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E. Celis, ed.)","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-9","title":"The biochemical mechanisms of T-cell anergy","abstract":null,"authors":"Atfield, AD., Liu, P., Penninger JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr. Immunol. Rev.","volume":"2","issue":null,"page":"73-99","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-10","title":"The renin angiotensin system in acute respiratory distress syndrome. ","abstract":null,"authors":"Imai, Y., Kuba, K., Penninger, JM., ","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Drug Discovery Today","volume":"3","issue":"","page":"225-229","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-12","title":"Angiotensin-converting enzyme 2 (ACE2)-mutant mice.","abstract":null,"authors":"Kuba, K., Imai, Y., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Respiratory Molecular Medicine","volume":"10","issue":null,"page":"38-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-13","title":"Chemotactic regulation of cancer cell migration and bone metastases by RANKL.","abstract":null,"authors":"Nakashima T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Experimental Medicine","volume":"24","issue":null,"page":"1777-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-15","title":"Live imaging of glioblastoma cells in brain tissue shows requirement of actin bundles for migration.","abstract":null,"authors":"Caspani, EM., Echevarria, D., Rottner, K., Small JV.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Neuron Glia Biology","volume":"2","issue":null,"page":"105-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-17","title":"Editorial overview; Cell structure and Dynamics.","abstract":null,"authors":"Small, JV., Glotzer, G.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Current Opinion in Cell Biology","volume":"18","issue":null,"page":"1-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8386298","title":"Receptor-mediated transport of DNA into eukaryotic cells.","abstract":null,"authors":"Cotten, M., Wagner, E., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Methods Enzymol","volume":"217","issue":null,"page":"618-44","pdf":null,"JrId":"5787","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16319966","title":"Pins for spines.","abstract":"","authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Cell Biol","volume":"7","issue":"12","page":"1157-8","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2006-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9722161","title":"Imprinting of the mouse Igf2r gene depends on an intronic CpG island.","abstract":"Gametic imprinting is a developmental process that uses cis-acting epigenetic mechanisms to induce parental-specific expression in autosomal and X-linked genes. From the limited knowledge we have of imprinted genes it seems clear that they play a role in regulating the growth and development of the placenta and embryo in utero, and also in the early post-natal phase. The biological function of imprinting in mammals is not yet understood but it may act to regulate the supply of nutrition to the embryo in order to maintain a balance between fetal demands and maternal resources. The molecular basis of imprinting any gene has not yet been disclosed. However. the current model proposes that single or clustered genes should be associated with a specific imprinting element which carries a reversible epigenetic imprinting signal, inherited from one parent and maintained on the same parental chromosome in diploid cells. A common imprinting recognition sequence has not been identified amongst the 20 known imprinted genes, but such an element is thought to exist from observations of mouse transgenes and transgenes of the imprinted H19 gene, which have shown that short DNA sequences can maintain imprinted expression at different chromosome locations. However, it is also clear from gene deletion experiments in the mouse and the analysis of deletions in the human Prader-Willi\/Angelman syndromes that imprinted genes are also influenced by distant DNA sequences. We have earlier proposed that CG rich sequences resembling CpG islands, which are associated with many imprinted genes and often subject to parental-specific methylation, could act as a common imprinting element. The mouse insulin-like growth factor type 2 receptor (Igf2r) gene contains a CpG island known as region2, in the second intron. Region2 was proposed as the imprinting element of this gene because it inherited a methylation imprint from the female gamete that was maintained only on the maternal chromosome in diploid cells. We have used YAC (yeast artificial chromosome) transgenes carrying the complete Igf2r locus, to test if imprinting and parental-specific methylation of the mouse Igf2r gene is maintained when transferred to other chromosomal locations and to test whether imprinting is dependent on the intronic CpG island proposed as the imprinting element for this gene. Gametic imprints are epigenetic modifications which are imposed onto the gametic chromosomes and cause parental-specific differences in the expression of a small number of genes in the embryo. As a consequence, correct imposition of the imprints in the parental germlines is a prerequisite for successful development of mammals and any anomaly in the expression of imprinted genes is often accompanied by aberration of embryonic growth. The link between imprinting and growth regulation is best exemplified by the Igf2 and Igf2r genes. Both genes show parental-specific expression patterns in the embryo. Igf2 is a general embryonic mitogen, and mice lacking Igf2 are markedly reduced in size (DeChiara, T.M., Robertson, E.J., Efstratiadis, A., 1991. Parental imprinting of the mouse insulin-like growth factor II gene. Cell 64, 849-859). Igf2r acts to fine tune the amount of growth factor, and embryos lacking this gene show overgrowth and die perinatally (Lau, M.M., Stewart, C.E., Liu, Z., Bhatt, H., Rotwein, P., Stewart, C.L., 1994. Loss of the imprinted IGF2\/cation-independent mannose 6-phosphate receptor results in fetal overgrowth and perinatal lethality. Genes Dev. 8, 2953 2963; Wang, Z.Q., Fung, M.R., Barlow, D.P., Wagner, E.F., 1994. Regulation of embryonic growth and lysosomal targeting by the imprinted Igf2\/Mpr gene. Nature 372, 464-467). The phenomenon of gametic imprinting is predicted to arise by an unusual regulation of the imposition and erasure of epigenetic modifications. There are three events which are required for imprinting: firstly, the imprint must be imposed in one of the gametes before fertilisat","authors":"Wutz, A., Barlow, DP.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Mol Cell Endocrinol","volume":"140","issue":"1-2","page":"9-14","pdf":null,"JrId":"3382","fulltextlink":null,"preprintlink":null,"articledate":"1998-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-18","title":"Discovering Biomolecular Mechanisms with Computational Biology.","abstract":null,"authors":"Eisenhaber F.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Georgetown: Landes Biosciences and Eurekah.com","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-20","title":"Prediction of the Protein Function: Two Basic Concepts and One Practical Recipe. Chapter 3 in ","abstract":null,"authors":"Eisenhaber F.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Georgetown: Landes Biosciences and Eurekah.com","volume":null,"issue":null,"page":"38-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-53","title":"Getting informed in bioinformatics","abstract":null,"authors":"Eisenhaber F.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Trends in Cell Biology","volume":"9","issue":"","page":"289","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-21","title":"Sequence complexity of proteins and its significance in annotation.","abstract":null,"authors":"Eisenhaber, B., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"\"Bioinformatics\" in the Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (Subramaniam, S., ed.)","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-27","title":"Polarized cell motility: microtubules show the way. ","abstract":null,"authors":"Small, JV., Kaverina, I.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell Migration in Development and Disease (Wedlich, D., ed)","volume":"","issue":"","page":"15-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-29","title":"Transcriptional mechanisms underlying neuropathic pain: DREAM, transcription factors and future pain management?","abstract":null,"authors":"Cheng, H.-YM., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Exp. Rev. Neurotherapeutics","volume":"2","issue":"","page":"677-89","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-30","title":"The potential role of CD45 as a drug target.","abstract":null,"authors":"Sasaki, T., Sasaki-Irie, J., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr. Topics Med. Chem.","volume":"131","issue":"","page":"495-501","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-31","title":"Infections and the immune response to cardiac antigens. Book chapter. ","abstract":null,"authors":"Penninger, JM., Bachmaier, K.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Epitope recognition since Landsteiner's discovery - 100 years since the discovery of human blood groups (Eibl, M., Mayr, WR., Thorbecke, GJ., eds.)","volume":"","issue":"","page":"103-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-5","title":"Epigenetics","abstract":null,"authors":"Allis, D., Jenuwein, T., Reinberg, D. (Editors), assisted by Caparros, M.L.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-32","title":"MKK7 couples stress signalling to G2\/M cell cycle progression and cellular senescence.","abstract":null,"authors":"Wada, T., Nishina, H., Katada, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Exper. Med. ","volume":"22","issue":"","page":"1398-400","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-33","title":"Polarized cell motility: microtubules show the way. 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Friedmann, T.)","volume":"","issue":"","page":"261-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-54","title":"Molecular calculations on the conformation of the HIV-1 reverse transcriptase inhibitor 1-[(2-Hydroxyethoxy)methyl]-6-[phenylthio]-thymine [HEPT].","abstract":null,"authors":"Lawtrakul, L., Hannongbua, S., Beyer, A., Wolschann, P.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Monatshefte f\u00fcr Chemie","volume":"130","issue":"","page":"1347-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-55","title":"Cell multiplication - editorial overview.","abstract":null,"authors":"Glotzer, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Current Opinion in Cell Biology ","volume":"10","issue":"","page":"739-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-56","title":"Endocytic organelles: Methods for preparation.","abstract":null,"authors":"Fialka, I., Huber, LA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Encyclopedia of Life Sciences (www.els.net)","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-48","title":"Hydrophobic regions on protein surfaces.","abstract":null,"authors":"Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Perspectives in Drug Discovery and Design","volume":"v. 17","issue":"N1","page":"27-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-50","title":"The puzzle of size control in organisms.","abstract":null,"authors":"Hochedlinger, K., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"B.I.F. Futura ","volume":"15","issue":"","page":"81-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-43","title":"High troughput mass-spectrometry for proteomics analysis.","abstract":null,"authors":"Sickmann, A., Mechtler, K., Sch\u00e4fer, H., Wagner, Y., Meyer, HE.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Transkript 2002","volume":"7","issue":"","page":"37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-44","title":"Feline tumour suppressor gene p53 - Mutation in a case of bronchial gland carcinoma ","abstract":null,"authors":"Mayr, B., Schaffner, G., Reifinger, M., Loupal, G.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Folia Veterinaria ","volume":"46","issue":"","page":"49-51","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-45","title":"Nuclear receptors in hematopoietic development: cooperation with growth factor receptors in regulation of proliferation and differentiation.","abstract":null,"authors":"Bauer, A., Gandrillon, O., Samarut, J., Beug, H.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Hematopoiesis. A developmental approach (Zon, L., ed.)","volume":"","issue":"","page":"368-390","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-46","title":"The role of PAX5 (BSAP) in early and late B-cell development.","abstract":null,"authors":"Horcher, M., Eberhard, D., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Transcription Factors: Normal and Malignant Development of Blood Cells (Ravid, K., Licht, Jd., eds.)","volume":"","issue":"","page":"217-228","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-47","title":"E-cadherin","abstract":null,"authors":"Herzig, M., Christofori, G.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cancer Research, an Encyclopedic Reference (Schwab, M., ed.)","volume":"","issue":"","page":"277-281","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18339545","title":"Neurobiology of behaviour.","abstract":null,"authors":"Dickson, BJ., Moser, EI.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Curr Opin Neurobiol","volume":"17","issue":"6","page":"672-4","pdf":null,"JrId":"2201","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18039964","title":"On the backroads to cellular asymmetry.","abstract":null,"authors":"Knoblich, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Development (Cambridge, England)","volume":"134","issue":"24","page":"4311-3","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8702151","title":"Pax genes and skeletal development.","abstract":null,"authors":"Balling, R., Helwig, U., Nadeau, J., Neub\u00fcser, A., Schmahl, W., Imai, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Ann N Y Acad Sci","volume":"785","issue":null,"page":"27-33","pdf":null,"JrId":"611","fulltextlink":null,"preprintlink":null,"articledate":"1996-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14532157","title":"Signalling in osteoclasts and the role of Fos\/AP1 proteins.","abstract":null,"authors":"Wagner, EF., Matsuo, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Ann Rheum Dis","volume":"62 Suppl 2","issue":null,"page":"ii83-5","pdf":null,"JrId":"640","fulltextlink":null,"preprintlink":null,"articledate":"2003-12-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11747804","title":"A prize for proliferation.","abstract":null,"authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell","volume":"107","issue":"6","page":"689-701","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11595914","title":"Exciting future planned for birthplace of genetics.","abstract":null,"authors":"Nasmyth, K., Schweizer, D.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nature","volume":"413","issue":"6856","page":"565","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9837810","title":"The tumor-suppressor function of E-cadherin.","abstract":null,"authors":"Semb, H., Christofori, G.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Am J Hum Genet","volume":"63","issue":"6","page":"1588-93","pdf":null,"JrId":"428","fulltextlink":null,"preprintlink":null,"articledate":"1999-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7915933","title":"SSCP\/SacI polymorphism in the PAX5 gene.","abstract":null,"authors":"Vorechovsk\u00fd, I., Kurzbauer, R., Kozm\u00edk, Z., Hammarstr\u00f6m, L., Smith, CI., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Hum Mol Genet","volume":"3","issue":"5","page":"839","pdf":null,"JrId":"2407","fulltextlink":null,"preprintlink":null,"articledate":"1994-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7894592","title":"Generation of alphoid DNA probes for fluorescence in situ hybridization (FISH) using the polymerase chain reaction.","abstract":null,"authors":"Lengauer, C., Dunham, I., Featherstone, T., Cremer, T.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Methods Mol Biol","volume":"33","issue":null,"page":"51-61","pdf":null,"JrId":"2488","fulltextlink":null,"preprintlink":null,"articledate":"1995-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8650001","title":"The human ubiquitin C promoter directs high ubiquitous expression of transgenes in mice.","abstract":null,"authors":"Schorpp, M., J\u00e4ger, R., Schellander, K., Schenkel, J., Wagner, EF., Weiher, H., Angel, P.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Nucleic Acids Res","volume":"24","issue":"9","page":"1787-8","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1996-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7894595","title":"FISH of Alu-PCR-amplified YAC clones and applications in tumor cytogenetics.","abstract":null,"authors":"Lengauer, C., Speicher, MR., Cremer, T.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Methods Mol Biol","volume":"33","issue":null,"page":"85-94","pdf":null,"JrId":"2488","fulltextlink":null,"preprintlink":null,"articledate":"1995-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7664329","title":"Spindle orientation and asymmetric cell fate.","abstract":null,"authors":"Rhyu, MS., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell","volume":"82","issue":"4","page":"523-6","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1995-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6248096","title":"Avian leukaemia viruses and haematopoietic cell differentiation.","abstract":null,"authors":"Graf, T., Beug, H., Roussel, M., Saule, S., Stehelin, D., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"Br J Cancer","volume":"41","issue":"4","page":"659-61","pdf":null,"JrId":"1765","fulltextlink":null,"preprintlink":null,"articledate":"1980-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"4610052","title":"A micromethod for routine measurement of cell agglutination and dissociation.","abstract":null,"authors":"Beug, H., Gerisch, G.","publication_status":"ppublish","journalpubyear":"1972","journaltitle":"J Immunol Methods","volume":"2","issue":"1","page":"49-57","pdf":null,"JrId":"4818","fulltextlink":null,"preprintlink":null,"articledate":"1975-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6309413","title":"Role of the v-erbA and v-erbB oncogenes of avian erythroblastosis virus in erythroid cell transformation.","abstract":null,"authors":"Graf, T., Beug, H.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Cell","volume":"34","issue":"1","page":"7-9","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1983-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1366621","title":"The in vivo application of ribozymes.","abstract":null,"authors":"Cotten, M.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Trends Biotechnol","volume":"8","issue":"7","page":"174-8","pdf":null,"JrId":"1560","fulltextlink":null,"preprintlink":null,"articledate":"1990-12-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"194785","title":"Isolation of clonal strains of chicken embryo fibroblasts.","abstract":null,"authors":"Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1977","journaltitle":"Exp Cell Res","volume":"107","issue":"2","page":"417-28","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1977-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"207439","title":"Transformation parameters in chicken fibroblasts transformed by AEV and MC29 avian leukemia viruses.","abstract":null,"authors":"Royer-Pokora, B., Beug, H., Claviez, M., Winkhardt, HJ., Friis, RR., Graf, T.","publication_status":"ppublish","journalpubyear":"1978","journaltitle":"Cell","volume":"13","issue":"4","page":"751-60","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1978-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15018931","title":"Development.","abstract":null,"authors":"Dickson, B., Walsh, CA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Opin Neurobiol","volume":"14","issue":"1","page":"1-5","pdf":null,"JrId":"2201","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14673982","title":"Rheumatoid arthritis therapy after tumor necrosis factor and interleukin-1 blockade.","abstract":null,"authors":"Redlich, K., Schett, G., Steiner, G., Hayer, S., Wagner, EF., Smolen, JS.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Arthritis Rheum","volume":"48","issue":"12","page":"3308-19","pdf":null,"JrId":"881","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10423040","title":"Function of Fos proteins in bone cell differentiation.","abstract":null,"authors":"Matsuo, K., Jochum, W., Owens, JM., Chambers, TJ., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Bone","volume":"25","issue":"1","page":"141","pdf":null,"JrId":"1710","fulltextlink":null,"preprintlink":null,"articledate":"1999-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-49","title":"Cullins and cell cycle control.","abstract":null,"authors":"Gieffers, C., Schleiffer, A., Peters, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Protoplasma","volume":"211","issue":"","page":"20-28","pdf":null,"JrId":"6729","fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8542285","title":"Cell cycle. The only way out of mitosis.","abstract":"The ubiquitination and destruction of cyclins provides the way out of mitosis. A multiprotein complex polyubiquitinates cyclin B and promotes the separation of sister chromatids.","authors":"Glotzer, M.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Curr Biol","volume":"5","issue":"9","page":"970-2","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1996-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2580642","title":"Transcription termination and 3' processing: the end is in site!","abstract":null,"authors":"Birnstiel, ML., Busslinger, M., Strub, K.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Cell","volume":"41","issue":"2","page":"349-59","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1985-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17611594","title":"Not miR-ly a splicing factor: hnRNP A1 succumbs to microRNA temptation.","abstract":null,"authors":"Nielsen, AF., Leuschner, PJ., Martinez, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Struct Mol Biol","volume":"14","issue":"7","page":"572-3","pdf":null,"JrId":"31761","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16753553","title":"Checkpoint activation: don't get mad too much.","abstract":"The Mad2 protein is required to delay sister chromatid separation until all chromosomes have been aligned on the mitotic spindle. Two recent studies provide new insights into how Mad2 contributes to this remarkable task.","authors":"L\u00e9n\u00e1rt, P., Peters, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr Biol","volume":"16","issue":"11","page":"R412-4","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11","title":"Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled beta-adrenergic antagonists.","abstract":"","authors":"Lefkowitz, RJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"18","page":"1651-8","pdf":null,"JrId":"1015","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22807655","title":"Regulation of DNA replication within the immunoglobulin heavy-chain locus during B cell commitment.","abstract":"The temporal order of replication of mammalian chromosomes appears to be linked to their functional organization, but the process that establishes and modifies this order during cell differentiation remains largely unknown. Here, we studied how the replication of the Igh locus initiates, progresses, and terminates in bone marrow pro-B cells undergoing B cell commitment. We show that many aspects of DNA replication can be quantitatively explained by a mechanism involving the stochastic firing of origins (across the S phase and the Igh locus) and extensive variations in their firing rate (along the locus). The firing rate of origins shows a high degree of coordination across Igh domains that span tens to hundreds of kilobases, a phenomenon not observed in simple eukaryotes. Differences in domain sizes and firing rates determine the temporal order of replication. During B cell commitment, the expression of the B-cell-specific factor Pax5 sharply alters the temporal order of replication by modifying the rate of origin firing within various Igh domains (particularly those containing Pax5 binding sites). We propose that, within the Igh C(H)-3'RR domain, Pax5 is responsible for both establishing and maintaining high rates of origin firing, mostly by controlling events downstream of the assembly of pre-replication complexes.","authors":"Demczuk, A., Gauthier, MG., Veras, I., Kosiyatrakul, S., Schildkraut, CL., Busslinger, M., Bechhoefer, J., Norio, P.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Biol","volume":"10","issue":"7","page":"e1001360","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8600472","title":"High primer concentration improves PCR amplification from random pools.","abstract":null,"authors":"Czerny, T.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Nucleic Acids Res","volume":"24","issue":"5","page":"985-6","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1996-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17115036","title":"fruitless regulates aggression and dominance in Drosophila.","abstract":"When competing for resources, two Drosophila melanogaster flies of the same sex fight each other. Males and females fight with distinctly different styles, and males but not females establish dominance relationships. Here we show that sex-specific splicing of the fruitless gene plays a critical role in determining who and how a fly fights, and whether a dominance relationship forms.","authors":"Vrontou, E., Nilsen, SP., Demir, E., Kravitz, EA., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nat Neurosci","volume":"9","issue":"12","page":"1469-71","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21310966","title":"Cortical constriction during abscission involves helices of ESCRT-III-dependent filaments.","abstract":"After partitioning of cytoplasmic contents by cleavage furrow ingression, animal cells remain connected by an intercellular bridge, which subsequently splits by abscission. Here, we examined intermediate stages of abscission in human cells by using live imaging, three-dimensional structured illumination microscopy, and electron tomography. We identified helices of 17-nanometer-diameter filaments, which narrowed the cortex of the intercellular bridge to a single stalk. The endosomal sorting complex required for transport (ESCRT)-III co-localized with constriction zones and was required for assembly of 17-nanometer-diameter filaments. Simultaneous spastin-mediated removal of underlying microtubules enabled full constriction at the abscission site. The identification of contractile filament helices at the intercellular bridge has broad implications for the understanding of cell division and of ESCRT-III-mediated fission of large membrane structures.","authors":"Guizetti, J., Schermelleh, L., M\u00e4ntler, J., Maar, S., Poser, I., Leonhardt, H., M\u00fcller-Reichert, T., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Science","volume":"331","issue":"6024","page":"1616-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17008915","title":"Cavitation of embryoid bodies requires optimal oxidative phosphorylation and AIF.","abstract":"","authors":"Feraud, O., Debili, N., Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell Death Differ","volume":"14","issue":"2","page":"385-7","pdf":null,"JrId":"20326","fulltextlink":null,"preprintlink":null,"articledate":"2007-03-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3375085","title":"Promoter of a somatic histone H2B gene of the sea urchin.","abstract":null,"authors":"Cosson, J., Kemler, I., Tanno, S., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Nucleic Acids Res","volume":"16","issue":"9","page":"4175","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1988-07-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2195639","title":"Cellular and molecular aspects of neurocarcinogenesis.","abstract":"Although the morphology of neural tumors induced in rats by N-ethyl-N-nitrosourea (NEU) and related alkylating agents has been extensively investigated, their histogenesis and the molecular basis of malignant transformation are still largely unknown. This review gives an account of the interaction of neurocarcinogenic agents with cellular DNA, the possible role of promutagenic O6-alkyldeoxyguanine and their deficient repair by the cerebral O6-alkylguanine-DNA alkyltransferase. A new experimental model is described in which neural tumors are induced in fetal brain transplants. Pregnant rats received a single iv dose of NEU (50 mg\/kg) on the 14th day of gestation. One day later, suspensions were prepared from the fetal forebrain and stereotactically injected into the caudoputamen of adult rats. After additional exposure to NEU of the host animals 8 days and 9 weeks post transplantation, all rats developed brain tumors within the neural graft. Histopathologically, all neoplasms were classified as olidogdendrogliomas. Other neoplasms typically induced by NEU transplacentally (astrocytomas, mixed gliomas, ependymomas) were absent. The selective induction of oligodendrogliomas indicates that neoplastic transformation in the nervous system can occur in a differentiated glial cell or a precursor cell committed to oligodendrocytic differentiation, and that transformation of a pluripotential stem cell is not necessary. Transplacental exposure of the donor fetuses to NEU alone, i.e., without additional postgrafting exposure, did not produce brain tumors in any of the experimental animals indicating that in the microenvironment of fetal brain transplants the multistep development of gliomas requires additional mutational events. Malignant schwanomas perinatally induced by NEU carry a point mutation in the transmembrane domain of the neu gene. The mode of oncogene activation in NEU-induced CNS gliomas has not yet been elucidated. We have used cerebral grafting techniques to study the effects of known oncogenes on the developing nervous system, taking advantage of efficient gene transfer by replication-defective retroviral vectors and of the extraordinary capacity of fetal CNS to differentiate in and fully integrate with the host brain. Rats carrying transplants exposed in vitro to the polyoma medium T-antigen developed endothelial hemangiomas in the graft which often led to fatal cerebral hemorrhage within 13-50 days after transplantation. Introduction of the viral src gene caused astrocytic and mesenchymal tumors after latency periods of 2-6 months. Following infection of fetal donor cells with a vector encoding the v-myc oncogene, only a single embryonal CNS tumor was observed whereas exposure to v-H-ras produced a low incidence of gliomas.(ABSTRACT TRUNCATED AT 400 WORDS)","authors":"Kleihues, P., Aguzzi, A., Wiestler, OD.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Toxicol Pathol","volume":"18","issue":"1 Pt 2","page":"193-203","pdf":null,"JrId":"7328","fulltextlink":null,"preprintlink":null,"articledate":"1990-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18246036","title":"Facing up to Mena: Tes(ting) times for EVH1 domains.","abstract":null,"authors":"Small, JV.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Cell Biol","volume":"10","issue":"2","page":"118-20","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11988751","title":"Conspiracy to disarm APC in interphase.","abstract":null,"authors":"Vodermaier, HC., Peters, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nat Cell Biol","volume":"4","issue":"5","page":"E119-20","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14584578","title":"K-ras protooncogene mutations in feline pancreatic adenocarcinomas.","abstract":null,"authors":"Mayr, B., Schaffner, G., Reifinger, M., Loupal, G.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Vet Rec","volume":"153","issue":"15","page":"468-9","pdf":null,"JrId":"7986","fulltextlink":null,"preprintlink":null,"articledate":"2003-12-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10465783","title":"Whose end is destruction: cell division and the anaphase-promoting complex.","abstract":null,"authors":"Zachariae, W., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Genes Dev","volume":"13","issue":"16","page":"2039-58","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1999-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8811733","title":"Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class.","abstract":"The success rates reported for secondary structural class prediction with different methods are contradictory. On one side, the problem of recognizing the secondary structural class of a protein knowing only its amino acid composition appears completely solved by simply applying jury decision with an elliptically scaled distance function. Chou and coworkers repeatedly (see Crit. Rev. Biochem. Mol. Biol. 30:275-349, 1995) published prediction accuracies near 100%. On the other hand, traditional secondary structure prediction techniques achieve success rates of about 70% for the secondary structural state per residue and about 75% for structural class only with extensive input information (full sequence of the query protein, its amino acid composition and length, multiple alignments with homologous sequences). In this article, we resolve the paradox and consider (1) the question of the secondary structural class definition, (2) the role of the representativity of the test set of protein tertiary structure for the current state of the Protein Data Bank (PDB); and (3) we estimate the real impact of amino acid composition on secondary structural class. We formulate three objective criteria for a reasonable definition of secondary structural classes and show that only the criterion of Nakashima et al. (J. Biochem. 99:153-162, 1986) complies with all of them. Only this definition matches the distribution of secondary structural content in representative PDB subsets, whereas other criteria leave many proteins (up to 65% of all PDB entries) simply unassigned. We review critically specialized secondary-structural class prediction methods, especially those of Chou and coworkers, which claim almost 100% accuracy using only amino acid composition, and resolve the paradox that these prediction accuracies are better than those from secondary structure predictions from multiple alignments. We show (i) that these techniques rely on a preselection of test sets which removes irregular proteins and other proteins without any class assignment (about 35% of all PDB entries); and (ii) that even for preselected representative test sets, the success rate drops to 60% and lower for a 4-type classification (alpha, beta, alpha + beta, alpha\/beta). The prediction accuracies fall to about 50% if the secondary structural class definition of Nakashima et al. is applied and only few irregular proteins are preselected and removed from automatically generated, representative subsets of the PDB. We have applied two new vector decomposition methods for secondary structural content prediction from amino acid composition alone, with and without consideration of amino acid compositional coupling in the learning set of tertiary structures respectively, to the problem of class prediction and achieve about 60% correct assignment among four classes (alpha, beta, mixed, irregular) as well as single sequence-based secondary structure prediction methods like GORIII and COMBI. Our results demonstrate that 60% correctness is the upper limit for a 4-type class prediction from amino acid composition alone for an unknown query protein and that consideration of compositional coupling does not improve the prediction success. The prediction program SSCP offering secondary structural class assignment for query compositions and sequences has been made available as a World Wide Web and E-mail service.","authors":"Eisenhaber, F., Fr\u00f6mmel, C., Argos, P.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Proteins","volume":"25","issue":"2","page":"169-79","pdf":null,"JrId":"6646","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8811732","title":"Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods.","abstract":"The predictive limits of the amino acid composition for the secondary structural content (percentage of residues in the secondary structural states helix, sheet, and coil) in proteins are assessed quantitatively. For the first time, techniques for prediction of secondary structural content are presented which rely on the amino acid composition as the only information on the query protein. In our first method, the amino acid composition of an unknown protein is represented by the best (in a least square sense) linear combination of the characteristic amino acid compositions of the three secondary structural types computed from a learning set of tertiary structures. The second technique is a generalization of the first one and takes into account also possible compositional couplings between any two sorts of amino acids. Its mathematical formulation results in an eigenvalue\/eigenvector problem of the second moment matrix describing the amino acid compositional fluctuations of secondary structural types in various proteins of a learning set. Possible correlations of the principal directions of the eigenspaces with physical properties of the amino acids were also checked. For example, the first two eigenvectors of the helical eigenspace correlate with the size and hydrophobicity of the residue types respectively. As learning and test sets of tertiary structures, we utilized representative, automatically generated subsets of Protein Data Bank (PDB) consisting of non-homologous protein structures at the resolution thresholds &lt; or = 1.8A, &lt; or = 2.0A, &lt; or = 2.5A, and &lt; or = 3.0 A. We show that the consideration of compositional couplings improves prediction accuracy, albeit not dramatically. Whereas in the self-consistency test (learning with the protein to be predicted), a clear decrease of prediction accuracy with worsening resolution is observed, the jackknife test (leave the predicted protein out) yielded best results for the largest dataset (&lt; or = 3.0A, almost no difference to the self-consistency test!), i.e., only this set, with more than 400 proteins, is sufficient for stable computation of the parameters in the prediction function of the second method. The average absolute error in predicting the fraction of helix, sheet, and coil from amino acid composition of the query protein are 13.7, 12.6, and 11.4%, respectively with r.m.s. deviations in the range of 8.6 divided by 11.8% for the 3.0 A dataset in a jackknife test. The absolute precision of the average absolute errors is in the range of 1 divided by 3% as measured for other representative subsets of the PDB. Secondary structural content prediction methods found in the literature have been clustered in accordance with their prediction accuracies. To our surprise, much more complex secondary structure prediction methods utilized for the same purpose of secondary structural content prediction achieve prediction accuracies very similar to those of the present analytic techniques, implying that all the information beyond the amino acid composition is, in fact, mainly utilized for positioning the secondary structural state in the sequence but not for determination of the overall number of residues in a secondary structural type. This result implies that higher prediction accuracies cannot be achieved relying solely on the amino acid composition of an unknown query protein as prediction input. Our prediction program SSCP has been made available as a World Wide Web and E-mail service.","authors":"Eisenhaber, F., Imperiale, F., Argos, P., Fr\u00f6mmel, C.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Proteins","volume":"25","issue":"2","page":"157-68","pdf":null,"JrId":"6646","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14517371","title":"The implications of angiogenesis on tumor invasiveness.","abstract":null,"authors":"Christofori, G.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Angiogenesis","volume":"2","issue":"1","page":"21-3","pdf":null,"JrId":"22063","fulltextlink":null,"preprintlink":null,"articledate":"2003-10-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12063850","title":"The Drosophila nervous system as a model for asymmetric cell division.","abstract":null,"authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Symp Soc Exp Biol","volume":null,"issue":"53","page":"75-89","pdf":null,"JrId":"7682","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9443906","title":"Photoreceptor development: breaking down the barriers.","abstract":"One form of the Tramtrack protein (Ttk88) acts as a general inhibitor of photoreceptor differentiation in developing Drosophila eyes. This inhibition is removed by targeting Ttk88 for degradation, which requires two proteins, Phyl and Sina, previously thought to act in the determination of specific photoreceptor subtypes.","authors":"Dickson, BJ.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Curr Biol","volume":"8","issue":"3","page":"R90-2","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1998-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9059326","title":"Transgenic mouse models of tumour angiogenesis: the angiogenic switch, its molecular controls, and prospects for preclinical therapeutic models.","abstract":null,"authors":"Hanahan, D., Christofori, G., Naik, P., Arbeit, J.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Eur J Cancer","volume":"32A","issue":"14","page":"2386-93","pdf":null,"JrId":"1697","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8722171","title":"Multiple roles for DNA methylation in gametic imprinting.","abstract":"Allele-specific DNA methylation has been observed for all tested imprinted genes and has a clear role in the imprinting mechanism. It remains to be resolved whether this role is to act as the gametic imprinting signal or to cause or maintain allele-specific expression.","authors":"Neumann, B., Barlow, DP.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Curr Opin Genet Dev","volume":"6","issue":"2","page":"159-63","pdf":null,"JrId":"2199","fulltextlink":null,"preprintlink":null,"articledate":"1996-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18685699","title":"Moving AHEAD with an international human epigenome project.","abstract":null,"authors":"","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"454","issue":"7205","page":"711-5","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18225947","title":"Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events.","abstract":null,"authors":"Holste, D., Ohler, U.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"PLoS Comput Biol","volume":"4","issue":"1","page":"e21","pdf":null,"JrId":"32534","fulltextlink":null,"preprintlink":null,"articledate":"2008-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9","title":"Radiochemical assay of glutathione S-epoxide transferase and its enhancement by phenobarbital in rat liver in vivo.","abstract":"","authors":"Marniemi, J., Parkki, MG.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"17","page":"1569-72","pdf":null,"JrId":"1015","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16401413","title":"Sexual behaviour: do a few dead neurons make the difference?","abstract":"Why do males and females behave so differently? Sexually dimorphic neural circuitry has just been found in parts of the fly's brain thought to control mating behaviour. Might this explain why males and females have such distinct sexual behaviours?","authors":"Yu, JY., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr Biol","volume":"16","issue":"1","page":"R23-5","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15964266","title":"Cyclin degradation: don't mes(s) with meiosis.","abstract":"Cyclin degradation is required for exit from mitosis and enables a new round of DNA replication in the subsequent S phase. A recent study in fission yeast shows that, during exit from meiosis I, the Mes1 protein partially inhibits cyclin degradation and thereby allows entry into meiosis II without an intervening S phase.","authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"12","page":"R461-3","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2005-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12781155","title":"Mitotic entry: tipping the balance.","abstract":"In the eukaryotic cell cycle, the G2-M transition is regulated by a counteracting kinase\/phosphatase mechanism. A novel player, Tome-1, has now been found to trigger entry into mitosis by interfering with this kinase\/phosphatase 'switch'.","authors":"Kraft, C.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"11","page":"R445-6","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12511871","title":"Is proteomics heading in the wrong direction?","abstract":"Proteomics is now considered to be one of the most important 'post-genome' approaches to help us understand gene function. In fact, several genomics companies have launched large-scale proteomics projects, and have started to annotate the entire human proteome. The 'holistic view' painted by a human proteome project is seductive, but is it realistic?","authors":"Huber, LA.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nat Rev Mol Cell Biol","volume":"4","issue":"1","page":"74-80","pdf":null,"JrId":"22271","fulltextlink":null,"preprintlink":null,"articledate":"2003-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29752447","title":"The beginning of totipotency.","abstract":null,"authors":"Tachibana, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Rev Mol Cell Biol","volume":"19","issue":"7","page":"417","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17443175","title":"Cell biology: the checkpoint brake relieved.","abstract":null,"authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"446","issue":"7138","page":"868-9","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2007-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17110561","title":"Cell biology. Sara splits the signal.","abstract":null,"authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Science","volume":"314","issue":"5802","page":"1094-6","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2006-11-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16950788","title":"Up-regulation of endogenous RGS2 mediates cross-desensitization between Gs and Gq signaling in osteoblasts.","abstract":"Regulator of G protein signaling (RGS) proteins limit G protein signals. In this study, we investigated the role of RGS2 in the control of G protein signaling cascades in osteoblasts, the cells responsible for bone formation. Expression of RGS2 was up-regulated in primary cultures of mouse calvarial osteoblasts by parathyroid hormone-related peptide (PTHrP)-(1-34), which stimulates G(s) signaling. RGS2 was also up-regulated by extracellular ATP, which selectively activates G(q), as well as by forskolin and phorbol myristate acetate, which activate targets downstream of G(s) and G(q), respectively. To assess the role of endogenous RGS2, we characterized G(s) and G(q) signaling in osteoblasts derived from wild type and rgs2(-\/-) mice. Under control conditions, nucleotide-stimulated calcium release, endothelin-stimulated accumulation of inositol phosphates, and PTHrP-stimulated cAMP accumulation were equivalent in osteoblasts isolated from wild type and rgs2(-\/-) mice. Thus, basal levels of endogenous RGS2 do not appear to regulate G(s) or G(q) signaling in osteoblasts. Interestingly, forskolin treatment of wild type but not rgs2(-\/-) osteoblasts suppressed both endothelin-stimulated accumulation of inositol phosphates and nucleotide-stimulated calcium release, indicating that up-regulation of RGS2 by G(s) signaling desensitizes G(q) signals. Furthermore, pretreatment with ATP suppressed PTHrP-dependent cAMP accumulation in wild type but not rgs2(-\/-) osteoblasts, implying that up-regulation of RGS2 by G(q) signaling desensitizes G(s) signals. Our findings demonstrate that endogenously expressed RGS2 can limit G(s) signaling. Moreover, up-regulation of RGS2 contributes to cross-desensitization of G(s)- and G(q)-coupled signals.","authors":"Roy, AA., Nunn, C., Ming, H., Zou, MX., Penninger, J., Kirshenbaum, LA., Dixon, SJ., Chidiac, P.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Biol Chem","volume":"281","issue":"43","page":"32684-93","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2006-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16843267","title":"STAT1 acts as a tumor promoter for leukemia development.","abstract":"The tumor suppressor STAT1 is considered a key regulator of the surveillance of developing tumors. Here, we describe an unexpected tumor-promoting role for STAT1 in leukemia. STAT1(-\/-) mice are partially protected from leukemia development, and STAT1(-\/-) tumor cells induce leukemia in RAG2(-\/-) and immunocompetent mice with increased latency. The low MHC class I protein levels of STAT1(-\/-) tumor cells enable efficient NK cell lysis and account for the enhanced tumor clearance. Strikingly, STAT1(-\/-) tumor cells acquire increased MHC class I expression upon leukemia progression. These findings define STAT1 as a tumor promoter in leukemia development. Furthermore, we describe the upregulation of MHC class I expression as a general mechanism that allows for the escape of hematopoietic malignancies from immune surveillance.","authors":"Kovacic, B., Stoiber, D., Moriggl, R., Weisz, E., Ott, RG., Kreibich, R., Levy, DE., Beug, H., Freissmuth, M., Sexl, V.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cancer Cell","volume":"10","issue":"1","page":"77-87","pdf":null,"JrId":"29778","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16806877","title":"Endosome dynamics during development.","abstract":"Endocytosis has traditionally been studied in isolated cells. More recently, however, the analysis of protein trafficking in whole organisms has revealed that it plays exciting roles during development. Endocytic trafficking of cell adhesion molecules regulates epithelial polarity and cell migration. Developmental signaling pathways are regulated by the trafficking of receptors and their ligands through the endocytic pathway. Finally, impairment of the endocytic machinery can affect proliferation control and contribute to tumor development.","authors":"Emery, G., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr Opin Cell Biol","volume":"18","issue":"4","page":"407-15","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16616850","title":"Lethal giant larvae take on a life of their own.","abstract":"Cell polarization requires the segregation of the plasma membrane into domains of distinct protein composition. The Lethal giant larvae (Lgl) protein of Drosophila, initially identified as a tumor suppressor, establishes such domains by localizing specific proteins to specific regions of the plasma membrane. However, how it does this remains puzzling and controversial. Recent studies of the yeast orthologs show a molecular pathway through which Lgl is activated locally to promote the targeted fusion of vesicles with the plasma membrane. Here, we reconcile these data with conflicting findings on the mechanism of Lgl in animals and consider if a similar model explains its role in epithelial polarity and asymmetric cell division.","authors":"Wirtz-Peitz, F., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Trends Cell Biol","volume":"16","issue":"5","page":"234-41","pdf":null,"JrId":"21041","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16127443","title":"Wnts send axons up and down the spinal cord.","abstract":"","authors":"Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Neurosci","volume":"8","issue":"9","page":"1130-2","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16564014","title":"Asymmetric segregation of the tumor suppressor brat regulates self-renewal in Drosophila neural stem cells.","abstract":"How stem cells generate both differentiating and self-renewing daughter cells is unclear. Here, we show that Drosophila larval neuroblasts-stem cell-like precursors of the adult brain-regulate proliferation by segregating the growth inhibitor Brat and the transcription factor Prospero into only one daughter cell. Like Prospero, Brat binds and cosegregates with the adaptor protein Miranda. In larval neuroblasts, both Brat and Prospero are required to inhibit self-renewal in one of the two daughter cells. While Prospero regulates cell-cycle gene transcription, Brat acts as a posttranscriptional inhibitor of dMyc. In brat or prospero mutants, both daughter cells grow and behave like neuroblasts leading to the formation of larval brain tumors. Similar defects are seen in lethal giant larvae (lgl) mutants where Brat and Prospero are not asymmetric. We have identified a molecular mechanism that may control self-renewal and prevent tumor formation in other stem cells as well.","authors":"Betschinger, J., Mechtler, K., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell","volume":"124","issue":"6","page":"1241-53","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7","title":"Maturation of the adrenal medulla--IV. Effects of morphine.","abstract":"","authors":"Anderson, TR., Slotkin, TA.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"16","page":"1469-74","pdf":null,"JrId":"1015","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15897174","title":"How might cohesin hold sister chromatids together?","abstract":"The sister chromatid cohesion essential for the bi-orientation of chromosomes on mitotic spindles depends on a multi-subunit complex called cohesin. This paper reviews the evidence that cohesin is directly responsible for holding sister DNAs together and considers how it might perform this function in the light of recent data on its structure.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"360","issue":"1455","page":"483-96","pdf":null,"JrId":"8277","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16466918","title":"A Wnt canon orchestrating osteoblastogenesis.","abstract":"Several transcription factors have been identified that control the differentiation of osteoblasts; however, relatively little is known about the signaling pathways involved in regulating the differentiation process. Recently, the canonical Wnt-beta-catenin pathway has been implicated in osteoblastogenesis. This review focuses on the role of the canonical Wnt-beta-catenin pathway during embryonic development, where it is required for the differentiation of osteoblasts from a precursor that is shared with the chondrocyte lineage and the requirement of this pathway during postnatal life in bone homeostasis. The recent findings covered in this review are major advances in our understanding of skeletal development and promise new therapeutic avenues for tissue engineering and treatment of osteoporosis.","authors":"Hartmann, C.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Trends Cell Biol","volume":"16","issue":"3","page":"151-8","pdf":null,"JrId":"21041","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16077006","title":"Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias.","abstract":"Deposition of variant histones provides a mechanism to reset and to potentially specify chromatin states. We determined the distribution of H3 and its variant H3.3 relative to chromatin structure and elongating polymerase. H3.3 is enriched throughout active genes similar to polymerase, yet its distribution is very distinct from that of several euchromatic histone modifications, which are highly biased toward the 5' part of active genes. Upon gene induction we observe displacement of both H3 and H3.3 followed by selective deposition of H3.3. These results support a model in which H3.3 deposition compensates for transcription-coupled nucleosomal displacement yet does not predetermine tail modifications.","authors":"Wirbelauer, C., Bell, O., Sch\u00fcbeler, D.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Genes Dev","volume":"19","issue":"15","page":"1761-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16061693","title":"The limited role of NH2-terminal c-Jun phosphorylation in neuronal apoptosis: identification of the nuclear pore complex as a potential target of the JNK pathway.","abstract":"c-Jun is induced in many neuronal death paradigms. A critical step in c-Jun regulation involves phosphorylation of Ser63\/Ser73 located in the NH2-terminal transactivation domain. To determine the importance of this phosphorylation for neuronal apoptosis, we analyzed the sympathetic neurons of mice carrying a mutant c-Jun gene that lacks Ser63\/Ser73 phosphorylation sites (jun aa). Trophic factor-deprivation or DNA damage-induced death was significantly delayed in jun aa\/aa neurons. Neuronal c-Jun induction was only partially inhibited, demonstrating that phosphorylation of Ser63\/73 is not required for c-Jun activation. The inductions of proapoptotic BH3-only proteins, Bim and PUMA\/Bbc3, were delayed during neuronal apoptosis in mutant neurons. These results demonstrate that NH2-terminal c-Jun phosphorylation is important, but not necessary, for the induction of proapoptotic genes and neuronal apoptosis. Thus, additional JNK substrates may be critical for neuronal death. As potential mediators, we identified additional nuclear MLK\/JNK substrates, including Nup214 subunit of the nuclear pore complex.","authors":"Besirli, CG., Wagner, EF., Johnson, EM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Cell Biol","volume":"170","issue":"3","page":"401-11","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2005-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16508672","title":"How APC\/C orders destruction.","abstract":"","authors":"Buschhorn, BA., Peters, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nat Cell Biol","volume":"8","issue":"3","page":"209-11","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16322747","title":"Immunity by ubiquitylation: a reversible process of modification.","abstract":"The conjugation of ubiquitin, a 76-amino-acid peptide, to a protein substrate provides a tag that either marks the labelled protein for degradation or modulates its function. The process of protein ubiquitylation--which is catalysed by coordinated enzymatic reactions that are mediated by enzymes known as E1, E2 and E3--has an important role in the modulation of immune responses. Importantly, protein ubiquitylation is a reversible process, and removal of ubiquitin molecules is mediated by de-ubiquitylating enzymes: for example, A20, which has been implicated in the regulation of immune responses. In addition, the conjugation of ubiquitin-like molecules, such as ISG15 (interferon-stimulated protein of 15 kDa), to proteins is also involved in immune regulation. This Review covers recent progress in our understanding of protein ubiquitylation in the immune system.","authors":"Liu, YC., Penninger, J., Karin, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Rev Immunol","volume":"5","issue":"12","page":"941-52","pdf":null,"JrId":"27017","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8181522","title":"Thymocyte apoptosis induced by elevated endogenous corticosterone levels.","abstract":"A well-known model of apoptosis is induction in thymocytes by injection of pharmacological doses of exogenous steroids. The aim of this study was to investigate whether this process also occurs under physiological conditions, i.e. by stimulation of endogenous glucocorticoid release, using the chicken as an experimental model. Endogenous glucocorticoid levels can be elevated by immunization with exogenous antigens or by injection of conditioned medium, e.g. supernatant of mitogen-stimulated spleen cells. This effect is mediated by so-called glucocorticoid-increasing factors, and is considered to act as an immunoregulatory principle. Thymocyte DNA of so treated birds showed a typical \"ladder\" pattern after electrophoresis in a 1.8% agarose gel, and degradation could be prevented by RU 38,486. This provides evidence that apoptosis can be induced by elevating endogenous corticosterone levels in vivo. By means of in situ nick translation (ISNT) and simultaneous immunofluorescence tests, it was possible to analyze various thymic subpopulations during apoptosis after treatment with exogenous glucocorticoids. Additionally, using confocal microscopical techniques, apoptosis of the same cells as analyzed by ISNT is shown. The possible role of elevated concentrations of endogenous glucocorticoids in regulating thymocyte cell death and autoimmune diseases is discussed.","authors":"Gruber, J., Sgonc, R., Hu, YH., Beug, H., Wick, G.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Eur J Immunol","volume":"24","issue":"5","page":"1115-21","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15746389","title":"Postsynaptic receptor trafficking underlying a form of associative learning.","abstract":"To elucidate molecular, cellular, and circuit changes that occur in the brain during learning, we investigated the role of a glutamate receptor subtype in fear conditioning. In this form of learning, animals associate two stimuli, such as a tone and a shock. Here we report that fear conditioning drives AMPA-type glutamate receptors into the synapse of a large fraction of postsynaptic neurons in the lateral amygdala, a brain structure essential for this learning process. Furthermore, memory was reduced if AMPA receptor synaptic incorporation was blocked in as few as 10 to 20% of lateral amygdala neurons. Thus, the encoding of memories in the lateral amygdala is mediated by AMPA receptor trafficking, is widely distributed, and displays little redundancy.","authors":"Rumpel, S., LeDoux, J., Zador, A., Malinow, R.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Science","volume":"308","issue":"5718","page":"83-8","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6","title":"Studies of oxygen binding energy to hemoglobin molecule.","abstract":"","authors":"Chow, YW., Pietranico, R., Mukerji, A.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Biophys Res Commun","volume":"66","issue":"4","page":"1424-31","pdf":null,"JrId":"1008","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15854913","title":"Phosphorylation of ZEN-4\/MKLP1 by aurora B regulates completion of cytokinesis.","abstract":"The central spindle regulates the formation and positioning of the contractile ring and is essential for completion of cytokinesis [1]. Central spindle assembly begins in early anaphase with the bundling of overlapping, antiparallel, nonkinetochore microtubules [2, 3], and these bundles become compacted and mature into the midbody. Prominent components of the central spindle include aurora B kinase and centralspindlin, a complex containing a Kinesin-6 protein (ZEN-4\/MKLP1) and a Rho family GAP (CYK-4\/MgcRacGAP) that is essential for central spindle assembly [4]. Centralspindlin localization depends on aurora B kinase [5]. Aurora B concentrates in the midbody and persists between daughter cells. Here, we show that in C. elegans embryos and in cultured human cells, respectively, ZEN-4 and MKLP1 are phosphorylated by aurora B in vitro and in vivo on conserved C-terminal serine residues. In C. elegans embryos, a nonphosphorylatable mutant of ZEN-4 localizes properly but does not efficiently support completion of cytokinesis. In mammalian cells, an inhibitor of aurora kinase acutely attenuates phosphorylation of MKLP1. Inhibition of aurora B in late anaphase causes cytokinesis defects without disrupting the central spindle. These data indicate a conserved role for aurora-B-mediated phosphorylation of ZEN-4\/MKLP1 in the completion of cytokinesis.","authors":"Guse, A., Mishima, M., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"8","page":"778-86","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2005-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15324689","title":"Dare to be different: asymmetric cell division in Drosophila, C. elegans and vertebrates.","abstract":"One widespread mechanism for the generation of diverse cell types is the unequal inheritance of cell fate determinants. Several such determinants have been identified in the fruitfly Drosophila melanogaster and the worm Caenorhabditis elegans and the molecular machinery responsible for their asymmetric segregation is beginning to be unraveled. To divide asymmetrically, cells establish an axis of polarity, orient the mitotic spindle along this axis and localize cell fate determinants to one side of the cell. During cytokinesis, determinants are then segregated into one of the two daughter cells where they direct cell fate. Here, we outline the steps and factors that are involved in this process in Drosophila and C. elegans and discuss their potential conservation in vertebrates.","authors":"Betschinger, J., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"16","page":"R674-85","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15621528","title":"Fragile X protein functions with lgl and the par complex in flies and mice.","abstract":"Fragile X syndrome, the most common form of inherited mental retardation, is caused by loss of function for the Fragile X Mental Retardation 1 gene (FMR1). FMR1 protein (FMRP) has specific mRNA targets and is thought to be involved in their transport to subsynaptic sites as well as translation regulation. We report a saturating genetic screen of the Drosophila autosomal genome to identify functional partners of dFmr1. We recovered 19 mutations in the tumor suppressor lethal (2) giant larvae (dlgl) gene and 90 mutations at other loci. dlgl encodes a cytoskeletal protein involved in cellular polarity and cytoplasmic transport and is regulated by the PAR complex through phosphorylation. We provide direct evidence for a Fmrp\/Lgl\/mRNA complex, which functions in neural development in flies and is developmentally regulated in mice. Our data suggest that Lgl may regulate Fmrp\/mRNA sorting, transport, and anchoring via the PAR complex.","authors":"Zarnescu, DC., Jin, P., Betschinger, J., Nakamoto, M., Wang, Y., Dockendorff, TC., Feng, Y., Jongens, TA., Sisson, JC., Knoblich, JA., Warren, ST., Moses, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Dev Cell","volume":"8","issue":"1","page":"43-52","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16047350","title":"Clonal divergence and genetic heterogeneity in clear cell renal cell carcinomas with sarcomatoid transformation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">16047350<\/PMID><DateCompleted><Year>2005<\/Year><Month>10<\/Month><Day>27<\/Day><\/DateCompleted><DateRevised><Year>2005<\/Year><Month>09<\/Month><Day>06<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0008-543X<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>104<\/Volume><Issue>6<\/Issue><PubDate><Year>2005<\/Year><Month>Sep<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Cancer<\/Title><ISOAbbreviation>Cancer<\/ISOAbbreviation><\/Journal><ArticleTitle>Clonal divergence and genetic heterogeneity in clear cell renal cell carcinomas with sarcomatoid transformation.<\/ArticleTitle><Pagination><MedlinePgn>1195-203<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Approximately 5% of clear cell renal cell carcinomas contain components with sarcomatoid differentiation. It has been suggested that the sarcomatoid elements arise from the clear cell tumors as a consequence of clonal expansions of neoplastic cells with progressively more genetic alterations. Analysis of the pattern of allelic loss and X-chromosome inactivation in both the clear cell and sarcomatoid components of the same tumor allows assessment of the genetic relationship of these tumor elements.","authors":"Jones, TD., Eble, JN., Wang, M., Maclennan, GT., Jain, S., Cheng, L.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cancer","volume":"104","issue":"6","page":"1195-203","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16036105","title":"Persistent STAT3 activation in colon cancer is associated with enhanced cell proliferation and tumor growth.","abstract":"Colorectal carcinoma (CRC) is a major cause of morbidity and mortality in Western countries. It has so far been molecularly defined mainly by alterations of the Wnt pathway. We show here for the first time that aberrant activities of the signal transducer and activator of transcription STAT3 actively contribute to this malignancy and, thus, are a potential therapeutic target for CRC. Constitutive STAT3 activity was found to be abundant in dedifferentiated cancer cells and infiltrating lymphocytes of CRC samples, but not in non-neoplastic colon epithelium. Cell lines derived from malignant colorectal tumors lost persistent STAT3 activity in culture. However, implantation of colon carcinoma cells into nude mice resulted in restoration of STAT3 activity, suggesting a role of an extracellular stimulus within the tumor microenvironment as a trigger for STAT activation. STAT3 activity in CRC cells triggered through interleukin-6 or through a constitutively active STAT3 mutant promoted cancer cell multiplication, whereas STAT3 inhibition through a dominant-negative variant impaired IL-6-driven proliferation. Blockade of STAT3 activation in CRC-derived xenograft tumors slowed down their development, arguing for a contribution of STAT3 to colorectal tumor growth.","authors":"Corvinus, FM., Orth, C., Moriggl, R., Tsareva, SA., Wagner, S., Pfitzner, EB., Baus, D., Kaufmann, R., Huber, LA., Zatloukal, K., Beug, H., Ohlschl\u00e4ger, P., Sch\u00fctz, A., Halbhuber, KJ., Friedrich, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Neoplasia","volume":"7","issue":"6","page":"545-55","pdf":null,"JrId":"21648","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9686439","title":"Novel p53 tumour suppressor mutations in cases of spindle cell sarcoma, pleomorphic sarcoma and fibrosarcoma in cats.","abstract":"Twenty feline neoplasms were sequenced in the region from exons 5 to 8 for the presence of tumour suppressor gene p53 mutations. In a spindle cell sarcoma of the bladder, a missense mutation (codon 164 AAG--&gt;GAG, lysine--&gt;glutamic acid) in exon 5 was detected. In a pleomorphic sarcoma, a 23 bp deletion involving the splicing junction between intron 5 and exon 6 was observed. In a fibrosarcoma, a 6 bp deletion of p53 covering 2 bp of exon 7 and 4 bp of intron 7, including the splicing junction, was found. The study demonstrates three new p53 mutations in different types of sarcomas in cats.","authors":"Mayr, B., Reifinger, M., Alton, K., Schaffner, G.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Vet Res Commun","volume":"22","issue":"4","page":"249-55","pdf":null,"JrId":"7996","fulltextlink":null,"preprintlink":null,"articledate":"1998-10-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15039780","title":"MKK7 couples stress signalling to G2\/M cell-cycle progression and cellular senescence.","abstract":"During the development of multicellular organisms, concerted actions of molecular signalling networks determine whether cells undergo proliferation, differentiation, death or ageing. Here we show that genetic inactivation of the stress signalling kinase, MKK7, a direct activator of JNKs in mice, results in embryonic lethality and impaired proliferation of hepatocytes. Beginning at passage 4-5, mkk7(-\/-) mouse embryonic fibroblasts (MEFs) display impaired proliferation, premature senescence and G2\/M cell cycle arrest. Similarly, loss of c-Jun or expression of a c-JunAA mutant in which the JNK phosphorylation sites were replaced with alanine results in a G2\/M cell-cycle block. The G2\/M cell-cycle kinase CDC2 was identified as a target for the MKK7-JNK-c-Jun pathway. These data show that the MKK7-JNK-c-Jun signalling pathway couples developmental and environmental cues to CDC2 expression, G2\/M cell cycle progression and cellular senescence in fibroblasts.","authors":"Wada, T., Joza, N., Cheng, HY., Sasaki, T., Kozieradzki, I., Bachmaier, K., Katada, T., Schreiber, M., Wagner, EF., Nishina, H., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nat Cell Biol","volume":"6","issue":"3","page":"215-26","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14993928","title":"Corecruitment of the Grg4 repressor by PU.1 is critical for Pax5-mediated repression of B-cell-specific genes.","abstract":"PU.1 and Pax5 are important regulators of immunoglobulin heavy-chain (IgH) gene expression in B lineage cells. We have previously shown that PU.1 can potentiate the transcription of an IgH HS1,2 enhancer-linked reporter gene, and that Pax5 represses the same enhancer in transient transfection assays. Here we report that PU.1, like Pax5, can recruit and physically interact with a member of the Groucho family of co-repressors, Grg4. As a consequence, PU.1 in conjunction with Pax5 represses enhancer function in a position-dependent manner when Grg4 is recruited. Interestingly, Grg4 levels decrease following B-cell activation, suggesting temporal regulation of Grg4. Moreover, the joining-chain promoter, with an activity pattern and architecture resembling HS1,2 can also be repressed by the combinatorial action of Pax5\/PU.1\/Grg4. These data indicate that Pax5 depends on PU.1, acting in cis, for stable recruitment of Grg co-repressors to B-cell-specific genes.","authors":"Linderson, Y., Eberhard, D., Malin, S., Johansson, A., Busslinger, M., Pettersson, S.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"EMBO Rep","volume":"5","issue":"3","page":"291-6","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14726687","title":"APC activators caught by their tails?","abstract":"The complexity of the Anaphase-Promoting Complex (APC), the major ubiquitin ligase in mitotic control, has been puzzling investigators ever since its discovery. Recent biochemical and genetic studies have now provided insights not only into the architecture of the complex, but also into how activators are recruited to the APC. In this article, we discuss the implications of these findings on our current understanding of APC activation.","authors":"Vodermaier, HC., Peters, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell Cycle","volume":"3","issue":"3","page":"265-6","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12906808","title":"Cytokinesis: a logical GAP.","abstract":"Two complexes localize to the central spindle and regulate completion of cytokinesis: one, centralspindlin, contains a kinesin-like protein and a Rho-family GAP; the second contains Aurora B kinase. Aurora B kinase is known to regulate localization of centralspindlin and may regulate the activity of the RhoGAP component of centralspindlin.","authors":"Mishima, M., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"15","page":"R589-91","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12820955","title":"Emi1 proteolysis: how SCF(beta-Trcp1) helps to activate the anaphase-promoting complex.","abstract":"Emi1 inhibits the anaphase-promoting complex (APC) during S and G2 phase. Two papers by Guardavaccaro et al. and Margottin-Goguet et al. in the June issue of Developmental Cell now show that Emi1 degradation in early mitosis is mediated by beta-Trcp1, an adaptor protein that recruits proteins to the SCF ubiquitin ligase.","authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Mol Cell","volume":"11","issue":"6","page":"1420-1","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16024645","title":"BCR\/ABL promotes dendritic cell-mediated natural killer cell activation.","abstract":"BCR\/ABL fusion gene, encoding a paradigmatic tyrosine kinase involved in chronic myelogenous leukemia (CML), can modulate the expression of genes involved in natural killer (NK) cell target recognition. Recent reports outline the role of allogeneic antileukemic NK effectors in the graft-versus-leukemia effect but the regulation of NK cell activation in the setting of graft-versus-leukemia effect remains unknown. Here we show that dendritic cells derived from monocytes of CML patients are selectively endowed with NK cell stimulatory capacity in vitro. We further show, using a gene transfer approach in mouse bone marrow progenitors, that ABL\/ABL is necessary to promote dendritic cell-mediated NK cell activation. The dendritic cell\/NK cell cross-talk in ABL\/ABL-induced CML seems unique because JunB or IFN consensus sequence binding protein loss of functions, associated with other myeloproliferative disorders, do not promote dendritic cell-mediated NK cell activation. NK cell activation by leukemic dendritic cells involves NKG2D activating receptors and is blocked by imatinib mesylate. Indeed, ABL\/ABL translocation enhances the expression levels of the NKG2D ligands on dendritic cells, which is counteracted by imatinib mesylate. Altogether, the clonal ABL\/ABL dendritic cells display the unique and selective ability to activate NK cells and may participate in the NK cell control of CML. This study also highlights the deleterious role of imatinib mesylate at the dendritic cell level for NK cell activation.","authors":"Terme, M., Borg, C., Guilhot, F., Masurier, C., Flament, C., Wagner, EF., Caillat-Zucman, S., Bernheim, A., Turhan, AG., Caignard, A., Zitvogel, L.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cancer Res","volume":"65","issue":"14","page":"6409-17","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2005-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14668816","title":"AP-1: a double-edged sword in tumorigenesis.","abstract":null,"authors":"Eferl, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nat Rev Cancer","volume":"3","issue":"11","page":"859-68","pdf":null,"JrId":"27016","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12857946","title":"In vivo dynamics of antigen-specific regulatory T cells not predicted from behavior in vitro.","abstract":"Adoptive transfer of antigen-specific CD25+CD4+ regulatory T cells was used to analyze the stability of their phenotype, their behavior after immunization, and their mode of suppressing cotransferred naive T cells in vivo. We found that regulatory T cells maintained their phenotype in the absence of antigen, were not anergic in vivo, and proliferated as extensively as naive CD4+ T cells after immunization without losing their suppressive function in vivo and in vitro. In vivo, the expansion of cotransferred naive T cells was suppressed relatively late in the response such that regulatory T cells expressing mostly IL-10 but not IL-2 or IFN-gamma represented the dominant subset of cells. Our results reveal properties of regulatory T cells that were not predicted from in vitro studies.","authors":"Klein, L., Khazaie, K., von Boehmer, H.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Proc Natl Acad Sci U S A","volume":"100","issue":"15","page":"8886-91","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12734430","title":"Fine tuning of kinetochore function by phosphorylation.","abstract":null,"authors":"Hauf, S.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cell Cycle","volume":"2","issue":"3","page":"228-9","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12702863","title":"Development. Wiring the brain with insulin.","abstract":null,"authors":"Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Science","volume":"300","issue":"5618","page":"440-1","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"121","title":"Proceedings: Evaluation of narcotic and narcotic antagonist analgesic drugs in the dog dental pulp stimulation test.","abstract":"","authors":"Marriott, AS., Skingle, M., Tyers, MB.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Pharmacol","volume":"55","issue":"2","page":"314P","pdf":null,"JrId":"1895","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"111","title":"[Oxygen affinity of haemoglobin (author's transl)].","abstract":"","authors":"Robert, M.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Bull Physiopathol Respir (Nancy)","volume":"11","issue":"1","page":"79-170","pdf":null,"JrId":"2470","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11051546","title":"The osteoclast differentiation factor osteoprotegerin-ligand is essential for mammary gland development.","abstract":"Osteoprotegerin-ligand (OPGL) is a key osteoclast differentiation\/activation factor essential for bone remodeling. We report that mice lacking OPGL or its receptor RANK fail to form lobulo-alveolar mammary structures during pregnancy, resulting in death of newborns. Transplantation and OPGL-rescue experiments in opgl-\/- and rank-\/- pregnant females showed that OPGL acts directly on RANK-expressing mammary epithelial cells. The effects of OPGL are autonomous to epithelial cells. The mammary gland defect in female opgl-\/- mice is characterized by enhanced apoptosis and failures in proliferation and PKB activation in lobulo-alveolar buds that can be reversed by recombinant OPGL treatment. These data provide a novel paradigm in mammary gland development and an evolutionary rationale for hormonal regulation and gender bias of osteoporosis in females.","authors":"Fata, JE., Kong, YY., Li, J., Sasaki, T., Irie-Sasaki, J., Moorehead, RA., Elliott, R., Scully, S., Voura, EB., Lacey, DL., Boyle, WJ., Khokha, R., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cell","volume":"103","issue":"1","page":"41-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-11-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12351775","title":"Molecular biology. An RNA-guided pathway for the epigenome.","abstract":null,"authors":"Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Science","volume":"297","issue":"5590","page":"2215-8","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11697883","title":"Protein localization during asymmetric cell division.","abstract":null,"authors":"Schaefer, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Exp Cell Res","volume":"271","issue":"1","page":"66-74","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16014714","title":"Selective lengthening of the cell cycle in the neurogenic subpopulation of neural progenitor cells during mouse brain development.","abstract":"During embryonic development of the mammalian brain, the average cell-cycle length of progenitor cells in the ventricular zone is known to increase. However, for any given region of the developing cortex and stage of neurogenesis, the length of the cell cycle is thought to be similar in the two coexisting subpopulations of progenitors [i.e., those undergoing (symmetric) proliferative divisions and those undergoing (either asymmetric or symmetric) neuron-generating divisions]. Using cumulative bromodeoxyuridine labeling of Tis21-green fluorescent protein knock-in mouse embryos, in which these two subpopulations of progenitors can be distinguished in vivo, we now show that at the onset as well as advanced stages of telencephalic neurogenesis, progenitors undergoing neuron-generating divisions are characterized by a significantly longer cell cycle than progenitors undergoing proliferative divisions. In addition, we find that the recently characterized neuronal progenitors dividing at the basal side of the ventricular zone and in the subventricular zone have a longer G(2) phase than those dividing at the ventricular surface. These findings are consistent with the hypothesis (Calegari and Huttner, 2003) that cell-cycle lengthening can causally contribute to neural progenitors switching from proliferative to neuron-generating divisions and may have important implications for the expansion of somatic stem cells in general.","authors":"Calegari, F., Haubensak, W., Haffner, C., Huttner, WB.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Neurosci","volume":"25","issue":"28","page":"6533-8","pdf":null,"JrId":"5035","fulltextlink":null,"preprintlink":null,"articledate":"2006-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12297047","title":"Regulation of myocardial contractility and cell size by distinct PI3K-PTEN signaling pathways.","abstract":"The PTEN\/PI3K signaling pathway regulates a vast array of fundamental cellular responses. We show that cardiomyocyte-specific inactivation of tumor suppressor PTEN results in hypertrophy, and unexpectedly, a dramatic decrease in cardiac contractility. Analysis of double-mutant mice revealed that the cardiac hypertrophy and the contractility defects could be genetically uncoupled. PI3Kalpha mediates the alteration in cell size while PI3Kgamma acts as a negative regulator of cardiac contractility. Mechanistically, PI3Kgamma inhibits cAMP production and hypercontractility can be reverted by blocking cAMP function. These data show that PTEN has an important in vivo role in cardiomyocyte hypertrophy and GPCR signaling and identify a function for the PTEN-PI3Kgamma pathway in the modulation of heart muscle contractility.","authors":"Crackower, MA., Oudit, GY., Kozieradzki, I., Sarao, R., Sun, H., Sasaki, T., Hirsch, E., Suzuki, A., Shioi, T., Irie-Sasaki, J., Sah, R., Cheng, HY., Rybin, VO., Lembo, G., Fratta, L., Oliveira-dos-Santos, AJ., Benovic, JL., Kahn, CR., Izumo, S., Steinberg, SF., Wymann, MP., Backx, PH., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cell","volume":"110","issue":"6","page":"737-49","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12049731","title":"The anaphase-promoting complex: proteolysis in mitosis and beyond.","abstract":"Key events in mitosis such as sister chromatid separation and subsequent inactivation of cyclin-dependent kinase 1 are regulated by ubiquitin-dependent proteolysis. These events are mediated by the anaphase-promoting complex (APC), a cell cycle-regulated ubiquitin ligase that assembles multiubiquitin chains on regulatory proteins such as securin and cyclins and thereby targets them for destruction by the 26S proteasome.","authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Cell","volume":"9","issue":"5","page":"931-43","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12015132","title":"Cytokinesis: regulated by destruction.","abstract":"Important transitions in the cell cycle are regulated by ubiquitin-dependent degradation of specific proteins. Recent data indicate that cytokinesis is also regulated by proteolysis.","authors":"Glotzer, M., Dechant, R.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"10","page":"R344-6","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11676939","title":"Cell cycle: Waiters serving the Destruction machinery.","abstract":"Targeting regulatory proteins for destruction, and thereby controlling progression through mitosis, is the crucial task for the anaphase-promoting complex (APC). Recent evidence suggests that essential APC activators, WD40 repeat proteins of the Cdc20 family, act as long-suspected receptors for APC substrates.","authors":"Vodermaier, HC.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Curr Biol","volume":"11","issue":"20","page":"R834-7","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11387251","title":"Establishment of normal, terminally differentiating mouse erythroid progenitors: molecular characterization by cDNA arrays.","abstract":null,"authors":"Dolznig, H., Boulm\u00e9, F., Stangl, K., Deiner, EM., Mikulits, W., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"FASEB J","volume":"15","issue":"8","page":"1442-4","pdf":null,"JrId":"3815","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8142898","title":"Structure of the membrane channel porin from Rhodopseudomonas blastica at 2.0 A resolution.","abstract":"The crystal structure of a membrane channel, homotrimeric porin from Rhodopseudomonas blastica has been determined at 2.0 A resolution by multiple isomorphous replacement and structural refinement. The current model has an R-factor of 16.5% and consists of 289 amino acids, 238 water molecules, and 3 detergent molecules per subunit. The partial protein sequence and subsequently the complete DNA sequence were determined. The general architecture is similar to those of the structurally known porins. As a particular feature there are 3 adjacent binding sites for n-alkyl chains at the molecular 3-fold axis. The side chain arrangement in the channel indicates a transverse electric field across each of the 3 pore eyelets, which may explain the discrimination against nonpolar solutes. Moreover, there are 2 significantly ordered girdles of aromatic residues at the nonpolar\/polar borderlines of the interface between protein and membrane. Possibly, these residues shield the polypeptide conformation against adverse membrane fluctuations.","authors":"Kreusch, A., Neub\u00fcser, A., Schiltz, E., Weckesser, J., Schulz, GE.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Protein Sci","volume":"3","issue":"1","page":"58-63","pdf":null,"JrId":"2312","fulltextlink":null,"preprintlink":null,"articledate":"1994-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"120","title":"Proceedings: Do anti-psychotic drugs act by dopamine receptor blockade in the nucleus accumbens.","abstract":"","authors":"Crow, TJ., Deakin, JF., Longden, A.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Pharmacol","volume":"55","issue":"2","page":"295P-296P","pdf":null,"JrId":"1895","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16001071","title":"Angiotensin-converting enzyme 2 protects from severe acute lung failure.","abstract":"Acute respiratory distress syndrome (ARDS), the most severe form of acute lung injury, is a devastating clinical syndrome with a high mortality rate (30-60%) (refs 1-3). Predisposing factors for ARDS are diverse and include sepsis, aspiration, pneumonias and infections with the severe acute respiratory syndrome (SARS) coronavirus. At present, there are no effective drugs for improving the clinical outcome of ARDS. Angiotensin-converting enzyme (ACE) and ACE2 are homologues with different key functions in the renin-angiotensin system. ACE cleaves angiotensin I to generate angiotensin II, whereas ACE2 inactivates angiotensin II and is a negative regulator of the system. ACE2 has also recently been identified as a potential SARS virus receptor and is expressed in lungs. Here we report that ACE2 and the angiotensin II type 2 receptor (AT2) protect mice from severe acute lung injury induced by acid aspiration or sepsis. However, other components of the renin-angiotensin system, including ACE, angiotensin II and the angiotensin II type 1a receptor (AT1a), promote disease pathogenesis, induce lung oedemas and impair lung function. We show that mice deficient for Ace show markedly improved disease, and also that recombinant ACE2 can protect mice from severe acute lung injury. Our data identify a critical function for ACE2 in acute lung injury, pointing to a possible therapy for a syndrome affecting millions of people worldwide every year.","authors":"Imai, Y., Kuba, K., Rao, S., Huan, Y., Guo, F., Guan, B., Yang, P., Sarao, R., Wada, T., Leong-Poi, H., Crackower, MA., Fukamizu, A., Hui, CC., Hein, L., Uhlig, S., Slutsky, AS., Jiang, C., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nature","volume":"436","issue":"7047","page":"112-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11232287","title":"Differentiation, dedifferentiation, and redifferentiation of B-lineage lymphocytes: roles of the surrogate light chain and the Pax5 gene.","abstract":null,"authors":"Rolink, A., Nutt, S., Busslinger, M., ten Boekel, E., Seidl, T., Andersson, J., Melchers, F.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"64","issue":null,"page":"21-5","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"2001-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11036769","title":"Making central T-cell tolerance efficient: thymic stromal cells sample distinct self-antigen pools.","abstract":null,"authors":"Kyewski, B., R\u00f6ttinger, B., Klein, L.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Curr Top Microbiol Immunol","volume":"251","issue":null,"page":"139-45","pdf":null,"JrId":"3237","fulltextlink":null,"preprintlink":null,"articledate":"2000-11-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11232328","title":"The molecular basis of B-cell lineage commitment.","abstract":null,"authors":"Nutt, SL., Rolink, AG., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"64","issue":null,"page":"51-9","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"2001-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10933595","title":"Fidelity and infidelity in commitment to B-lymphocyte lineage development.","abstract":"During B-lymphocyte development in mouse fetal liver and bone marrow, a pre-B I cell stage is reached in which the cells express B-lineage-specific genes, such as CD19, Ig alpha and Igbeta and VpreB and lambda5, which encode the surrogate light (SL) chain. In these pre-B I cells both alleles of the immunoglobulin heavy (IgH) chain locus are D(H)J(H) rearranged. Transplantation of pre-B I cells from wild-type (e.g. C57Bl\/6) mice in histocompatible RAG-deficient hosts leads to long-term reconstitution of some of the mature B-cell compartments and to the establishment of normal IgM levels, a third of the normal serum IgA levels, and IgG levels below the detection limit. Neither T-lineage nor myeloid cells of donor origin can be detected in the transplanted hosts, indicating that the pre-B I cells are committed to B-lineage differentiation. Consequently, the B-cell-reconstituted hosts respond to T-cell-independent antigens but not to T-cell-dependent antigens. Responses to T-cell-dependent antigens can be restored in the pre-B I-cell-transplanted, RAG-deficient hosts by the concomitant transplantation of mature CD4+ T cells. The transplanted wild-type pre-B I cells do not home back to the bone marrow and become undetectable shortly after transplantation. B-lymphocyte development in Pax-5-deficient mice becomes arrested at the transition of pre-B I to pre-B II cells i.e. at the stage when V(H) to D(H)J(H) rearrangements occur and when the pre-B-cell receptor, complete with muH chains and SL chains, is normally formed. T-lineage and myeloid cell development in these mice is normal. Pre-B I cells of Pax-5-deficient mice have a wild-type pre-B I-cell-like phenotype: while they do not express Pax-5-controlled CD19 gene, and express Ig alpha to a lesser extent, they express Igbeta, VpreB and lambda5, and proliferate normally in vitro on stromal cells in the presence of interleukin (IL)-7. Clones of these pre-B I cells carry characteristic D(H)J(H) rearrangements on both IgH chain alleles. However, removal of IL-7 from the tissue cultures, unlike wild-type pre-B I cells, does not induce B-cell differentiation to surface IgM-expressing B cells, but induces macrophage differentiation. This differentiation into macrophages requires either the presence of stromal cells or addition of macrophage colony-stimulating factor (M-CSF). Addition of M-CSF followed by granulocyte-macrophage colony-stimulating factor induces the differentiation to MHC class II-expressing, antigen-presenting dendritic cells. In vitro differentiation to granulocytes and osteoclasts can also be observed in the presence of the appropriate cytokines. Moreover, transplantation of Pax-5-deficient pre-B I clones into RAG-deficient hosts, while not allowing B-cell differentiation, leads to the full reconstitution of the thymus with all stages of CD4-CD8- and CD4+CD8+ thymocytes, to normal positive and negative selection of thymocytes in the thymus, and to the development of normal, reactive mature CD4+ and CD8+ T-cell compartments in the peripheral lymphoid tissues, all carrying the clone-specific D(H)J(H) rearrangements. On the other hand, Ig alpha, Igbeta, VpreB and lambda5 are turned off in the thymocytes, demonstrating that the expression of these genes does not commit cells irreversibly to the B lineage. Further more, Pax-5-deficient pre-B I cells are long-term reconstituting cells. They home back to the bone marrow of the RAG-deficient host, can be reisolated and regrown in tissue culture, and can be retransplanted into a secondary RAG-deficient host. This again develops thymocytes and mature T cells and allows the transplanted clonal pre-B I cells to home to the bone marrow.","authors":"Rolink, AG., Schaniel, C., Busslinger, M., Nutt, SL., Melchers, F.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Immunol Rev","volume":"175","issue":null,"page":"104-11","pdf":null,"JrId":"4161","fulltextlink":null,"preprintlink":null,"articledate":"2000-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15983402","title":"Hedgehog signaling controls dorsoventral patterning, blastema cell proliferation and cartilage induction during axolotl tail regeneration.","abstract":"Tail regeneration in urodeles requires the coordinated growth and patterning of the regenerating tissues types, including the spinal cord, cartilage and muscle. The dorsoventral (DV) orientation of the spinal cord at the amputation plane determines the DV patterning of the regenerating spinal cord as well as the patterning of surrounding tissues such as cartilage. We investigated this phenomenon on a molecular level. Both the mature and regenerating axolotl spinal cord express molecular markers of DV progenitor cell domains found during embryonic neural tube development, including Pax6, Pax7 and Msx1. Furthermore, the expression of Sonic hedgehog (Shh) is localized to the ventral floor plate domain in both mature and regenerating spinal cord. Patched1 receptor expression indicated that hedgehog signaling occurs not only within the spinal cord but is also transmitted to the surrounding blastema. Cyclopamine treatment revealed that hedgehog signaling is not only required for DV patterning of the regenerating spinal cord but also had profound effects on the regeneration of surrounding, mesodermal tissues. Proliferation of tail blastema cells was severely impaired, resulting in an overall cessation of tail regeneration, and blastema cells no longer expressed the early cartilage marker Sox9. Spinal cord removal experiments revealed that hedgehog signaling, while required for blastema growth is not sufficient for tail regeneration in the absence of the spinal cord. By contrast to the cyclopamine effect on tail regeneration, cyclopamine-treated regenerating limbs achieve a normal length and contain cartilage. This study represents the first molecular localization of DV patterning information in mature tissue that controls regeneration. Interestingly, although tail regeneration does not occur through the formation of somites, the Shh-dependent pathways that control embryonic somite patterning and proliferation may be utilized within the blastema, albeit with a different topography to mediate growth and patterning of tail tissues during regeneration.","authors":"Schnapp, E., Kragl, M., Rubin, L., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Development","volume":"132","issue":"14","page":"3243-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11084352","title":"Epithelial polarity: the ins and outs of the fly epidermis.","abstract":"Epithelial cells must polarize and establish apical and basolateral membrane domains during development. Recent experiments have shed light on how apical-basal polarity is generated during cellularization in Drosophila, when around 6000 epithelial cells are created synchronously from a syncytium.","authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Curr Biol","volume":"10","issue":"21","page":"R791-4","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2001-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10655052","title":"Generation of mice from wild-type and targeted ES cells by nuclear cloning.","abstract":null,"authors":"Rideout, WM., Wakayama, T., Wutz, A., Eggan, K., Jackson-Grusby, L., Dausman, J., Yanagimachi, R., Jaenisch, R.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nat Genet","volume":"24","issue":"2","page":"109-10","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2000-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10559946","title":"VASP dynamics during lamellipodia protrusion.","abstract":null,"authors":"Rottner, K., Behrendt, B., Small, JV., Wehland, J.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nat Cell Biol","volume":"1","issue":"5","page":"321-2","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"1999-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15981476","title":"Selection and behavior of CD4+ CD25+ T cells in vivo: lessons from T cell receptor transgenic models.","abstract":"Despite great interest in CD4+ CD25+ suppressor T cells, many of the fundamental properties of these cells remain enigmatic. This is in part due to experimental limitations inherent to the study of polyclonal suppressor T cells, and the extensive use of in vitro assays. This review article intends to outline recent advances in our understanding of the biology of suppressor T cells that have emerged from the analysis of T cell receptor (TCR) transgenic models. Several laboratories have taken advantage of model systems in which suppressor T cells of defined antigen-specificity are naturally selected in order to characterize the selection and behavior of these cells in vivo. In addition to providing valuable insights into the mechanism of differentiation of suppressor T cells, these systems now offer new possibilities for understanding the mode of action of suppressor T cells. For example, adoptive transfer of small numbers of ex vivo isolated TCR transgenic suppressor T cells allows for the visualization of the fate of such cells when confronted with cognate antigen in a quasi-normal, nonlymphopenic environment. Characteristic features of the currently available TCR transgenic models of suppressor T cells will be highlighted, and particular issues pertaining to the differentiation, function, and homeostasis of this T cell subset that have emerged from these models will be discussed.","authors":"Klein, L., Emmerich, J., d'Cruz, L., Aschenbrenner, K., Khazaie, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Top Microbiol Immunol","volume":"293","issue":null,"page":"73-87","pdf":null,"JrId":"3237","fulltextlink":null,"preprintlink":null,"articledate":"2005-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10203756","title":"Separating sister chromatids.","abstract":"Loss of cohesion between sister chromatids triggers their segregation during anaphase. Recent work has identified both a cohesin complex that holds sisters together and a sister-separating protein, separin, that destroys cohesion. Separins are bound by inhibitory proteins whose proteolysis at the metaphase-anaphase transition is mediated by the anaphase-promoting complex and its activator protein CDC20 (APCCDC20). When chromosomes are misaligned, a surveillance mechanism (checkpoint) blocks sister separation by inhibiting APCCDC20. Defects in this apparatus are implicated in causing aneuploidy in human cells.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Trends Biochem Sci","volume":"24","issue":"3","page":"98-104","pdf":null,"JrId":"7837","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9695832","title":"Wanted: subcellular localization of proteins based on sequence.","abstract":null,"authors":"Eisenhaber, F., Bork, P.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Trends Cell Biol","volume":"8","issue":"4","page":"169-70","pdf":null,"JrId":"21041","fulltextlink":null,"preprintlink":null,"articledate":"1998-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7655079","title":"Expression of the helix-loop-helix gene Id3 during murine embryonic development.","abstract":"The family of dominant-negative helix-loop-helix (dnHLH) transcriptional modulators consists of four mammalian genes known to date: Id1, Id2, Id3 (Id3 was formerly designated HLH462 or HEIR1 or HLH1R21), and Id4. We have performed a detailed study of Id3 expression in mouse embryos in order to gain insight into the possible developmental control functions of this gene and to compare its expression to that of other mammalian dnHLH genes. Employing RNA in situ hybridization on sectioned mouse embryos of gestational stages E9.5-17.5 and neonatal head, we generally detected a high abundance of transcripts at early stages that gradually declined at most sites toward E15.5. Expression of Id3 in embryos was detected in brain, spinal cord, olfactory system, branchial arches, limbs, sclerotome, endocardiac cushions, the outer lining of the gut, lung, retina, the collecting system of the kidney, and in tooth anlagen. Although the abundance of mRNA decreased toward later stages in most tissues, it remained high in teeth and kidney. This expression pattern suggests that Id3 functions both in undifferentiated tissues and in organs which are in the process of differentiation. When compared to the expression of other dnHLH genes, it becomes obvious that the pattern of Id3 mainly coincides with that of Id1. This may reflect a partial redundancy in gene function. Furthermore, previous experiments suggested a mutually exclusive expression of the proto-oncogene N-myc an Id3. The results of the present study confirm these data.","authors":"Ellmeier, W., Weith, A.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Dev Dyn","volume":"203","issue":"2","page":"163-73","pdf":null,"JrId":"1281","fulltextlink":null,"preprintlink":null,"articledate":"1995-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7657408","title":"Tumor vaccines: effects and fate of IL-2 transfected murine melanoma cells in vivo.","abstract":"We have previously demonstrated the general usefulness of the adenovirus-enhanced transferrinfection (AVET) in the generation of IL-2 producing tumor vaccines. By optimizing different parameters of the transfection protocol we were able to transform the poorly immunogenic M-3 mouse melanoma cell line into a potent immunogen. A long-lasting immunity was demonstrated after administration of the IL-2 releasing vaccine, since immunized animals successfully rejected native M-3 melanoma cells even after a period of more than 6 months. We also demonstrated that in vivo administration of such a vaccine is safe since transmission of the transfected IL-2 gene in host organs was not detected. IL-2 production ceased 2 days after injection because the engineered cells were destroyed. However, RT-PCR analysis of the site of vaccine injection suggests that IL-2 exerts its effects not only directly but also by inducing a set of other immunomodulator cytokines in situ that are probably indispensable in inducing a host response. We conclude that AVET of IL-2 into tumor cells is a safe and efficient method for the generation of tumor vaccines.","authors":"Maass, G., Schweighoffer, T., Berger, M., Schmidt, W., Herbst, E., Zatloukal, K., Buschle, M., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Int J Immunopharmacol","volume":"17","issue":"2","page":"65-73","pdf":null,"JrId":"4302","fulltextlink":null,"preprintlink":null,"articledate":"1995-10-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7538024","title":"Primary, self-renewing erythroid progenitors develop through activation of both tyrosine kinase and steroid hormone receptors.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">7538024<\/PMID><DateCompleted><Year>1995<\/Year><Month>06<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>5<\/Volume><Issue>2<\/Issue><PubDate><Year>1995<\/Year><Month>Feb<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Primary, self-renewing erythroid progenitors develop through activation of both tyrosine kinase and steroid hormone receptors.<\/ArticleTitle><Pagination><MedlinePgn>191-204<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Self renewal in the hematopoietic system is thought to be restricted to a class of pluripotent stem cells. The capacity of cells with the properties of committed progenitors to self renew in many leukemias is thought to be an abnormal property resulting from the mutations responsible for leukemic transformation. It is not known how cells that can self-renew differ from cells that cannot. The notion that only pluripotent stem cells self renew has recently been challenged: normal committed erythroid progenitors capable of sustained self renewal have been described. These cells, called SCF\/TGF alpha progenitors, co-express the c-Kit receptor tyrosine kinase and c-ErbB, the avian receptor for epidermal growth factor and transforming growth factor (TGF) alpha, and they undergo continuous self renewal in response to TGF alpha and estradiol. In contrast, common erythroid progenitors (termed SCF progenitors) express only c-Kit and undergo a limited number of cell divisions in response to the c-Kit ligand, stem cell factor (SCF). Both types of progenitor faithfully reproduce terminal erythroid differentiation in vitro when exposed to differentiation factors. Here, we have investigated the developmental origin of these two classes of self-renewing erythroid progenitors.","authors":"Steinlein, P., Wessely, O., Meyer, S., Deiner, EM., Hayman, MJ., Beug, H.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Curr Biol","volume":"5","issue":"2","page":"191-204","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9503030","title":"Assignment of the gene encoding the core promoter element binding protein (COPEB) to human chromosome 10p15 by somatic hybrid analysis and fluorescence in situ hybridization.","abstract":null,"authors":"Onyango, P., Koritschoner, NP., Patrito, LC., Zenke, M., Weith, A.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Genomics","volume":"48","issue":"1","page":"143-4","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"1998-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9500672","title":"Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases.","abstract":null,"authors":"Bork, P., Dandekar, T., Eisenhaber, F., Huynen, M.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Mol Med (Berl)","volume":"76","issue":"2","page":"77-9","pdf":null,"JrId":"8748","fulltextlink":null,"preprintlink":null,"articledate":"1998-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9461209","title":"Axon guidance. A Roundabout way of avoiding the midline.","abstract":null,"authors":"Dickson, B.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Nature","volume":"391","issue":"6666","page":"442-3","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1998-02-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9425339","title":"Cell multiplication.","abstract":null,"authors":"Hunt, T., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Curr Opin Cell Biol","volume":"9","issue":"6","page":"765-7","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"1998-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9151216","title":"Phase I study to the immunotherapy of metastatic malignant melanoma by a cancer vaccine consisting of autologous cancer cells transfected with the human IL-2 gene.","abstract":null,"authors":"Stingl, G., Br\u00f6cker, EB., Mertelsmann, R., Wolff, K., Schreiber, S., K\u00e4mpgen, E., Schneeberger, A., Trcka, J., Brennscheidt, U., Veelken, H., Birnstiel, ML., Zatloukal, K., Maass, G., Wagner, E., Buschle, M., Kempe, ER., Weber, HA., Voigt, T.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Mol Med (Berl)","volume":"75","issue":"4","page":"297-9","pdf":null,"JrId":"8748","fulltextlink":null,"preprintlink":null,"articledate":"1997-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8585961","title":"Self renewal and differentiation in primary avian hematopoietic cells: an alternative to mammalian in vitro models?","abstract":null,"authors":"Beug, H., Metz, T., M\u00fcllner, EW., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Curr Top Microbiol Immunol","volume":"211","issue":null,"page":"29-39","pdf":null,"JrId":"3237","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8578600","title":"Fos and bone cell development: lessons from a nuclear oncogene.","abstract":"Vertebrate embryologists are beginning to understand the early developmental decisions that control the origin and patterning of skeletal elements. However, the regulators governing the development of the cells that form the skeleton, namely, bone and cartilage cells, are poorly understood. Recent studies using transgenic and knockout mice have established a unique role for the proto-oncogene and nuclear transcription factor, Fos, in regulating the differentiation and activity of specific bone cell populations, both during normal development and in bone disease.","authors":"Grigoriadis, AE., Wang, ZQ., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Trends Genet","volume":"11","issue":"11","page":"436-41","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1339698","title":"Biogenesis of cell-surface polarity in epithelial cells and neurons.","abstract":null,"authors":"Simons, K., Dupree, P., Fiedler, K., Huber, LA., Kobayashi, T., Kurzchalia, T., Olkkonen, V., Pimplikar, S., Parton, R., Dotti, C.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"57","issue":null,"page":"611-9","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1993-11-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8","title":"Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal amidase-esterase.","abstract":"","authors":"Moroi, K., Sato, T.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"16","page":"1517-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"399368","title":"Some evidence for interhuman transmission of medieval plague.","abstract":null,"authors":"Ell, SR.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Rev Infect Dis","volume":"1","issue":"3","page":"563-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1980-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11238463","title":"Mammalian sprouty-1 and -2 are membrane-anchored phosphoprotein inhibitors of growth factor signaling in endothelial cells.","abstract":"Growth factor-induced signaling by receptor tyrosine kinases (RTKs) plays a central role in embryonic development and in pathogenesis and, hence, is tightly controlled by several regulatory proteins. Recently, Sprouty, an inhibitor of Drosophila development-associated RTK signaling, has been discovered. Subsequently, four mammalian Sprouty homologues (Spry-1-4) have been identified. Here, we report the functional characterization of two of them, Spry-1 and -2, in endothelial cells. Overexpressed Spry-1 and -2 inhibit fibroblast growth factor- and vascular endothelial growth factor-induced proliferation and differentiation by repressing pathways leading to p42\/44 mitogen-activating protein (MAP) kinase activation. In contrast, although epidermal growth factor-induced proliferation of endothelial cells was also inhibited by Spry-1 and -2, activation of p42\/44 MAP kinase was not affected. Biochemical and immunofluorescence analysis of endogenous and overexpressed Spry-1 and -2 reveal that both Spry-1 and -2 are anchored to membranes by palmitoylation and associate with caveolin-1 in perinuclear and vesicular structures. They are phosphorylated on serine residues and, upon growth factor stimulation, a subset is recruited to the leading edge of the plasma membrane. The data indicate that mammalian Spry-1 and -2 are membrane-anchored proteins that negatively regulate angiogenesis-associated RTK signaling, possibly in a RTK-specific fashion.","authors":"Impagnatiello, MA., Weitzer, S., Gannon, G., Compagni, A., Cotten, M., Christofori, G.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Cell Biol","volume":"152","issue":"5","page":"1087-98","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8994822","title":"Mitosis: don't get mad, get even.","abstract":"The 'mitotic spindle checkpoint' ensures that, before a cell exits from mitosis, all of its chromosomes are aligned on the spindle to form the metaphase plate. Mad2 is an essential component of this checkpoint system and it binds specifically to unattached kinetochores.","authors":"Glotzer, M.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Curr Biol","volume":"6","issue":"12","page":"1592-4","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1997-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8805380","title":"A homage to Giardia.","abstract":null,"authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Curr Biol","volume":"6","issue":"9","page":"1042","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1997-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8548277","title":"Cell polarity. The importance of being polar.","abstract":"Cell polarization is often accompanied by cytoskeletal rearrangements. Two signalling proteins, a GTPase and a kinase, are required for both actin and microtubule rearrangements. Are these two systems coupled?","authors":"Glotzer, M., Hyman, AA.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Curr Biol","volume":"5","issue":"10","page":"1102-5","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1996-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8664547","title":"The role of BSAP (Pax-5) in B-cell development.","abstract":"The hierarchy of transcriptional control in B-cell development has recently been analyzed by targeted gene inactivation in the mouse. In this manner, the paired box containing gene Pax-5, encoding the B cell specific transcription factor BSAP, has been shown to play a key role in early B lymphopoiesis. Other experimental strategies have implicated BSAP in the control of cell proliferation, isotype switching and transcription of the immunoglobulin heavy-chain gene at late stages of B-cell differentiation.","authors":"Busslinger, M., Urb\u00e1nek, P.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Curr Opin Genet Dev","volume":"5","issue":"5","page":"595-601","pdf":null,"JrId":"2199","fulltextlink":null,"preprintlink":null,"articledate":"1996-08-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8531702","title":"Avian hematopoietic cell culture: in vitro model systems to study oncogenic transformation of hematopoietic cells.","abstract":null,"authors":"Beug, H., Steinlein, P., Bartunek, P., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Methods Enzymol","volume":"254","issue":null,"page":"41-76","pdf":null,"JrId":"5787","fulltextlink":null,"preprintlink":null,"articledate":"1996-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7879657","title":"Oncogenic properties of the middle T antigens of polyomaviruses.","abstract":null,"authors":"Kiefer, F., Courtneidge, SA., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Adv Cancer Res","volume":"64","issue":null,"page":"125-57","pdf":null,"JrId":"262","fulltextlink":null,"preprintlink":null,"articledate":"1995-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8469984","title":"Methylation and imprinting: from host defense to gene regulation?","abstract":null,"authors":"Barlow, DP.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Science","volume":"260","issue":"5106","page":"309-10","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8062592","title":"Report and abstracts of the First International Workshop on Human Chromosome 1 Mapping 1994. Bethesda, Maryland, March 25-27, 1994.","abstract":null,"authors":"Dracopoli, NC., Bruns, GA., Brodeur, GM., Landes, GM., Matise, TC., Seldin, MF., Vance, JM., Weith, A.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Cytogenet Cell Genet","volume":"67","issue":"3","page":"144-65","pdf":null,"JrId":"3248","fulltextlink":null,"preprintlink":null,"articledate":"1994-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8259207","title":"Cell cycle. Dams and sluices.","abstract":null,"authors":"Nasmyth, K., Hunt, T.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Nature","volume":"366","issue":"6456","page":"634-5","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1994-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7939685","title":"c-Fos: a key regulator of osteoclast-macrophage lineage determination and bone remodeling.","abstract":"Mice lacking the proto-oncogene c-fos develop the bone disease osteopetrosis. Fos mutant mice were found to have a block in the differentiation of bone-resorbing osteoclasts that was intrinsic to hematopoietic cells. Bone marrow transplantation rescued the osteopetrosis, and ectopic c-fos expression overcame this differentiation block. The lack of Fos also caused a lineage shift between osteoclasts and macrophages that resulted in increased numbers of bone marrow macrophages. These results identify Fos as a key regulator of osteoclast-macrophage lineage determination in vivo and provide insights into the molecular mechanisms underlying metabolic bone diseases.","authors":"Grigoriadis, AE., Wang, ZQ., Cecchini, MG., Hofstetter, W., Felix, R., Fleisch, HA., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Science","volume":"266","issue":"5184","page":"443-8","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1994-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7880528","title":"Insights into erythroid differentiation obtained from studies on avian erythroblastosis virus.","abstract":"Analysis of the oncogenes v-erbB and v-erbA and their normal proto-oncogene counterparts has revealed several novel aspects of erythroid differentiation. A new erythroid progenitor capable of extended self-renewal has been described, tyrosine kinase receptors and steroid hormone receptors have been found to cooperate in controlling self-renewal, and dramatic alterations in the cell cycle have been found to accompany induction of terminal differentiation.","authors":"Beug, H., M\u00fcllner, EW., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Curr Opin Cell Biol","volume":"6","issue":"6","page":"816-24","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"1995-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8146914","title":"Electroporation of cosmid DNA into bacterial cells.","abstract":null,"authors":"Kubicka, P., Kramaric, G.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Trends Genet","volume":"10","issue":"1","page":"5","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"1994-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8061333","title":"Introduction: oncogenes and differentiation.","abstract":null,"authors":"Enrietto, PJ., Beug, H.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Semin Cancer Biol","volume":"5","issue":"2","page":"91-4","pdf":null,"JrId":"1211","fulltextlink":null,"preprintlink":null,"articledate":"1994-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8001127","title":"Complete block of early B cell differentiation and altered patterning of the posterior midbrain in mice lacking Pax5\/BSAP.","abstract":"The Pax5 gene, coding for the transcription factor BSAP, was mutated in the mouse germline by targeted disruption. Homozygous mutant mice were born alive, became growth retarded, and usually died within three weeks. About 5% of mutants survived to adulthood and were fertile, but severely runted. Morphogenesis of the posterior midbrain was affected as early as embryonic day 16.5, leading to a reduction of the inferior colliculus near the midline and to altered foliation of the anterior cerebellum. Moreover, all mutants failed to produce small pre-B, B, and plasma cells owing to a complete arrest of B cell development at an early precursor stage. These data define a key role for Pax5 in early B lymphopoiesis and midbrain patterning.","authors":"Urb\u00e1nek, P., Wang, ZQ., Fetka, I., Wagner, EF., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Cell","volume":"79","issue":"5","page":"901-12","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1995-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"5","title":"Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin.","abstract":"","authors":"Hendrickson, WA., Ward, KB.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Biophys Res Commun","volume":"66","issue":"4","page":"1349-56","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"4","title":"Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake.","abstract":"","authors":"Wiesmann, UN., DiDonato, S., Herschkowitz, NN.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Biophys Res Commun","volume":"66","issue":"4","page":"1338-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8402888","title":"Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins.","abstract":"In budding yeast, G1 cyclins such as CLN1 and CLN2 are expressed in G1 and S phases, while mitotic cyclins such as CLB1 and CLB2 are expressed in G2 and M phases. We find that the CLBs play a central role in the transition from CLNs to CLBs: the CLBs stimulate their own expression while repressing that of CLNs. This negative regulation of CLNs may occur via the transcription factor SWI4, because CLBs are necessary for G2 repression of SCB-regulated genes like CLN1 and CLN2 but not for repression of MCB-regulated genes like DNA polymerase and CLB5. Furthermore, SW14 associates with CLB2 protein and is a substrate for the CLB2-associated CDC28 kinase in vitro.","authors":"Amon, A., Tyers, M., Futcher, B., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Cell","volume":"74","issue":"6","page":"993-1007","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1993-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7532151","title":"The gene coding for the B cell surface protein CD19 is localized on human chromosome 16p11.","abstract":"The CD19 gene codes for one of the earliest markers of the human B cell lineage and is a target for the B lymphoid-specific transcription factor BSAP (Pax-5). The transmembrane protein CD19 has been implicated in controlling proliferation of mature B lymphocytes by modulating signal transduction through the antigen receptor. In this study, we have employed Southern blot and fluorescence in situ hybridization analyses to localize the CD19 gene to human chromosome 16p11.","authors":"Stapleton, P., Kozmik, Z., Weith, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Hum Genet","volume":"95","issue":"2","page":"223-5","pdf":null,"JrId":"4137","fulltextlink":null,"preprintlink":null,"articledate":"1995-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11179879","title":"Rho GTPases in growth cone guidance.","abstract":"It is now well established that the small GTPases of the Rho family--Rac, Cdc42 and Rho--regulate growth cone morphology. Less clear is their role in guiding the growth cone. Do they act permissively, providing the dynamic actin structures needed for guidance? Or do they act instructively, transducing specific guidance signals? Recent studies have provided the first strong evidence for an instructive role: extracellular guidance cues can modulate Rho GTPase activities in vitro, and Rho GTPase activators function in growth cone guidance in vivo. The pathways linking Rho GTPases and the actin cytoskeleton are also rapidly coming into view, revealing further points of regulation by extracellular guidance cues. The growth cone is therefore guided by signals transduced both via and independently of Rho GTPases.","authors":"Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Curr Opin Neurobiol","volume":"11","issue":"1","page":"103-10","pdf":null,"JrId":"2201","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7502071","title":"Gametic imprinting in mammals.","abstract":"Embryonic development in mammals is distinct from that in other vertebrates because it depends on a small number of imprinted genes that are specially expressed from either the maternal or paternal genome. Why mammals are uniquely dependent on sexual reproduction and how this dependency is dictated at a molecular level are questions that have been intensively investigated during the past 2 years. Gene inactivation experiments have confirmed predictions that imprinted genes regulate embryonic and placental growth and that DNA methylation is part of the imprinting mechanism. Despite these considerable achievements, the reason why imprinted hemizygosity is used as a mechanism to regulate the intrauterine growth of mammalian embryos remains elusive.","authors":"Barlow, DP.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Science","volume":"270","issue":"5242","page":"1610-3","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1996-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7764468","title":"Non-viral approaches to gene therapy.","abstract":"Several advances in non-viral gene transfer technology have been reported over the past year. Cationic lipids have been successfully used to deliver genes in vivo, providing a clear alternative to recombinant viruses. In addition, investigators have demonstrated that direct application of DNA via injection or particle bombardment can be used for vaccination. Analysis of the mechanisms employed by viruses to invade cells has demonstrated a crucial role for membrane-active proteins or peptides in the entry process. Several non-viral systems that include membrane-active elements are now available.","authors":"Cotten, M., Wagner, E.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Curr Opin Biotechnol","volume":"4","issue":"6","page":"705-10","pdf":null,"JrId":"1258","fulltextlink":null,"preprintlink":null,"articledate":"1994-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7736580","title":"A 20S complex containing CDC27 and CDC16 catalyzes the mitosis-specific conjugation of ubiquitin to cyclin B.","abstract":"Cyclin B is degraded at the onset of anaphase by a ubiquitin-dependent proteolytic system. We have fractionated mitotic Xenopus egg extracts to identify components required for this process. We find that UBC4 and at least one other ubiquitin-conjugating enzyme can support cyclin B ubiquitination. The mitotic specificity of cyclin ubiquitination is determined by a 20S complex that contains homologs of budding yeast CDC16 and CDC27. Because these proteins are required for anaphase in yeast and mammalian cells, we refer to this complex as the anaphase-promoting complex (APC). CDC27 antibodies deplete APC activity, while immunopurified CDC27 complexes are sufficient to complement either interphase extracts or a mixture of recombinant UBC4 and the ubiquitin-activating enzyme E1. These results suggest that APC functions as a regulated ubiquitin-protein ligase that targets cyclin B for destruction in mitosis.","authors":"King, RW., Peters, JM., Tugendreich, S., Rolfe, M., Hieter, P., Kirschner, MW.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell","volume":"81","issue":"2","page":"279-88","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24395427","title":"Engineered micro-objects as scaffolding elements in cellular building blocks for bottom-up tissue engineering approaches.","abstract":"A material-based bottom-up approach is proposed towards an assembly of cells and engineered micro-objects at the macroscale. We show how shape, size and wettability of engineered micro-objects play an important role in the behavior of cells on these objects. This approach can, among other applications, be used as a tool to engineer complex 3D tissues of clinically relevant size.","authors":"Leferink, A., Schipper, D., Arts, E., Vrij, E., Rivron, N., Karperien, M., Mittmann, K., van Blitterswijk, C., Moroni, L., Truckenm\u00fcller, R.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Adv Mater","volume":"26","issue":"16","page":"2592-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6274086","title":"Hematopoietic cells transformed in vitro by REVT avian reticuloendotheliosis virus express characteristics of very immature lymphoid cells.","abstract":null,"authors":"Beug, H., M\u00fcller, H., Grieser, S., Doederlein, G., Graf, T.","publication_status":"ppublish","journalpubyear":"1981","journaltitle":"Virology","volume":"115","issue":"2","page":"295-309","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1982-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6269281","title":"Clonal isolate of the simian sarcoma virus codes for a Gag-related 65,000-dalton protein.","abstract":null,"authors":"Matthews, TJ., Broughton, EM., Weinhold, KJ., Bolognesi, DP., Graf, T., Beug, H.","publication_status":"ppublish","journalpubyear":"1981","journaltitle":"Virology","volume":"114","issue":"1","page":"124-31","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1981-11-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20176920","title":"Automated microscopy for high-content RNAi screening.","abstract":"Fluorescence microscopy is one of the most powerful tools to investigate complex cellular processes such as cell division, cell motility, or intracellular trafficking. The availability of RNA interference (RNAi) technology and automated microscopy has opened the possibility to perform cellular imaging in functional genomics and other large-scale applications. Although imaging often dramatically increases the content of a screening assay, it poses new challenges to achieve accurate quantitative annotation and therefore needs to be carefully adjusted to the specific needs of individual screening applications. In this review, we discuss principles of assay design, large-scale RNAi, microscope automation, and computational data analysis. We highlight strategies for imaging-based RNAi screening adapted to different library and assay designs.","authors":"Conrad, C., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Cell Biol","volume":"188","issue":"4","page":"453-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15935765","title":"Neural circuitry that governs Drosophila male courtship behavior.","abstract":"Male-specific fruitless (fru) products (Fru(M)) are both necessary and sufficient to \"hardwire\" the potential for male courtship behavior into the Drosophila nervous system. Fru(M) is expressed in approximately 2% of neurons in the male nervous system, but not in the female. We have targeted the insertion of GAL4 into the fru locus, allowing us to visualize and manipulate the Fru(M)-expressing neurons in the male as well as their counterparts in the female. We present evidence that these neurons are directly and specifically involved in male courtship behavior and that at least some of them are interconnected in a circuit. This circuit includes olfactory neurons required for the behavioral response to sex pheromones. Anatomical differences in this circuit that might account for the dramatic differences in male and female sexual behavior are not apparent.","authors":"Stockinger, P., Kvitsiani, D., Rotkopf, S., Tiri\u00e1n, L., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell","volume":"121","issue":"5","page":"795-807","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"4993098","title":"Specific inhibition of cell contact formation in Dictyostelium by univalent antibodies.","abstract":null,"authors":"Beug, H., Gerisch, G., Kempff, S., Riedel, V., Cremer, G.","publication_status":"ppublish","journalpubyear":"1970","journaltitle":"Exp Cell Res","volume":"63","issue":"1","page":"147-58","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1971-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3472752","title":"Efficient expression of foreign genes in mice reconstituted with retrovirus-infected bone marrow cells.","abstract":null,"authors":"Keller, G., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"51 Pt 2","issue":null,"page":"1053-8","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1987-06-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3235154","title":"Cooperativity of viral oncogenes in avian leukaemia.","abstract":null,"authors":"Graf, T., Kahn, P., Leutz, A., Beug, H., Vennstr\u00f6m, B.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"IARC Sci Publ","volume":null,"issue":"92","page":"165-70","pdf":null,"JrId":"22092","fulltextlink":null,"preprintlink":null,"articledate":"1989-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2223991","title":"[Presentation of a mixed local area network with Apple Macintosh computers, MS-Dos compatible PC's and\/or a Sun workstation].","abstract":null,"authors":"Huber, LA., B\u00f6ck, G., Wick, G.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Biomed Tech (Berl)","volume":"35 Suppl 2","issue":null,"page":"20-2","pdf":null,"JrId":"1167","fulltextlink":null,"preprintlink":null,"articledate":"1990-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2209535","title":"EMBO medal review. On transferring genes into stem cells and mice.","abstract":null,"authors":"Wagner, EF.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"EMBO J","volume":"9","issue":"10","page":"3024-32","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1990-11-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1840270","title":"Some facts and thoughts on cell cycle control in yeast.","abstract":null,"authors":"Nasmyth, K., Dirick, L., Surana, U., Amon, A., Cvrckova, F.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"56","issue":null,"page":"9-20","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1992-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1797090","title":"Analysis of chromosome band 1p36 alterations by chromosomal in situ suppression hybridization with a microclone DNA bank.","abstract":"Alterations of the distal portion of chromosome Ip are a recurrent abnormality of several types of human cancer. In this study we show that chromosomal in situ suppression hybridization with a regional 1p36 DNA bank generated by microdissection and microcloning can be employed to detect translocations involving 1p36.","authors":"Zink, D., Weith, A., Martinsson, T., Schwab, M.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Genes Chromosomes Cancer","volume":"3","issue":"5","page":"407-10","pdf":null,"JrId":"1860","fulltextlink":null,"preprintlink":null,"articledate":"1992-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11163237","title":"Chronic myeloid leukemia with increased granulocyte progenitors in mice lacking junB expression in the myeloid lineage.","abstract":"The functions of JunB during myelopoiesis were studied in vivo. Transgenic mice specifically lacking JunB expression in the myeloid lineage (junB(-\/-)Ubi-junB mice) develop a transplantable myeloproliferative disease eventually progressing to blast crisis, which resembles human chronic myeloid leukemia. Similarly, mice reconstituted with ES cell-derived junB-\/- fetal liver cells also develop a myeloproliferative disease. In both cases, the absence of JunB expression results in increased numbers of granulocyte progenitors, which display enhanced GM-CSF-mediated proliferation and extended survival, associated with changes in the expression levels of the GM-CSFalpha receptor, the anti-apoptotic proteins Bcl2 and Bclx, and the cell cycle regulators p16(INK4a) and c-Jun. Importantly, ectopic expression of JunB fully reverts the immature and hyperproliferative phenotype of JunB-deficient myeloid cells. These results identify JunB as a key transcriptional regulator of myelopoiesis and a potential tumor suppressor gene.","authors":"Passegu\u00e9, E., Jochum, W., Schorpp-Kistner, M., M\u00f6hle-Steinlein, U., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell","volume":"104","issue":"1","page":"21-32","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2141913","title":"3 processing of histone RNA precursors.","abstract":null,"authors":"Vasserot, AP., Hoffmann, I., Tabiti, K., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Mol Biol Rep","volume":"14","issue":"2-3","page":"211-2","pdf":null,"JrId":"5917","fulltextlink":null,"preprintlink":null,"articledate":"1990-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11179212","title":"Vascular endothelial growth factor-C-mediated lymphangiogenesis promotes tumour metastasis.","abstract":"Metastasis is a frequent and lethal complication of cancer. Vascular endothelial growth factor-C (VEGF-C) is a recently described lymphangiogenic factor. Increased expression of VEGF-C in primary tumours correlates with dissemination of tumour cells to regional lymph nodes. However, a direct role for VEGF-C in tumour lymphangiogenesis and subsequent metastasis has yet to be demonstrated. Here we report the establishment of transgenic mice in which VEGF-C expression, driven by the rat insulin promoter (Rip), is targeted to beta-cells of the endocrine pancreas. In contrast to wild-type mice, which lack peri-insular lymphatics, RipVEGF-C transgenics develop an extensive network of lymphatics around the islets of Langerhans. These mice were crossed with Rip1Tag2 mice, which develop pancreatic beta-cell tumours that are neither lymphangiogenic nor metastatic. Double-transgenic mice formed tumours surrounded by well developed lymphatics, which frequently contained tumour cell masses of beta-cell origin. These mice frequently developed pancreatic lymph node metastases. Our findings demonstrate that VEGF-C-induced lymphangiogenesis mediates tumour cell dissemination and the formation of lymph node metastases.","authors":"Mandriota, SJ., Jussila, L., Jeltsch, M., Compagni, A., Baetens, D., Prevo, R., Banerji, S., Huarte, J., Montesano, R., Jackson, DG., Orci, L., Alitalo, K., Christofori, G., Pepper, MS.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"EMBO J","volume":"20","issue":"4","page":"672-82","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2001-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2004419","title":"DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein.","abstract":"We have studied the mechanism by which DNA methylation inhibits transcription both in cell-free nuclear extracts and in the living cell. Repression of transcription in vitro for four different promoters was shown to be an indirect effect. The mediator of repression had properties indistinguishable from those of a methyl-CpG binding protein (MeCP-1) that has been previously identified. Use of differentially methylated promoters and methylated competitors in transient transfection assays suggested that indirect repression via MeCP-1 also occurs in the living cell. This was supported by the fact that MeCP-1-deficient cells showed much reduced repression of methylated genes.","authors":"Boyes, J., Bird, A.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Cell","volume":"64","issue":"6","page":"1123-34","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1991-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1794045","title":"Maps of mouse chromosome 17: first report. Committee for Mouse Chromosome 17.","abstract":null,"authors":"","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Mamm Genome","volume":"1","issue":"1","page":"5-29","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"1992-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1498437","title":"Mouse chromosome 17.","abstract":null,"authors":"Silver, LM., Artzt, K., Barlow, D., Fischer-Lindahl, K., Lyon, MF., Klein, J., Snyder, L.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Mamm Genome","volume":"3 Spec No","issue":null,"page":"S241-60","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"1992-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1365873","title":"How do cells control the timing of DNA replication and mitosis?","abstract":null,"authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Harvey Lect","volume":"88","issue":null,"page":"141-71","pdf":null,"JrId":"3959","fulltextlink":null,"preprintlink":null,"articledate":"1995-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10959045","title":"Overview--burgeoning promise in metastasis research.","abstract":"","authors":"Wyke, JA.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Eur J Cancer","volume":"36","issue":"13 Spec No","page":"1589-94","pdf":null,"JrId":"1697","fulltextlink":null,"preprintlink":null,"articledate":"2000-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18376004","title":"The discovery of ACE2 and its role in acute lung injury.","abstract":"During several months of 2002, severe acute respiratory syndrome (SARS) caused by SARS-coronavirus (SARS-CoV) spread rapidly from China throughout the world causing more than 800 deaths due to the development of acute respiratory distress syndrome (ARDS), which is the severe form of acute lung injury (ALI). Interestingly, a novel homologue of angiotensin converting-enzyme (ACE), termed angiotensin converting enzyme 2 (ACE2) has been identified as a receptor for SARS-CoV. ACE and ACE2 share homology in their catalytic domain and provide different key functions in the renin-angiotensin system. ACE cleaves angiotensin I to generate angiotensin II that is a key effector peptide of the system and exerts multiple biological functions, whereas ACE2 reduces angiotensin II levels. Importantly, our recent studies using ACE2 knockout mice have demonstrated that ACE2 protects murine lungs from ARDS. Furthermore, SARS-CoV infections and the Spike protein of the SARS-CoV reduce ACE2 expression. Notably, injection of SARS-CoV Spike into mice worsens acute lung failure in vivo that can be attenuated by blocking the renin-angiotensin pathway, suggesting the activation of pulmonary RAS influences the pathogenesis of ALI\/ARDS and SARS.","authors":"Penninger, J., Imai, Y., Kuba, K.","publication_status":"aheadofprint","journalpubyear":"2008","journaltitle":"Exp Physiol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":"1614","fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19734049","title":"Mitotic phosphatases: from entry guards to exit guides.","abstract":"While the importance of protein kinases for the spatial and temporal control of mitotic events has long been recognized, mitotic phosphatases have only recently come into the limelight. It is now well established that protein phosphatases counteract mitotic kinases, so contributing to the generation of switch-like responses at mitotic stage transitions. In addition, the timely dephosphorylation of mitotic phosphoproteins by tightly regulated phosphatases is required for the assembly and stability of the mitotic spindle, the initiation of anaphase, and exit from mitosis. Mitotic phosphatases also emerge as effectors of the DNA damage and spindle assembly checkpoints. These new findings show that protein phosphatases regulate every step of mitosis and provide novel insights into the dynamic and versatile nature of mitotic phosphoregulation.","authors":"Bollen, M., Gerlich, DW., Lesage, B.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Trends Cell Biol","volume":"19","issue":"10","page":"531-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"972675","title":"Rotational diffusion of band 3 proteins in the human erythrocyte membrane.","abstract":null,"authors":"Cherry, RJ., B\u00fcrkli, A., Busslinger, M., Schneider, G., Parish, GR.","publication_status":"ppublish","journalpubyear":"1976","journaltitle":"Nature","volume":"263","issue":"5576","page":"389-93","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1976-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"566684","title":"Dictyostelium, a microbial model for biochemical studies on cell recognition.","abstract":null,"authors":"Gerisch, G., M\u00fcller, K., Beug, H.","publication_status":"ppublish","journalpubyear":"1978","journaltitle":"Biochem Soc Trans","volume":"6","issue":"3","page":"481-6","pdf":null,"JrId":"3328","fulltextlink":null,"preprintlink":null,"articledate":"1978-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1969136","title":"Requirement for the C-terminal domain of the v-erbA oncogene protein for biological function and transcriptional repression.","abstract":"In contrast to the normal thyroid hormone receptor, the v-erbA product fails to bind hormone due to mutations in the C-terminal ligand binding domain and thus appears to represent a hormone-independent, oncogenic transcription factor. Therefore, we asked whether or not the C-terminal domain of v-erbA is required for its biological activity and putative transcriptional control functions by analysing mutants with altered C-termini. A v-erbA protein truncated in the C-terminal domain lacked detectable biological activity in transformed erythroblasts and its transcriptional repression function with respect to the band 3 gene was abolished. The protein displayed a nuclear location and could still bind to DNA, indicating that the N-terminal region retained DNA-binding activity but was insufficient to produce characteristic v-erbA changes in erythroblasts. Another biologically defective v-erbA variant with a small frameshift towards the extreme C-terminus also failed to repress band 3, indicating a requirement for a specific C-terminal structure in repression. However, this mutant retained partial biological activity, stimulating erythroblasts to grow at a higher rate than cells containing a completely inactive, deleted v-erbA gene. The results demonstrate that the mutated hormone-binding domain, in addition to the DNA-binding region, is critical for v-erbA biological and transcriptional control functions.","authors":"Forrest, D., Mu\u00f1oz, A., Raynoschek, C., Vennstr\u00f6m, B., Beug, H.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Oncogene","volume":"5","issue":"3","page":"309-16","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1990-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15916952","title":"A REC8-dependent plant Shugoshin is required for maintenance of centromeric cohesion during meiosis and has no mitotic functions.","abstract":"During meiosis, sequential release of sister chromatid cohesion (SSC) during two successive nuclear divisions allows the production of haploid gametes from diploid progenitor cells. Release of SSC along chromosome arms allows first a reductional segregation of homologs, and, subsequently, release of centromeric cohesion at anaphase II allows the segregation of chromatids. The Shugoshin (SGO) protein family plays a major role in the protection of centromeric cohesion in Drosophila and yeast. We have isolated a maize mutant that displays premature loss of centromeric cohesion at anaphase I. We showed that this phenotype is due to the absence of ZmSGO1 protein, a maize shugoshin homolog. We also show that ZmSGO1 is localized to the centromeres. The ZmSGO1 protein is not found on mitotic chromosomes and has no obvious mitotic function. On the basis of these results, we propose that ZmSGO1 specifically maintains centromeric cohesion during meiosis I and therefore suggest that SGO1 core functions during meiosis are conserved across kingdoms and in large-genome species. However, in contrast to other Shugoshins, we observed an early and REC8-dependent recruitment of ZmSGO1 in maize, suggesting that control of SGO1 recruitment to chromosomes is different in plants than in other model organisms.","authors":"Hamant, O., Golubovskaya, I., Meeley, R., Fiume, E., Timofejeva, L., Schleiffer, A., Nasmyth, K., Cande, WZ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"10","page":"948-54","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2005-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19733077","title":"Cytokinetic abscission: cellular dynamics at the midbody.","abstract":"The intercellular canal containing the midbody is one of the most prominent structures in dividing animal cells, yet its function in the completion of cytokinesis by abscission remains largely unknown. This is because of its small size, which makes it difficult to investigate the cytoskeletal and membrane dynamics underlying abscission by standard light microscopy. The advent of new fluorescent probes and imaging technologies, along with sophisticated perturbation tools, provides new possibilities to elucidate the molecular control of this essential cell biological process. Here we discuss the control of midbody assembly and current models for the mechanism of abscission in animal cells. We highlight new methodologies that will facilitate testing and refining of these models.","authors":"Steigemann, P., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Trends Cell Biol","volume":"19","issue":"11","page":"606-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17979845","title":"From T-cell activation signals to signaling control of anti-cancer immunity.","abstract":"The activation of resting T cells is crucial to most immune processes. Recognition of foreign antigen by T-cell receptors has to be correctly translated into signal transduction events necessary for the induction of an effective immune response. In this review, we discuss the essential signals, molecules, and processes necessary to achieve full T-cell activation. In addition to describing these key biological events, we also discuss how T-cell receptor signaling may be harnessed to yield new therapeutic targets for a next generation of anti-cancer drugs.","authors":"Cronin, SJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Immunol Rev","volume":"220","issue":"","page":"151-68","pdf":null,"JrId":"4161","fulltextlink":null,"preprintlink":null,"articledate":"2008-01-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15909298","title":"The last but not the least: the origin and significance of trailing adhesions in fibroblastic cells.","abstract":"Mature adhesions in a motile fibroblast can be classified as stationary \"towing\" adhesions in the front and sliding trailing adhesions that resist the traction force. Adhesions formed at the front of motile fibroblasts rarely reach the trailing zone, due to disassembly promoted by intensive microtubule targeting. Here, we show that the majority of adhesions found at the trailing edge originate within small short-lived protrusions that extend laterally and backwards from the cell edge. These adhesions enlarge by sliding and by fusion with neighboring adhesions. A further subset of trailing adhesions is initiated at a novel site proximal to trailing stress fibre termini. Following tail retraction, trailing adhesions are actively regenerated and the stress fibre system is remodeled accordingly; the tensile forces elaborated by the contractile actin system are consequently redirected according to trailing adhesion location. We conclude that persistent and dynamic anchorage of the cell rear is needed for the maintenance of continuous unidirectional movement of fibroblasts.","authors":"Rid, R., Schiefermeier, N., Grigoriev, I., Small, JV., Kaverina, I.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell Motil Cytoskeleton","volume":"61","issue":"3","page":"161-71","pdf":null,"JrId":"2849","fulltextlink":null,"preprintlink":null,"articledate":"2005-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18670445","title":"Twenty years of cell-cycle conferences in Roscoff.","abstract":"At the end of April 2008, the cell-cycle community celebrated the twentieth anniversary of the Jacques-Monod cell-cycle conferences in Roscoff (France), where the discovery of Cdk1 as a key cell-cycle regulator was first discussed in 1988.","authors":"Vernos, I., Peters, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Cell Biol","volume":"10","issue":"8","page":"877-80","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15866163","title":"Canonical Wnt\/beta-catenin signaling prevents osteoblasts from differentiating into chondrocytes.","abstract":"Osteoblasts and chondrocytes are involved in building up the vertebrate skeleton and are thought to differentiate from a common mesenchymal precursor, the osteo-chondroprogenitor. Although numerous transcription factors involved in chondrocyte and osteoblast differentiation have been identified, little is known about the signals controlling lineage decisions of the two cell types. Here, we show by conditionally deleting beta-catenin in limb and head mesenchyme that beta-catenin is required for osteoblast lineage differentiation. Osteoblast precursors lacking beta-catenin are blocked in differentiation and develop into chondrocytes instead. In vitro experiments demonstrate that this is a cell-autonomous function of beta-catenin in an osteoblast precursor. Furthermore, detailed in vivo and in vitro loss- and gain-of-function analyses reveal that beta-catenin activity is necessary and sufficient to repress the differentiation of mesenchymal cells into Runx2- and Sox9-positive skeletal precursors. Thus, canonical Wnt\/beta-catenin signaling is essential for skeletal lineage differentiation, preventing transdifferentiation of osteoblastic cells into chondrocytes.","authors":"Hill, TP., Sp\u00e4ter, D., Taketo, MM., Birchmeier, W., Hartmann, C.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Dev Cell","volume":"8","issue":"5","page":"727-38","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18641637","title":"Epidermal JunB represses G-CSF transcription and affects haematopoiesis and bone formation.","abstract":"Mice that lack JunB in epidermal cells are born with normal skin; however, keratinocytes hyperproliferate in vitro and on TPA treatment in vivo. Loss of JunB expression in the epidermis of adult mice affects the skin, the proliferation of haematopoietic cells and bone formation. G-CSF is a direct transcriptional target of JunB and mutant epidermis releases large amounts of G-CSF that reach high systemic levels and cause skin ulcerations, myeloproliferative disease and low bone mass. The absence of G-CSF significantly improves hyperkeratosis and prevents the development of myeloproliferative disease, but does not affect bone loss. This study describes a mechanism by which the absence of JunB in epithelial cells causes multi-organ disease, suggesting that the epidermis can act as an endocrine-like organ.","authors":"Meixner, A., Zenz, R., Schonthaler, HB., Kenner, L., Scheuch, H., Penninger, JM., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Cell Biol","volume":"10","issue":"8","page":"1003-11","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18641461","title":"Efficient adult skeletal muscle regeneration in mice deficient in p38beta, p38gamma and p38delta MAP kinases.","abstract":"Adult skeletal muscle is a very stable tissue containing a small population of myofiber-associated quiescent satellite cells compared with late embryonic\/neonatal skeletal muscle, which contains highly proliferating myoblasts and small actively growing myofibers, suggesting that specific regulatory pathways may control myogenesis at distinct developmental stages. The p38 MAPK signaling pathway is central for myogenesis, based on studies using immortalized and neonatal primary myoblasts in vitro. However, the contribution of this pathway to adult myogenesis has never been investigated. Four p38 isoforms (p38alpha, p38beta, p38gamma and p38delta) exist in mammalian cells, being p38alpha and p38gamma the most abundantly expressed isoforms in adult skeletal muscle. Given the embryonic\/neonatal lethality of p38alpha-deficient mice, here we investigate the relative contribution of p38beta, p38gamma and p38delta to adult myogenesis. Regeneration and myofiber growth of adult muscle proceeds with similar efficiency in mice lacking p38beta, p38gamma and p38delta as in wild-type control mice. In agreement with this, there is no difference in adult primary myoblasts behavior in vitro among the different genotypes. Importantly, the pattern of p38 activation (ascribed to p38alpha) remains unperturbed during satellite cell-mediated myogenesis in vitro and adult muscle regeneration in wild type and p38beta-, p38gamma- and p38delta-deficient mice, rendering p38alpha as the essential p38 isoform sustaining adult myogenesis. This study constitutes the first analysis addressing the functionality of p38beta, p38gamma and p38delta in satellite cell-dependent adult muscle regeneration and growth.","authors":"Ruiz-Bonilla, V., Perdiguero, E., Gresh, L., Serrano, AL., Zamora, M., Sousa-Victor, P., Jard\u00ed, M., Wagner, EF., Mu\u00f1oz-C\u00e1noves, P.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell Cycle","volume":"7","issue":"14","page":"2208-14","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18636085","title":"When flies and mice develop cancer. Meeting on development and cancer.","abstract":null,"authors":"Gerlitz, O., Wagner, EF., Moreno, E.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO Rep","volume":"9","issue":"8","page":"730-4","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18604200","title":"EGFR signalling as a negative regulator of Notch1 gene transcription and function in proliferating keratinocytes and cancer.","abstract":"The Notch1 gene has an important role in mammalian cell-fate decision and tumorigenesis. Upstream control mechanisms for transcription of this gene are still poorly understood. In a chemical genetics screen for small molecule activators of Notch signalling, we identified epidermal growth factor receptor (EGFR) as a key negative regulator of Notch1 gene expression in primary human keratinocytes, intact epidermis and skin squamous cell carcinomas (SCCs). The underlying mechanism for negative control of the Notch1 gene in human cells, as well as in a mouse model of EGFR-dependent skin carcinogenesis, involves transcriptional suppression of p53 by the EGFR effector c-Jun. Suppression of Notch signalling in cancer cells counteracts the differentiation-inducing effects of EGFR inhibitors while, at the same time, synergizing with these compounds in induction of apoptosis. Thus, our data reveal a key role of EGFR signalling in the negative regulation of Notch1 gene transcription, of potential relevance for combinatory approaches for cancer therapy.","authors":"Kolev, V., Mandinova, A., Guinea-Viniegra, J., Hu, B., Lefort, K., Lambertini, C., Neel, V., Dummer, R., Wagner, EF., Dotto, GP.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Cell Biol","volume":"10","issue":"8","page":"902-11","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-172","title":"Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumor microenvironment and cross-resistance to immunotherapy in melanoma","abstract":null,"authors":"Haas L, Elewaut A, Gerard CL, Umkehrer C, Pedersen M, Leiendecker L, Krecioch I, Hoffmann D, Novatchkova M, Kuttke M, Neumann T, Pires de Silva I, Witthock H, Cuendet MA, Carotta S, Harrington KJ, Zuber J, Scolyer RA, Long GV, Wilmott JS, Michielin O, Vanharanta S, Wiesner T, Obenauf AC. ","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature Cancer ","volume":"2","issue":null,"page":"693\u2013708","pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.nature.com\/articles\/s43018-021-00221-9#citeas","preprintlink":null,"articledate":"2021-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19475385","title":"Automated live microscopy to study mitotic gene function in fluorescent reporter cell lines.","abstract":"Fluorescence live microscopy is a powerful technique to study complex cellular dynamics such as cell division. The availability of fluorescent markers based on GFP fusion proteins for virtually any cellular structure allows efficient visualization of specific processes, and the combination of different fluorophores can be used to study their coordination. In this chapter, we present methods for automated live cell microscopy to study mitotic gene function systematically and in high throughput. In particular, we provide protocols for efficient generation of fluorescent reporter cell lines stably expressing combinations of cellular markers, and provide detailed guidelines for optimizing imaging protocols for automated long-term live microscopy.","authors":"Schmitz, MH., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Methods Mol Biol","volume":"545","issue":null,"page":"113-34","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18562479","title":"Role of desmin in active force transmission and maintenance of structure during growth of urinary bladder.","abstract":"Role of the intermediate filament protein desmin in hypertrophy of smooth muscle was examined in desmin-deficient mice (Des(-\/-)). A partial obstruction of the urethra was created, and after 9-19 days bladder weight increased approximately threefold in both Des(-\/-) and wild type (Des(+\/+)) animals. Bladder growth was associated with the synthesis of actin and myosin. In the hypertrophic Des(+\/+) bladder, the relative content of desmin increased. In Des(-\/-)mice, desmin was absent. No alterations in the amount of vimentin were observed. Although Des(-\/-) obstructed bladders were capable of growth, they had structural changes with a partial disruption of the wall. Des(-\/-)bladders had slightly lower passive stress and significantly lower active stress compared with Des(+\/+). Des(-\/-)preparations had lower shortening velocity. During hypertrophy, these structural and mechanical alterations in the Des(-\/-)urinary bladder became more pronounced. In conclusion, desmin in the bladder smooth muscle is not needed for growth but has a role in active force transmission and maintenance of wall structure.","authors":"Scott, RS., Li, Z., Paulin, D., Uvelius, B., Small, JV., Arner, A.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Am J Physiol Cell Physiol","volume":"295","issue":"2","page":"C324-31","pdf":null,"JrId":"21623","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18544632","title":"Arabidopsis SMG7 protein is required for exit from meiosis.","abstract":"Meiosis consists of two nuclear divisions that are separated by a short interkinesis. Here we show that the SMG7 protein, which plays an evolutionarily conserved role in nonsense-mediated RNA decay (NMD) in animals and yeast, is essential for the progression from anaphase to telophase in the second meiotic division in Arabidopsis. Arabidopsis SMG7 is an essential gene, the disruption of which causes embryonic lethality. Plants carrying a hypomorphic smg7 mutation exhibit an elevated level of transcripts containing premature stop codons. This suggests that the role of SMG7 in NMD is conserved in plants. Furthermore, hypomorphic smg7 alleles render mutant plants sterile by causing an unusual cell-cycle arrest in anaphase II that is characterized by delayed chromosome decondensation and aberrant rearrangement of the meiotic spindle. The smg7 phenotype was mimicked by exposing meiocytes to the proteasome inhibitor MG115. Together, these data indicate that SMG7 counteracts cyclin-dependent kinase (CDK) activity at the end of meiosis, and reveal a novel link between SMG7 and regulation of the meiotic cell cycle.","authors":"Riehs, N., Akimcheva, S., Puizina, J., Bulankova, P., Idol, RA., Siroky, J., Schleiffer, A., Schweizer, D., Shippen, DE., Riha, K.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Cell Sci","volume":"121","issue":"Pt 13","page":"2208-16","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15855336","title":"G(-) anaerobes-reactive CD4+ T-cells trigger RANKL-mediated enhanced alveolar bone loss in diabetic NOD mice.","abstract":"Diabetic patients experience a higher risk for severe periodontitis; however, the underlying mechanism remains unclear. We investigated the contribution of antibacterial T-cell-mediated immunity to enhanced alveolar bone loss during periodontal infection in nonobese diabetic (NOD) mice by oral inoculation with Actinobacillus actinomycetemcomitans, a G(-) anaerobe responsible for juvenile and severe periodontitis. The results show that 1) inoculation with A. actinomycetemcomitans in pre-diabetic NOD mice does not alter the onset, incidence, and severity of diabetes; 2) after A. actinomycetemcomitans inoculation, diabetic NOD mice (blood glucose &gt;200 mg\/dl and with severe insulitis) exhibit significantly higher alveolar bone loss compared with pre-diabetic and nondiabetic NOD mice; and 3) A. actinomycetemcomitans-reactive CD4+ T-cells in diabetic mice exhibit significantly higher proliferation and receptor activator of nuclear factor kappaB ligand (RANKL) expression. When diabetic mice are treated with the RANKL antagonist osteoprotegerin (OPG), there is a significant reversal of alveolar bone loss, as well as reduced RANKL expression in A. actinomycetemcomitans-reactive CD4+ T-cells. This study clearly describes the impact of autoimmunity to anaerobic infection in an experimental periodontitis model of type 1 diabetes. Thus, microorganism-reactive CD4+ T-cells and the RANKL-OPG axis provide the molecular basis of the advanced periodontal breakdown in diabetes and, therefore, OPG may hold therapeutic potential for treating bone loss in diabetic subjects at high risk.","authors":"Mahamed, DA., Marleau, A., Alnaeeli, M., Singh, B., Zhang, X., Penninger, JM., Teng, YT.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Diabetes","volume":"54","issue":"5","page":"1477-86","pdf":null,"JrId":"3397","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18522989","title":"DNA double-strand breaks, but not crossovers, are required for the reorganization of meiotic nuclei in Tetrahymena.","abstract":"During meiosis, the micronuclei of the ciliated protist Tetrahymena thermophila elongate dramatically. Within these elongated nuclei, chromosomes are arranged in a bouquet-like fashion and homologous pairing and recombination takes place. We studied meiotic chromosome behavior in Tetrahymena in the absence of two genes, SPO11 and a homolog of HOP2 (HOP2A), which have conserved roles in the formation of meiotic DNA double-strand breaks (DSBs) and their repair, respectively. Single-knockout mutants for each gene display only a moderate reduction in chromosome pairing, but show a complete failure to form chiasmata and exhibit chromosome missegregation. The lack of SPO11 prevents the elongation of meiotic nuclei, but it is restored by the artificial induction of DSBs. In the hop2ADelta mutant, the transient appearance of gamma-H2A.X and Rad51p signals indicates the formation and efficient repair of DSBs; but this repair does not occur by interhomolog crossing over. In the absence of HOP2A, the nuclei are elongated, meaning that DSBs but not their conversion to crossovers are required for the development of this meiosis-specific morphology. In addition, by in silico homology searches, we compiled a list of likely Tetrahymena meiotic proteins as the basis for further studies of the unusual synaptonemal complex-less meiosis in this phylogenetically remote model organism.","authors":"Mochizuki, K., Novatchkova, M., Loidl, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Cell Sci","volume":"121","issue":"Pt 13","page":"2148-58","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19650157","title":"Angiotensin-converting-enzyme 2 inhibits liver fibrosis in mice.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19650157<\/PMID><DateCompleted><Year>2009<\/Year><Month>09<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1527-3350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>50<\/Volume><Issue>3<\/Issue><PubDate><Year>2009<\/Year><Month>Sep<\/Month><\/PubDate><\/JournalIssue><Title>Hepatology (Baltimore, Md.)<\/Title><ISOAbbreviation>Hepatology<\/ISOAbbreviation><\/Journal><ArticleTitle>Angiotensin-converting-enzyme 2 inhibits liver fibrosis in mice.<\/ArticleTitle><Pagination><MedlinePgn>929-38<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/hep.23104<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">The renin-angiotensin system (RAS) plays a major role in liver fibrosis. Recently, a homolog of angiotensin-converting-enzyme 1 (ACE1), termed ACE2, has been identified that appears to be a negative regulator of the RAS by degrading Ang II to Ang(1-7). The aim of this study was to characterize the long-term effects of gene deletion of ACE2 in the liver, to define the role of ACE2 in acute and chronic liver disease, and to characterize the role of Ang(1-7) in hepatic stellate cell (HSC) activation. Ace2 knockout (KO) mice and wild-type (wt) littermates underwent different models of acute and chronic liver injury. Liver pathology was analyzed by histology, immunohistochemistry, alpha smooth muscle actin (alpha-SMA) immunoblotting, and quantitative polymerase chain reaction (qPCR). Murine HSCs were isolated by collagenase-pronase-perfusion, and density gradient centrifugation. One-year-old ace2 KO mice spontaneously developed an inflammatory cell infiltration and mild hepatic fibrosis that was prevented by treatment with irbesartan. Ace2 KO mice showed increased liver fibrosis following bile duct ligation for 21 days or chronic carbon tetrachloride (CCl(4)) treatment. In contrast, ace2 KO mice subjected to acute liver injury models did not differ from wt littermates. Treatment with recombinant ACE2 attenuated experimental fibrosis in the course of cholestatic and toxic liver injury. HSCs express the Ang(1-7) receptor Mas and Ang(1-7) inhibited Ang II-induced phosphorylation of extracellular signal-regulated kinase (ERK)-1\/2 in cultured HSCs.","authors":"Osterreicher, CH., Taura, K., De Minicis, S., Seki, E., Penz-Osterreicher, M., Kodama, Y., Kluwe, J., Schuster, M., Oudit, GY., Penninger, JM., Brenner, DA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Hepatology","volume":"50","issue":"3","page":"929-38","pdf":null,"JrId":"4093","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29990461","title":"Developmental Biology: Morphogen in a Dish.","abstract":"Reconstitution of a Hedgehog morphogen gradient in&#xa0;vitro and in silico reveals the architectural features of the signal transduction pathway that ensure rapid formation of a robust signalling gradient.","authors":"Stapornwongkul, KS., Salbreux, G., Vincent, JP.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Curr Biol","volume":"28","issue":"13","page":"R755-R757","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-21","doi":"10.1016\/j.cub.2018.05.047","first_author":null,"corresponding_authors":null},{"pmid":"18511907","title":"Synergy of Eed and Tsix in the repression of Xist gene and X-chromosome inactivation.","abstract":"X-chromosome inactivation (XCI) depends on the noncoding Xist gene. Xist transcription is negatively regulated by its antisense partner Tsix, whose disruption results in nonrandom XCI in females. However, males can maintain Xist in a repressed state without Tsix, indicating participation of additional factor(s) in the protection of the single male X from inactivation. Here, we provide evidence that the histone methyltransferase Eed is also involved in the process. Male embryonic stem cells with Eed-null and Tsix mutations (X(Delta)Y Eed-\/-) showed Xist hyperactivation upon differentiation, whereas cells with either mutation alone did not. Impaired X-linked gene expression was observed in the X(Delta)Y Eed-\/- ES cells at the onset of differentiation. The Xist promoter in the X(Delta)Y Eed-\/- cells showed elevated histone H3-dimethyl lysine 4 modifications and lowered CpG methylation, which are characteristics of open chromatin. Hence, we identified Eed as an additional major player in the regulation of Xist expression. The synergy of Polycomb group proteins and antisense Tsix transcription in Xist gene regulation explains why males can repress Xist without Tsix.","authors":"Shibata, S., Yokota, T., Wutz, A.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO J","volume":"27","issue":"13","page":"1816-26","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18538592","title":"Instructive role of the transcription factor E2A in early B lymphopoiesis and germinal center B cell development.","abstract":"The transcription factor E2A controls the initiation of B lymphopoiesis, which is arrested at the pre-pro-B cell stage in E2A-deficient mice. Here, we demonstrate by conditional mutagenesis that E2A is essential for the development of pro-B, pre-B, and immature B cells in the bone marrow. E2A is, however, dispensable for the generation of mature B cells and plasma cells in peripheral lymphoid organs. In contrast, germinal center B cell development is impaired in the absence of E2A despite normal AID expression and class-switch recombination. Molecular analysis revealed that E2A is required not only for initiating but also for maintaining the expression of Ebf1, Pax5, and the B cell gene program in pro-B cells. Notably, precocious Pax5 transcription from the Ikzf1 locus promotes pro-B cell development in E2A-deficient mice, demonstrating that ectopic Pax5 expression is sufficient to activate the B lymphoid transcription program in vivo in the absence of E2A.","authors":"Kwon, K., Hutter, C., Sun, Q., Bilic, I., Cobaleda, C., Malin, S., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Immunity","volume":"28","issue":"6","page":"751-62","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18482566","title":"B young again.","abstract":"Hanna et al. (2008) report in a recent issue of Cell that a defined set of transcription factors can reprogram mature B cells back to pluripotent stem cells.","authors":"Graf, T., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Immunity","volume":"28","issue":"5","page":"606-8","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18505785","title":"Lack of nuclear factor-kappa B2\/p100 causes a RelB-dependent block in early B lymphopoiesis.","abstract":"Nuclear factor-kappaB (NF-kappaB) transcription factors regulate B-cell development and survival. However, whether they also have a role during early steps of B-cell differentiation is largely unclear. Here, we show that constitutive activation of the alternative NF-kappaB pathway in p100(-\/-) knockin mice resulted in a block of early B-cell development at the transition from the pre-pro-B to the pro-B-cell stage due to enhanced RelB activity. Expression of the essential B-cell transcription factors EBF and in particular Pax5 was reduced in p100(-\/-) B-cell precursors in a RelB-dependent manner, resulting in reduced mRNA levels of B lineage-specific genes. Moreover, enhanced RelB function in p100(-\/-) B-cell precursors was accompanied by increased expression of B lineage-inappropriate genes, such as C\/EBP alpha, correlating with a markedly increased myeloid differentiation potential of p100(-\/-) progenitor B cells. Ectopic expression of Pax5 in hematopoietic progenitors restored early B-cell development in p100(-\/-) bone marrow, suggesting that impaired early B lymphopoiesis in mice lacking the p100 inhibitor may be due to down-regulation of Pax5 expression. Thus, tightly controlled p100 processing and RelB activation is essential for normal B lymphopoiesis and lymphoid\/myeloid lineage decision in bone marrow.","authors":"Guo, F., T\u00e4nzer, S., Busslinger, M., Weih, F.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Blood","volume":"112","issue":"3","page":"551-9","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18499457","title":"The PDZ protein Canoe regulates the asymmetric division of Drosophila neuroblasts and muscle progenitors.","abstract":"Asymmetric cell division is a conserved mechanism to generate cellular diversity during animal development and a key process in cancer and stem cell biology. Despite the increasing number of proteins characterized, the complex network of proteins interactions established during asymmetric cell division is still poorly understood. This suggests that additional components must be contributing to orchestrate all the events underlying this tightly modulated process. The PDZ protein Canoe (Cno) and its mammalian counterparts AF-6 and Afadin are critical to regulate intracellular signaling and to organize cell junctions throughout development. Here, we show that Cno functions as a new effector of the apical proteins Inscuteable (Insc)-Partner of Inscuteable (Pins)-Galphai during the asymmetric division of Drosophila neuroblasts (NBs). Cno localizes apically in metaphase NBs and coimmunoprecipitates with Pins in vivo. Furthermore, Cno functionally interacts with the apical proteins Insc, Galphai, and Mushroom body defect (Mud) to generate correct neuronal lineages. Failures in muscle and heart lineages are also detected in cno mutant embryos. Our results strongly support a new function for Cno regulating key processes during asymmetric NB division: the localization of cell-fate determinants, the orientation of the mitotic spindle, and the generation of unequal-sized daughter cells.","authors":"Speicher, S., Fischer, A., Knoblich, J., Carmena, A.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Biol","volume":"18","issue":"11","page":"831-7","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"86","title":"Hybrids of chemical derivatives of Escherichia coli alkaline phosphatase.","abstract":"The activities of hybrid dimers of alkaline phosphatase containing two chemically modified subunits have been investigated. One hybrid species was prepared by dissociation and reconstitution of a mixture of two variants produced by chemical modification of the native enzyme with succinic anhydride and tetranitromethane, respectively. The succinyl-nitrotyrosyl hybrid was separated from the other members of the hybrid set by DEAE-Sephadex chromatography and then converted to a succinyl-aminotyrosyl hybrid by reduction of the modified tyrosine residues with sodium dithionite. A comparison of the activities of these two hybrids with the activities of the succinyl, nitrotyrosyl and aminotyrosyl derivatives has shown that either the subunits of alkaline phosphatase function independently or if the subunits turnover alternately in a reciprocating mechanism, then the intrinsic activity of each subunit must be strongly dependent on its partner subunit.","authors":"Meighen, E., Yue, R.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"2","page":"262-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35","title":"The effect of o-salicylate upon pentose phosphate pathway activity in normal and G6PD-deficient red cells.","abstract":"The effect of the major metabolite of aspirin, namely salicylic acid, upon the pentose phosphate pathway (PPP) of normal and G6PD-deficient red cells has been studied. Salicylic acid was shown to inhibit this pathway in proportion to the amount present. At any concentration of this substance there was greater inhibition of the PPP in G6PD-deficient than in normal red cells.","authors":"Worathumrong, N., Grimes, AJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Haematol","volume":"30","issue":"2","page":"225-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15713842","title":"Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing.","abstract":"Dicer is the enzyme that cleaves double-stranded RNA (dsRNA) into 21-25-nt-long species responsible for sequence-specific RNA-induced gene silencing at the transcriptional, post-transcriptional, or translational level. We disrupted the dicer-1 (dcr-1) gene in mouse embryonic stem (ES) cells by conditional gene targeting and generated Dicer-null ES cells. These cells were viable, despite being completely defective in RNA interference (RNAi) and the generation of microRNAs (miRNAs). However, the mutant ES cells displayed severe defects in differentiation both in vitro and in vivo. Epigenetic silencing of centromeric repeat sequences and the expression of homologous small dsRNAs were markedly reduced. Re-expression of Dicer in the knockout cells rescued these phenotypes. Our data suggest that Dicer participates in multiple, fundamental biological processes in a mammalian organism, ranging from stem cell differentiation to the maintenance of centromeric heterochromatin structure and centromeric silencing.","authors":"Kanellopoulou, C., Muljo, SA., Kung, AL., Ganesan, S., Drapkin, R., Jenuwein, T., Livingston, DM., Rajewsky, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Genes Dev","volume":"19","issue":"4","page":"489-501","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18448662","title":"The discovery of angiotensin-converting enzyme 2 and its role in acute lung injury in mice.","abstract":"During several months of 2002, severe acute respiratory syndrome (SARS) caused by SARS-coronavirus (SARS-CoV) spread rapidly from China throughout the world, causing more than 800 deaths due to the development of acute respiratory distress syndrome (ARDS), which is the severe form of acute lung injury (ALI). Interestingly, a novel homologue of angiotensin-converting enzyme, termed angiotensin-converting enzyme 2 (ACE2), has been identified as a receptor for SARS-CoV. Angiotensin-converting enzyme and ACE2 share homology in their catalytic domain and provide different key functions in the renin-angiotensin system (RAS). Angiotensin-converting enzyme cleaves angiotensin I to generate angiotensin II, which is a key effector peptide of the system and exerts multiple biological functions, whereas ACE2 reduces angiotensin II levels. Importantly, our recent studies using ACE2 knockout mice have demonstrated that ACE2 protects murine lungs from ARDS. Furthermore, SARS-CoV infections and the Spike protein of the SARS-CoV reduce ACE2 expression. Notably, injection of SARS-CoV Spike into mice worsens acute lung failure in vivo, which can be attenuated by blocking the renin-angiotensin pathway, suggesting that the activation of the pulmonary RAS influences the pathogenesis of ALI\/ARDS and SARS.","authors":"Imai, Y., Kuba, K., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Exp Physiol","volume":"93","issue":"5","page":"543-8","pdf":null,"JrId":"1614","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19471121","title":"An evolutionary conserved checkpoint controls abscission timing.","abstract":null,"authors":"Steigemann, P., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell Cycle","volume":"8","issue":"12","page":"1814-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18460602","title":"Different assemblies of the DAM1 complex follow shortening microtubules by distinct mechanisms.","abstract":"Mitotic chromosomes segregate at the ends of shortening spindle microtubules (MTs). In budding yeast, the Dam1 multiprotein complex supports this dynamic attachment, thereby contributing to accurate chromosome segregation. Purified Dam1 will track the end of a depolymerizing MT and can couple it to microbead transport in vitro. The processivity of such motions has been thought to depend on rings that the Dam1 complex can form around MTs, but the possibility that alternative coupling geometries contribute to these motilities has not been considered. Here, we demonstrate that both rings and nonencircling Dam1 oligomers can track MT ends and enable processive cargo movement in vitro. The coupling properties of these two assemblies are, however, quite different, so each may make a distinct contribution to chromosome motility.","authors":"Grishchuk, EL., Spiridonov, IS., Volkov, VA., Efremov, A., Westermann, S., Drubin, D., Barnes, G., Ataullakhanov, FI., McIntosh, JR.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Proc Natl Acad Sci U S A","volume":"105","issue":"19","page":"6918-23","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"78","title":"Studies on rat renal cortical cell kallikrein. I. Separation and measurement.","abstract":"A technique has been developed to separate and measure kallikrein in a heterogeneous population of rat renal cortical cells in suspension. After rat kidneys were perfused in situ in anaesthetized rats, viable, counted cortical cell suspensions were obtained. Cells were suspended in a sucrose\/Tris buffer containing 0.5% deoxycholate, homogenized, centrifuged, dialyzed, and gel filtered on Sephadex G-25. Column chromatography on DEAE-cellulose resulted in a single peak of esterase activity between 0.20 to 0.25 M NaCl\/sodium phosphate buffer. Subsequent elution yielded an alkaline esterase which was identical to kallikrein isolated from rat urine, insofar as pH optimum, effects of inhibitors, bioassay activity and immunological properties were concerned. Calculated yields were about 70% of the total esterase activity present in the parent cell homogenates. Recoveries of a purified rat urinary kallikrein added to the cell homogenates, the DEAE-cellulose columns, or the eluates from the columns ranged from 83-108% (mean 96%). Using this technique, it was found that the amount of kallikrein activity present in non-incubated renal cortical cells ranged from 0.6-10(-2) to 4.6 - 10(-2) alpha-N-tosyl-L-arginine methyl ester (Tos-Arg-OMe) esterase units per 10(8) cells. However, cells incubated in a nutrient medium at 37 degrees C for 3-8 h contained no measurable kallikrein activity, whereas the surrounding medium had kallikrein activity which could be significantly increased by aldosterone and decreased by spironolactone.","authors":"Kaizu, T., Margolius, HS.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"411","issue":"2","page":"305-15","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18438400","title":"The impact of target site accessibility on the design of effective siRNAs.","abstract":"Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downstream events in the RNA interference (RNAi) pathway, such as target site accessibility, have so far not been investigated extensively. In this study we present a comprehensive analysis of target RNA structure effects on RNAi by computing the accessibility of the target site for interaction with the siRNA. Based on our observations, we developed a novel siRNA design tool, RNAxs, by combining known siRNA functionality criteria with target site accessibility. We calibrated our method on two data sets comprising 573 siRNAs for 38 genes, and tested it on an independent set of 360 siRNAs targeting four additional genes. Overall, RNAxs proves to be a robust siRNA selection tool that substantially improves the prediction of highly efficient siRNAs.","authors":"Tafer, H., Ameres, SL., Obernosterer, G., Gebeshuber, CA., Schroeder, R., Martinez, J., Hofacker, IL.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Biotechnol","volume":"26","issue":"5","page":"578-83","pdf":null,"JrId":"20305","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18371441","title":"LIS1 and spindle orientation in neuroepithelial cells.","abstract":"Asymmetric stem cell division is thought to require precise orientation of the mitotic spindle. However, a recent study in Cell (Yingling et al., 2008) analyzes the role of LIS1 in the developing mouse brain and shows that spindle orientation is more important during early, symmetric progenitor cell divisions than for later asymmetric divisions.","authors":"Schwamborn, JC., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell Stem Cell","volume":"2","issue":"3","page":"193-4","pdf":null,"JrId":"34100","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35833838","title":"In preprints: morphogens in motion.","abstract":null,"authors":"Stapornwongkul, KS., Briscoe, J.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Development","volume":"149","issue":"14","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-18","doi":"10.1242\/dev.201066","first_author":null,"corresponding_authors":null},{"pmid":"18356559","title":"Distinct roles for angiotensin-converting enzyme 2 and carboxypeptidase A in the processing of angiotensins within the murine heart.","abstract":"Angiotensin-converting enzyme 2 (ACE2), a homologue of angiotensin-converting enzyme (ACE), converts angiotensin (Ang) I to Ang(1-9) and Ang II to Ang(1-7), but does not directly process Ang I to Ang II. Cardiac function is compromised in ACE2 null mice; however, the importance of ACE2 in the processing of angiotensin peptides within the murine heart is not known. We determined the metabolism of angiotensins in wild-type (WT), ACE (ACE(-\/-)) and ACE2 null mice (ACE2(-\/-)). Angiotensin II was converted almost exclusively to Ang(1-7) in the cardiac membranes of WT and ACE(-\/-) strains, although generation of Ang(1-7) was greater in the ACE(-\/-) mice (27.4 +\/- 4.1 versus 17.5 +\/- 3.2 nmol(-1) mg h(-1) for WT). The ACE2 inhibitor MLN4760 significantly attenuated Ang II metabolism and the subsequent formation of Ang(1-7) in both strains. In the ACE2(-\/-) hearts, Ang II metabolism and the generation of Ang(1-7) were significantly attenuated; however, the ACE2 inhibitor reduced the residual Ang(1-7)-forming activity in this strain. Angiotensin I was primarily converted to Ang(1-9) (WT, 28.9 +\/- 3.1 nmol(-1) mg h(-1); ACE(-\/-), 49.8 +\/- 5.3 nmol(-1) mg h(-1); and ACE2(-\/-), 35.9 +\/- 5.4 nmol(-1) mg h(-1)) and to smaller quantities of Ang(1-7) and Ang II. Although the ACE2 inhibitor had no effect on Ang(1-9) formation, the carboxypeptidase A inhibitor benzylsuccinate essentially abolished the formation of Ang(1-9) and increased the levels of Ang I in cardiac membranes. In conclusion, our studies in the murine heart suggest that ACE2 is the primary pathway for the metabolism of Ang II and the subsequent formation of Ang(1-7), a peptide that, in contrast to Ang II, exhibits both antifibrotic and antiproliferative actions.","authors":"Garabelli, PJ., Modrall, JG., Penninger, JM., Ferrario, CM., Chappell, MC.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Exp Physiol","volume":"93","issue":"5","page":"613-21","pdf":null,"JrId":"1614","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15673436","title":"Specific pathophysiological functions of JNK isoforms in the brain.","abstract":"We have investigated the effect of JNK1 ko, JNK2 ko, JNK3 ko, JNK2+3 ko and c-JunAA mutation on neuronal survival in adult transgenic mice following ischemia, 6-hydroxydopamine induced neurotoxicity, axon transection and kainic acid induced excitotoxicity. Deletion of JNK isoforms indicated the compartment-specific expression of JNK isoforms with 46-kDa JNK1 as the main phosphorylated JNK isoform. Permanent occlusion of the MCA significantly enlarged the infarct area in JNK1 ko, which showed an increased expression of JNK3 in the penumbra. Survival of dopaminergic neurons in the substantia nigra compacta (SNC) following intrastriatal injection of 6-hydroxydopamine was transiently improved in JNK3 ko and c-JunAA mice after 7 days, but not 60 days. Following transection of the medial forebrain bundle, however, JNK3 ko conferred persisting neuroprotection of axotomised SNC neurons. None of the JNK ko and c-JunAA mutation affected the survival of facial motoneurons following peripheral axotomy when investigated after 90 days. Finally, we determined the impact of JNK ko on the survival of animals and the degeneration of hippocampal neurons following kainic acid. JNK3 ko mice were substantially resistant against and survived kainic acid-induced seizures. JNK3 ko and JNK1 ko showed a nonsignificant tendency for decreased or increased death of hippocampal neurons, respectively. Surprisingly, the deletion of a single JNK isoform did not attenuate the immunocytochemical signal of phosphorylated c-Jun irrespective on the experimental set-up. This comprehensive study provides novel insights into the context-dependent physiological and pathological functions of JNK isoforms.","authors":"Brecht, S., Kirchhof, R., Chromik, A., Willesen, M., Nicolaus, T., Raivich, G., Wessig, J., Waetzig, V., Goetz, M., Claussen, M., Pearse, D., Kuan, CY., Vaudano, E., Behrens, A., Wagner, E., Flavell, RA., Davis, RJ., Herdegen, T.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Eur J Neurosci","volume":"21","issue":"2","page":"363-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15661635","title":"Developmentally regulated expression of the regulator of G-protein signaling gene 2 (Rgs2) in the embryonic mouse pituitary.","abstract":"During the development of the anterior pituitary gland, five distinct hormone-producing cell types emerge in a spatially and temporally regulated pattern from an invagination of oral ectoderm termed Rathke's Pouch. Evidence from mouse knockout and ectopic expression studies indicates that 12.5 days post coitum (dpc) to 14.5 dpc is a critical period for the expansion of the progenitor cell pool and the determination of most hormone-secreting cell types. While signaling proteins and transcription factors have been identified as having key roles in pituitary cell differentiation, little is known about the identity and function of proteins that mediate signal transduction in progenitor cells. To identify genes that are enriched in the embryonic pituitary gland, we compared gene expression in 14.5 dpc pituitary and 14.5 dpc embryo minus pituitary tissues using the NIA 15K microarray. Analysis of the data using the R program revealed that the Regulator of G Protein Signaling 2 (Rgs2) gene was 3.9-fold more abundant in the 14.5 dpc pituitary. In situ hybridisation confirmed this finding, and showed that Rgs2 expression in midline tissues was restricted to the pituitary and discrete regions of the nervous system. Within the pituitary, Rgs2 was expressed in undifferentiated cells, and was downregulated at the completion of the hormone cell differentiation. To investigate Rgs2 function in the pituitary, we examined hormone cell differentiation in Rgs2 null neonate mice. Pituitary cell differentiation and morphology appeared normal in the Rgs2 mutant animals, suggesting that other Rgs family members with similar activities may be present in the developing pituitary.","authors":"Wilson, LD., Ross, SA., Lepore, DA., Wada, T., Penninger, JM., Thomas, PQ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Gene Expr Patterns","volume":"5","issue":"3","page":"305-11","pdf":null,"JrId":"30259","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11106750","title":"JunD protects cells from p53-dependent senescence and apoptosis.","abstract":"JunD is the most broadly expressed member of the Jun family and the AP-1 transcription factor complex. Primary fibroblasts lacking JunD displayed p53-dependent growth arrest, upregulated p19(Arf) expression, and premature senescence. In contrast, immortalized cell lines lacking JunD showed increased proliferation and higher cyclinD1 levels. These properties are reminiscent of the effects of oncogenic Ras expression on primary and established cell cultures. Furthermore, JunD(-\/-) fibroblasts exhibited increased p53-dependent apoptosis upon ultraviolet irradiation and were sensitive to the cytotoxic effects of TNF-alpha. The antiapoptotic role of JunD was confirmed using an in vivo model of TNF-mediated hepatitis. We propose that JunD protects cells from senescence, or apoptotic responses to stress stimuli, by acting as a modulator of the signaling pathways that link Ras to p53.","authors":"Weitzman, JB., Fiette, L., Matsuo, K., Yaniv, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Cell","volume":"6","issue":"5","page":"1109-19","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18323525","title":"Phosphatidylinositol-3-kinase-gamma is integral to homing functions of progenitor cells.","abstract":"Endothelial progenitor cells (EPCs) and hematopoietic progenitor cells are recruited to ischemic regions, improving neovascularization. beta1 and beta2 integrins play a crucial role for progenitor cell homing to ischemic tissues. Integrin activity is regulated by chemokines and their respective G protein-coupled receptors. The phosphatidylinositol-3-kinase catalytic subunit gamma (PI3Kgamma) is the PI3K isoform that selectively transduces signals from G protein-coupled receptors. Here, we investigated the role of PI3Kgamma as a signaling intermediate in the chemokine-induced integrin-dependent homing functions of progenitor cells. A pharmacological PI3Kgamma inhibitor significantly reduced chemokine-induced chemotaxis and stromal cell-derived factor (SDF)1alpha-induced transmigration of human EPCs. Moreover, the PI3Kgamma inhibitor significantly reduced SDF1alpha-induced adhesion of EPCs to intercellular adhesion molecule-1 and human umbilical vein endothelial cell monolayers. These findings were corroborated with Lin(-) bone marrow-derived progenitor cells from PI3Kgamma-deficient mice that displayed reduced SDF1alpha-induced migration and intercellular adhesion molecule-1 adhesion as compared with wild-type cells. Pharmacological inhibition or genetic ablation of PI3Kgamma reduced SDF1alpha-induced integrin activation in human EPCs and in murine Lin(-) BM-derived progenitor cells, respectively. In vivo, the homing of PI3Kgamma-deficient Lin(-) progenitor cells to ischemic muscles after intravenous infusion in the model of hindlimb ischemia and their neovascularization-promoting capacity was reduced as compared with wild-type cells. In conclusion, PI3Kgamma is integral to the integrin-dependent homing of progenitor cells.","authors":"Chavakis, E., Carmona, G., Urbich, C., G\u00f6ttig, S., Henschler, R., Penninger, JM., Zeiher, AM., Chavakis, T., Dimmeler, S.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Circ Res","volume":"102","issue":"8","page":"942-9","pdf":null,"JrId":"2974","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27761821","title":"Generation of Tissue-Specific Mouse Models to Analyze HDAC Functions.","abstract":"Histone deacetylases (HDACs) play crucial roles during mammalian development and for cellular homeostasis. In addition, these enzymes are promising targets for small molecule inhibitors in the treatment of cancer and neurological diseases. Conditional HDAC knock-out mice are excellent tools for defining the functions of individual HDACs in vivo and for identifying the molecular targets of HDAC inhibitors in disease. Here, we describe the generation of tissue-specific HDAC knock-out mice and delineate a strategy for the generation of conditional HDAC knock-in mice.","authors":"Hagelkruys, A., Moser, MA., Seiser, C.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Methods Mol Biol","volume":"1510","issue":null,"page":"169-192","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18309327","title":"The molecular archaeology of a mitochondrial death effector: AIF in Drosophila.","abstract":"Apoptosis-inducing factor (AIF) is a phylogenetically conserved redox-active flavoprotein that contributes to cell death and oxidative phosphorylation in Saccharomyces cerevisiae, Caenorhabditis elegans, mouse and humans. AIF has been characterized as a caspase-independent death effector that is activated by its translocation from mitochondria to the cytosol and nucleus. Here, we report the molecular characterization of AIF in Drosophila melanogaster, a species in which most cell deaths occur in a caspase-dependent manner. Interestingly, knockout of zygotic D. melanogaster AIF (DmAIF) expression using gene targeting resulted in decreased embryonic cell death and the persistence of differentiated neuronal cells at late embryonic stages. Although knockout embryos hatch, they undergo growth arrest at early larval stages, accompanied by mitochondrial respiratory dysfunction. Transgenic expression of DmAIF misdirected to the extramitochondrial compartment (DeltaN-DmAIF), but not wild-type DmAIF, triggered ectopic caspase activation and cell death. DeltaN-DmAIF-induced death was not blocked by removal of caspase activator Dark or transgenic expression of baculoviral caspase inhibitor p35, but was partially inhibited by Diap1 overexpression. Knockdown studies revealed that DeltaN-DmAIF interacts genetically with the redox protein thioredoxin-2. In conclusion, we show that Drosophila AIF is a mitochondrial effector of cell death that plays roles in developmentally regulated cell death and normal mitochondrial function.","authors":"Joza, N., Galindo, K., Pospisilik, JA., Benit, P., Rangachari, M., Kanitz, EE., Nakashima, Y., Neely, GG., Rustin, P., Abrams, JM., Kroemer, G., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell Death Differ","volume":"15","issue":"6","page":"1009-18","pdf":null,"JrId":"20326","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18302922","title":"Checkpoint control: the journey continues.","abstract":"Mad2 and p31(comet) are components of the spindle assembly checkpoint which controls the fidelity of chromosome segregation. Two recent structural studies reveal new insight into how these proteins achieve this difficult task.","authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Biol","volume":"18","issue":"4","page":"R170-2","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18305480","title":"The Drosophila pheromone cVA activates a sexually dimorphic neural circuit.","abstract":"Courtship is an innate sexually dimorphic behaviour that can be observed in naive animals without previous learning or experience, suggesting that the neural circuits that mediate this behaviour are developmentally programmed. In Drosophila, courtship involves a complex yet stereotyped array of dimorphic behaviours that are regulated by Fru(M), a male-specific isoform of the fruitless gene. Fru(M) is expressed in about 2,000 neurons in the fly brain, including three subpopulations of olfactory sensory neurons and projection neurons (PNs). One set of Fru(+) olfactory neurons expresses the odorant receptor Or67d and responds to the male-specific pheromone cis-vaccenyl acetate (cVA). These neurons converge on the DA1 glomerulus in the antennal lobe. In males, activation of Or67d(+) neurons by cVA inhibits courtship of other males, whereas in females their activation promotes receptivity to other males. These observations pose the question of how a single pheromone acting through the same set of sensory neurons can elicit different behaviours in male and female flies. Anatomical or functional dimorphisms in this neural circuit might be responsible for the dimorphic behaviour. We therefore developed a neural tracing procedure that employs two-photon laser scanning microscopy to activate the photoactivatable green fluorescent protein. Here we show, using this technique, that the projections from the DA1 glomerulus to the protocerebrum are sexually dimorphic. We observe a male-specific axonal arbor in the lateral horn whose elaboration requires the expression of the transcription factor Fru(M) in DA1 projection neurons and other Fru(+) cells. The observation that cVA activates a sexually dimorphic circuit in the protocerebrum suggests a mechanism by which a single pheromone can elicit different behaviours in males and in females.","authors":"Datta, SR., Vasconcelos, ML., Ruta, V., Luo, S., Wong, A., Demir, E., Flores, J., Balonze, K., Dickson, BJ., Axel, R.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"452","issue":"7186","page":"473-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18295577","title":"Mechanisms of asymmetric stem cell division.","abstract":"Stem cells self-renew but also give rise to daughter cells that are committed to lineage-specific differentiation. To achieve this remarkable task, they can undergo an intrinsically asymmetric cell division whereby they segregate cell fate determinants into only one of the two daughter cells. Alternatively, they can orient their division plane so that only one of the two daughter cells maintains contact with the niche and stem cell identity. These distinct pathways have been elucidated mostly in Drosophila. Although the molecules involved are highly conserved in vertebrates, the way they act is tissue specific and sometimes very different from invertebrates.","authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell","volume":"132","issue":"4","page":"583-97","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11081625","title":"Cleavage of cohesin by the CD clan protease separin triggers anaphase in yeast.","abstract":"In eukaryotic cells, replicated DNA strands remain physically connected until their segregation to opposite poles of the cell during anaphase. This \"sister chromatid cohesion\" is essential for the alignment of chromosomes on the mitotic spindle during metaphase. Cohesion depends on the multisubunit cohesin complex, which possibly forms the physical bridges connecting sisters. Proteolytic cleavage of cohesin's Sccl subunit at the metaphase to anaphase transition is essential for sister chromatid separation and depends on a conserved protein called separin. We show here that separin is a cysteine protease related to caspases that alone can cleave Sccl in vitro. Cleavage of Sccl in metaphase arrested cells is sufficient to trigger the separation of sister chromatids and their segregation to opposite cell poles.","authors":"Uhlmann, F., Wernic, D., Poupart, MA., Koonin, EV., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cell","volume":"103","issue":"3","page":"375-86","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2000-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18281687","title":"Transcriptional regulation of EGR-1 by the interleukin-1-JNK-MKK7-c-Jun pathway.","abstract":"The proinflammatory cytokine interleukin (IL)-1 activates several hundred genes within the same cell. This occurs in part by activation of the MKK7-JNK-c-Jun signaling pathway whose precise role in the regulation of individual inflammatory genes is still incompletely understood. To identify the genes that are under specific control of activated JNK, we used a JNK-MKK7 fusion protein. Genome-wide microarray analysis revealed EGR-1 as the transcript that was most strongly induced by JNK-MKK7. IL-1-stimulated EGR-1 mRNA and protein expression were impaired in cells lacking JNK or c-Jun. Transcriptional activation of the EGR-1 promoter by JNK-MKK7 or by IL-1 required a single upstream AP-1 site and three distal serum-response elements (SRE). Reconstitution experiments in c-Jun-deficient cells revealed that c-Jun is required for EGR-1 transcription through both the AP-1 site and the distal SREs. By chromatin immunoprecipitation analysis, we found IL-1-inducible recruitment of c-Jun to the AP-1 site and to the region containing the three distal SREs. These experiments suggest that c-Jun plays a dual role in EGR-1 transcription. It directly binds to the AP-1 element, and at the same time it is essential for promoter activation through the three distal SREs by an indirect unknown mechanism. As predicted by TRANSFAC analysis and verified by ChIP experiments, IL-1-induced EGR-1 protein binds to the promoter regions of inflammatory mediators such as IL-6, IL-8, and CCL2. Furthermore, short interfering RNA-mediated suppression of EGR-1 partially suppresses IL-1-inducible transcription of IL-8, IL-6, and CCL2. In summary, we provide novel evidence for a complex c-Jun-mediated mechanism that is essential for inducible EGR-1 expression. We identify this pathway as a previously unrecognized part of a multistep gene regulatory network that controls cytokine and chemokine expression via the IL-1-MKK7-JNK-c-Jun-EGR-1 pathway.","authors":"Hoffmann, E., Ashouri, J., Wolter, S., Doerrie, A., Dittrich-Breiholz, O., Schneider, H., Wagner, EF., Troppmair, J., Mackman, N., Kracht, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Biol Chem","volume":"283","issue":"18","page":"12120-8","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"151","title":"[Basic phospholipase of Naja nigricollis venom].","abstract":"It is confirmed that N. nigricollis venom contains several phospholipases one of these is a basic phospholipase A. This enzyme is toxic for mice when injected intravenously. In vitro it reacts on egg yolk lecithin producing lysolecithin and prevents the phenomenon of blood clotting. An immunological identity has been established between this basic phospholipase and two acidic phospholipases present in the same venom.","authors":"Dumarey, C., Sket, D., Joseph, D., Boquet, P.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"C R Acad Hebd Seances Acad Sci D","volume":"280","issue":"13","page":"1633-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"55","title":"Subunit interactions in yeast glyceraldehyde-3-phosphate dehydrogenase.","abstract":"The spontaneous inactivation of yeast glyceraldehyde-3-phosphate dehydrogenase was found to fit a simple two-state model at pH 8.5 and 25 degrees. The first step is a relatively rapid dissociation of the tetramer to dimers with the equilibrium largely in favor of the tetramer. In the absence of NAD+ the dimer inactivates irreversibly. The apoenzyme is quite stable with a half-life for complete activity loss proportional to the square root of the enzyme concentration. Perturbances of the protein structure (by pH, ionic strength, and specific salts), which have no effect on the tetrameric state of the molecule, result in an alteration of the cooperativity of NAD+ binding, the reactivity of the active-site sulfhydryl group, and the catalytic activity of the enzyme. Covalent modification of two of the four active-site sulfhydryl groups has profound effects on the enzymic activity which are mediated by changes in the subunit interactions. Sedimentation analysis and hybridization studies indicate that the interaction between subunits remains strong after covalent modification. Under normal physiological and equilibrium dialysis conditions the protein is a tetramer. Equilibrium dialysis studies of NAD+ binding to the enzyme at pH 8.5 and 25 degrees reveal a mixed cooperativity pattern. A model consistent with these observations and the observed half-of-the-sites reactivity is that of ligand induced sequential conformational changes which are transferred across strongly interacting subunit domains. Methods for distinguishing negatively cooperative binding patterns from mixtures of denatured enzyme and multiple species are discussed.","authors":"Mockrin, SC., Byers, LD., Koshland, DE.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"25","page":"5428-37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18267092","title":"Cell-type-specific TEV protease cleavage reveals cohesin functions in Drosophila neurons.","abstract":"Cohesin is a highly conserved multisubunit complex that holds sister chromatids together in mitotic cells. At the metaphase to anaphase transition, proteolytic cleavage of the alpha kleisin subunit (Rad21) by separase causes cohesin's dissociation from chromosomes and triggers sister-chromatid disjunction. To investigate cohesin's function in postmitotic cells, where it is widely expressed, we have created fruit flies whose Rad21 can be cleaved by TEV protease. Cleavage causes precocious separation of sister chromatids and massive chromosome missegregation in proliferating cells, but not disaggregation of polytene chromosomes in salivary glands. Crucially, cleavage in postmitotic neurons is lethal. In mushroom-body neurons, it causes defects in axon pruning, whereas in cholinergic neurons it causes highly abnormal larval locomotion. These data demonstrate essential roles for cohesin in nondividing cells and also introduce a powerful tool by which to investigate protein function in metazoa.","authors":"Pauli, A., Althoff, F., Oliveira, RA., Heidmann, S., Schuldiner, O., Lehner, CF., Dickson, BJ., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Dev Cell","volume":"14","issue":"2","page":"239-51","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18249108","title":"Polo and Aurora kinases: lessons derived from chemical biology.","abstract":"During the cell division cycle, mitotic entry, spindle assembly, chromosome segregation, and cytokinesis must all be carefully coordinated to ensure that the two daughter cells inherit all the genetic material required for further growth and development. Central to this coordination are several protein kinases including Aurora A, Aurora B, and the Polo-like kinase, Plk1. A number of small-molecule Aurora and Plk1 inhibitors have been developed because these kinases are seen as attractive anticancer drug targets. These inhibitors are now being widely used as chemical biology tools to understand how these kinases ensure faithful genome transmission.","authors":"Taylor, S., Peters, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Opin Cell Biol","volume":"20","issue":"1","page":"77-84","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18239084","title":"Stat5 activation enables erythropoiesis in the absence of EpoR and Jak2.","abstract":"Erythropoiesis requires erythropoietin (Epo) and stem cell factor (SCF) signaling via their receptors EpoR and c-Kit. EpoR, like many other receptors involved in hematopoiesis, acts via the kinase Jak2. Deletion of EpoR or Janus kinase 2 (Jak2) causes embryonic lethality as a result of defective erythropoiesis. The contribution of distinct EpoR\/Jak2-induced signaling pathways (mitogen-activated protein kinase, phosphatidylinositol 3-kinase, signal transducer and activator of transcription 5 [Stat5]) to functional erythropoiesis is incompletely understood. Here we demonstrate that expression of a constitutively activated Stat5a mutant (cS5) was sufficient to relieve the proliferation defect of Jak2(-\/-) and EpoR(-\/-) cells in an Epo-independent manner. In addition, tamoxifen-induced DNA binding of a Stat5a-estrogen receptor (ER)* fusion construct enabled erythropoiesis in the absence of Epo. Furthermore, c-Kit was able to enhance signaling through the Jak2-Stat5 axis, particularly in lymphoid and myeloid progenitors. Although abundance of hematopoietic stem cells was 2.5-fold reduced in Jak2(-\/-) fetal livers, transplantation of Jak2(-\/-)-cS5 fetal liver cells into irradiated mice gave rise to mature erythroid and myeloid cells of donor origin up to 6 months after transplantation. Cytokine- and c-Kit pathways do not function independently of each other in hematopoiesis but cooperate to attain full Jak2\/Stat5 activation. In conclusion, activated Stat5 is a critical downstream effector of Jak2 in erythropoiesis\/myelopoiesis, and Jak2 functionally links cytokine- with c-Kit-receptor tyrosine kinase signaling.","authors":"Grebien, F., Kerenyi, MA., Kovacic, B., Kolbe, T., Becker, V., Dolznig, H., Pfeffer, K., Klingm\u00fcller, U., M\u00fcller, M., Beug, H., M\u00fcllner, EW., Moriggl, R.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Blood","volume":"111","issue":"9","page":"4511-22","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18227156","title":"T-cell receptor-induced NF-kappaB activation is negatively regulated by E3 ubiquitin ligase Cbl-b.","abstract":"It has previously been shown that E3 ubiquitin ligase Casitas B-lineage lymphoma-b (Cbl-b) negatively regulates T-cell activation, but the molecular mechanism(s) underlying this inhibition is not completely defined. In this study, we report that the loss of Cbl-b selectively results in aberrant activation of NF-kappaB upon T-cell antigen receptor (TCR) ligation, which is mediated by phosphatidylinositol 3-kinase (PI3-K)\/Akt and protein kinase C-theta (PKC-theta). TCR-induced hyperactivation of Akt in the absence of Cbl-b may potentiate the formation of caspase recruitment domain-containing membrane-associated guanylate kinase protein 1 (CARMA1)-B-cell lymphoma\/leukemia 10 (Bcl10)-mucosa-associated lymphatic tissue 1(MALT1) (CBM) complex, which appears to be independent of PKC-theta. Cbl-b associates with PKC-theta upon TCR stimulation and regulates TCR-induced PKC-theta activation via Vav-1, which couples PKC-theta to PI3-K and allows it to be phosphorylated. PKC-theta then couples IkappaB kinases (IKKs) to the CBM complex, resulting in the activation of the IKK complex. Therefore, our data provide the first evidence to demonstrate that the down-regulation of TCR-induced NF-kappaB activation by Cbl-b is mediated coordinately by both Akt-dependent and PKC-theta-dependent signaling pathways in primary T cells.","authors":"Qiao, G., Li, Z., Molinero, L., Alegre, ML., Ying, H., Sun, Z., Penninger, JM., Zhang, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Mol Cell Biol","volume":"28","issue":"7","page":"2470-80","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18200528","title":"How does noncoding transcription regulate Hox genes?","abstract":"Noncoding RNA has arrived at centre stage in recent years with the discovery of \"hidden transcriptomes\" in many higher organisms. Over two decades ago, noncoding transcripts were discovered in Drosophila Hox complexes, but their function has remained elusive. Recent studies1-3 have examined the role of these noncoding RNAs in Hox gene regulation, and have generated a fierce debate as to whether the noncoding transcripts are important for silencing or activation. Here we review the evidence, and show that, by taking developmental timing into account, some of these apparently conflicting results can be resolved. We examine current models that explain these data and explore alternative interpretations.","authors":"Lempradl, A., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Bioessays","volume":"30","issue":"2","page":"110-21","pdf":null,"JrId":"1014","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18226189","title":"Activator protein 1 (Fos\/Jun) functions in inflammatory bone and skin disease.","abstract":"Activator protein 1 (AP-1) (Fos\/Jun) is a transcriptional regulator composed of members of the Fos and Jun families of DNA binding proteins. The functions of AP-1 were initially studied in mouse development as well as in the whole organism through conventional transgenic approaches, but also by gene targeting using knockout strategies. The importance of AP-1 proteins in disease pathways including the inflammatory response became fully apparent through conditional mutagenesis in mice, in particular when employing gene inactivation in a tissue-specific and inducible fashion. Besides the well-documented roles of Fos and Jun proteins in oncogenesis, where these genes can function both as tumor promoters or tumor suppressors, AP-1 proteins are being recognized as regulators of bone and immune cells, a research area termed osteoimmunology. In the present article, we review recent data regarding the functions of AP-1 as a regulator of cytokine expression and an important modulator in inflammatory diseases such as rheumatoid arthritis, psoriasis and psoriatic arthritis. These new data provide a better molecular understanding of disease pathways and should pave the road for the discovery of new targets for therapeutic applications.","authors":"Zenz, R., Eferl, R., Scheinecker, C., Redlich, K., Smolen, J., Schonthaler, HB., Kenner, L., Tschachler, E., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Arthritis Res Ther","volume":"10","issue":"1","page":"201","pdf":null,"JrId":"30289","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18175296","title":"Allosteric activation of HtrA protease DegP by stress signals during bacterial protein quality control.","abstract":null,"authors":"Meltzer, M., Hasenbein, S., Hauske, P., Kucz, N., Merdanovic, M., Grau, S., Beil, A., Jones, D., Krojer, T., Clausen, T., Ehrmann, M., Kaiser, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Angew Chem Int Ed Engl","volume":"47","issue":"7","page":"1332-4","pdf":null,"JrId":"537","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18187451","title":"Paxillin-dependent stimulation of microtubule catastrophes at focal adhesion sites.","abstract":"An organized microtubule array is essential for the polarized motility of fibroblasts. Dynamic microtubules closely interact with focal adhesion sites in migrating cells. Here, we examined the effect of focal adhesions on microtubule dynamics. We observed that the probability of microtubule catastrophes (transitions from growth to shrinkage) was seven times higher at focal adhesions than elsewhere. Analysis of the dependence between the microtubule growth rate and catastrophe probability throughout the cytoplasm revealed that a nonspecific (mechanical or spatial) factor provided a minor contribution to the catastrophe induction by decreasing microtubule growth rate at adhesions. Strikingly, at the same growth rate, the probability of catastrophes was significantly higher at adhesions than elsewhere, indicative of a site-specific biochemical trigger. The observed catastrophe induction occurred at adhesion domains containing the scaffolding protein paxillin that has been shown previously to interact with tubulin. Furthermore, replacement of full-length paxillin at adhesion sites by microinjected paxillin LIM2-LIM3 domains suppressed microtubule catastrophes exclusively at adhesions. We suggest that paxillin influences microtubule dynamics at focal adhesions by serving as a scaffold for a putative catastrophe factor and\/or regulating its exposure to microtubules.","authors":"Efimov, A., Schiefermeier, N., Grigoriev, I., Ohi, R., Brown, MC., Turner, CE., Small, JV., Kaverina, I.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Cell Sci","volume":"121","issue":"Pt 2","page":"196-204","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18066048","title":"A receptor that mediates the post-mating switch in Drosophila reproductive behaviour.","abstract":"Mating in many species induces a dramatic switch in female reproductive behaviour. In most insects, this switch is triggered by factors present in the male's seminal fluid. How these factors exert such profound effects in females is unknown. Here we identify a receptor for the Drosophila melanogaster sex peptide (SP, also known as Acp70A), the primary trigger of post-mating responses in this species. Females that lack the sex peptide receptor (SPR, also known as CG16752), either entirely or only in the nervous system, fail to respond to SP and continue to show virgin behaviours even after mating. SPR is expressed in the female's reproductive tract and central nervous system. The behavioural functions of SPR map to the subset of neurons that also express the fruitless gene, a key determinant of sex-specific reproductive behaviour. SPR is highly conserved across insects, opening up the prospect of new strategies to control the reproductive and host-seeking behaviours of agricultural pests and human disease vectors.","authors":"Yapici, N., Kim, YJ., Ribeiro, C., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"451","issue":"7174","page":"33-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2008-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"45","title":"Bovine liver dihydrofolate reductase: purification and properties of the enzyme.","abstract":"A purification procedure is reported for obtaining bovine liver dihydrofolate reductase in high yield and amounts of 100-200 mg. A key step in the procedure is the use of an affinity gel prepared by coupling pteroyl-L-lysine to Sepharose. The purified reductase has a specific activity of about 100 units\/mg and is homogeneous as judged by analytical ultracentrifugation, polyacrylamide gel electrophoresis, and titration with methotrexate. The products of the first step of Edman degradation indicated a minimum purity of 79%. The reductase has a molecular weight of about 21500 on the basis of amino acid composition and 22100 +\/- 300 from equilibrium sedimentation. It is not inhibited by antiserum to the Streptococcus faecium reductase (isoenzyme 2). Unlike the reductase of many other vertebrate tissues, the bovine enzyme is inhibited by mercurials rather than activated and it has a single pH optimum at both low and high ionic strength. However, the position of the pH optimum is shifted and the activity increased by increasing ionic strength. Automatic Edman degradation has been used to determine 34 of the amino-terminal 37 amino acid residues. Considerable homology exists between this region and the corresponding regions of the reductase from S. faecium and from Escherichia coli. This strengthens the idea that this region contributes to the structure of the binding site for dihydrofolate.","authors":"Peterson, DL., Gleisner, JM., Blakley, RL.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"24","page":"5261-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22581641","title":"First annual meeting of the EpiGeneSys Network of Excellence: moving epigenetics towards systems biology.","abstract":"This meeting united participants from the fields of experimental epigenetics, mathematics and computational biology, to discuss results and challenges in the endeavour to explore points of synergy between these fields. The design shown here expresses the idea of moving complex biological phenomena (left nucleosome) towards precise mathematical descriptions (right nucleosome).","authors":"vandenBerg, A., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Bioessays","volume":"34","issue":"7","page":"620-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18059471","title":"14-3-3 proteins recognize a histone code at histone H3 and are required for transcriptional activation.","abstract":"Interphase phosphorylation of S10 at histone H3 is linked to transcriptional activation of a specific subset of mammalian genes like HDAC1. Recently, 14-3-3 proteins have been described as detectors for this phosphorylated histone H3 form. Here, we report that 14-3-3 binding is modulated by combinatorial modifications of histone H3. S10 phosphorylation is necessary for an interaction, but additional H3K9 or H3K14 acetylation increases the affinity of 14-3-3 for histone H3. Histone H3 phosphoacetylation occurs concomitant with K9 methylation in vivo, suggesting that histone phosphorylation and acetylation can synergize to overcome repressive histone methylation. Chromatin immunoprecipitation experiments reveal recruitment of 14-3-3 proteins to the HDAC1 gene in an H3S10ph-dependent manner. Recruitment of 14-3-3 to the promoter is enhanced by additional histone H3 acetylation and correlates with dissociation of the repressive binding module HP1gamma. Finally, siRNA-mediated loss of 14-3-3 proteins abolishes the transcriptional activation of HDAC1. Together our data indicate that 14-3-3 proteins are crucial mediators of histone phosphoacetylation signals.","authors":"Winter, S., Simboeck, E., Fischle, W., Zupkovitz, G., Dohnal, I., Mechtler, K., Ammerer, G., Seiser, C.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO J","volume":"27","issue":"1","page":"88-99","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2008-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18046317","title":"The phosphoinositide-3 kinase gamma-Akt pathway mediates renal tubular injury in cisplatin nephrotoxicity.","abstract":"Nephrotoxicity is a frequent complication of cisplatin-based chemotherapy often limiting its use. In this study, we attempted to the role of the phosphoinositide-3 kinase (PI3K)-gamma-Akt pathway in this form of acute kidney injury. Using PI3K-gamma knockout mice, we found that a conventional dose of cisplatin was more lethal in the knockout mice where the blood urea nitrogen and serum creatinine were significantly higher in them than in wild-type mice. Phosphorylation of Akt in the renal tubules was abrogated in the knockout mice with the severity of renal dysfunction and numbers of TUNEL (terminal deoxynucleotidyl transferase (TdT) mediated nick-end labeling)-positive renal tubule cells being higher in the knockout than in wild-type mice. Cisplatin treatment significantly increased. Caspase-3 activity, histone-associated DNA fragments, and number of annexin V-positive cells was significantly higher in cisplatin-treated primary cultured renal tubular epithelial cells of knockout mice. Transfection of dominant-active forms of Akt and PI3K-gamma ameliorated apoptosis of the tubule epithelial cells derived from the knockout mice. Our results suggest that the PI3K-gamma-Akt pathway lessens apoptosis and plays a critical role in the maintenance of renal function in cisplatin-induced acute kidney injury.","authors":"Kuwana, H., Terada, Y., Kobayashi, T., Okado, T., Penninger, JM., Irie-Sasaki, J., Sasaki, T., Sasaki, S.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Kidney Int","volume":"73","issue":"4","page":"430-45","pdf":null,"JrId":"5428","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18007596","title":"A conserved function for a Caenorhabditis elegans Com1\/Sae2\/CtIP protein homolog in meiotic recombination.","abstract":"Genome stability relies on faithful DNA repair both in mitosis and in meiosis. Here, we report on a Caenorhabditis elegans protein that we found to be homologous to the mammalian repair-related protein CtIP and to the budding yeast Com1\/Sae2 recombination protein. A com-1 mutant displays normal meiotic chromosome pairing but forms irregular chromatin aggregates instead of diakinesis bivalents. While meiotic DNA double-strand breaks (DSBs) are formed, they appear to persist or undergo improper repair. Despite the presence of DSBs, the recombination protein RAD-51, which is known to associate with single-stranded DNA (ssDNA) flanking DSBs, does not localize to meiotic chromosomes in the com-1 mutant. Exposure of the mutant to gamma-radiation, however, induces RAD-51 foci, which suggests that the failure of RAD-51 to load is specific to meiotic (SPO-11-generated) DSBs. These results suggest that C. elegans COM-1 plays a role in the generation of ssDNA tails that can load RAD-51, invade homologous DNA tracts and thereby initiate recombination. Extrapolating from the worm homolog, we expect similar phenotypes for mutations in the mammalian tumor suppressor CtIP.","authors":"Penkner, A., Portik-Dobos, Z., Tang, L., Schnabel, R., Novatchkova, M., Jantsch, V., Loidl, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"EMBO J","volume":"26","issue":"24","page":"5071-82","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18003702","title":"The complete removal of cohesin from chromosome arms depends on separase.","abstract":"Cohesin needs to be removed from chromosomes to allow sister chromatid separation in mitosis. In vertebrates, two pathways contribute to this process. The prophase pathway, which requires phosphorylation of the cohesin subunit SA2 and a cohesin-binding protein, called Wapl, removes the bulk of cohesin from the chromosome arms in early mitosis and allows the resolution of the chromosome arms. At anaphase onset, the protease separase removes centromere-enriched cohesin by proteolytic cleavage of another cohesin subunit, Scc1 (Rad21, Mcd1), which allows the separation of sister chromatids. When anaphase onset is delayed by the spindle-assembly checkpoint, the complete removal of cohesin from chromosome arms but not from centromeres generates typical X- or V-shaped chromosomes. Here, we found that cohesion between chromosome arms is preserved if mitosis is arrested with the proteasome inhibitor MG132. This arm cohesion depends on cohesin complexes that are protected by the shugoshin protein Sgo1, which appears to be distributed on chromosome arms as well as on centromeres in early mitosis. In cells lacking separase or expressing non-cleavable Scc1, arm cohesion was not efficiently removed during nocodazole arrest. Our observations suggest that a fraction of arm cohesin is protected by Sgo1, which prevents cohesin from being removed by the prophase pathway, and that separase is partly activated in nocodazole-arrested cells and removes the arm cohesin protected by Sgo1.","authors":"Nakajima, M., Kumada, K., Hatakeyama, K., Noda, T., Peters, JM., Hirota, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Cell Sci","volume":"120","issue":"Pt 23","page":"4188-96","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17981116","title":"Targeted deletion of AIF decreases mitochondrial oxidative phosphorylation and protects from obesity and diabetes.","abstract":"Type-2 diabetes results from the development of insulin resistance and a concomitant impairment of insulin secretion. Recent studies place altered mitochondrial oxidative phosphorylation (OxPhos) as an underlying genetic element of insulin resistance. However, the causative or compensatory nature of these OxPhos changes has yet to be proven. Here, we show that muscle- and liver-specific AIF ablation in mice initiates a pattern of OxPhos deficiency closely mimicking that of human insulin resistance, and contrary to current expectations, results in increased glucose tolerance, reduced fat mass, and increased insulin sensitivity. These results are maintained upon high-fat feeding and in both genetic mosaic and ubiquitous OxPhos-deficient mutants. Importantly, the effects of AIF on glucose metabolism are acutely inducible and reversible. These findings establish that tissue-specific as well as global OxPhos defects in mice can counteract the development of insulin resistance, diabetes, and obesity.","authors":"Pospisilik, JA., Knauf, C., Joza, N., Benit, P., Orthofer, M., Cani, PD., Ebersberger, I., Nakashima, T., Sarao, R., Neely, G., Esterbauer, H., Kozlov, A., Kahn, CR., Kroemer, G., Rustin, P., Burcelin, R., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell","volume":"131","issue":"3","page":"476-91","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20796172","title":"The E3-ubiquitin ligase TRIM2 regulates neuronal polarization.","abstract":"The establishment of a polarized morphology with a single axon and multiple dendrites is an essential step during neuronal differentiation. This cellular polarization is largely depending on changes in the dynamics of the neuronal cytoskeleton. Here, we show that the tripartite motif (TRIM)-NHL protein TRIM2 is regulating axon specification in cultured mouse hippocampal neurons, where one of several initially indistinguishable neurites is selected to become the axon. Suppression of TRIM2 by RNA interference results in the loss of neuronal polarity while over-expression of TRIM2 induces the specification of multiple axons. TRIM2 conducts its function during neuronal polarization by ubiquitination of the neurofilament light chain. Together, our results imply an important function of TRIM2 for axon outgrowth during development.","authors":"Khazaei, MR., Bunk, EC., Hillje, AL., Jahn, HM., Riegler, EM., Knoblich, JA., Young, P., Schwamborn, JC.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Neurochem","volume":"117","issue":"1","page":"29-37","pdf":null,"JrId":"5004","fulltextlink":null,"preprintlink":null,"articledate":"2011-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17965711","title":"Function of the Drosophila CPEB protein Orb2 in long-term courtship memory.","abstract":"Both long-term behavioral memory and synaptic plasticity require protein synthesis, some of which may occur locally at specific synapses. Cytoplasmic polyadenylation element-binding (CPEB) proteins are thought to contribute to the local protein synthesis that underlies long-term changes in synaptic efficacy, but a role has not been established for them in the formation of long-term behavioral memory. We found that the Drosophila melanogaster CPEB protein Orb2 is acutely required for long-term conditioning of male courtship behavior. Deletion of the N-terminal glutamine-rich region of Orb2 resulted in flies that were impaired in their ability to form long-term, but not short-term, memory. Memory was restored by expressing Orb2 selectively in fruitless (fru)-positive gamma neurons of the mushroom bodies and by providing Orb2 function in mushroom bodies only during and shortly after training. Our data thus demonstrate that a CPEB protein is important in long-term memory and map the molecular, spatial and temporal requirements for its function in memory formation.","authors":"Keleman, K., Kr\u00fcttner, S., Alenius, M., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Neurosci","volume":"10","issue":"12","page":"1587-93","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17940019","title":"Hepatocyte survival in acute hepatitis is due to c-Jun\/AP-1-dependent expression of inducible nitric oxide synthase.","abstract":"Analysis of the molecular factors determining hepatocyte survival or death in response to inflammatory stimuli is essential for understanding the pathogenesis of inflammatory liver disease and for identifying novel therapeutic approaches. c-Jun N-terminal kinase (JNK) is a major mediator of cytokine-induced cell death during hepatitis, but the signaling pathways downstream of JNK remain less well defined. Here we show that the transcription factor c-Jun\/AP-1, a prototypic target of JNK, is strongly expressed in the liver of patients with acute liver injury. The molecular function of c-Jun in inflammatory liver disease was analyzed in mice by using the Con A model of T cell-mediated hepatitis. Mice lacking c-Jun in hepatocytes display increased liver cell death and mortality upon Con A injection. This phenotype is caused by impaired expression of inducible nitric oxide synthase (nos2), a direct transcriptional target of c-Jun, and reduced production of hepatoprotective nitric oxide (NO). Moreover, increased hepatotoxicity in mutant mice is likely caused by hypoxia and oxidative stress and can be rescued pharmacologically by liver-specific NO delivery. These findings demonstrate that c-Jun\/AP-1 is hepatoprotective during acute hepatitis by regulating nos2\/NO expression and thus functionally antagonizes the cell death-promoting functions of JNK.","authors":"Hasselblatt, P., Rath, M., Komnenovic, V., Zatloukal, K., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Proc Natl Acad Sci U S A","volume":"104","issue":"43","page":"17105-10","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11034598","title":"Apoptosis control in syncytia induced by the HIV type 1-envelope glycoprotein complex: role of mitochondria and caspases.","abstract":"Syncytia arising from the fusion of cells expressing a lymphotropic HIV type 1-encoded envelope glycoprotein complex (Env) with cells expressing the CD4\/CXC chemokine receptor 4 complex spontaneously undergo cell death. Here we show that this process is accompanied by caspase activation and signs of mitochondrial membrane permeabilization (MMP), including the release of intermembrane proteins such as cytochrome c (Cyt-c) and apoptosis-inducing factor (AIF) from mitochondria. In Env-induced syncytia, caspase inhibition did not suppress AIF- and Cyt-c translocation, yet it prevented all signs of nuclear apoptosis. Translocation of Bax to mitochondria led to MMP, which was inhibited by microinjected Bcl-2 protein or bcl-2 transfection. Bcl-2 also prevented the subsequent nuclear chromatin condensation and DNA fragmentation. The release of AIF occurred before that of Cyt-c and before caspase activation. Microinjection of AIF into syncytia sufficed to trigger rapid, caspase-independent Cyt-c release. Neutralization of endogenous AIF by injection of an antibody prevented all signs of spontaneous apoptosis occurring in syncytia, including the Cyt-c release and nuclear apoptosis. In contrast, Cyt-c neutralization only prevented nuclear apoptosis, and did not affect AIF release. Our results establish that the following molecular sequence governs apoptosis of Env-induced syncytia: Bax-mediated\/Bcl-2-inhibited MMP --&gt; AIF release --&gt; Cyt-c release --&gt; caspase activation --&gt; nuclear apoptosis.","authors":"Ferri, KF., Jacotot, E., Blanco, J., Est\u00e9, JA., Zamzami, N., Susin, SA., Xie, Z., Brothers, G., Reed, JC., Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Exp Med","volume":"192","issue":"8","page":"1081-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-11-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17938245","title":"Regulation of the sigmaE stress response by DegS: how the PDZ domain keeps the protease inactive in the resting state and allows integration of different OMP-derived stress signals upon folding stress.","abstract":"The unfolded protein response of Escherichia coli is triggered by the accumulation of unassembled outer membrane proteins (OMPs) in the cellular envelope. The PDZ-protease DegS recognizes these mislocalized OMPs and initiates a proteolytic cascade that ultimately leads to the sigmaE-driven expression of a variety of factors dealing with folding stress in the periplasm and OMP assembly. The general features of how OMPs activate the protease function of DegS have not yet been systematically addressed. Furthermore, it is unknown how the PDZ domain keeps the protease inactive in the resting state, which is of crucial importance for the functioning of the entire sigmaE stress response. Here we show in atomic detail how DegS is able to integrate the information of distinct stress signals that originate from different OMPs containing a -x-Phe C-terminal motif. A dedicated loop of the protease domain, loop L3, serves as a versatile sensor for allosteric ligands. L3 is capable of interacting differently with ligands but reorients in a conserved manner to activate DegS. Our data also indicate that the PDZ domain directly inhibits protease function in the absence of stress signals by wedging loop L3 in a conformation that ultimately disrupts the proteolytic site. Thus, the PDZ domain and loop L3 of DegS define a novel molecular switch allowing strict regulation of the sigmaE stress response system.","authors":"Hasselblatt, H., Kurzbauer, R., Wilken, C., Krojer, T., Sawa, J., Kurt, J., Kirk, R., Hasenbein, S., Ehrmann, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genes Dev","volume":"21","issue":"20","page":"2659-70","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17869504","title":"X inactivation Xplained.","abstract":"Random inactivation of one of the two female X chromosomes establishes dosage compensation between XY males and XX females in placental mammals. X inactivation is controlled by the X inactivation center (Xic). Recent advances in genome sequencing show that the Xic has evolved from an ancestral vertebrate gene cluster in placental mammals and has undergone separate rearrangements in marsupials. The Xic ensures that all but one X chromosome per diploid genome are inactivated. Which chromosome remains active is randomly chosen. Pairing of Xic loci on the two X chromosomes and alternate states of the X chromosomes before inactivation have recently been implicated in the mechanism of random choice. Chromosome-wide silencing is then initiated by the noncoding Xist RNA, which evolved with the mammalian Xic and covers the inactive X chromosome.","authors":"Wutz, A., Gribnau, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Curr Opin Genet Dev","volume":"17","issue":"5","page":"387-93","pdf":null,"JrId":"2199","fulltextlink":null,"preprintlink":null,"articledate":"2008-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17851532","title":"Conversion of mature B cells into T cells by dedifferentiation to uncommitted progenitors.","abstract":"Lineage commitment and differentiation to a mature cell type are considered to be unidirectional and irreversible processes under physiological conditions. The commitment of haematopoietic progenitors to the B-cell lineage and their development to mature B lymphocytes critically depend on the transcription factor encoded by the paired box gene 5 (Pax5). Here we show that conditional Pax5 deletion in mice allowed mature B cells from peripheral lymphoid organs to dedifferentiate in vivo back to early uncommitted progenitors in the bone marrow, which rescued T lymphopoiesis in the thymus of T-cell-deficient mice. These B-cell-derived T lymphocytes carried not only immunoglobulin heavy- and light-chain gene rearrangements but also participated as functional T cells in immune reactions. Mice lacking Pax5 in mature B cells also developed aggressive lymphomas, which were identified by their gene expression profile as progenitor cell tumours. Hence, the complete loss of Pax5 in late B cells could initiate lymphoma development and uncovered an extraordinary plasticity of mature peripheral B cells despite their advanced differentiation stage.","authors":"Cobaleda, C., Jochum, W., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"449","issue":"7161","page":"473-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17846168","title":"Suv4-20h deficiency results in telomere elongation and derepression of telomere recombination.","abstract":"Mammalian telomeres have heterochromatic features, including trimethylated histone H3 at lysine 9 (H3K9me3) and trimethylated histone H4 at lysine 20 (H4K20me3). In addition, subtelomeric DNA is hypermethylated. The enzymatic activities responsible for these modifications at telomeres are beginning to be characterized. In particular, H4K20me3 at telomeres could be catalyzed by the novel Suv4-20h1 and Suv4-20h2 histone methyltransferases (HMTases). In this study, we demonstrate that the Suv4-20h enzymes are responsible for this histone modification at telomeres. Cells deficient for Suv4-20h2 or for both Suv4-20h1 and Suv4-20h2 show decreased levels of H4K20me3 at telomeres and subtelomeres in the absence of changes in H3K9me3. These epigenetic alterations are accompanied by telomere elongation, indicating a role for Suv4-20h HMTases in telomere length control. Finally, cells lacking either the Suv4-20h or Suv39h HMTases show increased frequencies of telomere recombination in the absence of changes in subtelomeric DNA methylation. These results demonstrate the importance of chromatin architecture in the maintenance of telomere length homeostasis and reveal a novel role for histone lysine methylation in controlling telomere recombination.","authors":"Benetti, R., Gonzalo, S., Jaco, I., Schotta, G., Klatt, P., Jenuwein, T., Blasco, MA.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Cell Biol","volume":"178","issue":"6","page":"925-36","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36","title":"The effects of processing of barley-based supplements on rumen pH, rate of digestion of voluntary intake of dried grass in sheep.","abstract":"1. In one experiment the effect on rumen pH of feeding with restricted amounts of whole or pelleted barley was studied. With whole barley there was little variation in rumen pH associated with feeding time, but with pelleted barley the pH decreased from about 7-0 before feeding to about 5-3, 2--3 h after feeding. 2. The rate of disappearance of dried grass during incubation in the rumens of sheep receiving either whole or pelleted barley was studied in a second experiment. After 24 h incubation only 423 mg\/g incubated had disappeared in the rumen of sheep receiving pelleted barley while 625 mg\/g incubated had disappeared when it was incubated in the rumen of sheep receiving whole barley. 3. The voluntary intake of dried grass of lambs was studied in a third experiment when they received supplements of either 25 or 50 g whole or pelleted barley\/kg live weight 0-75. At the high level, pelleted barley reduced intake of dried grass by 534 g\/kg but whole barley reduced it by only 352 g\/kg. The digestibility of acid-detergent fibre was reduced more by pelleted barley than by whole barley but there was a tendency for a small increase in digestibility of the barley due to processing. 4. The implications of these findings on supplementation of roughages with cereals are discussed.","authors":"Orskov, ER., Fraser, C.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Nutr","volume":"34","issue":"3","page":"493-500","pdf":null,"JrId":"1869","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17762881","title":"Antagonistic control of cell fates by JNK and p38-MAPK signaling.","abstract":"During the development and organogenesis of all multicellular organisms, cell fate decisions determine whether cells undergo proliferation, differentiation, or aging. Two independent stress kinase signaling pathways, p38-MAPK, and JNKs, have evolved that relay developmental and environmental cues to determine cell responses. Although multiple stimuli can activate these two stress kinase pathways, the functional interactions and molecular cross-talks between these common second signaling cascades are poorly elucidated. Here we report that JNK and p38-MAPK pathways antagonistically control cellular senescence, oncogenic transformation, and proliferation in primary mouse embryonic fibroblasts (MEFs). Similarly, genetic inactivation of the JNK pathway results in impaired proliferation of fetal hepatoblasts in vitro and defective adult liver regeneration in vivo, which is rescued by inhibition of the p38-MAPK pathway. Thus, the balance between the two stress-signaling pathways, MKK7-JNK and MKK3\/6-p38-MAPK, determines cell fate and links environmental and developmental stress to cell cycle arrest, senescence, oncogenic transformation, and adult tissue regeneration.","authors":"Wada, T., Stepniak, E., Hui, L., Leibbrandt, A., Katada, T., Nishina, H., Wagner, EF., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell Death Differ","volume":"15","issue":"1","page":"89-93","pdf":null,"JrId":"20326","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17546005","title":"Tandem affinity purification of functional TAP-tagged proteins from human cells.","abstract":"Tandem affinity purification (TAP) is a generic two-step affinity purification protocol for isolation of TAP-tagged proteins together with associated proteins. We used bacterial artificial chromosome to heterologously express TAP-tagged murine Sgo1 protein in human HeLa cells. This allowed us to test the functionality of the Sgo1-TAP protein by RNA interference-mediated depletion of the endogenous human Sgo1. Here, we present an optimized protocol for purification of TAP-tagged Sgo1 protein as well as KIAA1387 from HeLa cells with detailed instructions. The purification protocol can be completed in 1 day and it should be applicable to other proteins.","authors":"Gregan, J., Riedel, CG., Petronczki, M., Cipak, L., Rumpf, C., Poser, I., Buchholz, F., Mechtler, K., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Protoc","volume":"2","issue":"5","page":"1145-51","pdf":null,"JrId":"33047","fulltextlink":null,"preprintlink":null,"articledate":"2008-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17724470","title":"Sustained TGF beta exposure suppresses Smad and non-Smad signalling in mammary epithelial cells, leading to EMT and inhibition of growth arrest and apoptosis.","abstract":"To better understand the dual, tumour-suppressive and tumour-promoting function of transforming growth factor-beta (TGFbeta), we analysed mammary epithelial NMuMG cells in response to short and long-term TGFbeta exposure. NMuMG cells became proliferation-arrested and apoptotic after exposure to TGFbeta for 2-5 days, whereas surviving cells underwent epithelial-mesenchymal transition (EMT). After chronic TGFbeta exposure (2-3 weeks), however, NMuMG cells became resistant to proliferation arrest and apoptosis, showing sustained EMT instead (TD cells). EMT was fully reversed by a pharmacologic TGFbeta-receptor-I kinase inhibitor or withdrawal of TGFbeta for 6-12 days. Interestingly, both cell cycle arresting\/proapoptotic (Smads, p38 kinase) and antiapoptotic, proliferation and EMT-promoting signalling pathways (PI3K-PKB\/Akt, ERK) were co-suppressed to low, but significant levels. Except for PI3K-Akt, TGFbeta-dependent downregulation of these signalling pathways in transdifferentiated (TD) cells was fully reversed upon TGFbeta withdrawal, together with partial re-induction of proliferation arrest and apoptosis. Co-injection of non-tumorigenic NMuMG cells with tumour-forming CHO cells oversecreting exogenous TGFbeta1 (CHO-TGFbeta1) allowed outgrowth of epithelioid cells in CHO-TGFbeta1 cell-induced tumours. These epithelial islands enhanced CHO-TGFbeta1 tumour cell proliferation, possibly due to chemokines (for example, JE\/MCP-1) secreted by NMuMG\/TD cells. We conclude that suppression of antiproliferative, proapoptotic TGFbeta signalling in TD cells may permit TGFbeta-dependent proliferation, survival and EMT-enhancing signalling pathways to act at low levels. Thus, TGFbeta may modulate its own signalling to facilitate switching from tumour suppression to tumour progression.","authors":"Gal, A., Sj\u00f6blom, T., Fedorova, L., Imreh, S., Beug, H., Moustakas, A.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Oncogene","volume":"27","issue":"9","page":"1218-30","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17699747","title":"Life beyond cleavage: the case of Ago2 and hematopoiesis.","abstract":null,"authors":"Martinez, J., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genes Dev","volume":"21","issue":"16","page":"1983-8","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2007-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21532594","title":"Structural adaptation of the plant protease Deg1 to repair photosystem II during light exposure.","abstract":"Deg1 is a chloroplastic protease involved in maintaining the photosynthetic machinery. Structural and biochemical analyses reveal that the inactive Deg1 monomer is transformed into the proteolytically active hexamer at acidic pH. The change in pH is sensed by His244, which upon protonation, repositions a specific helix to trigger oligomerization. This system ensures selective activation of Deg1 during daylight, when acidification of the thylakoid lumen occurs and photosynthetic proteins are damaged.","authors":"Kley, J., Schmidt, B., Boyanov, B., Stolt-Bergner, PC., Kirk, R., Ehrmann, M., Knopf, RR., Naveh, L., Adam, Z., Clausen, T.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Struct Mol Biol","volume":"18","issue":"6","page":"728-31","pdf":null,"JrId":"31761","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17681633","title":"Xist function: bridging chromatin and stem cells.","abstract":"In mammals, dosage compensation is achieved by transcriptional silencing of one of the two female X chromosomes. X inactivation is dynamically regulated in development. The non-coding Xist RNA localizes to the inactive X, initiates gene repression in the early embryo, and later stabilizes the inactive state. Different functions of Xist are observed depending on which epigenetic regulatory pathways are active in a given cell. Because Xist has evolved recently, with the origin of placental mammals, the underlying pathways are also important in regulating developmental control genes. This review emphasizes the opportunity that Xist provides to functionally define epigenetic transitions in development, to understand cell identity, pluripotency and stem cell differentiation.","authors":"Wutz, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Trends Genet","volume":"23","issue":"9","page":"457-64","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17723215","title":"p110gamma and p110delta phosphoinositide 3-kinase signaling pathways synergize to control development and functions of murine NK cells.","abstract":"Phosphoinositide 3-kinases (PI-3Ks) are key enzymes for cell development, activation, and survival. Here we showed that PI-3K class IB and class IA catalytic subunits, p110gamma and p110delta, played a crucial role in the development and functions of murine NK cells. p110gamma deficiency and impairment of G protein-coupled receptor (GPRC) signaling prevented full NK cell maturation. Concomitant loss of p110gamma and p110delta exacerbated this defect, resulting in a very small population of NK cells with a highly immature phenotype in the bone marrow and periphery. Moreover, combined p110gamma and p110delta signals were required for cytotoxicity and activation of the kinase ERK during NK cell-target cell interaction. p110gamma played a major role in receptor-induced interferon-gamma (IFN-gamma) production through a pathway that involved the kinase ERK and 5-Lipoxigenase, which most likely generates lipid mediators activating GPRCs. Conversely, PI3Ks negatively regulated interleukin-12 (IL-12) and IL-18-induced IFN-gamma by modulating p38 kinase activation. Our data shed light on the multiple intersecting pathways through which PI3Ks control NK cell-mediated innate responses.","authors":"Tassi, I., Cella, M., Gilfillan, S., Turnbull, I., Diacovo, TG., Penninger, JM., Colonna, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Immunity","volume":"27","issue":"2","page":"214-27","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11027316","title":"Regulation of T cell activation, anxiety, and male aggression by RGS2.","abstract":"Regulators of G protein signaling (RGS) proteins accelerate the GTPase activity of Galpha protein subunits in vitro, negatively regulating G protein-coupled receptor signaling. The physiological role of mammalian RGS proteins is largely unknown. The RGS family member rgs2 was cloned as an immediate early response gene up-regulated in T lymphocytes after activation. To investigate the role of RGS2 in vivo, we generated rgs2-deficient mice. We show that targeted mutation of rgs2 in mice leads to reduced T cell proliferation and IL-2 production, which translates in an impaired antiviral immunity in vivo. Interestingly, rgs2(-\/-) mice also display increased anxiety responses and decreased male aggression in the absence of cognitive or motor deficits. RGS2 also controls synaptic development and basal electrical activity in hippocampal CA1 neurons. Thus, RGS2 plays an important role in T cell activation, synapse development in the hippocampus, and emotive behaviors.","authors":"Oliveira-Dos-Santos, AJ., Matsumoto, G., Snow, BE., Bai, D., Houston, FP., Whishaw, IQ., Mariathasan, S., Sasaki, T., Wakeham, A., Ohashi, PS., Roder, JC., Barnes, CA., Siderovski, DP., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Proc Natl Acad Sci U S A","volume":"97","issue":"22","page":"12272-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17673668","title":"Impaired heart contractility in Apelin gene-deficient mice associated with aging and pressure overload.","abstract":"Apelin constitutes a novel endogenous peptide system suggested to be involved in a broad range of physiological functions, including cardiovascular function, heart development, control of fluid homeostasis, and obesity. Apelin is also a catalytic substrate for angiotensin-converting enzyme 2, the key severe acute respiratory syndrome receptor. The in vivo physiological role of Apelin is still elusive. Here we report the generation of Apelin gene-targeted mice. Apelin mutant mice are viable and fertile, appear healthy, and exhibit normal body weight, water and food intake, heart rates, and heart morphology. Intriguingly, aged Apelin knockout mice developed progressive impairment of cardiac contractility associated with systolic dysfunction in the absence of histological abnormalities. We also report that pressure overload induces upregulation of Apelin expression in the heart. Importantly, in pressure overload-induced heart failure, loss of Apelin did not significantly affect the hypertrophy response, but Apelin mutant mice developed progressive heart failure. Global gene expression arrays and hierarchical clustering of differentially expressed genes in hearts of banded Apelin(-\/y) and Apelin(+\/y) mice showed concerted upregulation of genes involved in extracellular matrix remodeling and muscle contraction. These genetic data show that the endogenous peptide Apelin is crucial to maintain cardiac contractility in pressure overload and aging.","authors":"Kuba, K., Zhang, L., Imai, Y., Arab, S., Chen, M., Maekawa, Y., Leschnik, M., Leibbrandt, A., Markovic, M., Makovic, M., Schwaighofer, J., Beetz, N., Musialek, R., Neely, GG., Komnenovic, V., Kolm, U., Metzler, B., Ricci, R., Hara, H., Meixner, A., Nghiem, M., Chen, X., Dawood, F., Wong, KM., Sarao, R., Cukerman, E., Kimura, A., Hein, L., Thalhammer, J., Liu, PP., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Circ Res","volume":"101","issue":"4","page":"e32-42","pdf":null,"JrId":"2974","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17658281","title":"Transcription factor Pax5 activates the chromatin of key genes involved in B cell signaling, adhesion, migration, and immune function.","abstract":"The transcription factor Pax5 represses B lineage-inappropriate genes and activates B cell-specific genes in B lymphocytes. Here we have identified 170 Pax5-activated genes. Conditional mutagenesis demonstrated that the Pax5-regulated genes require continuous Pax5 activity for normal expression in pro-B and mature B cells. Expression of half of the Pax5-activated genes is either absent or substantially reduced upon Pax5 loss in plasma cells. Direct Pax5 target genes were identified based on their protein synthesis-independent activation by a Pax5-estrogen receptor fusion protein. Chromatin immunoprecipitation (ChIP) of Pax5 together with chromatin profiling by ChIP-on-chip analysis demonstrated that Pax5 directly activates the chromatin at promoters or putative enhancers of Pax5 target genes. The Pax5-activated genes code for key regulatory and structural proteins involved in B cell signaling, adhesion, migration, antigen presentation, and germinal-center B cell formation, thus revealing a complex regulatory network that is activated by Pax5 to control B cell development and function.","authors":"Schebesta, A., McManus, S., Salvagiotto, G., Delogu, A., Busslinger, GA., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Immunity","volume":"27","issue":"1","page":"49-63","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17658279","title":"Direct regulation of Gata3 expression determines the T helper differentiation potential of Notch.","abstract":"CD4(+) T helper cells differentiate into T helper 1 (Th1) or Th2 effector lineages, which orchestrate immunity to different types of microbes. Both Th1 and Th2 differentiation can be induced by Notch, but what dictates which of these programs is activated in response to Notch is not known. By using T cell-specific gene ablation of the Notch effector RBP-J or the Notch1 and 2 receptors, we showed here that Notch was required on CD4(+) T cells for physiological Th2 responses to parasite antigens. GATA-3 was necessary for Notch-induced Th2 differentiation, and we identified an upstream Gata3 promoter as a direct target for Notch signaling. Moreover, absence of GATA-3 turned Notch from a Th2 inducer into a powerful inducer of Th1 differentiation. Therefore, Gata3 is a critical element determining inductive Th2 differentiation and limiting Th1 differentiation by Notch.","authors":"Amsen, D., Antov, A., Jankovic, D., Sher, A., Radtke, F., Souabni, A., Busslinger, M., McCright, B., Gridley, T., Flavell, RA.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Immunity","volume":"27","issue":"1","page":"89-99","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17620408","title":"Ring1B is crucial for the regulation of developmental control genes and PRC1 proteins but not X inactivation in embryonic cells.","abstract":"The Polycomb group (PcG) gene Ring1B has been implicated in the repression of developmental control genes and X inactivation and is essential for embryogenesis. Ring1B protein contains a RING finger domain and functions as an E3 ubiquitin ligase that is crucial for the monoubiquitination of histone H2A (H2AK119ub1). Here, we study the function of Ring1B in mouse embryonic stem (ES) cells. The deletion of Ring1B causes the loss of several PcG proteins, showing an unanticipated function in the regulation of PcG protein levels. Derepression of lineage genes and an aberrant differentiation potential is observed in Ring1B-deficient ES cells. Despite a crucial function of Ring1B in establishing the chromosome-wide ubiquitination of histone H2A lysine 119 (H2AK119ub1) upon Xist expression in ES cells, the initiation of silencing by Xist is independent of Ring1B. Other chromatin marks associated with the initiation of X inactivation are not affected in Ring1B-deficient cells, suggesting compensation for the loss of Ring1B in X inactivation in contrast to the repression of lineage genes.","authors":"Leeb, M., Wutz, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Cell Biol","volume":"178","issue":"2","page":"219-29","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22580457","title":"Pat(ting) boosts meiosis.","abstract":"","authors":"Tachibana-Konwalski, K.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Cycle","volume":"11","issue":"10","page":"1876-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17634282","title":"A protein interaction map of the mitotic spindle.","abstract":"The mitotic spindle consists of a complex network of proteins that segregates chromosomes in eukaryotes. To strengthen our understanding of the molecular composition, organization, and regulation of the mitotic spindle, we performed a system-wide two-hybrid screen on 94 proteins implicated in spindle function in Saccharomyces cerevisiae. We report 604 predominantly novel interactions that were detected in multiple screens, involving 303 distinct prey proteins. We uncovered a pattern of extensive interactions between spindle proteins reflecting the intricate organization of the spindle. Furthermore, we observed novel connections between kinetochore complexes and chromatin-modifying proteins and used phosphorylation site mutants of NDC80\/TID3 to gain insights into possible phospho-regulation mechanisms. We also present analyses of She1p, a novel spindle protein that interacts with the Dam1 kinetochore\/spindle complex. The wealth of protein interactions presented here highlights the extent to which mitotic spindle protein functions and regulation are integrated with each other and with other cellular activities.","authors":"Wong, J., Nakajima, Y., Westermann, S., Shang, C., Kang, JS., Goodner, C., Houshmand, P., Fields, S., Chan, CS., Drubin, D., Barnes, G., Hazbun, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Biol Cell","volume":"18","issue":"10","page":"3800-9","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26420377","title":"Proliferation control in neural stem and progenitor cells.","abstract":"Neural circuit function can be drastically affected by variations in the number of cells that are produced during development or by a reduction in adult cell number owing to disease. For this reason, unique cell cycle and cell growth control mechanisms operate in the developing and adult brain. In Drosophila melanogaster and in mammalian neural stem and progenitor cells, these mechanisms are intricately coordinated with the developmental age and the nutritional, metabolic and hormonal state of the animal. Defects in neural stem cell proliferation that result in the generation of incorrect cell numbers or defects in neural stem cell differentiation can cause microcephaly or megalencephaly.","authors":"Homem, CC., Repic, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Rev Neurosci","volume":"16","issue":"11","page":"647-59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17632058","title":"Molecular basis for target RNA recognition and cleavage by human RISC.","abstract":"The RNA-Induced Silencing Complex (RISC) is a ribonucleoprotein particle composed of a single-stranded short interfering RNA (siRNA) and an endonucleolytically active Argonaute protein, capable of cleaving mRNAs complementary to the siRNA. The mechanism by which RISC cleaves a target RNA is well understood, however it remains enigmatic how RISC finds its target RNA. Here, we show, both in vitro and in vivo, that the accessibility of the target site correlates directly with the efficiency of cleavage, demonstrating that RISC is unable to unfold structured RNA. In the course of target recognition, RISC transiently contacts single-stranded RNA nonspecifically and promotes siRNA-target RNA annealing. Furthermore, the 5' part of the siRNA within RISC creates a thermodynamic threshold that determines the stable association of RISC and the target RNA. We therefore provide mechanistic insights by revealing features of RISC and target RNAs that are crucial to achieve efficiency and specificity in RNA interference.","authors":"Ameres, SL., Martinez, J., Schroeder, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell","volume":"130","issue":"1","page":"101-12","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19009524","title":"Impaired T-cell development in the absence of Vav1 and Itk.","abstract":"Vav1 and the Tec family kinase Itk act in similar T-cell activation pathways. Both molecules interact with members of the Cbl family of E3 ubiquitin ligases, and signaling defects in Vav1(-\/-) T cells are rescued upon deletion of Cbl-b. In this study we investigate the relation between Itk and Cbl-b or Vav1 by generating Itk\/Cbl-b and Itk\/Vav1 double-deficient mice. Deletion of Cbl-b in Itk(-\/-) CD4(+) T cells restored proliferation and partially IL-2 production, and also led to a variable rescue of IL-4 production. Thus, Itk and Vav1 act mechanistically similarly in peripheral T cells, since the defects in Itk(-\/-) T cells, as in Vav1(-\/-) T cells, are rescued if cells are released from the negative regulation mediated by Cbl-b. In addition, only few peripheral CD4(+) and CD8(+) T cells were present in Vav1(-\/-)Itk(-\/-) mice due to severely impaired thymocyte differentiation. Vav1(-\/-)Itk(-\/-) thymocyte numbers were strongly reduced compared with WT, Itk(-\/-) or Vav1(-\/-) mice, and double-positive thymocytes displayed increased cell death and impaired positive selection. Therefore, our data also reveal that the combined activity of Vav1 and Itk is required for proper T-cell development and the generation of the peripheral T-cell pool.","authors":"Raberger, J., Boucheron, N., Sakaguchi, S., Penninger, JM., Ellmeier, W.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Eur J Immunol","volume":"38","issue":"12","page":"3530-42","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17607691","title":"Simultaneous generation of fra-2 conditional and fra-2 knock-out mice.","abstract":"Loss of function mouse models comprise knock-out mice, where a gene is deleted in the germline, and conditional knock-out mice with somatic deletion of a floxed allele in defined tissues. Both types of mice are used for comprehensive studies of gene functions in vivo. Here, we describe a simple method for simultaneous generation of mice with conditional or knock-out alleles for the transcription factor fra-2 (Fos-related antigen 2) using a single embryonic stem (ES) cell clone. ES cells with a floxed fra-2 allele were transiently transfected with a Cre-recombinase expression plasmid and plated at low density. Most of the resulting ES cell colonies consisted of a mixture of cells that have either retained or lost the conditional allele. We demonstrate that these mixed ES cell clones can be directly used for generation of chimeras that give rise to offspring with conditional or knock-out alleles simultaneously. This strategy shortens the time and reduces the number of germline transmission events to generate genetically modified mice.","authors":"Eferl, R., Zenz, R., Theussl, HC., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genesis","volume":"45","issue":"7","page":"447-51","pdf":null,"JrId":"21590","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21558271","title":"Random mutagenesis of the prokaryotic peptide transporter YdgR identifies potential periplasmic gating residues.","abstract":"The peptide transporter (PTR) family represents a group of proton-coupled secondary transporters responsible for bulk uptake of amino acids in the form of di- and tripeptides, an essential process employed across species ranging from bacteria to humans. To identify amino acids critical for peptide transport in a prokaryotic PTR member, we have screened a library of mutants of the Escherichia coli peptide transporter YdgR using a high-throughput substrate uptake assay. We have identified 35 single point mutations that result in a full or partial loss of transport activity. Additional analysis, including homology modeling based on the crystal structure of the Shewanella oneidensis peptide transporter PepT(so), identifies Glu(56) and Arg(305) as potential periplasmic gating residues. In addition to providing new insights into transport by members of the PTR family, these mutants provide valuable tools for further study of the mechanism of peptide transport.","authors":"Malle, E., Zhou, H., Neuhold, J., Spitzenberger, B., Klepsch, F., Pollak, T., Bergner, O., Ecker, GF., Stolt-Bergner, PC.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Biol Chem","volume":"286","issue":"26","page":"23121-31","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2011-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17607745","title":"Annexin A2\/P11 interaction: new insights into annexin A2 tetramer structure by chemical crosslinking, high-resolution mass spectrometry, and computational modeling.","abstract":"During the past few years, the structural analysis of proteins and protein complexes by chemical crosslinking and mass spectrometry has enjoyed increasing popularity. With this approach we have investigated the quaternary structure of the complex between annexin A2 and p11, which is involved in numerous cellular processes. Although high-resolution data are available for both interaction partners as well as for the complex between two p11 subunits and two annexin A2 N-terminal peptides, the structure of the complete annexin A2\/p11 heterotetramer has not yet been solved at high resolution. Thus, the quaternary structure of the biologically relevant, membrane-bound annexin A2\/p11 complex is still under discussion, while the existence of a heterotetramer or a heterooctamer is the prevailing opinion. We gained further insight into the spatial organization of the annexin A2\/p11 heterotetramer by employing chemical crosslinking combined with high-resolution mass spectrometry. Furthermore, tandem mass spectrometry served as a tool for an exact localization of crosslinked amino acid residues and for a confirmation of crosslinked product assignment. On the basis of distance constraints from the crosslinking data we derived structural models of the annexin A2\/p11 heterotetramer by computational docking with Rosetta. We propose an octameric model for the annexin A2\/p11 complex, which exerts annexin A2 function. The proposed structure of the annexin A2\/p11 octamer differs from so far suggested models and sheds new light into annexin A2\/p11 interaction.","authors":"Schulz, DM., Kalkhof, S., Schmidt, A., Ihling, C., Stingl, C., Mechtler, K., Zsch\u00f6rnig, O., Sinz, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Proteins","volume":"69","issue":"2","page":"254-69","pdf":null,"JrId":"6646","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19170075","title":"Prostate cancer promotes CD11b positive cells to differentiate into osteoclasts.","abstract":"Bone is the preferred site of prostate cancer metastasis, contributing to the morbidity and mortality of this disease. A key step in the successful establishment of prostate cancer bone metastases is activation of osteoclasts with subsequent bone resorption causing the release of several growth factors from the bone matrix. CD11b+ cells in bone marrow are enriched for osteoclast precursors. Conditioned media from prostate cancer PC-3 cells induces CD11b+ cells from human peripheral blood to differentiate into functional osteoclasts with subsequent bone resorption. Analysis of PC-3 conditioned media revealed high amounts of IL-6 and IL-8. CD11b+ cells were cultured with M-CSF and RANKL, IL-6, IL-8, and CCL2, alone or in combination. All of these conditions induced osteoclast fusion, but cells cultured with M-CSF, IL-6, IL-8, and CCL2 were capable of limited bone resorption. Co-incubation with IL-6 and IL-8 and the RANK inhibitor, RANK-Fc, failed to inhibit osteoclast fusion and bone resorption, suggesting a potential RANKL-independent mechanism of functional osteoclast formation. This study demonstrates that functional osteoclasts can be derived from CD11b+ cells derived from human PBMCs. Prostate cancer cells secrete factors, including IL-6 and IL-8, that play an important role in osteoclast fusion by a RANKL-independent mechanism.","authors":"Mizutani, K., Sud, S., Pienta, KJ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Biochem","volume":"106","issue":"4","page":"563-9","pdf":null,"JrId":"4590","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17600118","title":"Loss of angiotensin-converting enzyme-2 (Ace2) accelerates diabetic kidney injury.","abstract":"Diabetic nephropathy is one of the most common causes of end-stage renal failure, but the factors responsible for the development of diabetic nephropathy have not been fully elucidated. We examined the effect of deletion of the angiotensin-convert-ing enzyme 2 (Ace2) gene on diabetic kidney injury. Ace2(-\/-) mice were crossed with Akita mice (Ins2(WT\/C96Y)), a model of type 1 diabetes mellitus, and four groups of mice were studied at 3 months of age: Ace2(+\/y)Ins2(WT\/WT), Ace2(-\/y)Ins2(WT\/WT), Ace2(+\/y) Ins2(WT\/C96Y), and Ace2(-\/y)Ins2(WT\/C96Y). Ace2(-\/y) Ins2(WT\/C96Y) mice exhibited a twofold increase in the urinary albumin excretion rate compared with Ace2(+\/y)Ins2(WT\/C96Y) mice despite similar blood glucose levels. Ace2(-\/y)Ins2(WT\/C96Y) mice were the only group to exhibit increased mesangial matrix scores and glomerular basement membrane thicknesses compared with Ace2(+\/y)Ins2(WT\/WT) mice, accompanied by increased fibronectin and alpha-smooth muscle actin immunostaining in the glomeruli of Ace2(-\/y) Ins2(WT\/C96Y) mice. There were no differences in blood pressure or heart function to account for the exacerbation of kidney injury. Although kidney levels of angiotensin (Ang) II were not increased in the diabetic mice, treatment with an Ang II receptor blocker reduced urinary albumin excretion rate in Ace2(-\/y)Ins2(WT\/C96Y) mice, suggesting that acceleration of kidney injury in these mice is Ang II-mediated. We conclude that ACE2 plays a protective role in the diabetic kidney, and ACE2 is an important determinant of diabetic nephropathy.","authors":"Wong, DW., Oudit, GY., Reich, H., Kassiri, Z., Zhou, J., Liu, QC., Backx, PH., Penninger, JM., Herzenberg, AM., Scholey, JW.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Am J Pathol","volume":"171","issue":"2","page":"438-51","pdf":null,"JrId":"449","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17571058","title":"Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections.","abstract":"Here we describe a method for sensitive and specific histological detection of microRNAs (miRNAs) by in situ hybridization. The protocol focuses on the use of locked nucleic acids (LNAs), which are bi-cyclic RNA analogs that allow a significant increase in the hybridization temperature and thereby an enhanced stringency for short probes as required for miRNA detection. The protocol is optimized for cryosections in order to study the spatial and temporal expression of miRNAs with high sensitivity and resolution. We detail how to construct probes, set up and conduct an LNA in situ hybridization experiment. In addition, we discuss alternative colorimetric strategies that can be used to effectively detect and visualize miRNAs including double staining with other markers. Setting up and conducting the in situ experiment is estimated to take approximately 1 week, assuming that all the component parts are readily available.","authors":"Obernosterer, G., Martinez, J., Alenius, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Protoc","volume":"2","issue":"6","page":"1508-14","pdf":null,"JrId":"33047","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17558469","title":"Angiotensin-converting enzyme 2 in acute respiratory distress syndrome.","abstract":"Angiotensin-converting enzyme (ACE) and ACE2 are highly homologous metalloproteases that provide essential catalytic functions in the renin-angiotensin system (RAS). Angiotensin II is one key effector peptide of the RAS, inducing vasoconstriction and exerting multiple biological functions. ACE cleaves angiotensin I to generate angiotensin II, whereas ACE2 reduces angiotensin II levels. Accumulating evidence has demonstrated a physiological and pathological role of ACE2 in the cardiovascular systems. Intriguingly, the SARS coronavirus, the cause of severe acute respiratory syndrome (SARS), utilizes ACE2 as an essential receptor for cell fusion and in vivo infections. Moreover, recent studies have demonstrated that ACE2 protects murine lungs from acute lung injury as well as SARS-Spike protein-mediated lung injury, suggesting a dual role of ACE2 in SARS infections and protection from ARDS.","authors":"Imai, Y., Kuba, K., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell Mol Life Sci","volume":"64","issue":"15","page":"2006-12","pdf":null,"JrId":"20436","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17560333","title":"Role of the polycomb repressive complex 2 in acute promyelocytic leukemia.","abstract":"Epigenetic changes are common alterations in cancer cells. Here, we have investigated the role of Polycomb group proteins in the establishment and maintenance of the aberrant silencing of tumor suppressor genes during transformation induced by the leukemia-associated PML-RARalpha fusion protein. We show that in leukemic cells knockdown of SUZ12, a key component of Polycomb repressive complex 2 (PRC2), reverts not only histone modification but also induces DNA demethylation of PML-RARalpha target genes. This results in promoter reactivation and granulocytic differentiation. Importantly, the epigenetic alterations caused by PML-RARalpha can be reverted by retinoic acid treatment of primary blasts from leukemic patients. Our results demonstrate that the direct targeting of Polycomb group proteins by an oncogene plays a key role during carcinogenesis.","authors":"Villa, R., Pasini, D., Gutierrez, A., Morey, L., Occhionorelli, M., Vir\u00e9, E., Nomdedeu, JF., Jenuwein, T., Pelicci, PG., Minucci, S., Fuks, F., Helin, K., Di Croce, L.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cancer Cell","volume":"11","issue":"6","page":"513-25","pdf":null,"JrId":"29778","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17521420","title":"A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.","abstract":"mtcPTM is an online repository of human and mouse phosphosites in which data are hierarchically organized to preserve biologically relevant experimental information, thus allowing straightforward comparisons of phosphorylation patterns found under different conditions. The database also contains the largest available collection of atomic models of phosphorylatable proteins. Detailed analysis of this structural dataset reveals that phosphorylation sites are found in a heterogeneous range of structural and sequence contexts. mtcPTM is available on the web http:\/\/www.mitocheck.org\/cgi-bin\/mtcPTM\/search.","authors":"Jim\u00e9nez, JL., Hegemann, B., Hutchins, JR., Peters, JM., Durbin, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genome Biol","volume":"8","issue":"5","page":"R90","pdf":null,"JrId":"21904","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"47","title":"The influence of pH on the interaction of inhibitors with triosephosphate isomerase and determination of the pKa of the active-site carboxyl group.","abstract":"Ionization effects on the binding of the potential transition state analogues 2-phosphoglycolate and 2-phosphoglycolohydroxamate appear to be attributable to the changing state of ionization of the ligands themselves, therefore it is unnecessary to postulate the additional involvement of an ionizing residue at the active site of triosephosphate isomerase to explain the influence of changing pH on Ki in the neutral range. The binding of the competitive inhibitor inorganic sulfate is insensitive to changing pH in the neutral range. 3-Chloroacetol sulfate, synthesized as an active-site-specific reagent for triosephosphate isomerase, is used to provide an indication of the pKa of the essential carboxyl group of this enzyme. Previously described active-site-specific reagents for the isomerase were phosphate esters, and their changing state of ionization (accompanied by possible changes in their affinity for the active site) may have complicated earlier attempts to determine the pKa of the essential carboxyl group from the pH dependence of the rate of inactivation. Being a strong monoprotic acid, chloroacetol sulfate is better suited to the determination of the pKa of the carboxyl group. Chloroacetol sulfate inactivates triosephosphate isomerase by the selective esterification of the same carboxyl group as that which is esterified by the phosphate esters described earlier. From the pH dependence of the rate of inactivation of yeast triosephosphate isomerase, the apparent pKa of the active-site carboxyl group is estimated as 3.9 +\/- 0.1.","authors":"Hartman, FC., LaMuraglia, GM., Tomozawa, Y., Wolfenden, R.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"24","page":"5274-9","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17504935","title":"Direct glucocorticoid receptor-Stat5 interaction in hepatocytes controls body size and maturation-related gene expression.","abstract":"The glucocorticoid receptor regulates transcription through DNA binding as well as through cross-talk with other transcription factors. In hepatocytes, the glucocorticoid receptor is critical for normal postnatal growth. Using hepatocyte-specific and domain-selective mutations in the mouse we show that Stat5 in hepatocytes is essential for normal postnatal growth and that it mediates the growth-promoting effect of the glucocorticoid receptor through a direct interaction involving the N-terminal tetramerization domain of Stat5b. This interaction mediates a selective and unexpectedly extensive part of the transcriptional actions of these molecules since it controls the expression of gene sets involved in growth and sexual maturation.","authors":"Engblom, D., Kornfeld, JW., Schwake, L., Tronche, F., Reimann, A., Beug, H., Hennighausen, L., Moriggl, R., Sch\u00fctz, G.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genes Dev","volume":"21","issue":"10","page":"1157-62","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2008-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15654976","title":"Fos and jun proteins are specifically expressed during differentiation of human keratinocytes.","abstract":"Activator protein 1 (AP-1) proteins play key roles in the regulation of cell proliferation and differentiation. In this study we investigated the expression of Fos and Jun proteins in different models of terminal differentiation of human keratinocytes and in skin from psoriasis patients. All Jun and Fos proteins, with the exception of FosB, were efficiently expressed in keratinocytes in monolayer cultures. In contrast, in normal epidermis as well as in organotypic epidermal cultures, the expression pattern of AP-1 proteins was dependent on the differentiation stage. Fos proteins were readily detected in nuclei of keratinocytes of basal and suprabasal layers. JunB and JunD were expressed in all layers of normal epidermis. Interestingly, expression of c-Jun started suprabasally, then disappeared and became detectable again in distinct cells of the outermost granular layer directly at the transition zone to the stratum corneum. In psoriatic epidermis, c-Jun expression was prominent in both hyperproliferating basal and suprabasal keratinocytes, whereas c-Fos expression was unchanged. These data indicate that AP-1 proteins are expressed in a highly specific manner during terminal differentiation of keratinocytes and that the enhanced expression of c-Jun in basal and suprabasal keratinocytes might contribute to the pathogenesis of psoriasis.","authors":"Mehic, D., Bakiri, L., Ghannadan, M., Wagner, EF., Tschachler, E.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Invest Dermatol","volume":"124","issue":"1","page":"212-20","pdf":null,"JrId":"4839","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19272526","title":"The expression and crucial roles of BMP signaling in development of smooth muscle progenitor cells in the mouse embryonic gut.","abstract":"Bone morphogenetic protein (BMP) signaling is essential for normal development of the gastrointestinal (GI) tract. BMPs also play multiple roles in vascular smooth muscle cells; however, the BMP signaling in the development of the GI musculature remains to be clarified. We investigated the expression of BMPs and their receptors in mouse embryonic GI tracts by immunohistochemistry and in situ hybridization. We demonstrated that BMP2, BMP receptor Ib and BMP receptor II were expressed in the smooth muscle progenitors from E12 to E13 for the first time. BMP signaling on smooth muscle differentiation was examined by implantation of agarose beads soaked with BMPs in the in vitro developmental model that is gut-like structures from mouse embryonic stem (ES) cells. BMP2 rather than BMP4 beads enhanced smooth muscle differentiation, and increased gut-like structures showing spontaneous contractions and expressing intensive alpha-smooth muscle actin immunoreactivity. This increase was confirmed by up-regulation of SM22 mRNA shown by real-time PCR. By addition of noggin beads or noggin to the medium at BMP2 bead implantation, the ratio of contractive gut-like structures decreased. Implantation of BMP2 beads at EB7 (EB--embryoid bodies) (corresponding to E12 or E13 of mouse embryo) showed the highest effects and up-regulation of transcription factors msx-1 after 24h. This increase was blocked by noggin, and msx-1 decreased to almost the control level after 60 h. BMP2 beads at EB7 increased platelet-derived growth factor-A (PDGF-A) in the differentiating smooth muscle cells. We have recently reported that PDGF-A is expressed in the developing inner circular smooth muscle and is crucial for the longitudinal smooth muscle differentiation. Taken together, BMP signaling was expressed for a short window in the smooth muscle progenitors and the signal, especially BMP2, plays an essential role in smooth muscle differentiation in cooperation with PDGF signaling.","authors":"Torihashi, S., Hattori, T., Hasegawa, H., Kurahashi, M., Ogaeri, T., Fujimoto, T.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Differentiation","volume":"77","issue":"3","page":"277-89","pdf":null,"JrId":"3402","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17499721","title":"c-Myc is required for transformation of FDC-P1 cells by EGFRvIII.","abstract":"In contrast to wtEGFR, its truncated version EGFRvIII transformed non-tumorigenic FDC-P1 cells only when c-Myc was coexpressed. In nude mice, EGFRvIII\/c-Myc coexpressing cells induced tumors, whereas wtEGFR-expressing EGF-dependent FDC-P1 cells did not. EGFRvIII function was required for both the induction and maintenance of tumor growth. Cellular proliferation was inhibited by a selective EGFR tyrosine kinase inhibitor indicating intrinsic tyrosine kinase activities for both receptors. Unlike wtEGFR, constitutive signaling by EGFRvIII was refractory to stimulation by the EGFR ligands EGF and TGF-alpha. Summarized, EGFRvIII is a constitutively active receptor tyrosine kinase whose transforming capacity is lower than that of EGF-stimulated wtEGFR.","authors":"Rath, O., Himmler, A., Baum, A., Sommergruber, W., Beug, H., Metz, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"FEBS Lett","volume":"581","issue":"13","page":"2549-56","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17494763","title":"ApoER2\/VLDL receptor and Dab1 in the rostral migratory stream function in postnatal neuronal migration independently of Reelin.","abstract":"Postnatal migration of interneuron precursors from the subventricular zone to the olfactory bulb occurs in chains that form the substrate for the rostral migratory stream. Reelin is suggested to induce detachment of neuroblasts from the chains when they arrive at the olfactory bulb. Here we show that ApoER2 and possibly very-low-density lipoprotein receptor (VLDLR) and their intracellular adapter protein Dab1 are involved in chain formation most likely independent of Reelin. F-spondin, which is present in the stream, may act as ligand for ApoER2 and VLDLR. In mice lacking either both receptors or Dab1 chain formation is severely compromised, and as a consequence the rostral migratory stream is virtually absent and neuroblasts accumulate in the subventricular zone. The mutant animals exhibit severe neuroanatomical defects in the subventricular zone and in the olfactory bulb. These data demonstrate a cell-autonomous function of ApoER2, and most likely VLDLR and Dab1, in postnatal migration of neuroblasts in the forebrain, which is suggested to depend on ligands other than Reelin.","authors":"Andrade, N., Komnenovic, V., Blake, SM., Jossin, Y., Howell, B., Goffinet, A., Schneider, WJ., Nimpf, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Proc Natl Acad Sci U S A","volume":"104","issue":"20","page":"8508-13","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17287245","title":"Acto-myosin reorganization and PAR polarity in C. elegans.","abstract":"The symmetry-breaking event during polarization of C. elegans embryos is an asymmetric rearrangement of the acto-myosin network, which dictates cell polarity through the differential recruitment of PAR proteins. The sperm-supplied centrosomes are required to initiate this cortical reorganization. Several questions about this event remain unanswered: how is the acto-myosin network regulated during polarization and how does acto-myosin reorganization lead to asymmetric PAR protein distribution? As we discuss, recent studies show that C. elegans embryos use two GTPases, RHO-1 and CDC-42, to regulate these two steps in polarity establishment. Although RHO-1 and CDC-42 control distinct aspects of polarization, they function interdependently to regulate polarity establishment in C. elegans embryos.","authors":"Cowan, CR., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Development","volume":"134","issue":"6","page":"1035-43","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10995794","title":"Functional human T-cell immunity and osteoprotegerin ligand control alveolar bone destruction in periodontal infection.","abstract":"Periodontitis, a prime cause of tooth loss in humans, is implicated in the increased risk of systemic diseases such as heart failure, stroke, and bacterial pneumonia. The mechanisms by which periodontitis and antibacterial immunity lead to alveolar bone and tooth loss are poorly understood. To study the human immune response to specific periodontal infections, we transplanted human peripheral blood lymphocytes (HuPBLs) from periodontitis patients into NOD\/SCID mice. Oral challenge of HuPBL-NOD\/SCID mice with Actinobacillus actinomycetemcomitans, a well-known Gram-negative anaerobic microorganism that causes human periodontitis, activates human CD4(+) T cells in the periodontium and triggers local alveolar bone destruction. Human CD4(+) T cells, but not CD8(+) T cells or B cells, are identified as essential mediators of alveolar bone destruction. Stimulation of CD4(+) T cells by A. actinomycetemcomitans induces production of osteoprotegerin ligand (OPG-L), a key modulator of osteoclastogenesis and osteoclast activation. In vivo inhibition of OPG-L function with the decoy receptor OPG diminishes alveolar bone destruction and reduces the number of periodontal osteoclasts after microbial challenge. These data imply that the molecular explanation for alveolar bone destruction observed in periodontal infections is mediated by microorganism-triggered induction of OPG-L expression on CD4(+) T cells and the consequent activation of osteoclasts. Inhibition of OPG-L may thus have therapeutic value to prevent alveolar bone and\/or tooth loss in human periodontitis.","authors":"Teng, YT., Nguyen, H., Gao, X., Kong, YY., Gorczynski, RM., Singh, B., Ellen, RP., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Clin Invest","volume":"106","issue":"6","page":"R59-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-10-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17488626","title":"The transmembrane protein Kon-tiki couples to Dgrip to mediate myotube targeting in Drosophila.","abstract":"Directed cell migration and target recognition are critical for the development of both the nervous and muscular systems. Molecular mechanisms that control these processes in the nervous system have been intensively studied, whereas those that act during muscle development are still largely uncharacterized. Here we identify a transmembrane protein, Kon-tiki (Kon), that mediates myotube target recognition in the Drosophila embryo. Kon is expressed in a specific subset of myotubes and is required autonomously for these myotubes to recognize their tendon cell targets and to establish a stable connection. Kon is enriched at myotube tips during targeting and signals through the intracellular adaptor Dgrip in a conserved molecular pathway. Forced overexpression of Kon stimulates muscle motility. We propose that Kon promotes directed myotube migration and transduces a target-derived signal that initiates the formation of a stable connection.","authors":"Schnorrer, F., Kalchhauser, I., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Dev Cell","volume":"12","issue":"5","page":"751-66","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15642358","title":"PREL1 provides a link from Ras signalling to the actin cytoskeleton via Ena\/VASP proteins.","abstract":"Ena\/VASP family proteins are important modulators of cell migration and localize to focal adhesions, stress fibres and the very tips of lamellipodia and filopodia. Proline-rich proteins like vinculin and zyxin are well established interaction partners, which mediate Ena\/VASP-recruitment via their EVH1-domains to focal adhesions and stress fibres. However, it is still unclear, which binding partners Ena\/VASP proteins may have at lamellipodia tips and how their recruitment to these cellular protrusions is regulated. Here, we report the identification of a novel protein with high similarity to the C. elegans MIG-10 protein, which we termed PREL1 (Proline Rich EVH1 Ligand). PREL1 is a 74 kDa protein and shares homology with the Grb7-family of signalling adaptors. We show that PREL1 directly binds to Ena\/VASP proteins and co-localizes with them at lamellipodia tips and at focal adhesions in response to Ras activation. Moreover, PREL1 directly binds to activated Ras in a phosphoinositide-dependent manner. Thus, our data pinpoint PREL1 as the first direct link between Ras signalling and cytoskeletal remodelling via Ena\/VASP proteins during cell migration and spreading.","authors":"Jenzora, A., Behrendt, B., Small, JV., Wehland, J., Stradal, TE.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"FEBS Lett","volume":"579","issue":"2","page":"455-63","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17488877","title":"Leukocyte PI3Kgamma and PI3Kdelta have temporally distinct roles for leukocyte recruitment in vivo.","abstract":"Phosphoinositide 3-kinases (PI3Ks) have been considered important in leukocyte motility. PI3Kgamma, the class I(B) PI3K, expressed prominently in leukocytes and also in endothelial cells, mediates leukocyte functional responses induced by chemoattractants. To reveal its role in leukocyte recruitment, we used intravital microscopy to directly visualize leukocyte rolling, adhesion, and emigration in postcapillary venules in PI3Kgamma-deficient (PI3Kgamma(-\/-)) mice. We report here that PI3Kgamma deficiency had no significant effects on leukocyte rolling flux or rolling velocity and minor effects on adhesion (30% to 35%) in response to CXC chemokine MIP-2 (CXCL2) or KC (CXCL1). However, leukocyte emigration was severely impaired in PI3Kgamma(-\/-) mice in an early (first 90 minutes) response to MIP-2 or KC. Chimeric mice receiving bone marrow transplants revealed that this early response was entirely dependent upon PI3Kgamma in neutrophils but not parenchymal cells (endothelium and others). Identical responses were observed when endogenous chemokine production was induced by TNFalpha; leukocyte emigration was reduced in PI3Kgamma(-\/-) mice. More prolonged responses to MIP-2 (for 4 to 5 hours) or TNFalpha (6 to 8 hours) were almost entirely PI3Kgamma independent and largely dependent on PI3Kdelta. Our results reveal that leukocyte emigration response to CXC chemokines is entirely dependent upon PI3Kgamma or PI3Kdelta, but these are nonoverlapping, temporally distinct events in inflamed tissues in vivo.","authors":"Liu, L., Puri, KD., Penninger, JM., Kubes, P.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Blood","volume":"110","issue":"4","page":"1191-8","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17486063","title":"The transcription factor ZEB1 (deltaEF1) promotes tumour cell dedifferentiation by repressing master regulators of epithelial polarity.","abstract":"Epithelial to mesenchymal transition (EMT) is implicated in the progression of primary tumours towards metastasis and is likely caused by a pathological activation of transcription factors regulating EMT in embryonic development. To analyse EMT-causing pathways in tumourigenesis, we identified transcriptional targets of the E-cadherin repressor ZEB1 in invasive human cancer cells. We show that ZEB1 repressed multiple key determinants of epithelial differentiation and cell-cell adhesion, including the cell polarity genes Crumbs3, HUGL2 and Pals1-associated tight junction protein. ZEB1 associated with their endogenous promoters in vivo, and strongly repressed promotor activities in reporter assays. ZEB1 downregulation in undifferentiated cancer cells by RNA interference was sufficient to upregulate expression of these cell polarity genes on the RNA and protein level, to re-establish epithelial features and to impair cell motility in vitro. In human colorectal cancer, ZEB1 expression was limited to the tumour-host interface and was accompanied by loss of intercellular adhesion and tumour cell invasion. In invasive ductal and lobular breast cancer, upregulation of ZEB1 was stringently coupled to cancer cell dedifferentiation. Our data show that ZEB1 represents a key player in pathologic EMTs associated with tumour progression.","authors":"Aigner, K., Dampier, B., Descovich, L., Mikula, M., Sultan, A., Schreiber, M., Mikulits, W., Brabletz, T., Strand, D., Obrist, P., Sommergruber, W., Schweifer, N., Wernitznig, A., Beug, H., Foisner, R., Eger, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Oncogene","volume":"26","issue":"49","page":"6979-88","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"63","title":"Enzymic reactions of fatty acid hydroperoxides in extracts of potato tuber. II. Conversion of 9- and 13-hydroperoxy-octadecadienoic acids to monohydroxydienoic acid, epoxyhydroxy- and trihydroxymonoenoic acid derivatives.","abstract":"1. Crude extracts and partially purified enzyme preparations from potato tubers catalyse, at pH 5-7, the conversion of linoleic acid hydroperoxides to a range of oxygenated fatty acid derivatives. 2. 9-D- and 13-L-hydroperoxide isomers are converted at similar rates to equivalent (isomeric) products. 3. The major products from the 13-hydroperoxide isomer were identified as the corresponding monohydroxydienoic acid derivative, threo-11-hydroxy-trans12,13-epoxy-octadec-cis9-enoic acid and 9,12,13-trihydroxy-octadec-trans10-enoic acid. The corresponding products from the 9-hydroperoxide were the monohydroxydienoic acid, 9,10-epoxy-11-hydroxy-octadec-12-enoic acid and 9,10,13-trihydroxy-octadec-11-enoic acid. 4. No separation of activities forming the different products was achieved by partial purification of enzyme extracts. 5. Product formation was unaffected by EDTA, CN-, sulphydryl reagents or glutathione but was reduced by boiling the extracts. 6. This system is compared with the 9-hydroperoxide-specific enzymic formation of divinyl ether derivatives by potato extracts.","authors":"Galliard, T., Phillips, DR., Matthew, JA.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"409","issue":"2","page":"157-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17471988","title":"[RNA directed DNA elimination in Tetrahymena].","abstract":null,"authors":"Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Tanpakushitsu Kakusan Koso","volume":"51","issue":"16 Suppl","page":"2624-30","pdf":null,"JrId":"6726","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17481880","title":"Polycomb comes of age: genome-wide profiling of target sites.","abstract":"The Polycomb group proteins are best known for their role as epigenetic regulators of the fly homeotic (Hox) gene clusters, but it has long been clear that these well conserved proteins have many other targets. For example, they are vital for maintaining both the pluripotency of stem cells and the identity of differentiated cells. However, a comprehensive list of experimentally defined targets has been lacking. Six new studies use genome wide profiling techniques to map Polycomb targets in stem cells and differentiated cells in vertebrates and flies. The findings of these studies demand that we rethink some of our current assumptions about Polycomb function.","authors":"Ringrose, L.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Curr Opin Cell Biol","volume":"19","issue":"3","page":"290-7","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17475820","title":"Increased renal responsiveness to vasopressin and enhanced V2 receptor signaling in RGS2-\/- mice.","abstract":"The antidiuretic effect of vasopressin is mediated by V2 receptors (V2R) that are located in kidney connecting tubules and collecting ducts. This study provides evidence that V2R signaling is negatively regulated by regulator of G protein signaling 2 (RGS2), a member of the family of RGS proteins. This study demonstrates that (1) RGS2 expression in the kidney is restricted to the vasopressin-sensitive part of the nephron (thick ascending limb, connecting tubule, and collecting duct); (2) expression of RGS2 is rapidly upregulated by vasopressin; (3) the vasopressin-dependent accumulation of cAMP, the principal messenger of V2R signaling, is significantly higher in collecting ducts that are microdissected from the RGS2(-\/-) mice compared with their wild-type littermates; and (4) analysis of urine output of mice that were exposed to water restriction followed by acute water loading revealed that RGS2(-\/-) mice exhibit an increased renal responsiveness to vasopressin. It is proposed that RGS2 is involved in negative feedback regulation of V2R signaling.","authors":"Zuber, AM., Singer, D., Penninger, JM., Rossier, BC., Firsov, D.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Am Soc Nephrol","volume":"18","issue":"6","page":"1672-8","pdf":null,"JrId":"1194","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15620645","title":"Spo13 facilitates monopolin recruitment to kinetochores and regulates maintenance of centromeric cohesion during yeast meiosis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15620645<\/PMID><DateCompleted><Year>2005<\/Year><Month>05<\/Month><Day>02<\/Day><\/DateCompleted><DateRevised><Year>2017<\/Year><Month>12<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>14<\/Volume><Issue>24<\/Issue><PubDate><Year>2004<\/Year><Month>Dec<\/Month><Day>29<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Spo13 facilitates monopolin recruitment to kinetochores and regulates maintenance of centromeric cohesion during yeast meiosis.<\/ArticleTitle><Pagination><MedlinePgn>2183-96<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Cells undergoing meiosis perform two consecutive divisions after a single round of DNA replication. During the first meiotic division, homologous chromosomes segregate to opposite poles. This is achieved by (1) the pairing of maternal and paternal chromosomes via recombination producing chiasmata, (2) coorientation of homologous chromosomes such that sister chromatids attach to the same spindle pole, and (3) resolution of chiasmata by proteolytic cleavage by separase of the meiotic-specific cohesin Rec8 along chromosome arms. Crucially, cohesin at centromeres is retained to allow sister centromeres to biorient at the second division. Little is known about how these meiosis I-specific events are regulated.","authors":"Katis, VL., Matos, J., Mori, S., Shirahige, K., Zachariae, W., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"24","page":"2183-96","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17428453","title":"Infarct volume after transient middle cerebral artery occlusion (MCAo) can be reduced by attenuation but not by inactivation of c-Jun action.","abstract":"Stroke therapy aims to save penumbral tissue from apoptosis that is activated in response to the ischemic injury. Since the c-Jun transcription factor plays a crucial role in promoting apoptosis, inhibition of its activation might reduce the final infarct size and thus increase functional outcome. To test this hypothesis we made use of four genetically modified mouse lines influencing the c-Jun pathway at various steps. Upon transient middle cerebral artery occlusion for 90 min and 24 h of reperfusion, infarct volume and number of ATF-2-, TUNEL- and cleaved Caspase-3-positive cells were determined in conditional c-Jun knock-out mice (cond. c-Jun), mice overexpressing JunB (JunBtg), mice lacking the phosphoacceptor serines 63 and 73 of c-Jun (JunAA) and in mice overexpressing Bcl-2 (Bcl-2tg). Cond. c-Jun as well as JunAA mice did not show significant differences in the infarct size when compared to their non-mutant controls. By contrast smaller infarct volumes were detected in transgenic mice merely attenuating c-Jun action (JunBtg and Bcl-2tg). ATF-2, TUNEL or cleaved Caspase-3 staining revealed no significant differences between the experimental groups. A complete lack of functional c-Jun might be compensated by other cellular mechanisms, in contrast to its reduced function. Thus, our data suggest that attenuation rather than a complete block of c-Jun action appears to be more promising for therapy of stroke.","authors":"Vogel, J., Weigand, MA., Behrens, A., Wagner, EF., Schorpp-Kistner, M., Zimmermann, M., Schenkel, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Brain Res","volume":"1151","issue":null,"page":"12-9","pdf":null,"JrId":"1920","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-207","title":"Metabolic control of germ layer proportions through regulation of Nodal and Wnt signalling","abstract":null,"authors":"Kristina S. Stapornwongkul; Elisa Hahn; Laura Salamo Palau; Krisztina Arato; Nicola Gritti; Kerim Anlas; Patryk Poli\u0144ski; Mireia Osuna Lopez; Miki Eibisuya; Vikas Trivedi","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"BioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2023.12.04.569862v1","articledate":"2023-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17411337","title":"Towards complete sets of farnesylated and geranylgeranylated proteins.","abstract":"Three different prenyltransferases attach isoprenyl anchors to C-terminal motifs in substrate proteins. These lipid anchors serve for membrane attachment or protein-protein interactions in many pathways. Although well-tolerated selective prenyltransferase inhibitors are clinically available, their mode of action remains unclear since the known substrate sets of the various prenyltransferases are incomplete. The Prenylation Prediction Suite (PrePS) has been applied for large-scale predictions of prenylated proteins. To prioritize targets for experimental verification, we rank the predictions by their functional importance estimated by evolutionary conservation of the prenylation motifs within protein families. The ranked lists of predictions are accessible as PRENbase (http:\/\/mendel.imp.univie.ac.at\/sat\/PrePS\/PRENbase) and can be queried for verification status, type of modifying enzymes (anchor type), and taxonomic distribution. Our results highlight a large group of plant metal-binding chaperones as well as several newly predicted proteins involved in ubiquitin-mediated protein degradation, enriching the known functional repertoire of prenylated proteins. Furthermore, we identify two possibly prenylated proteins in Mimivirus. The section HumanPRENbase provides complete lists of predicted prenylated human proteins-for example, the list of farnesyltransferase targets that cannot become substrates of geranylgeranyltransferase 1 and, therefore, are especially affected by farnesyltransferase inhibitors (FTIs) used in cancer and anti-parasite therapy. We report direct experimental evidence verifying the prediction of the human proteins Prickle1, Prickle2, the BRO1 domain-containing FLJ32421 (termed BROFTI), and Rab28 (short isoform) as exclusive farnesyltransferase targets. We introduce PRENbase, a database of large-scale predictions of protein prenylation substrates ranked by evolutionary conservation of the motif. Experimental evidence is presented for the selective farnesylation of targets with an evolutionary conserved modification site.","authors":"Maurer-Stroh, S., Koranda, M., Benetka, W., Schneider, G., Sirota, FL., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"PLoS Comput Biol","volume":"3","issue":"4","page":"e66","pdf":null,"JrId":"32534","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10995389","title":"Cell cycle- and cell growth-regulated proteolysis of mammalian CDC6 is dependent on APC-CDH1.","abstract":"CDC6 is conserved during evolution and is essential and limiting for the initiation of eukaryotic DNA replication. Human CDC6 activity is regulated by periodic transcription and CDK-regulated subcellular localization. Here, we show that, in addition to being absent from nonproliferating cells, CDC6 is targeted for ubiquitin-mediated proteolysis by the anaphase promoting complex (APC)\/cyclosome in G(1). A combination of point mutations in the destruction box and KEN-box motifs in CDC6 stabilizes the protein in G(1) and in quiescent cells. Furthermore, APC, in association with CDH1, ubiquitinates CDC6 in vitro, and both APC and CDH1 are required and limiting for CDC6 proteolysis in vivo. Although a stable mutant of CDC6 is biologically active, overexpression of this mutant or wild-type CDC6 is not sufficient to induce multiple rounds of DNA replication in the same cell cycle. The APC-CDH1-dependent proteolysis of CDC6 in early G(1) and in quiescent cells suggests that this process is part of a mechanism that ensures the timely licensing of replication origins during G(1).","authors":"Petersen, BO., Wagener, C., Marinoni, F., Kramer, ER., Melixetian, M., Lazzerini Denchi, E., Gieffers, C., Matteucci, C., Peters, JM., Helin, K.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Genes Dev","volume":"14","issue":"18","page":"2330-43","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2000-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"71","title":"Calcium-stimulated adenosine triphosphatase in the microsomal fraction of tooth germ from porcine fetus.","abstract":"The characterization and localization of a Ca(2+)-ATPase (ATP phosphohydrolase, EC 3.6.1.3) in the tooth germ of the porcine fetus are reported. This enzyme, a microsome fraction, is preferentially activated by Ca(2+). In the presence of 0.5 mM ATP, maximal enzyme activity is obtained at 0.5--1.0 mM CaCl2. The maximal rate of ATP hydrolysis is approx. 20 mumol per h per mg of protein as the enzyme preparation is used here. At optimal Ca(2+) concentration, the Mg(2+) has an inhibitory effect. The enzyme does not require Na+ or\/and K+ for activation by Ca(2+). Other nucleotide triphosphates may serve as the substrate, but V for ATP is the highest. The Km for ATP is 8.85 - 10(-5) M. The optimal pH for Ca(2+) activation of the enzyme lies around 9.2. Well known inhibitors of (Na+ + K+)-ATPase, mitochondria ATPase and Ca(2+)-ATPase in the erthrocyte do not inhibit the enzyme. In the subcellular order the enzyme may be assumed to be localized in the smooth endoplasmic reticulum fraction containing cell and Golgi body membrane fragments and in the tissue order in the enamel organ containing an ameloblast layer, stratum intermedium and stellate reticulum.","authors":"Yoshimura, F., Suzuki, T.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"167-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34411256","title":"Leukemia inhibitory factor modulates the differentiation of granulosa cells during sheep in vitro preantral to antral follicle development and improves oocyte meiotic competence.","abstract":"In vitro follicle development from cryopreserved ovarian tissue could become an invaluable assisted reproduction technology for women with early ovarian failure. The challenge lies in producing, from small follicles present in the ovarian cortex, high quality mature oocytes able to sustain embryo development. In vivo, an optimal combination of hormones and other factors coordinates the development of follicles and their enclosed oocyte. We have investigated the effect of the leukemia inhibitory factor (LIF) cytokine, alone or in combination with FSH, on sheep in vitro follicle development from the preantral stage onwards. LIF did not alter follicle growth or antrum formation, but it modulated the differentiation of granulosa cells, as revealed by decreased production of anti-Mullerian hormone and abolished FSH-induced stimulation of estradiol secretion. This modulatory role was also reflected in the abundance of mRNA from 35 genes, analysed by reverse-transcription coupled to microfluidic quantitative PCR. LIF stimulated or at least maintained the expression of genes involved in the dialogue between the oocyte and granulosa cells, through gap junctions (GJA4 encoding connexin 37) or paracrine signalling (Bone morphogenetic protein 15, KIT ligand and their receptors). Finally, the presence of both LIF and FSH during follicle growth strongly improved oocyte meiotic competence: most oocytes (56%) underwent subsequent nuclear maturation, a significant increase compared with their counterparts from follicles of similar size (550-900\u2009\u00b5m) cultured with FSH only (28%) or developed in vivo (9%). Their ability to sustain embryo development remains to be evaluated. Combined supplementation with FSH and LIF certainly merits investigation with human follicles.","authors":"Cadoret, V., Jarrier-Gaillard, P., Papillier, P., Monniaux, D., Gu\u00e9rif, F., Dalbies-Tran, R.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Mol Hum Reprod","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17391982","title":"Regulation of peripheral T cell tolerance by the E3 ubiquitin ligase Cbl-b.","abstract":"The family of the Casitas B-lineage Lymphoma (Cbl) proteins, c-Cbl, Cbl-b, and Cbl-3, function as E3 ubiquitin ligases and molecular adaptors. In particular, Cbl-b acts as a gatekeeper in T cell activation that controls activation thresholds and the requirement for co-stimulation. Loss of Cbl-b expression renders animals susceptible to antigen-triggered autoimmunity suggesting that Cbl-b is a key autoimmunity gene. In addition, Cbl-b plays a critical role in T cell anergy and escape from regulatory T cells (Treg) suppression. Modulation of Cbl-b might provide us with a unique opportunity for future immune treatment of human disorders such as autoimmunity, immunodeficiency, or cancer.","authors":"Loeser, S., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Semin Immunol","volume":"19","issue":"3","page":"206-14","pdf":null,"JrId":"1183","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17391671","title":"The transcription factor ZEB1 (deltaEF1) represses Plakophilin 3 during human cancer progression.","abstract":"Plakophilin 3 (PKP3) belongs to the p120ctn family of armadillo-related proteins predominantly functioning in desmosome formation. Here we report that PKP3 is transcriptionally repressed by the E-cadherin repressor ZEB1 in metastatic cancer cells. ZEB1 physically associates with two conserved E-box elements in the PKP3 promoter and partially represses the activity of corresponding human and mouse PKP3 promoter fragments in reporter gene assays. In human tumours ZEB1 is upregulated in invasive cancer cells at the tumour-host interface, which is accompanied by downregulation of PKP3 expression levels. Hence, the transcriptional repression of PKP3 by ZEB1 contributes to ZEB1-mediated disintegration of intercellular adhesion and epithelial to mesenchymal transition.","authors":"Aigner, K., Descovich, L., Mikula, M., Sultan, A., Dampier, B., Bonn\u00e9, S., van Roy, F., Mikulits, W., Schreiber, M., Brabletz, T., Sommergruber, W., Schweifer, N., Wernitznig, A., Beug, H., Foisner, R., Eger, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"FEBS Lett","volume":"581","issue":"8","page":"1617-24","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10882105","title":"A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation.","abstract":"Xist is required for X inactivation. To study the initiation of X inactivation, we have generated a full-length mouse Xist cDNA transgene and an inducible expression system facilitating controlled Xist expression in ES cells and differentiated cultures. In ES cells, transgenic Xist RNA was stable and caused long-range transcriptional repression in cis. Repression was reversible and dependent on continued Xist expression in ES cells and early ES cell differentiation. By 72 hr of differentiation, inactivation became irreversible and independent of Xist. Upon differentiation, autosomal transgenes did not effect counting, but transgenic Xist RNA induced late replication and histone H4 hypoacetylation. Xist had to be activated within 48 hr of differentiation to effect silencing, suggesting that reversible repression by Xist is a required initiation step that might occur during normal X inactivation in female cells.","authors":"Wutz, A., Jaenisch, R.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Cell","volume":"5","issue":"4","page":"695-705","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2000-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34314740","title":"BMP6 increases CD68 expression by up-regulating CTGF expression in human granulosa-lutein cells.","abstract":"Bone morphogenetic protein 6 (BMP6) and connective tissue growth factor (CTGF) are critical growth factors required for normal follicular development and luteal function. Cluster of Differentiation 68 (CD68) is an intraovarian marker of macrophages that plays an important role in modulating the physiological regression of the corpus luteum. The aim of this study was to investigate the effect of BMP6 on the expression of CTGF and the subsequent increase in CD68 expression as well as its underlying mechanisms. Primary and immortalized (SVOG) human granulosa cells obtained from infertile women undergoing in vitro fertilization treatment were used as cell models to conduct the in vitro experiments. Our results showed that BMP6 treatment significantly increased the expression levels of CTGF and CD68. Using BMP type I receptor inhibitors (dorsomorphin, DMH-1 and SB431542), we demonstrated that both activin receptor-like kinase (ALK)2 and ALK3 are involved in BMP6-induced stimulatory effects on the expression of CTGF and CD68. Additionally, SMAD4-knock down reversed the BMP6-induced up-regulation of CTGF and CD68, indicating that the canonical SMAD signaling pathway is required for these effects. Moreover, CTGF-knock down abolished the BMP6-induced up-regulation of CD68 expression. These findings indicate that intrafollicular CTGF mediates BMP6-induced increases in CD68 expression through the ALK2\/ALK3-mediated SMAD-dependent signaling pathway.","authors":"Zhang, XY., Chang, HM., Yi, Y., Zhu, H., Liu, RZ., Leung, PCK.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Mol Cell Endocrinol","volume":"536","issue":"","page":"111414","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17363905","title":"Phosphorylation and ubiquitination of the IkappaB kinase complex by two distinct signaling pathways.","abstract":"The IkappaB kinase (IKK) complex serves as the master regulator for the activation of NF-kappaB by various stimuli. It contains two catalytic subunits, IKKalpha and IKKbeta, and a regulatory subunit, IKKgamma\/NEMO. The activation of IKK complex is dependent on the phosphorylation of IKKalpha\/beta at its activation loop and the K63-linked ubiquitination of NEMO. However, the molecular mechanism by which these inducible modifications occur remains undefined. Here, we demonstrate that CARMA1, a key scaffold molecule, is essential to regulate NEMO ubiquitination upon T-cell receptor (TCR) stimulation. However, the phosphorylation of IKKalpha\/beta activation loop is independent of CARMA1 or NEMO ubiquitination. Further, we provide evidence that TAK1 is activated and recruited to the synapses in a CARMA1-independent manner and mediate IKKalpha\/beta phosphorylation. Thus, our study provides the biochemical and genetic evidence that phosphorylation of IKKalpha\/beta and ubiquitination of NEMO are regulated by two distinct pathways upon TCR stimulation.","authors":"Shambharkar, PB., Blonska, M., Pappu, BP., Li, H., You, Y., Sakurai, H., Darnay, BG., Hara, H., Penninger, J., Lin, X.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"EMBO J","volume":"26","issue":"7","page":"1794-805","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2007-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17360496","title":"PSD-95 is required for activity-driven synapse stabilization.","abstract":"The activity-dependent regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors and the stabilization of synapses are critical to synaptic development and plasticity. One candidate molecule implicated in maturation, synaptic strengthening, and plasticity is PSD-95. Here we find that acute knockdown of PSD-95 in brain slice cultures by RNAi arrests the normal development of synaptic structure and function that is driven by spontaneous activity. Surprisingly, PSD-95 is not necessary for the induction and early expression of long-term potentiation (LTP). However, knockdown of PSD-95 leads to smaller increases in spine size after chemically induced LTP. Furthermore, although at this age spine turnover is normally low and LTP produces a transient increase, in cells with reduced PSD-95 spine turnover is high and remains increased after LTP. Taken together, our data support a model in which appropriate levels of PSD-95 are required for activity-dependent synapse stabilization after initial phases of synaptic potentiation.","authors":"Ehrlich, I., Klein, M., Rumpel, S., Malinow, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Proc Natl Acad Sci U S A","volume":"104","issue":"10","page":"4176-81","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17362199","title":"Structures and functions of yeast kinetochore complexes.","abstract":"The kinetochore is a key cell division organelle that enables high-fidelity transmission of genetic information by coupling chromosomes to spindle microtubules during mitosis and meiosis. Despite its cytological description more than a century ago, remarkably little information is available on kinetochore function at a molecular level. Recently, important advances elucidating the overall organization of kinetochores, as well as information about the structures and molecular mechanisms of kinetochore function, have been achieved through a detailed analysis of the kinetochores of the budding yeast Saccharomyces cerevisiae. Here we review the current understanding of kinetochore function in budding yeast and draw comparisons to recent findings in other organisms.","authors":"Westermann, S., Drubin, DG., Barnes, G.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Annu Rev Biochem","volume":"76","issue":null,"page":"563-91","pdf":null,"JrId":"665","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15591903","title":"Effective use of high-dose chemotherapy and autologous stem cell rescue for relapsed adult Wilms' tumor and a novel alteration in intron 1 of the WT1 gene.","abstract":"Adult Wilms' tumor (AWT) is a very rare and aggressive malignancy, and little information is available on effective therapy in adults. Although mutations in WT1 have been found in 10% to 15% of childhood Wilms' tumor patients, to date WT1 mutations in AWT patients have not been described. The authors describe a 47-year-old man with relapsed AWT and a novel germline alteration in intron 1 of WT1: IVS1-6 C--&gt;A. This alteration may reduce the splicing efficiency for exon 2 and possibly results in exon skipping. The effective salvage chemotherapy contained ifosfamide, carboplatin, and etoposide and was followed by a high-dose chemotherapy that contained melphalan, carboplatin, and etoposide. Both chemotherapy regimens showed moderate treatment-related toxicity. This report is the first that indicates that adult nephroblastoma patients also may carry WT1 germline mutations.","authors":"Trappe, RU., Riess, H., Lippek, F., Plotkin, M., Schumacher, V., Royer-Pokora, B., Hildebrandt, B., Zuber, J., Mapara, MY., Oertel, S., D\u00f6rken, B.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Pediatr Hematol Oncol","volume":"26","issue":"12","page":"820-3","pdf":null,"JrId":"8621","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34314679","title":"Ovulation suppression protects against chromosomal abnormalities in mouse eggs at advanced maternal age.","abstract":"The frequency of egg aneuploidy and trisomic pregnancies increases with maternal age. To what extent individual approaches can delay the \"maternal age effect\" is unclear because multiple causes contribute to chromosomal abnormalities in mammalian eggs. We propose that ovulation frequency determines the physiological aging of oocytes, a key aspect of which is the ability to accurately segregate chromosomes and produce euploid eggs. To test this hypothesis, ovulations were reduced using successive pregnancies, hormonal contraception, and a pre-pubertal knockout mouse model, and the effects on chromosome segregation and egg ploidy were examined. We show that each intervention reduces chromosomal abnormalities in eggs of aged mice, suggesting that ovulation reduction delays oocyte aging. The protective effect can be partly explained by retention of chromosomal Rec8-cohesin that maintains sister chromatid cohesion in meiosis. In addition, single-nucleus Hi-C (snHi-C) revealed deterioration in the 3D chromatin structure including an increase in extruded loop sizes in long-lived oocytes. Artificial cleavage of Rec8 is sufficient to increase extruded loop sizes, suggesting that cohesin complexes maintaining cohesion restrict loop extrusion. These findings suggest that ovulation suppression protects against Rec8 loss, thereby maintaining both sister chromatid cohesion and 3D chromatin structure and promoting production of euploid eggs. We conclude that the maternal age effect can be delayed in mice. An implication of this work is that long-term ovulation-suppressing conditions can potentially reduce the risk of aneuploid pregnancies at advanced maternal age.","authors":"Chatzidaki, EE., Powell, S., Dequeker, BJH., Gassler, J., Silva, MCC., Tachibana, K.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Curr Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17349791","title":"Sororin is required for stable binding of cohesin to chromatin and for sister chromatid cohesion in interphase.","abstract":"Sister chromatid cohesion depends on cohesin [1-3]. Cohesin associates with chromatin dynamically throughout interphase [4]. During DNA replication, cohesin establishes cohesion [5], and this process coincides with the generation of a cohesin subpopulation that is more stably bound to chromatin [4]. In mitosis, cohesin is removed from chromosomes, enabling sister chromatid separation [6]. How cohesin associates with chromatin and establishes cohesion is poorly understood. By searching for proteins that are associated with chromatin-bound cohesin, we have identified sororin, a protein that was known to be required for cohesion [7]. To obtain further insight into sororin's function, we have addressed when during the cell cycle sororin is required for cohesion. We show that sororin is dispensable for the association of cohesin with chromatin but that sororin is essential for proper cohesion during G2 phase. Like cohesin, sororin is also needed for efficient repair of DNA double-strand breaks in G2. Finally, sororin is required for the presence of normal amounts of the stably chromatin-bound cohesin population in G2. Our data indicate that sororin interacts with chromatin-bound cohesin and functions during the establishment or maintenance of cohesion in S or G2 phase, respectively.","authors":"Schmitz, J., Watrin, E., L\u00e9n\u00e1rt, P., Mechtler, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Curr Biol","volume":"17","issue":"7","page":"630-6","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17334367","title":"Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes.","abstract":"Reversible contraction of immunoglobulin loci juxtaposes the variable (V) genes next to the (diversity)-joining-constant ((D)JC) gene domain, thus facilitating V-(D)J recombination. Here we show that the T cell receptor beta (Tcrb) and T cell receptor alphadelta (Tcra-Tcrd) loci also underwent long-range interactions by looping in double-negative and double-positive thymocytes, respectively. Contraction of the Tcrb and Tcra loci occurred in rearranging thymocytes and was reversed at the next developmental stage. Decontraction of the Tcrb locus probably prevented further V(beta)-DJ(beta) rearrangements in double-positive thymocytes by separating the V(beta) genes from the DJC(beta) domain. In most double-negative cells, one Tcrb allele was recruited to pericentromeric heterochromatin. Such allelic positioning may facilitate asynchronous V(beta)-DJ(beta) recombination. Hence, pericentromeric recruitment and locus 'decontraction' seem to contribute to the initiation and maintenance of allelic exclusion at the Tcrb locus.","authors":"Skok, JA., Gisler, R., Novatchkova, M., Farmer, D., de Laat, W., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Immunol","volume":"8","issue":"4","page":"378-87","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2007-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17347685","title":"Deficiency of Src homology 2 domain-containing inositol 5-phosphatase 1 affects platelet responses and thrombus growth.","abstract":"Platelets are critical for normal hemostasis. Their deregulation can lead to bleeding or to arterial thrombosis, a primary cause of heart attack and ischemic stroke. Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) is a 5-phosphatase capable of dephosphorylating the phosphatidylinositol 3,4,5-trisphosphate second messenger into phosphatidylinositol 3,4-bisphosphate. SHIP1 plays a critical role in regulating the level of these 2 lipids in platelets. Using SHIP1-deficient mice, we found that its loss affects platelet aggregation in response to several agonists with minor effects on fibrinogen binding and beta(3) integrin tyrosine phosphorylation. Accordingly, SHIP1-null mice showed defects in arterial thrombus formation in response to a localized laser-induced injury. Moreover, these mice had a prolonged tail bleeding time. Upon stimulation, SHIP1-deficient platelets showed large membrane extensions, abnormalities in the open canalicular system, and a dramatic decrease in close cell-cell contacts. Interestingly, SHIP1 appeared to be required for platelet contractility, thrombus organization, and fibrin clot retraction. These data indicate that SHIP1 is an important element of the platelet signaling machinery to support normal hemostasis. To our knowledge, this is the first report unraveling an important function of SHIP1 in the activation of hematopoietic cells, in contrast to its well-documented role in the negative regulation of lymphocytes.","authors":"S\u00e9verin, S., Gratacap, MP., Lenain, N., Alvarez, L., Hollande, E., Penninger, JM., Gachet, C., Plantavid, M., Payrastre, B.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Clin Invest","volume":"117","issue":"4","page":"944-52","pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33606988","title":"Unraveling the Developmental Roadmap toward Human Brown Adipose Tissue.","abstract":"Increasing brown adipose tissue (BAT) mass and activation is a therapeutic strategy to treat obesity and complications. Obese and diabetic patients possess low amounts of BAT, so an efficient way to expand their mass is necessary. There is limited knowledge about how human BAT develops, differentiates, and is optimally activated. Accessing human BAT is challenging, given its low volume and anatomical dispersion. These constraints make detailed BAT-related developmental and functional mechanistic studies in humans virtually impossible. We have developed and characterized functionally and molecularly a new chemically defined protocol for the differentiation of human pluripotent stem cells (hPSCs) into brown adipocytes (BAs) that overcomes current limitations. This protocol recapitulates step by step the physiological developmental path of human BAT. The BAs obtained express BA and thermogenic markers, are insulin\u00a0sensitive, and responsive to \u03b2-adrenergic stimuli. This new protocol is scalable, enabling the study of human BAs at early stages of development.","authors":"Carobbio, S., Guenantin, AC., Bahri, M., Rodriguez-Fdez, S., Honig, F., Kamzolas, I., Samuelson, I., Long, K., Awad, S., Lukovic, D., Erceg, S., Bassett, A., Mendjan, S., Vallier, L., Rosen, BS., Chiarugi, D., Vidal-Puig, A.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Stem Cell Reports","volume":"16","issue":"3","page":"641-655","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17333235","title":"Spatial organization of a ubiquitous eukaryotic kinetochore protein network in Drosophila chromosomes.","abstract":"Chromosome segregation during meiosis and mitosis depends on the assembly of functional kinetochores within centromeric regions. Centromeric DNA and kinetochore proteins show surprisingly little sequence conservation despite their fundamental biological role. However, our identification in Drosophila melanogaster of the most diverged orthologs identified so far, which encode components of a kinetochore protein network including the Ndc80 and Mis complexes, further emphasizes the notion of a shared eukaryotic kinetochore design. To determine its spatial organization, we have analyzed by quantitative light microscopy hundreds of native chromosomes from transgenic Drosophila strains coexpressing combinations of red and green fluorescent fusion proteins, fully capable of providing the essential wild-type functions. Thereby, Cenp-A\/Cid, Cenp-C, Mis12 and the Ndc80 complex were mapped along the inter sister kinetochore axis with a resolution below 10 nm. The C terminus of Cenp-C was found to be near but well separated from the innermost component Cenp-A\/Cid. The N terminus of Cenp-C is further out, clustered with Mis12 and the Spc25 end of the rod-like Ndc80 complex, which is known to bind to microtubules at its other more distal Ndc80\/Nuf2 end.","authors":"Schittenhelm, RB., Heeger, S., Althoff, F., Walter, A., Heidmann, S., Mechtler, K., Lehner, CF.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Chromosoma","volume":"116","issue":"4","page":"385-402","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34294896","title":"HUWE1 employs a giant substrate-binding ring to feed and regulate its HECT E3 domain.","abstract":"HUWE1 is a universal quality-control E3 ligase that marks diverse client proteins for proteasomal degradation. Although the giant HECT enzyme is an essential component of the ubiquitin-proteasome system closely linked with severe human diseases, its molecular mechanism is little understood. Here, we present the crystal structure of Nematocida HUWE1, revealing how a single E3 enzyme has specificity for a multitude of unrelated substrates. The protein adopts a remarkable snake-like structure, where the C-terminal HECT domain heads an extended alpha-solenoid body that coils in on itself and houses various protein-protein interaction modules. Our integrative structural analysis shows that this ring structure is highly dynamic, enabling the flexible HECT domain to reach protein targets presented by the various acceptor sites. Together, our data demonstrate how HUWE1 is regulated by its unique structure, adapting a promiscuous E3 ligase to selectively target unassembled orphan proteins.","authors":"Grabarczyk, DB., Petrova, OA., Deszcz, L., Kurzbauer, R., Murphy, P., Ahel, J., Vogel, A., Gogova, R., Faas, V., Kordic, D., Schleiffer, A., Meinhart, A., Imre, R., Lehner, A., Neuhold, J., Bader, G., Stolt-Bergner, P., B\u00f6ttcher, J., Wolkerstorfer, B., Fischer, G., Grishkovskaya, I., Haselbach, D., Kessler, D., Clausen, T.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Nat Chem Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25129144","title":"JAGN1 deficiency causes aberrant myeloid cell homeostasis and congenital neutropenia.","abstract":"The analysis of individuals with severe congenital neutropenia (SCN) may shed light on the delicate balance of factors controlling the differentiation, maintenance and decay of neutrophils. We identify 9 distinct homozygous mutations in the JAGN1 gene encoding Jagunal homolog 1 in 14 individuals with SCN. JAGN1-mutant granulocytes are characterized by ultrastructural defects, a paucity of granules, aberrant N-glycosylation of multiple proteins and increased incidence of apoptosis. JAGN1 participates in the secretory pathway and is required for granulocyte colony-stimulating factor receptor-mediated signaling. JAGN1 emerges as a factor that is necessary in the differentiation and survival of neutrophils.","authors":"Boztug, K., J\u00e4rvinen, PM., Salzer, E., Racek, T., M\u00f6nch, S., Garncarz, W., Gertz, EM., Sch\u00e4ffer, AA., Antonopoulos, A., Haslam, SM., Schieck, L., Pucha\u0142ka, J., Diestelhorst, J., Appaswamy, G., Lescoeur, B., Giambruno, R., Bigenzahn, JW., Elling, U., Pfeifer, D., Conde, CD., Albert, MH., Welte, K., Brandes, G., Sherkat, R., van der Werff Ten Bosch, J., Rezaei, N., Etzioni, A., Bellann\u00e9-Chantelot, C., Superti-Furga, G., Penninger, JM., Bennett, KL., von Blume, J., Dell, A., Donadieu, J., Klein, C.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Genet","volume":"46","issue":"9","page":"1021-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17297445","title":"JunB is a gatekeeper for B-lymphoid leukemia.","abstract":"Loss of JunB has been observed in human leukemia and lymphoma, but it remains unknown, whether this loss is relevant to disease progression. Here, we investigated the consequences of JunB deficiency using Abelson-induced B-lymphoid leukemia as a model system. Mice deficient in JunB expression succumbed to Abelson-induced leukemia with increased incidence and significantly reduced latency. Similarly, bcr\/abl p185-transformed JunB-deficient (junB(Delta\/Delta)) cells induced leukemia in RAG2(-\/-) mice displaying a more malignant phenotype. These observations indicated that cell intrinsic effects within the junB(Delta\/Delta) tumor cells accounted for the accelerated leukemia development. Indeed, explantated bcr\/abl p185 transformed junB(Delta\/Delta) cells proliferated faster than the control cells. The proliferative advantage emerged slowly after the initial transformation process and was associated with increased expression levels of the cell cycle kinase cdk6 and with decreased levels of the cell cycle inhibitor p16(INK4a). These alterations were due to irreversible reprogramming of the cell, because - once established - accelerated disease induced by junB(Delta\/Delta) cells was not reverted by re-introducing JunB. Consistent with this observation, we found that the p16 promoter was methylated. Thus, JunB functions as a gatekeeper during tumor evolution. In its absence, transformed leukemic cells acquire an enhanced proliferative capacity, which presages a more malignant disease.","authors":"Ott, RG., Simma, O., Kollmann, K., Weisz, E., Zebedin, EM., Schorpp-Kistner, M., Heller, G., Z\u00f6chbauer, S., Wagner, EF., Freissmuth, M., Sexl, V.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Oncogene","volume":"26","issue":"33","page":"4863-71","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33988504","title":"Spatiotemporal control of cell cycle acceleration during axolotl spinal cord regeneration.","abstract":"Axolotls are uniquely able to resolve spinal cord injuries, but little is known about the mechanisms underlying spinal cord regeneration. We previously found that tail amputation leads to reactivation of a developmental-like program in spinal cord ependymal cells (Rodrigo Albors et al., 2015), characterized by a high-proliferation zone emerging 4 days post-amputation (Rost et al., 2016). What underlies this spatiotemporal pattern of cell proliferation, however, remained unknown. Here, we use modeling, tightly linked to experimental data, to demonstrate that this regenerative response is consistent with a signal that recruits ependymal cells during ~85 hours after amputation within ~830 \u03bcm of the injury. We adapted Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) technology to axolotls (AxFUCCI) to visualize cell cycles in vivo. AxFUCCI axolotls confirmed the predicted appearance time and size of the injury-induced recruitment zone and revealed cell cycle synchrony between ependymal cells. Our modeling and imaging move us closer to understanding <i>bona fide<\/i> spinal cord regeneration.","authors":"Cura Costa, E., Otsuki, L., Rodrigo Albors, A., Tanaka, EM., Chara, O.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Elife","volume":"10","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3288656","title":"Dental materials: 1986 literature review. Part 2.","abstract":null,"authors":"van Noort, R., Causton, BE., Combe, EC., Sherriff, M., Strang, R., Waters, NE., Watts, DC.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"J Dent","volume":"16","issue":"1","page":"1-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1988-07-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17292401","title":"RNA degradation in fission yeast mitochondria is stimulated by a member of a new family of proteins that are conserved in lower eukaryotes.","abstract":"We report here on the role of open reading frame (ORF) SPCC1183.04c of Schizosaccharomyces pombe in mitochondrial RNA metabolism. A mutant deleted for this ORF on chromosome III accumulates mitochondrial transcripts with the exception of the cob mRNA. A detailed Northern blot analysis showed that the effect results from a decrease in RNA degradation but not from RNA processing deficiencies. Overexpression of the SPCC1183.04c gene in a S. pombe wild-type strain is characterized by slow growth at 37 degrees C on non-fermentable carbon sources and a significant reduction of steady-state levels of mitochondrial transcripts. A NCBI BLASTP search with the amino acid sequence deduced from the S. pombe gene identified significant similarity to a number of proteins in fungi (e.g. Ascomycota, Basidiomycota) and in some non-fungal eukaryotes (e.g. ciliate, slime mold, red algae). By heterologous expression of SPCC1183.04c in a Saccharomyces cerevisiae pet127Delta strain, we demonstrate that the fission yeast protein and Pet127p from S. cerevisiae function similarly: The fission yeast gene complemented the respiratory defect associated with the pet127Delta allele and partially restored the RNA processing phenotype. Although it lacks any recognizable targeting signal, the S. pombe protein is imported into S. cerevisiae mitochondria in vivo. We conclude from our results that the fission yeast SPCC1183.04c gene is a member of a new protein family that functions to stimulate mitochondrial RNA degradation, a function that is conserved within the mitochondria of lower eukaryotes but seems to have been replaced by alternative pathways in metazoans and higher plants.","authors":"Wiesenberger, G., Speer, F., Haller, G., Bonnefoy, N., Schleiffer, A., Schafer, B.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Mol Biol","volume":"367","issue":"3","page":"681-91","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2007-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17291758","title":"BI 2536, a potent and selective inhibitor of polo-like kinase 1, inhibits tumor growth in vivo.","abstract":"Fine-mapping of the cell-division cycle, notably the identification of mitotic kinase signaling pathways, provides novel opportunities for cancer-drug discovery. As a key regulator of multiple steps during mitotic progression across eukaryotic species, the serine\/threonine-specific Polo-like kinase 1 (Plk1) is highly expressed in malignant cells and serves as a negative prognostic marker in specific human cancer types . Here, we report the discovery of a potent small-molecule inhibitor of mammalian Plk1, BI 2536, which inhibits Plk1 enzyme activity at low nanomolar concentrations. The compound potently causes a mitotic arrest and induces apoptosis in human cancer cell lines of diverse tissue origin and oncogenome signature. BI 2536 inhibits growth of human tumor xenografts in nude mice and induces regression of large tumors with well-tolerated intravenous dose regimens. In treated tumors, cells arrest in prometaphase, accumulate phosphohistone H3, and contain aberrant mitotic spindles. This mitotic arrest is followed by a surge in apoptosis, detectable by immunohistochemistry and noninvasive optical and magnetic resonance imaging. For addressing the therapeutic potential of Plk1 inhibition, BI 2536 has progressed into clinical studies in patients with locally advanced or metastatic cancers.","authors":"Steegmaier, M., Hoffmann, M., Baum, A., L\u00e9n\u00e1rt, P., Petronczki, M., Krss\u00e1k, M., G\u00fcrtler, U., Garin-Chesa, P., Lieb, S., Quant, J., Grauert, M., Adolf, GR., Kraut, N., Peters, JM., Rettig, WJ.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Curr Biol","volume":"17","issue":"4","page":"316-22","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33707514","title":"Premating barriers in young sympatric snail species.","abstract":"Sympatric coexistence of recently diverged species raises the question of barriers restricting the gene flow between them. Reproductive isolation may be implemented at several levels, and the weakening of some, e.g. premating, barriers may require the strengthening of the others, e.g. postcopulatory ones. We analysed mating patterns and shell size of mates in recently diverged closely related species of the subgenus Littorina Neritrema (Littorinidae, Caenogastropoda) in order to assess the role of premating reproductive barriers between them. We compared mating frequencies observed in the wild with those expected based on relative densities using partial canonical correspondence analysis. We introduced the fidelity index (FI) to estimate the relative accuracy of mating with conspecific females and precopulatory isolation index (I<sub>PC<\/sub>) to characterize the strength of premating barriers. The species under study, with the exception of L. arcana, clearly demonstrated preferential mating with conspecifics. According to FI and I<sub>PC<\/sub>, L. fabalis and L. compressa appeared reliably isolated from their closest relatives within Neritrema. Individuals of these two species tend to be smaller than those of the others, highlighting the importance of shell size changes in gastropod species divergence. L. arcana males were often found in pairs with L. saxatilis females, and no interspecific size differences were revealed in this sibling species pair. We discuss the lack of discriminative mate choice in the sympatric populations of L. arcana and L. saxatilis, and possible additional mechanisms restricting gene flow between them.","authors":"Maltseva, AL., Varfolomeeva, MA., Lobov, AA., Tikanova, PO., Repkin, EA., Babkina, IY., Panova, M., Mikhailova, NA., Granovitch, AI.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Sci Rep","volume":"11","issue":"1","page":"5720","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17277772","title":"Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression.","abstract":"Posttranslational modifications of histones, such as methylation, regulate chromatin structure and gene expression. Recently, lysine-specific demethylase 1 (LSD1), the first histone demethylase, was identified. LSD1 interacts with the androgen receptor and promotes androgen-dependent transcription of target genes by ligand-induced demethylation of mono- and dimethylated histone H3 at Lys 9 (H3K9) only. Here, we identify the Jumonji C (JMJC) domain-containing protein JMJD2C as the first histone tridemethylase regulating androgen receptor function. JMJD2C interacts with androgen receptor in vitro and in vivo. Assembly of ligand-bound androgen receptor and JMJD2C on androgen receptor-target genes results in demethylation of trimethyl H3K9 and in stimulation of androgen receptor-dependent transcription. Conversely, knockdown of JMJD2C inhibits androgen-induced removal of trimethyl H3K9, transcriptional activation and tumour cell proliferation. Importantly, JMJD2C colocalizes with androgen receptor and LSD1 in normal prostate and in prostate carcinomas. JMJD2C and LSD1 interact and both demethylases cooperatively stimulate androgen receptor-dependent gene transcription. In addition, androgen receptor, JMJD2C and LSD1 assemble on chromatin to remove methyl groups from mono, di and trimethylated H3K9. Thus, our data suggest that specific gene regulation requires the assembly and coordinate action of demethylases with distinct substrate specificities.","authors":"Wissmann, M., Yin, N., M\u00fcller, JM., Greschik, H., Fodor, BD., Jenuwein, T., Vogler, C., Schneider, R., G\u00fcnther, T., Buettner, R., Metzger, E., Sch\u00fcle, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Cell Biol","volume":"9","issue":"3","page":"347-53","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17286585","title":"The 20S proteasome isolated from Alzheimer's disease brain shows post-translational modifications but unchanged proteolytic activity.","abstract":"Chronic neurodegenerative diseases are characterized by the accumulation of aggregated protein species, and functional impairment of the ubiquitin proteasome system has been hypothesized to contribute to neuronal cell loss. Decreased proteolytic activity of the 20S proteasome has been shown postmortem in crude brain lysates from Alzheimer's disease (AD) patients. In the present study, we demonstrate, however, that catalytic activity of the 20S proteasome increases during chromatographic purification from AD brains as compared with age-matched controls. By two-dimensional difference gel electrophoresis we detected pI shifts in several proteasome subunits in AD samples pointing to differential post-translational modifications. Moreover, we identified N-terminal acetylation and dephosphorylation of subunit alpha7 in AD by tandem mass spectrometry. Thus, reduced peptidase activity in AD brain extracts is not an intrinsic property of the 20S proteasome, but may be resulting from the presence of endogenous inhibitory proteins or substrates. Post-translational modifications of non-catalytic subunits in situ may contribute to the trend towards enhanced hydrolytic activity of the isolated 20S proteasome after removal of the endogenous inhibitors.","authors":"Gillardon, F., Kloss, A., Berg, M., Neumann, M., Mechtler, K., Hengerer, B., Dahlmann, B.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Neurochem","volume":"101","issue":"6","page":"1483-90","pdf":null,"JrId":"5004","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17284516","title":"LAP2alpha-binding protein LINT-25 is a novel chromatin-associated protein involved in cell cycle exit.","abstract":"Lamina-associated polypeptide 2alpha (LAP2alpha) is a nuclear protein dynamically associating with chromatin during the cell cycle. In addition, LAP2alpha interacts with A-type lamins and retinoblastoma protein and regulates cell cycle progression via the E2F-Rb pathway. Using yeast two-hybrid analysis and three independent in vitro binding assays we identified a new LAP2alpha interaction partner of hitherto unknown functions, which we termed LINT-25. LINT-25 protein levels were upregulated during G1 phase in proliferating cells and upon cell cycle exit in quiescence, senescence and differentiation. Upon cell cycle exit LINT-25 accumulated in heterochromatin foci, and LAP2alpha protein levels were downregulated by proteasomal degradation. Although LAP2alpha was not required for the upregulation and reorganization of LINT-25 during cell cycle exit, transient expression of LINT-25 in proliferating cells caused loss of LAP2alpha and subsequent cell death. Our data show a role of LINT-25 and LAP2alpha during cell cycle exit, in which LINT-25 acts upstream of LAP2alpha.","authors":"Naetar, N., Hutter, S., Dorner, D., Dechat, T., Korbei, B., Gotzmann, J., Beug, H., Foisner, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Cell Sci","volume":"120","issue":"Pt 5","page":"737-47","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33659463","title":"DigiTAG-a RNA Sequencing Approach to Analyze Transcriptomes of Rare Cell Populations in <i>Drosophila melanogaster<\/i>.","abstract":"Cell-type specific transcriptional programs underlie the development and maintenance of organs. Not only distinct cell types within a tissue, even cells with supposedly identical cell fates show a high degree of transcriptional heterogeneity. Inevitable, low cell numbers are a major hurdle to study transcriptomes of pure cell populations. Here we describe DigiTAG, a high-throughput method that combines transposase fragmentation and molecular barcoding to retrieve high quality transcriptome data of rare cell types in <i>Drosophila melanogaster<\/i>. The protocol showcases how DigiTAG can be used to analyse the transcriptome of rare neural stem cells (type II neuroblasts) of <i>Drosophila<\/i> larval brains, but can also be utilized for other cell types or model systems.","authors":"Landskron, L., Bonnay, F., Burkard, TR., Knoblich, JA.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Bio Protoc","volume":"10","issue":"21","page":"e3809","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33619734","title":"Wnt\/\u03b2-catenin signaling: Structure, assembly and endocytosis of the signalosome.","abstract":"Wnt\/\u03b2-catenin signaling is an ancient pathway that regulates key aspects of embryonic development, cell differentiation, proliferation, and adult stem cell homeostasis. Work from different laboratories has shed light on the molecular mechanisms underlying the Wnt pathway, including structural details of ligand-receptor interactions. One key aspect that has emerged from multiple studies is that endocytosis of the receptor complex plays a crucial role in fine-tuning Wnt\/\u03b2-catenin signaling. Endocytosis is a key process involved in both activation as well as attenuation of Wnt signaling, but how this is regulated is still poorly understood. Importantly, recent findings show that Wnt also regulates central metabolic pathways such as the acquisition of nutrients through actin-driven endocytic mechanisms. In this review, we propose that the Wnt pathway displays diverse characteristics that go beyond the regulation of gene expression, through a connection with the endocytic machinery.","authors":"Colozza, G., Koo, BK.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Dev Growth Differ","volume":"63","issue":"3","page":"199-218","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10924528","title":"G(olf)alpha mediates dopamine D1 receptor signaling.","abstract":"It is generally assumed that the coupling of dopamine D1 receptors to adenylyl cyclase is mediated by the stimulatory GTP-binding protein G(s). However, the striatum contains little G(s)alpha subunit, whereas it expresses high levels of G(olf)alpha, a close relative of G(s)alpha that is also expressed in olfactory receptor neurons. We used G(olf)alpha knockout mice to examine the functional coupling of D1 receptors. We found that these mice showed no hyperlocomotor response to either the D1 agonist SKF-81297 or the psychostimulant cocaine. Moreover, G(olf)alpha knockout mice did not display cocaine-induced c-fos expression in the striatum. Finally, in the absence of G(olf)alpha, striatal D1 receptors have a decreased affinity for dopamine. Thus coupling to G(olf)alpha appears to mediate D1 signaling in the striatum.","authors":"Zhuang, X., Belluscio, L., Hen, R.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Neurosci","volume":"20","issue":"16","page":"RC91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17224402","title":"Temporal target restriction of olfactory receptor neurons by Semaphorin-1a\/PlexinA-mediated axon-axon interactions.","abstract":"Axon-axon interactions have been implicated in neural circuit assembly, but the underlying mechanisms are poorly understood. Here, we show that in the Drosophila antennal lobe, early-arriving axons of olfactory receptor neurons (ORNs) from the antenna are required for the proper targeting of late-arriving ORN axons from the maxillary palp (MP). Semaphorin-1a is required for targeting of all MP but only half of the antennal ORN classes examined. Sema-1a acts nonautonomously to control ORN axon-axon interactions, in contrast to its cell-autonomous function in olfactory projection neurons. Phenotypic and genetic interaction analyses implicate PlexinA as the Sema-1a receptor in ORN targeting. Sema-1a on antennal ORN axons is required for correct targeting of MP axons within the antennal lobe, while interactions amongst MP axons facilitate their entry into the antennal lobe. We propose that Sema-1a\/PlexinA-mediated repulsion provides a mechanism by which early-arriving ORN axons constrain the target choices of late-arriving axons.","authors":"Sweeney, LB., Couto, A., Chou, YH., Berdnik, D., Dickson, BJ., Luo, L., Komiyama, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Neuron","volume":"53","issue":"2","page":"185-200","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33603169","title":"HACE1 blocks HIF1\u03b1 accumulation under hypoxia in a RAC1 dependent manner.","abstract":"Uncovering the mechanisms that underpin how tumor cells adapt to microenvironmental stress is essential to better understand cancer progression. The HACE1 (HECT domain and ankyrin repeat-containing E3 ubiquitin-protein ligase) gene is a tumor suppressor that inhibits the growth, invasive capacity, and metastasis of cancer cells. However, the direct regulatory pathways whereby HACE1 confers this tumor-suppressive effect remain to be fully elucidated. In this report, we establish a link between HACE1 and the major stress factor, hypoxia-inducible factor 1 alpha (HIF1\u03b1). We find that HACE1 blocks the accumulation of HIF1\u03b1 during cellular hypoxia through decreased protein stability. This property is dependent on HACE1 E3 ligase activity and loss of Ras-related C3 botulinum toxin substrate 1 (RAC1), an established target of HACE1 mediated ubiquitinylation and degradation. In vivo, genetic deletion of Rac1 reversed the increased HIF1\u03b1 expression observed in Hace1<sup>-\/-<\/sup> mice in murine KRas<sup>G12D<\/sup>-driven lung tumors. An inverse relationship was observed between HACE1 and HIF1\u03b1 levels in tumors compared to patient-matched normal kidney tissues, highlighting the potential pathophysiological significance of our findings. Together, our data uncover a previously unrecognized function for the HACE1 tumor suppressor in blocking HIF1\u03b1 accumulation under hypoxia in a RAC1-dependent manner.","authors":"Turgu, B., Zhang, F., El-Naggar, A., Negri, GL., Kogler, M., Tortola, L., Johnson, F., Ng, T., Li, A., Yapp, D., Lockwood, W., Martinez, D., Maris, JM., Daugaard, M., Penninger, JM., Hughes, CS., Sorensen, PH.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Oncogene","volume":"40","issue":"11","page":"1988-2001","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33459801","title":"Genetic engineering in organoids.","abstract":"Three-dimensional organoids have been widely used for developmental and disease modeling. Organoids are derived from both adult and pluripotent stem cells. Various types are available for mimicking almost all major organs and tissues in the mouse and human. While culture protocols for stepwise differentiation and long-term expansion are well established, methods for genetic manipulation in organoids still need further standardization. In this review, we summarized different methods for organoid genetics and provide the pros and cons of each method for designing an optimal strategy.","authors":"Teriyapirom, I., Batista-Rocha, AS., Koo, BK.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Mol Med (Berl)","volume":"99","issue":"4","page":"555-568","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17173042","title":"Control of cell polarity and motility by the PtdIns(3,4,5)P3 phosphatase SHIP1.","abstract":"Proper neutrophil migration into inflammatory sites ensures host defense without tissue damage. Phosphoinositide 3-kinase (PI(3)K) and its lipid product phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P(3)) regulate cell migration, but the role of PtdIns(3,4,5)P(3)-degrading enzymes in this process is poorly understood. Here, we show that Src homology 2 (SH2) domain-containing inositol-5-phosphatase 1 (SHIP1), a PtdIns(3,4,5)P(3) phosphatase, is a key regulator of neutrophil migration. Genetic inactivation of SHIP1 led to severe defects in neutrophil polarization and motility. In contrast, loss of the PtdIns(3,4,5)P(3) phosphatase PTEN had no impact on neutrophil chemotaxis. To study PtdIns(3,4,5)P(3) metabolism in living primary cells, we generated a novel transgenic mouse (AktPH-GFP Tg) expressing a bioprobe for PtdIns(3,4,5)P(3.) Time-lapse footage showed rapid, localized binding of AktPH-GFP to the leading edge membrane of chemotaxing ship1(+\/+)AktPH-GFP Tg neutrophils, but only diffuse localization in ship1(-\/-)AktPH-GFP Tg neutrophils. By directing where PtdIns(3,4,5)P(3) accumulates, SHIP1 governs the formation of the leading edge and polarization required for chemotaxis.","authors":"Nishio, M., Watanabe, K., Sasaki, J., Taya, C., Takasuga, S., Iizuka, R., Balla, T., Yamazaki, M., Watanabe, H., Itoh, R., Kuroda, S., Horie, Y., F\u00f6rster, I., Mak, TW., Yonekawa, H., Penninger, JM., Kanaho, Y., Suzuki, A., Sasaki, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Cell Biol","volume":"9","issue":"1","page":"36-44","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17170758","title":"The impact of small RNAs. Microsymposium on small RNAs.","abstract":"","authors":"Obernosterer, G., Meister, G., Poy, MN., Kuras, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"EMBO Rep","volume":"8","issue":"1","page":"23-7","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10828017","title":"Intramedullary and extramedullary B lymphopoiesis in osteopetrotic mice.","abstract":"Adult bone marrow is a major site for hematopoiesis, and reduction of the bone marrow cavity induces hematopoiesis in extramarrow tissues. To investigate the rudimentary intramarrow and the compensatory extramarrow hematopoiesis, particularly B lymphopoiesis, we used 3 osteopetrotic mouse strains [op\/op, mi\/mi, and Fos (-\/-)], which are severely deficient in functional osteoclasts and therefore form inadequate bone marrow cavities. We found that bone marrow in these osteopetrotic mice supports myelopoiesis but not B lymphopoiesis, although cells that have the potential to differentiate into B lineage cells are present in the bone marrow. Although B lymphopoiesis normally occurs both in the spleen and liver of newborn mice, compensatory B lymphopoiesis in adult op\/op and mi\/mi mice is observed only in the liver, while myelopoiesis is enhanced in both organs. Interestingly, mice lacking the Fos proto-oncogene exhibit B lymphopoiesis in the spleen as well as liver. The amounts of expression of steel factor, Flt3\/Flk-2 ligand, and interleukin-7 in the bone marrow, spleen, or liver were not significantly affected in these osteopetrotic mutants. These findings suggest that the volume of the bone marrow cavity regulates B lymphopoiesis without affecting the production of certain hematopoietic growth factors. The splenic microenvironments that support both myelopoiesis and B lymphopoiesis in the neonatal stage are lost in adults and are not reactivated even in the osteopetrotic adults unless the Fos gene is disrupted.","authors":"Tagaya, H., Kunisada, T., Yamazaki, H., Yamane, T., Tokuhisa, T., Wagner, EF., Sudo, T., Shultz, LD., Hayashi, SI.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Blood","volume":"95","issue":"11","page":"3363-70","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2000-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10766806","title":"The mitochondrial permeability transition augments Fas-induced apoptosis in mouse hepatocytes.","abstract":"Tumor necrosis factor-alpha receptor 1 and Fas recruit overlapping signaling pathways. To clarify the differences between tumor necrosis factor alpha (TNFalpha) and Fas pathways in hepatocyte apoptosis, primary mouse hepatocytes were treated with TNFalpha or an agonist anti-Fas antibody after infection with an adenovirus expressing an IkappaB superrepressor (Ad5IkappaB). Treatment with TNFalpha induced apoptosis in Ad5IkappaB-infected mouse hepatocytes, as we previously reported for rat hepatocytes. Ad5IkappaB plus anti-Fas antibody or actinomycin D plus anti-Fas antibody rapidly induced apoptosis, whereas anti-Fas antibody alone produced little cytotoxicity. The proteasome inhibitor (MG-132) and a dominant-negative mutant of nuclear factor-kappaB-inducing kinase also promoted TNFalpha- and Fas-mediated apoptosis. Expression of either crmA or a dominant-negative mutant of the Fas-associated death domain protein prevented TNFalpha- and Fas-mediated apoptosis. In addition, the caspase inhibitors, DEVD-cho and IETD-fmk, inhibited TNFalpha- and Fas-mediated apoptosis. In Ad5IkappaB-infected hepatocytes, caspases-3 and -8 were activated within 2 h after treatment with anti-Fas antibody or within 6 h after TNFalpha treatment. Confocal microscopy demonstrated onset of the mitochondrial permeability transition (MPT) and mitochondrial depolarization by 2-3 h after anti-Fas antibody treatment and 8-10 h after TNFalpha treatment, followed by cytochrome c release. The combination of the MPT inhibitors, cyclosporin A, and trifluoperazine, protected Ad5IkappaB-infected hepatocytes from TNFalpha-mediated apoptosis. After anti-Fas antibody, cyclosporin A and trifluoperazine decreased cytochrome c release but did not prevent caspase-3 activation and cell-death. In conclusion, nuclear factor-kappaB activation protects mouse hepatocytes against both TNFalpha- and Fas-mediated apoptosis. TNFalpha and Fas recruit similar but nonidentical, pathways signaling apoptosis. The MPT is obligatory for TNFalpha-induced apoptosis. In Fas-mediated apoptosis, the MPT accelerates the apoptogenic events but is not obligatory for them.","authors":"Hatano, E., Bradham, CA., Stark, A., Iimuro, Y., Lemasters, JJ., Brenner, DA.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Biol Chem","volume":"275","issue":"16","page":"11814-23","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2000-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17158252","title":"Phosphatidylinositol 3-kinase facilitates bile acid-induced Ca(2+) responses in pancreatic acinar cells.","abstract":"Bile acids are known to induce Ca(2+) signals in pancreatic acinar cells. We have recently shown that phosphatidylinositol 3-kinase (PI3K) regulates changes in free cytosolic Ca(2+) concentration ([Ca(2+)](i)) elicited by CCK by inhibiting sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA). The present study sought to determine whether PI3K regulates bile acid-induced [Ca(2+)](i) responses. In pancreatic acinar cells, pharmacological inhibition of PI3K with LY-294002 or wortmannin inhibited [Ca(2+)](i) responses to taurolithocholic acid 3-sulfate (TLC-S) and taurochenodeoxycholate (TCDC). Furthermore, genetic deletion of the PI3K gamma-isoform also decreased [Ca(2+)](i) responses to bile acids. Depletion of CCK-sensitive intracellular Ca(2+) pools or application of caffeine inhibited bile acid-induced [Ca(2+)](i) signals, indicating that bile acids release Ca(2+) from agonist-sensitive endoplasmic reticulum (ER) stores via an inositol (1,4,5)-trisphosphate-dependent mechanism. PI3K inhibitors increased the amount of Ca(2+) in intracellular stores during the exposure of acinar cells to bile acids, suggesting that PI3K negatively regulates SERCA-dependent Ca(2+) reloading into the ER. Bile acids inhibited Ca(2+) reloading into ER in permeabilized acinar cells. This effect was augmented by phosphatidylinositol (3,4,5)-trisphosphate (PIP(3)), suggesting that both bile acids and PI3K act synergistically to inhibit SERCA. Furthermore, inhibition of PI3K by LY-294002 completely inhibited trypsinogen activation caused by the bile acid TLC-S. Our results indicate that PI3K and its product, PIP(3), facilitate bile acid-induced [Ca(2+)](i) responses in pancreatic acinar cells through inhibition of SERCA-dependent Ca(2+) reloading into the ER and that bile acid-induced trypsinogen activation is mediated by PI3K. The findings have important implications for the mechanism of acute pancreatitis since [Ca(2+)](i) increases and trypsinogen activation mediate key pathological processes in this disorder.","authors":"Fischer, L., Gukovskaya, AS., Penninger, JM., Mareninova, OA., Friess, H., Gukovsky, I., Pandol, SJ.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Am J Physiol Gastrointest Liver Physiol","volume":"292","issue":"3","page":"G875-86","pdf":null,"JrId":"21621","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17143276","title":"Epidermal RANKL controls regulatory T-cell numbers via activation of dendritic cells.","abstract":"Regulatory CD4(+)CD25(+) T cells are important in suppressing immune responses. The requirements for the maintenance of peripheral CD4(+)CD25(+) T cells remain incompletely understood. Receptor activator of NF-kappaB (RANK) and its ligand (RANKL; also known as CD254, OPGL and TRANCE) are key regulators of bone remodeling, mammary gland formation, lymph node development and T-cell\/dendritic cell communication. Here we report that RANKL is expressed in keratinocytes of the inflamed skin. RANKL overexpression in keratinocytes resulted in functional alterations of epidermal dendritic cells and systemic increases of regulatory CD4(+)CD25(+) T cells. Thus, epidermal RANKL expression can change dendritic cell functions to maintain the number of peripheral CD4(+)CD25(+) regulatory T cells. Epidermal RANKL mediated ultraviolet-induced immunosuppression and overexpression of epidermal RANKL suppressed allergic contact hypersensitivity responses and the development of systemic autoimmunity. Therefore, environmental stimuli at the skin can rewire the local and systemic immune system by means of RANKL.","authors":"Loser, K., Mehling, A., Loeser, S., Apelt, J., Kuhn, A., Grabbe, S., Schwarz, T., Penninger, JM., Beissert, S.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nat Med","volume":"12","issue":"12","page":"1372-9","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17124183","title":"HPLC techniques for proteomics analysis--a short overview of latest developments.","abstract":"Due to the complex nature of the proteome, instrumentation and methods development for sample cleanup, fractionation, preconcentration, chromatographic separation and detection becomes urgent for the identification of peptides and proteins. Newly developed techniques and equipment for separation and detection, such as nano-HPLC and multidimensional HPLC for protein and peptide separation, enabled proteomics to experience dynamic growth during the past few years. In any proteomic analysis the most important and sometimes most difficult task is the separation of the complex mixture of proteins or peptides. This review describes some aspects and limitations of HPLC, both multidimensional and one-dimensional, in proteomics research without attempting to discuss all available HPLC methods, which would need far more space than available here.","authors":"Mitulovic, G., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Brief Funct Genomic Proteomic","volume":"5","issue":"4","page":"249-60","pdf":null,"JrId":"31949","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25712477","title":"Autophagy in malignant transformation and cancer progression.","abstract":"Autophagy plays a key role in the maintenance of cellular homeostasis. In healthy cells, such a homeostatic activity constitutes a robust barrier against malignant transformation. Accordingly, many oncoproteins inhibit, and several oncosuppressor proteins promote, autophagy. Moreover, autophagy is required for optimal anticancer immunosurveillance. In neoplastic cells, however, autophagic responses constitute a means to cope with intracellular and environmental stress, thus favoring tumor progression. This implies that at least in some cases, oncogenesis proceeds along with a temporary inhibition of autophagy or a gain of molecular functions that antagonize its oncosuppressive activity. Here, we discuss the differential impact of autophagy on distinct phases of tumorigenesis and the implications of this concept for the use of autophagy modulators in cancer therapy.","authors":"Galluzzi, L., Pietrocola, F., Bravo-San Pedro, JM., Amaravadi, RK., Baehrecke, EH., Cecconi, F., Codogno, P., Debnath, J., Gewirtz, DA., Karantza, V., Kimmelman, A., Kumar, S., Levine, B., Maiuri, MC., Martin, SJ., Penninger, J., Piacentini, M., Rubinsztein, DC., Simon, HU., Simonsen, A., Thorburn, AM., Velasco, G., Ryan, KM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"EMBO J","volume":"34","issue":"7","page":"856-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17115027","title":"Cyclin E-Cdk2 temporally regulates centrosome assembly and establishment of polarity in Caenorhabditis elegans embryos.","abstract":"Establishment of polarity in C. elegans embryos is dependent on the centrosome. The sperm contributes a pair of centrioles to the egg and these centrioles remain incapable of polarizing the cortex while the egg completes meiosis. Coincident with the establishment of polarity, the centrioles recruit centrosomal proteins, several of which are required for polarity, suggesting that the temporal regulation of centrosome assembly may control the initiation of polarization. We found that cyclin E-Cdk2 is required for the establishment of polarity. Cyclin E-Cdk2 controls the recruitment of centrosomal proteins specifically at the time of polarity establishment. Cyclin E is required for several examples of asymmetric cell division and fate determination in C. elegans and Drosophila. Here, we suggest a possible mechanism for cyclin E-Cdk2-dependent differentiation: the establishment of cortical polarity by the centrosome.","authors":"Cowan, CR., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nat Cell Biol","volume":"8","issue":"12","page":"1441-7","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2007-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17113138","title":"Wapl controls the dynamic association of cohesin with chromatin.","abstract":"Cohesin establishes sister-chromatid cohesion from S phase until mitosis or meiosis. To allow chromosome segregation, cohesion has to be dissolved. In vertebrate cells, this process is mediated in part by the protease separase, which destroys a small amount of cohesin, but most cohesin is removed from chromosomes without proteolysis. How this is achieved is poorly understood. Here, we show that the interaction between cohesin and chromatin is controlled by Wapl, a protein implicated in heterochromatin formation and tumorigenesis. Wapl is associated with cohesin throughout the cell cycle, and its depletion blocks cohesin dissociation from chromosomes during the early stages of mitosis and prevents the resolution of sister chromatids until anaphase, which occurs after a delay. Wapl depletion also increases the residence time of cohesin on chromatin in interphase. Our data indicate that Wapl is required to unlock cohesin from a particular state in which it is stably bound to chromatin.","authors":"Kueng, S., Hegemann, B., Peters, BH., Lipp, JJ., Schleiffer, A., Mechtler, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell","volume":"127","issue":"5","page":"955-67","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2007-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17108971","title":"Repression of p53 activity by Smyd2-mediated methylation.","abstract":"Specific sites of lysine methylation on histones correlate with either activation or repression of transcription. The tumour suppressor p53 (refs 4-7) is one of only a few non-histone proteins known to be regulated by lysine methylation. Here we report a lysine methyltransferase, Smyd2, that methylates a previously unidentified site, Lys 370, in p53. This methylation site, in contrast to the known site Lys 372, is repressing to p53-mediated transcriptional regulation. Smyd2 helps to maintain low concentrations of promoter-associated p53. We show that reducing Smyd2 concentrations by short interfering RNA enhances p53-mediated apoptosis. We find that Set9-mediated methylation of Lys 372 inhibits Smyd2-mediated methylation of Lys 370, providing regulatory cross-talk between post-translational modifications. In addition, we show that the inhibitory effect of Lys 372 methylation on Lys 370 methylation is caused, in part, by blocking the interaction between p53 and Smyd2. Thus, similar to histones, p53 is subject to both activating and repressing lysine methylation. Our results also predict that Smyd2 may function as a putative oncogene by methylating p53 and repressing its tumour suppressive function.","authors":"Huang, J., Perez-Burgos, L., Placek, BJ., Sengupta, R., Richter, M., Dorsey, JA., Kubicek, S., Opravil, S., Jenuwein, T., Berger, SL.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nature","volume":"444","issue":"7119","page":"629-32","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2007-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17084357","title":"The conserved c2 domain protein lethal (2) giant discs regulates protein trafficking in Drosophila.","abstract":"Drosophila sensory organ precursor (SOP) cells undergo several rounds of asymmetric cell division to generate the four different cell types that make up external sensory organs. Establishment of different fates among daughter cells of the SOP relies on differential regulation of the Notch pathway. Here, we identify the protein Lethal (2) giant discs (Lgd) as a critical regulator of Notch signaling in the SOP lineage. We show that lgd encodes a conserved C2 domain protein that binds to phospholipids present on early endosomes. When Lgd function is compromised, Notch and other transmembrane proteins accumulate in enlarged early endosomal compartments. These enlarged endosomes are positive for Rab5 and Hrs, a protein involved in trafficking into the degradative pathway. Our experiments suggest that Lgd is a critical regulator of endocytosis that is not present in yeast and acts in the degradative pathway after Hrs.","authors":"Gallagher, CM., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Dev Cell","volume":"11","issue":"5","page":"641-53","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2007-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17097932","title":"Application of different fragmentation techniques for the analysis of phosphopeptides using a hybrid linear ion trap-FTICR mass spectrometer.","abstract":"Electron capture dissociation (ECD) and infrared multiphoton dissociation (IRMPD) present complementary techniques for the fragmentation of peptides and proteins in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) in addition to the commonly used collisionally activated dissociation (CAD). Both IRMPD and ECD have been shown to be applicable for an efficient sequencing of peptides and proteins, whereas ECD has proven especially valuable for mapping labile posttranslational modifications (PTMs), such as phosphorylations. In this work, we compare the different fragmentation techniques and MS detection in a linear ion trap and the ICR cell with respect to their abilities to efficiently identify and characterize phosphorylated peptides. For optimizing fragmentation parameters, sets of synthetic peptides with molecular weights ranging from approximately 1 to 4 kDa and different levels of phosphorylation were analyzed. The influence of spectrum averaging for obtaining high-quality spectra was investigated. Our results show that the fragmentation methods CAD and ECD allow for a facilitated analysis of phosphopeptides; however, their general applicability for analyzing phosphopeptides has to be evaluated in each specific case with respect to the given analytical task. The major advantage of complementary peptide cleavages by combining different fragmentation methods is the increased amount of information that is obtained during MS\/MS analysis of modified peptides. On the basis of the obtained results, we are planning to design LC time-scale compatible, data-dependent MS\/MS methods using the different fragmentation techniques in order to improve the identification and characterization of phosphopeptides.","authors":"Stingl, C., Ihling, C., Ammerer, G., Sinz, A., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Biochim Biophys Acta","volume":"1764","issue":"12","page":"1842-52","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17043652","title":"Tumor progression induced by the loss of E-cadherin independent of beta-catenin\/Tcf-mediated Wnt signaling.","abstract":"E-cadherin-mediated cell-cell adhesion is frequently lost during the development of malignant epithelial cancers. Employing a transgenic mouse model of beta-cell carcinogenesis (Rip1Tag2) we have previously shown that the loss of E-cadherin is a rate-limiting step in the progression from adenoma to carcinoma. However, the mere loss of cell adhesion may not be sufficient and additional signals are required to cause tumor cells to permeate the basal membrane and to invade surrounding tissue. Besides being an important component of the E-cadherin cell-adhesion complex, beta-catenin plays a critical role in canonical Wnt signaling. We report here that beta-catenin-mediated Wnt signaling does not contribute to tumor progression in Rip1Tag2 mice. E-cadherin downregulates beta-catenin\/Tcf-mediated transcriptional activity by sequestrating beta-catenin into E-cadherin cell-adhesion complexes even in the presence of activated Wnt signaling. Upon loss of E-cadherin expression, beta-catenin is degraded and Tcf\/beta-catenin-mediated transcriptional activity is not induced. Moreover, forced expression of constitutive-active beta-catenin or genetic ablation of Tcf\/beta-catenin transcriptional activity in tumor cells of Rip1Tag2 transgenic mice does not affect tumor progression. Together, the data indicate that signals other than beta-catenin\/Tcf-mediated Wnt signaling are induced by the loss of E-cadherin during tumor progression in Rip1Tag2 transgenic mice.","authors":"Herzig, M., Savarese, F., Novatchkova, M., Semb, H., Christofori, G.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Oncogene","volume":"26","issue":"16","page":"2290-8","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2007-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17038539","title":"Constitutive activation of Stat5 promotes its cytoplasmic localization and association with PI3-kinase in myeloid leukemias.","abstract":"Persistent activation of Stat5 is frequently found in hematologic neoplasms. Studies conducted with constitutively active Stat5 mutants (Stat51*6 and cS5F) have shown that deregulated Stat5 activity promotes leukemogenesis. To investigate the oncogenic properties of these mutants, we used cS5F-expressing bone marrow cells which induce a multilineage leukemia when transplanted into recipient mice. Here, we show by immunocytochemistry that cS5F is localized mainly in the cytoplasmic compartment of leukemic cells, suggesting that the transforming nature of cS5F may be associated with a cytoplasmic function. In support of this hypothesis, we found that cS5F forms a complex with the p85 subunit of the phosphatidylinositol 3-kinase (PI3-K) and the scaffolding adapter Gab2 in leukemic bone marrow cells, resulting in the activation of Akt\/PKB, a crucial downstream target of PI3-K. By using transducible TAT-Gab2 or TAT-Akt recombinant proteins, we were able to demonstrate that activation of the PI3-kinase\/Akt pathway by cS5F molecules through Gab2 is essential for induction of cell growth. We also found that persistently phosphorylated Stat5 in primary cells from patients with myeloid leukemias has a cytoplasmic localization. These data suggest that oncogenic Stat5 proteins exert dual transforming capabilities not only as transcriptional activators but also as cytoplasmic signaling effectors.","authors":"Harir, N., Pecquet, C., Kerenyi, M., Sonneck, K., Kovacic, B., Nyga, R., Brevet, M., Dhennin, I., Gouilleux-Gruart, V., Beug, H., Valent, P., Lassoued, K., Moriggl, R., Gouilleux, F.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Blood","volume":"109","issue":"4","page":"1678-86","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2007-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17029581","title":"Regulation of commissural axon pathfinding by slit and its Robo receptors.","abstract":"Commissural axons grow along complex pathways toward, across, and beyond the midline of the central nervous system. Taking commissural axons in the vertebrate spinal cord and the Drosophila ventral nerve cord as examples, we examine how commissural axon pathfinding is regulated by the Slit family of guidance cues and their Robo family receptors. We extract several principles that seem likely to apply to other axons and other contexts, such as the reiterative use of the same guidance molecules in distinct pathfinding decisions, the transcriptional specification of a pathway, the posttranscriptional regulation of growth along the pathway, and the possible role of feedback mechanisms to ensure the fidelity of pathfinding choices. Such mechanisms may help explain how a relatively small number of guidance molecules can generate complex and stereotyped wiring patterns. We also highlight the many gaps in our understanding of commissural axon pathfinding and question some widely accepted views. We hope that this review encourages further efforts to tackle these questions, in the expectation that this system will continue to reveal the general principles of axon pathfinding.","authors":"Dickson, BJ., Gilestro, GF.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Annu Rev Cell Dev Biol","volume":"22","issue":null,"page":"651-75","pdf":null,"JrId":"20331","fulltextlink":null,"preprintlink":null,"articledate":"2006-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16983071","title":"Crystal structure of 12-oxophytodienoate reductase 3 from tomato: self-inhibition by dimerization.","abstract":"12-Oxophytodienoate reductase (OPR) 3, a homologue of old yellow enzyme (OYE), catalyzes the reduction of 9S,13S-12-oxophytodienoate to the corresponding cyclopentanone, which is subsequently converted to the plant hormone jasmonic acid (JA). JA and JA derivatives, as well as 12-oxophytodienoate and related cyclopentenones, are known to regulate gene expression in plant development and defense. Together with other oxygenated fatty acid derivatives, they form the oxylipin signature in plants, which resembles the pool of prostaglandins in animals. Here, we report the crystal structure of OPR3 from tomato and of two OPR3 mutants. Although the catalytic residues of OPR3 and related OYEs are highly conserved, several characteristic differences can be discerned in the substrate-binding regions, explaining the remarkable substrate stereoselectivity of OPR isozymes. Interestingly, OPR3 crystallized as an extraordinary self-inhibited dimer. Mutagenesis studies and biochemical analysis confirmed a weak dimerization of OPR3 in vitro, which correlated with a loss of enzymatic activity. Based on structural data of OPR3, a putative mechanism for a strong and reversible dimerization of OPR3 in vivo that involves phosphorylation of OPR3 is suggested. This mechanism could contribute to the shaping of the oxylipin signature, which is critical for fine-tuning gene expression in plants.","authors":"Breithaupt, C., Kurzbauer, R., Lilie, H., Schaller, A., Strassner, J., Huber, R., Macheroux, P., Clausen, T.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Proc Natl Acad Sci U S A","volume":"103","issue":"39","page":"14337-42","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16980619","title":"Hematopoietic precursor cells transiently reestablish permissiveness for X inactivation.","abstract":"Xist is the trigger for X inactivation in female mammals. The long noncoding Xist RNA localizes along one of the two female X chromosomes and initiates chromosome-wide silencing in the early embryo. In differentiated cells, Xist becomes dispensable for the maintenance of the inactive X, and its function for initiation of silencing is lost. How Xist mediates gene repression remains an open question. Here, we use an inducible Xist allele in adult mice to identify cells in which Xist can cause chromosome-wide silencing. We show that Xist has the ability to initiate silencing in immature hematopoietic precursor cells. In contrast, hematopoietic stem cells and mature blood cells are unable to initiate ectopic X inactivation. This indicates that pathways critical for silencing are transiently activated in hematopoietic differentiation. Xist-responsive cell types in normal female mice show a change of chromatin marks on the inactive X. However, dosage compensation is maintained throughout hematopoiesis. Therefore, Xist can initiate silencing in precursors with concomitant maintenance of dosage compensation. This suggests that Xist function is restricted in development by the limited activity of epigenetic pathways rather than by a change in the responsiveness of chromatin between embryonic and differentiated cell types.","authors":"Savarese, F., Flahndorfer, K., Jaenisch, R., Busslinger, M., Wutz, A.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Mol Cell Biol","volume":"26","issue":"19","page":"7167-77","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16968900","title":"Oncogenic role of Pax5 in the T-lymphoid lineage upon ectopic expression from the immunoglobulin heavy-chain locus.","abstract":"Four of 9 PAX transcription factor genes have been associated with chromosomal translocations in human tumors, although their oncogenic potential has not yet been demonstrated in transgenic mouse models. The B-lymphoidPAX5 gene participates in the generation of the t(9;14)(p13;q32) translocation in germinal center B cells, which leads to deregulated PAX5 expression under the control of the immunoglobulin heavy-chain (IgH) locus in a subset of B-cell non-Hodgkin lymphomas. Here we reconstructed a human t(9;14) translocation in a knock-in mouse by inserting a PAX5 minigene into the IgH locus. The IgH(P5ki) allele, which corresponds to a germline rather than somatic mutation, is activated in multipotent hematopoietic progenitors and is subsequently expressed in dendritic cells (DCs) and in natural killer (NK), T, and B cells. Ectopic Pax5 expression interferes with normal T-cell development and causes immature T-lymphoblastic lymphomas in IgH(P5ki\/+) and IgH(P5ki\/P5ki) mice. Aggressive T-cell lymphomas develop even faster in Ik(Pax5\/+) mice expressing Pax5 from the Ikaros locus. Pax5 expression in thymocytes activates B-cell-specific genes and represses T-lymphoid genes, suggesting that Pax5 contributes to lymphomagenesis by deregulating the T-cell gene-expression program. These data identify Pax5 as a potent oncogene and demonstrate that the T-lymphoid lineage is particularly sensitive to the oncogenic action of Pax5.","authors":"Souabni, A., Jochum, W., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Blood","volume":"109","issue":"1","page":"281-9","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16955515","title":"Cleaning of raw peptide MS\/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise.","abstract":"The dominant ions in MS\/MS spectra of peptides, which have been fragmented by low-energy CID, are often b-, y-ions and their derivatives resulting from the cleavage of the peptide bonds. However, MS\/MS spectra typically contain many more peaks. These can result not only from isotope variants and multiply charged replicates of the peptide fragmentation products but also from unknown fragmentation pathways, sample-specific or systematic chemical contaminations or from noise generated by the electronic detection system. The presence of this background complicates spectrum interpretation. Besides dramatically prolonged computation time, it can lead to incorrect protein identification, especially in the case of de novo sequencing algorithms. Here, we present an algorithm for detection and transformation of multiply charged peaks into singly charged monoisotopic peaks, removal of heavy isotope replicates, and random noise. A quantitative criterion for the recognition of some noninterpretable spectra has been derived as a byproduct. The approach is based on numerical spectral analysis and signal detection methods. The algorithm has been implemented in a stand-alone computer program called MS Cleaner that can be obtained from the authors upon request.","authors":"Mujezinovic, N., Raidl, G., Hutchins, JR., Peters, JM., Mechtler, K., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Proteomics","volume":"6","issue":"19","page":"5117-31","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2006-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16951341","title":"Receptor activator of NF-kappa B ligand and osteoprotegerin regulate proinflammatory cytokine production in mice.","abstract":"Receptor activator of NF-kappaB ligand (RANKL) is a membrane-bound or soluble cytokine essential for osteoclast differentiation, whereas the decoy receptor osteoprotegerin (OPG) masks RANKL activity. In mouse serum, both soluble RANKL and OPG are detectable. We observed that mice injected with LPS showed significantly down-regulated serum RANKL levels, whereas serum OPG levels were up-regulated. However, the roles of RANKL and OPG in innate immunity remain obscure. We found that RANKL pretreatment suppressed production of proinflammatory cytokines in macrophages in response to stimulation by bacteria and their components. Furthermore, such RANKL-induced tolerance in macrophages was inhibited by GM-CSF treatment, which blocks RANKL signaling. RANKL-induced tolerance occurred in the absence of c-Fos, which is essential for osteoclast differentiation. In mice lacking OPG, LPS-induced production of proinflammatory cytokines was reduced, whereas in mice lacking RANKL, it was increased, and lethality following LPS injection was also elevated, suggesting that constitutive activities of RANKL suppress cytokine responsiveness to LPS in vivo. Strikingly, prior administration of RANKL protected mice from LPS-induced death. These data reveal prophylactic potential of RANKL in acute inflammatory diseases.","authors":"Maruyama, K., Takada, Y., Ray, N., Kishimoto, Y., Penninger, JM., Yasuda, H., Matsuo, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Immunol","volume":"177","issue":"6","page":"3799-805","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32732418","title":"ANGEL2 is a member of the CCR4 family of deadenylases with 2',3'-cyclic phosphatase activity.","abstract":"RNA molecules are frequently modified with a terminal 2',3'-cyclic phosphate group as a result of endonuclease cleavage, exonuclease trimming, or de novo synthesis. During pre-transfer RNA (tRNA) and unconventional messenger RNA (mRNA) splicing, 2',3'-cyclic phosphates are substrates of the tRNA ligase complex, and their removal is critical for recycling of tRNAs upon ribosome stalling. We identified the predicted deadenylase angel homolog 2 (ANGEL2) as a human phosphatase that converts 2',3'-cyclic phosphates into 2',3'-OH nucleotides. We analyzed ANGEL2's substrate preference, structure, and reaction mechanism. Perturbing ANGEL2 expression affected the efficiency of pre-tRNA processing, X-box-binding protein 1 (<i>XBP1<\/i>) mRNA splicing during the unfolded protein response, and tRNA nucleotidyltransferase 1 (TRNT1)-mediated CCA addition onto tRNAs. Our results indicate that ANGEL2 is involved in RNA pathways that rely on the ligation or hydrolysis of 2',3'-cyclic phosphates.","authors":"Pinto, PH., Kroupova, A., Schleiffer, A., Mechtler, K., Jinek, M., Weitzer, S., Martinez, J.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Science","volume":"369","issue":"6503","page":"524-530","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32523996","title":"A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity.","abstract":"Tissue clearing combined with deep imaging has emerged as a powerful alternative to classical histological techniques. Whereas current techniques have been optimized for imaging selected nonpigmented organs such as the mammalian brain, natural pigmentation remains challenging for most other biological specimens of larger volume. We have developed a fast DEpigmEntation-Plus-Clearing method (DEEP-Clear) that is easily incorporated in existing workflows and combines whole system labeling with a spectrum of detection techniques, ranging from immunohistochemistry to RNA in situ hybridization, labeling of proliferative cells (EdU labeling) and visualization of transgenic markers. With light-sheet imaging of whole animals and detailed confocal studies on pigmented organs, we provide unprecedented insight into eyes, whole nervous systems, and subcellular structures in animal models ranging from worms and squids to axolotls and zebrafish. DEEP-Clear thus paves the way for the exploration of species-rich clades and developmental stages that are largely inaccessible by regular imaging approaches.","authors":"Pende, M., Vadiwala, K., Schmidbaur, H., Stockinger, AW., Murawala, P., Saghafi, S., Dekens, MPS., Becker, K., Revilla-I-Domingo, R., Papadopoulos, SC., Zurl, M., Pasierbek, P., Simakov, O., Tanaka, EM., Raible, F., Dodt, HU.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Adv","volume":"6","issue":"22","page":"eaba0365","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16917506","title":"Dissociating the dual roles of apoptosis-inducing factor in maintaining mitochondrial structure and apoptosis.","abstract":"The mitochondrial protein apoptosis-inducing factor (AIF) translocates to the nucleus and induces apoptosis. Recent studies, however, have indicated the importance of AIF for survival in mitochondria. In the absence of a means to dissociate these two functions, the precise roles of AIF remain unclear. Here, we dissociate these dual roles using mitochondrially anchored AIF that cannot be released during apoptosis. Forebrain-specific AIF null (tel. AifDelta) mice have defective cortical development and reduced neuronal survival due to defects in mitochondrial respiration. Mitochondria in AIF deficient neurons are fragmented with aberrant cristae, indicating a novel role of AIF in controlling mitochondrial structure. While tel. AifDelta Apaf1(-\/-) neurons remain sensitive to DNA damage, mitochondrially anchored AIF expression in these cells significantly enhanced survival. AIF mutants that cannot translocate into nucleus failed to induce cell death. These results indicate that the proapoptotic role of AIF can be uncoupled from its physiological function. Cell death induced by AIF is through its proapoptotic activity once it is translocated to the nucleus, not due to the loss of AIF from the mitochondria.","authors":"Cheung, EC., Joza, N., Steenaart, NA., McClellan, KA., Neuspiel, M., McNamara, S., MacLaurin, JG., Rippstein, P., Park, DS., Shore, GC., McBride, HM., Penninger, JM., Slack, RS.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"EMBO J","volume":"25","issue":"17","page":"4061-73","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16912274","title":"A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced.","abstract":"During early mammalian female development, one of the two X chromosomes becomes inactivated. Although X-chromosome coating by Xist RNA is essential for the initiation of X inactivation, little is known about how this signal is transformed into transcriptional silencing. Here we show that exclusion of RNA Polymerase II and transcription factors from the Xist RNA-coated X chromosome represents the earliest event following Xist RNA accumulation described so far in differentiating embryonic stem (ES) cells. Paradoxically, exclusion of the transcription machinery occurs before gene silencing is complete. However, examination of the three-dimensional organization of X-linked genes reveals that, when transcribed, they are always located at the periphery of, or outside, the Xist RNA domain, in contact with the transcription machinery. Upon silencing, genes shift to a more internal location, within the Xist RNA compartment devoid of transcription factors. Surprisingly, the appearance of this compartment is not dependent on the A-repeats of the Xist transcript, which are essential for gene silencing. However, the A-repeats are required for the relocation of genes into the Xist RNA silent domain. We propose that Xist RNA has multiple functions: A-repeat-independent creation of a transcriptionally silent nuclear compartment; and A-repeat-dependent induction of gene repression, which is associated with their translocation into this silent domain.","authors":"Chaumeil, J., Le Baccon, P., Wutz, A., Heard, E.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Genes Dev","volume":"20","issue":"16","page":"2223-37","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19923923","title":"Epigenetic control of the expression of a primate-specific microRNA cluster in human cancer cells.","abstract":"Many of the known microRNAs (miRNAs) are encoded by polycistronic transcripts and are thought to be co-expressed. In this study, we discovered that the expression of a large miRNA cluster (C19MC) on human chromosome 19 is upregulated by the demethylating agent, 5-aza-2'-deoxycytidine (5-Aza-dC), in AGS gastric cancer cells. We found that C19MC was rarely expressed in most cells, but its expression was restored through DNA demethylation. We confirmed that this miRNA cluster was mainly expressed in the placenta, as previously reported. Furthermore, its expression pattern was highly correlated with the methylation state of a distal CpG-rich region located about 17.6 kb upstream of the miRNA cluster. Using combined bisulfite restriction analysis (COBRA) and bisulfite-sequencing techniques, we determined that this CpG-rich region is hypermethylated in the AGS and HeLa cells, but hypomethylated in the placenta tissue. In conclusion, we demonstrated that the expression pattern of the C19MC was activated in human cancer cells through demethylation of a CpG-rich region.","authors":"Tsai, KW., Kao, HW., Chen, HC., Chen, SJ., Lin, WC.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Epigenetics","volume":"4","issue":"8","page":"587-92","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10429206","title":"Characterization of recombinant Arabidopsis thaliana threonine synthase.","abstract":"Threonine synthase (TS) catalyses the last step in the biosynthesis of threonine, the pyridoxal 5'-phosphate dependent conversion of L-homoserine phosphate (HSerP) into L-threonine and inorganic phosphate. Recombinant Arabidopsis thaliana TS (aTS) was characterized to compare a higher plant TS with its counterparts from Escherichia coli and yeast. This comparison revealed several unique properties of aTS: (a) aTS is a regulatory enzyme whose activity was increased up to 85-fold by S-adenosyl-L-methionine (SAM) and specifically inhibited by AMP; (b) HSerP analogues shown previously to be potent inhibitors of E. coli TS failed to inhibit aTS; and (c) aTS was a dimer, while the E. coli and yeast enzymes are monomers. The N-terminal region of aTS is essential for its regulatory properties and protects against inhibition by HSerP analogues, as an aTS devoid of 77 N-terminal residues was neither activated by SAM nor inhibited by AMP, but was inhibited by HSerP analogues. The C-terminal region of aTS seems to be involved in dimer formation, as the N-terminally truncated aTS was also found to be a dimer. These conclusions are supported by a multiple amino-acid sequence alignment, which revealed the existence of two TS subfamilies. aTS was classified as a member of subfamily 1 and its N-terminus is at least 35 residues longer than those of any nonplant TS. Monomeric E. coli and yeast TS are members of subfamily 2, characterized by C-termini extending about 50 residues over those of subfamily 1 members. As a first step towards a better understanding of the properties of aTS, the enzyme was crystallized by the sitting drop vapour diffusion method. The crystals diffracted to beyond 0.28 nm resolution and belonged to the space group P222 (unit cell parameters: a = 6.16 nm, b = 10.54 nm, c = 14.63 nm, alpha = beta = gamma = 90 degrees).","authors":"Laber, B., Maurer, W., Hanke, C., Gr\u00e4fe, S., Ehlert, S., Messerschmidt, A., Clausen, T.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Eur J Biochem","volume":"263","issue":"1","page":"212-21","pdf":null,"JrId":"3607","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16885984","title":"The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches.","abstract":"A classic textbook example of adaptive radiation under natural selection is the evolution of 14 closely related species of Darwin's finches (Fringillidae, Passeriformes), whose primary diversity lies in the size and shape of their beaks. Thus, ground finches have deep and wide beaks, cactus finches have long and pointed beaks (low depth and narrower width), and warbler finches have slender and pointed beaks, reflecting differences in their respective diets. Previous work has shown that even small differences in any of the three major dimensions (depth, width and length) of the beak have major consequences for the overall fitness of the birds. Recently we used a candidate gene approach to explain one pathway involved in Darwin's finch beak morphogenesis. However, this type of analysis is limited to molecules with a known association with craniofacial and\/or skeletogenic development. Here we use a less constrained, complementary DNA microarray analysis of the transcripts expressed in the beak primordia to find previously unknown genes and pathways whose expression correlates with specific beak morphologies. We show that calmodulin (CaM), a molecule involved in mediating Ca2+ signalling, is expressed at higher levels in the long and pointed beaks of cactus finches than in more robust beak types of other species. We validated this observation with in situ hybridizations. When this upregulation of the CaM-dependent pathway is artificially replicated in the chick frontonasal prominence, it causes an elongation of the upper beak, recapitulating the beak morphology of the cactus finches. Our results indicate that local upregulation of the CaM-dependent pathway is likely to have been a component of the evolution of Darwin's finch species with elongated beak morphology and provide a mechanistic explanation for the independence of beak evolution along different axes. More generally, our results implicate the CaM-dependent pathway in the developmental regulation of craniofacial skeletal structures.","authors":"Abzhanov, A., Kuo, WP., Hartmann, C., Grant, BR., Grant, PR., Tabin, CJ.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nature","volume":"442","issue":"7102","page":"563-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10712940","title":"Self-antigen presentation by thymic stromal cells: a subtle division of labor.","abstract":"Self-antigen-MHC complexes expressed by thymic stromal cells serve as ligands for TCR-mediated positive and negative selection, resulting in a self-MHC-restricted, self-tolerant T cell repertoire. It has recently become apparent that thymic stromal cells differ in their accessibility to antigen as well as their ability to process and present antigen. These differences result in the sampling by thymic stromal cells of largely nonoverlapping self-antigen pools and the display of self-peptide profiles specific for each cell type. In conjunction with single or serial cell-cell interactions between thymocytes and stromal cells, such differences in self-antigen display allow for maximal (re)presentation of 'self' in the thymus and optimize the efficacy of positive and negative selection.","authors":"Klein, L., Kyewski, B.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Curr Opin Immunol","volume":"12","issue":"2","page":"179-86","pdf":null,"JrId":"1461","fulltextlink":null,"preprintlink":null,"articledate":"2000-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20008139","title":"Nuclear beta-catenin induces an early liver progenitor phenotype in hepatocellular carcinoma and promotes tumor recurrence.","abstract":"Transforming growth factor-beta cooperates with oncogenic Ras to activate nuclear beta-catenin during the epithelial to mesenchymal transition of hepatocytes, a process relevant in the progression of hepatocellular carcinoma (HCC). In this study we investigated the role of beta-catenin in the differentiation of murine, oncogene-targeted hepatocytes and in 133 human HCC patients scheduled for orthotopic liver transplantation. Transforming growth factor-beta caused dissociation of plasma membrane E-cadherin\/beta-catenin complexes and accumulation of nuclear beta-catenin in Ras-transformed, but otherwise normal hepatocytes in p19(ARF)-\/- mice. Both processes were inhibited by Smad7-mediated disruption of transforming growth factor-beta signaling. Overexpression of constitutively active beta-catenin resulted in high levels of CK19 and M2-PK, whereas ablation of beta-catenin by axin overexpression caused strong expression of CK8 and CK18. Therefore, nuclear beta-catenin resulted in dedifferentiation of neoplastic hepatocytes to immature progenitor cells, whereas loss of nuclear beta-catenin led to a differentiated HCC phenotype. Poorly differentiated human HCC showed cytoplasmic redistribution or even loss of E-cadherin, suggesting epithelial to mesenchymal transition. Analysis of 133 HCC patient samples revealed that 58.6% of human HCC exhibited strong nuclear beta-catenin accumulation, which correlated with clinical features such as vascular invasion and recurrence of disease after orthotopic liver transplantation. These data suggest that activation of beta-catenin signaling causes dedifferentiation to malignant, immature hepatocyte progenitors and facilitates recurrence of human HCC after orthotopic liver transplantation.","authors":"Zulehner, G., Mikula, M., Schneller, D., van Zijl, F., Huber, H., Sieghart, W., Grasl-Kraupp, B., Waldh\u00f6r, T., Peck-Radosavljevic, M., Beug, H., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Am J Pathol","volume":"176","issue":"1","page":"472-81","pdf":null,"JrId":"449","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16896351","title":"The anaphase promoting complex\/cyclosome: a machine designed to destroy.","abstract":"The anaphase promoting complex\/cyclosome (APC\/C) is a ubiquitin ligase that has essential functions in and outside the eukaryotic cell cycle. It is the most complex molecular machine that is known to catalyse ubiquitylation reactions, and it contains more than a dozen subunits that assemble into a large 1.5-MDa complex. Recent discoveries have revealed an unexpected multitude of mechanisms that control APC\/C activity, and have provided a first insight into how this unusual ubiquitin ligase recognizes its substrates.","authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nat Rev Mol Cell Biol","volume":"7","issue":"9","page":"644-56","pdf":null,"JrId":"22271","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32090478","title":"Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration.","abstract":"The mechanisms of organ size control remain poorly understood. A key question is how cells collectively sense the overall status of a tissue. We addressed this problem focusing on mouse liver regeneration. Using digital tissue reconstruction and quantitative image analysis, we found that the apical surface of hepatocytes forming the bile canalicular network expands concomitant with an increase in F-actin and phospho-myosin, to compensate an overload of bile acids. These changes are sensed by the Hippo transcriptional co-activator YAP, which localizes to apical F-actin-rich regions and translocates to the nucleus in dependence of the integrity of the actin cytoskeleton. This mechanism tolerates moderate bile acid fluctuations under tissue homeostasis, but activates YAP in response to sustained bile acid overload. Using an integrated biophysical-biochemical model of bile pressure and Hippo signaling, we explained this behavior by the existence of a mechano-sensory mechanism that activates YAP in a switch-like manner. We propose that the apical surface of hepatocytes acts as a self-regulatory mechano-sensory system that responds to critical levels of bile acids as readout of tissue status.","authors":"Meyer, K., Morales-Navarrete, H., Seifert, S., Wilsch-Braeuninger, M., Dahmen, U., Tanaka, EM., Brusch, L., Kalaidzidis, Y., Zerial, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Mol Syst Biol","volume":"16","issue":"2","page":"e8985","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16876157","title":"Cohesin and DNA damage repair.","abstract":"Replicated DNA molecules are physically connected by cohesin complexes from the time of their synthesis in S-phase until they are segregated during anaphase of the subsequent mitosis or meiosis. This sister chromatid cohesion is essential for the biorientation of chromosomes on the mitotic or meiotic spindle. In addition, cohesion is also essential during G2-phase of the cell cycle to allow repair of DNA double-strand breaks by homologous recombination. Although cohesion can normally only be established during S-phase, recent work in yeast has shown that DNA double-strand breaks induce the recruitment of cohesin to the damage site and lead to the de novo formation of cohesion at this site. It is unknown if similar mechanisms operate in higher eukaryotes, but in mammalian cells phosphorylation of the cohesin subunit Smc1 by the protein kinase Atm has been shown to be important for DNA repair. We discuss how cohesin and sister chromatid cohesion might facilitate the repair of damaged DNA.","authors":"Watrin, E., Peters, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Exp Cell Res","volume":"312","issue":"14","page":"2687-93","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16858405","title":"Acetylation and MAPK phosphorylation cooperate to regulate the degradation of active GATA-1.","abstract":"Regulation of transcription requires mechanisms to both activate and terminate transcription factor activity. GATA-1 is a key haemopoietic transcription factor whose activity is increased by acetylation. We show here that acetylated GATA-1 is targeted for degradation via the ubiquitin\/proteasome pathway. Acetylation positively signals ubiquitination, suggesting that activation by acetylation simultaneously marks GATA-1 for degradation. Promoter-specific MAPK phosphorylation then cooperates with acetylation to execute protein loss. The requirement for both modifications is novel and suggests a way by which degradation of the active protein can be specifically regulated in response to external phosphorylation-mediated signalling. As many transcription factors are activated by acetylation, we suggest that this might be a general mechanism to control transcription factor activity.","authors":"Hernandez-Hernandez, A., Ray, P., Litos, G., Ciro, M., Ottolenghi, S., Beug, H., Boyes, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"EMBO J","volume":"25","issue":"14","page":"3264-74","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15574598","title":"Su(var) genes regulate the balance between euchromatin and heterochromatin in Drosophila.","abstract":"Histone lysine methylation is an epigenetic mark to index chromosomal subdomains. In Drosophila, H3-K9 di- and trimethylation is mainly controlled by the heterochromatic SU(VAR)3-9 HMTase, a major regulator of position-effect variegation (PEV). In contrast, H3-K27 methylation states are independently mediated by the Pc-group enzyme E(Z). Isolation of 19 point mutants demonstrates that the silencing potential of Su(var)3-9 increases with its associated HMTase activity. A hyperactive Su(var)3-9 mutant, pitkin(D), displays extensive H3-K9 di- and trimethylation within but also outside pericentric heterochromatin. Notably, mutations in a novel Su(var) gene, Su(var)3-1, severely restrict Su(var)3-9-mediated gene silencing. Su(var)3-1 was identified as \"antimorphic\" mutants of the euchromatic H3-S10 kinase JIL-1. JIL-1(Su(var)3-1) mutants maintain kinase activity and do not detectably impair repressive histone lysine methylation marks. However, analyses with seven different PEV rearrangements demonstrate a general role of JIL-1(Su(var)3-1) in controlling heterochromatin compaction and expansion. Our data provide evidence for a dynamic balance between heterochromatin and euchromatin, and define two distinct mechanisms for Su(var) gene function. Whereas the majority of Su(var)s encode inherent components of heterochromatin that can establish repressive chromatin structures [intrinsic Su(var)s], Su(var)3-1 reflects gain-of-function mutants of a euchromatic component that antagonize the expansion of heterochromatic subdomains [acquired Su(var)s].","authors":"Ebert, A., Schotta, G., Lein, S., Kubicek, S., Krauss, V., Jenuwein, T., Reuter, G.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genes Dev","volume":"18","issue":"23","page":"2973-83","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32049033","title":"Prospero Phase-Separating the Way to Neuronal Differentiation.","abstract":"Drosophila neural progenitors require the transcriptional repressor Prospero to promptly establish the neuronal fate of their daughter cells to avoid tumorigenesis. In this issue of Developmental Cell, Liu et\u00a0al. (2020) find that Prospero is mitotically implanted and forms liquid-like droplets mediating HP1a condensation to permanently repress its targets.","authors":"Bonnay, F., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Dev Cell","volume":"52","issue":"3","page":"251-252","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31805262","title":"Quiescence of Adult Mammalian Neural Stem Cells: A Highly Regulated Rest.","abstract":"Neural stem cells in the adult mammalian brain are the source of new neurons that contribute to complex sensory and cognitive functions. Most adult neural stem cells are maintained in a state of reversible cell cycle arrest, also called quiescence. Quiescent neural stem cells present a low rate of metabolic activity and a high sensitivity to their local signaling environment, and they can be activated by diverse physiological stimuli. The balance between stem cell quiescence and activity determines not only the rate of neurogenesis but also the long-term maintenance of the stem cell pool and the neurogenic capacity of the aging brain. In recent years, significant progress has been made in characterizing quiescent stem cells thanks to the introduction of new genomic and imaging techniques. We discuss in this review our current understanding of neural stem cell quiescence and its regulation by intrinsic and systemic factors.","authors":"Urb\u00e1n, N., Blomfield, IM., Guillemot, F.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Neuron","volume":"104","issue":"5","page":"834-848","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15541899","title":"Comparative analysis of transcriptional profiles between two apoptotic pathways of light-induced retinal degeneration.","abstract":"Light exposure can exacerbate the condition of a variety of human retinal diseases by increasing the rate of photoreceptor cell death. How light negatively affects photoreceptor cell survival is not yet fully understood. Previous studies involving light damage models have revealed two independent apoptotic pathways: low levels of light induce retinal degeneration in the arrestin -\/- mouse via constitutive activation of the phototransduction cascade, whereas strong light exposure to the retina, such as in an albino eye, elicits photoreceptor cell death via activator protein (AP-1) induction. In order to better understand the initial gene expression changes underlying light damage, dark-reared arrestin -\/- and albino BALB\/c mice were exposed to constant white light (2000 lux), and their retinal morphology was assessed as a function of time. The expression profiles of retinal transcripts were then compared between dark-adapted and light-exposed arrestin -\/-, pigmented wild-type and BALB\/c mice at a time point when morphological changes were minimal. As expected, the dark-adapted samples showed little difference in expression pattern between the three genotypes. Among the genes differentially regulated by light in BALB\/c, but not arrestin -\/- retinas, were c-fos and other stress-induced early response genes. In both mouse models, a marked increase in expression of the bZIP family of transcription factors was observed. Our results show a select group of unique and overlapping sets of genes induced by light in the two mouse models. These expression changes may constitute the underlying initiating events leading to the two distinct mechanisms of light damage.","authors":"Roca, A., Shin, KJ., Liu, X., Simon, MI., Chen, J.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Neuroscience","volume":"129","issue":"3","page":"779-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16788063","title":"Loss of Aif function causes cell death in the mouse embryo, but the temporal progression of patterning is normal.","abstract":"Apoptosis-inducing factor (AIF) is an evolutionarily conserved, ubiquitously expressed flavoprotein with NADH oxidase activity that is normally confined to mitochondria. In mammalian cells, AIF is released from mitochondria in response to apoptotic stimuli and translocates to the nucleus where it is thought to bind DNA and contribute to chromatinolysis and cell death in a caspase-independent manner. Here we describe the consequences of inactivating Aif in the early mouse embryo. Unexpectedly, we found that both the apoptosis-dependent process of cavitation in embryoid bodies and apoptosis associated with embryonic neural tube closure occur in the absence of AIF, indicating that Aif function is not required for apoptotic cell death in early mouse embryos. By embryonic day 9 (E9), loss of Aif function causes abnormal cell death, presumably because of reduced mitochondrial respiratory chain complex I activity. Because of this cell death, Aif null embryos fail to increase significantly in size after E9. Remarkably, patterning processes continue on an essentially normal schedule, such that E10 Aif null embryos with only approximately 1\/10 the normal number of cells have the same somite number as their wild-type littermates. These observations show that pattern formation in the mouse can occur independent of embryo size and cell number.","authors":"Brown, D., Yu, BD., Joza, N., B\u00e9nit, P., Meneses, J., Firpo, M., Rustin, P., Penninger, JM., Martin, GR.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Proc Natl Acad Sci U S A","volume":"103","issue":"26","page":"9918-23","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16783873","title":"PREL1 provides a link from Ras signalling to the actin cytoskeleton via Ena\/VASP proteins.","abstract":"Ena\/VASP family proteins are important modulators of cell migration and localize to focal adhesions, stress fibres and the very tips of lamellipodia and filopodia. Proline-rich proteins like vinculin and zyxin are well established interaction partners, which mediate Ena\/VASP-recruitment via their EVH1-domains to focal adhesions and stress fibres. However, it is still unclear, which binding partners Ena\/VASP proteins may have at lamellipodia tips and how their recruitment to these cellular protrusions is regulated. Here, we report the identification of a novel protein with high similarity to the C. elegans MIG-10 protein, which we termed PREL1 (Proline Rich EVH1 Ligand). PREL1 is a 74 kDa protein and shares homology with the Grb7-family of signalling adaptors. We show that PREL1 directly binds to Ena\/VASP proteins and co-localizes with them at lamellipodia tips and at focal adhesions in response to Ras activation. Moreover, PREL1 directly binds to activated Ras in a phosphoinositide-dependent manner. Thus, our data pinpoint PREL1 as the first direct link between Ras signalling and cytoskeletal remodelling via Ena\/VASP proteins during cell migration and spreading.","authors":"Jenzora, A., Behrendt, B., Small, JV., Wehland, J., Stradal, TE.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"FEBS Lett","volume":"580","issue":"12","page":"455-63","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16763550","title":"Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing.","abstract":"In mammals X inactivation is initiated by expression of Xist RNA and involves the recruitment of Polycomb repressive complex 1 (PRC1) and 2 (PRC2), which mediate chromosome-wide ubiquitination of histone H2A and methylation of histone H3, respectively. Here, we show that PRC1 recruitment by Xist RNA is independent of gene silencing. We find that Eed is required for the recruitment of the canonical PRC1 proteins Mph1 and Mph2 by Xist. However, functional Ring1b is recruited by Xist and mediates ubiquitination of histone H2A in Eed deficient embryonic stem (ES) cells, which lack histone H3 lysine 27 tri-methylation. Xist expression early in ES cell differentiation establishes a chromosomal memory, which allows efficient H2A ubiquitination in differentiated cells and is independent of silencing and PRC2. Our data show that Xist recruits PRC1 components by both PRC2 dependent and independent modes and in the absence of PRC2 function is sufficient for the establishment of Polycomb-based memory systems in X inactivation.","authors":"Schoeftner, S., Sengupta, AK., Kubicek, S., Mechtler, K., Spahn, L., Koseki, H., Jenuwein, T., Wutz, A.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"EMBO J","volume":"25","issue":"13","page":"3110-22","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16751808","title":"Raf plus TGFbeta-dependent EMT is initiated by endocytosis and lysosomal degradation of E-cadherin.","abstract":"Oncogenic Ras interferes with adhesive functions of epithelial cells, but requires tumor growth factor beta (TGFbeta) signaling to cause epithelial-mesenchymal transition (EMT) and tumor progression in model systems. To investigate the mechanisms by which Ras and TGFbeta pathways cooperate in EMT induction, we introduced a tamoxifen-inducible version of Raf-1 (RafER) into fully polarized, mammary epithelial cells (EpH4). EMT characterized by loss of E-cadherin expression and upregulation of invasiveness-promoting genes was induced by TGFbeta plus 4-hydroxytamoxifen (4HT) activation of RafER. Downregulation of E-cadherin by RafER plus TGFbeta was detectable in total cell lysates after 48 h and much earlier in detergent-insoluble fractions of E-cadherin. Both pathways cooperated to strongly enhance endocytosis of E-cadherin, mainly via the clathrin-dependent route. Pulse-chase experiments showed decreased E-cadherin protein stability in cells stimulated with TGFbeta and 4HT and increased E-cadherin half-life in the presence of monensin. Monensin and chloroquine prevented E-cadherin degradation to different extent, but only monensin effectively blocked the loss of E-cadherin from the junctional complexes. Both lysosome inhibitors caused accumulation of E-cadherin vesicles, some of which were positive for Cathepsin D and lysosome-associated membrane protein 1 (LAMP-1). In addition, TGFbeta and mitogen-activated protein kinase hyperactivation synergistically induced E-cadherin ubiquitination, suggesting that the cooperation of Raf and TGFbeta favors lysosomal degradation of E-cadherin instead of its recycling. Our data indicate that early stages of EMT involve cooperative, post-translational downregulation of E-cadherin, whereas loss of E-cadherin via transcriptional repression is a late event in EMT.","authors":"Janda, E., Nevolo, M., Lehmann, K., Downward, J., Beug, H., Grieco, M.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Oncogene","volume":"25","issue":"54","page":"7117-30","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2006-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16741576","title":"Autocrine PDGFR signaling promotes mammary cancer metastasis.","abstract":"Metastasis is the major cause of cancer morbidity, but strategies for direct interference with invasion processes are lacking. Dedifferentiated, late-stage tumor cells secrete multiple factors that represent attractive targets for therapeutic intervention. Here we show that metastatic potential of oncogenic mammary epithelial cells requires an autocrine PDGF\/PDGFR loop, which is established as a consequence of TGF-beta-induced epithelial-mesenchymal transition (EMT), a faithful in vitro correlate of metastasis. The cooperation of autocrine PDGFR signaling with oncogenic Ras hyperactivates PI3K and is required for survival during EMT. Autocrine PDGFR signaling also contributes to maintenance of EMT, possibly through activation of STAT1 and other distinct pathways. Inhibition of PDGFR signaling interfered with EMT and caused apoptosis in murine and human mammary carcinoma cell lines. Consequently, overexpression of a dominant-negative PDGFR or application of the established cancer drug STI571 interfered with experimental metastasis in mice. Similarly, in mouse mammary tumor virus-Neu (MMTV-Neu) transgenic mice, TGF-beta enhanced metastasis of mammary tumors, induced EMT, and elevated PDGFR signaling. Finally, expression of PDGFRalpha and -beta correlated with invasive behavior in human mammary carcinomas. Thus, autocrine PDGFR signaling plays an essential role during cancer progression, suggesting a novel application of STI571 to therapeutically interfere with metastasis.","authors":"Jechlinger, M., Sommer, A., Moriggl, R., Seither, P., Kraut, N., Capodiecci, P., Donovan, M., Cordon-Cardo, C., Beug, H., Gr\u00fcnert, S.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Clin Invest","volume":"116","issue":"6","page":"1561-70","pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16740476","title":"The Drosophila NuMA Homolog Mud regulates spindle orientation in asymmetric cell division.","abstract":"During asymmetric cell division, the mitotic spindle must be properly oriented to ensure the asymmetric segregation of cell fate determinants into only one of the two daughter cells. In Drosophila neuroblasts, spindle orientation requires heterotrimeric G proteins and the G alpha binding partner Pins, but how the Pins-G alphai complex interacts with the mitotic spindle is unclear. Here, we show that Pins binds directly to the microtubule binding protein Mud, the Drosophila homolog of NuMA. Like NuMA, Mud can bind to microtubules and enhance microtubule polymerization. In the absence of Mud, mitotic spindles in Drosophila neuroblasts fail to align with the polarity axis. This can lead to symmetric segregation of the cell fate determinants Brat and Prospero, resulting in the mis-specification of daughter cell fates and tumor-like over proliferation in the Drosophila nervous system. Our data suggest a model in which asymmetrically localized Pins-G alphai complexes regulate spindle orientation by directly binding to Mud.","authors":"Bowman, SK., Neum\u00fcller, RA., Novatchkova, M., Du, Q., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Dev Cell","volume":"10","issue":"6","page":"731-42","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31803201","title":"Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.","abstract":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host's immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant's responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. <i>Ustilago maydis<\/i>, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of <i>U. maydis<\/i> effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.","authors":"Alc\u00e2ntara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M., Uhse, S., Darino, MA., Olukayode, T., Reumann, D., Baggaley, L., Djamei, A.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Front Plant Sci","volume":"10","issue":null,"page":"1437","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16738660","title":"Assembly of the inner rod determines needle length in the type III secretion injectisome.","abstract":"Assembly of multi-component supramolecular machines is fundamental to biology, yet in most cases, assembly pathways and their control are poorly understood. An example is the type III secretion machine, which mediates the transfer of bacterial virulence proteins into host cells. A central component of this nanomachine is the needle complex or injectisome, an organelle associated with the bacterial envelope that is composed of a multi-ring base, an inner rod, and a protruding needle. Assembly of this organelle proceeds in sequential steps that require the reprogramming of the secretion machine. Here we provide evidence that, in Salmonella typhimurium, completion of the assembly of the inner rod determines the size of the needle substructure. Assembly of the inner rod, which is regulated by the InvJ protein, triggers conformational changes on the cytoplasmic side of the injectisome, reprogramming the secretion apparatus to stop secretion of the needle protein.","authors":"Marlovits, TC., Kubori, T., Lara-Tejero, M., Thomas, D., Unger, VM., Gal\u00e1n, JE.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nature","volume":"441","issue":"7093","page":"637-40","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16738409","title":"Post-transcriptional regulation of microRNA expression.","abstract":"microRNAs (miRNAs) are endogenous, noncoding approximately 22-nucleotide RNA molecules that have recently emerged as fundamental, post-transcriptional regulators of cognate target gene expression. Many mammalian miRNAs are expressed in a tissue-specific manner, a phenomenon that has so far been attributed to transcriptional regulation. We here show by Northern blots and in situ hybridization experiments that the expression of mammalian miRNAs can be regulated at the post-transcriptional level. In particular, miR-138 is spatially restricted to distinct cell types, while its precursor, pre-miR-138-2, is ubiquitously expressed throughout all tissues analyzed. Furthermore, pre-miR-138-2 is exported from the nucleus to the cytoplasm, suggesting that cleavage of this pre-miRNA by Dicer is restricted to certain tissues and cell types. Thus, differential processing of pre-miRNAs might be an alternative mechanism to control miRNA function.","authors":"Obernosterer, G., Leuschner, PJ., Alenius, M., Martinez, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"RNA","volume":"12","issue":"7","page":"1161-7","pdf":null,"JrId":"8792","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11444040","title":"Splitting the chromosome: cutting the ties that bind sister chromatids.","abstract":"In eukaryotic cells, replicated DNA molecules remain physically connected from their synthesis in S phase until they are separated during anaphase. This phenomenon, called sister chromatid cohesion, is essential for the temporal separation of DNA replication and mitosis and for the equal separation of the duplicated genome. Recent work has identified a number of chromosomal proteins required for cohesion. In this review we discuss how these proteins may connect sister chromatids and how they are removed from chromosomes to allow sister chromatid separation at the onset of anaphase.","authors":"Nasmyth, K., Peters, JM., Uhlmann, F.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Novartis Found Symp","volume":"237","issue":null,"page":"113-33; discussion 133-8, 158-63","pdf":null,"JrId":"20998","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16738407","title":"Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells.","abstract":"Histone lysine trimethyl states represent some of the most robust epigenetic modifications in eukaryotic chromatin. Using a candidate approach, we identified the subgroup of murine Jmjd2 proteins to antagonize H3K9me3 at pericentric heterochromatin. H3K27me3 and H4K20me3 marks are not impaired in inducible Jmjd2b-GFP cell lines, but Jmjd2b also reduces H3K36 methylation. Since recombinant Jmjd2b appears as a very poor enzyme, we applied metabolic labeling with heavy methyl groups to demonstrate Jmjd2b-mediated removal of chromosomal H3K9me3 as an active process that occurs well before replication of chromatin. These data reveal that certain members of the jmjC class of hydroxylases can work in a pathway that actively antagonizes a histone lysine trimethyl state.","authors":"Fodor, BD., Kubicek, S., Yonezawa, M., O'Sullivan, RJ., Sengupta, R., Perez-Burgos, L., Opravil, S., Mechtler, K., Schotta, G., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Genes Dev","volume":"20","issue":"12","page":"1557-62","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16713940","title":"Shared neural circuitry for female and male sexual behaviours in Drosophila.","abstract":"","authors":"Kvitsiani, D., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr Biol","volume":"16","issue":"10","page":"R355-6","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10669416","title":"Function of PI3Kgamma in thymocyte development, T cell activation, and neutrophil migration.","abstract":"Phosphoinositide 3-kinases (PI3Ks) regulate fundamental cellular responses such as proliferation, apoptosis, cell motility, and adhesion. Viable gene-targeted mice lacking the p110 catalytic subunit of PI3Kgamma were generated. We show that PI3Kgamma controls thymocyte survival and activation of mature T cells but has no role in the development or function of B cells. PI3Kgamma-deficient neutrophils exhibited severe defects in migration and respiratory burst in response to heterotrimeric GTP-binding protein (G protein)-coupled receptor (GPCR) agonists and chemotactic agents. PI3Kgamma links GPCR stimulation to the formation of phosphatidylinositol 3,4,5-triphosphate and the activation of protein kinase B, ribosomal protein S6 kinase, and extracellular signal-regulated kinases 1 and 2. Thus, PI3Kgamma regulates thymocyte development, T cell activation, neutrophil migration, and the oxidative burst.","authors":"Sasaki, T., Irie-Sasaki, J., Jones, RG., Oliveira-dos-Santos, AJ., Stanford, WL., Bolon, B., Wakeham, A., Itie, A., Bouchard, D., Kozieradzki, I., Joza, N., Mak, TW., Ohashi, PS., Suzuki, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Science","volume":"287","issue":"5455","page":"1040-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16717091","title":"The polycomb group protein EZH2 is required for mammalian circadian clock function.","abstract":"We examined the importance of histone methylation by the polycomb group proteins in the mouse circadian clock mechanism. Endogenous EZH2, a polycomb group enzyme that methylates lysine 27 on histone H3, co-immunoprecipitates with CLOCK and BMAL1 throughout the circadian cycle in liver nuclear extracts. Chromatin immunoprecipitation revealed EZH2 binding and di- and trimethylation of H3K27 on both the Period 1 and Period 2 promoters. A role of EZH2 in cryptochrome-mediated transcriptional repression of the clockwork was supported by overexpression and RNA interference studies. Serum-induced circadian rhythms in NIH 3T3 cells in culture were disrupted by transfection of an RNA interfering sequence targeting EZH2. These results indicate that EZH2 is important for the maintenance of circadian rhythms and extend the activity of the polycomb group proteins to the core clockwork mechanism of mammals.","authors":"Etchegaray, JP., Yang, X., DeBruyne, JP., Peters, AHFM., Weaver, DR., Jenuwein, T., Reppert, SM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Biol Chem","volume":"281","issue":"30","page":"21209-21215","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10613824","title":"Shaping of the autoreactive T-cell repertoire by a splice variant of self protein expressed in thymic epithelial cells.","abstract":"Intrathymic expression of tissue-specific self antigens may be involved in immunological tolerance and protection from autoimmune disease. We have analyzed the role of T-cell tolerance to proteolipid protein (PLP), the main protein of the myelin sheath, in susceptibility to experimental autoimmune encephalomyelitis (EAE), an animal model for multiple sclerosis. Intrathymic expression of PLP was largely restricted to the shorter splice variant, DM20. Expression of DM20 by thymic epithelium was sufficient to confer T-cell tolerance to all epitopes of PLP in EAE-resistant C57BL\/6 mice. In contrast, the major T-cell epitope in SJL\/J mice was only encoded by the central nervous system-specific exon of PLP, but not by thymic DM20. Thus, lack of tolerance to this epitope offers an explanation for the exquisite susceptibility of SJL\/J mice to EAE. As PLP expression in the human thymus is also restricted to the DM20 isoform, these findings have implications for selection of the autoimmune T-cell repertoire in multiple sclerosis.","authors":"Klein, L., Klugmann, M., Nave, KA., Tuohy, VK., Kyewski, B.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nat Med","volume":"6","issue":"1","page":"56-61","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"2000-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16687444","title":"Distinct roles of Polycomb group gene products in transcriptionally repressed and active domains of Hoxb8.","abstract":"To address the molecular mechanisms underlying Polycomb group (PcG)-mediated repression of Hox gene expression, we have focused on the binding patterns of PcG gene products to the flanking regions of the Hoxb8 gene in expressing and non-expressing tissues. In parallel, we followed the distribution of histone marks of transcriptionally active H3 acetylated on lysine 9 (H3-K9) and methylated on lysine 4 (H3-K4), and of transcriptionally inactive chromatin trimethylated on lysine 27 (H3-K27). Chromatin immunoprecipitation revealed that the association of PcG proteins, and H3-K9 acetylation and H3-K27 trimethylation around Hoxb8 were distinct in tissues expressing and not expressing the gene. We show that developmental changes of these epigenetic marks temporally coincide with the misexpression of Hox genes in PcG mutants. Functional analyses, using mutant alleles impairing the PcG class 2 component Rnf2 or the Suz12 mutation decreasing H3-K27 trimethylation, revealed that interactions between class 1 and class 2 PcG complexes, mediated by trimethylated H3-K27, play decisive roles in the maintenance of Hox gene repression outside their expression domain. Within the expression domains, class 2 PcG complexes appeared to maintain the transcriptionally active status via profound regulation of H3-K9 acetylation. The present study indicates distinct roles for class 2 PcG complexes in transcriptionally repressed and active domains of Hoxb8 gene.","authors":"Fujimura, Y., Isono, K., Vidal, M., Endoh, M., Kajita, H., Mizutani-Koseki, Y., Takihara, Y., van Lohuizen, M., Otte, A., Jenuwein, T., Deschamps, J., Koseki, H.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Development","volume":"133","issue":"12","page":"2371-81","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15207733","title":"Herpesvirus saimiri STP A11 protein interacts with STAT3 and stimulates its transcriptional activity.","abstract":"Herpesvirus saimiri (HVS) is an oncogenic gamma-2 herpesvirus that causes lymphoma in New World primates. HVS can be further divided into subgroups A, B, and C, based on sequence divergence. Saimiri transforming protein (STP) is coded for by the first open reading frame at the left end of the HVS genome and is responsible for its oncogenic potential. Here we show that STP A11 binds to signal transducers and activators of transcription 3 (STAT3), stimulates STAT3 phosphorylation, and activates STAT3-dependent transcription. STP A11 recruited c-Src kinase to phosphorylate STAT3 protein, and co-expression of STP A11 with c-Src dramatically increased STAT3 phosphorylation. We found that the amino terminal domain of STP A11 is required for both STAT3 interaction and activation, and that physical interaction is required for STAT3 activation.","authors":"Park, J., Seo, T., Jung, J., Choe, J.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Biochem Biophys Res Commun","volume":"320","issue":"1","page":"279-85","pdf":null,"JrId":"1008","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16675698","title":"Defective lipolysis and altered energy metabolism in mice lacking adipose triglyceride lipase.","abstract":"Fat tissue is the most important energy depot in vertebrates. The release of free fatty acids (FFAs) from stored fat requires the enzymatic activity of lipases. We showed that genetic inactivation of adipose triglyceride lipase (ATGL) in mice increases adipose mass and leads to triacylglycerol deposition in multiple tissues. ATGL-deficient mice accumulated large amounts of lipid in the heart, causing cardiac dysfunction and premature death. Defective cold adaptation indicated that the enzyme provides FFAs to fuel thermogenesis. The reduced availability of ATGL-derived FFAs leads to increased glucose use, increased glucose tolerance, and increased insulin sensitivity. These results indicate that ATGL is rate limiting in the catabolism of cellular fat depots and plays an important role in energy homeostasis.","authors":"Haemmerle, G., Lass, A., Zimmermann, R., Gorkiewicz, G., Meyer, C., Rozman, J., Heldmaier, G., Maier, R., Theussl, C., Eder, S., Kratky, D., Wagner, EF., Klingenspor, M., Hoefler, G., Zechner, R.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Science","volume":"312","issue":"5774","page":"734-7","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15530658","title":"Stress induced changes in cortical and hypothalamic c-fos expression are altered in fragile X mutant mice.","abstract":"Fragile X (FraX) syndrome is characterized by mental retardation and a behavioral phenotype that includes stress-related behaviors. Recently, FraX children were shown to have elevated glucocorticoid hormones under basal conditions and an exaggerated hormonal response to stress. In the present study, fragile X mental retardation 1-knockout (Fmr1-KO) and wild-type (WT) mice were subjected to immobilization stress for 30 min or 2 h, killed with paired controls, and the hippocampus, neocortex, and hypothalamic paraventricular nucleus (PVN) assessed by in situ hybridization for effects on c-fos mRNA. The main effect of stress in hippocampus was a reduction in mRNA levels within CA3-CA1 pyramidal cells in both genotypes. Stress significantly reduced CA1 c-fos mRNA in Fmr1-KOs at 30 min (-41%) and 2 h (-57%), whereas in WTs levels were significantly reduced only at 2 h (-57%). In neocortex, 30 min stress significantly increased c-fos mRNA in Fmr1-KOs only (+53%); however, by 2 h levels were reduced in both genotypes versus respective controls. In the paraventricular nucleus, c-fos mRNA levels were significantly, and equally, increased in both genotypes at 30 min. However, at 2 h, mRNA levels were still elevated in the Fmr1-KOs, whereas they had returned to control values in the WTs. Finally, immobilization stress significantly increased serum corticosterone levels in both genotypes at 30 min and 2 h, with Fmr1-KOs exhibiting greater levels than WTs; levels were statistically different at 2 h. These data indicate a greater response to stress in FraX mutants than in WTs, and further support the hypothesis of a dysregulated hypothalamic-pituitary-adrenal (HPA) axis in FraX syndrome.","authors":"Lauterborn, JC.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Brain Res Mol Brain Res","volume":"131","issue":"1-2","page":"101-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16627784","title":"Insulin-like growth factor-1 and PTEN deletion enhance cardiac L-type Ca2+ currents via increased PI3Kalpha\/PKB signaling.","abstract":"Ca2+ influx through the L-type Ca2+ channel (I(Ca,L)) is a key determinant of cardiac contractility and is modulated by multiple signaling pathways. Because the regulation of I(Ca,L) by phosphoinositide-3-kinases (PI3Ks) and phosphoinositide-3-phosphatase (PTEN) is unknown, despite their involvement in the regulation of myocardial growth and contractility, I(Ca,L) was recorded in myocytes isolated from mice overexpressing a dominant-negative p110alpha mutant (DN-p110alpha) in the heart, lacking the PI3Kgamma gene (PI3Kgamma(-\/-)) or with muscle-specific ablation of PTEN (PTEN(-\/-)). Combinations of these genetically altered mice were also examined. Although there were no differences in the expression level of CaV1.2 proteins, basal I(Ca,L) densities were larger (P&lt;0.01) in PTEN(-\/-) myocytes compared with littermate controls, PI3Kgamma(-\/-), or DN-p110alpha myocytes and showed negative shifts in voltage dependence of current activation. The I(Ca,L) differences seen in PTEN(-\/-) mice were eliminated by pharmacological inhibition of either PI3Ks or protein kinase B (PKB) as well as in PTEN(-\/-)\/DN-p110alpha double mutant mice but not in PTEN(-\/-)\/PI3Kgamma(-\/-) mice. On the other hand, application of insulin-like growth factor-1 (IGF-1), an activator of PKB, increased I(Ca,L) in control and PI3Kgamma(-\/-), while having no effects on I(Ca,L) in DN-p110alpha or PTEN(-\/-) mice. The I(Ca,L) increases induced by IGF-1 were abolished by PKB inhibition. Our results demonstrate that IGF-1 treatment or inactivation of PTEN enhances I(Ca,L) via PI3Kalpha-dependent increase in PKB activation.","authors":"Sun, H., Kerfant, BG., Zhao, D., Trivieri, MG., Oudit, GY., Penninger, JM., Backx, PH.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Circ Res","volume":"98","issue":"11","page":"1390-7","pdf":null,"JrId":"2974","fulltextlink":null,"preprintlink":null,"articledate":"2006-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16627581","title":"Osteoblasts provide a suitable microenvironment for the action of receptor activator of nuclear factor-kappaB ligand.","abstract":"Deficiency of osteoprotegerin (OPG), a soluble decoy receptor for receptor activator of nuclear factor-kappaB ligand (RANKL), in mice induces osteoporosis caused by enhanced bone resorption. Serum concentrations of RANKL are extremely high in OPG-deficient (OPG(-\/-)) mice, suggesting that circulating RANKL is involved in osteoclastogenesis. RANKL(-\/-) mice exhibit osteopetrosis, with the absence of osteoclasts. We examined the requirements for osteoclastogenesis using OPG(-\/-) mice, RANKL(-\/-) mice, and a system involving bone morphogenetic protein 2 (BMP-2)-induced ectopic bone formation. When collagen disks containing BMP-2 (BMP-2-disks) or vehicle were implanted into OPG(-\/-) mice, osteoclast-like cells (OCLs) and alkaline phosphatase-positive OCLs appeared in BMP-2-disks but not the control disks. F4\/80-positive osteoclast precursors were similarly distributed in both BMP-2- and control disks. Cells expressing RANKL were detected in the BMP-2-disks, and the addition of OPG to the disk inhibited OCL formation. Muscle cells in culture differentiated into alkaline phosphatase-positive cells in the presence of BMP-2 and accordingly expressed RANKL mRNA in response to PTH. This suggests that RANKL expressed by osteoblasts is a requirement for osteoclastogenesis. We then examined how osteoblasts are involved in osteoclastogenesis other than RANKL expression, using RANKL(-\/-) mice. BMP-2- and control disks were implanted into RANKL(-\/-) mice, which were injected with RANKL for 7 d. Many OCLs were observed in the BMP-2-disks and bone tissues but not the control disks. These results suggest that osteoblasts also play important roles in osteoclastogenesis through offering the critical microenvironment for the action of RANKL.","authors":"Yamamoto, Y., Udagawa, N., Matsuura, S., Nakamichi, Y., Horiuchi, H., Hosoya, A., Nakamura, M., Ozawa, H., Takaoka, K., Penninger, JM., Noguchi, T., Takahashi, N.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Endocrinology","volume":"147","issue":"7","page":"3366-74","pdf":null,"JrId":"3530","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31247106","title":"RNA profiling of human testicular cells identifies syntenic lncRNAs associated with spermatogenesis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31247106<\/PMID><DateCompleted><Year>2020<\/Year><Month>07<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>07<\/Month><Day>20<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1460-2350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>34<\/Volume><Issue>7<\/Issue><PubDate><Year>2019<\/Year><Month>07<\/Month><Day>08<\/Day><\/PubDate><\/JournalIssue><Title>Human reproduction (Oxford, England)<\/Title><ISOAbbreviation>Hum Reprod<\/ISOAbbreviation><\/Journal><ArticleTitle>RNA profiling of human testicular cells identifies syntenic lncRNAs associated with spermatogenesis.<\/ArticleTitle><Pagination><MedlinePgn>1278-1290<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/humrep\/dez063<\/ELocationID><Abstract><AbstractText Label=\"STUDY QUESTION\">Is the noncoding transcriptional landscape during spermatogenesis conserved between human and rodents?","authors":"Rolland, AD., Evrard, B., Darde, TA., Le B\u00e9guec, C., Le Bras, Y., Bensalah, K., Lavou\u00e9, S., Jost, B., Primig, M., Dejucq-Rainsford, N., Chalmel, F., J\u00e9gou, B.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Hum Reprod","volume":"34","issue":"7","page":"1278-1290","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16607286","title":"A crucial function of PDGF in TGF-beta-mediated cancer progression of hepatocytes.","abstract":"Polarized hepatocytes expressing hyperactive Ha-Ras adopt an invasive and metastatic phenotype in cooperation with transforming growth factor (TGF)-beta. This dramatic increase in malignancy is displayed by an epithelial to mesenchymal transition (EMT), which mimics the TGF-beta-mediated progression of human hepatocellular carcinomas. In culture, hepatocellular EMT occurs highly synchronously, facilitating the analysis of molecular events underlying the various stages of this process. Here, we show that in response to TGF-beta, phosphorylated Smads rapidly translocated into the nucleus and activated transcription of target genes such as E-cadherin repressors of the Snail superfamily, causing loss of cell adhesion. Within the TGF-beta superfamily of cytokines, TGF-beta1, -beta2 and -beta3 were specific for the induction of hepatocellular EMT. Expression profiling of EMT kinetics revealed 78 up- and 235 downregulated genes, which preferentially modulate metabolic activities, extracellular matrix composition, transcriptional activities and cell survival. Independent of the genetic background, platelet-derived growth factor (PDGF)-A ligand and both PDGF receptor subunits were highly elevated, together with autocrine secretion of bioactive PDGF. Interference with PDGF signalling by employing hepatocytes expressing the dominant-negative PDGF-alpha receptor revealed decreased TGF-beta-induced migration in vitro and efficient suppression of tumour growth in vivo. In conclusion, these results provide evidence for a crucial role of PDGF in TGF-beta-mediated tumour progression of hepatocytes and suggest PDGF as a target for therapeutic intervention in liver cancer.","authors":"Gotzmann, J., Fischer, AN., Zojer, M., Mikula, M., Proell, V., Huber, H., Jechlinger, M., Waerner, T., Weith, A., Beug, H., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Oncogene","volume":"25","issue":"22","page":"3170-85","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2006-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16581295","title":"Angiotensin-converting enzyme 2 in lung diseases.","abstract":"The renin-angiotensin system (RAS) plays a key role in maintaining blood pressure homeostasis, as well as fluid and salt balance. Angiotensin II, a key effector peptide of the system, causes vasoconstriction and exerts multiple biological functions. Angiotensin-converting enzyme (ACE) plays a central role in generating angiotensin II from angiotensin I, and capillary blood vessels in the lung are one of the major sites of ACE expression and angiotensin II production in the human body. The RAS has been implicated in the pathogenesis of pulmonary hypertension and pulmonary fibrosis, both commonly seen in chronic lung diseases such as chronic obstructive lung disease. Recent studies indicate that the RAS also plays a critical role in acute lung diseases, especially acute respiratory distress syndrome (ARDS). ACE2, a close homologue of ACE, functions as a negative regulator of the angiotensin system and was identified as a key receptor for SARS (severe acute respiratory syndrome) coronavirus infections. In the lung, ACE2 protects against acute lung injury in several animal models of ARDS. Thus, the RAS appears to play a critical role in the pathogenesis of acute lung injury. Indeed, increasing ACE2 activity might be a novel approach for the treatment of acute lung failure in several diseases.","authors":"Kuba, K., Imai, Y., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr Opin Pharmacol","volume":"6","issue":"3","page":"271-6","pdf":null,"JrId":"26801","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31374198","title":"Interconversion between Tumorigenic and Differentiated States in Acute Myeloid Leukemia.","abstract":"Tumors are composed of phenotypically heterogeneous cancer cells that often resemble various differentiation states of their lineage of origin. Within this\u00a0hierarchy, it is thought that an immature subpopulation of tumor-propagating cancer stem cells (CSCs) differentiates into non-tumorigenic progeny, providing a rationale for therapeutic strategies that specifically eradicate CSCs or induce their differentiation. The clinical success of these approaches depends on CSC differentiation being unidirectional rather than reversible, yet this question remains unresolved even in prototypically hierarchical malignancies, such as acute myeloid leukemia (AML). Here, we show in murine and human models of AML that, upon perturbation of endogenous expression of the lineage-determining transcription factor PU.1 or withdrawal of established differentiation therapies, some mature leukemia cells can de-differentiate and reacquire clonogenic and leukemogenic properties. Our results reveal plasticity of CSC maturation in AML, highlighting the need to therapeutically eradicate cancer cells across a range of differentiation states.","authors":"McKenzie, MD., Ghisi, M., Oxley, EP., Ngo, S., Cimmino, L., Esnault, C., Liu, R., Salmon, JM., Bell, CC., Ahmed, N., Erlichster, M., Witkowski, MT., Liu, GJ., Chopin, M., Dakic, A., Simankowicz, E., Pomilio, G., Vu, T., Krsmanovic, P., Su, S., Tian, L., Baldwin, TM., Zalcenstein, DA., DiRago, L., Wang, S., Metcalf, D., Johnstone, RW., Croker, BA., Lancaster, GI., Murphy, AJ., Naik, SH., Nutt, SL., Pospisil, V., Schroeder, T., Wall, M., Dawson, MA., Wei, AH., de Th\u00e9, H., Ritchie, ME., Zuber, J., Dickins, RA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell Stem Cell","volume":"25","issue":"2","page":"258-272.e9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26188070","title":"Pillars Article: Commitment to the B-lymphoid lineage depends on the transcription factor Pax5. Nature. 1999. 401: 556-562.","abstract":null,"authors":"Nutt, SL., Heavey, B., Rolink, AG., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Immunol","volume":"195","issue":"3","page":"766-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16571743","title":"Wiring stability of the adult Drosophila olfactory circuit after lesion.","abstract":"Neuronal wiring plasticity in response to experience or injury has been reported in many parts of the adult nervous system. For instance, visual or somatosensory cortical maps can reorganize significantly in response to peripheral lesions, yet a certain degree of stability is essential for neuronal circuits to perform their dedicated functions. Previous studies on lesion-induced neuronal reorganization have primarily focused on systems that use continuous neural maps. Here, we assess wiring plasticity in a discrete neural map represented by the adult Drosophila olfactory circuit. Using conditional expression of toxins, we genetically ablated specific classes of neurons and examined the consequences on their synaptic partners or neighboring classes in the adult antennal lobe. We find no alteration of connection specificity between olfactory receptor neurons (ORNs) and their postsynaptic targets, the projection neurons (PNs). Ablating an ORN class maintains PN dendrites within their glomerular borders, and ORN axons normally innervating an adjacent target do not expand. Likewise, ablating PN classes does not alter their partner ORN axon connectivity. Interestingly, an increase in the contralateral ORN axon terminal density occurs in response to the removal of competing ipsilateral ORNs. Therefore, plasticity in this circuit can occur but is confined within a glomerulus, thereby retaining the wiring specificity of ORNs and PNs. We conclude that, although adult olfactory neurons can undergo plastic changes in response to the loss of competition, the olfactory circuit overall is extremely stable in preserving segregated information channels in this discrete map.","authors":"Berdnik, D., Chihara, T., Couto, A., Luo, L.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Neurosci","volume":"26","issue":"13","page":"3367-76","pdf":null,"JrId":"5035","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31348016","title":"Organs by design: can bioprinting meet self-organization?","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Curated\" Owner=\"NLM\"><PMID Version=\"1\">31348016<\/PMID><DateCompleted><Year>2020<\/Year><Month>04<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>04<\/Month><Day>17<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1531-7013<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>24<\/Volume><Issue>5<\/Issue><PubDate><Year>2019<\/Year><Month>10<\/Month><\/PubDate><\/JournalIssue><Title>Current opinion in organ transplantation<\/Title><ISOAbbreviation>Curr Opin Organ Transplant<\/ISOAbbreviation><\/Journal><ArticleTitle>Organs by design: can bioprinting meet self-organization?<\/ArticleTitle><Pagination><MedlinePgn>562-567<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1097\/MOT.0000000000000679<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE OF REVIEW\">Engineering functional organs starting from stem or progenitor cells holds promise to address the urgent need for organ transplants. However, to date, the development of complex organ structures remains an open challenge.","authors":"Martin, I., Malda, J., Rivron, NC.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Curr Opin Organ Transplant","volume":"24","issue":"5","page":"562-567","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16547954","title":"Polycomb, trithorax and the decision to differentiate.","abstract":"For stem cells, life is full of potential: they have a high capacity to proliferate and a wide choice of future identities. When they differentiate, cells leave behind this freedom and become ever more committed to a single fate. Intriguingly, the Polycomb and Trithorax groups of proteins are vital to the very different natures of both stem cells and differentiated cells, but little is known about how they make the transition from one cell type to the other. A recent paper(1) throws light on this mystery, showing that the Polycomb proteins dramatically change their behaviour at a crucial moment of differentiation.","authors":"Ringrose, L.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Bioessays","volume":"28","issue":"4","page":"330-4","pdf":null,"JrId":"1014","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16533945","title":"Separase: a universal trigger for sister chromatid disjunction but not chromosome cycle progression.","abstract":"Separase is a protease whose liberation from its inhibitory chaperone Securin triggers sister chromatid disjunction at anaphase onset in yeast by cleaving cohesin's kleisin subunit. We have created conditional knockout alleles of the mouse Separase and Securin genes. Deletion of both copies of Separase but not Securin causes embryonic lethality. Loss of Securin reduces Separase activity because deletion of just one copy of the Separase gene is lethal to embryos lacking Securin. In embryonic fibroblasts, Separase depletion blocks sister chromatid separation but does not prevent other aspects of mitosis, cytokinesis, or chromosome replication. Thus, fibroblasts lacking Separase become highly polyploid. Hepatocytes stimulated to proliferate in vivo by hepatectomy also become unusually large and polyploid in the absence of Separase but are able to regenerate functional livers. Separase depletion in bone marrow causes aplasia and the presumed death of hematopoietic cells other than erythrocytes. Destruction of sister chromatid cohesion by Separase may be a universal feature of mitosis in eukaryotic cells.","authors":"Wirth, KG., Wutz, G., Kudo, NR., Desdouets, C., Zetterberg, A., Taghybeeglu, S., Seznec, J., Ducos, GM., Ricci, R., Firnberg, N., Peters, JM., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Cell Biol","volume":"172","issue":"6","page":"847-60","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16527894","title":"A balance between Raf-1 and Fas expression sets the pace of erythroid differentiation.","abstract":"Normal erythropoiesis critically depends on the balance between the renewal of precursor cells and their differentiation. If the renewal phase is shortened, the decrease in the precursor pool results in anemia; conversely, impaired differentiation increases the number of proliferating progenitors and the potential risk of leukemic transformation. Using gene ablation, we have discovered 2 self-sustaining signal transduction loops that antagonize each other and regulate erythroid progenitor proliferation and differentiation, respectively. We identify Raf-1 as the main activator of the MEK\/ERK cascade and as the key molecule in maintaining progenitor proliferation. Differentiation, in contrast, is mediated by Fas via the activation of both the ASK1\/JNK\/p38 module and the caspase cascade. The point of convergence between the 2 cascades is activated ERK, which positively feeds back on the proliferation pathway by maintaining the expression of Raf-1, while inhibiting the expression of Fas and therefore differentiation. In turn, Fas, once expressed, antagonizes proliferation by exerting a negative feedback on ERK activation and Raf-1 expression. Simultaneously, Fas-mediated caspase activation precipitates differentiation. These results identify Raf-1 and Fas as the key molecules whose expression finely tunes erythropoiesis and the extent of ERK activation as the switch that tips the balance between them.","authors":"Rubiolo, C., Piazzolla, D., Meissl, K., Beug, H., Huber, JC., Kolbus, A., Baccarini, M.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Blood","volume":"108","issue":"1","page":"152-9","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31240560","title":"A Data Structure for Real-Time Aggregation Queries of Big Brain Networks.","abstract":"Recent advances in neuro-imaging allowed big brain-initiatives and consortia to create vast resources of brain data that can be mined by researchers for their individual projects. Exploring the relationship between genes, brain circuitry, and behavior is one of the key elements of neuroscience research. This requires fusion of spatial connectivity data at varying scales, such as whole brain correlated gene expression, structural and functional connectivity. With ever-increasing resolution, these tend to exceed the past state-of-the art in size and complexity by several orders of magnitude. Since current analytical workflows in neuroscience involve time-consuming manual data-aggregation, incorporating efficient techniques for handling big connectivity data is a necessity. We propose a novel data structure enabling the interactive exploration of heterogeneous neurobiological connectivity data with billions of edges. Based on this data structure we realized Aggregation Queries, i.e. the aggregated connectivity from, to or between brain areas allows experts to compare the multimodal networks residing at different scales, or levels of hierarchically organized anatomical atlases. Executed on-demand on volumetric gene expression and connectivity data, they allow an interactive dissection of networks in real-time and based on their spatial context. The data structure is optimized in order to be accessible directly from the hard disk, since connectivity of large-scale networks typically exceeds the memory size of current consumer level PCs. This allows experts to embed and explore their own experimental data in the framework of public data resources without the need for their own large-scale infrastructure. Our data structure outperforms state-of-the-art graph engines in retrieving connectivity of arbitrary user defined local brain areas. We demonstrate the feasibility of our approach by analyzing fear-related functional neuroanatomy in mice. Further, we show its versatility by comparing multimodal brain networks linked to autism. Importantly, we achieve cross-species congruence in retrieving human psychiatric traits networks, which facilitates the selection of neural substrates to be further studied in mouse models.","authors":"Ganglberger, FJ., Kaczanowska, J., Haubensak, W., B\u00fchler, K.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Neuroinformatics","volume":"18","issue":"1","page":"131-149","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16429137","title":"Netrins guide Drosophila commissural axons at short range.","abstract":"Netrins are secreted axon guidance molecules required for commissure formation in a wide range of animal species, including Caenorhabditis elegans, Drosophila melanogaster and mice. They are generally thought to function as chemoattractants, acting at a distance to direct commissural axon growth toward the midline of the central nervous system. We show here, however, that D. melanogaster commissural axons still orient normally and reach the midline even in the complete absence of netrins, though some of them fail to cross the midline. Tethering endogenous netrin to the membrane selectively disrupts its long-range but not short-range activity, yet still allows normal commissure formation. We therefore propose that netrins act in commissural axon guidance as short-range cues that promote midline crossing, not as long-range chemoattractants.","authors":"Brankatschk, M., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nat Neurosci","volume":"9","issue":"2","page":"188-94","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16493008","title":"Clarifying the role of Stat5 in lymphoid development and Abelson-induced transformation.","abstract":"The Stat5 transcription factors Stat5a and Stat5b have been implicated in lymphoid development and transformation. Most studies have employed Stat5a\/b-deficient mice where gene targeting disrupted the first protein-coding exon, resulting in the expression of N-terminally truncated forms of Stat5a\/b (Stat5a\/b(DeltaN\/DeltaN) mice). We have now reanalyzed lymphoid development in Stat5a\/b(null\/null) mice having a complete deletion of the Stat5a\/b gene locus. The few surviving Stat5a\/b(null\/null) mice lacked CD8(+) T lymphocytes. A massive reduction of CD8(+) T cells was also found in Stat5a\/b(fl\/fl) lck-cre transgenic animals. While gammadelta T-cell receptor-positive (gammadeltaTCR(+)) cells were expressed at normal levels in Stat5a\/b(DeltaN\/DeltaN) mice, they were completely absent in Stat5a\/b(null\/null) animals. Moreover, B-cell maturation was abrogated at the pre-pro-B-cell stage in Stat5a\/b(null\/null) mice, whereas Stat5a\/b(DeltaN\/DeltaN) B-lymphoid cells developed to the early pro-B-cell stage. In vitro assays using fetal liver-cell cultures confirmed this observation. Most strikingly, Stat5a\/b(null\/null) cells were resistant to transformation and leukemia development induced by Abelson oncogenes, whereas Stat5a\/b(DeltaN\/DeltaN)-derived cells readily transformed. These findings show distinct lymphoid defects for Stat5a\/b(DeltaN\/DeltaN) and Stat5a\/b(null\/null) mice and define a novel functional role for the N-termini of Stat5a\/b in B-lymphoid transformation.","authors":"Hoelbl, A., Kovacic, B., Kerenyi, MA., Simma, O., Warsch, W., Cui, Y., Beug, H., Hennighausen, L., Moriggl, R., Sexl, V.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Blood","volume":"107","issue":"12","page":"4898-906","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15479736","title":"Hypophosphorylated SR splicing factors transiently localize around active nucleolar organizing regions in telophase daughter nuclei.","abstract":"Upon completion of mitosis, daughter nuclei assemble all of the organelles necessary for the implementation of nuclear functions. We found that upon entry into daughter nuclei, snRNPs and SR proteins do not immediately colocalize in nuclear speckles. SR proteins accumulated in patches around active nucleolar organizing regions (NORs) that we refer to as NOR-associated patches (NAPs), whereas snRNPs were enriched at other nuclear regions. NAPs formed transiently, persisting for 15-20 min before dissipating as nuclear speckles began to form in G1. In the absence of RNA polymerase II transcription, NAPs increased in size and persisted for at least 2 h, with delayed localization of SR proteins to nuclear speckles. In addition, SR proteins in NAPs are hypophosphorylated, and the SR protein kinase Clk\/STY colocalizes with SR proteins in NAPs, suggesting that phosphorylation releases SR proteins from NAPs and their initial target is transcription sites. This work demonstrates a previously unrecognized role of NAPs in splicing factor trafficking and nuclear speckle biogenesis.","authors":"Bubulya, PA., Prasanth, KV., Deerinck, TJ., Gerlich, D., Beaudouin, J., Ellisman, MH., Ellenberg, J., Spector, DL.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Cell Biol","volume":"167","issue":"1","page":"51-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-11-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16482219","title":"The mechanism of repression of the myeloid-specific c-fms gene by Pax5 during B lineage restriction.","abstract":"The transcription factor Pax5 (BSAP) is required for the expression of a B-cell-specific genetic program and for B-cell differentiation, and also to suppress genes of alternative lineages. The molecular mechanism by which repression of myeloid genes occurs during early B-lineage restriction is unknown and in this study we addressed this question. One of the genes repressed by Pax5 in B cells is the colony-stimulating factor receptor 1 gene (csf1r or c-fms). We examined the changes in chromatin caused by Pax5 activity, and we show that Pax5 is directly recruited to c-fms resulting in the rapid loss of RNA polymerase II binding, followed by loss of transcription factor binding and DNaseI hypersensitivity at all cis-regulatory elements. We also show that Pax5 targets the basal transcription machinery of c-fms by interacting with a binding site within the major transcription start sites. Our results support a model by which Pax5 does not lead to major alterations in chromatin modification, but inhibits transcription by interfering with the action of myeloid transcription factors.","authors":"Tagoh, H., Ingram, R., Wilson, N., Salvagiotto, G., Warren, AJ., Clarke, D., Busslinger, M., Bonifer, C.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"EMBO J","volume":"25","issue":"5","page":"1070-80","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22362668","title":"Induced heterodimerization and purification of two target proteins by a synthetic coiled-coil tag.","abstract":"A synthetic de novo designed heterodimeric coiled-coil was used to copurify two target fluorescent proteins, Venus and enhanced cyan fluorescent protein (ECFP). The coiled-coil consists of two 21-amino acid repetitive sequences, (EIAALEK)(3) and (KIAALKE)(3), named E3 and K3, respectively. These sequences were fused to the C-termini of ECFP or Venus followed by either a strep- or a his-tag, respectively, for affinity purification. Mixed lysates of Venus-K3 and ECFP-E3 were subjected to consecutive affinity purification and showed highly specific association between the coiled-coil pair by SDS-PAGE, gel filtration, isothermal titration calorimetry (ITC), and fluorescence resonance energy transfer (FRET). The tagged proteins eluted as heterodimers at the concentrations tested. FRET analysis further showed that the coiled-coil pair was stable in buffers commonly used for protein purification, including those containing high salt concentration and detergent. This study shows that the E3\/K3 pair is very well suited for the copurification of two target proteins expressed in vivo because of its high specificity: it forms exclusively heterodimers in solution, it does not interact with any cellular proteins and it is stable under different buffer conditions.","authors":"Fernandez-Rodriguez, J., Marlovits, TC.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Protein Sci","volume":"21","issue":"4","page":"511-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16467848","title":"Neuronal survival depends on EGFR signaling in cortical but not midbrain astrocytes.","abstract":"Mice lacking epidermal growth factor receptor (EGFR) develop a neurodegeneration of unknown etiology affecting exclusively the frontal cortex and olfactory bulbs. Here, we show that EGFR signaling controls cortical degeneration by regulating cortical astrocyte apoptosis. Whereas EGFR(-\/-) midbrain astrocytes are unaffected, mutant cortical astrocytes display increased apoptosis mediated by an Akt-caspase-dependent mechanism and are unable to support neuronal survival. The expression of many neurotrophic factors is unaltered in EGFR(-\/-) cortical astrocytes suggesting that neuronal loss occurs as a consequence of increased astrocyte apoptosis rather than impaired secretion of trophic factors. Neuron-specific expression of activated Ras can compensate for the deficiency of EGFR(-\/-) cortical astrocytes and prevent neuronal death. These results identify two functionally distinct astrocyte populations, which differentially depend on EGFR signaling for their survival and also for their ability to support neuronal survival. These spatial differences in astrocyte composition provide a mechanism for the region-specific neurodegeneration in EGFR(-\/-) mice.","authors":"Wagner, B., Natarajan, A., Gr\u00fcnaug, S., Kroismayr, R., Wagner, EF., Sibilia, M.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"EMBO J","volume":"25","issue":"4","page":"752-62","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20603323","title":"Disease-associated mutations in TUBA1A result in a spectrum of defects in the tubulin folding and heterodimer assembly pathway.","abstract":"Malformations of cortical development are characteristic of a plethora of diseases that includes polymicrogyria, periventricular and subcortical heterotopia and lissencephaly. Mutations in TUBA1A and TUBB2B, each a member of the multigene families that encode alpha- and beta-tubulins, have recently been implicated in these diseases. Here we examine the defects that result from nine disease-causing mutations (I188L, I238V, P263T, L286F, V303G, L397P, R402C, 402H, S419L) in TUBA1A. We show that the expression of all the mutant proteins in vitro results in the generation of tubulin heterodimers in varying yield and that these can co-polymerize with microtubules in vitro. We identify several kinds of defects that result from these mutations. Among these are various defects in the chaperone-dependent pathway leading to de novo tubulin heterodimer formation. These include a defective interaction with the chaperone prefoldin, a reduced efficiency in the generation of productive folding intermediates as a result of inefficient interaction with the cytosolic chaperonin, CCT, and, in several cases, a failure to stably interact with TBCB, one of five tubulin-specific chaperones that act downstream of CCT in the tubulin heterodimer assembly pathway. Other defects include structural instability in vitro, diminished stability in vivo, a compromised ability to co-assemble with microtubules in vivo and a suppression of microtubule growth rate in the neurites (but not the soma) of cultured neurons. Our data are consistent with the notion that some mutations in TUBA1A result in tubulin deficit, whereas others reflect compromised interactions with one or more MAPs that are essential to proper neuronal migration.","authors":"Tian, G., Jaglin, XH., Keays, DA., Francis, F., Chelly, J., Cowan, NJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Hum Mol Genet","volume":"19","issue":"18","page":"3599-613","pdf":null,"JrId":"2407","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15470252","title":"RNA polymerase II localizes in Tetrahymena thermophila meiotic micronuclei when micronuclear transcription associated with genome rearrangement occurs.","abstract":"The germ line micronucleus in Tetrahymena thermophila is transcriptionally silent in vegetatively growing cells. However, micronuclear transcription has been observed in the early (\"crescent\") stages of the sexual process, conjugation. This transcription is proposed to play a central role in identifying sites for subsequent genome rearrangements that accompany development of the somatic macronucleus from the micronucleus. RPB3 (cnjC), a gene encoding a protein homologous to the third largest subunit of RNA polymerase II (RNAP II), was previously reported to be expressed specifically during conjugation, suggesting a role in micronucleus-specific transcription. Rpb3p localized in the micronucleus only during the meiotic prophase, when micronuclear transcription occurs, and its intranuclear distribution is strikingly similar to that for previously described sites of micronuclear RNA synthesis. By contrast, Rpc5p, the homologous subunit shared by RNAPs I and III, was not detectable in the micronucleus at any stage of the life cycle. However, Rpb3p is not specific to the transcribing micronucleus. Like Rpc5p, it also localizes to macronuclei in all stages of the life cycle. Rpb3p is encoded by a unique, essential gene in Tetrahymena. Thus, RNAP II is associated with both somatic transcription and crescent transcription and probably has an important role in genome rearrangement.","authors":"Mochizuki, K., Gorovsky, MA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Eukaryot Cell","volume":"3","issue":"5","page":"1233-40","pdf":null,"JrId":"26862","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10544204","title":"Antigen receptor-induced activation and cytoskeletal rearrangement are impaired in Wiskott-Aldrich syndrome protein-deficient lymphocytes.","abstract":"The Wiskott-Aldrich syndrome protein (WASp) has been implicated in modulation of lymphocyte activation and cytoskeletal reorganization. To address the mechanisms whereby WASp subserves such functions, we have examined WASp roles in lymphocyte development and activation using mice carrying a WAS null allele (WAS(-)(\/)(-)). Enumeration of hemopoietic cells in these animals revealed total numbers of thymocytes, peripheral B and T lymphocytes, and platelets to be significantly diminished relative to wild-type mice. In the thymus, this abnormality was associated with impaired progression from the CD44(-)CD25(+) to the CD44(-)CD25(-) stage of differentiation. WASp-deficient thymocytes and T cells also exhibited impaired proliferation and interleukin (IL)-2 production in response to T cell antigen receptor (TCR) stimulation, but proliferated normally in response to phorbol ester\/ionomycin. This defect in TCR signaling was associated with a reduction in TCR-evoked upregulation of the early activation marker CD69 and in TCR-triggered apoptosis. While induction of TCR-zeta, ZAP70, and total protein tyrosine phosphorylation as well as mitogen-activated protein kinase (MAPK) and stress-activated protein\/c-Jun NH(2)-terminal kinase (SAPK\/JNK) activation appeared normal in TCR-stimulated WAS(-)(\/)(-) cells, TCR-evoked increases in intracellular calcium concentration were decreased in WASp-deficient relative to wild-type cells. WAS(-)(\/)(-) lymphocytes also manifested a marked reduction in actin polymerization and both antigen receptor capping and endocytosis after TCR stimulation, whereas WAS(-)(\/)(-) neutrophils exhibited reduced phagocytic activity. Together, these results provide evidence of roles for WASp in driving lymphocyte development, as well as in the translation of antigen receptor stimulation to proliferative or apoptotic responses, cytokine production, and cytoskeletal rearrangement. The data also reveal a role for WASp in modulating endocytosis and phagocytosis and, accordingly, suggest that the immune deficit conferred by WASp deficiency reflects the disruption of a broad range of cellular behaviors.","authors":"Zhang, J., Shehabeldin, A., da Cruz, LA., Butler, J., Somani, AK., McGavin, M., Kozieradzki, I., dos Santos, AO., Nagy, A., Grinstein, S., Penninger, JM., Siminovitch, KA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Exp Med","volume":"190","issue":"9","page":"1329-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15458642","title":"Roles of polo-like kinase 1 in the assembly of functional mitotic spindles.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15458642<\/PMID><DateCompleted><Year>2005<\/Year><Month>01<\/Month><Day>31<\/Day><\/DateCompleted><DateRevised><Year>2017<\/Year><Month>11<\/Month><Day>16<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>14<\/Volume><Issue>19<\/Issue><PubDate><Year>2004<\/Year><Month>Oct<\/Month><Day>05<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Roles of polo-like kinase 1 in the assembly of functional mitotic spindles.<\/ArticleTitle><Pagination><MedlinePgn>1712-22<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The stable association of chromosomes with both poles of the mitotic spindle (biorientation) depends on spindle pulling forces. These forces create tension across sister kinetochores and are thought to stabilize microtubule-kinetochore interactions and to silence the spindle checkpoint. Polo-like kinase 1 (Plk1) has been implicated in regulating centrosome maturation, mitotic entry, sister chromatid cohesion, the anaphase-promoting complex\/cyclosome (APC\/C), and cytokinesis, but it is unknown if Plk1 controls chromosome biorientation.","authors":"Sumara, I., Gim\u00e9nez-Abi\u00e1n, JF., Gerlich, D., Hirota, T., Kraft, C., de la Torre, C., Ellenberg, J., Peters, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"19","page":"1712-22","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24836920","title":"Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy.","abstract":"High-speed, large-scale three-dimensional (3D) imaging of neuronal activity poses a major challenge in neuroscience. Here we demonstrate simultaneous functional imaging of neuronal activity at single-neuron resolution in an entire Caenorhabditis elegans and in larval zebrafish brain. Our technique captures the dynamics of spiking neurons in volumes of \u223c700 \u03bcm \u00d7 700 \u03bcm \u00d7 200 \u03bcm at 20 Hz. Its simplicity makes it an attractive tool for high-speed volumetric calcium imaging.","authors":"Prevedel, R., Yoon, YG., Hoffmann, M., Pak, N., Wetzstein, G., Kato, S., Schr\u00f6del, T., Raskar, R., Zimmer, M., Boyden, ES., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Methods","volume":"11","issue":"7","page":"727-730","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16380111","title":"The adaptor protein X11Lalpha\/Dmint1 interacts with the PDZ-binding domain of the cell recognition protein Rst in Drosophila.","abstract":"The Drosophila cell adhesion molecule Rst plays key roles during the development of the embryonic musculature, spacing of ommatidia in the compound eye and of sensory organs on the antenna, as well as in the neuronal wiring of the optic lobe. In rst(CT) mutants lacking the cytoplasmic domain of the Rst protein, cell sorting and apoptosis in the eye are affected, suggesting a requirement of this domain for Rst function. To identify potential interacting proteins, yeast two-hybrid screens were performed using the cytoplasmic domains of Rst and its paralogue Kirre as baits. Among several putative interactors, two paralogous Drosophila PDZ motif proteins related to X11\/Mint were identified. X11\/Mint family members in C. elegans (LIN-10) and vertebrates are believed to function as adaptor proteins and to regulate the assembly of multi-subunit complexes at the synapse, thereby linking the vesicle cycle to cell adhesion. Using genetic, cell biological, and biochemical approaches, we show that the interaction of Rst with X11Lalpha is of biological significance. The proteins interact, for example, in the context of cell sorting in the pupal retina.","authors":"Vishnu, S., Hertenstein, A., Betschinger, J., Knoblich, JA., Gert de Couet, H., Fischbach, KF.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Dev Biol","volume":"289","issue":"2","page":"296-307","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10499801","title":"Identification of cohesin association sites at centromeres and along chromosome arms.","abstract":"A multisubunit cohesin complex holds sister chromatids together after DNA replication. Using chromatin immunoprecipitation, we detected cohesin association with centromeres and with discrete sites along chromosome arms from S phase until metaphase in S. cerevisiae. Short DNA sequences (130-280 bp) are sufficient to confer cohesin association. Cohesin association with a centromere depends on Mif2p, the centromere binding factor CBF3, and a centromere-specific histone variant, Cse4p. Because only active centromeres confer cohesin association with centromeric DNA, we suggest that cohesin is recruited by the same chromatin structure that confers the attachment of microtubules. Propagation of this structure might be partly epigenetic. Finally, cohesion associated with \"minimal\" centromeres is insufficient to resist the splitting force exerted by microtubules and appears to be reinforced by cohesion provided by their flanking DNA sequences.","authors":"Tanaka, T., Cosma, MP., Wirth, K., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cell","volume":"98","issue":"6","page":"847-58","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1999-10-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16364912","title":"Localization of the coactivator Cdh1 and the cullin subunit Apc2 in a cryo-electron microscopy model of vertebrate APC\/C.","abstract":"The anaphase-promoting complex\/cyclosome (APC\/C) is a ubiquitin ligase with essential functions in mitosis, meiosis, and G1 phase of the cell cycle. APC\/C recognizes substrates via coactivator proteins such as Cdh1, and bound substrates are ubiquitinated by E2 enzymes that interact with a hetero-dimer of the RING subunit Apc11 and the cullin Apc2. We have obtained three-dimensional (3D) models of human and Xenopus APC\/C by angular reconstitution and random conical tilt (RCT) analyses of negatively stained cryo-electron microscopy (cryo-EM) preparations, have determined the masses of these particles by scanning transmission electron microscopy (STEM), and have mapped the locations of Cdh1 and Apc2. These proteins are located on the same side of the asymmetric APC\/C, implying that this is where substrates are ubiquitinated. We have further identified a large flexible domain in APC\/C that adopts a different orientation upon Cdh1 binding. Cdh1 may thus activate APC\/C both by recruiting substrates and by inducing conformational changes.","authors":"Dube, P., Herzog, F., Gieffers, C., Sander, B., Riedel, D., M\u00fcller, SA., Engel, A., Peters, JM., Stark, H.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Mol Cell","volume":"20","issue":"6","page":"867-79","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2006-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16377621","title":"The role of human HtrA1 in arthritic disease.","abstract":"Human HtrA1 belongs to a widely conserved family of serine proteases involved in various aspects of protein quality control and cell fate. Although HtrA1 has been implicated in the pathology of several diseases, its precise biological functions remain to be established. Through identification of potential HtrA1 targets, studies presented herein propose that within the context of arthritis pathology HtrA1 contributes to cartilage degradation. Elevated synovial HtrA1 levels were detected in fluids obtained from rheumatoid and osteoarthritis patients, with synovial fibroblasts identified as a major source of secreted HtrA1. Mass spectrometry analysis of potential HtrA1 substrates within synovial fluids identified fibronectin as a candidate target, and treatment of fibronectin with recombinant HtrA1 led to the generation of fibronectin-degradation products that may be involved in cartilage catabolism. Consistently, treatment of synovial fibroblasts with HtrA1 or HtrA1-generated fibronectin fragments resulted in the specific induction of matrix metalloprotease 1 and matrix metalloprotease 3 expression, suggesting that HtrA1 contributes to the destruction of extracellular matrix through both direct and indirect mechanisms.","authors":"Grau, S., Richards, PJ., Kerr, B., Hughes, C., Caterson, B., Williams, AS., Junker, U., Jones, SA., Clausen, T., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Biol Chem","volume":"281","issue":"10","page":"6124-9","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9066627","title":"Folic acid-polylysine carrier improves efficacy of c-myc antisense oligodeoxynucleotides on human melanoma (M14) cells.","abstract":"Several polycations such as polylysine polymers are efficient transfection agents due to their capacity to bind DNA at physiological pH. By linking a ligand for a cell surface receptor to the polycation domain, a selective delivery of polyanionic compounds such as oligodeoxynucleotides (ODNs) without cell membrane-disruption can be achieved. Therefore, we aimed to develop this strategy to improve the uptake of oligomers in cancer cells. In particular, cationic polymers polylysine were covalently linked to a molecule of Folic Acid (FA) to deliver complexed ODNs in human melanoma (M-14) cells which express FA receptors. Since in these cells c-myc oncogene seems to play a crucial role in tumor growth, we used a c-myc antisense ODNs (15mer base antisense c-myc ODNs phosphorothioate) to inhibit its expression. The cellular uptake of the complexed ODNs was improved compared to the cellular uptake of free ODNs with a significant decrease in the intracellular c-myc protein level, resulting in a reduction of the growth rate and colony-forming capacity of the cells. No such effect was observed when ODNs in scrambled sequences were administered under the same experimental conditions. The efficacy of the uptake of the complex is receptor-related since a Transferrin-polylysine carrier produced no significant biological effects (in melanoma cells the Fe uptake is mediated by an oxidoreductase present in the cell membrane and not by Transferrin receptor pathway). Our results demonstrate that: a) By choosing the appropriate ligand for the membrane receptor present on the target cells, selective targeting of ODNs can be achieved. b) The uptake of the ODNs can be improved by receptor-mediated endocytosis. c) In a model system the complexed ODNs are capable of impairing gene product synthesis and function.","authors":"Ginobbi, P., Geiser, TA., Ombres, D., Citro, G.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Anticancer Res","volume":"17","issue":"1A","page":"29-35","pdf":null,"JrId":"592","fulltextlink":null,"preprintlink":null,"articledate":"1997-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15175151","title":"A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II.","abstract":null,"authors":"Bourbon, HM., Aguilera, A., Ansari, AZ., Asturias, FJ., Berk, AJ., Bjorklund, S., Blackwell, TK., Borggrefe, T., Carey, M., Carlson, M., Conaway, JW., Conaway, RC., Emmons, SW., Fondell, JD., Freedman, LP., Fukasawa, T., Gustafsson, CM., Han, M., He, X., Herman, PK., Hinnebusch, AG., Holmberg, S., Holstege, FC., Jaehning, JA., Kim, YJ., Kuras, L., Leutz, A., Lis, JT., Meisterernest, M., Naar, AM., Nasmyth, K., Parvin, JD., Ptashne, M., Reinberg, D., Ronne, H., Sadowski, I., Sakurai, H., Sipiczki, M., Sternberg, PW., Stillman, DJ., Strich, R., Struhl, K., Svejstrup, JQ., Tuck, S., Winston, F., Roeder, RG., Kornberg, RD.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Mol Cell","volume":"14","issue":"5","page":"553-7","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16338465","title":"Distribution of angiotensin-(1-7) and ACE2 in human placentas of normal and pathological pregnancies.","abstract":"This work was designed to study the expression of the vasodilator peptide angiotensin-(1-7) [Ang-(1-7)] and its generating enzyme (ACE2) in the uteroplacental interface. Placentas were obtained from 11 early pregnancy failures (5 miscarriages and 6 ectopic pregnancies), 15 normotensive, and 10 preeclamptic gestations. In placental villi, the main sites of immunocytochemical expression of Ang-(1-7) and ACE2 were the syncytiotrophoblast, cytotrophoblast, endothelium and vascular smooth muscle of primary and secondary villi. Syncitial Ang-(1-7) expression in samples obtained from miscarriages and ectopic pregnancies was increased compared to normal term pregnancy [2.0 (2.0-2.25 for the 25 and 75% interquartile range) vs 1.3 (1.0-1.9), p&lt;0.01]. In the maternal stroma, Ang-(1-7) and ACE2 were expressed in the invading and intravascular trophoblast and in decidual cells in all 3 groups. Ang-(1-7) and ACE2 staining was also found in arterial and venous endothelium and smooth muscle of the umbilical cord. The expression of Ang-(1-7) and ACE2 was similar in samples obtained from normal term or preeclamptic pregnancies, except for increased expression of ACE2 in umbilical arterial endothelium in preeclampsia [0.5 (0.5-0.8) vs 0.0 (0.0-0.0), p&lt;0.01]. The uteroplacental location of Ang-(1-7) and ACE2 in pregnancy suggests an autocrine function of Ang-(1-7) in the vasoactive regulation that characterizes placentation and established pregnancy.","authors":"Vald\u00e9s, G., Neves, LA., Anton, L., Corthorn, J., Chac\u00f3n, C., Germain, AM., Merrill, DC., Ferrario, CM., Sarao, R., Penninger, J., Brosnihan, KB.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Placenta","volume":"27","issue":"2-3","page":"200-7","pdf":null,"JrId":"6600","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30941720","title":"Generation and Analysis of Pluripotent Stem Cell-Derived Cardiomyocytes and Endothelial Cells for High Content Screening Purposes.","abstract":"Human-induced pluripotent stem cells (hiPSCs) and their differentiated derivatives became a new, promising source for in vitro screening techniques. Cell lines derived from healthy individuals can be applied for drug safety testing, while patient-derived cells provide a platform to model diseases in vitro and can be used as a tool for personalized medicine including specific drug efficacy testing and identification of new pharmacological targets as well as for tailoring pharmacological therapies. Efficient differentiation protocols yielding cardiomyocytes or endothelial cells derived from iPSCs have been developed recently. Phenotypic characterization and gene expression profiling of these derivatives can reveal clues for developmental and pathological questions. Moreover, functional analysis and cell-based assays using automated fluorescence imaging platform and high content analysis characterize cell type-specific profiles of hiPSC-derived cardiomyocytes (hiPSC-CM) and endothelial cells (hiPSC-EC) at the cellular and subcellular levels. This can be utilized in a platform which can provide multiple endpoint profiles of candidate compounds.","authors":"Berecz, T., Husv\u00e9th-T\u00f3th, M., Mioulane, M., Merkely, B., Ap\u00e1ti, \u00c1., F\u00f6ldes, G.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Methods Mol Biol","volume":"2150","issue":"","page":"57-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15384171","title":"New semidominant mutations that affect mouse development.","abstract":"Dominantly acting mutations that produce visible phenotypes are frequently recovered, either during routine maintenance of colonies or from mutagenesis experiments. We have studied 12 dominant mouse mutations that cause a tail dysmorphology, a coat spotting phenotype, or a combination of these. The majority of these mutations act in a semidominant manner with the homozygous state associated with embryonic lethality and a visible phenotype at or before midgestation. The homozygous phenotypes include axis truncation and neural crest cell defects, as may be expected from the heterozygous phenotypes. The majority of mutations, however, also produced other phenotypes that include neural tube closure defects and aberrant heart looping. In one coat spotting mutant the homozygous condition is lethal before neural crest cell production commences. The mutated genes often function in processes additional to those alluded to by the heterozygous phenotype.","authors":"Bogani, D., Warr, N., Elms, P., Davies, J., Tymowska-Lalanne, Z., Goldsworthy, M., Cox, RD., Keays, DA., Flint, J., Wilson, V., Nolan, P., Arkell, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genesis","volume":"40","issue":"2","page":"109-117","pdf":null,"JrId":"21590","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16319112","title":"Pax 2\/8-regulated Gata 3 expression is necessary for morphogenesis and guidance of the nephric duct in the developing kidney.","abstract":"The mammalian pro- and mesonephros are transient embryonic kidneys essential for urogenital system development. The nephric (Wolffian) duct, which is a central constituent of both structures, elongates caudally along a stereotypical path to reach the hindlimb level where it induces metanephros (adult kidney) formation, while the remaining duct gives rise to the male genital tract (epidydimis, vas deferens). The transcription factors Pax2 and Pax8 are essential for the initiation of pro- and mesonephros development. In a cDNA microarray screen for genes specifically expressed in the pro\/mesonephros and regulated by Pax proteins, we identified Gata3, a transcription factor gene associated with hypoparathyroidism, deafness and renal anomaly (HDR) syndrome. Gata3 is already expressed in the pronephric anlage, together with Pax2 and Pax8, suggesting that it may be a direct Pax2\/8 target gene. Inactivation of Gata3 by insertion of an Ires-GFP reporter gene resulted in a massive increase in nephric duct cellularity, which was accompanied by enhanced cell proliferation and aberrant elongation of the nephric duct. Interestingly, however, the nephrogenic cord extended, with delayed kinetics, along the entire caudal path up to the level of the hindlimb bud, indicating that extension of the nephric duct and cord is controlled by different guidance cues. At the molecular level, the nephric duct of Gata3(-\/-) embryos is characterized by the loss of Ret expression and signaling, which may contribute to the guidance defect of the nephric duct. Together, these results define Gata3 as a key regulator of nephric duct morphogenesis and guidance in the pro\/mesonephric kidney.","authors":"Grote, D., Souabni, A., Busslinger, M., Bouchard, M.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Development","volume":"133","issue":"1","page":"53-61","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30620907","title":"No evidence for a magnetite-based magnetoreceptor in the lagena of pigeons.","abstract":"It is well established that an array of avian species sense the Earth's magnetic field and use this information for orientation and navigation. While the existence of a magnetic sense can no longer be disputed, the underlying cellular and biophysical basis remains unknown. It has been proposed that pigeons exploit a magnetoreceptor based on magnetite crystals (Fe3O4) that are located within the lagena [1], a sensory epithelium of the inner ear. It has been hypothesised that these magnetic crystals form a bed of otoconia that stimulate hair cells transducing magnetic information into a neuronal impulse. We performed a systematic high-sensitivity screen for iron in the pigeon lagena using synchrotron X-ray fluorescence microscopy coupled with the analysis of serial sections by transmission electron microscopy. We find no evidence for extracellular magnetic otoconia or intracellular magnetite crystals, suggesting that if an inner ear magnetic sensor does exist it relies on a different biophysical mechanism.","authors":"Malkemper, EP., Kagerbauer, D., Ushakova, L., Nimpf, S., Pichler, P., Treiber, CD., de Jonge, M., Shaw, J., Keays, DA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Curr Biol","volume":"29","issue":"1","page":"R14-R15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15380095","title":"Comparative analysis of cytokinesis in budding yeast, fission yeast and animal cells.","abstract":"Cytokinesis is a temporally and spatially regulated process through which the cellular constituents of the mother cell are partitioned into two daughter cells, permitting an increase in cell number. When cytokinesis occurs in a polarized cell it can create daughters with distinct fates. In eukaryotes, cytokinesis is carried out by the coordinated action of a cortical actomyosin contractile ring and targeted membrane deposition. Recent use of model organisms with facile genetics and improved light-microscopy methods has led to the identification and functional characterization of many proteins involved in cytokinesis. To date, this analysis indicates that some of the basic components involved in cytokinesis are conserved from yeast to humans, although their organization into functional machinery that drives cytokinesis and the associated regulatory mechanisms bear species-specific features. Here, we briefly review the current status of knowledge of cytokinesis in the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe and animal cells, in an attempt to highlight both the common and the unique features. Although these organisms diverged from a common ancestor about a billion years ago, there are eukaryotes that are far more divergent. To evaluate the overall evolutionary conservation of cytokinesis, it will be necessary to include representatives of these divergent branches. Nevertheless, the three species discussed here provide substantial mechanistic diversity.","authors":"Balasubramanian, MK., Bi, E., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"18","page":"R806-18","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16275332","title":"Identification of cell cycle-dependent phosphorylation sites on the anaphase-promoting complex\/cyclosome by mass spectrometry.","abstract":"Phosphorylation has an almost universal role in controlling the properties of proteins that govern progression through mitosis and meiosis. The ubiquitin ligase anaphase-promoting complex\/cyclosome (APC\/C) and its cofactors are no exception to this rule. However, it is poorly understood how APC\/C pathway components are regulated by phosphorylation, i.e., little is known about which amino acid residues on subunits and regulators of the APC\/C are phosphorylated by which kinase, when during the cell cycle, where in the cell, and with which functional consequence. As a first step toward answering these questions we have established a procedure for the sensitive and relatively rapid identification of phosphorylation sites on small microgram amounts of the APC\/C and on associated regulatory proteins. This procedure will enable studies on the dynamic changes of APC\/C phosphorylation during the cell cycle and, in conjunction with chemical biology approaches, will allow one to determine which phosphorylation sites depend on the presence of which kinase activity in living cells.","authors":"Herzog, F., Mechtler, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Methods Enzymol","volume":"398","issue":null,"page":"231-45","pdf":null,"JrId":"5787","fulltextlink":null,"preprintlink":null,"articledate":"2005-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16300647","title":"Emerging themes of cancer stem cells: editorial--overview.","abstract":"","authors":"Sarraf, C.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell Prolif","volume":"38","issue":"6","page":"343-5","pdf":null,"JrId":"1103","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15352229","title":"Automated, on-line two-dimensional nano liquid chromatography tandem mass spectrometry for rapid analysis of complex protein digests.","abstract":"Evaluation of cellular processes and their changes at the level of protein expression and post-translational modifications may allow identification of novel proteins and the mechanisms involved in pathogenic processes. However, the number of proteins and, after tryptic digestion, of peptides from a single cell can be tremendously high. Separation and analysis of such complex peptide mixtures can be performed using multidimensional separation techniques such as two-dimensional gel electrophoresis or two-dimensional-high-performance liquid chromatography (2-D-HPLC). The aim of this work was to establish a fully automated on-line 2-D-HPLC separation method with column switching for the separation of complex tryptic digests. A model mixture of five proteins as well as a nuclear matrix protein sample were digested with trypsin and separated using a strong cation exchange (SCX) column in the first dimension and nano reversed phase in the second dimension. Separated peptides were detected using an ion trap mass spectrometer. The advantages of this new fully automated method are rapid sample loading, the possibility of injecting large volumes and no introduction of salt into the mass spectrometer. Furthermore, column switching allows the independent control and optimization of the two dimensions independently.","authors":"Mitulovi\u0107, G., Stingl, C., Smoluch, M., Swart, R., Chervet, JP., Steinmacher, I., Gerner, C., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Proteomics","volume":"4","issue":"9","page":"2545-57","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2005-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16281037","title":"Suppression of Polycomb group proteins by JNK signalling induces transdetermination in Drosophila imaginal discs.","abstract":"During the regeneration of Drosophila imaginal discs, cellular identities can switch fate in a process known as transdetermination. For leg-to-wing transdetermination, the underlying mechanism involves morphogens such as Wingless that, when activated outside their normal context, induce ectopic expression of the wing-specific selector gene vestigial. Polycomb group (PcG) proteins maintain cellular fates by controlling the expression patterns of homeotic genes and other developmental regulators. Here we report that transdetermination events are coupled to PcG regulation. We show that the frequency of transdetermination is enhanced in PcG mutant flies. Downregulation of PcG function, as monitored by the reactivation of a silent PcG-regulated reporter gene, is observed in transdetermined cells. This downregulation is directly controlled by the Jun amino-terminal kinase (JNK) signalling pathway, which is activated in cells undergoing regeneration. Accordingly, transdetermination frequency is reduced in a JNK mutant background. This regulatory interaction also occurs in mammalian cells, indicating that the role of this signalling cascade in remodelling cellular fates may be conserved.","authors":"Lee, N., Maurange, C., Ringrose, L., Paro, R.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nature","volume":"438","issue":"7065","page":"234-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16275763","title":"Autoamplification of NFATc1 expression determines its essential role in bone homeostasis.","abstract":"NFATc1 and NFATc2 are functionally redundant in the immune system, but it was suggested that NFATc1 is required exclusively for differentiation of osteoclasts in the skeletal system. Here we provide genetic evidence that NFATc1 is essential for osteoclast differentiation in vivo by adoptive transfer of NFATc1(-\/-) hematopoietic stem cells to osteoclast-deficient Fos(-\/-) mice, and by Fos(-\/-) blastocyst complementation, thus avoiding the embryonic lethality of NFATc1(-\/-) mice. However, in vitro osteoclastogenesis in NFATc1-deficient cells was rescued by ectopic expression of NFATc2. The discrepancy between the in vivo essential role of NFATc1 and the in vitro effect of NFATc2 was attributed to selective autoregulation of the NFATc1 gene by NFAT through its promoter region. This suggested that an epigenetic mechanism contributes to the essential function of NFATc1 in cell lineage commitment. Thus, this study establishes that NFATc1 represents a potential therapeutic target for bone disease and reveals a mechanism that underlies the essential role of NFATc1 in bone homeostasis.","authors":"Asagiri, M., Sato, K., Usami, T., Ochi, S., Nishina, H., Yoshida, H., Morita, I., Wagner, EF., Mak, TW., Serfling, E., Takayanagi, H.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Exp Med","volume":"202","issue":"9","page":"1261-9","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30369479","title":"[The effect of lnc-RAP3 on 3T3-L1 preadipocyte differentiation in mouse].","abstract":"The long non-coding RNAs (lncRNAs) are a type of RNAs with more than 200nt in length and without any long open reading frame, but often have mRNA structural features. They can regulate the expression of target genes in different manners at the transcriptional and post-transcriptional levels. In recent years, various studies demonstrated that lncRNAs play crucial roles in adipogenesis. The long non-coding RNA, lnc-RAP3, located on the mouse chromosome 17, possesses a significantly differential expression pattern during mouse adipocyte differentiation; but its specific biological function (s) remains unclear. To investigate the effect of lnc-RAP3 on adipogenesis in the mouse 3T3-L1 preadipocytes, we first constructed a eukaryotic expression vector pcDNA3.1-RAP3. pcDNA3.1-RAP3 and synthetic RAP3-siRNAs were transfected individually into 3T3-L1 preadipocytes by Lipofectamine <sup>TM<\/sup> 2000, thereby over-expressing and knocking-down lnc-RAP3 expression, respectively. The transfected preadipocytes were induced to undergo adipogenic differentiation. Oil Red O staining and qRT-PCR were used to detect the effects of lnc-RAP3 overexpression\/knockdown on 3T3-L1 preadipocyte differentiation. The results showed that overexpression of lnc-RAP3 led to a notable decrease in lipid accumulation (P&lt;0.05) and remarkably reduced the mRNA expression levels of C\/EBP\u03b1, Glut4, PPAR\u03b3, LPL and FAS on day 0, day 2, and day 4 post differentiation (P&lt;0.05, P&lt;0.01). In contrast, quantitative analysis of Oil Red O on day 4 of differentiation revealed that inhibition of lnc-RAP3 increased the formation of neutral lipid droplets (P&lt;0.05). In addition, silencing lnc-RAP3 also significantly increased the mRNA expression of PPAR\u03b3, LPL, C\/EBP\u03b1, FAS and Glut4 on day 0 and day 2 post differentiation (P&lt;0.05, P&lt;0.01). Our study suggests that lnc-RAP3 might suppress 3T3-L1 preadipocyte differentiation by affecting the expression of the genes involved in adipogenic differentiation.","authors":"Li, H., Feng, JC., Li, GL., Wang, X., Li, MZ., Liu, HF.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Yi Chuan","volume":"40","issue":"9","page":"758-766","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15350216","title":"Distinct roles for JNK1 and JNK2 in regulating JNK activity and c-Jun-dependent cell proliferation.","abstract":"Different c-Jun N-terminal kinases (JNKs) are activated by a plethora of signals and phosphorylate substrates such as c-Jun, which is required for efficient cell cycle progression. Although JNK1 and JNK2 were shown to differentially regulate fibroblast proliferation, the underlying mechanistic basis remains unclear. We found that Jnk2-\/- fibroblasts exit G1 and enter S phase earlier than wild-type counterparts, while Jnk1-\/- cells show the inverse phenotype. Moreover, Jnk2-\/- erythroblasts also exhibit a proliferative advantage. JNK2 deficiency results in elevated c-Jun phosphorylation and stability, whereas the absence of JNK1 reduces c-Jun phosphorylation and stability. Re-expression of JNK2 in Jnk2-\/- cells reverses the JNK2 null phenotype, whereas ectopic expression of JNK1 augments it. JNK2 is preferentially bound to c-Jun in unstimulated cells, thereby contributing to c-Jun degradation. In contrast, JNK1 becomes the major c-Jun interacting kinase after cell stimulation. These data provide mechanistic insights into the distinct roles of different JNK isoforms.","authors":"Sabapathy, K., Hochedlinger, K., Nam, SY., Bauer, A., Karin, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Mol Cell","volume":"15","issue":"5","page":"713-25","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30096312","title":"Divergent Routes toward Wnt and R-spondin Niche Independency during Human Gastric Carcinogenesis.","abstract":"Recent sequencing analyses have shed light on heterogeneous patterns of genomic aberrations in human gastric cancers (GCs). To explore how individual genetic events translate into cancer phenotypes, we established a biological library consisting of genetically engineered gastric organoids carrying various GC mutations and 37 patient-derived organoid lines, including rare genomically stable GCs. Phenotype analyses of GC organoids revealed divergent genetic and epigenetic routes to gain Wnt and R-spondin niche independency. An unbiased phenotype-based genetic screening identified a significant association between CDH1\/TP53 compound mutations and the R-spondin independency that was functionally validated by CRISPR-based knockout. Xenografting of GC organoids further established the feasibility of Wnt-targeting therapy for Wnt-dependent GCs. Our results collectively demonstrate that multifaceted genetic abnormalities render human GCs independent of the stem cell niche and highlight the validity of the genotype-phenotype screening strategy in gaining deeper understanding of human cancers.","authors":"Nanki, K., Toshimitsu, K., Takano, A., Fujii, M., Shimokawa, M., Ohta, Y., Matano, M., Seino, T., Nishikori, S., Ishikawa, K., Kawasaki, K., Togasaki, K., Takahashi, S., Sukawa, Y., Ishida, H., Sugimoto, S., Kawakubo, H., Kim, J., Kitagawa, Y., Sekine, S., Koo, BK., Kanai, T., Sato, T.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell","volume":"174","issue":"4","page":"856-869.e17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16204248","title":"TIS7 regulation of the beta-catenin\/Tcf-4 target gene osteopontin (OPN) is histone deacetylase-dependent.","abstract":"12-O-Tetradecanoylphorbol-13-acetate-induced sequence 7 (TIS7) acts as a transcriptional co-repressor interacting with SIN3, the histone deacetylase-containing complex. The overexpression of TIS7 down-regulates expression of a specific set of genes. Homozygous deletion of this gene in mice delays injury-induced muscle regeneration and inhibits muscle satellite cell differentiation and fusion of myoblasts in vitro. Osteopontin (OPN), a known beta-catenin\/T cell factor-4 (Tcf-4) downstream target gene, is up-regulated in tumors and in cells with increased motility such as muscle cells. OPN promoter sequence contains binding sites for Sp1, glucocorticoid receptor, E-box-binding factors, octamer motif-binding protein, c-Myc, and other transcription factors. Previously we have shown that TIS7 regulates the OPN expression through the inhibition of the Sp1-activating effects. Here we show that TIS7 has the capacity to inhibit OPN expression also through Lef-1, the second identified OPN regulatory element. TIS7 has the capacity to down-regulate beta-catenin\/Tcf-4 transcriptional activity. TIS7 homologous deletion in mouse embryonic fibroblasts increased not only the TOPflash reporter gene transcriptional activity but also the expression of c-Myc and OPN. Furthermore, we show that TIS7 overexpression leads to the beta-catenin interaction with enzymatically active histone deacetylases. We propose that TIS7 down-regulates the beta-catenin\/Tcf-4 transcriptional activity via its interaction with histone deacetylase-containing complex thereby inhibiting the expression of beta-catenin downstream target genes such as c-Myc and OPN. We hypothesize that TIS7 as a negative regulator of transcriptional activity represses expression of OPN and beta-catenin\/Tcf-4 target genes, which are involved in myogenesis, muscle maintenance, and regeneration in a histone deacetylase dependent manner.","authors":"Vietor, I., Kurzbauer, R., Brosch, G., Huber, LA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Biol Chem","volume":"280","issue":"48","page":"39795-801","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2006-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30250825","title":"Transforming Growth Factor-\u03b2-Induced Cell Plasticity in Liver Fibrosis and Hepatocarcinogenesis.","abstract":"The Transforming Growth Factor-beta (TGF-\u03b2) family plays relevant roles in the regulation of different cellular processes that are essential for tissue and organ homeostasis. In the case of the liver, TGF-\u03b2 signaling participates in different stages of disease progression, from initial liver injury toward fibrosis, cirrhosis and cancer. When a chronic injury takes place, mobilization of lymphocytes and other inflammatory cells occur, thus setting the stage for persistence of an inflammatory response. Macrophages produce profibrotic mediators, among them, TGF-\u03b2, which is responsible for activation -transdifferentiation- of quiescent hepatic stellate cells (HSC) to a myofibroblast (MFB) phenotype. MFBs are the principal source of extracellular matrix protein (ECM) accumulation and prominent mediators of fibrogenesis. TGF-\u03b2 also mediates an epithelial-mesenchymal transition (EMT) process in hepatocytes that may contribute, directly or indirectly, to increase the MFB population. In hepatocarcinogenesis, TGF-\u03b2 plays a dual role, behaving as a suppressor factor at early stages, but contributing to later tumor progression, once cells escape from its cytostatic effects. As part of its potential pro-tumorigenic actions, TGF-\u03b2 induces EMT in liver tumor cells, which increases its pro-migratory and invasive potential. In parallel, TGF-\u03b2 also induces changes in tumor cell plasticity, conferring properties of a migratory tumor initiating cell (TIC). The main aim of this review is to shed light about the pleiotropic actions of TGF-\u03b2 that explain its effects on the different liver cell populations. The cross-talk with other signaling pathways that contribute to TGF-\u03b2 effects, in particular the Epidermal Growth Factor Receptor (EGFR), will be presented. Finally, we will discuss the rationale for targeting the TGF-\u03b2 pathway in liver pathologies.","authors":"Fabregat, I., Caballero-D\u00edaz, D.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Front Oncol","volume":"8","issue":"","page":"357","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11413461","title":"Asymmetric cell division during animal development.","abstract":"Although most cells produce two equal daughters during mitosis, some can divide asymmetrically by segregating protein determinants into one of their two daughter cells. Interesting parallels exist between such asymmetric divisions and the polarity established in epithelial cells, and heterotrimeric G proteins might connect these aspects of cell polarity. The discovery of asymmetrically segregating proteins in vertebrates indicates that the results obtained in invertebrate model organisms might also apply to mammalian stem cells.","authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Rev Mol Cell Biol","volume":"2","issue":"1","page":"11-20","pdf":null,"JrId":"22271","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29946135","title":"Eukaryotic core promoters and the functional basis of transcription initiation.","abstract":"RNA polymerase II (Pol II) core promoters are specialized DNA sequences at transcription start sites of protein-coding and non-coding genes that support the assembly of the transcription machinery and transcription initiation. They enable the highly regulated transcription of genes by selectively integrating regulatory cues from distal enhancers and their associated regulatory proteins. In this Review, we discuss the defining properties of gene core promoters, including their sequence features, chromatin architecture and transcription initiation patterns. We provide an overview of molecular mechanisms underlying the function and regulation of core promoters and their emerging functional diversity, which defines distinct transcription programmes. On the basis of the established properties of gene core promoters, we discuss transcription start sites within enhancers and integrate recent results obtained from dedicated functional assays to propose a functional model of transcription initiation. This model can explain the nature and function of transcription initiation at gene starts and at enhancers and can explain the different roles of core promoters, of Pol II and its associated factors and of the activating cues provided by enhancers and the transcription factors and cofactors they recruit.","authors":"Haberle, V., Stark, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Rev Mol Cell Biol","volume":"19","issue":"10","page":"621-637","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15314684","title":"Critical roles of c-Jun signaling in regulation of NFAT family and RANKL-regulated osteoclast differentiation.","abstract":"Receptor activator of NF-kappaB ligand (RANKL) plays an essential role in osteoclast formation and bone resorption. Although genetic and biochemical studies indicate that RANKL regulates osteoclast differentiation by activating receptor activator of NF-kappaB and associated signaling molecules, the molecular mechanisms of RANKL-regulated osteoclast differentiation have not yet been fully established. We investigated the role of the transcription factor c-Jun, which is activated by RANKL, in osteoclastogenesis using transgenic mice expressing dominant-negative c-Jun specifically in the osteoclast lineage. We found that the transgenic mice manifested severe osteopetrosis due to impaired osteoclastogenesis. Blockade of c-Jun signaling also markedly inhibited soluble RANKL-induced osteoclast differentiation in vitro. Overexpression of nuclear factor of activated T cells 1 (NFAT1) (NFATc2\/NFATp) or NFAT2 (NFATc1\/NFATc) promoted differentiation of osteoclast precursor cells into tartrate-resistant acid phosphatase-positive (TRAP-positive) multinucleated osteoclast-like cells even in the absence of RANKL. Overexpression of NFAT1 also markedly transactivated the TRAP gene promoter. These osteoclastogenic activities of NFAT were abrogated by overexpression of dominant-negative c-Jun. Importantly, osteoclast differentiation and induction of NFAT2 expression by NFAT1 overexpression or soluble RANKL treatment were profoundly diminished in spleen cells of the transgenic mice. Collectively, these results indicate that c-Jun signaling in cooperation with NFAT is crucial for RANKL-regulated osteoclast differentiation.","authors":"Ikeda, F., Nishimura, R., Matsubara, T., Tanaka, S., Inoue, J., Reddy, SV., Hata, K., Yamashita, K., Hiraga, T., Watanabe, T., Kukita, T., Yoshioka, K., Rao, A., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Clin Invest","volume":"114","issue":"4","page":"475-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16137928","title":"Sec15, a component of the exocyst, promotes notch signaling during the asymmetric division of Drosophila sensory organ precursors.","abstract":"Asymmetric division of sensory organ precursors (SOPs) in Drosophila generates different cell types of the mature sensory organ. In a genetic screen designed to identify novel players in this process, we have isolated a mutation in Drosophila sec15, which encodes a component of the exocyst, an evolutionarily conserved complex implicated in intracellular vesicle transport. sec15(-) sensory organs contain extra neurons at the expense of support cells, a phenotype consistent with loss of Notch signaling. A vesicular compartment containing Notch, Sanpodo, and endocytosed Delta accumulates in basal areas of mutant SOPs. Based on the dynamic traffic of Sec15, its colocalization with the recycling endosomal marker Rab11, and the aberrant distribution of Rab11 in sec15 clones, we propose that a defect in Delta recycling causes cell fate transformation in sec15(-) sensory lineages. Our data indicate that Sec15 mediates a specific vesicle trafficking event to ensure proper neuronal fate specification in Drosophila.","authors":"Jafar-Nejad, H., Andrews, HK., Acar, M., Bayat, V., Wirtz-Peitz, F., Mehta, SQ., Knoblich, JA., Bellen, HJ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Dev Cell","volume":"9","issue":"3","page":"351-63","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16117651","title":"Trilogies of histone lysine methylation as epigenetic landmarks of the eukaryotic genome.","abstract":null,"authors":"Lachner, M., Sengupta, R., Schotta, G., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"69","issue":null,"page":"209-18","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"2005-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10488058","title":"Susceptibility to myocarditis is dependent on the response of alphabeta T lymphocytes to coxsackieviral infection.","abstract":"Viral myocarditis is an important cause of heart failure and dilated cardiomyopathy. T lymphocytes are implicated in myocardial damage in murine models of coxsackievirus B3 (CVB3) myocarditis. We used knockout mice lacking CD4 (CD4(-\/-)), CD8 (CD8(-\/-)), both coreceptors (CD4(-\/-)CD8(-\/-)), or the T-cell receptor beta chain (TCRbeta(-\/-)) to address the contribution of T-cell subpopulations to host susceptibility to CVB3 myocarditis. Severity of disease was magnified in CD8(-\/-) mice but attenuated in CD4(-\/-) mice, consistent with a pathogenic role for CD4(+) lymphocytes. Elimination of both CD4 and CD8 molecules from T lymphocytes by genetic knockout better protected mice from myocarditis, demonstrating that both CD4(+) and CD8(+) T cells contribute to host susceptibility. The same benefit occurred in TCRbeta(-\/-) mice, with prolonged survival and minimal myocardial disease observed after CVB3 infection. Elevated interferon-gamma and decreased tumor necrosis factor-alpha expression are associated with attenuated myocardial damage in CD4(-\/-)CD8(-\/-) mice. These results show that the presence of TCRalphabeta(+) T cells enhances host susceptibility to myocarditis. The severity of myocardial damage and associated mortality are dependent on the predominant T-cell type available to respond to CVB3 infection. One mechanism by which CD4(+) and CD8(+) T-cell subsets influence the pathogenesis of myocarditis may involve specific cytokine expression patterns.","authors":"Opavsky, MA., Penninger, J., Aitken, K., Wen, WH., Dawood, F., Mak, T., Liu, P.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Circ Res","volume":"85","issue":"6","page":"551-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16009709","title":"EZH2 and histone 3 trimethyl lysine 27 associated with Il4 and Il13 gene silencing in Th1 cells.","abstract":"Differentiation of na\u00efve CD4 T cells toward the T helper 1 (T(H)1) and T helper 2 (T(H)2) fates involves the transcriptional repression and enhancement, respectively, of Il4 and Il13, adjacent chromosome 11 genes encoding the canonical T(H)2 cytokines interleukin-4 and interleukin-13. Proper execution of this developmental fate choice during immune responses is critical to host defense and, when misregulated, leads to susceptibility to infectious microbes and to allergic and autoimmune diseases. Here, using chromatin immunoprecipitation and real time reverse transcription PCR we identify the Polycomb family histone methyltransferase EZH2 as the enzyme responsible for methylating lysine 27 of histone H3 at the Il4-Il13 locus of T(H)1 but not T(H)2 cells, implicating EZH2 in the mechanism of Il4 and Il13 transcriptional silencing.","authors":"Koyanagi, M., Baguet, A., Martens, J., Margueron, R., Jenuwein, T., Bix, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Biol Chem","volume":"280","issue":"36","page":"31470-7","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16979678","title":"Therapeutic applications of conotoxins that target the neuronal nicotinic acetylcholine receptor.","abstract":"Pain therapeutics discovered by molecular mining of the expressed genome of Australian predatory cone snails are providing lead compounds for the treatment of neurological diseases such as multiple sclerosis, shingles, diabetic neuropathy and other painful neurological conditions. The high specificity exhibited by these novel compounds for neuronal receptors and ion channels in the brain and nervous system indicates the high degree of selectivity that this class of neuropeptides can be expected to show when used therapeutically in humans. A lead compound, ACV1 (conotoxin Vc1.1 from Conus victoriae), has entered Phase II clinical trials and is being developed for the treatment for neuropathic pain. ACV1 will be targeted initially for the treatment of sciatica, shingles and diabetic neuropathy. The compound is a 16 amino acid peptide [Sandall et al., 2003. A novel alpha-conotoxin identified by gene sequencing is active in suppressing the vascular response to selective stimulation of sensory nerves in vivo. Biochemistry 42, 6904-6911], an antagonist of neuronal nicotinic acetylcholine receptors. It has potent analgesic activity following subcutaneous or intramuscular administration in several preclinical animal models of human neuropathic pain [Satkunanathan et al., 2005. Alpha conotoxin Vc1.1 alleviates neuropathic pain and accelerates functional recovery of injured neurons. Brain. Res. 1059, 149-158]. ACV1 may act as an analgesic by decreasing ectopic excitation in sensory nerves. In addition ACV1 appears to accelerate the recovery of injured nerves and tissues.","authors":"Livett, BG., Sandall, DW., Keays, D., Down, J., Gayler, KR., Satkunanathan, N., Khalil, Z.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Toxicon","volume":"48","issue":"7","page":"810-29","pdf":null,"JrId":"7772","fulltextlink":null,"preprintlink":null,"articledate":"2007-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16099152","title":"The comings and goings of actin: coupling protrusion and retraction in cell motility.","abstract":"Cells utilize actin filaments to produce protrusive and contractile arrays that cooperate to drive cell motility. The generation of the two arrays and the coupling between them result from the unique properties of the lamellipodium, a protrusive leaflet of cytoplasm at the cell edge. From the lamellipodium into the lamella behind, there is a transition from a fast retrograde flow of actin polymer driven by polymerization to a slow flow driven by the interaction of anti-parallel arrays of actin with myosin. In addition to driving protrusion, the lamellipodium appears to play a role in supplying filaments to the lamella for the assembly of the contractile network required for traction.","authors":"Small, JV., Resch, GP.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Opin Cell Biol","volume":"17","issue":"5","page":"517-23","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"2005-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16098727","title":"Molecular requirements for epithelial-mesenchymal transition during tumor progression.","abstract":"Epithelial-mesenchymal transitions (EMTs) occur as key steps during embryonic morphogenesis, and are now implicated in the progression of primary tumors towards metastases. Recent advances have fostered a more detailed understanding of molecular mechanisms and networks governing EMT in tumor progression. Besides TGFbeta and RTK\/Ras signaling, autocrine factors and Wnt-, Notch-, Hedgehog- and NF-kappaB-dependent pathways were found to contribute to EMT. Repression of E-cadherin by transcriptional regulators such as Snail or Twist emerges as one critical step driving EMT, and this stage is currently being molecularly linked with many of the new players. Increasing evidence suggests that EMT plays a specific role in the migration of cells from a primary tumor into the circulation and may provide a rationale for developing more effective cancer therapies.","authors":"Huber, MA., Kraut, N., Beug, H.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Opin Cell Biol","volume":"17","issue":"5","page":"548-58","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"2005-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16085484","title":"MicroRNAs: Loquacious speaks out.","abstract":"In Drosophila, Dicer-2 requires the double-stranded RNA binding protein R2D2, to mediate the assembly of short interfering RNAs into the RNA-induced silencing complex. New data show that Dicer-1 also requires a double-stranded RNA binding protein called Loquacious for efficient microRNA-mediated gene silencing.","authors":"Leuschner, PJ., Obernosterer, G., Martinez, J.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"15","page":"R603-5","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16079825","title":"Neurobiology: getting axons going.","abstract":"","authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nature","volume":"436","issue":"7051","page":"632-3","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2005-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29146670","title":"Three-Vessel Assessment of Coronary Microvascular Dysfunction in Patients With Clinical Suspicion of Ischemia: Prospective Observational Study With the Index of Microcirculatory Resistance.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">29146670<\/PMID><DateCompleted><Year>2018<\/Year><Month>07<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>07<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1941-7632<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>10<\/Volume><Issue>11<\/Issue><PubDate><Year>2017<\/Year><Month>Nov<\/Month><\/PubDate><\/JournalIssue><Title>Circulation. Cardiovascular interventions<\/Title><ISOAbbreviation>Circ Cardiovasc Interv<\/ISOAbbreviation><\/Journal><ArticleTitle>Three-Vessel Assessment of Coronary Microvascular Dysfunction in Patients With Clinical Suspicion of Ischemia: Prospective Observational Study With the Index of Microcirculatory Resistance.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">e005445<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/CIRCINTERVENTIONS.117.005445<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Difficulty directly visualizing the coronary microvasculature as opposed to the epicardial coronary artery makes its assessment challenging. The goal of this study is to measure the index of microcirculatory resistance (IMR) in all 3 major coronary vessels to identify the clinical and angiographic predictors of an abnormal IMR.","authors":"Kobayashi, Y., Lee, JM., Fearon, WF., Lee, JH., Nishi, T., Choi, DH., Zimmermann, FM., Jung, JH., Lee, HJ., Doh, JH., Nam, CW., Shin, ES., Koo, BK.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Circ Cardiovasc Interv","volume":"10","issue":"11","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10487860","title":"Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">10487860<\/PMID><DateCompleted><Year>1999<\/Year><Month>12<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>05<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">1367-4803<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>15<\/Volume><Issue>7-8<\/Issue><PubDate><MedlineDate>1999 Jul-Aug<\/MedlineDate><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.<\/ArticleTitle><Pagination><MedlinePgn>528-35<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"MOTIVATION\" NlmCategory=\"BACKGROUND\">Computer-based selection of entries from sequence databases with respect to a related functional description, e.g. with respect to a common cellular localization or contributing to the same phenotypic function, is a difficult task. Automatic semantic analysis of annotations is not only hampered by incomplete functional assignments. A major problem is that annotations are written in a rich, non-formalized language and are meant for reading by a human expert. This person can extract from the text considerably more information than is immediately apparent due to his extended biological background knowledge and logical reasoning.","authors":"Eisenhaber, F., Bork, P.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Bioinformatics","volume":"15","issue":"7-8","page":"528-35","pdf":null,"JrId":"20940","fulltextlink":null,"preprintlink":null,"articledate":"1999-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16007097","title":"A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury.","abstract":"During several months of 2003, a newly identified illness termed severe acute respiratory syndrome (SARS) spread rapidly through the world. A new coronavirus (SARS-CoV) was identified as the SARS pathogen, which triggered severe pneumonia and acute, often lethal, lung failure. Moreover, among infected individuals influenza such as the Spanish flu and the emergence of new respiratory disease viruses have caused high lethality resulting from acute lung failure. In cell lines, angiotensin-converting enzyme 2 (ACE2) has been identified as a potential SARS-CoV receptor. The high lethality of SARS-CoV infections, its enormous economic and social impact, fears of renewed outbreaks as well as the potential misuse of such viruses as biologic weapons make it paramount to understand the pathogenesis of SARS-CoV. Here we provide the first genetic proof that ACE2 is a crucial SARS-CoV receptor in vivo. SARS-CoV infections and the Spike protein of the SARS-CoV reduce ACE2 expression. Notably, injection of SARS-CoV Spike into mice worsens acute lung failure in vivo that can be attenuated by blocking the renin-angiotensin pathway. These results provide a molecular explanation why SARS-CoV infections cause severe and often lethal lung failure and suggest a rational therapy for SARS and possibly other respiratory disease viruses.","authors":"Kuba, K., Imai, Y., Rao, S., Gao, H., Guo, F., Guan, B., Huan, Y., Yang, P., Zhang, Y., Deng, W., Bao, L., Zhang, B., Liu, G., Wang, Z., Chappell, M., Liu, Y., Zheng, D., Leibbrandt, A., Wada, T., Slutsky, AS., Liu, D., Qin, C., Jiang, C., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Med","volume":"11","issue":"8","page":"875-9","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"2005-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29021213","title":"Whats, hows and whys of programmed DNA elimination in <i>Tetrahymena<\/i>.","abstract":"Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between transposable elements (TEs) and host genomes. DNA elimination in <i>Tetrahymena thermophila<\/i> removes approximately 12 000 internal eliminated sequences (IESs), which correspond to one-third of the genome, when the somatic macronucleus (MAC) differentiates from the germline micronucleus (MIC). More than half of the IESs, many of which show high similarity to TEs, are targeted for elimination in <i>cis<\/i> by the small RNA-mediated genome comparison of the MIC to the MAC. Other IESs are targeted for elimination in <i>trans<\/i> by the same small RNAs through repetitive sequences. Furthermore, the small RNA-heterochromatin feedback loop ensures robust DNA elimination. Here, we review an updated picture of the DNA elimination mechanism, discuss the physiological and evolutionary roles of DNA elimination, and outline the key questions that remain unanswered.","authors":"Noto, T., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Open Biol","volume":"7","issue":"10","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15983832","title":"Mutant meiotic chromosome core components in mice can cause apparent sexual dimorphic endpoints at prophase or X-Y defective male-specific sterility.","abstract":"Genetic modifications causing germ cell death during meiotic prophase in the mouse frequently have sexually dimorphic phenotypes where oocytes reach more advanced stages than spermatocytes. To determine to what extent these dimorphisms are due to differences in male versus female meiotic prophase development, we compared meiotic chromosome events in the two sexes in both wild-type and mutant mice. We report the abundance and time course of appearance of structural and recombination-related proteins of fetal oocyte nuclei. Oocytes at successive days post coitus show rapid, synchronous meiotic prophase development compared with the continuous spermatocyte development in adult testis. Consequently, a genetic defect requiring 2-3 days from the onset of prophase to reach arrest registers pachytene as the developmental endpoint in oocytes. Pachytene spermatocytes, on the other hand, which normally accumulate during days 4-10 after the onset of prophase, will be rare, giving the appearance of an earlier endpoint than in oocytes. We conclude that these different logistics create apparent sexually dimorphic endpoints. For more pronounced sexual dimorphisms, we examined meiotic prophase of mice with genetic modifications of meiotic chromosome core components that cause male but not female sterility. The correlations between male sterility and alterations in the organization of the sex chromosome cores and X-Y chromatin may indicate that impaired signals from the XY domain (XY chromosome cores, chromatin, dense body and sex body) may interfere with the progression of the spermatocyte through prophase. Oocytes, in the absence of the X-Y pair, do not suffer such defects.","authors":"Kolas, NK., Marcon, E., Crackower, MA., H\u00f6\u00f6g, C., Penninger, JM., Spyropoulos, B., Moens, PB.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Chromosoma","volume":"114","issue":"2","page":"92-102","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15249051","title":"Structural and functional impairment of an Old Yellow Enzyme homologue upon affinity tag incorporation.","abstract":"Recently, it has been reported that the previously uncharacterized YqjM protein from Bacillus subtilis is a true homologue of the physiologically enigmatic yeast Old Yellow Enzyme (OYE). In this study, it was also demonstrated that YqjM is involved in the oxidative stress response of B. subtilis, thus highlighting a novel direction to pursue the role of the OYE family of proteins in the cell. As part of an attempt to pin down the exact physiological role of these enzymes, both a N-terminal glutathione S-transferase and a C-terminal histidine-tagged form of the protein were created to enable \"pull-down\" assays and identify interacting partners which could aid in the functional definition. However, here we report on a comparison of the biochemical properties of the tagged forms with the native\/untagged YqjM, revealing critical differences in the catalytic activities and quaternary structure of the protein forms. UV-visible spectrophotometric features as well as steady state and individual half-reaction kinetic parameters show that the affinity tagged forms are severely impaired both in ligand binding and catalysis. Gel filtration and dynamic light scattering studies show that incorporation of a tag also has major effects on the quaternary structure of the protein by disrupting the native tetrameric conformation which may help to explain the observed differences. The study thus highlights important considerations for expression construct design when isolating members of the OYE family of proteins.","authors":"Fitzpatrick, TB., Auweter, S., Kitzing, K., Clausen, T., Amrhein, N., Macheroux, P.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Protein Expr Purif","volume":"36","issue":"2","page":"280-91","pdf":null,"JrId":"2218","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12824322","title":"Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.","abstract":"The detection of local structural patterns in proteins (e.g. active sites) can provide insights into protein function in the absence of sequence or fold similarity. Methods to detect such similarities are key during structural annotation, for example with results from Structural Genomics initiatives. PINTS (Patterns in Non-homologous Tertiary Structures, http:\/\/pints.embl.de) performs database searches for such patterns and most importantly provides a measure of statistical significance for any similarity uncovered. To aid functional annotation of proteins, we allow comparisons of pre-defined patterns against databases of complete structures and of entire structures to databases of particular residues likely to be functionally important.","authors":"Stark, A., Russell, RB.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nucleic Acids Res","volume":"31","issue":"13","page":"3341-4","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7864936","title":"Imprinting: a gamete's point of view.","abstract":"The recent isolation of imprinted mammalian genes has at last allowed the analysis of the molecular controls that regulate monoparental gene expression. Remarkably, many expectations as to how the imprinting mechanism works have been confounded by these studies. As a result, the time now seems right to reconsider our current understanding of the nature of imprinting, and how best it can be defined. Here, I discuss the past and present understanding of imprinting in the light of results obtained from studies of endogenous imprinted genes, and finally propose that the current multiplicity of imprinting terms and definitions be replaced by a single term and definition.","authors":"Barlow, DP.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Trends Genet","volume":"10","issue":"6","page":"194-9","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"1994-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28720652","title":"A framework for understanding the roles of miRNAs in animal development.","abstract":"MicroRNAs (miRNAs) contribute to the progressive changes in gene expression that occur during development. The combined loss of all miRNAs results in embryonic lethality in all animals analyzed, illustrating the crucial role that miRNAs play collectively. However, although the loss of some individual miRNAs also results in severe developmental defects, the roles of many other miRNAs have been challenging to uncover. This has been mostly attributed to their proposed function as tuners of gene expression or providers of robustness. Here, we present a view of miRNAs in the context of development as a hierarchical and canalized series of gene regulatory networks. In this scheme, only a fraction of embryonic miRNAs act at the top of this hierarchy, with their loss resulting in broad developmental defects, whereas most other miRNAs are expressed with high cellular specificity and play roles at the periphery of development, affecting the terminal features of specialized cells. This view could help to shed new light on our understanding of miRNA function in development, disease and evolution.","authors":"Alberti, C., Cochella, L.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Development","volume":"144","issue":"14","page":"2548-2559","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15960807","title":"Refinement and prediction of protein prenylation motifs.","abstract":"We refined the motifs for carboxy-terminal protein prenylation by analysis of known substrates for farnesyltransferase (FT), geranylgeranyltransferase I (GGT1) and geranylgeranyltransferase II (GGT2). In addition to the CaaX box for the first two enzymes, we identify a preceding linker region that appears constrained in physicochemical properties, requiring small or flexible, preferably hydrophilic, amino acids. Predictors were constructed on the basis of sequence and physical property profiles, including interpositional correlations, and are available as the Prenylation Prediction Suite (PrePS, http:\/\/mendel.imp.univie.ac.at\/sat\/PrePS) which also allows evaluation of evolutionary motif conservation. PrePS can predict partially overlapping substrate specificities, which is of medical importance in the case of understanding cellular action of FT inhibitors as anticancer and anti-parasite agents.","authors":"Maurer-Stroh, S., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Genome Biol","volume":"6","issue":"6","page":"R55","pdf":null,"JrId":"21904","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28522535","title":"ATP as a biological hydrotrope.","abstract":"Hydrotropes are small molecules that solubilize hydrophobic molecules in aqueous solutions. Typically, hydrotropes are amphiphilic molecules and differ from classical surfactants in that they have low cooperativity of aggregation and work at molar concentrations. Here, we show that adenosine triphosphate (ATP) has properties of a biological hydrotrope. It can both prevent the formation of and dissolve previously formed protein aggregates. This chemical property is manifested at physiological concentrations between 5 and 10 millimolar. Therefore, in addition to being an energy source for biological reactions, for which micromolar concentrations are sufficient, we propose that millimolar concentrations of ATP may act to keep proteins soluble. This may in part explain why ATP is maintained in such high concentrations in cells.","authors":"Patel, A., Malinovska, L., Saha, S., Wang, J., Alberti, S., Krishnan, Y., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Science","volume":"356","issue":"6339","page":"753-756","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15923635","title":"The erythroid phenotype of EKLF-null mice: defects in hemoglobin metabolism and membrane stability.","abstract":"Development of red blood cells requires the correct regulation of cellular processes including changes in cell morphology, globin expression and heme synthesis. Transcription factors such as erythroid Kruppel-like factor EKLF (Klf1) play a critical role in erythropoiesis. Mice lacking EKLF die around embryonic day 14 because of defective definitive erythropoiesis, partly caused by a deficit in beta-globin expression. To identify additional target genes, we analyzed the phenotype and gene expression profiles of wild-type and EKLF null primary erythroid progenitors that were differentiated synchronously in vitro. We show that EKLF is dispensable for expansion of erythroid progenitors, but required for the last steps of erythroid differentiation. We identify EKLF-dependent genes involved in hemoglobin metabolism and membrane stability. Strikingly, expression of these genes is also EKLF-dependent in primitive, yolk sac-derived, blood cells. Consistent with lack of upregulation of these genes we find previously undetected morphological abnormalities in EKLF-null primitive cells. Our data provide an explanation for the hitherto unexplained severity of the EKLF null phenotype in erythropoiesis.","authors":"Drissen, R., von Lindern, M., Kolbus, A., Driegen, S., Steinlein, P., Beug, H., Grosveld, F., Philipsen, S.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Mol Cell Biol","volume":"25","issue":"12","page":"5205-14","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15935764","title":"fruitless splicing specifies male courtship behavior in Drosophila.","abstract":"All animals exhibit innate behaviors that are specified during their development. Drosophila melanogaster males (but not females) perform an elaborate and innate courtship ritual directed toward females (but not males). Male courtship requires products of the fruitless (fru) gene, which is spliced differently in males and females. We have generated alleles of fru that are constitutively spliced in either the male or the female mode. We show that male splicing is essential for male courtship behavior and sexual orientation. More importantly, male splicing is also sufficient to generate male behavior in otherwise normal females. These females direct their courtship toward other females (or males engineered to produce female pheromones). The splicing of a single neuronal gene thus specifies essentially all aspects of a complex innate behavior.","authors":"Demir, E., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell","volume":"121","issue":"5","page":"785-94","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15905181","title":"Species specific membrane anchoring of nyctalopin, a small leucine-rich repeat protein.","abstract":"Mutations in the gene NYX, which encodes nyctalopin, lead to the retinal disorder congenital stationary night blindness which is characterized by defective night vision (nyctalopia) from birth. Nyctalopin is of unknown function but is predicted to be a secreted glycoprotein of the extracellular small leucine-rich repeat (SLRP) proteoglycan and protein family attached to the cell membrane in humans via a glycosylphosphatidylinositol (GPI) anchor but in mouse via a transmembrane domain. We investigated membrane association and attachment for human and mouse nyctalopin and show, conclusively, that human nyctalopin is a GPI anchored protein. In addition, the orthologous mouse protein, although it localizes to the cell surface, is not GPI anchored. We also confirm both mouse and human nyctalopins are glycosylated. Further sequence analysis suggests that chimp, dog and frog nyctalopins are likely to be GPI anchored but that rat nyctalopin is not. This is the first reported example of orthologous proteins which have different mechanisms of cell membrane attachment. Notably, the disease-causing mutations that have been identified to date in the human NYX gene are all distributed throughout the core LRR region and not in the C-terminal GPI anchor signal sequence. We propose that the presence of nyctalopin on the surface of the cell rather than the mechanism of anchoring is crucial to its function.","authors":"O'Connor, E., Eisenhaber, B., Dalley, J., Wang, T., Missen, C., Bulleid, N., Bishop, PN., Trump, D.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Hum Mol Genet","volume":"14","issue":"13","page":"1877-87","pdf":null,"JrId":"2407","fulltextlink":null,"preprintlink":null,"articledate":"2005-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28467904","title":"STAT3 Regulation of Citrate Synthase Is Essential during the Initiation of Lymphocyte Cell Growth.","abstract":"Citrate is a required carbon precursor for de novo fatty acid and membrane lipid synthesis. However, the pathways regulating intracellular citrate, particularly during the initial transition from a resting state to cell growth, remain unclear. Here, we show that STAT3 is among the first signaling events activated in resting lymphocytes following growth factor stimulation. During this period, the inhibition of STAT3 blocks the expression of citrate synthase (CS) and reduces the levels of intracellular citrate. As a consequence of CS loss and the reduction in citrate, cells are unable to grow or proliferate in response to extracellular growth factors. These effects were due to STAT3-dependent transcriptional regulation of CS, as exogenous addition of citrate could restore fatty acid synthesis, cell growth, and proliferation. Taken together, our studies reveal that transcription-dependent control of CS is essential for regulating the initiation of cell growth.","authors":"MacPherson, S., Horkoff, M., Gravel, C., Hoffmann, T., Zuber, J., Lum, JJ.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Rep","volume":"19","issue":"5","page":"910-918","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14691535","title":"Identification of Drosophila MicroRNA targets.","abstract":"MicroRNAs (miRNAs) are short RNA molecules that regulate gene expression by binding to target messenger RNAs and by controlling protein production or causing RNA cleavage. To date, functions have been assigned to only a few of the hundreds of identified miRNAs, in part because of the difficulty in identifying their targets. The short length of miRNAs and the fact that their complementarity to target sequences is imperfect mean that target identification in animal genomes is not possible by standard sequence comparison methods. Here we screen conserved 3' UTR sequences from the Drosophila melanogaster genome for potential miRNA targets. The screening procedure combines a sequence search with an evaluation of the predicted miRNA-target heteroduplex structures and energies. We show that this approach successfully identifies the five previously validated let-7, lin-4, and bantam targets from a large database and predict new targets for Drosophila miRNAs. Our target predictions reveal striking clusters of functionally related targets among the top predictions for specific miRNAs. These include Notch target genes for miR-7, proapoptotic genes for the miR-2 family, and enzymes from a metabolic pathway for miR-277. We experimentally verified three predicted targets each for miR-7 and the miR-2 family, doubling the number of validated targets for animal miRNAs. Statistical analysis indicates that the best single predicted target sites are at the border of significance; thus, target predictions should be considered as tentative until experimentally validated. We identify features shared by all validated targets that can be used to evaluate target predictions for animal miRNAs. Our initial evaluation and experimental validation of target predictions suggest functions for two miRNAs. For others, the screen suggests plausible functions, such as a role for miR-277 as a metabolic switch controlling amino acid catabolism. Cross-genome comparison proved essential, as it allows reduction of the sequence search space. Improvements in genome annotation and increased availability of cDNA sequences from other genomes will allow more sensitive screens. An increase in the number of confirmed targets is expected to reveal general structural features that can be used to improve their detection. While the screen is likely to miss some targets, our study shows that valid targets can be identified from sequence alone.","authors":"Stark, A., Brennecke, J., Russell, RB., Cohen, SM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"PLoS Biol","volume":"1","issue":"3","page":"E60","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15897173","title":"Introduction: dissection and simplification of chromosome segregation.","abstract":"","authors":"Yanagida, M., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"360","issue":"1455","page":"481","pdf":null,"JrId":"8277","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11044466","title":"Altered subcellular distribution of cadherin-5 in endothelial cells caused by the serum of pre-eclamptic patients.","abstract":"The main clinical features of pre-eclampsia are oedema and vascular leakage. Cadherin-5 mediates endothelial cell-cell contact in the vascular endothelium and may regulate permeability as a vascular function. Therefore, we addressed the question of whether pre-eclampsia alters cadherin-5 expression and intracellular distribution. Confluent human umbilical vein endothelial cells (HUVEC) were incubated with 20% serum from patients with pre-eclampsia (n = 18), haemolysis-elevated liver enzymes-low platelet syndrome (HELLP) (n = 12), pregnancy-induced hypertension (PIH) (n = 18) or normal pregnancy (n = 10). After incubation with sera from patients with pre-eclampsia, immunostaining analyses showed cadherin-5 accumulation in vesicular and tubular structures of the Golgi apparatus. Immunoblot analyses of HUVEC after pre-eclampsia serum incubation showed an increase of the stable form of cadherin-5 while degradation products decreased. Degradation of cadherin-5 takes place at the cell membrane, so this decrease may be due to a decrease of cadherin-5 in the cell membrane. The accumulation of cadherin-5 in the vesicular and tubular structures of the Golgi apparatus indicates that targeting of cadherin-5 to the plasma membrane could be disrupted. We suggest that intracellular retention of cadherin-5 caused by serum factors in patients with pre-eclampsia may decrease the number of adhesion complexes in the cell membrane, thereby contributing to endothelial dysfunction.","authors":"Groten, T., Kreienberg, R., Fialka, I., Huber, L., Wedlich, D.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Hum Reprod","volume":"6","issue":"11","page":"1027-32","pdf":null,"JrId":"20654","fulltextlink":null,"preprintlink":null,"articledate":"2000-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10417415","title":"Crystallization and preliminary X-ray analysis of human rhinovirus serotype 2 (HRV2).","abstract":"Human rhinoviruses, the major cause of mild recurrent infections of the upper respiratory tract, are small icosahedral particles. Over 100 different serotypes have been identified. The majority (91 serotypes) use intercellular adhesion molecule 1 as the cell-attachment site; ten serotypes (the minor group) bind to members of the low-density lipoprotein receptor. Three different crystal forms of the minor-group human rhinovirus serotype 2 (HRV2) were obtained by the hanging-drop vapour-diffusion technique using ammonium sulfate and sodium\/potassium phosphate as precipitants. Monoclinic crystals, space group P2(1), diffracted at least to 2.8 A resolution, and two complete virus particles were located in the crystal asymmetric unit. A second type of crystals had a compact cubic like morphology and diffracted beyond 2.5 A resolution. These crystals belong to a primitive orthorhombic space group, with unit-cell parameters a = 309.3, b = 353.5, c = 759.6 A, and contain one virus particle in the asymmetric unit. A third type of crystals, with a prismatic shape and belonging to space group I222, was also obtained under similar crystallization conditions. These latter crystals, with unit-cell parameters a = 308.7, b = 352.2, c = 380.5 A, diffracted to high resolution (beyond 1.8 A) and contained 15 protomers per asymmetric unit; this requires that three perpendicular crystal twofold axes coincide with three of the viral particle's dyad axes.","authors":"Verdaguer, N., Marlovits, TC., Bravo, J., Stuart, DI., Blaas, D., Fita, I.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Acta Crystallogr D Biol Crystallogr","volume":"55","issue":"Pt 8","page":"1459-61","pdf":null,"JrId":"20879","fulltextlink":null,"preprintlink":null,"articledate":"1999-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28009303","title":"Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain.","abstract":"Organoids derived from human pluripotent stem cells recapitulate the early three-dimensional organization of the human brain, but whether they establish the epigenomic and transcriptional programs essential for brain development is unknown. We compared epigenomic and regulatory features in cerebral organoids and human fetal brain, using genome-wide, base resolution DNA methylome and transcriptome sequencing. Transcriptomic dynamics in organoids faithfully modeled gene expression trajectories in early-to-mid human fetal brains. We found that early\u00a0non-CG methylation accumulation at super-enhancers in both fetal brain and organoids marks forthcoming transcriptional repression in the fully developed brain. Demethylated regions (74% of 35,627) identified during organoid differentiation overlapped with fetal brain regulatory elements. Interestingly, pericentromeric repeats showed widespread demethylation in multiple types of in\u00a0vitro human neural differentiation models but not in fetal brain. Our study reveals that organoids recapitulate many epigenomic features of mid-fetal human brain and also identified novel non-CG methylation signatures of brain development.","authors":"Luo, C., Lancaster, MA., Castanon, R., Nery, JR., Knoblich, JA., Ecker, JR.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Rep","volume":"17","issue":"12","page":"3369-3384","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15872005","title":"Identification of Pax2-regulated genes by expression profiling of the mid-hindbrain organizer region.","abstract":"The paired domain transcription factor Pax2 is required for the formation of the isthmic organizer (IsO) at the midbrain-hindbrain boundary, where it initiates expression of the IsO signal Fgf8. To gain further insight into the role of Pax2 in mid-hindbrain patterning, we searched for novel Pax2-regulated genes by cDNA microarray analysis of FACS-sorted GFP+ mid-hindbrain cells from wild-type and Pax2-\/- embryos carrying a Pax2(GFP) BAC transgene. Here, we report the identification of five genes that depend on Pax2 function for their expression in the mid-hindbrain boundary region. These genes code for the transcription factors En2 and Brn1 (Pou3f3), the intracellular signaling modifiers Sef and Tapp1, and the non-coding RNA Ncrms. The Brn1 gene was further identified as a direct target of Pax2, as two functional Pax2-binding sites in the promoter and in an upstream regulatory element of Brn1 were essential for lacZ transgene expression at the mid-hindbrain boundary. Moreover, ectopic expression of a dominant-negative Brn1 protein in chick embryos implicated Brn1 in Fgf8 gene regulation. Together, these data defined novel functions of Pax2 in the establishment of distinct transcriptional programs and in the control of intracellular signaling during mid-hindbrain development.","authors":"Bouchard, M., Grote, D., Craven, SE., Sun, Q., Steinlein, P., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Development","volume":"132","issue":"11","page":"2633-43","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2005-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15860757","title":"Cardiac sarcoplasmic reticulum calcium release and load are enhanced by subcellular cAMP elevations in PI3Kgamma-deficient mice.","abstract":"We recently showed that phosphoinositide-3-kinase-gamma-deficient (PI3Kgamma-\/-) mice have increased cardiac contractility without changes in heart size compared with control mice (ie, PI3Kgamma+\/+ or PI3Kgamma+\/-). In this study, we show that PI3Kgamma-\/- cardiomyocytes have elevated Ca2+ transient amplitudes with abbreviated decay kinetics compared with control under field-stimulation and voltage-clamp conditions. When Ca2+ transients were eliminated with high Ca2+ buffering, L-type Ca2+ currents (I(Ca,L)), K+ currents, and action potential duration (APD) were not different between the groups, whereas, in the presence of Ca2+ transients, Ca2+-dependent phase of I(Ca,L) inactivation was abbreviated and APD at 90% repolarization was prolonged in PI3Kgamma-\/- mice. Excitation-contraction coupling (ECC) gain, sarcoplasmic reticulum (SR) Ca2+ load, and SR Ca(2+) release fluxes measured as Ca2+ spikes, were also increased in PI3Kgamma-\/- cardiomyocytes without detectable changes in Ca2+ spikes kinetics. The cAMP inhibitor Rp-cAMP eliminated enhanced ECC and SR Ca2+ load in PI3Kgamma-\/- without effects in control myocytes. On the other hand, the beta-adrenergic receptor agonist isoproterenol increased I(Ca,L) and Ca2+ transient equally by approximately 2-fold in both PI3Kgamma-\/- and PI3Kgamma+\/- cardiomyocytes. Our results establish that PI3Kgamma reduces cardiac contractility in a highly compartmentalized manner by inhibiting cAMP-mediated SR Ca2+ loading without directly affecting other major modulators of ECC, such as AP and I(Ca,L).","authors":"Kerfant, BG., Gidrewicz, D., Sun, H., Oudit, GY., Penninger, JM., Backx, PH.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Circ Res","volume":"96","issue":"10","page":"1079-86","pdf":null,"JrId":"2974","fulltextlink":null,"preprintlink":null,"articledate":"2005-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28231465","title":"Time-Specific Effects of Spindle Positioning on Embryonic Progenitor Pool Composition and Adult Neural Stem Cell Seeding.","abstract":"The developmental mechanisms regulating the number of adult neural stem cells (aNSCs) are largely unknown. Here we show that the cleavage plane orientation in murine embryonic radial glia cells (RGCs) regulates the number of aNSCs in the lateral ganglionic eminence (LGE). Randomizing spindle orientation in RGCs by overexpression of Insc or a dominant-negative form of Lgn (dnLgn) reduces the frequency of self-renewing asymmetric divisions while favoring symmetric divisions generating two SNPs. Importantly, these changes during embryonic development result in reduced seeding of aNSCs. Interestingly, no effects on aNSC numbers were observed when Insc was overexpressed in postnatal RGCs or aNSCs. These data suggest a new mechanism for controlling aNSC numbers and show that the role of spindle orientation during brain development is highly time and region dependent.","authors":"Falk, S., Bugeon, S., Ninkovic, J., Pilz, GA., Postiglione, MP., Cremer, H., Knoblich, JA., G\u00f6tz, M.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Neuron","volume":"93","issue":"4","page":"777-791.e3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15848796","title":"Sugar codes for axons?","abstract":"Proteoglycans are complex macromolecules with the potential for extraordinary diversity. Several recent studies have demonstrated important roles for heparan sulfate and chondroitin sulfate proteoglycans (HSPGs and CSPGs) in axon pathfinding and have linked HSPGs to specific signaling pathways. More speculatively, there are hints of a \"sugar code,\" in which specific sugar modifications might act instructively in guidance decisions. This raises the intriguing possibility that the complexity of neuronal wiring may in part reflect the complexity of proteoglycan modifications.","authors":"Holt, CE., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Neuron","volume":"46","issue":"2","page":"169-72","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28273462","title":"Negative Regulators of an RNAi-Heterochromatin Positive Feedback Loop Safeguard Somatic Genome Integrity in Tetrahymena.","abstract":"RNAi-mediated positive feedback loops are pivotal for the maintenance of heterochromatin, but how they are downregulated at heterochromatin-euchromatin borders is not well understood. In the ciliated protozoan Tetrahymena, heterochromatin is formed exclusively on the sequences that are removed from the somatic genome by programmed DNA elimination, and an RNAi-mediated feedback loop is important for assembling heterochromatin on the eliminated sequences. In this study, we show that the heterochromatin protein 1 (HP1)-like protein Coi6p, its interaction partners Coi7p and Lia5p, and the histone demethylase Jmj1p are crucial for confining the production of small RNAs and the formation of heterochromatin to the eliminated sequences. The loss of Coi6p, Coi7p, or Jmj1p causes ectopic DNA elimination. The results provide direct evidence for the existence of a dedicated mechanism that counteracts a positive feedback loop between RNAi and heterochromatin at heterochromatin-euchromatin borders to maintain the integrity of the somatic genome.","authors":"Suhren, JH., Noto, T., Kataoka, K., Gao, S., Liu, Y., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Rep","volume":"18","issue":"10","page":"2494-2507","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15797376","title":"How do so few control so many?","abstract":"The separation of sister chromatids at the metaphase-to-anaphase transition is triggered by a protease called separase that is activated by the destruction of an inhibitory chaperone (securin). This process is mediated by a ubiquitin protein ligase called the anaphase-promoting complex or cyclosome (APC\/C), along with a protein called Cdc20. It is vital that separase not be activated before every single chromosome has been aligned on the mitotic spindle. Kinetochores that have not yet attached to microtubules catalyze the sequestration of Cdc20 by an inhibitor called Mad2. Recent experiments shed important insight into how Mad2 molecules bound to centromeres through their association with a protein called Mad1 might be transferred to Cdc20 and thereby inhibit securin's destruction.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell","volume":"120","issue":"6","page":"739-46","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11003657","title":"Nonperiodic activity of the human anaphase-promoting complex-Cdh1 ubiquitin ligase results in continuous DNA synthesis uncoupled from mitosis.","abstract":"Ubiquitin-proteasome-mediated destruction of rate-limiting proteins is required for timely progression through the main cell cycle transitions. The anaphase-promoting complex (APC), periodically activated by the Cdh1 subunit, represents one of the major cellular ubiquitin ligases which, in Saccharomyces cerevisiae and Drosophila spp., triggers exit from mitosis and during G(1) prevents unscheduled DNA replication. In this study we investigated the importance of periodic oscillation of the APC-Cdh1 activity for the cell cycle progression in human cells. We show that conditional interference with the APC-Cdh1 dissociation at the G(1)\/S transition resulted in an inability to accumulate a surprisingly broad range of critical mitotic regulators including cyclin B1, cyclin A, Plk1, Pds1, mitosin (CENP-F), Aim1, and Cdc20. Unexpectedly, although constitutively assembled APC-Cdh1 also delayed G(1)\/S transition and lowered the rate of DNA synthesis during S phase, some of the activities essential for DNA replication became markedly amplified, mainly due to a progressive increase of E2F-dependent cyclin E transcription and a rapid turnover of the p27(Kip1) cyclin-dependent kinase inhibitor. Consequently, failure to inactivate APC-Cdh1 beyond the G(1)\/S transition not only inhibited productive cell division but also supported slow but uninterrupted DNA replication, precluding S-phase exit and causing massive overreplication of the genome. Our data suggest that timely oscillation of the APC-Cdh1 ubiquitin ligase activity represents an essential step in coordinating DNA replication with cell division and that failure of mechanisms regulating association of APC with the Cdh1 activating subunit can undermine genomic stability in mammalian cells.","authors":"Sorensen, CS., Lukas, C., Kramer, ER., Peters, JM., Bartek, J., Lukas, J.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Cell Biol","volume":"20","issue":"20","page":"7613-23","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2000-10-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15767368","title":"Regulation of anaphylactic responses by phosphatidylinositol phosphate kinase type I {alpha}.","abstract":"The membrane phospholipid phosphatidylinositol 4, 5-bisphosphate [PI(4,5)P(2)] is a critical signal transducer in eukaryotic cells. However, the physiological roles of the type I phosphatidylinositol phosphate kinases (PIPKIs) that synthesize PI(4,5)P(2) are largely unknown. Here, we show that the alpha isozyme of PIPKI (PIPKIalpha) negatively regulates mast cell functions and anaphylactic responses. In vitro, PIPKIalpha-deficient mast cells exhibited increased degranulation and cytokine production after Fcepsilon receptor-I cross-linking. In vivo, PIPKIalpha(-\/-) mice displayed enhanced passive cutaneous and systemic anaphylaxis. Filamentous actin was diminished in PIPKIalpha(-\/-) mast cells, and enhanced degranulation observed in the absence of PIPKIalpha was also seen in wild-type mast cells treated with latrunculin, a pharmacological inhibitor of actin polymerization. Moreover, the association of FcepsilonRI with lipid rafts and FcepsilonRI-mediated activation of signaling proteins was augmented in PIPKIalpha(-\/-) mast cells. Thus, PIPKIalpha is a negative regulator of FcepsilonRI-mediated cellular responses and anaphylaxis, which functions by controlling the actin cytoskeleton and dynamics of FcepsilonRI signaling. Our results indicate that the different PIPKI isoforms might be functionally specialized.","authors":"Sasaki, J., Sasaki, T., Yamazaki, M., Matsuoka, K., Taya, C., Shitara, H., Takasuga, S., Nishio, M., Mizuno, K., Wada, T., Miyazaki, H., Watanabe, H., Iizuka, R., Kubo, S., Murata, S., Chiba, T., Maehama, T., Hamada, K., Kishimoto, H., Frohman, MA., Tanaka, K., Penninger, JM., Yonekawa, H., Suzuki, A., Kanaho, Y.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Exp Med","volume":"201","issue":"6","page":"859-70","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15765097","title":"Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer.","abstract":"CpG island hypermethylation and global genomic hypomethylation are common epigenetic features of cancer cells. Less attention has been focused on histone modifications in cancer cells. We characterized post-translational modifications to histone H4 in a comprehensive panel of normal tissues, cancer cell lines and primary tumors. Using immunodetection, high-performance capillary electrophoresis and mass spectrometry, we found that cancer cells had a loss of monoacetylated and trimethylated forms of histone H4. These changes appeared early and accumulated during the tumorigenic process, as we showed in a mouse model of multistage skin carcinogenesis. The losses occurred predominantly at the acetylated Lys16 and trimethylated Lys20 residues of histone H4 and were associated with the hypomethylation of DNA repetitive sequences, a well-known characteristic of cancer cells. Our data suggest that the global loss of monoacetylation and trimethylation of histone H4 is a common hallmark of human tumor cells.","authors":"Fraga, MF., Ballestar, E., Villar-Garea, A., Boix-Chornet, M., Espada, J., Schotta, G., Bonaldi, T., Haydon, C., Ropero, S., Petrie, K., Iyer, NG., P\u00e9rez-Rosado, A., Calvo, E., Lopez, JA., Cano, A., Calasanz, MJ., Colomer, D., Piris, MA., Ahn, N., Imhof, A., Caldas, C., Jenuwein, T., Esteller, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Genet","volume":"37","issue":"4","page":"391-400","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27789694","title":"The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli.","abstract":"When Escherichia coli encounters stress, the endoribonuclease MazF initiates a post-transcriptional response that results in the reprogramming of protein synthesis. By removing the 3\u0384-terminus of the 16S rRNA, MazF generates specialized ribosomes that selectively translate mRNAs likewise processed by MazF. Given the energy required for de novo ribosome biosynthesis, we considered the existence of a repair mechanism operating upon stress relief to recycle the modified ribosomes. Here, we show that the stress-ribosomes and the 3\u0384-terminal 16S rRNA fragment are stable during adverse conditions. Moreover, employing in vitro and in vivo approaches we demonstrate that the RNA ligase RtcB catalyzes the re-ligation of the truncated 16S rRNA present in specialized ribosomes Thereby their ability to translate canonical mRNAs is fully restored. Together, our findings not only provide a physiological function for the RNA ligase RtcB in bacteria but highlight the reversibility of ribosome heterogeneity, a crucial but hitherto undescribed concept for translational regulation.","authors":"Temmel, H., M\u00fcller, C., Sauert, M., Vesper, O., Reiss, A., Popow, J., Martinez, J., Moll, I.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nucleic Acids Res","volume":"45","issue":"8","page":"4708-4721","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15753127","title":"Raf-1 regulates Rho signaling and cell migration.","abstract":"Raf kinases relay signals inducing proliferation, differentiation, and survival. The Raf-1 isoform has been extensively studied as the upstream kinase linking Ras activation to the MEK\/ERK module. Recently, however, genetic experiments have shown that Raf-1 plays an essential role in counteracting apoptosis, and that it does so independently of its ability to activate MEK. By conditional gene ablation, we now show that Raf-1 is required for normal wound healing in vivo and for the migration of keratinocytes and fibroblasts in vitro. Raf-1-deficient cells show a symmetric, contracted appearance, characterized by cortical actin bundles and by a disordered vimentin cytoskeleton. These defects are due to the hyperactivity and incorrect localization of the Rho-effector Rok-alpha to the plasma membrane. Raf-1 physically associates with Rok-alpha in wild-type (WT) cells, and reintroduction of either WT or kinase-dead Raf-1 in knockout fibroblasts rescues their defects in shape and migration. Thus, Raf-1 plays an essential, kinase-independent function as a spatial regulator of Rho downstream signaling during migration.","authors":"Ehrenreiter, K., Piazzolla, D., Velamoor, V., Sobczak, I., Small, JV., Takeda, J., Leung, T., Baccarini, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Cell Biol","volume":"168","issue":"6","page":"955-64","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10359126","title":"The oncogene product Vav is a crucial regulator of primary cytotoxic T cell responses but has no apparent role in CD28-mediated co-stimulation.","abstract":"The guanine nucleotide-exchange factor Vav is a regulator of antigen-mediated cytoskeletal reorganization required for receptor clustering, proliferation and thymic selection. Moreover, Vav has been identified as a major substrate in the CD28 signal transduction pathway and overexpression of Vav enhances TCR-mediated IL-2 secretion in T cells. Here we show that CD3- plus CD28-mediated proliferation and IL-2 production were reduced in vav gene-deficient T cells. However, Vav had no apparent role in phorbol 12-myristate 13-acetate-plus CD28-mediated proliferation and IL-2 production, suggesting that Vav acts downstream of the TCR\/CD3 complex. In vivo, Vav expression was crucial to generate primary vesicular stomatitis virus (VSV)-specific cytotoxic T cell responses. In contrast, vav-\/- mice exhibited a reduced but significant footpad swelling after lymphocytic choriomeningitis virus (LCMV) infections and mounted a measurable primary cytotoxic T cell response to LCMV. Upon in vitro restimulation, cytotoxic T cell responses of both VSV- and LCMV-infected mice reached near normal levels. Our data provide the first genetic evidence that Vav is an important effector molecule that relays antigen receptor signaling to IL-2 production and activation of cytotoxic T cells.","authors":"Penninger, JM., Fischer, KD., Sasaki, T., Kozieradzki, I., Le, J., Tedford, K., Bachmaier, K., Ohashi, PS., Bachmann, MF.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Eur J Immunol","volume":"29","issue":"5","page":"1709-18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27596294","title":"Evaluation of expression profiles of microRNAs and two target genes, FOXO3a and RUNX2, effectively supports diagnostics and therapy predictions in breast cancer.","abstract":"Breast cancer (BC) including its progression into bone metastasis is a complex process involving changes in gene expression and function of both, microRNAs (miRNAs) and their target genes. Deregulation of miRNAs has been described as a crucial factor responsible for the initiation and progression of BC, and specific miRNA expression profiles have been found to be associated with particular disease states, histological tumor types, and BRCA1\/2 or HER status. BRCA1 tumor suppressor is involved in DNA damage response and repair and epigenetically controls miR-155 expression and its pre-cancerous potential. MiR-155 targets 3\u00b4UTR region of multiple components of the pro-oncogenic signaling cascades, including FOXO3a tumor suppressor and RUNX2 transcription factor regulating metastatic potential in BC. We employed qRT-PCR to determine expression level and examine possible regulatory role of selected miRNAs (miR-17, miR-18a, miR-19a, miR-20a, miR-21, miR-27a and miR-155) and their impact on expression modulation of FOXO3a and RUNX2 in peripheral blood mononuclear cells (PBMCs) in healthy individuals, in women carrying BRCA1 mutations with no disease manifestation, in women carrying BRCA1 mutations after tumor resection and therapy and in women with BC of unknown BRCA1 status in acute stage before tumor resection. Our results showed significant increase of miR-17, miR-19a, miR-21, miR-27, miR-155 and RUNX2 expression in PBMCs in BRCA1 patients and patients in acute stage, while FOXO3a expression was significantly decreased in these patients. MiR-18a and miR-20a expression was not affected. We propose that expressional changes reported in this study could provide significant additive information for early BC diagnosis, disease development prediction and therapy outcome monitoring.","authors":"Jurkovicova, D., Magyerkova, M., Sestakova, Z., Copakova, L., Bella, V., Konecny, M., Krivjanska, M., Kulcsar, L., Chovanec, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Neoplasma","volume":"63","issue":"6","page":"941-951","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27541193","title":"Chemical Biology Interrogates Protein Arginine Phosphorylation.","abstract":"Protein arginine phosphorylation has emerged as an important regulatory mechanism in Gram-positive bacteria, yet a couple of key mysteries remain. In this issue of Cell Chemical Biology, Fuhrmann et\u00a0al. (2016) use activity-based probes to demonstrate that the protein arginine phosphatase YwlE is inactivated upon oxidative stress to unleash heat-shock gene expression.","authors":"Suskiewicz, MJ., Clausen, T.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Chem Biol","volume":"23","issue":"8","page":"888-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15737063","title":"Dissociation of cohesin from chromosome arms and loss of arm cohesion during early mitosis depends on phosphorylation of SA2.","abstract":"Cohesin is a protein complex that is required to hold sister chromatids together. Cleavage of the Scc1 subunit of cohesin by the protease separase releases the complex from chromosomes and thereby enables the separation of sister chromatids in anaphase. In vertebrate cells, the bulk of cohesin dissociates from chromosome arms already during prophase and prometaphase without cleavage of Scc1. Polo-like kinase 1 (Plk1) and Aurora-B are required for this dissociation process, and Plk1 can phosphorylate the cohesin subunits Scc1 and SA2 in vitro, consistent with the possibility that cohesin phosphorylation by Plk1 triggers the dissociation of cohesin from chromosome arms. However, this hypothesis has not been tested yet, and in budding yeast it has been found that phosphorylation of Scc1 by the Polo-like kinase Cdc5 enhances the cleavability of cohesin, but does not lead to separase-independent dissociation of cohesin from chromosomes. To address the functional significance of cohesin phosphorylation in human cells, we have searched for phosphorylation sites on all four subunits of cohesin by mass spectrometry. We have identified numerous mitosis-specific sites on Scc1 and SA2, mutated them, and expressed nonphosphorylatable forms of both proteins stably at physiological levels in human cells. The analysis of these cells lines, in conjunction with biochemical experiments in vitro, indicate that Scc1 phosphorylation is dispensable for cohesin dissociation from chromosomes in early mitosis but enhances the cleavability of Scc1 by separase. In contrast, our data reveal that phosphorylation of SA2 is essential for cohesin dissociation during prophase and prometaphase, but is not required for cohesin cleavage by separase. The similarity of the phenotype obtained after expression of nonphosphorylatable SA2 in human cells to that seen after the depletion of Plk1 suggests that SA2 is the critical target of Plk1 in the cohesin dissociation pathway.","authors":"Hauf, S., Roitinger, E., Koch, B., Dittrich, CM., Mechtler, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"PLoS Biol","volume":"3","issue":"3","page":"e69","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15238529","title":"The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster.","abstract":"We describe a collection of P-element insertions that have considerable utility for generating custom chromosomal aberrations in Drosophila melanogaster. We have mobilized a pair of engineered P elements, p[RS3] and p[RS5], to collect 3243 lines unambiguously mapped to the Drosophila genome sequence. The collection contains, on average, an element every 35 kb. We demonstrate the utility of the collection for generating custom chromosomal deletions that have their end points mapped, with base-pair resolution, to the genome sequence. The collection was generated in an isogenic strain, thus affording a uniform background for screens where sensitivity to genetic background is high. The entire collection, along with a computational and genetic toolbox for designing and generating custom deletions, is publicly available. Using the collection it is theoretically possible to generate &gt;12,000 deletions between 1 bp and 1 Mb in size by simple eye color selection. In addition, a further 37,000 deletions, selectable by molecular screening, may be generated. We are now using the collection to generate a second-generation deficiency kit that is precisely mapped to the genome sequence.","authors":"Ryder, E., Blows, F., Ashburner, M., Bautista-Llacer, R., Coulson, D., Drummond, J., Webster, J., Gubb, D., Gunton, N., Johnson, G., O'Kane, CJ., Huen, D., Sharma, P., Asztalos, Z., Baisch, H., Schulze, J., Kube, M., Kittlaus, K., Reuter, G., Maroy, P., Szidonya, J., Rasmuson-Lestander, A., Ekstr\u00f6m, K., Dickson, B., Hugentobler, C., Stocker, H., Hafen, E., Lepesant, JA., Pflugfelder, G., Heisenberg, M., Mechler, B., Serras, F., Corominas, M., Schneuwly, S., Preat, T., Roote, J., Russell, S.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genetics","volume":"167","issue":"2","page":"797-813","pdf":null,"JrId":"3871","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15314029","title":"Conjugation-specific small RNAs in Tetrahymena have predicted properties of scan (scn) RNAs involved in genome rearrangement.","abstract":"We proposed a scan-RNA model for genome rearrangement based on finding small RNAs that hybridized preferentially to micronuclear-specific sequences and on the properties of Twi1p, a PPD protein required for both sequence elimination and small RNA accumulation in Tetrahymena. Here we show that Twi1p interacts with the small RNAs in both the old and the developing macronucleus, and is required for their stability. We show that the specificity of the small RNAs for micronuclear-limited sequences increases during conjugation. These results indicate that the small RNAs observed in conjugating cells have the properties predicted for scan RNAs.","authors":"Mochizuki, K., Gorovsky, MA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genes Dev","volume":"18","issue":"17","page":"2068-73","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27418510","title":"Return to quiescence of mouse neural stem cells by degradation of a proactivation protein.","abstract":"Quiescence is essential for long-term maintenance of adult stem cells. Niche signals regulate the transit of stem cells from dormant to activated states. Here, we show that the E3-ubiquitin ligase Huwe1 (HECT, UBA, and WWE domain-containing 1) is required for proliferating stem cells of the adult mouse hippocampus to return to quiescence. Huwe1 destabilizes proactivation protein Ascl1 (achaete-scute family bHLH transcription factor 1) in proliferating hippocampal stem cells, which prevents accumulation of cyclin Ds and promotes the return to a resting state. When stem cells fail to return to quiescence, the proliferative stem cell pool becomes depleted. Thus, long-term maintenance of hippocampal neurogenesis depends on the return of stem cells to a transient quiescent state through the rapid degradation of a key proactivation factor.","authors":"Urb\u00e1n, N., van den Berg, DL., Forget, A., Andersen, J., Demmers, JA., Hunt, C., Ayrault, O., Guillemot, F.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Science","volume":"353","issue":"6296","page":"292-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15688013","title":"Tumor cell invasiveness correlates with changes in integrin expression and localization.","abstract":"In nontumorigenic mammary epithelial cells (EpH4), transforming growth factor-beta (TGFbeta1) causes cell cycle arrest\/apoptosis, but induces epitheliomesenchymal transition (EMT) in Ha-Ras-transformed EpH4 cells (EpRas). EMT is closely correlated with late-stage tumor progression and results in fibroblastic, migratory cells displaying a mesenchymal gene expression program (FibRas). EpRas and FibRas cells showed strongly increased cell substrate adhesion to fibronectin, collagens I\/IV and laminin 1. Furthermore, Ras transformation caused enhanced or de-novo expression of the integrin subunits beta1, alpha2 and alpha3, or alpha5 and alpha6, respectively, the latter subunits being even more strongly expressed in FibRas cells. Importantly, polarized EpRas cells expressed integrin subunits beta1 and alpha6 at distinct (apical and lateral) membrane domains, while FibRas cells coexpressed these integrins and alpha5 at the entire plasma membrane. During EMT, EpRas cells formed an alpha5beta1 complex and deposited its ligand fibronectin into the extracellular matrix. Function-blocking alpha5 antibodies attenuated migration, and caused massive apoptosis in EpRas cells undergoing TGFbeta1-induced EMT in collagen gels, but failed to affect EpRas- or FibRas-derived structures. We conclude that functional alpha5beta1 integrin is centrally implicated in EMT induction. Importantly, FibRas cells also failed to deposit the alpha6beta4 ligand laminin 5, suggesting that alpha6beta4 is no longer functional after EMT and replaced by mesenchymal integrins such as alpha5beta1.","authors":"Maschler, S., Wirl, G., Spring, H., Bredow, DV., Sordat, I., Beug, H., Reichmann, E.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Oncogene","volume":"24","issue":"12","page":"2032-41","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15705598","title":"Integration of Ras subeffector signaling in TGF-beta mediated late stage hepatocarcinogenesis.","abstract":"Immortalized p19(ARF) null hepatocytes (MIM) feature a high degree of functional differentiation and are susceptible to transforming growth factor (TGF)-beta driven growth arrest and apoptosis. In contrast, polarized MIM hepatocytes expressing hyperactive Ha-Ras continue proliferation in cooperation with TGF-beta, and adopt an invasive phenotype by executing an epithelial to mesenchymal transition (EMT). In this study, we analyzed the involvement of Ras subeffectors in TGF-beta mediated hepatocellular EMT by employing MIM hepatocytes, which express Ras mutants allowing selective activation of either mitogen-activated protein kinase (MAPK) signaling (V12-S35) or phosphoinositide 3-OH (PI3)3 kinase (PI3K) signaling (V12-C40). We found that MAPK signaling in MIM-S35 hepatocytes was necessary and sufficient to promote resistance to TGF-beta mediated inhibition of proliferation in vitro and in vivo. MIM-S35 hepatocytes showed also PI3K activation during EMT, however, MAPK signaling on its own protected hepatocytes from apoptosis. Yet, MIM-C40 hepatocytes failed to form tumors and required additional MAPK stimulation to overcome TGF-beta mediated growth arrest. In vivo, the collaboration of MAPK signaling and TGF-beta activity drastically accelerated the cell-cycle progression of the hepatocytes, leading to vast tumor formation. From these data we conclude that MAPK is crucial for the cooperation with TGF-beta to regulate the proliferation as well as the survival of hepatocytes during EMT, and causes the fatal increase in hepatocellular tumor progression.","authors":"Fischer, AN., Herrera, B., Mikula, M., Proell, V., Fuchs, E., Gotzmann, J., Schulte-Hermann, R., Beug, H., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Carcinogenesis","volume":"26","issue":"5","page":"931-42","pdf":null,"JrId":"2665","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15703475","title":"Cell size control: new evidence for a general mechanism.","abstract":"Continuously proliferating cells have to precisely double their size during each cycle to maintain constant volumes. Time and again, this fact raised questions on the existence of an active cell size control mechanism in eukaryotic cells, which would prevent delayed or premature cell division at inadequate mass. We addressed this open issue by recapitulating in animal cells several long-standing experiments which had identified such a mechanism in yeast.","authors":"Grebien, F., Dolznig, H., Beug, H., Mullner, EW.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell Cycle","volume":"4","issue":"3","page":"418-21","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27224481","title":"Chromosome Compaction by Active Loop Extrusion.","abstract":"During cell division, chromosomes are compacted in length by more than a 100-fold. A wide range of experiments demonstrated that in their compacted state, mammalian chromosomes form arrays of closely stacked consecutive \u223c100 kb loops. The mechanism underlying the active process of chromosome compaction into a stack of loops is unknown. Here we test the hypothesis that chromosomes are compacted by enzymatic machines that actively extrude chromatin loops. When such loop-extruding factors (LEF) bind to chromosomes, they progressively bridge sites that are further away along the chromosome, thus extruding a loop. We demonstrate that collective action of LEFs leads to formation of a dynamic array of consecutive loops. Simulations and an analytically solved model identify two distinct steady states: a sparse state, where loops are highly dynamic but provide little compaction; and a dense state, where there are more stable loops and dramatic chromosome compaction. We find that human chromosomes operate at the border of the dense steady state. Our analysis also shows how the macroscopic characteristics of the loop array are determined by the microscopic properties of LEFs and their abundance. When the number of LEFs are used that match experimentally based estimates, the model can quantitatively reproduce the average loop length, the degree of compaction, and the general loop-array morphology of compact human chromosomes. Our study demonstrates that efficient chromosome compaction can be achieved solely by an active loop-extrusion process.","authors":"Goloborodko, A., Marko, JF., Mirny, LA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Biophys J","volume":"110","issue":"10","page":"2162-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15688012","title":"AP-1 dimers regulate transcription of the p14\/p19ARF tumor suppressor gene.","abstract":"Evidence is accumulating about the role of individual AP-1 components in cell proliferation and transformation. Notably, Ras-mediated transformation is characterized by the upregulation of particular AP-1 members, such as c-Jun and Fra-1. The p14\/p19ARF tumor suppressor gene is a key link between oncogenic Ras signaling and the p53 pathway. We explored the involvement of AP-1 dimers in the transcriptional regulation of the p14\/p19ARF gene. We demonstrate that both the human and mouse ARF promoters are transcriptional targets of selective AP-1 dimers. The ARF promoter is regulated specifically by AP-1 heterodimers containing Fra-1. Overexpression of c-Jun approximately Fra-1 dimers in primary murine fibroblast cells led to the upregulation of the endogenous ARF protein and growth arrest. Conversely, inhibition of c-Jun or Fra-1 protein levels resulted in decreased ARF expression. In addition, we show that AP-1 dimers cooperate with oncogenic Ras in the transcriptional activation of the p14\/p19ARF promoter. Thus, AP-1 heterodimers may contribute to the regulation of ARF expression upon oncogenic signaling.","authors":"Ameyar-Zazoua, M., Wisniewska, MB., Bakiri, L., Wagner, EF., Yaniv, M., Weitzman, JB.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Oncogene","volume":"24","issue":"14","page":"2298-306","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15674322","title":"DeltaEF1 is a transcriptional repressor of E-cadherin and regulates epithelial plasticity in breast cancer cells.","abstract":"Downregulation of E-cadherin is a crucial event for epithelial to mesenchymal transition (EMT) in embryonic development and cancer progression. Using the EpFosER mammary tumour model we show that during EMT, upregulation of the transcriptional regulator deltaEF1 coincided with transcriptional repression of E-cadherin. Ectopic expression of deltaEF1 in epithelial cells was sufficient to downregulate E-cadherin and to induce EMT. Analysis of E-cadherin promoter activity and chromatin immunoprecipitation identified deltaEF1 as direct transcriptional repressor of E-cadherin. In human cancer cells, transcript levels of deltaEF1 correlated directly with the extent of E-cadherin repression and loss of the epithelial phenotype. The protein was enriched in nuclei of human cancer cells and physically associated with the E-cadherin promoter. RNA interference-mediated downregulation of deltaEF1 in cancer cells was sufficient to derepress E-cadherin expression and restore cell to cell adhesion, suggesting that deltaEF1 is a key player in late stage carcinogenesis.","authors":"Eger, A., Aigner, K., Sonderegger, S., Dampier, B., Oehler, S., Schreiber, M., Berx, G., Cano, A., Beug, H., Foisner, R.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Oncogene","volume":"24","issue":"14","page":"2375-85","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15673575","title":"Thyroid hormone T3 acting through the thyroid hormone alpha receptor is necessary for implementation of erythropoiesis in the neonatal spleen environment in the mouse.","abstract":"Thyroid hormones (THs) mediate many physiological and developmental functions in vertebrates. All these functions are mediated by binding of the active form of the TH T3 to the specific nuclear receptors TRalpha and TRbeta, which are transcription factors. Using mutant mice lacking TRs or deficient for TH production, we show that T3 influences neonatal erythropoiesis through TRalpha. The effect of T3 and TRalpha is restricted to this developmental window and is specific for the spleen but not for other erythropoietic organs. We show that T3 via TRalpha affects late steps of erythrocytic development, promoting the proliferation of late basophilic erythroblasts. In vitro, this effect is exerted directly on erythrocytic cells. In vivo, the action of T3 is also intrinsic to spleen erythrocytic progenitors, as shown by grafting experiments of splenocytes derived from wildtype and TRalpha knockout (TRalpha(0\/0)) mice into wild-type and TRalpha(0\/0) irradiated recipients. Our results indicate that defective spleen erythropoiesis in hypothyroid and TRalpha(0\/0) mice results from impaired recognition of the spleen environment by the mutant erythrocytic progenitors. The data presented support a model in which T3 signaling through TRalpha is essential for the implementation of the transient spleen erythropoiesis at birth.","authors":"Angelin-Duclos, C., Domenget, C., Kolbus, A., Beug, H., Jurdic, P., Samarut, J.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Development","volume":"132","issue":"5","page":"925-34","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7541292","title":"In vivo LDL receptor and HMG-CoA reductase regulation in human lymphocytes and its alterations during aging.","abstract":"The LDL receptor and 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase play primary roles in the regulation of cellular cholesterol metabolism. To investigate the transcriptional regulation of lipid metabolism under physiological conditions ex vivo and its alterations during aging, we analyzed both the activity and mRNA concentration of the LDL receptor and HMG-CoA reductase in freshly isolated lymphocytes from healthy young and elderly donors. Data from fluorescent reverse transcriptase-polymerase chain reaction indicated that not only plasma LDL but also plasma HDL downregulates lymphocyte LDL receptor mRNA. Downregulation by HDL was three times more effective than that by LDL and presumably involved specific HDL binding sites. There was coordinate regulation of HMG-CoA reductase mRNA with LDL receptor mRNA that was independent of plasma lipoprotein concentrations. Despite elevated plasma concentrations of LDL, lymphocytes from elderly donors paradoxically expressed increased levels of the LDL receptor (P = .030) and HMG-CoA reductase mRNA (P = .062). The age-related dysregulation of the LDL receptor was predominantly due to impaired downregulation by plasma LDL rather than by HDL. Thus, not only LDL but also HDL and age significantly influences the transcriptional regulation of the LDL receptor in extrahepatic cells in vivo.","authors":"Stulnig, TM., Klocker, H., Harwood, HJ., J\u00fcrgens, G., Sch\u00f6nitzer, D., Jarosch, E., Huber, LA., Amberger, A., Wick, G.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Arterioscler Thromb Vasc Biol","volume":"15","issue":"7","page":"872-8","pdf":null,"JrId":"8623","fulltextlink":null,"preprintlink":null,"articledate":"1995-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15655111","title":"Distinct functions of junD in cardiac hypertrophy and heart failure.","abstract":"Cardiac hypertrophic stimuli induce both adaptive and maladaptive growth response pathways in heart. Here we show that mice lacking junD develop less adaptive hypertrophy in heart after mechanical pressure overload, while cardiomyocyte-specific expression of junD in mice results in spontaneous ventricular dilation and decreased contractility. In contrast, fra-1 conditional knock-out mice have a normal hypertrophic response, whereas hearts from fra-1 transgenic mice decompensate prematurely. Moreover, fra-1 transgenic mice simultaneously lacking junD reveal a spontaneous dilated cardiomyopathy associated with increased cardiomyocyte apoptosis and a primary mitochondrial defect. These data suggest that junD promotes both adaptive-protective and maladaptive hypertrophy in heart, depending on its expression levels.","authors":"Ricci, R., Eriksson, U., Oudit, GY., Eferl, R., Akhmedov, A., Sumara, I., Sumara, G., Kassiri, Z., David, JP., Bakiri, L., Sasse, B., Idarraga, MH., Rath, M., Kurz, D., Theussl, HC., Perriard, JC., Backx, P., Penninger, JM., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Genes Dev","volume":"19","issue":"2","page":"208-13","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15657595","title":"Comm function in commissural axon guidance: cell-autonomous sorting of Robo in vivo.","abstract":"Commissureless (Comm) controls axon guidance across the Drosophila melanogaster midline by regulating surface levels of Robo, the receptor for the midline repellent Slit. Two different models have been proposed for how Comm regulates Robo: a 'sorting' model and a 'clearance' model, both based on studies using heterologous cells in vitro. Here, we test these two models in vivo. We establish a genetic rescue assay for Comm, and use this assay to show that midline crossing does not require the presence of Comm in midline cells, as proposed by the clearance model. Moreover, by monitoring the trafficking of a Robo-green fluorescent protein (GFP) fusion in living embryos, we demonstrate that Comm prevents the delivery of Robo-GFP to the growth cone, as predicted by the sorting model. It has also been suggested that Comm must be ubiquitinated by the Nedd4 ubiquitin ligase. We show here, however, that ubiquitination of Comm is not required for its function in vitro or in vivo, and that Nedd4 is unlikely to function in axon guidance at the midline.","authors":"Keleman, K., Ribeiro, C., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Neurosci","volume":"8","issue":"2","page":"156-63","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15652752","title":"Stat5 tetramer formation is associated with leukemogenesis.","abstract":"Activation of Stat5 is frequently found in leukemias. To study the mechanism and role of Stat5 activation, we introduced a constitutively activated Stat5a mutant, cS5F, into murine bone marrow (BM) cells. BM transplantation with cS5F-transfected cells caused development of multilineage leukemias in lethally irradiated wild-type or nonirradiated Rag2(-\/-) mice. The leukemic cells showed strongly enhanced levels of cS5F tetramers but unchanged cS5F dimer levels in a DNA binding assay. Moreover, Stat5a mutants engineered to form only dimers, but not tetramers, failed to induce leukemias. In addition, Stat5 tetramers were found to accumulate in excess compared to dimers in various human leukemias. These data suggest that Stat5 tetramers are associated with leukemogenesis.","authors":"Moriggl, R., Sexl, V., Kenner, L., Duntsch, C., Stangl, K., Gingras, S., Hoffmeyer, A., Bauer, A., Piekorz, R., Wang, D., Bunting, KD., Wagner, EF., Sonneck, K., Valent, P., Ihle, JN., Beug, H.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cancer Cell","volume":"7","issue":"1","page":"87-99","pdf":null,"JrId":"29778","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15642137","title":"JNK1 is not essential for TNF-mediated joint disease.","abstract":"Tumour necrosis factor (TNF) signalling molecules are considered as promising therapeutic targets of antirheumatic therapy. Among them, mitogen-activated protein kinases are thought to be of central importance. Herein, we investigate the role in vivo of TNF-alpha signalling through c-Jun N-terminal kinase (JNK)1 in destructive arthritis. Human TNF transgenic (hTNFtg) mice, which develop inflammatory arthritis, were intercrossed with JNK1-deficient (JNK1-\/-) mice. Animals (n = 35) of all four genotypes (wild-type, JNK1-\/-, hTNFtg, JNK1-\/-hTNFtg) were assessed for clinical and histological signs of arthritis. Clinical features of arthritis (swelling and decreased grip strength) developed equally in hTNFtg and JNK1-\/-hTNFtg mice. Histological analyses revealed no differences in the quantity of synovial inflammation and bone erosions or in the cellular composition of the synovial infiltrate. Bone destruction and osteoclast formation were observed to a similar degree in hTNFtg and JNK1-\/-hTNFtg animals. Moreover, cartilage damage, as indicated by proteoglycan loss in the articular cartilage, was comparable in the two strains. Intact phosphorylation of JNK and c-Jun as well as expression of JNK2 in the synovial tissue of JNK1-\/-hTNFtg mice suggests that signalling through JNK2 may compensate for the deficiency in JNK1. Thus, JNK1 activation does not seem to be essential for TNF-mediated arthritis.","authors":"K\u00f6ller, M., Hayer, S., Redlich, K., Ricci, R., David, JP., Steiner, G., Smolen, JS., Wagner, EF., Schett, G.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Arthritis Res Ther","volume":"7","issue":"1","page":"R166-73","pdf":null,"JrId":"30289","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10330283","title":"T cell activation-associated epitopes of CD147 in regulation of the T cell response, and their definition by antibody affinity and antigen density.","abstract":"CD147 is a broadly expressed cell surface glycoprotein of the Ig superfamily whose expression is up-regulated upon T cell activation. In order to elucidate a possible role of CD147 in T cell biology, we established 15 specific mAb. Seven distinct epitopes were defined by the mAb panel. Most of the mAb bound only to phytohemagglutinin (PHA)-activated but not resting T cells. We demonstrate that this was not because of true expression of activation-dependent neoepitopes but rather due to bivalent binding of the relatively low-affinity mAb (affinity constant KA values between 2.25 x 10(8) and 7 x 10(9) M-1) to the more densely expressed and\/or more clustered CD147 molecules on the activated T cells. In contrast, the mAb with higher affinity (KA &gt; 7 x 10(9) M-1) could stably bind in a monovalent fashion even to the relatively low dense CD147 molecules on resting T cells. This model might more generally explain the nature of 'activation epitopes' described previously in other leukocyte surface molecules. Finally, we provide evidence that induction of ordered dimerization of CD147 by a mAb directed to a unique epitope results in strong inhibition of CD3-mediated T cell activation.","authors":"Koch, C., Staffler, G., H\u00fcttinger, R., Hilgert, I., Prager, E., Cern\u00fd, J., Steinlein, P., Majdic, O., Horejs\u00ed, V., Stockinger, H.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Int Immunol","volume":"11","issue":"5","page":"777-86","pdf":null,"JrId":"1837","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15632144","title":"Phosphoinositide binding by the disabled-1 PTB domain is necessary for membrane localization and Reelin signal transduction.","abstract":"Disabled-1 (Dab1) is an essential adaptor protein that functions in the Reelin signaling pathway and is required for the regulation of neuronal migration during embryonic development. Dab1 interacts with NPXY motifs in the cytoplasmic tails of the lipoprotein receptors ApoER2 and very low density lipoprotein receptor through an amino-terminal phosphotyrosine binding (PTB) domain. Binding of Reelin to these receptors leads to tyrosine phosphorylation of Dab1 and the initiation of a signaling cascade that results in remodeling of the cytoskeleton. Structural and biochemical studies of the Dab1 PTB domain have demonstrated that this domain binds to both the NPXY peptide motif in the lipoprotein receptor tails as well as to the head group of phosphoinositide 4,5-P2 through energetically independent mechanisms. Here we have investigated how phosphoinositide binding by the Dab1 PTB domain influences Reelin signal transduction. Our findings in cultured primary neurons that have been transduced with lentiviral constructs expressing mutant Dab1 forms reveal that phosphoinositide binding by the Dab1 PTB domain is necessary for proper membrane localization of Dab1 and for effective transduction of a Reelin signal.","authors":"Stolt, PC., Chen, Y., Liu, P., Bock, HH., Blacklow, SC., Herz, J.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Biol Chem","volume":"280","issue":"10","page":"9671-7","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15620348","title":"A crack in histone lysine methylation.","abstract":"Histone lysine methylation is regarded as a very stable modification with important functions in epigenetic gene control and for organizing chromatin domains. While more robust modifications of the chromatin template are essential to stabilize epigenetic information, there is now the first evidence for a histone lysine demethylase that reverts an activating methyl mark to the unmodified state (Shi et al., 2004 [this issue of Cell]).","authors":"Kubicek, S., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell","volume":"119","issue":"7","page":"903-6","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15598983","title":"A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase.","abstract":"Previous studies indicated that genome rearrangement involving DNA sequence elimination that occurs at late stages of conjugation in Tetrahymena is epigenetically controlled by siRNA-like scan (scn) RNAs produced from nongenic, heterogeneous, bidirectional, micronuclear transcripts synthesized at early stages of conjugation. Here, we show that Dcl1p, one of three Tetrahymena Dicer-like enzymes, is required for processing the micronuclear transcripts to scnRNAs. DCL1 is also required for methylation of histone H3 at Lys 9, which, in wild-type cells, specifically occurs on the sequences (IESs) being eliminated. These results argue that Dcl1p processes nongenic micronuclear transcripts to scnRNAs and is required for IES elimination. This is the first evidence linking nongenic micronuclear transcripts, scnRNAs, and genome rearrangement. Dcl1p also is required for proper mitotic and meiotic segregation of micronuclear chromosomes and for normal chromosome alignment in meiotic prophase, suggesting that DCL1 has multiple functions in regulating chromosome dynamics.","authors":"Mochizuki, K., Gorovsky, MA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Genes Dev","volume":"19","issue":"1","page":"77-89","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17584854","title":"Large spectrum of lissencephaly and pachygyria phenotypes resulting from de novo missense mutations in tubulin alpha 1A (TUBA1A).","abstract":"We have recently reported a missense mutation in exon 4 of the tubulin alpha 1A (Tuba1a) gene in a hyperactive N-ethyl-N-nitrosourea (ENU) induced mouse mutant with abnormal lamination of the hippocampus. Neuroanatomical similarities between the Tuba1a mutant mouse and mice deficient for Doublecortin (Dcx) and Lis1 genes, and the well-established functional interaction between DCX and microtubules (MTs), led us to hypothesize that mutations in TUBA1A (TUBA3, previous symbol), the human homolog of Tuba1a, might give rise to cortical malformations. This hypothesis was subsequently confirmed by the identification of TUBA1A mutations in two patients with lissencephaly and pachygyria, respectively. Here we report additional TUBA1A mutations identified in six unrelated patients with a large spectrum of brain dysgeneses. The de novo occurrence was shown for all mutations, including one recurrent mutation (c.790C&gt;T, p.R264C) detected in two patients, and two mutations that affect the same amino acid (c.1205G&gt;A, p.R402H; c.1204C&gt;T, p.R402C) detected in two other patients. Retrospective examination of MR images suggests that patients with TUBA1A mutations share not only cortical dysgenesis, but also cerebellar, hippocampal, corpus callosum, and brainstem abnormalities. Interestingly, the specific high level of Tuba1a expression throughout the period of central nervous system (CNS) development, shown by in situ hybridization using mouse embryos, is in accordance with the brain-restricted developmental phenotype caused by TUBA1A mutations. All together, these results, in combination with previously reported data, strengthen the relevance of the known interaction between MTs and DCX, and highlight the importance of the MTs\/DCX complex in the neuronal migration process.","authors":"Poirier, K., Keays, DA., Francis, F., Saillour, Y., Bahi, N., Manouvrier, S., Fallet-Bianco, C., Pasquier, L., Toutain, A., Tuy, FP., Bienvenu, T., Joriot, S., Odent, S., Ville, D., Desguerre, I., Goldenberg, A., Moutard, ML., Fryns, JP., van Esch, H., Harvey, RJ., Siebold, C., Flint, J., Beldjord, C., Chelly, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Hum Mutat","volume":"28","issue":"11","page":"1055-64","pdf":null,"JrId":"2408","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10583914","title":"Fast, convenient, and effective method to transiently transfect primary hippocampal neurons.","abstract":"Transfection of primary neurons in culture has proven to be experimentally challenging in the past. To overcome these limitations, we present a detailed transfection protocol for hippocampal neurons based on DNA\/Ca(2+)-phosphate coprecipitation. The main advantages being (1) the speed and convenience, (2) the remarkable efficiency of transfection for mature neurons, and (3) consistent health of the neurons upon transfection allowing subsequent manipulations. The strength of this protocol is convincingly demonstrated by the fact that the expressed protein can be detected biochemically on Western blots.","authors":"K\u00f6hrmann, M., Haubensak, W., Hemraj, I., Kaether, C., Lessmann, VJ., Kiebler, MA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Neurosci Res","volume":"58","issue":"6","page":"831-5","pdf":null,"JrId":"5310","fulltextlink":null,"preprintlink":null,"articledate":"2000-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17155450","title":"Quantized rotation of atoms from photons with orbital angular momentum.","abstract":"We demonstrate the coherent transfer of the orbital angular momentum of a photon to an atom in quantized units of variant Planck's over 2pi, using a 2-photon stimulated Raman process with Laguerre-Gaussian beams to generate an atomic vortex state in a Bose-Einstein condensate of sodium atoms. We show that the process is coherent by creating superpositions of different vortex states, where the relative phase between the states is determined by the relative phases of the optical fields. Furthermore, we create vortices of charge 2 by transferring to each atom the orbital angular momentum of two photons.","authors":"Andersen, MF., Ryu, C., Clad\u00e9, P., Natarajan, V., Vaziri, A., Helmerson, K., Phillips, WD.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Phys Rev Lett","volume":"97","issue":"17","page":"170406","pdf":null,"JrId":"21217","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23319436","title":"Interlaboratory studies and initiatives developing standards for proteomics.","abstract":"Proteomics is a rapidly transforming interdisciplinary field of research that embraces a diverse set of analytical approaches to tackle problems in fundamental and applied biology. This viewpoint article highlights the benefits of interlaboratory studies and standardization initiatives to enable investigators to address many of the challenges found in proteomics research. Among these initiatives, we discuss our efforts on a comprehensive performance standard for characterizing PTMs by MS that was recently developed by the Association of Biomolecular Resource Facilities (ABRF) Proteomics Standards Research Group (sPRG).","authors":"Ivanov, AR., Colangelo, CM., Dufresne, CP., Friedman, DB., Lilley, KS., Mechtler, K., Phinney, BS., Rose, KL., Rudnick, PA., Searle, BC., Shaffer, SA., Weintraub, ST.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proteomics","volume":"13","issue":"6","page":"904-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15572404","title":"Distinct functions of condensin I and II in mitotic chromosome assembly.","abstract":"Condensin is a protein complex associated with mitotic chromosomes that has been implicated in chromosome condensation. In vertebrates, two types of condensin complexes have recently been identified, called condensin I and II. Here, we show that in mammalian cells condensin II associates with chromatin in prophase, in contrast to condensin I which is cytoplasmic and can thus interact with chromosomes only after nuclear envelope breakdown. RNA interference experiments in conjunction with imaging of live and fixed cells revealed that condensin II is required for chromosome condensation in early prophase, whereas condensin I appears to be dispensable at this stage. By contrast, condensin I is required for the complete dissociation of cohesin from chromosome arms, for chromosome shortening and for normal timing of progression through prometaphase and metaphase, whereas normal condensin II levels are dispensable for these processes. After depletion of both condensin complexes, the onset of chromosome condensation is delayed until the end of prophase, but is then initiated rapidly before nuclear envelope breakdown. These results reveal that condensin II and I associate with chromosomes sequentially and have distinct functions in mitotic chromosome assembly.","authors":"Hirota, T., Gerlich, D., Koch, B., Ellenberg, J., Peters, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Cell Sci","volume":"117","issue":"Pt 26","page":"6435-45","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11460157","title":"Entanglement of the orbital angular momentum states of photons.","abstract":"Entangled quantum states are not separable, regardless of the spatial separation of their components. This is a manifestation of an aspect of quantum mechanics known as quantum non-locality. An important consequence of this is that the measurement of the state of one particle in a two-particle entangled state defines the state of the second particle instantaneously, whereas neither particle possesses its own well-defined state before the measurement. Experimental realizations of entanglement have hitherto been restricted to two-state quantum systems, involving, for example, the two orthogonal polarization states of photons. Here we demonstrate entanglement involving the spatial modes of the electromagnetic field carrying orbital angular momentum. As these modes can be used to define an infinitely dimensional discrete Hilbert space, this approach provides a practical route to entanglement that involves many orthogonal quantum states, rather than just two Multi-dimensional entangled states could be of considerable importance in the field of quantum information, enabling, for example, more efficient use of communication channels in quantum cryptography.","authors":"Mair, A., Vaziri, A., Weihs, G., Zeilinger, A.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nature","volume":"412","issue":"6844","page":"313-6","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15537535","title":"Heterotrimeric G proteins: new tricks for an old dog.","abstract":"Heterotrimeric G proteins are well known for their function in signal transduction downstream of seven transmembrane receptors. More recently, however, genetic analysis in C. elegans and in Drosophila has revealed a second, essential function of these molecules in positioning the mitotic spindle and attaching microtubules to the cell cortex. Five new publications in Cell (Afshar et al., 2004; Du and Macara, 2004 [this issue of Cell]; Hess et al., 2004), Developmental Cell (Martin-McCaffrey et al., 2004), and Current Biology (Couwenbergs et al., 2004) show that this function is conserved in vertebrates and--like the classical pathway--involves cycling of G proteins between GDP and GTP bound conformations.","authors":"Hampoelz, B., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell","volume":"119","issue":"4","page":"453-6","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15539952","title":"Epithelial-mesenchymal transition: NF-kappaB takes center stage.","abstract":"Activation of the transcription factor NF-kappaB occurs in many human tumors, and studies have shown that NF-kappaB can promote cell proliferation and oncogenesis, possibly by protecting cells from apoptosis. Little is known, however, about whether NF-kappaB is involved in tumor progression including epithelial-mesenchymal transition (EMT), a central process governing both morphogenesis and carcinoma progression in multicellular organisms. In a combined in vitro\/in vivo model of mammary carcinogenesis, NF-kappaB was essential both for the induction and maintenance of EMT and for in vivo metastasis. NF-kappaB and the signaling pathways that are involved in its activation should therefore receive attention as potential targets for the development of novel anti-metastatic cancer treatments.","authors":"Huber, MA., Beug, H., Wirth, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell Cycle","volume":"3","issue":"12","page":"1477-80","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15526035","title":"AIF deficiency compromises oxidative phosphorylation.","abstract":"Apoptosis-inducing factor (AIF) is a mitochondrial flavoprotein that, after apoptosis induction, translocates to the nucleus where it participates in apoptotic chromatinolysis. Here, we show that human or mouse cells lacking AIF as a result of homologous recombination or small interfering RNA exhibit high lactate production and enhanced dependency on glycolytic ATP generation, due to severe reduction of respiratory chain complex I activity. Although AIF itself is not a part of complex I, AIF-deficient cells exhibit a reduced content of complex I and of its components, pointing to a role of AIF in the biogenesis and\/or maintenance of this polyprotein complex. Harlequin mice with reduced AIF expression due to a retroviral insertion into the AIF gene also manifest a reduced oxidative phosphorylation (OXPHOS) in the retina and in the brain, correlating with reduced expression of complex I subunits, retinal degeneration, and neuronal defects. Altogether, these data point to a role of AIF in OXPHOS and emphasize the dual role of AIF in life and death.","authors":"Vahsen, N., Cand\u00e9, C., Bri\u00e8re, JJ., B\u00e9nit, P., Joza, N., Larochette, N., Mastroberardino, PG., Pequignot, MO., Casares, N., Lazar, V., Feraud, O., Debili, N., Wissing, S., Engelhardt, S., Madeo, F., Piacentini, M., Penninger, JM., Sch\u00e4gger, H., Rustin, P., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"EMBO J","volume":"23","issue":"23","page":"4679-89","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15528446","title":"Structural insights into the assembly of the type III secretion needle complex.","abstract":"Type III secretion systems (TTSSs) mediate translocation of virulence factors into host cells. We report the 17-angstrom resolution structures of a central component of Salmonella typhimurium TTSS, the needle complex, and its assembly precursor, the bacterial envelope-anchored base. Both the base and the fully assembled needle complex adopted multiple oligomeric states in vivo, and needle assembly was accompanied by recruitment of the protein PrgJ as a structural component of the base. Moreover, conformational changes during needle assembly created scaffolds for anchoring both PrgJ and the needle substructure and may provide the basis for substrate-specificity switching during type III secretion.","authors":"Marlovits, TC., Kubori, T., Sukhan, A., Thomas, DR., Gal\u00e1n, JE., Unger, VM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Science","volume":"306","issue":"5698","page":"1040-2","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15516908","title":"Hypertension with a grain of salt.","abstract":null,"authors":"Danilczyk, U., Penninger, J.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nat Med","volume":"10","issue":"11","page":"1163-4","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15510223","title":"Histone hypomethylation is an indicator of epigenetic plasticity in quiescent lymphocytes.","abstract":"Post-translational modifications of histone amino termini are thought to convey epigenetic information that extends the coding potential of DNA. In particular, histone lysine methylation has been implicated in conveying transcriptional memory and maintaining lineage fidelity. Here an analysis of histone lysine methylation in quiescent (G(0)) and cycling lymphocytes showed that methylation of histone H3 at lysines 4 (H3K4), 9 (H3K9), 27 (H3K27) and histone H4 at lysine 20 is markedly reduced in resting B lymphocytes as compared with cycling cells. Quiescent B cells also lacked heterochromatin-associated HP1beta and Ikaros at pericentric chromatin and expressed low levels of Ezh2 and ESET histone methyl transferases (HMTases). Nuclei from resting B or T cells were approximately three times more efficiently reprogrammed in nuclear transfer assays than cells in which HMTase expression, histone methylation and HP1beta binding had been restored following mitotic stimulation. These results showing local and global changes in histone lysine methylation levels in vivo demonstrate that constitutive heterochromatin organization is modified in resting lymphocytes and suggest that histone hypomethylation is a useful indicator of epigenetic plasticity.","authors":"Baxter, J., Sauer, S., Peters, A., John, R., Williams, R., Caparros, ML., Arney, K., Otte, A., Jenuwein, T., Merkenschlager, M., Fisher, AG.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"EMBO J","volume":"23","issue":"22","page":"4462-72","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15507213","title":"JunB deficiency leads to a myeloproliferative disorder arising from hematopoietic stem cells.","abstract":"The AP-1 transcription factor JunB is a transcriptional regulator of myelopoiesis. Inactivation of JunB in postnatal mice results in a myeloproliferative disorder (MPD) resembling early human chronic myelogenous leukemia (CML). Here, we show that JunB regulates the numbers of hematopoietic stem cells (HSC). JunB overexpression decreases the frequency of long-term HSC (LT-HSC), while JunB inactivation specifically expands the numbers of LT-HSC and granulocyte\/macrophage progenitors (GMP) resulting in chronic MPD. Further, we demonstrate that junB inactivation must take place in LT-HSC, and not at later stages of myelopoiesis, to induce MPD and that only junB-deficient LT-HSC are capable of transplanting the MPD to recipient mice. These results demonstrate a stem cell-specific role for JunB in normal and leukemic hematopoiesis and provide experimental evidence that leukemic stem cells (LSC) can reside at the LT-HSC stage of development in a mouse model of MPD.","authors":"Passegu\u00e9, E., Wagner, EF., Weissman, IL.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell","volume":"119","issue":"3","page":"431-43","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15492405","title":"Expansion and differentiation of immature mouse and human hematopoietic progenitors.","abstract":"A prerequisite for proper investigation of self-renewal and differentiation of hematopoietic cells is the possibility to obtain large quantities of homogenous primary progenitors under defined conditions, allowing meaningful biochemical and molecular analyses. These cells should show renewal and differentiation characteristics similar to the in vivo situation. The serum-free culture systems delineated in this chapter meet these requirements, employing primary hematopoietic cells derived from murine fetal liver and human umbilical cord blood, which show physiological self-renewal responses to cytokine\/hormone combinations, which in vivo are involved in stress hematopoiesis. We describe the expansion and sustained proliferation of multipotent (mouse) and erythroid (mouse and human) progenitors, responding to physiological signals. Moreover, both mouse and human erythroid progenitors can be induced to undergo synchronous terminal differentiation by addition of high levels of erythropoietin. If fetal liver cells from p53-\/- mice are used, respective multipotent and erythroid cells undergo immortalization without an obvious Hayflick crisis, but otherwise retain their primary cell characteristics. Finally, both primary and immortal mouse progenitors can be subjected to genetic manipulation via retroviral constructs with high efficiency.","authors":"Dolznig, H., Kolbus, A., Leberbauer, C., Schmidt, U., Deiner, EM., M\u00fcllner, EW., Beug, H.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Methods Mol Med","volume":"105","issue":null,"page":"323-44","pdf":null,"JrId":"27012","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15473847","title":"Asymmetric cell division in C. elegans: cortical polarity and spindle positioning.","abstract":"The one-cell Caenorhabditis elegans embryo divides asymmetrically into a larger and smaller blastomere, each with a different fate. How does such asymmetry arise? The sperm-supplied centrosome establishes an axis of polarity in the embryo that is transduced into the establishment of anterior and posterior cortical domains. These cortical domains define the polarity of the embryo, acting upstream of the PAR proteins. The PAR proteins, in turn, determine the subsequent segregation of fate determinants and the plane of cell division. We address how cortical asymmetry could be established, relying on data from C. elegans and other polarized cells, as well as from applicable models. We discuss how cortical polarity influences spindle position to accomplish an asymmetric division, presenting the current models of spindle orientation and anaphase spindle displacement. We focus on asymmetric cell division as a function of the actin and microtubule cytoskeletons, emphasizing the cell biology of polarity.","authors":"Cowan, CR., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Annu Rev Cell Dev Biol","volume":"20","issue":null,"page":"427-53","pdf":null,"JrId":"20331","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15483629","title":"Epigenetic silencing of the c-fms locus during B-lymphopoiesis occurs in discrete steps and is reversible.","abstract":"The murine c-fms (Csf1r) gene encodes the macrophage colony-stimulating factor receptor, which is essential for macrophage development. It is expressed at a low level in haematopoietic stem cells and is switched off in all non-macrophage cell types. To examine the role of chromatin structure in this process we studied epigenetic silencing of c-fms during B-lymphopoiesis. c-fms chromatin in stem cells and multipotent progenitors is in the active conformation and bound by transcription factors. A similar result was obtained with specified common myeloid and lymphoid progenitor cells. In developing B cells, c-fms chromatin is silenced in distinct steps, whereby first the binding of transcription factors and RNA expression is lost, followed by a loss of nuclease accessibility. Interestingly, regions of de novo DNA methylation in B cells overlap with an intronic antisense transcription unit that is differently regulated during lymphopoiesis. However, even at mature B cell stages, c-fms chromatin is still in a poised conformation and c-fms expression can be re-activated by conditional deletion of the transcription factor Pax5.","authors":"Tagoh, H., Schebesta, A., Lefevre, P., Wilson, N., Hume, D., Busslinger, M., Bonifer, C.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"EMBO J","volume":"23","issue":"21","page":"4275-85","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26743993","title":"Adaptive and Background-Aware GAL4 Expression Enhancement of Co-registered Confocal Microscopy Images.","abstract":"GAL4 gene expression imaging using confocal microscopy is a common and powerful technique used to study the nervous system of a model organism such as Drosophila melanogaster. Recent research projects focused on high throughput screenings of thousands of different driver lines, resulting in large image databases. The amount of data generated makes manual assessment tedious or even impossible. The first and most important step in any automatic image processing and data extraction pipeline is to enhance areas with relevant signal. However, data acquired via high throughput imaging tends to be less then ideal for this task, often showing high amounts of background signal. Furthermore, neuronal structures and in particular thin and elongated projections with a weak staining signal are easily lost. In this paper we present a method for enhancing the relevant signal by utilizing a Hessian-based filter to augment thin and weak tube-like structures in the image. To get optimal results, we present a novel adaptive background-aware enhancement filter parametrized with the local background intensity, which is estimated based on a common background model. We also integrate recent research on adaptive image enhancement into our approach, allowing us to propose an effective solution for known problems present in confocal microscopy images. We provide an evaluation based on annotated image data and compare our results against current state-of-the-art algorithms. The results show that our algorithm clearly outperforms the existing solutions.","authors":"Trapp, M., Schulze, F., Novikov, AA., Tirian, L., J Dickson, B., B\u00fchler, K.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Neuroinformatics","volume":"14","issue":"2","page":"221-33","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15470040","title":"Essential role of LFA-1 in activating Th2-like responses by alpha-galactosylceramide-activated NKT cells.","abstract":"NKT cells produce large amounts of cytokines associated with both the Th1 (IFN-gamma) and Th2 (IL-4) responses following stimulation of their invariant Valpha14 Ag receptor. The role of adhesion molecules in the activation of NKT cells by the Valpha14 ligand alpha-galactosylceramide (alpha-GalCer) remains unclear. To address this issue, LFA-1-\/- (CD11a-\/-) mice were used to investigate IL-4 and IFN-gamma production by NKT cells following alpha-GalCer stimulation. Intriguingly, LFA-1-\/- mice showed increased IL-4, IL-5, and IL-13 production and polarized Th2-type responses in response to alpha-GalCer in vitro and in vivo. Furthermore, the Th2-specific transcription factor GATA-3 was up-regulated in alpha-GalCer-activated NKT cells from LFA-1-\/- mice. These results provide the first genetic evidence that the adhesion receptor LFA-1 has a crucial role in Th2-polarizing functions of NKT cells.","authors":"Matsumoto, G., Kubota, E., Omi, Y., Lee, U., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Immunol","volume":"173","issue":"8","page":"4976-84","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15467726","title":"TCR affinity and negative regulation limit autoimmunity.","abstract":"Autoimmune diseases are often mediated by self-reactive T cells, which must be activated to cause immunopathology. One mechanism, known as molecular mimicry, proposes that self-reactive T cells may be activated by pathogens expressing crossreactive ligands. Here we have developed a model to investigate how the affinity of the T-cell receptor (TCR) for the activating agent influences autoimmunity. Our model shows that an approximately fivefold difference in the TCR affinity for the activating ligand results in a 50% reduction in the incidence of autoimmunity. A reduction in TCR-ligand affinity to approximately 20 times lower than normal does not induce autoimmunity despite the unexpected induction of cytotoxic T lymphocytes (CTLs) and insulitis. Furthermore, in the absence of a key negative regulatory molecule, Cbl-b, 100% of mice develop autoimmunity upon infection with viruses encoding the lower-affinity ligand. Therefore, autoimmune disease is sensitive both to the affinity of the activating ligand and to normal mechanisms that negatively regulate the immune response.","authors":"Gronski, MA., Boulter, JM., Moskophidis, D., Nguyen, LT., Holmberg, K., Elford, AR., Deenick, EK., Kim, HO., Penninger, JM., Odermatt, B., Gallimore, A., Gascoigne, NR., Ohashi, PS.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nat Med","volume":"10","issue":"11","page":"1234-9","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10199556","title":"Fra-1 potentiates osteoclastic differentiation in osteoclast-macrophage precursor cell lines.","abstract":"c-Fos, a component of the dimeric transcription factor AP-1, is necessary for osteoclast formation. To determine whether c-Fos can substitute for any or all of the stimuli needed for osteoclast induction, we infected osteoclast precursors with retroviral vectors expressing c-Fos or the Fos-related protein, Fra-1. The infected cells were incubated with or without osteoclast-inductive stimuli. Osteoclast formation from retroviral-infected precursors remained completely dependent on osteoclast-inductive stromal cells. Unexpectedly, infection of bipotential osteoclast-macrophage precursor cell lines with retroviruses expressing Fra-1 but not c-Fos caused a 10-100-fold increase in the number of precursors that developed calcitonin receptors associated with an increase in bone resorption. These observations suggest that, in the precursor cell lines, Fra-1 is a limiting factor for full responsiveness to the osteoclast-inductive environment. Fra-1 is therefore likely to play a role in osteoclast differentiation which is distinct from that of c-Fos.","authors":"Owens, JM., Matsuo, K., Nicholson, GC., Wagner, EF., Chambers, TJ.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Cell Physiol","volume":"179","issue":"2","page":"170-8","pdf":null,"JrId":"4586","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15449058","title":"SUMO conjugation in plants.","abstract":"Covalent attachment of small proteins to substrates can regulate protein activity in eukaryotes. SUMO, the small ubiquitin-related modifier, can be covalently linked to a broad spectrum of substrates. An understanding of SUMO's role in plant biology is still in its infancy. In this review, we briefly summarize the enzymology of SUMO conjugation (sumoylation), and the current knowledge of SUMO modification in Arabidopsis thaliana (L.) Heynh. and other plants, in comparison to animals and fungi. Furthermore, we assemble a list of potential pathway components in the genome of A. thaliana that have either been functionally defined, or are suggested by similarity to pathway components from other organisms.","authors":"Novatchkova, M., Budhiraja, R., Coupland, G., Eisenhaber, F., Bachmair, A.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Planta","volume":"220","issue":"1","page":"1-8","pdf":null,"JrId":"2296","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21043528","title":"Lesson from the stoichiometry determination of the cohesin complex: a short protease mediated elution increases the recovery from cross-linked antibody-conjugated beads.","abstract":"Affinity purification of proteins using antibodies coupled to beads and subsequent mass spectrometric analysis has become a standard technique for the identification of protein complexes. With the recent transfer of the isotope dilution mass spectrometry principle (IDMS) to the field of proteomics, quantitative analyses-such as the stoichiometry determination of protein complexes-have become achievable. Traditionally proteins were eluted from antibody-conjugated beads using glycine at low pH or using diluted acids such as HCl, TFA, or FA, but elution was often found to be incomplete. Using the cohesin complex and the anaphase promoting complex\/cyclosome (APC\/C) as examples, we show that a short 15-60 min predigestion with a protease such as LysC (modified on-bead digest termed protease elution) increases the elution efficiency 2- to 3-fold compared to standard acid elution protocols. While longer incubation periods-as performed in standard on-bead digestion-led to partial proteolysis of the cross-linked antibodies, no or only insignificant cleavage was observed after 15-60 min protease mediated elution. Using the protease elution method, we successfully determined the stoichiometry of the cohesin complex by absolute quantification of the four core subunits using LC-SRM analysis and 19 reference peptides generated with the EtEP strategy. Protease elution was 3-fold more efficient compared to HCl elution, but measurements using both elution techniques are in agreement with a 1:1:1:1 stoichiometry. Furthermore, using isoform specific reference peptides, we determined the exact STAG1:STAG2 stoichiometry within the population of cohesin complexes. In summary, we show that the protease elution protocol increases the recovery from affinity beads and is compatible with quantitative measurements such as the stoichiometry determination of protein complexes.","authors":"Holzmann, J., Fuchs, J., Pichler, P., Peters, JM., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Proteome Res","volume":"10","issue":"2","page":"780-9","pdf":null,"JrId":"30137","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15381145","title":"Autoimmune heart failure: new understandings of pathogenesis.","abstract":"Besides genetic susceptibility and infections with cardiotropic viruses, autoimmune responses against heart tissue play a major role in the pathogenesis of dilated cardiomyopathy, the most common cause of heart failure in young patients. Recent findings suggest that the combination of tissue damage resulting in release of self-antigens, together with non-specific activation of the innate immune system triggers various responses that are crucial for the development of heart-specific autoimmunity. Understanding these mechanisms is critical for the design and development of novel treatment strategies against devastating heart diseases in the future.","authors":"Eriksson, U., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Int J Biochem Cell Biol","volume":"37","issue":"1","page":"27-32","pdf":null,"JrId":"8630","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26659571","title":"RANKL blockade prevents and treats aggressive osteosarcomas.","abstract":"Osteosarcoma (OS) is the most common primary bone cancer, which occurs primarily in children and adolescents, severely affecting survivors' quality of life. Despite its chemosensitivity and treatment advances, long-term survival rates for OS patients have stagnated over the last 20 years. Thus, it is necessary to develop new molecularly targeted therapies for this metastatic bone cancer. Mutations in TP53 and RB are linked to OS predisposition and to the evolution of spontaneous OS. We established receptor activator of nuclear factor \u03baB ligand (RANKL) as a therapeutic target for suppression and prevention of OS. Combined conditional osteoblast-specific deletions of Rb, p53, and the protein kinase A (PKA) regulatory subunit Prkar1\u03b1 genes in genetically engineered mouse models (GEMMs) generate aggressive osteosarcomas, characterized by PKA, RANKL, and osteoclast hyperactivity. Whole-body Rankl deletion completely abrogates tumorigenesis. Although osteoblastic Rank deletion has little effect, osteoclastic Rank deletion delays tumorigenesis and prolongs life span. The latter is associated with inactivation of osteoclastogenesis and up-regulation of the tumor suppressor phosphatase and tensin homolog (PTEN). Further, we use these GEMMs as preclinical platforms to show that RANKL blockade with RANK-Fc arrests tumor progression and improves survival and also inhibits lung metastasis. Moreover, preemptive administration of RANK-Fc completely prevents tumorigenesis in mice highly predisposed to this aggressive cancer. Denosumab, a fully human monoclonal antibody against RANKL, is currently used to treat patients with osteoporosis or bone metastases. Our studies provide a strong rationale to consider RANKL blockade for the treatment and prevention of aggressive RANKL-overexpressing OS in humans.","authors":"Chen, Y., Di Grappa, MA., Molyneux, SD., McKee, TD., Waterhouse, P., Penninger, JM., Khokha, R.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Sci Transl Med","volume":"7","issue":"317","page":"317ra197","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15177032","title":"Sequential roles of Cdc42, Par-6, aPKC, and Lgl in the establishment of epithelial polarity during Drosophila embryogenesis.","abstract":"How epithelial cells subdivide their plasma membrane into an apical and a basolateral domain is largely unclear. In Drosophila embryos, epithelial cells are generated from a syncytium during cellularization. We show here that polarity is established shortly after cellularization when Par-6 and the atypical protein kinase C concentrate on the apical side of the newly formed cells. Apical localization of Par-6 requires its interaction with activated Cdc42 and dominant-active or dominant-negative Cdc42 disrupt epithelial polarity, suggesting that activation of this GTPase is crucial for the establishment of epithelial polarity. Maintenance of Par-6 localization requires the cytoskeletal protein Lgl. Genetic and biochemical experiments suggest that phosphorylation by aPKC inactivates Lgl on the apical side. On the basolateral side, Lgl is active and excludes Par-6 from the cell cortex, suggesting that complementary cortical domains are maintained by mutual inhibition of aPKC and Lgl on opposite sides of an epithelial cell.","authors":"Hutterer, A., Betschinger, J., Petronczki, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Dev Cell","volume":"6","issue":"6","page":"845-54","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15375666","title":"The Drosophila meiotic kleisin C(2)M functions before the meiotic divisions.","abstract":"Stepwise and regionally controlled resolution of sister chromatid cohesion is thought to be crucial for faithful chromosome segregation during meiotic divisions. In yeast, the meiosis-specific alpha-kleisin subunit of the cohesin complex, Rec8, is protected from cleavage by separase but only during meiosis I and specifically within the pericentromeric region. While the Drosophila genome does not contain an obvious Rec8 orthologue, as other animal and plant genomes, it includes c(2)M, which encodes a distant alpha-kleisin family member involved in female meiosis. C(2)M associates in vivo with the Smc3 cohesin subunit, as previously shown for yeast Rec8. In contrast to Rec8, however, C(2)M accumulates predominantly after the pre-meiotic S-phase. Moreover, after association with the synaptonemal complex, it disappears again and cannot be detected on meiotic chromosomes by metaphase I. C(2)M cleavage fragments are not observed during completion of the meiotic divisions, and mutations within putative separase cleavage sites do not interfere with meiotic chromosome segregation. Therefore, C(2)M appears to function within the synaptonemal complex during prophase I but possibly not thereafter. This suggests that C(2)M may not confer sister chromatid cohesion needed for meiosis I and II chromosome segregation.","authors":"Heidmann, D., Horn, S., Heidmann, S., Schleiffer, A., Nasmyth, K., Lehner, CF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Chromosoma","volume":"113","issue":"4","page":"177-87","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15343338","title":"Centrosomes direct cell polarity independently of microtubule assembly in C. elegans embryos.","abstract":"Polarity establishment requires a symmetry-breaking event, resulting in an axis along which determinants are segregated. In Caenorhabditis elegans, oocytes are apolar and are triggered to polarize rapidly along one axis after fertilization. The establishment of this first polarity axis is revealed by the asymmetric distribution of PAR proteins and cortical activity in the one-celled embryo. Current evidence suggests that the centrosome-pronucleus complex contributed by the sperm is involved in defining the polarization axis. Here we directly assess the contribution of the centrosome to polarity establishment by laser ablating the centrosome before and during polarization. We find that the centrosome is required to initiate polarity but not to maintain it. Initiation of polarity coincides with the proximity of the centrosome to the cortex and the assembly of pericentriolar material on the immature sperm centrosome. Depletion of microtubules or the microtubule nucleator gamma-tubulin did not affect polarity establishment. These results demonstrate that the centrosome provides an initiating signal that polarizes C. elegans embryos and indicate that this signalling event might be independent of the role of the centrosome as a microtubule nucleator.","authors":"Cowan, CR., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nature","volume":"431","issue":"7004","page":"92-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15356142","title":"Analysis of Notch1 function by in vitro T cell differentiation of Pax5 mutant lymphoid progenitors.","abstract":"Signaling through the Notch1 receptor is essential for T cell development in the thymus. Stromal OP9 cells ectopically expressing the Notch ligand Delta-like1 mimic the thymic environment by inducing hemopoietic stem cells to undergo in vitro T cell development. Notch1 is also expressed on Pax5-\/- pro-B cells, which are clonable lymphoid progenitors with a latent myeloid potential. In this study, we demonstrate that Pax5-\/- progenitors efficiently differentiate in vitro into CD4+CD8+ alphabeta and gammadelta T cells upon coculture with OP9-Delta-like1 cells. In vitro T cell development of Pax5-\/- progenitors strictly depends on Notch1 function and progresses through normal developmental stages by expressing T cell markers and rearranging TCRbeta, gamma, and delta loci in the correct temporal sequence. Notch-stimulated Pax5-\/- progenitors efficiently down-regulate the expression of B cell-specific genes, consistent with a role of Notch1 in preventing B lymphopoiesis in the thymus. At the same time, Notch signaling rapidly induces cell surface expression of the c-Kit receptor and transcription of the target genes Deltex1 and pre-Talpha concomitant with the activation of TCR Vbeta germline transcription and the regulatory genes GATA3 and Tcf1. These data suggest that Notch1 acts upstream of GATA3 and Tcf1 in early T cell development and regulates Vbeta-DJbeta rearrangements by controlling the chromatin accessibility of Vbeta genes at the TCRbeta locus.","authors":"H\u00f6flinger, S., Kesavan, K., Fuxa, M., Hutter, C., Heavey, B., Radtke, F., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Immunol","volume":"173","issue":"6","page":"3935-44","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15323557","title":"The dual-function disabled-1 PTB domain exhibits site independence in binding phosphoinositide and peptide ligands.","abstract":"While typical intracellular protein modules have only one ligand-binding site, there are rare examples of single modules that bind two different ligands at distinct binding sites. Here we present a detailed mutational and energetic analysis of one such domain, the phosphotyrosine binding (PTB) domain of Disabled-1 (Dab1), which binds to both peptide and phosphoinositide (PI) ligands simultaneously at structurally distinct binding sites. Through the techniques of isothermal titration calorimetry (ITC), analysis of Dab1 PTB domain mutants, and nuclear magnetic resonance (NMR), we have evaluated the characteristics of binding of the Dab1 PTB domain to various peptide and PI ligands. These studies reveal that the presence of saturating concentrations of one ligand has little effect on the binding constant for a second ligand at the other site. In addition, proteins with single-point mutations in the peptide-binding site retain native affinity for PI ligands, while proteins with mutations that prevent PI binding retain native affinity for peptide. NMR titrations show that the final structure of the ternary complex is the same independent of the order of addition of the two ligands. Together, these studies show that binding of peptide and PI ligands is energetically independent and noncooperative.","authors":"Stolt, PC., Vardar, D., Blacklow, SC.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Biochemistry","volume":"43","issue":"34","page":"10979-87","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9042861","title":"Essential functions of Pax5 (BSAP) in pro-B cell development: difference between fetal and adult B lymphopoiesis and reduced V-to-DJ recombination at the IgH locus.","abstract":"The Pax5 gene coding for the transcription factor BSAP has an essential role in B lymphopoiesis and midbrain development. Here we present a detailed analysis of the B-cell phenotype of Pax5 mutant mice that revealed a differential dependency of fetal and adult B lymphopoiesis on this transcriptional regulator. B-cell development is arrested in the bone marrow at the early pro-B (pre-BI) cell stage, which is characterized by expression of the early markers c-kit, CD43, lambda5, VpreB, and HSA and the absence of the later markers CD25 and BP-1. These pre-BI cells fail to express the BSAP target gene CD19 and are capable of long-term proliferation in vitro in the presence of stromal cells and IL-7. B-lymphoid progenitors could not be detected in the fetal liver of Pax5 mutant embryos. However, Pax5-deficient fetal liver cells gave rise to the development of pre-BI cells in bone marrow on transplantation into lethally irradiated mice. These data indicate different functions of Pax5 in the distinctive microenvironments of fetal liver and adult bone marrow. As shown by PCR analyses, the pre-BI cells in Pax5-deficient bone marrow have undergone D(H)-to-J(H) rearrangement of the immunoglobulin heavy-chain locus at normal frequency. In contrast, V(H)-to-D(H)J(H) rearrangements were reduced approximately 50-fold in Pax5-deficient pre-BI cells, suggesting a role for Pax5 in the developmental pathway controlling V-to-DJ recombination.","authors":"Nutt, SL., Urb\u00e1nek, P., Rolink, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Genes Dev","volume":"11","issue":"4","page":"476-91","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15342490","title":"Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint.","abstract":"We report on the function of the human ortholog of Saccharomyces cerevisiae Rif1 (Rap1-interacting factor 1). Yeast Rif1 associates with telomeres and regulates their length. In contrast, human Rif1 did not accumulate at functional telomeres, but localized to dysfunctional telomeres and to telomeric DNA clusters in ALT cells, a pattern of telomere association typical of DNA-damage-response factors. After induction of double-strand breaks (DSBs), Rif1 formed foci that colocalized with other DNA-damage-response factors. This response was strictly dependent on ATM (ataxia telangiectasia mutated) and 53BP1, but not affected by diminished function of ATR (ATM- and Rad3-related kinase), BRCA1, Chk2, Nbs1, and Mre11. Rif1 inhibition resulted in radiosensitivity and a defect in the intra-S-phase checkpoint. The S-phase checkpoint phenotype was independent of Nbs1 status, arguing that Rif1 and Nbs1 act in different pathways to inhibit DNA replication after DNA damage. These data reveal that human Rif1 contributes to the ATM-mediated protection against DNA damage and point to a remarkable difference in the primary function of this protein in yeast and mammals.","authors":"Silverman, J., Takai, H., Buonomo, SB., Eisenhaber, F., de Lange, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genes Dev","volume":"18","issue":"17","page":"2108-19","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15342493","title":"Vilse, a conserved Rac\/Cdc42 GAP mediating Robo repulsion in tracheal cells and axons.","abstract":"Slit proteins steer the migration of many cell types through their binding to Robo receptors, but how Robo controls cell motility is not clear. We describe the functional analysis of vilse, a Drosophila gene required for Robo repulsion in epithelial cells and axons. Vilse defines a conserved family of RhoGAPs (Rho GTPase-activating proteins), with representatives in flies and vertebrates. The phenotypes of vilse mutants resemble the tracheal and axonal phenotypes of Slit and Robo mutants at the CNS midline. Dosage-sensitive genetic interactions between vilse, slit, and robo mutants suggest that vilse is a component of robo signaling. Moreover, overexpression of Vilse in the trachea of robo mutants ameliorates the phenotypes of robo, indicating that Vilse acts downstream of Robo to mediate midline repulsion. Vilse and its human homolog bind directly to the intracellular domains of the corresponding Robo receptors and promote the hydrolysis of RacGTP and, less efficiently, of Cdc42GTP. These results together with genetic interaction experiments with robo, vilse, and rac mutants suggest a mechanism whereby Robo repulsion is mediated by the localized inactivation of Rac through Vilse.","authors":"Lundstr\u00f6m, A., Gallio, M., Englund, C., Steneberg, P., Hemph\u00e4l\u00e4, J., Aspenstr\u00f6m, P., Keleman, K., Falileeva, L., Dickson, BJ., Samakovlis, C.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genes Dev","volume":"18","issue":"17","page":"2161-71","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15322555","title":"Evidence for a size-sensing mechanism in animal cells.","abstract":"Continuously proliferating cells exactly double their mass during each cell cycle. Here we have addressed the controversial question of if and how cell size is sensed and regulated. We used erythroblasts that proliferate under the control of a constitutively active oncogene (v-ErbB) or under the control of physiological cytokines (stem cell factor, erythropoietin and v-ErbB inhibitor). The oncogene-driven cells proliferated 1.7 times faster and showed a 1.5-fold increase in cell volume. The two phenotypes could be converted into each other 24 h after altering growth factor signalling. The large cells had a higher rate of protein synthesis, together with a shortened G1 phase. Additional experiments with chicken erythroblasts and mouse fibroblasts, synchronized by centrifugal elutriation, provided further evidence that vertebrate cells can respond to cell size alterations (induced either through different growth factor signalling or DNA synthesis inhibitors) by compensatory shortening of the subsequent G1 phase. Taken together, these data suggest that an active size threshold mechanism exists in G1, which induces adjustment of cell-cycle length in the next cycle, thus ensuring maintenance of a proper balance between growth and proliferation rates in vertebrates.","authors":"Dolznig, H., Grebien, F., Sauer, T., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nat Cell Biol","volume":"6","issue":"9","page":"899-905","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26354919","title":"Predicting the Dynamics of Network Connectivity in the Neocortex.","abstract":"Dynamic remodeling of connectivity is a fundamental feature of neocortical circuits. Unraveling the principles underlying these dynamics is essential for the understanding of how neuronal circuits give rise to computations. Moreover, as complete descriptions of the wiring diagram in cortical tissues are becoming available, deciphering the dynamic elements in these diagrams is crucial for relating them to cortical function. Here, we used chronic in vivo two-photon imaging to longitudinally follow a few thousand dendritic spines in the mouse auditory cortex to study the determinants of these spines' lifetimes. We applied nonlinear regression to quantify the independent contribution of spine age and several morphological parameters to the prediction of the future survival of a spine. We show that spine age, size, and geometry are parameters that can provide independent contributions to the prediction of the longevity of a synaptic connection. In addition, we use this framework to emulate a serial sectioning electron microscopy experiment and demonstrate how incorporation of morphological information of dendritic spines from a single time-point allows estimation of future connectivity states. The distinction between predictable and nonpredictable connectivity changes may be used in the future to identify the specific adaptations of neuronal circuits to environmental changes. The full dataset is publicly available for further analysis. Significance statement: The neural architecture in the neocortex exhibits constant remodeling. The functional consequences of these modifications are poorly understood, in particular because the determinants of these changes are largely unknown. Here, we aimed to identify those modifications that are predictable from current network state. To that goal, we repeatedly imaged thousands of dendritic spines in the auditory cortex of mice to assess the morphology and lifetimes of synaptic connections. We developed models based on morphological features of dendritic spines that allow predicting future turnover of synaptic connections. The dynamic models presented in this paper provide a quantitative framework for adding putative temporal dynamics to the static description of a neuronal circuit from single time-point connectomics experiments.","authors":"Loewenstein, Y., Yanover, U., Rumpel, S.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Neurosci","volume":"35","issue":"36","page":"12535-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11001061","title":"Activation of heat-shock response by an adenovirus is essential for virus replication.","abstract":"Successful viral infection requires viruses to redirect host biochemistry to replicate the viral genome, and produce and assemble progeny virions. Cellular heat-shock responses, which are characterized as elevation and relocalization of heat-shock proteins, occur during replication of many viruses. Such responses might be host reactions to the synthesis of foreign protein, or might be irrelevant consequences of the viral need to activate transcription. Alternatively, as heat-shock proteins can facilitate protein folding, activating a heat-shock response might be a specific virus function ensuring proper synthesis of viral proteins and virions. It is not possible to determine whether heat-shock response is essential for virus replication, because the implicated viral genes (such as Ad5 EIA, ref. 10) also control other essential replication steps. Here we report that expression of Gam1, a protein encoded by the avian virus CELO (ref. 11), elevates and relocalizes hsp70 and hsp40. Gam1-negative CELO is replication-defective; however, Gam1 function can be partially replaced by either heat shock or forced hsp40 expression. Thus, an essential function of Gam1 during virus replication is to activate host heat-shock responses with hsp40 as a primary target.","authors":"Glotzer, JB., Saltik, M., Chiocca, S., Michou, AI., Moseley, P., Cotten, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nature","volume":"407","issue":"6801","page":"207-11","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2000-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26302790","title":"piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire.","abstract":"PIWI clade Argonaute proteins silence transposon expression in animal gonads. Their target specificity is defined by bound \u223c23- to 30-nucleotide (nt) PIWI-interacting RNAs (piRNAs) that are processed from single-stranded precursor transcripts via two distinct pathways. Primary piRNAs are defined by the endonuclease Zucchini, while biogenesis of secondary piRNAs depends on piRNA-guided transcript cleavage and results in piRNA amplification. Here, we analyze the interdependencies between these piRNA biogenesis pathways in developing Drosophila ovaries. We show that secondary piRNA-guided target slicing is the predominant mechanism that specifies transcripts\u2014including those from piRNA clusters\u2014as primary piRNA precursors and defines the spectrum of Piwi-bound piRNAs in germline cells. Post-transcriptional silencing in the cytoplasm therefore enforces nuclear transcriptional target silencing, which ensures the tight suppression of transposons during oogenesis. As target slicing also defines the nuclear piRNA pool during mouse spermatogenesis, our findings uncover an unexpected conceptual similarity between the mouse and fly piRNA pathways.","authors":"Senti, KA., Jurczak, D., Sachidanandam, R., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Genes Dev","volume":"29","issue":"16","page":"1747-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15308098","title":"Essential role of the E3 ubiquitin ligase Cbl-b in T cell anergy induction.","abstract":"Antigen-specific immunotolerance limits the expansion of self-reactive T cells involved in autoimmune diseases. Here, we show that the E3 ubiquitin ligase Cbl-b is upregulated in T cells after tolerizing signals. Loss of Cbl-b in mice results in impaired induction of T cell tolerance both in vitro and in vivo. Importantly, rechallenge of Cbl-b mutant mice with the tolerizing antigen results in massive lethality. Moreover, ablation of Cbl-b resulted in exacerbated autoimmunity. Mechanistically, loss of Cbl-b rescues reduced calcium mobilization of anergic T cells, which was attributed to Cbl-b-mediated regulation of PLCgamma-1 phosphorylation. Our results show a critical role for Cbl-b in the regulation of peripheral tolerance and anergy of T cells.","authors":"Jeon, MS., Atfield, A., Venuprasad, K., Krawczyk, C., Sarao, R., Elly, C., Yang, C., Arya, S., Bachmaier, K., Su, L., Bouchard, D., Jones, R., Gronski, M., Ohashi, P., Wada, T., Bloom, D., Fathman, CG., Liu, YC., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Immunity","volume":"21","issue":"2","page":"167-77","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15294934","title":"Cutting edge: differential roles for phosphoinositide 3-kinases, p110gamma and p110delta, in lymphocyte chemotaxis and homing.","abstract":"Despite the established role for PI3Ks in cell migration, the PI3Ks involved in lymphocyte chemotaxis are poorly defined. In this study, we report that p110gamma-deficient T cells, but not B cells, show reduced chemotactic responses to the lymphoid chemokines, CCL19, CCL21, and CXCL12. As B cell and T cell chemotactic responses were both sensitive to the general PI3K inhibitors, wortmannin (WMN) and LY294002, we explored whether B cell responses were affected in mice lacking p110delta, a major PI3K isoform in lymphocytes. B cells deficient in p110delta showed diminished chemotactic responses, especially to CXCL13. Adoptive transfer experiments with WMN-treated wild-type B cells and with p110delta-deficient B cells revealed diminished homing to Peyer's patches and splenic white pulp cords. WMN selectively inhibited CXCR5-dependent B cell homing to Peyer's patches. These observations establish that p110gamma and p110delta function in lymphocyte chemotaxis, and show differential roles for PI3K family members in B and T cell migration.","authors":"Reif, K., Okkenhaug, K., Sasaki, T., Penninger, JM., Vanhaesebroeck, B., Cyster, JG.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Immunol","volume":"173","issue":"4","page":"2236-40","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15288867","title":"Is chromatin remodeling required to build sister-chromatid cohesion?","abstract":"Chromosome segregation during mitosis and meiosis depends on the linkage of sister DNA molecules after replication. These links, known as sister-chromatid cohesion, are provided by a multi-subunit complex called cohesin. Recent papers suggest that chromatin-remodeling complexes also have a role in the generation of sister-chromatid cohesion. It remains unclear whether they do so by facilitating the recruitment of cohesin to specific chromosomal sequences or by modifying an event at replication forks giving rise to cohesion between sister DNAs.","authors":"Riedel, CG., Gregan, J., Gruber, S., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Trends Biochem Sci","volume":"29","issue":"8","page":"389-92","pdf":null,"JrId":"7837","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26066671","title":"Epigenetic Control of B Cell Development and B-Cell-Related Immune Disorders.","abstract":"B lymphocytes are generally recognized as the essential component of humoral immunity and also a regulator of innate immunity. The development of B cells is precisely regulated by a variety of factors via different mechanisms, including cytokine\/cytokine receptors, signal transduction molecules, and transcription factors. Recent findings suggest that epigenetic factors, such as DNA methylation, histone modification, and non-coding RNA, play critical roles in establishing B cell lineage-specific gene expression profiles to define and sustain B cell identity and function. Epigenetic modifications are also sensitive to external stimuli and might bridge genetic and environmental factors in the pathogenesis or control of B-cell-related immune disorders, such as autoimmune diseases, lymphoma, and leukemia. Better understanding of the epigenetic mechanisms for regulating B cell development and involving B cell abnormal differentiation and function will shed light on the design of new therapeutic approaches to B-cell-related diseases, and potential candidates of epigenetic modulators may be identified to target epigenetic pathways to prevent or treat B cell disorders. We summarize the relevance of epigenetic marks and landscapes in the stages of B cell development, discuss the interaction of the transcriptional networks and epigenetic changes, and review the involvement of epigenetic risk in the pathogenesis of B-cell-related diseases. Understanding how specific epigenetic alterations contribute to the development of B-cell-related autoimmunity and malignancies is instrumental to control B cell disorders.","authors":"Bao, Y., Cao, X.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Clin Rev Allergy Immunol","volume":"50","issue":"3","page":"301-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25891934","title":"The evolutionarily conserved transcription factor PRDM12 controls sensory neuron development and pain perception.","abstract":"PR homology domain-containing member 12 (PRDM12) belongs to a family of conserved transcription factors implicated in cell fate decisions. Here we show that PRDM12 is a key regulator of sensory neuronal specification in Xenopus. Modeling of human PRDM12 mutations that cause hereditary sensory and autonomic neuropathy (HSAN) revealed remarkable conservation of the mutated residues in evolution. Expression of wild-type human PRDM12 in Xenopus induced the expression of sensory neuronal markers, which was reduced using various human PRDM12 mutants. In Drosophila, we identified Hamlet as the functional PRDM12 homolog that controls nociceptive behavior in sensory neurons. Furthermore, expression analysis of human patient fibroblasts with PRDM12 mutations uncovered possible downstream target genes. Knockdown of several of these target genes including thyrotropin-releasing hormone degrading enzyme (TRHDE) in Drosophila sensory neurons resulted in altered cellular morphology and impaired nociception. These data show that PRDM12 and its functional fly homolog Hamlet are evolutionary conserved master regulators of sensory neuronal specification and play a critical role in pain perception. Our data also uncover novel pathways in multiple species that regulate evolutionary conserved nociception.","authors":"Nagy, V., Cole, T., Van Campenhout, C., Khoung, TM., Leung, C., Vermeiren, S., Novatchkova, M., Wenzel, D., Cikes, D., Polyansky, AA., Kozieradzki, I., Meixner, A., Bellefroid, EJ., Neely, GG., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell Cycle","volume":"14","issue":"12","page":"1799-808","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15254018","title":"Differential expression of a novel ankyrin containing E3 ubiquitin-protein ligase, Hace1, in sporadic Wilms' tumor versus normal kidney.","abstract":"We have analyzed the chromosome 6q21 breakpoint of a non-constitutional t(6;15)(q21;q21) rearrangement in sporadic Wilms' tumor. This identified a novel gene encoding a protein with six N-terminal ankyrin repeats linked to a C-terminal HECT ubiquitin-protein ligase domain. We therefore designated this gene HACE1 (HECT domain and Ankyrin repeat Containing E3 ubiquitin-protein ligase 1). HACE1 is widely expressed in human tissues, including mature and fetal kidney. We show that Hace1 protein possesses intrinsic ubiquitin ligase activity, utilizes UbcH7 as a candidate partner E2 enzyme and localizes predominantly to the endoplasmic reticulum. Although the HACE1 locus was not directly interrupted by the translocation in the index Wilms' case, its expression was markedly lower in tumor tissue compared with adjacent normal kidney. Moreover, HACE1 expression was virtually undetectable in the SK-NEP-1 Wilms' tumor cell line and in four of five additional primary Wilms' tumor cases compared with patient-matched normal kidney. We found no evidence of HACE1 mutations or deletions, but hypermethylation of two upstream CpG islands correlates with low HACE1 expression in tumor samples. Our findings implicate Hace1 as a novel ubiquitin-protein ligase and demonstrate that its expression is very low in primary Wilms' tumors.","authors":"Anglesio, MS., Evdokimova, V., Melnyk, N., Zhang, L., Fernandez, CV., Grundy, PE., Leach, S., Marra, MA., Brooks-Wilson, AR., Penninger, J., Sorensen, PH.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Hum Mol Genet","volume":"13","issue":"18","page":"2061-74","pdf":null,"JrId":"2407","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15273393","title":"Phosphorylation by cyclin B-Cdk underlies release of mitotic exit activator Cdc14 from the nucleolus.","abstract":"Budding yeast protein phosphatase Cdc14 is sequestered in the nucleolus in an inactive state during interphase by the anchor protein Net1. Upon entry into anaphase, the Cdc14 early anaphase release (FEAR) network initiates dispersal of active Cdc14 throughout the cell. We report that the FEARnetwork promotes phosphorylation of Net1 by cyclin-dependent kinase (Cdk) complexed with cyclin B1 or cyclin B2. These phosphorylations appear to be required for FEAR and sustain the proper timing of late mitotic events. Thus, a regulatory circuit exists to ensure that the arbiter of the mitotic state, Cdk, sets in motion events that culminate in exit from mitosis.","authors":"Azzam, R., Chen, SL., Shou, W., Mah, AS., Alexandru, G., Nasmyth, K., Annan, RS., Carr, SA., Deshaies, RJ.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Science","volume":"305","issue":"5683","page":"516-9","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25619250","title":"Pushing with actin: from cells to pathogens.","abstract":"Actin polymerization is harnessed by cells to generate lamellipodia for movement and by a subclass of pathogens to facilitate invasion of their infected hosts. Using electron tomography (ET), we have shown that lamellipodia are formed via the generation of subsets of actin filaments joined by branch junctions. Image averaging produced a 2.9\u00a0nm resolution model of branch junctions in situ and revealed a close fit to the electron density map of the actin-related protein 2\/3 (Arp2\/3)-actin complex in\u00a0vitro. Correlated live-cell imaging and ET was also used to determine how actin networks are created and remodelled during the initiation and inhibition of protrusion in lamellipodia. Listeria, Rickettsia and viruses, such as vaccinia virus and baculovirus, exploit the actin machinery of host cells to generate propulsive actin comet tails to disseminate their infection. By applying ET, we have shown that baculovirus generates at its rear a fishbone-like array of subsets of branched actin filaments, with an average of only four filaments engaged in pushing at any one time. In both of these studies, the application of ET of negatively stained cytoskeletons for higher filament resolution and cryo-ET for preserving overall 3D morphology was crucial for obtaining a complete structure-function analysis of actin-driven propulsion.","authors":"Small, JV.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Biochem Soc Trans","volume":"43","issue":"1","page":"84-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15242616","title":"Regulation of sister chromatid cohesion between chromosome arms.","abstract":"Sister chromatid separation in anaphase depends on the removal of cohesin complexes from chromosomes. In vertebrates, the bulk of cohesin is already removed from chromosome arms during prophase and prometaphase, whereas cohesin remains at centromeres until metaphase, when cohesin is cleaved by the protease separase. In unperturbed mitoses, arm cohesion nevertheless persists throughout metaphase and is principally sufficient to maintain sister chromatid cohesion. How arm cohesion is maintained until metaphase is unknown. Here we show that small amounts of cohesin can be detected in the interchromatid region of metaphase chromosome arms. If prometaphase is prolonged by treatment of cells with microtubule poisons, these cohesin complexes dissociate from chromosome arms, and arm cohesion is dissolved. If cohesin dissociation in prometaphase-arrested cells is prevented by depletion of Plk1 or inhibition of Aurora B, arm cohesion is maintained. These observations imply that, in unperturbed mitoses, small amounts of cohesin maintain arm cohesion until metaphase. When cells lacking Plk1 and Aurora B activity enter anaphase, chromatids lose cohesin. This loss is prevented by proteasome inhibitors, implying that it depends on separase activation. Separase may therefore be able to cleave cohesin at centromeres and on chromosome arms.","authors":"Gim\u00e9nez-Abi\u00e1n, JF., Sumara, I., Hirota, T., Hauf, S., Gerlich, D., de la Torre, C., Ellenberg, J., Peters, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"13","page":"1187-93","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-212","title":"Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity ","abstract":null,"authors":"Schwartz I,  Budroni V,  Meyenberg M,  Hornegger H,  Hacker K,  Schwartz S,  Hodakova  Z,  Grabarczyk DB,  Ehrmann JF ,  Scinicariello S,  Haselbach D, Menche J, Clausen T,  Karag\u00f6z E,  Versteeg GA","publication_status":"preprint","journalpubyear":"2024","journaltitle":"bioRxiv","volume":"2024.04.23.590688","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.04.23.590688v2","preprintlink":null,"articledate":"2024-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15252442","title":"A chromosomal memory triggered by Xist regulates histone methylation in X inactivation.","abstract":"We have elucidated the kinetics of histone methylation during X inactivation using an inducible Xist expression system in mouse embryonic stem (ES) cells. Previous reports showed that the ability of Xist to trigger silencing is restricted to an early window in ES cell differentiation. Here we show that this window is also important for establishing methylation patterns on the potential inactive X chromosome. By immunofluorescence and chromatin immunoprecipitation experiments we show that histone H3 lysine 27 trimethylation (H3K27m3) and H4 lysine 20 monomethylation (H4K20m1) are associated with Xist expression in undifferentiated ES cells and mark the initiation of X inactivation. Both marks depend on Xist RNA localisation but are independent of silencing. Induction of Xist expression after the initiation window leads to a markedly reduced ability to induce H3K27m3, whereas expression before the restrictive time point allows efficient H3K27m3 establishment. Our data show that Xist expression early in ES cell differentiation establishes a chromosomal memory, which is maintained in the absence of silencing. One consequence of this memory is the ability to introduce H3K27m3 efficiently after the restrictive time point on the chromosome that has expressed Xist early. Our results suggest that this silencing-independent chromosomal memory has important implications for the maintenance of X inactivation, where previously self-perpetuating heterochromatin structures were viewed as the principal form of memory.","authors":"Kohlmaier, A., Savarese, F., Lachner, M., Martens, J., Jenuwein, T., Wutz, A.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"PLoS Biol","volume":"2","issue":"7","page":"E171","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25737280","title":"Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt.","abstract":"Cellular morphology is an essential determinant of cellular function in all kingdoms of life, yet little is known about how cell shape is controlled. Here we describe a molecular program that controls the early morphology of neurons through a metazoan-specific zinc finger protein, Unkempt. Depletion of Unkempt in mouse embryos disrupts the shape of migrating neurons, while ectopic expression confers neuronal-like morphology to cells of different nonneuronal lineages. We found that Unkempt is a sequence-specific RNA-binding protein and identified its precise binding sites within coding regions of mRNAs linked to protein metabolism and trafficking. RNA binding is required for Unkempt-induced remodeling of cellular shape and is directly coupled to a reduced production of the encoded proteins. These findings link post-transcriptional regulation of gene expression with cellular shape and have general implications for the development and disease of multicellular organisms.","authors":"Murn, J., Zarnack, K., Yang, YJ., Durak, O., Murphy, EA., Cheloufi, S., Gonzalez, DM., Teplova, M., Curk, T., Zuber, J., Patel, DJ., Ule, J., Luscombe, NM., Tsai, LH., Walsh, CA., Shi, Y.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Genes Dev","volume":"29","issue":"5","page":"501-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25483092","title":"Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation.","abstract":"Phosphorylation by the cyclin-dependent kinase 1 (Cdk1) adjacent to nuclear localization signals (NLSs) is an important mechanism of regulation of nucleocytoplasmic transport. However, no systematic survey has yet been performed in human cells to analyze this regulatory process, and the corresponding cell-cycle dynamics have not yet been investigated. Here, we focused on the human proteome and found that numerous proteins, previously not identified in this context, are associated with Cdk1-dependent phosphorylation sites adjacent to their NLSs. Interestingly, these proteins are involved in key regulatory events of DNA repair, epigenetics, or RNA editing and splicing. This finding indicates that cell-cycle dependent events of genome editing and gene expression profiling may be controlled by nucleocytoplasmic trafficking. For in-depth investigations, we selected a number of these proteins and analyzed how point mutations, expected to modify the phosphorylation ability of the NLS segments, perturb nucleocytoplasmic localization. In each case, we found that mutations mimicking hyper-phosphorylation abolish nuclear import processes. To understand the mechanism underlying these phenomena, we performed a video microscopy-based kinetic analysis to obtain information on cell-cycle dynamics on a model protein, dUTPase. We show that the NLS-adjacent phosphorylation by Cdk1 of human dUTPase, an enzyme essential for genomic integrity, results in dynamic cell cycle-dependent distribution of the protein. Non-phosphorylatable mutants have drastically altered protein re-import characteristics into the nucleus during the G1 phase. Our results suggest a dynamic Cdk1-driven mechanism of regulation of the nuclear proteome composition during the cell cycle.","authors":"R\u00f3na, G., Borsos, M., Ellis, JJ., Mehdi, AM., Christie, M., K\u00f6rnyei, Z., Neubrandt, M., T\u00f3th, J., Boz\u00f3ky, Z., Buday, L., Madar\u00e1sz, E., Bod\u00e9n, M., Kobe, B., V\u00e9rtessy, BG.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell Cycle","volume":"13","issue":"22","page":"3551-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15233917","title":"The AP-1 transcription factor c-Jun is required for efficient axonal regeneration.","abstract":"Nerve injury triggers numerous changes in the injured neurons and surrounding nonneuronal cells that ultimately result in successful target reinnervation or cell death. c-Jun is a component of the heterodimeric AP-1 transcription factor, and c-Jun is highly expressed in response to neuronal trauma. Here we have investigated the role of c-jun during axonal regeneration using mice lacking c-jun in the central nervous system. After transection of the facial nerve, the absence of c-Jun caused severe defects in several aspects of the axonal response, including perineuronal sprouting, lymphocyte recruitment, and microglial activation. c-Jun-deficient motorneurons were atrophic, resistant to axotomy-induced cell death, and showed reduced target muscle reinnervation. Expression of CD44, galanin, and alpha7beta1 integrin, molecules known to be involved in regeneration, was greatly impaired, suggesting a mechanism for c-Jun-mediated axonal growth. Taken together, our results identify c-Jun as an important regulator of axonal regeneration in the injured central nervous system.","authors":"Raivich, G., Bohatschek, M., Da Costa, C., Iwata, O., Galiano, M., Hristova, M., Nateri, AS., Makwana, M., Riera-Sans, L., Wolfer, DP., Lipp, HP., Aguzzi, A., Wagner, EF., Behrens, A.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Neuron","volume":"43","issue":"1","page":"57-67","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10403247","title":"Sister-chromatid separation at anaphase onset is promoted by cleavage of the cohesin subunit Scc1.","abstract":"Cohesion between sister chromatids is established during DNA replication and depends on a multiprotein complex called cohesin. Attachment of sister kinetochores to the mitotic spindle during mitosis generates forces that would immediately split sister chromatids were it not opposed by cohesion. Cohesion is essential for the alignment of chromosomes in metaphase but must be abolished for sister separation to start during anaphase. In the budding yeast Saccharomyces cerevisiae, loss of sister-chromatid cohesion depends on a separating protein (separin) called Esp1 and is accompanied by dissociation from the chromosomes of the cohesion subunit Scc1. Here we show that Esp1 causes the dissociation of Scc1 from chromosomes by stimulating its cleavage by proteolysis. A mutant Scc1 is described that is resistant to Esp1-dependent cleavage and which blocks both sister-chromatid separation and the dissociation of Scc1 from chromosomes. The evolutionary conservation of separins indicates that the proteolytic cleavage of cohesion proteins might be a general mechanism for triggering anaphase.","authors":"Uhlmann, F., Lottspeich, F., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nature","volume":"400","issue":"6739","page":"37-42","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1999-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-208","title":"PITHD1: An Endogenous Inhibitor of the 26S Proteasome During Cellular Dormancy ","abstract":null,"authors":"Amann SJ, Dong K, Roehsner J, Krall D, Grishkovskaya I, Kotisch H, Schleiffer A, Roitinger E, Pauli A, Martin A, Haselbach D","publication_status":"preprint","journalpubyear":"2024","journaltitle":"bioRxiv ","volume":"2024.12.04.626795 ","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.12.04.626795v1","preprintlink":null,"articledate":"2024-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10102630","title":"FLI-1 inhibits differentiation and induces proliferation of primary erythroblasts.","abstract":"Friend virus-induced erythroleukemia involves two members of the ETS family of transcriptional regulators, both activated via proviral insertion in the corresponding loci. Spi-1\/PU.1 is expressed in the disease induced by the original Friend virus SFFV(F-MuLV) complex in adult mice. In contrast, FLI-1 is overexpressed in about 75% of the erythroleukemias induced by the F-MuLV helper virus in newborn mice. To analyse the consequences of the enforced expression of FLI-1 on erythroblast differentiation and proliferation and to compare its activity to that of PU.1\/Spi-1, we used a heterologous system of avian primary erythroblasts previously described to study the cooperation between Spi-1\/PU.1 and the other molecular alterations observed in SFFV-induced disease. FLI-1 was found: (i) to inhibit the apoptotic cell death program normally activated in erythroblasts following Epo deprivation; (ii) to inhibit the terminal differentiation program induced in these cells in response to Epo and; (iii) to induce their proliferation. However, in contrast to Spi-1\/PU.1, the effects of FLI-1 on erythroblast, differentiation and proliferation did not require its cooperation with an abnormally activated form of the EpoR. Enhanced survival of FLI-1 expressing erythroblasts correlated with the upregulation of bcl2 expression. FLI-1 also prevented the rapid downregulation of cyclin D2 and D3 expression normally observed during Epo-induced differentiation and delayed the downregulation of several other genes involved in cell cycle or cell proliferation control. Our results show that overexpression of FLI-1 profoundly deregulates the normal balance between differentiation and proliferation in primary erythroblasts. Thus, the activation of FLI-1 expression observed at the onset of F-MuLV-induced erythroleukemia may provide a proliferative advantage to virus infected cells that would otherwise undergo terminal differentiation or cell death.","authors":"Pereira, R., Quang, CT., Lesault, I., Dolznig, H., Beug, H., Ghysdael, J.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Oncogene","volume":"18","issue":"8","page":"1597-608","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15239950","title":"Muscle building; mechanisms of myotube guidance and attachment site selection.","abstract":"The complex muscle patterns of higher organisms arise as migrating myoblasts are guided toward and connect with specific attachment sites. We review here the current understanding of myotube migration, focusing on its dynamic nature and the few molecular cues that have been identified to date. Much of this knowledge comes from studies in Drosophila, where powerful methods for in vivo imaging and genetic manipulation can be used to tackle this important but largely unsolved problem in developmental biology.","authors":"Schnorrer, F., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Dev Cell","volume":"7","issue":"1","page":"9-20","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15196000","title":"The Btk inhibitor LFM-A13 is a potent inhibitor of Jak2 kinase activity.","abstract":"LFM-A13, or alpha-cyano-beta-hydroxy-beta-methyl-N-(2,5-dibromophenyl)propenamide, was shown to inhibit Bruton's tyrosine kinase (Btk). Here we show that LFM-A13 efficiently inhibits erythropoietin (Epo)-induced phosphorylation of the erythropoietin receptor, Janus kinase 2 (Jak2) and downstream signalling molecules. However, the tyrosine kinase activity of immunoprecipitated or in vitro translated Btk and Jak2 was equally inhibited by LFM-A13 in in vitro kinase assays. Finally, Epo-induced signal transduction was also inhibited in cells lacking Btk. Taken together, we conclude that LFM-A13 is a potent inhibitor of Jak2 and cannot be used as a specific tyrosine kinase inhibitor to study the role of Btk in Jak2-dependent cytokine signalling.","authors":"van den Akker, E., van Dijk, TB., Schmidt, U., Felida, L., Beug, H., L\u00f6wenberg, B., von Lindern, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Biol Chem","volume":"385","issue":"5","page":"409-13","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15229648","title":"The Fos-related antigen Fra-1 is an activator of bone matrix formation.","abstract":"Ectopic expression of the transcription factor Fra-1 in transgenic mice leads to osteosclerosis, a bone disorder characterized by increased bone mass. The molecular basis for this phenotype is unknown and Fra-1 functions cannot be studied by a conventional loss-of-function approach, since fra-1-knockout mice die in utero likely due to placental defects. Here we show that the lethality of fra-1-knockout mice can be rescued by specific deletion of Fra-1 only in the mouse embryo and not in the placenta. Mice lacking Fra-1 (fra-1(delta\/delta)) are viable and develop osteopenia, a low bone mass disease. Long bones of fra-1(delta\/delta) mice appear to have normal osteoclasts but express reduced amounts of bone matrix components produced by osteoblasts and chondrocytes such as osteocalcin, collagen1a2 and matrix Gla protein. The gene for matrix Gla protein seems to be a specific target of Fra-1 since its expression was markedly increased in the long bones of fra-1-transgenic mice. These results uncover a novel function of Fra-1 in regulating bone mass through bone matrix production by osteoblasts and chondrocytes.","authors":"Eferl, R., Hoebertz, A., Schilling, AF., Rath, M., Karreth, F., Kenner, L., Amling, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"EMBO J","volume":"23","issue":"14","page":"2789-99","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25128497","title":"CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma.","abstract":"One-year survival rates for newly diagnosed hepatocellular carcinoma (HCC) are &lt;50%, and unresectable HCC carries a dismal prognosis owing to its aggressiveness and the undruggable nature of its main genetic drivers. By screening a custom library of shRNAs directed toward known drug targets in a genetically defined Myc-driven HCC model, we identified cyclin-dependent kinase 9 (Cdk9) as required for disease maintenance. Pharmacological or shRNA-mediated CDK9 inhibition led to robust anti-tumor effects that correlated with MYC expression levels and depended on the role that both CDK9 and MYC exert in transcription elongation. Our results establish CDK9 inhibition as a therapeutic strategy for MYC-overexpressing liver tumors and highlight the relevance of transcription elongation in the addiction of cancer cells to MYC.","authors":"Huang, CH., Lujambio, A., Zuber, J., Tschaharganeh, DF., Doran, MG., Evans, MJ., Kitzing, T., Zhu, N., de Stanchina, E., Sawyers, CL., Armstrong, SA., Lewis, JS., Sherr, CJ., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genes Dev","volume":"28","issue":"16","page":"1800-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10972292","title":"Colorectal carcinomas in mice lacking the catalytic subunit of PI(3)Kgamma.","abstract":"Phosphoinositide-3-OH kinases (PI(3)Ks) constitute a family of evolutionarily conserved lipid kinases that regulate a vast array of fundamental cellular responses, including proliferation, transformation, differentiation and protection from apoptosis. PI(3)K-mediated activation of the cell survival kinase PKB\/Akt, and negative regulation of PI(3)K signalling by the tumour suppressor PTEN (refs 3, 4) are key regulatory events in tumorigenesis. Thus, a model has arisen that PI(3)Ks promote development of cancers. Here we report that genetic inactivation of the p110gamma catalytic subunit of PI(3)Kgamma (ref. 8) leads to development of invasive colorectal adenocarcinomas in mice. In humans, p110gamma protein expression is lost in primary colorectal adenocarcinomas from patients and in colon cancer cell lines. Overexpression of wild-type or kinase-dead p110gamma in human colon cancer cells with mutations of the tumour suppressors APC and p53, or the oncogenes beta-catenin and Ki-ras, suppressed tumorigenesis. Thus, loss of p110gamma in mice leads to spontaneous, malignant epithelial tumours in the colorectum and p110gamma can block the growth of human colon cancer cells.","authors":"Sasaki, T., Irie-Sasaki, J., Horie, Y., Bachmaier, K., Fata, JE., Li, M., Suzuki, A., Bouchard, D., Ho, A., Redston, M., Gallinger, S., Khokha, R., Mak, TW., Hawkins, PT., Stephens, L., Scherer, SW., Tsao, M., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nature","volume":"406","issue":"6798","page":"897-902","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15209214","title":"[Setting the stage for mitosis: kinase regulation of prophase].","abstract":null,"authors":"Hirota, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Tanpakushitsu Kakusan Koso","volume":"49","issue":"8","page":"1183-94","pdf":null,"JrId":"6726","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15203009","title":"Changing places. Interview by Graham Tebb.","abstract":"Kim Nasmyth is set to move from the Institute of Molecular Pathology in Vienna to take up a new post in Oxford. He talks to Graham Tebb about his reasons for returning to the UK and plans for the future.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"12","page":"R452-3","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15196465","title":"Small RNAs in genome rearrangement in Tetrahymena.","abstract":"Small RNAs produced by an RNAi-related mechanism are involved in DNA elimination during development of the somatic macronucleus from the germline micronucleus in Tetrahymena. The properties of these small RNAs can explain how the primary sequence of the parental macronucleus epigenetically controls genome rearrangement in the new macronucleus and provide the first demonstration of an RNAi-mediated process that directly alters DNA sequence organization. Methylation of histone H3 on lysine 9 and accumulation of chromodomain proteins, hallmarks of heterochromatin, also occur specifically on sequences undergoing elimination and are dependent on the small RNAs. These findings contribute to a new paradigm of chromatin biology: regulation of heterochromatin formation by RNAi-related mechanisms in eukaryotes.","authors":"Mochizuki, K., Gorovsky, MA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Opin Genet Dev","volume":"14","issue":"2","page":"181-7","pdf":null,"JrId":"2199","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24960695","title":"Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids.","abstract":"Membrane phospholipids typically contain fatty acids (FAs) of 16 and 18 carbon atoms. This particular chain length is evolutionarily highly conserved and presumably provides maximum stability and dynamic properties to biological membranes in response to nutritional or environmental cues. Here, we show that the relative proportion of C16 versus C18 FAs is regulated by the activity of acetyl-CoA carboxylase (Acc1), the first and rate-limiting enzyme of FA de novo synthesis. Acc1 activity is attenuated by AMPK\/Snf1-dependent phosphorylation, which is required to maintain an appropriate acyl-chain length distribution. Moreover, we find that the transcriptional repressor Opi1 preferentially binds to C16 over C18 phosphatidic acid (PA) species: thus, C16-chain containing PA sequesters Opi1 more effectively to the ER, enabling AMPK\/Snf1 control of PA acyl-chain length to determine the degree of derepression of Opi1 target genes. These findings reveal an unexpected regulatory link between the major energy-sensing kinase, membrane lipid composition, and transcription.","authors":"Hofbauer, HF., Schopf, FH., Schleifer, H., Knittelfelder, OL., Pieber, B., Rechberger, GN., Wolinski, H., Gaspar, ML., Kappe, CO., Stadlmann, J., Mechtler, K., Zenz, A., Lohner, K., Tehlivets, O., Henry, SA., Kohlwein, SD.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Dev Cell","volume":"29","issue":"6","page":"729-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25054083","title":"The taming of the shrew: Regulation of a catalytically active domesticated transposase.","abstract":"Transposons are mobile genetic elements that can be harmful for the host when mobilized. However, they are also genomic reservoirs for novel genes that can be evolutionarily beneficial. There are many examples of domesticated transposases, which play important roles in the hosts. In most cases domesticated transposases have lost their endonuclease activities and the hosts utilize their DNA-binding properties. However, some other domesticated transposases perform endonuclease activities for host biological processes. Because such a catalytically active transposase is potentially harmful for the integrity of the host genome, its activity should be tightly regulated. The catalytically active domesticated <i>piggyBac<\/i> transposase Tpb2p catalyzes programmed DNA elimination in the ciliate <i>Tetrahymena<\/i>. Here, we discuss the regulatory mechanism that prevents unintended DNA cleavage by Tpb2p and compare it to another well-studied catalytically active domesticated transposase, the RAG recombinase in V(D)J recombination. The regulatory mechanisms involve the temporarily regulated expression of the transposases, the target sequence preference of the endonuclease, and the recruitment of the transposases to locally restricted chromatin environments.","authors":"Vogt, A., Mochizuki, K.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Mob Genet Elements","volume":"4","issue":null,"page":"e29383","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15182311","title":"DREAM ablation selectively alters THC place aversion and analgesia but leaves intact the motivational and analgesic effects of morphine.","abstract":"DREAM (downstream regulatory element antagonistic modulator) is a novel transcriptional repressor for the prodynorphin gene, and genetic deletion of DREAM in mice results in a phenotype of ongoing analgesia by virtue of its effect on opioid gene expression. In the present study, we evaluated the motivational effects of opioids (morphine), cannabinoids [Delta(9)-tetrahydrocannabinol (THC)] and cocaine in mice lacking the dream gene (dream(-\/-)). The aversive effects of THC were potentiated in dream(-\/-) mice in a kappa-opioid receptor-dependent fashion, whereas morphine reward and the aversive effects of morphine withdrawal remained intact. The rewarding and aversive effects of cocaine were likewise unperturbed in dream(-\/-) mice. Moreover, the aversive properties of lithium chloride and naloxone were unaffected by the absence of DREAM, indicating that the effect of DREAM on THC-induced dysphoria is not due to a general involvement in the behavioral response to aversive stimuli. Additionally, physical dependence to morphine and the locomotor-sensitizing effects of cocaine were unaltered in these animals. Finally, whereas the absence of DREAM reduced the analgesic efficacy of THC, morphine analgesia was unaffected in dream(-\/-) mice.","authors":"Cheng, HY., Laviolette, SR., van der Kooy, D., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Eur J Neurosci","volume":"19","issue":"11","page":"3033-41","pdf":null,"JrId":"2607","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24766809","title":"Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function.","abstract":"CLP1 is a RNA kinase involved in tRNA splicing. Recently, CLP1 kinase-dead mice were shown to display a neuromuscular disorder with loss of motor neurons and muscle paralysis. Human genome analyses now identified a CLP1 homozygous missense mutation (p.R140H) in five unrelated families, leading to a loss of CLP1 interaction with the tRNA splicing endonuclease (TSEN) complex, largely reduced pre-tRNA cleavage activity, and accumulation of linear tRNA introns. The affected individuals develop severe motor-sensory defects, cortical dysgenesis, and microcephaly. Mice carrying kinase-dead CLP1 also displayed microcephaly and reduced cortical brain volume due to the enhanced cell death of neuronal progenitors that is associated with reduced numbers of cortical neurons. Our data elucidate a neurological syndrome defined by CLP1 mutations that impair tRNA splicing. Reduction of a founder mutation to homozygosity illustrates the importance of rare variations in disease and supports the clan genomics hypothesis.","authors":"Karaca, E., Weitzer, S., Pehlivan, D., Shiraishi, H., Gogakos, T., Hanada, T., Jhangiani, SN., Wiszniewski, W., Withers, M., Campbell, IM., Erdin, S., Isikay, S., Franco, LM., Gonzaga-Jauregui, C., Gambin, T., Gelowani, V., Hunter, JV., Yesil, G., Koparir, E., Yilmaz, S., Brown, M., Briskin, D., Hafner, M., Morozov, P., Farazi, TA., Bernreuther, C., Glatzel, M., Trattnig, S., Friske, J., Kronnerwetter, C., Bainbridge, MN., Gezdirici, A., Seven, M., Muzny, DM., Boerwinkle, E., Ozen, M., Clausen, T., Tuschl, T., Yuksel, A., Hess, A., Gibbs, RA., Martinez, J., Penninger, JM., Lupski, JR.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell","volume":"157","issue":"3","page":"636-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15166028","title":"Directed differentiation and mass cultivation of pure erythroid progenitors from mouse embryonic stem cells.","abstract":"Differentiating embryonic stem (ES) cells are an increasingly important source of hematopoietic progenitors, useful for both basic research and clinical applications. Besides their characterization in colony assays, protocols exist for the cultivation of lymphoid, myeloid, and erythroid cells. With the possible exception of mast cells, however, long-term expansion of pure hematopoietic progenitors from ES cells has not been possible without immortalization caused by overexpression of exogenous genes. Here, we describe for the first time an efficient yet easy strategy to generate mass cultures of pure, immature erythroid progenitors from mouse ES cells (ES-EPs), using serum-free medium plus recombinant cytokines and hormones. ES-EPs represent long-lived, adult, definitive erythroid progenitors that resemble immature erythroid cells expanding in vivo during stress erythropoiesis. When exposed to terminal differentiation conditions, ES-EPs differentiated into mature, enucleated erythrocytes. Importantly, ES-EPs injected into mice did not exhibit tumorigenic potential but differentiated into normal erythrocytes. Both the virtually unlimited supply of cells and the defined culture conditions render our system a valuable tool for the analysis of factors influencing proliferation and maturation of erythroid progenitors. In addition, the system allows detailed characterization of processes during erythroid proliferation and differentiation using wild-type (wt) and genetically modified ES cells.","authors":"Carotta, S., Pilat, S., Mairhofer, A., Schmidt, U., Dolznig, H., Steinlein, P., Beug, H.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Blood","volume":"104","issue":"6","page":"1873-80","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11070165","title":"Cbl-b is a negative regulator of receptor clustering and raft aggregation in T cells.","abstract":"Stimulation of T cells via the antigen and costimulatory receptors leads to the organization of a supramolecular activation cluster called the immune synapse. We report that loss of the molecular adaptor Cbl-b in T cells frees antigen receptor-triggered receptor clustering, lipid raft aggregation, and sustained tyrosine phosphorylation from the requirement for CD28 costimulation. Introduction of the cbl-b mutation into a vav1-\/- background relieved the functional defects of vav1-\/- T cells and caused spontaneous autoimmunity. Wiscott Aldrich Syndrome protein (WASP) was found to be essential for deregulated proliferation and membrane receptor reorganization of cbl-b mutant T cells. Antigen receptor-triggered Ca2+ mobilization, cytokine production, and receptor clustering can be genetically uncoupled in cbl-b mutant T cells. Thus, Cbl-b functions as a negative regulator of receptor clustering and raft aggregation in T cells.","authors":"Krawczyk, C., Bachmaier, K., Sasaki, T., Jones, RG., Snapper, SB., Bouchard, D., Kozieradzki, I., Ohashi, PS., Alt, FW., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Immunity","volume":"13","issue":"4","page":"463-73","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23132240","title":"Drosophila neuroblasts: a model for stem cell biology.","abstract":"Drosophila neuroblasts, the stem cells of the developing fly brain, have emerged as a key model system for neural stem cell biology and have provided key insights into the mechanisms underlying asymmetric cell division and tumor formation. More recently, they have also been used to understand how neural progenitors can generate different neuronal subtypes over time, how their cell cycle entry and exit are coordinated with development, and how proliferation in the brain is spared from the growth restrictions that occur in other organs upon starvation. In this Primer, we describe the biology of Drosophila neuroblasts and highlight the most recent advances made using neuroblasts as a model system.","authors":"Homem, CC., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Development","volume":"139","issue":"23","page":"4297-310","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15145825","title":"A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin.","abstract":"Histone lysine methylation is a central modification to mark functionally distinct chromatin regions. In particular, H3-K9 trimethylation has emerged as a hallmark of pericentric heterochromatin in mammals. Here we show that H4-K20 trimethylation is also focally enriched at pericentric heterochromatin. Intriguingly, H3-K9 trimethylation by the Suv39h HMTases is required for the induction of H4-K20 trimethylation, although the H4 Lys 20 position is not an intrinsic substrate for these enzymes. By using a candidate approach, we identified Suv4-20h1 and Suv4-20h2 as two novel SET domain HMTases that localize to pericentric heterochromatin and specifically act as nucleosomal H4-K20 trimethylating enzymes. Interaction of the Suv4-20h enzymes with HP1 isoforms suggests a sequential mechanism to establish H3-K9 and H4-K20 trimethylation at pericentric heterochromatin. Heterochromatic H4-K20 trimethylation is evolutionarily conserved, and in Drosophila, the Suv4-20 homolog is a novel PEV modifier to regulate position-effect variegation. Together, our data indicate a function for H4-K20 trimethylation in gene silencing and further suggest H3-K9 and H4-K20 trimethylation as important components of a repressive pathway that can index pericentric heterochromatin.","authors":"Schotta, G., Lachner, M., Sarma, K., Ebert, A., Sengupta, R., Reuter, G., Reinberg, D., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genes Dev","volume":"18","issue":"11","page":"1251-62","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15174131","title":"Prediction of sequence signals for lipid post-translational modifications: insights from case studies.","abstract":"In silico annotation techniques for post-translational modifications (PTMs) are important to generate biologically meaningful descriptions for sequences of experimentally uncharacterized proteins. Having previously contributed with predictors for lipid PTMs, we summarize our methodological experience. Rather than only looking for the sequence pattern in substrate sequences, a strategy aimed at creating a generalized model of substrate protein\/enzyme interaction appears more appropriate since the number of known substrate sequences is small, and some of them are not sufficiently verified experimentally. Such a physical approach (in contrast to a mere textual analysis of substrate sequences) can also take into account other, heterogeneous biological data (mutations of substrate sequences, kinetic data, enzyme sequences\/structures) with simple analytical expressions in the score function. Several lipid PTMs are encoded in the form of a small sequence region (with pronounced amino acid type preferences) that is connected to the substrate protein by a linker region with many conformationally flexible, hydrophilic residues. A score function composed of terms penalizing sequence properties known to be incompatible with productive substrate protein\/enzyme complexes essentially unselects inappropriate queries. Also, we estimate the number of nonredundant sequences necessary for robust profile computation with statistical criteria, a number that is not reached in most cases of PTM prediction. Finally, we discuss the usage of evolutionary information in evaluating the functional importance of predicted PTMs in cases of motif conservation within sequence families.","authors":"Eisenhaber, B., Eisenhaber, F., Maurer-Stroh, S., Neuberger, G.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Proteomics","volume":"4","issue":"6","page":"1614-25","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-210","title":"PHLPP2 is a pseudophosphatase that lost activity in the metazoan ancestor ","abstract":null,"authors":"Husremovi\u0107 T, Siess KM, Antonioli S, Meier V, Pi\u00ebch L, Grishkovskaya I, Kircheva N, Angelova SE, Brandst\u00e4tter A, Veis J, Mio\u010di\u0107-Sto\u0161i\u0107 F, Anrather D, Hartl M, Truebestein L, \u017dagrovi\u0107 B, Hann S, Bock C, Ogris E, Dudev T, Irwin NAT, Haselbach D, Leonard TA","publication_status":"preprint","journalpubyear":"2024","journaltitle":"bioRxiv","volume":"2024.12.03.625870 ","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.12.03.625870v2","preprintlink":null,"articledate":"2024-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24725403","title":"Differentiation of type 1 ILCs from a common progenitor to all helper-like innate lymphoid cell lineages.","abstract":"Innate lymphoid cells (ILCs) are a recently recognized group of lymphocytes that have important functions in protecting epithelial barriers against infections and in maintaining organ homeostasis. ILCs have been categorized into three distinct groups, transcriptional circuitry and effector functions of which strikingly resemble the various T helper cell subsets. Here, we identify a common, Id2-expressing progenitor to all interleukin 7 receptor-expressing, \"helper-like\" ILC lineages, the CHILP. Interestingly, the CHILP differentiated into ILC2 and ILC3 lineages, but not into conventional natural killer (cNK) cells that have been considered an ILC1 subset. Instead, the CHILP gave rise to a peculiar NKp46(+) IL-7R\u03b1(+) ILC lineage that required T-bet for specification and was distinct of cNK cells or other ILC lineages. Such ILC1s coproduced high levels of IFN-\u03b3 and TNF and protected against infections with the intracellular parasite Toxoplasma gondii. Our data significantly advance our understanding of ILC differentiation and presents evidence for a new ILC lineage that protects barrier surfaces against intracellular infections.","authors":"Klose, CSN., Flach, M., M\u00f6hle, L., Rogell, L., Hoyler, T., Ebert, K., Fabiunke, C., Pfeifer, D., Sexl, V., Fonseca-Pereira, D., Domingues, RG., Veiga-Fernandes, H., Arnold, SJ., Busslinger, M., Dunay, IR., Tanriver, Y., Diefenbach, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell","volume":"157","issue":"2","page":"340-356","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15107616","title":"Stress kinase MKK7: savior of cell cycle arrest and cellular senescence.","abstract":"The c-Jun N-terminal kinase (JNK\/SAPK) signaling cascade controls a spectrum of cellular processes, including cell growth, differentiation, transformation, and apoptosis. We recently demonstrated that stress kinase MKK7, a direct activator of JNKs, couples stress signaling to G2\/M cell cycle progression, CDC2 expression, and cellular senescence. We further explored other molecules involved in JNK pathway and found that both MKK4, another direct activator of JNK, and c-Jun, a direct substrate of JNK, have similar roles to MKK7. Here we discuss the importance of the MKK4\/MKK7-JNK-c-Jun pathway linking stress and developmental signals to cell proliferation, cell cycle progression, cellular senescence, and apoptosis including recent unpublished data from our lab.","authors":"Wada, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell Cycle","volume":"3","issue":"5","page":"577-9","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15166136","title":"In vivo analysis of synaptonemal complex formation during yeast meiosis.","abstract":"During meiotic prophase a synaptonemal complex (SC) forms between each pair of homologous chromosomes and is believed to be involved in regulating recombination. Studies on SCs usually destroy nuclear architecture, making it impossible to examine the relationship of these structures to the rest of the nucleus. In Saccharomyces cerevisiae the meiosis-specific Zip1 protein is found throughout the entire length of each SC. To analyze the formation and structure of SCs in living cells, a functional ZIP1::GFP fusion was constructed and introduced into yeast. The ZIP1::GFP fusion produced fluorescent SCs and rescued the spore lethality phenotype of zip1 mutants. Optical sectioning and fluorescence deconvolution light microscopy revealed that, at zygotene, SC assembly was initiated at foci that appeared uniformly distributed throughout the nuclear volume. At early pachytene, the full-length SCs were more likely to be localized to the nuclear periphery while at later stages the SCs appeared to redistribute throughout the nuclear volume. These results suggest that SCs undergo dramatic rearrangements during meiotic prophase and that pachytene can be divided into two morphologically distinct substages: pachytene A, when SCs are perinuclear, and pachytene B, when SCs are uniformly distributed throughout the nucleus. ZIP1::GFP also facilitated the enrichment of fluorescent SC and the identification of meiosis-specific proteins by MALDI-TOF mass spectroscopy.","authors":"White, EJ., Cowan, C., Cande, WZ., Kaback, DB.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genetics","volume":"167","issue":"1","page":"51-63","pdf":null,"JrId":"3871","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24654803","title":"Susceptibility quantitative trait loci for pathogenic leucocytosis in SCG\/Kj mice, a spontaneously occurring crescentic glomerulonephritis and vasculitis model.","abstract":"The spontaneous crescentic glomerulonephritis-forming\/Kinjoh (SCG\/Kj) mouse, a model of human crescentic glomerulonephritis (CrGN) and systemic vasculitis, is characterized by the production of myeloperoxidase-specific anti-neutrophil cytoplasmic autoantibody (MPO-ANCA) and marked leucocytosis. This study was performed to identify the specific populations of leucocytes associated with CrGN and susceptibility loci for pathogenic leucocytosis. Four hundred and twenty female (C57BL\/6\u2009\u00d7\u2009SCG\/Kj) F2 intercross mice were subjected to serial flow cytometry examination of the peripheral blood (PB). Kidney granulocytes and monocytes were examined histopathologically. Linkage analyses were performed with 109 polymorphic microsatellite markers. Correlation studies revealed that increase of the granulocytes, F4\/80(+) cells, CD3(+) CD4(-) CD8(-) T cells and dendritic cells (DCs) in peripheral blood (PB) were associated significantly with glomerulonephritis, crescent formation and vasculitis. In kidney sections, F4\/80(low) cells were observed in crescent, while F4\/80(high) cells were around the Bowman's capsules and in the interstitium. Numbers of F4\/80(+) cells in crescents correlated significantly with F4\/80(+) cell numbers in PB, but not with numbers of F4\/80(+) cells in the interstitium. Genome-wide quantitative trait locus (QTL) mapping revealed three SCG\/Kj-derived non-Fas\u2005QTLs for leucocytosis, two on chromosome 1 and one on chromosome 17. QTLs on chromosome 1 affected DCs, granulocytes and F4\/80(+) cells, but QTL on chromosome 17 affected DCs and granulocytes. We found CrGN-associated leucocytes and susceptibility QTLs with their positional candidate genes. F4\/80(+) cells in crescents are considered as recruited inflammatory macrophages. The results provide information for leucocytes to be targeted and genetic elements in CrGN and vasculitis.","authors":"Hamano, Y., Abe, M., Matsuoka, S., Zhang, D., Kondo, Y., Kagami, Y., Ishigami, A., Maruyama, N., Tsuruta, Y., Yumura, W., Suzuki, K.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Clin Exp Immunol","volume":"177","issue":"1","page":"353-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15077147","title":"Mitogen-activated protein kinases in apoptosis regulation.","abstract":"Cells are continuously exposed to a variety of environmental stresses and have to decide 'to be or not to be' depending on the types and strength of stress. Among the many signaling pathways that respond to stress, mitogen-activated protein kinase (MAPK) family members are crucial for the maintenance of cells. Three subfamilies of MAPKs have been identified: extracellular signal-regulated kinases (ERKs), c-Jun N-terminal kinases (JNKs), and p38-MAPKs. It has been originally shown that ERKs are important for cell survival, whereas JNKs and p38-MAPKs were deemed stress responsive and thus involved in apoptosis. However, the regulation of apoptosis by MAPKs is more complex than initially thought and often controversial. In this review, we discuss MAPKs in apoptosis regulation with attention to mouse genetic models and critically point out the multiple roles of MAPKs.","authors":"Wada, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Oncogene","volume":"23","issue":"16","page":"2838-49","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10086383","title":"Reduced expression of neural cell adhesion molecule induces metastatic dissemination of pancreatic beta tumor cells.","abstract":"As in the development of many human cancers, in a transgenic mouse model of beta-cell carcinogenesis (Rip1Tag2), expression of neural cell adhesion molecule (NCAM) changes from the 120-kDa isoform in normal tissue to the 140\/180-kDa isoforms in tumors. NCAM-deficient RiplTag2 mice, generated by crossing Rip1Tag2 mice with NCAM knockout mice, develop metastases, a tumor stage that is not seen in normal Rip1Tag2 mice. In contrast, overexpression of NCAM 120 in NCAM-deficient Rip1Tag2 mice prevents tumor metastasis. The results indicate that the loss of NCAM-mediated cell adhesion is one rate-limiting step in the actual metastatic dissemination of beta tumor cells.","authors":"Perl, AK., Dahl, U., Wilgenbus, P., Cremer, H., Semb, H., Christofori, G.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nat Med","volume":"5","issue":"3","page":"286-91","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15064766","title":"Tlx3 and Tlx1 are post-mitotic selector genes determining glutamatergic over GABAergic cell fates.","abstract":"Glutamatergic and GABAergic neurons mediate much of the excitatory and inhibitory neurotransmission, respectively, in the vertebrate nervous system. The process by which developing neurons select between these two cell fates is poorly understood. Here we show that the homeobox genes Tlx3 and Tlx1 determine excitatory over inhibitory cell fates in the mouse dorsal spinal cord. First, we found that Tlx3 was required for specification of, and expressed in, glutamatergic neurons. Both generic and region-specific glutamatergic markers, including VGLUT2 and the AMPA receptor Gria2, were absent in Tlx mutant dorsal horn. Second, spinal GABAergic markers were derepressed in Tlx mutants, including Pax2 that is necessary for GABAergic differentiation, Gad1\/2 and Viaat that regulate GABA synthesis and transport, and the kainate receptors Grik2\/3. Third, ectopic expression of Tlx3 was sufficient to suppress GABAergic differentiation and induce formation of glutamatergic neurons. Finally, excess GABA-mediated inhibition caused dysfunction of central respiratory circuits in Tlx3 mutant mice.","authors":"Cheng, L., Arata, A., Mizuguchi, R., Qian, Y., Karunaratne, A., Gray, PA., Arata, S., Shirasawa, S., Bouchard, M., Luo, P., Chen, CL., Busslinger, M., Goulding, M., Onimaru, H., Ma, Q.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nat Neurosci","volume":"7","issue":"5","page":"510-7","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21500343","title":"Proteomic analysis reveals a virtually complete set of proteins for translation and energy generation in elementary bodies of the amoeba symbiont Protochlamydia amoebophila.","abstract":"Chlamydiae belong to the most successful intracellular bacterial pathogens. They display a complex developmental cycle and an extremely broad host spectrum ranging from vertebrates to protozoa. The family Chlamydiaceae comprises exclusively well-known pathogens of humans and animals, whereas the members of its sister group, the Parachlamydiaceae, naturally occur as symbionts of free-living amoebae. Comparative analysis of these two groups provides valuable insights into chlamydial evolution and mechanisms for microbe-host interaction. Based on the complete genome sequence of the Acanthamoeba spp. symbiont Protochlamydia amoebophila UWE25, we performed the first detailed proteome analysis of the infectious stage of a symbiotic chlamydia. A 2-D reference proteome map was established and the analysis was extensively complemented by shotgun proteomics. In total, 472 proteins were identified, which represent 23.2% of all encoded proteins. These cover a wide range of functional categories, including typical house-keeping proteins, but also putative virulence-associated proteins. A number of proteins that are not encoded in genomes of Chlamydiaceae were observed and the expression of 162 proteins classified as hypothetical or unknown proteins could be demonstrated. Our findings indicate that P. amoebophila exploits its additional genetic repertoire (compared with the Chlamydiaceae), and that its elementary bodies are remarkably well equipped with proteins involved in transcription, translation, and energy generation.","authors":"Sixt, BS., Heinz, C., Pichler, P., Heinz, E., Montanaro, J., Op den Camp, HJ., Ammerer, G., Mechtler, K., Wagner, M., Horn, M.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Proteomics","volume":"11","issue":"10","page":"1868-92","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2011-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15150105","title":"Loss of vascular endothelial growth factor a activity in murine epidermal keratinocytes delays wound healing and inhibits tumor formation.","abstract":"The angiogenic cytokine vascular endothelial growth factor (VEGF)-A plays a central role in both wound healing and tumor growth. In the skin, epidermal keratinocytes are a major source of this growth factor. To study the contribution of keratinocyte-derived VEGF-A to these angiogenesis-dependent processes, we generated mice in which this cytokine was inactivated specifically in keratin 5-expressing tissues. The mutant mice were macroscopically normal, and the skin capillary system was well established, demonstrating that keratinocyte-derived VEGF-A is not essential for angiogenesis in the skin during embryonic development. However, healing of full-thickness wounds in adult animals was appreciably delayed compared with controls, with retarded crust shedding and the appearance of a blood vessel-free zone underneath the newly formed epidermis. When 9,12-dimethyl 1,2-benzanthracene was applied as both tumor initiator and promoter, a total of 143 papillomas developed in 20 of 23 (87%) of control mice. In contrast, only three papillomas arose in 2 of 17 (12%) of the mutant mice, whereas the rest merely displayed epidermal thickening and parakeratosis. Mutant mice also developed only 2 squamous cell carcinomas, whereas 11 carcinomas were found in seven of the control animals. These data demonstrate that whereas keratinocyte-derived VEGF-A is dispensable for skin vascularization under physiological conditions, it plays an important albeit nonessential role during epidermal wound healing and is crucial for the development of 9,12-dimethyl 1,2-benzanthracene-induced epithelial skin tumors.","authors":"Rossiter, H., Barresi, C., Pammer, J., Rendl, M., Haigh, J., Wagner, EF., Tschachler, E.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cancer Res","volume":"64","issue":"10","page":"3508-16","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15051068","title":"Myristoylation of viral and bacterial proteins.","abstract":null,"authors":"Maurer-Stroh, S., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Trends Microbiol","volume":"12","issue":"4","page":"178-85","pdf":null,"JrId":"8474","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15029240","title":"JunD regulates lymphocyte proliferation and T helper cell cytokine expression.","abstract":"Transgenic mice broadly expressing JunD (Ubi-junD(m)) appear phenotypically normal, but have strongly reduced numbers of peripheral lymphocytes. JunD overexpression in lymphocytes does not protect from numerous apoptotic insults; however, transgenic T cells proliferate poorly and exhibit impaired activation due to reduced levels of IL-4, CD25 and CD69. Consistently, in the absence of JunD (junD(-\/-)) T cells hyperproliferate following mitogen induction. Moreover, transgenic T helper (Th) 2 cells have decreased IL-4 and IL-10 expression, whereas junD(-\/-) Th2 cells secrete higher amounts of both Th2 cytokines. Th1-polarized junD(-\/-) CD4(+) T cells display enhanced IFN-gamma cytokine production associated with upregulated T-bet expression and downregulated expression of suppressor of cytokine signaling-1. These novel findings demonstrate a regulatory role of JunD in T lymphocyte proliferation and Th cell differentiation.","authors":"Meixner, A., Karreth, F., Kenner, L., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"EMBO J","volume":"23","issue":"6","page":"1325-35","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15037546","title":"Glucocorticoid receptor function in hepatocytes is essential to promote postnatal body growth.","abstract":"Mice carrying a hepatocyte-specific inactivation of the glucorticoid receptor (GR) gene show a dramatic reduction in body size. Growth hormone signaling mediated by the Stat5 transcription factors is impaired. We show that Stat5 proteins physically interact with GR and GR is present in vivo on Stat5-dependent IGF-I and ALS regulatory regions. Interestingly, mice with a DNA-binding-deficient GR but an unaltered ability to interact with STAT5 (GR(dim\/dim)) have a normal body size and normal levels of Stat5-dependent mRNAs. These findings strongly support the model in which GR acts as a coactivator for Stat5-dependent transcription upon GH stimulation and reveal an essential role of hepatic GR in the control of body growth.","authors":"Tronche, F., Opherk, C., Moriggl, R., Kellendonk, C., Reimann, A., Schwake, L., Reichardt, HM., Stangl, K., Gau, D., Hoeflich, A., Beug, H., Schmid, W., Sch\u00fctz, G.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genes Dev","volume":"18","issue":"5","page":"492-7","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15014946","title":"Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana.","abstract":"The Arabidopsis KRYPTONITE gene encodes a member of the Su(var)3-9 family of histone methyltransferases. Mutations of kryptonite cause a reduction of methylated histone H3 lysine 9, a loss of DNA methylation, and reduced gene silencing. Lysine residues of histones can be either monomethylated, dimethylated or trimethylated and recent evidence suggests that different methylation states are found in different chromatin domains. Here we show that bulk Arabidopsis histones contain high levels of monomethylated and dimethylated, but not trimethylated histone H3 lysine 9. Using both immunostaining of nuclei and chromatin immunoprecipitation assays, we show that monomethyl and dimethyl histone H3 lysine 9 are concentrated in heterochromatin. In kryptonite mutants, dimethyl histone H3 lysine 9 is nearly completely lost, but monomethyl histone H3 lysine 9 levels are only slightly reduced. Recombinant KRYPTONITE can add one or two, but not three, methyl groups to the lysine 9 position of histone H3. Further, we identify a KRYPTONITE-related protein, SUVH6, which displays histone H3 lysine 9 methylation activity with a spectrum similar to that of KRYPTONITE. Our results suggest that multiple Su(var)3-9 family members are active in Arabidopsis and that dimethylation of histone H3 lysine 9 is the critical mark for gene silencing and DNA methylation.","authors":"Jackson, JP., Johnson, L., Jasencakova, Z., Zhang, X., PerezBurgos, L., Singh, PB., Cheng, X., Schubert, I., Jenuwein, T., Jacobsen, SE.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Chromosoma","volume":"112","issue":"6","page":"308-15","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15003443","title":"A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe.","abstract":"The fungal transamidase complex that executes glycosylphosphatidylinositol (GPI) lipid anchoring of precursor proteins has overlapping but distinct sequence specificity compared with the animal system. Therefore, a taxon-specific prediction tool for the recognition of the C-terminal signal in fungal sequences is necessary. We have collected a learning set of fungal precursor protein sequences from the literature and fungal proteomes. Although the general four segment scheme of the recognition signal is maintained also in fungal precursors, there are taxon specificities in details. A fungal big-Pi predictor has been developed for the assessment of query sequence concordance with fungi-specific recognition signal requirements. The sensitivity of this predictor is close to 90%. The rate of false positive prediction is in the range of 0.1%. The fungal big-Pi tool successfully predicts the Gas1 mutation series described by C. Nuoffer and co-workers, and recognizes that the human PLAP C terminus is not a target for the fungal transamidase complex. Lists of potentially GPI lipid anchored proteins for five fungal proteomes have been generated and the hits have been functionally classified. The fungal big-Pi prediction WWW server as well as precursor lists are available at","authors":"Eisenhaber, B., Schneider, G., Wildpaner, M., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Mol Biol","volume":"337","issue":"2","page":"243-53","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15003124","title":"MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins.","abstract":"We evaluated the evolutionary conservation of glycine myristoylation within eukaryotic sequences. Our large-scale cross-genome analyses, available as MYRbase, show that the functional spectrum of myristoylated proteins is currently largely underestimated. We give experimental evidence for in vitro myristoylation of selected predictions. Furthermore, we classify five membrane-attachment factors that occur most frequently in combination with, or even replacing, myristoyl anchors, as some protein family examples show.","authors":"Maurer-Stroh, S., Gouda, M., Novatchkova, M., Schleiffer, A., Schneider, G., Sirota, FL., Wildpaner, M., Hayashi, N., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genome Biol","volume":"5","issue":"3","page":"R21","pdf":null,"JrId":"21904","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15122341","title":"Polyomavirus tumorantigens have a profound effect on gene expression in mouse fibroblasts.","abstract":"Polyomavirus (Py) large and small tumorantigens together are competent to induce S phase in growth-arrested mouse fibroblasts. The capacity of the large tumorantigen to bind the pocket proteins, pRB, p130 and p107, is important for the transactivation of DNA synthesis enzymes and the cyclins E and A, while the interference of small tumorantigen with protein phosphatase PP2A causes a destabilization of the cdk2 inhibitor p27, and thus leads to strong cyclin E- and cyclin A-dependent cdk2 activity. Py small tumorantigen, in addition, is able to transactivate cyclin A. Hence, this protein might have a much wider effect on gene expression in arrested mouse fibroblasts than hitherto suspected. This may have a profound part in the known capacity of Py to form tumors in mice. Therefore, it was interesting to gain an insight into the spectrum of transcriptional deregulation by Py tumorantigens. Accordingly, we performed microarray analysis of quiescent mouse fibroblasts in the absence and presence of small or large tumorantigen. We found that the viral proteins can induce or repress a great variety of genes beyond those involved in the S phase induction and DNA synthesis. The results of the microarray analysis were confirmed for selected genes by several methods, including real-time PCR. Interestingly, a mutation of the binding site for pocket proteins in case of LT and for PP2A in case of ST has a variable effect on the deregulation of genes by the viral proteins depending on the gene in question. In fact, some genes are transactivated by LT as well as ST completely independent of an interaction with their major cellular targets, pocket proteins and PP2A, respectively.","authors":"Klucky, B., Koch, B., Radolf, M., Steinlein, P., Wintersberger, E.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Oncogene","volume":"23","issue":"27","page":"4707-21","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24449838","title":"A single allele of Hdac2 but not Hdac1 is sufficient for normal mouse brain development in the absence of its paralog.","abstract":"The histone deacetylases HDAC1 and HDAC2 are crucial regulators of chromatin structure and gene expression, thereby controlling important developmental processes. In the mouse brain, HDAC1 and HDAC2 exhibit different developmental stage- and lineage-specific expression patterns. To examine the individual contribution of these deacetylases during brain development, we deleted different combinations of Hdac1 and Hdac2 alleles in neural cells. Ablation of Hdac1 or Hdac2 by Nestin-Cre had no obvious consequences on brain development and architecture owing to compensation by the paralog. By contrast, combined deletion of Hdac1 and Hdac2 resulted in impaired chromatin structure, DNA damage, apoptosis and embryonic lethality. To dissect the individual roles of HDAC1 and HDAC2, we expressed single alleles of either Hdac1 or Hdac2 in the absence of the respective paralog in neural cells. The DNA-damage phenotype observed in double knockout brains was prevented by expression of a single allele of either Hdac1 or Hdac2. Strikingly, Hdac1(-\/-)Hdac2(+\/-) brains showed normal development and no obvious phenotype, whereas Hdac1(+\/-)Hdac2(-\/-) mice displayed impaired brain development and perinatal lethality. Hdac1(+\/-)Hdac2(-\/-) neural precursor cells showed reduced proliferation and premature differentiation mediated by overexpression of protein kinase C, delta, which is a direct target of HDAC2. Importantly, chemical inhibition or knockdown of protein kinase C delta was sufficient to rescue the phenotype of neural progenitor cells in vitro. Our data indicate that HDAC1 and HDAC2 have a common function in maintaining proper chromatin structures and show that HDAC2 has a unique role by controlling the fate of neural progenitors during normal brain development.","authors":"Hagelkruys, A., Lagger, S., Krahmer, J., Leopoldi, A., Artaker, M., Pusch, O., Zezula, J., Weissmann, S., Xie, Y., Sch\u00f6fer, C., Schlederer, M., Brosch, G., Matthias, P., Selfridge, J., Lassmann, H., Knoblich, JA., Seiser, C.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Development","volume":"141","issue":"3","page":"604-616","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24243101","title":"Microtubules and neurodevelopmental disease: the movers and the makers.","abstract":"The development of the mammalian cortex requires the generation, migration and differentiation of neurons. Each of these cellular events requires a dynamic microtubule cytoskeleton. Microtubules are required for interkinetic nuclear migration, the separation of chromatids in mitosis, nuclear translocation during migration and the outgrowth of neurites. Their importance is underlined by the finding that mutations in a host of microtubule associated proteins cause detrimental neurological disorders. More recently, the structural subunits of microtubules, the tubulin proteins, have been implicated in a spectrum of human diseases collectively known as the tubulinopathies. This chapter reviews the discovery of microtubules, the role they play in neurodevelopment, and catalogues the tubulin isoforms associated with neurodevelopmental disease. Our focus is on the molecular and cellular mechanisms that underlie the pathology of tubulin-associated diseases. Finally, we reflect on whether different tubulin genes have distinct intrinsic functions.","authors":"Breuss, M., Keays, DA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Adv Exp Med Biol","volume":"800","issue":null,"page":"75-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15121008","title":"Normal mineralization and nanostructure of sclerotic bone in mice overexpressing Fra-1.","abstract":"Increased bone mass due to elevated number of active osteoblasts has been reported for transgenic mice overexpressing the transcription factor Fra-1. To explore the potential of the anabolic action of Fra-1 in treatment of osteoporosis, we examined the integrity of bone matrix generated in Fra-1 transgenic mice. Femora from Fra-1 transgenic (Fra-1 tg) and wild-type littermates were analyzed for bone mineralization density distribution (BMDD) and nanostructure using quantitative backscattered electron imaging (qBEI) and scanning small angle X-ray scattering (scanning-SAXS), respectively. For comparison, we studied mice lacking c-Fos (Fos-\/-), which develop osteopetrosis because of the absence of osteoclasts. Morphometrical analysis of metaphyseal spongiosa revealed an up to 5-fold increase in bone volume for Fra-1 transgenic compared to wild type. BMDD indicated a transient lower mineralization of bone for Fra-1 transgenic at 5 and 8 weeks, which became comparable to that of wild-type mice by 8 months. The homogeneity of mineralization was not altered in the Fra-1 transgenic mice at any ages examined. However, it was strikingly reduced in Fos-\/- due to an abundance of hypermineralized cartilage. The bone nanostructure did not show abnormalities in Fra-1 transgenic or Fos-\/-. These results provide a rationale for the development of therapeutic applications involving Fra-1-induced bone formation.","authors":"Roschger, P., Matsuo, K., Misof, BM., Tesch, W., Jochum, W., Wagner, EF., Fratzl, P., Klaushofer, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Bone","volume":"34","issue":"5","page":"776-82","pdf":null,"JrId":"1710","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23172725","title":"Studying the fragmentation behavior of peptides with arginine phosphorylation and its influence on phospho-site localization.","abstract":"Phospho-proteomic studies opened a broad view onto the main mechanisms of regulating cellular processes. Our recent discovery of a protein arginine kinase and its target in bacteria added a previously undescribed type of phosphorylation to control protein activity. Several challenges arise from large in vivo studies of this and other types of phosphorylations. The main factors impeding correct localization are low spectral quality, neutral loss of phosphoric acid, and gas-phase rearrangements, which have recently been described for phospho-serine, -threonine, and -tyrosine. Studies on histidine-phosphorylated peptides, a nitrogen-bound phosphorylation, also reported loss of phosphoric acid upon collision-induced dissociation. We were interested in studying the behaviour of arginine phosphorylation under different fragmentation conditions and its influence on site localization. First, we determined the percentage of false localizations obtained by three different search engines and a software tool dedicated for phospho-site determination. Next, we demonstrate that application of collisional activation for analysis of arginine-phosphorylated peptides leads to extensive elimination of phosphoric acid and increases the numbers of false localizations, while the modification is maintained on the arginine side chain upon electron-transfer dissociation. Furthermore, we also observed a rearrangement of the phosphorylation onto serine and glutamic acid side chains upon collisional activation.","authors":"Schmidt, A., Ammerer, G., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proteomics","volume":"13","issue":"6","page":"945-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14769860","title":"Mice lacking JunB are osteopenic due to cell-autonomous osteoblast and osteoclast defects.","abstract":"Because JunB is an essential gene for placentation, it was conditionally deleted in the embryo proper. JunBDelta\/Delta mice are born viable, but develop severe low turnover osteopenia caused by apparent cell-autonomous osteoblast and osteoclast defects before a chronic myeloid leukemia-like disease. Although JunB was reported to be a negative regulator of cell proliferation, junBDelta\/Delta osteoclast precursors and osteoblasts show reduced proliferation along with a differentiation defect in vivo and in vitro. Mutant osteoblasts express elevated p16(INK4a) levels, but exhibit decreased cyclin D1 and cyclin A expression. Runx2 is transiently increased during osteoblast differentiation in vitro, whereas mature osteoblast markers such as osteocalcin and bone sialoprotein are strongly reduced. To support a cell-autonomous function of JunB in osteoclasts, junB was inactivated specifically in the macrophage-osteoclast lineage. Mutant mice develop an osteopetrosis-like phenotype with increased bone mass and reduced numbers of osteoclasts. Thus, these data reveal a novel function of JunB as a positive regulator controlling primarily osteoblast as well as osteoclast activity.","authors":"Kenner, L., Hoebertz, A., Beil, FT., Beil, T., Keon, N., Karreth, F., Eferl, R., Scheuch, H., Szremska, A., Amling, M., Schorpp-Kistner, M., Angel, P., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Cell Biol","volume":"164","issue":"4","page":"613-23","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14738747","title":"Linking transcriptional mediators via the GACKIX domain super family.","abstract":null,"authors":"Novatchkova, M., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"2","page":"R54-5","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23973221","title":"Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.","abstract":"The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH-rearranged gene segment in the 3' proximal Igh domain. By using high-resolution mapping of long-range interactions, we demonstrate that local interaction domains established the three-dimensional structure of the extended Igh locus in lymphoid progenitors. In pro-B cells, these local domains engaged in long-range interactions across the Igh locus, which depend on the regulators Pax5, YY1, and CTCF. The large VH gene cluster underwent flexible long-range interactions with the more rigidly structured proximal domain, which probably ensures similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire. These long-range interactions appear to be an intrinsic feature of the VH gene cluster, because they are still generated upon mutation of the E\u03bc enhancer, IGCR1 insulator, or 3' regulatory region in the proximal Igh domain.","authors":"Medvedovic, J., Ebert, A., Tagoh, H., Tamir, IM., Schwickert, TA., Novatchkova, M., Sun, Q., Huis In 't Veld, PJ., Guo, C., Yoon, HS., Denizot, Y., Holwerda, SJ., de Laat, W., Cogn\u00e9, M., Shi, Y., Alt, FW., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Immunity","volume":"39","issue":"2","page":"229-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15116096","title":"Enhanced tenascin-C expression and matrix deposition during Ras\/TGF-beta-induced progression of mammary tumor cells.","abstract":"Overexpression of tenascin-C (TN-C) in breast carcinomas has been associated with a migratory or even invasive tumor cell phenotype. The mechanisms regulating expression and matrix deposition of TN-C in normal and cancerous breast tissues are, however, little understood. Here, we demonstrate that mouse mammary epithelial cells (EpH4) transformed by oncogenic Ha-Ras (EpRas) overexpress TN-C, which accumulates in the cytoplasm. When EpRas cells undergo epithelial-mesenchymal transition (EMT) in response to TGFbeta1, they secrete TN-C into the culture medium. In EpRas cells undergoing TGFbeta1-induced EMT in three-dimensional (3D)-collagen gel cultures, TN-C was deposited into an extracellular matrix (ECM) already containing fibronectin and perlecan. Under less physiological 2D plastic cultures, EpRas cells undergoing EMT failed to deposit TN-C into an (apparently incomplete) ECM. Ras-downstream signaling was dissected by pharmacological inhibitors and effector-specific Ras mutants (V12S35, V12C40), specifically inhibiting or activating ERK\/MAPK or PI3K signaling, respectively. We showed that TN-C overexpression required a hyperactive ERK\/MAPK-signaling pathway, while elevated PI3K signaling did not enhance TN-C expression. Similarly, tumors induced by cells exhibiting hyperactive ERK\/MAPK signaling showed expression of TN-C in the tumor cells themselves, while only endothelial cells expressed TN-C in tumors caused by the V12C40 mutant (incapable of EMT in vivo). Taken together, our data indicate that hyperactive ERK\/MAPK signaling causes enhanced expression of TN-C, while its secretion is induced by TGFbeta1 and both signals cooperate in TN-C matrix deposition. Importantly, both signals also cooperate to induce EMT in vitro and tumor progression\/metastasis in vivo.","authors":"Maschler, S., Grunert, S., Danielopol, A., Beug, H., Wirl, G.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Oncogene","volume":"23","issue":"20","page":"3622-33","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14711429","title":"Axon guidance: morphogens show the way.","abstract":"Hedgehog and Wnt family proteins can act as classic developmental morphogens to pattern a field of nai;ve cells. Surprising new studies show that members of these same protein families also act as guidance cues for growing axons in the developing nervous system.","authors":"Schnorrer, F., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"1","page":"R19-21","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14724179","title":"Loss of the anaphase-promoting complex in quiescent cells causes unscheduled hepatocyte proliferation.","abstract":"The anaphase-promoting complex or cyclosome (APC\/C) is an ubiquitin protein ligase that together with Cdc20 and Cdh1 targets mitotic proteins for degradation by the proteosome. APC-Cdc20 activity during mitosis triggers anaphase by destroying securin and cyclins. APC-Cdh1 promotes degradation of cyclins and other proteins during G(1). We show that loss of APC\/C during embryogenesis is early lethal before embryonic day E6.5 (E6.5). To investigate the role of APC\/C in quiescent cells, we conditionally inactivated the subunit Apc2 in mice. Deletion of Apc2 in quiescent hepatocytes caused re-entry into the cell cycle and arrest in metaphase, resulting in liver failure. Re-entry into the cell cycle either occurred without any proliferative stimulus or could be easily induced. We demonstrate that the APC has an additional function to prevent hepatocytes from unscheduled re-entry into the cell cycle.","authors":"Wirth, KG., Ricci, R., Gim\u00e9nez-Abi\u00e1n, JF., Taghybeeglu, S., Kudo, NR., Jochum, W., Vasseur-Cognet, M., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genes Dev","volume":"18","issue":"1","page":"88-98","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11169416","title":"Adhesion mediated by LFA-1 is required for efficient IL-12-induced NK and NKT cell cytotoxicity.","abstract":"Interleukin 12 (IL-12)-activated NK1.1+TCRalpha beta+ (NKT2) and NK1.1+TCRalpha beta- (NK) cells exhibit cytotoxic activity against a wide variety of tumor cells in the absence of prior sensitization. Here we demonstrate that the integrin adhesion receptor LFA-1 (CD11a\/CD18) regulates the cytotoxic activity of IL-12-activated NKT and NK cells against YAC-1 and EL-4 tumor cells. Differentiation in vivo and the expression of the cytolytic effector molecules perforin and Fas-L were comparable in both IL-12-activated NKT and NK cells from LFA-1-\/ - and LFA-1+\/+ mice. However, LFA-1-\/-IL-12-activated NKT and NK cells showed impaired conjugate formation with target cells. These results provide the first genetic evidence for a role for an adhesion receptor in killing by IL-12-activated NK cells.","authors":"Matsumoto, G., Omi, Y., Lee, U., Nishimura, T., Shindo, J., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Eur J Immunol","volume":"30","issue":"12","page":"3723-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23885867","title":"Multiple mechanisms contribute to centriole separation in C. elegans.","abstract":"Centrosome function in cell division requires their duplication, once, and only once, per cell cycle. Underlying centrosome duplication are alternating cycles of centriole assembly and separation. Work in vertebrates has implicated the cysteine protease separase in anaphase-coupled centriole separation (or disengagement) and identified this as a key step in licensing another round of assembly. Current models have separase cleaving a physical link between centrioles, potentially cohesin, that prevents reinitiation of centriole assembly unless disengaged. Here, we examine separase function in the C. elegans early embryo. We find that depletion impairs separation and consequently duplication of sperm-derived centrioles at the meiosis-mitosis transition. However, subsequent cycles proceed normally. Whereas mitotic centrioles separate in the context of cortical forces acting on a disassembling pericentriolar material, sperm centrioles are not associated with significant pericentriolar material or subject to strong forces. Increasing centrosomal microtubule nucleation restores sperm centriole separation and duplication in separase-depleted embryos, while forced pericentriolar material disassembly drives premature separation in mitosis. These results emphasize the critical role of cytoskeletal forces and the pericentriolar material in centriole separation. Separase contributes to separation where forces are limited, offering a potential explanation for results obtained in different experimental models.","authors":"Cabral, G., Sans, SS., Cowan, CR., Dammermann, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Curr Biol","volume":"23","issue":"14","page":"1380-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15099518","title":"Different EZH2-containing complexes target methylation of histone H1 or nucleosomal histone H3.","abstract":"Human Enhancer of Zeste homolog (Ezh2) is a histone lysine methyltransferase (HKMT) associated with transcriptional repression. Ezh2 is present in several distinct complexes, one of which, PRC2, we characterized previously. Here we report an additional Ezh2 complex, PRC3. We show that the Ezh2 complexes exhibit differential targeting of specific histones for lysine methylation dependent upon the context of the histone substrates. This differential targeting is a function of the associated Eed protein within each complex. We found that Eed protein is present in four isoforms, which represent alternate translation start site usage from the same mRNA. These Eed isoforms selectively associate with distinct Ezh2-containing complexes with resultant differential targeting of their associated HKMT activity toward histone H3-K27 or histone H1-K26. Our data provide evidence for a novel mechanism regulating the substrate specificity of a chromatin-modifying enzyme through disparate translational products of a regulatory subunit.","authors":"Kuzmichev, A., Jenuwein, T., Tempst, P., Reinberg, D.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Mol Cell","volume":"14","issue":"2","page":"183-93","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-211","title":"Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape ","abstract":null,"authors":"De La Concepcion JC,  Duverge H,  Kim Y,  Julian J,  Xu HD,  Ikene SA,  Bianchi A,  Grujic  N,  Papareddy RK,  Grishkovskaya I,  Haselbach D,  Murray DH,  Clavel M , Irwin NAT,  Dagdas Y","publication_status":"preprint","journalpubyear":"2024","journaltitle":"bioRxiv","volume":"2024.08.26.609756","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.08.26.609756v1","preprintlink":null,"articledate":"2024-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14706339","title":"Rhabdomyosarcoma development in mice lacking Trp53 and Fos: tumor suppression by the Fos protooncogene.","abstract":"The Fos protein, a major component of the AP-1 transcription factor, is essential for osteoclast differentiation, acts as an oncogene, potentiates transforming signals, and controls invasive growth and angiogenesis during tumor progression. To investigate a potential genetic interaction between the Trp53 and Fos pathways, Trp53\/Fos double knockout mice were generated. These mice develop highly proliferative and invasive rhabdomyosarcomas of the facial and orbital regions, with more than 90% penetrance at 6 months of age. Rhabdomyosarcoma cell lines established from the primary tumors express characteristic muscle-specific markers, and reexpression of Fos is associated with enhanced apoptosis in vitro. Moreover, Fos is able to repress Pax7 expression in rhabdomyosarcoma cell lines and primary myoblasts, suggesting a molecular link to genetic alterations involved in human rhabdomyosarcomas.","authors":"Fleischmann, A., Jochum, W., Eferl, R., Witowsky, J., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cancer Cell","volume":"4","issue":"6","page":"477-82","pdf":null,"JrId":"29778","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11099494","title":"X protein of hepatitis B virus inhibits Fas-mediated apoptosis and is associated with up-regulation of the SAPK\/JNK pathway.","abstract":"The X protein from a chronic strain of hepatitis B virus (HBx) was determined to inhibit Fas-mediated apoptosis and promote cell survival. Fas-mediated apoptosis is the major cause of hepatocyte damage during liver disease. Experiments demonstrated that cell death caused by anti-Fas antibodies was blocked by the expression of HBx in human primary hepatocytes and mouse embryo fibroblasts. This effect was also observed in mouse erythroleukemia cells that lacked p53, indicating that protection against Fas-mediated apoptosis was independent of p53. Components of the signal transduction pathways involved in this protection were studied. The SAPK\/JNK pathway has previously been suggested to be a survival pathway for some cells undergoing Fas-mediated apoptosis, and kinase assays showed that SAPK activity was highly up-regulated in cells expressing the HBx protein. Normal mouse fibroblasts expressing HBx were protected from death, whereas identical fibroblasts lacking the SEK1 component from the SAPK pathway succumbed to Fas-mediated apoptosis, whether HBx was present or not. Assays showed that caspase 3 and 8 activities and the release of cytochrome c from mitochondria were inhibited, in the presence of HBx, following stimulation with anti-Fas antibodies. Coprecipitation and confocal immunofluorescence microscopy experiments demonstrated that HBx localizes with a cytoplasmic complex containing MEKK1, SEK1, SAPK, and 14-3-3 proteins. Finally, mutational analysis of HBx demonstrated that a potential binding region for 14-3-3 proteins was essential for induction of SAPK\/JNK activity and protection from Fas-mediated apoptosis.","authors":"Diao, J., Khine, AA., Sarangi, F., Hsu, E., Iorio, C., Tibbles, LA., Woodgett, JR., Penninger, J., Richardson, CD.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Biol Chem","volume":"276","issue":"11","page":"8328-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18802077","title":"Inhibitory immunoglobulin-like receptors LILRB and PIR-B negatively regulate osteoclast development.","abstract":"Osteoclasts, multinucleated cells of myeloid-monocytic origin, are responsible for bone resorption, which is crucial for maintenance of bone homeostasis in concert with bone-forming osteoblasts of nonhematopoietic, mesenchymal origin. Receptor activator of NF-kappaB ligand (RANKL) and M-CSF, expressed on the surface of and secreted by osteoblasts, respectively, are essential factors that facilitate osteoclast formation. In contrast to the activation processes for osteoclast formation, inhibitory mechanisms for it are poorly understood. Herein we demonstrate that inhibitory Ig-like receptors recruiting Src homology 2 domain-containing tyrosine phosphatase 1 (SHP-1) are expressed on osteoclast precursor cells like other myeloid cells, and that they play a regulatory role in the development of osteoclasts. We detected cell-surface expression of paired Ig-like receptor (PIR)-B and four isoforms of leukocyte Ig-like receptor (LILR)B on cultured osteoclast precursor cells of mouse and human origin, respectively, and showed that all of these ITIM-harboring inhibitory receptors constitutively recruit SHP-1 in the presence of RANKL and M-CSF, and that some of them can suppress osteoclast development in vitro. Fluorescence energy transfer analyses have suggested that the constitutive binding of either murine PIR-B or its human ortholog LILRB1 to MHC class I molecules on the same cell surface comprises one of the mechanisms for developmental regulation. These results constitute the first evidence of the regulation of osteoclast formation by cell-surface, ITIM-harboring Ig-like receptors. Modulation of these regulatory receptors may be a novel way to control various skeletal system disorders and inflammatory arthritis.","authors":"Mori, Y., Tsuji, S., Inui, M., Sakamoto, Y., Endo, S., Ito, Y., Fujimura, S., Koga, T., Nakamura, A., Takayanagi, H., Itoi, E., Takai, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Immunol","volume":"181","issue":"7","page":"4742-51","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23766327","title":"Parallel neural pathways mediate CO2 avoidance responses in Drosophila.","abstract":"Different stimulus intensities elicit distinct perceptions, implying that input signals are either conveyed through an overlapping but distinct subpopulation of sensory neurons or channeled into divergent brain circuits according to intensity. In Drosophila, carbon dioxide (CO2) is detected by a single type of olfactory sensory neuron, but information is conveyed to higher brain centers through second-order projection neurons (PNs). Two distinct pathways, PN(v)-1 and PN(v)-2, are necessary and sufficient for avoidance responses to low and high CO2 concentrations, respectively. Whereas low concentrations activate PN(v)-1, high concentrations activate both PN(v)s and GABAergic PN(v)-3, which may inhibit PN(v)-1 pathway-mediated avoidance behavior. Channeling a sensory input into distinct neural pathways allows the perception of an odor to be further modulated by both stimulus intensity and context.","authors":"Lin, HH., Chu, LA., Fu, TF., Dickson, BJ., Chiang, AS.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Science","volume":"340","issue":"6138","page":"1338-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15095974","title":"Inhibitory effect of TIS7 on Sp1-C\/EBPalpha transcription factor module activity.","abstract":"The transcription factors C\/EBPalpha and Sp1 functionally interact to induce expression of specific genes during myeloid and epithelial cell differentiation. The C\/EBPalpha-Sp1 transcription factor \"module\" binds to enhancer elements within the upstream regulatory sequences of target genes. In our previous study we identified mouse TPA inducible sequence 7 (TIS7) as a novel co-repressor in epithelial cells undergoing loss of polarity. Increased levels of TIS7 down-regulate the transcription of a specific set of genes. Using bioinformatic analysis we identified a common binding site for the C\/EBPalpha-Spl transcription factor module within the upstream regulatory regions of TIS7-regulated genes. The inhibitory effect of TIS7 on C\/EBPalpha-Sp1-mediated transcription was confirmed by reporter assays. Our data showed that the TIS7 effect was mediated through specific interference with Sp1 transcriptional activity. Furthermore, TIS7 prevented formation of a complex between Sp1 protein and its consensus DNA binding site. Data presented here further specify the mechanism of action of the transcriptional co-repressor TIS7 as well as document the strength of a bioinformatic approach for the prediction and analysis of transcription factor modules.","authors":"Wick, N., Schleiffer, A., Huber, LA., Vietor, I.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Mol Biol","volume":"336","issue":"3","page":"589-95","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-213","title":"CowScape: Quantitative reconstruction of the conformational landscape of biological macromolecules from cryo-EM data","abstract":null,"authors":"Lambrecht F, Kr\u00f6pelin A, L\u00fcttich M, Habeck M, Haselbach D, Stark H","publication_status":"preprint","journalpubyear":"2024","journaltitle":"arXiv","volume":"2402.11589","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/arxiv.org\/abs\/2402.11589","preprintlink":null,"articledate":"2024-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10075979","title":"The cyclin-dependent kinase Cdk2 regulates thymocyte apoptosis.","abstract":"Aberrant activation of cell cycle molecules has been postulated to play a role in apoptosis (\"catastrophic cell cycle\"). Here we show that in noncycling developing thymocytes, the cyclin- dependent kinase Cdk2 is activated in response to all specific and nonspecific apoptotic stimuli tested, including peptide-specific thymocyte apoptosis. Cdk2 was found to function upstream of the tumor suppressor p53, transactivation of the death promoter Bax, alterations of mitochondrial permeability, Bcl-2, caspase activation, and caspase-dependent proteolytic cleavage of the retinoblastoma protein. Inhibition of Cdk2 completely protected thymocytes from apoptosis, mitochondrial changes, and caspase activation. These data provide the first evidence that Cdk2 activity is crucial for the induction of thymocyte apoptosis.","authors":"Hakem, A., Sasaki, T., Kozieradzki, I., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Exp Med","volume":"189","issue":"6","page":"957-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-05-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14678980","title":"Chemosensitization by a non-apoptogenic heat shock protein 70-binding apoptosis-inducing factor mutant.","abstract":"Heat shock protein 70 (HSP70) inhibits apoptosis and thereby increases the survival of cells exposed to a wide range of lethal stimuli. HSP70 has also been shown to increase the tumorigenicity of cancer cells in rodent models. The protective function of this chaperone involves interaction and neutralization of the caspase activator apoptotic protease activation factor-1 and the mitochondrial flavoprotein apoptosis-inducing factor (AIF). In this work, we determined by deletional mutagenesis that a domain of AIF comprised between amino acids 150 and 228 is engaged in a molecular interaction with the substrate-binding domain of HSP70. Computer calculations favored this conclusion. On the basis of this information, we constructed an AIF-derived protein, which is cytosolic, noncytotoxic, yet maintains its capacity to interact with HSP70. This protein, designated ADD70, sensitized different human cancer cells to apoptosis induced by a variety of death stimuli by its capacity to interact with HSP70 and therefore to sequester HSP70. Thus, its chemosensitizing effect was lost in cells in which inducible HSP70 genes had been deleted. These data delineate a novel strategy for the selective neutralization of HSP70.","authors":"Schmitt, E., Parcellier, A., Gurbuxani, S., Cande, C., Hammann, A., Morales, MC., Hunt, CR., Dix, DJ., Kroemer, RT., Giordanetto, F., J\u00e4\u00e4ttel\u00e4, M., Penninger, JM., Pance, A., Kroemer, G., Garrido, C.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cancer Res","volume":"63","issue":"23","page":"8233-40","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10022836","title":"JunB is essential for mammalian placentation.","abstract":"Lack of JunB, an immediate early gene product and member of the AP-1 transcription factor family causes embryonic lethality between E8.5 and E10.0. Although mutant embryos are severely retarded in growth and development, cellular proliferation is apparently not impaired. Retardation and embryonic death are caused by the inability of JunB-deficient embryos to establish proper vascular interactions with the maternal circulation due to multiple defects in extra-embryonic tissues. The onset of the phenotypic defects correlates well with high expression of junB in wild-type extra-embryonic tissues. In trophoblasts, the lack of JunB causes a deregulation of proliferin, matrix metalloproteinase-9 (MMP-9) and urokinase plasminogen activator (uPA) gene expression, resulting in a defective neovascularization of the decidua. As a result of downregulation of the VEGF-receptor 1 (flt-1), blood vessels in the yolk sac mesoderm appeared dilated. Mutant embryos which escape these initial defects finally die from a non-vascularized placental labyrinth. Injection of junB-\/- embryonic stem (ES) cells into tetraploid wild-type blastocysts resulted in a partial rescue, in which the ES cell-derived fetuses were no longer growth retarded and displayed a normal placental labyrinth. Therefore, JunB appears to be involved in multiple signaling pathways regulating genes involved in the establishment of a proper feto-maternal circulatory system.","authors":"Schorpp-Kistner, M., Wang, ZQ., Angel, P., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"EMBO J","volume":"18","issue":"4","page":"934-48","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23425860","title":"Complete cardiac regeneration in a mouse model of myocardial infarction.","abstract":"Cardiac remodeling and subsequent heart failure remain critical issues after myocardial infarction despite improved treatment and reperfusion strategies. Recently, complete cardiac regeneration has been demonstrated in fish and newborn mice following resection of the cardiac apex. However, it remained entirely unclear whether the mammalian heart can also completely regenerate following a complex cardiac ischemic injury. We established a protocol to induce a severe heart attack in one-day-old mice using left anterior descending artery (LAD) ligation. LAD ligation triggered substantial cardiac injury in the left ventricle defined by Caspase 3 activation and massive cell death. Ischemia-induced cardiomyocyte death was also visible on day 4 after LAD ligation. Remarkably, 7 days after the initial ischemic insult, we observed complete cardiac regeneration without any signs of tissue damage or scarring. This tissue regeneration translated into long-term normal heart functions as assessed by echocardiography. In contrast, LAD ligations in 7-day-old mice resulted in extensive scarring comparable to adult mice, indicating that the regenerative capacity for complete cardiac healing after heart attacks can be traced to the first week after birth. RNAseq analyses of hearts on day 1, day 3, and day 10 and comparing LAD-ligated and sham-operated mice surprisingly revealed a transcriptional programme of major changes in genes mediating mitosis and cell division between days 1, 3 and 10 postnatally and a very limited set of genes, including genes regulating cell cycle and extracellular matrix synthesis, being differentially regulated in the regenerating hearts. We present for the first time a mammalian model of complete cardiac regeneration following a severe ischemic cardiac injury. This novel model system provides the unique opportunity to uncover molecular and cellular pathways that can induce cardiac regeneration after ischemic injury, findings that one day could be translated to human heart attack patients.","authors":"Haubner, BJ., Adamowicz-Brice, M., Khadayate, S., Tiefenthaler, V., Metzler, B., Aitman, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Aging (Albany NY)","volume":"4","issue":"12","page":"966-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14657031","title":"Mitotic regulation of the human anaphase-promoting complex by phosphorylation.","abstract":"The anaphase-promoting complex (APC) or cyclosome is a ubiquitin ligase that initiates anaphase and mitotic exit. APC activation is thought to depend on APC phosphorylation and Cdc20 binding. We have identified 43 phospho-sites on APC of which at least 34 are mitosis specific. Of these, 32 sites are clustered in parts of Apc1 and the tetratricopeptide repeat (TPR) subunits Cdc27, Cdc16, Cdc23 and Apc7. In vitro, at least 15 of the mitotic phospho-sites can be generated by cyclin-dependent kinase 1 (Cdk1), and 3 by Polo-like kinase 1 (Plk1). APC phosphorylation by Cdk1, but not by Plk1, is sufficient for increased Cdc20 binding and APC activation. Immunofluorescence microscopy using phospho-antibodies indicates that APC phosphorylation is initiated in prophase during nuclear uptake of cyclin B1. In prometaphase phospho-APC accumulates on centrosomes where cyclin B ubiquitination is initiated, appears throughout the cytosol and disappears during mitotic exit. Plk1 depletion neither prevents APC phosphorylation nor cyclin A destruction in vivo. These observations imply that APC activation is initiated by Cdk1 already in the nuclei of late prophase cells.","authors":"Kraft, C., Herzog, F., Gieffers, C., Mechtler, K., Hagting, A., Pines, J., Peters, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"EMBO J","volume":"22","issue":"24","page":"6598-609","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23386380","title":"Non insulin producing cell line, MIA PaCa-2 is rendered insulin producing in vitro via mesenchymal epithelial transition.","abstract":"We used non-insulin producing pancreatic carcinoma cell line, MIA PaCa-2 and have modulated its culture conditions by using 1% matrigel as extracellular matrix, N2, B27 growth supplements and serum free conditions. Expression of markers was analyzed using qRT-PCR, immunofluorescence and in vitro functional assay for insulin and C-peptide release was assessed using insulin and C-peptide ELISA, respectively. The cells grown under this altered culture conditions have exhibited a transition in the morphology from mesenchymal to epithelial with extensive piling up of cells. A reduction in doubling time from 40 to 18 h, upregulation of beta islet specific markers like pancreatic duodenal homeobox-1 (Pdx-1), C-peptide, insulin, and disappearance of markers like vimentin were observed. On the functional level, the altered morphology bearing cells released high levels of insulin in response to 10 \u00b5M tolbutamide (an activator of insulin pathway) and reduced insulin secretion in response to 50 \u00b5M nifedipine (inhibitor of the pathway). On the contrary, the original cells (mesenchymal morphology) had failed to release any insulin in response to varying concentrations of glucose and also the activators and inhibitors of the insulin pathway. This investigation thus provides a basis for using this basic developmental biology phenomenon mesenchymal to epithelial transition as a strategy to generate a large number of functional islets from stem cells of mesenchymal origin.","authors":"Bose, B., Shenoy P, S.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Cell Biochem","volume":"114","issue":"7","page":"1642-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11261777","title":"Molecular motors involved in T cell receptor clusterings.","abstract":"Engagement of antigen receptors on T and B cells triggers reorganization of the cytoskeleton and ordered clustering of cell surface receptors. These receptor clusters constitute spatially organized signaling machines and form the immune synapse with antigen-presenting cells. Formation of supramolecular activation clusters appear to be essential to induce functional lymphocyte responses and have been implicated as molecular mechanisms of costimulation. The Vav1-Rho-GTPase-WASP pathway constitutes a molecular motor that relays antigen receptor stimulation to changes in the cytoskeleton and receptor clustering.","authors":"Krawczyk, C., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Leukoc Biol","volume":"69","issue":"3","page":"317-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23232409","title":"Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteins.","abstract":"The evolutionary origins of the gene network underlying cellular pluripotency, a central theme in developmental biology, have yet to be elucidated. In mammals, Oct4 is a factor crucial in the reprogramming of differentiated cells into induced pluripotent stem cells. The Oct4 and Pou2 genes evolved from a POU class V gene ancestor, but it is unknown whether pluripotency induced by Oct4 gene activity is a feature specific to mammals or was already present in ancestral vertebrates. Here we report that different vertebrate Pou2 and Oct4 homologues can induce pluripotency in mouse and human fibroblasts and that the inability of zebrafish Pou2 to establish pluripotency is not representative of all Pou2 genes, as medaka Pou2 and axolotl Pou2 are able to reprogram somatic cells into pluripotent cells. Therefore, our results indicate that induction of pluripotency is not a feature specific to mammals, but existed in the Oct4\/Pou2 common ancestral vertebrate.","authors":"Tapia, N., Reinhardt, P., Duemmler, A., Wu, G., Ara\u00fazo-Bravo, MJ., Esch, D., Greber, B., Cojocaru, V., Rascon, CA., Tazaki, A., Kump, K., Voss, R., Tanaka, EM., Sch\u00f6ler, HR.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nat Commun","volume":"3","issue":null,"page":"1279","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14644192","title":"Cytokinesis: progress on all fronts.","abstract":"Cell multiplication requires sequestration of the duplicated and segregated genome into two daughter cells. The mitotic spindle is critical for orchestrating sister chromatid separation and division plane positioning. During anaphase, spindle microtubules become bundled to form the central spindle, which is essential for completion of cytokinesis. Central spindle assembly is mediated by a microtubule-associated protein and a kinesin-RhoGAP complex, both of which are regulated by phosphorylation\/dephosphorylation. The central spindle also plays a role in cleavage furrow positioning, which appears to involve activation of RhoA. New results have provided some initial clues as to how furrow positioning is achieved. Particularly notable is the discovery that a protein activated by RhoA, formin, has actin nucleation activity.","authors":"Glotzer, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Opin Cell Biol","volume":"15","issue":"6","page":"684-90","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14634120","title":"IL-1R-associated kinase 4 is required for lipopolysaccharide-induced activation of APC.","abstract":"The bacterial product LPS is a critical stimulus for the host immune system in the response against the corresponding bacterial infection. LPS provides an activation stimulus for macrophages and a maturation signal for dendritic cells to set up innate and adaptive immune responses, respectively. The signaling cascade of myeloid differentiation factor 88--&gt;IL-1R-associated kinase (IRAK)--&gt;TNFR-associated factor 6 has been implicated in mediating LPS signaling. In this report, we studied the function of IRAK-4 in various LPS-induced signals. We found that IRAK-4-deficient cells were severely impaired in producing some IFN-regulated genes as well as inflammatory cytokines in response to LPS. Among the critical downstream signaling pathways induced by LPS, NF-kappaB activation but not IFN regulatory factor 3 or STAT1 activation was defective in cells lacking IRAK-4. IRAK-4 was also required for the proper maturation of dendritic cells by LPS stimulation, particularly in terms of cytokine production and the ability to stimulate Th cell differentiation. Our results demonstrate that IRAK-4 is critical for the LPS-induced activations of APCs.","authors":"Suzuki, N., Suzuki, S., Eriksson, U., Hara, H., Mirtosis, C., Chen, NJ., Wada, T., Bouchard, D., Hwang, I., Takeda, K., Fujita, T., Der, S., Penninger, JM., Akira, S., Saito, T., Yeh, WC.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Immunol","volume":"171","issue":"11","page":"6065-71","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14607918","title":"Granulocyte-macrophage colony-stimulating factor-based melanoma cell vaccines immunize syngeneic and allogeneic recipients via host dendritic cells.","abstract":"Subcutaneous injection of GM-CSF-expressing cancer cells into experimental animals results in protective cancer immunity. To delineate the mode of action of such vaccines, we used trinitrophenyl, the antigenic moiety of the contact allergen trinitrochlorobenzene, as surrogate Ag. Trinitrophenyl-derivatized bone marrow-derived dendritic cells were found to elicit a contact hypersensitivity response in syngeneic, but not in allogeneic recipients, compatible with their expected mode of direct Ag presentation. When expressing GM-CSF, haptenized M3 melanoma cells were also able to induce a contact hypersensitivity response but, in contrast to bone marrow-derived dendritic cells, not only in syngeneic but also in allogeneic recipients. This argues for a critical role of host APC. To identify their nature, we introduced the beta-galactosidase (betagal) gene into M3-GM cells. Their administration activated betagal-specific, L(d)-restricted CTL in syngeneic BALB\/c mice. Evaluation of lymph nodes draining M3-GM-betagal injection sites revealed the presence of cells presenting the respective L(d)-binding betagal peptide epitope. Based on their capacity to activate betagal-specific CTL, they were identified as being CD11c(+) dendritic cells. These experiments provide a rational basis for the use of GM-CSF-based melanoma cell vaccines in an allogeneic setting.","authors":"Schneeberger, A., L\u00fchrs, P., Kutil, R., Steinlein, P., Schild, H., Schmidt, W., Stingl, G.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Immunol","volume":"171","issue":"10","page":"5180-7","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14625544","title":"Dendritic cell-induced autoimmune heart failure requires cooperation between adaptive and innate immunity.","abstract":"Genetic susceptibility and autoimmunity triggered by microbial infections are factors implicated in the pathogenesis of dilated cardiomyopathy, the most common cause of heart failure in young patients. Here we show that dendritic cells (DCs) loaded with a heart-specific self peptide induce CD4+ T-cell-mediated myocarditis in nontransgenic mice. Toll-like receptor (TLR) stimulation, in concert with CD40 triggering of self peptide-loaded dendritic cells, was shown to be required for disease induction. After resolution of acute myocarditis, DC-immunized mice developed heart failure, and TLR stimulation of these mice resulted in relapse of inflammatory infiltrates. Injection of damaged, syngeneic cardiomyocytes also induced myocarditis in mice if TLRs were activated in vivo. DC-induced myocarditis provides a unifying theory as to how tissue damage and activation of TLRs during infection can induce autoimmunity, relapses and cardiomyopathy.","authors":"Eriksson, U., Ricci, R., Hunziker, L., Kurrer, MO., Oudit, GY., Watts, TH., Sonderegger, I., Bachmaier, K., Kopf, M., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nat Med","volume":"9","issue":"12","page":"1484-90","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14609947","title":"Bicaudal D induces selective dynein-mediated microtubule minus end-directed transport.","abstract":"Bicaudal D is an evolutionarily conserved protein, which is involved in dynein-mediated motility both in Drosophila and in mammals. Here we report that the N-terminal portion of human Bicaudal D2 (BICD2) is capable of inducing microtubule minus end-directed movement independently of the molecular context. This characteristic offers a new tool to exploit the relocalization of different cellular components by using appropriate targeting motifs. Here, we use the BICD2 N-terminal domain as a chimera with mitochondria and peroxisome-anchoring sequences to demonstrate the rapid dynein-mediated transport of selected organelles. Surprisingly, unlike other cytoplasmic dynein-mediated processes, this transport shows very low sensitivity to overexpression of the dynactin subunit dynamitin. The dynein-recruiting activity of the BICD2 N-terminal domain is reduced within the full-length molecule, indicating that the C-terminal part of the protein might regulate the interaction between BICD2 and the motor complex. Our findings provide a novel model system for dissection of the molecular mechanism of dynein motility.","authors":"Hoogenraad, CC., Wulf, P., Schiefermeier, N., Stepanova, T., Galjart, N., Small, JV., Grosveld, F., de Zeeuw, CI., Akhmanova, A.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"EMBO J","volume":"22","issue":"22","page":"6004-15","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15065662","title":"From a single double helix to paired double helices and back.","abstract":"The propagation of our genomes during cell proliferation depends on the movement of sister DNA molecules produced by DNA replication to opposite sides of the cell before it divides. This feat is achieved by microtubules in eukaryotic cells but it has long remained a mystery how cells ensure that sister DNAs attach to microtubules with opposite orientations, known as amphitelic attachment. It is currently thought that sister chromatid cohesion has a crucial role. By resisting the forces exerted by microtubules, sister chromatid cohesion gives rise to tension that is thought essential for stabilizing kinetochore-microtubule attachments. Efficient amphitelic attachment is therefore achieved by an error correction mechanism that selectively eliminates connections that do not give rise to tension. Cohesion between sister chromatids is mediated by a multisubunit complex called cohesin which forms a gigantic ring structure. It has been proposed that sister DNAs are held together owing to their becoming entrapped within a single cohesin ring. Cohesion between sister chromatids is destroyed at the metaphase to anaphase transition by proteolytic cleavage of cohesin's Scc1 subunit by a thiol protease called separase, which severs the ring and thereby releases sister DNAs.","authors":"Nasmyth, K., Schleiffer, A.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"359","issue":"1441","page":"99-108","pdf":null,"JrId":"8277","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23080501","title":"Elevated post-transfusion serum transaminase values associated with a highly significant trend for increasing prevalence of anti-Vesivirus antibody in Korean patients.","abstract":"A highly significant increase in anti-Vesivirus (family Caliciviridae) antibody prevalence, along the axis from healthy blood donors; donors with elevated transaminase; patients with clinical hepatitis; and patients with post-transfusion\/dialysis hepatitis, has been reported in human sera from the USA and Europe. Asian samples have now been tested retrospectively using serology and enzyme immunoassay (EIA) with a Vesivirus partial-capsid antigen expressed as a fusion protein. Anti-vesiviral antibodies were measured by optical densities (OD(650)) and compared in patients separated by age, gender and Groups A-F as follows: Control Group A, an Experimental Group B, which was divided further into Group C, patients with elevated enzymes (alanine transaminase (ALT), aspartate transaminase (AST), and \u03b3-glutamyl transpeptidase (\u03b3-GT); Group D, patients receiving transfused blood; Group E, patients with high enzyme levels after transfusion; and Group F, hepatitis B and C positive patients. Using multivariate logistic regression analyses, a significantly greater proportion of patients receiving transfusion(s), were positive for anti-Vesivirus antibody compared with non-transfused patients (P = 0.008; OR: 3.86, 95% CI: 1.43-10.43). Also, anti-Vesivirus antibody was significantly associated with elevated biochemical liver function tests: ALT \u2265 20\u2009IU or AST \u2265 120\u2009IU (P = 0.017; OR: 4.23, 95% CI: 1.30-13.80). In the blood transfusion group, anti-Vesivirus antibody was significantly correlated with high enzyme levels (ALT, P = 0.018; AST, P = 0.010; \u03b3-GT, P = 0.020). These data provide serologic evidence of vesiviral transfusion-transmission-associated disease, which could include infection of any organ system where cytopathology resulted in high levels of either ALT or AST.","authors":"Lee, H., Cho, YH., Park, JS., Kim, EC., Smith, AW., Ko, G.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Med Virol","volume":"84","issue":"12","page":"1943-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23081735","title":"Bone marrow endothelial progenitors augment atherosclerotic plaque regression in a mouse model of plasma lipid lowering.","abstract":"The major event initiating atherosclerosis is hypercholesterolemia-induced disruption of vascular endothelium integrity. In settings of endothelial damage, endothelial progenitor cells (EPCs) are mobilized from bone marrow into circulation and home to sites of vascular injury where they aid endothelial regeneration. Given the beneficial effects of EPCs in vascular repair, we hypothesized that these cells play a pivotal role in atherosclerosis regression. We tested our hypothesis in the atherosclerosis-prone mouse model in which hypercholesterolemia, one of the main factors affecting EPC homeostasis, is reversible (Reversa mice). In these mice, normalization of plasma lipids decreased atherosclerotic burden; however, plaque regression was incomplete. To explore whether endothelial progenitors contribute to atherosclerosis regression, bone marrow EPCs from a transgenic strain expressing green fluorescent protein (GFP) under the control of endothelial cell-specific Tie2 promoter (Tie2-GFP(+)) were isolated. These cells were then adoptively transferred into atheroregressing Reversa recipients where they augmented plaque regression induced by reversal of hypercholesterolemia. Advanced plaque regression correlated with engraftment of Tie2-GFP(+) EPCs into endothelium and resulted in an increase in atheroprotective nitric oxide and improved vascular relaxation. Similarly augmented plaque regression was also detected in regressing Reversa mice treated with the stem cell mobilizer AMD3100 which also mobilizes EPCs to peripheral blood. We conclude that correction of hypercholesterolemia in Reversa mice leads to partial plaque regression that can be augmented by AMD3100 treatment or by adoptive transfer of EPCs. This suggests that direct cell therapy or indirect progenitor cell mobilization therapy may be used in combination with statins to treat atherosclerosis.","authors":"Yao, L., Heuser-Baker, J., Herlea-Pana, O., Iida, R., Wang, Q., Zou, MH., Barlic-Dicen, J.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Stem Cells","volume":"30","issue":"12","page":"2720-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15062096","title":"Maintenance of cohesin at centromeres after meiosis I in budding yeast requires a kinetochore-associated protein related to MEI-S332.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15062096<\/PMID><DateCompleted><Year>2004<\/Year><Month>06<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2017<\/Year><Month>02<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>14<\/Volume><Issue>7<\/Issue><PubDate><Year>2004<\/Year><Month>Apr<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Maintenance of cohesin at centromeres after meiosis I in budding yeast requires a kinetochore-associated protein related to MEI-S332.<\/ArticleTitle><Pagination><MedlinePgn>560-72<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The halving of chromosome number that occurs during meiosis depends on three factors. First, homologs must pair and recombine. Second, sister centromeres must attach to microtubules that emanate from the same spindle pole, which ensures that homologous maternal and paternal pairs can be pulled in opposite directions (called homolog biorientation). Third, cohesion between sister centromeres must persist after the first meiotic division to enable their biorientation at the second.","authors":"Katis, VL., Galova, M., Rabitsch, KP., Gregan, J., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"7","page":"560-72","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23080365","title":"The coagulopathy of liver disease:  does vitamin K help?","abstract":"Vitamin K is frequently administered in cirrhotic patients to correct their coagulopathy, but evidence for such practice is lacking. We aimed to assess whether vitamin K administration increases the levels of the vitamin K-dependent factor VII (FVII), protein C, and protein S in patients with different stages of liver dysfunction. Eighty-nine patients were recruited into four groups: group 1 [hepatitis B virus (HBV) inactive carriers, n = 23]; group 2 [chronic HBV and hepatitis C virus (HCV) hepatitis, n = 21]; group 3 (cirrhosis, n = 24); group 4 (hepatocellular carcinoma, n = 21); and a healthy control group (n = 39). A single dose of 10 mg of vitamin K1 was administered subcutaneously to all patients. Prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT), fibrinogen, FVII, protein C, total and free protein S, and proteins induced by vitamin K absence (PIVKA)-II (des-gamma-carboxy prothrombin) were measured at baseline and 72 h after vitamin K administration. There was progressive increment in baseline PIVKA-II, and decrements in fibrinogen, FVII, protein C, and protein S across study groups (P &lt; 0.0001). Compared to baseline, vitamin K administration did not affect the measured parameters, whereas TT showed no reduction in any of the groups. Protein C levels declined in group 2, whereas FVII, total and free protein S did not increase in any group, for all parameters. Vitamin K therapy does not cause significant improvements in the majority of coagulation parameters and hence does not seem to be routinely indicated in patients with liver disease.","authors":"Saja, MF., Abdo, AA., Sanai, FM., Shaikh, SA., Gader, AG.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Blood Coagul Fibrinolysis","volume":"24","issue":"1","page":"10-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23080155","title":"CO(2) signaling in chemosensory neuroepithelial cells of the zebrafish gill filaments: role of intracellular Ca(2+) and pH.","abstract":"Adult zebrafish, Danio rerio, exhibit hyperventilatory responses to absolute environmental CO2 levels as low as 1.0 mmHg. The ability of zebrafish to detect and respond to low ambient CO2 appears to be mediated by chemosensory neuroepithelial cells (NECs) of the gill filaments. Recent electrophysiological characterization of this response revealed that the partial pressure-dependent depolarization of NECs in response to a hypercapnic stimulus is dependent on the rate of acidification associated with the hydration of CO2 and the inhibition of background K(+) channels. In order to further elucidate the signaling pathway underlying CO2 chemotransduction in NECs, we used microfluorimetric techniques to study intracellular changes in pH (pHi) and calcium ([Ca(2+)]i). Using the ratiometric indicators BCECF-AM and fura-2-AM, we found that a hypercapnic stimulus evoked a decrease in pHi and an increase in [Ca(2+)]i.","authors":"Abdallah, SJ., Perry, SF., Jonz, MG.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Adv Exp Med Biol","volume":"758","issue":"","page":"143-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10021388","title":"Deletion analysis of the Drosophila Inscuteable protein reveals domains for cortical localization and asymmetric localization.","abstract":"The Drosophila Inscuteable protein acts as a key regulator of asymmetric cell division during the development of the nervous system [1] [2]. In neuroblasts, Inscuteable localizes into an apical cortical crescent during late interphase and most of mitosis. During mitosis, Inscuteable is required for the correct apical-basal orientation of the mitotic spindle and for the asymmetric segregation of the proteins Numb [3] [4] [5], Prospero [5] [6] [7] and Miranda [8] [9] into the basal daughter cell. When Inscuteable is ectopically expressed in epidermal cells, which normally orient their mitotic spindle parallel to the embryo surface, these cells reorient their mitotic spindle and divide perpendicularly to the surface [1]. Like the Inscuteable protein, the inscuteable RNA is asymmetrically localized [10]. We show here that inscuteable RNA localization is not required for Inscuteable protein localization. We found that a central 364 amino acid domain - the Inscuteable asymmetry domain - was necessary and sufficient for Inscuteable localization and function. Within this domain, a separate 100 amino acid region was required for asymmetric localization along the cortex, whereas a 158 amino acid region directed localization to the cell cortex. The same 158 amino acid fragment could localize asymmetrically when coexpressed with the full-length protein, however, and could bind to Inscuteable in vitro, suggesting that this domain may be involved in the self-association of Inscuteable in vivo.","authors":"Knoblich, JA., Jan, LY., Jan, YN.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Curr Biol","volume":"9","issue":"3","page":"155-8","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1999-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14532126","title":"Formation of facultative heterochromatin in the absence of HP1.","abstract":"Facultative heterochromatin is a cytological manifestation of epigenetic mechanisms that regulate gene expression. Constitutive heterochromatin is marked by distinctive histone H3 methylation and the presence of HP1 proteins, but the chromatin modifications of facultative heterochromatin are less clear. We have examined histone modifications and HP1 in the facultative heterochromatin of nucleated erythrocytes and show that mouse and chicken erythrocytes have different mechanisms of heterochromatin formation. Mouse embryonic erythrocytes have abundant HP1, increased tri-methylation of H3 at K9 and loss of H3 tri-methylation at K27. In contrast, we show that HP1 proteins are lost during the differentiation of chicken erythrocytes, and that H3 tri-methylation at both K9 and K27 is reduced. This coincides with the appearance of the variant linker histone H5. HP1s are also absent from erythrocytes of Xenopus and zebrafish. Our data show that in the same cell lineage there are different mechanisms for forming facultative heterochromatin in vertebrates. To our knowledge, this is the first report of cell types that lack HP1s and that have gross changes in the levels of histone modifications.","authors":"Gilbert, N., Boyle, S., Sutherland, H., de Las Heras, J., Allan, J., Jenuwein, T., Bickmore, WA.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"EMBO J","volume":"22","issue":"20","page":"5540-50","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23063129","title":"Hedgehog partial agonism drives Warburg-like metabolism in muscle and brown fat.","abstract":"Diabetes, obesity, and cancer affect upward of 15% of the world's population. Interestingly, all three diseases juxtapose dysregulated intracellular signaling with altered metabolic state. Exactly which genetic factors define stable metabolic set points in vivo remains poorly understood. Here, we show that hedgehog signaling rewires cellular metabolism. We identify a cilium-dependent Smo-Ca(2+)-Ampk axis that triggers rapid Warburg-like metabolic reprogramming within minutes of activation and is required for proper metabolic selectivity and flexibility. We show that Smo modulators can uncouple the Smo-Ampk axis from canonical signaling and identify cyclopamine as one of a new class of \"selective partial agonists,\" capable of concomitant inhibition of canonical and activation of noncanonical hedgehog signaling. Intriguingly, activation of the Smo-Ampk axis in vivo drives robust insulin-independent glucose uptake in muscle and brown adipose tissue. These data identify multiple noncanonical endpoints that are pivotal for rational design of hedgehog modulators and provide a new therapeutic avenue for obesity and diabetes.","authors":"Teperino, R., Amann, S., Bayer, M., McGee, SL., Loipetzberger, A., Connor, T., Jaeger, C., Kammerer, B., Winter, L., Wiche, G., Dalgaard, K., Selvaraj, M., Gaster, M., Lee-Young, RS., Febbraio, MA., Knauf, C., Cani, PD., Aberger, F., Penninger, JM., Pospisilik, JA., Esterbauer, H.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell","volume":"151","issue":"2","page":"414-26","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14527956","title":"The human phosphatidylinositol phosphatase SAC1 interacts with the coatomer I complex.","abstract":"The Saccharomyces cerevisiae SAC1 gene encodes an integral membrane protein of the endoplasmic reticulum (ER) and the Golgi apparatus. Yeast SAC1 mutants display a wide array of phenotypes including inositol auxotrophy, cold sensitivity, secretory defects, disturbed ATP transport into the ER, or suppression of actin gene mutations. At present, it is not clear how these phenotypes relate to the finding that SAC1 displays polyphosphoinositide phosphatase activity. Moreover, it is still an open question whether SAC1 functions similarly in mammalian cells, since some phenotypes are yeast-specific. Potential protein interaction partners and, connected to that, possible regulatory circuits have not been described. Therefore, we have cloned human SAC1 (hSAC1), show that it behaves similar to ySac1p in terms of substrate specificity, demonstrate that the endogenous protein localizes to the ER and Golgi, and identify for the first time members of the coatomer I (COPI) complex as interaction partners of hSAC1. Mutation of a putative COPI interaction motif (KXKXX) at its C terminus abolishes interaction with COPI and causes accumulation of hSAC1 in the Golgi. In addition, we generated a catalytically inactive mutant, demonstrate that its lipid binding capacity is unaltered, and show that it accumulates in the Golgi, incapable of interacting with the COPI complex despite the presence of the KXKXX motif. These results open the possibility that the enzymatic function of hSAC1 provides a switch for accessibility of the COPI interaction motif.","authors":"Rohde, HM., Cheong, FY., Konrad, G., Paiha, K., Mayinger, P., Boehmelt, G.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Biol Chem","volume":"278","issue":"52","page":"52689-99","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23040479","title":"The Par complex and integrins direct asymmetric cell division in adult intestinal stem cells.","abstract":"The adult Drosophila midgut is maintained by intestinal stem cells (ISCs) that generate both self-renewing and differentiating daughter cells. How this asymmetry is generated is currently unclear. Here, we demonstrate that asymmetric ISC division is established by a unique combination of extracellular and intracellular polarity mechanisms. We show that Integrin-dependent adhesion to the basement membrane induces cell-intrinsic polarity and results in the asymmetric segregation of the Par proteins Par-3, Par-6, and aPKC into the apical daughter cell. Cell-specific knockdown and overexpression experiments suggest that increased activity of aPKC enhances Delta\/Notch signaling in one of the two daughter cells to induce terminal differentiation. Perturbing this mechanism or altering the orientation of ISC division results in the formation of intestinal tumors. Our data indicate that mechanisms for intrinsically asymmetric cell division can be adapted to allow for the flexibility in lineage decisions that is required in adult stem cells.","authors":"Goulas, S., Conder, R., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Stem Cell","volume":"11","issue":"4","page":"529-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15060170","title":"Muscle regeneration and myogenic differentiation defects in mice lacking TIS7.","abstract":"The tetradecanoyl phorbol acetate-induced sequence 7 gene (tis7) is regulated during cell fate processes and functions as a transcriptional coregulator. Here, we describe the generation and analysis of mice lacking the tis7 gene. Surprisingly, TIS7 knockout mice show no gross histological abnormalities and are fertile. Disruption of the tis7 gene by homologous recombination delayed muscle regeneration and altered the isometric contractile properties of skeletal muscles after muscle crush damage in TIS7(-\/-) mice. Cultured primary myogenic satellite cells (MSCs) from TIS7(-\/-) mice displayed marked reductions in differentiation potential and fusion index in a strictly cell-autonomous fashion. Loss of TIS7 caused the down-regulation of muscle-specific genes, such as those for MyoD, myogenin, and laminin-alpha2. Fusion potential in TIS7(-\/-) MSCs could be rescued by TIS7 expression or laminin supplementation. Therefore, TIS7 is not essential for mouse development but plays a novel regulatory role during adult muscle regeneration.","authors":"Vadivelu, SK., Kurzbauer, R., Dieplinger, B., Zweyer, M., Schafer, R., Wernig, A., Vietor, I., Huber, LA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Mol Cell Biol","volume":"24","issue":"8","page":"3514-25","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15048807","title":"Tissue-specific expression of cre recombinase from the Pax8 locus.","abstract":"The transcription factor Pax8 is expressed in the developing thyroid gland, inner ear, kidney, and mid-hindbrain region. Pax8 mutant mice die only postnatally due to a thyroid gland defect. Here we report the generation and expression analysis of a Pax8(cre) allele. Cre recombinase activity was detected in known Pax8 expression domains of Pax8(cre\/+) and Pax8(cre\/cre) embryos carrying the Z\/AP transgene, which expresses alkaline phosphatase only after Cre-mediated excision of lacZ sequences. Alkaline phosphatase expression was additionally detected in the adrenal gland and in the facial, vestibulocochlear, and cuneate nerves, which have so far not been associated with Pax8 expression. Our data indicate that the Pax8(cre) allele provides a novel important tool for conditional gene manipulation and lineage tracing in different Pax8 expression domains.","authors":"Bouchard, M., Souabni, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genesis","volume":"38","issue":"3","page":"105-9","pdf":null,"JrId":"21590","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12796471","title":"Normal incidence of diabetes in NOD mice tolerant to glutamic acid decarboxylase.","abstract":"Experiments in nonobese diabetic (NOD) mice that lacked expression of glutamic acid decarboxylase (GAD) in beta cells have suggested that GAD represents an autoantigen essential for initiating and maintaining the diabetogenic immune response. Several attempts of inducing GAD-specific recessive tolerance to support this hypothesis have failed. Here we report on successful tolerance induction by expressing a modified form of GAD under control of the invariant chain promoter resulting in efficient epitope display. In spite of specific tolerance insulitis and diabetes occurred with normal kinetics indicating that GAD is not an essential autoantigen in the pathogenesis of diabetes.","authors":"Jaeckel, E., Klein, L., Martin-Orozco, N., von Boehmer, H.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Exp Med","volume":"197","issue":"12","page":"1635-44","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12925580","title":"Mice humanised for the EGF receptor display hypomorphic phenotypes in skin, bone and heart.","abstract":"Mice lacking the epidermal growth factor receptor (EGFR) develop epithelial defects and a neurodegenerative disease and die within the first month of birth. By employing a conditional knock-in approach using the human EGFR cDNA mice humanised for EGFR (hEGFRKI\/KI) were generated. Homozygous hEGFRKI\/KI mice are viable and live up to six months. However, these mice are growth retarded and show skin and hair defects similar to Egfr-\/- mutants. Interestingly, the neurodegeneration is fully rescued in hEGFRKI\/KI mice, however, they develop a severe heart hypertrophy with semilunar valve abnormalities. Moreover, hEGFRKI\/KI mice display accelerated chondrocyte and osteoblast differentiation, a phenotype that is also present in Egfr-\/- mice and has not been previously described. The severity of the phenotypes correlates with the expression levels of the hEGFRKI allele, which is not efficiently expressed in epithelial and bone cells, but is expressed at similar and even higher levels as the endogenous Egfr in brain and heart. These results demonstrate that mice humanised for EGFR display tissue-specific hypomorphic phenotypes and describe a novel function for EGFR in bone development.","authors":"Sibilia, M., Wagner, B., Hoebertz, A., Elliott, C., Marino, S., Jochum, W., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Development","volume":"130","issue":"19","page":"4515-25","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2003-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15032574","title":"Transcriptional control of early B cell development.","abstract":"The generation of B-lymphocytes from hematopoietic stem cells is controlled by multiple transcription factors regulating distinct developmental aspects. Ikaros and PU.1 act in parallel pathways to control the development of lymphoid progenitors in part by regulating the expression of essential signaling receptors (Flt3, c-Kit, and IL-7R alpha). The generation of the earliest B cell progenitors depends on E2A and EBF, which coordinately activate the B cell gene expression program and immunoglobulin heavy-chain gene rearrangements at the onset of B-lymphopoiesis. Pax5 restricts the developmental options of lymphoid progenitors to the B cell lineage by repressing the transcription of lineage-inappropriate genes and simultaneously activating the expression of B-lymphoid signaling molecules. LEF1 and Sox4 contribute to the survival and proliferation of pro-B cells in response to extracellular signals. Finally, IRF4 and IRF8 together control the termination of pre-B cell receptor signaling and thus promote differentiation to small pre-B cells undergoing light-chain gene rearrangements.","authors":"Busslinger, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Annu Rev Immunol","volume":"22","issue":null,"page":"55-79","pdf":null,"JrId":"1564","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12946994","title":"Up-regulation of SLAP in FLI-1-transformed erythroblasts interferes with EpoR signaling.","abstract":"Rearrangement of the FLI-1 locus and ensuing overexpression of FLI-1 protein is an early event in Friend murine leukemia virus (F-MuLV)-induced erythroleukemia. When overexpressed in primary erythroblasts, FLI-1 converts erythropoietin (Epo)-induced terminal differentiation into a proliferative response. We found that SLAP, a gene encoding a recently described negative regulator of T-cell antigen receptor function during thymocyte development, is up-regulated both at the RNA and protein levels in FLI-1-transformed erythroblasts. Src-like adaptor protein (SLAP) was found in a specific complex with erythropoietin receptor (EpoR), a cytokine receptor essential to erythroid differentiation. Constitutive expression of SLAP severely impairs hemoglobinization and late survival during Epo-induced terminal differentiation of erythroblasts. This impairment is associated with the specific inhibition of several critical Epo-dependent signaling events, including signal transducer and activator of transcription 5 (STAT5) activation and up-regulation of the expression of the antiapoptotic BCL-X gene. Our data support a model by which FLI-1 inhibits normal erythroid differentiation through the deregulation of genes encoding adaptors\/effectors that modify the signaling output of cytokine receptors normally required for terminal differentiation.","authors":"Lebigot, I., Gardellin, P., Lefebvre, L., Beug, H., Ghysdael, J., Quang, CT.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Blood","volume":"102","issue":"13","page":"4555-62","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15020099","title":"Context-dependent stimulus presentation to freely moving animals in 3D.","abstract":"The presentation of controllable, dynamic sensory stimuli provides a powerful experimental paradigm, which has been extensively applied to explore sensory processing in walking and tethered flying insects. Recent advances in computer hardware and software technology provide the opportunity to track the 3D flight path of free-flying insects and process these data in real-time, opening up the possibility to present dynamic stimuli to free-flying animals. To accommodate for the increased complexity relating to 3D space, we partitioned experimental design, real-time data acquisition and stimulus control into multiple self-contained modules. 3D experimental scenarios were created in a stand-alone application by forging multiple 3D space-stimulus relationships. The use of dynamic cues is illustrated by an experiment, in which dynamic acoustic cues were presented to a free-flying parasitoid fly in a large 3D environment. The combination of loosely coupled modules provides robust and flexible solutions, allowing new paradigms to be readily implemented based on existing technologies. We demonstrate this with a test system that displayed a complex visual stimulus, controlled in real-time by the 2D position and orientation of a test object. The presented methods are applicable in a variety of novel experimental paradigms, including learning paradigms, for various sensory modalities in walking, swimming and flying animals.","authors":"Fry, SN., M\u00fcller, P., Baumann, HJ., Straw, AD., Bichsel, M., Robert, D.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Neurosci Methods","volume":"135","issue":"1-2","page":"149-57","pdf":null,"JrId":"5306","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15013811","title":"Computational identification of microRNA targets.","abstract":"Recent experiments have shown that the genomes of organisms such as worm, fly, human, and mouse encode hundreds of microRNA genes. Many of these microRNAs are thought to regulate the translational expression of other genes by binding to partially complementary sites in messenger RNAs. Phenotypic and expression analysis suggests an important role of microRNAs during development. Therefore, it is of fundamental importance to identify microRNA targets. However, no experimental or computational high-throughput method for target site identification in animals has been published yet. Our main result is a new computational method that is designed to identify microRNA target sites. This method recovers with high specificity known microRNA target sites that have previously been defined experimentally. Based on these results, we present a simple model for the mechanism of microRNA target site recognition. Our model incorporates both kinetic and thermodynamic components of target recognition. When we applied our method to a set of 74 Drosophila melanogaster microRNAs, searching 3'UTR sequences of a predefined set of fly mRNAs for target sites which were evolutionary conserved between D. melanogaster and Drosophila pseudoobscura, we found that many key developmental body patterning genes such as hairy and fushi-tarazu are likely to be translationally regulated by microRNAs.","authors":"Rajewsky, N., Socci, ND.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Dev Biol","volume":"267","issue":"2","page":"529-35","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33793889","title":"Membrane imaging in the plant endomembrane system.","abstract":"Recent studies on membrane imaging in the plant endomembrane system by 2-D\/3-D CLSM and TEM provide future perspectives of whole-cell ET and cryo-FIB-aided cryo-ET analysis.","authors":"Liu, Z., Gao, J., Cui, Y., Klumpe, S., Xiang, Y., Erdmann, PS., Jiang, L.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Plant Physiol","volume":"185","issue":"3","page":"562-576","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-11","doi":"10.1093\/plphys\/kiaa040","first_author":null,"corresponding_authors":null},{"pmid":"15004008","title":"Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene.","abstract":"The subnuclear location and chromatin state of the immunoglobulin heavy-chain (IgH) locus have been implicated in the control of VDJ recombination. VH-to-DJH rearrangement of distal, but not proximal V(H) genes, furthermore, depends on the B-lineage commitment factor Pax5 (BSAP). He e we demonstrate that ectopic Pax5 expression from the Ikaros promote induces proximal rather than distal VH-DJH rearrangements in Ik(Pax5\/+) thymocytes, thus recapitulating the loss-of-function phenotype of Pax5-\/- pro-B cells. The phenotypic similarities of both cell types include (1) chromatin accessibility of distal VH genes in the absence of VH-DJH rearrangements, (2) expression of the B-cell-specific regulator EBF, (3) central location of IgH alleles within the nucleus, and (4) physical separation of distal VH genes from proximal segments in an extended IgH locus. Reconstitution of Pax5 expression in Pax5-\/- pro-B cells induced large-scale contraction and distal VH-DJH rearrangements of the IgH locus. Hence, VH-DJH recombination is regulated in two steps during early B-lymphopoiesis. The IgH locus is first repositioned from its default location at the nuclear periphery toward the center of the nucleus, which facilitates proximal VH-DJH recombination. Pax5 subsequently activates locus contraction and distal VH-DJH rearrangements in collaboration with an unknown factor that is present in pro-B cells, but absent in thymocytes.","authors":"Fuxa, M., Skok, J., Souabni, A., Salvagiotto, G., Roldan, E., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genes Dev","volume":"18","issue":"4","page":"411-22","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12881423","title":"Myeloid lineage switch of Pax5 mutant but not wild-type B cell progenitors by C\/EBPalpha and GATA factors.","abstract":"The developmental potential of hematopoietic progenitors is restricted early on to either the erythromyeloid or lymphoid lineages. The broad developmental potential of Pax5(-\/-) pro-B cells is in apparent conflict with such a strict separation, although these progenitors realize the myeloid and erythroid potential with lower efficiency compared to the lymphoid cell fates. Here we demonstrate that ectopic expression of the transcription factors C\/EBPalpha, GATA1, GATA2 and GATA3 strongly promoted in vitro macrophage differentiation and myeloid colony formation of Pax5(-\/-) pro-B cells. GATA2 and GATA3 expression also resulted in efficient engraftment and myeloid development of Pax5(-\/-) pro-B cells in vivo. The myeloid transdifferentiation of Pax5(-\/-) pro-B cells was accompanied by the rapid activation of myeloid genes and concomitant repression of B-lymphoid genes by C\/EBPalpha and GATA factors. These data identify the Pax5(-\/-) pro-B cells as lymphoid progenitors with a latent myeloid potential that can be efficiently activated by myeloid transcription factors. The same regulators were unable to induce a myeloid lineage switch in Pax5(+\/+) pro-B cells, indicating that Pax5 dominates over myeloid transcription factors in B-lymphocytes.","authors":"Heavey, B., Charalambous, C., Cobaleda, C., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"EMBO J","volume":"22","issue":"15","page":"3887-97","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12923528","title":"Diverse cellular and molecular mechanisms contribute to epithelial plasticity and metastasis.","abstract":"In contrast to the aberrant control of proliferation, apoptosis, angiogenesis and lifespan, the cellular mechanisms that cause local invasion and metastasis of tumour cells are still poorly understood. New experimental approaches have identified different types of epithelial-plasticity changes in tumour cells towards fibroblastoid phenotypes as crucial events that occur during metastasis, and many molecules and signalling pathways cooperate to trigger these processes.","authors":"Gr\u00fcnert, S., Jechlinger, M., Beug, H.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nat Rev Mol Cell Biol","volume":"4","issue":"8","page":"657-65","pdf":null,"JrId":"22271","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9989411","title":"Molecular characterization of mitochondrial apoptosis-inducing factor.","abstract":"Mitochondria play a key part in the regulation of apoptosis (cell death). Their intermembrane space contains several proteins that are liberated through the outer membrane in order to participate in the degradation phase of apoptosis. Here we report the identification and cloning of an apoptosis-inducing factor, AIF, which is sufficient to induce apoptosis of isolated nuclei. AIF is a flavoprotein of relative molecular mass 57,000 which shares homology with the bacterial oxidoreductases; it is normally confined to mitochondria but translocates to the nucleus when apoptosis is induced. Recombinant AIF causes chromatin condensation in isolated nuclei and large-scale fragmentation of DNA. It induces purified mitochondria to release the apoptogenic proteins cytochrome c and caspase-9. Microinjection of AIF into the cytoplasm of intact cells induces condensation of chromatin, dissipation of the mitochondrial transmembrane potential, and exposure of phosphatidylserine in the plasma membrane. None of these effects is prevented by the wide-ranging caspase inhibitor known as Z-VAD.fmk. Overexpression of Bcl-2, which controls the opening of mitochondrial permeability transition pores, prevents the release of AIF from the mitochondrion but does not affect its apoptogenic activity. These results indicate that AIF is a mitochondrial effector of apoptotic cell death.","authors":"Susin, SA., Lorenzo, HK., Zamzami, N., Marzo, I., Snow, BE., Brothers, GM., Mangion, J., Jacotot, E., Costantini, P., Loeffler, M., Larochette, N., Goodlett, DR., Aebersold, R., Siderovski, DP., Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nature","volume":"397","issue":"6718","page":"441-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9973314","title":"Self-renewal, maturation, and differentiation of the rat myelomonocytic hematopoietic stem cell.","abstract":"Hematopoiesis is viewed as a differentiating system emanating from a pluripotent hematopoietic stem cell capable of both self-renewal and differentiation. By identifying and characterizing a novel and highly specific in vitro mitogenic response to the N-acetyl glucosamyl\/sialic acid specific, stem cell-binding lectin wheat germ agglutinin (WGA), we demonstrate the existance of a rare (0.1%), plastic adherent precursor in rat bone marrow capable of proliferation (two to seven divisions) in response to WGA. Stimulated cells possess a lineage (lin)low\/- immunophenotype and immature blastoid morphology (WGA blasts). A subsequent proliferative response to stem cell factor (SCF), the ligand for the proto-oncogene receptor tyrosine kinase c-kit, is characterized by an initial maturation in immunophenotype and subsequent self-renewal of cells (SCF blasts) without differentiation for at least 50 generations. Although granulocyte colony-stimulating factor (G-CSF), interleukin (IL) -6, IL-7, and IL-11 synergize with SCF to increase blast colony formation, cytokines such as granulocyte-macrophage CSF or IL-3 are without significant effect. At all time points in culture, however, cells rapidly differentiate to mature neutrophils with dexamethasone or to mainly monocytes\/macrophages in the presence of 1alpha,25-dihydroxyvitamin D3, characterized by cell morphology and cytochemistry. Removal of SCF during blast maturation, self-renewal, or induction of differentiation phases results in apoptotic cell death. Data indicate a pivotal role for SCF\/c-kit interaction during antigenic maturation, self-renewal, and apoptotic protection of these lineage-restricted progenitors during non-CSF-mediated induction of differentiation. This approach provides a source of many normal, proliferating myelomonocytic precursor cells, and introduces possible clinical applications of ex vivo expanded myeloid stem cells.","authors":"Lucas, T., Krugluger, W., Samorapoompichit, P., Gamperl, R., Beug, H., F\u00f6rster, O., Boltz-Nitulescu, G.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"FASEB J","volume":"13","issue":"2","page":"263-72","pdf":null,"JrId":"3815","fulltextlink":null,"preprintlink":null,"articledate":"1999-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12874086","title":"Enhanced renal immunocytochemical expression of ANG-(1-7) and ACE2 during pregnancy.","abstract":"Previously we demonstrated that kidney concentration and urinary excretion of angiotensin-(1-7) are increased during normal pregnancy in rats. Since this finding may reflect local kidney production of angiotensin-(1-7), we determined the immunocytochemical distribution of angiotensin-(1-7) and its newly described processing enzyme, ACE2, in kidneys of virgin and 19-day-pregnant Sprague-Dawley rats. Sprague-Dawley rats were killed at the 19th day of pregnancy, and tissues were prepared for immunocytochemical by using a polyclonal antibody to angiotensin- (1-7) or a monoclonal antibody to ACE2. Angiotensin-(1-7) immunostaining was predominantly localized to the renal tubules traversing both the inner cortex and outer medulla. ACE2 immunostaining was localized throughout the cortex and outer medulla and was visualized in the renal tubules of both virgin and pregnant rats. The quantification of angiotensin-(1-7) and ACE2 immunocytochemical staining showed that in pregnant animals, the intensity of the staining increased by 56% and 117%, respectively (P&lt;0.05). This first demonstration of the immunocytochemical distribution of angiotensin-(1-7) and ACE2 in kidneys of pregnant rats shows that pregnancy increases angiotensin-(1-7) immunocytochemical expression in association with increased ACE2 intensity of staining. The findings suggest that ACE2 may contribute to the local production and overexpression of angiotensin-(1-7) in the kidney during pregnancy.","authors":"Brosnihan, KB., Neves, LA., Joyner, J., Averill, DB., Chappell, MC., Sarao, R., Penninger, J., Ferrario, CM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Hypertension","volume":"42","issue":"4","page":"749-53","pdf":null,"JrId":"4217","fulltextlink":null,"preprintlink":null,"articledate":"2003-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9837974","title":"Soluble LDL minireceptors. Minimal structure requirements for recognition of minor group human rhinovirus.","abstract":"Soluble human low density lipoprotein minireceptors with less than seven ligand binding repeats (as are present in the native membrane receptor) were expressed in Sf9 insect cells with a hexa-His tag fused to the C terminus. The recombinant truncated proteins were affinity purified from the tissue culture supernatants by Ni-NTA column chromatography. Minireceptors with more than two repeats bound to rabbit beta very low density lipoprotein and could thus be further purified by affinity chromatography. Binding and cell protection assays indicated that two ligand binding repeats are sufficient for attachment of minor group human rhinoviruses to immobilized receptors, whereas at least three ligand binding repeats are required to protect HeLa cells against viral infection.","authors":"Marlovits, TC., Abrahamsberg, C., Blaas, D.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Biol Chem","volume":"273","issue":"50","page":"33835-40","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1999-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9811605","title":"Activation of the human anaphase-promoting complex by proteins of the CDC20\/Fizzy family.","abstract":"The initiation of anaphase and exit from mitosis depend on the activation of the cyclosome\/anaphase-promoting complex (APC) that ubiquitinates regulatory proteins such as anaphase inhibitors and mitotic cyclins [1-4]. Genetic experiments have demonstrated that two related WD40-repeat proteins--called Cdc20p and Hct1p\/Cdh1p in budding yeast and Fizzy and Fizzy-related in Drosophila--are essential for APC--dependent proteolysis [5-11]. Human orthologs of these proteins--hCDC20\/p55CDC [12] and hCDH1--have recently been found to associate with APC in a cell-cycle-dependent manner [13,14]. Here, we show that the amount of hCDC20 and hCDH1 bound to APC correlates with a high ubiquitination activity of APC and that binding of recombinant hCDC20 and hCDH1 can activate APC in vitro. Our results suggest that the association between hCDH1 and APC is regulated by post-translational mechanisms, whereas the amount of hCDC20 bound to APC may in addition be controlled by hCDC20 synthesis and destruction [15]. The temporally distinct association of hCDC20 and hCDH1 with APC suggests that these proteins are, respectively, mitosis-specific and G1-specific activating subunits of APC.","authors":"Kramer, ER., Gieffers, C., H\u00f6lzl, G., Hengstschl\u00e4ger, M., Peters, JM.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Curr Biol","volume":"8","issue":"22","page":"1207-10","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1999-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12857868","title":"Directed motion of telomeres in the formation of the meiotic bouquet revealed by time course and simulation analysis.","abstract":"Chromosome movement is critical for homologous chromosome pairing during meiosis. A prominent and nearly universal meiotic chromosome reorganization is the formation of the bouquet, characterized by the close clustering of chromosome ends at the nuclear envelope. We have used a novel method of in vitro culture of rye anthers combined with fluorescent in situ hybridization (FISH) detection of telomeres to quantitatively study bouquet formation. The three-dimensional distribution of telomeres over time was used to obtain a quantitative profile of bouquet formation intermediates. The bouquet formed through a gradual, continuous tightening of telomeres over approximately 6 h. To determine whether the motion of chromosomes was random or directed, we developed a computer simulation of bouquet formation to compare with our observations. We varied the diffusion rate of telomeres and the amount of directional bias in telomere movement. In our models, the bouquet was formed in a manner comparable to what we observed in cultured meiocytes only when the movement of telomeres was actively directed toward the bouquet site, whereas a wide range of diffusion rates were permitted. Directed motion, as opposed to random diffusion, was required to reproduce our observations, implying that an active process moves chromosomes to cause telomere clustering.","authors":"Carlton, PM., Cowan, CR., Cande, WZ.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Mol Biol Cell","volume":"14","issue":"7","page":"2832-43","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12856097","title":"An improved method for tracking and reducing the void volume in nano HPLC-MS with micro trapping columns.","abstract":"Tandem mass spectrometry coupled to HPLC is the state of the art technique in proteomic research. Here we describe a highly sensitive nano liquid chromatography system (nano HPLC) for analysis of protein digests. Using preconcentration in a column-switching set-up, we were able to inject large sample volumes (&lt; or =250 microL) without significant loss of sensitivity. The major problem with this type of preconcentration is usually the occurrence of void volumes. In order to diagnose void volumes a simple and easy test was developed by which the UV trace and the pressure profile in the separation column were monitored. Part by part replacement of connection tubing restored a void volume-free system. A major pre-requisite for handling samples in the femtomol range was found to be the use of protein\/peptide-saturated columns tryptic digests of cytochrome C were injected directly onto the reversed-phase nano separation column (75 microm inner diameter) and the separation results were compared with chromatograms obtained from separations using column switching. By using column switching we were able to inject large sample volumes in a short time period without losing resolution.","authors":"Mitulovi\u0107, G., Smoluch, M., Chervet, JP., Steinmacher, I., Kungl, A., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Anal Bioanal Chem","volume":"376","issue":"7","page":"946-51","pdf":null,"JrId":"27057","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12810588","title":"Mesenchymal patterning by Hoxa2 requires blocking Fgf-dependent activation of Ptx1.","abstract":"Hox genes are known key regulators of embryonic segmental identity, but little is known about the mechanisms of their action. To address this issue, we have analyzed how Hoxa2 specifies segmental identity in the second branchial arch. Using a subtraction approach, we found that Ptx1 was upregulated in the second arch mesenchyme of Hoxa2 mutants. This upregulation has functional significance because, in Hoxa2(-\/-);Ptx1(-\/-) embryos, the Hoxa2(-\/-) phenotype is partially reversed. Hoxa2 interferes with the Ptx1 activating process, which is dependent on Fgf signals from the epithelium. Consistently, Lhx6, another target of Fgf8 signaling, is also upregulated in the Hoxa2(-\/-) second arch mesenchyme. Our findings have important implications for the understanding of developmental processes in the branchial area and suggest a novel mechanism for mesenchymal patterning by Hox genes that acts to define the competence of mesenchymal cells to respond to skeletogenic signals.","authors":"Bobola, N., Carapu\u00e7o, M., Ohnemus, S., Kanzler, B., Leibbrandt, A., Neub\u00fcser, A., Drouin, J., Mallo, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Development","volume":"130","issue":"15","page":"3403-14","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12824382","title":"Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1.","abstract":"Many posttranslational modifications (N-myristoylation or glycosylphosphatidylinositol (GPI) lipid anchoring) and localization signals (the peroxisomal targeting signal PTS1) are encoded in short, partly compositionally biased regions at the N- or C-terminus of the protein sequence. These sequence signals are not well defined in terms of amino acid type preferences but they have significant interpositional correlations. Although the number of verified protein examples is small, the quantification of several physical conditions necessary for productive protein binding with the enzyme complexes executing the respective transformations can lead to predictors that recognize the signals from the amino acid sequence of queries alone. Taxon-specific prediction functions are required due to the divergent evolution of the active complexes. The big-Pi tool for the prediction of the C-terminal signal for GPI lipid anchor attachment is available for metazoan, protozoan and plant sequences. The myristoyl transferase (NMT) predictor recognizes glycine N-myristoylation sites (at the N-terminus and for fragments after processing) of higher eukaryotes (including their viruses) and fungi. The PTS1 signal predictor finds proteins with a C-terminus appropriate for peroxisomal import (for metazoa and fungi). Guidelines for application of the three WWW-based predictors (http:\/\/mendel.imp.univie.ac.at\/) and for the interpretation of their output are described.","authors":"Eisenhaber, F., Eisenhaber, B., Kubina, W., Maurer-Stroh, S., Neuberger, G., Schneider, G., Wildpaner, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nucleic Acids Res","volume":"31","issue":"13","page":"3631-4","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19542442","title":"Vav1 regulates the migration and adhesion of dendritic cells.","abstract":"Dendritic cells (DCs) are the most potent APCs for activating naive T cells, a process facilitated by the ability of immature DCs to mature and home to lymph nodes after encountering an inflammatory stimulus. Proteins involved in cytoskeletal rearrangement play an important role in regulating the adherence and motility of DCs. Vav1, a guanine nucleotide exchange factor for Rho family GTPases, mediates cytoskeletal rearrangement in hematopoietic cells following integrin ligation. We show that Vav1 is not required for the normal maturation of DCs in vitro; however, it is critical for DC binding to fibronectin and regulates the distribution but not the formation of podosomes. We also found that DC Vav1 was an important component of a signaling pathway involving focal adhesion kinase, phospholipase C-gamma2, and ERK1\/2 following integrin ligation. Surprisingly, Vav1(-\/-) DCs had increased rates of migration in vivo compared with wild-type control DCs. In vitro findings show that the presence of adhesive substrates such as fibronectin resulted in inhibition of migration. However, there was less inhibition in the absence of Vav1. These findings suggest that DC migration is negatively regulated by adhesion and integrin-mediated signaling and that Vav1 has a central role in this process.","authors":"Spurrell, DR., Luckashenak, NA., Minney, DC., Chaplin, A., Penninger, JM., Liwski, RS., Clements, JL., West, KA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Immunol","volume":"183","issue":"1","page":"310-8","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12810597","title":"Wnt signalling regulates myogenic differentiation in the developing avian wing.","abstract":"The limb musculature arises by delamination of premyogenic cells from the lateral dermomyotome. Initially the cells express Pax3 but, upon entering the limb bud, they switch on the expression of MyoD and Myf5 and undergo terminal differentiation into slow or fast fibres, which have distinct contractile properties that determine how a muscle will function. In the chick, the premyogenic cells express the Wnt antagonist Sfrp2, which is downregulated as the cells differentiate, suggesting that Wnts might regulate myogenic differentiation. Here, we have investigated the role of Wnt signalling during myogenic differentiation in the developing chick wing bud by gain- and loss-of-function studies in vitro and in vivo. We show that Wnt signalling changes the number of fast and\/or slow fibres. For example, in vivo, Wnt11 decreases and increases the number of slow and fast fibres, respectively, whereas overexpression of Wnt5a or a dominant-negative Wnt11 protein have the opposite effect. The latter shows that endogenous Wnt11 signalling determines the number of fast and slow myocytes. The distinct effects of Wnt5a and Wnt11 are consistent with their different expression patterns, which correlate with the ultimate distribution of slow and fast fibres in the wing. Overexpression of activated calmodulin kinase II mimics the effect of Wnt5a, suggesting that it uses this pathway. Finally, we show that overexpression of the Wnt antagonist Sfrp2 and DeltaLef1 reduces the number of myocytes. In Sfrp2-infected limbs, the number of Pax3 expressing cells was increased, suggesting that Sfrp2 blocks myogenic differentiation. Therefore, Wnt signalling modulates both the number of terminally differentiated myogenic cells and the intricate slow\/fast patterning of the limb musculature.","authors":"Anakwe, K., Robson, L., Hadley, J., Buxton, P., Church, V., Allen, S., Hartmann, C., Harfe, B., Nohno, T., Brown, AM., Evans, DJ., Francis-West, P.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Development","volume":"130","issue":"15","page":"3503-14","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22827382","title":"Follicle selection in the avian ovary.","abstract":"Follicle development in the highly efficient laying hen is characterized by a well-organized follicular hierarchy. This is not the case in other chickens such as the broiler breeder hen that has excessive follicle development and lower reproductive efficiency. Although management practices can optimize egg production in less productive breeds of chickens, the factors that contribute to this difference are not known. Interactions between the oocyte and surrounding somatic cells are believed to be involved in promoting follicle selection. Anti-M\u00fcllerian hormone (AMH) has been shown to have a role in regulating rate of follicle development in mammals. In hens, the expression of AMH is restricted to the growing population of follicles and, similar to mammals, is markedly decreased at around the time of follicle selection. The oocyte factors, growth and differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15), have been identified in the hen, and their expression pattern has been characterized. Anti-M\u00fcllerian hormone expression in hens is decreased by a protein factor from the oocyte (not GDF9) and is also decreased by vitamin D. Associated with the decrease in AMH expression by vitamin D, follicle-stimulating hormone receptor mRNA is increased. These data suggest that information about AMH regulation may enhance our understanding of follicle selection, particularly in birds with aberrant follicle development.","authors":"Johnson, PA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Reprod Domest Anim","volume":"47 Suppl 4","issue":"","page":"283-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12791272","title":"c-Jun regulates eyelid closure and skin tumor development through EGFR signaling.","abstract":"To investigate the function of c-Jun during skin development and skin tumor formation, we conditionally inactivated c-jun in the epidermis. Mice lacking c-jun in keratinocytes (c-jun(Deltaep)) develop normal skin but express reduced levels of EGFR in the eyelids, leading to open eyes at birth, as observed in EGFR null mice. Primary keratinocytes from c-jun(Deltaep) mice proliferate poorly, show increased differentiation, and form prominent cortical actin bundles, most likely because of decreased expression of EGFR and its ligand HB-EGF. In the absence of c-Jun, tumor-prone K5-SOS-F transgenic mice develop smaller papillomas, with reduced expression of EGFR in basal keratinocytes. Thus, using three experimental systems, we show that EGFR and HB-EGF are regulated by c-Jun, which controls eyelid development, keratinocyte proliferation, and skin tumor formation.","authors":"Zenz, R., Scheuch, H., Martin, P., Frank, C., Eferl, R., Kenner, L., Sibilia, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Dev Cell","volume":"4","issue":"6","page":"879-89","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12782685","title":"Nanometer targeting of microtubules to focal adhesions.","abstract":"Although cell movement is driven by actin, polarization and directional locomotion require an intact microtubule cytoskeleton that influences polarization by modulating substrate adhesion via specific targeting interactions with adhesion complexes. The fidelity of adhesion site targeting is precise; using total internal reflection fluorescence microscopy (TIRFM), we now show microtubule ends (visualized by incorporation of GFP tubulin) are within 50 nm of the substrate when polymerizing toward the cell periphery, but not when shrinking from it. Multiple microtubules sometimes followed similar tracks, suggesting guidance along a common cytoskeletal element. Use of TIRFM with GFP- or DsRed-zyxin in combination with either GFP-tubulin or GFP-CLIP-170 further revealed that the polymerizing microtubule plus ends that tracked close to the dorsal surface consistently targeted substrate adhesion complexes. This supports a central role for the microtubule tip complex in the guidance of microtubules into adhesion foci, and provides evidence for an intimate cross-talk between microtubule tips and substrate adhesions in the range of molecular dimensions.","authors":"Krylyshkina, O., Anderson, KI., Kaverina, I., Upmann, I., Manstein, DJ., Small, JV., Toomre, DK.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Cell Biol","volume":"161","issue":"5","page":"853-9","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12750306","title":"Organelle proteomics: implications for subcellular fractionation in proteomics.","abstract":"Functional proteome analysis is not restricted to the sequence information but includes the broad spectrum of structural modifications and quantitative changes of proteins to which they are subjected in different tissues and cell organelles and during the development of an organism. Cell biology has provided the means required for the analysis of the composition and properties of purified cellular elements. Subcellular fractionation is an approach universal across all cell types and tissues, including cardiac and vascular system. Subcellular fractionation and proteomics form an ideal partnership when it comes to enrichment and analysis of intracellular organelles and low abundant multiprotein complexes. Subcellular fractionation is a flexible and adjustable approach resulting in reduced sample complexity and is most efficiently combined with high-resolution 2D gel\/mass spectrometry analysis as well as with gel-independent techniques. In this study we introduce state of the art subcellular fractionation techniques and discuss their suitability, advantages, and limitations for proteomics research.","authors":"Huber, LA., Pfaller, K., Vietor, I.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Circ Res","volume":"92","issue":"9","page":"962-8","pdf":null,"JrId":"2974","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12765832","title":"The STIR-domain superfamily in signal transduction, development and immunity.","abstract":"We have identified a conserved sequence segment in transmembrane receptors (including SEFs, IL17Rs) and soluble factors (including CIKS\/ACT1) in eukaryotes and bacteria - the SEFIR domain. This sequence domain is part of the new STIR domain superfamily comprising also the TIR domain known to mediate TIR-TIR homotypic interactions. In TOLL\/IL1R-like pathways, the cytoplasmically localized TIR domain of a receptor and the TIR domain of a soluble adaptor interact physically and activate signalling. The similarity between the SEFIR and TIR domains involves the conserved boxes 1 and 2 of the TIR domain that are implicated in homotypic dimerization, but there is no sequence similarity between SEFIR domains and the TIR sequence box 3. By analogy, we suggest that SEFIR-domain proteins function as signalling components of Toll\/IL-1R-similar pathways and that their SEFIR domain mediates physical protein-protein interactions between pathway components.","authors":"Novatchkova, M., Leibbrandt, A., Werzowa, J., Neub\u00fcser, A., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Trends Biochem Sci","volume":"28","issue":"5","page":"226-9","pdf":null,"JrId":"7837","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12737822","title":"Origins of peptide selectivity and phosphoinositide binding revealed by structures of disabled-1 PTB domain complexes.","abstract":"Formation of the mammalian six-layered neocortex depends on a signaling pathway that involves Reelin, the very low-density lipoprotein receptor, the apolipoprotein E receptor-2 (ApoER2), and the adaptor protein Disabled-1 (Dab1). The 1.5 A crystal structure of a complex between the Dab1 phosphotyrosine binding (PTB) domain and a 14-residue peptide from the ApoER2 tail explains the unusual preference of Dab1 for unphosphorylated tyrosine within the NPxY motif of the peptide. Crystals of the complex soaked with the phosphoinositide PI-4,5P(2) (PI) show that PI binds to conserved basic residues on the PTB domain opposite the peptide binding groove. This finding explains how the Dab1 PTB domain can simultaneously bind PI and the ApoER2 tail. Recruitment of the Dab1 PTB domain to PI-rich regions of the plasma membrane may facilitate association with the Reelin receptor cytoplasmic tails to transduce a critical positional cue to migrating neurons.","authors":"Stolt, PC., Jeon, H., Song, HK., Herz, J., Eck, MJ., Blacklow, SC.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Structure","volume":"11","issue":"5","page":"569-79","pdf":null,"JrId":"22305","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12764197","title":"Essential role of Fkbp6 in male fertility and homologous chromosome pairing in meiosis.","abstract":"Meiosis is a critical stage of gametogenesis in which alignment and synapsis of chromosomal pairs occur, allowing for the recombination of maternal and paternal genomes. Here we show that FK506 binding protein (Fkbp6) localizes to meiotic chromosome cores and regions of homologous chromosome synapsis. Targeted inactivation of Fkbp6 in mice results in aspermic males and the absence of normal pachytene spermatocytes. Moreover, we identified the deletion of Fkbp6 exon 8 as the causative mutation in spontaneously male sterile as\/as mutant rats. Loss of Fkbp6 results in abnormal pairing and misalignments between homologous chromosomes, nonhomologous partner switches, and autosynapsis of X chromosome cores in meiotic spermatocytes. Fertility and meiosis are normal in Fkbp6 mutant females. Thus, Fkbp6 is a component of the synaptonemal complex essential for sex-specific fertility and for the fidelity of homologous chromosome pairing in meiosis.","authors":"Crackower, MA., Kolas, NK., Noguchi, J., Sarao, R., Kikuchi, K., Kaneko, H., Kobayashi, E., Kawai, Y., Kozieradzki, I., Landers, R., Mo, R., Hui, CC., Nieves, E., Cohen, PE., Osborne, LR., Wada, T., Kunieda, T., Moens, PB., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Science","volume":"300","issue":"5623","page":"1291-5","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34089875","title":"Cryo-EM structure of the cetacean morbillivirus nucleoprotein-RNA complex.","abstract":"Cetacean morbillivirus (CeMV) is an emerging and highly infectious paramyxovirus that causes outbreaks in cetaceans and occasionally in pinnipeds, representing a major threat to biodiversity and conservation of endangered marine mammal populations in both hemispheres. As for all non-segmented, negative-sense, single-stranded RNA (ssRNA) viruses, the morbilliviral genome is enwrapped by thousands of nucleoprotein (N) protomers. Each bound to six ribonucleotides, N protomers assemble to form a helical ribonucleoprotein (RNP) complex that serves as scaffold for nucleocapsid formation and as template for viral replication and transcription. While the molecular details on RNP complexes elucidated in human measles virus (MeV) served as paradigm model for these processes in all members of the Morbillivirus genus, no structural information has been obtained from other morbilliviruses, nor has any CeMV structure been solved so far. We report the structure of the CeMV RNP complex, reconstituted in vitro upon binding of recombinant CeMV N to poly-adenine ssRNA hexamers and solved to 4.0&#xa0;&#xc5; resolution by cryo-electron microscopy. In spite of the amino acid sequence similarity and consequently similar folding of the N protomer, the CeMV RNP complex exhibits different helical parameters as compared to previously reported MeV orthologs. The CeMV structure reveals exclusive interactions leading to more extensive protomer-RNA and protomer-protomer interfaces. We identified twelve residues, among those varying between CeMV strains, as putatively important for the stabilization of the RNP complex, which highlights the need to study the potential of CeMV N mutations that modulate nucleocapsid assembly to also affect viral phenotype and host adaptation.","authors":"Zinzula, L., Beck, F., Klumpe, S., Bohn, S., Pfeifer, G., Bollschweiler, D., Nagy, I., Plitzko, JM., Baumeister, W.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Struct Biol","volume":"213","issue":"3","page":"107750","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-04","doi":"10.1016\/j.jsb.2021.107750","first_author":null,"corresponding_authors":null},{"pmid":"12747830","title":"Flamingo regulates R8 axon-axon and axon-target interactions in the Drosophila visual system.","abstract":"Photoreceptors (R cells) in the Drosophila retina connect to targets in three distinct layers of the optic lobe of the brain: R1-R6 connect to the lamina, and R7 and R8 connect to distinct layers in the medulla. In each of these layers, R axon termini are arranged in evenly spaced topographic arrays. In a genetic screen for mutants with abnormal R cell connectivity, we recovered mutations in flamingo (fmi). fmi encodes a seven-transmembrane cadherin, previously shown to function in planar cell polarity and in dendritic patterning. Here, we show that fmi has two specific functions in R8 axon targeting: it facilitates competitive interactions between adjacent R8 axons to ensure their correct spacing, and it promotes the formation of stable connections between R8 axons and their target cells in the medulla. The former suggests a general role for Fmi in establishing nonoverlapping dendritic and axonal target fields. The latter, together with the finding that N-Cadherin has an analogous role in R7 axon-target interactions, points to a cadherin-based system for target layer specificity in the Drosophila visual system.","authors":"Senti, KA., Usui, T., Boucke, K., Greber, U., Uemura, T., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"10","page":"828-32","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22799003","title":"Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison.","abstract":"The conjugation of the small ubiquitin-related modifier, SUMO, to substrate proteins is a reversible and dynamic process, and an important response of plants to environmental challenges. Nevertheless, reliable data have so far been restricted largely to the model plant Arabidopsis thaliana. The increasing availability of genome information for other plant species offers the possibility to identify a core set of indispensable components, and to discover species-specific features of the sumoylation pathway. We analyzed the enzymes responsible for the conjugation of SUMO to substrates for their conservation between dicots and monocots. We thus assembled gene sets that relate the Arabidopsis SUMO conjugation system to that of the dicot species tomato, grapevine and poplar, and to four plant species from the monocot class: rice, Brachypodium distachyon, Sorghum bicolor and maize. We found that a core set of genes with clear assignment in Arabidopsis had highly conserved homologs in all tested plants. However, we also observed a variation in the copy number of homologous genes, and sequence variations that suggested monocot-specific variants. Generally, SUMO ligases and proteases showed the most pronounced differences. Finally, we identified potential SUMO chain-binding ubiquitin ligases, pointing to an in vivo function of SUMO chains as degradation signals in plants.","authors":"Novatchkova, M., Tomanov, K., Hofmann, K., Stuible, HP., Bachmair, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"New Phytol","volume":"195","issue":"1","page":"23-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22763434","title":"E3 ubiquitin ligase Cbl-b regulates Pten via Nedd4 in T cells independently of its ubiquitin ligase activity.","abstract":"E3 ubiquitin ligase Cbl-b plays a crucial role in T cell activation and tolerance induction. However, the molecular mechanism by which Cbl-b inhibits T cell activation remains unclear. Here, we report that Cbl-b does not inhibit PI3K but rather suppresses TCR\/CD28-induced inactivation of Pten. The elevated Akt activity in Cbl-b(-\/-) T cells is therefore due to heightened Pten inactivation. Suppression of Pten inactivation in T cells by Cbl-b is achieved by impeding the association of Pten with Nedd4, which targets Pten K13 for K63-linked polyubiquitination. Consistent with this finding, introducing Nedd4 deficiency into Cbl-b(-\/-) mice abrogates hyper-T cell responses caused by the loss of Cbl-b. Hence, our data demonstrate that Cbl-b inhibits T cell activation by suppressing Pten inactivation independently of its ubiquitin ligase activity.","authors":"Guo, H., Qiao, G., Ying, H., Li, Z., Zhao, Y., Liang, Y., Yang, L., Lipkowitz, S., Penninger, JM., Langdon, WY., Zhang, J.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Rep","volume":"1","issue":"5","page":"472-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12730288","title":"An epigenetic road map for histone lysine methylation.","abstract":null,"authors":"Lachner, M., O'Sullivan, RJ., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Cell Sci","volume":"116","issue":"Pt 11","page":"2117-24","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9778527","title":"Cohesion between sister chromatids must be established during DNA replication.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9778527<\/PMID><DateCompleted><Year>1999<\/Year><Month>01<\/Month><Day>19<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>8<\/Volume><Issue>20<\/Issue><PubDate><Year>1998<\/Year><Month>Oct<\/Month><Day>08<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Cohesion between sister chromatids must be established during DNA replication.<\/ArticleTitle><Pagination><MedlinePgn>1095-101<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Cohesion between sister chromatids, which opposes the splitting force exerted by the mitotic spindle during metaphase, is essential for their segregation to opposite poles of the cell during anaphase. In Saccharomyces cerevisiae, cohesion depends on a set of chromosomal proteins called cohesins, which include structural maintenance of chromosomes 1p (Smc1p), Smc3p and sister chromatid cohesion 1p (Scc1p). Strains with mutations in the genes encoding these proteins separate sister chromatids prematurely and fail to align them in metaphase. This leads to missegregation of chromosomes in the following anaphase.","authors":"Uhlmann, F., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Curr Biol","volume":"8","issue":"20","page":"1095-101","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1999-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12717442","title":"Polo-like kinase Cdc5 promotes chiasmata formation and cosegregation of sister centromeres at meiosis I.","abstract":"During meiosis, two rounds of chromosome segregation occur after a single round of DNA replication, producing haploid progeny from diploid progenitors. Three innovations in chromosome behaviour during meiosis I accomplish this unique division. First, crossovers between maternal and paternal sister chromatids (detected cytologically as chiasmata) bind replicated maternal and paternal chromosomes together. Second, sister kinetochores attach to microtubules from the same pole (mono-polar orientation), causing maternal and paternal centromere pairs (and not sister chromatids) to be separated. Third, sister chromatid cohesion near centromeres is preserved at anaphase I when cohesion along chromosome arms is destroyed. The finding that destruction of mitotic cohesion is regulated by Polo-like kinases prompted us to investigate the meiotic role of the yeast Polo-like kinase Cdc5. We show here that cells lacking Cdc5 synapse homologues and initiate recombination normally, but fail to efficiently resolve recombination intermediates as crossovers. They also fail to properly localize the Lrs4 (ref. 3) and Mam1 (ref. 4) monopolin proteins, resulting in bipolar orientation of sister kinetochores. Cdc5 is thus required both for the formation of chiasmata and for cosegregation of sister centromeres at meiosis I.","authors":"Clyne, RK., Katis, VL., Jessop, L., Benjamin, KR., Herskowitz, I., Lichten, M., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nat Cell Biol","volume":"5","issue":"5","page":"480-5","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22702730","title":"The DMRT gene family in amphioxus.","abstract":"Doublesex and Mab-3-related transcription factor (DMRT) gene family is widely known for its involvement in sex determination and\/or differentiation among different phyla. In this study, we identify eight DMRT genes in the cephalochordate amphioxus, a protochordate holding a key phylogenetic position. The eight DMRTs can be divided into two groups based on the conserved domain: BfDM044, BfDM045, BfDM55.1, BfDM115.1, and BfDM17.1 belong to the first group which have both DM and DMA domains, while BfDM246.1, BfDM084, and BfDM175 belong to the second group which have only DM domain. Most of the first group members have same genomic structure except BfDM17.1, while no regular pattern exists in the second group. Phylogenetic analysis of the DM domain sequences shows that DMRT genes in vertebrates form seven different independent clusters, and some even contain genes from invertebrates with high bootstrap. Notably, the first group members of amphioxus cluster with vertebrate DMRTs; while the second group members cluster into a single branch, which diverge from the vertebrate classes. The results suggest that several DMRT genes in vertebrates may evolve from homologous genes in invertebrates. As in nematode, drosophila, fish, and vertebrates, DMRT genes cluster is also found in amphioxus, which may be the result of gene duplication. Interspecific differences in the amphioxus DMRTs and sea squirt DMRTs may suggest post-speciation duplication of some DMRT genes.","authors":"Wang, F., Yu, Y., Ji, D., Li, H.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Biomol Struct Dyn","volume":"30","issue":"2","page":"191-200","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12707312","title":"CSC-1: a subunit of the Aurora B kinase complex that binds to the survivin-like protein BIR-1 and the incenp-like protein ICP-1.","abstract":"The Aurora B kinase complex is a critical regulator of chromosome segregation and cytokinesis. In Caenorhabditis elegans, AIR-2 (Aurora B) function requires ICP-1 (Incenp) and BIR-1 (Survivin). In various systems, Aurora B binds to orthologues of these proteins. Through genetic analysis, we have identified a new subunit of the Aurora B kinase complex, CSC-1. C. elegans embryos depleted of CSC-1, AIR-2, ICP-1, or BIR-1 have identical phenotypes. CSC-1, BIR-1, and ICP-1 are interdependent for their localization, and all are required for AIR-2 localization. In vitro, CSC-1 binds directly to BIR-1. The CSC-1\/BIR-1 complex, but not the individual subunits, associates with ICP-1. CSC-1 associates with ICP-1, BIR-1, and AIR-2 in vivo. ICP-1 dramatically stimulates AIR-2 kinase activity. This activity is not stimulated by CSC-1\/BIR-1, suggesting that these two subunits function as targeting subunits for AIR-2 kinase.","authors":"Romano, A., Guse, A., Krascenicova, I., Schnabel, H., Schnabel, R., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Cell Biol","volume":"161","issue":"2","page":"229-36","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12707311","title":"The small molecule Hesperadin reveals a role for Aurora B in correcting kinetochore-microtubule attachment and in maintaining the spindle assembly checkpoint.","abstract":"The proper segregation of sister chromatids in mitosis depends on bipolar attachment of all chromosomes to the mitotic spindle. We have identified the small molecule Hesperadin as an inhibitor of chromosome alignment and segregation. Our data imply that Hesperadin causes this phenotype by inhibiting the function of the mitotic kinase Aurora B. Mammalian cells treated with Hesperadin enter anaphase in the presence of numerous monooriented chromosomes, many of which may have both sister kinetochores attached to one spindle pole (syntelic attachment). Hesperadin also causes cells arrested by taxol or monastrol to enter anaphase within &lt;1 h, whereas cells in nocodazole stay arrested for 3-5 h. Together, our data suggest that Aurora B is required to generate unattached kinetochores on monooriented chromosomes, which in turn could promote bipolar attachment as well as maintain checkpoint signaling.","authors":"Hauf, S., Cole, RW., LaTerra, S., Zimmer, C., Schnapp, G., Walter, R., Heckel, A., van Meel, J., Rieder, CL., Peters, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Cell Biol","volume":"161","issue":"2","page":"281-94","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22665287","title":"DETSEL: an R-package to detect marker loci responding to selection.","abstract":"In the new era of population genomics, surveys of genetic polymorphism (\"genome scans\") offer the opportunity to distinguish locus-specific from genome-wide effects at many loci. Identifying presumably neutral regions of the genome that are assumed to be influenced by genome-wide effects only, and excluding presumably selected regions, is therefore critical to infer population demography and phylogenetic history reliably. Conversely, detecting locus-specific effects may help identify those genes that have been, or still are, targeted by natural selection. The software package DETSEL has been developed to identify markers that show deviation from neutral expectation in pairwise comparisons of diverging populations. Recently, two major improvements have been made: the analysis of dominant markers is now supported, and the estimation of empirical P-values has been implemented. These features, which are described below, have been incorporated into an R package, which replaces the stand-alone DETSEL software package.","authors":"Vitalis, R.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Methods Mol Biol","volume":"888","issue":"","page":"277-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14993250","title":"NF-kappaB and p53 are the dominant apoptosis-inducing transcription factors elicited by the HIV-1 envelope.","abstract":"The coculture of cells expressing the HIV-1 envelope glycoprotein complex (Env) with cells expressing CD4 results into cell fusion, deregulated mitosis, and subsequent cell death. Here, we show that NF-kappaB, p53, and AP1 are activated in Env-elicited apoptosis. The nuclear factor kappaB (NF-kappaB) super repressor had an antimitotic and antiapoptotic effect and prevented the Env-elicited phosphorylation of p53 on serine 15 and 46, as well as the activation of AP1. Transfection with dominant-negative p53 abolished apoptosis and AP1 activation. Signs of NF-kappaB and p53 activation were also detected in lymph node biopsies from HIV-1-infected individuals. Microarrays revealed that most (85%) of the transcriptional effects of HIV-1 Env were blocked by the p53 inhibitor pifithrin-alpha. Macroarrays led to the identification of several Env-elicited, p53-dependent proapoptotic transcripts, in particular Puma, a proapoptotic \"BH3-only\" protein from the Bcl-2 family known to activate Bax\/Bak. Down modulation of Puma by antisense oligonucleotides, as well as RNA interference of Bax and Bak, prevented Env-induced apoptosis. HIV-1-infected primary lymphoblasts up-regulated Puma in vitro. Moreover, circulating CD4+ lymphocytes from untreated, HIV-1-infected donors contained enhanced amounts of Puma protein, and these elevated Puma levels dropped upon antiretroviral therapy. Altogether, these data indicate that NF-kappaB and p53 cooperate as the dominant proapoptotic transcription factors participating in HIV-1 infection.","authors":"Perfettini, JL., Roumier, T., Castedo, M., Larochette, N., Boya, P., Raynal, B., Lazar, V., Ciccosanti, F., Nardacci, R., Penninger, J., Piacentini, M., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Exp Med","volume":"199","issue":"5","page":"629-40","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12703303","title":"Shedding light and electrons on the lamellipodium: imaging the motor of crawling cells.","abstract":"","authors":"Vignal, E., Resch, GP.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Biotechniques","volume":"34","issue":"4","page":"780-4, 786, 788-9","pdf":null,"JrId":"1595","fulltextlink":null,"preprintlink":null,"articledate":"2003-10-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12700890","title":"A story of two ACEs.","abstract":"According to the World Health Organization predictions cardiovascular diseases will be the leading cause of death by the year 2020. High blood pressure is a major risk factor for myocardial infarction, cerebrovascular disease, and stroke. Modulation of the renin-angiotensin system, particularly inhibition of the angiotensin-converting enzyme (ACE), has become a prime strategy in the treatment of hypertension and heart failure. Recently the gene of a new ACE, termed ACE2, has been characterized. The ACE2 gene maps to defined quantitative trait loci on the X chromosome in three different rat models of hypertension, suggesting ACE2 as a candidate gene for hypertension. In mice the targeted disruption of ACE2 resulted in increased systemic angiotensin II levels, impaired cardiac contractility, and upregulation of hypoxia-induced genes in the heart. Since mice deficient in both ACE2 and ACE show completely normal heart function, it appears that ACE and ACE2 negatively regulate each other. The mechanisms and physiological significance of the interplay between ACE and ACE2 are not yet elucidated, but it may involve several new peptides and peptide systems. In view of drug development the increasing complexity of the renin-angiotensin system offers both challenge and opportunity to develop new and refined treatment strategies against cardiovascular diseases.","authors":"Danilczyk, U., Eriksson, U., Crackower, MA., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Mol Med (Berl)","volume":"81","issue":"4","page":"227-34","pdf":null,"JrId":"8748","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12689588","title":"Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes.","abstract":"Previous studies have implicated the Eed-Enx1 Polycomb group complex in the maintenance of imprinted X inactivation in the trophectoderm lineage in mouse. Here we show that recruitment of Eed-Enx1 to the inactive X chromosome (Xi) also occurs in random X inactivation in the embryo proper. Localization of Eed-Enx1 complexes to Xi occurs very early, at the onset of Xist expression, but then disappears as differentiation and development progress. This transient localization correlates with the presence of high levels of the complex in totipotent cells and during early differentiation stages. Functional analysis demonstrates that Eed-Enx1 is required to establish methylation of histone H3 at lysine 9 and\/or lysine 27 on Xi and that this, in turn, is required to stabilize the Xi chromatin structure.","authors":"Silva, J., Mak, W., Zvetkova, I., Appanah, R., Nesterova, TB., Webster, Z., Peters, AH., Jenuwein, T., Otte, AP., Brockdorff, N.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Dev Cell","volume":"4","issue":"4","page":"481-95","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14975310","title":"Generation and characterization of methyl-lysine histone antibodies.","abstract":null,"authors":"Perez-Burgos, L., Peters, AH., Opravil, S., Kauer, M., Mechtler, K., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Methods Enzymol","volume":"376","issue":null,"page":"234-54","pdf":null,"JrId":"5787","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12697745","title":"Hypertension and prolonged vasoconstrictor signaling in RGS2-deficient mice.","abstract":"","authors":"Heximer, SP., Knutsen, RH., Sun, X., Kaltenbronn, KM., Rhee, MH., Peng, N., Oliveira-dos-Santos, A., Penninger, JM., Muslin, AJ., Steinberg, TH., Wyss, JM., Mecham, RP., Blumer, KJ.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Clin Invest","volume":"111","issue":"8","page":"1259","pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14972679","title":"Two fission yeast homologs of Drosophila Mei-S332 are required for chromosome segregation during meiosis I and II.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">14972679<\/PMID><DateCompleted><Year>2004<\/Year><Month>07<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>05<\/Month><Day>24<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>14<\/Volume><Issue>4<\/Issue><PubDate><Year>2004<\/Year><Month>Feb<\/Month><Day>17<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Two fission yeast homologs of Drosophila Mei-S332 are required for chromosome segregation during meiosis I and II.<\/ArticleTitle><Pagination><MedlinePgn>287-301<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Meiosis produces haploid gametes from diploid progenitor cells. This reduction is achieved by two successive nuclear divisions after one round of DNA replication. Correct chromosome segregation during the first division depends on sister kinetochores being oriented toward the same spindle pole while homologous kinetochores must face opposite poles. Segregation during the second division depends on retention of sister chromatid cohesion between centromeres until the onset of anaphase II, which in Drosophila melanogaster depends on a protein called Mei-S332 that binds to centromeres.","authors":"Rabitsch, KP., Gregan, J., Schleiffer, A., Javerzat, JP., Eisenhaber, F., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"4","page":"287-301","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22595677","title":"Protein phosphatase 4 cooperates with Smads to promote BMP signaling in dorsoventral patterning of zebrafish embryos.","abstract":"BMP signals play pivotal roles in dorsoventral patterning of vertebrate embryos. The role of Ppp4c, the catalytic subunit of ubiquitous protein phosphatase 4, in vertebrate embryonic development and underlying mechanisms is poorly understood. Here, we demonstrate that knockdown of zebrafish ppp4cb and\/or ppp4ca inhibits ventral development in embryos and also blocks ventralizing activity of ectopic Smad5. Biochemical analyses reveal that Ppp4c is a direct binding partner and transcriptional coactivator of Smad1\/Smad5. In response to BMP, Ppp4c is recruited to the Smad1-occupied promoter, and its phosphatase activity is essential in inhibiting HDAC3 activity and, consequently, potentiating transcriptional activation. Consistently, genetic or chemical interference of Hdac3 expression or activity compromises the dorsalizing phenotype induced by ppp4cb knockdown. We conclude that Ppp4c is a critical positive regulator of BMP\/Smad signaling during embryonic dorsoventral pattern formation in zebrafish.","authors":"Jia, S., Dai, F., Wu, D., Lin, X., Xing, C., Xue, Y., Wang, Y., Xiao, M., Wu, W., Feng, XH., Meng, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Dev Cell","volume":"22","issue":"5","page":"1065-78","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22508729","title":"In vivo Polycomb kinetics and mitotic chromatin binding distinguish stem cells from differentiated cells.","abstract":"Epigenetic memory mediated by Polycomb group (PcG) proteins must be maintained during cell division, but must also be flexible to allow cell fate transitions. Here we quantify dynamic chromatin-binding properties of PH::GFP and PC::GFP in living Drosophila in two cell types that undergo defined differentiation and mitosis events. Quantitative fluorescence recovery after photobleaching (FRAP) analysis demonstrates that PcG binding has a higher plasticity in stem cells than in more determined cells and identifies a fraction of PcG proteins that binds mitotic chromatin with up to 300-fold longer residence times than in interphase. Mathematical modeling examines which parameters best distinguish stem cells from differentiated cells. We identify phosphorylation of histone H3 at Ser 28 as a potential mechanism governing the extent and rate of mitotic PC dissociation in different lineages. We propose that regulation of the kinetic properties of PcG-chromatin binding is an essential factor in the choice between stability and flexibility in the establishment of cell identities.","authors":"Fonseca, JP., Steffen, PA., M\u00fcller, S., Lu, J., Sawicka, A., Seiser, C., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genes Dev","volume":"26","issue":"8","page":"857-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12667101","title":"When the DREAM is gone: from basic science to future prospectives in pain management and beyond.","abstract":"DREAM (downstream regulatory element antagonistic modulator) was identified as a novel calcium-binding protein with pleiotropic functions in vitro that are as varied as that of a transcription factor, a binding partner for presenilins, and a modulator of potassium channels. This review will discuss the findings that have implicated DREAM in its various roles. As a transcriptional repressor, DREAM may control the expression of the endogenous opioid gene prodynorphin amongst others, and itself is exquisitely regulated by second messenger molecules, protein kinases and other transcription factors. Recent genetic evidence has revealed a physiological role for DREAM in pain modulation. The interplay between DREAM and prodynorphin is discussed in light of our current understanding of this Janus-like opioid gene. The potential for the involvement of DREAM in other processes beyond pain modulation is considered at the end of this review.","authors":"Cheng, HY., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Expert Opin Ther Targets","volume":"7","issue":"2","page":"249-63","pdf":null,"JrId":"27020","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12654244","title":"Chromosomal cohesin forms a ring.","abstract":"The cohesin complex is essential for sister chromatid cohesion during mitosis. Its Smc1 and Smc3 subunits are rod-shaped molecules with globular ABC-like ATPases at one end and dimerization domains at the other connected by long coiled coils. Smc1 and Smc3 associate to form V-shaped heterodimers. Their ATPase heads are thought to be bridged by a third subunit, Scc1, creating a huge triangular ring that could trap sister DNA molecules. We address here whether cohesin forms such rings in vivo. Proteolytic cleavage of Scc1 by separase at the onset of anaphase triggers its dissociation from chromosomes. We show that N- and C-terminal Scc1 cleavage fragments remain connected due to their association with different heads of a single Smc1\/Smc3 heterodimer. Cleavage of the Smc3 coiled coil is sufficient to trigger cohesin release from chromosomes and loss of sister cohesion, consistent with a topological association with chromatin.","authors":"Gruber, S., Haering, CH., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cell","volume":"112","issue":"6","page":"765-77","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2003-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22441085","title":"Recombinant angiotensin-converting enzyme 2 suppresses pulmonary vasoconstriction in acute hypoxia.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22441085<\/PMID><DateCompleted><Year>2012<\/Year><Month>06<\/Month><Day>28<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1545-1534<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>23<\/Volume><Issue>1<\/Issue><PubDate><Year>2012<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>Wilderness &amp; environmental medicine<\/Title><ISOAbbreviation>Wilderness Environ Med<\/ISOAbbreviation><\/Journal><ArticleTitle>Recombinant angiotensin-converting enzyme 2 suppresses pulmonary vasoconstriction in acute hypoxia.<\/ArticleTitle><Pagination><MedlinePgn>24-30<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.wem.2011.09.002<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">Alveolar hypoxia as a result of high altitude leads to increased pulmonary arterial pressure. The renin-angiotensin system is involved in the regulation of pulmonary arterial pressure through angiotensin-converting enzyme 2 (ACE2). It remains unknown whether ACE2 administration alters pulmonary vascular pressure in hypoxia.","authors":"Kleinsasser, A., Pircher, I., Treml, B., Schwienbacher, M., Schuster, M., Janzek, E., Loibner, H., Penninger, JM., Loeckinger, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Wilderness Environ Med","volume":"23","issue":"1","page":"24-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12636915","title":"Centrosome separation and central spindle assembly act in redundant pathways that regulate microtubule density and trigger cleavage furrow formation.","abstract":"The mitotic spindle provides the spatial cue that coordinates cytokinesis with nuclear division. However, the specific property of the mitotic spindle that mediates this spatial regulation remains obscure, in part because different aspects of the mitotic spindle appear to have furrow inducing activity in different systems. We show that in C. elegans embryos, although the central spindle is usually dispensable for furrow initiation, it becomes essential for furrow formation when the extent of centrosome separation during anaphase is reduced. Measurements of microtubule density demonstrate that furrow formation occurs in the vicinity of a local minimum of microtubule density. Reduction of the extent of spindle elongation or disruption of the central spindle causes delayed formation of the cleavage furrow. These data suggest that reduced microtubule density triggers cleavage furrow initiation and demonstrate that redundant mechanisms direct efficient formation of the cleavage furrow.","authors":"Dechant, R., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Dev Cell","volume":"4","issue":"3","page":"333-44","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2003-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12629552","title":"The Par complex directs asymmetric cell division by phosphorylating the cytoskeletal protein Lgl.","abstract":"To generate different cell types, some cells can segregate protein determinants into one of their two daughter cells during mitosis. In Drosophila neuroblasts, the Par protein complex localizes apically and directs localization of the cell fate determinants Prospero and Numb and the adaptor proteins Miranda and Pon to the basal cell cortex, to ensure their segregation into the basal daughter cell. The Par protein complex has a conserved function in establishing cell polarity but how it directs proteins to the opposite side is unknown. We show here that a principal function of this complex is to phosphorylate the cytoskeletal protein Lethal (2) giant larvae (Lgl; also known as L(2)gl). Phosphorylation by Drosophila atypical protein kinase C (aPKC), a member of the Par protein complex, releases Lgl from its association with membranes and the actin cytoskeleton. Genetic and biochemical experiments show that Lgl phosphorylation prevents the localization of cell fate determinants to the apical cell cortex. Lgl promotes cortical localization of Miranda, and we propose that phosphorylation of Lgl by aPKC at the apical neuroblast cortex restricts Lgl activity and Miranda localization to the opposite, basal side of the cell.","authors":"Betschinger, J., Mechtler, K., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nature","volume":"422","issue":"6929","page":"326-30","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2003-04-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12408815","title":"The HtrA family of proteases: implications for protein composition and cell fate.","abstract":"Cells precisely monitor the concentration and functionality of each protein for optimal performance. Protein quality control involves molecular chaperones, folding catalysts, and proteases that are often heat shock proteins. One quality control factor is HtrA, one of a new class of oligomeric serine proteases. The defining feature of the HtrA family is the combination of a catalytic domain with at least one C-terminal PDZ domain. Here, we discuss the properties and roles of this ATP-independent protease chaperone system in protein metabolism and cell fate.","authors":"Clausen, T., Southan, C., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Cell","volume":"10","issue":"3","page":"443-55","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31851676","title":"A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a.","abstract":"Point-of-care testing (POCT) in low-resource settings requires tools that can operate independently of typical laboratory infrastructure. Due to its favorable signal-to-background ratio, a wide variety of biomedical tests utilize fluorescence as a readout. However, fluorescence techniques often require expensive or complex instrumentation and can be difficult to adapt for POCT. To address this issue, we developed a pocket-sized fluorescence detector costing less than $15 that is easy to manufacture and can operate in low-resource settings. It is built from standard electronic components, including an LED and a light dependent resistor, filter foils and 3D printed parts, and reliably reaches a lower limit of detection (LOD) of &#x2248; 6.8 nM fluorescein, which is sufficient to follow typical biochemical reactions used in POCT applications. All assays are conducted on filter paper, which allows for a flat detector architecture to improve signal collection. We validate the device by quantifying in vitro RNA transcription and also demonstrate sequence-specific detection of target RNAs with an LOD of 3.7 nM using a Cas13a-based fluorescence assay. Cas13a is an RNA-guided, RNA-targeting CRISPR effector with promiscuous RNase activity upon recognition of its RNA target. Cas13a sensing is highly specific and adaptable and in combination with our detector represents a promising approach for nucleic acid POCT. Furthermore, our open-source device may be used in educational settings, through providing low cost instrumentation for quantitative assays or as a platform to integrate hardware, software and biochemistry concepts in the future.","authors":"Katzmeier, F., Aufinger, L., Dupin, A., Quintero, J., Lenz, M., Bauer, L., Klumpe, S., Sherpa, D., D\u00fcrr, B., Honemann, M., Styazhkin, I., Simmel, FC., Heymann, M.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PLoS One","volume":"14","issue":"12","page":"e0220091","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-24","doi":"10.1371\/journal.pone.0220091","first_author":null,"corresponding_authors":null},{"pmid":"12624093","title":"Different properties of SEK1 and MKK7 in dual phosphorylation of stress-induced activated protein kinase SAPK\/JNK in embryonic stem cells.","abstract":"Stress-activated protein kinase\/c-Jun NH(2)-terminal kinase (SAPK\/JNK), belonging to the mitogen-activated protein kinase family, plays an important role in stress signaling. SAPK\/JNK activation requires the phosphorylation of both Thr and Tyr residues in its Thr-Pro-Tyr motif, and SEK1 and MKK7 have been identified as the dual specificity kinases. In this study, we generated mkk7(-\/-) mouse embryonic stem (ES) cells in addition to sek1(-\/-) cells and compared the two kinases in terms of the activation and phosphorylation of JNK. Although SAPK\/JNK activation by various stress signals was markedly impaired in both sek1(-\/-) and mkk7(-\/-) ES cells, there were striking differences in the dual phosphorylation profile. The severe impairment observed in mkk7(-\/-) cells was accompanied by a loss of the Thr phosphorylation of JNK without marked reduction in its Tyr-phosphorylated level. On the other hand, Thr phosphorylation of JNK in sek1(-\/-) cells was also attenuated in addition to a decreased level of its Tyr phosphorylation. Analysis in human embryonic kidney 293T cells transfected with a kinase-dead SEK1 or a Thr-Pro-Phe mutant of JNK1 revealed that SEK1-induced Tyr phosphorylation of JNK1 was followed by additional Thr phosphorylation by MKK7. Furthermore, SEK1 but not MKK7 was capable of binding to JNK1 in 293T cells. These results indicate that the Tyr and Thr residues of SAPK\/JNK are sequentially phosphorylated by SEK1 and MKK7, respectively, in the stress-stimulated ES cells.","authors":"Kishimoto, H., Nakagawa, K., Watanabe, T., Kitagawa, D., Momose, H., Seo, J., Nishitai, G., Shimizu, N., Ohata, S., Tanemura, S., Asaka, S., Goto, T., Fukushi, H., Yoshida, H., Suzuki, A., Sasaki, T., Wada, T., Penninger, JM., Nishina, H., Katada, T.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Biol Chem","volume":"278","issue":"19","page":"16595-601","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22365737","title":"Diverse functions of microRNAs in nervous system development.","abstract":"MicroRNAs (miRNAs) are integral parts of the gene regulatory networks that control most developmental processes. Through their regulatory action, miRNAs introduce an additional layer of genetic complexity that can translate into increased cellular diversity, something that is extremely relevant to nervous system structure. In addition, miRNAs sharpen the spatial and temporal boundaries between different cellular states during development. Here, we illustrate these roles with a number of specific miRNAs that act during distinct steps of neural development. We further discuss specific aspects of miRNA function that make these regulators particularly suited to provide the robustness and complexity that are essential for the dynamic nature of both the development and activity of the nervous system.","authors":"Cochella, L., Hobert, O.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Curr Top Dev Biol","volume":"99","issue":null,"page":"115-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17989254","title":"Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.","abstract":"MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing of small RNAs from Drosophila melanogaster to experimentally confirm and complement these predictions. In addition to validating 20 of our top 45 predictions for novel miRNA loci, the large-scale sequencing identified many miRNAs that had not been predicted. In total, 59 novel genes were identified, increasing our tally of confirmed fly miRNAs to 148. The large-scale sequencing also refined the identities of previously known miRNAs and provided insights into their biogenesis and expression. Many miRNAs were expressed in particular developmental contexts, with a large cohort of miRNAs expressed primarily in imaginal discs. Conserved miRNAs typically were expressed more broadly and robustly than were nonconserved miRNAs, and those conserved miRNAs with more restricted expression tended to have fewer predicted targets than those expressed more broadly. Predicted targets for the expanded set of microRNAs substantially increased and revised the miRNA-target relationships that appear conserved among the fly species. Insights were also provided into miRNA gene evolution, including evidence for emergent regulatory function deriving from the opposite arm of the miRNA hairpin, exemplified by mir-10, and even the opposite strand of the DNA, exemplified by mir-iab-4.","authors":"Ruby, JG., Stark, A., Johnston, WK., Kellis, M., Bartel, DP., Lai, EC.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genome Res","volume":"17","issue":"12","page":"1850-64","pdf":null,"JrId":"8754","fulltextlink":null,"preprintlink":null,"articledate":"2008-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12616501","title":"Visualizing the course of antigen-specific CD8 and CD4 T cell responses to a growing tumor.","abstract":"Spontaneous tumors frequently express antigens that can be recognized by the immune system but nevertheless manage to evade immune surveillance. To better understand the mechanism of evasion, we followed CD8 and CD4 T cells reacting against a subcutaneously growing tumor, modified to express influenza hemagglutinin (HA) as surrogate tumor antigen. Adoptive transfer of 8,000 antigen-specific CD8 T cells was sufficient to protect against challenge with 1x10(6) tumor cells, while larger numbers of T cells rejected established tumors. HA-specific CD4 T cells could not reject tumors on their own but helped rejection by CD8 T cells. Rejection of the tumor coincided with prolonged survival of expanded antigen-specific CD8 and CD4 T cells, while a failing anti-tumor response was accompanied by transient expansion followed by rapid elimination of antigen-specific T cells. Thus, a highly immunogenic tumor can evade immune surveillance because of an insufficient number of tumor-specific T cells and antigen overload, resulting in exhaustion of the immune response. In this scenario, adoptive immunotherapy rather than vaccination promises successful treatment.","authors":"Klein, L., Trautman, L., Psarras, S., Schnell, S., Siermann, A., Liblau, R., von Boehmer, H., Khazaie, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Eur J Immunol","volume":"33","issue":"3","page":"806-14","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"2003-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12600308","title":"Un m\u00e9nage \u00e0 quatre: the molecular biology of chromosome segregation in meiosis.","abstract":"Sexually reproducing organisms rely on the precise reduction of chromosome number during a specialized cell division called meiosis. Whereas mitosis produces diploid daughter cells from diploid cells, meiosis generates haploid gametes from diploid precursors. The molecular mechanisms controlling chromosome transmission during both divisions have started to be delineated. This review focuses on the four fundamental differences between mitotic and meiotic chromosome segregation that allow the ordered reduction of chromosome number in meiosis: (1) reciprocal recombination and formation of chiasmata between homologous chromosomes, (2) suppression of sister kinetochore biorientation, (3) protection of centromeric cohesion, and (4) inhibition of DNA replication between the two meiotic divisions.","authors":"Petronczki, M., Siomos, MF., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cell","volume":"112","issue":"4","page":"423-40","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2003-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12573607","title":"N-ras mutations in canine malignant melanomas.","abstract":null,"authors":"Mayr, B., Schaffner, G., Reifinger, M., Zwetkoff, S., Prodinger, B.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Vet J","volume":"165","issue":"2","page":"169-71","pdf":null,"JrId":"20585","fulltextlink":null,"preprintlink":null,"articledate":"2003-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12548401","title":"Quantitative measurement of cell migration using time-lapse videomicroscopy and non-linear system analysis.","abstract":"Epithelial cells of the mammary gland possess the inherent capacity to form epithelial monolayers in vitro. This requires coordination of cell migration, cell-cell contact formation, and cell proliferation. Using time-lapse phase contrast videomicroscopy we have observed mammary gland epithelial cells over different time scales. We show the generation of a complete polarized epithelial monolayer in real-time, starting from a few cells. We subsequently concentrated on the early stages of this process by tracking epithelial cells during phases of polarized migration. We performed migration analysis using fractal measures. With this technology the structure of seemingly random processes not accessible to the usual methods of linear analysis can be measured. As a control and proof of principle approach we applied infection of cells with an adenoviral vector, which is used as a gene targeting vector for many applications. Infection markedly influenced the patterns of migratory behavior. We, therefore, believe that time-lapse videomicroscopy in combination with fractal analysis can contribute to differential characterization of distinct cellular migration patterns. This will be useful in situations of long-term alterations in cell culture systems.","authors":"Wick, N., Thurner, S., Paiha, K., Sedivy, R., Vietor, I., Huber, LA.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Histochem Cell Biol","volume":"119","issue":"1","page":"15-20","pdf":null,"JrId":"8616","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12560555","title":"Maintenance of stable heterochromatin domains by dynamic HP1 binding.","abstract":"One function of heterochromatin is the epigenetic silencing by sequestration of genes into transcriptionally repressed nuclear neighborhoods. Heterochromatin protein 1 (HP1) is a major component of heterochromatin and thus is a candidate for establishing and maintaining the transcriptionally repressive heterochromatin structure. Here we demonstrate that maintenance of stable heterochromatin domains in living cells involves the transient binding and dynamic exchange of HP1 from chromatin. HP1 exchange kinetics correlate with the condensation level of chromatin and are dependent on the histone methyltransferase Suv39h. The chromodomain and the chromoshadow domain of HP1 are both required for binding to native chromatin in vivo, but they contribute differentially to binding in euchromatin and heterochromatin. These data argue against HP1 repression of transcription by formation of static, higher order oligomeric networks but support a dynamic competition model, and they demonstrate that heterochromatin is accessible to regulatory factors.","authors":"Cheutin, T., McNairn, AJ., Jenuwein, T., Gilbert, DM., Singh, PB., Misteli, T.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Science","volume":"299","issue":"5607","page":"721-5","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2003-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12471145","title":"Essential role of the adhesion receptor LFA-1 for T cell-dependent fulminant hepatitis.","abstract":"Viral hepatitis affects more than 2 billion people worldwide. In particular, no effective treatment exists to abrogate death and liver damage in fulminant hepatitis. Activation of T cells is an initial and critical event in the pathogenesis of liver damage in autoimmune and viral hepatitis. The precise molecular mechanisms that induce T cell-mediated hepatocyte injury remain largely unclear. In mice, T cell-dependent hepatitis and acute liver damage can be modeled using ConA. In this study, we examined the role of the adhesion receptor LFA-1 in ConA-induced acute hepatic damage using LFA-1(-\/-) (CD11a) mice. Massive liver cell apoptosis and metabolic liver damage were observed in LFA-1(+\/+) mice following ConA injection. By contrast, LFA-1(-\/-) mice were completely resistant to ConA-induced hepatitis and none of the LFA-1(-\/-) mice showed any hepatic damage. Whereas activated hepatic T cells remained in the liver in LFA-1(+\/+) mice, activated T cells were rapidly cleared from the livers of LFA-1(-\/-) mice. Mechanistically, T cells from LFA-1(-\/-) mice showed markedly reduced cytotoxicity toward liver cells as a result of impaired, activation-dependent adhesion. Importantly, adoptive transfer of hepatic T cells from LFA-1(+\/+) mice, but not from LFA-1(-\/-) mice, sensitized LFA-1(-\/-) mice to ConA-induced hepatitis. Thus, LFA-1 expression on T cells is necessary and sufficient for T cell-mediated liver damage in vivo. These results provide the first genetic evidence on an adhesion receptor, LFA-1, that has a crucial role in fulminant hepatitis. These genetic data identify LFA-1 as a potential key target for the treatment of T cell-mediated hepatitis and the prevention of liver damage.","authors":"Matsumoto, G., Tsunematsu, S., Tsukinoki, K., Ohmi, Y., Iwamiya, M., Oliveira-dos-Santos, A., Tone, D., Shindo, J., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Immunol","volume":"169","issue":"12","page":"7087-96","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2003-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11323691","title":"CD45: new jobs for an old acquaintance.","abstract":"Identified as the first and prototypic transmembrane protein tyrosine phosphatase (PTPase), CD45 has been extensively studied for over two decades and is thought to be important for positively regulating antigen-receptor signaling via the dephosphorylation of Src kinases. However, new evidence indicates that CD45 can function as a Janus kinase PTPase that negatively controls cytokine-receptor signaling. A point mutation in CD45, which appears to affect CD45 dimerization, and a genetic polymorphism that affects alternative CD45 splicing are implicated in autoimmunity in mice and multiple sclerosis in humans. CD45 is expressed in multiple isoforms and the modulation of specific CD45 splice variants with antibodies can prevent transplant rejections. In addition, loss of CD45 can affect microglia activation in a mouse model for Alzheimer's disease. Thus, CD45 is moving rapidly back into the spotlight as a drug target and central regulator involved in differentiation of multiple hematopoietic cell lineages, autoimmunity and antiviral immunity.","authors":"Penninger, JM., Irie-Sasaki, J., Sasaki, T., Oliveira-dos-Santos, AJ.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Immunol","volume":"2","issue":"5","page":"389-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22090513","title":"Stress-activated protein kinase MKK7 regulates axon elongation in the developing cerebral cortex.","abstract":"The c-Jun NH(2)-terminal protein kinase (JNK), which belongs to the mitogen-activated protein kinase family, plays important roles in a broad range of physiological processes. JNK is controlled by two upstream regulators, mitogen-activated protein kinase kinase (MKK) 7 and MKK4. To elucidate the physiological functions of MKK7, we used Nestin-Cre to generate a novel mouse model in which the mkk7 gene was specifically deleted in the nervous system (Mkk7(flox\/flox) Nestin-Cre mice). These mice were indistinguishable from their control littermates in gross appearance during embryogenesis but died immediately after birth without breathing. Histological examination showed that the mutants had severe defects in brain development, including enlarged ventricles, reduced striatum, and minimal axon tracts. Electron microscopy revealed abnormal accumulations of filamentous structures and autophagic vacuoles in Mkk7(flox\/flox) Nestin-Cre brain. Further analysis showed that MKK7 deletion decreased numbers of TAG-1-expressing axons and delayed neuronal migration in the cerebrum. Neuronal differentiation was not altered. In utero electroporation studies showed that contralateral projection of axons by layer 2\/3 neurons was impaired in the absence of MKK7. Moreover, MKK7 regulated axon elongation in a cell-autonomous manner in vivo, a finding confirmed in vitro. Finally, phosphorylation levels of JNK substrates, including c-Jun, neurofilament heavy chain, microtubule-associated protein 1B, and doublecortin, were reduced in Mkk7(flox\/flox) Nestin-Cre brain. Our findings demonstrate that the phenotype of Mkk7(flox\/flox) Nestin-Cre mice differs substantially from that of Mkk4(flox\/flox) Nestin-Cre mice, and establish that MKK7-mediated regulation of JNK is uniquely critical for both axon elongation and radial migration in the developing brain.","authors":"Yamasaki, T., Kawasaki, H., Arakawa, S., Shimizu, K., Shimizu, S., Reiner, O., Okano, H., Nishina, S., Azuma, N., Penninger, JM., Katada, T., Nishina, H.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Neurosci","volume":"31","issue":"46","page":"16872-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12471249","title":"Molecular mechanisms of axon guidance.","abstract":"Axons are guided along specific pathways by attractive and repulsive cues in the extracellular environment. Genetic and biochemical studies have led to the identification of highly conserved families of guidance molecules, including netrins, Slits, semaphorins, and ephrins. Guidance cues steer axons by regulating cytoskeletal dynamics in the growth cone through signaling pathways that are still only poorly understood. Elaborate regulatory mechanisms ensure that a given cue elicits the right response from the right axons at the right time but is otherwise ignored. With such regulatory mechanisms in place, a relatively small number of guidance factors can be used to generate intricate patterns of neuronal wiring.","authors":"Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Science","volume":"298","issue":"5600","page":"1959-64","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2003-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14962106","title":"Sheet preparations expose the dermal nerve plexus of human skin and render the dermal nerve end organ accessible to extensive analysis.","abstract":"Since vertical tissue sections used for the study of the human cutaneous nervous system inherently allow visualization of only a small part of the mainly horizontally oriented cutaneous nerves, we searched for possibilities to extend this view. We now propose a method based on the immuno-staining of dermal sheet preparations for subsequent analysis by electron-, light- or laser scanning microscopy. Dermal sheet preparations for the first time allowed the imaging of the complex structure of the nerve end organ over several cm2, and facilitated viewing of its topological relationship to other tissue components. We could visualize that the bulk of free ending nerve fibers ramified within 25 microm of the dermo-epidermal junction, whereas below that only larger nerve bundles were present. This method further allowed the detection and quantification of NCAM\/CD56+ non-myelinating Schwann cells which envelope terminal axons within the dermis. Depending on the body region, we detected between 140 to over 300 individual terminal Schwann cells per mm2 skin surface. Our method should allow the acquisition of new insights into the highly organized architecture of the skin nerve end organ. Its further application will give new impetus in the investigation of alterations of this skin compartment under pathological conditions.","authors":"Tschachler, E., Reinisch, CM., Mayer, C., Paiha, K., Lassmann, H., Weninger, W.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Invest Dermatol","volume":"122","issue":"1","page":"177-82","pdf":null,"JrId":"4839","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14755243","title":"beta-Catenin and TGFbeta signalling cooperate to maintain a mesenchymal phenotype after FosER-induced epithelial to mesenchymal transition.","abstract":"Several signalling pathways contribute to the regulation of epithelial to mesenchymal transition (EMT), either during developmentally regulated processes or in cancer progression and metastasis. Induction of EMT in fully polarized mouse mammary epithelial cells (EpH4) by an inducible c-fos estrogen receptor (FosER) oncoprotein involves loss of E-cadherin expression, nuclear translocation of beta-catenin, and autocrine production of TGFbeta. Reporter assays demonstrate that both beta-catenin\/LEF-TCF- and TGFbeta-Smad-dependent signalling activities are upregulated, probably coregulating mesenchymal-specific gene expression during EMT. Stable expression of E-cadherin in mesenchymal FosER cells decreased beta-catenin activity and reduced cell proliferation. However, these cells still exhibited a defect in epithelial polarization and expressed E-cadherin\/beta-catenin complexes in the entire plasma membrane. On the other hand, inhibition of TGFbeta-Smad signalling in mesenchymal FosER cells induced flat, cobblestone-like clusters of cells, which relocalized beta-catenin to the plasma membrane but still lacked detectable E-cadherin. Interestingly, inhibition of TGFbeta signalling in the E-cadherin-expressing mesenchymal FosER cells caused their reversion to a polarized epithelial phenotype, in which E-cadherin, beta-catenin, and ZO-1 were localized at their correct lateral plasma membrane domains. These results demonstrate that loss of E-cadherin can contribute to increased LEF\/TCF-beta-catenin signalling, which in turn cooperates with autocrine TGFbeta signalling to maintain an undifferentiated mesenchymal phenotype.","authors":"Eger, A., Stockinger, A., Park, J., Langkopf, E., Mikula, M., Gotzmann, J., Mikulits, W., Beug, H., Foisner, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Oncogene","volume":"23","issue":"15","page":"2672-2680","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12438425","title":"Raf-1 antagonizes erythroid differentiation by restraining caspase activation.","abstract":"The Raf kinases are key signal transducers activated by mitogens or oncogenes. The best studied Raf isoform, Raf-1, was identified as an inhibitor of apoptosis by conventional and conditional gene ablation in mice. c-raf-1(-)(\/)(-) embryos are growth retarded and anemic, and die at midgestation with anomalies in the placenta and fetal liver. Here, we show that Raf-1-deficient primary erythroblasts cannot be expanded in culture due to their accelerated differentiation into mature erythrocytes. In addition, Raf-1 expression is down-regulated in differentiating wild-type cells, whereas overexpression of activated Raf-1 delays differentiation. As recently described for human erythroid precursors, we find that caspase activation is necessary for the differentiation of murine fetal liver erythroblasts. Differentiation-associated caspase activation is accelerated in erythroid progenitors lacking Raf-1 and delayed by overexpression of the activated kinase. These results reveal an essential function of Raf-1 in erythropoiesis and demonstrate that the ability of Raf-1 to restrict caspase activation is biologically relevant in a context distinct from apoptosis.","authors":"Kolbus, A., Pilat, S., Husak, Z., Deiner, EM., Stengl, G., Beug, H., Baccarini, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Exp Med","volume":"196","issue":"10","page":"1347-53","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11551820","title":"New insights into the transmembrane protein tyrosine phosphatase CD45.","abstract":"CD45 is expressed on all nucleated haematopoietic cells and was originally identified as the first and prototypic transmembrane protein tyrosine phosphatase. In CD45 mutant cell lines, CD45-deficient mice and CD45-deficient human SCID patients, CD45 is required for signal transduction through antigen receptors. CD45 can operate as a positive as well as a negative regulator of Src-family kinases. Moreover, CD45 was identified as the elusive JAK tyrosine phosphatase that negatively regulates cytokine receptor activation involved in the differentiation, proliferation and antiviral immunity of haematopoietic cells. Modulation of CD45 splice variants provides a unique opportunity to design drugs that turn off or turn on antigen and cytokine receptor signaling in cancer, transplantation or autoimmunity","authors":"Sasaki, T., Sasaki-Irie, J., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Int J Biochem Cell Biol","volume":"33","issue":"11","page":"1041-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14734530","title":"FoxO3a regulates erythroid differentiation and induces BTG1, an activator of protein arginine methyl transferase 1.","abstract":"Erythropoiesis requires tight control of expansion, maturation, and survival of erythroid progenitors. Because activation of phosphatidylinositol-3-kinase (PI3K) is required for erythropoietin\/stem cell factor-induced expansion of erythroid progenitors, we examined the role of the PI3K-controlled Forkhead box, class O (FoxO) subfamily of Forkhead transcription factors. FoxO3a expression and nuclear accumulation increased during erythroid differentiation, whereas untimely induction of FoxO3a activity accelerated differentiation of erythroid progenitors to erythrocytes. We identified B cell translocation gene 1 (BTG1)\/antiproliferative protein 2 as a FoxO3a target gene in erythroid progenitors. Promoter studies indicated BTG1 as a direct target of FoxO3a. Expression of BTG1 in primary mouse bone marrow cells blocked the outgrowth of erythroid colonies, which required a domain of BTG1 that binds protein arginine methyl transferase 1. During erythroid differentiation, increased arginine methylation coincided with BTG1 expression. Concordantly, inhibition of methyl transferase activity blocked erythroid maturation without affecting expansion of progenitor cells. We propose FoxO3a-controlled expression of BTG1 and subsequent regulation of protein arginine methyl transferase activity as a novel mechanism controlling erythroid expansion and differentiation.","authors":"Bakker, WJ., Bl\u00e1zquez-Domingo, M., Kolbus, A., Besooyen, J., Steinlein, P., Beug, H., Coffer, PJ., L\u00f6wenberg, B., von Lindern, M., van Dijk, TB.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Cell Biol","volume":"164","issue":"2","page":"175-84","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21898588","title":"Lineage-committed osteoclast precursors circulate in blood and settle down into bone.","abstract":"Osteoclasts are derived from the monocyte\/macrophage lineage, but little is known about osteoclast precursors in circulation. We previously showed that cell cycle-arrested quiescent osteoclast precursors (QOPs) were detected along bone surfaces as direct osteoclast precursors. Here we show that receptor activator of NF-\u03baB (RANK)-positive cells isolated from bone marrow and peripheral blood possess characteristics of QOPs in mice. RANK-positive cells expressed c-Fms (receptors of macrophage colony-stimulating factor) at various levels, but scarcely expressed other monocyte\/granulocyte markers. RANK-positive cells failed to exert phagocytic and proliferating activities, and differentiated into osteoclasts but not into dendritic cells. To identify circulating QOPs, collagen disks containing bone morphogenetic protein-2 (BMP disks) were implanted into mice, which were administered bromodeoxyuridine daily. Most nuclei of osteoclasts detected in BMP-2-induced ectopic bone were bromodeoxyuridine-negative. RANK-positive cells in peripheral blood proliferated more slowly and had a much longer lifespan than F4\/80 (a macrophage marker)-positive macrophages. When BMP disks and control disks were implanted in RANK ligand-deficient mice, RANK-positive cells were observed in the BMP disks but not in the controls. F4\/80-positive cells were distributed in both disks. Administration of FYT720, a sphingosine 1-phosphate agonist, promoted the egress of RANK-positive cells from hematopoietic tissues into bloodstream. These results suggest that lineage-determined QOPs circulate in the blood and settle in the bone.","authors":"Muto, A., Mizoguchi, T., Udagawa, N., Ito, S., Kawahara, I., Abiko, Y., Arai, A., Harada, S., Kobayashi, Y., Nakamichi, Y., Penninger, JM., Noguchi, T., Takahashi, N.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Bone Miner Res","volume":"26","issue":"12","page":"2978-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12404120","title":"The C-terminal moiety of HIV-1 Vpr induces cell death via a caspase-independent mitochondrial pathway.","abstract":"Previous biochemical studies suggested that HIV-1-encoded Vpr may kill cells through an effect on the adenine nucleotide translocase (ANT), thereby causing mitochondrial membrane permeabilization (MMP). Here, we show that Vpr fails to activate caspases in conditions in which it induces cell killing. The knock-out of essential caspase-activators (Apaf-1 or caspase-9) or the knock-out of a mitochondrial caspase-independent death effector (AIF) does not abolish Vpr-mediated killing. In contrast, the cytotoxic effects of Vpr are reduced by transfection-enforced overexpression of two MMP-inhibitors, namely the endogenous protein Bcl-2 or the cytomegalovirus-encoded ANT-targeted protein vMIA. Vpr, which can elicit MMP through a direct effect on mitochondria, and HIV-1-Env, which causes MMP through an indirect pathway, exhibit additive (but not synergic) cytotoxic effects. In conclusion, it appears that Vpr induces apoptosis through a caspase-independent mitochondrial pathway.","authors":"Roumier, T., Vieira, HL., Castedo, M., Ferri, KF., Boya, P., Andreau, K., Druillennec, S., Joza, N., Penninger, JM., Roques, B., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cell Death Differ","volume":"9","issue":"11","page":"1212-9","pdf":null,"JrId":"20326","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19361491","title":"The C. elegans sex determination gene laf-1 encodes a putative DEAD-box RNA helicase.","abstract":"The Caenorhabditis elegans gene laf-1 is critical for both embryonic development and sex determination. Laf-1 is thought to promote male cell fates by negatively regulating expression of tra-2 in both hermaphrodites and males. We cloned laf-1 and established that it encodes a putative DEAD-box RNA helicase related to Saccharomycescerevisiae Ded1p and Drosophila Vasa. Three sequenced laf-1 mutations are missense alleles affecting a small region of the protein in or near helicase motif III. We demonstrate that the phenotypes resulting from laf-1 mutations are due to loss or reduction of laf-1 function, and that both laf-1 and a related helicase vbh-1 function in germline sex determination. Laf-1 mRNA is expressed in both males and hermaphrodites and in both the germline and soma of hermaphrodites. It is expressed at all developmental stages and is most abundant in embryos. LAF-1 is predominantly, if not exclusively, cytoplasmic and colocalizes with PGL-1 in P granules of germline precursor cells. Previous results suggest that laf-1 functions to negatively regulate expression of the sex determination protein TRA-2, and we find that the abundance of TRA-2 is modestly elevated in laf-1\/+ females. We discuss potential functions of LAF-1 as a helicase and its roles in sex determination.","authors":"Hubert, A., Anderson, P.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Dev Biol","volume":"330","issue":"2","page":"358-67","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12393755","title":"Distinct involvement of the Jun-N-terminal kinase and NF-kappaB pathways in the repression of the human COL1A2 gene by TNF-alpha.","abstract":"We used a gene knockout approach to elucidate the specific roles played by the Jun-N-terminal kinase (JNK) and NF-kappaB pathways downstream of TNF-alpha in the context of alpha(2) type I collagen gene (COL1A2) expression. In JNK1-\/--JNK2-\/- (JNK-\/-) fibroblasts, TNF-alpha inhibited basal COL1A2 expression but had no effect on TGF-beta-driven gene transactivation unless jnk1 was introduced ectopically. Conversely, in NF-kappaB essential modulator-\/- (NEMO-\/-) fibroblasts, lack of NF-kappaB activation did not influence the antagonism exerted by TNF-alpha against TGF-beta but prevented repression of basal COL1A2 gene expression. Similar regulatory mechanisms take place in dermal fibroblasts, as evidenced using transfected dominant-negative forms of MKK4 and IKK-alpha, critical kinases upstream of the JNK and NF-kappaB pathways, respectively. These results represent the first demonstration of an alternate usage of distinct signaling pathways by TNF-alpha to inhibit the expression of a given gene, COL1A2, depending on its activation state.","authors":"Verrecchia, F., Wagner, EF., Mauviel, A.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"EMBO Rep","volume":"3","issue":"11","page":"1069-74","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12387741","title":"Control of pre-BCR signaling by Pax5-dependent activation of the BLNK gene.","abstract":"The developmental progression from pro-B to pre-B cells is controlled by pre-B cell receptor (pre-BCR) signaling which depends on BLNK (SLP-65) for coupling the Syk kinase to its downstream effector pathways. Here we identified BLNK as a direct target of the transcription factor Pax5 (BSAP). Restoration of BLNK expression in Ig(mu) transgenic Pax5(-\/-) pro-B cells resulted in constitutive pre-BCR signaling and increased cell proliferation without inducing progression to the pre-B cell stage. Ig(mu)(+) Pax5(-\/-) pro-B cells expressing a BLNK-estrogen receptor fusion protein initiated signaling immediately upon hormone addition, which facilitated analysis of pre-BCR-induced gene expression changes. The pre-BCR was shown to execute its checkpoint function by regulating genes involved in cell proliferation, intracellular signaling, growth factor responsiveness, and V(D)J recombination.","authors":"Schebesta, M., Pfeffer, PL., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Immunity","volume":"17","issue":"4","page":"473-85","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2002-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33039147","title":"High-resolution structure and biophysical characterization of the nucleocapsid phosphoprotein dimerization domain from the Covid-19 severe acute respiratory syndrome coronavirus 2.","abstract":"Unprecedented by number of casualties and socio-economic burden occurring worldwide, the coronavirus disease 2019 (Covid-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the worst health crisis of this century. In order to develop adequate countermeasures against Covid-19, identification and structural characterization of suitable antiviral targets within the SARS-CoV-2 protein repertoire is urgently needed. The nucleocapsid phosphoprotein (N) is a multifunctional and highly immunogenic determinant of virulence and pathogenicity, whose main functions consist in oligomerizing and packaging the single-stranded RNA (ssRNA) viral genome. Here we report the structural and biophysical characterization of the SARS-CoV-2 N C-terminal domain (CTD), on which both N homo-oligomerization and ssRNA binding depend. Crystal structures solved at 1.44&#xa0;&#xc5; and 1.36&#xa0;&#xc5; resolution describe a rhombus-shape N CTD dimer, which stably exists in solution as validated by size-exclusion chromatography coupled to multi-angle light scattering and analytical ultracentrifugation. Differential scanning fluorimetry revealed moderate thermal stability and a tendency towards conformational change. Microscale thermophoresis demonstrated binding to a 7-bp SARS-CoV-2 genomic ssRNA fragment at micromolar affinity. Furthermore, a low-resolution preliminary model of the full-length SARS-CoV N in complex with ssRNA, obtained by cryo-electron microscopy, provides an initial understanding of self-associating and RNA binding functions exerted by the SARS-CoV-2 N.","authors":"Zinzula, L., Basquin, J., Bohn, S., Beck, F., Klumpe, S., Pfeifer, G., Nagy, I., Bracher, A., Hartl, FU., Baumeister, W.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Biochem Biophys Res Commun","volume":"538","issue":null,"page":"54-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-08","doi":"10.1016\/j.bbrc.2020.09.131","first_author":null,"corresponding_authors":null},{"pmid":"12379618","title":"Role of RANKL and RANK in bone loss and arthritis.","abstract":"The tumour necrosis factor family molecule RANKL (RANKL, TRANCE, ODF) and its receptor RANK are key regulators of bone remodelling and regulate T cell\/dendritic cell communications, and lymph node formation. Moreover, RANKL and RANK are expressed in mammary gland epithelial cells and control the development of a lactating mammary gland during pregnancy and the propagation of mammalian species. Importantly, RANKL and RANK are essential for the development and activation of osteoclasts and bone loss in response to virtually all triggers tested. Therapeutically, inhibition of RANKL function via the decoy receptor osteoprotegerin completely prevents bone loss at inflammed joints and has partially beneficial effects on cartilage destruction in all arthritis models studied. Modulation of these systems provides a unique opportunity to design novel treatments to inhibit bone loss and crippling in arthritis.","authors":"Jones, DH., Kong, YY., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Ann Rheum Dis","volume":"61 Suppl 2","issue":null,"page":"ii32-9","pdf":null,"JrId":"640","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21652647","title":"Ectodysplasin and Wnt pathways are required for salivary gland branching morphogenesis.","abstract":"The developing submandibular salivary gland (SMG) is a well-studied model for tissue interactions and branching morphogenesis. Its development shares similar features with other ectodermal appendages such as hair and tooth. The ectodysplasin (Eda) pathway is essential for the formation and function of several ectodermal organs. Mutations in the signaling components of the Eda pathway lead to a human syndrome known as hypohidrotic ectodermal dysplasia (HED), which is characterized by missing and malformed teeth, sparse hair and reduced sweating. Individuals with HED suffer also from dry mouth because of reduced saliva flow. In order to understand the underlying mechanism, we analyzed salivary gland development in mouse models with altered Eda pathway activities. We have found that Eda regulates growth and branching of the SMG via transcription factor NF-\u03baB in the epithelium, and that the hedgehog pathway is an important mediator of Eda\/NF-\u03baB. We also sought to determine whether a similar reciprocal interplay between the Eda and Wnt\/\u03b2-catenin pathways, which are known to operate in other skin appendages, functions in developing SMG. Surprisingly and unlike in developing hair follicles and teeth, canonical Wnt signaling activity did not colocalize with Edar\/NF-\u03baB in salivary gland epithelium. Instead, we observed high mesenchymal Wnt activity and show that ablation of mesenchymal Wnt signaling either in vitro or in vivo compromised branching morphogenesis. We also provide evidence suggesting that the effects of mesenchymal Wnt\/\u03b2-catenin signaling are mediated, at least in part, through regulation of Eda expression.","authors":"H\u00e4\u00e4r\u00e4, O., Fujimori, S., Schmidt-Ullrich, R., Hartmann, C., Thesleff, I., Mikkola, ML.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Development","volume":"138","issue":"13","page":"2681-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14716299","title":"AIF and cyclophilin A cooperate in apoptosis-associated chromatinolysis.","abstract":"Cyclophilin A (CypA) was determined to interact with apoptosis-inducing factor (AIF) by mass spectroscopy, coimmunoprecipitation, pull-down assays, and molecular modeling. During the initial, caspase-independent stage of chromatin condensation that accompanies apoptosis, AIF and CypA were found to coimmunolocalize in the nucleus. Recombinant AIF and CypA proteins synergized in vitro in the degradation of plasmid DNA, as well as in the capacity to induce DNA loss in purified nuclei. The apoptogenic cooperation between AIF and CypA did not rely on the CypA peptidyl-prolyl cis-trans isomerase activity. In Cyp-expressing cells, AIF overexpression augmented apoptotic chromatinolysis. The AIF-dependent large-scale DNA fragmentation was less pronounced in CypA knockout cells as compared to controls. AIF mutants lacking the CypA-binding domain were inefficient apoptosis sensitizers in transfection experiments. Moreover, AIF failed to sensitize CypA knockout cells to apoptosis induction, and this defect in the AIF response was reversed by reintroduction of the CypA gene into CypA-deficient cells. In summary, AIF and CypA collaborate in chromatinolysis.","authors":"Cand\u00e9, C., Vahsen, N., Kouranti, I., Schmitt, E., Daugas, E., Spahr, C., Luban, J., Kroemer, RT., Giordanetto, F., Garrido, C., Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Oncogene","volume":"23","issue":"8","page":"1514-21","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12297043","title":"Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena.","abstract":"During development of the somatic macronucleus from the germline micronucleus in ciliates, chromosome rearrangements occur in which specific regions of DNA are eliminated and flanking regions are healed, either by religation or construction of telomeres. We identified a gene, TWI1, in Tetrahymena thermophila that is homologous to piwi and is required for DNA elimination. We also found that small RNAs were specifically expressed prior to chromosome rearrangement during conjugation. These RNAs were not observed in TWI1 knockout cells and required PDD1, another gene required for rearrangement, for expression. We propose that these small RNAs function to specify sequences to be eliminated by a mechanism similar to RNA-mediated gene silencing.","authors":"Mochizuki, K., Fine, NA., Fujisawa, T., Gorovsky, MA.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cell","volume":"110","issue":"6","page":"689-99","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12202032","title":"Comm sorts robo to control axon guidance at the Drosophila midline.","abstract":"Axon growth across the Drosophila midline requires Comm to downregulate Robo, the receptor for the midline repellent Slit. We show here that comm is required in neurons, not in midline cells as previously thought, and that it is expressed specifically and transiently in commissural neurons. Comm acts as a sorting receptor for Robo, diverting it from the synthetic to the late endocytic pathway. A conserved cytoplasmic LPSY motif is required for endosomal sorting of Comm in vitro and for Comm to downregulate Robo and promote midline crossing in vivo. Axon traffic at the CNS midline is thus controlled by the intracellular trafficking of the Robo guidance receptor, which in turn depends on the precisely regulated expression of the Comm sorting receptor.","authors":"Keleman, K., Rajagopalan, S., Cleppien, D., Teis, D., Paiha, K., Huber, LA., Technau, GM., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cell","volume":"110","issue":"4","page":"415-27","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2002-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520315","title":"A model and scoring system to predict outcome of intrauterine pregnancies of uncertain viability.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520315<\/PMID><DateCompleted><Year>2011<\/Year><Month>06<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2016<\/Year><Month>11<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1469-0705<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>37<\/Volume><Issue>5<\/Issue><PubDate><Year>2011<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>Ultrasound in obstetrics &amp; gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology<\/Title><ISOAbbreviation>Ultrasound Obstet Gynecol<\/ISOAbbreviation><\/Journal><ArticleTitle>A model and scoring system to predict outcome of intrauterine pregnancies of uncertain viability.<\/ArticleTitle><Pagination><MedlinePgn>588-95<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/uog.9007<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\" NlmCategory=\"OBJECTIVE\">To define the incidence and outcome of intrauterine pregnancy of uncertain viability (PUV) and to develop and assess the performance of a model and a scoring system to predict ongoing viability.","authors":"Bottomley, C., Van Belle, V., Pexsters, A., Papageorghiou, AT., Mukri, F., Kirk, E., Van Huffel, S., Timmerman, D., Bourne, T.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Ultrasound Obstet Gynecol","volume":"37","issue":"5","page":"588-95","pdf":null,"JrId":"8585","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12213836","title":"The CeCDC-14 phosphatase is required for cytokinesis in the Caenorhabditis elegans embryo.","abstract":"In all eukaryotic organisms, the physical separation of two nascent cells must be coordinated with chromosome segregation and mitotic exit. In Saccharomyces cerevisiae and Schizosaccharomyces pombe this coordination depends on a number of genes that cooperate in intricate regulatory pathways termed mitotic exit network and septum initiation network, respectively. Here we have explored the function of potentially homologous genes in a metazoan organism, Caenorhabditis elegans, using RNA-mediated interference. Of all the genes tested, only depletion of CeCDC-14, the C. elegans homologue of the budding yeast dual-specificity phosphatase Cdc14p (Clp1\/Flp1p in fission yeast), caused embryonic lethality. We show that CeCDC-14 is required for cytokinesis but may be dispensable for progression of the early embryonic cell cycles. In response to depletion of CeCDC-14, embryos fail to establish a central spindle, and several proteins normally found at this structure are mislocalized. CeCDC-14 itself localizes to the central spindle in anaphase and to the midbody in telophase. It colocalizes with the mitotic kinesin ZEN-4, and the two proteins depend on each other for correct localization. These findings identify the CDC14 phosphatase as an important regulator of central spindle formation and cytokinesis in a metazoan organism.","authors":"Gruneberg, U., Glotzer, M., Gartner, A., Nigg, EA.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Cell Biol","volume":"158","issue":"5","page":"901-14","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2002-11-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21611889","title":"Recombinant human angiotensin-converting enzyme 2 as a new renin-angiotensin system peptidase for heart failure therapy.","abstract":"Angiotensin-converting enzyme 2 (ACE2) is a monocarboxypeptidase that metabolizes several peptides, including the degradation of angiotensin (Ang) II, a peptide with vasoconstrictive\/proliferative effects, to generate Ang 1-7, which exerts vasodilatory\/antiproliferative actions by acting through its receptor Mas. ACE2 is a multifunctional enzyme, and its actions on other vasoactive peptides, including the apelin-13 and apelin-17 peptides, also can contribute to its cardiovascular effects. The classical pathway of the renin-angiotensin system involving the ACE-Ang II-Ang II type-1 receptor axis is antagonized by the second arm constituted by the ACE2\/Ang 1-7\/Mas receptor axis. Loss of ACE2 enhances the adverse pathological remodeling susceptibility to pressure overload and myocardial infarction. Human recombinant ACE2 also is a negative regulator of Ang II-induced myocardial hypertrophy, fibrosis, and diastolic dysfunction and suppresses pressure overload-induced heart failure. Due to its characteristics, the ACE2\/Ang 1-7\/Mas axis may represent new possibilities for developing novel therapeutic strategies for the treatment of hypertension and heart failure. This review summarizes the beneficial effects of ACE2 in heart disease and the potential use of human recombinant ACE2 as a novel therapy for heart failure.","authors":"Oudit, GY., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Curr Heart Fail Rep","volume":"8","issue":"3","page":"176-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"81","title":"N-terminal spin label studies of hemoglobin, Ligand and pH dependence.","abstract":"Human hemoglobin was spin labeled with 4-isothiocanato-2,2,6,6-tetramethyl-piperdinooxyl, which is known to bind specifically to the N-terminal alpha-amino groups of proteins and slightly to the reactive sulfhydryl groups. Electron spin resonance (ESR) analysis indicated a partially resolved five-line spectrum, suggesting that the label was attached to at least two different binding sites. Using specific blocking reagents prior to spin labeling, the two binding sites were attributed to the sulfhydryl group of beta-93 (immobile) and the alpha-amino group of the N-terminal valines (mobile). The relative motion of the spin at one set of binding sites was restricted regardless of the state of ligation and pH, while the motion at the other site showed dependence on those parameters, e.g. the spin-labeled N-terminal ends of deoxyhemoglobin have restricted motion at all pH ranges studied, while those of oxyhemoglobin are relatively free to move at the basic pH range, but become more restricted in the acidic pH range.","authors":"Giangrande, M., Kim, YW., Mizukami, H.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"1","page":"187-93","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12194853","title":"The endocytic protein alpha-Adaptin is required for numb-mediated asymmetric cell division in Drosophila.","abstract":"During asymmetric cell division in Drosophila sensory organ precursor cells, the Numb protein localizes asymmetrically and segregates into one daughter cell, where it influences cell fate by repressing signal transduction via the Notch receptor. We show here that Numb acts by polarizing the distribution of alpha-Adaptin, a protein involved in receptor-mediated endocytosis. alpha-Adaptin binds to Numb and localizes asymmetrically in a Numb-dependent fashion. Mutant forms of alpha-Adaptin that no longer bind to Numb fail to localize asymmetrically and cause numb-like defects in asymmetric cell division. Our results suggest a model in which Numb influences cell fate by downregulating Notch through polarized receptor-mediated endocytosis, since Numb also binds to the intracellular domain of Notch.","authors":"Berdnik, D., T\u00f6r\u00f6k, T., Gonz\u00e1lez-Gait\u00e1n, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Dev Cell","volume":"3","issue":"2","page":"221-31","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14707076","title":"IL-10 induces regulatory T cell apoptosis by up-regulation of the membrane form of TNF-alpha.","abstract":"Numerous studies have demonstrated the role of regulatory T (Treg) cells in peripheral tolerance. Nevertheless, how the survival and death of Treg cells is controlled is largely unknown. In this study, we investigated the mechanisms involved in regulating the homeostasis of a subset of Ag-specific alphabetaTCR+ CD4-CD8- double negative (DN) Treg cells. We demonstrate that DN Treg cells are naturally resistant to TCR cross-linking-induced apoptosis. Administration of exogenous IL-10 renders DN Treg cells susceptible to apoptosis, and abolishes their suppressive function. Furthermore, TCR cross-linking of DN Treg cells in the presence of IL-10 leads to the up-regulation of the membrane-bound but not the soluble form of TNF-alpha. Interaction of membrane bound TNF-alpha with TNFR2 sends death signals to DN Treg cells. Blocking their interaction can reverse the effects of IL-10 on DN Treg cells. These results provide insights into the mechanisms that regulate the function and homeostasis of DN Treg cells.","authors":"Marra, LE., Zhang, ZX., Joe, B., Campbell, J., Levy, GA., Penninger, J., Zhang, L.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Immunol","volume":"172","issue":"2","page":"1028-35","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12142526","title":"Segregating sister genomes: the molecular biology of chromosome separation.","abstract":"During cell division, each daughter cell inherits one copy of every chromosome. Accurate transmission of chromosomes requires that the sister DNA molecules created during DNA replication are disentangled and then pulled to opposite poles of the cell before division. Defects in chromosome segregation produce cells that are aneuploid (containing an abnormal number of chromosomes)-a situation that can have dire consequences. Aneuploidy is a leading cause of spontaneous miscarriages in humans and is also a hallmark of many human cancer cells. Recent work with yeast, Xenopus, and other model systems has provided new information about the proteins that control chromosome segregation during cell division and how the activities of these proteins are coordinated with the cell cycle.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Science","volume":"297","issue":"5581","page":"559-65","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12103357","title":"Promiscuous gene expression and central T-cell tolerance: more than meets the eye.","abstract":null,"authors":"Kyewski, B., Derbinski, J., Gotter, J., Klein, L.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Trends Immunol","volume":"23","issue":"7","page":"364-71","pdf":null,"JrId":"22039","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21458673","title":"A rapid and scalable system for studying gene function in mice using conditional RNA interference.","abstract":"RNA interference is a powerful tool for studying gene function, however, the reproducible generation of RNAi transgenic mice remains a significant limitation. By combining optimized fluorescence-coupled miR30-based shRNAs with high efficiency ES cell targeting, we developed a fast, scalable pipeline for the production of shRNA transgenic mice. Using this system, we generated eight tet-regulated shRNA transgenic lines targeting Firefly and Renilla luciferases, Oct4 and tumor suppressors p53, p16(INK4a), p19(ARF) and APC and demonstrate potent gene silencing and GFP-tracked knockdown in a broad range of tissues in\u00a0vivo. Further, using an shRNA targeting APC, we illustrate how this approach can identify predicted phenotypes and also unknown functions for a well-studied gene. In addition, through regulated gene silencing we validate APC\/Wnt and p19(ARF) as potential therapeutic targets in T\u00a0cell acute lymphoblastic leukemia\/lymphoma and lung adenocarcinoma, respectively. This system provides a cost-effective and scalable platform for the production of RNAi transgenic mice targeting any mammalian gene. PAPERCLIP:","authors":"Premsrirut, PK., Dow, LE., Kim, SY., Camiolo, M., Malone, CD., Miething, C., Scuoppo, C., Zuber, J., Dickins, RA., Kogan, SC., Shroyer, KR., Sordella, R., Hannon, GJ., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Cell","volume":"145","issue":"1","page":"145-58","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2011-05-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14681680","title":"The MEK-1\/ERKs signalling pathway is differentially involved in the self-renewal of early and late avian erythroid progenitor cells.","abstract":"Making decisions between self-renewal and differentiation is a central ability of stem cells. Elucidation of molecular networks governing this decision is therefore of prime importance. A model of choice to explore this question is represented by chicken erythroid progenitors, in which self-renewal versus differentiation as well as progenitor maturation are regulated by external factor combinations. We used this system to study whether similar or different signalling pathways were involved in the self-renewal of early, immature or more mature erythroid progenitors. We show that a transforming growth factor (TGF)-alpha-activated Ras\/MEK-1\/ERK1\/2 pathway is strictly required for immature self-renewing cells but becomes fully dispensable when those cells are induced to differentiate. Consequently, pharmacological inhibition of this pathway led to spontaneous differentiation, only dependent on the presence of survival signals. Conversely, ectopic expression of a constitutive form of MEK-1 stimulates renewal and arrests differentiation process. Finally, we demonstrate that the ERK\/MAPK signalling pathway is required in early but not in late primary erythroid progenitors, which can be turned into each other by different growth factor combinations specifically driving their renewal. To the best of our knowledge, this is the first description of a central role of ERK\/MAPK signalling in regulating progenitor plasticity in the same cell type under different environmental conditions.","authors":"Dazy, S., Damiola, F., Parisey, N., Beug, H., Gandrillon, O.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Oncogene","volume":"22","issue":"58","page":"9205-16","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19596782","title":"Two GW repeat proteins interact with Tetrahymena thermophila argonaute and promote genome rearrangement.","abstract":"In conjugating Tetrahymena thermophila, massive DNA elimination occurs upon the development of the new somatic genome from the germ line genome. Small, approximately 28-nucleotide scan RNAs (scnRNAs) and Twi1p, an Argonaute family member, mediate H3K27me3 and H3K9me3 histone H3 modifications, which lead to heterochromatin formation and the excision of the heterochromatinized germ line-limited sequences. In our search for new factors involved in developmental DNA rearrangement, we identified two Twi1p-interacting proteins, Wag1p and CnjBp. Both proteins contain GW (glycine and tryptophan) repeats, which are characteristic of several Argonaute-interacting proteins in other organisms. Wag1p and CnjBp colocalize with Twi1p in the parental macronucleus early in conjugation and in the new developing macronucleus during later developmental stages. Around the time DNA elimination occurs, Wag1p forms multiple nuclear bodies in the developing macronuclei that do not colocalize with heterochromatic DNA elimination structures. Analyses of DeltaWAG1, DeltaCnjB, and double DeltaWAG1 DeltaCnjB knockout strains revealed that WAG1 and CnjB genes need to be deleted together to inhibit the downregulation of specific scnRNAs, the formation of DNA elimination structures, and DNA excision. Thus, Wag1p and CnjBp are two novel players with overlapping functions in RNA interference-mediated genome rearrangement in Tetrahymena.","authors":"Bednenko, J., Noto, T., DeSouza, LV., Siu, KW., Pearlman, RE., Mochizuki, K., Gorovsky, MA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Cell Biol","volume":"29","issue":"18","page":"5020-30","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12123597","title":"Epigenetics: SUPERMAN dresses up.","abstract":"DNA and histone methylation have been implicated in epigenetic gene regulation. Recent studies in Neurospora and now Arabidopsis indicate that histone methylation can direct DNA methylation, suggesting that these two methylation systems have been functionally linked during evolution.","authors":"Lachner, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"12","page":"R434-6","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12090776","title":"N-ras mutation in a feline lymphoma. Low frequency of N-ras mutations in a series of feline, canine and bovine lymphomas.","abstract":null,"authors":"Mayr, B., Winkler, G., Schaffner, G., Reifinger, M., Brem, G.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Vet J","volume":"163","issue":"3","page":"326-8","pdf":null,"JrId":"20585","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21385715","title":"Three-dimensional model of Salmonella's needle complex at subnanometer resolution.","abstract":"Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core structure, the needle complex (NC), is a ~3.5 megadalton-sized, oligomeric, membrane-embedded complex. Analyzing cryo-electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly.","authors":"Schraidt, O., Marlovits, TC.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Science","volume":"331","issue":"6021","page":"1192-5","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21108404","title":"Further evidence for the pathogenicity of 15q24 microduplications distal to the minimal critical regions.","abstract":"DNA copy number alterations in 15q24 have repeatedly been reported in patients exhibiting mild to moderate developmental delay and dysmorphic features. To date, mainly microdeletions have been described, and comparison of overlapping regions allowed the definition of minimal critical regions (MCRs) for microdeletions as well as microduplications. These MCRs are associated with distinct phenotypes. Recently, a family with a new microduplication distal to these MCRs was reported. However, for this alteration the typical phenotypical consequences could not yet be determined. Here we present another family with a nearly identical microduplication exhibiting a broad clinical spectrum including developmental delay, autistic traits and dysmorphic features. Our data suggest that microduplications adjacent and distal to the known MCRs are variable in expressivity and are associated with distinct features. They might represent a novel and recurrent microduplication syndrome.","authors":"Roetzer, KM., Schwarzbraun, T., Obenauf, AC., Hauser, E., Speicher, MR.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Am J Med Genet A","volume":"152A","issue":"12","page":"3173-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9653079","title":"CD4 T cell tolerance to human C-reactive protein, an inducible serum protein, is mediated by medullary thymic epithelium.","abstract":"Inducible serum proteins whose concentrations oscillate between nontolerogenic and tolerogenic levels pose a particular challenge to the maintenance of self-tolerance. Temporal restrictions of intrathymic antigen supply should prevent continuous central tolerization of T cells, in analogy to the spatial limitation imposed by tissue-restricted antigen expression. Major acute-phase proteins such as human C-reactive protein (hCRP) are typical examples for such inducible self-antigens. The circulating concentration of hCRP, which is secreted by hepatocytes, is induced up to 1,000-fold during an acute-phase reaction. We have analyzed tolerance to hCRP expressed in transgenic mice under its autologous regulatory regions. Physiological regulation of basal levels (&lt;10(-9) M) and inducibility (&gt;500-fold) are preserved in female transgenics, whereas male transgenics constitutively display induced levels. Surprisingly, crossing of hCRP transgenic mice to two lines of T cell receptor transgenic mice (specific for either a dominant or a subdominant epitope) showed that tolerance is mediated by intrathymic deletion of immature thymocytes, irrespective of widely differing serum levels. In the absence of induction, hCRP expressed by thymic medullary epithelial cells rather than liver-derived hCRP is necessary and sufficient to induce tolerance. Importantly, medullary epithelial cells also express two homologous mouse acute-phase proteins. These results support a physiological role of \"ectopic\" thymic expression in tolerance induction to acute-phase proteins and possibly other inducible self-antigens and have implications for delineating the relative contributions of central versus peripheral tolerance.","authors":"Klein, L., Klein, T., R\u00fcther, U., Kyewski, B.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Exp Med","volume":"188","issue":"1","page":"5-16","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"1998-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9619448","title":"Recombinant soluble low density lipoprotein receptor fragment inhibits minor group rhinovirus infection in vitro.","abstract":"A fragment of the low density lipoprotein receptor encompassing the seven ligand binding repeats was expressed in Sf9 insect cells as a fusion protein with a carboxyl-terminally linked hexa-his tag by using a baculovirus vector. Up to 10 mg\/l of the fusion protein was secreted into the medium. The material was soluble in the absence of detergent and active in binding beta very low density lipoprotein and a member of the minor group of human rhinoviruses (HRV2) in ligand blots from sodium dodecyl sulfate-polyacrylamide gels run under nonreducing conditions. The receptor fragment specifically inhibits viral infection of HeLa cells by minor group HRVs in a concentration-dependent manner. Viral infectivity is neutralized by aggregation.","authors":"Marlovits, TC., Zechmeister, T., Gruenberger, M., Ronacher, B., Schwihla, H., Blaas, D.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"FASEB J","volume":"12","issue":"9","page":"695-703","pdf":null,"JrId":"3815","fulltextlink":null,"preprintlink":null,"articledate":"1998-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"54","title":"Phospholipase A2 as a probe of phospholipid distribution in erythrocyte membranes. Factors influencing the apparent specificity of the reaction.","abstract":"The action of snake venom phospholipases A2 in intact human erythrocytes was investigated in detail. The basis phospholipase from Agkistrodon halys blomhifii was found to induce both hydrolysis of membrane phospholipids and total cell hemolysis under certain experimental conditions. The hydrolytic action of the basic enzyme was found to consist of two sequential events: (a) hydrolysis of 70% of the total cell ph osphatidylcholine without any evident hemolysis; and (b) complete hydrolysis of the remaining phosphatidylcholine, followed closely by extensive phosphatidylethanolamine hydrolysis and finally with onset of hemolysis, attack on the phosphatidylserine. At pH 7.4 and 10 mM Ca2+ only stage (a) occurred. However, a slight elevation of the pH of incubation to pH 8.0 and\/or inclusion of 40 mM Ca2+ in the reaction mixture caused both events (a) and (b) to occur. The addition of glucose limited the action of the enzyme to stage (a) under any reaction conditions. An investigation showed that enzymically induced hemolysis occurred under conditions where the intracellular ATP levels were lowered. Data are presented which suggest that stage (b) is mediated by in influx of Ca2+ into the cell when the levels of ATP are low. Interestingly the phosphllipase from Naja naja venom (Pakistan) yielded results similar to those observed with the basic enzyme from Agkistrodon venom. However, the enzyme from Crotalus adamanteus and the acidic enzyme also present in the Agkistrodon venom produced only slight hydrolysis or hemolysis under any of the conditions studied. Other species of erythrocytes, e.g., guinea pig, monkey, pig, and rat, were tested but only those from guinea pig behaved similarly to the human cells. Pig, monkey, and rat erythrocytes underwent very limited hydrolysis and hemolysis. It is evident that the use of these phospholipases to probe the localization of phospholipds in erythrocyte membranes must be approached with caution. Certain facets of this problem are discussed.","authors":"Martin, JK., Luthra, MG., Wells, MA., Watts, RP., Hanahan, DJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"25","page":"5400-8","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21141931","title":"Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications.","abstract":"The use of molecular simulations and ab initio calculations to predict thermodynamic properties of molecules has become routine. Such methods rely upon an accurate representation of the molecular partition function or configurational integral, which in turn often includes a rotational symmetry number. However, the reason for including the symmetry number is unclear to many practitioners, and there is also a need for a general prescription for evaluating the symmetry numbers of flexible molecules, i.e., for molecules with thermally active internal degrees of freedom, such as internal rotors. Surprisingly, we have been unable to find any complete and convincing explanations of these important issues in textbooks or the journal literature. The present paper aims to explain why symmetry numbers are needed and how their values should be determined. Both classical and quantum approaches are provided.","authors":"Gilson, MK., Irikura, KK.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Phys Chem B","volume":"114","issue":"49","page":"16304-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21111234","title":"Sororin mediates sister chromatid cohesion by antagonizing Wapl.","abstract":"Sister chromatid cohesion is essential for chromosome segregation and is mediated by cohesin bound to DNA. Cohesin-DNA interactions can be reversed by the cohesion-associated protein Wapl, whereas a stably DNA-bound form of cohesin is thought to mediate cohesion. In vertebrates, Sororin is essential for cohesion and stable cohesin-DNA interactions, but how Sororin performs these functions is unknown. We show that DNA replication and cohesin acetylation promote binding of Sororin to cohesin, and that Sororin displaces Wapl from its binding partner Pds5. In the absence of Wapl, Sororin becomes dispensable for cohesion. We propose that Sororin maintains cohesion by inhibiting Wapl's ability to dissociate cohesin from DNA. Sororin has only been identified in vertebrates, but we show that many invertebrate species contain Sororin-related proteins, and that one of these, Dalmatian, is essential for cohesion in Drosophila. The mechanism we describe here may therefore be widely conserved among different species.","authors":"Nishiyama, T., Ladurner, R., Schmitz, J., Kreidl, E., Schleiffer, A., Bhaskara, V., Bando, M., Shirahige, K., Hyman, AA., Mechtler, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell","volume":"143","issue":"5","page":"737-49","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21102610","title":"Asymmetric cell division: recent developments and their implications for tumour biology.","abstract":"The ability of cells to divide asymmetrically is essential for generating diverse cell types during development. The past 10 years have seen tremendous progress in our understanding of this important biological process. We have learned that localized phosphorylation events are responsible for the asymmetric segregation of cell fate determinants in mitosis and that centrosomes and microtubules play important parts in this process. The relevance of asymmetric cell division for stem cell biology has added a new dimension to the field, and exciting connections between asymmetric cell division and tumorigenesis have begun to emerge.","authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Rev Mol Cell Biol","volume":"11","issue":"12","page":"849-60","pdf":null,"JrId":"22271","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19822644","title":"Id2-, RORgammat-, and LTbetaR-independent initiation of lymphoid organogenesis in ocular immunity.","abstract":"The eye is protected by the ocular immunosurveillance system. We show that tear duct-associated lymphoid tissue (TALT) is located in the mouse lacrimal sac and shares immunological characteristics with mucosa-associated lymphoid tissues (MALTs), including the presence of M cells and immunocompetent cells for antigen uptake and subsequent generation of mucosal immune responses against ocularly encountered antigens and bacteria such as Pseudomonas aeruginosa. Initiation of TALT genesis began postnatally; it occurred even in germ-free conditions and was independent of signaling through organogenesis regulators, including inhibitor of DNA binding\/differentiation 2, retinoic acid-related orphan receptor gammat, lymphotoxin (LT) alpha1beta2-LTbetaR, and lymphoid chemokines (CCL19, CCL21, and CXCL13). Thus, TALT shares immunological features with MALT but has a distinct tissue genesis mechanism and plays a key role in ocular immunity.","authors":"Nagatake, T., Fukuyama, S., Kim, DY., Goda, K., Igarashi, O., Sato, S., Nochi, T., Sagara, H., Yokota, Y., Jetten, AM., Kaisho, T., Akira, S., Mimuro, H., Sasakawa, C., Fukui, Y., Fujihashi, K., Akiyama, T., Inoue, J., Penninger, JM., Kunisawa, J., Kiyono, H.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Exp Med","volume":"206","issue":"11","page":"2351-64","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2009-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14681532","title":"Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice.","abstract":"Posttranslational glycosylphosphatidylinositol (GPI) lipid anchoring is common not only for animal and fungal but also for plant proteins. The attachment of the GPI moiety to the carboxyl-terminus after proteolytic cleavage of a C-terminal propeptide is performed by the transamidase complex. Its four known subunits also have obvious full-length orthologs in the Arabidopsis and rice (Oryza sativa) genomes; thus, the mechanism of substrate protein processing appears similar for all eukaryotes. A learning set of plant proteins (substrates for the transamidase complex) has been collected both from the literature and plant sequence databases. We find that the plant GPI lipid anchor motif differs in minor aspects from the animal signal (e.g. the plant hydrophobic tail region can contain a higher fraction of aromatic residues). We have developed the \"big-Pi plant\" program for prediction of compatibility of query protein C-termini with the plant GPI lipid anchor motif requirements. Validation tests show that the sensitivity for transamidase targets is approximately 94%, and the rate of false positive prediction is about 0.1%. Thus, the big-Pi predictor can be applied as unsupervised genome annotation and target selection tool. The program is also suited for the design of modified protein constructs to test their GPI lipid anchoring capacity. The big-Pi plant predictor Web server and lists of potential plant precursor proteins in Swiss-Prot, SPTrEMBL, Arabidopsis, and rice proteomes are available at http:\/\/mendel.imp.univie.ac.at\/gpi\/plants\/gpi_plants.html. Arabidopsis and rice protein hits have been functionally classified. Several GPI lipid-anchored arabinogalactan-related proteins have been identified in rice.","authors":"Eisenhaber, B., Wildpaner, M., Schultz, CJ., Borner, GH., Dupree, P., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Plant Physiol","volume":"133","issue":"4","page":"1691-701","pdf":null,"JrId":"6478","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14653995","title":"Identification of a subunit of a novel Kleisin-beta\/SMC complex as a potential substrate of protein phosphatase 2A.","abstract":"Protein phosphatase 2A (PP2A) holoenzymes consist of a catalytic C subunit, a scaffolding A subunit, and one of several regulatory B subunits that recruit the AC dimer to substrates. PP2A is required for chromosome segregation, but PP2A's substrates in this process remain unknown. To identify PP2A substrates, we carried out a two-hybrid screen with the regulatory B\/PR55 subunit. We isolated a human homolog of C. elegans HCP6, a protein distantly related to the condensin subunit hCAP-D2, and we named this homolog hHCP-6. Both C. elegans HCP-6 and condensin are required for chromosome organization and segregation. HCP-6 binding partners are unknown, whereas condensin is composed of the structural maintenance of chromosomes proteins SMC2 and SMC4 and of three non-SMC subunits. Here we show that hHCP-6 becomes phosphorylated during mitosis and that its dephosphorylation by PP2A in vitro depends on B\/PR55, suggesting that hHCP-6 is a B\/PR55-specific substrate of PP2A. Unlike condensin, hHCP-6 is localized in the nucleus in interphase, but similar to condensin, hHCP-6 associates with chromosomes during mitosis. hHCP-6 is part of a complex that contains SMC2, SMC4, kleisin-beta, and the previously uncharacterized HEAT repeat protein FLJ20311. hHCP-6 is therefore part of a condensin-related complex that associates with chromosomes in mitosis and may be regulated by PP2A.","authors":"Yeong, FM., Hombauer, H., Wendt, KS., Hirota, T., Mudrak, I., Mechtler, K., Loregger, T., Marchler-Bauer, A., Tanaka, K., Peters, JM., Ogris, E.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"23","page":"2058-64","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14635253","title":"Building and breaking bridges between sister chromatids.","abstract":"Eukaryotic chromosomes undergo dramatic changes and movements during mitosis. These include the individualization and compaction of the two copies of replicated chromosomes (the sister chromatids) and their subsequent segregation to the daughter cells. Two multisubunit protein complexes termed 'cohesin' and 'condensin', both composed of SMC (Structural Maintenance of Chromosomes) and kleisin subunits, have emerged as crucial players in these processes. Cohesin is required for holding sister chromatids together whereas condensin, together with topoisomerase II, has an important role in organizing individual axes of sister chromatids prior to their segregation during anaphase. SMC and kleisin complexes also regulate the compaction and segregation of bacterial nucleoids. New research suggests that these ancient regulators of chromosome structure might function as topological devices that trap chromosomal DNA between 50 nm long coiled coils.","authors":"Haering, CH., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Bioessays","volume":"25","issue":"12","page":"1178-91","pdf":null,"JrId":"1014","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11973129","title":"Communication between the TCR and integrins: role of the molecular adapter ADAP\/Fyb\/Slap.","abstract":"TCR stimulation induces integrin-mediated adhesion, facilitating stabilization of conjugates between T cells and antigen-presenting cells and thereby contributing to T cell activation. Integrin activation has been shown to require cytoskeletal reorganization; however, the molecular mechanisms mediating communication between the TCR and integrins remain unclear. Recently the adapter protein ADAP\/Fyb\/Slap has been shown to couple TCR stimulation to integrin activation by mediating increased integrin avidity. ADAP may also play a role in transduction of external signals by integrins. Like other adapters, ADAP is a multifunctional protein and interacts with molecules such as Fyn, Slp-76, Ena\/VASP proteins, Vav1, WASP and the Arp2\/3 complex.","authors":"Griffiths, EK., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Opin Immunol","volume":"14","issue":"3","page":"317-22","pdf":null,"JrId":"1461","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14627834","title":"Genome-wide analysis of gene expression regulated by the HAT cofactor Trrap in conditional knockout cells.","abstract":"Transactivation\/transformation-domain associated protein (TRRAP) is a component of several multi-protein HAT complexes implicated in both transcriptional regulation and DNA repair. We recently identified Trrap, the murine ortholog of TRRAP, as an essential protein implicated in mitotic progression control, although its target genes are not known. In the present study, we analyzed the expression profiles of Trrap-responsive genes, using cDNA microarray in mitotic cells. From a panel of 17 664 transcript elements, we found that loss of Trrap leads to expression alteration of a large fraction of genes at mitotic stage. Functional classification of these genes indicates that Trrap influences a variety of cellular processes including cell cycle progression, cytoskeleton and cell adhesion, protein turnover, metabolism and signal transduction. The majority (71%) of differentially expressed genes was down-regulated in Trrap- deficient cells, whereas the rest were up-regulated, suggesting that Trrap may also play a role in transcriptional silencing. ChIP analysis revealed that Trrap might regulate gene expression by participating in acetylation of histone H4 and\/or H3 depending on target genes and cell cycle stage. Our study indicates that Trrap regulates the expression of a wide range of genes in both quiescence and mitotic stages. Removal of the Trrap protein is associated with both increased and decreased gene expression.","authors":"Herceg, Z., Li, H., Cuenin, C., Shukla, V., Radolf, M., Steinlein, P., Wang, ZQ.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nucleic Acids Res","volume":"31","issue":"23","page":"7011-23","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40045121","title":"Protein waste turned into antibiotics as a defence strategy of human cells.","abstract":null,"authors":"Clausen, T.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-03-05","doi":"10.1038\/d41586-025-00514-4","first_author":null,"corresponding_authors":null},{"pmid":"14625385","title":"Podosome formation in cultured A7r5 vascular smooth muscle cells requires Arp2\/3-dependent de-novo actin polymerization at discrete microdomains.","abstract":"Phorbol ester triggers the conversion of focal adhesions into podosomes in A7r5 smooth muscle cells. Here we followed the dynamics of podosome formation using dual fluorescence live video and confocal microscopy, as well as interference reflection and evanescent wave microscopy. We show that podosomes form at the outer region of stress fiber bundles, at specialized sites where they are embedded in adhesion plaques at the basal surface of the plasma membrane, and that cortactin resides constitutively at these microdomains. We further demonstrate that the formation of podosomes requires Arp2\/3-dependent actin polymerization at the stress fiber-focal adhesion interface. Concentration of Arp2\/3 coincides with podosome formation and precedes the engagement of SM22 and alpha-actinin, while the focal adhesion components zyxin and vinculin redistribute only at later stages of podosome development. We thus suggest that the genesis of podosomes includes two steps, one requiring the early de novo polymerization of actin filaments, and a second, late phase characterized by the recruitment of focal adhesion components. Moreover, we provide evidence for the existence of an as yet unidentified region in close proximity to the focal adhesion-stress fiber interface, which marks the site of actin cytoskeleton remodeling and is a novel site of Arp2\/3-dependent F-actin polymerization.","authors":"Kaverina, I., Stradal, TE., Gimona, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Cell Sci","volume":"116","issue":"Pt 24","page":"4915-24","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11970890","title":"Reaching a genetic and molecular understanding of skeletal development.","abstract":"In the last ten years, we have made considerable progress in our genetic and molecular understanding of all aspects of skeletal development, chondrogenesis, joint formation, and osteogenesis. This review addresses the role of the principal growth factors and transcription factors affecting these different processes and presents, in several cases, the genetic cascade leading to cell differentiation.","authors":"Karsenty, G., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Dev Cell","volume":"2","issue":"4","page":"389-406","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14622435","title":"Enhanced up-regulation of corticotropin-releasing hormone gene expression in response to restraint stress in the hypothalamic paraventricular nucleus of oxytocin gene-deficient male mice.","abstract":"The neuropeptide oxytocin is released not only into the blood, but also within the brain in response to various stressors. Accumulating evidence suggests that central oxytocin may play a major role in the regulation of neuroendocrine responses to stress. In the present study, using the oxytocin knockout mouse model, we tested whether oxytocin might act to attenuate stress-induced up-regulation of corticotropin-releasing hormone (CRH) mRNA expression in the brain. The expression of CRH mRNA in the paraventricular nucleus (PVN) after 4 h of restraint stress was examined in oxytocin gene-deficient (OTKO), wild-type and heterozygous male mice using in situ hybridization histochemistry. We found that basal levels of CRH mRNA were not different among the three genotypes. Although restraint stress resulted in a significant increase of CRH mRNA expression in the PVN regardless of genotype, the degree of stress induced-up-regulation was significantly higher in OTKO mice than in wild-type mice. The effects of restraint stress on the expression of the arginine vasopressin (AVP) and the oxytocin genes were also examined. Unlike CRH mRNA, basal expression (in nonstressed control groups) of AVP mRNA in OTKO mice, as well as oxytocin mRNA in heterozygous mice, was significantly lower in the PVN and the supraoptic nucleus than in wild-type mice. After restraint stress, the expression of AVP mRNA was significantly increased in the PVN of OTKO mice compared to the nonstressed control group, whereas the expression of both AVP and oxytocin mRNA were unchanged in the PVN and the supraoptic nucleus of wild-type and heterozygous mice. Finally, in a separate set of mice, restraint stress-induced Fos expression was also examined in several brain regions involved in stress response, including the lateral septum, the bed nucleus of the stria terminalis (BNST), the medial preoptic area, the PVN, the medial and central amygdala using immunohistochemistry. After 90 min of restraint stress, the number of Fos-expressing cells significantly increased in all brain regions examined regardless of genotype. However, the number of stress-induced Fos-expressing cells in the BNST and the medial amygdala of OTKO mice was significantly lower than in wild-type mice. Collectively, the findings in the present study suggest that oxytocin may regulate stress-induced CRH gene expression in the PVN. Furthermore, neuronal activity in the BNST and the medial amygdala may be involved in this neuroendocrine regulatory system.","authors":"Nomura, M., Saito, J., Ueta, Y., Muglia, LJ., Pfaff, DW., Ogawa, S.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Neuroendocrinol","volume":"15","issue":"11","page":"1054-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20075017","title":"A new acid mix enhances phosphopeptide enrichment on titanium- and zirconium dioxide for mapping of phosphorylation sites on protein complexes.","abstract":"The selective enrichment of phosphorylated peptides prior to reversed-phase separation and mass spectrometric detection significantly improves the analytical results in terms of higher number of detected phosphorylation sites and spectra of higher quality. Metal oxide chromatography (MOC) has been recently described for selective phosphopeptide enrichment (Pinkse et al., 2004; Larsen et al., 2005; Kweon and Hakansson, 2006; Cantin et al., 2007; Collins et al., 2007). In the present work we have tested the effect of a modified loading solvent containing a novel acid mix and optimized wash conditions on the efficiency of TiO(2)-based phosphopeptide enrichment in order to improve our previously published method (Mazanek et al., 2007). Applied to a test mixture of synthetic and BSA-derived peptides, the new method showed improved selectivity for phosphopeptides, whilst retaining a high recovery rate. Application of the new enrichment method to digested purified protein complexes resulted in the identification of a significantly higher number of phosphopeptides as compared to the previous method. Additionally, we have compared the performance of TiO(2) and ZrO(2) columns for the isolation and identification of phosphopeptides from purified protein complexes and found that for our test set, both media performed comparably well. In summary, our improved method is highly effective for the enrichment of phosphopeptides from purified protein complexes prior to mass spectrometry, and is suitable for large-scale phosphoproteomic projects that aim to elucidate phosphorylation-dependent cellular processes.","authors":"Mazanek, M., Roitinger, E., Hudecz, O., Hutchins, JR., Hegemann, B., Mitulovi\u0107, G., Taus, T., Stingl, C., Peters, JM., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Chromatogr B Analyt Technol Biomed Life Sci","volume":"878","issue":"5-6","page":"515-24","pdf":null,"JrId":"27040","fulltextlink":null,"preprintlink":null,"articledate":"2010-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11956231","title":"Cbfa1-independent decrease in osteoblast proliferation, osteopenia, and persistent embryonic eye vascularization in mice deficient in Lrp5, a Wnt coreceptor.","abstract":"The low-density lipoprotein receptor-related protein (Lrp)-5 functions as a Wnt coreceptor. Here we show that mice with a targeted disruption of Lrp5 develop a low bone mass phenotype. In vivo and in vitro analyses indicate that this phenotype becomes evident postnatally, and demonstrate that it is secondary to decreased osteoblast proliferation and function in a Cbfa1-independent manner. Lrp5 is expressed in osteoblasts and is required for optimal Wnt signaling in osteoblasts. In addition, Lrp5-deficient mice display persistent embryonic eye vascularization due to a failure of macrophage-induced endothelial cell apoptosis. These results implicate Wnt proteins in the postnatal control of vascular regression and bone formation, two functions affected in many diseases. Moreover, these features recapitulate human osteoporosis-pseudoglioma syndrome, caused by LRP5 inactivation.","authors":"Kato, M., Patel, MS., Levasseur, R., Lobov, I., Chang, BH., Glass, DA., Hartmann, C., Li, L., Hwang, TH., Brayton, CF., Lang, RA., Karsenty, G., Chan, L.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Cell Biol","volume":"157","issue":"2","page":"303-14","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14550415","title":"Cell differentiation and cell fate during urodele tail and limb regeneration.","abstract":"One of the most striking natural examples of adult tissue plasticity in vertebrates is limb and tail regeneration in urodele amphibians. In this setting, amputation triggers the destabilization of cell differentiation and the production of progenitor cells that extensively proliferate and pattern themselves to recreate a perfect replica of the missing part. A precise understanding of which cells dedifferentiate and how plastic they become has recently begun to emerge. Furthermore, information on which developmental gene programs are activated upon injury is becoming better understood. These studies indicate that, upon injury, an unusual cohort of genes are co-expressed. The future challenge will be to link the systems for studying dedifferentiation with activation of gene expression to understand on a molecular level how cells are 'pushed backward' to regenerate a complex structure such as a limb or tail.","authors":"Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Opin Genet Dev","volume":"13","issue":"5","page":"497-501","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14614819","title":"ATP hydrolysis is required for cohesin's association with chromosomes.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">14614819<\/PMID><DateCompleted><Year>2004<\/Year><Month>04<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>13<\/Volume><Issue>22<\/Issue><PubDate><Year>2003<\/Year><Month>Nov<\/Month><Day>11<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>ATP hydrolysis is required for cohesin's association with chromosomes.<\/ArticleTitle><Pagination><MedlinePgn>1941-53<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">A multi-subunit protein complex called cohesin is involved in holding sister chromatids together after DNA replication. Cohesin contains four core subunits: Smc1, Smc3, Scc1, and Scc3. Biochemical studies suggest that Smc1 and Smc3 each form 50 nm-long antiparallel coiled coils (arms) and bind to each other to form V-shaped heterodimers with globular ABC-like ATPases (created by the juxtaposition of N- and C-terminal domains) at their apices. These Smc \"heads\" are connected by Scc1, creating a tripartite proteinaceous ring.","authors":"Arumugam, P., Gruber, S., Tanaka, K., Haering, CH., Mechtler, K., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"22","page":"1941-53","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14581449","title":"Architecture of the budding yeast kinetochore reveals a conserved molecular core.","abstract":"How kinetochore proteins are organized to connect chromosomes to spindle microtubules, and whether any structural and organizational themes are common to kinetochores from distantly related organisms, are key unanswered questions. Here, we used affinity chromatography and mass spectrometry to generate a map of kinetochore protein interactions. The budding yeast CENP-C homologue Mif2p specifically copurified with histones H2A, H2B, and H4, and with the histone H3-like CENP-A homologue Cse4p, strongly suggesting that Cse4p replaces histone H3 in a specialized centromeric nucleosome. A novel four-protein Mtw1 complex, the Nnf1p subunit of which has homology to the vertebrate kinetochore protein CENP-H, also copurified with Mif2p and a variety of central kinetochore proteins. We show that Mif2 is a critical in vivo target of the Aurora kinase Ipl1p. Chromatin immunoprecipitation studies demonstrated the biological relevance of these associations. We propose that a molecular core consisting of CENP-A, -C, -H, and Ndc80\/HEC has been conserved from yeast to humans to link centromeres to spindle microtubules.","authors":"Westermann, S., Cheeseman, IM., Anderson, S., Yates, JR., Drubin, DG., Barnes, G.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Cell Biol","volume":"163","issue":"2","page":"215-22","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2003-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19058836","title":"Soluble TRAIL could enhance bone destruction acting on Rank-ligand in estrogen-independent human breast cancer cell line MDA-MB-231.","abstract":"The development and spread of tumors is associated with the ability of malignant cells to avoid detection and subsequent elimination by the immune system, to grow in non-native sites and to avoid programmed or induced cell death. In addition to the well-described role of osteoprotegerin in the regulation of bone turnover, there is an emerging evidence that osteoprotegerin may have an additional function due to its ability to bind and inhibit the members of the tumor necrosis factor (TNF)-superfamily, such as TNF-alpha and TNF-related apoptosis inducing ligand (TRAIL). We have shown that the breast cancer cell line MDA-MB-231 produces a sufficient amount of osteoprotegerin to bind TRAIL, resulting in an upregulation of receptor activator factor kappa B ligand (RANKL) expression. In conclusion, the presence of osteoprotegerin, as secreted by this cell line, acting as a paracrine factor, could affect breast cancer RANKL production inducing an enhancement of osteolysis and the perpetuation of a vicious cycle. A better understanding of the complex tumor cell-host cell interactions in the bone microenvironment, and of the autocrine and paracrine effects of the secreted (from tumor cells) and released (from bone matrix) factors may facilitate development of effective strategies to inhibit disease progression.","authors":"Nicolin, V., Narducci, P.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Acta Histochem","volume":"112","issue":"2","page":"189-92","pdf":null,"JrId":"81","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14562044","title":"Expression profiling of epithelial plasticity in tumor progression.","abstract":"Epithelial-to-mesenchymal transition (EMT), a switch of polarized epithelial cells to a migratory, fibroblastoid phenotype, is increasingly considered as an important event during malignant tumor progression and metastasis. To identify molecular players involved in EMT and metastasis, we performed expression profiling of a set of combined in vitro\/in vivo cellular models, based on clonal, fully polarized mammary epithelial cells. Seven closely related cell pairs were used, which were modified by defined oncogenes and\/or external factors and showed specific aspects of epithelial plasticity relevant to cell migration, local invasion and metastasis. Since mRNA levels do not necessarily reflect protein levels in cells, we used an improved expression profiling method based on polysome-bound RNA, suitable to analyse global gene expression on Affymetrix chips. A substantial fraction of all regulated genes was found to be exclusively controlled at the translational level. Furthermore, profiling of the above multiple cell pairs allowed one to identify small numbers of genes by cluster analysis, specifically correlating gene expression with EMT, metastasis, scattering and\/or oncogene function. A small set of genes specifically regulated during EMT was identified, including key regulators and signaling pathways involved in cell proliferation, epithelial polarity, survival and trans-differentiation to mesenchymal-like cells with invasive behavior.","authors":"Jechlinger, M., Grunert, S., Tamir, IH., Janda, E., L\u00fcdemann, S., Waerner, T., Seither, P., Weith, A., Beug, H., Kraut, N.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Oncogene","volume":"22","issue":"46","page":"7155-69","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2003-11-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14550787","title":"Cortical and retinal defects caused by dosage-dependent reductions in VEGF-A paracrine signaling.","abstract":"To determine the function of VEGF-A in nervous system development, we have utilized the Nestin promoter-driven Cre recombinase transgene, in conjunction with a conditional and hypomorphic VEGF-A allele, to lower VEGF-A activity in neural progenitor cells. Mice with intermediate levels of VEGF-A activity showed decreased blood vessel branching and density in the cortex and retina, resulting in a thinner retina and aberrant structural organization of the cortex. Severe reductions in VEGF-A led to decreases in vascularity and subsequent hypoxia, resulting in the specific degeneration of the cerebral cortex and neonatal lethality. Decreased neuronal proliferation and hypoxia was evident at E11.5, leading to increased neuronal apoptosis in the cortex by E15.5. In order to address whether the observed changes in the structural organization of the nervous system were due to a direct and autocrine role of VEGF-A on the neural population, we conditionally inactivated the main VEGF-A receptor, Flk1, specifically in neuronal lineages, by using the Nestin Cre transgene. The normality of these mice ruled out the possibility that VEGF-A\/Flk1 signaling has a significant autocrine role in CNS development. VEGF-A dosage is therefore a critical parameter regulating the density of the vascular plexus in the developing CNS that is in turn a key determinant in the development and architectural organization of the nervous system.","authors":"Haigh, JJ., Morelli, PI., Gerhardt, H., Haigh, K., Tsien, J., Damert, A., Miquerol, L., Muhlner, U., Klein, R., Ferrara, N., Wagner, EF., Betsholtz, C., Nagy, A.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Dev Biol","volume":"262","issue":"2","page":"225-41","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2003-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14530369","title":"The hemopoietic Rho\/Rac guanine nucleotide exchange factor Vav1 regulates N-formyl-methionyl-leucyl-phenylalanine-activated neutrophil functions.","abstract":"Vav1 is a hemopoietic-specific Rho\/Rac guanine nucleotide exchange factor that plays a prominent role in responses to multisubunit immune recognition receptors in lymphoid cells, but its contribution to regulation of neutrophil functions is unknown. Activated Rho family GTPases are critical participants in neutrophil signaling cascades initiated by binding of FMLP and other chemoattractants to their cognate G protein-coupled receptors. Therefore, we investigated whether Vav1 regulates chemoattractant-induced responses in neutrophils. We found that superoxide production elicited by FMLP in Vav1(-\/-) murine neutrophils isolated from either bone marrow or from peritoneal exudates was substantially reduced compared with that of wild type. Filamentous actin generation in FMLP-stimulated Vav1(-\/-) neutrophils was also markedly reduced, whereas it was normal in response to IL-8 or leukotriene B(4). FMLP induced tyrosine phosphorylation of Vav1, whereas IL-8 or leukotriene B(4) did not, correlating with the requirement for Vav1 in chemoattractant-stimulated filamentous actin generation. Neutrophil motility in vitro and neutrophil mobilization into peripheral blood in vivo elicited by FMLP were both decreased in Vav1(-\/-) mice. Hence, this study defines a new role for Vav1 in regulating granulocytic leukocytes as well as linking Vav1 to specific cellular responses downstream of a seven transmembrane domain receptor.","authors":"Kim, C., Marchal, CC., Penninger, J., Dinauer, MC.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Immunol","volume":"171","issue":"8","page":"4425-30","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11923871","title":"Severe impairment of interleukin-1 and Toll-like receptor signalling in mice lacking IRAK-4.","abstract":"Toll-like receptors (TLRs), which recognize pathogen-associated molecular patterns, and members of the pro-inflammatory interleukin-1 receptor (IL-1R) family, share homologies in their cytoplasmic domains called Toll\/IL-1R\/plant R gene homology (TIR) domains. Intracellular signalling mechanisms mediated by TIRs are similar, with MyD88 (refs 5-8) and TRAF6 (refs 9, 10) having critical roles. Signal transduction between MyD88 and TRAF6 is known to involve the serine-threonine kinase IL-1 receptor-associated kinase 1 (IRAK-1) and two homologous proteins, IRAK-2 (ref. 12) and IRAK-M. However, the physiological functions of the IRAK molecules remain unclear, and gene-targeting studies have shown that IRAK-1 is only partially required for IL-1R and TLR signalling. Here we show by gene-targeting that IRAK-4, an IRAK molecule closely related to the Drosophila Pelle protein, is indispensable for the responses of animals and cultured cells to IL-1 and ligands that stimulate various TLRs. IRAK-4-deficient animals are completely resistant to a lethal dose of lipopolysaccharide (LPS). In addition, animals lacking IRAK-4 are severely impaired in their responses to viral and bacterial challenges. Our results indicate that IRAK-4 has an essential role in innate immunity.","authors":"Suzuki, N., Suzuki, S., Duncan, GS., Millar, DG., Wada, T., Mirtsos, C., Takada, H., Wakeham, A., Itie, A., Li, S., Penninger, JM., Wesche, H., Ohashi, PS., Mak, TW., Yeh, WC.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nature","volume":"416","issue":"6882","page":"750-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14499603","title":"The relationship between sequence and interaction divergence in proteins.","abstract":"There is currently a gap in knowledge between complexes of known three-dimensional structure and those known from other experimental methods such as affinity purifications or the two-hybrid system. This gap can sometimes be bridged by methods that extrapolate interaction information from one complex structure to homologues of the interacting proteins. To do this, it is important to know if and when proteins of the same type (e.g. family, superfamily or fold) interact in the same way. Here, we study interactions of known structure to address this question. We found all instances within the structural classification of proteins database of the same domain pairs interacting in different complexes, and then compared them with a simple measure (interaction RMSD). When plotted against sequence similarity we find that close homologues (30-40% or higher sequence identity) almost invariably interact the same way. Conversely, similarity only in fold (i.e. without additional evidence for a common ancestor) is only rarely associated with a similarity in interaction. The results suggest that there is a twilight zone of sequence similarity where it is not possible to say whether or not domains will interact similarly. We also discuss the rare instances of fold similarities interacting the same way, and those where obviously homologous proteins interact differently.","authors":"Aloy, P., Ceulemans, H., Stark, A., Russell, RB.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Mol Biol","volume":"332","issue":"5","page":"989-98","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2003-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12956947","title":"TPR subunits of the anaphase-promoting complex mediate binding to the activator protein CDH1.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">12956947<\/PMID><DateCompleted><Year>2004<\/Year><Month>01<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>13<\/Volume><Issue>17<\/Issue><PubDate><Year>2003<\/Year><Month>Sep<\/Month><Day>02<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>TPR subunits of the anaphase-promoting complex mediate binding to the activator protein CDH1.<\/ArticleTitle><Pagination><MedlinePgn>1459-68<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Chromosome segregation and mitotic exit depend on activation of the anaphase-promoting complex (APC) by the substrate adaptor proteins CDC20 and CDH1. The APC is a ubiquitin ligase composed of at least 11 subunits. The interaction of APC2 and APC11 with E2 enzymes is sufficient for ubiquitination reactions, but the functions of most other subunits are unknown.","authors":"Vodermaier, HC., Gieffers, C., Maurer-Stroh, S., Eisenhaber, F., Peters, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"17","page":"1459-68","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11909551","title":"Axon guidance: growth cones make an unexpected turn.","abstract":"Axonal growth cones can turn in response to minute concentration differences in extracellular guidance cues. Surprising new work suggests that these cues might steer the growth cone by inducing rapid local changes in protein levels.","authors":"Dickson, BJ., Senti, KA.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"6","page":"R218-20","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11882300","title":"Netrins.","abstract":null,"authors":"Dickson, BJ., Keleman, K.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"5","page":"R154-5","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11869895","title":"Transcriptional control of B-cell development.","abstract":"Significant progress has recently been made in our understanding of how transcription factors such as PU.1, Notch1, E2A, EBF, Pax5, Bcl6, Blimp1 and XBP1 control different developmental decisions during the onset and terminal phase of B-lymphopoiesis. One emerging theme is that negative regulatory networks play an important role in suppressing alternative gene programs and their corresponding cell fates throughout B-cell development.","authors":"Schebesta, M., Heavey, B., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Opin Immunol","volume":"14","issue":"2","page":"216-23","pdf":null,"JrId":"1461","fulltextlink":null,"preprintlink":null,"articledate":"2002-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11861618","title":"RANK-L and RANK: T cells, bone loss, and mammalian evolution.","abstract":"TNF and TNFR family proteins play important roles in the control of cell death, proliferation, autoimmunity, the function of immune cells, or the organogenesis of lymphoid organs. Recently, novel members of this large family have been identified that have critical functions in immunity and that couple lymphoid cells with other organ systems such as bone morphogenesis and mammary gland formation in pregnancy. The TNF-family molecule RANK-L (RANK-L, TRANCE, ODF) and its receptor RANK are key regulators of bone remodeling, and they are essential for the development and activation of osteoclasts. Intriguingly, RANK-L\/RANK interactions also regulate T cell\/dendritic cell communications, dendritic cell survival, and lymph node formation; T cell-derived RANK-L can mediate bone loss in arthritis and periodontal disease. Moreover, RANK-L and RANK are expressed in mammary gland epithelial cells, and they control the development of a lactating mammary gland during pregnancy and the propagation of mammalian species. Modulation of these systems provides us with a unique opportunity to design novel therapeutics to inhibit bone loss in arthritis, periodontal disease, and osteoporosis.","authors":"Theill, LE., Boyle, WJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Annu Rev Immunol","volume":"20","issue":null,"page":"795-823","pdf":null,"JrId":"1564","fulltextlink":null,"preprintlink":null,"articledate":"2002-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20371351","title":"A global in vivo Drosophila RNAi screen identifies NOT3 as a conserved regulator of heart function.","abstract":"Heart diseases are the most common causes of morbidity and death in humans. Using cardiac-specific RNAi-silencing in Drosophila, we knocked down 7061 evolutionarily conserved genes under conditions of stress. We present a first global roadmap of pathways potentially playing conserved roles in the cardiovascular system. One critical pathway identified was the CCR4-Not complex implicated in transcriptional and posttranscriptional regulatory mechanisms. Silencing of CCR4-Not components in adult Drosophila resulted in myofibrillar disarray and dilated cardiomyopathy. Heterozygous not3 knockout mice showed spontaneous impairment of cardiac contractility and increased susceptibility to heart failure. These heart defects were reversed via inhibition of HDACs, suggesting a mechanistic link to epigenetic chromatin remodeling. In humans, we show that a common NOT3 SNP correlates with altered cardiac QT intervals, a known cause of potentially lethal ventricular tachyarrhythmias. Thus, our functional genome-wide screen in Drosophila can identify candidates that directly translate into conserved mammalian genes involved in heart function.","authors":"Neely, GG., Kuba, K., Cammarato, A., Isobe, K., Amann, S., Zhang, L., Murata, M., Elm\u00e9n, L., Gupta, V., Arora, S., Sarangi, R., Dan, D., Fujisawa, S., Usami, T., Xia, CP., Keene, AC., Alayari, NN., Yamakawa, H., Elling, U., Berger, C., Novatchkova, M., Koglgruber, R., Fukuda, K., Nishina, H., Isobe, M., Pospisilik, JA., Imai, Y., Pfeufer, A., Hicks, AA., Pramstaller, PP., Subramaniam, S., Kimura, A., Ocorr, K., Bodmer, R., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell","volume":"141","issue":"1","page":"142-53","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12956414","title":"Protein prenyltransferases: anchor size, pseudogenes and parasites.","abstract":"Lipid modification of eukaryotic proteins by protein prenyltransferases is required for critical signaling pathways, cell cycle progression, cytoskeleton remodeling, induction of apoptosis and vesicular trafficking. This review analyzes the influence of distinct states of sequential posttranslational processing that can be obtained after single or double prenylation, reversible palmitoylation, proteolytic cleavage of the C-terminus and possible reversible carboxymethylation. This series of modifications, as well as the exact length of the prenyl anchor, are determinants in protein-membrane and specific protein-protein interactions of protein prenyltransferase substrates. Furthermore, the occurrence and distribution of pseudogenes of protein prenyltransferase subunits are discussed. Besides being developed as anti-cancer agents, prenyltransferase inhibitors are effective against an increasing number of parasitic diseases. Extensive screens for protein prenyltransferases in genomic data of fungal and protozoan pathogens unveil a series of new pharmacologic targets for prenyltransferase inhibition, including the parasites Brugia malayi, Onchocerca volvulus, Aspergillus nidulans, Pneumocystis carinii, Entamoeba histolytica, Strongyloides stercoralis, Trichinella spiralis and Cryptosporidium parvum.","authors":"Maurer-Stroh, S., Washietl, S., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Biol Chem","volume":"384","issue":"7","page":"977-89","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11839280","title":"Histone H3 lysine 9 methylation occurs rapidly at the onset of random X chromosome inactivation.","abstract":"In female mammals, a single X chromosome is stably and heritably silenced early in embryogenesis. The inactive X is characterized by asynchronous DNA replication and epigenetic chromatin modifications, including DNA methylation, histone H3\/H4 hypoacetylation, and incorporation of a variant histone macroH2A. X inactivation is initiated by a cis-acting RNA molecule, the X-inactive specific transcript (Xist), which coats the chromosome. However, the mechanism by which Xist induces chromosome silencing is poorly understood. An important approach towards answering this question has been to determine the temporal order of epigenetic chromatin modifications in an in vitro model system, differentiating XX embryonic stem (ES) cells, and thereby to identify candidate targets for Xist RNA. To date, these studies have demonstrated that, following accumulation of Xist RNA, the transition to late replication of the X chromosome is the earliest detectable event. H4 hypoacetylation, macroH2A1.2 incorporation, and DNA methylation all occur subsequently. Recently, it has been shown that chromatin of the inactive X is also characterized by methylation of histone H3 at lysine 9 (H3-K9). Here we show that H3-K9 methylation is a very early event in the process of X inactivation, which closely parallels the onset of Xist RNA accumulation.","authors":"Mermoud, JE., Popova, B., Peters, AH., Jenuwein, T., Brockdorff, N.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"3","page":"247-51","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11818961","title":"JunB can substitute for Jun in mouse development and cell proliferation.","abstract":"The Jun and JunB components of the AP-1 transcription factor are known to have antagonistic functions. Here we show, by a knock-in strategy and a transgenic complementation approach, that Junb can substitute for absence of Jun during mouse development. Junb can rescue both liver and cardiac defects in Jun-null mice in a manner dependent on gene dosage. JunB restores the expression of genes regulated by Jun\/Fos, but not those regulated by Jun\/ATF, thereby rescuing Jun-dependent defects in vivo as well as in primary fibroblasts and fetal hepatoblasts in vitro. Thus, the transcriptionally less active JunB has the potential to substitute for Jun, indicating that the spatial and temporal regulation of expression of the transcription factor AP-1 may be more important than the coding sequence of its components.","authors":"Passegu\u00e9, E., Jochum, W., Behrens, A., Ricci, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nat Genet","volume":"30","issue":"2","page":"158-66","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20362898","title":"Morphologic, functional, and occlusal characterization of mandibular lateral displacement malocclusion.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20362898<\/PMID><DateCompleted><Year>2010<\/Year><Month>05<\/Month><Day>04<\/Day><\/DateCompleted><DateRevised><Year>2010<\/Year><Month>04<\/Month><Day>05<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1097-6752<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>137<\/Volume><Issue>4<\/Issue><PubDate><Year>2010<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics<\/Title><ISOAbbreviation>Am J Orthod Dentofacial Orthop<\/ISOAbbreviation><\/Journal><ArticleTitle>Morphologic, functional, and occlusal characterization of mandibular lateral displacement malocclusion.<\/ArticleTitle><Pagination><MedlinePgn>454.e1-9; discussion 454-5<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.ajodo.2009.10.031<\/ELocationID><Abstract><AbstractText Label=\"INTRODUCTION\" NlmCategory=\"BACKGROUND\">Mandibular lateral displacement (MLD) is clinically characterized by deviation of the chin, facial asymmetry, dental midline discrepancy, crossbite in the posterior region, and high prevalence of internal derangement of the temporomandibular joint. Morphologic and functional characteristics of MLD should be clarified to correct and prevent this malocclusion.","authors":"Ishizaki, K., Suzuki, K., Mito, T., Tanaka, EM., Sato, S.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Am J Orthod Dentofacial Orthop","volume":"137","issue":"4","page":"454.e1-9; discussion 454-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11790801","title":"Ras and TGF[beta] cooperatively regulate epithelial cell plasticity and metastasis: dissection of Ras signaling pathways.","abstract":"Multistep carcinogenesis involves more than six discrete events also important in normal development and cell behavior. Of these, local invasion and metastasis cause most cancer deaths but are the least well understood molecularly. We employed a combined in vitro\/in vivo carcinogenesis model, that is, polarized Ha-Ras-transformed mammary epithelial cells (EpRas), to dissect the role of Ras downstream signaling pathways in epithelial cell plasticity, tumorigenesis, and metastasis. Ha-Ras cooperates with transforming growth factor beta (TGFbeta) to cause epithelial mesenchymal transition (EMT) characterized by spindle-like cell morphology, loss of epithelial markers, and induction of mesenchymal markers. EMT requires continuous TGFbeta receptor (TGFbeta-R) and oncogenic Ras signaling and is stabilized by autocrine TGFbeta production. In contrast, fibroblast growth factors, hepatocyte growth factor\/scatter factor, or TGFbeta alone induce scattering, a spindle-like cell phenotype fully reversible after factor withdrawal, which does not involve sustained marker changes. Using specific inhibitors and effector-specific Ras mutants, we show that a hyperactive Raf\/mitogen-activated protein kinase (MAPK) is required for EMT, whereas activation of phosphatidylinositol 3-kinase (PI3K) causes scattering and protects from TGFbeta-induced apoptosis. Hyperactivation of the PI3K pathway or the Raf\/MAPK pathway are sufficient for tumorigenesis, whereas EMT in vivo and metastasis required a hyperactive Raf\/MAPK pathway. Thus, EMT seems to be a close in vitro correlate of metastasis, both requiring synergism between TGFbeta-R and Raf\/MAPK signaling.","authors":"Janda, E., Lehmann, K., Killisch, I., Jechlinger, M., Herzig, M., Downward, J., Beug, H., Gr\u00fcnert, S.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Cell Biol","volume":"156","issue":"2","page":"299-313","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21629305","title":"Comment on 'Jobs for the boys'.","abstract":null,"authors":"K\u00f6cher, T.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"EMBO Rep","volume":"12","issue":"6","page":"488","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11784082","title":"FGF signaling is necessary for the specification of the odontogenic mesenchyme.","abstract":"Tooth development is initiated by signals from the oral ectoderm which induce gene expression required for tooth development in the underlying mesenchyme. In this study, we have used Su5402, an inhibitor of FGF receptor signaling, to analyze the requirement of FGF signaling during early tooth development. We show that FGF signaling is necessary for expression of Pax9, a transcription factor required for development of all teeth, in prospective incisor and molar mesenchyme until E11.0. Expression of the LIM homeobox gene Lhx7 also requires FGF signaling until E11.0 whereas expression of its homologue Lhx6 and the homeobox transcription factor Barx1 already becomes independent of FGF signaling at E10.75. In contrast, ectodermal expression of several genes thought to be important for tooth development was unaffected by the block of FGF signaling. Finally, we show that expression of the TGFbeta antagonist Dan in prospective tooth mesenchyme requires ectodermal signals and can be induced by FGF-soaked beads but is maintained in mandibular explants in the absence of FGF signaling. Together, these results demonstrate that FGF signaling is required for development of both molar and incisor teeth and suggest that specification of tooth mesenchyme involves at least two FGF-dependent steps.","authors":"Mandler, M., Neub\u00fcser, A.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Dev Biol","volume":"240","issue":"2","page":"548-59","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11782313","title":"Central spindle assembly and cytokinesis require a kinesin-like protein\/RhoGAP complex with microtubule bundling activity.","abstract":"A late step in cytokinesis requires the central spindle, which forms during anaphase by the bundling of antiparallel nonkinetochore microtubules. Microtubule bundling and completion of cytokinesis require ZEN-4\/CeMKLP-1, a kinesin-like protein, and CYK-4, which contains a RhoGAP domain. We show that CYK-4 and ZEN-4 exist in a complex in vivo that can be reconstituted in vitro. The N terminus of CYK-4 binds the central region of ZEN-4, including the neck linker. Genetic suppression data prove the functional significance of this interaction. An analogous complex, containing equimolar amounts of a CYK-4 ortholog and MKLP-1, was purified from mammalian cells. Biochemical studies indicate that this complex, named centralspindlin, is a heterotetramer. Centralspindlin, but not its individual components, strongly promotes microtubule bundling in vitro.","authors":"Mishima, M., Kaitna, S., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Dev Cell","volume":"2","issue":"1","page":"41-54","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20230747","title":"Rec8 phosphorylation by casein kinase 1 and Cdc7-Dbf4 kinase regulates cohesin cleavage by separase during meiosis.","abstract":"During meiosis, two rounds of chromosome segregation after a single round of DNA replication produce haploid gametes from diploid precursors. At meiosis I, maternal and paternal kinetochores are pulled toward opposite poles, and chiasmata holding bivalent chromosomes together are resolved by cleavage of cohesin's alpha-kleisin subunit (Rec8) along chromosome arms. This creates dyad chromosomes containing a pair of chromatids joined solely by cohesin at centromeres that had resisted cleavage. The discovery that centromeric Rec8 is protected from separase during meiosis I by shugoshin\/MEI-S332 proteins that bind PP2A phosphatase suggests that phosphorylation either of separase or cohesin may be necessary for Rec8 cleavage. We show here that multiple phosphorylation sites within Rec8 as well as two different kinases, casein kinase 1delta\/epsilon (CK1delta\/epsilon) and Dbf4-dependent Cdc7 kinase (DDK), are required for Rec8 cleavage and meiosis I nuclear division. Rec8 with phosphomimetic mutations is no longer protected from separase at centromeres and is cleaved even when the two kinases are inhibited. Our data suggest that PP2A protects centromeric cohesion by opposing CK1delta\/epsilon- and DDK-dependent phosphorylation of Rec8.","authors":"Katis, VL., Lipp, JJ., Imre, R., Bogdanova, A., Okaz, E., Habermann, B., Mechtler, K., Nasmyth, K., Zachariae, W.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Dev Cell","volume":"18","issue":"3","page":"397-409","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12918079","title":"Effects of oral UFT combined with or without zoledronic acid on bone metastasis in the 4T1\/luc mouse breast cancer.","abstract":"Bone metastasis is one of the major causes of increased morbidity and eventual mortality in breast cancer patients. Therefore, intervention of bone metastases is one of the important targets in the management of breast cancer. In the present study, we examined the effects of the orally administrable chemotherapeutic agent UFT (a combination of tegafur and uracil at a molar ratio of 1:4) on bone metastases using an animal model of the 4T1\/luc mouse breast cancer. The 4T1\/luc cells developed spontaneous metastases to bone following orthotopic cell inoculation. Oral daily administration of UFT (20 mg\/kg\/day) significantly reduced the orthotopic tumor burden; however, the lower dose (15 mg\/kg\/day) did not. In contrast, histologic examination showed that both doses of UFT significantly suppressed bone metastases in a dose-dependent manner. Since clinical studies have demonstrated that bisphosphonates (BPs), specific inhibitors of osteoclastic bone resorption, are beneficial for breast cancer patients with bone metastases, we next examined the effects of UFT combined with the BP zoledronic acid (ZOL) on established bone metastases. The combination of UFT (20 mg\/kg\/day) with ZOL (250 microg\/kg) caused an enhanced reduction of bone metastases compared with UFT alone. In vitro studies showed that 5-fluorouracil (5-FU), an active metabolite of UFT, and ZOL increased apoptosis in 4T1\/luc cells and inhibited osteoclast-like cell formation in an additive fashion. Our results suggest that oral UFT is an effective chemotherapeutic agent for advanced breast cancer accompanying bone metastases and that the combination with BP increases its benefits for bone metastases.","authors":"Hiraga, T., Ueda, A., Tamura, D., Hata, K., Ikeda, F., Williams, PJ., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Int J Cancer","volume":"106","issue":"6","page":"973-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12900441","title":"Consequences of the depletion of zygotic and embryonic enhancer of zeste 2 during preimplantation mouse development.","abstract":"Enhancer of zeste 2 (Ezh2), a SET domain-containing protein, is crucial for development in many model organisms, including early mouse development. In mice, Ezh2 is detected as a maternally inherited protein in the oocyte but its function at the onset of development is unknown. We have used a conditional allele of Ezh2 to deplete the oocyte of this maternal inheritance. We show that the loss of maternal Ezh2 has a long-term effect causing severe growth retardation of neonates despite 'rescue' through embryonic transcription from the paternal allele. This phenotypic effect on growth could be attributed to the asymmetric localisation of the Ezh2\/Eed complex and the associated histone methylation pattern to the maternal genome, which is disrupted in Ezh2 mutant zygotes. During subsequent development, we detect distinct histone methylation patterns in the trophectoderm and the pluripotent epiblast. In the latter where Oct4 expression continues from the zygote onwards, the Ezh2\/Eed complex apparently establishes a unique epigenetic state and plasticity, which probably explains why loss of Ezh2 is early embryonic lethal and obligatory for the derivation of pluripotent embryonic stem cells. By contrast, in the differentiating trophectoderm cells where Oct4 expression is progressively downregulated Ezh2\/Eed complex is recruited transiently to one X chromosome in female embryos at the onset of X-inactivation. This accumulation and the associated histone methylation are also lost in Ezh2 mutants, suggesting a role in X inactivation. Thus, Ezh2 has significant and diverse roles during early development, as well as during the establishment of the first differentiated cells, the trophectoderm, and of the pluripotent epiblast cells.","authors":"Erhardt, S., Su, IH., Schneider, R., Barton, S., Bannister, AJ., Perez-Burgos, L., Jenuwein, T., Kouzarides, T., Tarakhovsky, A., Surani, MA.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Development","volume":"130","issue":"18","page":"4235-48","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2003-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20028656","title":"The alarmin cytokine, high mobility group box 1, is produced by viable cardiomyocytes and mediates the lipopolysaccharide-induced myocardial dysfunction via a TLR4\/phosphatidylinositol 3-kinase gamma pathway.","abstract":"High mobility group box 1 (HMGB1) is an alarmin actively secreted by immune cells and passively released by necrotic nonimmune cells. HMGB1 has been implicated in both cardiac contractile dysfunction and the lethality associated with sepsis\/endotoxemia. The aim of the current study was to assess whether viable cardiomyocytes could produce HMGB1 and whether HMGB1 can affect myocardial contractility. LPS was used as a model of sepsis\/endotoxemia in mice and isolated cardiac myocytes. LPS increased myocardial expression of HMGB1 in vivo (immunohistochemistry) and production and secretion of HMGB1 by viable cardiac myocytes in vitro (Western). LPS increased the phosphorylation status of PI3Kgamma in cardiac myocytes, an effect not observed in TLR4(-\/-) myocytes. Genetic (PI3Kgamma(-\/-)) or pharmacologic (AS605240) blockade of PI3Kgamma ameliorated the LPS-induced 1) cardiomyocyte production and secretion of HMGB1 in vitro and 2) HMGB1 expression in the myocardium in vivo. The LPS-induced depression of myocardial contractility was prevented by the HMGB1 antagonist, A-box. Genetic (PI3Kgamma(-\/-)) or pharmacologic (AS605240) blockade of PI3Kgamma ameliorated the LPS-induced decrease in myocardial contractility. No evidence of inflammatory infiltrate was noted in any of the in vivo studies. The findings of the current study indicate that 1) LPS can induce HMGB1 secretion by viable cardiac myocytes through a TLR4\/PI3Kgamma signaling pathway, and 2) HMGB1 plays a role in the LPS-induced myocardial contractile dysfunction. The results of the current study also have broader implications (i.e., that viable parenchymal cells, such as cardiac myocytes, participate in the alarmin response).","authors":"Xu, H., Su, Z., Wu, J., Yang, M., Penninger, JM., Martin, CM., Kvietys, PR., Rui, T.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Immunol","volume":"184","issue":"3","page":"1492-8","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21984922","title":"Activation-induced cytidine deaminase (AID)-associated multigene signature to assess impact of AID in etiology of diseases with inflammatory component.","abstract":"Activation-induced cytidine deaminase (AID) is expressed in B cells within germinal centers and is critically involved in class switch recombination and somatic hypermutation of immunoglobulin loci. Functionally active AID can additionally be detected within ectopic follicular structures developed at sites of chronic inflammation. Furthermore, AID may target non-Ig genes in B- and non-B-cell background. Therefore, AID-associated effects are of increasing interest in disease areas such as allergy, inflammation, autoimmunity, and cancer.Pathway- or disease-relevant multigene signatures have attracted substantial attention for therapeutic target proposal, diagnostic tools, and monitoring of therapy response. To delineate the impact of AID in etiology of multifactorial diseases, we designed the AID-associated 25-gene signature. Chronic rhinosinusitis with nasal polyps was used as an inflammation-driven airway disease model; high levels of IgE have been previously shown to be present within polyp tissue. Expression levels of 16 genes were found to be modulated in polyps including AID, IgG and IgE mature transcripts which reflect AID activity; clustering algorithm revealed an AID-specific gene signature for the disease state with nasal polyp. Complementary, AID-positive ectopic lymphoid structures were detected within polyp tissues by in situ immunostaining. Our data demonstrate the class switch recombination and somatic hypermutation events likely taking place locally in the airways and in addition to the previously highlighted markers and\/or targets as IL5 and IgE suggest novel candidate genes to be considered for treatment of nasal polyposis including among others IL13 and CD23. Thus, the algorithm presented herein including the multigene signature approach, analysis of co-regularities and creation of AID-associated functional network gives an integrated view of biological processes and might be further applied to assess role of altered AID expression in etiology of other diseases, in particular, aberrant immunity and cancer.","authors":"Mechtcheriakova, D., Sobanov, Y., Holtappels, G., Bajna, E., Svoboda, M., Jaritz, M., Bachert, C., Jensen-Jarolim, E.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"PLoS One","volume":"6","issue":"10","page":"e25611","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12517702","title":"Microtubules meet substrate adhesions to arrange cell polarity.","abstract":"Cell movement is driven by the regulated and polarised turnover of the actin cytoskeleton and of the adhesion complexes that link it to the extracellular matrix. For most cells, polarisation requires the engagement of microtubules, which exert their effect by mediating changes in the activity of the Rho GTPases. Evidence suggests that these changes are effected in a very localised fashion at sites of substrate adhesion, via specific microtubule-targeting interactions. Targeting serves to bring molecular complexes bound at the tips and along microtubules in close proximity with adhesion complexes, to promote adhesion disassembly and remodelling of the actin cytoskeleton.","authors":"Small, JV., Kaverina, I.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Opin Cell Biol","volume":"15","issue":"1","page":"40-7","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12885297","title":"SH2-containing inositol 5-phosphatases 1 and 2 in blood platelets: their interactions and roles in the control of phosphatidylinositol 3,4,5-trisphosphate levels.","abstract":"Src homology domain 2-containing inositol 5-phosphatases 1 and 2 (SHIP1 and SHIP2) are capable of dephosphorylating the second messenger PtdIns(3,4,5) P3 (phosphatidylinositol 3,4,5-trisphosphate) and interacting with several signalling proteins. SHIP1 is essentially expressed in haematopoietic cells, whereas SHIP2, a closely related enzyme, is ubiquitous. In the present study, we show that SHIP1 and SHIP2 are expressed as functional PtdIns(3,4,5) P3 5-phosphatases in human blood platelets and are capable of interacting when these two lipid phosphatases are co-expressed, either naturally (platelets and A20 B lymphoma cells) or artificially (COS-7 cells). Using COS-7 cells transfected with deletion mutants of SHIP2, we demonstrate that the Src homology domain 2 of SHIP2 is the minimal and sufficient protein motif responsible for the interaction between the two phosphatases. These results prompted us to investigate the relative importance of SHIP1 and SHIP2 in the control of PtdIns(3,4,5) P3 levels in platelets using homozygous or heterozygous SHIP1- or SHIP2-deficient mice. Our results strongly suggest that SHIP1, rather than SHIP2, plays a major role in controlling PtdIns(3,4,5) P3 levels in response to thrombin or collagen activation of mouse blood platelets.","authors":"Giuriato, S., Pesesse, X., Bodin, S., Sasaki, T., Viala, C., Marion, E., Penninger, J., Schurmans, S., Erneux, C., Payrastre, B.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Biochem J","volume":"376","issue":"Pt 1","page":"199-207","pdf":null,"JrId":"1011","fulltextlink":null,"preprintlink":null,"articledate":"2003-12-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11726933","title":"Genetic mapping with SNP markers in Drosophila.","abstract":"Map-based positional cloning of Drosophila melanogaster genes is hampered by both the time-consuming, error-prone nature of traditional methods for genetic mapping and the difficulties in aligning the genetic and cytological maps with the genome sequence. The identification of sequence polymorphisms in the Drosophila genome will make it possible to map mutations directly to the genome sequence with high accuracy and resolution. Here we report the identification of 7,223 single-nucleotide polymorphisms (SNPs) and 1,392 insertions\/deletions (InDels) in common laboratory strains of Drosophila. These sequence polymorphisms define a map of 787 autosomal marker loci with a resolution of 114 kb. We have established PCR product-length polymorphism (PLP) or restriction fragment-length polymorphism (RFLP) assays for 215 of these markers. We demonstrate the use of this map by delimiting two mutations to intervals of 169 kb and 307 kb, respectively. Using a local high-density SNP map, we also mapped a third mutation to a resolution of approximately 2 kb, sufficient to localize the mutation within a single gene. These methods should accelerate the rate of positional cloning in Drosophila.","authors":"Berger, J., Suzuki, T., Senti, KA., Stubbs, J., Schaffner, G., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Genet","volume":"29","issue":"4","page":"475-81","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11734999","title":"Expression of Xist RNA is sufficient to initiate macrochromatin body formation.","abstract":"MacroH2A1 is a histone variant that is found as a component of the inactive X chromosome where it is detected as a dense accumulation called a macrochromatin body (MCB). Macrochromatin bodies co-localize with Xist RNA, which is an untranslated RNA that is expressed exclusively from the inactive X chromosome of placental mammals. However, no studies to date have investigated whether Xist RNA expression is necessary or sufficient to cause the formation of MCBs. Here we show that expression of Xist RNA is sufficient to cause the formation of MCBs even when Xist is expressed from an inducible transgene at ectopic autosomal sites. Macrochromatin bodies form at sites of transgenic Xist expression in differentiating mouse ES cell lines and transgenic fibroblasts, but MCBs cannot form in undifferentiated ES cells even after prolonged Xist expression. The kinetics of MCB formation revealed that Xist expression precedes MCB formation and that differentiating ES cells undergo a rapid and synchronous transition that renders them competent to form MCBs. Once MCBs have formed, continued expression of Xist is required for their maintenance. These results show that Xist RNA and macroH2A1 function in a common pathway. Expression of Xist in a permissive nuclear environment is sufficient to initiate a chromatin-remodeling event culminating in the incorporation of macroH2A1. The results also strongly suggest the existence of additional regulatory factors for X inactivation that are regulated developmentally. In addition, we present evidence that macroH2A1 density is not simply a measure of the general degree of DNA compaction.","authors":"Rasmussen, TP., Wutz, AP., Pehrson, JR., Jaenisch, RR.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Chromosoma","volume":"110","issue":"6","page":"411-20","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19160501","title":"Serine phosphorylation of ephrinB2 regulates trafficking of synaptic AMPA receptors.","abstract":"Plasticity in the brain is essential for maintaining memory and learning and is associated with the dynamic membrane trafficking of AMPA receptors. EphrinB proteins, ligands for EphB receptor tyrosine kinases, are transmembrane molecules with signaling capabilities that are required for spine morphogenesis, synapse formation and synaptic plasticity. Here, we describe a molecular mechanism for ephrinB2 function in controlling synaptic transmission. EphrinB2 signaling is critical for the stabilization of AMPA receptors at the cellular membrane. Mouse hippocampal neurons from conditional ephrinB2 knockouts showed enhanced constitutive internalization of AMPA receptors and reduced synaptic transmission. Mechanistically, glutamate receptor interacting proteins bridge ephrinB ligands and AMPA receptors. Moreover, this function involved a regulatory aspect of ephrinB reverse signaling that involves the phosphorylation of a single serine residue in their cytoplasmic tails. In summary, our findings uncover a model of cooperative AMPA receptor and ephrinB reverse signaling at the synapse.","authors":"Essmann, CL., Martinez, E., Geiger, JC., Zimmer, M., Traut, MH., Stein, V., Klein, R., Acker-Palmer, A.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Neurosci","volume":"11","issue":"9","page":"1035-43","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11726661","title":"Osteoprotegerin ligand induces beta-casein gene expression through the transcription factor CCAAT\/enhancer-binding protein beta.","abstract":"Osteoprotegerin ligand (OPGL, also known as RANKL), a member of the tumor necrosis factor superfamily, is essential for mammary gland development during pregnancy in addition to key roles in the immune system and bone development. Here we show that OPGL induces beta-casein transcription through the CCAAT\/enhancer-binding protein beta (C\/EBPbeta). In both HC11 cell lines and primary mammary epithelial cells, OPGL stimulation triggers rapid nuclear translocation of C\/EBPbeta, which is critical for the expression of the beta-casein gene. Mutation of C\/EBbeta binding sites in the beta-casein gene promoter completely abrogated OPGL-induced beta-casein promoter activity. By contrast, OPGL stimulation did not result in STAT5 phosphorylation. In vivo immunohistochemistry studies further demonstrated defective nuclear translocation of C\/EBPbeta, but normal STAT5 activation, in OPGL-deficient mice. These data show that OPGL is a critical activator of beta-casein gene expression via the transcription factor C\/EBPbeta. Our data provide new insights into the understanding of the molecular events involved in milk protein gene expression.","authors":"Kim, HJ., Yoon, MJ., Lee, J., Penninger, JM., Kong, YY.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Biol Chem","volume":"277","issue":"7","page":"5339-44","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12874451","title":"Lymphatic microvessels in the rat remnant kidney model of renal fibrosis: aminopeptidase p and podoplanin are discriminatory markers for endothelial cells of blood and lymphatic vessels.","abstract":"ABSTRACT. Rat remnant kidney is an established model of renal tubulointerstitial fibrosis and progression to end-stage renal failure. The morphologic lesions comprise nephron loss and regeneratory tubular hypertrophy, interstitial infiltration, predominately by macrophages, and progressive fibrosis. A critical role in this complex pathology was assigned to tubulointerstitial blood microvessels that regulate the supply of oxygen and nutrients of tubuli. Whereas some investigations reported a rarefaction of the vascular network in association with the degenerative cortical changes, others observed an increase in vascularization. Here these discrepant findings are addressed by reinvestigation of the vascularization of rat remnant kidneys by the use of two novel endothelial lineage specific, discriminatory markers, i.e., the membrane mucoprotein podoplanin with specificity for lymphatic endothelia, and the glycosyl-phosphatidylinositol (GPI)-anchored membrane enzyme aminopeptidase P that is recognized by a monoclonal antibody designated JG12 and that is specifically expressed by endothelial cells of blood vessels only. The results obtained confirm a regional rarefaction of aminopeptidase P-positive blood microvessels; they also establish major changes in the renal lymphatic vasculature. Massive proliferation of lymphatic vessels was observed in fibrotic tubulointerstitial regions, whereas in kidneys of sham-operated rats, only a few lymphatic vessels were found adjoined with arteries. The lymphatic vessels frequently contained mononuclear cells that were also encountered in the interstitial spaces and expressed relative large amounts of vascular endothelial growth factor-C mRNA by in situ hybridization. Collectively, these results indicate that a large proportion of the microvessels encountered in the cortex of remnant kidneys are of lymphatic origin and cannot be discriminated by common endothelial markers, such as CD34, that are expressed by both lymphatic and blood endothelia cells. As lymphatic endothelial cells secrete chemokines that attract dendritic cells, it is possible that the increase in lymphatic vascularization could enhance the immunologic surveillance of remnant kidneys.","authors":"Matsui, K., Nagy-Bojarsky, K., Laakkonen, P., Krieger, S., Mechtler, K., Uchida, S., Geleff, S., Kang, DH., Johnson, RJ., Kerjaschki, D., Kang, DH.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Am Soc Nephrol","volume":"14","issue":"8","page":"1981-9","pdf":null,"JrId":"1194","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12853486","title":"Early mitotic degradation of the homeoprotein HOXC10 is potentially linked to cell cycle progression.","abstract":"Hox proteins are transcription factors involved in controlling axial patterning, leukaemias and hereditary malformations. Here, we show that HOXC10 oscillates in abundance during the cell cycle, being targeted for degradation early in mitosis by the ubiquitin-dependent proteasome pathway. Among abdominal-B subfamily members, the mitotic proteolysis of HOXC10 appears unique, since the levels of the paralogous HOXD10 and the related homeoprotein HOXC13 are constant throughout the cell cycle. When two destruction box motifs (D-box) are mutated, HOXC10 is stabilized and cells accumulate in metaphase. HOXC10 appears to be a new prometaphase target of the anaphase-promoting complex (APC), since its degradation coincides with cyclin A destruction and is suppressed by expression of a dominant-negative form of UbcH10, an APC-associated ubiquitin-conjugating enzyme. Moreover, HOXC10 co-immunoprecipitates the APC subunit CDC27, and its in vitro degradation is reduced in APC-depleted extracts or by competition with the APC substrate cyclin A. These data imply that HOXC10 is a homeoprotein with the potential to influence mitotic progression, and might provide a link between developmental regulation and cell cycle control.","authors":"Gabellini, D., Colaluca, IN., Vodermaier, HC., Biamonti, G., Giacca, M., Falaschi, A., Riva, S., Peverali, FA.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"EMBO J","volume":"22","issue":"14","page":"3715-24","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11719202","title":"Short- and long-range repulsion by the Drosophila Unc5 netrin receptor.","abstract":"Netrins are bifunctional guidance molecules, attracting some axons and repelling others. They act through receptors of the DCC and UNC5 families. DCC receptors have been implicated in both attraction and repulsion by Netrins. UNC5 receptors are required only for repulsion. In Drosophila, Netrins are expressed by midline cells of the CNS and by specific muscles in the periphery. They attract commissural and motor axons expressing the DCC family receptor Frazzled. Here we report the identification of the Drosophila Unc5 receptor, and show that it is a repulsive Netrin receptor likely to contribute to motor axon guidance. Ectopic expression of Unc5 on CNS axons can elicit either short- or long-range repulsion from the midline. Both short- and long-range repulsion require Netrin function, but only long-range repulsion requires Frazzled.","authors":"Keleman, K., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Neuron","volume":"32","issue":"4","page":"605-17","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11703469","title":"Insulin promotes functional induction of silent synapses in differentiating rat neocortical neurons.","abstract":"Long-term synaptic plasticity is thought to underlie synaptic reorganization phenomena that occur during neocortical development. Recently, it has been proposed, that the functional induction of AMPA receptors at silent glutamatergic synapses is of major importance in activity-dependent, developmental plasticity. To investigate the mechanisms involved in the developmental regulation of silent synapses, we analysed the functional maturation of the thalamocortical projection in culture. A large proportion of the thalamocortical synapses were functionally silent at an early stage in vitro. During further differentiation, the incidence of silent synapses decreased drastically, indicating a conversion of silent into functional synapses. Chronic blockade of spontaneous network activity by addition of tetrodotoxin to the culture medium strongly impaired this developmental maturation. Moreover, the developmental decline in the proportion of silent synapses was dramatically accelerated by chronic addition of the neurotrophic factor, insulin. This effect of insulin was partly dependent on spontaneous activity. Thus, insulin appears to be involved in the modulation of long-term developmental plasticity at immature glutamatergic synapses.","authors":"Plitzko, D., Rumpel, S., Gottmann, K.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Eur J Neurosci","volume":"14","issue":"8","page":"1412-5","pdf":null,"JrId":"2607","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20087860","title":"Overexpression of the oncogenic signal transducer Gab2 occurs early in breast cancer development.","abstract":"Gab2, a docking-type signaling protein with demonstrated oncogenic potential, is overexpressed in breast cancer, but its prognostic significance and role in disease evolution remain unclear. Immunohistochemical detection of Gab2 in a large cohort of primary human breast cancers of known outcome revealed that while Gab2 expression was positively correlated with increased tumor grade, it did not correlate with disease recurrence or breast cancer-related death in the total cohort or in patients stratified according to lymph node, estrogen receptor (ER) or HER2 status. Interestingly, analysis of a \"progression series\" that included premalignant and preinvasive breast lesions as well as samples of metastatic disease revealed that Gab2 expression was significantly enhanced in the earliest lesion examined, usual ductal hyperplasia, with a further increase detected in ductal carcinoma in situ (DCIS). Furthermore, expression was less in invasive cancers and lymph node metastases than in DCIS, but still higher than in normal breast. These findings indicate that while Gab2 expression is not prognostic in breast cancer, its role in early disease evolution warrants further analysis, as Gab2 and its effectors may provide targets for novel strategies aimed at preventing breast cancer development.","authors":"Fleuren, ED., O'Toole, S., Millar, EK., McNeil, C., Lopez-Knowles, E., Boulghourjian, A., Croucher, DR., Schramek, D., Brummer, T., Penninger, JM., Sutherland, RL., Daly, RJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Int J Cancer","volume":"127","issue":"6","page":"1486-92","pdf":null,"JrId":"4284","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12782712","title":"Preferential signaling and induction of allergy-promoting lymphokines upon weak stimulation of the high affinity IgE receptor on mast cells.","abstract":"Mast cell degranulation and de novo cytokine production is a consequence of antigen-aggregation of the immunoglobulin E (IgE)-occupied high affinity receptor for IgE (Fc epsilon RI). Herein, we report that lymphokines that promote allergic inflammation, like MCP-1, were potently induced at low antigen (Ag) concentrations or at low receptor occupancy with IgE whereas some that down-regulate this response, like interleukin (IL)-10, required high receptor occupancy. Weak stimulation of mast cells caused minimal degranulation whereas a half-maximal secretory response was observed for chemokines and, with the exception of TNF-alpha, a weaker cytokine secretory response was observed. The medium from weakly stimulated mast cells elicited a monocyte\/macrophage chemotactic response similar to that observed at high receptor occupancy. Weak stimulation also favored the phosphorylation of Gab2 and p38MAPK, while LAT and ERK2 phosphorylation was induced by a stronger stimulus. Gab2-deficient mast cells were severely impaired in chemokine mRNA induction whereas LAT-deficient mast cells showed a more pronounced defect in cytokines. These findings demonstrate that perturbation of small numbers of IgE receptors on mast cells favors certain signals that contribute to a lymphokine response that can mediate allergic inflammation.","authors":"Gonzalez-Espinosa, C., Odom, S., Olivera, A., Hobson, JP., Martinez, ME., Oliveira-Dos-Santos, A., Barra, L., Spiegel, S., Penninger, JM., Rivera, J.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Exp Med","volume":"197","issue":"11","page":"1453-65","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12771026","title":"Induction of DNA synthesis in primary mouse hepatocytes is associated with nuclear pro-transforming growth factor alpha and erbb-1 and is independent of c-jun.","abstract":"For growth stimulation of liver cells by hepatocyte growth factor (HGF) or transforming growth factor alpha (TGFalpha) via receptor tyrosine kinases, c-fos\/c-jun has been considered a point of intersection for cross-talk between the different signal transduction pathways. Recent evidence strongly implicates translocation of pro-TGFalpha into the nucleus as an important step preceding the initiation of hepatic DNA synthesis. We asked whether an active c-jun is required for the nuclear translocation of pro-TGFalpha and its stimulatory effect on DNA synthesis. For this purpose we used mice with c-jun inactivated post partum in hepatocytes by the Cre-loxP recombination system (c-jun(Deltaliver)). Nuclear fractions from control and c-jun(Deltaliver) mouse livers contained TGFalpha as pro-form of 17 kDa and the epidermal growth factor receptor (erbb-1) with molecular weights of 170 and 150 kDa (truncated form). Hepatocytes were isolated by collagenase perfusion and cultivated. A lack of c-jun did not alter the apoptotic activity but significantly suppressed DNA synthesis in the cultured hepatocytes. In control and c-jun(Deltaliver) cells DNA synthesis was almost always associated with nuclear presence of pro-TGFalpha. 76.5 +\/- 6.8% of hepatocytes with pro-TGFalpha positive nuclei and only 4.52 +\/- 1.31% of hepatocytes with negative nuclei exhibited DNA replication. About 85% of the pro-TGFalpha positive nuclei also contained erbb-1. Treatment of cultures with mature TGFalpha or HGF elevated the frequency of pro-TGFalpha positive nuclei replicating DNA; HGF and TGFalpha-induced nuclear pro-TGFalpha and DNA synthesis significantly more in c-jun(Deltaliver) than in control hepatocytes. These results suggest that (i) a lack of c-jun suppresses basal rates of DNA replication in hepatocytes; (ii) c-jun deficient hepatocytes show a pronounced growth response towards HGF or TGFalpha; (iii) nuclear translocation of pro-TGFalpha together with erbb-1 and its association with DNA synthesis are independent of c-jun.","authors":"Schausberger, E., Eferl, R., Parzefall, W., Chabicovsky, M., Breit, P., Wagner, EF., Schulte-Hermann, R., Grasl-Kraupp, B., Chabikovsky, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Carcinogenesis","volume":"24","issue":"5","page":"835-41","pdf":null,"JrId":"2665","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12706718","title":"Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence.","abstract":"Peroxisomal matrix proteins have to be imported into their target organelle post-translationally. The major translocation pathway depends on a C-terminal targeting signal, termed PTS1. Our previous analysis of sequence variability in the PTS1 motif revealed that, in addition to the known C-terminal tripeptide, at least nine residues directly upstream are important for signal recognition in the PTS1-Pex5 receptor complex. The refined PTS1 motif description was implemented in a prediction tool composed of taxon-specific functions (metazoa, fungi, remaining taxa), capable of recognising potential PTS1s in query sequences. The composite score function consists of classical profile terms and additional terms penalising deviations from the derived physical property pattern over sequence segments. The prediction algorithm has been validated with a self-consistency and three different cross-validation tests. Additionally, we tested the tool on a large set of non-peroxisomal negatives, on mutation data, and compared the prediction rate to the PTS1 component of the PSORT2 program. The sensitivity of our predictor in recognising documented PTS1 signal containing proteins is close to 90% for reliable prediction. The predictor distinguishes even SKL-appended non-peroxisomally targeted proteins such as a mouse dihydrofolate reductase-SKL construct. The corresponding rate of false positives is not worse than 0.8%; thus, the tool can be applied for large-scale unsupervised sequence database annotation. A scan of public protein databases uncovered a number of yet uncharacterised proteins for which the PTS1 signal might be critical for biological function. The predicted presence of a PTS1 signal implies peroxisomal localisation in the absence of N-terminal targeting sequences such as the mitochondrial import signal.","authors":"Neuberger, G., Maurer-Stroh, S., Eisenhaber, B., Hartig, A., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Mol Biol","volume":"328","issue":"3","page":"581-92","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21245337","title":"Membrane lipidome of an epithelial cell line.","abstract":"Tissue differentiation is an important process that involves major cellular membrane remodeling. We used Madin-Darby canine kidney cells as a model for epithelium formation and investigated the remodeling of the total cell membrane lipidome during the transition from a nonpolarized morphology to an epithelial morphology and vice versa. To achieve this, we developed a shotgun-based lipidomics workflow that enabled the absolute quantification of mammalian membrane lipidomes with minimal sample processing from low sample amounts. Epithelial morphogenesis was accompanied by a major shift from sphingomyelin to glycosphingolipid, together with an increase in plasmalogen, phosphatidylethanolamine, and cholesterol content, whereas the opposite changes took place during an epithelial-to-mesenchymal transition. Moreover, during polarization, the sphingolipids became longer, more saturated, and more hydroxylated as required to generate an apical membrane domain that serves as a protective barrier for the epithelial sheet.","authors":"Sampaio, JL., Gerl, MJ., Klose, C., Ejsing, CS., Beug, H., Simons, K., Shevchenko, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Proc Natl Acad Sci U S A","volume":"108","issue":"5","page":"1903-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12456873","title":"On filtering false positive transmembrane protein predictions.","abstract":"While helical transmembrane (TM) region prediction tools achieve high (&gt;90%) success rates for real integral membrane proteins, they produce a considerable number of false positive hits in sequences of known nontransmembrane queries. We propose a modification of the dense alignment surface (DAS) method that achieves a substantial decrease in the false positive error rate. Essentially, a sequence that includes possible transmembrane regions is compared in a second step with TM segments in a sequence library of documented transmembrane proteins. If the performance of the query sequence against the library of documented TM segment-containing sequences in this test is lower than an empirical threshold, it is classified as a non-transmembrane protein. The probability of false positive prediction for trusted TM region hits is expressed in terms of E-values. The modified DAS method, the DAS-TMfilter algorithm, has an unchanged high sensitivity for TM segments ( approximately 95% detected in a learning set of 128 documented transmembrane proteins). At the same time, the selectivity measured over a non-redundant set of 526 soluble proteins with known 3D structure is approximately 99%, mainly because a large number of falsely predicted single membrane-pass proteins are eliminated by the DAS-TMfilter algorithm.","authors":"Cserz\u00f6, M., Eisenhaber, F., Eisenhaber, B., Simon, I.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Protein Eng","volume":"15","issue":"9","page":"745-52","pdf":null,"JrId":"6619","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1234567","title":"The effect of castration and peroral estrogen therapy on some psychological functions.","abstract":null,"authors":"Rauramo, L., Lagerspetz, K., Engblom, P., Punnonen, R.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Front Horm Res","volume":"3","issue":null,"page":"94-104","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1977-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20025329","title":"An integrated approach to NMR spin relaxation in flexible biomolecules: application to beta-D-glucopyranosyl-(1--&gt;6)-alpha-D-mannopyranosyl-OMe.","abstract":"The description of the reorientational dynamics of flexible molecules is a challenging task, in particular when the rates of internal and global motions are comparable. The commonly used simple mode-decoupling models are based on the assumption of statistical independence between these motions. This assumption is not valid when the time scale separation between their rates is small, a situation that was found to arise in oligosaccharides in the context of certain internal motions. To make possible the interpretation of NMR spin relaxation data from such molecules, we developed a comprehensive approach generally applicable to flexible rotators with one internal degree of freedom. This approach integrates a stochastic description of coupled global tumbling and internal torsional motion, quantum chemical calculations of the local potential and the local geometry at the site of the restricted torsion, and hydrodynamics-based calculations of the diffusive properties. The method is applied to the disaccharide beta-D-Glcp-(1--&gt;6)-alpha-D-[6-(13)C]-Manp-OMe dissolved in a DMSO-d(6)\/D(2)O cryosolvent. The experimental NMR relaxation parameters, associated with the (13)CH(2) probe residing at the glycosidic linkage, include (13)C T(1) and T(2) and (13)C-{(1)H} nuclear Overhauser enhancement (NOE) as well as longitudinal and transverse dipole-dipole cross-correlated relaxation rates, acquired in the temperature range of 253-293 K. These data are predicted successfully by the new theory with only the H-C-H angle allowed to vary. Previous attempts to fit these data using mode-decoupling models failed.","authors":"Zerbetto, M., Polimeno, A., Kotsyubynskyy, D., Ghalebani, L., Kowalewski, J., Meirovitch, E., Olsson, U., Widmalm, G.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Chem Phys","volume":"131","issue":"23","page":"234501","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20016617","title":"Photothermal measurement of absorption and scattering losses in thin films excited by surface plasmons.","abstract":"We present a novel noncontact, photothermal technique, based on the focus error signal of a commercial CD pickup head that allows direct determination of absorption in thin films. Combined with extinction methods, this technique yields the scattering contribution to the losses. Surface plasmon polaritons are excited using the Kretschmann configuration in thin Au films of varying thickness. By measuring the extinction and absorption simultaneously, it is shown that dielectric constants and thickness retrieval leads to inconsistencies if the model does not account for scattering.","authors":"Domen\u00e9, EA., Balzarotti, F., Bragas, AV., Mart\u00ednez, OE.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Opt Lett","volume":"34","issue":"24","page":"3797-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11562346","title":"Bidirectional action of the Igf2r imprint control element on upstream and downstream imprinted genes.","abstract":"Imprinting of the maternally-expressed Igf2r gene is controlled by an intronic imprint control element (ICE) known as Region2 that contains the promoter of the noncoding Air RNA, whose transcript overlaps the silenced paternal Igf2r promoter in an antisense orientation. Two novel imprinted genes, Slc22a2 and Slc22a3 are described here that lie 110 and 155 kb 3' to Igf2r and that are not overlapped by the Air transcript but are regulated by the Igf2r-ICE, as previously shown for Igf2r. These results identify a new cluster of imprinted genes whose repression by the bidirectional action of the Region2-ICE is independent of transcript overlap by the Air RNA.","authors":"Zwart, R., Sleutels, F., Wutz, A., Schinkel, AH., Barlow, DP.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Genes Dev","volume":"15","issue":"18","page":"2361-6","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2001-10-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12706717","title":"Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences.","abstract":"Eukaryote peroxisomes, plant glyoxysomes and trypanosomal glycosomes belong to the microbody family of organelles that compartmentalise a variety of biochemical processes. The interaction between the PTS1 signal and its cognate receptor Pex5 initiates the major import mechanism for proteins into the matrix of these organelles. Relying on the analysis of amino acid sequence variability of known PTS1-targeted proteins and PTS1-containing peptides that interact with Pex5 in the yeast two-hybrid assay, on binding site studies of the Pex5-ligand complex crystal structure, 3D models and sequences of Pex5 proteins from various taxa, we derived the requirements for a C-terminal amino acid sequence to interact productively with Pex5. We found evidence that, at least the 12 C-terminal residues of a given substrate protein are implicated in PTS1 signal recognition. This motif can be structurally and functionally divided into three regions: (i) the C-terminal tripeptide, (ii) a region interacting with the surface of Pex5 (about four residues further upstream), and (iii) a polar, solvent-accessible and unstructured region with linker function (the remaining five residues). Specificity differences are confined to taxonomic subgroups (metazoa and fungi) and are connected with amino acid type preferences in region 1 and deviating hydrophobicity patterns in region 2.","authors":"Neuberger, G., Maurer-Stroh, S., Eisenhaber, B., Hartig, A., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Mol Biol","volume":"328","issue":"3","page":"567-79","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11559704","title":"Molecular cloning and characterization of EndoGlyx-1, an EMILIN-like multisubunit glycoprotein of vascular endothelium.","abstract":"EndoGlyx-1, the antigen identified with the monoclonal antibody H572, is a pan-endothelial human cell surface glycoprotein complex composed of four different disulfide-bonded protein species with an apparent molecular mass of approximately 500 kDa. Here, we report the purification and peptide analysis of two EndoGlyx-1 subunits, p125 and p140, and the identification of a common, full-length cDNA with an open reading frame of 2847 base pairs. The EndoGlyx-1 cDNA encodes a protein of 949 amino acids with a predicted molecular mass of 105 kDa, found as an entry for an unnamed protein with unknown function in public data bases. A short sequence tag matching the cDNA of this gene was independently discovered by serial analysis of gene expression profiling as a pan-endothelial marker, PEM87. Bioinformatic evaluation classifies EndoGlyx-1 as an EMILIN-like protein composed of a signal sequence, an N-terminal EMI domain, and a C-terminal C1q-like domain, separated from each other by a central coiled-coil-rich region. Biochemical and carbohydrate analysis revealed that p125, p140, and the two additional EndoGlyx-1 subunits, p110 and p200, are exposed on the cell surface. The three smaller subunits show a similar pattern of N-linked and O-linked carbohydrates, as shown by enzyme digestion. Because the two globular domains of EndoGlyx-1 p125\/p140 show structural features shared by EMILIN-1 and Multimerin, two oligomerizing glycoproteins implicated in cell-matrix adhesion and hemostasis, it will be of interest to explore similar functions for EndoGlyx-1 in human vascular endothelium.","authors":"Christian, S., Ahorn, H., Novatchkova, M., Garin-Chesa, P., Park, JE., Weber, G., Eisenhaber, F., Rettig, WJ., Lenter, MC.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Biol Chem","volume":"276","issue":"51","page":"48588-95","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9521908","title":"Equivalence of the fly orthodenticle gene and the human OTX genes in embryonic brain development of Drosophila.","abstract":"Members of the orthodenticle gene family are essential for embryonic brain development in animals as diverse as insects and mammals. In Drosophila, mutational inactivation of the orthodenticle gene results in deletions in anterior parts of the embryonic brain and in defects in the ventral nerve cord. In the mouse, targeted elimination of the homologous Otx2 or Otx1 genes causes defects in forebrain and\/or midbrain development. To determine the morphogenetic properties and the extent of evolutionary conservation of the orthodenticle gene family in embryonic brain development, genetic rescue experiments were carried out in Drosophila. Ubiquitous overexpression of the orthodenticle gene rescues both the brain defects and the ventral nerve cord defects in orthodenticle mutant embryos; morphology and nervous system-specific gene expression are restored. Two different time windows exist for the rescue of the brain versus the ventral nerve cord. Ubiquitous overexpression of the human OTX1 or OTX2 genes also rescues the brain and ventral nerve cord phenotypes in orthodenticle mutant embryos; in the brain, the efficiency of morphological rescue is lower than that obtained with overexpression of orthodenticle. Overexpression of either orthodenticle or the human OTX gene homologs in the wild-type embryo results in ectopic neural structures. The rescue of highly complex brain structures in Drosophila by either fly or human orthodenticle gene homologs indicates that these genes are interchangeable between vertebrates and invertebrates and provides further evidence for an evolutionarily conserved role of the orthodenticle gene family in brain development.","authors":"Leuzinger, S., Hirth, F., Gerlich, D., Acampora, D., Simeone, A., Gehring, WJ., Finkelstein, R., Furukubo-Tokunaga, K., Reichert, H.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Development","volume":"125","issue":"9","page":"1703-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19952104","title":"Dividing cellular asymmetry: asymmetric cell division and its implications for stem cells and cancer.","abstract":"Cell division is commonly thought to involve the equal distribution of cellular components into the two daughter cells. During many cell divisions, however, proteins, membrane compartments, organelles, or even DNA are asymmetrically distributed between the two daughter cells. Here, we review the various types of asymmetries that have been described in yeast and in animal cells. Asymmetric segregation of protein determinants is particularly relevant for stem cell biology. We summarize the relevance of asymmetric cell divisions in various stem cell systems and discuss why defects in asymmetric cell division can lead to the formation of tumors.","authors":"Neum\u00fcller, RA., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genes Dev","volume":"23","issue":"23","page":"2675-99","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11554494","title":"Lack of sequence variation in sporadic bovine leucosis in regions of tumour suppressor genes p53 and p16.","abstract":"Regions of the promoter and exons 5-8 of the tumour suppressor gene p53 were analysed in 25 cases of sporadic bovine leucosis. The study included 17 cases of juvenile leucosis, five cases of adult leucosis and three cases of skin leucosis. Exon 2 of tumour suppressor gene p16 was also investigated in the same samples. No sequence variations were present in the analysed areas of the genes. In p53, this fact represents a clear difference in comparison with enzootic bovine leucosis. In p16, no comparative data are available.","authors":"Mayr, B., Gr\u00fcneis, C., Brem, G., Reifinger, M., Schaffner, G., Hochsteiner, W.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Vet Med A Physiol Pathol Clin Med","volume":"48","issue":"6","page":"365-71","pdf":null,"JrId":"21739","fulltextlink":null,"preprintlink":null,"articledate":"2001-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19934782","title":"Combining functional magnetic resonance imaging with mouse genomics: new options in pain research.","abstract":"This functional magnetic imaging study investigated the functional implications of genetic modification and pharmacological intervention on cerebral processing of heat-induced nociception in mice. Comparing dynorphin-overexpressing dream(-\/-) with wild-type mice, smaller activated cortical and limbic brain structure sizes could be observed. Moreover, significantly reduced blood oxygenation level-dependent signal amplitudes were found in pain-related brain structures: sensory input, thalamic regions, sensory cortex, limbic system, basal ganglia, hypothalamus and periaqueductal grey. Administration of the specific kappa-opioid-receptor antagonist nor-binaltorphimine to dream(-\/-) mice reversed this reduction to wild-type level in the same brain structures. These results show that blood oxygenation level-dependent functional magnetic imaging in the pain system of (transgenic) mice is feasible. Genetic modifications and pharmacological interventions modify brain responses in a structure-specific manner.","authors":"Heindl-Erdmann, C., Axmann, R., Kreitz, S., Zwerina, J., Penninger, J., Schett, G., Brune, K., Hess, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Neuroreport","volume":"21","issue":"1","page":"29-33","pdf":null,"JrId":"1199","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11509732","title":"Cohesin cleavage by separase required for anaphase and cytokinesis in human cells.","abstract":"Cell division depends on the separation of sister chromatids in anaphase. In yeast, sister separation is initiated by cleavage of cohesin by the protease separase. In vertebrates, most cohesin is removed from chromosome arms by a cleavage-independent mechanism. Only residual amounts of cohesin are cleaved at the onset of anaphase, coinciding with its disappearance from centromeres. We have identified two separase cleavage sites in the human cohesin subunit SCC1 and have conditionally expressed noncleavable SCC1 mutants in human cells. Our results indicate that cohesin cleavage by separase is essential for sister chromatid separation and for the completion of cytokinesis.","authors":"Hauf, S., Waizenegger, IC., Peters, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Science","volume":"293","issue":"5533","page":"1320-3","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9029148","title":"The glucocorticoid receptor is a key regulator of the decision between self-renewal and differentiation in erythroid progenitors.","abstract":"During development and in regenerating tissues such as the bone marrow, progenitor cells constantly need to make decisions between proliferation and differentiation. We have used a model system, normal erythroid progenitors of the chicken, to determine the molecular players involved in making this decision. The molecules identified comprised receptor tyrosine kinases (c-Kit and c-ErbB) and members of the nuclear hormone receptor superfamily (thyroid hormone receptor and estrogen receptor). Here we identify the glucocorticoid receptor (GR) as a key regulator of erythroid progenitor self-renewal (i.e. continuous proliferation in the absence of differentiation). In media lacking a GR ligand or containing a GR antagonist, erythroid progenitors failed to self-renew, even if c-Kit, c-ErbB and the estrogen receptor were activated simultaneously. To induce self-renewal, the GR required the continuous presence of an activated receptor tyrosine kinase and had to cooperate with the estrogen receptor for full activity. Mutant analysis showed that DNA binding and a functional AF-2 transactivation domain are required for proliferation stimulation and differentiation arrest. c-myb was identified as a potential target gene of the GR in erythroblasts. It could be demonstrated that delta c-Myb, an activated c-Myb protein, can functionally replace the GR.","authors":"Wessely, O., Deiner, EM., Beug, H., von Lindern, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"EMBO J","volume":"16","issue":"2","page":"267-80","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"39354071","title":"Modelling and deciphering tumour metabolism in CRISPR screens.","abstract":null,"authors":"Zuber, J., Palm, W.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nat Rev Cancer","volume":"25","issue":"1","page":"1-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-00-01","doi":"10.1038\/s41568-024-00758-8","first_author":null,"corresponding_authors":null},{"pmid":"12640676","title":"Profile of gene expression induced by the tumour promotor TPA in murine epithelial cells.","abstract":"Malignant transformation of mouse skin by chemical carcinogens and tumour promoters, such as the phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA), is a multistage process that leads to squamous cell carcinoma (SCC) formation. In an effort to identify tumour-associated genes, we studied the influence of short-term TPA-treatment on the gene expression profile of murine skin. A comprehensive microarray with some 5,000 murine gene specific cDNA fragments was established and hybridised with pooled RNA derived from control and TPA-treated dorsal skin samples. Of these genes, 54 were up- and 35 were down-regulated upon TPA application. Additionally, we performed suppression subtractive hybridisation (SSH) with respective RNA pools to generate and analyse a cDNA library enriched for TPA-inducible genes. Expression data of selected genes were confirmed by quantitative real-time PCR and Northern blot analysis. Comparison of microarray and SSH data revealed that 26% of up-regulated genes identified by expression profiling matched with those present in the SSH library. Besides numerous known genes, we identified a large set of unknown cDNAs that represent previously unrecognised TPA-regulated genes in murine skin with potential function in tumour promotion. Additionally, some TPA-induced genes, such as Sprr1A, Saa3, JunB, Il4ralpha, Gp38, RalGDS and Slpi exhibit high basal level in advanced stages of skin carcinogenesis, suggesting that at least a subgroup of the identified TPA-regulated genes may contribute to tumour progression and metastasis.","authors":"Schlingemann, J., Hess, J., Wrobel, G., Breitenbach, U., Gebhardt, C., Steinlein, P., Kramer, H., F\u00fcrstenberger, G., Hahn, M., Angel, P., Lichter, P.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Int J Cancer","volume":"104","issue":"6","page":"699-708","pdf":null,"JrId":"4284","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12614352","title":"Thymic selection revisited: how essential is it?","abstract":"Intrathymic T cell development represents one of the best studied paradigms of mammalian development. Lymphoid committed precursors enter the thymus and the Notch1 receptor plays an essential role in committing them to the T cell lineages. The pre-T cell receptor (TCR), as an autonomous cell signaling receptor, commits cells to the alphabeta lineage while its rival, the gammadeltaTCR, is involved in generating the gammadelta lineage of T cells. Positive and negative selection of immature alphabetaTCR-expressing cells are essential mechanisms for generating mature T cells, committing them to the CD4 and CD8 lineages and avoiding autoimmunity. Additional lineages of alphabetaT cells, such as the natural killer T cell lineage and the CD25+ regulatory T cell lineage, are formed when the alphabetaTCR encounters specific ligands in suitable microenvironments. Thus, positive selection and receptor-instructed lineage commitment represent a hallmark of the thymus. Ectopically expressed organ-specific antigens contribute to thymic self-nonself discrimination, which represents an essential feature for the evolutionary fitness of mammalian species.","authors":"von Boehmer, H., Aifantis, I., Gounari, F., Azogui, O., Haughn, L., Apostolou, I., Jaeckel, E., Grassi, F., Klein, L.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Immunol Rev","volume":"191","issue":null,"page":"62-78","pdf":null,"JrId":"4161","fulltextlink":null,"preprintlink":null,"articledate":"2003-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12553907","title":"Liver tumor development. c-Jun antagonizes the proapoptotic activity of p53.","abstract":"The transcription factor c-Jun mediates several cellular processes, including proliferation and survival, and is upregulated in many carcinomas. Liver-specific inactivation of c-Jun at different stages of tumor development was used to study its role in chemically induced hepatocellular carcinomas (HCCs) in mice. The requirement for c-jun was restricted to early stages of tumor development, and the number and size of hepatic tumors was dramatically reduced when c-jun was inactivated after the tumor had initiated. The impaired tumor development correlated with increased levels of p53 and its target gene noxa, resulting in the induction of apoptosis without affecting cell proliferation. Primary hepatocytes lacking c-Jun showed increased sensitivity to TNF-alpha-induced apoptosis, which was abrogated in the absence of p53. These data indicate that c-Jun prevents apoptosis by antagonizing p53 activity, illustrating a mechanism that might contribute to the early stages of human HCC development.","authors":"Eferl, R., Ricci, R., Kenner, L., Zenz, R., David, JP., Rath, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cell","volume":"112","issue":"2","page":"181-92","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2003-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21460858","title":"Interstitial lung disease induced by gefitinib and toll-like receptor ligands is mediated by Fra-1.","abstract":"The role of the AP-1 transcription factor Fra-1 (encoded by Fosl1) in inflammatory responses associated with lung disease is largely unknown. Here, we show that Fra-1 overexpression in mice reduced proinflammatory cytokine production in response to injection of lipopolysaccharide (LPS), a Toll-like receptor (TLR)-ligand. Unexpectedly, Fra-1 transgenic mice died rapidly following LPS treatment, showing severe interstitial lung disease and displaying massive accumulation of macrophages and overproduction of several chemokines, including macrophage chemoattractant protein-1 (MCP-1, encoded by Ccl2). To assess the clinical relevance of Fra-1 in lung pathology, mice were treated with the anticancer drug gefitinib (Iressa), which can lead to interstitial lung disease in patients. Gefitinib-treated mice showed increased Fosl1 and Ccl2 expression and developed interstitial lung disease in response to LPS, endogenous TLR ligands and chemotherapy. Moreover, deletion of Fra-1 or blocking MCP-1 receptor signaling in mice attenuated gefitinib-enhanced lethality in response to LPS. Importantly, human alveolar macrophages showed enhanced LPS-induced FOSL1 and CCL2 expression after gefitinib treatment. These results indicate that Fra-1 is an important mediator of interstitial lung disease following gefitinib treatment.","authors":"Takada, Y., Gresh, L., Bozec, A., Ikeda, E., Kamiya, K., Watanabe, M., Kobayashi, K., Asano, K., Toyama, Y., Wagner, EF., Matsuo, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Oncogene","volume":"30","issue":"36","page":"3821-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-11-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12546794","title":"Evolution of eukaryotic cell cycle regulation: stepwise addition of regulatory kinases and late advent of the CDKs.","abstract":"Protein kinases regulate a number of critical events in mitosis and meiosis. A study of the evolution of kinases involved in cell cycle control (CCC) might shed light on the evolution of the eukaryotic cell cycle. In particular, applying quantitative phylogenetic methods to key CCC kinases could provide information on the relative timing of gene duplication events. To investigate the evolution of CCC kinases, we constructed phylogenetic trees for the CDC28 family and performed statistical tests of the tree topology. This family includes the cyclin-dependent kinases (CDKs), which are key regulators of the eukaryotic cell cycle, as well as other CCC kinases. We found that CDKs and, in particular, the principal cell cycle regulator Cdc28p, branch off the phylogenetic tree at a late stage, after several other kinases involved in either mitosis or meiosis regulation. On the basis of this tree topology, it is proposed that, at early stages of evolution, the eukaryotic cell cycle was not controlled by CDKs and that only a subset of extant kinases, notably the DNA damage checkpoint kinase Chk1p, were in place. During subsequent evolution, a series of duplications of kinase genes occurred, gradually adding more kinases to the CCC system, the CDKs being among the last major additions.","authors":"Krylov, DM., Nasmyth, K., Koonin, EV.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"2","page":"173-7","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12441295","title":"Impaired intervertebral disc formation in the absence of Jun.","abstract":"Jun is a major component of the heterodimeric transcription factor AP-1 and is essential for embryonic development, as foetuses that lack Jun die at mid-gestation. Ubiquitous mosaic inactivation of a conditional Jun allele by cre\/LoxP-mediated recombination was used to screen for novel functions of Jun and revealed that its absence results in severe malformations of the axial skeleton. More-specific Jun deletion by collagen2a1-cre demonstrated the essential function of Jun in the notochord and sclerotome. Mutant notochordal cells showed increased apoptosis, resulting in hypocellularity of the intervertebral discs. Subsequently, fusion of vertebral bodies caused a scoliosis of the axial skeleton. Thus, Jun is required for axial skeletogenesis by regulating notochord survival and intervertebral disc formation.","authors":"Behrens, A., Haigh, J., Mechta-Grigoriou, F., Nagy, A., Yaniv, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Development","volume":"130","issue":"1","page":"103-9","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2003-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11406393","title":"The Brix domain protein family -- a key to the ribosomal biogenesis pathway?","abstract":"Six (one archaean and five eukaryotic) protein families have similar domain architecture that includes a central globular Brix domain, and optional N- and obligatory C-terminal segments, both with charged low-complexity regions. Biological data for some proteins in this superfamily suggest a role in ribosome biogenesis and rRNA binding.","authors":"Eisenhaber, F., Wechselberger, C., Kreil, G.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Trends Biochem Sci","volume":"26","issue":"6","page":"345-7","pdf":null,"JrId":"7837","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12435636","title":"Nephric lineage specification by Pax2 and Pax8.","abstract":"The mammalian kidney develops in three successive steps from the initial pronephros via the mesonephros to the adult metanephros. Although the nephric lineage is specified during pronephros induction, no single regulator, including the transcription factor Pax2 or Pax8, has yet been identified to control this initial phase of kidney development. In this paper, we demonstrate that mouse embryos lacking both Pax2 and Pax8 are unable to form the pronephros or any later nephric structures. In these double-mutant embryos, the intermediate mesoderm does not undergo the mesenchymal-epithelial transitions required for nephric duct formation, fails to initiate the kidney-specific expression of Lim1 and c-Ret, and is lost by apoptosis 1 d after failed pronephric induction. Conversely, retroviral misexpression of Pax2 was sufficient to induce ectopic nephric structures in the intermediate mesoderm and genital ridge of chick embryos. Together, these data identify Pax2 and Pax8 as critical regulators that specify the nephric lineage.","authors":"Bouchard, M., Souabni, A., Mandler, M., Neub\u00fcser, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Genes Dev","volume":"16","issue":"22","page":"2958-70","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12419187","title":"GTP binding induces filament assembly of a recombinant septin.","abstract":"The septins are a family of GTPases involved in cytokinesis in budding yeast, Drosophila, and vertebrates (see for review). Septins are associated with a system of 10 nm filaments at the S. cerevisiae bud neck, and heteromultimeric septin complexes have been isolated from cell extracts in a filamentous state. A number of septins have been shown to bind and hydrolyze guanine nucleotide. However, the role of GTP binding and hydrolysis in filament formation has not been elucidated. Furthermore, several lines of evidence suggest that not all the subunits of the septin complex are required for all aspects of septin function. To address these questions, we have reconstituted filament assembly in vitro by using a recombinant Xenopus septin, Xl Sept2. Filament assembly is GTP dependent; moreover, the coiled-coil domain common to most septins is not essential for filament formation. Septin polymerization is preceded by a lag phase, suggesting a cooperative assembly mechanism. The slowly hydrolyzable GTP analog, GTP-gamma-S, also induces polymerization, indicating that polymerization does not require GTP hydrolysis. If the properties of Xl Sept2 filaments reflect those of native septin complexes, these results imply that the growth or stability of septin filaments, or both, is regulated by the state of bound nucleotide.","authors":"Mendoza, M., Hyman, AA., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"21","page":"1858-63","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19926510","title":"Rheumatic diseases: environment and genetics.","abstract":"Rheumatology deals with many different entities among which dys\/autoimmune diseases occupy a position of preponderance. This review focuses on the concept of complex genetic disease, which is illustrated by three different chronic inflammatory joint diseases: rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis. Genetic studies have established that a common genetic background is shared by many autoimmune disorders. Interestingly, although common genetic factors are shared by diseases that produce different phenotypes, risk variants can exert a strong influence on the phenotype of a given disease. Genetics cannot fully explain the determinism of complex genetic diseases. Future genetic studies must incorporate data on exposure to potential environmental factors. The next step in unravelling complex genetic diseases will involve investigations not only of gene-gene and gene-environment interactions, but also of epigenetics, defined as transmissible and reversible changes in gene expression that are not related to changes in the DNA sequence. The past decade has witnessed an impressive accumulation of data on the determinism of complex diseases, and the next will probably bring further insights into the pathophysiology of dys\/autoimmune diseases.","authors":"Dieud\u00e9, P.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Joint Bone Spine","volume":"76","issue":"6","page":"602-7","pdf":null,"JrId":"21697","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11371343","title":"Phosphorylation of the cohesin subunit Scc1 by Polo\/Cdc5 kinase regulates sister chromatid separation in yeast.","abstract":"At the onset of anaphase, a caspase-related protease (separase) destroys the link between sister chromatids by cleaving the cohesin subunit Scc1. During most of the cell cycle, separase is kept inactive by binding to an inhibitory protein called securin. Separase activation requires proteolysis of securin, which is mediated by an ubiquitin protein ligase called the anaphase-promoting complex. Cells regulate anaphase entry by delaying securin ubiquitination until all chromosomes have attached to the mitotic spindle. Though no longer regulated by this mitotic surveillance mechanism, sister separation remains tightly cell cycle regulated in yeast mutants lacking securin. We show here that the Polo\/Cdc5 kinase phosphorylates serine residues adjacent to Scc1 cleavage sites and strongly enhances their cleavage. Phosphorylation of separase recognition sites may be highly conserved and regulates sister chromatid separation independently of securin.","authors":"Alexandru, G., Uhlmann, F., Mechtler, K., Poupart, MA., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell","volume":"105","issue":"4","page":"459-72","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12379619","title":"Functions of AP1 (Fos\/Jun) in bone development.","abstract":"Genetically modified mice and cells have provided important insights into the biological functions of the dimeric transcription factor complex AP1, in particular into its role in skeletal development. Data obtained from knockout mice revealed that some components, such as c-Fos are key regulators of bone cell differentiation, whereas others, like c-Jun, JunB and Fra-1 are essential in embryonic and\/or postnatal development. Apart from identifying the specific roles of AP1 proteins in developmental processes, researchers are beginning to obtain a better molecular understanding of their cell-context dependent functions, their downstream target genes and how they regulate bone cell proliferation, differentiation, and apoptosis.","authors":"Wagner, EF.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Ann Rheum Dis","volume":"61 Suppl 2","issue":null,"page":"ii40-2","pdf":null,"JrId":"640","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12376563","title":"JNK1 modulates osteoclastogenesis through both c-Jun phosphorylation-dependent and -independent mechanisms.","abstract":"Phosphorylation of the N-terminal domain of Jun by the Jun kinases (JNKs) modulates the transcriptional activity of AP-1, a dimeric transcription factor typically composed of c-Jun and c-Fos, the latter being essential for osteoclast differentiation. Using mice lacking JNK1 or JNK2, we demonstrate that JNK1, but not JNK2, is specifically activated by the osteoclast-differentiating factor RANKL. Activation of JNK1, but not JNK2, is required for efficient osteoclastogenesis from bone marrow monocytes (BMMs). JNK1 protects BMMs from RANKL-induced apoptosis during differentiation. In addition, BMMs from mice carrying a mutant of c-Jun phosphorylation sites (JunAA\/JunAA), as well as cells lacking either c-Jun or JunD, which is another JNK substrate, revealed that c-Jun phosphorylation and c-Jun itself, but not JunD, are essential for efficient osteoclastogenesis. Moreover, JNK1-dependent c-Jun phosphorylation in response to RANKL is not involved in the anti-apoptotic function of JNK1. Thus, these data provide genetic evidence that JNK1 activation modulates osteoclastogenesis through both c-Jun-phosphorylation-dependent and -independent mechanisms.","authors":"David, JP., Sabapathy, K., Hoffmann, O., Idarraga, MH., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Cell Sci","volume":"115","issue":"Pt 22","page":"4317-25","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12324217","title":"Mechanisms of muscle dedifferentiation during regeneration.","abstract":"For many years people have known that amphibians have an amazing ability to regenerate lost body parts. In contrast humans have limited regeneration capacity and even simple wound healing results in scarring. Despite more than a century of scientific inquiry, this remarkable phenomenon remains poorly understood. Recent research has begun to provide insight into how this unique process that is now fully accepted to occur via the reversal of cell differentiation is executed at the molecular level. As more and more is known about regeneration and dedifferentiation we can begin to address the question: if given the right signals could mammals also regenerate body structures?","authors":"Echeverri, K., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Semin Cell Dev Biol","volume":"13","issue":"5","page":"353-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12237450","title":"A CH domain-containing N terminus in NuMA?","abstract":"Nuclear mitotic apparatus protein (NuMA) is an essential vertebrate component in organizing microtubule ends at spindle poles. The NuMA-dynactin\/dynein motor multiprotein complex not only explains the transport of NuMA along spindle fibers but also is linked to the process of microtubule focusing. The interaction sites of NuMA to dynein\/dynactin have not been mapped. In the yet functionally uncharacterized N terminus of NuMA, we predict a calponin-homology (CH) domain, a motif with binding activity for actin-like molecules. We substantiate the primary sequence analysis-based prediction with secondary structure and fold recognition analysis, and we propose the N-terminal CH domain of NuMA as a likely interaction site for actin-related protein 1 (Arp1) protein of the dynactin\/dynein complex.","authors":"Novatchkova, M., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Protein Sci","volume":"11","issue":"10","page":"2281-4","pdf":null,"JrId":"2312","fulltextlink":null,"preprintlink":null,"articledate":"2003-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12235286","title":"Reorganization and polarization of the meiotic bouquet-stage cell can be uncoupled from telomere clustering.","abstract":"Striking cellular reorganizations mark homologous pairing during meiotic prophase. We address the interdependence of chromosomal and cellular polarization during meiotic telomere clustering, the defining feature of the bouquet stage, by examining nuclear positioning and microtubule and nuclear pore reorganization. Polarization of meiotic cellular architecture was coincident with telomere clustering: microtubules were focused on the nuclear surface opposite the telomere cluster, the nucleus was positioned eccentrically in the cell such that the telomeres faced the direction of nuclear displacement and nuclear pores were clustered in a single region of the nuclear surface opposite the telomeres. Treatment of pre-bouquet stage cells with colchicine inhibited telomere clustering. Asymmetric nuclear positioning and nuclear pore clustering were normal in the presence of unclustered telomeres resulting from colchicine treatment. Nuclear pores were positioned normally with respect to the cell cortex in the absence of telomere clustering, indicating that telomere positioning is not required for polarization. This work provides evidence of meiotic cell polarization and suggests that telomeres may be positioned relative to an asymmetry present in the cell at the time of bouquet formation.","authors":"Cowan, CR., Carlton, PM., Cande, WZ.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Cell Sci","volume":"115","issue":"Pt 19","page":"3757-66","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2003-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11336713","title":"Three-dimensional structure of the anaphase-promoting complex.","abstract":"The anaphase-promoting complex (APC) is a cell cycle-regulated ubiquitin-protein ligase, composed of at least 11 subunits, that controls progression through mitosis and G1. Using cryo-electron microscopy and angular reconstitution, we have obtained a three-dimensional model of the human APC at a resolution of 24 A. The APC has a complex asymmetric structure 140 A x 140 A x 135 A in size, in which an outer protein wall surrounds a large inner cavity. We discuss the possibility that this cavity represents a reaction chamber in which ubiquitination reactions take place, analogous to the inner cavities formed by other protein machines such as the 26S proteasome and chaperone complexes. This cage hypothesis could help to explain the great subunit complexity of the APC.","authors":"Gieffers, C., Dube, P., Harris, JR., Stark, H., Peters, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Mol Cell","volume":"7","issue":"4","page":"907-13","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12213570","title":"The c-Jun N-terminal kinases in cerebral microglia: immunological functions in the brain.","abstract":"The c-Jun N-terminal kinases (JNKs) exert a pleiotrophy of physiological and pathological actions. This is also true for the immune system. Disruption of the JNK locus results in substantial functional deficits of peripheral T-cells. In contrast to circulating immune cells and the role of p38, the presence and function of JNKs in the immune cells of the brain remain to be defined. Here, we report on the expression and activation of JNKs in cultivated microglia from neonatal rats and from mice with targeted disruption of the JNK locus and the N-terminal mutation of c-Jun (c-JunAA), respectively. JNK1, 2 and 3 mRNA and proteins were all expressed in microglia. Following stimulation with LPS (100 ng\/mL), a classical activator of microglia, JNKs were rapidly activated and this activation returns to basal levels within 4 hr. Following LPS and other stimuli such as thrombin (10-50 unit\/mL), the activation of JNKs went along with the N-terminal phosphorylation of c-Jun which persisted for at least 8 hr. Indirect inhibition of JNK by CEP-11004 (0.5-2 microM), an inhibitor of mixed-lineage kinases (MLK), reduced the LPS-induced phosphorylation of both, JNK and c-Jun, by around 50%, and attentuated the LPS-induced the alterations in microglial morphology. Finally, JNKs are involved in the control of cytokine release since both, incubation with CEP-11004 and disruption of the JNK1 locus enhanced the release of TNFalpha, IL-6 and IL-12. Our findings provide insight in so far unknown functions of JNKs in cerebral immune cells. These observations are also important for the wide spread efforts to develop JNK-inhibitors as neuroprotective drugs which, however, might trigger pro-inflammatory processes.","authors":"Hidding, U., Mielke, K., Waetzig, V., Brecht, S., Hanisch, U., Behrens, A., Wagner, E., Herdegen, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Biochem Pharmacol","volume":"64","issue":"5-6","page":"781-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19917252","title":"Hierarchical rules for Argonaute loading in Drosophila.","abstract":"Drosophila Argonaute-1 and Argonaute-2 differ in function and small RNA content. AGO2 binds to siRNAs, whereas AGO1 is almost exclusively occupied by microRNAs. MicroRNA duplexes are intrinsically asymmetric, with one strand, the miR strand, preferentially entering AGO1 to recognize and regulate the expression of target mRNAs. The other strand, miR*, has been viewed as a byproduct of microRNA biogenesis. Here, we show that miR*s are often loaded as functional species into AGO2. This indicates that each microRNA precursor can potentially produce two mature small RNA strands that are differentially sorted within the RNAi pathway. miR* biogenesis depends upon the canonical microRNA pathway, but loading into AGO2 is mediated by factors traditionally dedicated to siRNAs. By inferring and validating hierarchical rules that predict differential AGO loading, we find that intrinsic determinants, including structural and thermodynamic properties of the processed duplex, regulate the fate of each RNA strand within the RNAi pathway.","authors":"Czech, B., Zhou, R., Erlich, Y., Brennecke, J., Binari, R., Villalta, C., Gordon, A., Perrimon, N., Hannon, GJ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Cell","volume":"36","issue":"3","page":"445-56","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11306551","title":"Perturbation of the tight junction permeability barrier by occludin loop peptides activates beta-catenin\/TCF\/LEF-mediated transcription.","abstract":"Here we show that interference with the integrity of the transepithelial permeability barrier of mouse mammary epithelial cells by treatment with synthetic peptides, homologous to the second extracellular domain of occludin, decreased the amount of occludin protein present at tight junctions and led to the formation of multilayered, unpolarized cell clusters. In addition, transcription of the adherens junction protein beta-catenin was induced. Following accumulation of soluble beta-catenin protein, transcription by beta-catenin\/TCF\/LEF was increased, as revealed by transcriptional assays following transient transfection of the reporter construct. Furthermore, treatment with occludin-II peptides up-regulated RNA levels of the known beta-catenin\/TCF\/LEF downstream target gene c-myc. The data presented imply a functional cross-talk between tight and adherens junctions that possibly contributes to the stepwise transformation during oncogenesis.","authors":"Vietor, I., Bader, T., Paiha, K., Huber, LA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"EMBO Rep","volume":"2","issue":"4","page":"306-12","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11287197","title":"Cloning and expression of a novel cysteine-rich secreted protein family member expressed in thyroid and pancreatic mesoderm within the chicken embryo.","abstract":"We have isolated a new chicken gene that is a member of the cysteine-rich secreted protein family (CRISP). The CRISP family is composed of over 70 members that are found in many phyla of organisms, including: vertebrates, plants, fungi, yeast, and insects. Here we describe the cloning of a novel member of this family, SugarCrisp, and its expression pattern throughout chicken embryogenesis. We also describe its utility as a marker of thyroid and pancreatic mesoderm in the developing chicken embryo and its expression within the human and mouse in glandular tissue.","authors":"Smith, DM., Collins-Racie, LA., Marigo, VA., Roberts, DJ., Davis, NM., Hartmann, C., Schweitzer, R., LaVallie, ER., Gamer, L., McCoy, J., Tabin, CJ.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Mech Dev","volume":"102","issue":"1-2","page":"223-6","pdf":null,"JrId":"1825","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12206776","title":"Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis.","abstract":"Pyridoxine 5'-phosphate (PNP) synthase is the last enzyme in the de novo biosynthesis of vitamin B(6) catalyzing the complicated ring-closure reaction between 1-deoxy-D-xylulose-5-phosphate and 1-amino-acetone-3-phosphate. Here we present the crystal structures of four PNP synthase complexes with substrates and substrate analogs. While the overall fold of the enzyme is conserved in all complexes, characteristic readjustments were observed in the active site. The complementary structural information allowed us to postulate a detailed reaction mechanism. The observed binding mode of substrates indicates how the first reaction intermediate, the Schiff-base conjugate, is formed. The most important mechanistic features are the presence of two phosphate-binding sites with distinct affinities and the existence of a water relay system for the release of reaction water molecules. Furthermore, the complexes provide the basis to rationalize the open-closed transition of a flexible loop located on the C-terminal side of the TIM-barrel. Binding of both substrate molecules to the active site seems to be a prerequisite to trigger this transition. Highly conserved mechanistically important residues in the PNP synthase family imply a similar active site organization and reaction mechanism for all family members. Due to the exclusive presence of PNP synthase in a subset of eubacteria, including several well-known pathogens, and due to its outstanding physiological importance for these organisms, the enzyme appears to be a promising novel target for antibacterial drug design.","authors":"Garrido-Franco, M., Laber, B., Huber, R., Clausen, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Mol Biol","volume":"321","issue":"4","page":"601-12","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"48","title":"Monoanion inhibition and 35Cl nuclear magnetic resonance studies of renal dipeptidase.","abstract":"Kinetic analyses of monoanion inhibition and 15Cl nuclear magnetic resonance at 5.88 MHz were employed to study monoanion interactions with the zinc metalloenzyme, renal dipeptidase. The enzyme-catalyzed hydrolysis of glycyldehydrophenylalanine exhibited competitive inhibition when the reaction rate was determined in the presence of the monovalent anions fluoride, chloride, bromide, iodide, azide, nitrate, or thiocyanate or upon the addition of the divalent anion, sulfate. Competitive inhibition was produced by these anions. One anion was bound per enzyme molecule, and except in the case of fluoride all of the anions appeared to bind at the same site. Cyanide ion produced a much more effective inhibition of renal dipeptidase than the other monoanions, and it was shown that two cyanide ions were bound per enzyme molecule. An investigation of the effect of pH upon monoanion inhibition suggested that the anion inhibitors bind to the group with a pK of approximately 7.8. Complete dissociation of this group (approximately pH 8.4) eliminates the inhibitory effect of anions. The 35Cl line broadening produced by renal dipeptidase in 0.5 M NaCl solutions was 100 times more effective than that produced by equivalent concentrations of aquozinc(II). The line broadening was dependent upon the concentration of the metalloenzyme and independent of the frequency of the exciting radiation. When zinc ion was removed from the metalloenzyme by dialysis or when chloride was titrated from the metalloenzyme by cyanide, line broadening was decreased. Treatment of renal dipeptidase with saturating concentrations of the competitive inhibitor, guanosine triphosphate, in the presence of 0.5 M NaCl also produced a significant decrease in the 35Cl line width. The 35Cl line broadening produced by renal dipeptidase was shown to decrease with increasing pH through the range pH 5.8-10.8. This line-width variation with pH appeared to result from the titration of a site on the metalloprotein with an approximate pK of 7.4. Temperature studies of 35Cl line broadening by the metalloenzyme in the presence of chloride and cyanide inhibitors suggest that the fast exchange process pertains and that the dominant relaxation mechanism is quadrupolar in nature.","authors":"Ferren, LG., Ward, RL., Campbell, BJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"24","page":"5280-5","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11199207","title":"Comparative studies in the promoter and exon 1 regions of tumour suppressor p53 in several mammalian species: absence of mutations in a panel of spontaneous domestic animal tumours.","abstract":"Tumour suppressor p53 is critical in a broad panel of tumour types in human, mouse and other mammals. Regions of the promoter and exon 1 play an important role in expression of p53. In the present study, the DNA sequences of promoter and exon 1 regions of four domestic animal species (dog, cat, horse and cattle) are determined and compared with experimental rodents (mouse, rat and hamster) and man. A broad panel of tumour types have been investigated for mutations in this regulatory area in 90 canine, 136 feline, 25 equine and 10 bovine patients. No mutation was detected in any of the tumours analysed.","authors":"Mayr, B., Resch, S., Hepperle, S., Brem, G., Reifinger, M., Schaffner, G.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Vet Med A Physiol Pathol Clin Med","volume":"47","issue":"10","page":"593-7","pdf":null,"JrId":"21739","fulltextlink":null,"preprintlink":null,"articledate":"2001-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22855833","title":"Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena.","abstract":"The ciliated protozoan Tetrahymena undergoes extensive programmed DNA elimination when the germline micronucleus produces the new macronucleus during sexual reproduction. DNA elimination is epigenetically controlled by DNA sequences of the parental macronuclear genome, and this epigenetic regulation is mediated by small RNAs (scan RNAs [scnRNAs]) of \u223c28-30 nucleotides that are produced and function by an RNAi-related mechanism. Here, we examine scnRNA production and turnover by deep sequencing. scnRNAs are produced exclusively from the micronucleus and nonhomogeneously from a variety of chromosomal locations. scnRNAs are preferentially derived from the eliminated sequences, and this preference is mainly determined at the level of transcription. Despite this bias, a significant fraction of scnRNAs is also derived from the macronuclear-destined sequences, and these scnRNAs are degraded during the course of sexual reproduction. These results indicate that the pattern of DNA elimination in the new macronucleus is shaped by the biased transcription in the micronucleus and the selective degradation of scnRNAs in the parental macronucleus.","authors":"Schoeberl, UE., Kurth, HM., Noto, T., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genes Dev","volume":"26","issue":"15","page":"1729-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23776409","title":"Co-expression of VAL- and TMT-opsins uncovers ancient photosensory interneurons and motorneurons in the vertebrate brain.","abstract":"The functional principle of the vertebrate brain is often paralleled to a computer: information collected by dedicated devices is processed and integrated by interneuron circuits and leads to output. However, inter- and motorneurons present in today's vertebrate brains are thought to derive from neurons that combined sensory, integration, and motor function. Consistently, sensory inter-motorneurons have been found in the simple nerve nets of cnidarians, animals at the base of the evolutionary lineage. We show that light-sensory motorneurons and light-sensory interneurons are also present in the brains of vertebrates, challenging the paradigm that information processing and output circuitry in the central brain is shielded from direct environmental influences. We investigated two groups of nonvisual photopigments, VAL- and TMT-Opsins, in zebrafish and medaka fish; two teleost species from distinct habitats separated by over 300 million years of evolution. TMT-Opsin subclasses are specifically expressed not only in hypothalamic and thalamic deep brain photoreceptors, but also in interneurons and motorneurons with no known photoreceptive function, such as the typeXIV interneurons of the fish optic tectum. We further show that TMT-Opsins and Encephalopsin render neuronal cells light-sensitive. TMT-Opsins preferentially respond to blue light relative to rhodopsin, with subclass-specific response kinetics. We discovered that tmt-opsins co-express with val-opsins, known green light receptors, in distinct inter- and motorneurons. Finally, we show by electrophysiological recordings on isolated adult tectal slices that interneurons in the position of typeXIV neurons respond to light. Our work supports \"sensory-inter-motorneurons\" as ancient units for brain evolution. It also reveals that vertebrate inter- and motorneurons are endowed with an evolutionarily ancient, complex light-sensory ability that could be used to detect changes in ambient light spectra, possibly providing the endogenous equivalent to an optogenetic machinery.","authors":"Fischer, RM., Fontinha, BM., Kirchmaier, S., Steger, J., Bloch, S., Inoue, D., Panda, S., Rumpel, S., Tessmar-Raible, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"PLoS Biol","volume":"11","issue":"6","page":"e1001585","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11266357","title":"Making connections. Meeting: axon guidance and neural plasticity.","abstract":null,"authors":"Dickson, BJ., Cline, H., Polleux, F., Ghosh, A.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"EMBO Rep","volume":"2","issue":"3","page":"182-6","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11245282","title":"Molecular mechanisms of tumor angiogenesis and tumor progression.","abstract":"The formation of new blood vessels (angiogenesis) is crucial for the growth and persistence of primary solid tumors and their metastases. Furthermore, angiogenesis is also required for metastatic dissemination, since an increase in vascular density will allow easier access of tumor cells to the circulation. Induction of angiogenesis precedes the formation of malignant tumors, and increased vascularization seems to correlate with the invasive properties of tumors and thus with the malignant tumor phenotype. In the last few years, the discovery and characterization of tumor-derived angiogenesis modulators greatly contributed to our understanding of how tumors regulate angiogenesis. However, although angiogenesis appears to be a rate-limiting event in tumor growth and metastatic dissemination, a direct connection between the induction of angiogenesis and the progression to tumor malignancy is less well understood. In this review, we discuss the most recent observations concerning the modulation of angiogenesis and their implications in tumor progression, as well as their potential impact on cancer therapy.","authors":"Cavallaro, U., Christofori, G.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Neurooncol","volume":"50","issue":"1-2","page":"63-70","pdf":null,"JrId":"5024","fulltextlink":null,"preprintlink":null,"articledate":"2001-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11245196","title":"Developmental neuroscience.   Moving on.","abstract":null,"authors":"Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Science","volume":"291","issue":"5510","page":"1910-1","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12198164","title":"TIS7 interacts with the mammalian SIN3 histone deacetylase complex in epithelial cells.","abstract":"The mammalian SIN3 complex consists of histone deacetylases (HDAC1, HDAC2), several known proteins (SAP30, N-CoR) and as yet unidentified proteins. Here we show that the mouse tetradecanoyl phorbol acetate induced sequence 7 (TIS7) protein is a novel transcriptional co-repressor that can associate with the SIN3 complex. We have identified tis7 as a gene that is up-regulated upon loss of polarity in a mouse mammary gland epithelial cell line expressing an estrogen-inducible c-JunER fusion protein. In unpolarized cells, TIS7 protein levels increase and TIS7 translocates into the nucleus. Overexpression of tis7 causes loss of polarity and represses a set of genes, as revealed by cDNA microarray analysis. We have shown that TIS7 protein interacts with several proteins of the SIN3 complex (mSin3B, HDAC1, N-CoR and SAP30) by yeast two-hybrid screening and co-immunoprecipitations. TIS7 co-immunoprecipitated HDAC complex is enzymatically active and represses a GAL4-dependent reporter transcription. The transcriptional repression of endogenous genes by tis7 overexpression is HDAC dependent. Thus, we propose TIS7 as a transcriptional co-repressor affecting the expression of specific genes in a HDAC activity-dependent manner during cell fate decisions, e.g. scattering.","authors":"Vietor, I., Vadivelu, SK., Wick, N., Hoffman, R., Cotten, M., Seiser, C., Fialka, I., Wunderlich, W., Haase, A., Korinkova, G., Brosch, G., Huber, LA.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"EMBO J","volume":"21","issue":"17","page":"4621-31","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12169632","title":"MLL-ENL cooperates with SCF to transform primary avian multipotent cells.","abstract":"The MLL gene is targeted by chromosomal translocations, which give rise to heterologous MLL fusion proteins and are associated with distinct types of acute lymphoid and myeloid leukaemia. To determine how MLL fusion proteins alter the proliferation and\/or differentiation of primary haematopoietic progenitors, we introduced the MLL-AF9 and MLL-ENL fusion proteins into primary chicken bone marrow cells. Both fusion proteins caused the sustained outgrowth of immature haematopoietic cells, which was strictly dependent on stem cell factor (SCF). The renewing cells have a long in vitro lifespan exceeding the Hayflick limit of avian cells. Analysis of clonal cultures identified the renewing cells as immature, multipotent progenitors, expressing erythroid, myeloid, lymphoid and stem cell surface markers. Employing a two-step commitment\/differentiation protocol involving the controlled withdrawal of SCF, the MLL-ENL-transformed progenitors could be induced to terminal erythroid or myeloid differentiation. Finally, in cooperation with the weakly leukaemogenic receptor tyrosine kinase v-Sea, the MLL-ENL fusion protein gave rise to multilineage leukaemia in chicks, suggesting that other activated, receptor tyrosine kinases can substitute for ligand-activated c-Kit in vivo.","authors":"Schulte, CE., von Lindern, M., Steinlein, P., Beug, H., Wiedemann, LM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"EMBO J","volume":"21","issue":"16","page":"4297-306","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2002-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11239392","title":"Wnt-14 plays a pivotal role in inducing synovial joint formation in the developing appendicular skeleton.","abstract":"The long bones of the vertebrate appendicular skeleton arise from initially continuous condensations of mesenchymal cells that subsequently segment and cavitate to form discrete elements separated by synovial joints. Little is known, however, about the molecular mechanisms of joint formation. We present evidence that Wnt-14 plays a central role in initiating synovial joint formation in the chick limb. Wnt-14 is expressed in joint-forming regions prior to the segmentation of the cartilage elements, and local misexpression of Wnt-14 induces morphological and molecular changes characteristic of the first steps of joint formation. Induction of an ectopic joint-like region by Wnt-14 suppresses the formation of the immediately adjacent endogenous joint, potentially providing insight into the spacing of joints.","authors":"Hartmann, C., Tabin, CJ.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell","volume":"104","issue":"3","page":"341-51","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19885848","title":"The cytotoxic effect of Bowman-Birk isoinhibitors, IBB1 and IBBD2, from soybean (Glycine max) on HT29 human colorectal cancer cells is related to their intrinsic ability to inhibit serine proteases.","abstract":"Bowman-Birk inhibitors (BBI) from soybean and related proteins are naturally occurring protease inhibitors with potential health-promoting properties within the gastrointestinal tract. In this work, we have investigated the effects of soybean BBI proteins on HT29 colon adenocarcinoma cells, compared with non-malignant colonic fibroblast CCD-18Co cells. Two major soybean isoinhibitors, IBB1 and IBBD2, showing considerable amino acid sequence divergence within their inhibitory domains, were purified in order to examine their functional properties, including their individual effects on the proliferation of HT29 colon cancer cells. IBB1 inhibited both trypsin and chymotrypsin whereas IBBD2 inhibited trypsin only. Despite showing significant differences in their enzyme inhibitory properties, the median inhibitory concentration values determined for IBB1 and IBBD2 on HT29 cell growth were not significantly different (39.9+\/-2.3 and 48.3+\/-3.5 microM, respectively). The cell cycle distribution pattern of HT29 colon cancer cells was affected by BBI treatment in a dose-dependent manner, with cells becoming blocked in the G0-G1 phase. Chemically inactive soybean BBI had a weak but non-significant effect on the proliferation of HT29 cells. The anti-proliferative properties of BBI isoinhibitors from soybean reveal that both trypsin- and chymotrypsin-like proteases involved in carcinogenesis should be considered as potential targets of BBI-like proteins.","authors":"Clemente, A., Moreno, FJ., Mar\u00edn-Manzano, Mdel C., Jim\u00e9nez, E., Domoney, C.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Mol Nutr Food Res","volume":"54","issue":"3","page":"396-405","pdf":null,"JrId":"32150","fulltextlink":null,"preprintlink":null,"articledate":"2010-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11171403","title":"Lilliputian: an AF4\/FMR2-related protein that controls cell identity and cell growth.","abstract":"Members of the AF4\/FMR2 family of nuclear proteins are involved in human diseases such as acute lymphoblastic leukemia and mental retardation. Here we report the identification and characterization of the Drosophila lilliputian (lilli) gene, which encodes a nuclear protein related to mammalian AF4 and FMR2. Mutations in lilli suppress excessive neuronal differentiation in response to a constitutively active form of Raf in the eye. In the wild type, Lilli has a partially redundant function in the Ras\/MAPK pathway in differentiation but it is essential for normal growth. Loss of Lilli function causes an autonomous reduction in cell size and partially suppresses the increased growth associated with loss of PTEN function. These results suggest that Lilli acts in parallel with the Ras\/MAPK and the PI3K\/PKB pathways in the control of cell identity and cellular growth.","authors":"Wittwer, F., van der Straten, A., Keleman, K., Dickson, BJ., Hafen, E.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Development","volume":"128","issue":"5","page":"791-800","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2001-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12169269","title":"FIP-2, an IkappaB-kinase-gamma-related protein, is associated with the Golgi apparatus and translocates to the marginal band during chicken erythroblast differentiation.","abstract":"Using an antiserum directed against marginal band associated proteins of chicken erythrocytes we isolated clones encoding the chicken homolog of 14.7K-interacting protein 2 (FIP-2), a protein potentially involved in tumor necrosis factor-alpha\/nuclear factor-kappaB signaling, from a chicken erythroblast cDNA library. We found that chicken FIP-2 was expressed in a variety of tissues and cell types, but unlike its human counterpart, alternative splicing does not appear to take place. Analysis of intracellular localization revealed that FIP-2 was concentrated at the Golgi apparatus in most cells. Perturbation of the Golgi structure without loss of Golgi function (by treatment with nocodazole) resulted in a retention of FIP-2 at the dispersed Golgi fragments. In contrast, disruption of both Golgi structure and function (by brefeldin A) led to a loss of FIP-2 from Golgi membranes. Remarkably, during erythroblast differentiation FIP-2 was found to translocate from the Golgi to the marginal band. Our results support the hypothesis of a function of the Golgi apparatus in signal transduction. Moreover, our results raise the possibility that the marginal band of chicken erythrocytes, in addition to its role in morphogenesis, has a function in signal transduction and that FIP-2 is in some way involved in its formation.","authors":"Stroissnigg, H., Repitz, M., Miloloza, A., Linhartova, I., Beug, H., Wiche, G., Propst, F.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Exp Cell Res","volume":"278","issue":"2","page":"133-45","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"2002-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12140765","title":"Oncogenic Ras\/Her-2 mediate hyperproliferation of polarized epithelial cells in 3D cultures and rapid tumor growth via the PI3K pathway.","abstract":"Carcinogenesis by oncogenic Ras and Her-2 involves enhanced proliferation of epithelial cells in vivo. However, hyperproliferation induced by these oncogenes, or their downstream pathways in vitro has mainly been studied in cultured, fibroblastic cell lines. Here, we demonstrate that oncogenic Ha-Ras or constitutively active Her-2 cause increased proliferation and cyclin D1 upregulation in fully polarized, mammary epithelial cells (EpH4), if cultivated as organotypic structures in three-dimensional collagen\/matrigel matrices. Under standard culture conditions, however, these oncogenes failed to induce hyperproliferation. Using both specific low molecular weight inhibitors and Ras-effector-specific mutants, we dissected signaling pathways downstream of oncogenic Ras (PI3K, Mek1\/MAPK) with respect to (i) hyperproliferation in collagen gels and tumorigenesis in mice and (ii) epithelial\/mesenchymal transition (EMT). We show that the Ras-activated PI3K pathway is required to induce rapid tumor growth and enhanced proliferation of EpH4 cells in collagen gels, but fails to cause EMT in vitro and in vivo. On the other hand, Ras-dependent activation of the Mek1\/MAPK pathway in EpH4 cells (previously shown to cause EMT and metastasis) did not induce hyperproliferation in collagen gels and caused only slow tumor growth. Our data thus indicate that Ras-dependent signaling through the PI3K- and MAPK pathways fulfil distinct, but complementary functions during carcinogenesis.","authors":"Janda, E., Litos, G., Gr\u00fcnert, S., Downward, J., Beug, H.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Oncogene","volume":"21","issue":"33","page":"5148-59","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12123707","title":"Gene expression profiling in RAS oncogene-transformed cell lines and in solid tumors using subtractive suppression hybridization and cDNA arrays.","abstract":null,"authors":"Sers, C., Tchernitsa, OI., Zuber, J., Diatchenko, L., Zhumabayeva, B., Desai, S., Htun, S., Hyder, K., Wiechen, K., Agoulnik, A., Scharff, KM., Siebert, PD., Sch\u00e4fer, R.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Adv Enzyme Regul","volume":"42","issue":null,"page":"63-82","pdf":null,"JrId":"278","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11163265","title":"Crossing the midline: roles and regulation of Robo receptors.","abstract":"In the Drosophila CNS, the midline repellent Slit acts at short range through its receptor Robo to control midline crossing. Longitudinal axons express high levels of Robo and avoid the midline; commissural axons that cross the midline express only low levels of Robo. Robo levels are in turn regulated by Comm. Here, we show that the Slit receptors Robo2 and Robo3 ensure the fidelity of this crossing decision: rare crossing errors occur in both robo2 and robo3 single mutants. In addition, low levels of either Robo or Robo2 are required to drive commissural axons through the midline: only in robo,robo2 double mutants do axons linger at the midline as they do in slit mutants. Robo2 and Robo3 levels are also tightly regulated, most likely by a mechanism similar to but distinct from the regulation of Robo by Comm.","authors":"Rajagopalan, S., Nicolas, E., Vivancos, V., Berger, J., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Neuron","volume":"28","issue":"3","page":"767-77","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11163190","title":"Functional genomics identifies monopolin: a kinetochore protein required for segregation of homologs during meiosis i.","abstract":"The orderly reduction in chromosome number that occurs during meiosis depends on two aspects of chromosome behavior specific to the first meiotic division. These are the retention of cohesion between sister centromeres and their attachment to microtubules that extend to the same pole (monopolar attachment). By deleting genes that are upregulated during meiosis, we identified in Saccharomyces cerevisiae a kinetochore associated protein, Mam1 (Monopolin), which is essential for monopolar attachment. We also show that the meiosis-specific cohesin, Rec8, is essential for maintaining cohesion between sister centromeres but not for monopolar attachment. We conclude that monopolar attachment during meiosis I requires at least one meiosis-specific protein and is independent of the process that protects sister centromere cohesion.","authors":"T\u00f3th, A., Rabitsch, KP., G\u00e1lov\u00e1, M., Schleiffer, A., Buonomo, SB., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cell","volume":"103","issue":"7","page":"1155-68","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11163180","title":"Selecting a longitudinal pathway: Robo receptors specify the lateral position of axons in the Drosophila CNS.","abstract":"On each side of the midline of the Drosophila CNS, axons are organized into a series of parallel pathways. Here we show that the midline repellent Slit, previously identified as a short-range signal that regulates midline crossing, also functions at long range to pattern these longitudinal pathways. In this long-range function, Slit signals through the receptors Robo2 and Robo3. Axons expressing neither, one, or both of these receptors project in one of three discrete lateral zones, each successively further from the midline. Loss of robo2 or robo3 function repositions axons closer to the midline, while gain of robo2 or robo3 function shifts axons further from the midline. Local cues further refine the lateral position. Together, these long- and short-range guidance cues allow growth cones to select with precision a specific longitudinal pathway.","authors":"Rajagopalan, S., Vivancos, V., Nicolas, E., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cell","volume":"103","issue":"7","page":"1033-45","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11160745","title":"Microtubule-independent motility and nuclear targeting of adenoviruses with fluorescently labeled genomes.","abstract":"A novel adenovirus system for analyzing the adenovirus entry pathway has been developed that contains green fluorescent protein bound to the encapsidated viral DNA (AdLite viruses). AdLite viruses enter host cells and accumulate around the nuclei and near the microtubule organizing centers (MTOC). In live cells, individual AdLite particles were observed trafficking both toward and away from the nucleus. Depolymerization of microtubules during infection prevented AdLite accumulation around the MTOC; however, it did not abolish perinuclear localization of AdLite particles. Furthermore, depolymerization of microtubules did not affect AdLite motility and did not affect gene expression from wild-type adenovirus and adenovirus-derived vectors. These data revealed that adenovirus intracellular motility and nuclear targeting can be supported by a mechanism that does not rely on the microtubule network.","authors":"Glotzer, JB., Michou, AI., Baker, A., Saltik, M., Cotten, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Virol","volume":"75","issue":"5","page":"2421-34","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9011180","title":"Avian erythropoiesis and erythroleukemia: towards understanding the role of the biomolecules involved.","abstract":null,"authors":"Beug, H., Bauer, A., Dolznig, H., von Lindern, M., Lobmayer, L., Mellitzer, G., Steinlein, P., Wessely, O., Mullner, E.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Biochim Biophys Acta","volume":"1288","issue":"3","page":"M35-47","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1997-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20678469","title":"Phosphoinositide 3-kinase-gamma expression is upregulated in brain microglia and contributes to ischemia-induced microglial activation in acute experimental stroke.","abstract":"Microglia, the resident microphages of the CNS, are rapidly activated after ischemic stroke. Inhibition of microglial activation may protect the brain by attenuating blood-brain barrier damage and neuronal apoptosis after ischemic stroke. However, the mechanisms by which microglia is activated following cerebral ischemia is not well defined. In this study, we investigated the expression of PI3Kgamma in normal and ischemic brains and found that PI3Kgamma mRNA and protein are constitutively expressed in normal brain microvessels, but significantly upregulated in postischemic brain primarily in activated microglia following cerebral ischemia. In vitro, the expression of PI3Kgamma mRNA and protein was verified in mouse brain endothelial and microglial cell lines. Importantly, absence of PI3Kgamma blocked the early microglia activation (at 4h) and subsequent expansion (at 24-72 h) in PI3Kgamma knockout mice. The results suggest that PI3Kgamma is an ischemia-responsive gene in brain microglia and contributes to ischemia-induced microglial activation and expansion.","authors":"Jin, R., Yu, S., Song, Z., Quillin, JW., Deasis, DP., Penninger, JM., Nanda, A., Granger, DN., Li, G.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Biochem Biophys Res Commun","volume":"399","issue":"3","page":"458-64","pdf":null,"JrId":"1008","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12101246","title":"Selective interactions between vertebrate polycomb homologs and the SUV39H1 histone lysine methyltransferase suggest that histone H3-K9 methylation contributes to chromosomal targeting of Polycomb group proteins.","abstract":"Polycomb group (PcG) proteins form multimeric chromatin-associated protein complexes that are involved in heritable repression of gene activity. Two distinct human PcG complexes have been characterized. The EED\/EZH2 PcG complex utilizes histone deacetylation to repress gene activity. The HPC\/HPH PcG complex contains the HPH, RING1, BMI1, and HPC proteins. Here we show that vertebrate Polycomb homologs HPC2 and XPc2, but not M33\/MPc1, interact with the histone lysine methyltransferase (HMTase) SUV39H1 both in vitro and in vivo. We further find that overexpression of SUV39H1 induces selective nuclear relocalization of HPC\/HPH PcG proteins but not of the EED\/EZH2 PcG proteins. This SUV39H1-dependent relocalization concentrates the HPC\/HPH PcG proteins to the large pericentromeric heterochromatin domains (1q12) on human chromosome 1. Within these PcG domains we observe increased H3-K9 methylation. Finally, we show that H3-K9 HMTase activity is associated with endogenous HPC2. Our findings suggest a role for the SUV39H1 HMTase and histone H3-K9 methylation in the targeting of human HPC\/HPH PcG proteins to modified chromatin structures.","authors":"Sewalt, RG., Lachner, M., Vargas, M., Hamer, KM., den Blaauwen, JL., Hendrix, T., Melcher, M., Schweizer, D., Jenuwein, T., Otte, AP.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Cell Biol","volume":"22","issue":"15","page":"5539-53","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12086464","title":"FGF signaling regulates expression of Tbx2, Erm, Pea3, and Pax3 in the early nasal region.","abstract":"Fgf8 is required for normal development of the nasal region. Here, we have used a candidate approach to identify genes that are induced in chick nasal mesenchyme in response to FGF signaling. Using an explant culture system, we show that expression of the transcription factors Tbx2, Erm, Pea3, and Pax3, but not Pax7, in nasal mesenchyme is regulated by ectodermal signals in a stage-dependent manner. Using beads soaked in recombinant FGF protein and an FGF receptor antagonist, we furthermore demonstrate that FGF signaling is necessary and sufficient for expression of Tbx2, Erm, Pea3, and Pax3, but has no effect on Pax7 expression. We also show that, within the nasal mesenchyme, competence to respond to FGF signaling is initially widespread and uniform but becomes restricted to regions normally exposed to FGF at later stages of development, coincident with changes in FGF receptor expression. Finally, we provide evidence that FGF8 also regulates Erm and Pea3 expression in the nasal placodes. Together, these results identify Tbx2, Erm, Pea3, and Pax3 as downstream targets of FGF signaling in the facial area and suggest that these genes may mediate some of the effects of FGF8 during development of the nasal region.","authors":"Firnberg, N., Neub\u00fcser, A.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Dev Biol","volume":"247","issue":"2","page":"237-50","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11146625","title":"DmPAR-6 directs epithelial polarity and asymmetric cell division of neuroblasts in Drosophila.","abstract":"The Drosophila protein Bazooka is required for both apical-basal polarity in epithelial cells and directing asymmetric cell division in neuroblasts. Here we show that the PDZ-domain protein DmPAR-6 cooperates with Bazooka for both of these functions. DmPAR-6 colocalizes with Bazooka at the apical cell cortex of epithelial cells and neuroblasts, and binds to Bazooka in vitro. DmPAR-6 localization requires Bazooka, and mislocalization of Bazooka through overexpression redirects DmPAR-6 to ectopic sites of the cell cortex. In the absence of DmPAR-6, Bazooka fails to localize apically in neuroblasts and epithelial cells, and is distributed in the cytoplasm instead. Epithelial cells lose their apical-basal polarity in DmPAR-6 mutants, asymmetric cell divisions in neuroblasts are misorientated, and the proteins Numb and Miranda do not segregate correctly into the basal daughter cell. Bazooka and DmPAR-6 are Drosophila homologues of proteins that direct asymmetric cell division in early Caenorhabditis elegans embryos, and our results indicate that homologous protein machineries may direct this process in worms and flies.","authors":"Petronczki, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Cell Biol","volume":"3","issue":"1","page":"43-9","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11124802","title":"TGF-beta inhibits p70 S6 kinase via protein phosphatase 2A to induce G(1) arrest.","abstract":"On TGF-beta binding, the TGF-beta receptor directly phosphorylates and activates the transcription factors Smad2\/3, leading to G(1) arrest. Here, we present evidence for a second, parallel, TGF-beta-dependent pathway for cell cycle arrest, achieved via inhibition of p70(s6k). TGF-beta induces association of its receptor with protein phosphatase-2A (PP2A)-Balpha. Concomitantly, three PP2A-subunits, Balpha, Abeta, and Calpha, associate with p70(s6k), leading to its dephosphorylation and inactivation. Although either pathway is sufficient to induce G(1) arrest, abrogation of both, the inhibition of p70(s6k), and transcription through Smad proteins is required for release of epithelial cells from TGF-beta-induced G(1) arrest. TGF-beta thereby modulates the translational and posttranscriptional control of cell cycle progression.","authors":"Petritsch, C., Beug, H., Balmain, A., Oft, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Genes Dev","volume":"14","issue":"24","page":"3093-101","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2001-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12070303","title":"Enhanced ERK-1\/2 activation in mice susceptible to coxsackievirus-induced myocarditis.","abstract":"Group B coxsackieviral (CVB) infection commonly causes viral myocarditis. Mice are protected from CVB3 myocarditis by gene-targeted knockout of p56(Lck)(Lck), the Src family kinase (Src) essential for T cell activation. Extracellular signal-regulated kinase 1 and 2 (ERK-1\/2) can influence cell function downstream of Lck. Using T cell lines and neonatal cardiac myocytes we investigated the role of ERK-1\/2 in CVB3 infection. In Jurkat T cells ERK-1\/2 is rapidly activated by CVB3; but, this response is absent in Lck-negative JCaM T cells. Inhibition of ERK-1\/2 with UO126 reduced CVB3 titers in Jurkat cells, but not in JCaM cells. In cardiac myocytes CVB3 activation of ERK-1\/2 is blocked by the Src inhibitor PP2. In addition, viral production in myocytes is decreased by Src or ERK-1\/2 inhibition. In vitro, in both immune and myocardial cells, ERK-1\/2 is activated by CVB3 downstream of Lck and other Src's and is necessary for efficient CVB3 replication. In vivo, following CVB3 infection, ERK-1\/2 activation is evident in the myocardium. ERK-1\/2 activation is intense in the hearts of myocarditis-susceptible A\/J mice. In contrast, significantly less ERK-1\/2 activation is found in the hearts of myocarditis-resistant C57BL\/6 mice. Therefore, the ERK-1\/2 response to CVB3 infection may contribute to differential host susceptibility to viral myocarditis.","authors":"Opavsky, MA., Martino, T., Rabinovitch, M., Penninger, J., Richardson, C., Petric, M., Trinidad, C., Butcher, L., Chan, J., Liu, PP.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Clin Invest","volume":"109","issue":"12","page":"1561-9","pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12070039","title":"Transferrin receptor hyperexpression in primary erythroblasts is lost on transformation by avian erythroblastosis virus.","abstract":"In primary chicken erythroblasts (stem cell factor [SCF] erythroblasts), transferrin receptor (TfR) messenger RNA (mRNA) and protein were hyperexpressed as compared to nonerythroid chicken cell types. This erythroid-specific hyperexpression was abolished in transformed erythroblasts (HD3E22 cells) expressing the v-ErbA and v-ErbB oncogenes of avian erythroblastosis virus. TfR expression in HD3E22 cells could be modulated by changes in exogenous iron supply, whereas expression in SCF erythroblasts was not subject to iron regulation. Measurements of TfR mRNA half-life indicated that hyperexpression in SCF erythroblasts was due to a massive stabilization of transcripts even in the presence of high iron levels. Changes in mRNA binding activity of iron regulatory protein 1 (IRP1), the primary regulator of TfR mRNA stability in these cells, correlated well with TfR mRNA expression; IRP1 activity in HD3E22 cells and other nonerythroid cell types tested was iron dependent, whereas IRP1 activity in primary SCF erythroblasts could not be modulated by iron administration. Analysis of avian erythroblasts expressing v-ErbA alone indicated that v-ErbA was responsible for these transformation-specific alterations in the regulation of iron metabolism. In SCF erythroblasts high amounts of TfR were detected on the plasma membrane, but a large fraction was also located in early and late endosomal compartments, potentially concealing temporary iron stores from the IRP regulatory system. In contrast, TfR was almost exclusively located to the plasma membrane in HD3E22 cells. In summary, stabilization of TfR mRNA and redistribution of Fe-Tf\/TfR complexes to late endosomal compartments may contribute to TfR hyperexpression in primary erythroblasts, effects that are lost on leukemic transformation.","authors":"Lobmayr, L., Sauer, T., Killisch, I., Schranzhofer, M., Wilson, RB., Ponka, P., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Blood","volume":"100","issue":"1","page":"289-98","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11136975","title":"The mammalian UV response: c-Jun induction is required for exit from p53-imposed growth arrest.","abstract":"The mammalian UV response results in rapid and dramatic induction of c-jun. Induction of a protooncogene, normally involved in mitogenic responses, by a genotoxic agent that causes growth arrest seems paradoxical. We now provide an explanation for the role of c-Jun in the UV response of mouse fibroblasts. c-Jun is necessary for cell-cycle reentry of UV-irradiated cells, but does not participate in the response to ionizing radiation. Cells lacking c-Jun undergo prolonged cell-cycle arrest, but resist apoptosis, whereas cells that express c-Jun constitutively do not arrest and undergo apoptosis. This function of c-Jun is exerted through negative regulation of p53 association with the p21 promoter. Cells lacking c-Jun exhibit prolonged p21 induction, whereas constitutive c-Jun inhibits UV-mediated p21 induction.","authors":"Shaulian, E., Schreiber, M., Piu, F., Beeche, M., Wagner, EF., Karin, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cell","volume":"103","issue":"6","page":"897-907","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11081627","title":"Two distinct pathways remove mammalian cohesin from chromosome arms in prophase and from centromeres in anaphase.","abstract":"In yeast, anaphase depends on cohesin cleavage. How anaphase is controlled in vertebrates is unknown because their cohesins dissociate from chromosomes before anaphase. We show that residual amounts of the cohesin SCC1 remain associated with human centromeres until the onset of anaphase when a similarly small amount of SCC1 is cleaved. In Xenopus extracts, SCC1 cleavage depends on the anaphase-promoting complex and separin. Separin immunoprecipitates are sufficient to cleave SCC1, indicating that separin is associated with a protease activity. Separin activation coincides with securin destruction and partial separin cleavage, suggesting that several mechanisms regulate separin activity. We propose that in vertebrates, a cleavage-independent pathway removes cohesin from chromosome arms during prophase, whereas a separin-dependent pathway cleaves centromeric cohesin at the metaphase-anaphase transition.","authors":"Waizenegger, IC., Hauf, S., Meinke, A., Peters, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cell","volume":"103","issue":"3","page":"399-410","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2000-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12067650","title":"The many faces of histone lysine methylation.","abstract":"Diverse post-translational modifications of histone amino termini represent an important epigenetic mechanism for the organisation of chromatin structure and the regulation of gene activity. Within the past two years, great progress has been made in understanding the functional implications of histone methylation; in particular through the characterisation of histone methyltransferases that direct the site-specific methylation of, for example, lysine 9 and lysine 4 positions in the histone H3 amino terminus. All known histone methyltransferases of this type contain the evolutionarily conserved SET domain and appear to be able to stimulate either gene repression or gene activation. Methylation of H3 Lys9 and Lys4 has been visualised in native chromatin, indicating opposite roles in structuring repressive or accessible chromatin domains. For example, at the mating-type loci in Schizosaccharomyces pombe, at pericentric heterochromatin and at the inactive X chromosome in mammals, striking differences between these distinct marks have been observed. H3 Lys9 methylation is also important to direct additional epigenetic signals such as DNA methylation--for example, in Neurospora crassa and in Arabidopsis thaliana. Together, the available data strongly establish histone lysine methylation as a central modification for the epigenetic organisation of eukaryotic genomes.","authors":"Lachner, M., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Opin Cell Biol","volume":"14","issue":"3","page":"286-98","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"2002-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20883686","title":"Wnt\/\u03b2-catenin signaling in the dental mesenchyme regulates incisor development by regulating Bmp4.","abstract":"Loss- and gain-of function approaches modulating canonical Wnt\/\u03b2-catenin activity have established a role for the Wnt\/\u03b2-catenin pathway during tooth development. Here we show that Wnt\/\u03b2-catenin signaling is required in the dental mesenchyme for normal incisor development, as locally restricted genetic inactivation of \u03b2-catenin results in a splitting of the incisor placode, giving rise to two incisors. Molecularly this is first associated with down-regulation of Bmp4 and subsequent splitting of the Shh domain at a subsequent stage. The latter phenotype can be mimicked by ectopic application of the BMP antagonist Noggin. Conditional genetic inactivation of Bmp4 in the mesenchyme reveals that mesenchymal BMP4 activity is required for maintenance of Shh expression in the dental ectoderm. Taken together our results indicate that \u03b2-catenin together with Lef1 and Tcf1 are required to activate Bmp4 expression in order to maintain Shh expression in the dental ectoderm. This provides a mechanism whereby the number of incisors arising from one placode can be varied through local alterations of a mesenchymal signaling circuit involving \u03b2-catenin, Lef1, Tcf1 and Bmp4.","authors":"Fujimori, S., Novak, H., Weissenb\u00f6ck, M., Jussila, M., Gon\u00e7alves, A., Zeller, R., Galloway, J., Thesleff, I., Hartmann, C.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Dev Biol","volume":"348","issue":"1","page":"97-106","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19724917","title":"LIV-1 enhances the aggressive phenotype through the induction of epithelial to mesenchymal transition in human pancreatic carcinoma cells.","abstract":"LIV-1 is a downstream target of STAT3 and is essential for the nuclear localization of Snail, a master regulator of epithelial to mesenchymal transition (EMT). Little is known about the association of LIV-1 with pancreatic carcinoma development, therefore, expression of LIV-1 mRNA was analyzed by real-time reverse transcriptase polymerase chain reaction (RT-PCR) in 9 cultured cell lines (8 carcinoma and 1 normal duct cell lines) and 24 pancreatic tissues (12 carcinoma and 12 normal tissues). Localization of this gene product was investigated by immunohistochemistry in 72 pancreatic carcinoma and the relation between its expression and clinicopathological findings was examined. To assess the function of LIV-1 in pancreatic carcinoma cells, stable siRNA expressing Panc-1 cells were generated. Higher expression of LIV-1 mRNA was found in both pancreatic carcinoma cell lines and pancreatic carcinoma tissues compared to normal duct cell line and histologically normal tissues, respectively. Immunohistochemical analysis revealed that LIV-1 expression was frequently found in 76.4% of pancreatic carcinoma tissues and its expression level was associated with tumor size and lymphatic infiltration. Down-regulated LIV-1 cells showed significant inhibition of anchorage-dependent or -independent proliferation and cell motility in vitro and reduction of tumor growth and metastasis in vivo. Furthermore, nuclear expression of Snail was decreased and E-cadherin expression was restored in LIV-1 siRNA expressing pancreatic carcinoma cells. These findings indicate that LIV-1 may be involved in acquisition of the aggressive phenotype of human pancreatic carcinoma cells through the induction of epithelial to mesenchymal transition.","authors":"Unno, J., Satoh, K., Hirota, M., Kanno, A., Hamada, S., Ito, H., Masamune, A., Tsukamoto, N., Motoi, F., Egawa, S., Unno, M., Horii, A., Shimosegawa, T.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Int J Oncol","volume":"35","issue":"4","page":"813-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19625504","title":"Role of cleavage by separase of the Rec8 kleisin subunit of cohesin during mammalian meiosis I.","abstract":"Proteolytic activity of separase is required for chiasma resolution during meiosis I in mouse oocytes. Rec8, the meiosis-specific alpha-kleisin subunit of cohesin, is a key target of separase in yeast. Is the equivalent protein also a target in mammals? We show here that separase cleaves mouse Rec8 at three positions in vitro but only when the latter is hyper-phosphorylated. Expression of a Rec8 variant (Rec8-N) that cannot be cleaved in vitro at these sites causes sterility in male mice. Their seminiferous tubules lack a normal complement of 2 C secondary spermatocytes and 1 C spermatids and contain instead a high proportion of cells with enlarged nuclei. Chromosome spreads reveal that Rec8-N expression has no effect in primary spermatocytes but produces secondary spermatocytes and spermatids with a 4 C DNA content, suggesting that the first and possibly also the second meiotic division is abolished. Expression of Rec8-N in oocytes causes chromosome segregation to be asynchronous and delays its completion by 2-3 hours during anaphase I, probably due to inefficient proteolysis of Rec8-N by separase. Despite this effect, chromosome segregation must be quite accurate as Rec8-N does not greatly reduce female fertility. Our data is consistent with the notion that Rec8 cleavage is important and probably crucial for the resolution of chiasmata in males and females.","authors":"Kudo, NR., Anger, M., Peters, AH., Stemmann, O., Theussl, HC., Helmhart, W., Kudo, H., Heyting, C., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Sci","volume":"122","issue":"Pt 15","page":"2686-98","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11081626","title":"Disjunction of homologous chromosomes in meiosis I depends on proteolytic cleavage of the meiotic cohesin Rec8 by separin.","abstract":"It has been proposed but never proven that cohesion between sister chromatids distal to chiasmata is responsible for holding homologous chromosomes together while spindles attempt to pull them toward opposite poles during metaphase of meiosis I. Meanwhile, the mechanism by which disjunction of homologs is triggered at the onset of anaphase I has remained a complete mystery. In yeast, cohesion between sister chromatid arms during meiosis depends on a meiosis-specific cohesin subunit called Rec8, whose mitotic equivalent, Sccl, is cleaved at the metaphase to anaphase transition by an endopeptidase called separin. We show here that cleavage of Rec8 by separin at one of two different sites is necessary for the resolution of chiasmata and the disjunction of homologous chromosomes during meiosis.","authors":"Buonomo, SB., Clyne, RK., Fuchs, J., Loidl, J., Uhlmann, F., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cell","volume":"103","issue":"3","page":"387-98","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2000-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20043281","title":"ConteXt of change--X inactivation and disease.","abstract":"Epigenetic regulation is important for stable maintenance of cell identity. For continued function of organs and tissues, illegitimate changes in cell identity must be avoided. Failure to do so can trigger tumour development and disease. How epigenetic patterns are established during cell differentiation has been explored by studying model systems such as X inactivation. Mammals balance the X-linked gene dosage between the sexes by silencing of one of the two X chromosomes in females. This is initiated by expression of the non-coding X-inactive specific transcript (Xist) RNA and depends on specific cellular contexts, in which essential silencing factors are expressed. Normally X inactivation is initiated in early embryogenesis, but recent reports identified instances where Xist is expressed and can initiate gene repression. Here we describe the features that characterize the cellular permissivity to initiation of X inactivation and note that these can also occur in cancer cells and in specific haematopoietic progenitors. We propose that embryonic pathways for epigenetic regulation are re-established in adult progenitor cells and tumour cells. Understanding their reactivation will deepen our understanding of tumourigenesis and may be exploited for cancer therapy.","authors":"Agrelo, R., Wutz, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"EMBO Mol Med","volume":"2","issue":"1","page":"6-15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11044407","title":"Placental vascularisation requires the AP-1 component fra1.","abstract":"Fra1 is an immediate-early gene encoding a member of the AP-1 transcription factor family, which has diverse roles in development and oncogenesis. To determine the function of Fra1 in mouse development, the gene was inactivated by gene targeting. Foetuses lacking Fra1 were severely growth retarded and died between E10.0 and E10.5, owing to defects in extra-embryonic tissues. The placental labyrinth layer, where X-gal staining revealed expression of Fra1, was reduced in size and largely avascular, owing to a marked decrease in the number of vascular endothelial cells, as shown by the lack of Flk1 expression. In contrast, the spongiotrophoblast layer was unaffected and expressed the marker genes 4311 (Tpbp) and Flt1. Furthermore, mutant foetuses exhibited yolk-sac defects that may contribute to their growth retardation and lethality. Importantly, when the placental defect was rescued by injection of Fra1(-)(\/)(-) ES cells into tetraploid wild-type blastocysts, Fra1(-)(\/)(-) pups were obtained that were no longer growth retarded and survived up to 2 days after birth without apparent phenotypic defects. These data indicate that a defect in the extra-embryonic compartment is causal to the observed lethality, and suggest that Fra1 plays a crucial role in establishing normal vascularisation of the placenta.","authors":"Schreiber, M., Wang, ZQ., Jochum, W., Fetka, I., Elliott, C., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Development","volume":"127","issue":"22","page":"4937-48","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2001-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19320758","title":"Two hsp23 genes in the Mediterranean fruit fly, Ceratitis capitata: structural characterization, heat shock regulation and developmental expression.","abstract":"In the present study, we characterized a 3320-bp genomic DNA fragment encoding two medfly (Ceratitis capitata) homologues of the Drosophila melanogaster heat shock protein 23 (hsp23) gene, named Cchsp23-alphaand -beta. The two medfly hsp23 genes are transcribed in opposite directions and encode two almost identical proteins. Furthermore, the two genes exhibit a very high degree of similarity in their 5' untranslated and proximal promoter regions. Phylogenetic analysis indicated that the CcHsp23 proteins are orthologous to Drosophila Hsp23 and Sarcophaga crassipalpis Hsp23. Structural analysis of the 5' flanking regions of the Cchsp23 genes revealed the presence of several putative heat shock elements. Both CcHsp23 genes are induced by heat in a similar manner. In addition to heat-induction, the Cchsp23 genes are expressed at several stages of normal development as well as in ovaries and testes. In general, the developmental expression patterns of the medfly genes are similar, suggesting that they are under similar regulatory mechanisms. However, the expression of the Cchsp23 genes differs significantly from the expression of the Drosophila hsp23 gene in certain embryonic and larval stages, suggesting differential regulation of the hsp23 genes in the two dipteran species. The expression of both Cchsp23 genes in adult flies is increased with age, especially in males.","authors":"Kokolakis, G., Kritsidima, M., Tkachenko, T., Mintzas, AC.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Insect Mol Biol","volume":"18","issue":"2","page":"171-81","pdf":null,"JrId":"2608","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10990462","title":"Activation of the beta globin locus by transcription factors and chromatin modifiers.","abstract":"Locus control regions (LCRs) alleviate chromatin-mediated transcriptional repression. Incomplete LCRs partially lose this property when integrated in transcriptionally restrictive genomic regions such as centromeres. This frequently results in position effect variegation (PEV), i.e. the suppression of expression in a proportion of the cells. Here we show that this PEV is influenced by the heterochromatic protein SUV39H1 and by the Polycomb group proteins M33 and BMI-1. A concentration variation of these proteins modulates the proportion of cells expressing human globins in a locus-dependent manner. Similarly, the transcription factors Sp1 or erythroid Kr\u00fcppel-like factor (EKLF) also influence PEV, characterized by a change in the number of expressing cells and the chromatin structure of the locus. However, in contrast to results obtained in a euchromatic locus, EKLF influences the expression of the gamma- more than the beta-globin genes, suggesting that the relief of silencing is caused by the binding of EKLF to the LCR and that genes at an LCR proximal position are more likely to be in an open chromatin state than genes at a distal position.","authors":"McMorrow, T., van den Wijngaard, A., Wollenschlaeger, A., van de Corput, M., Monkhorst, K., Trimborn, T., Fraser, P., van Lohuizen, M., Jenuwein, T., Djabali, M., Philipsen, S., Grosveld, F., Milot, E.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"EMBO J","volume":"19","issue":"18","page":"4986-96","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2000-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10976802","title":"Characterisation of the rubber elongation factor from ammoniated latex by electrophoresis and mass spectrometry.","abstract":"Rubber elongation factor (REF) is considered as one of the major allergens present in latex. An extraction and purification protocol for preparation of REF standards has been modified. A protein fraction was extracted from ammoniated latex sap and purified by gel filtration chromatography. The purified and concentrated proteins were separated by sodium dodecylsulfate-polyacrylamide gel electrophoresis into two major bands. These bands were further characterised by matrix-assisted laser desorption\/ionisation time-of-flight and nano-electrospray ionization mass spectrometry. REF and a truncated form could be ascertained by the mass and fragmentation pattern of the tryptic peptides. In the faster migrating band an additional peptide could be identified. This peptide is also present in Hevb3 and a Mr 27000 latex allergen. Our findings indicate that conventional REF preparations as standards may contain additional allergenic proteins.","authors":"D\u00fcrauer, A., Csaszar, E., Mechtler, K., Jungbauer, A., Schmid, E.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Chromatogr A","volume":"890","issue":"1","page":"145-58","pdf":null,"JrId":"2582","fulltextlink":null,"preprintlink":null,"articledate":"2000-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8984634","title":"Viewpoint: putting the cell cycle in order.","abstract":null,"authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Science","volume":"274","issue":"5293","page":"1643-5","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1997-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12049770","title":"Transrepression of AP-1 by nuclear receptors in Drosophila.","abstract":"Mammalian cell culture studies have shown that several members of the nuclear receptor super family such as glucocorticoid receptor, retinoic acid receptor and thyroid hormone receptor can repress the activity of AP-1 proteins by a mechanism that does not require the nuclear receptor to bind to DNA directly, but that is otherwise poorly understood. Several aspects of nuclear receptor function are believed to rely on this inhibitory mechanism, which is referred to as transrepression. This study presents evidence that nuclear receptor-mediated transrepression of AP-1 occurs in Drosophila melanogaster. In two different developmental situations, embryonic dorsal closure and wing development, several nuclear receptors, including Seven up, Tailless, and Eagle antagonize AP-1. The inhibitory interactions with nuclear receptors are integrated with other modes of AP-1 regulation, such as mitogen-activated protein kinase signaling. A potential role of nuclear receptors in setting a threshold of AP-1 activity required for the manifestation of a cellular response is discussed.","authors":"Gritzan, U., Weiss, C., Brennecke, J., Bohmann, D.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mech Dev","volume":"115","issue":"1-2","page":"91-100","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12037666","title":"Stabilization of beta-catenin induces lesions reminiscent of prostatic intraepithelial neoplasia, but terminal squamous transdifferentiation of other secretory epithelia.","abstract":"The present study documents that stabilization of beta-catenin is sufficient to induce lesions reminiscent of prostate intraepithelial neoplasia (PIN). Such lesions were present in all compound mutant mice and all prostate acini expressing stabilized beta-catenin. High grade PIN-like lesions resembling early human prostate cancer were detected as early as 10 weeks of age. Surprisingly, stabilization of beta-catenin in other secretory epithelia including salivary, preputial, harderian, and mammary glands induced extensive squamous metaplasia and keratinization associated with terminal differentiation of the target cells, but failed to cause neoplastic transformation. Epidermal hyperplasia, hair follicle cysts, and odontomas were also observed. The prostatic lesions exhibited upregulation of c-myc, increased rate of cellular proliferation, loss of the Na-K-Cl co-transporter NKCC1, and expression of androgen receptor. Basal cell markers such as p63 and keratin 5 were not expressed by the masses of PIN-like lesions, but were present in small foci of proliferating beta-catenin expressing basal cells. Our observations indicate that beta-catenin stabilization is a crucial event for the initiation of PIN-like lesions, but induces squamous metaplasia rather than tumorigenesis in secretory epithelia other than the prostate.","authors":"Gounari, F., Signoretti, S., Bronson, R., Klein, L., Sellers, WR., Kum, J., Siermann, A., Taketo, MM., von Boehmer, H., Khazaie, K.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Oncogene","volume":"21","issue":"26","page":"4099-107","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10964660","title":"Regulation of ferritin mRNA translation in primary erythroblasts: exogenous c-Kit plus EpoR signaling mimics v-ErbA oncoprotein activity.","abstract":"In general, translation efficiency of ferritin mRNAs is modulated by variations in iron supply. In primary avian erythroblasts undergoing short-term proliferation, however, ferritin heavy chain (ferH) mRNA is repressed at all iron levels. Yet, expression of v-ErbA oncoprotein is sufficient to reinduce ferH mRNA utilization at physiological iron concentrations. Since overexpression of the receptor tyrosine kinase c-Kit and erythropoietin receptor (EpoR) stimulates long-term proliferation of primary erythroblasts like v-ErbA, we analyzed the impact of cooperation between c-Kit and EpoR on the regulation of iron storage. Whereas endogenous c-Kit in combination with exogenous EpoR had no significant effect, ectopic overexpression of both receptors abolished translational repression of ferH mRNA upon iron administration. Thus, high-intensity signaling through c-Kit plus EpoR pathways mimics the v-ErbA-mediated regulatory phenotype.","authors":"Mikulits, W., Schranzhofer, M., Deiner, EM., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Biochem Biophys Res Commun","volume":"275","issue":"2","page":"292-4","pdf":null,"JrId":"1008","fulltextlink":null,"preprintlink":null,"articledate":"2000-10-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10973316","title":"Increased bone formation and osteosclerosis in mice overexpressing the transcription factor Fra-1.","abstract":"Bone formation by osteoblasts is essential for skeletal growth and remodeling. Fra-1 is a c-Fos-related protein belonging to the AP-1 family of transcription factors. Here we show that transgenic mice overexpressing Fra-1 in various organs develop a progressive increase in bone mass leading to osteosclerosis of the entire skeleton, which is due to a cell-autonomous increase in the number of mature osteoblasts. Moreover, osteoblast differentiation, but not proliferation, was enhanced and osteoclastogenesis was also elevated in vitro. These data indicate that, unlike c-Fos, which causes osteosarcomas, Fra-1 specifically enhances bone formation, which may be exploited to stimulate bone formation in pathological conditions.","authors":"Jochum, W., David, JP., Elliott, C., Wutz, A., Plenk, H., Matsuo, K., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nat Med","volume":"6","issue":"9","page":"980-4","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"2000-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10943841","title":"The EGF receptor provides an essential survival signal for SOS-dependent skin tumor development.","abstract":"The EGF receptor (EGFR) is required for skin development and is implicated in epithelial tumor formation. Transgenic mice expressing a dominant form of Son of Sevenless (SOS-F) in basal keratinocytes develop skin papillomas with 100% penetrance. However, tumor formation is inhibited in a hypomorphic (wa2) and null EGFR background. Similarly, EGFR-deficient fibroblasts are resistant to transformation by SOS-F and rasV12, however, tumorigenicity is restored by expression of the anti-apoptotic bcl-2 gene. The K5-SOS-F papillomas and primary keratinocytesfrom wa2 mice display increased apoptosis, reduced Akt phosphorylation and grafting experiments imply a cell-autonomous requirement for EGFR in keratinocytes. Therefore, EGFR functions as a survival factor in oncogenic transformation and provides a valuable target for therapeutic intervention in a broader range of tumors than anticipated.","authors":"Sibilia, M., Fleischmann, A., Behrens, A., Stingl, L., Carroll, J., Watt, FM., Schlessinger, J., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cell","volume":"102","issue":"2","page":"211-20","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2000-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10930469","title":"The recycling endosome of Madin-Darby canine kidney cells is a mildly acidic compartment rich in raft components.","abstract":"We present a biochemical and morphological characterization of recycling endosomes containing the transferrin receptor in the epithelial Madin-Darby canine kidney cell line. We find that recycling endosomes are enriched in molecules known to regulate transferrin recycling but lack proteins involved in early endosome membrane dynamics, indicating that recycling endosomes are distinct from conventional early endosomes. We also find that recycling endosomes are less acidic than early endosomes because they lack a functional vacuolar ATPase. Furthermore, we show that recycling endosomes can be reached by apically internalized tracers, confirming that the apical endocytic pathway intersects the transferrin pathway. Strikingly, recycling endosomes are enriched in the raft lipids sphingomyelin and cholesterol as well as in the raft-associated proteins caveolin-1 and flotillin-1. These observations may suggest that a lipid-based sorting mechanism operates along the Madin-Darby canine kidney recycling pathway, contributing to the maintenance of cell polarity. Altogether, our data indicate that recycling endosomes and early endosomes differ functionally and biochemically and thus that different molecular mechanisms regulate protein sorting and membrane traffic at each step of the receptor recycling pathway.","authors":"Gagescu, R., Demaurex, N., Parton, RG., Hunziker, W., Huber, LA., Gruenberg, J.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Biol Cell","volume":"11","issue":"8","page":"2775-91","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2000-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10928999","title":"Isolation of translationally controlled mRNAs by differential screening.","abstract":"Translationalregulation plays an important role in the control of gene expression. Changes in translation initiation rates are the most common translation-regulating mechanisms, resulting in alterations in mRNA loading of ribosomes. This differential mobilization of mRNAs onto polyribosomes was used in differential screening to directly identify cDNAs whose transcripts are translationally controlled during antigenic stimulation of primary human T lymphocytes. Ribosome-free and polysome-bound mRNAs were prepared from quiescent and activated T cells and used as templates to synthesize four cDNA pools. These in turn were used as probes to hybridize four identical replicas of a T cell library or, alternatively, four cDNA arrays. Translational activation was indicated by redistribution of the hybridization signals from the ribosome-free fraction in resting T cells to the polysome-associated fraction in activated T cells. Translational repression corresponded to the opposite hybridization pattern. Fifty-two cDNAs were identified as translationally controlled by screening 472 genes in a cDNA array; 12 additional ones were obtained by screening a cDNA library. Several of the transcripts corresponded to mRNAs previously reported to be translationally controlled, thus validating the method. For the majority, however, such regulation had not yet been described. Translational control was verified for representative examples by demonstrating the redistribution of the corresponding mRNAs on polysome gradients in response to T cell activation. Our strategy therefore provides an efficient tool to directly isolate or identify translationally controlled mRNAs in a variety of physiological situations. Moreover, differential screening using arrays enables simultaneous analysis of both transcriptional and translational regulation, further enhancing the power of gene expression analysis.","authors":"Mikulits, W., Pradet-Balade, B., Habermann, B., Beug, H., Garcia-Sanz, JA., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"FASEB J","volume":"14","issue":"11","page":"1641-52","pdf":null,"JrId":"3815","fulltextlink":null,"preprintlink":null,"articledate":"2000-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19298200","title":"Cuscuta chinensis extract promotes osteoblast differentiation and mineralization in human osteoblast-like MG-63 cells.","abstract":"The aim of the present study was to investigate whether the aqueous extract of To-Sa-Za (TSZ-AE), the seed of Cuscuta chinensis Lam., which is a traditional medicinal herb commonly used in Korea and other oriental countries, could induce osteogenic activity in human osteoblast-like MG-63 cells. TSZ-AE treatment mildly promoted the proliferation of MG-63 cells at doses of 500 and 1,000 microg\/mL in the 24-hour culture period. Dose-dependent increases in alkaline phosphatase (ALP) activity and collagen synthesis were shown at 48 and 72 hours of incubation. The release of bone morphogenetic protein (BMP)-2 but not osteocalcin in the MG-63 cells was induced by TSZ-AE at 72 hours (100-1,000 microg\/mL). In addition, TSZ-AE markedly increased mRNA expression of ALP, collagen, and BMP-2 in the MG-63 cells in a dose-dependent manner. Mineralization in the culture of MG-63 cells was significantly induced at 500 and 1,000 microg\/mL TSZ-AE treatment. In conclusion, this study shows that TSZ-AE enhanced ALP activity, collagen synthesis, BMP-2 expression, and mineralization in MG-63 cells. These results strongly suggest that C. chinensis can play an important role in osteoblastic bone formation and may possibly lead to the development of bone-forming drugs.","authors":"Yang, HM., Shin, HK., Kang, YH., Kim, JK.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Med Food","volume":"12","issue":"1","page":"85-92","pdf":null,"JrId":"30114","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10871885","title":"Automated annotation of GPI anchor sites: case study C. elegans.","abstract":null,"authors":"Eisenhaber, B., Bork, P., Yuan, Y., L\u00f6ffler, G., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Trends Biochem Sci","volume":"25","issue":"7","page":"340-1","pdf":null,"JrId":"7837","fulltextlink":null,"preprintlink":null,"articledate":"2000-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19249272","title":"Sensory neurons in the Drosophila genital tract regulate female reproductive behavior.","abstract":"Females of many animal species behave very differently before and after mating. In Drosophila melanogaster, changes in female behavior upon mating are triggered by the sex peptide (SP), a small peptide present in the male's seminal fluid. SP activates a specific receptor, the sex peptide receptor (SPR), which is broadly expressed in the female reproductive tract and nervous system. Here, we pinpoint the action of SPR to a small subset of internal sensory neurons that innervate the female uterus and oviduct. These neurons express both fruitless (fru), a marker for neurons likely to have sex-specific functions, and pickpocket (ppk), a marker for proprioceptive neurons. We show that SPR expression in these fru+ ppk+ neurons is both necessary and sufficient for behavioral changes induced by mating. These neurons project to regions of the central nervous system that have been implicated in the control of reproductive behaviors in Drosophila and other insects.","authors":"H\u00e4semeyer, M., Yapici, N., Heberlein, U., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Neuron","volume":"61","issue":"4","page":"511-8","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19270159","title":"Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome.","abstract":"Duplication of eukaryotic genomes during S phase is coordinated in space and time. In order to identify zones of initiation and cell-type- as well as gender-specific plasticity of DNA replication, we profiled replication timing, histone acetylation, and transcription throughout the Drosophila genome. We observed two waves of replication initiation with many distinct zones firing in early-S phase and multiple, less defined peaks at the end of S phase, suggesting that initiation becomes more promiscuous in late-S phase. A comparison of different cell types revealed widespread plasticity of replication timing on autosomes. Most occur in large regions, but only half coincide with local differences in transcription. In contrast to confined autosomal differences, a global shift in replication timing occurs throughout the single male X chromosome. Unlike in females, the dosage-compensated X chromosome replicates almost exclusively early. This difference occurs at sites that are not transcriptionally hyperactivated, but show increased acetylation of Lys 16 of histone H4 (H4K16ac). This suggests a transcription-independent, yet chromosome-wide process related to chromatin. Importantly, H4K16ac is also enriched at initiation zones as well as early replicating regions on autosomes during S phase. Together, our study reveals novel organizational principles of DNA replication of the Drosophila genome and suggests that H4K16ac is more closely correlated with replication timing than is transcription.","authors":"Schwaiger, M., Stadler, MB., Bell, O., Kohler, H., Oakeley, EJ., Sch\u00fcbeler, D.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genes Dev","volume":"23","issue":"5","page":"589-601","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10921888","title":"Targeting of N-CoR and histone deacetylase 3 by the oncoprotein v-erbA yields a chromatin infrastructure-dependent transcriptional repression pathway.","abstract":"Transcriptional repression by nuclear hormone receptors is thought to result from a unison of targeting chromatin modification and disabling the basal transcriptional machinery. We used Xenopus oocytes to compare silencing effected by the thyroid hormone receptor (TR) and its mutated version, the oncoprotein v-ErbA, on partly and fully chromatinized TR-responsive templates in vivo. Repression by v-ErbA was not as efficient as that mediated by TR, was significantly more sensitive to histone deacetylase (HDAC) inhibitor treatment and, unlike TR, v-ErbA required mature chromatin to effect repression. We find that both v-ErbA and TR can recruit the corepressor N-CoR, but, in contrast to existing models, show a concomitant enrichment for HDAC3 that occurs without an association with Sin3, HDAC1\/RPD3, Mi-2 or HDAC5. We propose a requirement for chromatin infrastructure in N-CoR\/HDAC3-effected repression and suggest that the inability of v-ErbA to silence on partly chromatinized templates may stem from its impaired capacity to interfere with basal transcriptional machinery function. In support of this notion, we find v-ErbA to be less competent than TR for binding to TFIIB in vitro and in vivo.","authors":"Urnov, FD., Yee, J., Sachs, L., Collingwood, TN., Bauer, A., Beug, H., Shi, YB., Wolffe, AP.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"EMBO J","volume":"19","issue":"15","page":"4074-90","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2000-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10894549","title":"Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2\/M-specific promoters.","abstract":"Many cell-cycle-specific events are supported by stage-specific gene expression. In budding yeast, at least three different nuclear factors seem to cooperate in the periodic activation of G2\/M-specific genes. Here we show, by using chromatin immunoprecipitation polymerase chain reaction assays, that a positive regulator, Ndd1, becomes associated with G2\/M promoter regions in manner that depends on the stage in cell cycle. Its recruitment depends on a permanent protein-DNA complex consisting of the MADS box protein, Mcm1, and a recently identified partner Fkh2, a forkhead\/winged helix related transcription factor. The lethality of Ndd1 depletion is suppressed by fkh2 null mutations, which indicates that Fkh2 may also have a negative regulatory role in the transcription of G2\/M-induced RNAs. We conclude that Ndd1-Fkh2 interactions may be the transcriptionally important process targeted by Cdk activity.","authors":"Koranda, M., Schleiffer, A., Endler, L., Ammerer, G.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nature","volume":"406","issue":"6791","page":"94-8","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2000-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10879517","title":"Genetics. Reverse gear for Drosophila.","abstract":null,"authors":"Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nature","volume":"405","issue":"6789","page":"896-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2000-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10856241","title":"JunB suppresses cell proliferation by transcriptional activation of p16(INK4a) expression.","abstract":"A role for the transcription factor JunB in proliferation control was investigated in genetically modified mouse fibroblasts. Increased JunB expression induced high levels of the cyclin-dependent kinase inhibitor p16(INK4a), leading to premature senescence in primary cells and reduced proliferation in 3T3 cells, whereas lack of JunB expression results in decreased p16 levels. Furthermore, JunB-mediated p16 induction in 3T3 cells completely abolished cyclin D-associated kinase activity, resulting in reduced pRb hyperphosphorylation and G(1)-phase extension. Moreover, three AP1-like binding sites were identified in the p16 promoter through which JunB directly activates p16 transcription. Elevated JunB expression in 3T3 cells also inhibited Ras- and Src-mediated transformation and tumour growth in vivo. The suppressive effect of JunB on cell proliferation was shown to be dependent on p16 since it did not occur in INK4a(-\/-) fibroblasts that lack both p16 and p19(ARF). These results demonstrate that p16 is a direct transcriptional target gene of JunB and identify JunB as a negative regulator of cell proliferation.","authors":"Passegu\u00e9, E., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"EMBO J","volume":"19","issue":"12","page":"2969-79","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2000-08-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10862751","title":"Dual roles of Wnt signaling during chondrogenesis in the chicken limb.","abstract":"Long bones of the appendicular skeleton are formed from a cartilage template in a process known as endochondral bone development. Chondrocytes within this template undergo a progressive program of differentiation from proliferating to postmitotic prehypertrophic to hypertrophic chondrocytes, while mesenchymal cells immediately surrounding the early cartilage template form the perichondrium. Recently, members of the Wnt family of secreted signaling molecules have been implicated in regulating chondrocyte differentiation. We find that Wnt-5a, Wnt-5b and Wnt-4 genes are expressed in chondrogenic regions of the chicken limb: Wnt-5a is expressed in the perichondrium, Wnt-5b is expressed in a subpopulation of prehypertrophic chondrocytes and in the outermost cell layer of the perichondrium, and Wnt-4 is expressed in cells of the joint region. Misexpression experiments demonstrate that two of these Wnt molecules, Wnt-5a and Wnt-4, have opposing effects on the differentiation of chondrocytes and that these effects are mediated through divergent signaling pathways. Specifically, Wnt-5a misexpression delays the maturation of chondrocytes and the onset of bone collar formation, while Wnt-4 misexpression accelerates these two processes. Misexpression of a stabilized form of beta-catenin also results in accelerated chondrogenesis, suggesting that a beta-catenin\/TCF-LEF complex is involved in mediating the positive regulatory effect of Wnt-4. A number of the genes involved in Wnt signal tranduction, including two members of the Frizzled gene family, which are believed to encode Wnt-receptors, show very dynamic and distinct expression patterns in cartilaginous elements of developing chicken limbs. Misexpression of putative dominant-negative forms of the two Frizzled proteins results in severe shortening of the infected cartilage elements due to a delay in chondrocyte maturation, indicating that an endogenous Wnt signal does indeed function to promote chondrogenic differentiation.","authors":"Hartmann, C., Tabin, CJ.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Development","volume":"127","issue":"14","page":"3141-59","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2000-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10865206","title":"Osteoclast lineage commitment of bone marrow precursors through expression of membrane-bound TRANCE.","abstract":"Osteoclast formation from hemopoietic precursors is induced by TRANCE (also called RANKL, ODF, and OPGL), a membrane-bound ligand expressed by bone marrow stromal cells. Because soluble recombinant TRANCE is a suboptimal osteoclastogenic stimulus, and to eliminate the need for such dependence on stromal cells, membrane-bound TRANCE was expressed in hematopoietic precursors using retroviral gene transfer. Four TRANCE-expressing osteoclast cell lines were established that continuously generate large numbers of multinucleated cells and express tartrate-resistant acid phosphatase and calcitonin receptors. The multinuclear cells are long-lived and either fuse continuously with each other and with mononuclear cells to form enormous syncytia, or separate to form daughter multinuclear cells. When formed on bone, but not on plastic, the majority of multinuclear cells develop actin rings on bone, and resorb bone, suggesting that bone matrix may provide additional signals that facilitate osteoclastic functional maturation. Surprisingly, multinuclear cells originate from fusion of proliferating mononuclear cells that strongly express the mature macrophage markers F4\/80 and Fc receptor, which are not expressed by osteoclasts. These results indicate that osteoclasts can be derived from F4\/80-positive and Fc receptor-positive cells, and that TRANCE induces osteoclastic differentiation partly by suppressing the macrophage phenotype.","authors":"Lean, JM., Matsuo, K., Fox, SW., Fuller, K., Gibson, FM., Draycott, G., Wani, MR., Bayley, KE., Wong, BR., Choi, Y., Wagner, EF., Chambers, TJ.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Bone","volume":"27","issue":"1","page":"29-40","pdf":null,"JrId":"1710","fulltextlink":null,"preprintlink":null,"articledate":"2000-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-204","title":"A molecular switch orchestrates the nuclear export of human messenger RNA","abstract":null,"authors":"Hohmann, U., Graf, M., Schellhaas, U., Pacheco-Fiallos, B., Fin, L., Riabov-Bassat, D., P\u00fchringer, T., Szalay, MF., Tiri\u00e1n, L., Handler, D., Brennecke, J., Plaschka, C.","publication_status":"preprint","journalpubyear":"2024","journaltitle":"BioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.03.24.586400v1","preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.03.24.586400v1","articledate":"2024-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10858955","title":"Erythroid cell development and leukemic transformation: interplay between signal transduction, cell cycle control and oncogenes.","abstract":"Studies using genetically modified mice and ex vivo tissue culture of erythroid progenitors converge to show that generation of mature erythroid cells depends on the interplay between specific transcriptional regulators and intracellular signals controlled by cytokines and growth factors. These studies also show that terminal differentiation in the erythroid lineage is unusual since the acquisition of the phenotypic traits of mature cells occurs while the cells are still actively dividing. Furthermore, under specific stress conditions, a massive and sustained self-renewal of committed erythroid progenitors can take place to replenish the pool of terminally differentiated cells. We review here how the erythroid genetic program and its interplay with specific cytokines, growth factors and hormones controls survival, proliferation and differentiation of erythroid progenitors both in normal and stress conditions. Special emphasis is laid on our present understanding of the differences in cell cycle control, which result either in self-renewal of erythroid progenitors or in the particular cell divisions which accompany terminal differentiation. Finally, we discuss how deregulation of the various aspects of the physiological control of erythroid progenitor survival, proliferation and differentiation can lead to erythroblast transformation and erythroleukemia.","authors":"Ghysdael, J., Tran Quang, C., Deiner, EM., Dolznig, H., M\u00fcllner, EW., Beug, H.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Pathol Biol (Paris)","volume":"48","issue":"3","page":"211-26","pdf":null,"JrId":"6376","fulltextlink":null,"preprintlink":null,"articledate":"2000-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12020798","title":"Recent advances in cancer research: mouse models of tumorigenesis.","abstract":"Over the past 20 years, cancer research has gained major insights into the complexity of tumor development, in particular into the molecular mechanisms that underlie the progressive transformation of normal cells into highly malignant derivatives. It is estimated that the transformation of a normal cell to a malignant tumor cell is dependent upon a small number of genetic alterations, estimated to be within the range of four to seven rate-limiting events. Critical events in the evolution of neoplastic disease include the loss of proliferative control, the failure to undergo programmed cell death (apoptosis), the onset of neoangiogenesis, tissue remodeling, invasion of tumor cells into surrounding tissue and, finally, metastatic dissemination of tumor cells to distant organs. In patients, the molecular analysis of these multiple steps is hampered by the unavailability of tumor biopsies from all tumor stages. In contrast, mouse models of tumorigenesis allow the reproducible isolation of all tumor stages, including normal tissue, which are then amenable to pathological, genetic and biochemical analyses and, hence, have been instrumental in investigating cancer-related genes and their role in carcinogenesis. In this review, we discuss mouse tumor models that have contributed substantially to the identification and characterization of novel tumor pathways. In particular, we focus on transgenic and knockout mouse models that closely mimic human cancer and thus can be used as model systems for cancer research.","authors":"Herzig, M., Christofori, G.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Biochim Biophys Acta","volume":"1602","issue":"2","page":"97-113","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10851065","title":"Oncogenic transformation by ras and fos is mediated by c-Jun N-terminal phosphorylation.","abstract":"The nuclear phosphoprotein c-Jun is a major component of the AP-1 transcription factor, whose activity is augmented by many oncogenes. An important mechanism to stimulate AP-1 function is N-terminal phosphorylation of c-Jun at the serine residues 63 and 73 by the c-JunN-terminal kinases (JNKs). Mice and cells harboring a mutant allele of c-jun, which has the JNK phosphoacceptor serines changed to alanines (junAA), were used to determine the function of c-Jun N-terminal phosphorylation (JNP) during oncogenic transformation in vitro and in vivo. JunAA immortalized fibroblasts expressing v-ras and v-fos showed reduced tumorigenicity in nude mice, but the efficiency of v-src transformation was unaffected by the lack of JNP. To assess the significance of JNP in tumour development in vivo, two transgenic mouse tumour models were employed. Skin tumour development caused by constitutive activation of the ras pathway by K5-SOS-F expression and c-fos-induced osteosarcoma formation were impaired in mice lacking JNP. Inhibition of JNP may, therefore, be a novel therapeutic strategy to inhibit tumour growth in vivo. Oncogene (2000).","authors":"Behrens, A., Jochum, W., Sibilia, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Oncogene","volume":"19","issue":"22","page":"2657-63","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2000-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10847683","title":"Trio combines with dock to regulate Pak activity during photoreceptor axon pathfinding in Drosophila.","abstract":"Correct pathfinding by Drosophila photoreceptor axons requires recruitment of p21-activated kinase (Pak) to the membrane by the SH2-SH3 adaptor Dock. Here, we identify the guanine nucleotide exchange factor (GEF) Trio as another essential component in photoreceptor axon guidance. Regulated exchange activity of one of the two Trio GEF domains is critical for accurate pathfinding. This GEF domain activates Rac, which in turn activates Pak. Mutations in trio result in projection defects similar to those observed in both Pak and dock mutants, and trio interacts genetically with Rac, Pak, and dock. These data define a signaling pathway from Trio to Rac to Pak that links guidance receptors to the growth cone cytoskeleton. We propose that distinct signals transduced via Trio and Dock act combinatorially to activate Pak in spatially restricted domains within the growth cone, thereby controlling the direction of axon extension.","authors":"Newsome, TP., Schmidt, S., Dietzl, G., Keleman, K., Asling, B., Debant, A., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cell","volume":"101","issue":"3","page":"283-94","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2000-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10827941","title":"Splitting the chromosome: cutting the ties that bind sister chromatids.","abstract":"In eukaryotic cells, sister DNA molecules remain physically connected from their production at S phase until their separation during anaphase. This cohesion is essential for the separation of sister chromatids to opposite poles of the cell at mitosis. It also permits chromosome segregation to take place long after duplication has been completed. Recent work has identified a multisubunit complex called cohesin that is essential for connecting sisters. Proteolytic cleavage of one of cohesin's subunits may trigger sister separation at the onset of anaphase.","authors":"Nasmyth, K., Peters, JM., Uhlmann, F.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Science","volume":"288","issue":"5470","page":"1379-85","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2000-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9376370","title":"Slow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study.","abstract":"The pyridoxal 5'-phosphate (PLP)-dependent cystathionine beta-lyase (CBL) was previously found to be inhibited by the natural toxins rhizobitoxine and l-aminoethoxyvinylglycine (AVG). The present study characterizes the interaction of Escherichia coli CBL with AVG and methoxyvinylglycine (MVG) by a combination of kinetic methods and X-ray crystallography. Upon AVG treatment, time-dependent, slow-binding inhibition [Morrison, J. F. (1982) Trends Biochem. Sci. 7, 102-105] was observed due to the generation of a long-lived, slowly dissociating enzyme-inhibitor complex. Kinetic analysis revealed a one-step inhibition mechanism (CBL + AVG --&gt; CBLAVG, Ki = 1.1 +\/- 0.3 microM) with an association rate constant (k1) of 336 +\/- 40 M-1 s-1. This value is several orders of magnitude lower than typical bimolecular rate constants of ES formation, suggesting that additional steps occur before formation of the first detectable CBLAVG complex. Loss of activity is paralleled by the conversion of the pyridoxaldimine 426 nm chromophore to a 341 nm-absorbing species. On the basis of the recently solved structure of native CBL [Clausen, T., et al. (1996) J. Mol. Biol. 262, 202-224], it was possible to elucidate the X-ray structure of the CBLAVG complex and to refine it to an R-factor of 16.4% at 2.2 A resolution. The refined structure reveals the geometry of the bound inhibitor and its interactions with residues in the active site of CBL. Both the X-ray structure and the absorbance spectrum of the CBLAVG complex are compatible with a ketimine as the reaction product. Thus, the inhibitor seems to bind in a similar way to CBL as the substrate, but after alpha-proton abstraction, the reaction proceeds in a CBL nontypical manner, i.e. protonation of PLP-C4', resulting in the \"dead-end\" ketimine PLP derivative. The CBLAVG structure furthermore suggests a binding mode for rhizobitoxine and explains the failure of MVG to inhibit CBL.","authors":"Clausen, T., Huber, R., Messerschmidt, A., Pohlenz, HD., Laber, B.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Biochemistry","volume":"36","issue":"41","page":"12633-43","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1997-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16551260","title":"A central role for central tolerance.","abstract":"Recent elucidation of the role of central tolerance in preventing organ-specific autoimmunity has changed our concepts of self\/nonself discrimination. This paradigmatic shift is largely attributable to the discovery of promiscuous expression of tissue-restricted self-antigens (TRAs) by medullary thymic epithelial cells (mTECs). TRA expression in mTECs mirrors virtually all tissues of the body, irrespective of developmental or spatio-temporal expression patterns. This review summarizes current knowledge on the cellular and molecular regulation of TRA expression in mTECs, outlines relevant mechanisms of antigen presentation and modes of tolerance induction, and discusses implications for the pathogenesis of autoimmune diseases and other biological processes such as fertility, pregnancy, puberty, and tumor defense.","authors":"Kyewski, B., Klein, L.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Annu Rev Immunol","volume":"24","issue":null,"page":"571-606","pdf":null,"JrId":"1564","fulltextlink":null,"preprintlink":null,"articledate":"2006-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12015116","title":"The aurora B kinase AIR-2 regulates kinetochores during mitosis and is required for separation of homologous Chromosomes during meiosis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">12015116<\/PMID><DateCompleted><Year>2002<\/Year><Month>10<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>12<\/Volume><Issue>10<\/Issue><PubDate><Year>2002<\/Year><Month>May<\/Month><Day>14<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The aurora B kinase AIR-2 regulates kinetochores during mitosis and is required for separation of homologous Chromosomes during meiosis.<\/ArticleTitle><Pagination><MedlinePgn>798-812<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Mitotic chromosome segregation depends on bi-orientation and capture of sister kinetochores by microtubules emanating from opposite spindle poles and the near synchronous loss of sister chromatid cohesion. During meiosis I, in contrast, sister kinetochores orient to the same pole, and homologous kinetochores are captured by microtubules emanating from opposite spindle poles. Additionally, mechanisms exist that prevent complete loss of cohesion during meiosis I. These features ensure that homologs separate during meiosis I and sister chromatids remain together until meiosis II. The mechanisms responsible for orienting kinetochores in mitosis and for causing asynchronous loss of cohesion during meiosis are not well understood.","authors":"Kaitna, S., Pasierbek, P., Jantsch, M., Loidl, J., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"10","page":"798-812","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12006614","title":"A ubiquitin C-terminal hydrolase is required to maintain osmotic balance and execute actin-dependent processes in the early C. elegans embryo.","abstract":"In the early Caenorhabditis elegans embryo, establishment of cell polarity and cytokinesis are both dependent upon reorganization of the actin cytoskeleton. Mutations in the cyk-3 gene cause maternal effect embryonic lethality. Embryos produced by homozygous cyk-3 mutant animals become multinucleate. We have further analyzed the cyk-3 mutant phenotype and have found that cyk-3 mutant embryos fail to properly polarize the actin cytoskeleton and fail to segregate germline determinants. In addition, they fail to assemble an intact cleavage furrow. However, we have found that cyk-3 mutant embryos are intrinsically defective in osmotic regulation and that the cytokinesis defects can be partially rescued by providing osmotic support. The cyk-3 gene has been identified and found to encode a ubiquitin C-terminal hydrolase that is active against model substrates. These data indicate that the deubiquitination of certain substrates by CYK-3 is crucial for cellular osmoregulation. Defects in osmoregulation appear to indirectly affect actin-dependent processes.","authors":"Kaitna, S., Schnabel, H., Schnabel, R., Hyman, AA., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Cell Sci","volume":"115","issue":"Pt 11","page":"2293-302","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10760256","title":"Crystal structure of the cystine C-S lyase from Synechocystis: stabilization of cysteine persulfide for FeS cluster biosynthesis.","abstract":"FeS clusters are versatile cofactors of a variety of proteins, but the mechanisms of their biosynthesis are still unknown. The cystine C-S lyase from Synechocystis has been identified as a participant in ferredoxin FeS cluster formation. Herein, we report on the crystal structure of the lyase and of a complex with the reaction products of cystine cleavage at 1.8- and 1.55-A resolution, respectively. The sulfur-containing product was unequivocally identified as cysteine persulfide. The reactive persulfide group is fixed by a hydrogen bond to His-114 in the center of a hydrophobic pocket and is thereby shielded from the solvent. Binding and stabilization of the cysteine persulfide represent an alternative to the generation of a protein-bound persulfide by NifS-like proteins and point to the general importance of persulfidic compounds for FeS cluster assembly.","authors":"Clausen, T., Kaiser, JT., Steegborn, C., Huber, R., Kessler, D.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Proc Natl Acad Sci U S A","volume":"97","issue":"8","page":"3856-61","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2000-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10714213","title":"[Loss of junB expression causes a myeloproliferative syndrome resembling chronic myeloid leukemia].","abstract":"JunB, a member of the AP-1 family of transcription factors, has been implicated in the control of proliferation and differentiation of various cell types including myeloid cells. We found that absence of junB expression in the myeloid lineage of mice lead to a myeloproliferative syndrome resembling human chronic myeloid leukaemia. The disease was due to a cell autonomous increase in the proliferation of immature myeloid cells. These results suggest that junB is a negative regulator of myelopoiesis.","authors":"Jochum, W., Passegue, E., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Verh Dtsch Ges Pathol","volume":"83","issue":null,"page":"216-7","pdf":null,"JrId":"7961","fulltextlink":null,"preprintlink":null,"articledate":"2000-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10742604","title":"A versatile assay to study cellular uptake of gene transfer complexes by flow cytometry.","abstract":"In this study, we present a simple and reliable method to analyse the first steps of DNA-based gene delivery into eucaryotic cells, i. e. binding and internalisation of transfection complexes. Taking advantage of flow cytometry, it is possible to discriminate quantitatively between total and internal DNA on a single-cell level. Here, we use two fluorescent dyes with high specificity and affinity to double-stranded DNA that cannot penetrate the extracellular membrane of living cells. Total DNA is stained prior to complexation with the first dye and complexes are added to cells. After the incubation, only extracellular DNA remains accessible to the second dye. Cell associated fluorescence is measured simultaneously using a flow cytometer and data are analysed using a computer program capable of calculating the ratio of fluorescence intensities on a single-cell level. These ratios are indicative of the binding and internalisation kinetics of gene transfer complexes.","authors":"Ogris, M., Wagner, E., Steinlein, P.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Biochim Biophys Acta","volume":"1474","issue":"2","page":"237-43","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"2000-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10725329","title":"Hyaluronic acid (HA) binding to CD44 activates Rac1 and induces lamellipodia outgrowth.","abstract":"Both cell adhesion protein CD44 and its main ligand hyaluronic acid (HA) are thought to be involved in several processes ultimately requiring cytoskeleton rearrangements. Here, we show that the small guanine nucleotide (GTP)-binding protein, Rac1, can be activated upon HA binding to CD44. When applied locally to a passive cell edge, HA promoted the formation of lamellipodial protrusions in the direction of the stimulus. This process was inhibited by the prior injection of cells with dominant-negative N17Rac recombinant protein or by pretreatment of cells with monoclonal anti-CD44 antibodies, interfering with HA binding, implying the direct involvement of CD44 in signaling to Rac1.","authors":"Oliferenko, S., Kaverina, I., Small, JV., Huber, LA.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Cell Biol","volume":"148","issue":"6","page":"1159-64","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2000-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9021154","title":"Isolation of the Pax9 cDNA from adult human esophagus.","abstract":null,"authors":"Peters, H., Schuster, G., Neub\u00fcser, A., Richter, T., H\u00f6fler, H., Balling, R.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Mamm Genome","volume":"8","issue":"1","page":"62-4","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10712946","title":"Lineage commitment in lymphopoiesis.","abstract":"The mechanisms controlling the commitment of hematopoietic progenitor cells to the lymphoid lineages are still mostly unknown. Recent findings indicate that the earliest phase of B cell development may proceed in two steps. At the onset of B-lymphopoiesis, the transcription factors E2A and EBF coordinately activate the B-cell-specific gene expression program. Subsequently, Pax5 appears to repress the promiscuous transcription of lineage-inappropriate genes and thus commits progenitor cells to the B-lymphoid pathway by suppressing alternative cell fates. B-lineage commitment by Pax5 seems to occur in a stochastic manner in the bone marrow, as indicated by the random activation of only one of the two Pax5 alleles in early pro-B cells. In contrast, loss- and gain-of-function analyses have implicated the Notch1 receptor in the specification of the T cell fate, which may thus be controlled by instructive signals in the thymus.","authors":"Busslinger, M., Nutt, SL., Rolink, AG.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Curr Opin Immunol","volume":"12","issue":"2","page":"151-8","pdf":null,"JrId":"1461","fulltextlink":null,"preprintlink":null,"articledate":"2000-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11987132","title":"Identification of vaccine candidate antigens of Staphylococcus aureus by serological proteome analysis.","abstract":"In this study we applied serological proteome analysis (Klade, C. S. et al. Proteomics 2001, 1, 890-898) for identification of bacterial vaccine candidate antigens. First, approximately one hundred sera from healthy individuals and patients suffering from Staphylococcus aureus infections were screened for antibodies against staphylococcal lysates and recombinant proteins representing surface antigens. Two pools (healthy donors, patients) each consisting of five sera with the highest antiproteinaceous IgG reactivity were selected. Second, S. aureus COL was grown under different conditions and the number of antigens expressed was monitored by Western blot analysis. Third, surface proteins were enriched by digesting the bacterial cell wall under isotonic conditions and subsequent removal of protoplasts. These protein preparations were resolved by two-dimensional electrophoresis (2-DE) (pI 4-7). 2-DE immunoblotting using the preselected serum pools at 1:10 000-1:100 000 dilutions revealed a number of highly immunogenic staphylococcal proteins. Twenty-one spots were isolated by preparative 2-DE, and analysed by matrix-assisted laser desorption\/ionization mass spectrometry and tandem mass spectrometry sequencing of tryptic peptides. This led to the identification of 15 proteins including known and novel vaccine candidates. Seroreactivity of several antigens including serine-aspartate repeat containing protein D, immuno-dominant staphylococcal antigen and a novel 309 amino acid lipoprotein was independently confirmed by enzyme-linked immunosorbent assay and Western blot analysis of purified recombinant proteins. In conclusion, serological proteome analysis proved to be a powerful tool for the identification of novel staphylococcal antigens, which provide a basis for rational vaccine design.","authors":"Vytvytska, O., Nagy, E., Bl\u00fcggel, M., Meyer, HE., Kurzbauer, R., Huber, LA., Klade, CS.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Proteomics","volume":"2","issue":"5","page":"580-90","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11983165","title":"EphrinB phosphorylation and reverse signaling: regulation by Src kinases and PTP-BL phosphatase.","abstract":"Ephrins are cell surface-associated ligands for Eph receptors and are important regulators of morphogenic processes such as axon guidance and angiogenesis. Transmembrane ephrinB ligands act as \"receptor-like\" signaling molecules, in part mediated by tyrosine phosphorylation and by engagement with PDZ domain proteins. However, the underlying cell biology and signaling mechanisms are poorly understood. Here we show that Src family kinases (SFKs) are positive regulators of ephrinB phosphorylation and phosphotyrosine-mediated reverse signaling. EphB receptor engagement of ephrinB causes rapid recruitment of SFKs to ephrinB expression domains and transient SFK activation. With delayed kinetics, ephrinB ligands recruit the cytoplasmic PDZ domain containing protein tyrosine phosphatase PTP-BL and are dephosphorylated. Our data suggest the presence of a switch mechanism that allows a shift from phosphotyrosine\/SFK-dependent signaling to PDZ-dependent signaling.","authors":"Palmer, A., Zimmer, M., Erdmann, KS., Eulenburg, V., Porthin, A., Heumann, R., Deutsch, U., Klein, R.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Cell","volume":"9","issue":"4","page":"725-37","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2002-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10699141","title":"A syndrome involving intrauterine growth retardation, microcephaly, cerebellar hypoplasia, B lymphocyte deficiency, and progressive pancytopenia.","abstract":"We report a new complex syndrome involving profound failure to thrive with severe intrauterine growth retardation, cerebellar abnormalities, microcephaly, a complete lack of B lymphocyte development, and secondary, progressive marrow aplasia. B cell differentiation was found to be blocked at the pro-B cell stage. Although not strictly proven, a genetic origin is likely, according to similar cases reported in the literature. Three candidate genes, PAX5, encoding B cell-specific activator protein, a factor involved in B cell lineage commitment, stromal cell-derived factor 1, and CXCR4, encoding a chemokine and its receptor, respectively, were thought to be responsible for this disease, given the similarity between the phenotype of the corresponding knock-out mice and the clinical features of the patient. However, the genomic DNA sequences of these 3 genes were normal, and normal amounts of stromal cell-derived factor 1 and CXCR4 were present. These data strongly suggest that another molecule is involved in early B cell differentiation, hematopoiesis, and cerebellar development in humans.","authors":"Revy, P., Busslinger, M., Tashiro, K., Arenzana, F., Pillet, P., Fischer, A., Durandy, A.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Pediatrics","volume":"105","issue":"3","page":"E39","pdf":null,"JrId":"6405","fulltextlink":null,"preprintlink":null,"articledate":"2000-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10698925","title":"X-ray structure of MalY from Escherichia coli: a pyridoxal 5'-phosphate-dependent enzyme acting as a modulator in mal gene expression.","abstract":"MalY represents a bifunctional pyridoxal 5'-phosphate-dependent enzyme acting as a beta-cystathionase and as a repressor of the maltose regulon. Here we present the crystal structures of wild-type and A221V mutant protein. Each subunit of the MalY dimer is composed of a large pyridoxal 5'-phosphate-binding domain and a small domain similar to aminotransferases. The structural alignment with related enzymes identifies residues that are generally responsible for beta-lyase activity and depicts a unique binding mode of the pyridoxal 5'-phosphate correlated with a larger, more flexible substrate-binding pocket. In a screen for MalY mutants with reduced mal repressor properties, mutations occurred in three clusters: I, 83-84; II, 181-189 and III, 215-221, which constitute a clearly distinguished region in the MalY crystal structure far away from the cofactor. The tertiary structure of one of these mutants (A221V) demonstrates that positional rearrangements are indeed restricted to regions I, II and III. Therefore, we propose that a direct protein-protein interaction with MalT, the central transcriptional activator of the maltose system, underlies MalY-dependent repression of the maltose system.","authors":"Clausen, T., Schlegel, A., Peist, R., Schneider, E., Steegborn, C., Chang, YS., Haase, A., Bourenkov, GP., Bartunik, HD., Boos, W.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"EMBO J","volume":"19","issue":"5","page":"831-42","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2000-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11931760","title":"The dissociation of cohesin from chromosomes in prophase is regulated by Polo-like kinase.","abstract":"The separation of sister chromatids in anaphase depends on the dissociation of cohesin from chromosomes. In vertebrates, some cohesin is removed from chromosomes at the onset of anaphase by proteolytic cleavage. In contrast, the bulk of cohesin is removed from chromosomes already in prophase and prometaphase by an unknown mechanism that does not involve cohesin cleavage. We show that Polo-like kinase is required for the cleavage-independent dissociation of cohesin from chromosomes in Xenopus. Cohesin phosphorylation depends on Polo-like kinase and reduces the ability of cohesin to bind to chromatin. These results suggest that Polo-like kinase regulates the dissociation of cohesin from chromosomes early in mitosis.","authors":"Sumara, I., Vorlaufer, E., Stukenberg, PT., Kelm, O., Redemann, N., Nigg, EA., Peters, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Cell","volume":"9","issue":"3","page":"515-25","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10671371","title":"Mitotic phosphorylation of SUV39H1, a novel component of active centromeres, coincides with transient accumulation at mammalian centromeres.","abstract":"Centromeres of eukaryotes are frequently associated with constitutive heterochromatin and their activity appears to be coregulated by epigenetic modification of higher order chromatin. Recently, we isolated murine (Suv39h1) and human (SUV39H1) homologues of the dominant Drosophila suppressor of position effect variegation Su(var)3-9, which is also related to the S. pombe silencing factor Clr4. We have shown that mammalian Su(var)3-9 homologues encode novel centromeric proteins on metaphase-arrested chromosomes. Here, we describe a detailed analysis of the chromatin distribution of human SUV39H1 during the cell cycle. Although there is significant heterochromatic overlap between SUV39H1 and M31 (HP1(beta)) during interphase, mitotic SUV39H1 displays a more restricted spatial and temporal association pattern with metaphase chromosomes than M31 (HP1(beta)), or the related HP1(&amp;agr;) gene product. SUV39H1 specifically accumulates at the centromere during prometaphase but dissociates from centromeric positions at the meta- to anaphase transition. In addition, SUV39H1 selectively associates with the active centromere of a dicentric chromosome and also with a neocentromere. Interestingly, SUV39H1 is shown to be a phosphoprotein with modifications at serine and, to a lesser degree, also at threonine residues. Whereas SUV39H1 steady-state protein levels appear constant during the cell cycle, two additional phosphorylated isoforms are detected in mitotic extracts. This intriguing localisation and modification pattern would be consistent with a regulatory role(s) for SUV39H1 in participating in higher order chromatin organisation at mammalian centromeres.","authors":"Aagaard, L., Schmid, M., Warburton, P., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Cell Sci","volume":"113 ( Pt 5)","issue":null,"page":"817-29","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2000-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10655067","title":"Fosl1 is a transcriptional target of c-Fos during osteoclast differentiation.","abstract":"Osteoclasts are bone-resorbing cells derived from haematopoietic precursors of the monocyte-macrophage lineage. Mice lacking Fos (encoding c-Fos) develop osteopetrosis due to an early differentiation block in the osteoclast lineage. c-Fos is a component of the dimeric transcription factor activator protein-1 (Ap-1), which is composed mainly of Fos (c-Fos, FosB, Fra-1 and Fra-2) and Jun proteins (c-Jun, JunB and JunD). Unlike Fra-1 (encoded by Fosl1), c-Fos contains transactivation domains required for oncogenesis and cellular transformation. The mechanism by which c-Fos exerts its specific function in osteoclast differentiation is not understood. Here we show by retroviral-gene transfer that all four Fos proteins, but not the Jun proteins, rescue the differentiation block in vitro. Structure-function analysis demonstrated that the major carboxy-terminal transactivation domains of c-Fos and FosB are dispensable and that Fra-1 (which lacks transactivation domains) has the highest rescue activity. Moreover, a transgene expressing Fra-1 rescues the osteopetrosis of c-Fos-mutant mice in vivo. The osteoclast differentiation factor Rankl (also known as TRANCE, ODF and OPGL; refs 8-11) induces transcription of Fosl1 in a c-Fos-dependent manner, thereby establishing a link between Rank signalling and the expression of Ap-1 proteins in osteoclast differentiation.","authors":"Matsuo, K., Owens, JM., Tonko, M., Elliott, C., Chambers, TJ., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nat Genet","volume":"24","issue":"2","page":"184-7","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2000-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19203582","title":"Aurora B-mediated abscission checkpoint protects against tetraploidization.","abstract":"Genomic abnormalities are often seen in tumor cells, and tetraploidization, which results from failures during cytokinesis, is presumed to be an early step in cancer formation. Here, we report a cell division control mechanism that prevents tetraploidization in human cells with perturbed chromosome segregation. First, we found that Aurora B inactivation promotes completion of cytokinesis by abscission. Chromosome bridges sustained Aurora B activity to posttelophase stages and thereby delayed abscission at stabilized intercellular canals. This was essential to suppress tetraploidization by furrow regression in a pathway further involving the phosphorylation of mitotic kinesin-like protein 1 (Mklp1). We propose that Aurora B is part of a sensor that responds to unsegregated chromatin at the cleavage site. Our study provides evidence that in human cells abscission is coordinated with the completion of chromosome segregation to protect against tetraploidization by furrow regression.","authors":"Steigemann, P., Wurzenberger, C., Schmitz, MH., Held, M., Guizetti, J., Maar, S., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"136","issue":"3","page":"473-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10684760","title":"Presence of p53 mutations in feline neoplasms.","abstract":"A region from exon 4 to 8 of the tumour suppressor gene p53 was analysed in 60 feline tumours (30 fibrosarcomas, seven malignant histiocytomas, three lymphosarcomas, five basal cell tumours, five squamous cell carcinomas, two adenocarcinomas of tubular skin glands, one undifferentiated carcinoma of the skin, seven mammary carcinomas). Missense mutations were detected in two fibrosarcomas, one malignant fibrous histiocytoma, the undifferentiated carcinoma of the skin and one mammary carcinoma. One nonsense mutation was detected in one fibrosarcoma and one deletion\/frameshift-mutation was observed in one squamous cell carcinoma.","authors":"Mayr, B., Blauensteiner, J., Edlinger, A., Reifinger, M., Alton, K., Schaffner, G., Brem, G.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Res Vet Sci","volume":"68","issue":"1","page":"63-70","pdf":null,"JrId":"6920","fulltextlink":null,"preprintlink":null,"articledate":"2000-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18984389","title":"Longitudinal alteration of the occlusal plane and development of different dentoskeletal frames during growth.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18984389<\/PMID><DateCompleted><Year>2008<\/Year><Month>11<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2016<\/Year><Month>11<\/Month><Day>24<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1097-6752<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>134<\/Volume><Issue>5<\/Issue><PubDate><Year>2008<\/Year><Month>Nov<\/Month><\/PubDate><\/JournalIssue><Title>American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics<\/Title><ISOAbbreviation>Am J Orthod Dentofacial Orthop<\/ISOAbbreviation><\/Journal><ArticleTitle>Longitudinal alteration of the occlusal plane and development of different dentoskeletal frames during growth.<\/ArticleTitle><Pagination><MedlinePgn>602.e1-11; discussion 602-3<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.ajodo.2008.02.017<\/ELocationID><Abstract><AbstractText Label=\"INTRODUCTION\" NlmCategory=\"BACKGROUND\">Valuable information about growth and development in different types of occlusions and skeletal frames can be obtained by analyzing longitudinal data, particularly the functional significance of the occlusal plane; this information is important for understanding the etiology, diagnosis, and treatment of malocclusion. The purpose of this study was to investigate the relationship between the cant of the occlusal plane and mandibular position to establish a functional determinant in the development of different dentoskeletal frames in longitudinal growth samples.","authors":"Tanaka, EM., Sato, S.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Am J Orthod Dentofacial Orthop","volume":"134","issue":"5","page":"602.e1-11; discussion 602-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18757399","title":"Podoplanin is a novel fos target gene in skin carcinogenesis.","abstract":"Expression and function of the oncogenic transcription factor activator protein (AP-1; mainly composed of Jun and Fos proteins) is required for neoplastic transformation of keratinocytes in vitro and tumor promotion as well as malignant progression in vivo. Here, we describe the identification of 372 differentially expressed genes comparing skin tumor samples of K5-SOS-F transgenic mice (Fos(f\/f) SOS(+)) with samples derived from animals with a specific deletion of c-Fos in keratinocytes (Fos(Deltaep) SOS(+)). Fos-dependent transcription of selected genes was confirmed by quantitative real-time PCR analysis using tumor samples and mouse back skin treated with the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA). One of the most differentially expressed genes encodes the small mucin-like glycoprotein Podoplanin (Pdpn), whose expression correlates with malignant progression in mouse tumor model systems and human cancer. We found Pdpn and Fos expression in chemically induced mouse skin tumors, and detailed analysis of the Pdpn gene promoter revealed impaired activity in Fos-deficient mouse embryonic fibroblasts, which could be restored by ectopic Fos expression. Direct Fos protein binding to the Pdpn promoter was shown by chromatin immunoprecipitation and a TPA-induced complex at a TPA-responsive element-like motif in the proximal promoter was identified by electrophoretic mobility shift assays. In summary, we could define a Fos-dependent genetic program in a well-established model of skin tumors. Systematic analysis of these novel target genes will guide us in elucidating the molecular mechanisms of AP-1-regulated pathways that are critically implicated in neoplastic transformation and\/or malignant progression.","authors":"Durchdewald, M., Guinea-Viniegra, J., Haag, D., Riehl, A., Lichter, P., Hahn, M., Wagner, EF., Angel, P., Hess, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cancer Res","volume":"68","issue":"17","page":"6877-83","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10648243","title":"Analysis of Drosophila photoreceptor axon guidance in eye-specific mosaics.","abstract":"During development of the adult Drosophila visual system, axons of the eight photoreceptors in each ommatidium fasciculate together and project as a single bundle towards the optic lobes of the brain. Within the brain, individual photoreceptor axons from each bundle then seek specific targets in distinct layers of the optic lobes. The axons of photoreceptors R1-R6 terminate in the lamina, while R7 and R8 axons pass through the lamina to terminate in separate layers of the medulla. To identify genes required for photoreceptor axon guidance, including those with essential functions during early development, we have devised a strategy for the simple and efficient generation of genetic mosaics in which mutant photoreceptor axons innervate a predominantly wild-type brain. In a large-scale saturation mutagenesis performed using this system, we recovered new alleles of the gene encoding the receptor tyrosine phosphatase PTP69D. PTP69D has previously been shown to function in the correct targeting of motor axons in the embryo and R1-R6 axons in the visual system. Here, we show that PTP69D is also required for correct targeting of R7 axons. Whereas mutant R1-R6 axons occasionally extend beyond their normal targets in the lamina, mutant R7 axons often fail to reach their targets in the medulla, stopping instead at the same level as the R8 axon. These targeting errors are difficult to reconcile with models in which PTP69D plays an instructive role in photoreceptor axon targeting, as previously proposed. Rather, we suggest that PTP69D plays a permissive role, perhaps reducing the adhesion of R1-R6 and R7 growth cones to the pioneer R8 axon so that they can respond independently to their specific targeting cues.","authors":"Newsome, TP., Asling, B., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Development","volume":"127","issue":"4","page":"851-60","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2000-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18755006","title":"Filopodia formation induced by active mDia2\/Drf3.","abstract":"Filopodia are rod-shaped cell surface protrusions composed of a parallel bundle of actin filaments. Since filopodia frequently emanate from lamellipodia, it has been proposed that they form exclusively by the convergence and elongation of actin filaments generated in lamellipodia networks. However, filopodia form without Arp2\/3-complex, which is essential for lamellipodia formation, indicating that actin filaments in filopodia may be generated by other nucleators. Here we analyzed the effects of ectopic expression of GFP-tagged full length or a constitutively active variant of the human formin mDia2\/Drf3. By contrast to the full-length molecule, which did not affect cell behaviour and was entirely cytosolic, active Drf3 lacking the C-terminal regulatory region (Drf3DeltaDAD) induced the formation of filopodia and accumulated at their tips. Low expression of Drf3DeltaDAD induced rod-shaped or tapered filopodia, whereas over-expression resulted in multiple, club-shaped filopodia. The clubs were filled with densely bundled actin filaments, whose number but not packing density decreased further away from the tip. Interestingly, clubs frequently increased in width after protrusion beyond the cell periphery, which correlated with increased amounts of Drf3DeltaDAD at their tips. These data suggest Drf3-induced filopodia form and extend by de novo nucleation of actin filaments instead of convergent elongation. Finally, Drf3DeltaDAD also induced the formation of unusual, lamellipodia-like structures, which contained both lamellipodial markers and the prominent filopodial protein fascin. Microarray analyses revealed highly variable Drf3 expression levels in different commonly used cell lines, reflecting the need for more detailed analyses of the functions of distinct formins in actin cytoskeleton turnover and different cell types.","authors":"Block, J., Stradal, TE., H\u00e4nisch, J., Geffers, R., K\u00f6stler, SA., Urban, E., Small, JV., Rottner, K., Faix, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Microsc","volume":"231","issue":"3","page":"506-17","pdf":null,"JrId":"4961","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11955008","title":"N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence.","abstract":"Myristoylation by the myristoyl-CoA:protein N-myristoyltransferase (NMT) is an important lipid anchor modification of eukaryotic and viral proteins. Automated prediction of N-terminal N-myristoylation from the substrate protein sequence alone is necessary for large-scale sequence annotation projects but it requires a low rate of false positive hits in addition to a sufficient sensitivity. Our previous analysis of substrate protein sequence variability, NMT sequences and 3D structures has revealed motif properties in addition to the known PROSITE motif that are utilized in a new predictor described here. The composite prediction function (with separate ad hoc parameterization (a) for queries from non-fungal eukaryotes and their viruses and (b) for sequences from fungal species) consists of terms evaluating amino acid type preferences at sequences positions close to the N terminus as well as terms penalizing deviations from the physical property pattern of amino acid side-chains encoded in multi-residue correlation within the motif sequence. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set as well as with kinetic data for model substrates. The sensitivity in recognizing documented NMT substrates is above 95 % for both taxon-specific versions. The corresponding rate of false positive prediction (for sequences with an N-terminal glycine residue) is close to 0.5 %; thus, the technique is applicable for large-scale automated sequence database annotation. The predictor is available as public WWW-server with the URL http:\/\/mendel.imp.univie.ac.at\/myristate\/. Additionally, we propose a version of the predictor that identifies a number of proteolytic protein processing sites at internal glycine residues and that evaluates possible N-terminal myristoylation of the protein fragments.A scan of public protein databases revealed new potential NMT targets for which the myristoyl modification may be of critical importance for biological function. Among others, the list includes kinases, phosphatases, proteasomal regulatory subunit 4, kinase interacting proteins KIP1\/KIP2, protozoan flagellar proteins, homologues of mitochondrial translocase TOM40, of the neuronal calcium sensor NCS-1 and of the cytochrome c-type heme lyase CCHL. Analyses of complete eukaryote genomes indicate that about 0.5 % of all encoded proteins are apparent NMT substrates except for a higher fraction in Arabidopsis thaliana ( approximately 0.8 %).","authors":"Maurer-Stroh, S., Eisenhaber, B., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Mol Biol","volume":"317","issue":"4","page":"541-57","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11953459","title":"Fra-1 substitutes for c-Fos in AP-1-mediated signal transduction in retinal apoptosis.","abstract":"Lack of the AP-1 member c-Fos protects photoreceptors against light-induced apoptosis, a model for retinal degeneration. In mice, light damage increases the activity of the transcription factor AP-1, while pharmacological suppression of AP-1 prevents apoptosis, suggesting the involvement of pro-apoptotic AP-1 target genes. Recently, however, it was shown that photoreceptors expressing Fra-1 in place of c-Fos (Fos (Fosl1\/Fosl1) ) are apoptosis competent despite the lack of transactivation domains in Fra-1. Here, we show that morphological features of light-induced apoptosis were indistinguishable in Fos (Fosl1\/Fosl1) and wild-type mice. Furthermore, light exposure comparably increased AP-1 activity in both genotypes. Opposite to wild-type mice, Fra-1, but not c-Fos, was detectable in AP-1 complexes of Fos (Fosl1\/Fosl1) mice. Importantly, AP-1 responsiveness for glucocorticoid receptor-mediated inhibition was preserved in Fos (Fosl1\/Fosl1) mice. Thus, Fra-1 takes over for c-Fos in pro- and anti-apoptotic signal transduction. As Fra-1 lacks transactivation domains, AP-1 may not induce, but rather suppress genes in retinal light damage.","authors":"Wenzel, A., Iseli, HP., Fleischmann, A., Hafezi, F., Grimm, C., Wagner, EF., Rem\u00e9, CE.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Neurochem","volume":"80","issue":"6","page":"1089-94","pdf":null,"JrId":"5004","fulltextlink":null,"preprintlink":null,"articledate":"2002-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10619433","title":"Dispatched, a novel sterol-sensing domain protein dedicated to the release of cholesterol-modified hedgehog from signaling cells.","abstract":"Members of the Hedgehog (Hh) family of secreted signaling proteins function as potent short-range organizers in animal development. Their range of action is limited by a C-terminal cholesterol tether and the upregulation of Patched (Ptc) receptor levels. Here we identify a novel segment-polarity gene in Drosophila, dispatched (disp), and demonstrate that its product is required in sending cells for normal Hh function. In the absence of Disp, cholesterol-modified but not cholesterol-free Hh is retained in these cells, indicating that Disp functions to release cholesterol-anchored Hh. Despite their opposite roles, Disp and Ptc share structural homology in the form of a sterol-sensing domain, suggesting that release and sequestration of cholesterol-modified Hh may be based on related molecular pathways.","authors":"Burke, R., Nellen, D., Bellotto, M., Hafen, E., Senti, KA., Dickson, BJ., Basler, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cell","volume":"99","issue":"7","page":"803-15","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2000-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10580006","title":"The glucocorticoid receptor is required for stress erythropoiesis.","abstract":"The glucocorticoid receptor (GR) coordinates a multitude of physiological responses in vivo. In vitro, glucocorticoids are required for sustained proliferation of erythroid progenitors (ebls). Here, we analyze the impact of the GR on erythropoiesis in vivo, using GR-deficient mice or mice expressing a GR defective for transactivation. In vitro, sustained proliferation of primary ebls requires an intact GR. In vivo, the GR is required for rapid expansion of ebls under stress situations like erythrolysis or hypoxia. A particular, GR-sensitive progenitor could be identified as being responsible for the stress response. Thus, GR-mediated regulation of ebl proliferation is essential for stress erythropoiesis in vivo.","authors":"Bauer, A., Tronche, F., Wessely, O., Kellendonk, C., Reichardt, HM., Steinlein, P., Sch\u00fctz, G., Beug, H.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Genes Dev","volume":"13","issue":"22","page":"2996-3002","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2000-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11948429","title":"Differential effects of JNK1 and JNK2 on signal specific induction of apoptosis.","abstract":"The c-Jun N-terminal kinases (JNKs) are activated by a variety of stress inducing agents and are thought to regulate apoptosis in a cell type and signal-specific manner. We have used fibroblasts lacking JNK1 or JNK2 to define their roles in response to different stress signals. Lack of JNK1 results in reduced c-Jun phosphorylation and resistance to UV-induced cell death. JNK2 deficient cells show increased sensitivity to UV irradiation which correlates with elevated and sustained phosphorylation of JNK1 and c-Jun. On the contrary, both Jnk1-\/- and Jnk2-\/- cells were more sensitive to tumor necrosis factor - alpha (TNF-alpha) and sorbitol-induced cell death. Treatment of Jnk1-\/- cells with these reagents resulted in reduced JNK activity and a concomitant reduction of c-Jun phosphorylation, suggesting that phosphorylation of c-Jun does not influence TNF-alpha and sorbitol-induced apoptosis in fibroblasts. Moreover, both JNK1 and JNK2 appear to negatively regulate apoptosis independent of c-Jun phosphorylation. These data provide genetic evidence that although the JNK pathway is activated by a plethora of signals, it is required only for the induction of UV-induced cell death in a c-Jun phosphorylation-dependent manner, but not for TNF-alpha and sorbitol-induced apoptosis.","authors":"Hochedlinger, K., Wagner, EF., Sabapathy, K.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Oncogene","volume":"21","issue":"15","page":"2441-5","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2002-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10559486","title":"Defective neural tube morphogenesis and altered apoptosis in the absence of both JNK1 and JNK2.","abstract":"Mice lacking both c-Jun-NH(2)-terminal kinases (JNK1 and JNK2) were generated to define their roles in development. Jnk1\/jnk2 double mutant fetuses die around embryonic day 11 (E11) and were found to display an open neural tube (exencephaly) at the hindbrain level with reduced apoptosis in the hindbrain neuroepithelium at E9.25. In contrast, a dramatic increase in cell death was observed one day later at E10.5 in both the hindbrain and forebrain regions. Moreover, about 25% of jnk1-\/-jnk2+\/- fetuses display exencephaly probably due to reduced levels of JNK proteins, whereas jnk1+\/-jnk2-\/- mice are viable. These results assign both pro- and anti-apoptotic functions for JNK1 and JNK2 in the development of the fetal brain.","authors":"Sabapathy, K., Jochum, W., Hochedlinger, K., Chang, L., Karin, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Mech Dev","volume":"89","issue":"1-2","page":"115-24","pdf":null,"JrId":"1825","fulltextlink":null,"preprintlink":null,"articledate":"2000-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17931617","title":"Distinct and overlapping roles of single-repeat MYB genes in root epidermal patterning.","abstract":"Cell specification in the root epidermis of Arabidopsis generates a position-dependent pattern of root-hair cells and non-hair cells. Here we conduct a comprehensive analysis of the five members of a single-repeat R3 MYB gene family, including CAPRICE (CPC), TRIPTYCHON (TRY), ENHANCER of TRY and CPC 1, 2, and 3 (ETC1, ETC2, and ETC3), and study their role and functional relationship in root epidermal cell specification. Based on genetic and expression analyses, CPC, TRY and ETC1, but not ETC2 or ETC3, promote the hair cell fate by inhibiting non-hair specification. Further, we find that single-repeat MYB activity is required for epidermal patterning throughout root development, beginning during embryogenesis. We also identify a novel regulatory interaction whereby GLABRA2 (GL2) promotes TRY (but not CPC or ETC1) expression in the root epidermis, which generates a second lateral inhibition feedback loop. Gene fusion experiments combining CPC regulatory elements with protein-coding regions of each single-repeat MYB gene suggest that all five proteins are functionally similar, although TRY and ETC2 exhibit distinctions from CPC\/ETC1\/ETC3. These results provide new insight into the function of these single-repeat MYBs and suggest that divergence of their regulatory sequences is largely responsible for their distinct roles in epidermal cell patterning.","authors":"Simon, M., Lee, MM., Lin, Y., Gish, L., Schiefelbein, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Dev Biol","volume":"311","issue":"2","page":"566-78","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11944946","title":"Dcas is required for importin-alpha3 nuclear export and mechano-sensory organ cell fate specification in Drosophila.","abstract":"We have studied the in vivo function and tissue specificity of Dcas, the Drosophila ortholog of CAS, the importin beta-like export receptor for importin alpha. While dcas mRNA is specifically expressed in the embryonic central nervous system, Dcas protein is maternally supplied to all embryonic cells and its nuclear\/cytoplasmic distribution varies in different tissues and times in development. Unexpectedly, hypomorphic alleles of dcas show specific transformations in mechano-sensory organ cell identity, characteristic of mutations that increase Notch signaling. Dcas is essential for efficient importin-alpha3 nuclear export in mechano-sensory cells and the surrounding epidermal cells and is indirectly required for the import of one component of the Notch pathway, but not others tested. We interpret the specificity of the dcas phenotype as indicating that one or more Notch signaling components are particularly sensitive to a disruption in nuclear protein import. We propose that mutations in house keeping genes often cause specific developmental phenotypes, such as those observed in many human genetic disorders.","authors":"Tekotte, H., Berdnik, D., T\u00f6r\u00f6k, T., Buszczak, M., Jones, LM., Cooley, L., Knoblich, JA., Davis, I.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Dev Biol","volume":"244","issue":"2","page":"396-406","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10524622","title":"Commitment to the B-lymphoid lineage depends on the transcription factor Pax5.","abstract":"The Pax5 gene encoding the B-cell-specific activator protein (BSAP) is expressed within the haematopoietic system exclusively in the B-lymphoid lineage, where it is required in vivo for progression beyond the pro-B-cell stage. However, Pax5 is not essential for in vitro propagation of pro-B cells in the presence of interleukin-7 and stromal cells. Here we show that pro-B cells lacking Pax5 are also incapable of in vitro B-cell differentiation unless Pax5 expression is restored by retroviral transduction. Pax5-\/- pro-B cells are not restricted in their lineage fate, as stimulation with appropriate cytokines induces them to differentiate into functional macrophages, osteoclasts, dendritic cells, granulocytes and natural killer cells. As expected for a clonogenic haematopoietic progenitor with lymphomyeloid developmental potential, the Pax5-\/- pro-B cell expresses genes of different lineage-affiliated programmes, and restoration of Pax5 activity represses this lineage-promiscuous transcription. Pax5 therefore plays an essential role in B-lineage commitment by suppressing alternative lineage choices.","authors":"Nutt, SL., Heavey, B., Rolink, AG., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nature","volume":"401","issue":"6753","page":"556-62","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1999-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10500174","title":"Expression of the CDH1-associated form of the anaphase-promoting complex in postmitotic neurons.","abstract":"The anaphase-promoting complex\/cyclosome (APC) is a tightly cell cycle-regulated ubiquitin-protein ligase that targets cyclin B and other destruction box-containing proteins for proteolysis at the end of mitosis and in G1. Recent work has shown that activation of the APC in mitosis depends on CDC20, whereas APC is maintained active in G1 via association with the CDC20-related protein CDH1. Here we show that the mitotic activator CDC20 is the only component of the APC ubiquitination pathway whose expression is restricted to proliferating cells, whereas the APC and CDH1 are also expressed in several mammalian tissues that predominantly contain differentiated cells, such as adult brain. Immunocytochemical analyses of cultured rat hippocampal neurons and of mouse and human brain sections indicate that the APC and CDH1 are ubiquitously expressed in the nuclei of postmitotic terminally differentiated neurons. The APC purified from brain contains all core subunits known from proliferating cells and is tightly associated with CDH1. Purified brain APC(CDH1) has a high cyclin B ubiquitination activity that depends less on the destruction box than on the activity of mitotic APC(CDC20). On the basis of these results, we propose that the functions of APC(CDH1) are not restricted to controlling cell-cycle progression but may include the ubiquitination of yet unidentified substrates in differentiated cells.","authors":"Gieffers, C., Peters, BH., Kramer, ER., Dotti, CG., Peters, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Proc Natl Acad Sci U S A","volume":"96","issue":"20","page":"11317-22","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1999-10-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11552264","title":"[Involvement of phosphoinositide 3-kinases and phosphoinositide phosphatases in immune responses, glucose metabolism and tumorigenesis].","abstract":null,"authors":"Sasaki, T., Sasaki, J., Suzuki, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Tanpakushitsu Kakusan Koso","volume":"46","issue":"12","page":"1820-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10498682","title":"Vertebrate Sprouty genes are induced by FGF signaling and can cause chondrodysplasia when overexpressed.","abstract":"The Drosophila sprouty gene encodes an antagonist of FGF and EGF signaling whose expression is induced by the signaling pathways that it inhibits. Here we describe a family of vertebrate Sprouty homologs and demonstrate that the regulatory relationship with FGF pathways has been conserved. In both mouse and chick embryos, Sprouty genes are expressed in intimate association with FGF signaling centers. Gain- and loss-of-function experiments demonstrate that FGF signaling induces Sprouty gene expression in various tissues. Sprouty overexpression obtained by infecting the prospective wing territory of the chick embryo with a retrovirus containing a mouse Sprouty gene causes a reduction in limb bud outgrowth and other effects consistent with reduced FGF signaling from the apical ectodermal ridge. At later stages of development in the infected limbs there was a dramatic reduction in skeletal element length due to an inhibition of chondrocyte differentiation. The results provide evidence that vertebrate Sprouty proteins function as FGF-induced feedback inhibitors, and suggest a possible role for Sprouty genes in the pathogenesis of specific human chondrodysplasias caused by activating mutations in Fgfr3.","authors":"Minowada, G., Jarvis, LA., Chi, CL., Neub\u00fcser, A., Sun, X., Hacohen, N., Krasnow, MA., Martin, GR.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Development","volume":"126","issue":"20","page":"4465-75","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"1999-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10477820","title":"Stabilization of gene delivery systems by freeze-drying.","abstract":"Freeze-drying of three different forms of gene delivery systems was performed using a controlled two-step drying process and 10% sucrose as lyoprotectant. Complexes of pCMVL plasmid with transferrin-conjugated polyethylenimine, adenovirus-enhanced transferrinfection consisting of pCMVL\/transferrin-polylysine complexes linked to inactivated adenovirus particles, and a recombinant, E1-defective adenovirus expressing a luciferase reporter gene were tested. Three weeks after freeze-drying the reagents were rehydrated with water and tested for transfection activity. Luciferase gene expression levels were retained at high levels in all three systems, in contrast to reagents stored in solution. The use of the lyoprotectant was essential. In the absence of sucrose the transfection activities dropped by a factor of 100-1000. The data suggest freeze-drying as a useful method for stabilization and storage of standardized batches of transfection agents.","authors":"Talsma, H., Cherng, J., Lehrmann, H., Kursa, M., Ogris, M., Hennink, WE., Cotten, M., Wagner, E.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Int J Pharm","volume":"157","issue":"2","page":"233-238","pdf":null,"JrId":"21201","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11397097","title":"Surface map comparison: studying function diversity of homologous proteins.","abstract":"A simplified protein surface cartography approach has been developed to assist in the analysis of surface features in homologous families, and thus to predict conservation or divergence of protein functions and protein-protein interaction patterns. A spherical approximation of protein surface was used, with a focus on charged and hydrophobic residues. The resulting surface map allows for qualitative analysis and comparison of surfaces of proteins, but can also be used to define a simple numerical measure of map similarity between two or more proteins. The latter was shown to be useful for function based classifications within large protein families. Surface map analysis was tested on several test cases: haemoglobins, death domains and TRAF domains. It was shown that surface map comparison allows a better function prediction than general sequence analysis methods and can reproduce known examples of functional variation within a divergent group of proteins. In another example, we predict novel, unexpected sets of common functional properties for seemingly distant members of a large group of divergent proteins. The method was also shown to be robust enough to allow using protein models from comparative modelling instead of experimental structures.","authors":"Pawlowski, K., Godzik, A.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Mol Biol","volume":"309","issue":"3","page":"793-806","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10438597","title":"The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity.","abstract":"Cystathionine gamma-synthase catalyses the committed step of de novo methionine biosynthesis in micro-organisms and plants, making the enzyme an attractive target for the design of new antibiotics and herbicides. The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum has been solved by Patterson search techniques using the structure of Escherichia coli cystathionine gamma-synthase. The model was refined at 2.9 A resolution to a crystallographic R -factor of 20.1 % (Rfree25.0 %). The physiological substrates of the enzyme, L-homoserine phosphate and L-cysteine, were modelled into the unliganded structure. These complexes support the proposed ping-pong mechanism for catalysis and illustrate the dissimilar substrate specificities of bacterial and plant cystathionine gamma-synthases on a molecular level. The main difference arises from the binding modes of the distal substrate groups (O -acetyl\/succinyl versusO -phosphate). Central in fixing the distal phosphate of the plant CGS substrate is an exposed lysine residue that is strictly conserved in plant cystathionine gamma-synthases whereas bacterial enzymes carry a glycine residue at this position. General insight regarding the reaction specificity of transsulphuration enzymes is gained by the comparison to cystathionine beta-lyase from E. coli, indicating the mechanistic importance of a second substrate binding site for L-cysteine which leads to different chemical reaction types.","authors":"Steegborn, C., Messerschmidt, A., Laber, B., Streber, W., Huber, R., Clausen, T.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Mol Biol","volume":"290","issue":"5","page":"983-96","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1999-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18641959","title":"Purification of Drosophila protein complexes for mass spectrometry.","abstract":"Drosophila melanogaster is one of the best characterized model systems for genetic analysis. Protein biochemical methods have lagged behind for quite some time but meanwhile have reached a state where protein interaction networks can be elucidated at a similar speed and accuracy as genetic interactions. Therefore, Drosophila now offers the advantages of both genetic and biochemical approaches. Here, we present a basic method for the purification of the endogenous Par-6\/aPKC protein complex, which plays a central role in orchestrating asymmetric cell divisions in the developing nervous system of Drosophila. The procedure can be subdivided into the following steps: acquisition of sufficient starting material, complex stabilization by crosslinking (optional), purification of the protein complex by immunoprecipitation, separation of the isolated material on a polyacrylamide gel, sample preparation for mass spectrometry, and sample analysis. The protocol can easily be adapted to different affinity-tagged or endogenous protein complexes of interest.","authors":"J\u00fcschke, C., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Methods Mol Biol","volume":"420","issue":null,"page":"347-58","pdf":null,"JrId":"2488","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9333292","title":"[Receptor mediated gene transfer in squamous epithelial carcinoma of the head-neck area].","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9333292<\/PMID><DateCompleted><Year>1997<\/Year><Month>10<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2012<\/Year><Month>11<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0935-8943<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>76<\/Volume><Issue>7<\/Issue><PubDate><Year>1997<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>Laryngo- rhino- otologie<\/Title><ISOAbbreviation>Laryngorhinootologie<\/ISOAbbreviation><\/Journal><ArticleTitle>[Receptor mediated gene transfer in squamous epithelial carcinoma of the head-neck area].<\/ArticleTitle><Pagination><MedlinePgn>411-4<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The \"Adeno-Virus-Enhanced-Receptor-Mediated\" (AVET)-System uses the receptor-mediated endocytosis route to introduce DNA into mammalian cells. By the help of a replication defective adenovirus with endosomolytic activity the coentry of receptor-bound DNA particles is faciliated. The transport to the nucleus followed by gene expression is multifold enhanced.","authors":"Wollenberg, B., Schmidt, W., Schmitt, B., Lang, S., Zeidler, R.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Laryngorhinootologie","volume":"76","issue":"7","page":"411-4","pdf":null,"JrId":"1306","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10421570","title":"Chromosome segregation: Samurai separation of Siamese sisters.","abstract":"How do cells ensure that sister chromatids are precisely partitioned in mitosis? New studies on budding yeast have revealed that sister chromatid separation at anaphase requires endoproteolytic cleavage of a protein that maintains the association between sister chromatids.","authors":"Glotzer, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Curr Biol","volume":"9","issue":"14","page":"R531-4","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1999-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18634584","title":"Live imaging of glioblastoma cells in brain tissue shows requirement of actin bundles for migration.","abstract":"Live-cell imaging of glioblastoma U373 and U87 cells transfected with actin cytoskeleton markers has been used to study there-arrangements that are associated with migration in two- and three-dimensional matrices and in brain tissue. In collagen gels and in brain slices, both cell types developed neuronal-like processes with ruffling membranes and filopodia. Blebbing cells were also observed, but these were mainly immobile. The retraction of trailing cell processes in a tissue environment was associated with the transient development and contraction of bundles of axial stress fibers. The inhibition of Rho-kinase caused glioblastoma cells in brain slices to become immobile and develop neurite-like processes at random, which indicates the requirement of Rho signaling and contractility for migration. Actin stress fibers were also observed in glioblastoma cells injected into the brains of living mice. Thus, invading glioblastoma cells use neurite-like extensions to penetrate between neuronal fibers and contractile actin bundles for traction of the cell body.","authors":"Caspani, EM., Echevarria, D., Rottner, K., Small, JV.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Neuron Glia Biol","volume":"2","issue":"2","page":"105-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-09-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9310335","title":"Specific muscle identities are regulated by Kr\u00fcppel during Drosophila embryogenesis.","abstract":"During Drosophila embryogenesis, mesodermal cells are recruited to form a complex pattern of larval muscles. The formation of the pattern is initiated by the segregation of a special class of founder myoblasts. Single founders fuse with neighbouring nonfounder myoblasts to form the precursors of individual muscles. Founders and the muscles that they give rise to have specific patterns of gene expression and it has been suggested that it is the expression of these founder cell genes that determines individual muscle attributes such as size, shape, insertion sites and innervation. We find that the segmentation gene Kr\u00fcppel is expressed in a subset of founders and muscles, regulates specific patterns of gene expression in these cells and is required for the acquisition of proper muscle identity. We show that gain and loss of Kr\u00fcppel expression in sibling founder cells is sufficient to switch these cells, and the muscles that they give rise to, between alternative cell fates.","authors":"Ruiz-G\u00f3mez, M., Romani, S., Hartmann, C., J\u00e4ckle, H., Bate, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Development","volume":"124","issue":"17","page":"3407-14","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11927562","title":"Impaired postnatal hepatocyte proliferation and liver regeneration in mice lacking c-jun in the liver.","abstract":"Mice lacking the AP-1 transcription factor c-jun die at mid-gestation showing heart defects and impaired hepatogenesis. To inactivate c-jun in hepatocytes, mice carrying a floxed c-jun allele were generated. Perinatal liver-specific c-jun deletion caused reduced hepatocyte proliferation and decreased body size. After partial hepatectomy, half of the mutants died and liver regeneration was impaired. This phenotype was not present in mice lacking the N-terminal phosphorylation sites of c-Jun. The failure to regenerate was accompanied by increased cell death and lipid accumulation in hepatocytes. Moreover, cyclin-dependent kinases and several cell cycle regulators were affected, resulting in inefficient G(1)-S phase progression. These studies identify c-Jun as a critical regulator of hepatocyte proliferation and survival during liver development and regeneration.","authors":"Behrens, A., Sibilia, M., David, JP., M\u00f6hle-Steinlein, U., Tronche, F., Sch\u00fctz, G., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"EMBO J","volume":"21","issue":"7","page":"1782-90","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2002-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8978760","title":"Report of the second international workshop on human chromosome 1 mapping 1995.","abstract":null,"authors":"Weith, A., Brodeur, GM., Bruns, GA., Matise, TC., Mischke, D., Nizetic, D., Seldin, MF., van Roy, N., Vance, J.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Cytogenet Cell Genet","volume":"72","issue":"2-3","page":"114-44","pdf":null,"JrId":"3248","fulltextlink":null,"preprintlink":null,"articledate":"1997-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10412984","title":"A central role for cohesins in sister chromatid cohesion, formation of axial elements, and recombination during yeast meiosis.","abstract":"A multisubunit complex, called cohesin, containing Smc1p, Smc3p, Scc1p, and Scc3p, is required for sister chromatid cohesion in mitotic cells. We show here that Smc3p and a meiotic version of Scc1p called Rec8p are required for cohesion between sister chromatids, for formation of axial elements, for reciprocal recombination, and for preventing hyperresection of double-strand breaks during meiosis. Both Rec8p and Smc3p colocalize with chromosome cores independently of synapsis during prophase I and largely disappear from chromosome arms after pachytene but persist in the neighborhood of centromeres until the onset of anaphase II. The eukaryotic cell's cohesion apparatus is required both for the repair of recombinogenic lesions and for chromosome segregation and therefore appears to lie at the heart of the meiotic process.","authors":"Klein, F., Mahr, P., Galova, M., Buonomo, SB., Michaelis, C., Nairz, K., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cell","volume":"98","issue":"1","page":"91-103","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10397722","title":"The glucocorticoid receptor cooperates with the erythropoietin receptor and c-Kit to enhance and sustain proliferation of erythroid progenitors in vitro.","abstract":"Although erythropoietin (Epo) is essential for the production of mature red blood cells, the cooperation with other factors is required for a proper balance between progenitor proliferation and differentiation. In avian erythroid progenitors, steroid hormones cooperate with tyrosine kinase receptors to induce renewal of erythroid progenitors. We examined the role of corticosteroids in the in vitro expansion of primary human erythroid cells in liquid cultures and colony assays. Dexamethasone (Dex), a synthetic glucocorticoid hormone, cooperated with Epo and stem cell factor to induce erythroid progenitors to undergo 15 to 22 cell divisions, corresponding to a 10(5)- to 10(6)-fold amplification of erythroid cells. Dex acted directly on erythroid progenitors and maintained the colony-forming capacity of the progenitor cells expanded in liquid cultures. The hormone delayed terminal differentiation into erythrocytes, which was assayed by morphology, hemoglobin accumulation, and the expression of genes characteristic for immature cells. Sustained proliferation of erythroid progenitors could be induced equally well from purified erythroid burst-forming units (BFU-E), from CD34(+) blast cells, and from bone marrow depleted from CD34(+) cells.","authors":"von Lindern, M., Zauner, W., Mellitzer, G., Steinlein, P., Fritsch, G., Huber, K., L\u00f6wenberg, B., Beug, H.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Blood","volume":"94","issue":"2","page":"550-9","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18620484","title":"Rapid large-scale expansion of functional mesenchymal stem cells from unmanipulated bone marrow without animal serum.","abstract":"Adult mesenchymal stem cells (MSCs) are considered as valuable mediators for tissue regeneration and cellular therapy. This study was performed to develop conditions for regularly propagating a clinical quantity of &gt; 2 x 10(8) MSCs without animal serum from small bone marrow (BM) aspiration volumes within short time. We established optimized culture conditions with pooled human platelet lysate (pHPL) replacing fetal bovine serum (FBS) for MSC propagation. MSC quality, identity, purity, and function were assessed accordingly. Biologic safety was determined by bacterial\/fungal\/mycoplasma\/endotoxin testing and genomic stability by array comparative genomic hybridization (CGH). We demonstrate that unmanipulated BM can be used to efficiently initiate MSC cultures without the need for cell separation. Just diluting 1.5-5 mL heparinized BM per 500 mL minimum essential medium supplemented with L-glutamine, heparin, and 10% pHPL sufficiently supported the safe propagation of 7.8 +\/- 1.5 x 10(8) MSCs within a single 11- to 16-day primary culture under defined conditions. This procedure also resulted in sustained MSC colony recovery. MSC purity, immune phenotype, and in vitro differentiation potential fully matched current criteria. Despite high proliferation rate, MSCs showed genomic stability in array CGH. This easy single-phase culture procedure can build the basis for standardized manufacturing of MSC-based therapeutics under animal serum-free conditions for dose-escalated cellular therapy and tissue engineering.","authors":"Schallmoser, K., Rohde, E., Reinisch, A., Bartmann, C., Thaler, D., Drexler, C., Obenauf, AC., Lanzer, G., Linkesch, W., Strunk, D.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Tissue Eng Part C Methods","volume":"14","issue":"3","page":"185-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-05-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14562846","title":"4D imaging to assay complex dynamics in live specimens.","abstract":"A full understanding of cellular dynamics is often difficult to obtain from time-lapse microscopy of single optical sections. New microscopes and image-processing software are now making it possible to rapidly record three-dimensional images over time. This four-dimensional imaging allows precise quantitative analysis and enhances visual exploration of data by allowing cellular structures to be interactively displayed from many angles. It has become a key tool for understanding the complex organization of biological processes in live specimens.","authors":"Gerlich, D., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nat Cell Biol","volume":"Suppl","issue":null,"page":"S14-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-10-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10407276","title":"Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines.","abstract":"Epitope tagging of proteins as a strategy for the analysis of function, interactions and the subcellular distribution of proteins has become widely used. In the yeast Saccharomyces cerevisiae, molecular biological techniques have been developed that use a simple PCR-based strategy to introduce epitope tags to chromosomal loci (Wach et al., 1994). To further employ the power of this strategy, a variety of novel tags was constructed. These tags were combined with different selectable marker genes, resulting in PCR amplificable modules. Only one set of primers is required for the amplification of any module. Furthermore, convenient laboratory techniques are described that facilitate the genetic manipulations of yeast strains, as well as the analysis of the epitope-tagged proteins.","authors":"Knop, M., Siegers, K., Pereira, G., Zachariae, W., Winsor, B., Nasmyth, K., Schiebel, E.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Yeast","volume":"15","issue":"10B","page":"963-72","pdf":null,"JrId":"8252","fulltextlink":null,"preprintlink":null,"articledate":"1999-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11919635","title":"Rac GTPases control axon growth, guidance and branching.","abstract":"Growth, guidance and branching of axons are all essential processes for the precise wiring of the nervous system. Rho family GTPases transduce extracellular signals to regulate the actin cytoskeleton. In particular, Rac has been implicated in axon growth and guidance. Here we analyse the loss-of-function phenotypes of three Rac GTPases in Drosophila mushroom body neurons. We show that progressive loss of combined Rac1, Rac2 and Mtl activity leads first to defects in axon branching, then guidance, and finally growth. Expression of a Rac1 effector domain mutant that does not bind Pak rescues growth, partially rescues guidance, but does not rescue branching defects of Rac mutant neurons. Mosaic analysis reveals both cell autonomous and non-autonomous functions for Rac GTPases, the latter manifesting itself as a strong community effect in axon guidance and branching. These results demonstrate the central role of Rac GTPases in multiple aspects of axon development in vivo, and suggest that axon growth, guidance and branching could be controlled by differential activation of Rac signalling pathways.","authors":"Ng, J., Nardine, T., Harms, M., Tzu, J., Goldstein, A., Sun, Y., Dietzl, G., Dickson, BJ., Luo, L.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nature","volume":"416","issue":"6879","page":"442-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19259264","title":"A toolkit and robust pipeline for the generation of fosmid-based reporter genes in C. elegans.","abstract":"Engineering fluorescent proteins into large genomic clones, contained within BACs or fosmid vectors, is a tool to visualize and study spatiotemporal gene expression patterns in transgenic animals. Because these reporters cover large genomic regions, they most likely capture all cis-regulatory information and can therefore be expected to recapitulate all aspects of endogenous gene expression. Inserting tags at the target gene locus contained within genomic clones by homologous recombination (\"recombineering\") represents the most straightforward method to generate these reporters. In this methodology paper, we describe a simple and robust pipeline for recombineering of fosmids, which we apply to generate reporter constructs in the nematode C. elegans, whose genome is almost entirely covered in an available fosmid library. We have generated a toolkit that allows for insertion of fluorescent proteins (GFP, YFP, CFP, VENUS, mCherry) and affinity tags at specific target sites within fosmid clones in a virtually seamless manner. Our new pipeline is less complex and, in our hands, works more robustly than previously described recombineering strategies to generate reporter fusions for C. elegans expression studies. Furthermore, our toolkit provides a novel recombineering cassette which inserts a SL2-spliced intercistronic region between the gene of interest and the fluorescent protein, thus creating a reporter controlled by all 5' and 3' cis-acting regulatory elements of the examined gene without the direct translational fusion between the two. With this configuration, the onset of expression and tissue specificity of secreted, sub-cellular compartmentalized or short-lived gene products can be easily detected. We describe other applications of fosmid recombineering as well. The simplicity, speed and robustness of the recombineering pipeline described here should prompt the routine use of this strategy for expression studies in C. elegans.","authors":"Tursun, B., Cochella, L., Carrera, I., Hobert, O.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS One","volume":"4","issue":"3","page":"e4625","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11919634","title":"Rac function and regulation during Drosophila development.","abstract":"Rac GTPases regulate the actin cytoskeleton to control changes in cell shape. To date, the analysis of Rac function during development has relied heavily on the use of dominant mutant isoforms. Here, we use loss-of-function mutations to show that the three Drosophila Rac genes, Rac1, Rac2 and Mtl, have overlapping functions in the control of epithelial morphogenesis, myoblast fusion, and axon growth and guidance. They are not required for the establishment of planar cell polarity, as had been suggested on the basis of studies using dominant mutant isoforms. The guanine nucleotide exchange factor, Trio, is essential for Rac function in axon growth and guidance, but not for epithelial morphogenesis or myoblast fusion. Different Rac activators thus act in different developmental processes. The specific cellular response to Rac activation may be determined more by the upstream activator than the specific Rac protein involved.","authors":"Hakeda-Suzuki, S., Ng, J., Tzu, J., Dietzl, G., Sun, Y., Harms, M., Nardine, T., Luo, L., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nature","volume":"416","issue":"6879","page":"438-42","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10384316","title":"Nuclear matrix attachment regions confer long-range function upon the immunoglobulin mu enhancer.","abstract":null,"authors":"Fern\u00e1ndez, LA., Winkler, M., Forrester, W., Jenuwein, T., Grosschedl, R.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"63","issue":null,"page":"515-24","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1999-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11884518","title":"Hepatocytes convert to a fibroblastoid phenotype through the cooperation of TGF-beta1 and Ha-Ras: steps towards invasiveness.","abstract":"In hepatocarcinogenesis, it is an open question whether transforming growth factor (TGF)-beta1 provides a tumor-suppressive or a tumor-promoting role. To address this question, we employed immortalized murine hepatocytes, which display a high degree of differentiation and, expectedly, arrest in the G1 phase under exposure to TGF-beta1. These hepatocytes maintain epithelial polarization upon expression of oncogenic Ha-Ras. However, Ras-transformed hepatocytes rapidly convert to a spindle-shaped, fibroblastoid morphology upon treatment with TGF-beta1, which no longer inhibits proliferation. This epithelial to fibroblastoid conversion (EFC) is accompanied by disruption of intercellular contacts and remodeling of the cytoskeletal framework. Fibroblastoid derivatives form elongated branching cords in collagen gels and grow to severely vascularized tumors in vivo, indicating their increased malignancy and even invasive phenotype. Additionally, fibroblastoid cells secrete strongly enhanced levels of TGF-beta1, suggesting an autocrine regulation of TGF-beta signaling. Expression profiling further revealed that the loss of the adhesion component E-cadherin correlates with the upregulation of its transcriptional repressor Snail in fibroblastoid cells. Moreover, the phosphoinositide 3-OH (PI3) kinase pathway was required for the maintenance of EFC, as inhibition of PI3 kinase reverted fibroblastoid cells to an epithelial-like phenotype. Taken together, these data indicate a dual role of TGF-beta1 in hepatocytes: it induces proliferation arrest but provides a crucial function in promoting late malignant events in collaboration with activated Ha-Ras.","authors":"Gotzmann, J., Huber, H., Thallinger, C., Wolschek, M., Jansen, B., Schulte-Hermann, R., Beug, H., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Cell Sci","volume":"115","issue":"Pt 6","page":"1189-202","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10329618","title":"Sister chromatid separation and chromosome re-duplication are regulated by different mechanisms in response to spindle damage.","abstract":"In yeast, anaphase entry depends on Pds1 proteolysis, while chromosome re-duplication in the subsequent S-phase involves degradation of mitotic cyclins such as Clb2. Sequential proteolysis of Pds1 and mitotic cyclins is mediated by the anaphase-promoting complex (APC). Lagging chromosomes or spindle damage are detected by surveillance mechanisms (checkpoints) which block anaphase onset, cytokinesis and DNA re-replication. Until now, the MAD and BUB genes implicated in this regulation were thought to function in a single pathway that blocks APC activity. We show that spindle damage blocks sister chromatid separation solely by inhibiting APCCdc20-dependent Pds1 proteolysis and that this process requires Mad2. Blocking APCCdh1-mediated Clb2 proteolysis and chromosome re-duplication does not require Mad2 but a different protein, Bub2. Our data imply that Mad1, Mad2, Mad3 and Bub1 regulate APCCdc20, whereas Bub2 regulates APCCdh1.","authors":"Alexandru, G., Zachariae, W., Schleiffer, A., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"EMBO J","volume":"18","issue":"10","page":"2707-21","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1999-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9295023","title":"Normal thymic selection, normal viability and decreased lymphoproliferation in T cell receptor-transgenic CTLA-4-deficient mice.","abstract":"CTLA-4 is a T cell surface receptor essential for the negative regulation of T cell activation. In the CTLA-4-deficient mouse, a dramatic accumulation of activated peripheral T cells effects extensive damage to host tissues, resulting in mortality within 5 weeks of age. To determine whether the accumulation of activated T cells in CTLA-4(-\/-) mice is due to a defect in thymic selection, we examined negative selection in CTLA-4(-\/-) mice using two transgenic T cell receptor (TCR) models of thymic selection. Neither the H-Y-specific TCR nor the lymphocytic choriomeningitis virus (LCMV)-specific TCR transgenic models revealed a defect in positive or negative selection in CTLA-4(-\/-) mice in vivo or in vitro. In fact, the negatively selecting phenotype of male H-YTCR-transgenic mice greatly mitigated the accumulation of activated peripheral T cells. Further, peripheral CTLA-4(-\/-) T cells expressing a single LMCV-specific transgenic TCR did not have an activated phenotype, indicating that CTLA-4(-\/-) T cells require specific antigen for proliferation. These results demonstrate that specific antigen is required for the lymphoproliferation observed in CTLA-4(-\/-) mice, and that CTLA-4 deficiency does not lead to a gross defect in negative selection.","authors":"Waterhouse, P., Bachmann, MF., Penninger, JM., Ohashi, PS., Mak, TW.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Eur J Immunol","volume":"27","issue":"8","page":"1887-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11867540","title":"Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing.","abstract":"Su(var)3-9 is a dominant modifier of heterochromatin-induced gene silencing. Like its mammalian and Schizosaccharomyces pombe homologues, Su(var) 3-9 encodes a histone methyltransferase (HMTase), which selectively methylates histone H3 at lysine 9 (H3-K9). In Su(var)3-9 null mutants, H3-K9 methylation at chromocentre heterochromatin is strongly reduced, indicating that SU(VAR)3-9 is the major heterochromatin-specific HMTase in Drosophila. SU (VAR)3-9 interacts with the heterochromatin-associated HP1 protein and with another silencing factor, SU(VAR)3-7. Notably, SU(VAR)3-9-HP1 interaction is interdependent and governs distinct localization patterns of both proteins. In Su(var)3-9 null mutants, concentration of HP1 at the chromocentre is nearly lost without affecting HP1 accumulation at the fourth chromosome. By contrast, in HP1 null mutants SU(VAR)3-9 is no longer restricted at heterochromatin but broadly dispersed across the chromosomes. Despite this interdependence, Su(var)3-9 dominates the PEV modifier effects of HP1 and Su(var)3-7 and is also epistatic to the Y chromosome effect on PEV. Finally, the human SUV39H1 gene is able to partially rescue Su(var)3-9 silencing defects. Together, these data indicate a central role for the SU(VAR)3-9 HMTase in heterochromatin-induced gene silencing in Drosophila.","authors":"Schotta, G., Ebert, A., Krauss, V., Fischer, A., Hoffmann, J., Rea, S., Jenuwein, T., Dorn, R., Reuter, G.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"EMBO J","volume":"21","issue":"5","page":"1121-31","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11739945","title":"Stem cells. PTEN--coupling tumor suppression to stem cells?","abstract":null,"authors":"Penninger, JM., Woodgett, J.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Science","volume":"294","issue":"5549","page":"2116-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10210145","title":"Efficient gene delivery into human dendritic cells by adenovirus polyethylenimine and mannose polyethylenimine transfection.","abstract":"Gene-modified human dendritic cells (DCs) were generated by transfection with adenovirus polyethylenimine DNA (Ad\/PEI\/DNA) and mannose polyethylenimine DNA (ManPEI\/DNA) complexes. Ad\/PEI\/DNA complexes have plasmid DNA bound to adenovirus particles by PEI and deliver DNA into cells via the adenovirus infection route. Such transfection complexes yield high transduction levels and sustained expression of luciferase and green fluorescent protein reporter genes and were almost as effective as recombinant adenovirus vectors. ManPEI\/DNA complexes rely on uptake by receptor-mediated endocytosis via mannose receptor, which is highly expressed on DCs. While gene delivery by ManPEI\/DNA complexes was less efficient than by Ad\/PEI transfection, incorporation of adenovirus particles in ManPEI\/DNA transfection complexes further enhanced transduction efficiencies and transgene expression. We also demonstrate that Ad\/PEI-transfected DCs are competent in stimulating T cell proliferation in allogeneic and autologous mixed lymphocyte reactions, and in activating T cells from T cell receptor (TCR)-transgenic mice in an antigen-specific manner. Thus, the present study establishes the following relative order of transduction efficiencies of viral and nonviral gene delivery systems for primary human DCs: recombinant adenovirus &gt; Ad\/PEI = Ad\/ManPEI &gt; ManPEI &gt; PEI. Ad\/PEI and ManPEI transfection modes represent particularly versatile transduction systems for DCs, with ManPEI being built up exclusively of synthetic compounds.","authors":"Diebold, SS., Lehrmann, H., Kursa, M., Wagner, E., Cotten, M., Zenke, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Hum Gene Ther","volume":"10","issue":"5","page":"775-86","pdf":null,"JrId":"1041","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11815965","title":"Precise microdissection of human bladder carcinomas reveals divergent tumor subclones in the same tumor.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11815965<\/PMID><DateCompleted><Year>2002<\/Year><Month>02<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>20<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0008-543X<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>94<\/Volume><Issue>1<\/Issue><PubDate><Year>2002<\/Year><Month>Jan<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Cancer<\/Title><ISOAbbreviation>Cancer<\/ISOAbbreviation><\/Journal><ArticleTitle>Precise microdissection of human bladder carcinomas reveals divergent tumor subclones in the same tumor.<\/ArticleTitle><Pagination><MedlinePgn>104-10<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Human bladder carcinoma is thought to arise from a field change that affects the entire urothelium. Whether independently transformed urothelial cell populations exist in the same patient is uncertain.","authors":"Cheng, L., Gu, J., Ulbright, TM., MacLennan, GT., Sweeney, CJ., Zhang, S., Sanchez, K., Koch, MO., Eble, JN.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cancer","volume":"94","issue":"1","page":"104-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10212249","title":"Kinetics and inhibition of recombinant human cystathionine gamma-lyase. Toward the rational control of transsulfuration.","abstract":"The gene encoding human cystathionine gamma-lyase was cloned from total cellular Hep G2 RNA. Fusion to a T7 promoter allowed expression in Escherichia coli, representing the first mammalian cystathionine gamma-lyase overproduced in a bacterial system. About 90% of the heterologous gene product was insoluble, and renaturation experiments from purified inclusion bodies met with limited success. About 5 mg\/liter culture of human cystathionine gamma-lyase could also be extracted from the soluble lysis fraction, employing a three-step native procedure. While the enzyme showed high gamma-lyase activity toward L-cystathionine (Km = 0.5 mM, Vmax = 2.5 units\/mg) with an optimum pH of 8.2, no residual cystathionine beta-lyase behavior and only marginal reactivity toward L-cystine and L-cysteine were detected. Inhibition studies were performed with the mechanism-based inactivators propargylglycine, trifluoroalanine, and aminoethoxyvinylglycine. Propargylglycine inactivated human cystathionine gamma-lyase much more strongly than trifluoroalanine, in agreement with the enzyme's preference for C-gamma-S bonds. Aminoethoxyvinylglycine showed slow and tight binding characteristics with a Ki of 10.5 microM, comparable with its effect on cystathionine beta-lyase. The results have important implications for the design of specific inhibitors for transsulfuration components.","authors":"Steegborn, C., Clausen, T., Sondermann, P., Jacob, U., Worbs, M., Marinkovic, S., Huber, R., Wahl, MC.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Biol Chem","volume":"274","issue":"18","page":"12675-84","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10222126","title":"Subunits and substrates of the anaphase-promoting complex.","abstract":"The initiation of anaphase and exit from mitosis depend on a ubiquitination complex called the anaphase-promoting complex (APC) or cyclosome. The APC is composed of more than 10 constitutive subunits and associates with additional regulatory factors in mitosis and during the G1 phase of the cell cycle. At the metaphase-anaphase transition the APC ubiquitinates proteins such as Pds1 in budding yeast and Cut2 in fission yeast whose subsequent degradation by the 26S proteasome is essential for the initiation of sister chromatid separation. Later in anaphase and telophase the APC promotes the inactivation of the mitotic cyclin-dependent protein kinase 1 by ubiquitinating its activating subunit cyclin B. The APC also mediates the ubiquitin-dependent proteolysis of several other mitotic regulators, including other protein kinases, APC activators, spindle-associated proteins, and inhibitors of DNA replication.","authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Exp Cell Res","volume":"248","issue":"2","page":"339-49","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1999-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10318877","title":"Characterization of the DOC1\/APC10 subunit of the yeast and the human anaphase-promoting complex.","abstract":"The anaphase-promoting complex\/cyclosome (APC) is a ubiquitin-protein ligase whose activity is essential for progression through mitosis. The vertebrate APC is thought to be composed of 8 subunits, whereas in budding yeast several additional APC-associated proteins have been identified, including a 33-kDa protein called Doc1 or Apc10. Here, we show that Doc1\/Apc10 is a subunit of the yeast APC throughout the cell cycle. Mutation of Doc1\/Apc10 inactivates the APC without destabilizing the complex. An ortholog of Doc1\/Apc10, which we call APC10, is associated with the APC in different vertebrates, including humans and frogs. Biochemical fractionation experiments and mass spectrometric analysis of a component of the purified human APC show that APC10 is a genuine APC subunit whose cellular levels or association with the APC are not cell cycle-regulated. We have further identified an APC10 homology region, which we propose to call the DOC domain, in several protein sequences that also contain either cullin or HECT domains. Cullins are present in several ubiquitination complexes including the APC, whereas HECT domains represent the catalytic core of a different type of ubiquitin-protein ligase. DOC domains may therefore be important for reactions catalyzed by several types of ubiquitin-protein ligases.","authors":"Grossberger, R., Gieffers, C., Zachariae, W., Podtelejnikov, AV., Schleiffer, A., Nasmyth, K., Mann, M., Peters, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Biol Chem","volume":"274","issue":"20","page":"14500-7","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18516089","title":"Atypical ubiquitin chains: new molecular signals. 'Protein Modifications: Beyond the Usual Suspects' review series.","abstract":"Ubiquitin (Ub) is a small protein modifier that regulates many biological processes, including gene transcription, cell-cycle progression, DNA repair, apoptosis, virus budding and receptor endocytosis. Ub can be conjugated to target proteins either as a monomer or as Ub chains that vary in length and linkage type. The various types of Ub modification are linked to distinct physiological functions in cells. MonoUb, for example, regulates DNA repair and receptor endocytosis, whereas lysine 48-linked Ub chains label proteins for proteasomal degradation. More recently, the importance of chains conjugated through the other six lysines in Ub, known as atypical Ub chains, has been revealed. Atypical chains can be homotypic, sequentially using the same lysine residue in Ub for conjugation; mixed-linkage, utilizing several distinct lysines to connect consecutive Ub moieties; or heterologous, connecting Ub with other Ub-like modifiers. Here, we describe recent progress in the understanding of atypical Ub chain assembly and their recognition by Ub-binding domains, and we discuss further their functional roles in vivo.","authors":"Ikeda, F., Dikic, I.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO Rep","volume":"9","issue":"6","page":"536-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18498734","title":"Mind bomb 1-expressing intermediate progenitors generate notch signaling to maintain radial glial cells.","abstract":"Notch signaling is critical for the stemness of radial glial cells (RGCs) during embryonic neurogenesis. Although Notch-signal-receiving events in RGCs have been well characterized, the signal-sending mechanism by the adjacent cells is poorly understood. Here, we report that conditional inactivation of mind bomb-1 (mib1), an essential component for Notch ligand endocytosis, in mice using the nestin and hGFAP promoters resulted in complete loss of Notch activation, which leads to depletion of RGCs, and premature differentiation into intermediate progenitors (IPs) and finally neurons, which were reverted by the introduction of active Notch1. Interestingly, Mib1 expression is restricted in the migrating IPs and newborn neurons, but not in RGCs. Moreover, sorted Mib1+ IPs and neurons can send the Notch signal to neighboring cells. Our results reveal that not only newborn neurons but also IPs are essential Notch-ligand-presenting cells for maintaining RGC stemness during both symmetric and asymmetric divisions.","authors":"Yoon, KJ., Koo, BK., Im, SK., Jeong, HW., Ghim, J., Kwon, MC., Moon, JS., Miyata, T., Kong, YY.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Neuron","volume":"58","issue":"4","page":"519-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18451846","title":"Neuroscience: hidden female talent.","abstract":null,"authors":"Yu, JY., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"453","issue":"7191","page":"41-2","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17545586","title":"DNA methylation and complete transcriptional silencing of cancer genes persist after depletion of EZH2.","abstract":"Recent work suggests a link between the polycomb group protein EZH2 and mediation of gene silencing in association with maintenance of DNA methylation. However, we show that whereas basally expressed target cancer genes with minimal DNA methylation have increased transcription during EZH2 knockdown, densely DNA hypermethylated and silenced genes retain their methylation and remain transcriptionally silent. These results suggest that EZH2 can modulate transcription of basally expressed genes but not silent genes that are densely DNA methylated.","authors":"McGarvey, KM., Greene, E., Fahrner, JA., Jenuwein, T., Baylin, SB.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cancer Res","volume":"67","issue":"11","page":"5097-102","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18428249","title":"Preparation of adenovirus-polylysine-DNA complexes.","abstract":"This unit describes preparation of adenovirus-polylysine-DNA complexes, which is useful for transfection of DNA into a variety of cell types. A DNA complex is prepared with biotinylated adenovirus and streptavidin-polylysine, coupled to transferrin, and used to transfect cells. Several support protocols describe methods for adenovirus growth and purification, biotinylation, inactivation with psoralen, and quantitation of the adenovirus particles. Additional support protocols describes preparation of streptavidin-polylysine and transferrin-polylysine, necessary for the basic procedure. The DNA used for transfection must be free of lipopolysaccharide (LPS), and two methods for removing LPS are described. A more direct polylysine-virus linkage that is simple and requires no exotic reagents can be used for transfection. This protocol requires polylysine-modified adenovirus, prepared as described. An alternate protocol describes transfecting cells with free virus and DNA condensed with a polycation.","authors":"Cotten, M., Baker, A., Birnstiel, ML., Zatloukal, K., Wagner, E.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Curr Protoc Hum Genet","volume":"Chapter 12","issue":null,"page":"Unit 12.3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-05-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10195434","title":"Conformational study of the HIV-1 reverse transcriptase inhibitor 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT).","abstract":"The conformations of the HIV-1 reverse transcriptase inhibitor 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) are calculated by semiempirical and mainly by ab initio methods in order to estimate the potential for the rotation around the carbon sulfur single bond. The results are compared to X-ray structures of HEPT associated to the HIV-1 reverse transcriptase. The NMR spectra of the compound are calculated to obtain some information about its structure in solution. The structure of HEPT in the complex is analysed to study the intermolecular interactions between the inhibitor and the surrounding protein, which determine the geometry of the inhibition complex.","authors":"Lawtrakul, L., Hannongbua, S., Beyer, A., Wolschann, P.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Biol Chem","volume":"380","issue":"2","page":"265-7","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10195416","title":"The IMP and European molecular biology: moving the centre eastwards. Institute of Molecular Pathology.","abstract":null,"authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Biol Chem","volume":"380","issue":"2","page":"113-4","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9288898","title":"Isolation and amino acid sequence analysis reveal an ancient evolutionary origin of the cleavage stage (CS) histones of the sea urchin.","abstract":"The cleavage stage (CS) H1, H2A, and H2B histones of the sea urchin, which have previously been identified by their distinct electrophoretic mobility on Triton\/acid\/urea gels, are known to be maternally expressed during oogenesis and have been implicated in chromatin remodeling of the male pronucleus following fertilization. Here, we describe the isolation of these three CS histones by reverse-phase HPLC chromatography. Moreover, a novel CS H3 protein was identified by the same purification procedure. A low incorporation of radioactive amino acids into the CS histones during early development revealed that the bulk of these proteins in the blastula embryo are derived from the maternal pool of the egg. Amino acid analysis, together with the previously described electrophoretic mobilities, unequivocally identified the purified proteins as CS histones. Peptide sequence analysis confirmed the novel nature of the CS variants as they are distantly related to the early, late, and sperm histone subtypes of the sea urchin. The CS H1 protein displays highest sequence similarity with the H1M (B4) histone of Xenopus laevis, indicating that the frog H1M protein may be a vertebrate homologue of the CS H1 histone. These data suggest an ancient evolutionary origin and wide distribution of the CS histone variants.","authors":"Brandt, WF., Schwager, SU., Rodrigues, JA., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Eur J Biochem","volume":"247","issue":"3","page":"784-91","pdf":null,"JrId":"3607","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10949293","title":"Regulation of chromatin structure by site-specific histone H3 methyltransferases.","abstract":"The organization of chromatin into higher-order structures influences chromosome function and epigenetic gene regulation. Higher-order chromatin has been proposed to be nucleated by the covalent modification of histone tails and the subsequent establishment of chromosomal subdomains by non-histone modifier factors. Here we show that human SUV39H1 and murine Suv39h1--mammalian homologues of Drosophila Su(var)3-9 and of Schizosaccharomyces pombe clr4--encode histone H3-specific methyltransferases that selectively methylate lysine 9 of the amino terminus of histone H3 in vitro. We mapped the catalytic motif to the evolutionarily conserved SET domain, which requires adjacent cysteine-rich regions to confer histone methyltransferase activity. Methylation of lysine 9 interferes with phosphorylation of serine 10, but is also influenced by pre-existing modifications in the amino terminus of H3. In vivo, deregulated SUV39H1 or disrupted Suv39h activity modulate H3 serine 10 phosphorylation in native chromatin and induce aberrant mitotic divisions. Our data reveal a functional interdependence of site-specific H3 tail modifications and suggest a dynamic mechanism for the regulation of higher-order chromatin.","authors":"Rea, S., Eisenhaber, F., O'Carroll, D., Strahl, BD., Sun, ZW., Schmid, M., Opravil, S., Mechtler, K., Ponting, CP., Allis, CD., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nature","volume":"406","issue":"6796","page":"593-9","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2000-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10086388","title":"Mice lacking the poly(ADP-ribose) polymerase gene are resistant to pancreatic beta-cell destruction and diabetes development induced by streptozocin.","abstract":"Human type 1 diabetes results from the selective destruction of insulin-producing pancreatic beta cells during islet inflammation. Cytokines and reactive radicals released during this process contribute to beta-cell death. Here we show that mice with a disrupted gene coding for poly (ADP-ribose) polymerase (PARP-\/- mice) are completely resistant to the development of diabetes induced by the beta-cell toxin streptozocin. The mice remained normoglycemic and maintained normal levels of total pancreatic insulin content and normal islet ultrastructure. Cultivated PARP-\/- islet cells resisted streptozocin-induced lysis and maintained intracellular NAD+ levels. Our results identify NAD+ depletion caused by PARP activation as the dominant metabolic event in islet-cell destruction, and provide information for the development of strategies to prevent the progression or manifestation of the disease in individuals at risk of developing type 1 diabetes.","authors":"Burkart, V., Wang, ZQ., Radons, J., Heller, B., Herceg, Z., Stingl, L., Wagner, EF., Kolb, H.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nat Med","volume":"5","issue":"3","page":"314-9","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"105","title":"[Effect of carbidine on conditioned defense reflexes].","abstract":"Chronic experiments were conducted on rats and rabbits; a study was made of the effect of carbidine on the conditioned defence reflexes in stimulation of the mesencephalic part of the reticular formation. Carbidine prevented the depression of the conditioned defence reflexes caused by stimulation of the mesencephalic portion of the reticular formation. This pointed to its depressive influence on the mentioned structures, and was confirmed by experiments on rabbits in recording changes in biocurrents under conditions of stimulation of the mesencephalic reticular formation.","authors":"Barkov, NK., Ostrovskaia, RU.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biull Eksp Biol Med","volume":"79","issue":"4","page":"61-4","pdf":null,"JrId":"1214","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18362182","title":"Building the actin cytoskeleton: filopodia contribute to the construction of contractile bundles in the lamella.","abstract":"Filopodia are rodlike extensions generally attributed with a guidance role in cell migration. We now show in fish fibroblasts that filopodia play a major role in generating contractile bundles in the lamella region behind the migrating front. Filopodia that developed adhesion to the substrate via paxillin containing focal complexes contributed their proximal part to stress fiber assembly, and filopodia that folded laterally contributed to the construction of contractile bundles parallel to the cell edge. Correlated light and electron microscopy of cells labeled for actin and fascin confirmed integration of filopodia bundles into the lamella network. Inhibition of myosin II did not subdue the waving and folding motions of filopodia or their entry into the lamella, but filopodia were not then integrated into contractile arrays. Comparable results were obtained with B16 melanoma cells. These and other findings support the idea that filaments generated in filopodia and lamellipodia for protrusion are recycled for seeding actomyosin arrays for use in retraction.","authors":"Nemethova, M., Auinger, S., Small, JV.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Cell Biol","volume":"180","issue":"6","page":"1233-44","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11809716","title":"Overexpression of vascular endothelial growth factor-A165 enhances tumor angiogenesis but not metastasis during beta-cell carcinogenesis.","abstract":"The pivotal role of vascular endothelial growth factor (VEGF-A) in the regulation of angiogenesis, in particular in the onset and maintenance of tumor angiogenesis, has been demonstrated repeatedly in experimental model systems and, more recently, in clinical trials. Experimental evidence has also suggested that up-regulated expression of VEGF-A may cooperate with other genetic or epigenetic changes to induce or accelerate tumor progression to invasive and metastatic cancers. Here we report the generation of transgenic mouse lines that express human VEGF-A165 under the control of the rat insulin promoter in the beta cells of pancreatic islets of Langerhans (Rip1VEGF-A). These mice do not exhibit detectable changes in islet development, vascularization, or physiology. Intercrosses of these mice with a transgenic mouse model of pancreatic beta cell carcinogenesis (Rip1Tag2) result in an earlier onset of tumor angiogenesis and with it accelerated tumor growth and mortality. The transition from benign tumors (adenoma) to malignant tumors (carcinoma) is modestly accelerated; however, tumor metastases are not observed. Our findings indicate that in beta-cell tumorigenesis, overexpression of VEGF-A165 accelerates the onset of tumor angiogenesis and with it tumor progression but is not sufficient to induce tumor metastasis.","authors":"Gannon, G., Mandriota, SJ., Cui, L., Baetens, D., Pepper, MS., Christofori, G.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cancer Res","volume":"62","issue":"2","page":"603-8","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29059181","title":"Magnetoreception-A sense without a receptor.","abstract":"Evolution has equipped life on our planet with an array of extraordinary senses, but perhaps the least understood is magnetoreception. Despite compelling behavioral evidence that this sense exists, the cells, molecules, and mechanisms that mediate sensory transduction remain unknown. So how could animals detect magnetic fields? We introduce and discuss 3 concepts that attempt to address this question: (1) a mechanically sensitive magnetite-based magnetoreceptor, (2) a light-sensitive chemical-based mechanism, and (3) electromagnetic induction within accessory structures. In discussing the merits and issues with each of these ideas, we draw on existing precepts in sensory biology. We argue that solving this scientific mystery will require the development of new genetic tools in magnetosensitive species, coupled with an interdisciplinary approach that bridges physics, behavior, anatomy, physiology, molecular biology, and genetics.","authors":"Nordmann, GC., Hochstoeger, T., Keays, DA.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"PLoS Biol","volume":"15","issue":"10","page":"e2003234","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10098402","title":"The role of the cell-adhesion molecule E-cadherin as a tumour-suppressor gene.","abstract":"E-cadherin-mediated cell-cell adhesion is lost during the development of most epithelial cancers. Recent evidence indicates that the loss of E-cadherin function, besides causing loss of cell-cell adhesion, might also convey signals that actively induce tumour-cell invasion and metastasis.","authors":"Christofori, G., Semb, H.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Trends Biochem Sci","volume":"24","issue":"2","page":"73-6","pdf":null,"JrId":"7837","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10051331","title":"The murine polycomb-group genes Ezh1 and Ezh2 map close to Hox gene clusters on mouse chromosomes 11 and 6.","abstract":null,"authors":"Laible, G., Haynes, AR., Lebersorger, A., O'Carroll, D., Mattei, MG., Denny, P., Brown, SD., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Mamm Genome","volume":"10","issue":"3","page":"311-4","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"1999-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10075850","title":"Distinct neural stem cells proliferate in response to EGF and FGF in the developing mouse telencephalon.","abstract":"Multipotent, self-renewing neural stem cells reside in the embryonic mouse telencephalic germinal zone. Using an in vitro neurosphere assay for neural stem cell proliferation, we demonstrate that FGF-responsive neural stem cells are present as early as E8.5 in the anterior neural plate, but EGF-responsive neural stem cells emerge later in development in a temporally and spatially specific manner. By separately blocking EGF and FGF2 signaling, we also show that EGF alone and FGF2 alone can independently elicit neural stem cell proliferation and at relatively high cell densities separate cell nonautonomous effects can substantially enhance the mitogen-induced proliferation. At lower cell densities, neural stem cell proliferation is additive in the presence of EGF and FGF2 combined, revealing two different stem cell populations. However, both FGF-responsive and EGF-responsive neural stem cells retain their self-renewal and multilineage potential, regardless of growth factor conditions. These results support a model in which separate, lineage-related EGF- and FGF-responsive neural stem cells are present in the embryonic telencephalic germinal zone.","authors":"Tropepe, V., Sibilia, M., Ciruna, BG., Rossant, J., Wagner, EF., van der Kooy, D.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Dev Biol","volume":"208","issue":"1","page":"166-88","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"1999-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18341990","title":"The transmembrane protein Golden goal regulates R8 photoreceptor axon-axon and axon-target interactions.","abstract":"During Drosophila visual system development, photoreceptor (R) axons choose their correct paths and targets in a step-wise fashion. R axons with different identities make specific pathfinding decisions at different stages during development. We show here that the transmembrane protein Golden goal (Gogo), which is dynamically expressed in all R neurons and localizes predominantly to growth cones, is required in two distinct steps of R8 photoreceptor axon pathfinding: Gogo regulates axon-axon interactions and axon-target interactions in R8 photoreceptor axons. gogo loss-of-function and gain-of-function phenotypes suggest that Gogo mediates repulsive axon-axon interaction between R8 axons to maintain their proper spacing, and it promotes axon-target recognition at the temporary layer to enable R8 axons to enter their correct target columns in the medulla. From detailed structure-function experiments, we propose that Gogo functions as a receptor that binds an unidentified ligand through its conserved extracellular domain.","authors":"Tomasi, T., Hakeda-Suzuki, S., Ohler, S., Schleiffer, A., Suzuki, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Neuron","volume":"57","issue":"5","page":"691-704","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10068135","title":"Subcellular fractionation, electromigration analysis and mapping of organelles.","abstract":"Subcellular fractionation has provided the means required to analyze the composition and properties of purified cellular elements. In particular, subcellular fractionation has helped to define membrane boundaries and became necessary for the development of cell-free assays that reconstitute complicated cellular processes. Although cell fractionation techniques have improved over the last decades the purification of organelles to homogeneity is still a barely accessible goal in cell biology. In this article, we will first briefly review the basic principles of subcellular fractionation, and the establishment of different organelle fractions by density centrifugation, using tissue culture cells as a paradigm. Then we will discuss some of the intrinsic problems and will compare gradient purification of cellular extracts with electromigration analysis. Finally, we will describe alternative approaches, such as immunoisolation and flow cytometry to purify organelles from tissue culture cells.","authors":"Pasquali, C., Fialka, I., Huber, LA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Chromatogr B Biomed Sci Appl","volume":"722","issue":"1-2","page":"89-102","pdf":null,"JrId":"20702","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10072388","title":"Control of cell cycle progression by c-Jun is p53 dependent.","abstract":"The c-jun proto-oncogene encodes a component of the mitogen-inducible immediate-early transcription factor AP-1 and has been implicated as a positive regulator of cell proliferation and G1-to-S-phase progression. Here we report that fibroblasts derived from c-jun-\/- mouse fetuses exhibit a severe proliferation defect and undergo a prolonged crisis before spontaneous immortalization. The cyclin D1- and cyclin E-dependent kinases (CDKs) and transcription factor E2F are poorly activated, resulting in inefficient G1-to-S-phase progression. Furthermore, the absence of c-Jun results in elevated expression of the tumor suppressor gene p53 and its target gene, the CDK inhibitor p21, whereas overexpression of c-Jun represses p53 and p21 expression and accelerates cell proliferation. Surprisingly, protein stabilization, the common mechanism of p53 regulation, is not involved in up-regulation of p53 in c-jun-\/- fibroblasts. Rather, c-Jun regulates transcription of p53 negatively by direct binding to a variant AP-1 site in the p53 promoter. Importantly, deletion of p53 abrogates all defects of cells lacking c-Jun in cell cycle progression, proliferation, immortalization, and activation of G1 CDKs and E2F. These results demonstrate that an essential, rate-limiting function of c-Jun in fibroblast proliferation is negative regulation of p53 expression, and establish a mechanistic link between c-Jun-dependent mitogenic signaling and cell-cycle regulation.","authors":"Schreiber, M., Kolbus, A., Piu, F., Szabowski, A., M\u00f6hle-Steinlein, U., Tian, J., Karin, M., Angel, P., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Genes Dev","volume":"13","issue":"5","page":"607-19","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18232104","title":"Analysis of microRNA-target interactions by a target structure based hybridization model.","abstract":"MicroRNAs (miRNAs) are small non-coding RNAs that repress protein synthesis by binding to target messenger RNAs (mRNAs) in multicellular eukaryotes. The mechanism by which animal miRNAs specifically recognize their targets is not well understood. We recently developed a model for modeling the interaction between a miRNA and a target as a two-step hybridization reaction: nucleation at an accessible target site, followed by hybrid elongation to disrupt local target secondary structure and form the complete miRNA-target duplex. Nucleation potential and hybridization energy are two key energetic characteristics of the model. In this model, the role of target secondary structure on the efficacy of repression by miRNAs is considered, by employing the Sfold program to address the likelihood of a population of structures that co-exist in dynamic equilibrium for a specific mRNA molecule. This model can accurately account for the sensitivity to repression by let-7 of both published and rationally designed mutant forms of the Caenorhabditis elegans lin-41 3' UTR, and for the behavior of many other experimentally-tested miRNA-target interactions in C. elegans and Drosophila melanogaster. The model is particularly effective in accounting for certain false positive predictions obtained by other methods. In this study, we employed this model to analyze a set of miRNA-target interactions that were experimentally tested in mammalian models. These include targets for both mammalian miRNAs and viral miRNAs, and a viral target of a human miRNA. We found that our model can well account for both positive interactions and negative interactions. The model provides a unique explanation for the lack of function of a conserved seed site in the 3' UTR of the viral target, and predicts a strong interaction that cannot be predicted by conservation-based methods. Thus, the findings from this analysis and the previous analysis suggest that target structural accessibility is generally important for miRNA function in a broad class of eukaryotic systems. The model can be combined with other algorithms to improve the specificity of predictions by these algorithms. Because the model does not involve sequence conservation, it is readily applicable to target identification for microRNAs that lack conserved sites, non-conserved human miRNAs, and poorly conserved viral mRNAs. StarMir is a new Sfold application module developed for the implementation of the structure-based model, and is available through Sfold Web server at http:\/\/sfold.wadsworth.org.","authors":"Long, D., Chan, CY., Ding, Y.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Pac Symp Biocomput","volume":"","issue":"","page":"64-74","pdf":null,"JrId":"20660","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11807024","title":"The activation and maintenance of Pax2 expression at the mid-hindbrain boundary is controlled by separate enhancers.","abstract":"Pax2 is the earliest known gene to be expressed throughout the mid-hindbrain region in late gastrula embryos of the mouse and is essential for the formation of an organizing center at the midbrain-hindbrain boundary (MHB), which controls midbrain and cerebellum development. We have used transgenic analysis to identify three MHB-specific enhancers in the upstream region of the mouse Pax2 gene. A 120 bp enhancer (at -3.7 kb) in cooperation with the endogenous promoter was sufficient to induce transgene expression in the anterior neural plate of late gastrula embryos, while it was already inactivated again at the MHB during somitogenesis. The activity of this early enhancer was severely reduced by mutation of three homeodomain-binding sites, two of which are part of a recognition sequence for POU homeodomain proteins. Oct3\/4 (Pou5f1), the mouse ortholog of zebrafish Pou2, efficiently bound to this sequence, suggesting its involvement in the regulation of the early Pax2 enhancer. Starting at the four-somite stage, Pax2 is expressed at the MHB under the control of two enhancers located at -4.1 kb and -2.8 kb. The distal late enhancer contains a 102 bp sequence that is not only highly conserved between the mouse and pufferfish Pax2 genes, but also contributes to the enhancer activity of both genes in transgenic mice. The proximal 410 bp enhancer, which overlaps with a kidney-specific regulatory element, contains a functional Pax2\/5\/8-binding site and thus maintains Pax2 expression at the MHB under auto- and cross-regulatory control by Pax2\/5\/8 proteins. Importantly, the early and proximal late enhancers are not only sufficient but also necessary for expression at the MHB in the genomic context of the Pax2 locus, as their specific deletion interfered with correct temporal expression of a large Pax2 BAC transgene. Hence, separate enhancers under the control of distinct transcription factors activate and maintain Pax2 expression at the MHB.","authors":"Pfeffer, PL., Payer, B., Reim, G., di Magliano, MP., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Development","volume":"129","issue":"2","page":"307-18","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11804738","title":"Cadherins and the tumour progression: is it all in a switch?","abstract":"Progression to tumour malignancy involves changes in a tumour cell's capabilities to adhere and communicate with neighboring cells and with its extracellular environment. Correlation studies in human cancer specimen and functional experiments with cultured tumour cells and transgenic mouse models have indicated that the loss of the cell adhesion molecule E-cadherin is causally involved in the formation of epithelial cancers (carcinomas). More recently, it has been observed that the function of E-cadherin is replaced or overruled by the expression of mesenchymal cadherins, such as N-cadherin. Although the functional implication of such a 'cadherin switch' remains to be elucidated, recent experimental results demonstrating an interaction of cadherins with tyrosine kinase receptors suggest that changes in cadherin expression may not only modulate tumour cell adhesion but also affect signal transduction and, hence, the malignant phenotype.","authors":"Cavallaro, U., Schaffhauser, B., Christofori, G.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cancer Lett","volume":"176","issue":"2","page":"123-8","pdf":null,"JrId":"2780","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9990856","title":"Yeast cohesin complex requires a conserved protein, Eco1p(Ctf7), to establish cohesion between sister chromatids during DNA replication.","abstract":"Sister chromatid cohesion is crucial for chromosome segregation during mitosis. Loss of cohesion very possibly triggers sister separation at the metaphase --&gt; anaphase transition. This process depends on the destruction of anaphase inhibitory proteins like Pds1p (Cut2p), which is thought to liberate a sister-separating protein Esp1p (Cut1p). By looking for mutants that separate sister centromeres in the presence of Pds1p, this and a previous study have identified six proteins essential for establishing or maintaining sister chromatid cohesion. Four of these proteins, Scc1p, Scc3p, Smc1p, and Smc3p, are subunits of a 'Cohesin' complex that binds chromosomes from late G1 until the onset of anaphase. The fifth protein, Scc2p, is not a stoichiometric Cohesin subunit but it is required for Cohesin's association with chromosomes. The sixth protein, Eco1p(Ctf7p), is not a Cohesin subunit. It is necessary for the establishment of cohesion during DNA replication but not for its maintenance during G2 and M phases.","authors":"T\u00f3th, A., Ciosk, R., Uhlmann, F., Galova, M., Schleiffer, A., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Genes Dev","volume":"13","issue":"3","page":"320-33","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9922458","title":"Neural cell adhesion molecule (N-CAM) is required for cell type segregation and normal ultrastructure in pancreatic islets.","abstract":"Classical cell dissociation\/reaggregation experiments with embryonic tissue and cultured cells have established that cellular cohesiveness, mediated by cell adhesion molecules, is important in determining the organization of cells within tissue and organs. We have employed N-CAM-deficient mice to determine whether N-CAM plays a functional role in the proper segregation of cells during the development of islets of Langerhans. In N-CAM-deficient mice the normal localization of glucagon-producing alpha cells in the periphery of pancreatic islets is lost, resulting in a more randomized cell distribution. In contrast to the expected reduction of cell-cell adhesion in N-CAM-deficient mice, a significant increase in the clustering of cadherins, F-actin, and cell-cell junctions is observed suggesting enhanced cadherin-mediated adhesion in the absence of proper N-CAM function. These data together with the polarized distribution of islet cell nuclei and Na+\/K+-ATPase indicate that islet cell polarity is also affected. Finally, degranulation of beta cells suggests that N-CAM is required for normal turnover of insulin-containing secretory granules. Taken together, our results confirm in vivo the hypothesis that a cell adhesion molecule, in this case N-CAM, is required for cell type segregation during organogenesis. Possible mechanisms underlying this phenomenon may include changes in cadherin-mediated adhesion and cell polarity.","authors":"Esni, F., T\u00e4ljedal, IB., Perl, AK., Cremer, H., Christofori, G., Semb, H.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Cell Biol","volume":"144","issue":"2","page":"325-37","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1999-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18056405","title":"Stefan Westermann: a close look at kinetochore function. Interviewed by Caitlin Sedwick.","abstract":"Stefan Westermann is probing the structure and function of the yeast kinetochore.","authors":"Westermann, S.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Cell Biol","volume":"179","issue":"5","page":"810-1","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9914180","title":"SCF and APC: the Yin and Yang of cell cycle regulated proteolysis.","abstract":"Progression through the cell cycle requires the activity of two ubiquitination complexes, the Skp1-cullin-F-box-protein complex (SCF) and the anaphase-promoting complex\/cyclosome (APC). Observations in the past year have revealed unexpected similarities between the SCF and the APC and have allowed detailed insight into the regulation of their activities. Both complexes are now known to exist in different forms that target different substrates for ubiquitin-dependent proteolysis.","authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Curr Opin Cell Biol","volume":"10","issue":"6","page":"759-68","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"1999-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9882345","title":"Mutational analysis of the avian adenovirus CELO, which provides a basis for gene delivery vectors.","abstract":"The avian adenovirus CELO is being developed as a gene transfer tool. Using homologous recombination in Escherichia coli, the CELO genome was screened for regions that could be deleted and would tolerate the insertion of a marker gene (luciferase or enhanced green fluorescent protein). For each mutant genome, the production of viable virus able to deliver the transgene to target cells was monitored. A series of mutants in the genome identified a set of open reading frames that could be deleted but which must be supplied in trans for virus replication. A region of the genome which is dispensable for viral replication and allows the insertion of an expression cassette was identified and a vector based on this mutation was evaluated as a gene delivery reagent. Transduction of avian cells occurs at 10- to 100-fold greater efficiency (per virus particle) than with an adenovirus type 5 (Ad5)-based vector carrying the same expression cassette. Most important for gene transfer applications, the CELO vector transduced mammalian cells as efficiently as an Ad5 vector. The CELO vector is exceptionally stable, can be grown inexpensively in chicken embryos, and provides a useful alternative to Ad5-based vectors.","authors":"Michou, AI., Lehrmann, H., Saltik, M., Cotten, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Virol","volume":"73","issue":"2","page":"1399-410","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1999-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17851526","title":"Dscam diversity is essential for neuronal wiring and self-recognition.","abstract":"Neurons are thought to use diverse families of cell-surface molecules for cell recognition during circuit assembly. In Drosophila, alternative splicing of the Down syndrome cell adhesion molecule (Dscam) gene potentially generates 38,016 closely related transmembrane proteins of the immunoglobulin superfamily, each comprising one of 19,008 alternative ectodomains linked to one of two alternative transmembrane segments. These ectodomains show isoform-specific homophilic binding, leading to speculation that Dscam proteins mediate cell recognition. Genetic studies have established that Dscam is required for neural circuit assembly, but the extent to which isoform diversity contributes to this process is not known. Here we provide conclusive evidence that Dscam diversity is essential for circuit assembly. Using homologous recombination, we reduced the entire repertoire of Dscam ectodomains to just a single isoform. Neural circuits in these mutants are severely disorganized. Furthermore, we show that it is crucial for neighbouring neurons to express distinct isoforms, but that the specific identity of the isoforms expressed in an individual neuron is unimportant. We conclude that Dscam diversity provides each neuron with a unique identity by which it can distinguish its own processes from those of other neurons, and that this self-recognition is essential for wiring the Drosophila brain.","authors":"Hattori, D., Demir, E., Kim, HW., Viragh, E., Zipursky, SL., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"449","issue":"7159","page":"223-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2007-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12543067","title":"Quantitative motion analysis and visualization of cellular structures.","abstract":"The availability of cellular markers tagged with the green fluorescent protein (GFP) has recently allowed a large number of cell biological studies to be carried out in live cells, thereby addressing the dynamic organization of cellular structures. Typically, microscopes capable of video recording are used to generate time-resolved data sets. Dynamic imaging data are complex and often difficult to interpret by pure visual inspection. Therefore, specialized image processing methods for object detection, motion estimation, visualization, and quantitation are required. In this review, we discuss concepts for automated analysis of multidimensional image data from live cell microscopy and their application to the dynamics of cell nuclear subcompartments.","authors":"Gerlich, D., Mattes, J., Eils, R.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Methods","volume":"29","issue":"1","page":"3-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-07-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9857075","title":"Neisseria gonorrhoeae porin modulates phagosome maturation.","abstract":"The porin (PorB) of Neisseria gonorrhoeae has been implicated in the pathogenesis of this species. Porin is believed to translocate from the bacterial outer membrane into target cell membranes affecting various cell functions. Here we investigated the effect of porin on phagosome maturation. Phagocytosis of latex beads by human macrophages was allowed in the presence or absence of purified porin. Isolation of latex bead-containing phagosomes and subsequent two-dimensional gel electrophoresis revealed substantial differences in the phagosomal protein composition. Immunoblotting detected higher amounts of annexin II and the early endocytic markers Rab5 and transferrin receptor and decreased levels of the late endocytic markers Rab7 and cathepsin D in phagosomes obtained in the presence of porin compared with those obtained in its absence. Furthermore, association of Rab4 with the latex bead-containing phagosomes was revealed by flow cytometry. The amount of this small GTPase was markedly higher in the phagosomes isolated in the presence of porin. The data thus indicate that neisserial porin is itself able to arrest phagosome maturation within macrophages.","authors":"Mosleh, IM., Huber, LA., Steinlein, P., Pasquali, C., G\u00fcnther, D., Meyer, TF.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Biol Chem","volume":"273","issue":"52","page":"35332-8","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1999-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17679087","title":"Active and repressive chromatin are interspersed without spreading in an imprinted gene cluster in the mammalian genome.","abstract":"The Igf2r imprinted cluster is an epigenetic silencing model in which expression of a ncRNA silences multiple genes in cis. Here, we map a 250 kb region in mouse embryonic fibroblast cells to show that histone modifications associated with expressed and silent genes are mutually exclusive and localized to discrete regions. Expressed genes were modified at promoter regions by H3K4me3 + H3K4me2 + H3K9Ac and on putative regulatory elements flanking active promoters by H3K4me2 + H3K9Ac. Silent genes showed two types of nonoverlapping profile. One type spread over large domains of tissue-specific silent genes and contained H3K27me3 alone. A second type formed localized foci on silent imprinted gene promoters and a nonexpressed pseudogene and contained H3K9me3 + H4K20me3 +\/- HP1. Thus, mammalian chromosome arms contain active chromatin interspersed with repressive chromatin resembling the type of heterochromatin previously considered a feature of centromeres, telomeres, and the inactive X chromosome.","authors":"Regha, K., Sloane, MA., Huang, R., Pauler, FM., Warczok, KE., Melikant, B., Radolf, M., Martens, JH., Schotta, G., Jenuwein, T., Barlow, DP.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Cell","volume":"27","issue":"3","page":"353-66","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9831566","title":"Control of cyclin ubiquitination by CDK-regulated binding of Hct1 to the anaphase promoting complex.","abstract":"Proteolysis of mitotic cyclins depends on a multisubunit ubiquitin-protein ligase, the anaphase promoting complex (APC). Proteolysis commences during anaphase, persisting throughout G1 until it is terminated by cyclin-dependent kinases (CDKs) as cells enter S phase. Proteolysis of mitotic cyclins in yeast was shown to require association of the APC with the substrate-specific activator Hct1 (also called Cdh1). Phosphorylation of Hct1 by CDKs blocked the Hct1-APC interaction. The mutual inhibition between APC and CDKs explains how cells suppress mitotic CDK activity during G1 and then establish a period with elevated kinase activity from S phase until anaphase.","authors":"Zachariae, W., Schwab, M., Nasmyth, K., Seufert, W.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Science","volume":"282","issue":"5394","page":"1721-4","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1998-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20887897","title":"Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5.","abstract":"Activation-induced cytidine deaminase (AID) initiates antibody gene diversification by creating U:G mismatches. However, AID is not specific for antibody genes; Off-target lesions can activate oncogenes or cause chromosome translocations. Despite its importance in these transactions little is known about how AID finds its targets. We performed an shRNA screen to identify factors required for class switch recombination (CSR) of antibody loci. We found that Spt5, a factor associated with stalled RNA polymerase II (Pol II) and single stranded DNA (ssDNA), is required for CSR. Spt5 interacts with AID, it facilitates association between AID and Pol II, and AID recruitment to its Ig and non-Ig targets. ChIP-seq experiments reveal that Spt5 colocalizes with AID and stalled Pol II. Further, Spt5 accumulation at sites of Pol II stalling is predictive of AID-induced mutation. We propose that AID is targeted to sites of Pol II stalling in part via its association with Spt5.","authors":"Pavri, R., Gazumyan, A., Jankovic, M., Di Virgilio, M., Klein, I., Ansarah-Sobrinho, C., Resch, W., Yamane, A., Reina San-Martin, B., Barreto, V., Nieland, TJ., Root, DE., Casellas, R., Nussenzweig, MC.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell","volume":"143","issue":"1","page":"122-33","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9851980","title":"Drosophila Cyclin B3 is required for female fertility and is dispensable for mitosis like Cyclin B.","abstract":"Cyclin B3 has been conserved during higher eukaryote evolution as evidenced by its identification in chicken, nematodes, and insects. We demonstrate that Cyclin B3 is present in addition to Cyclins A and B in mitotically proliferating cells and not detectable in endoreduplicating tissues of Drosophila embryos. Cyclin B3 is coimmunoprecipitated with Cdk1(Cdc2) but not with Cdk2(Cdc2c). It is degraded abruptly during mitosis like Cyclins A and B. In contrast to these latter cyclins, which accumulate predominantly in the cytoplasm during interphase, Cyclin B3 is a nuclear protein. Genetic analyses indicate functional redundancies. Double and triple mutant analyses demonstrate that Cyclins A, B, and B3 cooperate to regulate mitosis, but surprisingly single mutants reveal that neither Cyclin B3 nor Cyclin B is required for mitosis. However, both are required for female fertility and Cyclin B also for male fertility.","authors":"Jacobs, HW., Knoblich, JA., Lehner, CF.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Genes Dev","volume":"12","issue":"23","page":"3741-51","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1999-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17627824","title":"The kinetochore proteins Pcs1 and Mde4 and heterochromatin are required to prevent merotelic orientation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">17627824<\/PMID><DateCompleted><Year>2007<\/Year><Month>12<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>17<\/Volume><Issue>14<\/Issue><PubDate><Year>2007<\/Year><Month>Jul<\/Month><Day>17<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The kinetochore proteins Pcs1 and Mde4 and heterochromatin are required to prevent merotelic orientation.<\/ArticleTitle><Pagination><MedlinePgn>1190-200<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Accurate chromosome segregation depends on the establishment of correct-amphitelic-kinetochore orientation. Merotelic kinetochore orientation is an error that occurs when a single kinetochore attaches to microtubules emanating from opposite spindle poles, a condition that hinders segregation of the kinetochore to a spindle pole in anaphase. To avoid chromosome missegregation resulting from merotelic kinetochore orientation, cells have developed mechanisms to prevent or correct merotelic attachment. A protein called Pcs1 has been implicated in preventing merotelic attachment in mitosis and meiosis II in the fission yeast S. pombe.","authors":"Gregan, J., Riedel, CG., Pidoux, AL., Katou, Y., Rumpf, C., Schleiffer, A., Kearsey, SE., Shirahige, K., Allshire, RC., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Curr Biol","volume":"17","issue":"14","page":"1190-200","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11781114","title":"Cell adhesion in tumor invasion and metastasis: loss of the glue is not enough.","abstract":"Tumor cells often show a decrease in cell-cell and\/or cell-matrix adhesion. An increasing body of evidence indicates that this reduction in cell adhesion correlates with tumor invasion and metastasis. Two main groups of adhesion molecules, cadherins and CAMs, have been implicated in tumor malignancy. However, the specific role that these proteins play in the context of tumor progression remains to be elucidated. In this review, we discuss recent data pointing to a causal relationship between the loss of cell adhesion molecules and tumor progression. In addition, the direct involvement of these molecules in specific signal transduction pathways will be considered, with particular emphasis on the alterations of such pathways in transformed cells. Finally, we review recent observations on the molecular mechanisms underlying metastatic dissemination. In many cases, spreading of tumor cells from the primary site to distant organs has been characterized as an active process involving the loss of cell-cell adhesion and gain of invasive properties. On the other hand, various examples of metastases exhibiting a relatively benign (i.e. not invasive) phenotype have been reported. Together with our recent results on a mouse tumor model, these findings indicate that 'passive' metastatic dissemination can occur, in particular as a consequence of impaired cell-matrix adhesion and of tumor tissue disaggregation.","authors":"Cavallaro, U., Christofori, G.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Biochim Biophys Acta","volume":"1552","issue":"1","page":"39-45","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17543861","title":"The nuclear envelope protein Matefin\/SUN-1 is required for homologous pairing in C. elegans meiosis.","abstract":"We identify a highly specific mutation (jf18) in the Caenorhabditis elegans nuclear envelope protein matefin MTF-1\/SUN-1 that provides direct evidence for active involvement of the nuclear envelope in homologous chromosome pairing in C. elegans meiosis. The reorganization of chromatin in early meiosis is disrupted in mtf-1\/sun-1(jf18) gonads, concomitant with the absence of presynaptic homolog alignment. Synapsis is established precociously and nonhomologously. Wild-type leptotene\/zygotene nuclei show patch-like aggregations of the ZYG-12 protein, which fail to develop in mtf-1\/sun-1(jf18) mutants. These patches remarkably colocalize with a component of the cis-acting chromosomal pairing center (HIM-8) rather than the centrosome. Our data on this mtf-1\/sun-1 allele challenge the previously postulated role of the centrosome\/spindle organizing center in chromosome pairing, and clearly support a role for MTF-1\/SUN-1 in meiotic chromosome reorganization and in homolog recognition, possibly by mediating local aggregation of the ZYG-12 protein in meiotic nuclei.","authors":"Penkner, A., Tang, L., Novatchkova, M., Ladurner, M., Fridkin, A., Gruenbaum, Y., Schweizer, D., Loidl, J., Jantsch, V.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Dev Cell","volume":"12","issue":"6","page":"873-85","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9790834","title":"Predicting function: from genes to genomes and back.","abstract":"Predicting function from sequence using computational tools is a highly complicated procedure that is generally done for each gene individually. This review focuses on the added value that is provided by completely sequenced genomes in function prediction. Various levels of sequence annotation and function prediction are discussed, ranging from genomic sequence to that of complex cellular processes. Protein function is currently best described in the context of molecular interactions. In the near future it will be possible to predict protein function in the context of higher order processes such as the regulation of gene expression, metabolic pathways and signalling cascades. The analysis of such higher levels of function description uses, besides the information from completely sequenced genomes, also the additional information from proteomics and expression data. The final goal will be to elucidate the mapping between genotype and phenotype.","authors":"Bork, P., Dandekar, T., Diaz-Lazcoz, Y., Eisenhaber, F., Huynen, M., Yuan, Y.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Mol Biol","volume":"283","issue":"4","page":"707-25","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1998-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9732271","title":"Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities.","abstract":"Pax genes have been shown to play important roles in mammalian development and organogenesis. Pax9, a member of this transcription factor family, is expressed in somites, pharyngeal pouches, mesenchyme involved in craniofacial, tooth, and limb development, as well as other sites during mouse embryogenesis. To analyze its function in vivo, we generated Pax9 deficient mice and show that Pax9 is essential for the development of a variety of organs and skeletal elements. Homozygous Pax9-mutant mice die shortly after birth, most likely as a consequence of a cleft secondary palate. They lack a thymus, parathyroid glands, and ultimobranchial bodies, organs which are derived from the pharyngeal pouches. In all limbs, a supernumerary preaxial digit is formed, but the flexor of the hindlimb toes is missing. Furthermore, craniofacial and visceral skeletogenesis is disturbed, and all teeth are absent. In Pax9-deficient embryos tooth development is arrested at the bud stage. At this stage, Pax9 is required for the mesenchymal expression of Bmp4, Msx1, and Lef1, suggesting a role for Pax9 in the establishment of the inductive capacity of the tooth mesenchyme. In summary, our analysis shows that Pax9 is a key regulator during the development of a wide range of organ primordia.","authors":"Peters, H., Neub\u00fcser, A., Kratochwil, K., Balling, R.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Genes Dev","volume":"12","issue":"17","page":"2735-47","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1998-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17440452","title":"Pax5: the guardian of B cell identity and function.","abstract":"The transcription factor Pax5 is essential for commitment of lymphoid progenitors to the B lymphocyte lineage. Pax5 fulfils a dual role by repressing B lineage 'inappropriate' genes and simultaneously activating B lineage-specific genes. This transcriptional reprogramming restricts the broad signaling capacity of uncommitted progenitors to the B cell pathway, regulates cell adhesion and migration, induces V(H)-DJ(H) recombination, facilitates (pre-)B cell receptor signaling and promotes development to the mature B cell stage. Conditional Pax5 inactivation in early and late B lymphocytes revealed an essential role for Pax5 in controlling the identity and function of B cells throughout B lymphopoiesis. PAX5 has also been implicated in human B cell malignancies, as it is deregulated by chromosomal translocations in a subset of acute lymphoblastic leukemias and non-Hodgkin lymphomas.","authors":"Cobaleda, C., Schebesta, A., Delogu, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Immunol","volume":"8","issue":"5","page":"463-70","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17406492","title":"High-throughput knockout screen in fission yeast.","abstract":"We have designed the most efficient strategy to knock out genes in fission yeast Schizosaccharomyces pombe on a large scale. Our technique is based on knockout constructs that contain regions homologous to the target gene cloned into vectors carrying dominant drug-resistance markers. Most of the steps are carried out in a 96-well format, allowing simultaneous deletion of 96 genes in one batch. Based on our knockout technique, we designed a strategy for cloning knockout constructs for all predicted fission yeast genes, which is available in a form of a searchable database http:\/\/mendel.imp.ac.at\/Pombe_deletion\/. We validated this technique in a screen where we identified novel genes required for chromosome segregation during meiosis. Here, we present our protocol with detailed instructions. Using this protocol, one person can knock out 96 S. pombe genes in 8 days.","authors":"Gregan, J., Rabitsch, PK., Rumpf, C., Novatchkova, M., Schleiffer, A., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nat Protoc","volume":"1","issue":"5","page":"2457-64","pdf":null,"JrId":"33047","fulltextlink":null,"preprintlink":null,"articledate":"2007-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11776394","title":"Expression of collagenase-3 (MMP-13) in c-fos-induced osteosarcomas and chondrosarcomas is restricted to a subset of cells of the osteo-\/chondrogenic lineage.","abstract":"The interstitial collagenases have been suggested to play a critical role in bone formation, remodeling, and cancerogenesis. We have previously shown that during mouse development expression of collagenase-3 (MMP-13) is restricted to bone and cartilage (Gack et al., 1995; Tuckermann et al., 2000) and is affected in mice with altered c-Fos and Cbfa-1 expression (Gack et al., 1994; Porte et al., 1999). In this study, using immunohistochemistry (IHC) and in situ hybridization (ISH) techniques, we have identified cells of the osteoblastic lineage to be the origin of strongly enhanced levels of MMP-13 transcripts in c-fos-induced osteosarcomas. Expression in these cells is further increased in c-fos\/c-jun double transgenic mice and paralleled by Cbfa-1 expression. Similarly, in spontaneous and radiation-induced osteosarcomas, both c-Fos and MMP-13 proteins are detectable, suggesting that overexpression of both genes is a characteristic feature of osteosarcomas of different origin. We also observed high levels of MMP-13 in c-Fos-induced chondrosarcomas. In osteoblast-like cells and in cells of late chondrocyte differentiation such as hypertrophic chondrocytes, high levels of MMP-13 transcripts were found. In contrast, in anaplastic areas of the tumors representing highly proliferating chondrocytes, no MMP-13 expression is detectable, suggesting that in addition to Fos\/AP-1, bone-specific transcription factors are responsible for restricted expression of collagenase-3\/MMP-13 in a specific subset of cells of bone and cartilage in physiology and pathology.","authors":"Tuckermann, JP., Vallon, R., Gack, S., Grigoriadis, AE., Porte, D., Lutz, A., Wagner, EF., Schmidt, J., Angel, P.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Differentiation","volume":"69","issue":"1","page":"49-57","pdf":null,"JrId":"3402","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17353275","title":"Differential regulation of Foxo3a target genes in erythropoiesis.","abstract":"The cooperation of stem cell factor (SCF) and erythropoietin (Epo) is required to induce renewal divisions in erythroid progenitors, whereas differentiation to mature erythrocytes requires the presence of Epo only. Epo and SCF activate common signaling pathways such as the activation of protein kinase B (PKB) and the subsequent phosphorylation and inactivation of Foxo3a. In contrast, only Epo activates Stat5. Both Foxo3a and Stat5 promote erythroid differentiation. To understand the interplay of SCF and Epo in maintaining the balance between renewal and differentiation during erythroid development, we investigated differential Foxo3a target regulation by Epo and SCF. Expression profiling revealed that a subset of Foxo3a targets was not inhibited but was activated by Epo. One of these genes was Cited2. Transcriptional control of Epo\/Foxo3a-induced Cited2 was studied and compared with that of the Epo-repressed Foxo3a target Btg1. We show that in response to Epo, the allegedly growth-inhibitory factor Foxo3a associates with the allegedly growth-stimulatory factor Stat5 in the nucleus, which is required for Epo-induced Cited2 expression. In contrast, Btg1 expression is controlled by the cooperation of Foxo3a with cyclic AMP- and Jun kinase-dependent Creb family members. Thus, Foxo3a not only is an effector of PKB but also integrates distinct signals to regulate gene expression in erythropoiesis.","authors":"Bakker, WJ., van Dijk, TB., Parren-van Amelsvoort, M., Kolbus, A., Yamamoto, K., Steinlein, P., Verhaak, RG., Mak, TW., Beug, H., L\u00f6wenberg, B., von Lindern, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Cell Biol","volume":"27","issue":"10","page":"3839-3854","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21357543","title":"Regulation of GATA-3 expression during CD4 lineage differentiation.","abstract":"GATA-3 is necessary for the development of MHC class II-restricted CD4 T cells, and its expression is increased during positive selection of these cells. TCR signals drive this upregulation, but the signaling pathways that control this process are not well understood. Using genetic and pharmacological approaches, we show that GATA-3 upregulation during thymocyte-positive selection is the result of additive inputs from the Ras\/MAPK and calcineurin pathways. This upregulation requires the presence of the transcription factor c-Myb. Furthermore, we show that TH-POK can also upregulate GATA-3 in double-positive thymocytes, suggesting the existence of a positive feedback loop that contributes to lock in the initial commitment to the CD4 lineage during differentiation.","authors":"Gimferrer, I., Hu, T., Simmons, A., Wang, C., Souabni, A., Busslinger, M., Bender, TP., Hernandez-Hoyos, G., Alberola-Ila, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Immunol","volume":"186","issue":"7","page":"3892-8","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8939846","title":"How proteolysis drives the cell cycle.","abstract":"Oscillations in the activity of cyclin-dependent kinases (CDKs) promote progression through the eukaryotic cell cycle. This review examines how proteolysis regulates CDK activity-by degrading CDK activators or inhibitors-and also how proteolysis may directly trigger the transition from metaphase to anaphase. Proteolysis during the cell cycle is mediated by two distinct ubiquitin-conjugation pathways. One pathway, requiring CDC34, initiates DNA replication by degrading a CDK inhibitor. The second pathway, involving a large protein complex called the anaphase-promoting complex or cyclosome, initiates chromosome segregation and exit from mitosis by degrading anaphase inhibitors and mitotic cyclins. Proteolysis therefore drives cell cycle progression not only by regulating CDK activity, but by directly influencing chromosome and spindle dynamics.","authors":"King, RW., Deshaies, RJ., Peters, JM., Kirschner, MW.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Science","volume":"274","issue":"5293","page":"1652-9","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1997-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9601022","title":"Making sense of imprinting the mouse and human IGF2R loci.","abstract":"The mouse and human IGF2R genes are similar in terms of expression pattern, gene structure and organization. Both genes have features that are common to imprinted genes. These common features are allele-specific methylation and replication asynchrony, plus the ability to restrict expression to one parental allele in diploid cells despite the presence of two functional parental alleles. In inbred laboratory mice Igf2r is initially expressed from both parental chromosomes in preimplantation embryos, it then shows maternal-specific monoallelic expression in all tissues of the postimplantation embryo and adult. The human gene is similarly monoallelically expressed in preterm postimplantation embryonic tissues (preimplantation embryos have not been examined). The behaviour of the human gene then diverges from that observed in inbred mice because it shows biallelic expression in term embryonic tissues and in the adult. An extra difference displayed by the human gene is that monoallelic expression is polymorphic and only occurs in 50% of individuals. The mechanism of IGF2R imprinting will be discussed with relevance to these similarities and differences between the mouse and human genes.","authors":"Wutz, A., Smrzka, OW., Barlow, DP.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Novartis Found Symp","volume":"214","issue":null,"page":"251-9; discussion 260-3","pdf":null,"JrId":"20998","fulltextlink":null,"preprintlink":null,"articledate":"1998-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20534708","title":"Navigating intermediate targets: the nervous system midline.","abstract":"In a bilaterally symmetric animal, the midline plays a key role in directing axon growth during wiring of the nervous system. Midline cells provide a variety of guidance cues for growing axons, to which different types of axons respond in different ways and at different times. For some axons, the midline is an intermediate target. They first seek it out, but then move on towards their final targets on the opposite side. For others, the midline is a repulsive barrier that keeps them on their own side of the midline. And for many of these axons the midline provides signals that guide them along specific lateral pathways or up and down the longitudinal axis.","authors":"Dickson, BJ., Zou, Y.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cold Spring Harb Perspect Biol","volume":"2","issue":"8","page":"a002055","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23559217","title":"Analysis of meiotic protein complexes from Arabidopsis and Brassica using affinity-based proteomics.","abstract":"The application of proteomics techniques to the study of plant meiosis has the potential to make a valuable contribution to our understanding of the molecular events underpinning meiotic processes. Here we describe the preparation of meiotic protein complexes from Arabidopsis thaliana and its close crop relative, Brassica oleracea, by co-immunoprecipitation for in-solution analysis by tandem mass spectrometry (MS\/MS). Early results using these techniques have proved encouraging, enabling the identification of candidate AtASY1-interacting proteins in A. thaliana and providing evidence of an in planta interaction between BoASY1 and BoASY3 in B. oleracea. The detection of phospho-modified peptides of BoASY1 and BoASY3 suggests that this approach may be useful for studying meiotic protein modification events.","authors":"Osman, K., Roitinger, E., Yang, J., Armstrong, S., Mechtler, K., Franklin, FC.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Methods Mol Biol","volume":"990","issue":null,"page":"215-26","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9598338","title":"Asymmetric segregation of the Drosophila numb protein during mitosis: facts and speculations.","abstract":null,"authors":"Knoblich, JA., Jan, LY., Jan, YN.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"62","issue":null,"page":"71-7","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1998-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9244230","title":"iNOS expression and nitrotyrosine formation in the myocardium in response to inflammation is controlled by the interferon regulatory transcription factor 1.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9244230<\/PMID><DateCompleted><Year>1997<\/Year><Month>08<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2013<\/Year><Month>11<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0009-7322<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>96<\/Volume><Issue>2<\/Issue><PubDate><Year>1997<\/Year><Month>Jul<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>iNOS expression and nitrotyrosine formation in the myocardium in response to inflammation is controlled by the interferon regulatory transcription factor 1.<\/ArticleTitle><Pagination><MedlinePgn>585-91<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Production of NO by inducible NO synthase (iNOS) has been implicated in the pathology of spontaneous and antigen-induced autoimmune diseases, and iNOS is expressed in the myocardium of patients with heart failure. It is not clear whether inflammatory murine autoimmune heart disease, an experimental model for human postviral heart disease, is characterized by increased iNOS expression within the heart and whether iNOS and NO are essential in the pathogenesis of autoimmune myocarditis.","authors":"Bachmaier, K., Neu, N., Pummerer, C., Duncan, GS., Mak, TW., Matsuyama, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Circulation","volume":"96","issue":"2","page":"585-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17203100","title":"Xist and the order of silencing.","abstract":"X inactivation is the mechanism by which mammals adjust the genetic imbalance that arises from the different numbers of gene-rich X-chromosomes between the sexes. The dosage difference between XX females and XY males is functionally equalized by silencing one of the two X chromosomes in females. This dosage-compensation mechanism seems to have arisen concurrently with early mammalian evolution and is based on the long functional Xist RNA, which is unique to placental mammals. It is likely that previously existing mechanisms for other cellular functions have been recruited and adapted for the evolution of X inactivation. Here, we critically review our understanding of dosage compensation in placental mammals and place these findings in the context of other cellular processes that intersect with mammalian dosage compensation.","authors":"Ng, K., Pullirsch, D., Leeb, M., Wutz, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"EMBO Rep","volume":"8","issue":"1","page":"34-9","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11750659","title":"The paradox of plastid transit peptides: conservation of function despite divergence in primary structure.","abstract":"Transit peptides are N-terminal extensions that facilitate the targeting and translocation of cytosolically synthesized precursors into plastids via a post-translational mechanism. With the complete Arabidopsis genome in hand, it is now evident that transit peptides direct more than 3500 different proteins into the plastid during the life of a typical plant. Deciphering a common mechanism for how this multitude of targeting sequences function has been hampered by the realization that at a primary sequence level, transit peptides are highly divergent in length, composition, and organization. This review addresses recent findings on several of the diverse functions that transit peptides must perform, including direct interaction with envelope lipids, association with a cis-acting guidance complex, recognition by envelope receptors, insertion into the Toc\/Tic translocon, interaction with molecular motors, and finally, recognition\/cleavage by the stromal processing peptidase. In addition to higher plants, transit peptides also direct the import of proteins into complex plastids derived from secondary endosymbiosis. An emerging concept suggests that transit peptides contain multiple domains that provide either distinct or possibly overlapping functions. Although still poorly characterized, evolutionary processes could yield transit peptides with alternative domain organizations.","authors":"Bruce, BD.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Biochim Biophys Acta","volume":"1541","issue":"1-2","page":"2-21","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9557730","title":"Structure of a neutralizing antibody bound monovalently to human rhinovirus 2.","abstract":"The structure of a complex between human rhinovirus 2 (HRV2) and the Fab fragment of neutralizing monoclonal antibody (MAb) 3B10 has been determined to 25-A resolution by cryoelectron microscopy and three-dimensional reconstruction techniques. The footprint of 3B10 on HRV2 is very similar to that of neutralizing MAb 8F5, which binds bivalently across the icosahedral twofold axis. However, the 3B10 Fab fragment (Fab-3B10) is bound in an orientation, inclined at approximately 45 degrees to the surface of the virus capsid, which is compatible only with monovalent binding of the antibody. The canyon around the fivefold axis is not directly obstructed by the bound Fab. The X-ray structures of a closely related HRV (HRV1A) and a Fab fragment were fitted to the density maps of the HRV2-Fab-3B10 complex obtained by cryoelectron microscope techniques. The footprint of 3B10 on the viral surface is largely on VP2 but also covers the VP3 loop centered on residue 3064 and the VP1 loop centered on residue 1267. MAb 3B10 can interact directly with VP2 residue 2164, the site of an escape mutation on VP2, and with VP1 residues 1264 to 1267, the site of a deletion escape mutation. Deletion of these residues shortens the VP1 loop, moving it away from the MAb binding site. All structural and biochemical evidence indicates that MAb 3B10 binds to a conformation epitope on HRV2.","authors":"Hewat, EA., Marlovits, TC., Blaas, D.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Virol","volume":"72","issue":"5","page":"4396-402","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1998-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19879387","title":"Defining the conserved internal architecture of a protein kinase.","abstract":"Protein kinases constitute a large protein family of important regulators in all eukaryotic cells. All of the protein kinases have a similar bilobal fold, and their key structural features have been well studied. However, the recent discovery of non-contiguous hydrophobic ensembles inside the protein kinase core shed new light on the internal organization of these molecules. Two hydrophobic \"spines\" traverse both lobes of the protein kinase molecule, providing a firm but flexible connection between its key elements. The spine model introduces a useful framework for analysis of intramolecular communications, molecular dynamics, and drug design.","authors":"Kornev, AP., Taylor, SS.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Biochim Biophys Acta","volume":"1804","issue":"3","page":"440-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16959614","title":"ILEI: a cytokine essential for EMT, tumor formation, and late events in metastasis in epithelial cells.","abstract":"Erk\/MAPK and TGFbeta signaling cause epithelial to mesenchymal transition (EMT) and metastasis in mouse mammary epithelial cells (EpH4) transformed with oncogenic Ras (EpRas). In trials to unravel underlying mechanisms, expression profiling for EMT-specific genes identified a secreted interleukin-related protein (ILEI), upregulated exclusively at the translational level. Stable overexpression of ILEI in EpH4 and EpRas cells caused EMT, tumor growth, and metastasis, independent of TGFbeta-R signaling and enhanced by Bcl2. RNAi-mediated knockdown of ILEI in EpRas cells before and after EMT (EpRasXT) prevented and reverted TGFbeta-dependent EMT, also abrogating metastasis formation. ILEI is overexpressed and\/or altered in intracellular localization in multiple human tumors, an event strongly correlated to invasion\/EMT, metastasis formation, and survival in human colon and breast cancer.","authors":"Waerner, T., Alacakaptan, M., Tamir, I., Oberauer, R., Gal, A., Brabletz, T., Schreiber, M., Jechlinger, M., Beug, H.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cancer Cell","volume":"10","issue":"3","page":"227-39","pdf":null,"JrId":"29778","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17055978","title":"Cohesin's ATPase activity is stimulated by the C-terminal Winged-Helix domain of its kleisin subunit.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">17055978<\/PMID><DateCompleted><Year>2006<\/Year><Month>12<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>16<\/Volume><Issue>20<\/Issue><PubDate><Year>2006<\/Year><Month>Oct<\/Month><Day>24<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Cohesin's ATPase activity is stimulated by the C-terminal Winged-Helix domain of its kleisin subunit.<\/ArticleTitle><Pagination><MedlinePgn>1998-2008<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Cohesin, a multisubunit protein complex conserved from yeast to humans, holds sister chromatids together from the onset of replication to their separation during anaphase. Cohesin consists of four core subunits, namely Smc1, Smc3, Scc1, and Scc3. Smc1 and Smc3 proteins are characterized by 50-nm-long anti-parallel coiled coils flanked by a globular hinge domain and an ABC-like ATPase head domain. Whereas Smc1 and Smc3 heterodimerize via their hinge domains, the kleisin subunit Scc1 connects their ATPase heads, and this results in the formation of a large ring. Biochemical studies suggest that cohesin might trap sister chromatids within its ring, and genetic evidence suggests that ATP hydrolysis is required for the stable association of cohesin with chromosomes. However, the precise role of the ATPase domains remains enigmatic.","authors":"Arumugam, P., Nishino, T., Haering, CH., Gruber, S., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr Biol","volume":"16","issue":"20","page":"1998-2008","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9230080","title":"CDK1 inactivation regulates anaphase spindle dynamics and cytokinesis in vivo.","abstract":"Through association with CDK1, cyclin B accumulation and destruction govern the G2\/M\/G1 transitions in eukaryotic cells. To identify CDK1 inactivation-dependent events during late mitosis, we expressed a nondestructible form of cyclin B (cyclin BDelta90) by microinjecting its mRNA into prometaphase normal rat kidney cells. The injection inhibited chromosome decondensation and nuclear envelope formation. Chromosome disjunction occurred normally, but anaphase-like movement persisted until the chromosomes reached the cell periphery, whereupon they often somersaulted and returned to the cell center. Injection of rhodamine-tubulin showed that this movement occurred in the absence of a central anaphase spindle. In 82% of cells cytokinesis was inhibited; the remainder split themselves into two parts in a process reminiscent of Dictyostelium cytofission. In all cells injected, F-actin and myosin II were diffusely localized with no detectable organization at the equator. Our results suggest that a primary effect of CDK1 inactivation is on spindle dynamics that regulate chromosome movement and cytokinesis. Prolonged CDK1 activity may prevent cytokinesis through inhibiting midzone microtubule formation, the behavior of proteins such as TD60, or through the phosphorylation of myosin II regulatory light chain.","authors":"Wheatley, SP., Hinchcliffe, EH., Glotzer, M., Hyman, AA., Sluder, G., Wang, Yl.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Cell Biol","volume":"138","issue":"2","page":"385-93","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1997-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11746235","title":"Can molecular mechanisms of biological processes be extracted from expression profiles? Case study: endothelial contribution to tumor-induced angiogenesis.","abstract":"Whereas the genome contains all potential developmental programs, expression profiles permit the determination of genes that are actively transcribed under defined physiological conditions. In this article, the idea of extracting biological mechanisms from expression data is tested. Molecular processes of the endothelial contribution to angiogenesis are derived from recently published expression profiles. The analysis reveals the sensitivity limits of experimental detection of transcriptional changes and how sequence-analytic techniques can help to identify the function of genes in question. We conclude that the transcripts (http:\/\/mendel.imp.univie.ac.at\/SEQUENCES\/TEMS\/) found to be up-regulated in angiogenesis are involved in extracellular matrix remodeling, cellular migration, adhesion, cell-cell communication rather than in angiogenesis initiation or integrative control. Comparison with tissue-specific patterns of EST occurrence shows that, indeed, the presumptive tumor-specific endothelial markers are more generally expressed by cell types involved in migration and matrix remodeling processes. This exemplary study demonstrates how bioinformatics approaches can be helpful in deriving mechanistic information from diverse sources of experimental data.","authors":"Novatchkova, M., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Bioessays","volume":"23","issue":"12","page":"1159-75","pdf":null,"JrId":"1014","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9469815","title":"Identification of a cullin homology region in a subunit of the anaphase-promoting complex.","abstract":"The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). The remaining four human APC subunits, APC2, APC4, APC5, and APC7, as well as human CDC23, were cloned. APC7 contains multiple copies of the tetratrico peptide repeat, similar to CDC16, CDC23, and CDC27. Whereas APC4 and APC5 share no similarity to proteins of known function, APC2 contains a region that is similar to a sequence in cullins, a family of proteins implicated in the ubiquitination of G1 phase cyclins and cyclin-dependent kinase inhibitors. The APC2 gene is essential in Saccharomyces cerevisiae, and apc2 mutants arrest at metaphase and are defective in the degradation of Pds1p. APC2 and cullins may be distantly related members of a ubiquitin ligase family that targets cell cycle regulators for degradation.","authors":"Yu, H., Peters, JM., King, RW., Page, AM., Hieter, P., Kirschner, MW.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Science","volume":"279","issue":"5354","page":"1219-22","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16920972","title":"Immune interactions with CD4+ T cells promote the development of functional osteoclasts from murine CD11c+ dendritic cells.","abstract":"Dendritic cells (DC) are innate immune effectors and are critically involved in regulating T cell immunity. Osteoclasts (OC) are bone-resorbing cells derived from the monocyte\/macrophage lineage in response to receptor activator of NF-kappaB ligand (RANKL). DC and T cells form aggregates in the inflammatory infiltrates at active disease sites in human and in experimental rheumatoid arthritis and periodontitis. We investigated whether DC interactions with T cells in the bone environment can support the development of functional OC. In the present study, we demonstrate that upon proper activation by microbial or protein Ags (namely Actinobacillus actinomycetemcomitans, bovine insulin, and outer membrane protein-1) and during immune interactions with CD4+ T cells in vitro, murine BM-derived and splenic CD11c+ DC (CD11b- F4\/80- Ly-6C- CD31-) develop into TRAP+ CT-R+ cathepsin-k+ functional OC in a RANKL\/RANK-dependent manner. Rescue and blocking experiments using CD11c+ DC derived from Csf-1(-\/-) op\/op mice show that M-CSF is required \"before\" developing such osteoclastogenic potential upstream of RANKL\/RANK signaling, suggesting that immature CD11c+ DC can indeed act like OC precursors. In addition, these CD11c+ DC-derived OC are capable of inducing bone loss after adoptive transfer in vivo. These data suggest a direct contribution of DC during immune interactions with CD4+ T cells to inflammation-induced osteoclastogenesis. Therefore, our findings not only provide further evidence for DC plasticity, but also extend the current paradigm of osteoimmunology.","authors":"Alnaeeli, M., Penninger, JM., Teng, YT.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Immunol","volume":"177","issue":"5","page":"3314-26","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9479473","title":"Translational fidelity: error-prone versus hyper-accurate ribosomes.","abstract":"Decoding mRNA is a multistep process involving the RNA and protein components of the ribosome, and external factors; little is known about the mechanism, however. New evidence suggests that a central region in small ribosomal RNA switches between two helices in translation to maintain translational fidelity.","authors":"von Ahsen, U.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Chem Biol","volume":"5","issue":"1","page":"R3-6","pdf":null,"JrId":"20384","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16871217","title":"Electrical signals control wound healing through phosphatidylinositol-3-OH kinase-gamma and PTEN.","abstract":"Wound healing is essential for maintaining the integrity of multicellular organisms. In every species studied, disruption of an epithelial layer instantaneously generates endogenous electric fields, which have been proposed to be important in wound healing. The identity of signalling pathways that guide both cell migration to electric cues and electric-field-induced wound healing have not been elucidated at a genetic level. Here we show that electric fields, of a strength equal to those detected endogenously, direct cell migration during wound healing as a prime directional cue. Manipulation of endogenous wound electric fields affects wound healing in vivo. Electric stimulation triggers activation of Src and inositol-phospholipid signalling, which polarizes in the direction of cell migration. Notably, genetic disruption of phosphatidylinositol-3-OH kinase-gamma (PI(3)Kgamma) decreases electric-field-induced signalling and abolishes directed movements of healing epithelium in response to electric signals. Deletion of the tumour suppressor phosphatase and tensin homolog (PTEN) enhances signalling and electrotactic responses. These data identify genes essential for electrical-signal-induced wound healing and show that PI(3)Kgamma and PTEN control electrotaxis.","authors":"Zhao, M., Song, B., Pu, J., Wada, T., Reid, B., Tai, G., Wang, F., Guo, A., Walczysko, P., Gu, Y., Sasaki, T., Suzuki, A., Forrester, JV., Bourne, HR., Devreotes, PN., McCaig, CD., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nature","volume":"442","issue":"7101","page":"457-60","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16844996","title":"DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity.","abstract":"DOUTfinder is a web-based tool facilitating protein domain detection among related protein sequences in the twilight zone of sequence similarity. The sequence set required for this analysis can be provided by the user or will be collected using PSI-BLAST if a single sequence is given as an input. The obtained sequence family is analyzed for known Pfam and SMART domains, and the thereby identified subsignificant domain similarities are evaluated further. Domains with several subthreshold hits in the query set are ranked based on a sum-score function and likely homologous domains are suggested according to established cut-offs. By providing a post-filtering procedure for subsignificant domain hits DOUTfinder allows the detection of non-trivial domain relationships and can thereby lead to new insights into the function and evolution of distantly related sequence families. DOUTfinder is available at http:\/\/mendel.imp.ac.at\/dout\/.","authors":"Novatchkova, M., Schneider, G., Fritz, R., Eisenhaber, F., Schleiffer, A.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nucleic Acids Res","volume":"34","issue":"Web Server issue","page":"W214-8","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16568946","title":"The role of histone modifications in epigenetic transitions during normal and perturbed development.","abstract":"Epigenetic mechanisms control eukaryotic development beyond DNA-stored information. DNA methylation, histone modifications and variants, nucleosome remodeling and noncoding RNAs all contribute to the dynamic make-up of chromatin under distinct developmental options. In particular, the great diversity of covalent histone tail modifications has been proposed to be ideally suited for imparting epigenetic information. While most of the histone tail modifications represent transient marks at transcriptionally permissive chromatin, some modifications appear more robust at silent chromatin regions, where they index repressive epigenetic states with functions also outside transcriptional regulation. Under-representation of repressive histone marks could be indicative of epigenetic plasticity in stem, young and tumor cells, while committed and senescent (old) cells often display increased levels of these more stable modifications. Here, we discuss profiles of normal and aberrant histone lysine methylation patterns, as they occur during the transition of an embryonic to a differentiated cell or in controlled self-renewal vs pro-neoplastic or metastatic conditions. Elucidating these histone modification patterns promises to have important implications for novel advances in stem cell research, nuclear reprogramming and cancer, and may offer novel targets for the combat of tumor cells, potentially leading to new diagnostic and therapeutic avenues in human biology and disease.","authors":"Kubicek, S., Schotta, G., Lachner, M., Sengupta, R., Kohlmaier, A., Perez-Burgos, L., Linderson, Y., Martens, JH., O'Sullivan, RJ., Fodor, BD., Yonezawa, M., Peters, AH., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Ernst Schering Res Found Workshop","volume":null,"issue":"57","page":"1-27","pdf":null,"JrId":"21783","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7981748","title":"Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9.","abstract":"In the human paired box-containing (PAX) gene family, only two members, PAX-3 and PAX-6, which are associated with Waardenburg's syndrome and aniridia, respectively have been mapped to human chromosomes. We have now isolated cosmids for six additional human PAX genes (PAX-1,-2,-5,-7,-8,-9) and a polymerase chain reaction fragment for PAX-4. PAX-9 is a novel family member which is closely related in its paired domain to PAX-1. The chromosomal location of all cloned PAX genes was determined by analysis of somatic cell hybrids and (except PAX-4) by fluorescence in situ hybridization to metaphase chromosomes. PAX-1 and PAX-7 map to chromosomal regions containing previously assigned disease loci.","authors":"Stapleton, P., Weith, A., Urb\u00e1nek, P., Kozmik, Z., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Nat Genet","volume":"3","issue":"4","page":"292-8","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"1995-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16493086","title":"Regulatory networks induced by live parasites impair both Th1 and Th2 pathways in patent lymphatic filariasis: implications for parasite persistence.","abstract":"Patent lymphatic filariasis is characterized by a profound down-regulation of immune responses with both parasite Ag-specific tolerance and bystander suppression. Although this down-regulation is confined to the Th1 arm of the immune system in response to parasite Ag, we hypothesized a more generalized suppression in response to live parasites. Indeed, when we examined the cytokine profile of a cohort of filaria-infected (n = 10) and uninfected (n = 10) individuals in response to live infective-stage larvae or microfilariae of Brugia malayi, we found significant impairment of both Th1 and Th2 cytokines characterized by diminished production of IFN-gamma, TNF-alpha, IL-4, IL-5, and IL-10 in infected patients. The molecular basis of this impaired Th1\/Th2 response was examined, and we identified three major networks of immunoregulation and tolerance. First, impaired induction of T-bet and GATA-3 mRNA underlies the Th1\/Th2 deficiency in infected individuals. Second, regulatory networks, as evidenced by significantly increased expression of Foxp3 (natural regulatory T cell marker) and regulatory effectors such as TGF-beta, CTLA-4, PD-1, ICOS, and indoleamine 2,3-dioxygenase play an important role in immunosuppression. Third, the compromise of effector T cell function is mediated by the enhanced induction of anergy-inducing factors cbl-b, c-cbl (cbl is abbreviation for Casitas B lymphoma), Itch, and Nedd4. Indeed, blocking CTLA-4 or neutralizing TGF-beta restored the ability to mount Th1\/Th2 responses to live parasites and reversed the induction of anergy-inducing factors. Hence, we conclude that a profound impairment of live parasite-specific Th1 and Th2 immune responses occurs in lymphatic filariasis that is governed at the transcriptional level by a complex interplay of inhibitory mediators.","authors":"Babu, S., Blauvelt, CP., Kumaraswami, V., Nutman, TB.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Immunol","volume":"176","issue":"5","page":"3248-56","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16428453","title":"Receptor activator of NF-kappaB ligand regulates the proliferation of mammary epithelial cells via Id2.","abstract":"Receptor activator of NF-kappaB ligand (RANKL) is a key regulator for mammary gland development during pregnancy. RANKL-deficient mice display impaired development of lobulo-alveolar mammary structures. Similar mammary gland defects have been reported in mice lacking Id2. Here we report that RANKL induces the proliferation of mammary epithelial cells via Id2. RANKL triggers marked nuclear translocation of Id2 in mammary epithelial cells. In vivo studies further demonstrated the defective nuclear translocation of Id2, but the normal expression of cyclin D1, in the mammary epithelial cells of rankl-\/- mice. In vitro studies with nuclear localization sequence-tagged Id2 revealed that the nuclear localization of Id2 itself is critical for the downregulation of p21 promoter activity. Moreover, RANKL stimulation failed to induce cell growth and to downregulate p21 expression in Id2-\/- mammary epithelial cells. Our results indicate that the inhibitor of helix-loop-helix protein, Id2, is critical to control the proliferation of mammary epithelial cells in response to RANKL stimulation.","authors":"Kim, NS., Kim, HJ., Koo, BK., Kwon, MC., Kim, YW., Cho, Y., Yokota, Y., Penninger, JM., Kong, YY.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Mol Cell Biol","volume":"26","issue":"3","page":"1002-13","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2006-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16051156","title":"Fidelity in protein synthesis.","abstract":null,"authors":"Cochella, L., Green, R.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"14","page":"R536-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9312023","title":"Cooperation of Spi-1\/PU.1 with an activated erythropoietin receptor inhibits apoptosis and Epo-dependent differentiation in primary erythroblasts and induces their Kit ligand-dependent proliferation.","abstract":"Spi-1\/PU.1 is a myeloid- and B-cell specific transcription factor which is also involved in Friend virus-induced murine erythroleukemia. The pre-leukemic phase of Friend erythroleukemia results from activation of the erythropoietin receptor (EpoR) by the spleen focus forming virus (SFFV) envelope glycoprotein, followed by the emergence of leukemic clones characterized by overexpression of Spi-1 and mutation of the p53 tumor suppressor gene. We developed a heterologous system to analyze the contribution of these alterations to the induction of primary erythroblast transformation. Avian erythroblasts expressing the activated mouse EpoR(R129C) differentiated into erythrocytes in response to hEpo. Expression of Spi-1 in these cells inhibited this ability to differentiate and rescued the cells from the apoptotic cell death program normally induced upon hEpo withdrawal. Although devoid of any effect by itself, a mutant p53 cooperated with Spi-1 and EpoR(R129C) to reinforce both phenotypes. Analysis of erythroblasts co-expressing Spi-1 and the wild-type mouse EpoR showed that differentiation arrest and inhibition of apoptosis depended on specific cooperation between Spi-1 and EpoR(R129C). This cooperation was also required to induce the sustained proliferation of differentiation-blocked erythroblasts in response to ligand activation of the endogenous tyrosine kinase receptor c-Kit. These results show that Spi-1\/PU.1 requires signals emanating from specific cytokine and growth factor receptors to affect the survival, proliferation and differentiation control of primary erythroblasts. They also suggest that the function of Spi-1\/PU.1 in the late phase of Friend leukemia requires specific signaling from the gp55-modified EpoR generated during the early phase of the disease.","authors":"Quang, CT., Wessely, O., Pironin, M., Beug, H., Ghysdael, J.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"EMBO J","volume":"16","issue":"18","page":"5639-53","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1997-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9218607","title":"STAT5 involvement in the differentiation response of primary chicken myeloid progenitor cells to chicken myelomonocytic growth factor.","abstract":"We have investigated the activation of the STAT5 protein during the differentiation of myelomonocytic cells. In the human U937 promonocytic cell line, STAT5 activation occurred in response to several inducers of monocytic differentiation (phorbol ester, 1alpha,25-dihydroxyvitamin D3, and retinoic acid). In the promyelocytic HL60 cell line, STAT5 was activated in the course of either phorbol ester-induced monocytic differentiation or DMSO-induced granulocytic differentiation. To test for involvement of STAT5 in the differentiation of primary nonimmortalized cells, chicken myeloid progenitor cells transfected with the ts21-E26 avian retrovirus were studied. At 37 degrees C the temperature-sensitive oncoprotein of the ts21-E26 virus (p135(gag-myb-ets)) installs a differentiation block that is released by a shift to the nonpermissive temperature (42 degrees C). Both proliferation and differentiation of ts21-E26-transfected myeloblasts require the continuous presence of chicken myelomonocytic growth factor (cMGF). Addition of cMGF to growth factor-starved cells rapidly caused STAT5 tyrosine phosphorylation, DNA binding, and transcriptional activity at both permissive and nonpermissive temperatures. Moreover, the temperature shift-induced onset of myelomonocytic differentiation strictly correlated with the appearance of activated STAT5 in ts21-E26-infected myeloblasts, but not in cells infected with wtE26 retrovirus. These data position STAT5 in a nuclear signaling cascade induced by the cMGF receptor and suggest a contribution of STAT5 to the process of myelomonocytic differentiation or to the functional changes that accompany the maturation of myeloid progenitor cells to a terminally differentiated stage.","authors":"Woldman, I., Mellitzer, G., Kieslinger, M., Buchhart, D., Meinke, A., Beug, H., Decker, T.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Immunol","volume":"159","issue":"2","page":"877-86","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"1997-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16275329","title":"Large-scale purification of the vertebrate anaphase-promoting complex\/cyclosome.","abstract":"The anaphase-promoting complex or cyclosome (APC\/C) is a ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC\/C is a 1.5-MDa complex composed of at least 12 different core subunits. At different stages of mitosis and G1, the APC\/C associates with a variety of regulatory proteins, such as the activator proteins Cdc20 and Cdh1 and the mitotic checkpoint complex (MCC), which regulate APC\/C activity in a substrate-specific manner. Although APC\/C and its regulators have been under intense investigation, it is still poorly understood how substrates are recognized and ubiquitinated by the APC\/C, why so many subunits are required for these processes, and how regulators of the APC\/C control its ubiquitin ligase activity in a substrate-specific manner. This chapter describes a simple and rapid procedure that allows the isolation of APC\/C from vertebrate cells and tissues with reasonable purity and at high concentrations, yielding up to 0.5 mg of APC\/C. This procedure should facilitate biochemical, biophysical, and structural analyses of the APC\/C that will be needed for a better mechanistic understanding of its function and regulation.","authors":"Herzog, F., Peters, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Methods Enzymol","volume":"398","issue":null,"page":"175-95","pdf":null,"JrId":"5787","fulltextlink":null,"preprintlink":null,"articledate":"2005-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16219685","title":"E-cadherin endocytosis regulates the activity of Rap1: a traffic light GTPase at the crossroads between cadherin and integrin function.","abstract":"The coordinate modulation of cadherin and integrin functions plays an essential role in fundamental physiological and pathological processes, including morphogenesis and cancer. However, the molecular mechanisms underlying the functional crosstalk between cadherins and integrins are still elusive. Here, we demonstrate that the small GTPase Rap1, a crucial regulator of the inside-out activation of integrins, is a target for E-cadherin-mediated outside-in signaling. In particular, we show that a strong activation of Rap1 occurs upon adherens junction disassembly that is triggered by E-cadherin internalization and trafficking along the endocytic pathway. By contrast, Rap1 activity is not influenced by integrin outside-in signaling. Furthermore, we demonstrate that the E-cadherin endocytosis-dependent activation of Rap1 is associated with and controlled by an increased Src kinase activity, and is paralleled by the colocalization of Rap1 and E-cadherin at the perinuclear Rab11-positive recycling endosome compartment, and the association of Rap1 with a subset of E-cadherin-catenin complexes that does not contain p120ctn. Conversely, Rap1 activity is suppressed by the formation of E-cadherin-dependent cell-cell junctions as well as by agents that inhibit either Src activity or E-cadherin internalization and intracellular trafficking. Finally, we demonstrate that the E-cadherin endocytosis-dependent activation of Rap1 is associated with and is required for the formation of integrin-based focal adhesions. Our findings provide the first evidence of an E-cadherin-modulated endosomal signaling pathway involving Rap1, and suggest that cadherins may have a novel modulatory role in integrin adhesive functions by fine-tuning Rap1 activation.","authors":"Balzac, F., Avolio, M., Degani, S., Kaverina, I., Torti, M., Silengo, L., Small, JV., Retta, SF.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Cell Sci","volume":"118","issue":"Pt 20","page":"4765-83","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9305773","title":"Structure and erythroid cell-restricted expression of a chicken cDNA encoding a novel zinc finger protein of the Cys + His class.","abstract":"We report the cloning, sequence analysis and expression pattern of chGfi, a zinc finger protein (Zfp)-encoding cDNA that was isolated from a cDNA library constructed with RNA from avian erythroblastosis virus (AEV)-transformed primary chicken erythroblasts. The 1387-bp-long chGfi cDNA encodes a full-length 337-amino-acid (aa) protein that contains six zinc fingers (Zf) of the 2Cys + 2His class at its C-terminus. Immunoblotting experiments with extracts from bone marrow cells detected a 38-kDa protein that corresponds to the M(r) of 38,690 calculated for the protein deduced from chGfi. The chGfi protein is most homologous to the rat Gfi-1 showing a sequence similarity of 92% over the Zf region and only two exchanges within the N-terminal 19 aa that constitute the Gfi-1 repressor domain. Expression of chGfi is only detected in transformed primary erythroblasts, in erythroid cells of the primitive and definitive lineage and in bone marrow cells. chGfi activity does not vary significantly during differentiation of transformed primary erythroblasts of the definitive lineage. No chGfi expression is detected in cells of the myeloid and lymphoid lineages or in a total of nine different organs of adult origin. Our results indicate that chGfi expression is restricted to erythroid cells of the primitive and definitive lineage.","authors":"Fuchs, B., Wagner, T., R\u00f6ssel, N., Antoine, M., Beug, H., Niessing, J.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Gene","volume":"195","issue":"2","page":"277-84","pdf":null,"JrId":"3886","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16143109","title":"The molecular clock mediates leptin-regulated bone formation.","abstract":"The hormone leptin is a regulator of bone remodeling, a homeostatic function maintaining bone mass constant. Mice lacking molecular-clock components (Per and Cry), or lacking Per genes in osteoblasts, display high bone mass, suggesting that bone remodeling may also be subject to circadian regulation. Moreover, Per-deficient mice experience a paradoxical increase in bone mass following leptin intracerebroventricular infusion. Thus, clock genes may mediate the leptin-dependent sympathetic regulation of bone formation. We show that expression of clock genes in osteoblasts is regulated by the sympathetic nervous system and leptin. Clock genes mediate the antiproliferative function of sympathetic signaling by inhibiting G1 cyclin expression. Partially antagonizing this inhibitory loop, leptin also upregulates AP-1 gene expression, which promotes cyclin D1 expression, osteoblast proliferation, and bone formation. Thus, leptin determines the extent of bone formation by modulating, via sympathetic signaling, osteoblast proliferation through two antagonistic pathways, one of which involves the molecular clock.","authors":"Fu, L., Patel, MS., Bradley, A., Wagner, EF., Karsenty, G.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell","volume":"122","issue":"5","page":"803-15","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9285404","title":"Selection of a broad repertoire of CD4+ T cells in H-2Ma0\/0 mice.","abstract":"According to past reports, H-2Ma0\/0 mice express a single major histocompatiblity complex class II molecule, A(b), heavily loaded with a single peptide derived from the invariant chain, CLIP. Despite the highly restricted diversity of the class II:peptide complexes expressed on thymic stromal cells in the mutant animals, a large and diverse population of CD4+ T cells is positively selected. However, two important issues remained unresolved and are addressed here: Just how preponderant is CLIP occupancy of the class II molecules from H-2M0\/0 mice? How extensive and functionally competent is the CD4+ population selected in the mutant animals? Our results argue that a single class II:peptide complex can select a very broad, though not complete, repertoire of CD4+ T cells.","authors":"Tourne, S., Miyazaki, T., Oxenius, A., Klein, L., Fehr, T., Kyewski, B., Benoist, C., Mathis, D.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Immunity","volume":"7","issue":"2","page":"187-95","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"1997-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9244299","title":"Antagonistic interactions between FGF and BMP signaling pathways: a mechanism for positioning the sites of tooth formation.","abstract":"Vertebrate organogenesis is initiated at sites that are often morphologically indistinguishable from the surrounding region. Here we have identified Pax9 as a marker for prospective tooth mesenchyme prior to the first morphological manifestation of odontogenesis. We provide evidence that the sites of Pax9 expression in the mandibular arch are positioned by the combined activity of two signals, one (FGF8) that induces Pax9 expression and the other (BMP2 and BMP4) that prevents this induction. Thus it appears that the position of the teeth is determined by a combination of two different types of signaling molecules produced in wide but overlapping domains rather than by a single localized inducer. We suggest that a similar mechanism may be used for specifying the sites of development of other organs.","authors":"Neub\u00fcser, A., Peters, H., Balling, R., Martin, GR.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Cell","volume":"90","issue":"2","page":"247-55","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1997-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"142","title":"Effects of zinc-smelter emissions on forest soil microflora.","abstract":"Within 2 km of a zinc (Zn) smelter in Palmerton, Pennsylvania, near the Lehigh Water Gap, up to 13.5% Zn by weight has been measured in the O2 horizon of the soil, and up to 8% Zn in the A1 horizon. The total numbers of bacteria, actinomycetes, and fungi (measured by dilution plate counts) were greatly reduced in the most severely Zn-contaminated soils compared with control soils. The reduction of microbial populations may be a partial cause of the decreased rate of litter decomposition at Lehigh Gap. Growth of most bacteria from control sites was reduced by 100 to 200 muM Zn, most actinomycetes by 100 muM Zn, and most fungi by 100 to 1000 muM Zn in thin-Pablum extract agar (TPab). All the tested actinomycetes and non-spore-forming bacteria isolated from Zn-contaminated Lehigh Gap soils were Zn-tolerant, growing normally in media containing 600-2000 muM Zn. Most fungi, regardless of source, were capable of at least 50% of normal growth at 700 muM Zn. Zinc-tolerant bacteria, actinomycetes, and fungi were readily isolated from low-Zn soils, suggesting that selection for Zn tolerance may proceed rapidly. Acidophilic Mortierella species have been selectively eliminated near the smelter, apparently because of elevated soil pH. Peryronellaea glomerata (Corda) Goidanich and Coniothyrium spp. were found only in the high-Zn soils.","authors":"Jordan, MJ., Lechevalier, MP.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Microbiol","volume":"21","issue":"11","page":"1855-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15980439","title":"PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets.","abstract":"The analysis of taxonomic distribution and lineage-specific variation of domains and domain combinations is an important step in the assessment of their functional roles and potential interoperability. In the study of eukaryote sequence sets with many multi-domain proteins, it can become laborious to evaluate the phylogenetic context of the many occurring domains and their mutual relationships. PhyloDome is an answer to that problem. It provides a fast overview on the taxonomic spreading and potential interrelation of domains that are either given as a list of names and PFAM\/SMART accessions or derived from a user-defined set of sequences. This taxonomic distribution analysis can be helpful in protein function and interaction assignment as the comparative study of potential Hedgehog pathway members in C.elegans shows. An implementation of PhyloDome is accessible for public use as a WWW-Service at http:\/\/mendel.imp.univie.ac.at\/phylodome\/. Software components are available on request.","authors":"Novatchkova, M., Wildpaner, M., Schweizer, D., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nucleic Acids Res","volume":"33","issue":"Web Server issue","page":"W121-5","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"2005-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15897281","title":"I{kappa}B kinase (IKK){beta}, but not IKK{alpha}, is a critical mediator of osteoclast survival and is required for inflammation-induced bone loss.","abstract":"Transcription factor, nuclear factor kappaB (NF-kappaB), is required for osteoclast formation in vivo and mice lacking both of the NF-kappaB p50 and p52 proteins are osteopetrotic. Here we address the relative roles of the two catalytic subunits of the IkappaB kinase (IKK) complex that mediate NF-kappaB activation, IKKalpha and IKKbeta, in osteoclast formation and inflammation-induced bone loss. Our findings point out the importance of the IKKbeta subunit as a transducer of signals from receptor activator of NF-kappaB (RANK) to NF-kappaB. Although IKKalpha is required for RANK ligand-induced osteoclast formation in vitro, it is not needed in vivo. However, IKKbeta is required for osteoclastogenesis in vitro and in vivo. IKKbeta also protects osteoclasts and their progenitors from tumor necrosis factor alpha-induced apoptosis, and its loss in hematopoietic cells prevents inflammation-induced bone loss.","authors":"Ruocco, MG., Maeda, S., Park, JM., Lawrence, T., Hsu, LC., Cao, Y., Schett, G., Wagner, EF., Karin, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Exp Med","volume":"201","issue":"10","page":"1677-87","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15578054","title":"Wobble during decoding: more than third-position promiscuity.","abstract":null,"authors":"Cochella, L., Green, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nat Struct Mol Biol","volume":"11","issue":"12","page":"1160-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11743722","title":"Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.","abstract":"The complexity of biological systems provides for a great diversity of relationships between genes. The current analysis of whole-genome expression data focuses on relationships based on global correlation over a whole time-course, identifying clusters of genes whose expression levels simultaneously rise and fall. There are, of course, other potential relationships between genes, which are missed by such global clustering. These include activation, where one expects a time-delay between related expression profiles, and inhibition, where one expects an inverted relationship. Here, we propose a new method, which we call local clustering, for identifying these time-delayed and inverted relationships. It is related to conventional gene-expression clustering in a fashion analogous to the way local sequence alignment (the Smith-Waterman algorithm) is derived from global alignment (Needleman-Wunsch). An integral part of our method is the use of random score distributions to assess the statistical significance of each cluster. We applied our method to the yeast cell-cycle expression dataset and were able to detect a considerable number of additional biological relationships between genes, beyond those resulting from conventional correlation. We related these new relationships between genes to their similarity in function (as determined from the MIPS scheme) or their having known protein-protein interactions (as determined from the large-scale two-hybrid experiment); we found that genes strongly related by local clustering were considerably more likely than random to have a known interaction or a similar cellular role. This suggests that local clustering may be useful in functional annotation of uncharacterized genes. We examined many of the new relationships in detail. Some of them were already well-documented examples of inhibition or activation, which provide corroboration for our results. For instance, we found an inverted expression profile relationship between genes YME1 and YNT20, where the latter has been experimentally documented as a bypass suppressor of the former. We also found new relationships involving uncharacterized yeast genes and were able to suggest functions for many of them. In particular, we found a time-delayed expression relationship between J0544 (which has not yet been functionally characterized) and four genes associated with the mitochondria. This suggests that J0544 may be involved in the control or activation of mitochondrial genes. We have also looked at other, less extensive datasets than the yeast cell-cycle and found further interesting relationships. Our clustering program and a detailed website of clustering results is available at http:\/\/www.bioinfo.mbb.yale.edu\/expression\/cluster (or http:\/\/www.genecensus.org\/expression\/cluster).","authors":"Qian, J., Dolled-Filhart, M., Lin, J., Yu, H., Gerstein, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Mol Biol","volume":"314","issue":"5","page":"1053-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11741272","title":"DNA\/polyethylenimine transfection particles: influence of ligands, polymer size, and PEGylation on internalization and gene expression.","abstract":"Receptor-binding ligands have been incorporated into DNA\/polyethylenimine (PEI) complexes to enhance cell binding and cellular internalization. This study characterizes receptor-mediated uptake of DNA\/PEI complexes on a cellular basis. A novel assay based on flow cytometry was applied, discriminating between total cell-associated and extracellularly bound DNA complexes. Receptor-mediated uptake of ligand-containing DNA\/PEI (molecular weight, 800 kd) complexes was found to occur quickly (within 1 hour), whereas unspecific uptake through adsorptive endocytosis is less efficient or requires extended periods to reach the same degree of internalization. Rapid, receptor-mediated internalization requires a small complex size; however, large, aggregated complexes show higher gene expression. Using PEI 25 kd conjugated to large proteins such as transferrin or antibodies, improper condensation with DNA leads to suboptimal uptake and gene expression, whereas partial replacement of ligand-PEI with unconjugated PEI increases both uptake and transfection. In contrast, the 8 kd protein epidermal growth factor conjugated to PEI 25 kd properly condenses DNA and mediates specific uptake into human adenocarcinoma (KB) cells. Modification of the complex surface with appropriate amounts of poly(ethylene glycol) (PEG) does not block ligand-mediated internalization. A higher degree of PEGylation reduces the internalization of transferrin or antibody-containing complexes to a level similar to that of ligand-free complexes. In contrast, epidermal growth factor \"mediated uptake is less effected by excessive PEGylation.","authors":"Ogris, M., Steinlein, P., Carotta, S., Brunner, S., Wagner, E.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"AAPS PharmSci","volume":"3","issue":"3","page":"E21","pdf":null,"JrId":"22454","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11740938","title":"Scc1\/Rad21\/Mcd1 is required for sister chromatid cohesion and kinetochore function in vertebrate cells.","abstract":"Proteolytic cleavage of the cohesin subunit Scc1 is a consistent feature of anaphase onset, although temporal differences exist between eukaryotes in cohesin loss from chromosome arms, as distinct from centromeres. We describe the effects of genetic deletion of Scc1 in chicken DT40 cells. Scc1 loss caused premature sister chromatid separation but did not disrupt chromosome condensation. Scc1 mutants showed defective repair of spontaneous and induced DNA damage. Scc1-deficient cells frequently failed to complete metaphase chromosome alignment and showed chromosome segregation defects, suggesting aberrant kinetochore function. Notably, the chromosome passenger INCENP did not localize normally to centromeres, while the constitutive kinetochore proteins CENP-C and CENP-H behaved normally. These results suggest a role for Scc1 in mitotic regulation, along with cohesion.","authors":"Sonoda, E., Matsusaka, T., Morrison, C., Vagnarelli, P., Hoshi, O., Ushiki, T., Nojima, K., Fukagawa, T., Waizenegger, IC., Peters, JM., Earnshaw, WC., Takeda, S.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Dev Cell","volume":"1","issue":"6","page":"759-70","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15808511","title":"PARP-1 determines specificity in a retinoid signaling pathway via direct modulation of mediator.","abstract":"We show that PARP-1 is indispensable to retinoic acid receptor (RAR)-mediated transcription from the RARbeta2 promoter in a highly purified, reconstituted transcription system and that RA-inducible expression of all RARbeta isoforms is abrogated in PARP-1(-\/-) cells in vivo. Importantly, PARP-1 activity was independent of its catalytic domain. PARP-1 directly interacts with RAR and Mediator. Chromatin immunoprecipitation experiments confirmed the presence of PARP-1 and Mediator on RAR-responsive promoters in vivo. Importantly, Mediator was inactive (Cdk8+) under basal conditions but was activated (Cdk8-) upon induction. However, in PARP-1(-\/-) cells, Mediator was retained in its inactive state (Cdk8+) upon induction consistent with the absence of gene expression. PARP-1 became dispensable for ligand-dependent transcription in a chromatin reconstituted transcription assay when Mediator was devoid of the Cdk8 module (CRSP). PARP-1 appears to function as a specificity factor regulating the RA-induced switch of Mediator from the inactive (Cdk8+) to the active (Cdk8-) state in RAR-dependent transcription.","authors":"Pavri, R., Lewis, B., Kim, TK., Dilworth, FJ., Erdjument-Bromage, H., Tempst, P., de Murcia, G., Evans, R., Chambon, P., Reinberg, D.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Mol Cell","volume":"18","issue":"1","page":"83-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15781582","title":"CD44 is a determinant of inflammatory bone loss.","abstract":"Chronic inflammation is a major trigger of local and systemic bone loss. Disintegration of cell-matrix interaction is a prerequisite for the invasion of inflammatory tissue into bone. CD44 is a type I transmembrane glycoprotein that connects a variety of extracellular matrix proteins to the cell surface. Tumor necrosis factor (TNF) is a major inducer of chronic inflammation and its overexpression leads to chronic inflammatory arthritis. By generating CD44(-\/-) human TNF-transgenic (hTNFtg) mice, we show that destruction of joints and progressive crippling is far more severe in hTNFtg mice lacking CD44, which also develop severe generalized osteopenia. Mutant mice exhibit an increased bone resorption due to enhanced number, size, and resorptive capacity of osteoclasts, whereas bone formation and osteoblast differentiation are not affected. Responsiveness of CD44-deficient osteoclasts toward TNF is enhanced and associated with increased activation of the p38 mitogen-activated protein kinase. These data identify CD44 as a critical inhibitor of TNF-driven joint destruction and inflammatory bone loss.","authors":"Hayer, S., Steiner, G., G\u00f6rtz, B., Reiter, E., Tohidast-Akrad, M., Amling, M., Hoffmann, O., Redlich, K., Zwerina, J., Skriner, K., Hilberg, F., Wagner, EF., Smolen, JS., Schett, G.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Exp Med","volume":"201","issue":"6","page":"903-14","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15774750","title":"The molecular requirements for cytokinesis.","abstract":"After anaphase onset, animal cells build an actomyosin contractile ring that constricts the plasma membrane to generate two daughter cells connected by a cytoplasmic bridge. The bridge is ultimately severed to complete cytokinesis. Myriad techniques have been used to identify proteins that participate in cytokinesis in vertebrates, insects, and nematodes. A conserved core of about 20 proteins are individually involved with cytokinesis in most animal cells. These components are found in the contractile ring, on the central spindle, within the RhoA pathway, and on vesicles that expand the membrane and sever the bridge. Cytokinesis involves additional proteins, but they, or their requirement in cytokinesis, are not conserved among animal cells.","authors":"Glotzer, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Science","volume":"307","issue":"5716","page":"1735-9","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11714200","title":"Correction of hyperglycemia in diabetic mice transplanted with reversibly immortalized pancreatic beta cells controlled by the tet-on regulatory system.","abstract":"Pancreatic beta cell lines may offer an abundant source of cells for beta-cell replacement in type I diabetes. Using regulatory elements of the bacterial tetracycline (tet) operon for conditional expression of SV40 T antigen oncoprotein in transgenic mouse beta cells, we have shown that reversible immortalization is an efficient approach for regulated beta-cell expansion, accompanied by enhanced cell differentiation upon growth arrest. The original system employed the tet-off approach, in which the cells proliferate in the absence of tet ligands and undergo growth arrest in their presence. The disadvantage of this system is the need for continuous treatment with the ligand in vivo for maintaining growth arrest. Here we utilized the tet-on regulatory system to generate beta cell lines in which proliferation is regulated in reverse: these cells divide in the presence of tet ligands, and undergo growth arrest in their absence, as judged by [3H]thymidine and BrdU incorporation assays. These cell lines were derived from insulinomas, which heritably developed in transgenic mice continuously treated with the tet derivative doxycycline (dox). The cells produce and secrete high amounts of insulin, and can restore and maintain euglycemia in syngeneic streptozotocin-induced diabetic mice in the absence of dox. Such a system is more suitable for transplantation, compared with cells regulated by the tet-off approach, because ligand treatment is limited to cell expansion in culture and is not required for long-term maintenance of growth arrest in vivo.","authors":"Milo-Landesman, D., Surana, M., Berkovich, I., Compagni, A., Christofori, G., Fleischer, N., Efrat, S.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell Transplant","volume":"10","issue":"7","page":"645-50","pdf":null,"JrId":"8477","fulltextlink":null,"preprintlink":null,"articledate":"2002-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15664196","title":"Formation of a dynamic kinetochore- microtubule interface through assembly of the Dam1 ring complex.","abstract":"How kinetochore proteins form a dynamic interface with microtubules is largely unknown. In budding yeast, the 10-protein Dam1 complex is an Aurora kinase target that plays essential roles maintaining the integrity of the mitotic spindle and regulating interactions with the kinetochore. Here, we investigated the biochemical properties of purified Dam1 complex. The complex oligomerized into rings around microtubules. Ring formation was facilitated by microtubules but could occur in their absence. Mutant alleles led to partially assembled complexes or reduced microtubule binding. The interaction between rings and microtubules is mediated by the C termini of both Dam1 and alphabeta-tubulin. Ring formation promotes microtubule assembly, stabilizes against disassembly, and promotes bundling. A GTP-tubulin lattice is the preferred binding partner for the complex, and Dam1 rings can exhibit lateral mobility on microtubules. These observations suggest a mechanism by which the kinetochore can recognize and stay attached to the plus ends of microtubules.","authors":"Westermann, S., Avila-Sakar, A., Wang, HW., Niederstrasser, H., Wong, J., Drubin, DG., Nogales, E., Barnes, G.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Mol Cell","volume":"17","issue":"2","page":"277-90","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8461380","title":"Direct in vivo gene transfer to airway epithelium employing adenovirus-polylysine-DNA complexes.","abstract":"Adenovirus-polylysine-DNA complexes were evaluated for their capacity to accomplish direct in vivo gene transfer to airway epithelium employing a rodent model. Binary complexes containing transferrin or adenovirus, or combination complexes containing both transferrin and adenovirus, were evaluated. The highest in vitro gene transfer efficiency in primary cultures of airway epithelial cells was accomplished by the combination complexes. This result was paralleled in vivo. Transient gene expression of up to 1 week was observed with localization of the transduced cells to the region of the small airways. These results establish the feasibility of this type of approach for gene therapy applications.","authors":"Gao, L., Wagner, E., Cotten, M., Agarwal, S., Harris, C., R\u00f8mer, M., Miller, L., Hu, PC., Curiel, D.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Hum Gene Ther","volume":"4","issue":"1","page":"17-24","pdf":null,"JrId":"1041","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15649045","title":"Chemical cross-linking and high-performance Fourier transform ion cyclotron resonance mass spectrometry for protein interaction analysis: application to a calmodulin\/target peptide complex.","abstract":"Chemical cross-linking has proved successful in combination with mass spectrometry as a tool for low-resolution structure determination of proteins. The integration of chemical cross-linking with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to determine protein interfaces was tested on the calcium-dependent complex between calmodulin (CaM) and a 26-amino acid peptide derived from the skeletal muscle myosin light chain kinase (M13). Different amine-reactive, homobifunctional cross-linkers and a \"zero-length\" cross-linker were employed. The covalently attached complexes were separated from nonreacted proteins by one-dimensional gel electrophoresis, and the bands of interest were excised and in-gel digested with trypsin. Digestion of the cross-linked complexes resulted in complicated peptide mixtures, which were analyzed by nano-HPLC\/nano-ESI-FTICR mass spectrometry. The distance constraints obtained by chemical cross-linking were in agreement with the published NMR structure of the CaM\/M13 complex, pointing to residues Lys-18 and Lys-19 of M13 being cross-linked with the central alpha-helix of CaM. Thus, the integrated approach described herein has proven to be an efficient tool for mapping the topology of the CaM\/M13 complex. As such it is applicable as a general strategy for the investigation of the spatial organization of protein complexes and complements existing techniques, such as X-ray crystallography and NMR spectroscopy.","authors":"Kalkhof, S., Ihling, C., Mechtler, K., Sinz, A.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Anal Chem","volume":"77","issue":"2","page":"495-503","pdf":null,"JrId":"519","fulltextlink":null,"preprintlink":null,"articledate":"2007-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9159073","title":"The cytoskeleton in mRNA localization and cell differentiation.","abstract":"Asymmetric distribution of cytoplasmic proteins and messenger RNAs has been implicated in several instances of cell differentiation. Microtubules have been suggested to direct mRNA localization in Drosophila and Xenopus oocytes but motor proteins that might transport mRNAs have not yet been identified. Recent data imply that in Drosophila, Caenorhabditis elegans and budding yeast, proteins of the actin cytoskeleton, including unconventional myosins, play active roles in the segregation of differentiation factors and mRNAs.","authors":"Nasmyth, K., Jansen, RP.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Curr Opin Cell Biol","volume":"9","issue":"3","page":"396-400","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"1997-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15568990","title":"Proteolysis as a regulatory mechanism.","abstract":"Proteases can play key roles in regulation by controlling the levels of critical components of, for example, signal transduction pathways. Proteolytic processing can remove regulatory proteins when they are not needed, while transforming others from the dormant into the biologically active state. The latter mechanism often involves a subsequent change of cellular localization such as the movement from the membrane to the nucleus. The investigation of these processes has revealed a new type of proteolytic activity, regulated intramembrane proteolysis, and a reversible switch in activity occurring in the HtrA family of serine proteases. The bacterial RseA and the human amyloid precursor processing pathways are used as models to review these novel principles that are evolutionarily conserved and have wide biological implications.","authors":"Ehrmann, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Annu Rev Genet","volume":"38","issue":null,"page":"709-24","pdf":null,"JrId":"668","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15546623","title":"Distinct contributions of histone H3 lysine 9 and 27 methylation to locus-specific stability of polycomb complexes.","abstract":"The Polycomb group of proteins (PcG) maintains stable epigenetic silencing of over 100 genes via PcG response elements (PREs). Here we investigate the relationship between Polycomb binding, transcriptional status, and histone H3 methylation at lysine 9 (H3K9Me) and 27 (H3K27Me) for over 30 PcG targets in Drosophila. We show that H3K9Me and H3K27Me have distinct distributions at different loci. Our data show that Polycomb binding and histone methylation at the promoter do not prevent strong transcriptional activity, and indicate instead that silencing requires methylation of both PRE and promoter. In addition, we show that trimethylated H3K9 and H3K27 peptides can compete Polycomb from polytene chromosomes, with different effects at different loci, which correlate with differences in methylation status and transcriptional activity. We use mathematical modeling to examine these data, and propose that weak Polycomb-histone tail interactions enable PcG complexes to bind dynamically to chromatin, offering opportunities for regulation.","authors":"Ringrose, L., Ehret, H., Paro, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Mol Cell","volume":"16","issue":"4","page":"641-53","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15520247","title":"The molecular adapter Carma1 controls entry of IkappaB kinase into the central immune synapse.","abstract":"Carma1 (also known as caspase recruitment domain [CARD]11, Bimp3) is a CARD-containing membrane-associated guanylate kinase family protein that plays an essential role in antigen receptor-induced nuclear factor kappaB activation. We investigated the role of Carma1 in the assembly of signaling molecules at the immune synapse using a peptide-specific system. We report that Carma1 is essential for peptide-induced interleukin 2 and interferon gamma production, but dispensable for proliferation in T cells. Recruitment and distribution of T cell receptor, lymphocyte function associated 1, lipid rafts, and protein kinase C (PKC)theta; to central and peripheral immune synapse regions occur normally in Carma1-\/- T cells. Carma1 controls entry of IkappaB kinase (IKK) into lipid raft aggregates and the central region of the immune synapse, as well as activation of IKK downstream of PKC. Our data provide the first genetic evidence on a new class of molecular scaffold that controls entry of defined signaling components, IKK, into the central supramolecular activation cluster at T cell-antigen-presenting cell interfaces without having any apparent effect on the overall organization and formation of immune synapses.","authors":"Hara, H., Bakal, C., Wada, T., Bouchard, D., Rottapel, R., Saito, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Exp Med","volume":"200","issue":"9","page":"1167-77","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15567863","title":"Requirement of JNK2 for scavenger receptor A-mediated foam cell formation in atherogenesis.","abstract":"In vitro studies suggest a role for c-Jun N-terminal kinases (JNKs) in proatherogenic cellular processes. We show that atherosclerosis-prone ApoE-\/- mice simultaneously lacking JNK2 (ApoE-\/- JNK2-\/- mice), but not ApoE-\/- JNK1-\/- mice, developed less atherosclerosis than do ApoE-\/- mice. Pharmacological inhibition of JNK activity efficiently reduced plaque formation. Macrophages lacking JNK2 displayed suppressed foam cell formation caused by defective uptake and degradation of modified lipoproteins and showed increased amounts of the modified lipoprotein-binding and -internalizing scavenger receptor A (SR-A), whose phosphorylation was markedly decreased. Macrophage-restricted deletion of JNK2 was sufficient to decrease atherogenesis. Thus, JNK2-dependent phosphorylation of SR-A promotes uptake of lipids in macrophages, thereby regulating foam cell formation, a critical step in atherogenesis.","authors":"Ricci, R., Sumara, G., Sumara, I., Rozenberg, I., Kurrer, M., Akhmedov, A., Hersberger, M., Eriksson, U., Eberli, FR., Becher, B., Bor\u00e9n, J., Chen, M., Cybulsky, MI., Moore, KJ., Freeman, MW., Wagner, EF., Matter, CM., L\u00fcscher, TF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Science","volume":"306","issue":"5701","page":"1558-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15458643","title":"The E2-C vihar is required for the correct spatiotemporal proteolysis of cyclin B and itself undergoes cyclical degradation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15458643<\/PMID><DateCompleted><Year>2005<\/Year><Month>01<\/Month><Day>31<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>14<\/Volume><Issue>19<\/Issue><PubDate><Year>2004<\/Year><Month>Oct<\/Month><Day>05<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The E2-C vihar is required for the correct spatiotemporal proteolysis of cyclin B and itself undergoes cyclical degradation.<\/ArticleTitle><Pagination><MedlinePgn>1723-33<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Proteolytic degradation of mitotic regulatory proteins first requires these targets to be ubiquitinated. This is regulated at the level of conjugation of ubiquitin to substrates by the anaphase-promoting complex\/cyclosome (APC\/C) ubiquitin-protein ligase. Substrate specificity and temporal activity of the APC\/C has been thought to lie primarily with its two activators, Cdc20\/Fizzy and Cdh1\/Fizzy-related.","authors":"M\u00e1th\u00e9, E., Kraft, C., Giet, R., De\u00e1k, P., Peters, JM., Glover, DM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"19","page":"1723-33","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15509771","title":"The AP1 transcription factor Fra2 is required for efficient cartilage development.","abstract":"The Fos-related AP1 transcription factor Fra2 (encoded by Fosl2) is expressed in various epithelial cells as well as in cartilaginous structures. We studied the role of Fra2 in cartilage development. The absence of Fra2 in embryos and newborns leads to reduced zones of hypertrophic chondrocytes and impaired matrix deposition in femoral and tibial growth plates, probably owing to impaired differentiation into hypertrophic chondrocytes. In addition, hypertrophic differentiation and ossification of primordial arches of the developing vertebrae are delayed in Fra2-deficient embryos. Primary Fosl2-\/- chondrocytes exhibit decreased hypertrophic differentiation and remain in a proliferative state longer than wild-type cells. As pups lacking Fra2 die shortly after birth, we generated mice carrying 'floxed' Fosl2 alleles and crossed them to coll2a1-Cre mice, allowing investigation of postnatal cartilage development. The coll2a1-Cre, Fosl2f\/f mice die between 10 and 25 days after birth, are growth retarded and display smaller growth plates similar to Fosl2-\/- embryos. In addition, these mice suffer from a kyphosis-like phenotype, an abnormal bending of the spine. Hence, Fra2 is a novel transcription factor important for skeletogenesis by affecting chondrocyte differentiation.","authors":"Karreth, F., Hoebertz, A., Scheuch, H., Eferl, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Development","volume":"131","issue":"22","page":"5717-25","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11709169","title":"Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11709169<\/PMID><DateCompleted><Year>2002<\/Year><Month>02<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>09<\/Month><Day>16<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0969-2126<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>9<\/Volume><Issue>11<\/Issue><PubDate><Year>2001<\/Year><Month>Nov<\/Month><\/PubDate><\/JournalIssue><Title>Structure (London, England : 1993)<\/Title><ISOAbbreviation>Structure<\/ISOAbbreviation><\/Journal><ArticleTitle>Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization.<\/ArticleTitle><Pagination><MedlinePgn>1051-60<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">MalT from Escherichia coli, the best-studied member of the MalT family of ATP-dependent transcriptional activators, regulates the genes for malto-oligosaccharide utilization. The active form of this 4 domain protein is a homooligomer, and its multimerization is induced by the binding of maltotriose. Domains II and III of MalT were suggested to mediate the oligomerization process, but its molecular mechanism and the specific functions of these domains remain to be identified.","authors":"Steegborn, C., Danot, O., Huber, R., Clausen, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Structure","volume":"9","issue":"11","page":"1051-60","pdf":null,"JrId":"22305","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15479877","title":"DREAMing about arthritic pain.","abstract":"The experience of acute pain serves a crucial biological purpose: it alerts a living organism to environmental dangers, inducing behavioural responses which protect the organism from further damage. In contrast, chronic pain arising from disease states and\/or pathological functioning of the nervous system offers no advantage and may be debilitating to those afflicted. Despite recent advances in our understanding of pain mechanisms, the satisfactory management of pathological pain eludes current treatment strategies. We have demonstrated in a previous study on dream deficient mice the pivotal role of downstream regulatory element antagonistic modulator (DREAM) in modulating pain sensitivity in a number of behavioural models, including acute and chronic neuropathic pain. DREAM is a novel calcium binding transcriptional repressor for the prodynorphin gene in spinal cord neurones. The marked attenuation in pain behaviour exhibited by dream-\/- mice was shown, by pharmacological and biochemical analyses, to be due to increased activation of the endogenous kappa-opioid system. Importantly, loss of DREAM also attenuated inflammatory pain. Thus, DREAM and the DREAM pathway constitute a novel therapeutic paradigm for the treatment of chronic pain in arthritis.","authors":"Cheng, HY., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Ann Rheum Dis","volume":"63 Suppl 2","issue":null,"page":"ii72-ii75","pdf":null,"JrId":"640","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9115401","title":"Cytokinesis.","abstract":null,"authors":"Glotzer, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Curr Biol","volume":"7","issue":"5","page":"R274-6","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15380093","title":"APC\/C and SCF: controlling each other and the cell cycle.","abstract":"Regulated protein degradation has emerged as a key recurring theme in multiple aspects of cell-cycle regulation. Importantly, the irreversible nature of proteolysis makes it an invaluable complement to the intrinsically reversible regulation through phosphorylation and other post-translational modifications. Consequently, ubiquitin-protein ligases, the protagonists of regulated protein destruction, have gained prominence that compares to that of the cyclin-dependent kinases (Cdks) in driving the eukaryotic cell-cycle clock. This review will focus on the two main players, the related ubiquitin-protein ligases APC\/C and SCF, and how they control cell-cycle progression. I will also try to delineate the regulation and interplay of these destruction mechanisms, which are intricately connected to the kinase network as well as to extrinsic signals. Moreover, cell-cycle ubiquitin-protein ligases are themselves subject to proteolytic control in cis as well as in trans. Finally, a careful comparison of the functions and regulation of APC\/C and SCF shows that, in certain aspects, their logic of action is fundamentally different.","authors":"Vodermaier, HC.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"18","page":"R787-96","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15353547","title":"Quantitative kinetic analysis of nucleolar breakdown and reassembly during mitosis in live human cells.","abstract":"One of the great mysteries of the nucleolus surrounds its disappearance during mitosis and subsequent reassembly at late mitosis. Here, the relative dynamics of nucleolar disassembly and reformation were dissected using quantitative 4D microscopy with fluorescent protein-tagged proteins in human stable cell lines. The data provide a novel insight into the fates of the three distinct nucleolar subcompartments and their associated protein machineries in a single dividing cell. Before the onset of nuclear envelope (NE) breakdown, nucleolar disassembly started with the loss of RNA polymerase I subunits from the fibrillar centers. Dissociation of proteins from the other subcompartments occurred with faster kinetics but commenced later, coincident with the process of NE breakdown. The reformation pathway also follows a reproducible and defined temporal sequence but the order of reassembly is shown not to be dictated by the order in which individual nucleolar components reaccumulate within the nucleus after mitosis.","authors":"Leung, AK., Gerlich, D., Miller, G., Lyon, C., Lam, YW., Lleres, D., Daigle, N., Zomerdijk, J., Ellenberg, J., Lamond, AI.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Cell Biol","volume":"166","issue":"6","page":"787-800","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15276015","title":"The role of phosphoinositide-3 kinase and PTEN in cardiovascular physiology and disease.","abstract":"Phosphoinositide-3 kinases (PI3Ks) are a family of evolutionary conserved lipid kinases that mediate many cellular responses in both physiologic and pathophysiologic states. Class I PI3K can be activated by either receptor tyrosine kinase (RTK)\/cytokine receptor activation (class I(A)) or G-protein-coupled receptors (GPCR) (class I(B)). Once activated PI3Ks generate phosphatidylinositols (PtdIns) (3,4,5)P(3) leading to the recruitment and activation of Akt\/protein kinase B (PKB), PDK1 and monomeric G-proteins (e.g. Rac-GTPases), which then activate a range of downstream targets including glycogen synthase kinase-3beta (GSK-3beta), mammalian target of rapamycin (mTOR), p70S6 kinase, endothelial nitric oxide synthase (eNOS) and several anti-apoptotic effectors. Class I(A) (PI3Kalpha, beta and delta) and class I(B) (PI3Kgamma) PI3Ks mediate distinct phenotypes in the heart and under negative control by the 3'-lipid phosphatase, phosphatase and tensin homolog on chromosome ten (PTEN) which dephosphorylate PtdIns(3,4,5)P(3) into PtdIns(4,5)P(2). PI3Kalpha, gamma and PTEN are expressed in cardiomyocytes, fibroblasts, endothelial cells and vascular smooth muscle cells where they modulate cell survival\/apoptosis, hypertrophy, contractility, metabolism and mechanotransduction. Several transgenic and knockout models support a fundamental role of PI3K\/PTEN signaling in the regulation of myocardial contractility and hypertrophy. Consequently the PI3K\/PTEN signaling pathways are involved in a wide variety of diseases including cardiac hypertrophy, heart failure, preconditioning and hypertension. In this review, we discuss the biochemistry and molecular biology of PI3K (class I isoforms) and PTEN and their critical role in cardiovascular physiology and diseases.","authors":"Oudit, GY., Sun, H., Kerfant, BG., Crackower, MA., Penninger, JM., Backx, PH.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Mol Cell Cardiol","volume":"37","issue":"2","page":"449-71","pdf":null,"JrId":"4968","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15251138","title":"Negative regulation of T cell receptor signals.","abstract":"T cells undergo clonal expansion upon encountering cognate antigen in peripheral lymphoid tissues. They require signals through both the T cell receptor and the costimulatory receptor CD28 for this process to occur. In the absence of CD28 stimulation, T cell receptor signals are repressed by the ubiquitin ligase Cbl-b, which negatively regulates the activity of the downstream effectors PI3Kp85 and Vav1. CD28 signals overcome this repression, at least in part, by ubiquitinating and degrading Cbl-b itself. CD28 signals induce clustering of cell-surface receptors, cell division and optimal interleukin-2 production. The Cbl-b\/CD28 regulatory axis has profound implications for pathological conditions ranging from autoimmunity to cancer.","authors":"Rangachari, M., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Opin Pharmacol","volume":"4","issue":"4","page":"415-22","pdf":null,"JrId":"26801","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9095407","title":"Intracellular delivery of lipopolysaccharide during DNA transfection activates a lipid A-dependent cell death response that can be prevented by polymyxin B.","abstract":"The presence of lipopolysaccharide (LPS) as a contaminant in plasmid DNA prepared from Escherichia coli is well documented, and we have previously demonstrated that LPS internalization during adenovirus-mediated gene transfer can generate a toxicity in some primary cell types. We demonstrate here that in addition to adenoviral systems, several commonly used nonviral methods of gene transfer also activate this cell death response in the presence of LPS. Subcomponents of LPS were analyzed and the toxicity was found to be due to the lipid A component of LPS. The LPS-chelating antibiotic polymyxin B, when present at concentration of 10-30 micrograms\/ml, can block this toxicity.","authors":"Cotten, M., Saltik, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Hum Gene Ther","volume":"8","issue":"5","page":"555-61","pdf":null,"JrId":"1041","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15240402","title":"Catecholamine synthesizing enzymes and their modulation by immobilization stress in knockout mice.","abstract":"The c-fos knockout mice (c-fos KO) and corticotropin-releasing hormone knockout mice (CRH KO) can serve as interesting models for studying mechanisms involved in response of the organism to stress, focused mainly on the hypothalamic-pituitary-adrenal (HPA) axis and sympathoadrenal system (SAS). The present study focused on the investigation of changes in gene expression of catecholamine biosynthesizing enzymes tyrosine hydroxylase (TH), dopamine-beta-hydroxylase (DBH), and phenylethanolamine N-methyltransferase (PNMT) in adrenal medulla of c-fos KO and CRH KO mice stressed by immobilization. Levels of TH, DBH, and PNMT mRNA were determined by reverse transcription-polymerase chain reaction (RT-PCR). Single immobilization for 2 h significantly increased adrenomedullary TH, DBH, and PNMT mRNA levels in both c-fos KO and wild-type (WT) mice compared to unstressed controls. In CRH KO mice, PNMT gene expression was not increased to the same extent after single, but especially after repeated immobilization as in WT mice, in contrast to TH and DBH mRNA levels. Thus, our data indicate that CRH deficiency can influence the PNMT mRNA level in adrenal medulla during stress, confirming the idea that the HPA axis plays the crucial role in PNMT gene regulation in mice. On the other hand, c-Fos protein probably does not play a crucial role in TH, DBH, and PNMT gene expression in adrenal medulla under stress conditions.","authors":"Kubovcakova, L., Tybitanclova, K., Sabban, EL., Majzoub, J., Zorad, S., Vietor, I., Wagner, EF., Krizanova, O., Kvetnansky, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Ann N Y Acad Sci","volume":"1018","issue":null,"page":"458-65","pdf":null,"JrId":"611","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15226405","title":"S. pombe meiotic linear elements contain proteins related to synaptonemal complex components.","abstract":"The fission yeast Schizosaccharomyces pombe does not form synaptonemal complexes (SCs) in meiotic prophase nuclei. Instead, thin threads, the so-called linear elements (LEs), are observed at the corresponding stages by electron microscopy. Here, we demonstrate that S. pombe Rec10 is a protein related to the Saccharomyces cerevisiae SC protein Red1 and that it localizes to LEs. Moreover, a homologue to S. cerevisiae Hop1 does exist in S. pombe and we show by in situ immunostaining that it, and the kinase Mek1 (a homologue of which is also known to be associated with SCs), localizes to LEs. These observations indicate the evolutionary relationship of LEs with the lateral elements of SCs and suggest that these structures might exert similar functions in S. cerevisiae and S. pombe.","authors":"Lorenz, A., Wells, JL., Pryce, DW., Novatchkova, M., Eisenhaber, F., McFarlane, RJ., Loidl, J.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Cell Sci","volume":"117","issue":"Pt 15","page":"3343-51","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15186742","title":"The Caenorhabditis elegans centrosomal protein SPD-2 is required for both pericentriolar material recruitment and centriole duplication.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15186742<\/PMID><DateCompleted><Year>2004<\/Year><Month>07<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2017<\/Year><Month>02<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>14<\/Volume><Issue>10<\/Issue><PubDate><Year>2004<\/Year><Month>May<\/Month><Day>25<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The Caenorhabditis elegans centrosomal protein SPD-2 is required for both pericentriolar material recruitment and centriole duplication.<\/ArticleTitle><Pagination><MedlinePgn>863-73<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The centrosome is composed of a centriole pair and pericentriolar material (PCM). By marking the site of PCM assembly, the centrioles define the number of centrosomes present in the cell. The PCM, in turn, is responsible for the microtubule (MT) nucleation activity of centrosomes. Therefore, in order to assemble a functional bipolar mitotic spindle, a cell needs to control both centriole duplication and PCM recruitment. To date, however, the molecular mechanisms that govern these two processes still remain poorly understood.","authors":"Pelletier, L., Ozl\u00fc, N., Hannak, E., Cowan, C., Habermann, B., Ruer, M., M\u00fcller-Reichert, T., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Curr Biol","volume":"14","issue":"10","page":"863-73","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9083111","title":"Glutaconate CoA-transferase from Acidaminococcus fermentans: the crystal structure reveals homology with other CoA-transferases.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9083111<\/PMID><DateCompleted><Year>1997<\/Year><Month>06<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>09<\/Month><Day>14<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0969-2126<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>5<\/Volume><Issue>3<\/Issue><PubDate><Year>1997<\/Year><Month>Mar<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Structure (London, England : 1993)<\/Title><ISOAbbreviation>Structure<\/ISOAbbreviation><\/Journal><ArticleTitle>Glutaconate CoA-transferase from Acidaminococcus fermentans: the crystal structure reveals homology with other CoA-transferases.<\/ArticleTitle><Pagination><MedlinePgn>415-26<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Coenzyme A-transferases are a family of enzymes with a diverse substrate specificity and subunit composition. Members of this group of enzymes are found in anaerobic fermenting bacteria, aerobic bacteria and in the mitochondria of humans and other mammals, but so far none have been crystallized. A defect in the human gene encoding succinyl-CoA: 3-oxoacid CoA-transferase causes a metabolic disease which leads to severe ketoacidosis, thus reflecting the importance of this family of enzymes. All CoA-transferases share a common mechanism in which the CoA moiety is transferred from a donor (e.g. acetyl CoA) to an acceptor, (R)-2-hydroxyglutarate, whereby acetate is formed. The transfer has been described by a ping-pong mechanism in which CoA is bound to the active-site residue of the enzyme as a covalent thiol ester intermediate. We describe here the crystal structure of glutaconate CoA-transferase (GCT) from the strictly anaerobic bacterium Acidaminococcus fermentans. This enzyme activates (R)-2-hydroxyglutarate to (R)-2-hydroxyglutaryl-CoA in the pathway of glutamate fermentation. We initiated this project to gain further insight into the function of this enzyme and the structural basis for the characteristics of CoA-transferases.","authors":"Jacob, U., Mack, M., Clausen, T., Huber, R., Buckel, W., Messerschmidt, A.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Structure","volume":"5","issue":"3","page":"415-26","pdf":null,"JrId":"22305","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15171245","title":"The indexing potential of histone lysine methylation.","abstract":"Diverse post-translational modifications of histone N-termini represent an important epigenetic mechanism for the organization of chromatin structure and the regulation of gene activity. Within the last three years, great progress has been made in understanding the functional implications of histone methylation, in particular through the characterization of histone methyltransferases (HMTases) that direct the site-specific methylation of lysine positions in the histone H3 N-terminus. Histone lysine methylation has been linked with pericentric heterochromatin formation, X-inactivation, Polycomb group (Pc-G)-dependent gene repression and epigenetic control of transcription units at euchromatic positions. Together, these regulatory roles have strongly established histone lysine methylation as a central epigenetic modification for the organization of eukaryotic chromatin. However, they also create a paradox: if histone lysine methylation is present at so many chromatin regions, how can it impart epigenetic information? We provide evidence that differences in distinct methylation states (mono- vs. di- vs. trimethylation) and selective combinations of individually methylated lysine positions can indeed index chromatin regions, resulting in epigenetic landmarks for the partitioning of eukaryotic chromatin.","authors":"Schotta, G., Lachner, M., Peters, AH., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Novartis Found Symp","volume":"259","issue":null,"page":"22-37; discussion 37-47, 163-9","pdf":null,"JrId":"20998","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15137941","title":"Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease.","abstract":"Gram-negative bacteria respond to misfolded proteins in the cell envelope with the sigmaE-driven expression of periplasmic proteases\/chaperones. Activation of sigmaE is controlled by a proteolytic cascade that is initiated by the DegS protease. DegS senses misfolded protein in the periplasm, undergoes autoactivation, and cleaves the antisigma factor RseA. Here, we present the crystal structures of three distinct states of DegS from E. coli. DegS alone exists in a catalytically inactive form. Binding of stress-signaling peptides to its PDZ domain induces a series of conformational changes that activates protease function. Backsoaking of crystals containing the DegS-activator complex revealed the presence of an active\/inactive hybrid structure and demonstrated the reversibility of activation. Taken together, the structural data illustrate in molecular detail how DegS acts as a periplasmic stress sensor. Our results suggest a novel regulatory role for PDZ domains and unveil a novel mechanism of reversible protease activation.","authors":"Wilken, C., Kitzing, K., Kurzbauer, R., Ehrmann, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell","volume":"117","issue":"4","page":"483-94","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15128777","title":"IL-4 confers NK stimulatory capacity to murine dendritic cells: a signaling pathway involving KARAP\/DAP12-triggering receptor expressed on myeloid cell 2 molecules.","abstract":"Dendritic cells (DC) regulate NK cell functions, but the signals required for the DC-mediated NK cell activation, i.e., DC-activated NK cell (DAK) activity, remain poorly understood. Upon acute inflammation mimicked by LPS or TNF-alpha, DC undergo a maturation process allowing T and NK cell activation in vitro. Chronic inflammation is controlled in part by Th2 cytokines. In this study, we show that IL-4 selectively confers to DC NK but not T cell stimulatory capacity. IL-4 is mandatory for mouse bone marrow-derived DC grown in GM-CSF (DC(GM\/IL-4)) to promote NK cell activation in the draining lymph nodes. IL-4-mediated DAK activity depends on the KARAP\/DAP12-triggering receptor expressed on myeloid cell 2 signaling pathway because: 1) gene targeting of the adaptor molecule KARAP\/DAP12, a transmembrane polypeptide with an intracytoplasmic immunoreceptor tyrosine-based activation motif, suppresses the DC(GM\/IL-4) capacity to activate NK cells, and 2) IL-4-mediated DAK activity is significantly blocked by soluble triggering receptor expressed on myeloid cell 2 Fc molecules. These data outline a novel role for Th2 cytokines in the regulation of innate immune responses through triggering receptors expressed on myeloid cells.","authors":"Terme, M., Tomasello, E., Maruyama, K., Cr\u00e9pineau, F., Chaput, N., Flament, C., Marolleau, JP., Angevin, E., Wagner, EF., Salomon, B., Lemonnier, FA., Wakasugi, H., Colonna, M., Vivier, E., Zitvogel, L.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Immunol","volume":"172","issue":"10","page":"5957-66","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15064704","title":"Transcriptional basis of KRAS oncogene-mediated cellular transformation in ovarian epithelial cells.","abstract":"To understand the relationship between oncogenic signaling and the reprogramming of gene expression, we performed transcriptional profiling in rat ovarian surface epithelial cells (ROSE), in which neoplastic transformation is driven by a mutated KRAS oncogene. We identified &gt;200 genes whose expression was elevated or reduced following permanent KRAS expression. Deregulated KRAS-responsive genes encode transcriptional regulators, signaling effectors, proteases, extracellular matrix and adhesion proteins, transformation-suppressing proteins and negative growth regulators. Many of them have not been previously identified in cells expressing oncogenic RAS genes or in other well-studied models of oncogenic signaling. The number of critical genes related to the execution of anchorage-independent proliferation and epithelial-mesenchymal transition was narrowed down to 79 by selectively inhibiting the mitogen-activated protein kinase (MAPK\/ERK) and phosphatidylinositol 3-kinase (PI3K) pathways. Blocking MAPK\/ERK-signaling caused reversion to the normal epithelial phenotype in conjunction with the reversal of deregulated target transcription to pretransformation levels. In addition, silencing of the overexpressed transcriptional regulator Fra-1 by RNA interference resulted in growth reduction, suggesting that this factor partially contributes to, but is not sufficient for the proliferative capacity of KRAS-transformed epithelial cells.","authors":"Tchernitsa, OI., Sers, C., Zuber, J., Hinzmann, B., Grips, M., Schramme, A., Lund, P., Schwendel, A., Rosenthal, A., Sch\u00e4fer, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Oncogene","volume":"23","issue":"26","page":"4536-55","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14644190","title":"Dynamics of chromosome positioning during the cell cycle.","abstract":"The arrangement and dynamics of chromosomes inside the nucleus of mammalian cells have been studied intensively over the last two years. Although chromosomes are relatively immobile and occupy non-random positions in interphase, their dynamic movements in mitosis have traditionally been assumed to randomize this arrangement. New methods of live cell imaging now make it possible to follow chromosome movements directly and quantitatively in single cells. Such studies have generated models of chromosome positioning throughout the cell cycle and provide a new basis to address the underlying mechanisms in future experiments.","authors":"Gerlich, D., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Opin Cell Biol","volume":"15","issue":"6","page":"664-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9010925","title":"Hydrophobic regions on protein surfaces: definition based on hydration shell structure and a quick method for their computation.","abstract":"The hydrophobic part of the solvent-accessible surface of a typical monomeric globular protein consists of a single, large interconnected region formed from faces of apolar atoms and constituting approximately 60% of the solvent-accessible surface area. Therefore, the direct delineation of the hydrophobic surface patches on an atom-wise basis is impossible. Experimental data indicate that, in a two-state hydration model, a protein can be considered to be unified with its first hydration shell in its interaction with bulk water. We show that, if the surface area occupied by water molecules bound at polar protein atoms as generated by AUTOSOL is removed, only about two-thirds of the hydrophobic part of the protein surface remains accessible to bulk solvent. Moreover, the organization of the hydrophobic part of the solvent-accessible surface experiences a drastic change, such that the single interconnected hydrophobic region disintegrates into many smaller patches, i.e. the physical definition of a hydrophobic surface region as unoccupied by first hydration shell water molecules can distinguish between hydrophobic surface clusters and small interconnecting channels. It is these remaining hydrophobic surface pieces that probably play an important role in intra- and intermolecular recognition processes such as ligand binding, protein folding and protein-protein association in solution conditions. These observations have led to the development of an accurate and quick analytical technique for the automatic determination of hydrophobic surface patches of proteins. This technique is not aggravated by the limiting assumptions of the methods for generating explicit water hydration positions. Formation of the hydrophobic surface regions owing to the structure of the first hydration shell can be computationally simulated by a small radial increment in solvent-accessible polar atoms, followed by calculation of the remaining exposed hydrophobic patches. We demonstrate that a radial increase of 0.35-0.50 A resembles the effect of tightly bound water on the organization of the hydrophobic part of the solvent-accessible surface.","authors":"Eisenhaber, F., Argos, P.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Protein Eng","volume":"9","issue":"12","page":"1121-33","pdf":null,"JrId":"6619","fulltextlink":null,"preprintlink":null,"articledate":"1997-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8985178","title":"Anaphase initiation in Saccharomyces cerevisiae is controlled by the APC-dependent degradation of the anaphase inhibitor Pds1p.","abstract":"Anaphase initiation has been postulated to be controlled through the ubiquitin-dependent proteolysis of an unknown inhibitor. This process involves the anaphase promoting complex (APC), a specific ubiquitin ligase that has been shown to be involved in mitotic cyclin degradation. Previous studies demonstrated that in Saccharomyces cerevisiae, Pds1 protein is an anaphase inhibitor and suggested that it may be an APC target. Here we show that in yeast cells and in mitotic Xenopus extracts Pds1p is degraded in an APC-dependent manner. In addition, Pds1p is directly ubiquitinated by the Xenopus APC. In budding yeast Pds1p is degraded at the time of anaphase initiation and nondegradable derivatives of Pds1p inhibit the onset of anaphase. We conclude that Pds1p is an anaphase inhibitor whose APC-dependent degradation is required for the initiation of anaphase.","authors":"Cohen-Fix, O., Peters, JM., Kirschner, MW., Koshland, D.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Genes Dev","volume":"10","issue":"24","page":"3081-93","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1997-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14871811","title":"Tissue-wide expression profiling using cDNA subtraction and microarrays to identify tumor-specific genes.","abstract":"With the objective of discovering novel putative intervention sites for anticancer therapy, we compared transcriptional profiles of breast cancer, lung squamous cell cancer (LSCC), lung adenocarcinoma (LAC), and renal cell cancer (RCC). Each of these tumor types still needs improvement in medical treatment. Our intention was to search for genes not only highly expressed in the majority of patient samples but which also exhibit very low or even absence of expression in a comprehensive panel of 16 critical (vital) normal tissues. To achieve this goal, we combined two powerful technologies, PCR-based cDNA subtraction and cDNA microarrays. Seven subtractive libraries consisting of approximately 9250 clones were established and enriched for tumor-specific transcripts. These clones, together with approximately 1750 additional tumor-relevant genes, were used for cDNA microarray preparation. Hybridizations were performed using a pool of 16 critical normal tissues as a reference in all experiments. In total, we analyzed 20 samples of breast cancer, 11 of LSCC, 11 of LAC, and 8 of RCC. To select for genes with low or even no expression in normal tissues, expression profiles of 22 different normal tissues were additionally analyzed. Importantly, this tissue-wide expression profiling allowed us to eliminate genes, which exhibit also high expression in normal tissues. Similarly, expression signatures of genes, which are derived from infiltrating cells of the immune system, were eliminated as well. Cluster analysis resulted in the identification of 527 expressed sequence tags specifically up-regulated in these tumors. Gene-wise hierarchical clustering of these clones clearly separated the different tumor types with RCC exhibiting the most homogeneous and LAC the most diverse expression profile. In addition to already known tumor-associated genes, the majority of identified genes have not yet been brought into context with tumorigenesis such as genes involved in bone matrix mineralization (OSN, OPN, and OSF-2) in lung, breast, and kidney cancer or genes controlling Ca(2+) homeostasis (RCN1,CALCA, S100 protein family). EGLN3, which recently has been shown to be involved in regulation of hypoxia-inducible factor, was found to be highly up-regulated in all RCCs and in half of the LSCCs analyzed. Furthermore, 42 genes, the expression level of which correlated with the overall survival of breast cancer patients, were identified. The gene dendogram clearly separates two groups of genes, those up-regulated such as cyclin B1, TGF-beta 3, B-Myb, Erg2, VCAM-1, and CD44 and those down-regulated such as MIG-6, Esp15, and CAK in patients with short survival time.","authors":"Amatschek, S., Koenig, U., Auer, H., Steinlein, P., Pacher, M., Gruenfelder, A., Dekan, G., Vogl, S., Kubista, E., Heider, KH., Stratowa, C., Schreiber, M., Sommergruber, W.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cancer Res","volume":"64","issue":"3","page":"844-56","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14693825","title":"TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">14693825<\/PMID><DateCompleted><Year>2004<\/Year><Month>05<\/Month><Day>19<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">1367-4803<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>20<\/Volume><Issue>1<\/Issue><PubDate><Year>2004<\/Year><Month>Jan<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.<\/ArticleTitle><Pagination><MedlinePgn>136-7<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"UNLABELLED\">Web-based servers implementing the DAS-TMfilter algorithm have been launched at three mirror sites and their usage is described. The underlying computer program is an upgraded and modified version of the DAS-prediction method. The new server is (approximately 1 among 100 unrelated queries) while the high efficiency of the original algorithm locating TM segments in queries is preserved (sensitivity of approximately 95% among documented proteins with helical TM regions).","authors":"Cserzo, M., Eisenhaber, F., Eisenhaber, B., Simon, I.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Bioinformatics","volume":"20","issue":"1","page":"136-7","pdf":null,"JrId":"20940","fulltextlink":null,"preprintlink":null,"articledate":"2004-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7553851","title":"An NSF-like ATPase, p97, and NSF mediate cisternal regrowth from mitotic Golgi fragments.","abstract":"Golgi cisternae regrew in a cell-free system from mitotic Golgi fragments incubated with buffer alone. Pretreatment with NEM or salt washing inhibited regrowth, but this could be restored either by p97, an NSF-like ATPase, or by NSF together with SNAPs and p115, a vesicle docking protein. The morphology of cisternae regrown with p97 and NSF-SNAPs-p115 differed, suggesting that they play distinct roles in rebuilding Golgi cisternae after mitosis.","authors":"Rabouille, C., Levine, TP., Peters, JM., Warren, G.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell","volume":"82","issue":"6","page":"905-14","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1995-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14762792","title":"Phosphatidylinositide 3-kinase gamma regulates key pathologic responses to cholecystokinin in pancreatic acinar cells.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">14762792<\/PMID><DateCompleted><Year>2004<\/Year><Month>03<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>07<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0016-5085<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>126<\/Volume><Issue>2<\/Issue><PubDate><Year>2004<\/Year><Month>Feb<\/Month><\/PubDate><\/JournalIssue><Title>Gastroenterology<\/Title><ISOAbbreviation>Gastroenterology<\/ISOAbbreviation><\/Journal><ArticleTitle>Phosphatidylinositide 3-kinase gamma regulates key pathologic responses to cholecystokinin in pancreatic acinar cells.<\/ArticleTitle><Pagination><MedlinePgn>554-66<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\" NlmCategory=\"OBJECTIVE\">Early events in the pancreatic acinar cell critical for development of pancreatitis include activation of the transcription factor nuclear factor kappa B (NF-kappa B), abnormal Ca(2+) responses, and trypsinogen activation. Mechanisms underlying these responses, which can be studied in isolated pancreatic acini stimulated with supraphysiologic doses of cholecystokinin (CCK-8), remain poorly understood. We here report that these responses are regulated by phosphatidylinositide 3-kinase (PI3K) gamma.","authors":"Gukovsky, I., Cheng, JH., Nam, KJ., Lee, OT., Lugea, A., Fischer, L., Penninger, JM., Pandol, SJ., Gukovskaya, AS.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Gastroenterology","volume":"126","issue":"2","page":"554-66","pdf":null,"JrId":"3841","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8934819","title":"Cell cycle regulation and erythroid differentiation.","abstract":null,"authors":"M\u00fcllner, EW., Dolznig, H., Beug, H.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Curr Top Microbiol Immunol","volume":"212","issue":null,"page":"175-94","pdf":null,"JrId":"3237","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14999681","title":"Immortalized p19ARF null hepatocytes restore liver injury and generate hepatic progenitors after transplantation.","abstract":"Primary hepatocytes are blocked in mitotic activity and well-defined culture conditions only allow the limited expansion of these cells. Various genetic modifications have therefore been employed to establish immortalized hepatic cell lines, but, unfortunately, proper hepatocyte cultures conducting a faithful hepatic gene expression program and lacking malignancy are hardly available. Here we report the immortalization of primary hepatocytes isolated from p19(ARF) null mice using the rationale that loss of p19(ARF) lowers growth-suppressive functions of p53 and bypasses cellular senescence without losing genetic stability. The established hepatocytes, called MIM, express liver-specific markers, show a nontumorigenic phenotype, and competence to undergo Fas-mediated apoptosis. Intrasplenic transplantation of GFP-expressing parental MIM cells into Fas-injured livers of SCID mice revealed liver-reconstituting activity. In the regenerated liver, MIM cells localized in small-sized clusters and showed presence in structures comparable to canals of Hering, the site of oval cells. Transplantation of MIM-Bcl-X(L) cells, which are protected against apoptosis, and successive Fas-induced liver damage, enhanced donor-derived liver repopulation by showing differentiation into cholangiocytes and cells expressing markers characteristic of both fetal hepatocytes and oval cells. In conclusion, these data indicate that long-term cultivated p19(ARF) null hepatocytes are capable of generating hepatic progenitor cells during liver restoration, and thus represent a highly valuable tool to study the differentiation repertoire of hepatocytes.","authors":"Mikula, M., Fuchs, E., Huber, H., Beug, H., Schulte-Hermann, R., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Hepatology","volume":"39","issue":"3","page":"628-34","pdf":null,"JrId":"4093","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14681481","title":"GermOnline, a cross-species community knowledgebase on germ cell differentiation.","abstract":"GermOnline provides information and microarray expression data for genes involved in mitosis and meiosis, gamete formation and germ line development across species. The database has been developed, and is being curated and updated, by life scientists in cooperation with bioinformaticists. Information is contributed through an online form using free text, images and the controlled vocabulary developed by the GeneOntology Consortium. Authors provide up to three references in support of their contribution. The database is governed by an international board of scientists to ensure a standardized data format and the highest quality of GermOnline's information content. Release 2.0 provides exclusive access to microarray expression data from Saccharomyces cerevisiae and Rattus norvegicus, as well as curated information on approximately 700 genes from various organisms. The locus report pages include links to external databases that contain relevant annotation, microarray expression and proteome data. Conversely, the Saccharomyces Genome Database (SGD), S.cerevisiae GeneDB and Swiss-Prot link to the budding yeast section of GermOnline from their respective locus pages. GermOnline, a fully operational prototype subject-oriented knowledgebase designed for community annotation and array data visualization, is accessible at http:\/\/www.germonline.org. The target audience includes researchers who work on mitotic cell division, meiosis, gametogenesis, germ line development, human reproductive health and comparative genomics.","authors":"Wiederkehr, C., Basavaraj, R., Sarrauste de Menthi\u00e8re, C., Hermida, L., Koch, R., Schlecht, U., Amon, A., Brachat, S., Breitenbach, M., Briza, P., Caburet, S., Cherry, M., Davis, R., Deutschbauer, A., Dickinson, HG., Dumitrescu, T., Fellous, M., Goldman, A., Grootegoed, JA., Hawley, R., Ishii, R., J\u00e9gou, B., Kaufman, RJ., Klein, F., Lamb, N., Maro, B., Nasmyth, K., Nicolas, A., Orr-Weaver, T., Philippsen, P., Pineau, C., Rabitsch, KP., Reinke, V., Roest, H., Saunders, W., Schr\u00f6der, M., Schedl, T., Siep, M., Villeneuve, A., Wolgemuth, DJ., Yamamoto, M., Zickler, D., Esposito, RE., Primig, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nucleic Acids Res","volume":"32","issue":"Database issue","page":"D560-7","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14675543","title":"Molecular shredders: how proteasomes fulfill their role.","abstract":"The 20S proteasome is a large, cylinder-shaped protease that is found in all domains of life and plays a crucial role in cellular protein turnover. It has multiple catalytic centers located within the hollow cavity of a molecular cage. This architecture prevents unwanted degradation of endogenous proteins and promotes processive degradation of substrates by restricting the dissociation of partially digested polypeptides. Although this kind of self-compartmentalization is generally conserved, the proteasomes of bacteria, archaea and eukaryotes show many differences in architecture, subunit composition and regulation. The structure of the 20S proteasome and its inherent role in the regulation of proteasome function are gradually being elucidated.","authors":"Groll, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Opin Struct Biol","volume":"13","issue":"6","page":"665-73","pdf":null,"JrId":"8602","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14602076","title":"Genome-wide prediction of Polycomb\/Trithorax response elements in Drosophila melanogaster.","abstract":"Polycomb\/Trithorax response elements (PRE\/TREs) maintain transcriptional decisions to ensure correct cell identity during development and differentiation. There are thought to be over 100 PRE\/TREs in the Drosophila genome, but only very few have been identified due to the lack of a defining consensus sequence. Here we report the definition of sequence criteria that distinguish PRE\/TREs from non-PRE\/TREs. Using this approach for genome-wide PRE\/TRE prediction, we identify 167 candidate PRE\/TREs, which map to genes involved in development and cell proliferation. We show that candidate PRE\/TREs are bound and regulated by Polycomb proteins in vivo, thus demonstrating the validity of PRE\/TRE prediction. Using the larger data set thus generated, we identify three sequence motifs that are conserved in PRE\/TRE sequences.","authors":"Ringrose, L., Rehmsmeier, M., Dura, JM., Paro, R.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Dev Cell","volume":"5","issue":"5","page":"759-71","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2003-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8871553","title":"p72: a human nuclear DEAD box protein highly related to p68.","abstract":"P72, a novel human member of the DEAD box family of putative RNA-dependent ATPases and ATP-dependent RNA helicases was isolated from a HeLa cDNA library. The predicted amino acid sequence of p72 is highly homologous to that of the prototypic DEAD box protein p68. In addition to the conserved core domains characteristic of DEAD box proteins, p72 contains several N-terminal RGG RNA-binding domains and a serine\/glycine rich C-terminus likely involved in mediating protein-protein interactions. A p72-specific probe detects two mRNAs of approximately 5300 and 9300 bases which, although ubiquitously expressed, show variability in their expression levels in different tissues. Purified recombinant p72 exhibits ATPase activity in the presence of a range of RNA moieties. Immunocytochemical studies of p68 and p72 show that these proteins localise to similar locations in the nucleus of HeLa cells, suggesting their involvement in a nuclear process.","authors":"Lamm, GM., Nicol, SM., Fuller-Pace, FV., Lamond, AI.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Nucleic Acids Res","volume":"24","issue":"19","page":"3739-47","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12930946","title":"Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes.","abstract":"Micro-RNAs are a class of small non-coding regulatory RNAs that impair translation by imperfect base pairing to mRNAs. For analysis of their cellular function we injected different miRNA-specific DNA antisense oligonucleotides in Drosophila embryos. In four cases we observed severe interference with normal development, one had a moderate impact and six oligonucleotides did not cause detectable phenotypes. We further used the miR-13a DNA antisense oligonucleotide as a PCR primer on a cDNA library template. In this experimental way we identified nine Drosophila genes, which are characterised by 3' untranslated region motifs that allow imperfect duplex formation with miR-13 or related miRNAs. These genes, which include Sos and Myd88, represent putative targets for miRNA regulation. Mutagenesis of the target motif of two genes followed by transfection in Drosophila Schneider 2 (S2) cells and subsequent reporter gene analysis confirmed the hypothesis that the binding potential of miR-13 is inversely correlated with gene expression.","authors":"Boutla, A., Delidakis, C., Tabler, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nucleic Acids Res","volume":"31","issue":"17","page":"4973-80","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11707517","title":"Inscuteable-dependent apical localization of the microtubule-binding protein Cornetto suggests a role in asymmetric cell division.","abstract":"Drosophila neuroblasts divide asymmetrically along the apical-basal axis. The Inscuteable protein localizes to the apical cell cortex in neuroblasts from interphase to metaphase, but disappears in anaphase. Inscuteable is required for correct spindle orientation and for asymmetric localization of cell fate determinants to the opposite (basal) cell cortex. Here, we show that Inscuteable also directs asymmetric protein localization to the apical cell cortex during later stages of mitosis. In a two-hybrid screen for Inscuteable-binding proteins, we have identified the coiled-coil protein Cornetto, which shows a highly unusual subcellular distribution in neuroblasts. Although the protein is uniformly distributed in the cytoplasm during metaphase, it concentrates apically in anaphase and forms an apical crescent during telophase in an inscuteable-dependent manner. Upon overexpression, Cornetto localizes to astral microtubules and microtubule spin-down experiments demonstrate that Cornetto is a microtubule-binding protein. After disruption of the actin cytoskeleton, Cornetto localizes with microtubules throughout the cell cycle and decorates the mitotic spindle during metaphase. Our results reveal a novel pattern of asymmetric protein localization in Drosophila neuroblasts and are consistent with a function of Cornetto in anchoring the mitotic spindle during late phases of mitosis, even though our cornetto mutant analysis suggests that this function might be obscured by genetic redundancy.","authors":"Bulgheresi, S., Kleiner, E., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Cell Sci","volume":"114","issue":"Pt 20","page":"3655-62","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11707407","title":"Modes of spindle pole body inheritance and segregation of the Bfa1p-Bub2p checkpoint protein complex.","abstract":"Yeast spindle pole bodies (SPBs) duplicate once per cell cycle by a conservative mechanism resulting in a pre-existing 'old' and a newly formed SPB. The two SPBs of yeast cells are functionally distinct. It is only the SPB that migrates into the daughter cell, the bud, which carries the Bfa1p-Bub2p GTPase-activating protein (GAP) complex, a component of the spindle positioning checkpoint. We investigated whether the functional difference of the two SPBs correlates with the time of their assembly. We describe that in unperturbed cells the 'old' SPB always migrates into the bud. However, Bfa1p localization is not determined by SPB inheritance. It is the differential interaction of cytoplasmic microtubules with the mother and bud cortex that directs the Bfa1p-Bub2p GAP to the bud-ward-localized SPB. In response to defects of cytoplasmic microtubules to interact with the cell cortex, the Bfa1p-Bub2p complex binds to both SPBs. This may provide a mechanism to delay cell cycle progression when cytoplasmic microtubules fail to orient the spindle. Thus, SPBs are able to sense cytoplasmic microtubule properties and regulate the Bfa1p-Bub2p GAP accordingly.","authors":"Pereira, G., Tanaka, TU., Nasmyth, K., Schiebel, E.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"EMBO J","volume":"20","issue":"22","page":"6359-70","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8824784","title":"Gaining insight into a complex organelle, the phagosome, using two-dimensional gel electrophoresis.","abstract":"Phagosomes are the organelles formed de novo in a variety of cells by the internalization of large particulate materials, including a wide range of pathogenic microorganisms. We present here a systematic approach that can be used to study the polypeptide composition of phagosomes\/phagolysosomes and to yield analytical information on the characteristics of their proteins. A density shift approach was used to isolate pure preparations of phagosomes filled with low density latex beads from mouse J774 and human U937 macrophages. High resolution two-dimensional (2-D) gel electrophoresis was performed to generate a map of the overall [35S]methionine-labeled protein profile of the isolated phagosomes. The resulting map showed the minimal presence of over 200 polypeptides, indicating the complexity of this organelle. Comigration experiments showed that several phagosome polypeptides, among them several known proteins, are shared by the two species. Extraction with Triton X-114 and sodium carbonate was performed to distinguish between membrane and soluble proteins, and sensitivity to a panel of proteases was measured to identify proteins exposed on the cytoplasmic face of the phagosome membrane. The general value of the 2-D gel approach in the mapping of organelle proteins is discussed.","authors":"Burkhardt, J., Huber, LA., Dieplinger, H., Blocker, A., Griffiths, G., Desjardins, M.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Electrophoresis","volume":"16","issue":"12","page":"2249-57","pdf":null,"JrId":"3579","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"5106016","title":"Cell dissociation: univalent antibodies as a possible alternative to proteolytic enzymes.","abstract":"Univalent antibody fragments directed against special membrane antigens dissociate multicellular bodies of the cellular slime mold Dictyostelium discoideum completely into single cells. This provides a gentle method for cell dissociation and demonstrates that a nonenzyme protein can disintegrate a tissue","authors":"Beug, H., Gerisch, G., M\u00fcller, E.","publication_status":"ppublish","journalpubyear":"1971","journaltitle":"Science","volume":"173","issue":"3998","page":"742-3","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1971-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12850142","title":"Using a neural network and spatial clustering to predict the location of active sites in enzymes.","abstract":"Structural genomics projects aim to provide a sharp increase in the number of structures of functionally unannotated, and largely unstudied, proteins. Algorithms and tools capable of deriving information about the nature, and location, of functional sites within a structure are increasingly useful therefore. Here, a neural network is trained to identify the catalytic residues found in enzymes, based on an analysis of the structure and sequence. The neural network output, and spatial clustering of the highly scoring residues are then used to predict the location of the active site.A comparison of the performance of differently trained neural networks is presented that shows how information from sequence and structure come together to improve the prediction accuracy of the network. Spatial clustering of the network results provides a reliable way of finding likely active sites. In over 69% of the test cases the active site is correctly predicted, and a further 25% are partially correctly predicted. The failures are generally due to the poor quality of the automatically generated sequence alignments. We also present predictions identifying the active site, and potential functional residues in five recently solved enzyme structures, not used in developing the method. The method correctly identifies the putative active site in each case. In most cases the likely functional residues are identified correctly, as well as some potentially novel functional groups.","authors":"Gutteridge, A., Bartlett, GJ., Thornton, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Mol Biol","volume":"330","issue":"4","page":"719-34","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11687493","title":"Animal cell cytokinesis.","abstract":"Cytokinesis creates two daughter cells endowed with a complete set of chromosomes and cytoplasmic organelles. This conceptually simple event is mediated by a complex and dynamic interplay between the microtubules of the mitotic spindle, the actomyosin cytoskeleton, and membrane fusion events. For many decades the study of cytokinesis was driven by morphological studies on specimens amenable to physical manipulation. The studies led to great insights into the cellular structures that orchestrate cell division, but the underlying molecular machinery was largely unknown. Molecular and genetic approaches have now allowed the initial steps in the development of a molecular understanding of this fundamental event in the life of a cell. This review provides an overview of the literature on cytokinesis with a particular emphasis on the molecular pathways involved in the division of animal cells.","authors":"Glotzer, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Annu Rev Cell Dev Biol","volume":"17","issue":null,"page":"351-86","pdf":null,"JrId":"20331","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8786109","title":"Cloning and characterization of CpG islands of the human chromosome 1p36 region.","abstract":"CpG islands were identified and localized to chromosome 1p36 by means of pulsed-field gel blot hybridization with 1p36-specific microclone probes. Five CpG islands, designated CpG17, CpG28, CpG60, CpG112a, and CpG112b, were molecularly cloned from corresponding cosmids. All five islands are associated with transcribed sequences, as shown by RNA blot hybridizations. Screening of cDNA libraries with the island-specific genomic probes led to the isolation of two cDNA clones to date. These encode the human transcription factor E2F-2 and the dominant-negative helix-loop-helix gene ID3, respectively. Pulsed-field gel electrophoresis analysis also revealed that these two genes are located next to each other at a distance of about 25 kb.","authors":"Ellmeier, W., Barnas, C., Kobrna, A., Kleiner, E., Kurzbauer, R., Weith, A.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Genomics","volume":"32","issue":"1","page":"155-8","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"1996-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8780645","title":"Genetic analysis of Netrin genes in Drosophila: Netrins guide CNS commissural axons and peripheral motor axons.","abstract":"Two tandem Netrin genes in Drosophila are expressed at the midline of the developing CNS and in different subsets of neurons, muscles, and epidermal patches. In embryos carrying a small deficiency that deletes both genes, CNS axon commissures are partially missing or thinner. This phenotype is rescued by expressing either Netrin gene at the midline. Pan-neural expression of either gene causes disruption of commissural and longitudinal tracts, indicating that the pattern of Netrin expression is crucial and that Netrins function as instructive cues. The double mutant also shows defects in motor axon projections. Expression of either Netrin gene in all muscles also results in aberrant motor projections. Thus, Drosophila Netrins are required for the guidance of commissural axons at the midline, and of motor axons to their target muscles.","authors":"Mitchell, KJ., Doyle, JL., Serafini, T., Kennedy, TE., Tessier-Lavigne, M., Goodman, CS., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Neuron","volume":"17","issue":"2","page":"203-15","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"1996-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11683993","title":"Cell-autonomous and -nonautonomous functions of LAR in R7 photoreceptor axon targeting.","abstract":"During Drosophila visual system development, photoreceptors R7 and R8 project axons to targets in distinct layers of the optic lobe. We show here that the LAR receptor tyrosine phosphatase is required in the eye for correct targeting of R7 axons. In LAR mutants, R7 axons initially project to their correct target layer, but then retract to the R8 target layer. This targeting defect can be fully rescued by transgenic expression of LAR in R7, and partially rescued by expression of LAR in R8. The phosphatase domains of LAR are required for its activity in R7, but not in R8. These data suggest that LAR can act both as a receptor in R7, and as a ligand provided by R8. Genetic interactions implicate both Enabled and Trio in LAR signal transduction.","authors":"Maurel-Zaffran, C., Suzuki, T., Gahmon, G., Treisman, JE., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Neuron","volume":"32","issue":"2","page":"225-35","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11533664","title":"Heat-shock protein 70 antagonizes apoptosis-inducing factor.","abstract":"Heat-shock protein 70 (Hsp70) has been reported to block apoptosis by binding apoptosis protease activating factor-1 (Apaf-1), thereby preventing constitution of the apoptosome, the Apaf-1\/cytochrome c\/caspase-9 activation complex [1,2]. Here we show that overexpression of Hsp70 protects Apaf-1-\/- cells against death induced by serum withdrawal, indicating that Apaf-1 is not the only target of the anti-apoptotic action of Hsp70. We investigated the effect of Hsp70 on apoptosis mediated by the caspase-independent death effector apoptosis inducing factor (AIF), which is a mitochondrial intermembrane flavoprotein [3,4]. In a cell-free system, Hsp70 prevented the AIF-induced chromatin condensation of purified nuclei. Hsp70 specifically interacted with AIF, as shown by ligand blots and co-immunoprecipitation. Cells overexpressing Hsp70 were protected against the apoptogenic effects of AIF targeted to the extramitochondrial compartment. In contrast, an anti-sense Hsp70 complementary DNA, which reduced the expression of endogenous Hsp70, increased sensitivity to the lethal effect of AIF. The ATP-binding domain of Hsp70 seemed to be dispensable for inhibiting cell death induced by serum withdrawal, AIF binding and AIF inhibition, although it was required for Apaf-1 binding. Together, our data indicate that Hsp70 can inhibit apoptosis by interfering with target proteins other than Apaf-1, one of which is AIF.","authors":"Ravagnan, L., Gurbuxani, S., Susin, SA., Maisse, C., Daugas, E., Zamzami, N., Mak, T., J\u00e4\u00e4ttel\u00e4, M., Penninger, JM., Garrido, C., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Cell Biol","volume":"3","issue":"9","page":"839-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-10-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"4354075","title":"Defective cyclic adenosine-3', 5'-phosphate-phosphodiesterase regulation in morphogenetic mutants of Dictyostelium discoideum.","abstract":null,"authors":"Riedel, V., Gerisch, G., M\u00fcller, E., Beug, H.","publication_status":"ppublish","journalpubyear":"1973","journaltitle":"J Mol Biol","volume":"74","issue":"4","page":"573-85","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1973-11-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11518531","title":"Crystal structures of cystathionine gamma-synthase inhibitor complexes rationalize the increased affinity of a novel inhibitor.","abstract":"Cystathionine gamma-synthase catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of antimicrobials and herbicides. We solved the crystal structures of complexes of cystathionine gamma-synthase (CGS) from Nicotiana tabacum with inhibitors of different compound classes. The complex with the substrate analog dl-E-2-amino-5-phosphono-3-pentenoic acid verifies the carboxylate-binding function of Arg423 and identifies the phosphate-binding pocket of the active site. The structure shows the function of Lys165 in specificity determination and suggests a role for the flexible side-chain of Tyr163 in catalysis. The importance of hydrophobic interactions for binding to the active-site center is highlighted by the complex with 3-(phosphonomethyl)pyridine-2-carboxylic acid. The low affinity of this compound is due to the non-optimal arrangement of the functional groups binding to the phosphate and carboxylate-recognition site, respectively. The newly identified inhibitor 5-carboxymethylthio-3-(3'-chlorophenyl)-1,2,4-oxadiazol, in contrast, shows the highest affinity to CGS reported so far. This affinity is due to binding to an additional active-site pocket not used by the physiological substrates. The inhibitor binds to the carboxylate-recognition site, and its tightly bent conformation enables it to occupy the novel binding pocket between Arg423 and Ser388. The described structures suggest improvements for known inhibitors and give guidelines for the development of new lead compounds.","authors":"Steegborn, C., Laber, B., Messerschmidt, A., Huber, R., Clausen, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Mol Biol","volume":"311","issue":"4","page":"789-801","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2001-10-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12717814","title":"RNAs templating chromatin structure for dosage compensation in animals.","abstract":"The role of RNA as a messenger in the expression of the genome has been long appreciated, but its functions in regulating chromatin and chromosome structure are no less interesting. Recent results have shown that small RNAs guide chromatin-modifying complexes to chromosomal regions in a sequence-specific manner to elicit transcriptional repression. However, sequence-specific targeting by means of base pairing seems to be only one mechanism by which RNA is employed for epigenetic regulation. The focus of this review is on large RNAs that act in the dosage-compensation pathways of flies and mammals. These RNAs associate with chromatin over the length of whole chromosomes and are crucial for spreading epigenetic changes in chromatin structure. They do not appear to act in a sequence-specific manner but might provide scaffolds for co-operative binding of chromatin-associated complexes that enable spreading of chromatin modifications.","authors":"Wutz, A.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Bioessays","volume":"25","issue":"5","page":"434-42","pdf":null,"JrId":"1014","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12707582","title":"RANKL and RANK as novel therapeutic targets for arthritis.","abstract":"The TNF-family molecule receptor activator of nuclear factor kappa B (NFkappaB) ligand (RANKL) (OPGL, TRANCE, ODF) and its receptor activator of NFkappaB (RANK) are key regulators of bone remodeling and regulate T cell\/dendritic cell communications, and lymph node formation. Moreover, RANKL and RANK are expressed in mammary gland epithelial cells and control the development of a lactating mammary gland during pregnancy. Genetically, RANKL and RANK are essential for the development and activation of osteoclasts and bone loss in response to virtually all triggers tested. Inhibition of RANKL function via the natural decoy receptor osteoprotegerin (OPG, TNFRSF11B) prevents bone loss in postmenopausal osteoporosis and cancer metastases. Importantly, RANKL appears to be the pathogenetic principle that causes bone and cartilage destruction in arthritis, and OPG treatment prevents bone loss at inflamed joints and has partially beneficial effects on cartilage destruction in all arthritis models studied so far. Modulation of these systems provides a unique opportunity to design novel therapeutics to inhibit bone loss and crippling in arthritis.","authors":"Nakashima, T., Wada, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Opin Rheumatol","volume":"15","issue":"3","page":"280-7","pdf":null,"JrId":"1774","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8909137","title":"At the heart of the budding yeast cell cycle.","abstract":"It might now seem obvious that the mechanisms regulating cell division would be found to be a highly conserved feature of eukaryotic cells. This was less clear 20 years ago when the pioneering genetic studies of the cell cycle were initiated. This article presents one view as to what lies at the heart of the budding yeast cell cycle. It is written on the premise that most of the key players, such as cyclin-dependent kinases, the anaphase-promoting complex, the origin recognition complex, Cdc6p and Mcm proteins, were performing similar functions in the common ancestor of yeast and man. Ideas about the budding yeast cell cycle might, therefore, have universal significance for other eukaryotic cells.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Trends Genet","volume":"12","issue":"10","page":"405-12","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26367798","title":"Transcriptional plasticity promotes primary and acquired resistance to BET inhibition.","abstract":"Following the discovery of BRD4 as a non-oncogene addiction target in acute myeloid leukaemia (AML), bromodomain and extra terminal protein (BET) inhibitors are being explored as a promising therapeutic avenue in numerous cancers. While clinical trials have reported single-agent activity in advanced haematological malignancies, mechanisms determining the response to BET inhibition remain poorly understood. To identify factors involved in primary and acquired BET resistance in leukaemia, here we perform a chromatin-focused RNAi screen in a sensitive MLL-AF9;Nras(G12D)-driven AML mouse model, and investigate dynamic transcriptional profiles in sensitive and resistant mouse and human leukaemias. Our screen shows that suppression of the PRC2 complex, contrary to effects in other contexts, promotes BET inhibitor resistance in AML. PRC2 suppression does not directly affect the regulation of Brd4-dependent transcripts, but facilitates the remodelling of regulatory pathways that restore the transcription of key targets such as Myc. Similarly, while BET inhibition triggers acute MYC repression in human leukaemias regardless of their sensitivity, resistant leukaemias are uniformly characterized by their ability to rapidly restore MYC transcription. This process involves the activation and recruitment of WNT signalling components, which compensate for the loss of BRD4 and drive resistance in various cancer models. Dynamic chromatin immunoprecipitation sequencing and self-transcribing active regulatory region sequencing of enhancer profiles reveal that BET-resistant states are characterized by remodelled regulatory landscapes, involving the activation of a focal MYC enhancer that recruits WNT machinery in response to BET inhibition. Together, our results identify and validate WNT signalling as a driver and candidate biomarker of primary and acquired BET resistance in leukaemia, and implicate the rewiring of transcriptional programs as an important mechanism promoting resistance to BET inhibitors and, potentially, other chromatin-targeted therapies.","authors":"Rathert, P., Roth, M., Neumann, T., Muerdter, F., Roe, JS., Muhar, M., Deswal, S., Cerny-Reiterer, S., Peter, B., Jude, J., Hoffmann, T., Bory\u0144, \u0141M., Axelsson, E., Schweifer, N., Tontsch-Grunt, U., Dow, LE., Gianni, D., Pearson, M., Valent, P., Stark, A., Kraut, N., Vakoc, CR., Zuber, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nature","volume":"525","issue":"7570","page":"543-547","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"4341653","title":"Cell communication by chemical signals and the regulation of cyclic AMP in the development of a microorganism, Dictyostelium discoideum.","abstract":null,"authors":"Gerisch, G., Malchow, D., Riedel, V., Beug, H.","publication_status":"ppublish","journalpubyear":"1972","journaltitle":"Hoppe Seylers Z Physiol Chem","volume":"353","issue":"5","page":"684-5","pdf":null,"JrId":"4075","fulltextlink":null,"preprintlink":null,"articledate":"1972-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8668535","title":"Extrachromosomal recombination occurs efficiently in cells defective in various DNA repair systems.","abstract":"A series of different frameshift mutations of a firefly luciferase reporter plasmid was created so that no activity was obtained when they were transfected into mammalian cells. Co-transfection of these constructs with short fragments of the original sequence resulted in luciferase activity in different cell lines (A-549, NIH 3T3 and Jurkat). The level of this activity was dependent on the length of the fragment, regardless of cell line examined. Two different transfection techniques (lipofection and adenovirus-enhanced gene transfer) gave similar results. It was shown by polymerase chain reaction that expression of detectable luciferase required recombination of the transfected molecules. Cells with defined defects in DNA repair pathways were examined for their ability to perform this extrachromosomal recombination. Cells lacking normal Ku p80, (ADP-ribosyl)transferase, MLH1 or XP-C were all capable of restoring expression to the frameshifted constructs. Given the pivotal roles of the above molecules in the pathways of DNA repair, it seems that this recombination derives from a different activity.","authors":"Morrison, C., Wagner, E.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Nucleic Acids Res","volume":"24","issue":"11","page":"2053-8","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1996-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9209486","title":"Analysis of the requirement for beta 2-microglobulin for expression and formation of human CD1 antigens.","abstract":"Human CD1 form a group of nonpolymorphic leukocyte surface molecules with homology to major histocompatibility complex (MHC) proteins. Recent findings in human and in mouse demonstrate the capacity of CD1 molecules to present nonpeptide components like lipids or lipoglycans as well as peptides. We studied the involvement of beta 2-microglobulin (beta 2m) in expression of the classic human CD1 proteins CD1a, CD1b, and CD1c. The beta 2m-deficient human melanoma cell line FO-1 was transiently transfected with either CD1a, CD1b, or CD1c DNA alone, or in combination with beta 2m using the adenovirus-enhanced receptor-mediated transfer infection system. Only co-transfection of FO-1 cells with CD1+ beta 2m resulted in the detection of CD1 Ag by monoclonal antibodies (mAb). This indicated that CD1 mAb recognized determinants are dependent on beta 2m and raised the question whether beta 2m-free forms of CD1 can be expressed. Therefore, to visualize CD1 molecule expression independently of beta 2m, we expressed tagged recombinant forms. A full-length CD1b construct tagged at the very C terminus with a small peptide was transported to the plasma membrane only when beta 2m was co-transfected. beta 2m involvement in the transport of CD1 was confirmed by expression of soluble forms of CD1a, CD1b, and CD1c in three different cell types. Analogous to tagged full-length CD1b, secretion of the soluble CD1 constructs was strictly dependent on beta 2m. The soluble CD1 chimeras were secreted as complexes with endogenous beta 2m. Thus, similar to its role for MHC class I expression, beta 2m is essential for processing and surface transport of the classic human CD1 molecules CD1a, CD1b, and CD1c.","authors":"Bauer, A., H\u00fcttinger, R., Staffler, G., Hansmann, C., Schmidt, W., Majdic, O., Knapp, W., Stockinger, H.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Eur J Immunol","volume":"27","issue":"6","page":"1366-73","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"1997-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8895471","title":"Identification of subunits of the anaphase-promoting complex of Saccharomyces cerevisiae.","abstract":"Entry into anaphase and proteolysis of B-type cyclins depend on a complex containing the tetratricopeptide repeat proteins Cdc16p, Cdc23p, and Cdc27p. This particle, called the anaphase-promoting complex (APC) or cyclosome, functions as a cell cycle-regulated ubiquitin-protein ligase. Two additional subunits of the budding yeast APC were identified: The largest subunit, encoded by the APC1 gene, is conserved between fungi and vertebrates and shows similarity to BIMEp from Aspergillus nidulans. A small heat-inducible subunit is encoded by the CDC26 gene. The yeast APC is a 36S particle that contains at least seven different proteins.","authors":"Zachariae, W., Shin, TH., Galova, M., Obermaier, B., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Science","volume":"274","issue":"5290","page":"1201-4","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12688129","title":"N-ras mutation in a canine lymphoma: short communication.","abstract":"Lymphomas of dogs were investigated by molecular genetic methods. Regions of exon 1 and 2 of the N-ras gene, which harbours the mutation hot spots (codons 12, 13 and 61) were screened. A GGT [symbol: see text] GAT (glycine [symbol: see text] aspartic acid) mutation in codon 13 was present in a multicentric-type lymphoma of a 1-year-old male dog.","authors":"Mayr, B., Holzheu, M., Schaffner, G., Reifinger, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Acta Vet Hung","volume":"51","issue":"1","page":"91-4","pdf":null,"JrId":"221","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8657298","title":"Retinoblastoma protein. Another role rolls in.","abstract":null,"authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Nature","volume":"382","issue":"6586","page":"28-9","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1996-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12667442","title":"Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners.","abstract":"We describe a superfamily of eukaryotic and prokaryotic proteins (kleisins) that includes ScpA, Scc1, Rec8, and Barren. Scc1 interacts with SMC proteins through N- and C-terminal domains to form a ring-like structure. Since these are the only domains conserved among kleisins, we suggest that ring formation with SMC proteins may define this family.","authors":"Schleiffer, A., Kaitna, S., Maurer-Stroh, S., Glotzer, M., Nasmyth, K., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Mol Cell","volume":"11","issue":"3","page":"571-5","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8641288","title":"The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE).","abstract":"The MSN2 and MSN4 genes encode homologous and functionally redundant Cys2His2 zinc finger proteins. A disruption of both MSN2 and MSN4 genes results in a higher sensitivity to different stresses, including carbon source starvation, heat shock and severe osmotic and oxidative stresses. We show that MSN2 and MSN4 are required for activation of several yeast genes such as CTT1, DDR2 and HSP12, whose induction is mediated through stress-response elements (STREs). Msn2p and Msn4p are important factors for the stress-induced activation of STRE dependent promoters and bind specifically to STRE-containing oligonucleotides. Our results suggest that MSN2 and MSN4 encode a DNA-binding component of the stress responsive system and it is likely that they act as positive transcription factors.","authors":"Mart\u00ednez-Pastor, MT., Marchler, G., Sch\u00fcller, C., Marchler-Bauer, A., Ruis, H., Estruch, F.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"EMBO J","volume":"15","issue":"9","page":"2227-35","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1996-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8627818","title":"Hybrid proteins between Pseudomonas aeruginosa exotoxin A and poliovirus 2Apro cleave p220 in HeLa cells.","abstract":"Cleavage of p220, a component of the initiation factor eIF-4F, has been correlated with the inhibition of host translation during poliovirus infection. To obtain p220 cleavage in the absence of any other poliovirus gene products, hybrid proteins containing Pseudomonas aeruginosa exotoxin A and poliovirus protease 2Apro have been constructed. The addition of the hybrid molecules to cultured cells did not lead to substantial p220 cleavage. However, the simultaneous presence of the hybrid toxin with replicationally inactive chicken adenovirus particles results in efficient cleavage of p220 in the intact cells. Under these conditions, cellular translation continues unabated for several hours, arguing against a direct requirement for intact p220 in each round of the initiation of translation of cellular mRNAs.","authors":"Novoa, I., Cotten, M., Carrasco, L.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"J Virol","volume":"70","issue":"5","page":"3319-24","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1996-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12616489","title":"Weak agonist self-peptides promote selection and tuning of virus-specific T cells.","abstract":"Recent progress has begun to define the interactions and signaling pathways that are triggered during positive selection. To identify and further examine self-peptides that can mediate positive selection, we searched a protein-database to find peptides that have minimal homology with the viral peptide (p33) that activates a defined P14 transgenic TCR. We identified four peptides that could bind the restriction element H-2D(b) and induce proliferation of P14 transgenic splenocytes at high concentration. Two of the four peptides (DBM and RPP) were able to positively select the virus-specific TCR in fetal thymic organ culture but were unable to induce clonal deletion. Reverse-phase HPLC and mass spectrometry demonstrated that these peptides were presented by H-2D(b) molecules on thymic epithelial cell lines. We also examined whether the selecting ligands altered T cell responsiveness in vitro. DBM-selected T cells lost their ability to respond to the positively selecting ligand DBM, whereas RPP-selected T cells only retained their ability to respond to high concentrations of RPP. These results demonstrate that self-peptides that mediate positive selection can differentially \"tune\" the activation threshold of T cells and alter the functional repertoire of T cells.","authors":"Saibil, SD., Ohteki, T., White, FM., Luscher, M., Zakarian, A., Elford, A., Shabanowitz, J., Nishina, H., Hugo, P., Penninger, J., Barber, B., Hunt, DF., Ohashi, PS.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Eur J Immunol","volume":"33","issue":"3","page":"685-96","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"2003-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8625407","title":"Mother cell-specific HO expression in budding yeast depends on the unconventional myosin myo4p and other cytoplasmic proteins.","abstract":"Certain cell types give rise to progeny that adopt different patterns of gene expression in the absence of any differences in their environment. Cells of budding yeast give birth to mother and daughter cells that differ in that only mother cells express the HO endonuclease gene and thereby switch mating types. We describe the identification of five genes, called SHE1-SHE5, that encode cytoplasmic proteins required for mother-specific HO expression. She1p, which is identical to the minimyosin Myo4p, and She3p are not, however, mother-specific proteins. On the contrary, they accumulate in growing buds. She proteins might be required for the transport of factors that promote HO repression from the mother cell into its bud. In an accompanying paper, we show that SHE genes are needed for the accumulation in daughter nuclei of Ash1p, a repressor of HO.","authors":"Jansen, RP., Dowzer, C., Michaelis, C., Galova, M., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Cell","volume":"84","issue":"5","page":"687-97","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1996-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12557220","title":"Electroporation as a tool to study in vivo spinal cord regeneration.","abstract":"Tailed amphibians such as axolotls and newts have the unique ability to fully regenerate a functional spinal cord throughout life. Where the cells come from and how they form the new structure is still poorly understood. Here, we describe the development of a technique that allows the visualization of cells in the living animal during spinal cord regeneration. A microelectrode needle is inserted into the lumen of the spinal cord and short rapid pulses are applied to transfer the plasmids encoding the green or red fluorescent proteins into ependymal cells close to the plane of amputation. The use of small, transparent axolotls permits imaging with epifluorescence and differential interference contrast microscopy to track the transfected cells as they contribute to the spinal cord. This technique promises to be useful in understanding how neural progenitors are recruited to the regenerating spinal cord and opens up the possibility of testing gene function during this process.","authors":"Echeverri, K., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Dev Dyn","volume":"226","issue":"2","page":"418-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21454566","title":"Monoglyceride lipase deficiency in mice impairs lipolysis and attenuates diet-induced insulin resistance.","abstract":"Monoglyceride lipase (MGL) influences energy metabolism by at least two mechanisms. First, it hydrolyzes monoacylglycerols (MG) into fatty acids and glycerol. These products can be used for energy production or synthetic reactions. Second, MGL degrades 2-arachidonoyl glycerol (2-AG), the most abundant endogenous ligand of cannabinoid receptors (CBR). Activation of CBR affects energy homeostasis by central orexigenic stimuli, by promoting lipid storage, and by reducing energy expenditure. To characterize the metabolic role of MGL in vivo, we generated an MGL-deficient mouse model (MGL-ko). These mice exhibit a reduction in MG hydrolase activity and a concomitant increase in MG levels in adipose tissue, brain, and liver. In adipose tissue, the lack of MGL activity is partially compensated by hormone-sensitive lipase. Nonetheless, fasted MGL-ko mice exhibit reduced plasma glycerol and triacylglycerol, as well as liver triacylglycerol levels indicative for impaired lipolysis. Despite a strong elevation of 2-AG levels, MGL-ko mice exhibit normal food intake, fat mass, and energy expenditure. Yet mice lacking MGL show a pharmacological tolerance to the CBR agonist CP 55,940 suggesting that the elevated 2-AG levels are functionally antagonized by desensitization of CBR. Interestingly, however, MGL-ko mice receiving a high fat diet exhibit significantly improved glucose tolerance and insulin sensitivity in comparison with wild-type controls despite equal weight gain. In conclusion, our observations implicate that MGL deficiency impairs lipolysis and attenuates diet-induced insulin resistance. Defective degradation of 2-AG does not provoke cannabinoid-like effects on feeding behavior, lipid storage, and energy expenditure, which may be explained by desensitization of CBR.","authors":"Taschler, U., Radner, FP., Heier, C., Schreiber, R., Schweiger, M., Schoiswohl, G., Preiss-Landl, K., Jaeger, D., Reiter, B., Koefeler, HC., Wojciechowski, J., Theussl, C., Penninger, JM., Lass, A., Haemmerle, G., Zechner, R., Zimmermann, R.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Biol Chem","volume":"286","issue":"20","page":"17467-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8605583","title":"Mutations in tumour suppressor gene p53 in two feline fibrosarcomas.","abstract":"Exons 5-7 of the tumour suppressor gene p53 were investigated in genomic DNA of tumours of domestic cats. In one fibrosarcoma investigated we observed a mutation GAG--&gt;AAG (glutamic acid--&gt;lysine) in codon 180; in another there was a mutation CGG--&gt;TGG (arginine--&gt;tryptophane) in codon 248.","authors":"Mayr, B., Schaffner, G., Kurzbauer, R., Schneider, A., Reifinger, M., Loupal, G.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Br Vet J","volume":"151","issue":"6","page":"707-13","pdf":null,"JrId":"1916","fulltextlink":null,"preprintlink":null,"articledate":"1996-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12399316","title":"Roles of the Homothorax\/Meis\/Prep homolog UNC-62 and the Exd\/Pbx homologs CEH-20 and CEH-40 in C. elegans embryogenesis.","abstract":"Co-factor homeodomain proteins such as Drosophila Homothorax (Hth) and Extradenticle (Exd) and their respective vertebrate homologs, the Meis\/Prep and Pbx proteins, can increase the DNA-binding specificity of Hox protein transcription factors and appear to be required for many of their developmental functions. We show that the unc-62 gene encodes the C. elegans ortholog of Hth, and that maternal-effect unc-62 mutations can cause severe posterior disorganization during embryogenesis (Nob phenotype), superficially similar to that seen in embryos lacking function of either the two posterior-group Hox genes nob-1 and php-3 or the caudal homolog pal-1. Other zygotically acting unc-62 alleles cause earlier embryonic arrest or incompletely penetrant larval lethality with variable morphogenetic defects among the survivors, suggesting that unc-62 functions are required at several stages of development. The differential accumulation of four unc-62 transcripts is consistent with multiple functions. The C. elegans exd homologs ceh-20 and ceh-40 interact genetically with unc-62 and may have overlapping roles in embryogenesis: neither CEH-20 nor CEH-40 appears to be required when the other is present, but loss of both functions causes incompletely penetrant embryonic lethality in the presence of unc-62(+) and complete embryonic lethality in the presence of an unc-62 hypomorphic allele.","authors":"Van Auken, K., Weaver, D., Robertson, B., Sundaram, M., Saldi, T., Edgar, L., Elling, U., Lee, M., Boese, Q., Wood, WB.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Development","volume":"129","issue":"22","page":"5255-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12589053","title":"Differential roles of Smad1 and p38 kinase in regulation of peroxisome proliferator-activating receptor gamma during bone morphogenetic protein 2-induced adipogenesis.","abstract":"Bone morphogenetic protein 2 (BMP2) promotes the differentiation of undifferentiated mesenchymal cells into adipocytes. To investigate the molecular mechanisms that regulate this differentiation process, we studied the relationship between BMP2 signaling and peroxisome proliferator-activating receptor gamma (PPARgamma) during adipogenesis of mesenchymal cells by using pluripotent mesenchymal cell line C3H10T1\/2. In C3H10T1\/2 cells, BMP2 induced expression of PPARgamma along with adipogenesis. Overexpression of Smad6, a natural antagonist for Smad1, blocked PPARgamma expression and adipocytic differentiation induced by BMP2. Overexpression of dominant-negative PPARgamma also diminished adipocytic differentiation of C3H10T1\/2 cells, suggesting the central role of PPARgamma in BMP2-induced adipocytic differentiation. Specific inhibitors for p38 kinase inhibited BMP2-induced adipocytic differentiation and transcriptional activation of PPARgamma, whereas overexpression of Smad6 had no effect on transcriptional activity of PPARgamma. Furthermore, activation of p38 kinase by overexpression of TAK1 and TAB1, without affecting PPARgamma expression, led the up-regulation of transcriptional activity of PPARgamma. These results suggest that both Smad and p38 kinase signaling are concomitantly activated and responsible for BMP2-induced adipocytic differentiation by inducing and up-regulating PPARgamma, respectively. Thus, BMP2 controls adipocytic differentiation by using two distinct signaling pathways that play differential roles in this process in C3H10T1\/2 cells.","authors":"Hata, K., Nishimura, R., Ikeda, F., Yamashita, K., Matsubara, T., Nokubi, T., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Mol Biol Cell","volume":"14","issue":"2","page":"545-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8568896","title":"Principles of helix-helix packing in proteins: the helical lattice superposition model.","abstract":"The geometry of helix-helix packing in globular proteins is comprehensively analysed within the model of the superposition of two helix lattices which result from unrolling the helix cylinders onto a plane containing points representing each residue. The requirements for the helix geometry (the radius R, the twist angle omega and the rise per residue delta) under perfect match of the lattices are studied through a consistent mathematical model that allows consideration of all possible associations of all helix types (alpha-, pi- and 3(10)). The corresponding equations have three well-separated solutions for the interhelical packing angle, omega, as a function of the helix geometric parameters allowing optimal packing. The resulting functional relations also show unexpected behaviour. For a typically observed alpha-helix (omega = 99.1 degrees, delta = 1.45 A), the three optimal packing angles are omega a,b,c = -37.1 degrees, -97.4 degrees and +22.0 degrees with a periodicity of 180 degrees and respective helix radii Ra,b,c = 3.0 A, 3.5 A and 4.3 A. However, the resulting radii are very sensitive to variations in the twist angle omega. At omega triple = 96.9 degrees, all three solutions yield identical radii at delta = 1.45 A where Rtriple = 3.46 A. This radius is close to that of a poly(Ala) helix, indicating a great packing flexibility when alanine is involved in the packing core, and omega triple is close to the mean observed twist angle. In contrast, the variety of possible theoretical solutions is limited for the other two helix types. Besides the perfect matches, novel suboptimal \"knobs into holes\" hydrophobic packing patterns as a function of the helix radius are described. Alternative \"knobs onto knobs\" and mixed models can be applied in cases where salt bridges, hydrogen bonds, disulphide bonds and tight hydrophobic head-to-head contacts are involved in helix-helix associations. An analysis of the experimentally observed packings in proteins confirmed the conclusions of the theoretical model. Nonetheless, the observed alpha-helix packings showed deviations from the 180 degrees periodicity expected from the model. An investigation of the actual three-dimensional geometry of helix-helix packing revealed an explanation for the observed discrepancies where a decisive role was assigned to the defined orientation of the C alpha-C beta vectors of the side-chains. As predicted form the model, helices with different radii (differently sized side-chains in the packing core) were observed to utilize different packing cells (packing patterns). In agreement with the coincidence between Rtriple and the radius of a poly(Ala) helix, Ala was observed to show greatest propensity to build the packing core. The application of the helix lattice superposition model suggests that the packing of amino acid residues is best described by a \"knobs into holes\" scheme rather than \"ridges into grooves\". The various specific packing modes made salient by the model should be useful in protein engineering and design.","authors":"Walther, D., Eisenhaber, F., Argos, P.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"J Mol Biol","volume":"255","issue":"3","page":"536-53","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12419208","title":"Just the beginning: novel functions for angiotensin-converting enzymes.","abstract":"Cardiovascular disease is predicted to be the commonest cause of death worldwide by the year 2020. Diabetes, smoking and hypertension are the main risk factors. The renin-angiotensin system plays a key role in regulating blood pressure and fluid and electrolyte homeostasis in mammals. The discovery of specific drugs that block either the key enzyme of the renin-angiotensin system, angiotensin-converting enzyme (ACE), or the receptor for its main effector angiotensin II, was a major step forward in the treatment of hypertension and heart failure. In recent years, however, the renin-angiotensin system has been shown to be a far more complex system than initially thought. It has become clear that additional peptide mediators are involved. Furthermore, a new ACE, angiotensin-converting enzyme 2 (ACE2), has been discovered which appears to negatively regulate the renin-angiotensin system. In the heart, ACE2 deficiency results in severe impairment of cardiac contractility and upregulation of hypoxia-induced genes. We shall discuss the interplay of the various effector peptides generated by angiotensin-converting enzymes ACE and ACE2, highlighting the role of ACE2 as a negative regulator of the renin-angiotensin system.","authors":"Eriksson, U., Danilczyk, U., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"21","page":"R745-52","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11516655","title":"Bazooka and PAR-6 are required with PAR-1 for the maintenance of oocyte fate in Drosophila.","abstract":"The anterior-posterior axis of C. elegans is defined by the asymmetric division of the one-cell zygote, and this is controlled by the PAR proteins, including PAR-3 and PAR-6, which form a complex at the anterior of the cell, and PAR-1, which localizes at the posterior [1-4]. PAR-1 plays a similar role in axis formation in Drosophila: the protein localizes to the posterior of the oocyte and is necessary for the localization of the posterior and germline determinants [5, 6]. PAR-1 has recently been shown to have an earlier function in oogenesis, where it is required for the maintenance of oocyte fate and the posterior localization of oocyte-specific markers [7, 8]. Here, we show that the homologs of PAR-3 (Bazooka) and PAR-6 are also required to maintain oocyte fate. Germline clones of mutants in either gene give rise to egg chambers that develop 16 nurse cells and no oocyte. Furthermore, oocyte-specific factors, such as Orb protein and the centrosomes, still localize to one cell but fail to move from the anterior to the posterior cortex. Thus, PAR-1, Bazooka, and PAR-6 are required for the earliest polarity in the oocyte, providing the first example in Drosophila where the three homologs function in the same process. Although these PAR proteins therefore seem to play a conserved role in early anterior-posterior polarity in C. elegans and Drosophila, the relationships between them are different, as the localization of PAR-1 does not require Bazooka or PAR-6 in Drosophila, as it does in the worm.","authors":"Huynh, JR., Petronczki, M., Knoblich, JA., St Johnston, D.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Curr Biol","volume":"11","issue":"11","page":"901-6","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8892942","title":"Structural requirements for low-pH-induced rearrangements in the envelope glycoprotein of tick-borne encephalitis virus.","abstract":"The exposure of the flavivirus tick-borne encephalitis (TBE) virus to an acidic pH is necessary for virus-induced membrane fusion and leads to a quantitative and irreversible conversion of the envelope protein E dimers to trimers. To study the structural requirements for this oligomeric rearrangement, the effect of low-pH treatment on the oligomeric state of different isolated forms of protein E was investigated. Full-length E dimers obtained by solubilization of virus with the detergent Triton X-100 formed trimers at low pH, whereas truncated E dimers lacking the stem-anchor region underwent a reversible dissociation into monomers without forming trimers. These data suggest that the low-pH-induced rearrangement in virions is a two-step process involving a reversible dissociation of the E dimers followed by an irreversible formation of trimers, a process which requires the stem-anchor portion of the protein. This region contains potential amphipathic alpha-helical and conserved structural elements whose interactions may contribute to the rearrangements which initiate the fusion process.","authors":"Stiasny, K., Allison, SL., Marchler-Bauer, A., Kunz, C., Heinz, FX.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"J Virol","volume":"70","issue":"11","page":"8142-7","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26379026","title":"Erratum: Pharmacological targeting of the Wdr5-MLL interaction in C\/EBP\u03b1 N-terminal leukemia.","abstract":null,"authors":"Grebien, F., Vedadi, M., Getlik, M., Giambruno, R., Grover, A., Avellino, R., Skucha, A., Vittori, S., Kuznetsova, E., Smil, D., Barsyte-Lovejoy, D., Li, F., Poda, G., Schapira, M., Wu, H., Dong, A., Senisterra, G., Stukalov, A., Huber, KV., Sch\u00f6negger, A., Marcellus, R., Bilban, M., Bock, C., Brown, PJ., Zuber, J., Bennett, KL., Al-Awar, R., Delwel, R., Nerlov, C., Arrowsmith, CH., Superti-Furga, G.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Chem Biol","volume":"11","issue":"10","page":"815","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3903518","title":"Expression of a foreign gene in myeloid and lymphoid cells derived from multipotent haematopoietic precursors.","abstract":"Bone marrow cells infected with retroviral vectors carrying the bacterial neomycin resistance (neo) gene as a marker were used for long-term reconstitution of the haematopoietic system of irradiated mice. The neo gene is expressed in the myeloid and lymphoid lineages of these animals and an analysis of the sites of viral integration indicates that these lineages are derived from the same primitive multipotent cells.","authors":"Keller, G., Paige, C., Gilboa, E., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Nature","volume":"318","issue":"6042","page":"149-54","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1985-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21441458","title":"Lymphotoxin signal promotes thymic organogenesis by eliciting RANK expression in the embryonic thymic stroma.","abstract":"It has recently become clear that signals mediated by members of the TNFR superfamily, including lymphotoxin-\u03b2 receptor (LT\u03b2R), receptor activator for NF-\u03baB (RANK), and CD40, play essential roles in organizing the integrity of medullary thymic epithelial cells (mTECs) required for the establishment of self-tolerance. However, details of the mechanism responsible for the unique and cooperative action of individual and multiple TNFR superfamily members during mTEC differentiation still remain enigmatic. In this study, we show that the LT\u03b2R signal upregulates expression of RANK in the thymic stroma, thereby promoting accessibility to the RANK ligand necessary for mTEC differentiation. Cooperation between the LT\u03b2R and RANK signals for optimal mTEC differentiation was underscored by the exaggerated defect of thymic organogenesis observed in mice doubly deficient for these signals. In contrast, we observed little cooperation between the LT\u03b2R and CD40 signals. Thus, the LT\u03b2R signal exhibits a novel and unique function in promoting RANK activity for mTEC organization, indicating a link between thymic organogenesis mediated by multiple cytokine signals and the control of autoimmunity.","authors":"Mouri, Y., Yano, M., Shinzawa, M., Shimo, Y., Hirota, F., Nishikawa, Y., Nii, T., Kiyonari, H., Abe, T., Uehara, H., Izumi, K., Tamada, K., Chen, L., Penninger, JM., Inoue, J., Akiyama, T., Matsumoto, M.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Immunol","volume":"186","issue":"9","page":"5047-57","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12235285","title":"Meiotic telomere clustering is inhibited by colchicine but does not require cytoplasmic microtubules.","abstract":"Telomere clustering, the defining feature of the bouquet, is an almost universal feature of meiotic prophase, yet its mechanism remains unknown. The microtubule-depolymerizing agent colchicine was found to inhibit bouquet formation. Telomeres in colchicine-treated cells remained scattered in the nuclear periphery, whereas untreated cells exhibited a prominent telomere cluster. Colchicine administered after the bouquet had formed did not affect telomere dispersal. The effect of colchicine on bouquet formation appeared to be separable from its effect on cytoplasmic microtubules; amiprophos methyl, a highly effective plant microtubule-depolymerizing drug, did not affect telomere clustering. Inhibition of bouquet formation was limited to colchicine and the related drug podophyllotoxin out of the variety of microtubule-depolymerizing drugs tested, suggesting that the target involved in bouquet formation has a structural specificity.","authors":"Cowan, CR., Cande, WZ.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Cell Sci","volume":"115","issue":"Pt 19","page":"3747-56","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2003-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8538771","title":"An essential role for the Cdc6 protein in forming the pre-replicative complexes of budding yeast.","abstract":"Origins of DNA replication in Saccharomyces cerevisiae are bound by two protein complexes during the cell cycle. Post-replicative complexes closely resemble those generated in vitro by purified origin recognition complex (ORC), which is essential for DNA replication in vivo. Pre-replicative complexes (pre-RCs) are characterized by an extended region of nuclease protection overlapping the ORC footprint. We show here that the Cdc6 protein (Cdc6p), which is necessary for origin firing in vivo, is essential for the establishment and maintenance of pre-RCs, suggesting that it is a component of these complexes. Without Cdc6p, G1 origins closely resemble post-replicative origins, providing evidence that ORC is also a component of pre-RCs. These results suggest that pre-RCs play an essential role in initiating DNA replication and support a two-step mechanism for the assembly of functional initiation complexes.","authors":"Cocker, JH., Piatti, S., Santocanale, C., Nasmyth, K., Diffley, JF.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Nature","volume":"379","issue":"6561","page":"180-2","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1996-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8557712","title":"Cell cycle regulation of p70 S6 kinase and p42\/p44 mitogen-activated protein kinases in Swiss mouse 3T3 fibroblasts.","abstract":"We show here using synchronized Swiss mouse 3T3 fibroblasts that p70 S6 kinase (p70S6k) and mitogen-activated protein kinases (p42mapk\/p44mapk) are not only activated at the G0\/G1 boundary, but also in cells progressing from M into G1. p70S6k activity increases 20-fold in G1 cells released from G0. Throughout G1, S, and G2 it decreases constantly, so that during M phase low kinase activity is measured. The kinase is reactivated 10-fold when cells released from a nocodazole-induced metaphase block enter G1 of the next cell cycle. p42mapk\/p44mapk in G0 cells are activated transiently early in G1 and are reactivated late in mitosis after nocodazole release. p70S6k activity is dependent on permanent signaling from growth factors at all stages of the cell cycle. Immunofluorescence studies showed that p70S6k and its isoform p85S6k become concentrated in localized spots in the nucleus at certain stages in the cell cycle. Cell cycle-dependent changes in p70S6k activity are associated with alterations in the phosphorylation state of the protein. However, examination of the regulation of a p70S6k mutant in which the four carboxyl-terminal phosphorylation sites are changed to acidic amino acids suggests that a mechanism independent of these phosphorylation sites controls the activity of the enzyme during the cell cycle.","authors":"Edelmann, HM., K\u00fchne, C., Petritsch, C., Ballou, LM.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"J Biol Chem","volume":"271","issue":"2","page":"963-71","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1996-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8547228","title":"Transformation of erythroid progenitors by viral and cellular tyrosine kinases.","abstract":"Recently, two different normal avian erythroid progenitors were described. They differ in the receptor tyrosine kinases they express and in their ability to undergo self-renewal in culture. A common progenitor, termed stem cell factor (SCF) progenitor, expresses the receptor for avian SCF c-Kit, and undergoes short-term self-renewal when grown in the presence of avian SCF. A second progenitor, referred to as SCF\/transforming growth factor-alpha progenitor, coexpresses c-Kit and the avian epidermal growth factor receptor homologue c-ErbB. These progenitors undergo sustained self-renewal when grown in the presence of transforming growth factor-alpha plus estradiol. The phenotype of the normal SCF\/transforming growth factor-alpha progenitors closely corresponded to that of erythroid cells transformed by the tyrosine kinase oncogenes v-erbB or v-sea. This suggested that these cells, but not the SCF progenitors, would be the target cells for erythroblast transformation by these oncogenes. However, we demonstrate that both progenitor cells can be transformed by the v-erbB and v-sea oncogenes and also by the ligand-activated proto-oncogene product c-ErbB. We conclude that the target cell specificity of certain tyrosine kinase oncoproteins for erythroid cells is a reflection of their ability to provide signals for self-renewal that normally emanate from the endogenous c-ErbB protein.","authors":"Beug, H., Schroeder, C., Wessely, O., Deiner, E., Meyer, S., Ischenko, ID., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell Growth Differ","volume":"6","issue":"8","page":"999-1008","pdf":null,"JrId":"1848","fulltextlink":null,"preprintlink":null,"articledate":"1996-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34550333","title":"Erratum to: Severe Coronavirus Disease 2019 (COVID-19) is Associated With Elevated Serum Immunoglobulin (Ig) A and Antiphospholipid IgA Antibodies.","abstract":null,"authors":"Hasan Ali, O., Bomze, D., Risch, L., Brugger, SD., Paprotny, M., Weber, M., Thiel, S., Kern, L., Albrich, WC., Kohler, P., Kahlert, CR., Vernazza, P., B\u00fchler, PK., Sch\u00fcpbach, RA., G\u00f3mez-Mejia, A., Popa, AM., Bergthaler, A., Penninger, JM., Flatz, L.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Clin Infect Dis","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8504932","title":"Ectopic expression of a conditional GATA-2\/estrogen receptor chimera arrests erythroid differentiation in a hormone-dependent manner.","abstract":"The GATA factors are a family of transcriptional regulatory proteins in eukaryotes that share extensive homology in their DNA-binding domains. One enigmatic aspect of GATA factor expression is that several GATA proteins, which ostensibly share the same DNA-binding site specificity, are coexpressed in erythroid cells. To elucidate the roles of individual GATA factors in erythropoiesis, conditional alleles of GATA-1, GATA-2, and GATA-3 were prepared by fusing each of the factors to the hormone-binding domain of the human estrogen receptor (ER). These GATA\/ER chimeric factors were shown to be hormone-inducible trans-activating proteins in transient transfection assays. When stably introduced into primary erythroblasts or conditionally transformed erythroid progenitors cells, exogenous GATA-2\/ER promoted proliferation and inhibited terminal differentiation in an estrogen-dependent manner. These phenotypic effects are specifically attributable to the action of ectopically expressed GATA-2\/ER because erythroblasts expressing exogenous GATA-2 are constitutively arrested in differentiation and because erythroid progenitors expressing either Gal\/ER or GATA-3\/ER do not display a hormone-responsive block in differentiation. Thus, the GATA-2 transcription factor appears to play a role in regulating the self-renewal capacity of early erythroid progenitor cells.","authors":"Briegel, K., Lim, KC., Plank, C., Beug, H., Engel, JD., Zenke, M.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Genes Dev","volume":"7","issue":"6","page":"1097-109","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1993-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12112320","title":"Inhibition of proliferation and expression of T1 and cyclin D1 genes by thyroid hormone in mammary epithelial cells.","abstract":"The relationship between thyroid hormone (triiodothyronine, T(3)) and breast cancer is unclear. We studied the effect of the c-erbA\/TR alpha proto-oncogene encoding a functional T(3) receptor (TR alpha 1), of its ligand T(3), and of its retroviral, mutated counterpart, the v-erbA oncogene, on the proliferation capacity of nontumorigenic mammary epithelial cells (EpH4). We found that EpH4 cells expressing ectopically TR (EpH4 + TR alpha 1) or v-erbA (EpH4 + v-erbA) proliferated faster than parental EpH4 cells that contained low levels of endogenous TR. T(3) inhibited DNA synthesis and proliferation in EpH4 + TR alpha 1 cells but not EpH4 or EpH4 + v-erbA cells. The study of cell-cycle genes showed that T(3) decreased cyclin D1 RNA and protein levels in EpH4 + TR alpha 1 cells. In addition, T(3) downregulated the expression of T1, a gene that is overexpressed in human breast adenocarcinomas and is induced by mitogens, serum, and several oncogenes and cytokines. Inhibition of the T1 gene by T(3) required both de novo mRNA and protein synthesis. Furthermore, T(3) abolished the induction of T1 by the tumor promoter 12-O-tetradecanoylphorbol-13-acetate and inhibited the activity of an activation protein 1-dependent promoter (-73-Col-CAT) in EpH4 + TR alpha 1 cells, suggesting that interference with activation protein 1 transcription factor plays a part in the inhibition of the T1 gene. Our results showed that T(3) reduced the proliferation of mammary epithelial cells and inhibited the expression of cyclin D1 and T1 genes.","authors":"Gonz\u00e1lez-Sancho, JM., Figueroa, A., L\u00f3pez-Barahona, M., L\u00f3pez, E., Beug, H., Mu\u00f1oz, A.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Carcinog","volume":"34","issue":"1","page":"25-34","pdf":null,"JrId":"1399","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8491189","title":"Destruction of the CDC28\/CLB mitotic kinase is not required for the metaphase to anaphase transition in budding yeast.","abstract":"It is widely assumed that degradation of mitotic cyclins causes a decrease in mitotic cdc2\/CDC28 kinase activity and thereby triggers the metaphase to anaphase transition. Two observations made on the budding yeast Saccharomyces cerevisiae are inconsistent with this scenario: (i) anaphase occurs in the presence of high levels of kinase in cdc15 mutants and (ii) overproduction of a B-type mitotic cyclin causes arrest not in metaphase as previously reported but in telophase. Kinase destruction is therefore implicated in the exit from mitosis rather than the entry into anaphase. The behaviour of esp1 mutants shows in addition that kinase destruction can occur in the absence of anaphase completion. The execution of anaphase and the destruction of CDC28 kinase activity therefore appear to take place independently of one another.","authors":"Surana, U., Amon, A., Dowzer, C., McGrew, J., Byers, B., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"EMBO J","volume":"12","issue":"5","page":"1969-78","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1993-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11500832","title":"Sampling of complementing self-antigen pools by thymic stromal cells maximizes the scope of central T cell tolerance.","abstract":"Expression of peripheral antigens in the thymus has been implicated in T cell tolerance and autoimmunity, yet the identity of cells involved remains elusive. Here we show that antigen expression in a minor fraction of medullary thymic epithelial cells leads to deletion of specific CD4 T cells. Strikingly, this deletion is not dependent on cross-presentation by hemopoietic antigen-presenting cells, which have been ascribed a predominant role in negative selection. By contrast, when the same antigen enters the thymus via the blood stream, negative selection is strictly dependent on antigen presentation by hemopoietic cells. These findings imply that the (re)-presentation of \"self\" by thymic stromal cells is non-redundant, and that different thymic antigen-presenting cells instead cover complementing sets of self-antigens, thus maximizing the scope of central tolerance","authors":"Klein, L., Roettinger, B., Kyewski, B.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Eur J Immunol","volume":"31","issue":"8","page":"2476-86","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11484034","title":"Gene regulation. Cycling silence.","abstract":"","authors":"Ringrose, L., Paro, R.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nature","volume":"412","issue":"6846","page":"493-4","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8462104","title":"Maternal-specific methylation of the imprinted mouse Igf2r locus identifies the expressed locus as carrying the imprinting signal.","abstract":"The mouse insulin-like growth factor type 2 receptor (Igf2r) is imprinted and expressed exclusively from the maternally inherited chromosome. To investigate whether methylation could function as the imprinting signal, we have cloned 130 kb from the Igf2r locus and searched for sequences methylated in a parental-specific manner. Two regions have been identified: region 1 contains the start of transcription and is methylated only on the silent paternal chromosome; region 2 is contained in an intron and is methylated only on the expressed maternal chromosome. Methylation of region 1 is acquired after fertilization, in contrast with the methylation of region 2, which is inherited from the female gamete. Methylation of region 2 may mark the maternal Igf2r locus in a manner that could act as an imprinting signal. These data suggest that the expressed locus carries a potential imprinting signal and imply that methylation is necessary for expression of the Igf2r gene.","authors":"St\u00f6ger, R., Kubicka, P., Liu, CG., Kafri, T., Razin, A., Cedar, H., Barlow, DP.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Cell","volume":"73","issue":"1","page":"61-71","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1993-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"96","title":"Polymer concentration dependence of the helix to random coil transition of a charged polypeptide in aqueous salt solution.","abstract":"The helix to coil transition of poly(L-glutamic acid) was investigated in 0.05 and 0.005 M aqueous potassium chloride solutions by use of potentiometric titration and circular dichroism measurement. Polymer concentration dependence of the transition was observed in the range from 0.006 to 0.04 monomol\/e in 0.005 M KG1 solution. The polymer concentration dependence can be interpreted by current theories of the transition of charged polypeptides and of titration curves of linear weak polyelectrolytes taking the effect of polymer concentration into consideration.","authors":"Nitta, K., Yoneyama, M.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biophys Chem","volume":"3","issue":"4","page":"323-9","pdf":null,"JrId":"1175","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8463214","title":"Binding-incompetent adenovirus facilitates molecular conjugate-mediated gene transfer by the receptor-mediated endocytosis pathway.","abstract":"Molecular conjugate vectors may be constructed that accomplish high efficiency gene transfer by the receptor-mediated endocytosis pathway. In order to mediate escape from lysosomal degradation, we have incorporated adenoviruses into the functional design of the conjugate. In doing so, however, we have introduced an additional ligand, which can bind to receptors on the cell surface, undermining the potential for cell specific targeting. To overcome this, we have treated the adenovirus with a monoclonal anti-fiber antibody, which renders the virus incapable of binding to its receptor. The result is a multi-functional molecular conjugate vector, which has preserved its binding specificity while at the same time being capable of preventing lysosomal degradation of endosome-internalized conjugate-DNA complexes. This finding indicates that adenoviral binding is not a prerequisite for adenoviral-mediated endosome disruption.","authors":"Michael, SI., Huang, CH., R\u00f8mer, MU., Wagner, E., Hu, PC., Curiel, DT.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Biol Chem","volume":"268","issue":"10","page":"6866-9","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12068919","title":"Stage-specific chromosomal association of Drosophila dMBD2\/3 during genome activation.","abstract":"The Drosophila gene dMBD2\/3 encodes a protein with significant homologies to the mammalian methyl-DNA binding proteins MBD2 and MBD3. These proteins are essential components of chromatin complexes involved in epigenetic gene regulation. Because the available in vitro data on dMBD2\/3 are conflicting we have started an in vivo characterization of dMBD2\/3. We detected expression of two isoforms specifically during embryonic development. Staining of whole embryos combined with high-resolution confocal microscopy revealed a highly regulated spatial distribution. During the syncytial blastoderm stage, dMBD2\/3 formed speckles that localized to the cytoplasm. Shortly after, during the cellular blastoderm stage, the protein entered the nucleus and formed bright foci that associated with DNA. This rapid transition coincided with the activation of the embryonic genome. A similar observation was made during activation of the spermatocyte genome as dMBD2\/3 formed distinct foci associated with the activated Y chromosome. Our results indicate that dMBD2\/3 forms specialized nuclear compartments to keep certain genes epigenetically silenced during genome activation.","authors":"Marhold, J., Zbylut, M., Lankenau, DH., Li, M., Gerlich, D., Ballestar, E., Mechler, BM., Lyko, F.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Chromosoma","volume":"111","issue":"1","page":"13-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8462098","title":"A Drosophila SH2-SH3 adaptor protein implicated in coupling the sevenless tyrosine kinase to an activator of Ras guanine nucleotide exchange, Sos.","abstract":"A Drosophila gene (drk) encodes a widely expressed protein with a single SH2 domain and two flanking SH3 domains, which is homologous to the Sem-5 protein of C. elegans and mammalian GRB2. Genetic analysis suggests that drk function is essential for signaling by the sevenless receptor tyrosine kinase. Drk biological activity correlates with binding of its SH2 domain to activated receptor tyrosine kinases and concomitant localization of drk to the plasma membrane. In vitro, drk also binds directly to the C-terminal tail of Sos, a Ras guanine nucleotide-releasing protein (GNRP), which, like Ras1 and drk, is required for sevenless signaling. These results suggest that drk binds autophosphorylated receptor tyrosine kinases with its SH2 domain and the Sos GNRP through its SH3 domains, thereby coupling receptor tyrosine kinases to Ras activation. The conservation of these signaling proteins during evolution indicates that this is a general mechanism for linking tyrosine kinases to Ras.","authors":"Olivier, JP., Raabe, T., Henkemeyer, M., Dickson, B., Mbamalu, G., Margolis, B., Schlessinger, J., Hafen, E., Pawson, T.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Cell","volume":"73","issue":"1","page":"179-91","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1993-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8413205","title":"Alternative splicing of Pax-8 gene transcripts is developmentally regulated and generates isoforms with different transactivation properties.","abstract":"Pax-8, a member of the paired box-containing gene family, was shown to be coexpressed with Pax-2 in several human kidney carcinoma cell lines. Four different Pax-8 mRNA isoforms, a to d, were cloned from one of these cell lines by polymerase chain reaction amplification, and the Pax-8 gene was isolated from a human cosmid library. Analysis of the exon-intron structure of Pax-8 revealed that the four mRNA isoforms arise by alternative splicing, resulting in inclusion or exclusion of exon 7 and\/or exon 8 sequences. All four Pax-8 proteins retain the paired domain as their DNA-binding motif and recognize DNA in the same manner as do the closely related Pax-2 and BSAP (Pax-5) proteins. The Pax-8a and Pax-8b isoforms end in a serine\/threonine\/tyrosine-rich sequence, while the C terminus of Pax-8c and Pax-8d is translated in a different, proline-rich reading frame. Transient transfection experiments revealed that Pax-8 isoforms a and b, but not c and d, strongly stimulate transcription from a promoter containing six copies of a paired-domain recognition sequence. The same four mRNA variants were also detected by RNase protection analysis in the mouse embryo and adult kidney, thus indicating evolutionary conservation of Pax-8 mRNA splicing. A different splice pattern was observed in the developing placenta, which expresses two new variants, Pax-8e and Pax-8f, instead of transcripts b to d. Expression of these mRNAs is high at embryonic day 9.5 and is gradually reduced until Pax-8a is the predominant transcript in the 12.5-day placenta. In the embryo, however, the synthesis of mRNAs b to d is initially low and then increases relative to that of Pax-8a. Hence, alternative splicing of Pax-8 gene transcripts not only generates six different Pax-8 variants but is also temporally and spatially regulated during early mouse development.","authors":"Kozmik, Z., Kurzbauer, R., D\u00f6rfler, P., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Mol Cell Biol","volume":"13","issue":"10","page":"6024-35","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1993-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8428595","title":"Synergistic action of Drosophila cyclins A and B during the G2-M transition.","abstract":"A variety of different cyclin proteins have been identified in higher eukaryotes. In the case of cyclin B, functional analyses have clearly demonstrated an important role in the control of entry into mitosis. The function of cyclin A is more complex. It appears to function in the control of both S- and M-phase. The results of our genetic analyses in Drosophila demonstrate that cyclin A has a mitotic function and that it acts synergistically with cyclin B during the G2-M transition. In double mutant embryos that express neither cyclin A nor cyclin B zygotically, cell cycle progression is blocked just before the exhaustion of the maternally contributed cyclin A and B stores. BrdU-labeling experiments indicate that cell cycle progression is blocked in G2 before entry into the fifteenth round of mitosis. Expression of either cyclin A or B from heat-inducible transgenes is sufficient to overcome this cell cycle block. This block is also not observed in single mutant embryos deficient for either cyclin A or B. In cyclin B deficient embryos, cell cycle progression continues after the apparent exhaustion of the maternal contribution, suggesting that cyclin B might not be essential for mitosis. However, mitotic spindles are clearly abnormal and progression through mitosis is delayed in these cyclin B deficient embryos.","authors":"Knoblich, JA., Lehner, CF.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"EMBO J","volume":"12","issue":"1","page":"65-74","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1993-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20833046","title":"Dicing with dogma: de-branching the lamellipodium.","abstract":"The primary event in the movement of a migrating eukaryotic cell is the extension of cytoplasmic sheets termed lamellipodia composed of networks of actin filaments. Lamellipodia networks are thought to arise through the branching of new filaments from the sides of old filaments, producing a dendritic array. Recent studies by electron tomography have revealed the three dimensional organization of lamellipodia and show, contrary to previous evidence, that actin filaments do not form dendritic arrays in vivo. These findings signal a reconsideration of the structural basis of protrusion and about the roles of the different actin nucleating and elongating complexes involved in the process.","authors":"Small, JV.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Trends Cell Biol","volume":"20","issue":"11","page":"628-33","pdf":null,"JrId":"21041","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8449406","title":"SWI5 instability may be necessary but is not sufficient for asymmetric HO expression in yeast.","abstract":"Homothallic haploid yeast cells divide to produce a mother cell that switches mating type and a daughter cell that does not. This pattern is the result of HO endonuclease transcription exclusively in mother cells, and there only transiently in late G1 as cells undergo Start. SWI5 encodes an HO transcription factor that is expressed during the S, G2, and M phases of the cell cycle. The lack of synthesis of SWI5 during G1 is essential to prevent HO transcription in daughter cells. Thus, HO must be activated by SWI5 protein synthesized in the previous cell cycle if it is to be properly regulated. SWI5 is inherited by both mother and daughter cells, and we show here that most of it is rapidly degraded during early G1. More stable mutant SWI5 proteins cause daughter cells to switch mating type, suggesting that SWI5 destruction is necessary to prevent HO expression in daughters. We show further that mother cells can still express HO when stimulated to undergo Start after arrest in early G1 for several hours. We propose that a small fraction of the SWI5 protein inherited by mother cells is extremely stable and that the crucial difference between mothers and daughters with regard to HO transcription is their differential ability to sequester SWI5 in a stable form, possibly as a component of transcription complexes on the HO promoter.","authors":"Tebb, G., Moll, T., Dowzer, C., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Genes Dev","volume":"7","issue":"3","page":"517-28","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1993-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8446579","title":"A selective transcriptional induction system for mammalian cells based on Gal4-estrogen receptor fusion proteins.","abstract":"Most mammalian cells neither express any Gal4-like activity nor endogenous estrogen receptor, thus rendering estrogen an inert signal for them. For these two reasons we have developed a selective induction system based on the estrogen-regulable transcription factor Gal-ER. Gal-ER consists of the DNA-binding domain of the yeast Gal4 protein fused to the hormone-binding domain of the human estrogen receptor and hence should exclusively regulate a transfected gene under the control of a Gal4-responsive promoter in mammalian cells. Two major improvements of this induction system were made. First, a synthetic Gal4-responsive promoter was constructed which consisted of four Gal4-binding sites, an inverted CCAAT element, a TATA box, and the adenovirus major late initiation region. This promoter showed extremely low basal activity in the absence and high inducibility in the presence of ligand-activated Gal-ER. Second, the transcription factor Gal-ER was rendered more potent and less susceptible to cell type-specific variation by fusing the strong activating domain of the herpesvirus protein VP16 onto its C terminus. In response to estrogen, Gal-ER-VP16 induced the Gal4-responsive promoter at least 100-fold in transiently transfected NIH 3T3 and P19 cells. Rat fibroblast cell lines expressing integrated Gal-ER and Gal4-responsive fos genes were transformed in a strictly estrogen-dependent manner. The exogenous fos gene was rapidly induced to maximal levels within 1-2 hr of estrogen addition. Elevated Fos activity in turn stimulated transcription of the endogenous fra-1 gene. These data demonstrate the utility of the Gal-ER induction system as a powerful genetic switch for regulating heterologous genes and, in particular, for identifying Fos targets in mammalian cells.","authors":"Braselmann, S., Graninger, P., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Proc Natl Acad Sci U S A","volume":"90","issue":"5","page":"1657-61","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1993-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8391932","title":"Anaphase is initiated by proteolysis rather than by the inactivation of maturation-promoting factor.","abstract":"We have used frog egg extracts that assemble mitotic spindles to identify the event that triggers sister chromatid separation. Adding a nondegradable form of cyclin B prevents maturation-promoting factor (MPF) inactivation but does not block sister chromatid separation, showing that MPF inactivation is not needed to initiate anaphase. In contrast, adding an N-terminal fragment of cyclin, which acts as a specific competitor for cyclin degradation, produces a dose-dependent delay in MPF inactivation and sister chromatid separation. Methylated ubiquitin, which inhibits ubiquitin-mediated proteolysis, also delays sister chromatid separation, suggesting that ubiquitin-mediated proteolysis is necessary to initiate anaphase. The N-terminal cyclin fragment inhibits chromosome separation even in extracts that contain only nondegradable forms of cyclin, suggesting that proteins other than the known cyclins must be degraded to dissolve the linkage between sister chromatids.","authors":"Holloway, SL., Glotzer, M., King, RW., Murray, AW.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Cell","volume":"73","issue":"7","page":"1393-402","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1993-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9185869","title":"Generation of effective cancer vaccines genetically engineered to secrete cytokines using adenovirus-enhanced transferrinfection (AVET).","abstract":"Cancer vaccines are based on the concept that tumors express novel antigens and thus differ from their normal tissue counterparts. Such putative tumor-specific antigens should be recognizable by the immune system. However, malignant cells are of self origin and only poorly immunogenic, which limits their capability to induce an anticancer immune response. To overcome this problem, tumor cells have been isolated, genetically engineered to secrete cytokine gene products and administered as cancer vaccines. We used adenovirus-enhanced transferrinfection (AVET), which allows high-level transient transgene expression, to introduce cytokine gene expression vectors into murine melanoma cells. The efficiency of AVET makes laborious selection and cloning procedures obsolete. We administered such modified tumor cells as cancer vaccines to syngeneic animals and investigated their impact on the induction of anticancer immunity. We found that IL-2 or GM-CSF gene-transfected murine melanoma cells are highly effective vaccines. Both of these cytokine-secreting vaccines cured 80% of animals which bore a subcutaneous micrometastasis prior to treatment, and induced potent antitumor immunity. The generation of antitumor immunity by these cytokine-secreting vaccines requires three different steps: (1) tumor antigen uptake and processing by antigen-presenting cells (APCs) at the site of vaccination; (2) migration of these APCs into the regional lymph nodes where T-cell priming occurs; (3) recirculation of specific, activated T-cells that recognize distinct tumor load and initiate its elimination. Extending our previously reported studies, we have now comprehensively analysed the requirements for effective antitumor vaccination in animals. This may also become the basis for treatment of human cancer patients.","authors":"Schmidt, W., Maass, G., Buschle, M., Schweighoffer, T., Berger, M., Herbst, E., Schilcher, F., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Gene","volume":"190","issue":"1","page":"211-6","pdf":null,"JrId":"3886","fulltextlink":null,"preprintlink":null,"articledate":"1997-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8406005","title":"The immunoglobulin mu enhancer core establishes local factor access in nuclear chromatin independent of transcriptional stimulation.","abstract":"Factor access in chromatin has been proposed to be facilitated by transcriptional enhancers. With the aim of uncoupling factor access from transcriptional stimulation by protein-protein contacts, we analyzed the potential of enhancer fragments to confer accessibility upon a linked promoter for prokaryotic T7 RNA polymerase. Access to the T7 promoter in pre-B cells from transgenic mice was examined by transcribing chromatin of isolated nuclei with T7 RNA polymerase. A 95-bp immunoglobulin mu enhancer core element was necessary and sufficient to confer accessibility upon the T7 promoter independent of its chromosomal position. This enhancer-dependent factor access could be uncoupled from an active transcriptional state of the transgene and was not accompanied by the formation of pronounced DNase I hypersensitive sites. Additional mu enhancer sequences comprising previously identified matrix attachment regions and a cryptic promoter were required to induce DNase I hypersensitivity. Together, these data provide evidence that the 95-bp mu enhancer core can establish localized factor access in nuclear chromatin independent of detectable transcription by endogenous polymerases and suggest that multiple steps are involved in the alteration of chromatin structure.","authors":"Jenuwein, T., Forrester, WC., Qiu, RG., Grosschedl, R.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Genes Dev","volume":"7","issue":"10","page":"2016-32","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1993-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8408203","title":"Rab8, a small GTPase involved in vesicular traffic between the TGN and the basolateral plasma membrane.","abstract":"Small GTP-binding proteins of the rab family have been implicated as regulators of membrane traffic along the biosynthetic and endocytic pathways in eukaryotic cells. We have investigated the localization and function of rab8, closely related to the yeast YPT1\/SEC4 gene products. Confocal immunofluorescence microscopy and immunoelectron microscopy on filter-grown MDCK cells demonstrated that, rab8 was localized to the Golgi region, vesicular structures, and to the basolateral plasma membrane. Two-dimensional gel electrophoresis showed that rab8p was highly enriched in immuno-isolated basolateral vesicles carrying vesicular stomatitis virus-glycoprotein (VSV-G) but was absent from vesicles transporting the hemagglutinin protein (HA) of influenza virus to the apical cell surface. Using a cytosol dependent in vitro transport assay in permeabilized MDCK cells we studied the functional role of rab8 in biosynthetic membrane traffic. Transport of VSV-G from the TGN to the basolateral plasma membrane was found to be significantly inhibited by a peptide derived from the hypervariable COOH-terminal region of rab8, while transport of the influenza HA from the TGN to the apical surface and ER to Golgi transport were unaffected. We conclude that rab8 plays a role in membrane traffic from the TGN to the basolateral plasma membrane in MDCK cells.","authors":"Huber, LA., Pimplikar, S., Parton, RG., Virta, H., Zerial, M., Simons, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Cell Biol","volume":"123","issue":"1","page":"35-45","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1993-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20702731","title":"Conditional deletion of histone deacetylase 1 in T cells leads to enhanced airway inflammation and increased Th2 cytokine production.","abstract":"Chromatin modifications, such as reversible histone acetylation, play a key role in the regulation of T cell development and function. However, the role of individual histone deacetylases (HDACs) in T cells is less well understood. In this article, we show by conditional gene targeting that T cell-specific loss of HDAC1 led to an increased inflammatory response in an in vivo allergic airway inflammation model. Mice with HDAC1-deficient T cells displayed an increase in all critical parameters in this Th2-type asthma model, such as eosinophil recruitment into the lung, mucus hypersecretion, parenchymal lung inflammation, and enhanced airway resistance. This correlated with enhanced Th2 cytokine production in HDAC1-deficient T cells isolated from diseased mice. In vitro-polarized HDAC1-deficient Th2 cells showed a similar enhancement of IL-4 expression, which was evident already at day 3 of Th2 differentiation cultures and restricted to T cell subsets that underwent several rounds of cell divisions. HDAC1 was recruited to the Il4 gene locus in ex vivo isolated nonstimulated CD4(+) T cells, indicating a direct control of the Il4 gene locus. Our data provide genetic evidence that HDAC1 is an essential HDAC that controls the magnitude of an inflammatory response by modulating cytokine expression in effector T cells.","authors":"Grausenburger, R., Bilic, I., Boucheron, N., Zupkovitz, G., El-Housseiny, L., Tschismarov, R., Zhang, Y., Rembold, M., Gaisberger, M., Hartl, A., Epstein, MM., Matthias, P., Seiser, C., Ellmeier, W.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Immunol","volume":"185","issue":"6","page":"3489-97","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8372350","title":"A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase.","abstract":"In budding yeast genes that encode G1 cyclins and proteins involved in DNA synthesis are transcriptionally activated in late G1. A transcription factor, called SBF, is composed of Swi4 and Swi6 proteins and activates transcription of G1 cyclin genes. A different, but related, complex called MBF binds to MCB elements (Mlu I cell cycle box) found in the promoter of most DNA synthesis genes. MBF contains Swi6 and a 120-kilodalton protein (p120). MBF was purified and the gene encoding p120 (termed MBP1) was cloned. A deletion of MBP1 was not lethal but led to deregulated expression of DNA synthesis genes, indicating a direct regulatory role for MBF in MCB-driven transcription. Mbp1 is related to Swi4. Strains deleted for both MBP1 and SWI4 were inviable, demonstrating that transcriptional activation by MBF and SBF has an important role in the transition from G1 to S phase.","authors":"Koch, C., Moll, T., Neuberg, M., Ahorn, H., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Science","volume":"261","issue":"5128","page":"1551-7","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1993-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8351016","title":"Titin antibodies in myasthenia gravis: identification of a major immunogenic region of titin.","abstract":"Approximately 15% of patients with myasthenia gravis (MG) have thymus neoplasia. These MG with thymoma (MGT) patients show autoantibodies to striated muscle as well as autoantibodies to acetylcholine receptor. To characterize these thymoma-associated muscle antigens, we cloned a number of immunopositive cDNAs by immunoscreening muscle cDNA libraries with sera from MGT patients. Analysis of the isolated cDNAs show that all share a common sequence encoding a distinct region of the titin gene. We expressed this main immunogenic region (MIR) of titin in Escherichia coli, and determined autoantibody serum titers directed against the obtained recombinant antigen in a variety of patients. We could detect titin MIR autoantibodies in 97% of sera from MGT patients but not in control sera from healthy blood donors. Therefore, expressed titin from the MIR of the molecule is a sensitive marker antigen for evaluating the presence of thymoma in MG.","authors":"Gautel, M., Lakey, A., Barlow, DP., Holmes, Z., Scales, S., Leonard, K., Labeit, S., Mygland, A., Gilhus, NE., Aarli, JA.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Neurology","volume":"43","issue":"8","page":"1581-5","pdf":null,"JrId":"6069","fulltextlink":null,"preprintlink":null,"articledate":"1993-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8349690","title":"Rab GDP dissociation inhibitor as a general regulator for the membrane association of rab proteins.","abstract":"Rab proteins comprise a family of small GTPases that serve a regulatory role in membrane traffic. These proteins are in part cytosolic and in part associated with the membranes of specific exocytic and endocytic organelles. Smg p25A\/rab3A GDI, a cytosolic protein which inhibits the dissociation of GDP from smg p25A\/rab3A, Sec4p, and rab11, has also been found to prevent association of rab3A with the membrane. In this study, we have used Madin-Darby canine kidney cells permeabilized with the bacterial toxin streptolysin O to test the general activity of rab3A GDI in modulating the membrane association of various small GTP-binding proteins. Rab3A GDP dissociation inhibitor (GDI) removed from the membrane all rab proteins we have tested and inhibited the membrane binding of in vitro translated rab proteins. However, rab3A GDI had a limited effect on the membrane association of a mutant rab5 protein which contained a farnesylated cysteine motif. Finally, we found that, although rab3A GDI resides primarily in the cytosol, it is also associated with compartments of the exocytic and endocytic pathways. Since rab3A GDI can modulate the membrane association of various rab proteins, we propose to rename it rab GDI.","authors":"Ullrich, O., Stenmark, H., Alexandrov, K., Huber, LA., Kaibuchi, K., Sasaki, T., Takai, Y., Zerial, M.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Biol Chem","volume":"268","issue":"24","page":"18143-50","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1993-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8350651","title":"Estimation of reference intervals from a SENIEUR protocol compatible aged population for immunogerontological studies.","abstract":"Because many laboratory values change with age, the study of healthy aging as well as diagnosis of disease in geriatric patients requires specific age-corrected reference intervals. We have established such reference intervals for a healthy population aged 65-74 years by selection of a sample group applying the clinical criteria of the SENIEUR protocol and we have compared them with those of a young control group (20-33 years) fulfilling the same criteria. Significant or minor elevations were seen, e.g. for plasma concentrations of fasting glucose, urea, total and LDL-cholesterol, triglycerides, gamma-glutamyl-transferase, alkaline phosphatase, erythrocyte sedimentation rate and serum neopterin levels. These reference intervals can be used for selecting a SENIEUR compatible population aged between 65 and 74 years. Additionally, plasma lipid parameters (cholesterol, triglycerides) are proposed to be included in the SENIEUR protocol.","authors":"Stulnig, T., Mair, A., Jarosch, E., Schober, M., Sch\u00f6nitzer, D., Wick, G., Huber, LA.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Mech Ageing Dev","volume":"68","issue":"1-3","page":"105-15","pdf":null,"JrId":"5571","fulltextlink":null,"preprintlink":null,"articledate":"1993-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8364198","title":"Rescue of W-associated mast cell defects in W\/Wv bone marrow cells by ectopic expression of normal and mutant epidermal growth factor receptors.","abstract":"The normal human epidermal growth factor receptor (EGF-R) (HERc), a chimeric EGF-R\/v-erbB (HERerbB) receptor, and the ligand-independent oncogenic EGF-R variant (v-erbB) were used to correct the mast cell defects in W\/Wv bone marrow (BM) cells. In culture, all three receptor molecules transduced functional mitogenic signals in infected interleukin-3 (IL-3)-dependent bone marrow-derived mast cells (BMMCs) and enabled their differentiation into safranin-positive mast cells resembling connective tissue-type mast cells (CTMCs). Furthermore, expression of these receptors restored the capacity of W\/Wv BMMCs to colonize the peritoneal cavity of mast cell-deficient W\/Wv mice where they differentiated to safranin-positive cells with similar frequencies as wild-type BMMCs. These experiments show that expression of normal and mutant EGF-Rs in W\/Wv BM cells is able to complement the function of the c-kit-encoded Steel factor receptor (SLF-R) in mast cell development. We conclude that signal transduction by normal and mutant EGF-Rs in murine hematopoietic cells apparently involves components also used by the SLF-R, which suggests that these receptors use overlapping pathways for signal transduction.","authors":"von R\u00fcden, T., Stingl, L., Ullrich, A., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Blood","volume":"82","issue":"5","page":"1463-70","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"1993-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8358828","title":"The glycerol kinase (GUT1) gene of Saccharomyces cerevisiae: cloning and characterization.","abstract":"The GUT1 gene of Saccharomyces cerevisiae, encoding glycerol kinase, was cloned and sequenced. The cloned genomic DNA fragment contains an open reading frame potentially coding for a protein of 709 amino acids with homology to bacterial glycerol kinases (40.8% identity over 502 amino acids, and 42.1% identity over 496 amino acids, in comparison to the smaller E. coli and B. subtilis enzymes). Disruption of GUT1 showed that the gene is required for growth on glycerol, but not on glucose or ethanol media. No glycerol kinase activity was detected in the disruption mutant. According to enzyme activity and transcript analysis, synthesis of glycerol kinase is repressed by glucose, and derepression is ADR1-dependent.","authors":"Pavlik, P., Simon, M., Schuster, T., Ruis, H.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Curr Genet","volume":"24","issue":"1-2","page":"21-5","pdf":null,"JrId":"2877","fulltextlink":null,"preprintlink":null,"articledate":"1993-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11967568","title":"The crystal structure of the mouse apoptosis-inducing factor AIF.","abstract":"Mitochondria play a key role in apoptosis due to their capacity to release potentially lethal proteins. One of these latent death factors is cytochrome c, which can stimulate the proteolytic activation of caspase zymogens. Another important protein is apoptosis-inducing factor (AIF), a flavoprotein that can stimulate a caspase-independent cell-death pathway required for early embryonic morphogenesis. Here, we report the crystal structure of mouse AIF at 2.0 A. Its active site structure and redox properties suggest that AIF functions as an electron transferase with a mechanism similar to that of the bacterial ferredoxin reductases, its closest evolutionary homologs. However, AIF structurally differs from these proteins in some essential features, including a long insertion in a C-terminal beta-hairpin loop, which may be related to its apoptogenic functions.","authors":"Mat\u00e9, MJ., Ortiz-Lombard\u00eda, M., Boitel, B., Haouz, A., Tello, D., Susin, SA., Penninger, J., Kroemer, G., Alzari, PM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nat Struct Biol","volume":"9","issue":"6","page":"442-6","pdf":null,"JrId":"8610","fulltextlink":null,"preprintlink":null,"articledate":"2002-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8319908","title":"CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae.","abstract":"The functions of the Cdc28 protein kinase in DNA replication and mitosis in Saccharomyces cerevisiae are thought to be determined by the type of cyclin subunit with which it is associated. G1-specific cyclins encoded by CLN1, CLN2, and CLN3 are required for entry into the cell cycle (Start) and thereby for S phase, whereas G2-specific B-type cyclins encoded by CLB1, CLB2, CLB3, and CLB4 are required for mitosis. We describe a new family of B-type cyclin genes, CLB5 and CLB6, whose transcripts appear in late G1 along with those of CLN1, CLN2, and many genes required for DNA replication. Deletion of CLB6 has little or no effect, but deletion of CLB5 greatly extends S phase, and deleting both genes prevents the timely initiation of DNA replication. Transcription of CLB5 and CLB6 is normally dependent on Cln activity, but ectopic CLB5 expression allows cells to proliferate in the absence of Cln cyclins. Thus, the kinase activity associated with Clb5\/6 and not with Cln cyclins may be responsible for S-phase entry. Clb5 also has a function, along with Clb3 and Clb4, in the formation of mitotic spindles. Our observation that CLB5 is involved in the initiation of both S phase and mitosis suggests that a single primordial B-type cyclin might have been sufficient for regulating the cell cycle of the common ancestor of many, if not all, eukaryotes.","authors":"Schwob, E., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Genes Dev","volume":"7","issue":"7A","page":"1160-75","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1993-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11477548","title":"Overexpression of Pax5 is not sufficient for neoplastic transformation of mouse neuroectoderm.","abstract":"The developmental control genes of the Pax family are essential for brain development. Several Pax genes are also involved in chromosomal translocations causing malignancies in humans, and Pax5 expression is deregulated in medulloblastomas. We have investigated whether Pax5 can induce tumors in the developing mouse brain. Primary mouse embryonic neuroectodermal cells were retrovirally transduced with mouse Pax5 and transplanted into the brain of syngeneic host mice. No tumors developed in 36 transplants after one year, and there were no alterations in the differentiation pattern of the neural transplants. We then generated transgenic mice expressing human Pax5 under control of the Engrailed-2 promoter, which is expressed in the cerebellar external granule cell layer and in medulloblastomas. Sustained expression was achieved in the cerebellum of transgenic animals throughout lifetime. Expression levels were similar to those observed in human medulloblastomas. Again, cerebellar morphogenesis was undisturbed, and no tumors arose. These results strongly argue against a dominant transforming activity of PAX5 in NEC and in cerebellar granule cell precursors of mice, and underline the restricted tissue-specificity of PAX5 related oncogenesis.","authors":"Steinbach, JP., Kozmik, Z., Pfeffer, P., Aguzzi, A.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Int J Cancer","volume":"93","issue":"4","page":"459-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11472838","title":"Tissue specific regulation of VEGF expression during bone development requires Cbfa1\/Runx2.","abstract":"Vascular endothelial growth factor (VEGF) is a critical regulator of angiogenesis during development, but little is known about the factors that control its expression. We provide the first example of tissue specific loss of VEGF expression as a result of targeting a single gene, Cbfa1\/Runx2. During endochondral bone formation, invasion of blood vessels into cartilage is associated with upregulation of VEGF in hypertrophic chondrocytes and increased expression of VEGF receptors in the perichondrium. This upregulation is lacking in Cbfa1 deficient mice, and cartilage angiogenesis does not occur. Finally, over-expression of Cbfa1 in fibroblasts induces an increase in their VEGF mRNA level and protein production by stimulating VEGF transcription. The results demonstrate that Cbfa1 is a necessary component of a tissue specific genetic program that regulates VEGF during endochondral bone formation.","authors":"Zelzer, E., Glotzer, DJ., Hartmann, C., Thomas, D., Fukai, N., Soker, S., Olsen, BR.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Mech Dev","volume":"106","issue":"1-2","page":"97-106","pdf":null,"JrId":"1825","fulltextlink":null,"preprintlink":null,"articledate":"2001-10-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11961557","title":"RANKL maintains bone homeostasis through c-Fos-dependent induction of interferon-beta.","abstract":"Osteoclasts are cells of monocyte\/macrophage origin that erode bone matrix: regulation of their differentiation is central to the understanding of the pathogenesis and treatment of bone diseases such as osteoporosis. Signalling by RANKL (receptor activator of NF-kappaB ligand), also known as Tnfsf11, is essential for the induction of osteoclast differentiation, and it must be strictly regulated to maintain bone homeostasis. But it is not known whether RANKL signalling to the cell interior is linked to any regulatory mechanisms. Here we show that RANKL induces the interferon-beta (IFN-beta) gene in osteoclast precursor cells, and that IFN-beta inhibits the differentiation by interfering with the RANKL-induced expression of c-Fos, an essential transcription factor for the formation of osteoclasts. This IFN-beta gene induction mechanism is distinct from that induced by virus, and is dependent on c-Fos itself. Thus an autoregulatory mechanism operates-the RANKL-induced c-Fos induces its own inhibitor. The importance of this regulatory mechanism for bone homeostasis is emphasized by the observation that mice deficient in IFN-beta signalling exhibit severe osteopenia (loss of bone mass) accompanied by enhanced osteoclastogenesis. Our study places the IFN-beta system in a new context, and may offer a molecular basis for the treatment of bone diseases.","authors":"Takayanagi, H., Kim, S., Matsuo, K., Suzuki, H., Suzuki, T., Sato, K., Yokochi, T., Oda, H., Nakamura, K., Ida, N., Wagner, EF., Taniguchi, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nature","volume":"416","issue":"6882","page":"744-9","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8276260","title":"Somatic gene therapy for cancer: the utility of transferrinfection in generating 'tumor vaccines'.","abstract":"The last few years have seen the development of a branch of somatic gene therapy which aims at strengthening the immune surveillance of the body, leading to eradication of disseminated cancer tumor cells and occult micrometastases after surgical removal of the primary tumor. Such a tumor vaccination protocol calls for cultivation of the primary tumor tissue and the insertion of one of three types of genes into the isolated cultured tumor cells followed by irradiation of the transfected or transduced cells to render them incapable of further proliferation. The cells so treated constitute the 'tumor vaccine'. A review of the literature suggests that for mouse models, in the initial period after inoculation, rejection of the tumor cells is usually effected by non-T-cell immunity, whereas the long-term systemic immune response is based on cytotoxic T-cells. High expression of the gene inserted into the tumor cells may be critical for the success of the vaccination procedure. Examples are given which indicate that transferrinfection, a procedure to introduce genes by adenovirus-augmented receptor-mediated endocytosis, meets some important prerequisites for successful application of this type of gene therapy.","authors":"Zatloukal, K., Schmidt, W., Cotten, M., Wagner, E., Stingl, G., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Gene","volume":"135","issue":"1-2","page":"199-207","pdf":null,"JrId":"3886","fulltextlink":null,"preprintlink":null,"articledate":"1994-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8268678","title":"Encyclopedia of the mouse genome III. October 1993. Mouse chromosome 17.","abstract":null,"authors":"Himmelbauer, H., Artzt, K., Barlow, D., Fischer-Lindahl, K., Lyon, M., Klein, J., Silver, LM.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Mamm Genome","volume":"4 Spec No","issue":null,"page":"S230-52","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"1994-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10385629","title":"Cdc53\/cullin and the essential Hrt1 RING-H2 subunit of SCF define a ubiquitin ligase module that activates the E2 enzyme Cdc34.","abstract":"SCFCdc4 (Skp1, Cdc53\/cullin, F-box protein) defines a family of modular ubiquitin ligases (E3s) that regulate diverse processes including cell cycle, immune response, and development. Mass spectrometric analysis of proteins copurifying with Cdc53 identified the RING-H2 finger protein Hrt1 as a subunit of SCF. Hrt1 shows striking similarity to the Apc11 subunit of anaphase-promoting complex. Conditional inactivation of hrt1(ts) results in stabilization of the SCFCdc4 substrates Sic1 and Cln2 and cell cycle arrest at G1\/S. Hrt1 assembles into recombinant SCF complexes and individually binds Cdc4, Cdc53 and Cdc34, but not Skp1. Hrt1 stimulates the E3 activity of recombinant SCF potently and enables the reconstitution of Cln2 ubiquitination by recombinant SCFGrr1. Surprisingly, SCF and the Cdc53\/Hrt1 subcomplex activate autoubiquitination of Cdc34 E2 enzyme by a mechanism that does not appear to require a reactive thiol. The highly conserved human HRT1 complements the lethality of hrt1Delta, and human HRT2 binds CUL-1. We conclude that Cdc53\/Hrt1 comprise a highly conserved module that serves as the functional core of a broad variety of heteromeric ubiquitin ligases.","authors":"Seol, JH., Feldman, RM., Zachariae, W., Shevchenko, A., Correll, CC., Lyapina, S., Chi, Y., Galova, M., Claypool, J., Sandmeyer, S., Nasmyth, K., Deshaies, RJ., Shevchenko, A., Deshaies, RJ.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Genes Dev","volume":"13","issue":"12","page":"1614-26","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8262070","title":"Yeast G1 cyclins CLN1 and CLN2 and a GAP-like protein have a role in bud formation.","abstract":"Cyclin-dependent protein kinases have a central role in cell cycle regulation. In Saccharomyces cerevisiae, Cdc28 kinase and the G1 cyclins Cln1, 2 and 3 are required for DNA replication, duplication of the spindle pole body and bud emergence. These three independent processes occur simultaneously in late G1 when the cells reach a critical size, an event known as Start. At least one of the three Clns is necessary for Start. Cln3 is believed to activate Cln1 and Cln2, which can then stimulate their own accumulation by means of a positive feedback loop. They (or Cln3) also activate another pair of cyclins, Clb5 and 6, involved in initiating S phase. Little is known about the role of Clns in spindle pole body duplication and budding. We report here the isolation of a gene (CLA2\/BUD2\/ERC25) that codes for a homologue of mammalian Ras-associated GTPase-activating proteins (GAPs) and is necessary for budding only in cln1 cln2 cells. This suggests that Cln1 and Cln2 may have a direct role in bud formation.","authors":"Cvrckov\u00e1, F., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"EMBO J","volume":"12","issue":"13","page":"5277-86","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1994-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8224244","title":"Rab11, a small GTPase associated with both constitutive and regulated secretory pathways in PC12 cells.","abstract":"A specific polyclonal antibody was used to investigate the subcellular distribution of the small GTPase, rab11p, in the neuroendocrine cell line, PC12. We took advantage of a previously described pulse-chase protocol based on sulfation to examine the distribution of rab11 along the secretory pathway. Using the rab11 antiserum, but not serum depleted of rab11 antibodies, we were able to specifically immunoisolate markers of the constitutive and the regulated secretory pathway in the trans-Golgi network (TGN) as well as after their exit from this compartment (constitutive secretory vesicles, immature, and mature secretory granules). We therefore conclude that rab11p is associated with the TGN and with TGN-derived vesicles of both the constitutive and the regulated secretory pathway in PC12 cells.","authors":"Urb\u00e9, S., Huber, LA., Zerial, M., Tooze, SA., Parton, RG.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"FEBS Lett","volume":"334","issue":"2","page":"175-82","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"1993-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8202466","title":"An improved pair potential to recognize native protein folds.","abstract":"We present a novel method to improve a simple pair potential of mean force, derived from experimentally determined protein structures, in such a way that it recognizes native protein folds with high reliability. This improvement is based on the use of mutation data matrices to overcome difficulties arising from the poor statistics of small sample sizes. A set of 167 protein chains taken from the Brookhaven Protein Structure Data Base, selected from high-resolution structures and avoiding homologous proteins, is used for generation of the potential set. The potential describes interresidue pair energies depending on distance and sequential separation, and is calculated using the Boltzmann equation. Its performance is evaluated by jackknife tests that try to identify the native fold for a given sequence among a large number of possible threadings on all structures in the set without allowing for gaps. Up to 94% of the protein chains are correctly assigned to their native folds, so that all proper single-chain domains are recognized.","authors":"Bauer, A., Beyer, A.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Proteins","volume":"18","issue":"3","page":"254-61","pdf":null,"JrId":"6646","fulltextlink":null,"preprintlink":null,"articledate":"1994-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11439328","title":"Leukemic transformation of normal murine erythroid progenitors: v- and c-ErbB act through signaling pathways activated by the EpoR and c-Kit in stress erythropoiesis.","abstract":"Primary erythroid progenitors can be expanded by the synergistic action of erythropoietin (Epo), stem cell factor (SCF) and glucocorticoids. While Epo is required for erythropoiesis in general, glucocorticoids and SCF mainly contribute to stress erythropoiesis in hypoxic mice. This ability of normal erythroid progenitors to undergo expansion under stress conditions is targeted by the avian erythroblastosis virus (AEV), harboring the oncogenes v-ErbB and v-ErbA. We investigated the signaling pathways required for progenitor expansion under stress conditions and in leukemic transformation. Immortal strains of erythroid progenitors, able to undergo normal, terminal differentiation under appropriate conditions, were established from fetal livers of p53-\/- mice. Expression and activation of the EGF-receptor (HER-1\/c-ErbB) or its mutated oncogenic version (v-ErbB) in these cells abrogated the requirement for Epo and SCF in expansion of these progenitors and blocked terminal differentiation. Upon inhibition of ErbB function, differentiation into erythrocytes occurred. Signal transducing molecules important for renewal induction, i.e. Stat5- and phosphoinositide 3-kinase (PI3K), are utilized by both EpoR\/c-Kit and v\/c-ErbB. However, while v-ErbB transformed cells and normal progenitors depended on PI3K signaling for renewal, c-ErbB also induces progenitor expansion by PI3K-independent mechanisms.","authors":"von Lindern, M., Deiner, EM., Dolznig, H., Parren-Van Amelsvoort, M., Hayman, MJ., Mullner, EW., Beug, H.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Oncogene","volume":"20","issue":"28","page":"3651-64","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11433297","title":"N-CAM modulates tumour-cell adhesion to matrix by inducing FGF-receptor signalling.","abstract":"Loss of expression of neural cell-adhesion molecule (N-CAM) is implicated in the progression of tumour metastasis. Here we show that N-CAM modulates neurite outgrowth and matrix adhesion of beta-cells from pancreatic tumours by assembling a fibroblast-growth-factor receptor-4 (FGFR-4) signalling complex, which consists of N-cadherin, FGFR-4, phospholipase C gamma (PLC-gamma), the adaptor protein FRS2, pp60(c-src), cortactin and growth-associated protein-43 (GAP-43). Dominant-negative FGFR-4, inhibitors of FGFR signalling and anti-beta(1)-integrin antibodies repress matrix adhesion induced by N-CAM. FGF ligands can replace N-CAM in promoting matrix adhesion but not neurite outgrowth. The results indicate that N-CAM stimulates beta1-integrin-mediated cell-matrix adhesion by activating FGFR signalling. This is a potential mechanism for preventing the dissemination of metastatic tumour cells.","authors":"Cavallaro, U., Niedermeyer, J., Fuxa, M., Christofori, G.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Cell Biol","volume":"3","issue":"7","page":"650-7","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8193542","title":"Genetics of signal transduction in invertebrates.","abstract":"Receptor tyrosine kinases regulate a number of different cell fate decisions during invertebrate development. Genetic analysis of the signal transduction pathways activated by these kinases suggests that they converge upon a common pathway involving Ras and a cascade of cytoplasmic kinases, diverging again in the nucleus with the regulation of specific transcription factors.","authors":"Dickson, B., Hafen, E.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Curr Opin Genet Dev","volume":"4","issue":"1","page":"64-70","pdf":null,"JrId":"2199","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9141636","title":"Permeabilization of mammalian cells to proteins: poliovirus 2A(pro) as a probe to analyze entry of proteins into cells.","abstract":"Two hybrid protein molecules containing the poliovirus protease 2A (MBP-2A(pro)) (maltose-binding protein-2A(pro) and MBP-Pseudomonas exotoxin A-2A(pro)) have been constructed and purified. Both hybrid proteins efficiently cleave the translation initiation factor eIF-4G when they are co-internalized into cells with adenovirus particles. Almost no intact eIF-4G can be detected in cells incubated with these proteins following this method. Reovirus infectious subviral particles also promote the delivery of MBP-2A(pro) into cells, although less efficiently than adenovirus particles. None of the other methods employed to permeabilize cells to MBP-2A(pro) achieves the degree of eIF-4G cleavage observed with adenovirus particles. By comparison about 30% of cells electroporated with MBP-2A(pro) still contain intact eIF-4G. More drastic electroporation conditions lead to a significant decrease of cell survival. Osmotic lysis of pinocytic vesicles resulted in 30% of the eIF-4G being cleaved in cells treated in suspension. Delivery of MBP-2A(pro) by pH-sensitive liposomes leads to poor hydrolysis of eIF-4G. Taken together our results indicate that permeabilization of cells with adenovirus particles is the most efficient method for introducing MBP-2A(pro) into cells.","authors":"Novoa, I., Benavente, J., Cotten, M., Carrasco, L.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Exp Cell Res","volume":"232","issue":"1","page":"186-90","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8186386","title":"Molecular dissection of multi-stage tumorigenesis in transgenic mice.","abstract":"The epidemiology of cancer in humans and in animal models suggests that multiple genetic events are responsible for the genesis of malignant tumors. During development of many tumors, distinctive changes can be recognized: normal unaffected tissue, hyperplasia with a high incidence of proliferating cells, induction of tumor angiogenesis with the new growth of capillaries, solid tumors (neoplasia), and finally metastasis. The molecular analysis of tumorigenesis is often hampered by the unavailability of tissue specimens from the multiple stages. For this reason, the genetic reproducibility and the accessibility of tissue specimens have made transgenic mice a valuable tool to study the molecular events that are involved in the stepwise progression to the tumor phenotype. Many transgenic mouse models of human cancer, for example mammary epithelia, skin and liver, exhibit similar patterns of stepwise tumor development. In this review we discuss possible strategies to investigate the molecular events that are involved in multi-stage tumor development. Then we present in some detail the molecular dissection of tumor development in two transgenic models of fibrosarcomas of the skin, and a third transgenic mouse line that develops tumors of the beta cells in the islets of Langerhans (insulinomas). In particular, approaches to the molecular characterization of tumor cell proliferation and tumor angiogenesis are discussed.","authors":"Christofori, G., Hanahan, D.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Semin Cancer Biol","volume":"5","issue":"1","page":"3-12","pdf":null,"JrId":"1211","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8186146","title":"A two-step mode of stripe formation in the Drosophila blastoderm requires interactions among primary pair rule genes.","abstract":"The stripe pattern of pair rule gene expression along the anterior-posterior axis of the Drosophila blastoderm embryo represents the first sign of periodicity during the process of segmentation. Striped gene expression can be mediated by distinct cis-acting elements that give rise to individual stripe expression domains in direct response to maternal and first zygotic factors. Here we show that the expression of stripes can also be generated by a different, two-step mode which involves regulatory interactions among the primary pair rule genes hairy (h) and runt (run). Expression of h stripes 3 and 4 is directed by a common cis-acting element that results in an initial broad band of gene expression covering three stripe equivalents. Subsequently, this expression domain is split by repression in the forthcoming interstripe region, a process mediated by a separate cis-acting element that responds to run activity. This second mode of pair rule stripe formation may have evolutionary implications.","authors":"Hartmann, C., Taubert, H., J\u00e4ckle, H., Pankratz, MJ.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Mech Dev","volume":"45","issue":"1","page":"3-13","pdf":null,"JrId":"1825","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11792323","title":"Nuclear envelope breakdown proceeds by microtubule-induced tearing of the lamina.","abstract":"The mechanism of nuclear envelope breakdown (NEBD) was investigated in live cells. Early spindle microtubules caused folds and invaginations in the NE up to one hour prior to NEBD, creating mechanical tension in the nuclear lamina. The first gap in the NE appeared before lamin B depolymerization, at the site of maximal tension, by a tearing mechanism. Gap formation relaxed this tension and dramatically accelerated the rate of chromosome condensation. The hole produced in the NE then rapidly expanded over the nuclear surface. NE fragments remaining on chromosomes were removed toward the centrosomes in a microtubule-dependent manner, suggesting a mechanism mediated by a minus-end-directed motor.","authors":"Beaudouin, J., Gerlich, D., Daigle, N., Eils, R., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cell","volume":"108","issue":"1","page":"83-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21526793","title":"General statistical modeling of data from protein relative expression isobaric tags.","abstract":"Quantitative comparison of the protein content of biological samples is a fundamental tool of research. The TMT and iTRAQ isobaric labeling technologies allow the comparison of 2, 4, 6, or 8 samples in one mass spectrometric analysis. Sound statistical models that scale with the most advanced mass spectrometry (MS) instruments are essential for their efficient use. Through the application of robust statistical methods, we developed models that capture variability from individual spectra to biological samples. Classical experimental designs with a distinct sample in each channel as well as the use of replicates in multiple channels are integrated into a single statistical framework. We have prepared complex test samples including controlled ratios ranging from 100:1 to 1:100 to characterize the performance of our method. We demonstrate its application to actual biological data sets originating from three different laboratories and MS platforms. Finally, test data and an R package, named isobar, which can read Mascot, Phenyx, and mzIdentML files, are made available. The isobar package can also be used as an independent software that requires very little or no R programming skills.","authors":"Breitwieser, FP., M\u00fcller, A., Dayon, L., K\u00f6cher, T., Hainard, A., Pichler, P., Schmidt-Erfurth, U., Superti-Furga, G., Sanchez, JC., Mechtler, K., Bennett, KL., Colinge, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Proteome Res","volume":"10","issue":"6","page":"2758-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11420047","title":"Pax5\/BSAP maintains the identity of B cells in late B lymphopoiesis.","abstract":"The B lineage commitment factor Pax5 (BSAP) is expressed throughout B cell development. To investigate its late function, we generated a mouse strain carrying a floxed Pax5 allele that was conditionally inactivated by CD19-cre or Mx-cre expression. Pax5 deletion resulted in the preferential loss of mature B cells, inefficient lymphoblast formation, and reduced serum IgG levels. Mature B cells radically changed their gene expression pattern in response to Pax5 inactivation. Most B cell antigens were downregulated on the cell surface, and the transcription of B cell-specific genes was decreased, whereas the expression of non-B lymphoid genes was activated in Pax5-deficient B cells. These data demonstrate that Pax5 is essential for maintaining the identity and function of B cells during late B lymphopoiesis.","authors":"Horcher, M., Souabni, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Immunity","volume":"14","issue":"6","page":"779-90","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11853667","title":"Evidence that the Ipl1-Sli15 (Aurora kinase-INCENP) complex promotes chromosome bi-orientation by altering kinetochore-spindle pole connections.","abstract":"How sister kinetochores attach to microtubules from opposite spindle poles during mitosis (bi-orientation) remains poorly understood. In yeast, the ortholog of the Aurora B-INCENP protein kinase complex (Ipl1-Sli15) may have a role in this crucial process, because it is necessary to prevent attachment of sister kinetochores to microtubules from the same spindle pole. We investigated IPL1 function in cells that cannot replicate their chromosomes but nevertheless duplicate their spindle pole bodies (SPBs). Kinetochores detach from old SPBs and reattach to old and new SPBs with equal frequency in IPL1+ cells, but remain attached to old SPBs in ipl1 mutants. This raises the possibility that Ipl1-Sli15 facilitates bi-orientation by promoting turnover of kinetochore-SPB connections until traction of sister kinetochores toward opposite spindle poles creates tension in the surrounding chromatin.","authors":"Tanaka, TU., Rachidi, N., Janke, C., Pereira, G., Galova, M., Schiebel, E., Stark, MJ., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cell","volume":"108","issue":"3","page":"317-29","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8156587","title":"Cyclin E controls S phase progression and its down-regulation during Drosophila embryogenesis is required for the arrest of cell proliferation.","abstract":"Most cells of the dorsal epidermis exit from the mitotic cycle after division 16 in Drosophila embryogenesis. This exit is dependent on the down-regulation of Drosophila cyclin E (DmcycE) during the final mitotic cycle. Ectopic expression of DmcycE after the final mitosis induces entry into S phase and reaccumulation of G2 cyclins and results in progression through a complete additional cell cycle. Conversely, analyses in DmcycE mutant embryos indicate that cyclin E is required for progression through S phase of the mitotic cycle. Moreover, endoreplication, which occurs in late wild-type embryos in the same pattern as DmcycE expression, is not observed in the mutant embryos. Therefore, Drosophila cyclin E, which forms a complex with the Dmcdc2c kinase, controls progression through S phase and its down-regulation limits embryonic proliferation.","authors":"Knoblich, JA., Sauer, K., Jones, L., Richardson, H., Saint, R., Lehner, CF.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Cell","volume":"77","issue":"1","page":"107-20","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1994-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8137820","title":"Down-regulation of wild-type p53 activity interferes with apoptosis of IL-3-dependent hematopoietic cells following IL-3 withdrawal.","abstract":"Overexpression of wild-type p53 in p53-deficient leukemic cells induces apoptosis, which can be inhibited by hematopoietic survival factors. This suggests that p53 may contribute to survival factor dependence. To assess the role of wild-type p53 in mediating apoptosis following survival factor withdrawal, we interfered with endogenous p53 activity in interleukin-3 (IL-3)-dependent cells. Extended survival without IL-3 was conferred by recombinant retroviruses encoding either a full-length p53 mutant or a C-terminal p53 miniprotein, both of which can act as negative-dominant inhibitors of wild-type p53. On the other hand, excess wild-type p53 activity failed to elicit apoptosis as long as IL-3 was present. We propose that p53 is a positive, though not exclusive, mediator of survival factor dependence in hematopoietic cells.","authors":"Gottlieb, E., Haffner, R., von R\u00fcden, T., Wagner, EF., Oren, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"EMBO J","volume":"13","issue":"6","page":"1368-74","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1994-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8157002","title":"The Drosophila rolled locus encodes a MAP kinase required in the sevenless signal transduction pathway.","abstract":"Mitogen-activated protein (MAP) kinases have been proposed to play a critical role in receptor tyrosine kinase (RTK)-mediated signal transduction pathways. Although genetic and biochemical studies of RTK pathways in Caenorhabditis elegans, Drosophila melanogaster and mammals have revealed remarkable similarities, a genetic requirement for MAP kinases in RTK signaling has not been established. During retinal development in Drosophila, the sevenless (Sev) RTK is required for development of the R7 photoreceptor cell. Components of the signal transduction pathway activated by Sev in the R7 precursor include proteins encoded by the gap1, drk, Sos, ras1 and raf loci. In this report we present evidence that a Drosophila MAP kinase, ERK-A, is encoded by the rolled locus and is required downstream of raf in the Sev signal transduction pathway.","authors":"Biggs, WH., Zavitz, KH., Dickson, B., van der Straten, A., Brunner, D., Hafen, E., Zipursky, SL.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"EMBO J","volume":"13","issue":"7","page":"1628-35","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1994-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20034073","title":"Expression and regulation of ANTXR1 in the chick embryo.","abstract":"Anthrax Toxin Receptor 1 (ANTXR1; also known as Tumor Endothelial Marker 8, TEM8) is one of several genes that was recently found to be up-regulated in tumor-associated endothelial cells. In vitro, the protein can link extracellular matrix components with the actin cytoskeleton to promote cell adhesion and cell spreading. Both, ANTXR1 and the closely related ANTXR2 can bind anthrax toxin and interact with lipoprotein receptor-related protein 5 and 6, which also work as coreceptors in the WNT signaling pathway. Here, we report the cloning of chick ANTXR1 from a suppression subtractive hybridization screen for fibroblast growth factor (FGF) -inducible genes in chicken embryonic facial mesenchyme. We show that chicken ANTXR1 is dynamically expressed throughout embryogenesis, starting from Hamburger and Hamilton stage 10. Furthermore, we demonstrate that FGF signaling is sufficient, but not necessary, to induce ANTXR1 expression in chicken facial mesenchyme.","authors":"Herrmann, D., Ferrer-Vaquer, A., Lahsnig, C., Firnberg, N., Leibbrandt, A., Neub\u00fcser, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Dev Dyn","volume":"239","issue":"2","page":"680-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8120091","title":"Biogenesis of phagolysosomes proceeds through a sequential series of interactions with the endocytic apparatus.","abstract":"We have examined the modifications occurring during the transformation of phagosomes into phagolysosomes in J-774 macrophages. The use of low density latex beads as markers of phagosomes (latex bead compartments, LBC) allowed the isolation of these organelles by flotation on a simple sucrose gradient. Two-dimensional gel electrophoresis, immunocytochemistry, and biochemical assays have been used to characterize the composition of LBC at different time points after their formation, as well as their interactions with the organelles of the endocytic pathway. Our results show that LBC acquire and lose various markers during their transformation into phagolysosomes. Among these are members of the rab family of small GTPases as well as proteins of the lamp family. The transfer of the LBC of lamp 2, a membrane protein associated with late endocytic structures, was shown to be microtubule dependent. Video-microscopy showed that newly formed phagosomes were involved in rapid multiple contacts with late components of the endocytic pathway. Collectively, these observations suggest that phagolysosome formation is a highly dynamic process that involves the gradual and regulated acquisition of markers from endocytic organelles.","authors":"Desjardins, M., Huber, LA., Parton, RG., Griffiths, G.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"J Cell Biol","volume":"124","issue":"5","page":"677-88","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1994-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18555781","title":"Transport through the Golgi apparatus by rapid partitioning within a two-phase membrane system.","abstract":"The prevailing view of intra-Golgi transport is cisternal progression, which has a key prediction--that newly arrived cargo exhibits a lag or transit time before exiting the Golgi. Instead, we find that cargo molecules exit at an exponential rate proportional to their total Golgi abundance with no lag. Incoming cargo molecules rapidly mix with those already in the system and exit from partitioned domains with no cargo privileged for export based on its time of entry into the system. Given these results, we constructed a new model of intra-Golgi transport that involves rapid partitioning of enzymes and transmembrane cargo between two lipid phases combined with relatively rapid exchange among cisternae. Simulation and experimental testing of this rapid partitioning model reproduced all the key characteristics of the Golgi apparatus, including polarized lipid and protein gradients, exponential cargo export kinetics, and cargo waves.","authors":"Patterson, GH., Hirschberg, K., Polishchuk, RS., Gerlich, D., Phair, RD., Lippincott-Schwartz, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell","volume":"133","issue":"6","page":"1055-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-07-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11753375","title":"Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus.","abstract":"Promyelocytic leukaemia (PML) nuclear bodies are present in most mammalian cell nuclei. PML bodies are disrupted by PML retinoic acid receptor alpha (RAR alpha) oncoproteins in acute promyelocytic leukaemia. These bodies contain numerous proteins, including Sp100, SUMO-1, HAUSP(USP7), CBP and BLM, and they have been implicated in aspects of transcriptional regulation or as nuclear storage depots. Here, we show that three classes of PML nuclear bodies can be distinguished, on the basis of their dynamic properties in living cells. One class of PML bodies is particularly noteworthy in that it moves by a metabolic-energy-dependent mechanism. This represents the first example of metabolic-energy-dependent transport of a nuclear body within the mammalian cell nucleus.","authors":"Muratani, M., Gerlich, D., Janicki, SM., Gebhard, M., Eils, R., Spector, DL.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nat Cell Biol","volume":"4","issue":"2","page":"106-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8098843","title":"A conserved C-terminal sequence that is deleted in v-ErbA is essential for the biological activities of c-ErbA (the thyroid hormone receptor).","abstract":"The thyroid hormone (T3) receptor type alpha, the c-ErbA alpha proto-oncoprotein, stimulates transcription of T3-dependent promoters, interferes with AP-1 activity, and induces erythroid differentiation in a ligand-dependent manner. The v-ErbA oncoprotein does not bind hormone and has lost all of these activities. Using c-ErbA\/v-ErbA chimeras, we found that a deletion of 9 amino acids, conserved among many members of the nuclear receptor superfamily, which are located at the extreme carboxy terminus of c-ErbA alpha is responsible for loss of both transactivation and transcriptional interference activities. Single, double, and triple amino acid substitutions within this region completely abolished T3-dependent transcriptional activation, interference with AP-1 activity, and decreased T3 binding by c-ErbA alpha. However, the lower T3 binding by these mutants does not fully account for the loss of transactivation and transcriptional interference, since a c-ErbA\/v-ErbA chimera which was similarly reduced in T3 binding activity has retained both of these functions. Deletion of homologous residues in the retinoic acid receptor alpha (RAR alpha) resulted in a similar loss of transactivation and transcriptional interference activities. The ability of c-ErbA alpha to induce differentiation of transformed erythroblasts is also impaired by all of the mutations introduced into the conserved carboxy-terminal sequence. We conclude that this 9-amino-acid conserved region is essential for normal biological function of c-ErbA alpha and RAR alpha and possibly other T3 and RA receptors.","authors":"Saatcioglu, F., Bartunek, P., Deng, T., Zenke, M., Karin, M.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Mol Cell Biol","volume":"13","issue":"6","page":"3675-85","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1993-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11402193","title":"The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity.","abstract":"The pyridoxal 5'-phosphate-dependent enzyme cystathionine beta-lyase (CBL) catalyzes the penultimate step in the de novo biosynthesis of Met in microbes and plants. Absence of CBL in higher organisms makes it an important target for the development of antibiotics and herbicides. The three-dimensional structure of cystathionine beta-lyase from Arabidopsis was determined by Patterson search techniques, using the structure of tobacco (Nicotiana tabacum) cystathionine gamma-synthase as starting point. At a resolution of 2.3 A, the model was refined to a final crystallographic R-factor of 24.9%. The overall structure is very similar to other pyridoxal 5'-phosphate-dependent enzymes of the gamma-family. Exchange of a few critical residues within the active site causes the different substrate preferences between Escherichia coli and Arabidopsis CBL. Loss of interactions at the alpha-carboxyl site is the reason for the poorer substrate binding of Arabidopsis CBL. In addition, the binding pocket of Arabidopsis CBL is larger than that of E. coli CBL, explaining the similar binding of L-cystathionine and L-djenkolate in Arabidopsis CBL in contrast to E. coli CBL, where the substrate binding site is optimized for the natural substrate cystathionine.","authors":"Breitinger, U., Clausen, T., Ehlert, S., Huber, R., Laber, B., Schmidt, F., Pohl, E., Messerschmidt, A.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Plant Physiol","volume":"126","issue":"2","page":"631-42","pdf":null,"JrId":"6478","fulltextlink":null,"preprintlink":null,"articledate":"2001-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11390355","title":"A Caenorhabditis elegans cohesion protein with functions in meiotic chromosome pairing and disjunction.","abstract":"We have studied four Caenorhabditis elegans homologs of the Rad21\/Scc1\/Rec8 sister-chromatid cohesion protein family. Based on the RNAi phenotype and protein localization, it is concluded that one of them, W02A2.6p, is the likely worm ortholog of yeast Rec8p. The depletion of C. elegans W02A2.6p (called REC-8) by RNAi, induced univalent formation and splitting of chromosomes into sister chromatids at diakinesis. Chromosome synapsis at pachytene was defective, but primary homology recognition seemed unaffected, as a closer-than-random association of homologous fluorescence in situ hybridization (FISH) signals at leptotene\/zygotene was observed. Depletion of REC-8 also induced chromosome fragmentation at diakinesis. We interpret these fragments as products of unrepaired meiotic double-stranded DNA breaks (DSBs), because fragmentation was suppressed in a spo-11 background. Thus, REC-8 seems to be required for successful repair of DSBs. The occurrence of DSBs in REC-8-depleted meiocytes suggests that DSB formation does not depend on homologous synapsis. Anti-REC-8 immunostaining decorated synaptonemal complexes (SCs) at pachytene and chromosomal axes in bivalents and univalents at diakinesis. Between metaphase I and metaphase II, REC-8 is partially lost from the chromosomes. The partial loss of REC-8 from chromosomes between metaphase I and metaphase II suggests that worm REC-8 might function similarly to yeast Rec8p. The loss of yeast Rec8p from chromosome arms at meiosis I and centromeres at meiosis II coordinates the disjunction of homologs and sister chromatids at the two meiotic divisions.","authors":"Pasierbek, P., Jantsch, M., Melcher, M., Schleiffer, A., Schweizer, D., Loidl, J.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Genes Dev","volume":"15","issue":"11","page":"1349-60","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8061331","title":"Oncogenes and epithelial cell transformation.","abstract":"More than 80% of the tumors occurring in man are carcinomas. Despite the prevalence of these epithelial tumors most in vitro studies of oncogenesis have employed mesenchymal rather than epithelial cells. As a result, a detailed understanding of the molecular mechanisms of carcinoma formation and an exact definition of the malignant transformed epithelial phenotype are lacking. Taking into account that the genesis of a carcinoma involves alterations in multiple genes, giving rise to complex phenotypic changes, the question arises whether each single, mutational step can be correlated with distinct alterations of the epithelial phenotype. To approach this question, oncogenes that are both critically positioned in growth factor receptor-driven signaling pathways and relevant in carcinoma development, such as ras, src, myc and fos, have been expressed in epithelial cells. The results indicate that epithelial cells transformed by oncogenes in vitro alter their gene expression programs, thereby losing certain features of cell polarity and cell adhesion. However, as with true tumor cells, these changes occur in distinct combinations, to different degrees and are influenced by the local environment of the cells.","authors":"Reichmann, E.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Semin Cancer Biol","volume":"5","issue":"2","page":"157-65","pdf":null,"JrId":"1211","fulltextlink":null,"preprintlink":null,"articledate":"1994-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10679003","title":"Quantitative imaging of pre-mRNA splicing factors in living cells.","abstract":null,"authors":"Eils, R., Gerlich, D., Tvarusk\u00f3, W., Spector, DL., Misteli, T.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Biol Cell","volume":"11","issue":"2","page":"413-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8096810","title":"Unliganded T3R, but not its oncogenic variant, v-erbA, suppresses RAR-dependent transactivation by titrating out RXR.","abstract":"V-erbA is thought to be an antagonist of thyroid hormone receptor (T3R) function. Here we show that unliganded T3R, but not v-erbA, suppresses retinoic acid (RA)-dependent induction of the RAR-beta 2 promoter by competing for the common dimerization partner, the retinoid X receptor (RXR). Firstly, T3R suppression can be alleviated by co-transfection of RXR. Secondly, T3R, but not v-erbA, competes with RAR for RXR and causes the dissociation of a preformed RAR\/RXR-RARE ternary complex in vitro. A single point mutation located in the dimerization interface of v-erbA (Pro349 to Ser) abolishes the transdominant phenotype when introduced at the respective position in T3R. The hypertransforming v-erbA variant r12, in which this mutation is reversed (Ser349 to Pro) suppresses RA-induced differentiation in chicken erythroid progenitors, while v-erbA does not. Our data thus suggest that unliganded T3R and v-erbA act as dominant suppressors through mechanistically distinct pathways.","authors":"Barettino, D., Bugge, TH., Bartunek, P., Vivanco Ruiz, MD., Sonntag-Buck, V., Beug, H., Zenke, M., Stunnenberg, HG.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"EMBO J","volume":"12","issue":"4","page":"1343-54","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11704761","title":"Distinct regulators control the expression of the mid-hindbrain organizer signal FGF8.","abstract":"Local expression of FGF8 at the mid\/hindbrain boundary (MHB) governs the development of multiple neurons and support cells. Here we show that the paired-domain protein Pax2 is necessary and sufficient for the induction of FGF8 in part by regulating the expression of Pax5&amp;8. A network of transcription and secreted factors, including En1, Otx2, Gbx2, Grg4 and Wnt1&amp;4, that is established independently of Pax2, further refines the expression domain and level of FGF8 at the MHB through opposing effects on Pax2 activity. Our results indicate that the expression of local organizing factors is controlled by combinatorial interaction between inductive and modulatory factors.","authors":"Ye, W., Bouchard, M., Stone, D., Liu, X., Vella, F., Lee, J., Nakamura, H., Ang, SL., Busslinger, M., Rosenthal, A.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Neurosci","volume":"4","issue":"12","page":"1175-81","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8066460","title":"Dependence of enhancer-mediated transcription of the immunoglobulin mu gene on nuclear matrix attachment regions.","abstract":"Transcription of the immunoglobulin mu heavy chain locus is regulated by an intronic enhancer that is flanked on both sides by nuclear matrix attachment regions (MARs). These MARs have now been shown to be essential for transcription of a rearranged mu gene in transgenic B lymphocytes, but they were not required in stably transfected tissue culture cells. Normal rates of transcriptional initiation at a variable region promoter and the formation of an extended deoxyribonuclease I (DNase I)--sensitive chromatin domain were dependent on MARs, although DNase I hypersensitivity at the enhancer was detected in the absence of MARs. Thus, transcriptional activation of the mu gene during normal lymphoid development requires a synergistic collaboration between the enhancer and flanking MARs.","authors":"Forrester, WC., van Genderen, C., Jenuwein, T., Grosschedl, R.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Science","volume":"265","issue":"5176","page":"1221-5","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1994-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8031870","title":"Mechanical loading triggers specific biochemical responses in mandibular condylar chondrocytes.","abstract":"The effect of mechanical loading on the phosphorylation state of condylar cartilage proteins was investigated by high resolution electrophoretic analysis of 32P-labelled proteins from mechanically stimulated rat mandibular condylar chondrocytes. Specific dephosphorylation (and\/or loss) of an acidic, 35-36 kDa protein(s) and of proteins overlapping with members of the ras superfamily of small GTP-binding proteins was observed. These responses may constitute part of a mechanically induced transduction system which establishes the differentiated phenotype.","authors":"Basdra, EK., Huber, LA., Komposch, G., Papavassiliou, AG.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Biochim Biophys Acta","volume":"1222","issue":"2","page":"315-22","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1994-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8026445","title":"Mapping small GTP-binding proteins on high-resolution two-dimensional gels by a combination of GTP binding and labeling with in situ periodate-oxidized GTP.","abstract":"We compared two approaches to identify and map small GTP-binding proteins in combination with high-resolution two-dimensional (2-D) gel electrophoresis. The first approach involved direct GTP ligand binding after a renaturing transfer onto nitrocellulose. In the second, affinity labeling with in situ periodate-oxidized GTP was used in permeabilized cells (Peter, M. E., She, J., Huber, L. A. and Terhorst, C. Anal. Biochem. 1993, 210, 77-85). Analysis by 2-D gel electrophoresis revealed a number of distinct intracellular small GTP-binding proteins in Madine-darby canine kidney strain II cells (MDCKII). Using specific antibodies the electrophoretic coordinates of rab4, rap1a\/b, and rap2 were identified for native as well as for crosslinked GTPases. These methods allow the identification of small GTP-binding proteins in total cell lysates and purified subcellular fractions, providing excellent markers throughout the course of differentiation and development.","authors":"Huber, LA., Peter, ME.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Electrophoresis","volume":"15","issue":"2","page":"283-8","pdf":null,"JrId":"3579","fulltextlink":null,"preprintlink":null,"articledate":"1994-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8043272","title":"The involvement of the small GTP-binding protein Rab5a in neuronal endocytosis.","abstract":"Rab5a is a small GTPase that regulates fusion of endocytic vesicles to early endosomes. We investigated whether Rab5a is involved in early endocytic traffic in both the axonal and the somatodendritic domains of polarized neurons. Using immunofluorescence, endogenous Rab5a was detected in axons and dendrites. Its localization in axons strongly overlapped that of the synaptic vesicle protein synaptophysin. Indeed, Rab5a co-immunoisolated with synaptophysin-containing vesicles, and antibodies against Rab5a labeled synaptic vesicle-like structures in nerve terminals. The functional association of Rab5a with dendritic and axonal early endosomes was assayed by electron microscopy after overexpression of wild-type and mutant Rab5a in cultured hippocampal neurons. This induced the formation of abnormal endosomes in both the somatodendritic and the axonal domains. These results show a role for Rab5a in axonal and dendritic endocytosis, and the presence of Rab5a on synaptic vesicles indicates that the axonal endosomes participate in the biogenesis of these vesicles.","authors":"de Hoop, MJ., Huber, LA., Stenmark, H., Williamson, E., Zerial, M., Parton, RG., Dotti, CG.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Neuron","volume":"13","issue":"1","page":"11-22","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"1994-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8055873","title":"Two-dimensional gel mapping of small GTPases reveals transformation-specific changes during oncogenesis.","abstract":"Epithelial cells transformed by oncogenes in vitro change their gene expression program, thereby losing features of cell polarity and cell adhesion. Using ras-transformed mammary epithelial cells, we have investigated the expression of other small GTP-binding proteins by high-resolution two-dimensional gel electrophoresis and direct GTP ligand binding after renaturing transfer onto nitrocellulose. Ras-transformed cells lost the expression of one epithelial-specific GTP-binding protein (21-22 kDa, pI 4.5-4.8) and instead expressed a fibroblast GTP-binding protein (21-22 kDa, pI 4.8-5.0).","authors":"Huber, LA., Beug, H., Simons, K., Reichmann, E.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Electrophoresis","volume":"15","issue":"3-4","page":"469-73","pdf":null,"JrId":"3579","fulltextlink":null,"preprintlink":null,"articledate":"1994-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8034017","title":"Myelin membrane biogenesis by oligodendrocytes. Developmental regulation of low molecular weight GTP-binding proteins.","abstract":"Oligodendrocytes synthesize dramatic amounts of myelin membrane. We hypothesized that this requires unique aspects of vesicular trafficking. Specific stages of the oligodendrocyte lineage were assayed for low molecular weight GTP-binding proteins implicated in the regulation of vesicular transport pathway (two dimensional gel electrophoresis, [alpha-32P]GTP overlay). Consistent with the hypothesis, as oligodendrocytes differentiate from early progenitors to mature myelin-producing cells, &gt; or = 12 small GTP-binding proteins become up-regulated. Myelin membrane also has a complex pattern of GTP-binding proteins. Several of these proteins may be specific to oligodendrocytes, suggesting that oligodendrocytes may utilize cell-type specific GTP-binding proteins for biogenesis and maintenance of the myelin membrane.","authors":"Huber, LA., Madison, DL., Simons, K., Pfeiffer, SE.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"FEBS Lett","volume":"347","issue":"2-3","page":"273-8","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"1994-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7985232","title":"Proteasomes: protein degradation machines of the cell.","abstract":"20 S proteasomes are cylinder-shaped protein complexes that play an important role in intracellular protein degradation in eukaryotes and certain archaebacteria. Although 20 S proteasomes were first described many years ago, it has been discovered only recently that these particles can assemble with other protein complexes, presumably of regulatory function. One of the macromolecular assemblies formed, the 26 S proteasome complex, functions as an ATP-dependent protease in the ubiquitin pathway, which has been implicated in the degradation of abnormal proteins, degradation of short-lived regulatory proteins and antigen presentation.","authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Trends Biochem Sci","volume":"19","issue":"9","page":"377-82","pdf":null,"JrId":"7837","fulltextlink":null,"preprintlink":null,"articledate":"1995-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7956097","title":"Role of enhancer sequences in regulating accessibility of DNA in nuclear chromatin.","abstract":null,"authors":"Jenuwein, T., Forrester, W., Grosschedl, R.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"58","issue":null,"page":"97-103","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1994-11-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7984240","title":"Regulation of embryonic growth and lysosomal targeting by the imprinted Igf2\/Mpr gene.","abstract":"The receptor for insulin-like growth factor type 2, also known as the cation-independent mannose-6-phosphate receptor (Igf2\/Mpr), is a multifunctional receptor thought to play a role in lysosomal targeting, cell growth and signal transduction. Igf2\/Mpr has been mapped to the mouse Tme locus and shown to be an imprinted gene, which further suggests a role in embryonic growth regulation. To define the functions of Igf2\/Mpr, we have generated mice lacking this gene. We report here that maternal inheritance of an Igf2\/Mpr null allele (-\/+) as well as homozygosity for the inactive allele (-\/-) is generally lethal at birth and mutants are about 30% larger, indicating that maternal expression of Igf2\/Mpr is essential for late embryonic development and growth regulation. The phenotype is probably caused by an excess of Igf2 because the introduction of an Igf2 null allele rescued the Igf2\/Mpr mutant mice. Mutant mice also have organ and skeletal abnormalities and missort mannose-6-phosphate-tagged proteins. A few (-\/+) mice reactivated their paternal Igf2\/Mpr allele in some tissues and survived to adults. But no (-\/-) mice survived, indicating a role for the reactivated paternal allele in postnatal survival.","authors":"Wang, ZQ., Fung, MR., Barlow, DP., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Nature","volume":"372","issue":"6505","page":"464-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1994-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7954792","title":"The B-type cyclin kinase inhibitor p40SIC1 controls the G1 to S transition in S. cerevisiae.","abstract":"When yeast cells reach a critical size, they initiate bud formation, spindle pole body duplication, and DNA replication almost simultaneously. All three events depend on activation of Cdc28 protein kinase by the G1 cyclins Cln1, -2, and -3. We show that DNA replication also requires activation of Cdc28 by B-type (Clb) cyclins. A sextuple clb1-6 mutant arrests as multibudded G1 cells that resemble cells lacking the Cdc34 ubiquitin-conjugating enzyme. cdc34 mutants cannot enter S phase because they fail to destroy p40SIC1, which is a potent inhibitor of Clb but not Cln forms of the Cdc28 kinase. In wild-type cells, p40SIC1 protein appears at the end of mitosis and disappears shortly before S phase. Proteolysis of a cyclin-specific inhibitor of Cdc28 is therefore an essential aspect of the G1 to S phase transition.","authors":"Schwob, E., B\u00f6hm, T., Mendenhall, MD., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Cell","volume":"79","issue":"2","page":"233-44","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1994-11-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11581013","title":"Mammary gland development and lactation are controlled by different glucocorticoid receptor activities.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11581013<\/PMID><DateCompleted><Year>2001<\/Year><Month>12<\/Month><Day>04<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>09<\/Month><Day>06<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0804-4643<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>145<\/Volume><Issue>4<\/Issue><PubDate><Year>2001<\/Year><Month>Oct<\/Month><\/PubDate><\/JournalIssue><Title>European journal of endocrinology<\/Title><ISOAbbreviation>Eur J Endocrinol<\/ISOAbbreviation><\/Journal><ArticleTitle>Mammary gland development and lactation are controlled by different glucocorticoid receptor activities.<\/ArticleTitle><Pagination><MedlinePgn>519-27<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">Regulation of physiological processes by glucocorticoids is achieved by binding to the glucocorticoid receptor (GR) and subsequent modulation of gene expression, either by DNA binding-dependent mechanisms or via protein-protein interaction with other transcription factors. The purpose of this study was to define the molecular mechanism of GR underlying the control of mammary gland development and lactation.","authors":"Reichardt, HM., Horsch, K., Gr\u00f6ne, HJ., Kolbus, A., Beug, H., Hynes, N., Sch\u00fctz, G.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Eur J Endocrinol","volume":"145","issue":"4","page":"519-27","pdf":null,"JrId":"2590","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9115362","title":"Delivery of bacterial artificial chromosomes into mammalian cells with psoralen-inactivated adenovirus carrier.","abstract":"Molecular biology has many applications where the introduction of large (&gt;100 kb) DNA molecules is required. The current methods of large DNA transfection are very inefficient. We reasoned that two limits to improving transfection methods with these large DNA molecules were the difficulty of preparing workable quantities of clean DNA and the lack of rapid assays to determine transfection success. We have used bacterial artificial chromosomes (BACs) based on the Escherichia coli F factor plasmid system, which are simple to manipulate and purify in microgram quantities. Because BAC plasmids are kept at one to two copies per cell, the problems of rearrangement observed with YACs are eliminated. We have generated two series of BAC vectors bearing marker genes for luciferase and green fluorescent protein (GFP). Using these reagents, we have developed methods of delivering BACs of up to 170 kb into mammalian cells with transfection efficiency comparable to 5-10 kb DNA. Psoralen-inactivated adenovirus is used as the carrier, thus eliminating the problems associated with viral gene expression. The delivered DNA is linked to the carrier virus with a condensing polycation. Further improvements in gene delivery were obtained by replacing polylysine with low molecular weight polyethylenimine (PEI) as the DNA condensing agent.","authors":"Baker, A., Cotten, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Nucleic Acids Res","volume":"25","issue":"10","page":"1950-6","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7926774","title":"pct1+, which encodes a new DNA-binding partner of p85cdc10, is required for meiosis in the fission yeast Schizosaccharomyces pombe.","abstract":"The transcriptional activation of genes at late G1 is an important regulatory step in the commitment to a new cell division cycle. In Schizosaccharomyces pombe, this regulation is mediated by MCB elements that serve as binding sites for the MBF\/DSC-1 complex. The cdc10(+)-encoded protein is a component of this complex. We report the cloning of a new gene, pct1+, encoding a 73-kD protein that interacts with p85cdc10 to form an MCB-binding heteromer. Pct1+ is related to, but distinct from, the res1+\/sct1+ gene that also encodes a p85cdc10 partner. p73pct1 has centrally located ankyrin repeats and a putative amino-terminal DNA-binding domain that has extensive sequence similarity to the DNA-binding domains of the Saccharomyces cerevisiae SWI4 and MBP1 proteins. The p73pct1\/p85cdc10 complex binds both in vitro and in vivo to MCB but not SCB or E2F sites. Overexpression of pct1+ is sufficient to rescue the growth of the cdc10-129 temperature-sensitive mutant at the restrictive temperature, although it is unable to rescue a cdc10 null mutation. A deletion of pct1+ is not lethal but does result in a severe meiotic defect. Our results indicate that there are two cdc10-containing heteromeric complexes that bind to MCB elements and play differential roles in mitotic division and meiosis.","authors":"Zhu, Y., Takeda, T., Nasmyth, K., Jones, N.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Genes Dev","volume":"8","issue":"8","page":"885-98","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1994-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7923380","title":"Positive regulation of the cAMP-responsive activator CREM by the p70 S6 kinase: an alternative route to mitogen-induced gene expression.","abstract":"Activation of the adenylyl cyclase signaling pathway elicits the induction of genes via activators binding to cAMP-responsive elements (CREs). Nuclear factor CRE modulator (CREM) is activated by PKA-mediated phosphorylation on a serine at position 117. We show that Ser-117 is also phosphorylated by the mitogen-activated p70 S6 kinase (p70S6K) in vitro. Activation of cellular p70S6K by serum factors enhances Ser-117 phosphorylation and CREM transactivation. Coexpression of p70S6K significantly increases transactivation by a GAL4-CREM fusion. The macrolide rapamycin, a potent and specific inhibitor of p70S6K in vivo, completely blocks CREM activation induced by serum and by p70S6K. Thus, CREM constitutes a target for mitogenic signaling through p70S6K and may acts as a nuclear effector in which transduction pathways may converge and cross-talk.","authors":"de Groot, RP., Ballou, LM., Sassone-Corsi, P.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Cell","volume":"79","issue":"1","page":"81-91","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1994-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9111337","title":"Long-range interactions at the HO promoter.","abstract":"The SWI5 gene encodes a zinc finger DNA-binding protein required for the transcriptional activation of the yeast HO gene. There are two Swi5p binding sites in the HO promoter, site A at -1800 and site B at -1300. Swi5p binding at site B has been investigated in some detail, and we have shown that Swi5p binds site B in a mutually cooperative fashion with Pho2p, a homeodomain protein. In this report, we demonstrate that Swi5p and Pho2p bind cooperatively to both sites A and B but that there are differences in binding to these two promoter sites. It has been shown previously that point mutations in either Swi5p binding site only modestly reduce HO expression in a PHO2 strain. We show that these mutant promoters are completely inactive in a pho2 mutant. We have created stronger point mutations at the two Swi5p binding sites within the HO promoter, and we show that the two binding sites, separated by 500 bp, are both absolutely required for HO expression, independent of PHO2. These results create an apparent dilemma, as the strong mutations at the Swi5p binding sites show that both binding sites are required for HO expression, but the earlier binding site mutations allow Swi5p to activate HO, but only in the presence of Pho2p. To explain these results, a model is proposed in which physical interaction between Swi5p proteins bound to these two sites separated by 500 bp is required for activation of the HO promoter. Experimental evidence is presented that supports the model. In addition, through deletion analysis we have identified a region near the amino terminus of Swi5p that is required for PHO2-independent activation of HO, suggesting that this region mediates the long-range interactions between Swi5p molecules bound at the distant sites.","authors":"McBride, HJ., Brazas, RM., Yu, Y., Nasmyth, K., Stillman, DJ.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Mol Cell Biol","volume":"17","issue":"5","page":"2669-78","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1997-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7915168","title":"An intragenic TaqI RFLP at the PAX5 locus.","abstract":null,"authors":"Vorechovsk\u00fd, I., Kozm\u00edk, Z., Hammarstr\u00f6m, L., Smith, CI., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Hum Mol Genet","volume":"3","issue":"4","page":"681","pdf":null,"JrId":"2407","fulltextlink":null,"preprintlink":null,"articledate":"1994-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7917338","title":"Cell cycle regulated transcription in yeast.","abstract":"At least four different classes of cell cycle regulated gene exist in yeast: G1 cyclins and DNA synthesis genes are expressed in late G1; histone genes in S phase; genes for transcription factors, cell cycle regulators and replication initiation proteins in G2; and genes needed for cell separation as cells enter G1. Early and late G1-specific transcription is mediated by the Swi5\/Ace2 and Swi4\/Swi6 classes of factor, respectively. Changes in cyclin\/Cdc28 kinases may be involved in all classes of regulation. Transcriptional control of cyclin genes has an important role in regulating cell cycle progression.","authors":"Koch, C., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Curr Opin Cell Biol","volume":"6","issue":"3","page":"451-9","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"1994-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7889400","title":"Generation of normal T and B lymphocytes by c-jun deficient embryonic stem cells.","abstract":"To determine the potential roles of c-jun in lymphocyte development, we generated somatic chimeric mice by injecting homozygous c-jun mutant embryonic stem (ES) cells into blastocysts from recombination activating gene-2 (RAG-2)-deficient mice. Chimeric mice had poor restoration of thymocytes, but contained substantial numbers of mature T and B lymphocytes in the periphery. Stimulation of c-jun-\/- B cells resulted in normal levels of proliferation and immunoglobulin secretion. Likewise, stimulation of c-jun-\/- T cells resulted in essentially normal levels of IL-2R alpha expression, IL-2 secretion, and proliferation. We further showed that the relatively normal activation responses of the c-jun-\/- T cells probably results from the fact that other members of the Jun family contribute to the bulk of the activator protein-1 (AP-1) complexes in normal T cells and, as a result, AP-1 complexes are found at relatively normal levels in c-jun-\/- T cells.","authors":"Chen, J., Stewart, V., Spyrou, G., Hilberg, F., Wagner, EF., Alt, FW.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Immunity","volume":"1","issue":"1","page":"65-72","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"1995-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7859287","title":"Control of Drosophila photoreceptor cell fates by phyllopod, a novel nuclear protein acting downstream of the Raf kinase.","abstract":"The phyllopod (phyl) gene regulates the fates of a subset of cells in the developing Drosophila eye; in the absence of phyl function, the R1, R6, and R7 photoreceptors are transformed into additional cone cells, whereas ectopic phyl expression in the cone cell precursors transforms these cells into additional R7 cells. Within this group of cells, phyl expression thus mimics activation of the Raf pathway in its ability to induce photoreceptor rather than cone cell development. Furthermore, the transformation of cone cells into R7 cells in response to Raf activation is both accompanied by and dependent upon ectopic phyl expression. phyl thus represents a possible target gene of the Raf pathway during eye development, controlling the fates of a novel subset of photoreceptors.","authors":"Dickson, BJ., Dom\u00ednguez, M., van der Straten, A., Hafen, E.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell","volume":"80","issue":"3","page":"453-62","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1995-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7845679","title":"Induction of the mitogen-activated p70 S6 kinase by adenovirus E1A.","abstract":"Adenovirus E1A proteins can transform primary cells in culture in conjunction with other oncogenes, such as E1B or activated ras. The modulation of various cell cycle regulators by E1A is thought to be involved in this transformation process. In this paper we show that E1A enhances the expression of the mitogen-inducible p70 S6 kinase (p70s6k), a kinase which is essential for G1 progression. p70s6k mRNA and protein levels are enhanced 3-4-fold in various E1A-expressing cell lines. Similarly, the activity of p70s6k is enhanced in E1A-expressing cells in a manner partially independent of enhanced expression of p70s6k. The induction of p70s6k correlates with the presence of conserved region 1 (CR1) of E1A and with morphological transformation by E1A. These results suggest that induction of p70s6k by E1A might be involved in transformation by E1A.","authors":"de Groot, RP., Schouten, GJ., de Wit, L., Ballou, LM., van der Eb, AJ., Zantema, A.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Oncogene","volume":"10","issue":"3","page":"543-8","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1995-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7834754","title":"Dendritic cell progenitor is transformed by a conditional v-Rel estrogen receptor fusion protein v-RelER.","abstract":"A conditional v-Rel estrogen receptor fusion protein, v-RelER, causes estrogen-dependent but otherwise unaltered v-rel-specific transformation of chicken bone marrow cells. Here, we demonstrate that such v-relER-transformed cells exhibit B lymphoid determinants in line with earlier studies on v-rel-transformed cells. However, following inactivation of v-RelER oncoprotein activity by administration of an estrogen antagonist, cells differentiate into antigen-presenting dendritic cells as judged by several morphological and functional criteria. Additionally, under yet different culture conditions, v-relER cells differentiate into cells resembling polymorphonuclear neutrophils. Our studies therefore suggest that the conditional v-RelER, and probably also the authentic v-Rel, transform a common progenitor for neutrophils and dendritic cells.","authors":"Boehmelt, G., Madruga, J., D\u00f6rfler, P., Briegel, K., Schwarz, H., Enrietto, PJ., Zenke, M.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell","volume":"80","issue":"2","page":"341-52","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1995-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11564170","title":"Keratinocyte-specific onset of serine protease BSSP expression in experimental carcinogenesis.","abstract":"Malignant transformation of mouse skin by chemical carcinogens and tumor promoters, such as the phorbol ester 12-O-tetradecanoylphorbol-13-acetate, is a multistage process leading to the formation of squamous cell carcinomas. In an effort to identify target genes whose expression is associated with skin tumorigenesis we combined elements of suppression subtractive hybridization with differential screening to isolate genes that are differentially upregulated in mouse skin after short-term treatment with 12-O-tetradecanoylphorbol-13-acetate and that exhibit a high constitutive expression in squamous cell carcinomas. Here, we report the detailed analysis of one of these cDNAs encoding the serine protease BSSP in mouse skin. Phorbol ester application increases BSSP expression in keratinocytes of the epidermis and the hair follicle several-fold starting 4 h post- treatment. Transcriptional activation of BSSP by 12-O-tetradecanoylphorbol-13-acetate was found to be independent of c-Fos expression and resistant to downregulation by glucocorticoids. By monitoring BSSP expression throughout experimental skin carcinogenesis we found strong constitutive expression in hyperplastic epidermis as well as in proliferatively active keratinocytes of benign and malignant skin tumors. These results establish a novel link between expression of an as yet ill-defined serine protease and skin carcinogenesis.","authors":"Breitenbach, U., Tuckermann, JP., Gebhardt, C., Richter, KH., F\u00fcrstenberger, G., Christofori, G., Angel, P.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Invest Dermatol","volume":"117","issue":"3","page":"634-40","pdf":null,"JrId":"4839","fulltextlink":null,"preprintlink":null,"articledate":"2001-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7824281","title":"Cell proliferation and cell cycle progression are not impaired in fibroblasts and ES cells lacking c-Fos.","abstract":"The transcription factor AP-1 is thought to play an important role in the control of cell proliferation, but the function of individual Fos and Jun family members is a largely unresolved issue. To directly analyse the function of c-Fos in the control of cell proliferation we have used embryonic stem (ES) cells and fibroblasts lacking c-Fos due to a disruption of the c-fos gene by homologous recombination. Our results demonstrate that proliferation of normally cycling cells and reentry of quiescent cells into the cell cycle following serum stimulation are not c-Fos-dependent and occur with similar efficiency in c-fos-\/- and control cells. We also show that there is no compensatory overexpression or activation of other known Fos or Jun family members. On the contrary, the c-fos-\/- cells showed a reduced induction of fra-1 after serum stimulation which is in agreement with the previous identification of fra-1 as a c-Fos target gene. Comparison of the AP-1 binding and transactivation activities in c-fos-\/- and +\/+ fibroblasts by electrophoretic mobility antibody supershift and CAT assays suggests that c-Fos is not a major component of AP-1 complexes in these cells. It is therefore conceivable that the lack of any detectable effect on cell proliferation in c-fos-\/- cells might be due to a functional redundancy among the different AP-1 family members.","authors":"Br\u00fcsselbach, S., M\u00f6hle-Steinlein, U., Wang, ZQ., Schreiber, M., Lucibello, FC., M\u00fcller, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Oncogene","volume":"10","issue":"1","page":"79-86","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1995-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-139","title":"New Tools for Visualization and Quantification in Dynamic Processes: Applicati to the Nuclear Envelope Dynamics during Mitosis","abstract":null,"authors":"J. Mattes, J. Fieres, J. Beaudoin, D. Gerlich, J. Ellenberg, R. Eils","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Proceedings of MICCAI","volume":"","issue":"","page":"1323-1325","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11544187","title":"The transcriptional repressor CDP (Cutl1) is essential for epithelial cell differentiation of the lung and the hair follicle.","abstract":"The mammalian Cutl1 gene codes for the CCAAT displacement protein (CDP), which has been implicated as a transcriptional repressor in diverse processes such as terminal differentiation, cell cycle progression, and the control of nuclear matrix attachment regions. To investigate the in vivo function of Cutl1, we have replaced the C-terminal Cut repeat 3 and homeodomain exons with an in-frame lacZ gene by targeted mutagenesis in the mouse. The CDP-lacZ fusion protein is retained in the cytoplasm and fails to repress gene transcription, indicating that the Cutl1(lacZ) allele corresponds to a null mutation. Cutl1 mutant mice on inbred genetic backgrounds are born at Mendelian frequency, but die shortly after birth because of retarded differentiation of the lung epithelia, which indicates an essential role of CDP in lung maturation. A less pronounced delay in lung development allows Cutl1 mutant mice on an outbred background to survive beyond birth. These mice are growth-retarded and develop an abnormal pelage because of disrupted hair follicle morphogenesis. The inner root sheath (IRS) is reduced, and the transcription of Sonic hedgehog and IRS-specific genes is deregulated in Cutl1 mutant hair follicles, consistent with the specific expression of Cutl1 in the progenitors and cell lineages of the IRS. These data implicate CDP in cell-lineage specification during hair follicle morphogenesis, which resembles the role of the related Cut protein in specifying cell fates during Drosophila development.","authors":"Ellis, T., Gambardella, L., Horcher, M., Tschanz, S., Capol, J., Bertram, P., Jochum, W., Barrandon, Y., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Genes Dev","volume":"15","issue":"17","page":"2307-19","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2001-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7779400","title":"Generation of high-titer retroviral vectors following receptor-mediated, adenovirus-augmented transfection.","abstract":"A new procedure is described for the generation of high-titer, helper-free retrovirus vectors employing receptor-mediated, adenovirus-augmented transfection into a standard packaging cell line. Viral titers are increased 30-fold to 100-fold in transiently (&gt; 10(5) infectious units per mL) and stable (&gt; 10(7) infectious units per mL) transfected cells as compared with either CaPO4-mediated transfection or retroviral infection of a packaging cell line. Further, expression of the transduced genes was drastically increased in the transfected cells, but, as expected, there was no difference in transduction efficiency and gene expression in the infected target cells. The increases in viral titers were most likely due to the high number of stable, integrated copies of the vector plasmid DNA in the resulting packaging lines following G418 selection. In addition, experiments generating recombinant retroviruses from non-packaging cell lines are presented. The results suggest that this procedure may be of use to generate high-titer retrovirus vectors in packaging cell lines as well as in primary cells, thus providing a technical basis for in vivo gene transfer upon transplantation of these cells into various organs.","authors":"von R\u00fcden, T., Stingl, L., Cotten, M., Wagner, E., Zatloukal, K.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Biotechniques","volume":"18","issue":"3","page":"484-9","pdf":null,"JrId":"1595","fulltextlink":null,"preprintlink":null,"articledate":"1995-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7797073","title":"Distinct modes of cyclin E\/cdc2c kinase regulation and S-phase control in mitotic and endoreduplication cycles of Drosophila embryogenesis.","abstract":"Drosophila cyclin E (DmcycE) is required in embryos for S phase of mitotic and endoreduplication cycles. Here, we describe regulatory differences characteristic for these two cell cycle types. While DmcycE transcript levels decline in DmcycE mutant cells programmed for mitotic proliferation, they are maintained and no longer restricted to transient pulses in DmcycE mutant cells programmed for endoreduplication. Moreover, DmcycE expression in endoreduplicating cells is down-regulated by ectopic expression of a heat-inducible cyclin E transgene. DmcycE expression in endoreduplicating tissues, therefore, is restricted by a negative feedback to the transient pulse triggering entry into S-phase. Conversely, during mitotic cycles, where S phase entry is not only dependent on cyclin E but also on progression through M phase, cyclin E and associated Dmcdc2c kinase activity are present throughout the cell cycle. Reinitiation of DNA replication during the G2 phase of the mitotic cell cycle, therefore, is prevented by cyclin E\/Dmcdc2c kinase-independent regulation. Observations in cyclin A mutants implicate G2 cyclins in this regulation. Our results suggest molecular explanations for the different rules governing S phase during mitotic and endoreduplication cycles.","authors":"Sauer, K., Knoblich, JA., Richardson, H., Lehner, CF.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Genes Dev","volume":"9","issue":"11","page":"1327-39","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1995-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7791782","title":"Transcriptional activation of the fra-1 gene by AP-1 is mediated by regulatory sequences in the first intron.","abstract":"Constitutive expression of c-Fos, FosB, Fra-1, or c-Jun in rat fibroblasts leads to up-regulation of the immediate-early gene fra-1. Using the posttranslational FosER induction system, we demonstrate that this AP-1-dependent stimulation of fra-1 expression is rapid, depends on a functional DNA-binding domain of FosER, and is a general phenomenon observed in different cell types. In vitro mutagenesis and functional analysis of the rat fra-1 gene in stably transfected Rat-1A-FosER fibroblasts indicated that basal and AP-1-regulated expression of the fra-1 gene depends on regulatory sequences in the first intron which comprise a consensus AP-1 site and two AP-1-like elements. We have also investigated the transactivating and transforming properties of the Fra-1 protein to address the significance of fra-1 up-regulation. The entire Fra-1 protein fused to the DNA-binding domain of Ga14 is shown to lack any transactivation function, and yet it possesses oncogenic potential, as overexpression of Fra-1 in established rat fibroblasts results in anchorage-independent growth in vitro and tumor development in athymic mice, fra-1 is therefore not only induced by members of the Fos family, but its gene product may also contribute to cellular transformation by these proteins. Together, these data identify fra-1 as a unique member of the fos gene family which is under positive control by AP-1 activity.","authors":"Bergers, G., Graninger, P., Braselmann, S., Wrighton, C., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Mol Cell Biol","volume":"15","issue":"7","page":"3748-58","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1995-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7777574","title":"Deregulated expression of PAX5 in medulloblastoma.","abstract":"Medulloblatoma is a pediatric brain tumor originating in the human cerebellum. A collection of 23 medulloblastomas was analyzed for expression of the developmental control genes of the PAX and EN gene families by RNase protection and in situ hybridization. Of all nine PAX genes investigated, only PAX5 and PAX6 were consistently expressed in most medulloblastomas (70 and 78% of all cases, respectively), as were the genes EN1 (57%) and EN2 (78%). EN1, EN2, and PAX6 genes were also expressed in normal cerebellar tissue, and their expression in medulloblastoma is consistent with the hypothesis that this tumor originates in the external granular layer of the developing cerebellum. PAX5 transcripts were, however, not detected in the neonatal cerebellum, indicating that this gene is deregulated in medulloblastoma. In the desmoplastic variant of medulloblastoma, PAX5 expression was restricted to the reticulin-producing proliferating tumor areas containing undifferentiated cells; PAX5 was not expressed in the reticulin-free nonproliferating islands undergoing neuronal differentiation. These data suggest that deregulated expression of PAX5 correlates positively with cell proliferation and inversely with neuronal differentiation in desmoplastic medulloblastoma.","authors":"Kozmik, Z., Sure, U., R\u00fcedi, D., Busslinger, M., Aguzzi, A.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Proc Natl Acad Sci U S A","volume":"92","issue":"12","page":"5709-13","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1995-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7739566","title":"DNA-binding and transactivation properties of Pax-6: three amino acids in the paired domain are responsible for the different sequence recognition of Pax-6 and BSAP (Pax-5).","abstract":"Pax-6 is known to be a key regulator of vertebrate eye development. We have now isolated cDNA for an invertebrate Pax-6 protein from sea urchin embryos. Transcripts of this gene first appear during development at the gastrula stage and are later expressed at high levels in the tube foot of the adult sea urchin. The sea urchin Pax-6 protein is highly homologous throughout the whole protein to its vertebrate counterpart with the paired domain and homeodomain being virtually identical. Consequently, we found that the DNA-binding and transactivation properties of the sea urchin and mouse Pax-6 proteins are very similar, if not identical. A potent activation domain capable of stimulating transcription from proximal promoter and distal enhancer positions was localized within the C-terminal sequences of both the sea urchin and mouse Pax-6 proteins. The homeodomain of Pax-6 was shown to cooperatively dimerize on DNA sequences consisting of an inverted repeat of the TAAT motif with a preferred spacing of 3 nucleotides. The consensus recognition sequence of the Pax-6 paired domain deviates primarily only at one position from that of BSAP (Pax-5), and yet the two proteins exhibit largely different binding specificities for individual, naturally occurring sites. By creating Pax-6-BSAP fusion proteins, we were able to identify a short amino acid stretch in the N-terminal part of the paired domain which is responsible for these differences in DNA-binding specificity. Mutation of three Pax-6-specific residues in this region (at positions 42, 44, and 47 of the paired domain) to the corresponding amino acids of BSAP resulted in a complete switch of the DNA-binding specificity from Pax-6 to BSAP. These three amino acids were furthermore shown to discriminate between the Pax-6- and BSAP-specific nucleotide at the divergent position of the two consensus recognition sequences.","authors":"Czerny, T., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Mol Cell Biol","volume":"15","issue":"5","page":"2858-71","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7777545","title":"Priming of tumor-specific T cells in the draining lymph nodes after immunization with interleukin 2-secreting tumor cells: three consecutive stages may be required for successful tumor vaccination.","abstract":"Although both CD4+ and CD8+ T cells are clearly required to generate long-lasting anti-tumor immunity induced by s.c. vaccination with interleukin 2 (IL-2)-transfected, irradiated M-3 clone murine melanoma cells, some controversy continues about the site and mode of T-cell activation in this system. Macrophages, granulocytes, and natural killer cells infiltrate the vaccination site early after injection into either syngeneic euthymic DBA\/2 mice or athymic nude mice and eliminate the inoculum within 48 hr. We could not find T cells at the vaccination site, which argues against the concept that T-cell priming by the IL-2-secreting cancer cells occurs directly at that location. However, reverse transcription-PCR revealed transcripts indicative of T-cell activation and expansion in the draining lymph nodes of mice immunized with the IL-2-secreting vaccine but not in mice vaccinated with untransfected, irradiated M-3 cells. We therefore propose that the antigen-presenting cells, which invade the vaccination site, process tumor-derived antigens and, subsequently, initiate priming of tumor-specific T lymphocytes in lymphoid organs. These findings suggest a three-stage process for the generation of effector T cells after vaccination with IL-2-secreting tumor cells: (i) tumor-antigen uptake and processing at the site of injection by antigen-presenting cells, (ii) migration of antigen-presenting cells into the regional draining lymph nodes, where T-cell priming occurs, and (iii) circulation of activated T cells that either perform or initiate effector mechanisms leading to tumor cell destruction.","authors":"Maass, G., Schmidt, W., Berger, M., Schilcher, F., Koszik, F., Schneeberger, A., Stingl, G., Birnstiel, ML., Schweighoffer, T.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Proc Natl Acad Sci U S A","volume":"92","issue":"12","page":"5540-4","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1995-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11524682","title":"Crystal structure of the APC10\/DOC1 subunit of the human anaphase-promoting complex.","abstract":"The anaphase-promoting complex (APC), or cyclosome, is a cell cycle-regulated ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC is composed of at least 11 subunits; no structure has been determined for any of these subunits. The subunit APC10\/DOC1, a one-domain protein consisting of 185 amino acids, has a conserved core (residues 22-161) that is homologous to domains found in several other putative ubiquitin ligases and, therefore, may play a role in ubiquitination reactions. Here we report the crystal structure of human APC10 at 1.6 A resolution. The core of the protein is formed by a beta-sandwich that adopts a jellyroll fold. Unexpectedly, this structure is highly similar to ligand-binding domains of several bacterial and eukaryotic proteins, such as galactose oxidase and coagulation factor Va, raising the possibility that APC10 may function by binding a yet unidentified ligand. We further provide biochemical evidence that the C-terminus of APC10 binds to CDC27\/APC3, an APC subunit that contains multiple tetratrico peptide repeats.","authors":"Wendt, KS., Vodermaier, HC., Jacob, U., Gieffers, C., Gmachl, M., Peters, JM., Huber, R., Sondermann, P.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Struct Biol","volume":"8","issue":"9","page":"784-8","pdf":null,"JrId":"8610","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7753870","title":"Cancer vaccines: the interleukin 2 dosage effect.","abstract":"Cancer vaccines genetically engineered to produce interleukin 2 have been investigated intensively in a series of animal models and are at the point of entering into clinical trials. In this study we demonstrate a strong correlation between the rate of interleukin 2 production and the protection efficiency of murine S91 melanoma cell (clone M-3) vaccines. Best immunization is achieved with vaccines producing medium interleukin 2 levels of 1000-3000 units per 10(5) cells per day. Reduced interleukin 2 production evokes a corresponding decline in the number of successfully treated animals. Unexpectedly, when interleukin 2 expression is raised to high levels of 5000-7500 units per 10(5) cells per day, protection is completely absent because of impaired generation of tumor-specific cytotoxic T lymphocytes. In comparison, granulocyte-macrophage colony-stimulating factor as immunomodulator induces substantial immunization even at a moderate level of secretion and protects all animals at the maximal obtainable level of secretion. Our findings demonstrate the importance of the interleukin 2 level produced by genetically modified tumor cells and may have substantial impact for the clinical application of cancer vaccines.","authors":"Schmidt, W., Schweighoffer, T., Herbst, E., Maass, G., Berger, M., Schilcher, F., Schaffner, G., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Proc Natl Acad Sci U S A","volume":"92","issue":"10","page":"4711-4","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11402336","title":"AP-1 in mouse development and tumorigenesis.","abstract":"Genetically modified mice have provided important insights into the biological functions of the dimeric transcription factor complex AP-1. Extensive analyses of mice and cells with genetically modified Fos or Jun proteins provide novel insights into the physiological functions of AP-1 proteins. Using knock-out strategies it was found that some components, such as c-Fos, FosB and JunD are dispensable, whereas others, like c-Jun, JunB and Fra-1 are essential in embryonic development and\/or in the adult organism. Besides the specific roles of AP-1 proteins in developmental processes, we are beginning to obtain a better molecular understanding of the cell-context dependent function of AP-1 in cell proliferation and apoptosis, in bone biology as well as in multistep tumorigenesis.","authors":"Jochum, W., Passegu\u00e9, E., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Oncogene","volume":"20","issue":"19","page":"2401-12","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7732572","title":"Nuclear factors in sevenless signalling.","abstract":"Recent studies in both vertebrates and invertebrates support an 'hourglass' model for signal transduction from receptor tyrosine kinases: Ras channels signals from diverse receptor tyrosine kinases into a common cytoplasmic kinase cascade, the targets of which are an even more diverse collection of nuclear proteins. What are these nuclear factors, and how do they interact to direct specific cellular responses to a generic signal? The past year has brought considerable progress in our quest to answer these questions in one model genetic system, the Drosophila eye.","authors":"Dickson, B.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Trends Genet","volume":"11","issue":"3","page":"106-11","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"1995-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11389834","title":"Emi1 is a mitotic regulator that interacts with Cdc20 and inhibits the anaphase promoting complex.","abstract":"We have discovered an early mitotic inhibitor, Emi1, which regulates mitosis by inhibiting the anaphase promoting complex\/cyclosome (APC). Emi1 is a conserved F box protein containing a zinc binding region essential for APC inhibition. Emi1 accumulates before mitosis and is ubiquitylated and destroyed in mitosis, independent of the APC. Emi1 immunodepletion from cycling Xenopus extracts strongly delays cyclin B accumulation and mitotic entry, whereas nondestructible Emi1 stabilizes APC substrates and causes a mitotic block. Emi1 binds the APC activator Cdc20, and Cdc20 can rescue an Emi1-induced block to cyclin B destruction. Our results suggest that Emi1 regulates progression through early mitosis by preventing premature APC activation, and may help explain the well-known delay between cyclin B\/Cdc2 activation and cyclin B destruction.","authors":"Reimann, JD., Freed, E., Hsu, JY., Kramer, ER., Peters, JM., Jackson, PK.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell","volume":"105","issue":"5","page":"645-55","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7736579","title":"Genes involved in sister chromatid separation are needed for B-type cyclin proteolysis in budding yeast.","abstract":"B-type cyclin destruction is necessary for exit from mitosis and the initiation of a new cell cycle. Through the isolation of mutants, we have identified three essential yeast genes, CDC16, CDC23, and CSE1, which are required for proteolysis of the B-type cyclin CLB2 but not of other unstable proteins. cdc23-1 mutants are defective in both entering and exiting anaphase. Their failure to exit anaphase can be explained by defective cyclin proteolysis. CDC23 is required at the metaphase\/anaphase transition to separate sister chromatids, and we speculate that it might promote proteolysis of proteins that hold sister chromatids together. Proteolysis of CLB2 is initiated in early anaphase, but a fraction of CLB2 remains stable until anaphase is complete.","authors":"Irniger, S., Piatti, S., Michaelis, C., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell","volume":"81","issue":"2","page":"269-78","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11448778","title":"Sister chromatid cohesion is required for postreplicative double-strand break repair in Saccharomyces cerevisiae.","abstract":"The repair of DNA double-strand breaks by recombination requires the presence of an undamaged copy that is used as a template during the repair process. Because cells acquire resistance to gamma irradiation during DNA replication and because sister chromatids are the preferred partner for double-strand break repair in mitotic diploid yeast cells, it has long been suspected that cohesion between sister chromatids might be crucial for efficient repair. This hypothesis is consistent with the sensitivity to gamma irradiation of mutants defective in the cohesin complex that holds sister chromatids together from DNA replication until the onset of anaphase (reviewed in) . It is also in accordance with the finding that surveillance mechanisms (checkpoints) that sense DNA damage arrest cell cycle progression in yeast by causing stabilization of the securin Pds1, thereby blocking sister chromatid separation. The hypersensitivity to irradiation of cohesin mutants could, however, be due to a more direct involvement of the cohesin complex in the process of DNA repair. We show here that passage through S phase in the presence of cohesin, and not cohesin per se, is essential for efficient double-strand break repair during G2 in yeast. Proteins needed to load cohesin onto chromosomes (Scc2) and to generate cohesion during S phase (Eco1) are also shown to be required for repair. Our results confirm what has long been suspected but never proven, that cohesion between sister chromatids is essential for efficient double-strand break repair in mitotic cells.","authors":"Sj\u00f6gren, C., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Curr Biol","volume":"11","issue":"12","page":"991-5","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8723940","title":"Glycerol enhancement of ligand-polylysine\/DNA transfection.","abstract":"Primary human fibroblasts and a series of cell lines (A549, BNL CL.2, H225, NIH 3T3 and Rat-1) are efficiently transfected by using positively charged complexes of plasmid DNA and transferrin-polylysine or polylysine in the presence of glycerol (1 molar to 1.8 molar, depending on the cell type). An increase in gene expression of up to several-hundredfold (compared to complexes without glycerol) is obtained if the transfection mixture is incubated with the cells for 3-4 h at 37 degrees C. This simple method has been used for transient expression of luciferase, beta-galactosidase and interleukin-2, and also for the generation of stably transfected cells.","authors":"Zauner, W., Kichler, A., Schmidt, W., Sinski, A., Wagner, E.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Biotechniques","volume":"20","issue":"5","page":"905-13","pdf":null,"JrId":"1595","fulltextlink":null,"preprintlink":null,"articledate":"1996-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7704015","title":"Characteristics of imprinted genes.","abstract":null,"authors":"Neumann, B., Kubicka, P., Barlow, DP.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Nat Genet","volume":"9","issue":"1","page":"12-3","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"1995-05-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8682095","title":"The role of transgenic knockout models in defining the pathogenesis of viral heart disease.","abstract":"The pathogenesis of viral myocarditis involves contributions from the virus, the immune system and myocytes. In defining the molecular contributions in the disease process, modulations of the components of the immune system through transgenic knockout models provide useful insights. Advantages of the transgenic knockout models are that they allow biological evaluation of the importance of a particular molecule in the physiological context of an intact organism. Furthermore, the techniques of transgenic knockout models are now standardized, even though they are still technically challenging and time consuming. An example in myocarditis is the IRF-1 knockout mouse, where there is a complete absence of the inducible form of nitric oxide synthetase in the tissues. These animals are exquisitely sensitive to coxsackieviral infection, with extremely high mortality. On the other hand, CD4 knockouts appear to still have myocarditis in an autoimmune myocarditis model, while p56lck knockouts (the T-cell tyrosine kinase signalling molecule) appears to be free of viral myocarditis. These elegant systems of molecular manipu-lation should allow us unique insights into the pathogenesis of myocarditis.","authors":"Liu, P., Penninger, J., Aitken, K., Sole, M., Mak, T.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Eur Heart J","volume":"16 Suppl O","issue":null,"page":"25-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1996-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9989492","title":"The actin cytoskeleton and lymphocyte activation.","abstract":null,"authors":"Penninger, JM., Crabtree, GR.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cell","volume":"96","issue":"1","page":"9-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-03-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"39","title":"Formation of transient complexes in the glutamate dehydrogenase catalyzed reaction.","abstract":"The reaction of glutamate dehydrogenase and glutamate (gl) with NAD+ and NADP+ has been studied with stopped-flow techniques. The enzyme was in all experiments present in excess of the coenzyme. The results indicate that the ternary complex (E-NAD(P)H-kg) is present as an intermediate in the formation of the stable complex (E-NAD(P)H-gl). The identification of the complexes is based on their absorption spectra. The binding of the coenzyme to (E-gl) is the rate-limiting step in the formation of (E-NAD(P)H-kg) while the dissociation of alpha-ketoglutarate (kg) from this complex is the rate-limiting step in the formation of (E-NAD(P)H-gl). The Km for glutamate was 20-25 mM in the first reaction and 3 mM in the formation of the stable complex. The Km values were independent of the coenzyme. The reaction rates with NAD+ were approximately 50% greater than those with NADP+. Furthermore, high glutamate concentration inhibited the formation of (E-NADH-kg) while no substrate inhibition was found with NADP+ as coenzyme. ADP enhanced while GTP reduced the rate of (E-NAD(P)H-gl) formation. The rate of formation of (E-NAD(P)H-kg) was inhibited by ADP, while it increased at high glutamate concentration when small amounts of GTP were added. The results show that the higher activity found with NAD+ compared to NADP+ under steady-state assay conditions do not necessarily involve binding of NAD+ to the ADP activating site of the enzyme. Moreover, the substrate inhibition found at high glutamate concentration under steady-state assay condition is not due to the formation of (E-NAD(P)H-gl) as this complex is formed with Km of 3 mM glutamate, and the substrate inhibition is only significant at 20-30 times this concentration.","authors":"Sanner, T.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"23","page":"5094-8","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25","title":"Pharmacological properties of new neuroleptic compounds.","abstract":"RMI 61 140, RMI 61 144 and RMI 61 280 are newly synthetized N-[8-R-dibenzo(b,f)oxepin-10-yl]-N'-methyl-piperazine-maleates which show interesting psychopharmacologic effects. This work contains the results of a study performed with these three compounds, in order to demonstrate their neuropsycholeptic activity in comparison with chloropromazine (CPZ) and chlordiazepoxide (CPD). The inhibition of motility observed in mice shows that the compounds reduce the normal spontaneous motility as well as the muscle tone. The central-depressant activity is evidenced by increased barbiturate-induced sleep and a remarkable eyelid ptosis can also be observed. Our compounds do not show any activity on electroshock just as do CPZ and CPD. As to the antipsychotic outline, our compounds show strong reduction of lethality due to amphetamine in grouped mice and a strong antiapomorphine activity. They show also an antiaggressive effect and an inhibitory activity on avoidance behaviour much stronger than CPZ. We have also found extrapyramidal effects, as catalepsy, common to many tranquillizers of the kind of the standards used by us. As for vegetative phenomena, the compounds show hypotensive dose related action ranging from moderate to strong, probably due to an a-receptor inhibition. Adrenolytic activity against lethal doses of adrenaline, antiserotonin and antihistaminic effects, as well as other actions (hypothermia, analgesia, etc.) confirm that RMI 61 140, RMI 61 144 and RMI 61 280 are endowed with pharmacologic properties similar and more potent than those of CPZ. Studies on the metabolism of brain catecholamines show that they are similar to CPZ, although with less effect on dopamine level.","authors":"Coscia, L., Causa, P., Giuliani, E., Nunziata, A.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Arzneimittelforschung","volume":"25","issue":"9","page":"1436-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9096381","title":"Cell-free tumor antigen peptide-based cancer vaccines.","abstract":"The central role that tumor antigen-derived peptides play in induction of antitumor immunity makes them ideal candidates for peptide-based cancer vaccines. We have demonstrated that \"transloading\" is an efficient strategy for importing short peptide ligands into antigen-presenting cells in vitro. Postulating that the transloading procedure might effect peptide uptake by antigen-presenting cells in vivo as well, we tested this approach for the generation of peptide-based cancer vaccines. In the P815 mastocytoma system, we vaccinated mice by s.c. injection of a single, known natural peptide derived from JAK-1 kinase. Whereas vaccination with peptide alone or mixed with incomplete Freund's adjuvant was ineffective, application of the peptide in conjunction with the polycation poly-L-lysine protected a significant number of animals against tumor challenge. Dependent upon the type of poly-L-lysine applied, protection against tumor take was comparable to that achieved with irradiated whole-cell vaccines, genetically modified to secrete granulocyte-macrophage colony-stimulating factor. In the murine melanoma M-3, a combination of four putative tumor antigen-derived peptides was tested as a cancer vaccine. Administered in combination with polycations, these peptides evoked potent antitumor immunity that could not be obtained with the peptides alone or peptides emulsified in incomplete Freund's adjuvant. However, peptide-polycation vaccines applied to the M-3 model were not as efficient as cellular control vaccines, consisting of irradiated interleukin 2 or granulocyte-macrophage colony-stimulating factor-secreting tumor cells.","authors":"Schmidt, W., Buschle, M., Zauner, W., Kirlappos, H., Mechtler, K., Trska, B., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Proc Natl Acad Sci U S A","volume":"94","issue":"7","page":"3262-7","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1997-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7663515","title":"Deregulation of both imprinted and expressed alleles of the insulin-like growth factor 2 gene during beta-cell tumorigenesis.","abstract":"In a mouse model of multistage carcinogenesis elicited by the SV40 large T-antigen (Tag) oncogene in pancreatic beta cells, the gene for insulin-like growth factor IGF2 is focally up-regulated and functionally implicated in tumour development. The IGF2 gene is differentially regulated in normal tissues: the paternal allele is transiently expressed during embryogenesis, whereas the maternal allele is genomically imprinted and inactive. Crossbred mice carrying the Tag oncogene and a disruption of either the paternal or maternal allele of IGF2 reveal that both alleles are co-activated early during tumour development, and that each contributes to malignant hyperproliferation and consequent tumour volume.","authors":"Christofori, G., Naik, P., Hanahan, D.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Nat Genet","volume":"10","issue":"2","page":"196-201","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"1995-10-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7662710","title":"Rab and rho GTPases are involved in specific response of periodontal ligament fibroblasts to mechanical stretching.","abstract":"To investigate the contribution of ras-related signalling molecules to the mechanotransduction process, stretch-sensing human periodontal ligament (PDL) fibroblasts were isolated and cultured in dishes with a flexible bottom. The cells were stimulated by stretching the bottom of the dishes and membrane fractions were prepared and analysed at the level of mapping small GTP-binding proteins by high resolution two-dimensional gel electrophoresis followed by renaturing transfer and an [alpha-32P]GTP-overlay procedure. This analysis revealed that mechanically-stretched PDL fibroblasts exhibit complete down-regulation of rhoA and induction of rab6, rab17 and a putative member of the rab3 subfamily in a cell type-specific manner.","authors":"Basdra, EK., Papavassiliou, AG., Huber, LA.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Biochim Biophys Acta","volume":"1268","issue":"2","page":"209-13","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1995-10-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34392423","title":"Giant Y79 retinoblastoma cells contain functionally active T-type calcium channels.","abstract":"Retinoblastoma is the most common malignant intraocular tumor in children. Y79 human retinoblastoma cells are in vitro models of retinal tumors used for drug screening. Undifferentiated Y79 cells originate from a primitive multi-potential neuroectodermal cell and express neuronal and glial properties. However, the nature of cellular heterogeneity in Y79 cells is unclear because functional methods to characterize neurons or glial cells have not been employed to Y79 cells. Here, we perform patch-clamp recordings to characterize electrophysiological properties in retinoblastoma cells. We identified a population of large-sized Y79 cells (i.e., giant cells,\u2009~\u200940-\u00b5m diameter), hyperpolarized resting membrane potential (-54\u00a0mV), and low input resistance (~\u2009600 M\u03a9), indicating electrically mature cells. We also found that giant Y79 cells contain increased density of T-type calcium channels. Finally, we found that T-type calcium channels are active only in giant cells suggesting that cancer treatments aimed to prevent calcium influx in retinoblastomas should be tested in giant cells.","authors":"Kim, S., Guzman, SJ., Jo, DH., Cho, CS., Kim, JH.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Pflugers Arch","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10234557","title":"Osteoprotegerin ligand: a common link between osteoclastogenesis, lymph node formation and lymphocyte development.","abstract":"The TNF-family molecule osteoprotegerin ligand (OPGL; also known as TRANCE, RANKL or ODF) has been identified as the osteoclast differentiation factor and a regulator of T cell-dendritic cell interactions in the immune system. Surprisingly, the same molecule was identified as a crucial factor in early lymphocyte development and lymph node organogenesis. We will discuss the role of OPGL in bone remodelling and the immune system.","authors":"Kong, YY., Boyle, WJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Immunol Cell Biol","volume":"77","issue":"2","page":"188-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11342298","title":"Pax5 determines the identity of B cells from the beginning to the end of B-lymphopoiesis.","abstract":"Despite being one of the most intensively studied cell types, the molecular basis of B cell specification is largely unknown. The Pax5 gene encoding the transcription factor BSAP is required for progression of B-lymphopoiesis beyond the pro-B cell stage. Pax5-deficient pro-B cells are, however, not yet committed to the B-lymphoid lineage, but instead have a broad lymphomyeloid developmental potential. Pax5 appears to mediate B-lineage commitment by repressing the transcription of non-B-lymphoid genes and by simultaneously activating the expression of B-lineage-specific genes. Pax5 thus functions both as a transcriptional repressor and activator, depending on its interactions with corepressors of the Groucho protein family or with positive regulators such as the TATA-binding protein. Once committed to the B-lineage, B cells require Pax5 function to maintain their B-lymphoid identity throughout B cell development.","authors":"Nutt, SL., Eberhard, D., Horcher, M., Rolink, AG., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Int Rev Immunol","volume":"20","issue":"1","page":"65-82","pdf":null,"JrId":"4890","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9081706","title":"In vitro targeting and specific transfection of human neuroblastoma cells by chCE7 antibody-mediated gene transfer.","abstract":"We developed a new vector for gene targeting of neuroblastoma (NB) cells, based on the utilization o a monoclonal antibody (chCE7) covalently linked to polylysine (PL). In the presence of chloroquine, chCE7-PL-DNA complexes transfected NB cells as efficiently as DOTAP, transfectam, TF-X50, or lipofectamine. This was demonstrated by transfection of the luciferase or beta-galactosidase reporter genes in three different NB cell lines. This transfection was specific, since it was inhibited in the presence of competing unconjugated chCE7 antibody (Ab), and was not observed in cell lines negative for the CE7 antigen. We tested the potential biological activity of a plasmid coding for gamma-interferon (gamma IFN) transfected with chCE7-PL. HLA ABC expression on NB cells was induced after transfection with pCMV-gamma IFN at a higher level than after incubation with 1000 IU\/ml of purified gamma IFN. Moreover, these HLA ABC-positive NB cells were able to activate autologous cytotoxic T lymphocytes in vitro. Thus chCE7-PL is able to target a plasmid to NB cells and to allow the expression of the transfected gene in a biologically active form.","authors":"Coll, JL., Wagner, E., Combaret, V., Metchler, K., Amstutz, H., Iacono-Di-Cacito, I., Simon, N., Favrot, MC.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Gene Ther","volume":"4","issue":"2","page":"156-61","pdf":null,"JrId":"8603","fulltextlink":null,"preprintlink":null,"articledate":"1997-04-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7641874","title":"Mapping cells and sub-cellular organelles on 2-D gels: 'new tricks for an old horse'.","abstract":"Nowadays, investigators in all fields are faced with the identification of unknown, up- or down-regulated, modified proteins that they are trying to identify. Two-dimensional (2-D) gel electrophoresis, with its ability to resolve several thousand proteins, is an extremely powerful technique. The current resolution and reproducibility of 2-D gel technology and the establishment of computer assisted 2-D gel protein databases have paved new ways for the identification of proteins.","authors":"Huber, LA.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"FEBS Lett","volume":"369","issue":"1","page":"122-5","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"1995-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7640960","title":"Sequence of an exon of tumour suppressor p53 gene--a comparative study in domestic animals: mutation in a feline solid mammary carcinoma.","abstract":"Partial sequence determinations were performed on exon 8 of tumour suppressor gene p53 of cattle, sheep, goat, horse and pig. High sequence homology between these species and other species including dog, cat, chicken and man is demonstrated. A mutation CGG--&gt;TGG (arginine--&gt;tryptophan) was detected in a feline solid carcinoma of the mammary gland.","authors":"Mayr, B., Schaffner, G., Kurzbauer, R., Reifinger, M., Schellander, K.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Br Vet J","volume":"151","issue":"3","page":"325-9","pdf":null,"JrId":"1916","fulltextlink":null,"preprintlink":null,"articledate":"1995-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11172026","title":"Jun N-terminal kinase 2 modulates thymocyte apoptosis and T cell activation through c-Jun and nuclear factor of activated T cell (NF-AT).","abstract":"The Jun N-terminal kinases (JNKs) recently have been shown to be required for thymocyte apoptosis and T cell differentiation and\/or proliferation. To investigate the molecular targets of JNK signaling in lymphoid cells, we used mice in which the serines phosphorylated by JNK in c-Jun were replaced by homologous recombination with alanines (junAA mice). Lymphocytes from these mice showed no phosphorylation of c-Jun in response to activation stimuli, whereas c-Jun was rapidly phosphorylated in wild-type cells. Despite the fact that c-jun is essential for early development, junAA mice develop normally; however, c-Jun N-terminal phosphorylation was required for efficient T cell receptor-induced and tumor necrosis factor-alpha-induced thymocyte apoptosis. In contrast, c-Jun phosphorylation by JNK is not required for T cell proliferation or differentiation. Because jnk2-\/- T cells display a proliferation defect, we concluded that JNK2 must have other substrates required for lymphocyte function. Surprisingly, jnk2-\/- T cells showed reduced NF-AT DNA-binding activity after activation. Furthermore, overexpression of JNK2 in Jurkat T cells strongly enhanced NF-AT-dependent transcription. These results demonstrate that JNK signaling differentially uses c-Jun and NF-AT as molecular effectors during thymocyte apoptosis and T cell proliferation.","authors":"Behrens, A., Sabapathy, K., Graef, I., Cleary, M., Crabtree, GR., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Proc Natl Acad Sci U S A","volume":"98","issue":"4","page":"1769-74","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2001-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34423833","title":"In vitro models of the human heart.","abstract":"Cardiac congenital disabilities are the most common organ malformations, but we still do not understand how they arise in the human embryo. Moreover, although cardiovascular disease is the most common cause of death globally, the development of new therapies is lagging compared with other fields. One major bottleneck hindering progress is the lack of self-organizing human cardiac models that recapitulate key aspects of human heart development, physiology and disease. Current in vitro cardiac three-dimensional systems are either engineered constructs or spherical aggregates of cardiomyocytes and other cell types. Although tissue engineering enables the modeling of some electro-mechanical properties, it falls short of mimicking heart development, morphogenetic defects and many clinically relevant aspects of cardiomyopathies. Here, we review different approaches and recent efforts to overcome these challenges in the field using a new generation of self-organizing embryonic and cardiac organoids.","authors":"Hofbauer, P., Jahnel, SM., Mendjan, S.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Development","volume":"148","issue":"16","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7618085","title":"Strain-dependent epithelial defects in mice lacking the EGF receptor.","abstract":"Mice and cells lacking the epidermal growth factor receptor (EGFR) were generated to examine its physiological role in vivo. Mutant fetuses are retarded in growth and die at mid-gestation in a 129\/Sv genetic background, whereas in a 129\/Sv x C57BL\/6 cross some survive until birth and even to postnatal day 20 in a 129\/Sv x C57BL\/6 x MF1 background. Death in utero probably results from a defect in the spongiotrophoblast layer of the placenta. Newborn mutant mice have open eyes, rudimentary whiskers, immature lungs, and defects in the epidermis, correlating with the expression pattern of the EGFR as monitored by beta-galactosidase activity. These defects are probably cell-autonomous because chimeric mice generated with EGFR-\/- embryonic stem cells contribute small amounts of mutant cells to some organs. These results indicate that the EGFR regulates epithelial proliferation and differentiation and that the genetic background influences the resulting phenotype.","authors":"Sibilia, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Science","volume":"269","issue":"5221","page":"234-8","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1995-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7629057","title":"Low affinity binding of interleukin-1 beta and intracellular signaling via NF-kappa B identify Fit-1 as a distant member of the interleukin-1 receptor family.","abstract":"The fit-1 gene gives rise to two different mRNA isoforms, which code for soluble (Fit-1S) and membrane-bound (Fit-1M) proteins related to the type I interleukin (IL)-1 receptor. To investigate IL-1 binding, we have synthesized and purified histidine-tagged polypeptides corresponding to Fit-1S and the extracellular domain of the type I IL-1 receptor using a vaccinia expression system. Fit-1S is shown to interact with IL-1 beta, but not with IL-1 alpha. However, Fit-1S binds IL-1 beta only with low affinity in contrast to the IL-1 receptor, suggesting that IL-1 beta is not a physiological ligand of Fit-1S. Moreover, expression of the membrane-bound protein Fit-1M in transiently transfected Jurkat cells did not result in activation of the transcription factor NF-kappa B following IL-1 beta treatment. However, a chimeric protein consisting of the extracellular domain of the type I IL-1 receptor and of the transmembrane and intracellular regions of Fit-1M stimulated NF-kappa B-dependent transcription as efficiently as the full-length type I IL-1 receptor. These data indicate that Fit-1M is a signaling molecule belonging to the IL-1 receptor family.","authors":"Reikerstorfer, A., Holz, H., Stunnenberg, HG., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Biol Chem","volume":"270","issue":"30","page":"17645-8","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1995-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7607706","title":"The PAX5 gene: a linkage and mutation analysis in candidate human primary immunodeficiencies.","abstract":null,"authors":"Vorechovsk\u00fd, I., Koskinen, S., Paganelli, R., Smith, CI., Busslinger, M., Hammarstr\u00f6m, L.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Immunogenetics","volume":"42","issue":"2","page":"149-52","pdf":null,"JrId":"4198","fulltextlink":null,"preprintlink":null,"articledate":"1995-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8668141","title":"EGT2 gene transcription is induced predominantly by Swi5 in early G1.","abstract":"In a screen for cell cycle-regulated genes in the yeast Saccharomyces cerevisiae, we have identified a gene, EGT2, which is involved in cell separation in the G1 stage of the cell cycle. Transcription of EGT2 is tightly regulated in a cell cycle-dependent manner. Transcriptional levels peak at the boundary of mitosis and early G1 The transcription factors responsible for EGT2 expression in early G1 are Swi5 and, to a lesser extent, Ace2. Swi5 is involved in the transcriptional activation of the HO gene during late G1 and early S phase, and Ace2 induces CTS1 transcription during early and late G1 We show that Swi5 activates EGT2 transcription as soon as it enters the nucleus at the end of mitosis in a concentration-dependent manner. Since Swi5 is unstable in the nucleus, its level drops rapidly, causing termination of EGT2 transcription before cells are committed to the next cell cycle. However, Swi5 is still able to activate transcription of HO in late G1 in conjunction with additional activators such as Swi4 and Swi6.","authors":"Kovacech, B., Nasmyth, K., Schuster, T.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Mol Cell Biol","volume":"16","issue":"7","page":"3264-74","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1996-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34423297","title":"Impaired dopamine metabolism is linked to fatigability in mice and fatigue in Parkinson's disease patients.","abstract":"Fatigue is a common symptom of Parkinson's disease that compromises significantly the patients' quality of life. Despite that, fatigue has been under-recognized as symptom, its pathophysiology remains poorly understood, and there is no adequate treatment so far. Parkinson's disease is characterized by the progressive loss of midbrain dopaminergic neurons, eliciting the classical motor symptoms including slowing of movements, muscular rigidity and resting tremor. The dopamine synthesis is mediated by the rate-limiting enzyme tyrosine hydroxylase, which requires tetrahydrobiopterin as a mandatory cofactor. Here, we showed that reserpine administration (1\u2009mg\/kg, two intraperitoneal injections with an interval of 48\u2009h) in adult Swiss male mice (8-10\u2009weeks; 35-45\u2009g) provoked striatal depletion of dopamine and tetrahydrobiopterin, and intolerance to exercise. The poor exercise performance of reserpinized mice was not influenced by emotional or anhedonic factors, mechanical nociceptive thresholds, electrocardiogram pattern alterations or muscle-impaired bioenergetics. The administration of levodopa (100\u2009mg\/kg; i.p.) plus benserazide (50\u2009mg\/kg; i.p.) rescued reserpine-induced fatigability-like symptoms and restored striatal dopamine and tetrahydrobiopterin levels. Remarkably, it was observed, for the first time, that impaired blood dopamine metabolism inversely and idependently correlated with fatigue scores in eighteen idiopathic Parkinson's disease patients (male <i>n\u2009<\/i>=<i>\u2009<\/i>13; female <i>n\u2009<\/i>=<i>\u2009<\/i>5; age 61.3\u2009\u00b1\u20099.59\u2009years). Altogether, this study provides new experimental and clinical evidence that fatigue symptoms might be caused by the impaired striatal dopaminergic neurotransmission, pointing to a central origin of fatigue in Parkinson's disease.","authors":"Scheffer, DDL., Freitas, FC., Aguiar, AS., Ward, C., Guglielmo, LGA., Prediger, RD., Cronin, SJF., Walz, R., Andrews, NA., Latini, A.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Brain Commun","volume":"3","issue":"3","page":"fcab116","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7587278","title":"Protein structure prediction: recognition of primary, secondary, and tertiary structural features from amino acid sequence.","abstract":"This review attempts a critical stock-taking of the current state of the science aimed at predicting structural features of proteins from their amino acid sequences. At the primary structure level, methods are considered for detection of remotely related sequences and for recognizing amino acid patterns to predict posttranslational modifications and binding sites. The techniques involving secondary structural features include prediction of secondary structure, membrane-spanning regions, and secondary structural class. At the tertiary structural level, methods for threading a sequence into a mainchain fold, homology modeling and assigning sequences to protein families with similar folds are discussed. A literature analysis suggests that, to date, threading techniques are not able to show their superiority over sequence pattern recognition methods. Recent progress in the state of ab initio structure calculation is reviewed in detail. The analysis shows that many structural features can be predicted from the amino acid sequence much better than just a few years ago and with attendant utility in experimental research. Best prediction can be achieved for new protein sequences that can be assigned to well-studied protein families. For single sequences without homologues, the folding problem has not yet been solved.","authors":"Eisenhaber, F., Persson, B., Argos, P.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Crit Rev Biochem Mol Biol","volume":"30","issue":"1","page":"1-94","pdf":null,"JrId":"3208","fulltextlink":null,"preprintlink":null,"articledate":"1995-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7584089","title":"Receptor-mediated gene delivery employing lectin-binding specificity.","abstract":"Selective targeting of malignant cells will be necessary to implement many of the gene therapy strategies being designed to combat cancer. Targeting can be achieved by transductional or transcriptional approaches. Transductional targeting can be accomplished by exploiting differences in the molecules or receptors expressed on the cell surface of malignant versus normal cells. Given that malignant cells can be distinguished from normal by differences in the expression of cell surface carbohydrates, we hypothesized that transductional targeting would be feasible by molecular conjugate vectors which achieve cell binding by virtue of lectins directed against the cell surface glycocalyx. We have shown that gene transfer can be accomplished by these novel lectin-targeted molecular conjugate vectors and that lectin binding specificities may serve as a means for potential targeting of cancer cells for the purposes of gene therapy.","authors":"Batra, RK., Wang-Johanning, F., Wagner, E., Garver, RI., Curiel, DT.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Gene Ther","volume":"1","issue":"4","page":"255-60","pdf":null,"JrId":"8603","fulltextlink":null,"preprintlink":null,"articledate":"1995-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7555081","title":"Adenovirus-augmented, receptor-mediated gene delivery and some solutions to the common toxicity problems.","abstract":null,"authors":"Cotten, M.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Curr Top Microbiol Immunol","volume":"199 ( Pt 3)","issue":null,"page":"283-95","pdf":null,"JrId":"3237","fulltextlink":null,"preprintlink":null,"articledate":"1995-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34408281","title":"Correction: Gastric organoids-an in vitro model system for the study of gastric development and road to personalized medicine.","abstract":null,"authors":"Seidlitz, T., Koo, BK., Stange, DE.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Cell Death Differ","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11121682","title":"Molecular control of bone remodeling and osteoporosis.","abstract":"Osteoprotegerin ligand (OPGL, TNFS11) and its receptor RANK (TNFRS11A) are essential for the development and activation of osteoclasts and critical regulators of physiological bone remodeling and osteoporosis. Production of OPGL by activated T cells can directly regulate osteoclastogenesis and bone remodeling. This may explain why autoimmune diseases, cancers, leukemias, asthma and chronic viral infections such as hepatitis and HIV result in systemic and local bone loss. OPGL is also the pathogenetic factor that causes bone and cartilage destruction and clinical crippling in arthritis. Inhibition of OPGL binding to RANK via the natural decoy receptor osteoprotegerin (OPG) prevents bone loss in postmenopausal osteoporosis and cancer metastases and completely blocks crippling in a rat model of arthritis. Moreover, OPG expression is induced by estrogen which provides a molecular explanation of postmenopausal osteoporosis in women.","authors":"Kong, YY., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Exp Gerontol","volume":"35","issue":"8","page":"947-56","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7548275","title":"Receptor-mediated gene transfer into human T lymphocytes via binding of DNA\/CD3 antibody particles to the CD3 T cell receptor complex.","abstract":"Retrovirus-mediated gene transfer is currently the method of choice for the transfection of human T lymphocytes for applications in gene therapy. Use of retroviral vectors, however, is hampered by limits on the size of the genetic material to be transferred, the requirement of dividing target cells, and by potential safety questions. Synthetic peptide-enhanced or adenovirus-enhanced receptor-mediated transferrinfection of DNA (SPET and AVET, respectively) is a powerful method for the introduction of genetic material into mammalian cells. Although transferrin has proven to be a useful ligand for gene transfer in many cell types, gene expression in T cells with transferrin\/DNA complexes is usually not satisfactory. To improve gene transfer to T cells, antibodies directed against the CD3-T cell receptor complex were tested for their ability to function as ligands for DNA delivery. In T cell lines, up to 50% of the cells expressed a beta-galactosidase reporter gene using anti-CD3 gene transfer complexes. Applying optimized conditions, prestimulated primary peripheral blood lymphocytes were also transfected successfully, although at a lesser efficiency (5%).","authors":"Buschle, M., Cotten, M., Kirlappos, H., Mechtler, K., Schaffner, G., Zauner, W., Birnstiel, ML., Wagner, E.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Hum Gene Ther","volume":"6","issue":"6","page":"753-61","pdf":null,"JrId":"1041","fulltextlink":null,"preprintlink":null,"articledate":"1995-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8647170","title":"Human CD4 and human major histocompatibility complex class II (DQ6) transgenic mice: supersensitivity to superantigen-induced septic shock.","abstract":"Rodents are significantly less sensitive to enterotoxin-induced shock, and are thus not valid human disease models. Here, we describe a mouse strain carrying the human CD4 and human major histocompatibility complex (MHC) class II (DQ6) transgenes in an endogenous CD4- and CD8-deficient background. T lymphocytes from these animals react to minute amounts (10-100 times less than control mice) of staphylococcal enterotoxin B (SEB) in vitro, similar to concentrations to which human cells react. In vivo, these double-transgenic, double-knockout mice succumb to normally sublethal amounts of SEB. This sensitivity is not due to a biased T cell receptor V beta repertoire, increased T cell reactivity, or increased sensitivity to macrophage-derived cytokines. Rather, tumor necrosis factor (TNF)-alpha production by T cells and serum levels of TNF-alpha correlate precisely with the clinical syndrome, showing a biphasic T cell-dependent response. These data show that both human CD4 and MHC class II molecules can render mice supersensitive to superantigen-induced septic shock syndrome. This animal model mimics the progression of septic shock in man by transforming normally resistant mice into hypersensitive SEB responders, a trait that is characteristic of humans. Mice that have been humanized by exchanging autochthonous superantigen ligands by their human equivalents may be useful to decipher superantigen responses in vivo and to assess the pathogenesis of superantigen-associated diseases.","authors":"Yeung, RS., Penninger, JM., K\u00fcndig, T., Khoo, W., Ohashi, PS., Kroemer, G., Mak, TW.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Eur J Immunol","volume":"26","issue":"5","page":"1074-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1996-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17442891","title":"Ihh\/Gli2 signaling promotes osteoblast differentiation by regulating Runx2 expression and function.","abstract":"Genetic and cell biological studies have indicated that Indian hedgehog (Ihh) plays an important role in bone development and osteoblast differentiation. However, the molecular mechanism by which Ihh regulates osteoblast differentiation is complex and remains to be fully elucidated. In this study, we investigated the role of Ihh signaling in osteoblast differentiation using mesenchymal cells and primary osteoblasts. We observed that Ihh stimulated alkaline phosphatase (ALP) activity, osteocalcin expression, and calcification. Overexpression of Gli2- but not Gli3-induced ALP, osteocalcin expression, and calcification of these cells. In contrast, dominant-negative Gli2 markedly inhibited Ihh-dependent osteoblast differentiation. Ihh treatment or Gli2 overexpression also up-regulated the expression of Runx2, an essential transcription factor for osteoblastogenesis, and enhanced the transcriptional activity and osteogenic action of Runx2. Coimmunoprecipitation analysis demonstrated a physical interaction between Gli2 and Runx2. Moreover, Ihh or Gli2 overexpression failed to increase ALP activity in Runx2-deficient mesenchymal cells. Collectively, these results suggest that Ihh regulates osteoblast differentiation of mesenchymal cells through up-regulation of the expression and function of Runx2 by Gli2.","authors":"Shimoyama, A., Wada, M., Ikeda, F., Hata, K., Matsubara, T., Nifuji, A., Noda, M., Amano, K., Yamaguchi, A., Nishimura, R., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Biol Cell","volume":"18","issue":"7","page":"2411-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7533981","title":"Genetic modification of cells by receptor-mediated adenovirus-augmented gene delivery: a new approach for immunotherapy of cancer.","abstract":"Most concepts of gene therapy of cancer are based on the generation of an enhanced immune response against the cancer by means of vaccination with gene-modified cancer cells. We have investigated the applicability of a new gene transfer technique which uses the receptor-mediated endocytosis pathway and the endosome disruption activity of adenovirus for the generation of a cancer vaccine consisting of interleukin-2 (IL-2)-transfected, irradiated murine melanoma cells (clone M-3). This technique resulted in very high IL-2 expression (in the range of 30,000 Units IL-2\/10(6) cells\/24 hrs) in the transfected cells without the need to selection of stably expressing cell clones. We found that this high IL-2 expression of the melanoma cells correlates with high efficacy of the vaccine. Immunization of animals with this vaccine elicits a systemic T-cell-mediated immune response which protects from tumor development after implantation of highly tumorigenic doses of wild-type melanoma cells.","authors":"Zatloukal, K., Schneeberger, A., Berger, M., Koszik, F., Schmidt, W., Wagner, E., Cotten, M., Buschle, M., Maass, G., Stingl, G.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Verh Dtsch Ges Pathol","volume":"78","issue":null,"page":"171-6","pdf":null,"JrId":"7961","fulltextlink":null,"preprintlink":null,"articledate":"1995-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34288709","title":"The Fertilization Enigma: How Sperm and Egg Fuse.","abstract":"Fertilization is a multistep process that culminates in the fusion of sperm and egg, thus marking the beginning of a new organism in sexually reproducing species. Despite its importance for reproduction, the molecular mechanisms that regulate this singular event, particularly sperm-egg fusion, have remained mysterious for many decades. Here, we summarize our current molecular understanding of sperm-egg interaction, focusing mainly on mammalian fertilization. Given the fundamental importance of sperm-egg fusion yet the lack of knowledge of this process in vertebrates, we discuss hallmarks and emerging themes of cell fusion by drawing from well-studied examples such as viral entry, placenta formation, and muscle development. We conclude by identifying open questions and exciting avenues for future studies in gamete fusion. Expected final online publication date for the <i>Annual Review of Cell and Developmental Biology<\/i>, Volume 37 is October 2021. Please see http:\/\/www.annualreviews.org\/page\/journal\/pubdates for revised estimates.","authors":"Deneke, VE., Pauli, A.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Annu Rev Cell Dev Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34328418","title":"McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation.","abstract":"In Gram-positive bacteria, the McsB protein arginine kinase is central to protein quality control, labeling aberrant molecules for degradation by the ClpCP protease. Despite its importance for stress response and pathogenicity, it is still elusive how the bacterial degradation labeling is regulated. Here, we delineate the mechanism how McsB targets aberrant proteins during stress conditions. Structural data reveal a self-compartmentalized kinase, in which the active sites are sequestered in a molecular cage. The 'closed' octamer interconverts with other oligomers in a phosphorylation-dependent manner and, unlike these 'open' forms, preferentially labels unfolded proteins. In vivo data show that heat-shock triggers accumulation of higher order oligomers, of which the octameric McsB is essential for surviving stress situations. The interconversion of open and closed oligomers represents a distinct regulatory mechanism of a degradation labeler, allowing the McsB kinase to adapt its potentially dangerous enzyme function to the needs of the bacterial cell.","authors":"Hajdusits, B., Suskiewicz, MJ., Hundt, N., Meinhart, A., Kurzbauer, R., Leodolter, J., Kukura, P., Clausen, T.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Elife","volume":"10","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.09.08.287243v1","articledate":"2021-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8614412","title":"Vascular endothelial growth factor and its receptors, flt-1 and flk-1, are expressed in normal pancreatic islets and throughout islet cell tumorigenesis.","abstract":"Endocrine organs, such as the pancreatic islets of Langerhans, contain permeable, fenestrated endothelium that allows direct access of endocrine cells to the blood stream. Factors that control differentiation and maintenance of this highly specialized endothelium remain unknown. Vascular endothelial growth factor (VEGF) is a multifunctional growth factor that may be responsible for the homeostasis of endocrine endothelium; it is a selective mitogen for endothelial cells and is able to permeabilize endothelium. We have analyzed the expression of VEGF mRNA and protein in pancreatic islet cells of normal mice and during the different stages of tumor progression in a transgenic mouse model of beta-cell carcinogenesis. The 120-amino acid and the 164-amino acid isoforms of VEGF are expressed in normal islets of Langerhans and are moderately up-regulated during the stages of tumor development. Two high-affinity receptors for VEGF, flt-1 and flk-1, are expressed by endothelial cells both in normal islets and in the stages of tumorigenesis; these receptors are not up-regulated during this process. Our data raise the possibility that VEGF is involved in the maintenance of permeable endothelium in islets of Langerhans, an observation that may have implications for islet cell physiology and diabetes. While VEGF may also play an important role in the growth of new blood vessels during islet cell tumorigenesis, it cannot be the only factor required for the activation of tumor angiogenesis.","authors":"Christofori, G., Naik, P., Hanahan, D.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Mol Endocrinol","volume":"9","issue":"12","page":"1760-70","pdf":null,"JrId":"5920","fulltextlink":null,"preprintlink":null,"articledate":"1996-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7520302","title":"Oncogenes in the study of endothelial cell growth and differentiation.","abstract":"During embryogenesis endothelial cells differentiate from mesodermal blood islands, proliferate and form new blood vessels throughout embryonic and early postnatal life by the processes of vasculogenesis and angiogenesis. Proliferation then ceases and is very low in the adult, although it resumes under certain physiological and pathological conditions, such as wound healing, tumor growth and hemangiomatous diseases. Expression of the polyoma middle T (PymT) oncogene in mouse endothelial cells leads to their rapid transformation and to the development of hemangiomas. These endothelial tumors allow the establishment of endothelioma (End) cell lines, which resemble normal endothelial cells yet exhibit a drastically altered proteolytic activity. The specific effects of PymT on the growth of endothelial cells appear in part to be mediated through the activation of cellular tyrosine kinases.","authors":"Wagner, EF., Risau, W.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Semin Cancer Biol","volume":"5","issue":"2","page":"137-45","pdf":null,"JrId":"1211","fulltextlink":null,"preprintlink":null,"articledate":"1994-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16937268","title":"Critical role of cortactin in actin ring formation and osteoclastic bone resorption.","abstract":"Tyrosine kinase c-Src plays an essential role in ruffled border formation and bone resorption in osteoclasts; however, it is unclear how c-Src controls ruffled border formation during bone resorption. To address this question, we investigated the role of cortactin, a c-Src substrate, in osteoclasts. We found that cortactin showed colocalization with c-Src and actin rings in osteoclasts. Overexpression of cortactin stimulated actin ring formation in RAW 264.7 cells. In contrast, overexpression of Csk inhibited tyrosine phosphorylation of cortactin and binding of cortactin to c-Src. More importantly, overexertion of a mutant cortactin strongly suppressed actin ring formation and bone resorbing activity in osteoclasts. Collectively, our data indicate that cortactin controls osteoclastic bone resorption by regulating actin organization.","authors":"Matsubara, T., Myoui, A., Ikeda, F., Hata, K., Yoshikawa, H., Nishimura, R., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Bone Miner Metab","volume":"24","issue":"5","page":"368-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7495723","title":"Role of the OCTA site in regulation of IgH chain gene transcription during B cell activation.","abstract":"We have evaluated the importance of the OCTA site in both the promoter and enhancer regions for the induction of enhancement of IgH chain gene transcription after B cell activation. These studies show that although occupancy of the OCTA site in the promoter is critical for basal transcription of the mu gene, it is not necessary for the increase in transcription induced by in vivo activation. On the other hand, the OCTA site in the enhancer is necessary for neither basal transcription nor in vivo activation of transcription; however, occupancy of this site is required for further up-regulation in transcription of the mu gene in pre-activated cells. These results indicate that different mechanisms may be involved in the activation of resting versus in vivo stimulated B lymphocytes. The findings are discussed in relation to the phenotype described for Oct-2-deficient mice.","authors":"Yuan, D., Dang, T., Hawley, J., Jenuwein, T., Grosschedl, R.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Int Immunol","volume":"7","issue":"8","page":"1163-72","pdf":null,"JrId":"1837","fulltextlink":null,"preprintlink":null,"articledate":"1996-01-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34475534","title":"Release of Notch activity coordinated by IL-1\u03b2 signalling confers differentiation plasticity of airway progenitors via Fosl2 during alveolar regeneration.","abstract":"While the acquisition of cellular plasticity in adult stem cells is essential for rapid regeneration after tissue injury, little is known about the underlying mechanisms governing this process. Our data reveal the coordination of airway progenitor differentiation plasticity by inflammatory signals during alveolar regeneration. Following damage, interleukin-1\u03b2 (IL-1\u03b2) signalling-dependent modulation of Jag1 and Jag2 expression in ciliated cells results in the inhibition of Notch signalling in secretory cells, which drives the reprogramming and acquisition of differentiation plasticity. We identify the transcription factor Fosl2 (also known as Fra2) for secretory cell fate conversion to alveolar type 2 cells that retain the distinct genetic and epigenetic signatures of secretory lineages. We also reveal that human secretory cells positive for KDR (also known as FLK-1) display a conserved capacity to generate alveolar type 2 cells via Notch inhibition. Our results demonstrate the functional role of an IL-1\u03b2-Notch-Fosl2 axis in the fate decision of secretory cells during injury repair, proposing a potential therapeutic target for human lung alveolar regeneration.","authors":"Choi, J., Jang, YJ., Dabrowska, C., Iich, E., Evans, KV., Hall, H., Janes, SM., Simons, BD., Koo, BK., Kim, J., Lee, JH.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Nat Cell Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7489720","title":"The Drosophila fork head domain protein crocodile is required for the establishment of head structures.","abstract":"The fork head (fkh) domain defines the DNA-binding region of a family of transcription factors which has been implicated in regulating cell fate decisions across species lines. We have cloned and molecularly characterized the crocodile (croc) gene which encodes a new family member from Drosophila. croc is expressed in the head anlagen of the blastoderm embryo under the control of the anterior, the dorsoventral and the terminal maternal organizer systems. The croc mutant phenotype indicates that the croc wild-type gene is required to function as an early patterning gene in the anterior-most blastoderm head segment anlage and for the establishment of a specific head skeletal structure that derives from the non-adjacent intercalary segment at a later stage of embryogenesis. As an early patterning gene, croc exerts unusual properties which do not allow it to be grouped among the established segmentation genes. A single-site mutation within the croc fkh domain, which causes a replacement of the first out of four conserved amino acid residues thought to be involved in the coordinate binding of Mg2+, abolishes the DNA binding of the protein in vitro. In view of the resulting lack-of-function mutant phenotype, it appears likely that metal binding by the affected region of the fkh domain is crucial for proper folding of the DNA-binding structure.","authors":"H\u00e4cker, U., Kaufmann, E., Hartmann, C., J\u00fcrgens, G., Kn\u00f6chel, W., J\u00e4ckle, H.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"EMBO J","volume":"14","issue":"21","page":"5306-17","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1996-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9068618","title":"Stem cell factor stimulates chicken osteoclast activity in vitro.","abstract":"Stem cell factor (SCF) is a polypeptide growth factor active on multiple cell types, mainly of hematopoietic origin. We studied the effects of avian SCF on the differentiation of chicken osteoclasts from their putative progenitors as well as on the bone-resorbing activity of terminally differentiated osteoclasts. Osteoclast formation was analyzed in long-term cocultures of osteoblasts and nonadherent, osteoclast-depleted bone marrow cells. Osteoclast activity was studied in short-term (48 h) cultures of bone marrow cell populations enriched for osteoclasts, on dentine slices. SCF strongly enhanced osteoclast differentiation. The IL-6-related chicken myelomonocytic growth factor (cMGF) had a similar effect, and the effects of SCF and cMGF were additive. SCF, but not cMGF, also stimulated the bone-resorbing activity of existing osteoclasts. As osteoblasts have been found to regulate osteoclast activity and formation, chicken osteoblasts were tested for their ability to express and secrete SCF. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis showed that osteoblasts express SCF mRNA and that parathyroid hormone increases expression levels about fourfold. SCF did not accumulate in the culture medium, but remained cell (osteoblasts) surface associated.","authors":"van't Hof, RJ., von Lindern, M., Nijweide, PJ., Beug, H.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"FASEB J","volume":"11","issue":"4","page":"287-93","pdf":null,"JrId":"3815","fulltextlink":null,"preprintlink":null,"articledate":"1997-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7489723","title":"Fos is an essential component of the mammalian UV response.","abstract":"Mouse 3T3 fibroblasts lacking c-fos were employed to demonstrate an essential function of the UV-inducible transcription factor AP-1 (Fos\/Jun) in the response to the cytotoxic effects of short-wavelength ultraviolet (UVC) radiation. Clonogenic survival and proliferation of cells lacking c-fos were drastically reduced following UV irradiation. This UV hypersensitivity manifests itself primarily in increased cell death, partly by apoptosis, and prolonged recovery time from UV-induced cell cycle arrest. Co-culture with wild-type cells did not ameliorate the hypersensitivity of mutant cells. Transcriptional induction of the c-Fos target genes collagenase I, stromelysin-1 and stromelysin-2 by UV is almost absent in cells lacking c-fos which correlates with a reduced UV induction of AP-1 DNA-binding and transactivation activity. The repair of UV-induced DNA lesions was not affected, as shown by unscheduled DNA synthesis and host cell reactivation assays. These data demonstrate that c-Fos is involved in a novel protective function other than DNA repair against the harmful consequences of UVC.","authors":"Schreiber, M., Baumann, B., Cotten, M., Angel, P., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"EMBO J","volume":"14","issue":"21","page":"5338-49","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1996-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34507999","title":"MSX2 safeguards syncytiotrophoblast fate of human trophoblast stem cells.","abstract":"Multiple placental pathologies are associated with failures in trophoblast differentiation, yet the underlying transcriptional regulation is poorly understood. Here, we discovered msh homeobox 2 (MSX2) as a key transcriptional regulator of trophoblast identity using the human trophoblast stem cell model. Depletion of MSX2 resulted in activation of the syncytiotrophoblast transcriptional program, while forced expression of MSX2 blocked it. We demonstrated that a large proportion of the affected genes were directly bound and regulated by MSX2 and identified components of the SWItch\/Sucrose nonfermentable (SWI\/SNF) complex as strong MSX2 interactors and target gene cobinders. MSX2 cooperated specifically with the SWI\/SNF canonical BAF (cBAF) subcomplex and cooccupied, together with H3K27ac, a number of differentiation genes. Increased H3K27ac and cBAF occupancy upon MSX2 depletion imply that MSX2 prevents premature syncytiotrophoblast differentiation. Our findings established MSX2 as a repressor of the syncytiotrophoblast lineage and demonstrated its pivotal role in cell fate decisions that govern human placental development and disease.","authors":"Hornbachner, R., Lackner, A., Papuchova, H., Haider, S., Kn\u00f6fler, M., Mechtler, K., Latos, PA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Proc Natl Acad Sci U S A","volume":"118","issue":"37","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9060680","title":"Identification of a novel antiapoptotic protein, GAM-1, encoded by the CELO adenovirus.","abstract":"We have developed a simple screening method to identify genes that mimic bcl-2 or adenovirus E1B 19K in enhancing cell survival after transfection and have used this method to identify such a gene in the avian adenovirus CELO. The gene encodes a novel 30-kDa nuclear protein, which we have named GAM-1, that functions comparably to Bcl-2 and adenovirus E1B 19K in blocking apoptosis. However, GAM-1 has no sequence homology to Bcl-2, E1B 19K, or any other known antiapoptotic proteins and thus defines a novel antiapoptotic function.","authors":"Chiocca, S., Baker, A., Cotten, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Virol","volume":"71","issue":"4","page":"3168-77","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1997-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7319290","title":"Structure of the lysozyme gene and expression in the oviduct and macrophages.","abstract":null,"authors":"Hauser, H., Graf, T., Beug, H., Greiser-Wilke, I., Lindenmaier, W., Grez, M., Land, H., Giesecke, K., Sch\u00fctz, G.","publication_status":"ppublish","journalpubyear":"1981","journaltitle":"Haematol Blood Transfus","volume":"26","issue":null,"page":"175-8","pdf":null,"JrId":"30276","fulltextlink":null,"preprintlink":null,"articledate":"1982-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7111278","title":"Phenotypic analysis of globin gene expression: the thalassaemias.","abstract":null,"authors":"Flavell, RA., Moschonas, NK., deBoer, E., Grosveld, GC., Busslinger, M., Dahl, HH., Grosveld, FG.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Prog Clin Biol Res","volume":"85 Pt A","issue":null,"page":"25-39","pdf":null,"JrId":"6671","fulltextlink":null,"preprintlink":null,"articledate":"1982-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36449170","title":"Epigenetic Manipulation of Transposable and Repetitive Elements.","abstract":"This protocol describes methods to design, assemble, and validate tools for targeted activation or repression of single-copy and multi-copy genes, including repetitive and transposable elements. It uses transcription activator-like effector (TALE) technology combined with VP64 activator or Kruppel-associated box (KRAB) repressor, both of which are potent transcriptional regulators that modify the epigenetic state of endogenous DNA loci. This protocol has been successfully used to simultaneously modify expression patterns of thousands of LINE-1 transposable elements and satellite repeats, both in cell culture model systems and in preimplantation mouse embryos.","authors":"Jachowicz, JW.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Methods Mol Biol","volume":"2607","issue":null,"page":"355-368","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6985893","title":"Development of Escherichia coli virus T1. The role of the proton-motive force.","abstract":"In the interaction between Escherichia coli virus T1 and its host cell, which leads to reorientation of macromolecule synthesis, the alteration of the host cell membrane is an important step: The proton-motive force is rapidly reduced. This became apparent from selective changes in energy-coupled transports: proton-motive force- and ATP-dependent transports are inhibited in wild type cells. However, in ATPase-deficient (unc-) cells the ATP-driven transports are not affected by T1. The membrane potential is reduced by T1 as was measured by triphenylmethylphosphonium ion distribution. The potassium gradient is dissipated and calcium ions are accumulated by the cells. However, the residual (but reduced) membrane energy is essential for T1 development since the addition of uncouplers prevents any viral production. Consistently, the cell membrane remains intact after T1 infection: proteins, like beta-galactoside, amino acids, and alpha-methylglucoside cannot passively penetrate the membrane of T1-infected cells.","authors":"Wagner, EF., Ponta, H., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"J Biol Chem","volume":"255","issue":"2","page":"534-9","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1980-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6954007","title":"Hormone-dependent terminal differentiation in vitro of chicken erythroleukemia cells transformed by ts mutants of avian erythroblastosis virus.","abstract":"Chicken erythroblast cell strains and a cell line transformed by ts mutants of avian erythroblastosis virus (AEV) terminally differentiate when shifted to the nonpermissive temperature (42 degrees C). The differentiated cells resemble mature erythrocytes with respect to morphology and ultrastructure, expression of differentiation-specific cell-surface antigens, pattern of protein synthesis and hemoglobin content. Terminal differentiation is dependent on conditions favoring the differentiation of normal erythroid progenitor cells, including an erythropoietin-like factor. Colonies of ts AEV cells grown at 42 degrees C semisolid medium resemble erythrocyte colonies derived from normal erythroid progenitor cells. The colonies obtained were comparable in size or slightly larger than the late erythroid precursor (CFU-E) colonies. These results suggest that AEV-transformed cells are blocked at a stage of differentiation that is more advanced than that of the uninfected target cells. ts AEV cells are irreversibly committed to terminal differentiation within 20 to 30 hr after shift to 42 degrees C.","authors":"Beug, H., Palmieri, S., Freudenstein, C., Zentgraf, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Cell","volume":"28","issue":"4","page":"907-19","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1982-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10934469","title":"Cohesin ensures bipolar attachment of microtubules to sister centromeres and resists their precocious separation.","abstract":"The multisubunit protein complex cohesin is required to establish cohesion between sister chromatids during S phase and to maintain it during G2 and M phases. Cohesin is essential for mitosis, and even partial defects cause very high rates of chromosome loss. In budding yeast, cohesin associates with specific sites which are distributed along the entire length of a chromosome but are more dense in the vicinity of the centromere. Real-time imaging of individual centromeres tagged with green fluorescent protein suggests that cohesin bound to centromeres is important for bipolar attachment to microtubules. This cohesin is, however, incapable of resisting the consequent force, which leads to sister centromere splitting and chromosome stretching. Meanwhile, cohesin bound to sequences flanking the centromeres prevents sister chromatids from completely unzipping and is required to pull back together sister centromeres that have already split. Cohesin therefore has a central role in generating a dynamic tension between microtubules and sister chromatid cohesion at centromeres, which lasts until chromosome segregation is finally promoted by separin-dependent cleavage of the cohesin subunit Scc1p.","authors":"Tanaka, T., Fuchs, J., Loidl, J., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nat Cell Biol","volume":"2","issue":"8","page":"492-9","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2000-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6664997","title":"DNA methylation and the regulation of globin gene expression.","abstract":null,"authors":"Busslinger, M., Flavell, RA.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Prog Clin Biol Res","volume":"134","issue":null,"page":"193-203","pdf":null,"JrId":"6671","fulltextlink":null,"preprintlink":null,"articledate":"1984-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34492159","title":"GSK3-mediated phosphorylation of DEK3 regulates chromatin accessibility and stress tolerance in Arabidopsis.","abstract":"Chromatin dynamics enable the precise control of transcriptional programmes. The balance between restricting and opening of regulatory sequences on the DNA needs to be adjusted to prevailing conditions and is fine-tuned by chromatin remodelling proteins. DEK is an evolutionarily conserved chromatin architectural protein regulating important chromatin-related processes. However, the molecular link between DEK-induced chromatin reconfigurations and upstream signalling events remains unknown. Here, we show that ASK\u03b2\/AtSK31 is a salt stress-activated glycogen synthase kinase 3 (GSK3) from Arabidopsis thaliana that phosphorylates DEK3. This specific phosphorylation alters nuclear DEK3 protein complex composition and affects nucleosome occupancy and chromatin accessibility that is translated into changes in gene expression, contributing to salt stress tolerance. These findings reveal that DEK3 phosphorylation is critical for chromatin function and cellular stress response and provide a mechanistic example of how GSK3-based signalling is directly linked to chromatin, facilitating a transcriptional response.","authors":"Waidmann, S., Petutschnig, E., Rozhon, W., Moln\u00e1r, G., Popova, O., Mechtler, K., Jonak, C.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"FEBS J","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6541297","title":"Differentiation of F9 teratocarcinoma stem cells after transfer of c-fos proto-oncogenes.","abstract":"Transfer of mouse or human c-fos proto-oncogenes into F9 teratocarcinoma stem cells results in expression of c-fos mRNA and protein. This is accompanied by the appearance of morphologically altered cells which express several specific markers characteristic of differentiated cells, suggesting that c-fos plays a role in cellular differentiation.","authors":"M\u00fcller, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1984","journaltitle":"Nature","volume":"311","issue":"5985","page":"438-42","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1984-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6340981","title":"Escherichia coli virus T1: genetic controls during virus infection.","abstract":null,"authors":"Wagner, EF., Auer, B., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Curr Top Microbiol Immunol","volume":"102","issue":null,"page":"131-52","pdf":null,"JrId":"3237","fulltextlink":null,"preprintlink":null,"articledate":"1983-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6329725","title":"Myeloblasts transformed by the avian acute leukemia virus E26 are hormone-dependent for growth and for the expression of a putative myb-containing protein, p135 E26.","abstract":"Avian leukemia virus E26 contains the myb oncogene and transforms erythroid and myeloid hematopoietic cells in vivo and in vitro. E26-transformed nonproducer myeloblasts but not avian erythroleukemia virus (AEV)-transformed erythroblasts nor MC29-transformed macrophages were shown to be dependent for growth on factor(s) present in supernatants from Concanavalin A-stimulated chicken spleen cells. The same factor enhanced the synthesis of p135 E26, the candidate transforming protein of E26, but did not induce the synthesis of the transforming proteins of AEV and MC29 viruses nor that of helper virus-derived structural proteins. P135 E26 was shown to contain sequences related to the viral gag gene as well as sequences which may be related to the myb gene product. P135 E26 might constitute the first example of a viral onc protein whose synthesis is regulated directly or indirectly by an exogenous hematopoietic growth factor.","authors":"Beug, H., Hayman, MJ., Graf, T.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"EMBO J","volume":"1","issue":"9","page":"1069-73","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1984-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8595419","title":"Conservation of a maternal-specific methylation signal at the human IGF2R locus.","abstract":"The human IGF2R gene has been reported to be either biallelically or very rarely monoallelically expressed, in contrast to the maternally expressed mouse counterpart. We describe here an analysis of the 5' portion of the human IGF2R gene and show that it contains a maternally methylated CpG island in the second intron. A similar maternally methylated intronic element has been proposed to be the imprinting box for the mouse gene and although the relevance of this element has yet to be directly demonstrated, methylation has been reported to be essential to maintain allele-specific expression of imprinted genes. Allelic expression analysis of human IGF2R in 70 lymphoblastoid cell lines identified only one line showing monoallelic expression. Thus, in this tissue monoparental methylation of the IGF2R gene does not correlate with allele-specific expression. We also confirm here that the human IGF2R gene is located in an asynchronously replicating chromosomal region, as are all other imprinted genes so far analyzed. The mouse and human IGF2R intronic CpG islands both contain numerous large direct repeats that are methylated following maternal, but not paternal, transmittance. Thus features that attract maternal-specific methylation are conserved between the mouse and human genes. Since these intronic CpG islands share organizational rather than sequence homology, this suggests that secondary DNA structure may play a role in attracting a maternal methylation imprint.","authors":"Smrzka, OW., Fa\u00e9, I., St\u00f6ger, R., Kurzbauer, R., Fischer, GF., Henn, T., Weith, A., Barlow, DP.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Hum Mol Genet","volume":"4","issue":"10","page":"1945-52","pdf":null,"JrId":"2407","fulltextlink":null,"preprintlink":null,"articledate":"1996-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6305573","title":"Structure and expression of the human globin genes and murine histocompatibility antigen genes.","abstract":null,"authors":"Flavell, RA., Grosveld, F., Busslinger, M., de Boer, E., Kioussis, D., Mellor, AL., Golden, L., Weiss, E., Hurst, J., Bud, H., Bullman, H., Simpson, E., James, R., Townsend, AR., Taylor, PM., Schmidt, W., Ferluga, J., Leben, L., Santamaria, M., Atfield, G., Festenstein, H.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"47 Pt 2","issue":null,"page":"1067-78","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1983-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34545368","title":"Clinical grade ACE2 as a universal agent to block SARS-CoV-2 variants.","abstract":"The recent emergence of multiple SARS-CoV-2 variants has caused considerable concern due to reduced vaccine efficacy and escape from neutralizing antibody therapeutics. It is therefore paramount to develop therapeutic strategies that inhibit all known and future SARS-CoV-2 variants. Here we report that all SARS-CoV-2 variants analyzed, including variants of concern (VOC) Alpha, Beta, Gamma, and Delta, exhibit enhanced binding affinity to clinical grade and phase 2 tested recombinant human soluble ACE2 (APN01). Importantly, soluble ACE2 neutralized infection of VeroE6 cells and human lung epithelial cells by multiple VOC strains with markedly enhanced potency when compared to reference SARS-CoV-2 isolates. Effective inhibition of infections with SARS-CoV-2 variants was validated and confirmed in two independent laboratories. These data show that SARS-CoV-2 variants that have emerged around the world, including current VOC and several variants of interest, can be inhibited by soluble ACE2, providing proof of principle of a pan-SARS-CoV-2 therapeutic.","authors":"Wirnsberger, G., Monteil, V., Eaton, B., Postnikova, E., Murphy, M., Braunsfeld, B., Crozier, I., Kricek, F., Niederh\u00f6fer, J., Schwarzb\u00f6ck, A., Breid, H., Sanchez Jimenez, A., Bugajska-Schretter, A., Dohnal, A., Ruf, C., Gugenberger, R., Hagelkruys, A., Montserrat, N., Holbrook, MR., Oostenbrink, C., Shoemaker, RH., Mirazimi, A., Penninger, JM.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10922056","title":"The RING-H2 finger protein APC11 and the E2 enzyme UBC4 are sufficient to ubiquitinate substrates of the anaphase-promoting complex.","abstract":"The anaphase-promoting complex (APC) is a cell cycle-regulated ubiquitin-protein ligase that targets cyclin B, securin and other destruction box containing proteins for proteolysis. Nine APC subunits have been identified in vertebrates and eleven in yeast, but for none of them it is known how they contribute to the catalysis of ubiquitination reactions. Here we report the mass spectrometric identification of CDC26 and of the RING-H2 finger protein APC11 in the human APC. We have expressed these proteins and several other APC subunits in Escherichia coli and have tested their activities in vitro. We find that APC11 alone is sufficient to allow the synthesis of multiubiquitin chains in the presence of E1 and UBC4. These multiubiquitin chains are partly unanchored and partly bound to APC11 itself. APC11 and UBC4 are also able to ubiquitinate securin and cyclin B, but these reactions show a decreased dependency on the destruction box. The integrity of the putative zinc binding RING-H2 finger is required for the ability of APC11 to support ubiquitination reactions. These results suggest that APC11 and UBC4 catalyze the formation of isopeptide bonds in APC-mediated ubiquitination reactions.","authors":"Gmachl, M., Gieffers, C., Podtelejnikov, AV., Mann, M., Peters, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Proc Natl Acad Sci U S A","volume":"97","issue":"16","page":"8973-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2000-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6298806","title":"The structure and expression of mammalian gene clusters.","abstract":null,"authors":"Flavell, RA., Bud, H., Bullman, H., Busslinger, M., deBoer, E., deKleine, A., Golden, L., Groffen, J., Grosveld, FG., Mellor, AL., Moschonas, N., Weiss, E.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Prog Clin Biol Res","volume":"103 Pt A","issue":null,"page":"37-55","pdf":null,"JrId":"6671","fulltextlink":null,"preprintlink":null,"articledate":"1983-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6279674","title":"Erythroblast cell lines transformed by a temperature-sensitive mutant of avian erythroblastosis virus: a model system to study erythroid differentiation in vitro.","abstract":"A continuous chicken erythroblast cell line transformed by the temperature-sensitive mutant ts34 of avian erythroblastosis virus was developed. This cell line, designated HD3, could be induced to terminally differentiate by shift to the nonpermissive temperature. The differentiated cells resembled erythrocytes as judged by morphology, expression of hemoglobin as determined by benzidine staining and radioimmunoassay, and by the expression of differentiation-specific cell surface antigens. Terminal differentiation was dependent on an erythropoietin-like activity present in anemic chicken serum. In contrast, induction of differentiation in the same cells by butyric acid was erythropoietin independent and did not lead to the formation of erythrocytes. In addition, we found that the responsiveness to temperature inducibility and to butyric acid could be dissociated in variant sublines of HD3 and that both types of differentiation inducers appear to act via different pathways.","authors":"Beug, H., Doederlein, G., Freudenstein, C., Graf, T.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"J Cell Physiol Suppl","volume":"1","issue":null,"page":"195-207","pdf":null,"JrId":"4587","fulltextlink":null,"preprintlink":null,"articledate":"1982-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34545364","title":"Development of a novel, pan-variant aerosol intervention for COVID-19.","abstract":"To develop a universal strategy to block SARS-CoV-2 cellular entry and infection represents a central aim for effective COVID-19 therapy. The growing impact of emerging variants of concern increases the urgency for development of effective interventions. Since ACE2 is the critical SARS-CoV-2 receptor and all tested variants bind to ACE2, some even at much increased affinity (see accompanying paper), we hypothesized that aerosol administration of clinical grade soluble human recombinant ACE2 (APN01) will neutralize SARS-CoV-2 in the airways, limit spread of infection in the lung and mitigate lung damage caused by deregulated signaling in the renin-angiotensin (RAS) and Kinin pathways. Here we show that intranasal administration of APN01 in a mouse model of SARS-CoV-2 infection dramatically reduced weight loss and prevented animal death. As a prerequisite to a clinical trial, we evaluated both virus binding activity and enzymatic activity for cleavage of Ang II following aerosolization. We report successful aerosolization for APN01, retaining viral binding as well as catalytic RAS activity. Dose range-finding and IND-enabling repeat-dose aerosol toxicology testing were conducted in dogs. Twice daily aerosol administration for two weeks at the maximum feasible concentration revealed no notable toxicities. Based on these results, a Phase I clinical trial in healthy volunteers can now be initiated, with subsequent Phase II testing in individuals with SARS-CoV-2 infection. This strategy could be used to develop a viable and rapidly actionable therapy to prevent and treat COVID-19, against all current and future SARS-CoV-2 variants.","authors":"Shoemaker, RH., Panettieri, RA., Libutti, SK., Hochster, HS., Watts, NR., Wingfield, PT., Starkl, P., Pimenov, L., Gawish, R., Hladik, A., Knapp, S., Boring, D., White, JM., Lawrence, Q., Boone, J., Marshall, JD., Matthews, RL., Cholewa, BD., Richig, JW., Chen, BT., McCormick, DL., Gugensberger, R., H\u00f6ller, S., Penninger, JM., Wirnsberger, G.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6297279","title":"The structure and expression of the haemoglobin genes.","abstract":null,"authors":"Grosveld, F., Busslinger, M., Grosveld, G., Groffen, J., DeKleine, A., Flavell, RA.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Adv Exp Med Biol","volume":"158","issue":null,"page":"65-80","pdf":null,"JrId":"280","fulltextlink":null,"preprintlink":null,"articledate":"1983-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6297746","title":"Expression of a chicken lysozyme recombinant gene is regulated by progesterone and dexamethasone after microinjection into oviduct cells.","abstract":"We transferred a chicken lysozyme gene recombinant by microinjection into primary cultures of chicken oviduct cells. The recombinant gene is a fusion between the lysozyme promoter, including 1.4 kb of upstream sequences, and the coding region of the gene for SV40 T antigen (plys-T). The expression of plys-T is stimulated by the steroid hormones progesterone and dexamethasone, but not by estradiol. The number of oviduct cells expressing coinjected or separately injected control genes is not increased by steroids. A deletion mutant lacking the lysozyme sequences between -161 and +15 does not express T antigen, indicating that transcription of plys-T starts within the lysozyme promoter region. By screening different cell types we found that microinjected plys-T is expressed in chicken oviduct cells but not in chicken macrophages or fibroblasts or in rat II fibroblasts.","authors":"Renkawitz, R., Beug, H., Graf, T., Matthias, P., Grez, M., Sch\u00fctz, G.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Cell","volume":"31","issue":"1","page":"167-76","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1983-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6294978","title":"Isolation and characterization of four new temperature-sensitive mutants of avian erythroblastosis virus (AEV).","abstract":null,"authors":"Palmieri, S., Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Virology","volume":"123","issue":"2","page":"296-311","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1983-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6287575","title":"Human beta-globin gene sequences injected into mouse eggs, retained in adults, and transmitted to progeny.","abstract":"Foreign gene sequences were retained in two adult mice (out of 62 analyzed) from fertilized eggs injected with a recombinant plasmid containing the human beta-globin genomic region and the herpes simplex viral thymidine kinase gene. The intact human and viral genes were found in DNA of one of the animals and, in the other, at least part of the human globin gene was present. The latter individual transmitted these sequences to its progeny in a Mendelian ration. Thus, human DNA may be incorporated into the germ line of mice for in vivo studies of regulation of gene expression in development, genetic diseases, and malignancy.","authors":"Steward, TA., Wagner, EF., Mintz, B.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Science","volume":"217","issue":"4564","page":"1046-8","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1982-10-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6258948","title":"Characterization of the hematopoietic target cells of AEV, MC29 and AMV avian leukemia viruses.","abstract":null,"authors":"Graf, T., von Kirchbach, A., Beug, H.","publication_status":"ppublish","journalpubyear":"1981","journaltitle":"Exp Cell Res","volume":"131","issue":"2","page":"331-43","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1981-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34459017","title":"Autophagy in major human diseases.","abstract":"Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discuss preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.","authors":"Klionsky, DJ., Petroni, G., Amaravadi, RK., Baehrecke, EH., Ballabio, A., Boya, P., Bravo-San Pedro, JM., Cadwell, K., Cecconi, F., Choi, AMK., Choi, ME., Chu, CT., Codogno, P., Colombo, MI., Cuervo, AM., Deretic, V., Dikic, I., Elazar, Z., Eskelinen, EL., Fimia, GM., Gewirtz, DA., Green, DR., Hansen, M., J\u00e4\u00e4ttel\u00e4, M., Johansen, T., Juh\u00e1sz, G., Karantza, V., Kraft, C., Kroemer, G., Ktistakis, NT., Kumar, S., Lopez-Otin, C., Macleod, KF., Madeo, F., Martinez, J., Mel\u00e9ndez, A., Mizushima, N., M\u00fcnz, C., Penninger, JM., Perera, RM., Piacentini, M., Reggiori, F., Rubinsztein, DC., Ryan, KM., Sadoshima, J., Santambrogio, L., Scorrano, L., Simon, HU., Simon, AK., Simonsen, A., Stolz, A., Tavernarakis, N., Tooze, SA., Yoshimori, T., Yuan, J., Yue, Z., Zhong, Q., Galluzzi, L., Pietrocola, F.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"EMBO J","volume":null,"issue":null,"page":"e108863","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10793135","title":"Mitotic regulation of the APC activator proteins CDC20 and CDH1.","abstract":"The ordered activation of the ubiquitin protein ligase anaphase-promoting complex (APC) or cyclosome by CDC20 in metaphase and by CDH1 in telophase is essential for anaphase and for exit from mitosis, respectively. Here, we show that CDC20 can only bind to and activate the mitotically phosphorylated form of the Xenopus and the human APC in vitro. In contrast, the analysis of phosphorylated and nonphosphorylated forms of CDC20 suggests that CDC20 phosphorylation is neither sufficient nor required for APC activation. On the basis of these results and the observation that APC phosphorylation correlates with APC activation in vivo, we propose that mitotic APC phosphorylation is an important mechanism that controls the proper timing of APC(CDC20) activation. We further show that CDH1 is phosphorylated in vivo during S, G2, and M phase and that CDH1 levels fluctuate during the cell cycle. In vitro, phosphorylated CDH1 neither binds to nor activates the APC as efficiently as does nonphosphorylated CDH1. Nonphosphorylatable CDH1 mutants constitutively activate APC in vitro and in vivo, whereas mutants mimicking the phosphorylated form of CDH1 are constitutively inactive. These results suggest that mitotic kinases have antagonistic roles in regulating APC(CDC20) and APC(CDH1); the phosphorylation of APC subunits is required to allow APC activation by CDC20, whereas the phosphorylation of CDH1 prevents activation of the APC by CDH1. These mechanisms can explain the temporal order of APC activation by CDC20 and CDH1 and may help to ensure that exit from mitosis is not initiated before anaphase has occurred.","authors":"Kramer, ER., Scheuringer, N., Podtelejnikov, AV., Mann, M., Peters, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Biol Cell","volume":"11","issue":"5","page":"1555-69","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2000-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6253196","title":"Three new types of viral oncogenes in defective avian leukemia viruses. II. Biological, genetic, and immunochemical evidence.","abstract":null,"authors":"Graf, T., Beug, H., von Kirchbach, A., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"44 Pt 2,","issue":null,"page":"1225-34","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1981-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6243431","title":"Transformation parameters of chicken embryo fibroblasts infected with the ts34 mutant of avian erythroblastosis virus.","abstract":null,"authors":"Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"Virology","volume":"100","issue":"2","page":"348-56","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1980-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6095268","title":"src- and fps-containing avian sarcoma viruses transform chicken erythroid cells.","abstract":"We report here that several oncogene-transducing avian sarcoma virus strains, namely Rous sarcoma virus (src), Fujinami sarcoma virus (fps), and PRCII (fps), transform avian erythroid cells in vitro and in vivo. The src- and fps-transformed erythroblasts grow in vitro for 20-30 generations, require special growth conditions, and tend to differentiate spontaneously. In these properties, they resemble erythroid cells transformed with the erbB-containing H strain of avian erythroblastosis virus (AEV-H) but differ from those transformed with AEV-ES4 (erbA, erbB), which grow under standard culture conditions and rarely differentiate spontaneously. Erythroblasts transformed with viruses carrying temperature-sensitive mutations in the src or fps oncogene and then shifted to the nonpermissive temperature in the presence of anemic serum (as a source of an erythropoietin-like factor) differentiate terminally into erythrocytes. These results demonstrate that several members of the src gene family other than erbB have the capacity to transform erythroid cells.","authors":"Kahn, P., Adkins, B., Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1984","journaltitle":"Proc Natl Acad Sci U S A","volume":"81","issue":"22","page":"7122-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1985-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34556579","title":"The conserved fertility factor SPACA4\/Bouncer has divergent modes of action in vertebrate fertilization.","abstract":"Fertilization is the fundamental process that initiates the development of a new individual in all sexually reproducing species. Despite its importance, our understanding of the molecular players that govern mammalian sperm-egg interaction is incomplete, partly because many of the essential factors found in nonmammalian species do not have obvious mammalian homologs. We have recently identified the lymphocyte antigen-6 (Ly6)\/urokinase-type plasminogen activator receptor (uPAR) protein Bouncer as an essential fertilization factor in zebrafish [S. Herberg, K. R. Gert, A. Schleiffer, A. Pauli, <i>Science<\/i> 361, 1029-1033 (2018)]. Here, we show that Bouncer's homolog in mammals, Sperm Acrosome Associated 4 (SPACA4), is also required for efficient fertilization in mice. In contrast to fish, in which Bouncer is expressed specifically in the egg, SPACA4 is expressed exclusively in the sperm. Male knockout mice are severely subfertile, and sperm lacking SPACA4 fail to fertilize wild-type eggs in vitro. Interestingly, removal of the zona pellucida rescues the fertilization defect of <i>Spaca4<\/i>-deficient sperm in vitro, indicating that SPACA4 is not required for the interaction of sperm and the oolemma but rather of sperm and the zona pellucida. Our work identifies SPACA4 as an important sperm protein necessary for zona pellucida penetration during mammalian fertilization.","authors":"Fujihara, Y., Herberg, S., Blaha, A., Panser, K., Kobayashi, K., Larasati, T., Novatchkova, M., Theussl, HC., Olszanska, O., Ikawa, M., Pauli, A.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Proc Natl Acad Sci U S A","volume":"118","issue":"39","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.05.02.442348v1","articledate":"2021-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9032246","title":"The five cleavage-stage (CS) histones of the sea urchin are encoded by a maternally expressed family of replacement histone genes: functional equivalence of the CS H1 and frog H1M (B4) proteins.","abstract":"The cleavage-stage (CS) histones of the sea urchin are known to be maternally expressed in the egg, have been implicated in chromatin remodeling of the male pronucleus following fertilization, and are the only histone variants present in embryonic chromatin up to the four-cell stage. With the help of partial peptide sequence information, we have isolated and identified CS H1, H2A, H2B, H3, and H4 cDNAs from egg poly(A)+ mRNA of the sea urchin Psammechinus miliaris. All five CS proteins correspond to replacement histone variants which are encoded by replication-independent genes containing introns, poly(A) addition signals, and long nontranslated sequences. Transcripts of the CS histone genes could be detected only during oogenesis and in development up to the early blastula stage. The CS proteins, with the exception of H4, are unique histones which are distantly related in sequence to the early, late, and sperm histone subtypes of the sea urchin. In contrast, the CS H1 protein displays highest sequence homology with the H1M (B4) histone of Xenopus laevis. Both H1 proteins are replacement histone variants with very similar developmental expression profiles in their respective species, thus indicating that the frog H1M (B4) gene is a vertebrate homolog of the CS H1 gene. These data furthermore suggest that the CS histones are of ancient evolutionary origin and may perform similar conserved functions during oogenesis and early development in different species.","authors":"Mandl, B., Brandt, WF., Superti-Furga, G., Graninger, PG., Birnstiel, ML., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Mol Cell Biol","volume":"17","issue":"3","page":"1189-200","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6165135","title":"Production and characterization of antisera specific for the erb-portion of p75, the presumptive transforming protein of avian erythroblastosis virus.","abstract":null,"authors":"Beug, H., Graf, T., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1981","journaltitle":"Virology","volume":"111","issue":"1","page":"201-10","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1981-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8565834","title":"Pax1 is expressed during development of the thymus epithelium and is required for normal T-cell maturation.","abstract":"Pax1 is a transcriptional regulatory protein expressed during mouse embryogenesis and has been shown to have an important function in vertebral column development. Expression of Pax1 mRNA in the embryonic thymus has been reported previously. Here we show that Pax1 protein expression in thymic epithelial cells can be detected throughout thymic development and in the adult. Expression starts in the early endodermal epithelium lining the foregut region and includes the epithelium of the third pharyngeal pouch, a structure giving rise to part of the thymus epithelium. In early stages of thymus development a large proportion of thymus cells expresses Pax1. With increasing age, the proportion of Pax1-expressing cells is reduced and in the adult mouse only a small fraction of cortical thymic stromal cells retains strong Pax1 expression. Expression of Pax1 in thymus epithelium is necessary for establishing the thymus microenvironment required for normal T cell maturation. Mutations in the Pax-1 gene in undulated mice affect not only the total size of the thymus but also the maturation of thymocytes. The number of thymocytes is reduced about 2- to 5-fold, affecting mainly the CD4+8+ immature and CD4+ mature thymocyte subsets. The expression levels of major thymocyte surface markers remains unchanged with the exception of Thy-1 which was found to be expressed at 3- to 4-fold higher levels.","authors":"Wallin, J., Eibel, H., Neub\u00fcser, A., Wilting, J., Koseki, H., Balling, R.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Development","volume":"122","issue":"1","page":"23-30","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34557919","title":"Wnt\/\u03b2-catenin signalling is dispensable for adult neural stem cell homeostasis and activation.","abstract":"Adult mouse hippocampal neural stem cells (NSCs) generate new neurons that integrate into existing hippocampal networks and modulate mood and memory. These NSCs are largely quiescent and are stimulated by niche signals to activate and produce neurons. Wnt\/\u03b2-catenin signalling acts at different steps along the hippocampal neurogenic lineage, but whether it has a direct role in the regulation of NSCs remains unclear. Here, we used Wnt\/\u03b2-catenin reporters and transcriptomic data from in vivo and in vitro models to show that adult NSCs respond to Wnt\/\u03b2-catenin signalling. Wnt\/\u03b2-catenin stimulation instructed the neuronal differentiation of proliferating NSCs and promoted the activation or differentiation of quiescent NSCs in a dose-dependent manner. However, deletion of \u03b2-catenin in NSCs did not affect either their activation or maintenance of their stem cell characteristics. Together, these results indicate that, although NSCs do respond to Wnt\/\u03b2-catenin stimulation in a dose-dependent and state-specific manner, Wnt\/\u03b2-catenin signalling is not cell-autonomously required to maintain NSC homeostasis, which reconciles some of the contradictions in the literature as to the role of Wnt\/\u03b2-catenin signalling in adult hippocampal NSCs.","authors":"Austin, SHL., Gabarr\u00f3-Solanas, R., Rigo, P., Paun, O., Harris, L., Guillemot, F., Urb\u00e1n, N.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Development","volume":"148","issue":"20","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6011388","title":"[Rhythm of cell orientation and velocity of movement in the chemotactic reaction system of Dictyostelium discoideum].","abstract":null,"authors":"Gerisch, G., Normann, I., Beug, H.","publication_status":"ppublish","journalpubyear":"1966","journaltitle":"Naturwissenschaften","volume":"53","issue":"23","page":"618","pdf":null,"JrId":"6013","fulltextlink":null,"preprintlink":null,"articledate":"1968-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"5391200","title":"[Monovalent fragments of antibodies for the analysis of cell membrane functions].","abstract":null,"authors":"Beug, H., Gerisch, G.","publication_status":"ppublish","journalpubyear":"1969","journaltitle":"Naturwissenschaften","volume":"56","issue":"7","page":"374","pdf":null,"JrId":"6013","fulltextlink":null,"preprintlink":null,"articledate":"1970-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9012505","title":"Regulation and function of transcription factor GATA-1 during red blood cell differentiation.","abstract":"The tissue-specific transcription factor GATA-1 is a key regulator of red blood cell differentiation. One seemingly contradictory aspect of GATA-1 function is that, while it is abundant in erythroid progenitor cells prior to the onset of overt differentiation, it does not significantly activate known GATA-1 target genes in those cells. To investigate the mechanisms underlying GATA-1 function during the transition from early to late erythropoiesis, we have examined its expression and activity in normal avian erythroid progenitor cells before and after induction of differentiation. In these primary progenitor cells, GATA-1 protein was predominantly located in the cytoplasm, while induction of differentiation caused its rapid relocalization to the nucleus, suggesting that nuclear translocation constitutes an important regulatory step in GATA-1 activation. As an alternative way of addressing the same question, we also ectopically expressed a GATA-1\/estrogen receptor fusion protein (GATA-1\/ER) in red blood cell progenitors, where nuclear translocation of, and transcriptional activation by, this hybrid factor are conditionally controlled by estrogen. We found that hormone-activated GATA-1\/ER protein accelerated red blood cell differentiation, and concomitantly suppressed cell proliferation. These phenotypic effects were accompanied by a simultaneous suppression of c-myb and GATA-2 transcription, two genes thought to be involved in the proliferative capacity of hematopoietic progenitor cells. Thus, GATA-1 appears to promote differentiation in committed erythroid progenitor cells both by inducing differentiation-specific genes and by simultaneously suppressing genes involved in cell proliferation.","authors":"Briegel, K., Bartunek, P., Stengl, G., Lim, KC., Beug, H., Engel, JD., Zenke, M.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Development","volume":"122","issue":"12","page":"3839-50","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"1997-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3868504","title":"Gene transfer into murine stem cells and mice using retroviral vectors.","abstract":null,"authors":"Wagner, EF., Keller, G., Gilboa, E., R\u00fcther, U., Stewart, C.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"50","issue":null,"page":"691-700","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1986-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3868501","title":"Regulation of histone gene expression.","abstract":null,"authors":"Busslinger, M., Sch\u00fcmperli, D., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"50","issue":null,"page":"665-70","pdf":null,"JrId":"3100","fulltextlink":null,"preprintlink":null,"articledate":"1986-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3625115","title":"The expression of retroviral vectors in murine stem cells and transgenic mice.","abstract":null,"authors":"Stewart, CL., R\u00fcther, U., Garber, C., Vanek, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"J Embryol Exp Morphol","volume":"97 Suppl","issue":null,"page":"263-75","pdf":null,"JrId":"4712","fulltextlink":null,"preprintlink":null,"articledate":"1987-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3607873","title":"Mutually exclusive interaction of the CCAAT-binding factor and of a displacement protein with overlapping sequences of a histone gene promoter.","abstract":"The sperm histone H2B-1 gene of the sea urchin Psammechinus miliaris contains two octamer sequences (ATTTGCAT) and two CCAAT motifs upstream of its TATA box. The CCAAT-binding factors present in nuclear extracts from testis and from blastula and gastrula embryos are indistinguishable by mobility shift and methylation interference analysis. However, there is a testis-specific octamer-binding factor in addition to the ubiquitous form. In DNAase I protection experiments, the CCAAT-binding factor of only the testis extract is able to interact with the sperm H2B promoter. In the two embryonic extracts a novel factor binds with high affinity to sequences overlapping the proximal CCAAT element, thus preventing the DNA interaction of the CCAAT-binding factor in the embryo where the sperm H2B gene is not expressed. This CCAAT displacement protein may therefore act as a repressor of sperm H2B gene transcription.","authors":"Barberis, A., Superti-Furga, G., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Cell","volume":"50","issue":"3","page":"347-59","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1987-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3396543","title":"Specific contacts between mammalian U7 snRNA and histone precursor RNA are indispensable for the in vitro 3' RNA processing reaction.","abstract":"We have made a detailed molecular analysis of the reactions leading to the formation of mature 3' ends in mammalian histone mRNAs. Using two analytical protocols we have identified an essential sequence motif in the downstream spacer which is consistently present, albeit in diffuse form, mammalian histone genes. Tampering with this sequence element completely abolishes 3' processing. However, 3' cleavage in vitro, although at a very much reduced rate, can be detected when the conserved hairpin is deleted from histone precursor mRNAs. U7 snRNA, previously shown to be essential for the maturation of sea urchin histone messages, was isolated from murine cells and the sequence was determined. The approximately 63-nucleotide, trimethyl-G-capped, murine U7 snRNA possesses a sequence shown in the sea urchin U7 to be required for Sm-precipitability, and like the sea urchin U7, the 3' end of murine U7 is encased in a hairpin structure. The 5' sequence of murine U7 exhibits extensive sequence complementarity to the conserved downstream motif of the histone precursor. As expected, oligo-nucleotide-directed RNase H cleavage of this portion of murine U7 inhibits the in vitro processing reaction. These experiments identify a set of specific contacts between mammalian U7 and histone precursor RNA which is indispensable for the maturation reaction.","authors":"Cotten, M., Gick, O., Vasserot, A., Schaffner, G., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"EMBO J","volume":"7","issue":"3","page":"801-8","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1988-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3486230","title":"Introduction of a selectable gene into murine T-lymphoblasts by a retroviral vector.","abstract":"A recombinant retroviral vector with an inserted bacterial neomycin resistance (neo) gene was used to transfer in vitro neomycin resistance (neoR) into murine cytotoxic lymphocyte precursors (CLP). The infection protocol involved co-cultivation of mitogen-activated splenic T-blasts with irradiated cells that produced either the recombinant retrovirus plus a helper virus, or exclusively the recombinant retrovirus. Infected T-blasts were subsequently cultured under limiting dilution (LD) conditions that supported clonal in vitro development of a large fraction of murine CLP. In infected T-blast populations, frequency estimates were obtained for CLP that developed into functional cytotoxic T-lymphocyte (CTL) populations under G418-selected or non-selected conditions; from these frequency estimates, an efficiency of transduction of the neoR phenotype into murine CLP of 2-8% was calculated. Some conditions were defined that influenced transduction efficiency, i.e., the density of the infecting monolayer cells; the presence of interleukin 2-containing conditioned medium and mitogenic lectins during the co-culture period; a delayed onset of G418 selection after infection. It was demonstrated that the neoR phenotype of functional CTL populations derived from infected CLP resulted from expressed recombinant retrovirus.","authors":"Reimann, J., Heeg, K., Wagner, H., Keller, G., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"J Immunol Methods","volume":"89","issue":"1","page":"93-101","pdf":null,"JrId":"4818","fulltextlink":null,"preprintlink":null,"articledate":"1986-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3481753","title":"ts-oncogene-transformed erythroleukemic cells: a novel test system for purifying and characterizing avian erythroid growth factors.","abstract":null,"authors":"Kowenz, E., Leutz, A., D\u00f6derlein, G., Graf, T., Beug, H.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Haematol Blood Transfus","volume":"31","issue":null,"page":"199-209","pdf":null,"JrId":"30276","fulltextlink":null,"preprintlink":null,"articledate":"1988-05-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10769751","title":"Analysis of fast dynamic processes in living cells: high-resolution and high-speed dual-color imaging combined with automated image analysis.","abstract":"The generation of spectral mutants of the green fluorescent protein (GFP) set the stage for multiple-color imaging in living cells. However, the use of this technique has been limited by a spectral overlap of the available GFP mutants and\/or by insufficient resolution in both time and space. Using a new setup for dual-color imaging, we demonstrate here the visualization of small, fast moving vesicular structures with a high time resolution. Two GFP-fusion proteins were generated: human chromogranin B, a secretory granule matrix protein, and phogrin, a secretory granule membrane protein. They were tagged with enhanced yellow fluorescent protein (EYFP) and enhanced cyan fluorescent protein (ECFP), respectively. Both fusion proteins were cotransfected in Vero cells, a cell line from green monkey kidney. EYFP and ECFP were excited sequentially at high time rates using a monochromator. Charged coupled device (CCD)-based image acquisition resulted in 5-8 dual-color images per second, with a resolution sufficient to detect transport vesicles in mammalian cells. Under these conditions, a fully automated time-resolved analysis of the movement of color-coded objects was achieved. The development of specialized software permitted the analysis of the extent of colocalization between the two differentially labeled sets of cellular structures over time. This technical advance will provide an important tool to study the dynamic interactions of subcellular structures in living cells.","authors":"Rustom, A., Gerlich, D., Rudolf, R., Heinemann, C., Eils, R., Gerdes, HH.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Biotechniques","volume":"28","issue":"4","page":"722-8, 730","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3456476","title":"Monoclonal antibodies to novel erythroid differentiation antigens reveal specific effects of oncogenes on the leukaemic cell phenotype.","abstract":"A panel of new monoclonal antibodies to antigens on the surface of chick erythroid progenitor cells is described. These are characterised with respect to their binding to different classes of normal haemopoietic cells of both the erythroid and myeloid lineages. Using these antibodies, we have examined the phenotype of avian leukaemic cells transformed by retroviruses carrying defined oncogenes. Our data show that these cells, although similar to the normal haematopoietic precursor from which they are derived, aberrantly express certain markers in an oncogene specific manner.","authors":"Schmidt, JA., Marshall, J., Hayman, MJ., Doderlein, G., Beug, H.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Leuk Res","volume":"10","issue":"3","page":"257-72","pdf":null,"JrId":"5304","fulltextlink":null,"preprintlink":null,"articledate":"1986-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10692154","title":"A new mechanism for the control of a prokaryotic transcriptional regulator: antagonistic binding of positive and negative effectors.","abstract":"MalT, the transcriptional activator of the Escherichia coli maltose regulon, self-associates, binds promoter DNA and activates initiation of transcription only in the presence of ATP and maltotriose, the inducer. In vivo studies have revealed that MalT action is negatively controlled by the MalY protein. Using a biochemical approach, we analyse here the mechanism whereby MalY represses MalT activity. We show that MalY inhibits transcription activation by MalT in a purified transcription system. In vitro, a constitutive MalT variant (which is partially active in the absence of maltotriose) is less sensitive than wild-type MalT to repression by MalY, as observed in vivo. We demonstrate that MalY forms a complex with MalT only in the absence of maltotriose and that, conversely, MalY inhibits maltotriose binding by MalT. Together, these results establish that MalY acts directly upon MalT without the help of any factor, and that MalY is a negative effector of MalT competing with the inducer for MalT binding.","authors":"Schreiber, V., Steegborn, C., Clausen, T., Boos, W., Richet, E.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Microbiol","volume":"35","issue":"4","page":"765-76","pdf":null,"JrId":"5753","fulltextlink":null,"preprintlink":null,"articledate":"2000-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3349438","title":"Immunoglobulin allotypes Gm and Km in hematologic malignancies.","abstract":"Immunoglobulin allotypes of the Gm and Km systems have been compared in patients with various forms of hematologic malignancies and healthy controls of the same ethnographic background. These comparisons found an increased frequency of the haplotype Gm and a decreased frequency of Gm in patients with Hodgkin's disease; a decreased frequency of Gm in diffuse, large-cell lymphoma patients; a decreased frequency of Gm and an increased frequency of Gm in acute myeloid leukemia patients; a decreased frequency of Gm in chronic myeloid leukemia patients, and an increased frequency of the phenotype Km(1+) in chronic lymphocytic leukemia patients. These results support previous suggestions of the involvement of immunoglobulin allotypes in the susceptibility to some forms of human hematologic malignancy.","authors":"Janardhana, V., Propert, DN., Cooper, I., Wolf, M., Garson, OM., Hopper, JL., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Cancer Genet Cytogenet","volume":"31","issue":"2","page":"179-86","pdf":null,"JrId":"2778","fulltextlink":null,"preprintlink":null,"articledate":"1988-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"77","title":"Kinetic studies and effects of anions on creatine phosphokinase from skeletal muscle of rhesus monkey (Macaca mulatta).","abstract":"A purification procedure for creatine kinase (EC 2.7.3.2) from muscle of the monke35--170 muequiv H+\/mg protein per min at 30 degrees C and a yield of approx. 0.5 g\/kg muscle. Assuming equilibrium kinetics, synergistic binding of substrates at one catalytic site is found for both the forward and back reactions. Kinetic constants for the binding of each substrate to the free enzyme and the enzyme-second substrate complex are determined and are compared with those for the enzyme from other species. Inhibition by small anions is determined in the presence of different combinations of substrates and products. SO4(2-) inhibits by simple competitive inhibition and probably binds at the site of the transferrable phosphoryl group. Inhibition by NO3-, NO2-, SCN- and Cl- is more complex and these ions are suggested to mimic the transferrable phosphoryl group in a planar transition-state complex. These anions stabilize the dead-end complex, enzyme-creatine-MgADP, which lacks the transferable phosphoryl group. The effects of these anions on the dissociation constants of the enzyme-substrate complexes is reported and is in accord with the above hypothesis. The dead-end complex in the absence of anion does not protect the essential thiol group against inhibition by iodoacetamide. Addition of NO3- or Cl- to the dead-end complex or a substrate equilibrium mixture without anion confers protection. The essential thiol group is inhibited by iodoacetamide at a rate which is essentially independent of pH over the normal stability range of the enzyme. Contrary to our previous report this pH independence is not altered by the presence of dead-end complex, creatine plus MgADP, in the presence or absence of anion or in the presence of a substrate equilibrium mixture. It is  inferred that the 'essential' thiol group of the monkey enzyme has essentially the same properties as that of the rabbit enzyme. In consequence, the inferences made about the role of this group based on our previous work on the monkey enzyme are no longer valid. The present findings are compatible with the essential thiol group playing a conformational role in the catalytic process.","authors":"Chegwidden, WR., Watts, DC.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"99-114","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3181130","title":"The -117 mutation in Greek HPFH affects the binding of three nuclear factors to the CCAAT region of the gamma-globin gene.","abstract":"The Greek form of hereditary persistence of fetal hemoglobin (HPFH) is associated with a point mutation immediately upstream of the distal of the two CCAAT elements of the A gamma-globin gene. Three proteins present in nuclear extracts of erythroleukemia cells bind to this CCAAT region and contact the nucleotide mutated in Greek HPFH. The ubiquitous CCAAT-binding factor CP1 interacts preferentially with the proximal CCAAT sequence. An erythroid cell-specific factor, referred to as NF-E, binds with a higher affinity to the distal CCAAT region and interacts only with sequences flanking the CCAAT motif. The third protein is the vertebrate homologue of the sea urchin CCAAT displacement protein and recognizes sequences in both CCAAT elements and their flanking sequences. While the point mutation in Greek HPFH slightly strengthens the binding of CP1 and the CCAAT displacement protein, the same base change strongly reduces the binding of NF-E to the distal CCAAT region, suggesting a possible role of NF-E in the repression of gamma-globin genes in adult erythroid cells.","authors":"Superti-Furga, G., Barberis, A., Schaffner, G., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"EMBO J","volume":"7","issue":"10","page":"3099-107","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1988-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"74","title":"Yeast glutathione reductase. Studies of the kinetics and stability of the enzyme as a function of pH and salt concentration.","abstract":"1. The pH dependencies of the apparent Michaelis constant for oxidized glutathione and the apparent turnover number of yeast glutathione reductase (EC 1.6.4.2) have been determined at a fixed concentration of 0.1 mM NADPH in the range pH 4.5--8.0. Between pH 5.5 and 7.6, both of these parameters are relatively constant. The principal effect of low pH on the kinetics of the enzyme-catalyzed reaction is the observation of a pH-dependent substrate inhibition by oxidized glutathione at pH less than or equal 7, which is shown to correlate with the binding of oxidized glutathione to the oxidized form of the enzyme. 2. The catalytic activity of yeast glutathione reductase at pH 5.5 is affected by the sodium acetate buffer concentration. The stability of the oxidized and reduced forms of the enzyme at pH 5.5 and 25 degrees C in the absence of bovine serum albumin was studied as a function of sodium acetate concentration. The results show that activation of the catalytic activity of the enzyme at low sodium acetate concentration correlates with an effect of sodium acetate on a reduced form of the enzyme. In contrast, inhibition of the catalytic activity of the enzyme at high sodium acetate concentration correlates with an effect of sodium acetate on the oxidized form of the enzyme.","authors":"Moroff, G., Brandt, KG.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"21-31","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10742150","title":"The tyrosine kinase p56lck is essential in coxsackievirus B3-mediated heart disease.","abstract":"Infections are thought to be important in the pathogenesis of many heart diseases. Coxsackievirus B3 (CVB3) has been linked to chronic dilated cardiomyopathy, a common cause of progressive heart disease, heart failure and sudden death. We show here that the sarcoma (Src) family kinase Lck (p56lck) is required for efficient CVB3 replication in T-cell lines and for viral replication and persistence in vivo. Whereas infection of wild-type mice with human pathogenic CVB3 caused acute and very severe myocarditis, meningitis, hepatitis, pancreatitis and dilated cardiomyopathy, mice lacking the p56lck gene were completely protected from CVB3-induced acute pathogenicity and chronic heart disease. These data identify a previously unknown function of Src family kinases and indicate that p56lck is the essential host factor that controls the replication and pathogenicity of CVB3.","authors":"Liu, P., Aitken, K., Kong, YY., Opavsky, MA., Martino, T., Dawood, F., Wen, WH., Kozieradzki, I., Bachmaier, K., Straus, D., Mak, TW., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nat Med","volume":"6","issue":"4","page":"429-34","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3345558","title":"Embryonic lethalities and endothelial tumors in chimeric mice expressing polyoma virus middle T oncogene.","abstract":"The effect of the middle T oncogene of polyoma virus was studied in vivo using a replication-defective selectable retrovirus. Injection of virus into newborn and adult mice resulted in the rapid appearance of cavernous hemangiomas. Infection of embryos did not yield transgenic mice; therefore, embryonal stem (ES) cells were used as an alternative system. Several infected ES cell clones were established that constitutively expressed middle T and its associated tyrosine kinase activity. Chimeric embryos obtained by blastocyst injection of individual ES cell clones were specifically arrested at midgestation, when multiple hemangiomas disrupted blood vessel formation. From these tumors endothelial cell lines were established that retained expression of von Willebrand factor yet were tumorigenic in vivo. These results suggest that middle T acts in endothelial cells as a single-step oncogene and that ES cells provide a valuable system for the study of growth control during embryogenesis.","authors":"Williams, RL., Courtneidge, SA., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Cell","volume":"52","issue":"1","page":"121-31","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1988-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10647015","title":"APC(Cdc20) promotes exit from mitosis by destroying the anaphase inhibitor Pds1 and cyclin Clb5.","abstract":"Ubiquitin-mediated proteolysis due to the anaphase-promoting complex\/cyclosome (APC\/C) is essential for separation of sister chromatids, requiring degradation of the anaphase inhibitor Pds1, and for exit from mitosis, requiring inactivation of cyclin B Cdk1 kinases. Exit from mitosis in yeast involves accumulation of the cyclin kinase inhibitor Sic1 as well as cyclin proteolysis mediated by APC\/C bound by the activating subunit Cdh1\/Hct1 (APC(Cdh1)). Both processes require the Cdc14 phosphatase, whose release from the nucleolus during anaphase causes dephosphorylation and thereby activation of Cdh1 and accumulation of another protein, Sic1 (refs 4-7). We do not know what determines the release of Cdc14 and enables it to promote Cdk1 inactivation, but it is known to be dependent on APC\/C bound by Cdc20 (APC(Cdc20)) (ref. 4). Here we show that APC(Cdc20) allows activation of Cdc14 and promotes exit from mitosis by mediating proteolysis of Pds1 and the S phase cyclin Clb5 in the yeast Saccharomyces cerevisiae. Degradation of Pds1 is necessary for release of Cdc14 from the nucleolus, whereas degradation of Clb5 is crucial if Cdc14 is to overwhelm Cdk1 and activate its foes (Cdh1 and Sic1). Remarkably, cells lacking both Pds1 and Clb5 can proliferate in the complete absence of Cdc20.","authors":"Shirayama, M., T\u00f3th, A., G\u00e1lov\u00e1, M., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nature","volume":"402","issue":"6758","page":"203-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2000-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3330781","title":"Isolation and structural analysis of a biologically active chicken c-fos cDNA: identification of evolutionarily conserved domains in fos protein.","abstract":"To identify functionally important domains in the fos gene product we have studied the evolutionary divergence between chicken and mammalian fos proteins. A cDNA containing the entire chicken c-fos coding region was isolated and its nucleotide sequence determined. The deduced 367-amino acid sequence was compared to that of the mouse and human proteins. This comparison revealed a highly conserved domain (98% homology between mouse and chicken) in the center of the protein (85 amino acids) that coincides with a region known to be indispensible for transforming activity. This highly charged domain presumably contains contact sites for DNA and other proteins as well as a nuclear location signal sequence. Two other regions, that are dispensable for transformation, are also highly conserved and may thus be important for the physiological function of c-fos. These are the N-terminal 88 amino acids (85% homology) and the C-terminal 62 amino acids (92% homology). The C-terminus not only contains a potential DNA-binding Zn-finger structure but is also the least divergent region in the protein at the nucleotide level (92% conservation between chicken and mouse), supporting the hypothesis that mRNA secondary structures in this region may contribute to post-transcriptional regulatory mechanisms. In contrast, the domains between the terminal sequences and the center region of fos protein show considerable divergence (39% and 45% homology, respectively), indicating a minor role, if any, for these sequences. The significance of these conclusions is emphasized by the observation that the chicken c-fos protein, expressed from the cDNA inserted into a retrovirally-derived expression vector, efficiently induces morphological transformation in rat fibroblasts. The chicken c-fos gene product could be identified by immunoprecipitation and in vitro transcription\/translation of the isolated cDNA as a protein of Mr approximately 60 K.","authors":"M\u00f6lders, H., Jenuwein, T., Adamkiewicz, J., M\u00fcller, R.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Oncogene","volume":"1","issue":"4","page":"377-85","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1988-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17956251","title":"Ubiquitin signals in the NF-kappaB pathway.","abstract":"The NF-kappaB (nuclear factor kappaB) transcription factors control cell survival, proliferation and innate and adaptive immune response. Post-translational modifications of key components of the NF-kappaB pathway provide the molecular basis for signal transmission from the cell membrane to the nucleus. Here, we describe the involvement of different types of ubiquitin modification in the regulation of the NF-kappaB signalling pathway.","authors":"Terzic, J., Marinovic-Terzic, I., Ikeda, F., Dikic, I.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Biochem Soc Trans","volume":"35","issue":"Pt 5","page":"942-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10655059","title":"A genome-wide survey of RAS transformation targets.","abstract":"An important aspect of multi-step tumorigenesis is the mutational activation of genes of the RAS family, particularly in sporadic cancers of the pancreas, colon, lung and myeloid system. RAS genes encode small GTP-binding proteins that affect gene expression in a global way by acting as major switches in signal transduction processes, coupling extracellular signals with transcription factors. Oncogenic forms of RAS are locked in their active state and transduce signals essential for transformation, angiogenesis, invasion and metastasis via downstream pathways involving the RAF\/MEK\/ERK cascade of cytoplasmic kinases, the small GTP-binding proteins RAC and RHO, phosphatidylinositol 3-kinase and others. We have used subtractive suppression hybridization (SSH), a PCR-based cDNA subtraction technique, to contrast differential gene expression profiles in immortalized, non-tumorigenic rat embryo fibroblasts and in HRAS- transformed cells. Sequence and expression analysis of more than 1,200 subtracted cDNA fragments revealed transcriptional stimulation or repression of 104 ESTs, 45 novel sequences and 244 known genes in HRAS- transformed cells compared with normal cells. Furthermore, we identified common and distinct targets in cells transformed by mutant HRAS, KRAS and NRAS, as well as 61 putative target genes controlled by the RAF\/MEK\/ERK pathway in reverted cells treated with the MEK-specific inhibitor PD 98059.","authors":"Zuber, J., Tchernitsa, OI., Hinzmann, B., Schmitz, AC., Grips, M., Hellriegel, M., Sers, C., Rosenthal, A., Sch\u00e4fer, R.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nat Genet","volume":"24","issue":"2","page":"144-52","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2000-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3263272","title":"Truncation of the human EGF receptor leads to differential transforming potentials in primary avian fibroblasts and erythroblasts.","abstract":"The transforming capacity of the normal and mutant human EGF receptor (EGFR) was investigated in primary chicken cells. In fibroblasts, both N- and C-terminal truncations resulted in a weak, additive oncogenic activity. However, not even double truncations caused a v-erbB-like phenotype. Upon EGF-binding, on the other hand, both normal and C-terminally truncated EGFRs resembled v-erbB in their fibroblast transforming potential. In erythroblasts, N-terminal truncation was sufficient to induce constitutive self-renewal, which was enhanced by deletion of 32 C-terminal amino acids but abolished by a larger truncation of 202 amino acids. In contrast to the normal EGFR, the receptor lacking 32 C-terminal amino acids resembled v-erbB in conferring erythropoietin independence for spontaneous differentiation to the transformed erythroblasts. Our results indicate that the C-terminal domain of the EGFR is non-essential in fibroblast transformation, but seems to be crucial for both self renewal induction and specificity of receptor function in erythroblasts.","authors":"Khazaie, K., Dull, TJ., Graf, T., Schlessinger, J., Ullrich, A., Beug, H., Vennstr\u00f6m, B.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"EMBO J","volume":"7","issue":"10","page":"3061-71","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1988-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3167107","title":"[Structure of the hydration envelope of the B-form of polydeoxyribonucleotides poly(dA-dC).poly(dG-dT) and poly(dA-dG).poly(dTs-dT) from the data of Monte-Carlo simulation].","abstract":"The results of a Monte Carlo simulation of the hydration shell of two polynucleotides poly (dA-dC).poly(dG-dT) and poly(dA-dG).poly(dC-dT) are reported. This study is a part of a series of Monte Carlo computations of the hydration of regular polydeoxyribonucleotides with dinucleotide repeat aimed at looking for dependences of hydration shell structure on base sequence. The coordinates of the main local maximal of water density near the polymers and the topology of the most probable one- and two-membered water bridges are published. For most of the sequences a common primary hydration of base edges of successive base pairs is characteristic. The AT-homopolymeric sequence represents an exception with autonomous primary hydration of a base pair in both grooves, which correlates with the sequence-dependent flexibility and the occurrence of bends of DNA.","authors":"Eisenhaber, F., Tumanian, VG.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Biofizika","volume":"33","issue":"3","page":"422-9","pdf":null,"JrId":"1060","fulltextlink":null,"preprintlink":null,"articledate":"1988-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3053164","title":"Expression of functional human EGF receptor on murine bone marrow cells.","abstract":"The human epidermal growth factor-receptor (EGF-R) was introduced into primary mouse bone marrow cells (BMC), utilizing retrovirus mediated gene transfer. Cultivation of infected BMC in the presence of interleukin-3 (IL-3) led to the outgrowth of IL-3 dependent myeloid cells, which efficiently expressed functional EGF-R, exhibiting its two characteristic affinity states. EGF acts on these cells synergistically with IL-3 in stimulating DNA synthesis and cell proliferation even under IL-3 saturation conditions. However, EGF was not sufficient to replace the requirement for IL-3. In contrast, EGF was able to maintain proliferation of a factor-dependent hemopoietic cell line (FDC-P1) infected with the EGF-R retrovirus in the absence of IL-3, but these cells did not respond to EGF in the presence of IL-3. No influence of EGF on IL-3 induced mast cell differentiation of BMC expressing the EGF-R could be observed by histological criteria. These data show that the expression of EGF-R alone is not sufficient to induce or maintain cell proliferation in IL-3 dependent bone marrow derived cells, although it can do so in established hemopoietic cell lines.","authors":"von R\u00fcden, T., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"EMBO J","volume":"7","issue":"9","page":"2749-56","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1988-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3133119","title":"c-fos expression interferes with thymus development in transgenic mice.","abstract":"To study the function of the proto-oncogene c-fos in hematopoietic tissues, transgenic mice were generated that express c-fos from the H2-Kb promoter in several organs. These H2-c-fos mice have enlarged spleens and hyperplastic thymuses containing an increased number of thymic epithelial cells. The exogenous c-fos expression specifically affects T cell development in the thymus, thereby increasing the fraction of mature thymocytes. Results obtained with bone marrow radiation chimeras suggest that the altered distribution of T cell subsets is not a direct effect of c-fos expression within the T cell lineage. No changes in the proportion of hematopoietic cell lineages are seen in the spleen, and these mice do not develop lymphoid malignancies. B and T cell function, however, is impaired, and H2-c-fos mice are immune deficient. It appears that c-fos specifically stimulates the proliferation of thymic epithelial cells, and may thus indirectly affect T cell development.","authors":"R\u00fcther, U., M\u00fcller, W., Sumida, T., Tokuhisa, T., Rajewsky, K., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Cell","volume":"53","issue":"6","page":"847-56","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1988-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8188271","title":"A physical map of the region encompassing the human interleukin-1 alpha, interleukin-1 beta, and interleukin-1 receptor antagonist genes.","abstract":"We have constructed a restriction map of the human genomic region containing the genes encoding the three members of the interleukin-1 (IL-1) family, IL-1 alpha, IL-1 beta, and IL-1 receptor antagonist (IL-1 ra). For this purpose, pulsed-field gel electrophoresis blots were hybridized with probes derived from the three genes. The genes (IL1A, IL1B, and IL1RN, respectively) were found to map to a common restriction fragment of approximately 430 kb that is flanked by two clusters of sites for methylation-sensitive rare-cutter restriction enzymes (putative CpG islands). A likely third internal CpG island was marked by two rare-cutter sites. CpG and non-CpG-specific enzymes were used to map the three genes. Relative to one terminal CpG island, the three genes were mapped to the following intervals: IL1A was between +0 and +35 kb, IL1B was between +70 and +110 kb, and IL1RN was between +330 and +430 kb.","authors":"Nicklin, MJ., Weith, A., Duff, GW.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Genomics","volume":"19","issue":"2","page":"382-4","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3143916","title":"Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells.","abstract":"Embryonic stem (ES) cells, the totipotent outgrowths of blastocysts, can be cultured and manipulated in vitro and then returned to the embryonic environment where they develop normally and can contribute to all cell lineages. Maintenance of the stem-cell phenotype in vitro requires the presence of a feeder layer of fibroblasts or of a soluble factor, differentiation inhibitory activity (DIA) produced by a number of sources; in the absence of DIA the ES cells differentiate into a wide variety of cell types. We recently noted several similarities between partially purified DIA and a haemopoietic regulator, myeloid leukaemia inhibitory factor (LIF), a molecule which induces differentiation in M1 myeloid leukaemic cells and which we have recently purified, cloned and characterized. We demonstrate here that purified, recombinant LIF can substitute for DIA in the maintenance of totipotent ES cell lines that retain the potential to form chimaeric mice.","authors":"Williams, RL., Hilton, DJ., Pease, S., Willson, TA., Stewart, CL., Gearing, DP., Wagner, EF., Metcalf, D., Nicola, NA., Gough, NM.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Nature","volume":"336","issue":"6200","page":"684-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1989-01-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3028645","title":"Structure-function analysis of fos protein: a single amino acid change activates the immortalizing potential of v-fos.","abstract":"We have undertaken a detailed structure-function analysis of v-fos protein, taking the ability to induce transformation and immortalization as criteria of biological activity. Our results demonstrate that the evolutionarily conserved center region of fos, comprising ca. 28% of the protein, is indispensable for its function. A single amino acid change (Glu 138----Val 138) in this region activates the immortalizing potential of v-fos without affecting its transforming capacity. The presence of additional either N- or C-terminal amino acids, however, is required for efficient expression of a stable protein, and significantly increases its biological activity. In contrast, sequences in the C-terminal half (between positions 228 and 267) strongly downmodulate the transforming activity of v-fos protein without decreasing its immortalizing potential.","authors":"Jenuwein, T., M\u00fcller, R.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Cell","volume":"48","issue":"4","page":"647-57","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1987-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3027573","title":"Deregulated c-fos expression interferes with normal bone development in transgenic mice.","abstract":"Transgenic mice were generated expressing c-fos genes under the control of the human metallothionein promoter. Although high levels of c-fos messenger RNA were detectable in a variety of tissues, deregulated c-fos expression specifically interfered with normal bone development without inducing malignant tumours.","authors":"R\u00fcther, U., Garber, C., Komitowski, D., M\u00fcller, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Nature","volume":"325","issue":"6103","page":"412-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1987-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34301800","title":"Pax5 regulates B cell immunity by promoting PI3K signaling via PTEN down-regulation.","abstract":"The transcription factor Pax5 controls B cell development, but its role in mature B cells is largely enigmatic. Here, we demonstrated that the loss of Pax5 by conditional mutagenesis in peripheral B lymphocytes led to the strong reduction of B-1a, marginal zone (MZ), and germinal center (GC) B cells as well as plasma cells. Follicular (FO) B cells tolerated the loss of Pax5 but had a shortened half-life. The Pax5-deficient FO B cells failed to proliferate upon B cell receptor or Toll-like receptor stimulation due to impaired PI3K-AKT signaling, which was caused by increased expression of PTEN, a negative regulator of the PI3K pathway. Pax5 restrained PTEN protein expression at the posttranscriptional level, likely involving <i>Pten<\/i>-targeting microRNAs. Additional PTEN loss in <i>Pten,Pax5<\/i> double-mutant mice rescued FO B cell numbers and the development of MZ B cells but did not restore GC B cell formation. Hence, the posttranscriptional down-regulation of PTEN expression is an important function of Pax5 that facilitates the differentiation and survival of mature B cells, thereby promoting humoral immunity.","authors":"Calder\u00f3n, L., Schindler, K., Malin, SG., Schebesta, A., Sun, Q., Schwickert, T., Alberti, C., Fischer, M., Jaritz, M., Tagoh, H., Ebert, A., Minnich, M., Liston, A., Cochella, L., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Sci Immunol","volume":"6","issue":"61","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21111228","title":"What determines the specificity and outcomes of ubiquitin signaling?","abstract":"Ubiquitin signals and ubiquitin-binding domains are implicated in almost every cellular process, but how is their functionality achieved in cells? We assess recent advances in monitoring the dynamics and specificity of ubiquitin networks in vivo and discuss challenges ahead.","authors":"Ikeda, F., Crosetto, N., Dikic, I.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell","volume":"143","issue":"5","page":"677-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9002521","title":"Stress-signalling kinase Sek1 protects thymocytes from apoptosis mediated by CD95 and CD3.","abstract":"Distinct and evolutionarily conserved signal transduction cascades mediate survival or death in response to developmental and environmental cues. The stress-activated protein kinases, or Jun N-terminal kinases (SAPKs\/JNKs), are activated in response to a variety of cellular stresses such as changes in osmolarity and metabolism, DNA damage, heat shock, ischaemia, or inflammatory cytokines. Sek1 (JNKK\/MKK4) is a direct activator of SAPKs\/JNKs in response to environmental stresses or mitogenic factors. Here we investigate the role of Sek1 in development and apoptosis by deleting sek1 in embryonic stem (ES) cells by homologous recombination. We provide genetic evidence that different stresses utilize distinct signalling pathways for SAPK\/JNK activation. sek1(-\/-) rag2(-\/-) chimaeric mice have normal numbers of mature T cells but fewer immature CD4+CD8+ thymocytes. The sek1 mutation did not affect the induction of apoptosis in response to environmental stresses in ES and T cells: instead, sek1 protected thymocytes from CD95 (Fas)- and CD3-mediated apoptosis. These data indicate that SEK1 mediates survival signals in T-cell development.","authors":"Nishina, H., Fischer, KD., Radvanyi, L., Shahinian, A., Hakem, R., Rubie, EA., Bernstein, A., Mak, TW., Woodgett, JR., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Nature","volume":"385","issue":"6614","page":"350-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3013419","title":"Control of erythroid differentiation: possible role of the transferrin cycle.","abstract":"A monoclonal antibody to the chicken transferrin receptor (JS-8) blocked temperature-induced and spontaneous differentiation of avian erythroid cells transformed by ts- and wt-retroviral oncogenes. In cells committed to differentiate, JS-8 caused an arrest at the erythroblast or early reticulocyte stage, followed by premature cell death, whereas proliferation of noncommitted erythroid cells or other hematopoietic cells remained unaffected. JS-8 had no effect on transferrin binding or internalization, but blocked subsequent receptor-recycling resulting in reduced iron uptake. Restoration of high intracellular iron levels neutralized the action of JS-8, whereas an inhibitor of porphyrine biosynthesis (4,6-dioxoheptanoic acid) closely mimicked the effect of JS-8. This suggests that erythroid differentiation might involve coordinate synthesis of erythrocyte proteins subject to regulation by hemin or hemoglobin.","authors":"Schmidt, JA., Marshall, J., Hayman, MJ., Ponka, P., Beug, H.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Cell","volume":"46","issue":"1","page":"41-51","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1986-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34525339","title":"Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response.","abstract":"Cell fate decisions during early B cell activation determine the outcome of responses to pathogens and vaccines. We examined the early B cell response to T-dependent antigen in mice by single-cell RNA sequencing. Early after immunization, a homogeneous population of activated precursors (APs) gave rise to a transient wave of plasmablasts (PBs), followed a day later by the emergence of germinal center B cells (GCBCs). Most APs rapidly exited the cell cycle, giving rise to non-GC-derived early memory B cells (eMBCs) that retained an AP-like transcriptional profile. Rapid decline of antigen availability controlled these events; provision of excess antigen precluded cell cycle exit and induced a new wave of PBs. Fate mapping revealed a prominent contribution of eMBCs to the MBC pool. Quiescent cells with an MBC phenotype dominated the early response to immunization in primates. A reservoir of APs\/eMBCs may enable rapid readjustment of the immune response when failure to contain a threat is manifested by increased antigen availability.","authors":"Glaros, V., Rauschmeier, R., Artemov, AV., Reinhardt, A., Ols, S., Emmanouilidi, A., Gustafsson, C., You, Y., Mirabello, C., Bj\u00f6rklund, \u00c5K., Perez, L., King, NP., M\u00e5nsson, R., Angeletti, D., Lor\u00e9, K., Adameyko, I., Busslinger, M., Kreslavsky, T.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Immunity","volume":"54","issue":"9","page":"2005-2023.e10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3006340","title":"Analysis of the autophosphorylation activity of transformation defective mutants of avian erythroblastosis virus.","abstract":"The v-erb B protein of avian erythroblastosis virus (AEV) possesses an associated protein kinase activity in vitro. Analysis of temperature-sensitive mutants, and nonconditional host range mutants of AEV demonstrated that there was no simple correlation between this autophosphorylation activity and the transformation ability of the various AEV mutants. These data suggest that although this kinase activity may be central to transformation by AEV it is in itself insufficient.","authors":"Hayman, MJ., Kitchener, G., Knight, J., McMahon, J., Watson, R., Beug, H.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Virology","volume":"150","issue":"1","page":"270-5","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1986-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9505088","title":"Molecular and cellular mechanisms of T lymphocyte apoptosis.","abstract":null,"authors":"Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Adv Immunol","volume":"68","issue":null,"page":"51-144","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3004938","title":"Activation of c-erbB in avian leukosis virus-induced erythroblastosis leads to the expression of a truncated EGF receptor kinase.","abstract":"Chicken erythroblastosis caused by avian leukosis virus (ALV) is thought to be mediated by activation of the c-erbB\/EGF receptor oncogene by a promoter-insertion mechanism. Here we study the proteins expressed by two ALV-induced leukemias and compare them with the avian EGF receptor and with the oncogene product of avian erythroblastosis virus (v-erbB) which was shown to be a truncated EGF receptor. It appears that the two leukemias express truncated EGF receptors of slightly different sizes with intrinsic tyrosine kinase activity. Hence, acute and chronic retroviruses utilize a common pathway for transformation. Moreover, the proteins expressed in the leukemias are similar to the avian EGF receptor with respect to their phosphopeptide maps, suggesting that they do not carry the C-terminal deletion characteristic of v-erbB.","authors":"Lax, I., Kris, R., Sasson, I., Ullrich, A., Hayman, MJ., Beug, H., Schlessinger, J.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"EMBO J","volume":"4","issue":"12","page":"3179-82","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1986-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2999798","title":"The putative transforming protein of S13 avian erythroblastosis virus is a transmembrane glycoprotein with an associated protein kinase activity.","abstract":"S13 is an avian retrovirus that transforms both fibroblasts and erythroblasts. The gene product responsible for the oncogenic effects of S13 is the env-related glycoprotein gp155. In this report we show that gp155 is a transmembrane protein with a 55-kDa cytoplasmic domain. Pulse-chase analysis shows that gp155 was cleaved posttranslationally into two glycosylated proteins, gp85 and gp70. In addition, we show that a tyrosine protein kinase activity is associated only with the gp70 protein in microsomes and in immune complexes.","authors":"Hayman, MJ., Kitchener, G., Vogt, PK., Beug, H.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Proc Natl Acad Sci U S A","volume":"82","issue":"23","page":"8237-41","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1986-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2993119","title":"Characterization of hematopoietic cells transformed in vitro by AEV-H, a v-erbB-containing avian erythroblastosis virus.","abstract":null,"authors":"Beug, H., Kahn, P., Doederlein, G., Hayman, MJ., Graf, T.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Haematol Blood Transfus","volume":"29","issue":null,"page":"290-7","pdf":null,"JrId":"30276","fulltextlink":null,"preprintlink":null,"articledate":"1985-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2993118","title":"Characterization of the number of carbohydrate chains on the avian erythroblastosis virus erb B gene product and their role in transformation.","abstract":null,"authors":"Hayman, MJ., Schmidt, JA., Kitchener, G., Marshall, J., Beug, H.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Haematol Blood Transfus","volume":"29","issue":null,"page":"284-9","pdf":null,"JrId":"30276","fulltextlink":null,"preprintlink":null,"articledate":"1985-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8486736","title":"Rab17, a novel small GTPase, is specific for epithelial cells and is induced during cell polarization.","abstract":"The rab subfamily of small GTPases has been demonstrated to play an important role in the regulation of membrane traffic in eukaryotic cells. Compared with nonpolarized cells, epithelial cells have distinct apical and basolateral transport pathways which need to be separately regulated. This raises the question whether epithelial cells require specific rab proteins. However, all rab proteins identified so far were found to be equally expressed in polarized and nonpolarized cells. Here we report the identification of rab17, the first epithelial cell-specific small GTPase. Northern blot analysis on various mouse organs, revealed that the rab17 mRNA is present in kidney, liver, and intestine but not in organs lacking epithelial cells nor in fibroblasts. To determine whether rab17 is specific for epithelial cells we studied its expression in the developing kidney. We found that rab17 is absent from the mesenchymal precursors but is induced upon their differentiation into epithelial cells. In situ hybridization studies on the embryonic kidney and intestine revealed that rab17 is restricted to epithelial cells. By immunofluorescence and immunoelectron microscopy on kidney sections, rab17 was localized to the basolateral plasma membrane and to apical tubules. Rab proteins associated with two distinct compartments have been found to regulate transport between them. Therefore, our data suggest that rab17 might be involved in transcellular transport.","authors":"L\u00fctcke, A., Jansson, S., Parton, RG., Chavrier, P., Valencia, A., Huber, LA., Lehtonen, E., Zerial, M.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Cell Biol","volume":"121","issue":"3","page":"553-64","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1993-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1974172","title":"High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines.","abstract":"CpG islands are normally methylation free in cells of the animal, even when the associated gene is transcriptionally silent. In mouse NIH 3T3 and L cells, however, over half of the islands are heavily methylated. Near identity of the methylated subset in the two cell lines suggested that methylation is confined to genes that are nonessential in culture. In agreement with this, islands at several tissue-specific genes, but not at housekeeping genes, have become methylated in many human and mouse cell lines. At the chromatin level, methylated islands are Mspl resistant compared with their nonmethylated counterparts. We suggest that mutation-like gene inactivation due to CpG island methylation is widespread in many cell lines and could explain the loss of cell type-specific functions in culture.","authors":"Antequera, F., Boyes, J., Bird, A.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Cell","volume":"62","issue":"3","page":"503-14","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1990-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34233950","title":"Down-regulation of A20 promotes immune escape of lung adenocarcinomas.","abstract":"Inflammation is a well-known driver of lung tumorigenesis. One strategy by which tumor cells escape tight homeostatic control is by decreasing the expression of the potent anti-inflammatory protein tumor necrosis factor alpha-induced protein 3 (TNFAIP3), also known as A20. We observed that tumor cell intrinsic loss of A20 markedly enhanced lung tumorigenesis and was associated with reduced CD8<sup>+<\/sup> T cell-mediated immune surveillance in patients with lung cancer and in mouse models. In mice, we observed that this effect was completely dependent on increased cellular sensitivity to interferon-\u03b3 (IFN-\u03b3) signaling by aberrant activation of TANK-binding kinase 1 (TBK1) and increased downstream expression and activation of signal transducer and activator of transcription 1 (STAT1). Interrupting this autocrine feed forward loop by knocking out IFN-\u03b1\/\u03b2 receptor completely restored infiltration of cytotoxic T cells and rescued loss of A20 depending tumorigenesis. Downstream of STAT1, programmed death ligand 1 (PD-L1) was highly expressed in A20 knockout lung tumors. Accordingly, immune checkpoint blockade (ICB) treatment was highly efficient in mice harboring A20-deficient lung tumors. Furthermore, an A20 loss-of-function gene expression signature positively correlated with survival of melanoma patients treated with anti-programmed cell death protein 1. Together, we have identified A20 as a master immune checkpoint regulating the TBK1-STAT1-PD-L1 axis that may be exploited to improve ICB therapy in patients with lung adenocarcinoma.","authors":"Breitenecker, K., Homolya, M., Luca, AC., Lang, V., Trenk, C., Petroczi, G., Mohrherr, J., Horvath, J., Moritsch, S., Haas, L., Kurnaeva, M., Eferl, R., Stoiber, D., Moriggl, R., Bilban, M., Obenauf, AC., Ferran, C., Dome, B., Laszlo, V., Gy\u0151rffy, B., Dezso, K., Moldvay, J., Casanova, E., Moll, HP.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Sci Transl Med","volume":"13","issue":"601","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2963370","title":"Identification of transcripts of the T cell antigen receptor beta chain gene and major histocompatibility complex class II genes in antigen-presenting cloned BK-BI-2.6.C6 cells.","abstract":"The cloned murine cell line BK-BI-2.6.C6 has previously been shown to exhibit T cell characteristics, to synthesize and express MHC class II molecules, and to present protein antigens to antigen-dependent T cell clones. As a more definitive proof of the T-cell nature of these cells, transcripts of the rearranged T cell antigen receptor (TcR) beta gene were assessed by Northern blot analysis. BK-BI-2.6.C6 cells constitutively transcribe mRNA for the light chain of TcR and express the disulphide-linked alpha, beta TcR heterodimer at the cell surface. In addition mRNA for the polymorphic MHC class II subunits A alpha and A beta as well as for the invariant gamma chain were detected. BK-BI-2.6.C6 T cells effectively stimulated bovine insulin-reactive T hybridoma cells to lymphokine production in the presence of this antigen. Since the antigen-presenting and the responding T cell populations are maintained in culture in the absence of feeder cells, contamination by conventional accessory cells is excluded. These data unequivocally demonstrate that cloned murine Ia-expressing T cells can act as antigen-presenting accessory cells.","authors":"Reske-Kunz, AB., R\u00fcck, G., Steinlein, P., Reske, K.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Scand J Immunol","volume":"27","issue":"1","page":"107-12","pdf":null,"JrId":"7415","fulltextlink":null,"preprintlink":null,"articledate":"1988-02-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2985272","title":"DNA-binding activity is associated with purified myb proteins from AMV and E26 viruses and is temperature-sensitive for E26 ts mutants.","abstract":"Oncogene protein products from avian myeloblastosis virus, p48v-myb, and from avian leukemia virus E26, p135gag-myb-ets, are located predominantly in the nucleus of nonproducer bone marrow cell clones, as revealed by indirect immunofluorescence. Both oncogene proteins were purified by immunoaffinity chromatography using monoclonal antibodies against p19 and immunoglobulins specific for myb, which was expressed in bacteria for antibody production. The purified proteins bind to DNA in vitro. In contrast, purified p135gag-myb-ets proteins from several mutants of E26 virus, temperature-sensitive for myeloblast transformation, either lost their abilities to bind to DNA or exhibited highly thermolabile DNA-protein interactions in vitro. DNA binding of AMV and E26 oncogene proteins is inhibited by myb-specific immunoglobulins. Our results suggest that lesions in the myb oncogene affect transformation as well as DNA binding of myb proteins in vitro.","authors":"Moelling, K., Pfaff, E., Beug, H., Beimling, P., Bunte, T., Schaller, HE., Graf, T.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Cell","volume":"40","issue":"4","page":"983-90","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1985-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8464066","title":"Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins.","abstract":"Originally, rotamers were defined as side-chain torsion (chi-angle) combinations corresponding to the local minima of potential energy (van-der-Waals and torsion terms) for the side-chain of a terminally blocked amino acid. If at least one chi-angle differed by more than 20 degrees from that of a rotamer, the side-chain was considered as deviant both from energetic (increase in potential energy of no less than 1 to 2 kcal\/mol) and geometric (precision of atom positioning is worse than 0.5 A) aspects. In this work the distribution of side-chain conformations in protein crystal structures is analysed. Large deviations from rotameric chi-values occur systematically and cannot be attributed merely to errors in crystal structure determination. The \"rotamericity\" (the fraction of residues within +\/- 20 degrees of the chi-angles of a rotamer) not only remains substantially below 100% (70 to 95% for various amino acids) with improving crystallographic resolution but actually decreases for 8 out of 17 amino acid types after a critical resolution limit is crossed. This effect has been observed for external as well as for internal residues. The set of amino acid side-chain conformations in globular proteins cannot be considered as normally distributed around some rotamer points. Outliers occur systematically. The rotamericity of an amino acid depends essentially on the different environments the amino acid meets in real protein structures. Factors such as the backbone torsion angles of the residue itself, the secondary structure and tertiary contacts influence the rotamericity. The deviations in regions of regular main-chain structure from the average g-:t:g+ relationship in the chi 1-angle become much more evident if, in addition to the typical secondary structure assignments, the actual backbone torsion angles of the residue are taken into account. In alpha-helices the t:g+ distribution in the chi 1-angle correlates with physical properties describing volume, extension and flexibility of the side-chain. In beta-strands the factors influencing the t:g+ distribution in the chi 1-angle are the polarity and hydrophobicity of the side-chain. Nevertheless, a considerable number of residues do not comply with the statistical preferences observed for the side-chain conformation. Large deviations from the rotamer values are observed especially in cases when normally advantageous chi 1-values are not allowed and adjustments in chi 2 become necessary to accommodate the side-chain.(ABSTRACT TRUNCATED AT 400 WORDS)","authors":"Schrauber, H., Eisenhaber, F., Argos, P.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Mol Biol","volume":"230","issue":"2","page":"592-612","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1993-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34604863","title":"A summary of current NKG2D-based CAR clinical trials.","abstract":"Cancer immunotherapies have significantly improved patient survival and treatment options in recent years. Nonetheless, the success of immunotherapy is limited to certain cancer types and specific subgroups of patients, making the development of new therapeutic approaches a topic of ongoing research. Chimeric antigen receptor (CAR) cells are engineered immune cells that are programmed to specifically eliminate cancer cells. Ideally, a CAR recognizes antigens that are restricted to tumor cells to avoid off-target effects. NKG2D is an activating immunoreceptor and an important player in anti-tumor immunity due to its ability to recognize tumor cells and initiate an anti-tumor immune response. Ligands for NKG2D are expressed on malignant or stressed cells and typically absent from healthy tissue, making it a promising CAR candidate. Here, we provide a summary of past and ongoing NKG2D-based CAR clinical trials and comment on potential pitfalls.","authors":"Curio, S., Jonsson, G., Marinovi\u0107, S.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Immunother Adv","volume":"1","issue":"1","page":"ltab018","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2878364","title":"A single amino acid substitution in v-erbB confers a thermolabile phenotype to ts167 avian erythroblastosis virus-transformed erythroid cells.","abstract":"A library of recombinant bacteriophage was prepared from ts167 avian erythroblastosis virus-transformed erythroid precursor cells (HD6), and integrated proviruses from three distinct genomic loci were isolated. A subclone of one of these proviruses (pAEV1) was shown to confer temperature-sensitive release from transformation of erythroid precursor cells in vitro. The predicted amino acid sequence of the v-erbB polypeptide from the mutant had a single amino acid change when compared with the wild-type parental virus. When the wild-type amino acid was introduced into the temperature-sensitive avian erythroblastosis virus provirus in pAEV1, all erythroid clones produced in vitro were phenotypically wild type. The mutation is a change from a histidine to an aspartic acid in the temperature-sensitive v-erbB polypeptide. It is located in the center of the tyrosine-specific protein kinase domain and corresponds to amino acid position 826 of the human epidermal growth factor receptor sequence.","authors":"Choi, OR., Trainor, C., Graf, T., Beug, H., Engel, JD.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Mol Cell Biol","volume":"6","issue":"5","page":"1751-9","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1987-01-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2879242","title":"The c-erb-A protein is a high-affinity receptor for thyroid hormone.","abstract":"Hormone binding and localization of the c-erb-A protein suggest that it is a receptor for thyroid hormone, a nuclear protein that binds to DNA and activates transcription. In contrast, the product of the viral oncogene v-erb-A is defective in binding the hormone but is still located in the nucleus.","authors":"Sap, J., Mu\u00f1oz, A., Damm, K., Goldberg, Y., Ghysdael, J., Leutz, A., Beug, H., Vennstr\u00f6m, B.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Nature","volume":"324","issue":"6098","page":"635-40","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1987-02-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2866519","title":"How do retroviral oncogenes induce transformation in avian erythroid cells?","abstract":"The v-erb B oncogene, as well as other oncogenes of the src-gene family transform immature erythroid cells from chick bone marrow in vivo and in vitro. The erb B-transformed erythroid cells differ from normal late erythroid precursors (CFU-E) in that they have acquired the capacity to undergo self-renewal as well as to differentiate terminally. They also do not require the normal erythroid differentiation hormone, erythropoietin, for either process. Cooperation of v-erb B with a second oncogene, v-erb A, results in a differentiation arrest of the transformed cells, which now only use the self-renewal pathway. Studies with conditional and non-conditional mutants in both v-erb B and v-erb A will be presented to elucidate further how the transforming proteins encoded by these oncogenes, gp74erb B and gp75gag-erb A, affect the differentiation programme of the infected erythroid precursor with the outcome of hormone-independent leukaemic cells arrested at an early stage of erythroid differentiation.","authors":"Beug, H., Kahn, P., Vennstr\u00f6m, B., Hayman, MJ., Graf, T.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Proc R Soc Lond B Biol Sci","volume":"226","issue":"1242","page":"121-6","pdf":null,"JrId":"6660","fulltextlink":null,"preprintlink":null,"articledate":"1986-01-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2850165","title":"Cytolytic T cells recognize a chimeric MHC class I antigen expressed in influenza A infected transgenic mice.","abstract":"A chimeric H-2Kd\/Kk gene, called pC31, contains the extracellular alpha 1 domain of Kd origin whereas the rest of the molecule is of Kk origin. Disruption of the syngeneic alpha 1-alpha 2 structure results in a total abrogation of the function of the C31 protein as a restriction element for H-2Kd and Kk restricted T cells during virus infection. In an attempt to obtain information on the functional polymorphism of MHC class I antigens as restriction elements, we have introduced the pC31 gene into the germ line of C3H\/He mice (H-2k). The pC31 gene was transcribed in all tissues examined and the expression pattern paralleled the endogenous H-2Kk gene. However, the mRNA for the transgene was approximately 10-times more abundant, which was reflected in an elevated expression of the C31 protein in transgenic splenocytes. Most of the C31 antigen was found intracellularly. The C31 antigen could condition transgenic cytotoxic T lymphocytes in a specific manner during influenza A virus infection and functioned as the restricting element during T cell lysis of the infected cells. These results suggest that entire exons may be exchanged between MHC class I genes and that this exchange can generate novel and functional restriction elements.","authors":"Jefferies, WA., R\u00fcther, U., Wagner, EF., Kvist, S.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"EMBO J","volume":"7","issue":"11","page":"3423-31","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1989-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18470659","title":"Signal transduction and transcriptional regulation during mesenchymal cell differentiation.","abstract":null,"authors":"Nishimura, R., Hata, K., Ikeda, F., Ichida, F., Shimoyama, A., Matsubara, T., Wada, M., Amano, K., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Bone Miner Metab","volume":"26","issue":"3","page":"203-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22499256","title":"Reconstructing the orientation distribution of actin filaments in the lamellipodium of migrating keratocytes from electron microscopy tomography data.","abstract":"Migration of motile cells on flat substrates is usually driven by the polymerization of a flat actin filament network. Theoretical models have made different predictions regarding the distribution of the filament orientation in the lamellipodium with respect to the direction of motion. Here we show how one can automatically reconstruct the orientation distribution of actin filaments in the lamellipodium of migrating keratocytes from electron microscopy tomography data. We use two different image analysis methods, an algorithm which explicitly extracts an abstract network representation and an analysis of the gray scale information based on the structure tensor. We show that the two approaches give similar results, both for simulated data and for electron microscopy tomography data from migrating keratocytes. For the lamellipodium at the leading edge of fast moving cells, we find an orientation distribution that is peaked at +35\/-35 degrees. For the lamellipodium at the leading edge of slow moving cells as well as for the lamellipodium at the flanks of fast moving cells, one broad peak around 0 degree dominates the distribution.","authors":"Weichsel, J., Urban, E., Small, JV., Schwarz, US.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cytometry A","volume":"81","issue":"6","page":"496-507","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9558087","title":"Differential requirement for p56lck in fetal and adult thymopoiesis.","abstract":"The protein tyrosine kinase p56lck is critical for the generation of mature thymocytes in adult mice. However its requirement during the maturation of thymocytes from the fetal to the adult stage has not been clearly defined. We analyzed prenatal and postnatal thymocyte maturation in mice deficient for p56lck (lck[-\/-]). Before birth, lck appears to play a crucial role in the expansion and proliferation of CD4+CD8+ double positive thymocytes, whereas proliferation and absolute numbers of CD4-CD8- double negative thymocyte precursors remained within the normal range until the end of the second week postnatal. Three weeks after birth, the total numbers of double negative and immature single positive thymocytes underwent a dramatic reduction that correlated with a decrease in the double positive population. This ontogenic defect was associated with a significant decrease in the proliferation rates of thymocyte precursors. Our data suggest that signaling via p56lck kinase is differentially required within a given phenotypically defined thymocyte subpopulation, depending on its stage of thymocyte maturation.","authors":"Molina, TJ., Perrot, JY., Penninger, J., Ramos, A., Audouin, J., Briand, P., Mak, TW., Diebold, J.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Immunol","volume":"160","issue":"8","page":"3828-34","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2834683","title":"Abnormal glycosylation of the env-sea oncogene product inhibits its proteolytic cleavage and blocks its transforming ability.","abstract":"Cells transformed by the avian erythroblastosis virus S13 contain three proteins derived from the v-sea oncogene, gp155, gp70 (a cleavage product of gp155), and p38. It is not clear whether only one or all three of these proteins are required for transformation by S13. S13 transformed erythroblasts and fibroblasts revert to a normal morphology in the presence of the alpha glucosidase-1 inhibitor castanospermine, whereas cells transformed by the v-src or v-erbB oncogenes are unaffected by this drug. Treatment with castanospermine does not alter the tyrosine kinase autophosphorylation activity of any of the v-sea products, and the synthesis and processing of p38 is unaffected. Castanospermine modifies the structure of the carbohydrate chains of gp155 such that the glucose residues are retained, thereby inhibiting complex chain formation. Analysis of revertant S13 transformed cells shows that the proteolytic cleavage of the modified form of gp155 is inhibited, resulting in a very low yield of a modified form of gp70. There is no detectable effect of castanospermine on the transport of v-sea gene products to the cell surface. However, due to the inhibition of proteolytic cleavage, the modified form of gp155 is now the major v-sea encoded protein expressed on the cell surface. Thus it appears that the cell surface expression of a v-sea encoded protein with tyrosine kinase autophosphorylating activity is insufficient for cell transformation.","authors":"Knight, J., Beug, H., Marshall, J., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Oncogene","volume":"2","issue":"4","page":"317-26","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1988-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10497036","title":"Prediction of potential GPI-modification sites in proprotein sequences.","abstract":"Glycosylphosphatidylinositol (GPI) lipid anchoring is a common posttranslational modification known mainly from extracellular eukaryotic proteins. Attachment of the GPI moiety to the carboxyl terminus (omega-site) of the polypeptide follows after proteolytic cleavage of a C-terminal propeptide. For the first time, a new prediction technique locating potential GPI-modification sites in precursor sequences has been applied for large-scale protein sequence database searches. The composite prediction function (with separate parametrisation for metazoan and protozoan proteins) consists of terms evaluating both amino acid type preferences at sequence positions near a supposed omega-site as well as the concordance with general physical properties encoded in multi-residue correlation within the motif sequence. The latter terms are especially successful in rejecting non-appropriate sequences from consideration. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set of fully annotated sequences from the SWISS-PROT database as well as with a newly created database \"big-Pi\" (more than 300 GPI-motif mutations extracted from original literature sources). The accuracy of predicting the effect of mutations in the GPI sequence motif was above 83 %. Lists of potential precursor proteins which are non-annotated in SWISS-PROT and SPTrEMBL are presented on the WWW-page http:\/\/www.embl-heidelberg.de\/beisenha\/gpi\/gpi_p rediction. html The algorithm has been implemented in the prototype software \"big-Pi predictor\" which may find application as a genome annotation and target selection tool.","authors":"Eisenhaber, B., Bork, P., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Mol Biol","volume":"292","issue":"3","page":"741-58","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1999-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8876239","title":"The Drosophila Numb protein inhibits signaling of the Notch receptor during cell-cell interaction in sensory organ lineage.","abstract":"Specification of unequal daughter cell fates in the Drosophila external sense organ lineage requires asymmetric localization of the intrinsic determinant Numb as well as cell-cell interactions mediated by the Delta ligand and Notch receptor. Previous genetic studies indicated that numb acts upstream of Notch, and biochemical studies revealed that Numb can bind Notch. For a functional assay of the action of Numb on Notch signaling, we expressed these proteins in cultured Drosophila cells and used nuclear translocation of Suppressor of Hairless [Su(H)] as a reporter for Notch activity. We found that Numb interfered with the ability of Notch to cause nuclear translocation of Su(H); both the C-terminal half of the phosphotyrosine binding domain and the C terminus of Numb are required to inhibit Notch. Overexpression of Numb during wing development, which is sensitive to Notch dosage, revealed that Numb is also able to inhibit the Notch receptor in vivo. In the external sense organ lineage, the phosphotyrosine binding domain of Numb was found to be essential for the function but not for asymmetric localization of Numb. Our results suggest that Numb determines daughter cell fates in the external sense organ lineage by inhibiting Notch signaling.","authors":"Frise, E., Knoblich, JA., Younger-Shepherd, S., Jan, LY., Jan, YN.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Proc Natl Acad Sci U S A","volume":"93","issue":"21","page":"11925-32","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2784063","title":"The protein CDP, but not CP1, footprints on the CCAAT region of the gamma-globin gene in unfractionated B-cell extracts.","abstract":"We have identified, by DNase I footprinting, six different factors that interact with the promoter of the human A gamma-globin gene in nuclear extracts of the B-cell line BJA-B. Among them is the vertebrate homologue of the sea-urchin CCAAT displacement protein (CDP) which footprints over the entire duplicated CCAAT region. The CCAAT-binding factor CP1, a potential activator of the gamma-globin promoter, is able to bind to its proximal recognition sequence only once it has been partially enriched and separated from CDP. The factor CDP has an apparent molecular mass of 200 kDa and differs from CP1 by its footprint pattern and competition behavior.","authors":"Superti-Furga, G., Barberis, A., Schreiber, E., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Biochim Biophys Acta","volume":"1007","issue":"2","page":"237-42","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1989-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2821499","title":"A universal retroviral vector for efficient constitutive expression of exogenous genes.","abstract":null,"authors":"Boulter, CA., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Nucleic Acids Res","volume":"15","issue":"17","page":"7194","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1987-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2780325","title":"The testis-specific octamer-binding protein of the sea urchin has a molecular weight of 85 kDa.","abstract":null,"authors":"Barberis, A., Superti-Furga, G., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Nucleic Acids Res","volume":"17","issue":"17","page":"7114","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1989-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34590075","title":"A probabilistic framework for cellular lineage reconstruction using integrated single-cell 5-hydroxymethylcytosine and genomic DNA sequencing.","abstract":"Lineage reconstruction is central to understanding tissue development and maintenance. To overcome the limitations of current techniques that typically reconstruct clonal trees using genetically encoded reporters, we report scPECLR, a probabilistic algorithm to endogenously infer lineage trees at a single-cell-division resolution by using 5-hydroxymethylcytosine (5hmC). When applied to 8-cell pre-implantation mouse embryos, scPECLR predicts the full lineage tree with greater than 95% accuracy. In addition, we developed scH&amp;G-seq to sequence both 5hmC and genomic DNA from the same cell. Given that genomic DNA sequencing yields information on both copy number variations and single-nucleotide polymorphisms, when combined with scPECLR it enables more accurate lineage reconstruction of larger trees. Finally, we show that scPECLR can also be used to map chromosome strand segregation patterns during cell division, thereby providing a strategy to test the \"immortal strand\" hypothesis. Thus, scPECLR provides a generalized method to endogenously reconstruct lineage trees at an individual-cell-division resolution.","authors":"Wangsanuwat, C., Chialastri, A., Aldeguer, JF., Rivron, NC., Dey, SS.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell Rep Methods","volume":"1","issue":"4","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2721491","title":"In vivo and in vitro expression of U7 snRNA genes: cis- and trans-acting elements required for RNA polymerase II-directed transcription.","abstract":"Three of five genes coding for U7 small nuclear (sn) RNA of the sea urchin Psammechinus miliaris were shown to be expressed during early embryogenesis by microinjection into sea urchin eggs followed by fertilization. Both in vivo and in nuclear extracts of blastula embryos, a minimal promoter of 80 bp of 5' flanking sequence is essential for their expression. Sequences upstream of position -80 enhance transcription in vivo, but not in vitro, approximately 5-fold. In vitro, transcription initiates at nucleotide +1 of the U7 snRNA and is directed by RNA polymerase II. Protein-DNA binding studies and site-directed mutagenesis demonstrate the presence of multiple proteins interacting with sequences between -57 and -26, which are essential for selection of the correct initiation site and for efficient in vitro transcription. Three of these factors recognize a TATA-like regulatory element between positions -53 and -45, suggesting a role for TATA-binding proteins in the initiation of sea urchin U7 snRNA transcription.","authors":"Southgate, C., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"EMBO J","volume":"8","issue":"2","page":"539-49","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1989-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16713556","title":"CYLD in ubiquitin signaling and tumor pathogenesis.","abstract":"Absence of CYLD, which encodes a deubiquitinating enzyme, causes an inherited disease characterized by benign skin tumors. In this issue of Cell, Massoumi et al. (2006) show that CYLD deubiquitinates the coactivator Bcl-3, thereby preventing its translocation into the nucleus, where it normally interacts with NF-kappaB and activates transcription of proliferation genes in response to growth signals.","authors":"Ikeda, F., Dikic, I.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell","volume":"125","issue":"4","page":"643-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2744459","title":"Developmental and tissue-specific regulation of a novel transcription factor of the sea urchin.","abstract":"We have identified a novel transcription factor that interacts with the promoter of four tissue-specific late histone H2A-2 and H2B-2 genes of the sea urchin by DNase I footprint, mobility shift, and methylation interference analyses. The binding site for this factor is required for efficient transcription of the H2B-2.1 gene both in vitro in nuclear extracts of gastrula embryos and in vivo in microinjected sea urchin embryos. This factor binds with equal affinity to the recognition sequences of all four histone genes in cross-competition assays. Moreover, the binding site of the H2B-2.2 promoter can functionally substitute for that of the H2B-2.1 gene in in vivo expression experiments. Nevertheless, all four binding sites share little sequence homology with each other. This transcription factor increases in abundance during embryogenesis and has been detected in the adult sea urchin only in the tube feet, where the late H2A-2 and H2B-2 genes are expressed specifically. Therefore, we refer to this factor as tissue-specific activator protein (TSAP). The close correlation between the presence of TSAP and the expression pattern of the late H2A-2 and H2B-2 genes suggests that this transcription factor is directly responsible for the developmental and tissue-specific regulation of these genes.","authors":"Barberis, A., Superti-Furga, G., Vitelli, L., Kemler, I., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Genes Dev","volume":"3","issue":"5","page":"663-75","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1989-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2736622","title":"Endothelioma cells expressing the polyoma middle T oncogene induce hemangiomas by host cell recruitment.","abstract":"Mouse endothelioma cells expressing the polyoma middle T oncogene induced hemangiomas in a variety of species such as mice, rats, chicks, and quails. In embryos and newborn mice the hemangiomas expanded within 10-18 hr of injection, disrupting the vasculature and causing the death of the animal. In contrast, the hemangiomas formed a stable structure reminiscent of benign human hemangiomas in adult mice within 5 days. Analysis of the cells comprising the hemangioma revealed that over 95% of the endothelial cells were host derived. No induction of host cell proliferation was detected, and no endothelial mitogens were secreted by the endothelioma cells in vitro. The maintenance of the hemangioma appeared to require the continuous presence of endothelioma cells. The results indicate that these endothelioma cells act as a potent stimulating agent in the rapid formation of hemangiomas by recruiting nonproliferating host endothelial cells.","authors":"Williams, RL., Risau, W., Zerwes, HG., Drexler, H., Aguzzi, A., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Cell","volume":"57","issue":"6","page":"1053-63","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1989-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1979040","title":"Phosphorylation of the v-erbA protein is required for its function as an oncogene.","abstract":"The v-erbA oncogene of avian erythroblastosis virus (AEV) encodes a ligand-independent mutated version of the chicken c-erbA alpha-encoded thyroid hormone receptor. The v-erbA gene product, a 75-kD gag\/v-erbA fusion protein, is phosphorylated on Ser-16\/17 of its v-erbA-encoded domain, and phosphorylation at this site is increased in vivo after activation of either the PKA or PKC signal transduction pathways. To test the hypothesis that phosphorylation of Ser-16\/17 regulates gag\/v-erbA protein function, mutant proteins in which Ser-16\/17 had been changed to alanine or threonine residues were analyzed for their ability to inhibit erythroid differentiation of ts v-erbB or ts v-sea-transformed erythroblasts at nonpermissive temperature. Conversion of Ser-16\/17 into alanine, although not affecting nuclear localization or DNA binding of the gag\/erbA protein, prevented phosphorylation of the v-erbA-encoded domain of the protein both in unstimulated cells or after stimulation by PKA and PKC activators. The nonphosphorylatable AA-gag\/v-erbA protein proved unable to inhibit temperature-induced differentiation of ts v-erbB and ts v-sea-transformed erythroblasts and to block expression of the erythrocyte-specific genes band 3 and carbonic anhydrase II. Back mutation of these alanine residues to serine resulted in the recovery of both normal phosphorylation levels and wild-type biological activity. In contrast, substitution of Ser-16\/17 for threonine, which preserved phosphorylation in unstimulated cells but not PKA- and PKC-enhanced phosphorylation, resulted in a partially active gag\/v-erbA protein. These results, together with the fact that the protein kinase inhibitor H7 resulted in both a dose-dependent inhibition of gag\/v-erbA protein phosphorylation and the induction of terminal differentiation of AEV-transformed erythroblasts show that phosphorylation of gag\/v-erbA protein is required for full biological activity. These results support the hypothesis that phosphorylation of the gag\/v-erbA protein is important for transcriptional repression of at least some of its target genes in erythroid cells.","authors":"Glineur, C., Zenke, M., Beug, H., Ghysdael, J.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Genes Dev","volume":"4","issue":"10","page":"1663-76","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1991-01-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8458346","title":"The estrogen receptor cooperates with the TGF alpha receptor (c-erbB) in regulation of chicken erythroid progenitor self-renewal.","abstract":"A unique combination of growth promoting factors is described that allows growth of large amounts (10(10)-10(11)) of normal erythroid progenitors from chick bone marrow. These erythroid progenitors express the estrogen receptor (ER) as well as the receptor tyrosine kinase TGF alpha R\/c-erbB. They require both TGF alpha and estradiol for sustained self-renewal in vitro, but terminally differentiate upon withdrawal of TGF alpha and inactivation of the ER by an antagonist (ICI 164.384). Overexpression of the human ER in erythroblasts devoid of endogenous ER revealed that the hormone-activated ER alone arrested erythroid differentiation and repressed a large group of erythrocyte genes. When similarly overexpressed, TGF alpha R\/c-erbB inhibited the expression of a distinct, but overlapping, set of genes. The endogenous ER and TGF alpha R\/c-erbB affect erythrocyte gene expression in a similar, but less pronounced fashion. Surprisingly, suppression of ER function by antagonist efficiently inhibited erythroblast transformation by tyrosine kinase oncogenes, suggesting a role of the endogenous ER in leukemogenesis. We speculate that the oncogenes v-erbB and v-erbA cooperate in erythroleukemia induction by a mechanism that is employed by TGF alpha R\/c-erbB and ER to regulate normal progenitor self-renewal in response to external signals.","authors":"Schroeder, C., Gibson, L., Nordstr\u00f6m, C., Beug, H.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"EMBO J","volume":"12","issue":"3","page":"951-60","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1993-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34661293","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration.","abstract":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling.","authors":"Bajaj, S., Bagley, JA., Sommer, C., Vertesy, A., Nagumo Wong, S., Krenn, V., L\u00e9vi-Strauss, J., Knoblich, JA.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"EMBO J","volume":null,"issue":null,"page":"e108714","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2655927","title":"Dangerous liaisons: spermatozoa as natural vectors for foreign DNA?","abstract":null,"authors":"Birnstiel, ML., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Cell","volume":"57","issue":"5","page":"701-2","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1989-07-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2568314","title":"Expression of v-src induces a myeloproliferative disease in bone-marrow-reconstituted mice.","abstract":"A recombinant retrovirus, N-TK-src, was used to introduce the v-src oncogene into mouse hematopoietic cells. This vector efficiently expresses both the neo and v-src genes in different hematopoietic lineages in culture as well as in mice reconstituted with infected bone marrow cells. Expression of v-src had no dramatic effect on the proliferative and differentiative capacity of hematopoietic precursors when assayed in methyl cellulose cultures. However, in mice reconstituted with N-TK-src-infected bone marrow cells, expression of v-src leads to the rapid development of a severe myeloproliferative disease, characterized by splenomegaly, anemia, and a shift of hematopoiesis from the bone marrow to the spleen.","authors":"Keller, G., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Genes Dev","volume":"3","issue":"6","page":"827-37","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1989-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2560752","title":"The mutated, myeloid cell-specific growth factor receptor v-fms transforms avian erythroid but not myeloid cells.","abstract":"In avian hematopoietic cells, transformation by tyrosine kinase oncogenes is restricted to the erythroid lineage. To study the mechanism of this striking target cell specificity, we constructed an avian retrovirus correctly expressing the feline v-fms protein, an oncogenic version of the myeloid-specific CSF-1 receptor. Similar to other tyrosine kinase oncogenes (erbB, src, fps, sea), the v-fms oncogene induced progenitor cells to self-renew in an erythropoietin-independent manner. Spontaneous differentiation of the transformed cells was arrested by v-erbA. v-fms failed to induce transformation of myeloid cells but caused myeloid cells transformed by the v-myb oncogene, as well as normal macrophages, to proliferate independent of cMGF (chicken myelomonocytic growth factor). Unlike the other tyrosine kinases, v-fms did not induce cMGF secretion in myb-myeloblasts, suggesting a nonautocrine mechanism of growth factor independence.","authors":"Fuhrmann, U., Vennstr\u00f6m, B., Beug, H.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Genes Dev","volume":"3","issue":"12B","page":"2072-82","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1990-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2559851","title":"Co-operation between viral oncogenes in avian erythroid and myeloid leukaemia.","abstract":null,"authors":"Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Eur J Clin Invest","volume":"19","issue":"6","page":"491-502","pdf":null,"JrId":"3611","fulltextlink":null,"preprintlink":null,"articledate":"1990-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2555793","title":"Two classes of observed frequency for rare-cutter sites in CpG islands.","abstract":null,"authors":"Bird, AP.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Nucleic Acids Res","volume":"17","issue":"22","page":"9485","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1990-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8844856","title":"Hydrophobic regions on protein surfaces. Derivation of the solvation energy from their area distribution in crystallographic protein structures.","abstract":"For the first time, a direct approach for the derivation of an atomic solvation parameter from macromolecular structural data alone is presented. The specific free energy of solvation for hydrophobic surface regions of proteins is delineated from the area distribution of hydrophobic surface patches. The resulting value is 18 cal\/(mol.A2), with a statistical uncertainty of +\/-2 cal\/mol.A2) at the 5% significance level. It compares favorably with the parameters for carbon obtained by other authors who use the the crystal geometry of succinic acid or energies of transfer from hydrophobic solvent to water for small organic compounds. Thus, the transferability of atomic solvation parameters for hydrophobic atoms to macromolecules has been directly demonstrated. A careful statistical analysis demonstrates that surface energy parameters derived from thermodynamic data of protein mutation experiments are clearly less confident.","authors":"Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Protein Sci","volume":"5","issue":"8","page":"1676-86","pdf":null,"JrId":"2312","fulltextlink":null,"preprintlink":null,"articledate":"1997-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21153314","title":"Selective binding of linear ubiquitin chains to NEMO in NF-kappaB activation.","abstract":null,"authors":"Ikeda, F., Rahighi, S., Wakatsuki, S., Dikic, I.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Adv Exp Med Biol","volume":"691","issue":null,"page":"107-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8387733","title":"Labeling of adenine and guanine nucleotide-binding proteins in permeabilized cells with in situ periodate-oxidized nucleotides.","abstract":"A novel approach for identification of adenine and guanine nucleotide-binding proteins in permeabilized cells is described. Cells were incubated for various periods with alpha-32P-labeled nucleotides and then briefly treated with periodate. Condensation products formed in situ between the protein bound alpha-32P-labeled oxidized nucleotide (NTPoxi) and a lysine residue near the nucleotide-binding sites were rapidly stabilized by the addition of cyanoborohydride. Analysis by two-dimensional isoelectric focusing\/sodium dodecylsulfate-poly-acrylamide gel electrophoresis showed that in the human leukemic T-cell line Jurkat a number of distinct intracellular proteins could be labeled with ATPoxi (M(r) 40,000-200,000) or GTPoxi (M(r) 19,000-80,000). Competition with deoxyribonucleotides confirmed the selectivity of these affinity labeling reactions. To test this method two classical GTP-binding proteins were further examined. First the alpha-subunits of the Gs and Gi-2 proteins were specifically labeled with [alpha-32P]GTPoxi but not with [alpha-32P]ATPoxi. Second, p21ras was crosslinked specifically to [alpha-32P]GTPoxi or to its bound endogenous ligand. Surprisingly, under optimized conditions 60% of the ras protein was specifically modified, demonstrating the high efficiency and sensitivity of the method. As a first step toward isolation of hitherto unidentified nucleotide-binding proteins, rabbit antisera specific for the modified amino acid residues were raised. The presented labeling method can be applied for identification of nucleotide-binding proteins in all eukaryotic cells.","authors":"Peter, ME., She, J., Huber, LA., Terhorst, C.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Anal Biochem","volume":"210","issue":"1","page":"77-85","pdf":null,"JrId":"518","fulltextlink":null,"preprintlink":null,"articledate":"1993-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2546254","title":"Further liaisons with sperm.","abstract":null,"authors":"Birnstiel, ML., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Science","volume":"245","issue":"4915","page":"243-4","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1989-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2505228","title":"Cloning of cDNAs coding for human HMG I and HMG Y proteins: both are capable of binding to the octamer sequence motif.","abstract":"In human B lymphocytes and placenta HMG I and its smaller isoform HMG Y are encoded by two distinct but structurally highly similar mRNAs which arise most likely by alternative splicing of a single primary transcript. Both have been cloned as cDNAs. On Northern blots an abundant mRNA species 2000 nucleotides in length was detected in all cell lines examined. Exclusively in erythroid cells an additional rare 3800 nucleotides long mRNA species was noted. In quiescent cells the mRNA levels of HMG I\/Y were not significantly down-regulated. Southern blot analysis indicated that at least four genes are present per haploid human genome. Both proteins when expressed in bacteria bind specifically to A-T rich stretches of DNA suggesting that no posttranslational modifications are necessary for specific DNA binding. Interestingly, HMG I as well as HMG Y are capable of binding to the octamer transcriptional regulatory sequence motif.","authors":"Eckner, R., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Nucleic Acids Res","volume":"17","issue":"15","page":"5947-59","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1989-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34655654","title":"CellFIE: CRISPR- and cell fusion-based two-hybrid interaction mapping of endogenous proteins.","abstract":"Numerous genetic methods facilitate the detection of binary protein-protein interactions (PPIs) by exogenous overexpression, which can lead to false results. Here, we describe CellFIE, a CRISPR- and cell fusion-based PPI detection method, which enables the mapping of interactions between endogenously tagged two-hybrid proteins. We demonstrate the specificity and reproducibility of CellFIE in a matrix mapping approach, validating the interactions of VCP with ASPL and UBXD1, and the self-interaction of TDP-43 under endogenous conditions. Furthermore, we show that CellFIE can be used to quantify changes of endogenous PPIs upon stress induction or drug treatment. For the first time, CellFIE facilitates systematic mapping of interactions between endogenously tagged proteins and represents a novel tool to characterize PPIs in live cells under dynamic conditions.","authors":"Secker, C., Kostova, S., Niederlechner, H., Beetz, S., Wendland, I., Liebich, MJ., Polzer, O., Groh, M., Schnoegl, S., Trepte, P., Wanker, EE.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"J Mol Biol","volume":null,"issue":null,"page":"167305","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2499906","title":"The specific consequences of c-fos expression in transgenic mice.","abstract":null,"authors":"R\u00fcther, U., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Prog Nucleic Acid Res Mol Biol","volume":"36","issue":null,"page":"235-45","pdf":null,"JrId":"6716","fulltextlink":null,"preprintlink":null,"articledate":"1989-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10383411","title":"Mannose polyethylenimine conjugates for targeted DNA delivery into dendritic cells.","abstract":"Cell surface-bound receptors represent suitable entry sites for gene delivery into cells by receptor-mediated endocytosis. Here we have taken advantage of the mannose receptor that is highly expressed on antigen-presenting dendritic cells for targeted gene transfer by employing mannosylpolyethylenimine (ManPEI) conjugates. Several ManPEI conjugates were synthesized and used for formation of ManPEI\/DNA transfection complexes. Conjugates differed in the linker between mannose and polyethylenimine (PEI) and in the size of the PEI moiety. We demonstrate that ManPEI transfection is effective in delivering DNA into mannose receptor-expressing cells. Uptake of ManPEI\/DNA complexes is receptor-specific, since DNA delivery can be competed with mannosylated albumin. Additionally, incorporation of adenovirus particles into transfection complexes effectively enhances transgene expression. This is particularly important for primary immunocompetent dendritic cells. It is demonstrated here that dendritic cells transfected with ManPEI\/DNA complexes containing adenovirus particles are effective in activating T cells of T cell receptor transgenic mice in an antigen-specific fashion.","authors":"Diebold, SS., Kursa, M., Wagner, E., Cotten, M., Zenke, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Biol Chem","volume":"274","issue":"27","page":"19087-94","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1999-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10400747","title":"Characterization of CELO virus proteins that modulate the pRb\/E2F pathway.","abstract":"The avian adenovirus CELO can, like the human adenoviruses, transform several mammalian cell types, yet it lacks sequence homology with the transforming, early regions of human adenoviruses. In an attempt to identify how CELO virus activates the E2F-dependent gene expression important for S phase in the host cell, we have identified two CELO virus open reading frames that cooperate in activating an E2F-inducible reporter system. The encoded proteins, GAM-1 and Orf22, were both found to interact with the retinoblastoma protein (pRb), with Orf22 binding to the pocket domain of pRb, similar to other DNA tumor virus proteins, and GAM-1 interacting with pRb regions outside the pocket domain. The motif in Orf22 responsible for the pRb interaction is essential for Orf22-mediated E2F activation, yet it is remarkably unlike the E1A LxCxD and may represent a novel form of pRb-binding peptide.","authors":"Lehrmann, H., Cotten, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Virol","volume":"73","issue":"8","page":"6517-25","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36475526","title":"In preprints: improving and interrogating embryo models.","abstract":null,"authors":"Scialdone, A., Rivron, N.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Development","volume":"149","issue":"23","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2412222","title":"Synthesis of sperm and late histone cDNAs of the sea urchin with a primer complementary to the conserved 3' terminal palindrome: evidence for tissue-specific and more general histone gene variants.","abstract":"We have cloned histone cDNAs from total RNA isolated from testis and from gastrula-stage embryos of the sea urchin Psammechinus miliaris. The reverse transcription of histone mRNAs was specifically primed with an oligonucleotide that is complementary to the conserved palindromic sequence present at the 3' end of nonpolyadenylated histone mRNAs. Two sperm H2B, two late H2B, and three late H2A variant cDNA clones were isolated and characterized by DNA sequence analysis. These cDNA clones were used to study the accumulation of histone mRNA during sea urchin embryogenesis. The different late H2A and H2B mRNAs are present in as few as 200 copies in the egg and each accumulate to 3-5 X 10(5) molecules in the gastrula embryo. One of the late mRNAs, the H2A-3 mRNA, is also abundant in testis RNA and codes for the H2A variant present in sperm chromatin. The late H2A-3 protein is therefore a more prevalent H2A variant of the sea urchin. In contrast, the two sperm H2B mRNAs are found in testes but not ovaries and embryos of the sea urchin, suggesting that the sperm H2B genes are expressed only during spermatogenesis. In addition, evidence for gene conversion between two late H2A gene variants is presented.","authors":"Busslinger, M., Barberis, A.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Proc Natl Acad Sci U S A","volume":"82","issue":"17","page":"5676-80","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1985-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16847348","title":"Geminin is essential to prevent endoreduplication and to form pluripotent cells during mammalian development.","abstract":"In multicellular eukaryotes, geminin prevents overreplication of DNA in proliferating cells. Here, we show that genetic ablation of geminin in the mouse prevents formation of inner cell mass (ICM) and causes premature endoreduplication at eight cells, rather than 32 cells. All cells in geminin-deficient embryos commit to the trophoblast cell lineage and consist of trophoblast giant cells (TGCs) only. Geminin is also down-regulated in TGCs of wild-type blastocysts during S and gap-like phases by proteasome-mediated degradation, suggesting that loss of geminin is part of the mechanism regulating endoreduplication.","authors":"Gonzalez, MA., Tachibana, KE., Adams, DJ., van der Weyden, L., Hemberger, M., Coleman, N., Bradley, A., Laskey, RA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Genes Dev","volume":"20","issue":"14","page":"1880-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"148","title":"The effects of the continuous administration of N,N-dimethyl-4-phenylazoaniline (DAB) on the activities and the inducibilities of some drug-metabolizing enzymes in rat liver.","abstract":"(1) The effect of feeding a relatively low-protein diet containing 0.06% DAB for 29 weeks on the activity of DAB-azoreductase, nitroreductase (p-nitrobenzoic acid), N-oxidase (N,N-dimethylaniline), N-demethylase (DAB), cytochrome P-450, NADPH-cytochrome c reductase, beta-glucuronidase and arylsulphatase A were studied. Rapid decreases occurred in the activities of the first six enzymes, reaching minimal values at between 4 and 8 weeks. Activities then increased in all cases to control or nearly control levels. This rate of increase was least for cytochrome P-450. At 4 weeks azoreductase activity with the chemotherapeutic agent CB10-252 (I) as substrate was significantly higher than in control rats. Early increases occurred in the activities of beta-glucuronidase and arylsulphatase A and the activity of the latter never dropped below the control level. (2) An investigation was made of the differential effects of dye feeding on some of the enzyme activities in the two major liver lobes and differences were found. (3) The effect of phenobarbital (PB) pretreatment on the DAB-fed rats was studied at 4-week intervals. The activities of DAB-azoreductase and of nitroreductase increased throughout the whole period, while the activities of the lysosomal enzymes were decreased. (4) After feeding DAB for 4 weeks the effect of PB and 3-methylcholanthrene (MC) on the activities of DAB-azoreductase, CB10-252-azoreductase and components of the azoreductases-cytochrome P-450, NADPH-cytochrome c reductase, the CO-CB10-252-azoreductase was not induced by PB or MC, and CO did not inhibit its reduction. Its reduction depended only slightly on NADH. CO caused a greater relative decrease in the activity of DAB-azoreductase in dye-fed animals and also in animals following PB and MC pretreatment, implying a greater role of  cytochrome P-450 in dye-fed animals.","authors":"Autrup, H., Thurlow, BJ., Warwick, GP.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Chem Biol Interact","volume":"11","issue":"5","page":"313-28","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10376527","title":"Role of the ATFa\/JNK2 complex in Jun activation.","abstract":"The ATFa proteins, which are members of the CREB\/ATF family of transcription factors, display quite versatile properties. We have previously shown that they interact with the adenovirus E1a oncoprotein, mediating part of its transcriptional activity and heterodimerize with the Jun, Fos or related transcription factors, thereby modulating their DNA-binding specificity. In the present study, we report the sequence requirement of the N-terminal activation domain of ATFa and demonstrate the importance of specific threonine residues (Thr51 and Thr53) in addition to that of the metal-binding domain, in transcriptional activation processes. We also show that the N-terminal domain of ATFa which stably binds the Jun N-terminal kinase-2 (JNK2) (Bocco et al., 1996), is not a substrate for this kinase in vivo but, instead, serves as a JNK2-docking site for ATFa-associated partners like JunD, allowing them to be phosphorylated by the bound kinase.","authors":"De Graeve, F., Bahr, A., Sabapathy, KT., Hauss, C., Wagner, EF., Kedinger, C., Chatton, B.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Oncogene","volume":"18","issue":"23","page":"3491-500","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16397411","title":"Geminin regulates multiple steps of the chromosome inheritance cycle.","abstract":"Centrosome duplication like DNA replication must occur exactly once per cell cycle to maintain genomic stability. Cell fusion and microinjection assays gave rise to the concept of \"licensing\" and uncovered nuclear-intrinsic blocks to genomic overreplication and recently also centrosome-intrinsic blocks to overduplication. The chromatin licence has been defined in molecular terms as the pre-replication complex (preRC) antagonised by its regulator geminin. Geminin prevents preRC assembly and overreplication in S and G(2) phases. However, the mechanisms that limit centrosome duplication including a potential centrosome licence remain poorly understood. Here, we discuss our recent data demonstrating that loss of the licensing inhibitor geminin causes centrosome overduplication in addition to genomic overreplication. We present further evidence that geminin is an inhibitor of centrosome duplication. Therefore, geminin is involved in regulating multiple steps of the chromosome inheritance cycle, including DNA replication, centrosome duplication and chromosome segregation.","authors":"Tachibana, KE., Nigg, EA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell Cycle","volume":"5","issue":"2","page":"151-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2201907","title":"A conserved sequence in histone H2A which is a ubiquitination site in higher eucaryotes is not required for growth in Saccharomyces cerevisiae.","abstract":"Histones H2A and H2B are modified by ubiquitination of specific lysine residues in higher and lower eucaryotes. To identify functions of ubiquitinated histone H2A, we studied an organism in which genetic analysis of histones is feasible, the yeast Saccharomyces cerevisiae. Surprisingly, immunoblotting experiments using both anti-ubiquitin and anti-H2A antibodies gave no evidence that S. cerevisiae contains ubiquitinated histone H2A. The immunoblot detected a variety of other ubiquitinated species. A sequence of five residues in S. cerevisiae histone H2A that is identical to the site of H2A ubiquitination in higher eucaryotes was mutated to substitute arginines for lysines. Any ubiquitination at this site would be prevented by these mutations. Yeast organisms carrying this mutation were indistinguishable from the wild type under a variety of conditions. Thus, despite the existence in S. cerevisiae of several gene products, such as RAD6 and CDC34, which are capable of ubiquitinating histone H2A in vitro, ubiquitinated histone H2A is either scarce in or absent from S. cerevisiae. Furthermore, the histone H2A sequence which serves as a ubiquitination site in higher eucaryotes is not essential for yeast growth, sporulation, or resistance to either heat stress or UV radiation.","authors":"Swerdlow, PS., Schuster, T., Finley, D.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Mol Cell Biol","volume":"10","issue":"9","page":"4905-11","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1990-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8385673","title":"Thyroid hormone receptor\/c-erbA: control of commitment and differentiation in the neuronal\/chromaffin progenitor line PC12.","abstract":"The c-erbA proto-oncogenes encode nuclear receptors for thyroid hormone (T3), a hormone intimately involved in mammalian brain maturation. To study thyroid hormone receptor (TR) action on neuronal cells in vitro, we expressed the chicken c-erbA\/TR alpha-1 as well as its oncogenic variant v-erbA in the adrenal medulla progenitor cell line PC12. In the absence of T3, exogenous TR alpha-1 inhibits NGF-induced neuronal differentiation and represses neuron-specific gene expression. In contrast, TR alpha-1 allows normal differentiation and neuronal gene expression to occur in the presence of T3. Finally, TR alpha-1-expressing cells become NGF-responsive for proliferation when T3 is absent, but NGF-dependent for survival in presence of T3. A similar differentiation induction by NGF plus T3 was observed in a central nervous system-derived neuronal cell line (E 18) expressing exogenous TR alpha-1. Together with the finding that TR alpha-1 constitutively blocked dexamethasone-induced differentiation of PC12 cells into the chromaffin pathway, these results suggest that TR alpha-1 plays an important role in regulating commitment and maturation of neuronal progenitors. In contrast, the v-erbA oncogene, a mutated, oncogenic version of TR alpha-1, partially but constitutively inhibited NGF-induced neuronal differentiation of PC12 cells and potentiated dexamethasone-induced chromaffin differentiation, giving rise to an aberrant \"interlineage\" cell phenotype.","authors":"Mu\u00f1oz, A., Wrighton, C., Seliger, B., Bernal, J., Beug, H.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Cell Biol","volume":"121","issue":"2","page":"423-38","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34646120","title":"PRDM12 Is Transcriptionally Active and Required for Nociceptor Function Throughout Life.","abstract":"PR domain-containing member 12 (PRDM12) is a key developmental transcription factor in sensory neuronal specification and survival. Patients with rare deleterious variants in <i>PRDM12<\/i> are born with congenital insensitivity to pain (CIP) due to the complete absence of a subtype of peripheral neurons that detect pain. In this paper, we report two additional CIP cases with a novel homozygous <i>PRDM12<\/i> variant. To elucidate the function of PRDM12 during mammalian development and adulthood, we generated temporal and spatial conditional mouse models. We find that PRDM12 is expressed throughout the adult nervous system. We observed that loss of PRDM12 during mid-sensory neurogenesis but not in the adult leads to reduced survival. Comparing cellular biophysical nociceptive properties in developmental and adult-onset PRDM12 deletion mouse models, we find that PRDM12 is necessary for proper nociceptive responses throughout life. However, we find that PRDM12 regulates distinct age-dependent transcriptional programs. Together, our results implicate PRDM12 as a viable therapeutic target for specific pain therapies even in adults.","authors":"Kokotovi\u0107, T., Langeslag, M., Lenartowicz, EM., Manion, J., Fell, CW., Alehabib, E., Tafakhori, A., Darvish, H., Bellefroid, EJ., Neely, GG., Kress, M., Penninger, JM., Nagy, V.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Front Mol Neurosci","volume":"14","issue":null,"page":"720973","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8953634","title":"Development of a rapid means of estimating the haemoglobin F content of candidate fetal cells isolated from maternal blood using HPLC.","abstract":"Prenatal diagnosis of genetic disorders in nucleated fetal red blood cells present in maternal blood requires methods to detect and enrich for such cells. Here we describe a rapid high performance liquid chromatography (HPLC) method that allows one to determine as few as 100 cells containing haemoglobin F (HbF) in the presence of a vast excess of haemoglobin A (HbA)-producing cells. The HPLC separations of haemoglobins were performed with a weak cation exchange column-silica gel-bound asparaginic acid-and ammonium phosphate buffer as the mobile phase. Separations were carried out in 7 min. When applied to estimation of the recovery of fetal cells from maternal blood, the HPLC method indicates in a timely manner whether or not to proceed with further techniques (i.e., FISH or PCR). Several current techniques such as Ficoll gradients and fluorescence (FACS) or magnetic (MACS) activated cell sorting were thus evaluated. Unexpectedly, our method indicates high cell losses with both single gradient and triple density Ficoll pre-enrichment methods. Less than 20 per cent of the nucleated red blood cells can be recovered in the most optimal setting. Lysis of erythrocytes may be an alternative technique that leaves nucleated red blood cells of all maturation stages intact. Thus, any further improvements in the technology for fetal cell recovery may be aided by monitoring the yield with HPLC.","authors":"Huber, K., Wolf, H., Van Lindern, M., Worofka, B., Rosen, A., Hafner, E., Beug, H., Philipp, K., Bauer, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Prenat Diagn","volume":"16","issue":"11","page":"1011-9","pdf":null,"JrId":"6583","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10352021","title":"Functions of c-Jun in liver and heart development.","abstract":"Mice lacking the AP-1 transcription factor c-Jun die around embryonic day E13.0 but little is known about the cell types affected as well as the cause of embryonic lethality. Here we show that a fraction of mutant E13.0 fetal livers exhibits extensive apoptosis of both hematopoietic cells and hepatoblasts, whereas the expression of 15 mRNAs, including those of albumin, keratin 18, hepatocyte nuclear factor 1, beta-globin, and erythropoietin, some of which are putative AP-1 target genes, is not affected. Apoptosis of hematopoietic cells in mutant livers is most likely not due to a cell-autonomous defect, since c-jun-\/- fetal liver cells are able to reconstitute all hematopoietic compartments of lethally irradiated recipient mice. A developmental analysis of chimeras showed contribution of c-jun-\/- ES cell derivatives to fetal, but not to adult livers, suggesting a role of c-Jun in hepatocyte turnover. This is in agreement with the reduced mitotic and increased apoptotic rates found in primary liver cell cultures derived from c-jun-\/- fetuses. Furthermore, a novel function for c-Jun was found in heart development. The heart outflow tract of c-jun-\/- fetuses show malformations that resemble the human disease of a truncus arteriosus persistens. Therefore, the lethality of c-jun mutant fetuses is most likely due to pleiotropic defects reflecting the diversity of functions of c-Jun in development, such as a role in neural crest cell function, in the maintenance of hepatic hematopoiesis and in the regulation of apoptosis.","authors":"Eferl, R., Sibilia, M., Hilberg, F., Fuchsbichler, A., Kufferath, I., Guertl, B., Zenz, R., Wagner, EF., Zatloukal, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Cell Biol","volume":"145","issue":"5","page":"1049-61","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1999-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8895470","title":"Identification of BIME as a subunit of the anaphase-promoting complex.","abstract":"The initiation of anaphase and exit from mitosis require the activation of a proteolytic system that ubiquitinates and degrades cyclin B. The regulated component of this system is a large ubiquitin ligase complex, termed the anaphase-promoting complex (APC) or cyclosome. Purified Xenopus laevis APC was found to be composed of eight major subunits, at least four of which became phosphorylated in mitosis. In addition to CDC27, CDC16, and CDC23, APC contained a homolog of Aspergillus nidulans BIME, a protein essential for anaphase. Because mutation of bimE can bypass the interphase arrest induced by either nimA mutation or unreplicated DNA, it appears that ubiquitination catalyzed by APC may also negatively regulate entry into mitosis.","authors":"Peters, JM., King, RW., H\u00f6\u00f6g, C., Kirschner, MW.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Science","volume":"274","issue":"5290","page":"1199-201","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2261635","title":"FAR-reaching discoveries about the regulation of START.","abstract":null,"authors":"Nasmyth, KA.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Cell","volume":"63","issue":"6","page":"1117-20","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1991-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10229821","title":"Regulation of apoptosis in mature alphabeta+CD4-CD8- antigen-specific suppressor T cell clones.","abstract":"The regulation of apoptosis in mature CD4+ or CD8+ alphabeta+ T cells has been well studied. How the survival and death is regulated in peripheral CD4-CD8- (double negative, DN) alphabeta+ T cells remains unknown. Recent studies suggest that peripheral DN T cells may play an important role in the regulation of the immune responses mediated by CD4+ or CD8+ T cells. Here, we used immunosuppressive DN T cell clones to elucidate the mechanisms involved in the regulation of death and survival of alphabeta+ DN T cells. The DN T cell clones were generated from the spleen cells of 2C transgenic mice, which express the transgenic TCR specific for Ld and permanently accepted Ld+ skin allografts after pretransplant infusion of Ld+ lymphocytes. We report that 1) the mature DN T cells are highly resistant to TCR cross-linking-induced apoptosis in the presence of exogenous IL-4; 2) Fas\/Fas-ligand and TNF-alpha\/TNFR pathways do not play an apparent role in regulating apoptosis in DN T cells; 3) the DN T cells constitutively express a high level of Bcl-xL, but not Bcl-2; 4) both Bcl-xL and Bcl-2 are up-regulated following TCR-cross-linking; and 5) IL-4 stimulation significantly up-regulates Bcl-xL and c-Jun expression and leads to mitogen-activated protein kinase phosphorylation in DN T cells, which may contribute to the resistance to apoptosis in these T cells. Taken together, these results provide us with an insight into how mature DN T cells resist activation-induced apoptosis to provide a long-term suppressor function in vivo.","authors":"Khan, Q., Penninger, JM., Yang, L., Marra, LE., Kozieradzki, I., Zhang, L.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Immunol","volume":"162","issue":"10","page":"5860-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8335693","title":"Osteoblasts are target cells for transformation in c-fos transgenic mice.","abstract":"We have generated transgenic mice expressing the proto-oncogene c-fos from an H-2Kb class I MHC promoter as a tool to identify and isolate cell populations which are sensitive to altered levels of Fos protein. All homozygous H2-c-fosLTR mice develop osteosarcomas with a short latency period. This phenotype is specific for c-fos as transgenic mice expressing the fos- and jun-related genes, fosB and c-jun, from the same regulatory elements do not develop any pathology despite high expression in bone tissues. The c-fos transgene is not expressed during embryogenesis but is expressed after birth in bone tissues before the onset of tumor formation, specifically in putative preosteoblasts, bone-forming osteoblasts, osteocytes, as well as in osteoblastic cells present within the tumors. Primary and clonal cell lines established from c-fos-induced tumors expressed high levels of exogenous c-fos as well as the bone cell marker genes, type I collagen, alkaline phosphatase, and osteopontin\/2ar. In contrast, osteocalcin\/BGP expression was either low or absent. All cell lines were tumorigenic in vivo, some of which gave rise to osteosarcomas, expressing exogenous c-fos mRNA, and Fos protein in osteoblastic cells. Detailed analysis of one osteogenic cell line, P1, and several P1-derived clonal cell lines indicated that bone-forming osteoblastic cells were transformed by Fos. The regulation of osteocalcin\/BGP and alkaline phosphatase gene expression by 1,25-dihydroxyvitamin D3 was abrogated in P1-derived clonal cells, whereas glucocorticoid responsiveness was unaltered. These results suggest that high levels of Fos perturb the normal growth control of osteoblastic cells and exert specific effects on the expression of the osteoblast phenotype.","authors":"Grigoriadis, AE., Schellander, K., Wang, ZQ., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Cell Biol","volume":"122","issue":"3","page":"685-701","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1993-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34645873","title":"The expression, localisation and interactome of pigeon CRY2.","abstract":"Cryptochromes (CRY) are highly conserved signalling molecules that regulate circadian rhythms and are candidate radical pair based magnetoreceptors. Birds have at least four cryptochromes (CRY1a, CRY1b, CRY2, and CRY4), but few studies have interrogated their function. Here we investigate the expression, localisation and interactome of clCRY2 in the pigeon retina. We report that clCRY2 has two distinct transcript variants, clCRY2a, and a previously unreported splice isoform, clCRY2b which is larger in size. We show that clCRY2a mRNA is expressed in all retinal layers and clCRY2b is enriched in the inner and outer nuclear layer. To define the localisation and interaction network of clCRY2 we generated and validated a monoclonal antibody that detects both clCRY2 isoforms. Immunohistochemical studies revealed that clCRY2a\/b is present in all retinal layers and is enriched in the outer limiting membrane and outer plexiform layer. Proteomic analysis showed clCRY2a\/b interacts with typical circadian molecules (PER2, CLOCK, ARTNL), cell junction proteins (CTNNA1, CTNNA2) and components associated with the microtubule motor dynein (DYNC1LI2, DCTN1, DCTN2, DCTN3) within the retina. Collectively these data show that clCRY2 is a component of the avian circadian clock and unexpectedly associates with the microtubule cytoskeleton.","authors":"Balay, SD., Hochstoeger, T., Vilceanu, A., Malkemper, EP., Snider, W., D\u00fcrnberger, G., Mechtler, K., Schuechner, S., Ogris, E., Nordmann, GC., Ushakova, L., Nimpf, S., Keays, DA.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Sci Rep","volume":"11","issue":"1","page":"20293","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10195435","title":"Transient transfection of mammary epithelial cells with a PEI\/DNA\/adenovirus system.","abstract":"Studies on epithelial cells often require the transient expression of exogenous proteins in polarized epithelial cells. However, the major limitation of this approach has been the difficulty of obtaining transient gene expression in polarized epithelial cell cultures. We report here on the application of a polyethylenimine (PEI)\/DNA\/adenovirus system for efficient transient gene expression in mammary epithelial cells. Based on luciferase assay and FACScan analysis the PEI\/DNA\/adenovirus system is shown to be an effective and simple method for transfecting epithelial cells.","authors":"Bischof, J., Vietor, I., Cotten, M., Huber, LA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Biol Chem","volume":"380","issue":"2","page":"269-73","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16179947","title":"Depletion of licensing inhibitor geminin causes centrosome overduplication and mitotic defects.","abstract":"Metazoans limit origin firing to once per cell cycle by oscillations in cyclin-dependent kinases and the replication licensing inhibitor geminin. Geminin inhibits pre-replication complex assembly by preventing Cdt1 from recruiting the minichromosome maintenance proteins to chromatin. Geminin depletion results in genomic over-replication in Drosophila and human cell lines. Here, we show that loss of geminin affects other cell cycle-dependent events in addition to DNA replication. Geminin inactivation causes centrosome overduplication without passage through mitosis in human normal and cancer cells. Centrosomes are microtubule-organizing centres that are duplicated during S phase and have an important role in the fidelity of chromosome transmission by nucleating the mitotic spindle. Consistent with this, geminin-depleted cells show multiple mitotic defects, including multipolar spindles, when driven into mitosis by checkpoint abrogation. These results show that the consequences of geminin loss exceed its immediate role in DNA replication and extend to promoting chromosome mis-segregation in mitosis.","authors":"Tachibana, KE., Gonzalez, MA., Guarguaglini, G., Nigg, EA., Laskey, RA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"EMBO Rep","volume":"6","issue":"11","page":"1052-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-193","title":"Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming","abstract":null,"authors":"Pinheiro,D., Kardos,R., Hannezo, E., Heisenberg,CP.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"nature physics","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.nature.com\/articles\/s41567-022-01787-6","preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.05.16.492018v1.abstract","articledate":"2022-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10197586","title":"The partial homeodomain of the transcription factor Pax-5 (BSAP) is an interaction motif for the retinoblastoma and TATA-binding proteins.","abstract":"Pax-5 codes for the transcription factor BSAP, which plays an important role in midbrain patterning, B cell development, and lymphoma formation. Pax-5 is known to control gene expression by recognizing its target genes via the NH2-terminal paired domain and by regulating transcription through a COOH-terminal regulatory module consisting of activating and inhibitory sequences. The central region of Pax-5 contains a sequence with significant homology to the first alpha-helix of the paired-type homeodomain. This partial homeodomain has been highly conserved throughout vertebrate evolution because it is found not only in Pax-5 but also in the related Pax-2 and Pax-8 members of the same Pax subfamily. Here we report that the partial homeodomain binds the TATA-binding protein (TBP) and retinoblastoma (Rb) gene product. Both TBP and Rb were shown by coimmunoprecipitation experiments to directly associate with Pax-5 in vivo. The conserved core domain of TBP and the pocket region as well as COOH-terminal sequences of Rb are required for interaction with the partial homeodomain of Pax-5 in in vitro binding assays. Furthermore, Pax-5 was specifically bound only by the underphosphorylated form of Rb. These data indicate that Pax-5 is able to contact the basal transcription machinery through the TBP-containing initiation factor TFIID, and that its activity can be controlled by the cell cycle-regulated association with Rb.","authors":"Eberhard, D., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cancer Res","volume":"59","issue":"7 Suppl","page":"1716s-1724s; discussion 1724s-1725s","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9695188","title":"Vav links antigen-receptor signaling to the actin cytoskeleton.","abstract":"The haematopoietic-specific Rho-family guanine-nucleotide exchange factor Vav is a regulator of lymphocyte antigen receptor signaling leading to proliferation of B and T cells, generation of the B1 cell lineage and IL-2 production and maturation in T cells. The specific role it plays in these events, however, has not yet been resolved. Recent findings suggest that Vav is recruited to activated antigen receptors and requires both tyrosine phosphorylation and the presence of activating phospholipids for catalytic activity towards Rho-family GTPases. Studies form vav-deficient mice show that in response to antigen receptor activation, Vav is not essential for activation of JNK kinase pathways, but is required for actin polymerisation and T cell capping. We discuss Vav function in the light of these new findings.","authors":"Fischer, KD., Tedford, K., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Semin Immunol","volume":"10","issue":"4","page":"317-27","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34663934","title":"Methods in organoids: a model that goes beyond our imagination.","abstract":null,"authors":"Koo, BK.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Exp Mol Med","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10195426","title":"A novel way to induce erythroid progenitor self renewal: cooperation of c-Kit with the erythropoietin receptor.","abstract":"Red blood cells are of vital importance for oxygen transport in vertebrates. Thus, their formation during development and homeostasis requires tight control of both progenitor proliferation and terminal red cell differentiation. Self renewal (i.e. long-term proliferation without differentiation) of committed erythroid progenitors has recently been shown to contribute to this regulation. Avian erythroid progenitors expressing the EGF receptor\/c-ErbB (SCF\/TGFalpha progenitors) can be induced to long-term proliferation by the c-ErbB ligand transforming growth factor alpha and the steroids estradiol and dexamethasone. These progenitors have not yet been described in mammals and their factor requirements are untypical for adult erythroid progenitors. Here we describe a second, distinct type of erythroid progenitor (EpoR progenitors) which can be established from freshly isolated bone marrow and is induced to self renew by ligands relevant for erythropoiesis, i.e. erythropoietin, stem cell factor, the ligand for c-Kit and the glucocorticoid receptor ligand dexamethasone. Limiting dilution cloning indicates that these EpoR progenitors are derived from normal BFU-E\/CFU-E. For a detailed study, mEpoR progenitors were generated by retroviral expression of the murine Epo receptor in bone marrow erythroblasts. These progenitors carry out the normal erythroid differentiation program in recombinant differentiation factors only. We show that mEpoR progenitors are more mature than SCF\/TGFalpha progenitors and also do no longer respond to transforming growth factor alpha and estradiol. In contrast they are now highly sensitive to low levels of thyroid hormone, facilitating their terminal maturation into erythrocytes.","authors":"Wessely, O., Bauer, A., Quang, CT., Deiner, EM., von Lindern, M., Mellitzer, G., Steinlein, P., Ghysdael, J., Beug, H.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Biol Chem","volume":"380","issue":"2","page":"187-202","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2078295","title":"Lipoprotein interactions with T cells: an update.","abstract":"The role of plasma lipoproteins in atherogenesis is well recognized but the physiological relevance of their immunoregulatory properties is still questioned. Here Karine Traill and colleagues outline the recent advances that have been made towards unravelling the mechanisms of immunoregulation by lipoproteins in vitro and consider whether any of these mechanisms are operative in vivo. In particular they address the possible detrimental effects of high serum lipoprotein levels on immune function and the question of whether hyperlipidemia (or hypercholesterolemia) should be considered a risk factor for diminished immunity, for example in old age.","authors":"Traill, KN., Huber, LA., Wick, G., J\u00fcrgens, G.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Immunol Today","volume":"11","issue":"11","page":"411-7","pdf":null,"JrId":"1390","fulltextlink":null,"preprintlink":null,"articledate":"1991-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2034670","title":"Transferrin-polycation-DNA complexes: the effect of polycations on the structure of the complex and DNA delivery to cells.","abstract":"We have previously described a gene delivery system based upon the receptor-mediated endocytosis of DNA complexed with transferrin-polycation conjugates. This delivery system has been found to be very effective for both the internalization and the expression of genetic material in cells that have many transferrin receptors. Upon scrutinization of the parameters involved in this method, which we have termed transferrinfection, we note two important features of the process: the polycation in polycation-transferrin conjugates, as expected, serves to attach the transferrin moiety to the DNA and, in addition, the polycation functions to condense the DNA into a doughnut structure. Electron microscopic analysis of a range of poorly active to highly active transferrinfection samples reveals a strong correlation between DNA condensation and cellular DNA uptake. Furthermore, we demonstrate that the transfection activity of the DNA complex can be increased by addition of free polycation as long as a sufficient quantity of polycation-transferrin conjugates remains in the complex to ensure its binding to the cellular receptor.","authors":"Wagner, E., Cotten, M., Foisner, R., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Proc Natl Acad Sci U S A","volume":"88","issue":"10","page":"4255-9","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1991-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8263938","title":"Structural features of the 26 S proteasome complex.","abstract":"Proteasomes play a key role in the degradation of abnormal proteins, of short-lived regulatory proteins and in antigen processing. Evidence is accumulating that the 20 S proteasome represents the proteolytic core of the 26 S protease complex (26 S proteasome) which contains several additional subunits implicated in regulation and substrate recognition. Using electron microscopy and digital image analysis we obtained first insights into the structure of this complex which has an estimated molecular weight of approximately 2000 kDa. Two highly asymmetric masses which presumably contain the regulatory subunits of the 26 S complex are attached to both ends of the dimeric 20 S proteasome clearly reflecting its C2 symmetry. The structural uniformity of the complex, i.e. the absence of significant inter-image variations, has important implications for the structure of the latter: It indicates that, in spite of their sequence similarities, the various alpha-type and beta-type subunits of the 20 S proteasome are not promiscuous but occupy precisely defined positions.","authors":"Peters, JM., Cejka, Z., Harris, JR., Kleinschmidt, JA., Baumeister, W.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Mol Biol","volume":"234","issue":"4","page":"932-7","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1994-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1992439","title":"Cell type-specific tumor induction in neural transplants by retrovirus-mediated oncogene transfer.","abstract":"Using a neural transplantation model which mimics structural and functional properties of the normal rat brain to a high extent, we have taken a novel approach to study the transforming potential of activated oncogenes in the developing brain. Single cell suspensions prepared from fetal rat brains were infected with replication-defective retroviral vectors encoding oncogenes and stereotaxically injected into the caudoputamen of adult F344 rats. Rats carrying transplants expressing the polyoma middle T antigen developed endothelial hemangiomas in the graft which in 70% of the recipient animals led to fatal cerebral hemorrhage within 13-50 days after transplantation. Expression of the v-src gene caused astrocytic and mesenchymal tumors with a 70% incidence after latency periods of 2-6 months, but no endothelial lesions. It was found by in situ hybridization that these oncogenes are expressed in all cell types present in the graft. This indicates that cell-type specific transformation is due to differential susceptibility of the respective target cell to the oncogenes, rather than selective integration or expression of the retroviral construct. The highly efficient gene transfer by retroviral vectors into fetal brain transplants provides a challenging experimental strategy to study differentiation and oncogenesis in the CNS.","authors":"Aguzzi, A., Kleihues, P., Heckl, K., Wiestler, OD.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Oncogene","volume":"6","issue":"1","page":"113-8","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1991-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15660109","title":"Control of DNA replication and its potential clinical exploitation.","abstract":"Multiple conserved mechanisms limit DNA replication to once per cell cycle. One vital level of control focuses on the loading of the heterohexameric ring of minichromosome maintenance proteins (MCMs) onto chromatin in the hierarchical assembly of the pre-replication complex at origins of replication. An essential role in proliferation for MCMs and their regulators makes them potentially important biomarkers for routine clinical use in cancer detection and prognosis.","authors":"Gonzalez, MA., Tachibana, KE., Laskey, RA., Coleman, N.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Rev Cancer","volume":"5","issue":"2","page":"135-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2016745","title":"A general approach to the isolation of cell cycle-regulated genes in the budding yeast, Saccharomyces cerevisiae.","abstract":"We describe a general approach to the isolation of cell cycle-dependently regulated transcripts in Saccharomyces cerevisiae. This approach is based on the physical identification of cell cycle-regulated transcripts by Northern hybridization using as probes yeast DNA isolated from an ordered S. cerevisiae genomic library. The purpose of this is twofold; first, to assess the importance of transcriptional regulation in cell cycle control; and second, to identify novel genes that may have important roles in the eukaryotic cell cycle. We report the isolation of two previously uncharacterized genes that are transcribed at points in the cell cycle to which specific transcriptional activation has not been assigned: namely, mitosis and early G1 phase. It is argued that these transcripts serve as important landmarks for cell cycle events that are not readily distinguished by either morphological or cytological criteria. The cell cycle-dependent transcription of the RNR1 and CLN1 genes is also described and the implications for cell cycle control, in G1, are discussed with reference to these two genes.","authors":"Price, C., Nasmyth, K., Schuster, T.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"J Mol Biol","volume":"218","issue":"3","page":"543-56","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1991-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1969681","title":"Microdissection and microcloning of human chromosome 7q22-32 region.","abstract":"Genetic information contributing to cystic fibrosis in addition to the CF gene is suggested to reside on the long arm of the human chromosome 7. In our attempt to analyze this genomic region in detail, we generated a region-specific DNA probe library by microdissection and microcloning of the midpiece of the chromosome 7q arm. Microdissection was performed in unstained metaphase spreads from a human x mouse hybrid cell line containing chromosome 7 as the only human chromosome. We obtained 593 clones from 75 dissected chromosomal fragments. At least 88% of the microclones were true recombinants; 40% of the clones contained repetitive sequences as determined by plaque hybridization with genomic DNA as probe. The overall mean fragment size of insert fragments was 3.2 kb, the median size was 3.5 kb. Regional mapping of 30 DNA fragments was performed by the aid of hybrid cell lines containing different segments of human chromosome 7; 50% of the microcloned inserts were found to map to 7q22-32.","authors":"Weber, J., Weith, A., Kaiser, R., Grzeschik, KH., Olek, K.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Somat Cell Mol Genet","volume":"16","issue":"2","page":"123-8","pdf":null,"JrId":"7582","fulltextlink":null,"preprintlink":null,"articledate":"1990-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1840381","title":"Developmental expression of IL-2-receptor light chain (CD25) in the chicken embryo.","abstract":"Thymocyte differentiation obeys the same fundamental principles in mammals as in avian species. This parallelism does not only affect the developmentally controlled acquisition of CD3, 4, 8, and TcR isotype expression, but also concerns CD25, the light chain of the interleukin-2 receptor (IL-2R). On chicken thymocytes, surface CD25, which is recognized by the monoclonal antibody INN Ch16, is first observed during day 11 of embryonic life, and peaks at day 14, when it is expressed by about one-third of all lymphoid cells. CD25 is found on subsets of all thymocyte populations as defined by TcR alpha beta, TcR gamma delta, 2, CD4, and CD8 expression, cortical or medullary localization, and is also present on a subset of intrathymic nurse-cell lymphocytes. These findings suggest phylogenetic conservation of the IL-2\/IL-2R-triggered differentiation pathway previously described for mammalian species, thus underlining its probable functional importance.","authors":"Fedecka-Bruner, B., Penninger, J., Vaigot, P., Lehmann, A., Mart\u00ednez, C., Kroemer, G.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Dev Immunol","volume":"1","issue":"3","page":"237-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1992-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34308839","title":"Cdc4 phospho-degrons allow differential regulation of Ame1<sup>CENP-U<\/sup> protein stability across the cell cycle.","abstract":"Kinetochores are multi-subunit protein assemblies that link chromosomes to microtubules of the mitotic and meiotic spindle. It is still poorly understood how efficient, centromere-dependent kinetochore assembly is accomplished from hundreds of individual protein building blocks in a cell cycle-dependent manner. Here, by combining comprehensive phosphorylation analysis of native Ctf19<sup>CCAN<\/sup> subunits with biochemical and functional assays in the model system budding yeast, we demonstrate that Cdk1 phosphorylation activates phospho-degrons on the essential subunit Ame1<sup>CENP-U<\/sup>, which are recognized by the E3 ubiquitin ligase complex SCF-Cdc4. Gradual phosphorylation of degron motifs culminates in M-phase and targets the protein for degradation. Binding of the Mtw1<sup>Mis12<\/sup> complex shields the proximal phospho-degron, protecting kinetochore-bound Ame1 from the degradation machinery. Artificially increasing degron strength partially suppresses the temperature sensitivity of a <i>cdc4<\/i> mutant, while overexpression of Ame1-Okp1 is toxic in SCF mutants, demonstrating the physiological importance of this mechanism. We propose that phospho-regulated clearance of excess CCAN subunits facilitates efficient centromere-dependent kinetochore assembly. Our results suggest a novel strategy for how phospho-degrons can be used to regulate the assembly of multi-subunit complexes.","authors":"B\u00f6hm, M., Killinger, K., Dudziak, A., Pant, P., J\u00e4nen, K., Hohoff, S., Mechtler, K., \u00d6rd, M., Loog, M., Sanchez-Garcia, E., Westermann, S.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Elife","volume":"10","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8131748","title":"Alternative promoter usage of the Fos-responsive gene Fit-1 generates mRNA isoforms coding for either secreted or membrane-bound proteins related to the IL-1 receptor.","abstract":"Fit-1 has been identified previously as a Fos-responsive gene of rat fibroblasts. Here we show that Fit-1 is directly regulated by the estrogen-inducible transcription factor Fos-ER and that it belongs to the family of delayed early genes. Two different mRNA isoforms are expressed from the Fit-1 gene. The Fit-1M mRNA isolated from spleen codes for a membrane-bound protein which is most closely related in its extracellular, transmembrane and intracellular domains to the type I interleukin-1 (IL-1) receptor. The Fit-1S mRNA of fibroblasts directs, instead, the synthesis of a secreted protein consisting of only the extracellular domain. Analysis of the exon-intron structure of the Fit-1 gene indicated that the Fit-1S and Fit-1M mRNAs are transcribed from two different promoters and that the sequence differences at their 3' ends result from alternative 3' processing. Northern blot analysis with specific 5' and 3' probes directly demonstrated tight coupling between alternative promoter usage and 3' processing of the Fit-1 transcripts. The orthologous gene of the mouse (known as T1 or ST2) is expressed during ontogeny first in the fetal liver of the embryo and then in lung and hematopoietic tissues of the adult. The mRNA coding for the membrane-bound protein is more abundantly expressed in all of these tissues, while the transcript for the secreted form predominates in fibroblasts and mammary epithelial cells. Differential regulation of two distinct promoters is thus used to determine the ratio between secreted and membrane-bound forms of Fit-1 (T1\/ST2) which may modulate signaling in response to IL-1.","authors":"Bergers, G., Reikerstorfer, A., Braselmann, S., Graninger, P., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"EMBO J","volume":"13","issue":"5","page":"1176-88","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1994-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8103939","title":"Transcription factors important for starting the cell cycle in yeast.","abstract":"Unlike early embryonic cleavage divisions in certain animals, cell-cycle progression in yeast and probably also in all metazoan somatic cells requires the periodic transcriptional activation of certain key genes. Thus far, the only clear examples are genes that encode a class of unstable 'cyclin' proteins, which bind and activate the cdc2\/Cdc28 protein kinase: the G1-specific cyclins encoded by CLN1 and CLN2, a B-type cyclin implicated in DNA replication encoded by CLB5; and four B-type cyclins involved in mitosis encoded by CLB1, 2, 3, 4. CLN1, CLN2, and CLB5 are transcribed in late G1, as cells undergo Start. A transcription factor composed of Swi4 and Swi6 proteins (called SBF) activates CLN1 and CLN2 transcription via a positive feedback loop in which Cln proteins activate their own transcription. A different but related transcription factor called MBF seems responsible for the late G1-specific transcription of most DNA replication genes including CLB5. We have purified MBF and shown that it contains Swi6 and a 110-120 kDa protein distinct from Swi4 (p120) that contacts DNA. Thus, we propose that SBF and MBF share a common regulatory subunit (Swi6) but recognize their promoter elements via distinct DNA binding subunits.","authors":"Moll, T., Schwob, E., Koch, C., Moore, A., Auer, H., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"340","issue":"1293","page":"351-60","pdf":null,"JrId":"8277","fulltextlink":null,"preprintlink":null,"articledate":"1993-10-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10021384","title":"JNK2 is required for efficient T-cell activation and apoptosis but not for normal lymphocyte development.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">10021384<\/PMID><DateCompleted><Year>1999<\/Year><Month>03<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>9<\/Volume><Issue>3<\/Issue><PubDate><Year>1999<\/Year><Month>Feb<\/Month><Day>11<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>JNK2 is required for efficient T-cell activation and apoptosis but not for normal lymphocyte development.<\/ArticleTitle><Pagination><MedlinePgn>116-25<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The Jun N-terminal kinase (JNK) signaling pathway has been implicated in cell proliferation and apoptosis, but its function seems to depend on the cell type and inducing signal. In T cells, JNK has been implicated in both antigen-induced activation and apoptosis.","authors":"Sabapathy, K., Hu, Y., Kallunki, T., Schreiber, M., David, JP., Jochum, W., Wagner, EF., Karin, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Curr Biol","volume":"9","issue":"3","page":"116-25","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1999-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1967981","title":"Cyclin is a component of maturation-promoting factor from Xenopus.","abstract":"Highly purified maturation-promoting factor (MPF) from Xenopus eggs contains both cyclin B1 and cyclin B2 as shown by Western blotting and immunoprecipitation using Xenopus anti-B-type cyclin antibodies. Immunoprecipitates with these antibodies display the histone H1 kinase activity characteristic of MPF, for which exogenously added B1 and B2 cyclins are both substrates. Protein kinase activity against cyclin oscillates in maturing oocytes and activated eggs with the same kinetics as p34cdc2 kinase activity. These data indicate that B-type cyclin is the other component of MPF besides p34cdc2.","authors":"Gautier, J., Minshull, J., Lohka, M., Glotzer, M., Hunt, T., Maller, JL.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Cell","volume":"60","issue":"3","page":"487-94","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1990-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8099627","title":"Chicken adenovirus (CELO virus) particles augment receptor-mediated DNA delivery to mammalian cells and yield exceptional levels of stable transformants.","abstract":"Delivery of genes via receptor-mediated endocytosis is severely limited by the poor exit of endocytosed DNA from the endosome. A large enhancement in delivery efficiency has been obtained by including human adenovirus particles in the delivery system. This enhancement is probably a function of the natural adenovirus entry mechanism, which must include passage through or disruption of the endosomal membrane. In an effort to identify safer virus particles useful in this application, we have tested the chicken adenovirus CELO virus for its ability to augment receptor-mediated gene delivery. We report here that CELO virus possesses pH-dependent, liposome disruption activity similar to that of human adenovirus type 5. Furthermore, the chicken adenovirus can be used to augment receptor-mediated gene delivery to levels comparable to those found for the human adenovirus when it is physically linked to polylysine ligand-condensed DNA particles. The chicken adenovirus has the advantage of being produced inexpensively in embryonated eggs, and the virus is naturally replication defective in mammalian cells, even in the presence of wild-type human adenovirus.","authors":"Cotten, M., Wagner, E., Zatloukal, K., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Virol","volume":"67","issue":"7","page":"3777-85","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1993-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8097581","title":"Mutational analysis of the role of the carboxy-terminal region of the v-erbB protein in erythroid cell transformation.","abstract":"The v-erbB protein encoded by the avian erythroblastosis virus AEV-H is responsible for the transformation of fibroblasts and erythroblasts by this virus. Deletion of amino acids 961-1102, which lie carboxy terminal to the kinase domain of the v-erbB protein, destroys the ability of the virus to transform erythroid cells without severely affecting fibroblast transformation. This region is termed the E-domain and has been postulated to contain a region important for erythroid cell transformation. In-frame deletions of approximately 23 amino acids were introduced throughout the E-domain in an attempt to locate a specific region that was essential for erythroid cell transformation. Several of the deletions gave rise to a partial transformed phenotype, although no single deletion that completely abolished erythroid cell transformation was found. Interestingly, deletion of amino acids 1031-1055 resulted in a superactivated v-erbB protein that was more active for erythroid cell transformation than the wild-type AEV-H v-erbB protein. This indicates that there is a negative regulatory region located within this region that normally partially suppresses the transforming activity of the v-erbB protein for erythroid cells. These data suggest that the E-domain contains both negative and positive regulatory regions that function in erythroid cells, and complete deletion of the region is necessary to abolish erythroid cell transformation.","authors":"Lee, EB., Beug, H., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Oncogene","volume":"8","issue":"5","page":"1317-27","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8041776","title":"The H1A histone variant is an in vivo repressor of oocyte-type 5S gene transcription in Xenopus laevis embryos.","abstract":"Previous in vitro transcription studies have pointed to the importance of histone H1 for repression of oocyte-type 5S genes of Xenopus laevis. It has been previously reported that in development up to the early gastrula stage, Xenopus embryos contain a large pool of the maternal histone H1 variant H1M but are virtually devoid of histone H1A, H1B, and H1C proteins. At the early gastrula stage, there is an increase in H1A protein synthesis and H1A becomes the predominant H1 histone variant. Concomitant with the significant appearance of H1A protein in chromatin, oocyte 5S transcription is repressed. Here it is shown that there appears to be a direct link between H1A accumulation and inhibition of oocyte-type 5S RNA synthesis. Inhibition of H1A synthesis by a ribozyme targeted to H1A mRNA leads to the continued expression of oocyte 5S genes. H1A is proposed to inhibit major oocyte 5S gene transcription by sealing the nucleosome that is positioned over the major oocyte 5S coding sequences and by driving major oocyte 5S gene chromatin into a higher-order structure in which histone H1A molecules interact cooperatively.","authors":"Kandolf, H.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Proc Natl Acad Sci U S A","volume":"91","issue":"15","page":"7257-61","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1994-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34667177","title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.","abstract":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.","authors":"Appel, LM., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., Schoeberl, UE., Puchinger, MG., Kostrhon, S., Ebenwaldner, C., Sebesta, M., Beltzung, E., Mechtler, K., Lin, G., Vlasova, A., Leeb, M., Pavri, R., Stark, A., Akalin, A., Stefl, R., Bernecky, C., Djinovic-Carugo, K., Slade, D.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"6078","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1859092","title":"The decline of the immune response during aging: the role of an altered lipid metabolism.","abstract":null,"authors":"Wick, G., Huber, LA., Xu, QB., Jarosch, E., Sch\u00f6nitzer, D., J\u00fcrgens, G.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Ann N Y Acad Sci","volume":"621","issue":null,"page":"277-90","pdf":null,"JrId":"611","fulltextlink":null,"preprintlink":null,"articledate":"1991-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34718559","title":"A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary.","abstract":"Argonaute proteins of the PIWI clade complexed with PIWI-interacting RNAs (piRNAs) protect the animal germline genome by silencing transposable elements. One of the leading experimental systems for studying piRNA biology is the Drosophila melanogaster ovary. In addition to classical mutagenesis, transgenic RNA interference (RNAi), which enables tissue-specific silencing of gene expression, plays a central role in piRNA research. Here, we establish a versatile toolkit focused on piRNA biology that combines germline transgenic RNAi, GFP marker lines for key proteins of the piRNA pathway, and reporter transgenes to establish genetic hierarchies. We compare constitutive, pan-germline RNAi with an equally potent transgenic RNAi system that is activated only after germ cell cyst formation. Stage-specific RNAi allows us to investigate the role of genes essential for germline cell survival, for example nuclear RNA export or the SUMOylation pathway, in piRNA-dependent and independent transposon silencing. Our work forms the basis for an expandable genetic toolkit provided by the Vienna Drosophila Resource Center.","authors":"ElMaghraby, MF., Tirian, L., Senti, KA., Meixner, K., Brennecke, J.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Genetics","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1829507","title":"Positive feedback in the activation of G1 cyclins in yeast.","abstract":"Yeast cells become committed to the mitotic cell cycle at a stage during G1 called Start. To enter Start, cells must grow to a critical size. They also require the CDC28 protein kinase and at least one of three G1-specific cyclins encoded by CLN1, 2, and 3. It is thought that Start is triggered by the accumulation of G1 cyclins that bind to the CDC28 kinase and activate it. So what determines the accumulation of G1 cyclins? For CLN1 and CLN2, transcriptional activation could be involved because their RNAs appear transiently during the cell cycle as cells undergo Start. Here we report that the appearance of CLN1 and CLN2 RNAs depends on an active CDC28 kinase and is stimulated by CLN3 activity. We propose that CDC28 kinase activity due to CLN1 and CLN2 proteins arises through a positive feedback loop which allows CLN proteins to promote their own synthesis.","authors":"Dirick, L., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Nature","volume":"351","issue":"6329","page":"754-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1991-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9083114","title":"Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9083114<\/PMID><DateCompleted><Year>1997<\/Year><Month>06<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>09<\/Month><Day>14<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0969-2126<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>5<\/Volume><Issue>3<\/Issue><PubDate><Year>1997<\/Year><Month>Mar<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Structure (London, England : 1993)<\/Title><ISOAbbreviation>Structure<\/ISOAbbreviation><\/Journal><ArticleTitle>Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis.<\/ArticleTitle><Pagination><MedlinePgn>349-58<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">During the cell cycle, cells progress through four distinct phases, G1, S, G2 and M; transcriptional controls play an important role at the transition between these phases. MCB-binding factor (MBF), a transcription factor from budding yeast, binds to the so-called MCB (MluI cell-cycle box) elements found in the promoters of many DNA synthesis genes, and activates the transcription of those at the G1--&gt;S phase transition. MBF is comprised of two proteins, Mbp1 and Swi6.","authors":"Xu, RM., Koch, C., Liu, Y., Horton, JR., Knapp, D., Nasmyth, K., Cheng, X.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Structure","volume":"5","issue":"3","page":"349-58","pdf":null,"JrId":"22305","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1846030","title":"Cyclin is degraded by the ubiquitin pathway.","abstract":"Cyclin degradation is the key step governing exit from mitosis and progress into the next cell cycle. When a region in the N terminus of cyclin is fused to a foreign protein, it produces a hybrid protein susceptible to proteolysis at mitosis. During the course of degradation, both cyclin and the hybrid form conjugates with ubiquitin. The kinetic properties of the conjugates indicate that cyclin is degraded by ubiquitin-dependent proteolysis. Thus anaphase may be triggered by the recognition of cyclin by the ubiquitin-conjugating system.","authors":"Glotzer, M., Murray, AW., Kirschner, MW.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Nature","volume":"349","issue":"6305","page":"132-8","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1991-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1840543","title":"Primary structure and expression of a chicken cDNA encoding a protein with zinc-finger motifs.","abstract":"We report the cloning and sequence analysis of a chicken nearly full-length cDNA clone, cKr1, encoding a protein of 509 amino acids which contains ten 2Cys + 2His-type zinc-finger motifs arranged in two separate sets of five zinc fingers each. The cKr1 transcripts are detected in organs of the adult chicken, predominantly in the brain and lung. At day 4 of embryonic development strong cKr1 hybridization signals are found in the brain and neural tube, in the mesonephros and in the gut, respectively.","authors":"Benn, A., Antoine, M., Beug, H., Niessing, J.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Gene","volume":"106","issue":"2","page":"207-12","pdf":null,"JrId":"3886","fulltextlink":null,"preprintlink":null,"articledate":"1991-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1832338","title":"The role of SWI4 and SWI6 in the activity of G1 cyclins in yeast.","abstract":"Entry into the mitotic cycle (START) requires a protein kinase encoded by the CDC28 gene and one of three redundant G1-specific cyclins encoded by CLN1, -2, and -3. SWI4 and SWI6 are transcription factors required for the START-dependent activation of the HO endonuclease gene. They also fulfill an overlapping but essential role for cell division since cells deleted for both genes are inviable. We show that the essential role of SWI4 and SWI6 is to ensure the activity of G1-specific cyclin genes. SWI4 and SWI6 appear necessary for the transcription of CLN1 and CLN2, but not for that of CLN3. CLN3 function is, however, also dependent on SWI4 and SWI6.","authors":"Nasmyth, K., Dirick, L.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Cell","volume":"66","issue":"5","page":"995-1013","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1991-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34715055","title":"Reprogramming CBX8-PRC1 function with a positive allosteric modulator.","abstract":"Canonical targeting of Polycomb repressive complex 1 (PRC1) to repress developmental genes is mediated by cell-type-specific, paralogous chromobox (CBX) proteins (CBX2, 4, 6, 7, and 8). Based on their central role in silencing and their dysregulation associated with human disease including cancer, CBX proteins are attractive targets for small-molecule chemical probe development. Here, we have used a quantitative and target-specific cellular assay to discover a potent positive allosteric modulator (PAM) of CBX8. The PAM activity of UNC7040 antagonizes H3K27me3 binding by CBX8 while increasing interactions with nucleic acids. We show that treatment with UNC7040 leads to efficient and selective eviction of CBX8-containing PRC1 from chromatin, loss of silencing, and reduced proliferation across different cancer cell lines. Our discovery and characterization of UNC7040 not only reveals the most cellularly potent CBX8-specific chemical probe to date, but also corroborates a mechanism of Polycomb regulation by non-specific CBX nucleotide binding activity.","authors":"Suh, JL., Bsteh, D., Hart, B., Si, Y., Weaver, TM., Pribitzer, C., Lau, R., Soni, S., Ogana, H., Rectenwald, JM., Norris, JL., Cholensky, SH., Sagum, C., Umana, JD., Li, D., Hardy, B., Bedford, MT., Mumenthaler, SM., Lenz, HJ., Kim, YM., Wang, GG., Pearce, KH., James, LI., Kireev, DB., Musselman, CA., Frye, SV., Bell, O.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Cell Chem Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9658173","title":"Regulation of the cyclin B degradation system by an inhibitor of mitotic proteolysis.","abstract":"The initiation of anaphase and exit from mitosis depend on the anaphase-promoting complex (APC), which mediates the ubiquitin-dependent proteolysis of anaphase-inhibiting proteins and mitotic cyclins. We have analyzed whether protein phosphatases are required for mitotic APC activation. In Xenopus egg extracts APC activation occurs normally in the presence of protein phosphatase 1 inhibitors, suggesting that the anaphase defects caused by protein phosphatase 1 mutation in several organisms are not due to a failure to activate the APC. Contrary to this, the initiation of mitotic cyclin B proteolysis is prevented by inhibitors of protein phosphatase 2A such as okadaic acid. Okadaic acid induces an activity that inhibits cyclin B ubiquitination. We refer to this activity as inhibitor of mitotic proteolysis because it also prevents the degradation of other APC substrates. A similar activity exists in extracts of Xenopus eggs that are arrested at the second meiotic metaphase by the cytostatic factor activity of the protein kinase mos. In Xenopus eggs, the initiation of anaphase II may therefore be prevented by an inhibitor of APC-dependent ubiquitination.","authors":"Vorlaufer, E., Peters, JM.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Mol Biol Cell","volume":"9","issue":"7","page":"1817-31","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"1999-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7964466","title":"Human CD4-major histocompatibility complex class II (DQw6) transgenic mice in an endogenous CD4\/CD8-deficient background: reconstitution of phenotype and human-restricted function.","abstract":"To reconstitute the human immune system in mice, transgenic mice expressing human CD4 and human major histocompatibility complex (MHC) class II (DQw6) molecules in an endogenous CD4- and CD8-deficient background (mCD4\/8-\/-), after homologous recombination, have been generated. We report that expression of human CD4 molecule in mCD4\/8-\/- mice rescues thymocyte development and completely restores the T cell compartment in peripheral lymphoid organs. Upon vesicular stomatitis virus (VSV) challenge, the reconstituted mature T cell population effectively provide T help to B cells in immunoglobulin class switching from IgM to specific IgG-neutralizing antibodies. Human CD4+DQw6+ double transgenic mice are tolerant to DQw6 and the DQw6 molecule functions in antigen presentation, effectively generating a human MHC class II-restricted T cell response to streptococcal M6C2 peptide. These data show that both the hCD4 and DQw6 molecules are functional in mCD4\/8-\/- mice, fully and stably reconstituting this limb of the human immune system in mice. This animal model provides a powerful in vivo tool to dissect the human CD4-human class II MHC interaction, especially its role in human autoimmune diseases, superantigen-mediated diseases, and acquired immunodeficiency syndrome (AIDS).","authors":"Yeung, RS., Penninger, JM., K\u00fcndig, TM., Law, Y., Yamamoto, K., Kamikawaji, N., Burkly, L., Sasazuki, T., Flavell, R., Ohashi, PS., Mak, TW.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"J Exp Med","volume":"180","issue":"5","page":"1911-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1994-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1756728","title":"The DNA binding and oligomerization domain of MCM1 is sufficient for its interaction with other regulatory proteins.","abstract":"The MCM1 gene encodes an essential DNA binding protein that, in cooperation with the transactivators alpha 1 and STE12 and the repressor alpha 2, confers mating specificity to haploid yeast cells. We show that the amino-terminal third of the MCM1 protein is sufficient for the physical interaction with these factors. A strain expressing just 98 amino acids encompassing the oligomerization and DNA binding domains of MCM1 is viable and mating competent. This motif exhibits considerable similarity to a domain of the mammalian transcription factor SRF. A 98 amino acid hybrid gene coding for the MCM1 DNA binding domain and SRF dimerization domain is sufficient for viability but not for the expression of mating type specific genes. In vitro binding studies suggest that a region of approximately 50 amino acids of MCM1 is essential for providing contacts with alpha 1, alpha 2 and STE12.","authors":"Primig, M., Winkler, H., Ammerer, G.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"EMBO J","volume":"10","issue":"13","page":"4209-18","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1992-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1799805","title":"Mouse chromosome 17.","abstract":null,"authors":"Artzt, K., Barlow, D., Dove, WF., Fischer-Lindahl, K., Klein, J., Lyon, MF., Silver, LM.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Mamm Genome","volume":"1 Spec No","issue":null,"page":"S280-300","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"1992-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1772904","title":"DNA-binding transferrin conjugates as functional gene-delivery agents: synthesis by linkage of polylysine or ethidium homodimer to the transferrin carbohydrate moiety.","abstract":"We have previously demonstrated that transferrin-polycation conjugates are efficient carrier molecules for the introduction of genes into eukaryotic cells. We describe here a more specific method for conjugation of transferrin with DNA-binding compounds involving attachment at the transferrin carbohydrate moiety. We used the polycation poly(L-lysine) or the DNA intercalator, ethidium homodimer as DNA-binding domains. Successful transferrin-receptor-mediated delivery and expression of the Photinus pyralis luciferase gene in K562 cells has been shown with these new transferrin conjugates. The activity of the transferrin-ethidium homodimer (TfEtD) conjugates is low relative to transferrin-polylysine conjugates; probably because of incomplete condensation of the DNA. However, DNA delivery with TfEtD is drastically improved when ternary complexes of the DNA with TfEtD and the DNA condensing agent polylysine are prepared. The gene delivery with the carbohydrate-linked transferrin-polylysine conjugates is equal or superior to described conjugates containing disulfide linkage. The new ligation method facilitates the synthesis of large quantities (greater than 100 mg) of conjugates.","authors":"Wagner, E., Cotten, M., Mechtler, K., Kirlappos, H., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Bioconjug Chem","volume":"2","issue":"4","page":"226-31","pdf":null,"JrId":"1061","fulltextlink":null,"preprintlink":null,"articledate":"1992-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1751449","title":"Multiple regions of v-Fos protein involved in the activation of AP1-dependent transcription: is trans-activation crucial for transformation?","abstract":"We show that trans-activation by v-Fos requires several functionally separable regions, including the leucine repeat, the basic DNA-binding region, a directly adjacent acidic cluster, and additional flanking sequences. Structural alterations in the flanking regions are in part responsible for the greater trans-activating potential of the fos gene product of the Finkel-Biskis-Reilly mouse osteosarcoma virus, FBR-MuSV. A point mutation in the acidic cluster, which is known to activate the immortalizing potential of Fos, leads to a significant increase in trans-activation. However, comparison of the trans-activating and transforming properties of mutant Fos proteins suggests that functions other than trans-activation are involved in the induction of transformation.","authors":"Lucibello, FC., Neuberg, M., Jenuwein, T., M\u00fcller, R.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"New Biol","volume":"3","issue":"7","page":"671-7","pdf":null,"JrId":"1880","fulltextlink":null,"preprintlink":null,"articledate":"1992-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1718741","title":"Expression of functional c-kit receptors rescues the genetic defect of W mutant mast cells.","abstract":"Loss-of-function mutations in the gene for the c-kit tyrosine kinase receptor are strongly implicated in the developmental abnormalities of W mutant mice. To dissect further the relationship between kit and the W phenotype, retroviruses carrying the normal murine c-kit gene were constructed. In infected cells, the level of c-kit expression from these vectors varied markedly with different promoter elements, the 5' viral LTR proving to be the most effective. When introduced into cells which normally do not express c-kit, ectopic kit receptors transduced a ligand (Steel factor)-dependent proliferative signal in IL-3-dependent DA-1 myeloid cells and induced transformation in fibroblasts. Primary mutant mast cells were used to examine the effects of reconstituting functional kit expression in cells affected by W mutations. Exogenous c-kit expression rescued the defective proliferative response to Steel factor of cells from both W\/Wv and W\/W mutant mice. Moreover, functional kit expression also restored the capacity of W\/Wv mast cells to survive and differentiate in vivo. These results imply that defective c-kit receptor function is sufficient to generate the W mutant phenotype.","authors":"Alexander, WS., Lyman, SD., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"EMBO J","volume":"10","issue":"12","page":"3683-91","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1991-12-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-175","title":"Maternally-inherited anti-sense piRNAs antagonize transposon expression in teleost embryos","abstract":null,"authors":"Guo,Y., Gert,KR., Lebedeva,S., Potok,ME., Wike,CL., Grow,EJ., Ketting,RF., Pauli,A., Cairns,B.","publication_status":"preprint","journalpubyear":"2021","journaltitle":"bioRxiv ","volume":"2021.11.03.467172","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.11.03.467172v1","preprintlink":null,"articledate":"2021-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9712036","title":"Receptor-specific allelic exclusion of TCRV alpha-chains during development.","abstract":"Expression of a single Ag receptor on lymphocytes is maintained via allelic exclusion that generates cells with a clonal receptor repertoire. We show in normal mice and mice expressing functionally rearranged TCR alphabeta transgenes that allelic exclusion at the TCR alpha locus is not operational in immature thymocytes, whereas most mature T cells express a single TCRV alpha-chain. TCRV alpha allelic exclusion in mature thymocytes is regulated through a CD45 tyrosine phosphatase-mediated signal during positive selection. Using functional and genetic systems for selection of immature double TCRV alpha+ thymocytes, we show that peptide-specific ligand recognition provides the signal for allelic exclusion, i.e., mature T cells maintain expression of the ligand-specific TCRV alpha-chain, but lose the nonfunctional receptor. Whereas activation of TCRV beta-chains or CD3epsilon leads to receptor internalization, TCRV alpha ligation promotes retention of the TCR on the cell surface. Although both TCRV alpha- and TCRV beta-chains trigger phosphotyrosine signaling, only the TCRV beta-chain mediates membrane recruitment of the GTPase dynamin. These data indicate that TCRV alpha-directed signals for positive selection control allelic exclusion in T cells, and that developmental signals can select for single receptor usage.","authors":"Boyd, R., Kozieradzki, I., Chidgey, A., Mittr\u00fccker, HW., Bouchard, D., Timms, E., Kishihara, K., Ong, CJ., Chui, D., Marth, JD., Mak, TW., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Immunol","volume":"161","issue":"4","page":"1718-27","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"152","title":"[Spontaneous mortality and vascular lesions in 3 rat strains with different blood pressure levels].","abstract":"We have observed a high and significant mortality in spontaneously hypertensive rats compared to normotensive and hypotensive controls, in the fifth generation. The hypertensive rats exhibited a high frequency of cerebral haemorrhage and periarteritis nodosa.","authors":"Dupont, J., Dupont, JC., Milon, H., Froment, A.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"C R Acad Hebd Seances Acad Sci D","volume":"280","issue":"13","page":"1637-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7927211","title":"Expression of three- and four-repeat tau isoforms in mouse liver.","abstract":"Tau protein is a member of the family of microtubule-associated proteins, which support microtubule polymerization and stability. Under pathological conditions, tau is a major constituent of neurofibrillary tangles in nerve cells of patients with Alzheimer's disease. Neurofibrillary tangles share some morphological, biochemical and immunological properties with cytoplasmic inclusions associated with other diseases, such as Mallory bodies in the livers of patients with alcoholic hepatitis and in corresponding mouse models. Recently a Mallory body component was identified that in molecular mass and isoelectric point resembles the abnormally phosphorylated tau of neurofibrillary tangles. There has been, however, so far no report describing the occurrence of tau in normal liver. We now demonstrate the expression of two tau isoforms containing three and four repeats, respectively, of the microtubule-binding domains in normal mouse liver and kidney. This finding provides evidence for a physiological role of tau in the liver and, consequently, the basis for the involvement of tau in pathological situations.","authors":"Kenner, L., el-Shabrawi, Y., Hutter, H., Forstner, M., Zatloukal, K., Hoefler, G., Preisegger, KH., Kurzbauer, R., Denk, H.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Hepatology","volume":"20","issue":"4 Pt 1","page":"1086-9","pdf":null,"JrId":"4093","fulltextlink":null,"preprintlink":null,"articledate":"1994-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9705955","title":"Early function of Pax5 (BSAP) before the pre-B cell receptor stage of B lymphopoiesis.","abstract":"The formation of the pre-B cell receptor (BCR) corresponds to an important checkpoint in B cell development that selects pro-B (pre-BI) cells expressing a functionally rearranged immunoglobulin mu (Igmu) heavy chain protein to undergo the transition to the pre-B (pre-BII) cell stage. The pre-BCR contains, in addition to Igmu, the surrogate light chains lambda5 and VpreB and the signal transducing proteins Igalpha and Igbeta. The absence of one of these pre-BCR components is known to arrest B cell development at the pre-BI cell stage. Disruption of the Pax5 gene, which codes for the B cell-specific activator protein (BSAP), also blocks adult B lymphopoiesis at the pre-BI cell stage. Moreover, expression of the mb-1 (Igalpha) gene and VH-to-DHJH recombination at the IgH locus are reduced in Pax5-deficient B lymphocytes approximately 10- and approximately 50-fold, respectively. Here we demonstrate that complementation of these deficiencies in pre-BCR components by expression of functionally rearranged Ig mu and chimeric Igmu-Igbeta transgenes fails to advance B cell development to the pre-BII cell stage in Pax5 (-\/-) mice in contrast to RAG2 (-\/-) mice. Furthermore, the pre-BCR is stably expressed on cultured pre-BI cells from Igmu transgenic, Pax5-deficient bone marrow, but is unable to elicit its normal signaling responses. In addition, the early developmental block is unlikely to be caused by the absence of a survival signal, as it could not be rescued by expression of a bcl2 transgene in Pax5-deficient pre-BI cells. Together, these data demonstrate that the absence of Pax5 arrests adult B lymphopoiesis at an early developmental stage that is unresponsive to pre-BCR signaling.","authors":"Th\u00e9venin, C., Nutt, SL., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Exp Med","volume":"188","issue":"4","page":"735-44","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"1998-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-174","title":"Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing","abstract":null,"authors":"Gert,KR., Cabrera Quio,LE., Novatchkova,M., Guo,Y., Cairns,BR., Pauli,A.","publication_status":"preprint","journalpubyear":"2021","journaltitle":"bioRxiv ","volume":"2021.11.03.467109","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.11.03.467109v1","preprintlink":null,"articledate":"2021-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1685095","title":"Cell cycle research proliferates. The Research Institute of Molecular Pathology (I.M.P.). Fourth International Conference on the Control of Proliferation in Normal and Malignant Cells, Vienna, Austria, May 3-5, 1991.","abstract":null,"authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"New Biol","volume":"3","issue":"10","page":"955-8","pdf":null,"JrId":"1880","fulltextlink":null,"preprintlink":null,"articledate":"1992-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1696685","title":"Cell cycle-dependent regulation of histone precursor mRNA processing by modulation of U7 snRNA accessibility.","abstract":"Histone gene expression is regulated both during and after transcription, with the turnover of histone messenger RNA and the regulation of its 3' processing being the principal factors that determine the size of the histone mRNA pool during the cell cycle. The mature ends of the replication-dependent histone mRNAs are generated during 3' processing by endonucleolytic cleavage of a large primary transcript. This reaction depends on a highly conserved stem-loop structure also included in the mature RNA, and a purine-rich sequence lying downstream within the spacer transcript. Three factors involved in this reaction which act in trans have been identified: the U7 small nuclear ribonucleoprotein particle (snRNP), the heat-labile factor, and the hairpin-binding factor. Here we show how U7 snRNP participates in the regulation of 3' processing: the 5' sequences of the U7 snRNA that hybridize with the downstream spacer motif during 3' processing are occluded in the G0 stage of the cell cycle but are exposed and free to interact with histone pre-mRNA during S phase, when histone mRNA synthesis is at its peak.","authors":"Hoffmann, I., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Nature","volume":"346","issue":"6285","page":"665-8","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1990-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7897222","title":"Elicitation of a systemic and protective anti-melanoma immune response by an IL-2-based vaccine. Assessment of critical cellular and molecular parameters.","abstract":"We have established a model for the immunologic rejection of melanoma cells. Using a receptor-mediated, adenovirus-augmented gene delivery system (transferrinfection) we have shown that, upon transfection with an IL-2 gene construct, MHC class I+\/class II- murine M-3 cells lose their tumorigenicity in both athymic and euthymic mice. More importantly, we found that these melanoma cells, which produce high levels of IL-2, can be used to induce a long-lasting anti-tumor immune response in syngeneic euthymic DBA\/2 mice but not in athymic animals. This immune response, which can also be elicited by coadministration of nonmodified, irradiated M-3 cells and IL-2-transduced fibroblasts, results in the rejection of a subsequent challenge with M-3 cells or, in the elimination of preexisting M-3 cancer cell deposits. We found that transfer of T cell-enriched, but not of T cell-depleted, splenocytes from immunized mice conferred protection against M-3 cells, but not against unrelated KLN 205 cancer cells. Transfer of either CD4+ or CD8+ T cells led to only partial protection against challenge with wild-type M-3 cells. Our further observations that T cell-enriched, but not T cell-depleted splenocytes of immunized animals are capable of tumor-specific lytic activity and that this activity resides in the CD8+ cell population are compatible with the assumption that MHC class I-restricted T cell cytotoxicity is a biologically relevant effector mechanism in this model. That other mechanisms also contribute to melanoma cell destruction is evidenced by the presence of large numbers of macrophages and granulocytes in addition to T cells at the challenge sites of immunized mice.","authors":"Zatloukal, K., Schneeberger, A., Berger, M., Schmidt, W., Koszik, F., Kutil, R., Cotten, M., Wagner, E., Buschle, M., Maass, G.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Immunol","volume":"154","issue":"7","page":"3406-19","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"1995-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1672293","title":"Genetic maps of mouse chromosome 17 including 12 new anonymous DNA loci and 25 anchor loci.","abstract":"An interspecific backcross between lab mice and Mus spretus was used to construct a multilocus map of Chromosome 17 consisting of 12 new anonymous loci and 9 anchor loci. In addition, 7 anonymous DNA loci were added to the Chr 17 map for the BXD strains. Although we were able to identify readily the most likely gene order in the interspecific backcross, we found no evidence for an unambiguous gene order using the BXD recombinant inbred strains. Comparison of the interspecific backcross map and the BXD RI strain map revealed evidence in the interspecific backcross for a longer total genetic length, enhanced recombination distal to H-2, a segment showing suppressed recombination, and strong interference.","authors":"Nadeau, JH., Herrmann, B., Bucan, M., Burkart, D., Crosby, JL., Erhart, MA., Kosowsky, M., Kraus, JP., Michiels, F., Schnattinger, A.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Genomics","volume":"9","issue":"1","page":"78-89","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"1991-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34725484","title":"Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis.","abstract":"Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N\ufeff- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.","authors":"Kawahara, R., Chernykh, A., Alagesan, K., Bern, M., Cao, W., Chalkley, RJ., Cheng, K., Choo, MS., Edwards, N., Goldman, R., Hoffmann, M., Hu, Y., Huang, Y., Kim, JY., Kletter, D., Liquet, B., Liu, M., Mechref, Y., Meng, B., Neelamegham, S., Nguyen-Khuong, T., Nilsson, J., Pap, A., Park, GW., Parker, BL., Pegg, CL., Penninger, JM., Phung, TK., Pioch, M., Rapp, E., Sakalli, E., Sanda, M., Schulz, BL., Scott, NE., Sofronov, G., Stadlmann, J., Vakhrushev, SY., Woo, CM., Wu, HY., Yang, P., Ying, W., Zhang, H., Zhang, Y., Zhao, J., Zaia, J., Haslam, SM., Palmisano, G., Yoo, JS., Larson, G., Khoo, KH., Medzihradszky, KF., Kolarich, D., Packer, NH., Thaysen-Andersen, M.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Methods","volume":"18","issue":"11","page":"1304-1316","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7836914","title":"A novel class of autoantigens of anti-neutrophil cytoplasmic antibodies in necrotizing and crescentic glomerulonephritis: the lysosomal membrane glycoprotein h-lamp-2 in neutrophil granulocytes and a related membrane protein in glomerular endothelial cells.","abstract":"Necrotizing and crescentic glomerulonephritis (NCGN) is frequently associated with circulating antineutrophil cytoplasmic autoantibodies (ANCA). It is established that ANCA are specific for soluble enzymes of granules of polymorphonuclear neutrophil granulocytes (PMN), such as myeloperoxidase (MPO) or protease 3 (PR3). The purpose of this study was to identify membrane proteins of PMNs, and\/or glomerular cells, as additional autoantigenic ANCA targets. When membrane protein fractions were prepared from PMNs and isolated human glomeruli, and immunoblotted with ANCA sera of NCGN patients, two bands with apparent molecular masses of 170 and 80-110 kD (gp170\/80-110) were labeled in PMNs, and a 130-kD glycoprotein (gp130) in glomeruli. Gp130 was purified, and monoclonal and rabbit antibodies (Abs) were produced which showed the same double specificity as the patient's ANCA. Using these probes, evidence was provided that gp170\/80-110 is identical with human lysosomal-associated membrane protein 2 (h-lamp-2), because both proteins were immunologically cross-reactive and screening of a cDNA expression library from human promyelocytic leukemia cells with anti-gp130 Ab yielded a clone derived from h-lamp-2. Gp170\/80-110 was localized primarily in granule membranes of resting PMNs, and was translocated to the cell surfaces by activation with FMLP. By contrast, gp130 was localized in the surface membranes of endothelial cells of human glomerular and renal interstitial capillaries, rather than in lysosomes, as found for h-lamp-2. Potential clinical relevance of autoantibodies to gp170\/80-110 and gp130 was assessed in a preliminary trial, in which ANCA sera of patients (n = 16) with NCGN were probed with purified or recombinant antigens. Specific reactivity was detected in approximately 90% of cases with active phases of NCGN, and frequently also in combination with autoantibodies specific for PR3 or MPO. Collectively, these data provide evidence that h-lamp-2 in PMNs and a different, structurally related 130-kD membrane protein on the cell surface of renal microvascular endothelial cells are autoantigenic targets for ANCA in patients with active NCGN.","authors":"Kain, R., Matsui, K., Exner, M., Binder, S., Schaffner, G., Sommer, EM., Kerjaschki, D.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Exp Med","volume":"181","issue":"2","page":"585-97","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"1995-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6444298","title":"Development of escherichia coli virus T1. ATP-mediated discrimination of gene expression.","abstract":"The mechanism of host shut-off following virus T1 infection was studied using Escherichia coli wild type and ATPase deficient (unc-) cells. Host protein synthesis measured either as amino acid incorporation into proteins or as enzyme synthesis is immediately inhibited in T1-infected wild type cells. In contrast, host repression in the ATPase-deficient cells is almost unaffected after T1 infection. The continuation of host macromolecule synthesis in the unc- cells is due to constant ATP concentrations after infection, whereas an immediate drop in intracellular ATP levels in T1-infected wild type cells causes repression of host protein synthesis. This result is confirmed when host protein synthesis is determined at decreasing ATP concentrations following the starvation of cells.","authors":"Wagner, EF., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"J Biol Chem","volume":"255","issue":"2","page":"540-2","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1980-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1633717","title":"A chimaeric mouse model for autosomal-dominant polycystic kidney disease.","abstract":null,"authors":"Boulter, CA., Aguzzi, A., Evans, MJ., Affara, N.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Contrib Nephrol","volume":"97","issue":null,"page":"60-70","pdf":null,"JrId":"3171","fulltextlink":null,"preprintlink":null,"articledate":"1992-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1631096","title":"Coupling of adenovirus to transferrin-polylysine\/DNA complexes greatly enhances receptor-mediated gene delivery and expression of transfected genes.","abstract":"We are developing efficient methods for gene transfer into tissue culture cells. We have previously shown that coupling of a chimeric adenovirus with polylysine allowed the construction of an adenovirus-polylysine-reporter-gene complex that transferred the transporter gene with great efficiency into HeLa cells. We have now explored simpler, biochemical means for coupling adenovirus to DNA\/polylysine complexes and show that such complexes yield virtually 100% transfection in tissue culture cell lines. In these methods adenovirus is coupled to polylysine, either enzymatically through the action of transglutaminase or biochemically by biotinylating adenovirus and streptavidinylating the polylysine moiety. Combination complexes containing DNA, adenovirus-polylysine, and transferrin-polylysine have the capacity to transfer the reporter gene into adenovirus-receptor- and\/or transferrin-receptor-rich cells.","authors":"Wagner, E., Zatloukal, K., Cotten, M., Kirlappos, H., Mechtler, K., Curiel, DT., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Proc Natl Acad Sci U S A","volume":"89","issue":"13","page":"6099-103","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1992-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7811058","title":"Synthesis and anti-HIV activity of thiocholesteryl-coupled phosphodiester antisense oligonucleotides incorporated into immunoliposomes.","abstract":"Encapsulation of oligonucleotides in antibody-targeted liposomes (immunoliposomes) which bind to target cells permits intracellular delivery of the oligonucleotides. This approach circumvents problems of extracellular degradation by nucleases and poor membrane permeability which free phosphodiester oligonucleotides are subject to, but leaves unresolved the inefficiency of encapsulation of oligonucleotides in liposomes. We have coupled oligonucleotides to cholesterol via a reversible disulfide bond. This modification of oligonucleotides improved their association with immunoliposomes by a factor of about 10 in comparison to unmodified oligonucleotides. The presence of cholesteryl-modified oligonucleotides incorporated in the bilayer of liposomes did not interfere with the coupling of the targeting protein to the liposome surface. Free or cholesterol coupled oligonucleotides associated with liposomes and directed against the tat gene of HIV-1 were tested for inhibition of HIV-1 proliferation in acutely infected cells. We demonstrate that the cholesteryl-modified as well as unmodified oligonucleotides acquire the target specificity of the antibody on the liposome. Their antiviral activity when delivered into cells is sequence-specific. The activity of these modified or unmodified oligonucleotides to inhibit the replication of HIV was the same on an equimolar basis (EC50 around 0.1 microM). Cholesterol coupled oligonucleotides thus offer increased liposome association without loss of antiviral activity.","authors":"Zelphati, O., Wagner, E., Leserman, L.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Antiviral Res","volume":"25","issue":"1","page":"13-25","pdf":null,"JrId":"688","fulltextlink":null,"preprintlink":null,"articledate":"1995-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1577279","title":"Immortalization of conditionally transformed chicken cells: loss of normal p53 expression is an early step that is independent of cell transformation.","abstract":"Clones of mortal chicken fibroblasts and erythroblasts transformed by temperature-sensitive v-src and v-erb B oncoproteins have been developed into immortal cell lines that retain the conditional transformed phenotype. The expressions of two tumor suppressor genes, the retinoblastoma (Rb) gene and the p53 gene, were investigated during senescence, crisis, and cell line establishment. In temperature-sensitive (ts)-v-erb B erythroblasts and ts-v-src fibroblasts (as well as in v-myc macrophages), loss of p53 mRNA or expression of a mutated p53 gene invariably occurred in the early phase of immortalization. In contrast, expression of the Rb gene was unchanged at all stages of immortalization. Inactivation of the original temperature-sensitive oncogene led to loss of the transformed phenotype in fibroblasts and to differentiation in erythroblasts, even in lines that were immortal and lacked p53. The results demonstrate that the process of immortalization is distinct from cell transformation, probably requiring different mutational events.","authors":"Ulrich, E., Boehmelt, G., Bird, A., Beug, H.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Genes Dev","volume":"6","issue":"5","page":"876-87","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1992-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1549463","title":"Evolutionary conserved multiprotein complexes interact with the 3' untranslated region of histone transcripts.","abstract":"The replication dependent histone transcripts terminate with a highly conserved stem-loop structure. This feature distinguishes them from most other eukaryotic mRNAs which end with a poly(A) tail. The 3' terminus of histone mRNA is a main determinant for rapid turnover of these transcripts. In this study, we report the identification of two cytoplasmic protein complexes that interact in a sequence specific fashion with 3' terminal sequences of a mouse histone H4 and a human histone H2A mRNA. The binding activities are conserved from frog to man. At least a fraction of one of the protein complexes appears to be specifically associated with polysomes. The evidence for an involvement of the observed protein complexes in turnover of histone transcripts is discussed.","authors":"Eckner, R., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Nucleic Acids Res","volume":"20","issue":"5","page":"1023-30","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1992-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1540389","title":"Gene transfer to respiratory epithelial cells via the receptor-mediated endocytosis pathway.","abstract":"Gene-based therapies for a variety of inherited and acquired pulmonary diseases will require the development of vectors capable of safe and efficient transfer of DNA to the respiratory epithelium. The present study examined the feasibility of delivering DNA to respiratory epithelial cells by the receptor-mediated endocytosis pathway. This strategy employs molecular conjugates consisting of a cognate moiety, in this case human transferrin, covalently linked to a DNA-binding moiety, such as a cationic polyamine. Complexes were formed between transferrin-polylysine conjugates (hTfpL) and plasmid DNA carrying the firefly luciferase reporter gene (pRSVL). The conjugate-DNA complexes were added directly to cells in tissue culture and incubated for 24 h, after which cell lysates were analyzed for luciferase enzyme activity by luminometry. An immortalized human respiratory epithelial cell line (HBE1) treated with the transferrin-polylysine-DNA complexes exhibited luciferase enzyme activity significantly augmented over background levels. This respiratory epithelial cell line exhibited greater susceptibility to gene transfer by the transferrin-polylysine conjugates than did non-respiratory epithelial cell lines known to possess high levels of transferrin receptors. Effective gene transfer was shown to require both the DNA-binding moiety and cognate moiety for the cell surface receptor. Specific internalization of the conjugates by the transferrin pathway was verified by competition for the transferrin receptor. In addition, treatment with agents that either increased transferrin receptor number or decreased lysosomal degradation markedly augmented gene expression mediated by the conjugates. Thus, respiratory epithelial cells possess receptors for transferrin that can be exploited to accomplish gene transfer by the receptor-mediated endocytosis pathway.","authors":"Curiel, DT., Agarwal, S., R\u00f8mer, MU., Wagner, E., Cotten, M., Birnstiel, ML., Boucher, RC.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Am J Respir Cell Mol Biol","volume":"6","issue":"3","page":"247-52","pdf":null,"JrId":"1625","fulltextlink":null,"preprintlink":null,"articledate":"1992-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7249085","title":"Cell-surface glycoprotein synthesis during differentiation of chicken erythroblasts transformed by temperature-sensitive avian erythroblastosis virus.","abstract":"Chicken erythroblasts transformed by a temperature-sensitive mutant of avian erythroblastosis virus (ts34 AEV) have a greatly increased haemoglobin content (Graf, T., N. Ade and H. Beug: Nature 275, 496-501 (1978)) if allowed to grow for 3-5 days at the non-permissive temperature (41 degrees C), instead of the permissive temperature (35 degrees C) of the virus. Cell-surface molecular changes during this differentiation were investigated by examining the glycoproteins synthesized by a ts34-transformed erythroblast cell line. These cells synthesized a greatly increased amount of a 94,000 molecular weight erythrocyte cell-surface glycoprotein beginning 2-6 h after a shift in growth temperature from 35 degrees to 41 degrees C, consistent with the proposal that such a shift releases these transformed cells from a differentiation block.","authors":"Savin, KW., Beug, H.","publication_status":"ppublish","journalpubyear":"1981","journaltitle":"Cell Differ","volume":"10","issue":"3","page":"163-71","pdf":null,"JrId":"2832","fulltextlink":null,"preprintlink":null,"articledate":"1981-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34755089","title":"The ubiquitin ligase HOIL-1L regulates immune responses by interacting with linear ubiquitin chains.","abstract":"The Linear Ubiquitin Chain Assembly Complex (LUBAC), composed of HOIP, HOIL-1L, and SHARPIN, promotes tumor necrosis factor (TNF)-dependent NF-\u03baB signaling in diverse cell types. HOIL-1L contains an Npl4 Zinc Finger (NZF) domain that specifically recognizes linear ubiquitin chains, but its physiological role <i>in\u00a0vivo<\/i> has remained unclear. Here, we demonstrate that the HOIL-1L NZF domain has important regulatory functions in inflammation and immune responses in mice. We generated knockin mice (<i>Hoil-1l<\/i> <sup><i>T201A;R208A\/T201A;R208A<\/i><\/sup> ) expressing a HOIL-1L NZF mutant and observed attenuated responses to TNF- and LPS-induced shock, including prolonged survival, stabilized body temperature, reduced cytokine production, and\u00a0liver damage markers. Cells derived from <i>Hoil-1l<\/i> <sup><i>T201A;R208A\/T201A;R208A<\/i><\/sup> mice show reduced TNF-dependent NF-\u03baB activation and incomplete recruitment of HOIL-1L into TNF Receptor (TNFR) Complex I. We further show that HOIL-1L NZF cooperates with SHARPIN to prevent TNFR-dependent skin inflammation. Collectively, our data suggest that linear ubiquitin-chain binding by HOIL-1L regulates immune responses and inflammation <i>in\u00a0vivo<\/i>.","authors":"Gomez-Diaz, C., Jonsson, G., Schodl, K., Deszcz, L., Bestehorn, A., Eislmayr, K., Almagro, J., Kavirayani, A., Seida, M., Fennell, LM., Hagelkruys, A., Kovarik, P., Penninger, JM., Ikeda, F.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"iScience","volume":"24","issue":"11","page":"103241","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8843198","title":"TGF-beta1 and Ha-Ras collaborate in modulating the phenotypic plasticity and invasiveness of epithelial tumor cells.","abstract":"Metastasis of epithelial tumor cells can be associated with the acquisition of fibroblastoid features and the ability to invade stroma and blood vessels. Using matched in vivo and in vitro culture systems employing fully polarized, mammary epithelial cells, we report here that TGF-beta1 brings about these changes in Ras-transformed cells but not in normal cells. When grown in collagen gels in the absence of TGF-beta, both normal and Ras-transformed mammary epithelial cells form organ-like structures in which the cells maintain their epithelial characteristics. Under these conditions, treatment of normal cells with TGF-beta results in growth arrest. The same treatment renders Ras-transformed epithelial cells fibroblastoid, invasive, and resistant to growth inhibition by TGF-beta. After this epithelial-fibroblastoid conversion, the Ras-transformed cells start to secrete TGF-beta themselves, leading to autocrine maintenance of the invasive phenotype and recruitment of additional cells to become fibroblastoid and invasive. More important, this cooperation of activated Ha-Ras with TGF-beta1 is operative during in vivo tumorigenesis and, as in wound healing processes, is dependent on epithelial-stromal interactions.","authors":"Oft, M., Peli, J., Rudaz, C., Schwarz, H., Beug, H., Reichmann, E.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Genes Dev","volume":"10","issue":"19","page":"2462-77","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1996-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1521499","title":"Amphibian oocytes and sphere organelles: are the U snRNA genes amplified?","abstract":"The sphere organelles (spheres) of Xenopus and other amphibian oocytes are known to contain small nuclear ribonucleoprotein particles (snRNPs) and have been suggested to play a role in snRNP complex assembly. Coupled with the similarities that exist between spheres and nucleoli and the quantitative and kinetic aspects of snRNA synthesis in the Xenopus oocyte, we have investigated whether or not the U snRNA encoding genes are amplified in Xenopus oogenesis, the spheres being possible sites for the location of such extrachromosomal gene copies. By applying a number of quantitative nucleic acid hybridization procedures to both total and fractionated oocyte and somatic DNA, employing both homologous and heterologous U snRNA gene probes and suitable amplification and non-amplification control probes, we show that the U snRNA genes do not undergo any major amplification in Xenopus oogenesis. Therefore, the analogy between the sphere organelles and nucleoli appears to be limited. The role of the spheres and their relationship to other snRNP containing structures, specifically B snurposomes, and the sphere organizer loci remains obscure.","authors":"Phillips, S., Cotten, M., Laengle-Rouault, F., Schaffner, G., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Chromosoma","volume":"101","issue":"9","page":"549-56","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"1992-10-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34793982","title":"Comparative proteome signatures of trace samples by multiplexed Data-Independent Acquisition.","abstract":"Single cell transcriptomics has revolutionized our understanding of basic biology and disease. Since transcript levels often do not correlate with protein expression, it is crucial to complement transcriptomics approaches with proteome analyses at single cell resolution. Despite continuous technological improvements in sensitivity, mass spectrometry-based single cell proteomics ultimately faces the challenge of reproducibly comparing the protein expression profiles of thousands of individual cells. Here, we combine two hitherto opposing analytical strategies, DIA and Tandem-Mass-Tag (TMT)-multiplexing, to generate highly reproducible, quantitative proteome signatures from ultra-low input samples. We developed a novel, identification-independent proteomics data-analysis pipeline that allows to quantitatively compare DIA-TMT proteome signatures across hundreds of samples independent of their biological origin to identify cell types and single protein knockouts. These proteome signatures overcome the need to impute quantitative data due to accumulating detrimental amounts of missing data in standard multi-batch TMT experiments. We validate our approach using integrative data analysis of different human cell lines and standard database searches for knockouts of defined proteins. Our data establish a novel and reproducible approach to markedly expand the numbers of proteins one detects from ultra-low input samples.","authors":"Ctortecka, C., Kr\u0161\u0161\u00e1kov\u00e1, G., Stejskal, K., Penninger, JM., Mendjan, S., Mechtler, K., Stadlmann, J.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Mol Cell Proteomics","volume":null,"issue":null,"page":"100177","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7720705","title":"Thyroid hormone regulates stromelysin expression, protease secretion and the morphogenetic potential of normal polarized mammary epithelial cells.","abstract":"Stromelysins are a group of proteases which degrade the extracellular matrix and activate other secreted proteases. Stromelysin (ST)-1 and ST-2 genes are induced by tumor promoters, oncogenes and growth factors, and have been involved in acquisition of the malignant phenotype. We show here that the thyroid hormone (T3) increases ST-1 and ST-2 expression in a non-transformed mouse mammary epithelial cell line (EpH4) in a way that is dependent on the level of thyroid receptor\/c-erbA (TR alpha-1) expression. In agreement with this, T3 increases the secreted stromelysin activity and enhances the gelatinolytic activity of type IV collagenase. We have also demonstrated that T3 affects the epithelial polarity of EpH4 cells, diminishing the transepithelial electrical resistance of monolayers cultured on permeable filters, causing an abnormal distribution of polarization markers and the disruption of the organized 3-D structures formed by these cells in type I collagen gels. These results indicate that the ligand-activated TR alpha-1 plays an important role in regulating the morphogenetic and invasive capacities of mammary epithelial cells. Because the c-erbA locus is altered in several types of carcinoma, an altered or deregulated TR alpha-1 expression may also be important for breast cancer development and metastasis.","authors":"L\u00f3pez-Barahona, M., Fialka, I., Gonz\u00e1lez-Sancho, JM., Asunci\u00f3n, M., Gonz\u00e1lez, M., Iglesias, T., Bernal, J., Beug, H., Mu\u00f1oz, A.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"EMBO J","volume":"14","issue":"6","page":"1145-55","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1995-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7738098","title":"rab8 in retinal photoreceptors may participate in rhodopsin transport and in rod outer segment disk morphogenesis.","abstract":"Small GTP-binding protein rab8 regulates transport from the TGN to the basolateral plasma membrane in epithelial cells and to the dendritic plasma membrane in cultured hippocampal neurons. In our approach to identify proteins involved in rhodopsin transport and sorting in retinal photoreceptors, we have found, using [32P]GTP overlays of 2D gel blots, that six small GTP-binding proteins are tightly bound to the post-Golgi membranes immunoisolated with a mAb to the cytoplasmic domain of frog rhodopsin. We report here that one of these proteins is rab8. About 50% of photoreceptor rab8 is membrane associated and approximately 13% is tightly bound to the post-Golgi vesicles. By confocal microscopy, antibody to rab8 specifically labels calycal processes and the actin bundles of the photoreceptor inner segment that extend inward to the junctional complexes that comprise the outer limiting membrane. Anti-rab8 shows a striking periodicity of high density labeling at 1 +\/- 0.12 microns intervals along the actin bundles. Rhodopsin-bearing post-Golgi membranes cluster around the base of the cilium where rab8 and actin are also co-localized, as revealed by confocal microscopy of retinal sections double labeled with anti-rab8 and phalloidin. Microfilaments have been implicated in rod outer segment (ROS) disk morphogenesis. Our data suggest that rab6, which we have previously localized to the post-Golgi compartment, and rab8 associate with the post-Golgi membranes sequentially at different stages of transport. rab8 may mediate later steps that involve interaction of transport membranes with actin filaments and may participate in microfilament-dependent ROS disk morphogenesis.","authors":"Deretic, D., Huber, LA., Ransom, N., Mancini, M., Simons, K., Papermaster, DS.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Cell Sci","volume":"108 ( Pt 1)","issue":null,"page":"215-24","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1465144","title":"Bone and haematopoietic defects in mice lacking c-fos.","abstract":"The proto-oncogene c-fos is the cellular homologue of v-fos originally isolated from murine osteosarcoma. Fos protein is a major component of the AP-1 transcription factor complex, which includes members of the jun family. Stable expression of c-fos in mice has been demonstrated in developing bones and teeth, haematopoietic cells, germ cells and in the central nervous system. It has been proposed that c-fos has an important role in signal transduction, cell proliferation and differentiation. We have previously demonstrated that overexpression of c-fos in transgenic and chimaeric mice specifically affects bone, cartilage and haematopoietic cell development. To understand better the function of c-fos in vivo, we used gene targeting in embryonic stem cells to generate cells and mice lacking c-fos. Here we report that heterozygous fos +\/- mice appear normal, although females exhibit a distorted transmission frequency. All homozygous fos -\/- mice are growth-retarded, develop osteopetrosis with deficiencies in bone remodelling and tooth eruption, and have altered haematopoiesis. These data define the c-Fos protein as an essential molecule for the development of specific cellular compartments.","authors":"Wang, ZQ., Ovitt, C., Grigoriadis, AE., M\u00f6hle-Steinlein, U., R\u00fcther, U., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Nature","volume":"360","issue":"6406","page":"741-5","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1993-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1483353","title":"Cyclins and cdc2 kinases in Drosophila: genetic analyses in a higher eukaryote.","abstract":"Cyclin proteins and the kinases with which they associate are encoded by gene families in multicellular eukaryotes. A variety of cyclin\/kinase complexes with different functions may exist. We have started a genetic dissection of this complexity in Drosophila. We have done experiments to investigate a potential functional overlap between two kinases (Dmcdc2 and Dmcdc2c) and two cyclins (cyclin A and cyclin B). No functional overlap was observed between the Dmcdc2 and the Dmcdc2c kinases. The phenotype resulting from mutations in Dmcdc2 was not affected by altering the level of Dmcdc2c. Our results concerning cyclin A and cyclin B strongly suggest that these two cyclins have largely overlapping functions. Cell proliferation was observed in the absence of either cyclin A or cyclin B, but not if both cyclins were absent. Cyclin A also has essential functions that cannot be taken over by cyclin B, but these functions appear to be required at defined developmental stages in specific tissues only.","authors":"Lehner, CF., Ried, G., Stern, B., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Ciba Found Symp","volume":"170","issue":null,"page":"97-109; discussion 110-4","pdf":null,"JrId":"2951","fulltextlink":null,"preprintlink":null,"articledate":"1993-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34815389","title":"ACE2-like carboxypeptidase B38-CAP protects from SARS-CoV-2-induced lung injury.","abstract":"Angiotensin-converting enzyme 2 (ACE2) is a receptor for cell entry of SARS-CoV-2, and recombinant soluble ACE2 protein inhibits SARS-CoV-2 infection as a decoy. ACE2 is a carboxypeptidase that degrades angiotensin II, thereby improving the pathologies of cardiovascular disease or acute lung injury. Here we show that B38-CAP, an ACE2-like enzyme, is protective against SARS-CoV-2-induced lung injury. Endogenous ACE2 expression is downregulated in the lungs of SARS-CoV-2-infected hamsters, leading to elevation of angiotensin II levels. Recombinant Spike also downregulates ACE2 expression and worsens the symptoms of acid-induced lung injury. B38-CAP does not neutralize cell entry of SARS-CoV-2. However, B38-CAP treatment improves the pathologies of Spike-augmented acid-induced lung injury. In SARS-CoV-2-infected hamsters or human ACE2 transgenic mice, B38-CAP significantly improves lung edema and pathologies of lung injury. These results provide the first in vivo evidence that increasing ACE2-like enzymatic activity is a potential therapeutic strategy to alleviate lung pathologies in COVID-19 patients.","authors":"Yamaguchi, T., Hoshizaki, M., Minato, T., Nirasawa, S., Asaka, MN., Niiyama, M., Imai, M., Uda, A., Chan, JF., Takahashi, S., An, J., Saku, A., Nukiwa, R., Utsumi, D., Kiso, M., Yasuhara, A., Poon, VK., Chan, CC., Fujino, Y., Motoyama, S., Nagata, S., Penninger, JM., Kamada, H., Yuen, KY., Kamitani, W., Maeda, K., Kawaoka, Y., Yasutomi, Y., Imai, Y., Kuba, K.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"6791","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1451114","title":"Avian erythroblastosis: a model system to study oncogene co-operation in leukemia.","abstract":"Avian erythroblastosis virus, AEV-ES4, provides an ideal in vitro system to study oncogene co-operation in the development of erythroid leukaemias in chickens. Two oncogenes that use distinct signal transduction pathways have been identified; these act to produce a highly malignant phenotype and are an oncogenic version of a plasma membrane growth factor receptor that regulates haematopoietic progenitor self renewal and a mutated version of a transcription factor that suppresses specific gene expression. These two diverse types of oncogenes act together to generate a more malignant phenotype than would be expected merely from a summation of the individual oncogene effects. The aspects of normal growth control and the regulation of differentiation, which are altered in this system to generate the leukaemic phenotype, include changes in the balance between proliferation versus maturation, altered expression of differentiation genes and changes in growth factor responsiveness. These are exactly those features that are altered in human leukaemias. Thus, the avian leukaemia virus model has taught us important lessons that will help us to understand the basic molecular mechanisms that give rise to human leukaemia.","authors":"Hayman, MJ., Beug, H.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Cancer Surv","volume":"15","issue":null,"page":"53-68","pdf":null,"JrId":"2787","fulltextlink":null,"preprintlink":null,"articledate":"1993-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"229630","title":"Transforming capacities and defectiveness of avian leukemia viruses OK10 and E 26.","abstract":null,"authors":"Graf, T., Oker-Blom, N., Todorov, TG., Beug, H.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Virology","volume":"99","issue":"2","page":"431-6","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1980-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1425595","title":"Hormone-regulated v-rel estrogen receptor fusion protein: reversible induction of cell transformation and cellular gene expression.","abstract":"We describe the construction of a v-rel estrogen receptor fusion protein (v-relER) which allows the regulation of v-rel oncoprotein activity by hormone. In the presence of estrogen, v-relER readily transformed primary chicken fibroblasts and bone marrow cells in vitro. In both cell types, v-rel-specific transformation was critically dependent on the presence of estrogen or the estrogen agonist 4-hydroxytamoxifen (OHT). Withdrawal of estrogen or application of an estrogen antagonist, ICI164,384 (ICI) caused a reversal of the transformed phenotype. We also demonstrate that the v-relER protein binds to NF-kappa B sites in an estrogen-dependent manner, thereby showing that sequence-specific DNA binding of v-relER is critical for the activation of its transforming capacity. In transient transfection experiments, we failed to demonstrate a clear repressor or activator function of the v-rel moiety in v-relER. However, in v-relER-transformed bone marrow cells, estrogen and OHT induced elevated mRNA levels of two cellular genes whose expression is constitutive and high in v-rel-transformed cells. These results suggest that v-rel might exert part of its activity as an activator of rel-responsive genes.","authors":"Boehmelt, G., Walker, A., Kabrun, N., Mellitzer, G., Beug, H., Zenke, M., Enrietto, PJ.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"EMBO J","volume":"11","issue":"12","page":"4641-52","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1992-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1387566","title":"Characterization of four B-type cyclin genes of the budding yeast Saccharomyces cerevisiae.","abstract":"The previously described CLB1 and CLB2 genes encode a closely related pair of B-type cyclins. Here we present the sequences of another related pair of B-type cyclin genes, which we term CLB3 and CLB4. Although CLB1 and CLB2 mRNAs rise in abundance at the time of nuclear division, CLB3 and CLB4 are turned on earlier, rising early in S phase and declining near the end of nuclear division. When all possible single and multiple deletion mutants were constructed, some multiple mutations were lethal, whereas all single mutants were viable. All lethal combinations included the clb2 deletion, whereas the clb1 clb3 clb4 triple mutant was viable, suggesting a key role for CLB2. The inviable multiple clb mutants appeared to have a defect in mitosis. Conditional clb mutants arrested as large budded cells with a G2 DNA content but without any mitotic spindle. Electron microscopy showed that the spindle pole bodies had duplicated but not separated, and no spindle had formed. This suggests that the Clb\/Cdc28 kinase may have a relatively direct role in spindle formation. The two groups of Clbs may have distinct roles in spindle formation and elongation.","authors":"Fitch, I., Dahmann, C., Surana, U., Amon, A., Nasmyth, K., Goetsch, L., Byers, B., Futcher, B.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Mol Biol Cell","volume":"3","issue":"7","page":"805-18","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"1992-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"153","title":"Effects of decreasing arterial blood pressure on cerebral blood flow in the baboon. Influence of the sympathetic nervous system.","abstract":"The influence of the sympathetic nervous system on the cerebral circulatory response to graded reductions in mean arterial blood pressure was studied in anesthetized baboons. Cerebral blood flow was measured by the 133Xe clearance method, and arterial blood pressure was decreased by controlled hemorrhage. In normal baboons, the constancy of cerebral blood flow was maintained until mean arterial blood pressure was approximately 65% of the base-line value; thereafter, cerebral blood flow decreased when arterial blood pressure was reduced. Superior cervical sympathectomy of 2-3 weeks duration did not affect the normal response. In contrast, both acute surgical sympathectomy (cervical trunk division) and alpha-receptor blockade (1.5 mg\/kg of phenoxybenzamine) enhanced the maintenance of cerebral blood flow in the face of hemorrhagic hypotension in that cerebral blood flow did not decrease until mean arterial blood pressure was approximately 35% of the base-line value. The results indicate that the sympathetic nervous system is not involved in the maintenance of cerebral blood flow in the face of a fall in arterial blood pressure. Indeed, the implication is that the sympathicoadrenal discharge accompanying hemorrhagic hypotension is detrimental to, rather than responsible for,  cerebral autoregulation.","authors":"Fitch, W., MacKenzie, ET., Harper, AM.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Circ Res","volume":"37","issue":"5","page":"550-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1408132","title":"The v-ski oncogene cooperates with the v-sea oncogene in erythroid transformation by blocking erythroid differentiation.","abstract":"The avian retrovirus oncogene v-ski was analysed for its ability to alter the differentiation program of erythroid cells and to cooperate with tyrosine kinase oncogenes in leukemogenesis. For this, a retrovirus combining v-ski with a temperature-sensitive version of the v-sea oncogene was constructed. In transformed erythroblasts, v-ski disturbed the concerted expression of several erythrocyte genes, leading to an abnormal erythroblast phenotype. Expression levels of hemoglobin and erythrocyte anion transporter (band 3) were elevated, while expression of the erythroid-specific histone H5 was strongly suppressed. v-ski could also be shown to repress or severely retard the temperature-induced erythroid differentiation of v-ski\/ts-v-sea-transformed cells. The undifferentiated cells had an abnormal erythroblast or early reticulocyte phenotype characterized by unusually low levels of histone H5. In chicks, the v-ski\/ts-v-sea virus displayed enhanced leukemogenicity compared with viruses containing just the single oncogenes. Thus, v-ski cooperates with tyrosine kinase oncogenes in a similar fashion to the v-erbA oncogene, however the pattern of genes affected by these two oncogenes is different.","authors":"Larsen, J., Beug, H., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Oncogene","volume":"7","issue":"10","page":"1903-11","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1992-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1406694","title":"Identification of a new set of cell cycle-regulatory genes that regulate S-phase transcription of histone genes in Saccharomyces cerevisiae.","abstract":"Histone mRNA synthesis is tightly regulated to S phase of the yeast Saccharomyces cerevisiae cell cycle as a result of transcriptional and posttranscriptional controls. Moreover, histone gene transcription decreases rapidly if DNA replication is inhibited by hydroxyurea or if cells are arrested in G1 by the mating pheromone alpha-factor. To identify the transcriptional controls responsible for cycle-specific histone mRNA synthesis, we have developed a selection for mutations which disrupt this process. Using this approach, we have isolated five mutants (hpc1, hpc2, hpc3, hpc4, and hpc5) in which cell cycle regulation of histone gene transcription is altered. All of these mutations are recessive and belong to separate complementation groups. Of these, only one (hpc1) falls in one of the three complementation groups identified previously by other means (M. A. Osley and D. Lycan, Mol. Cell. Biol. 7:4204-4210, 1987), indicating that at least seven different genes are involved in the cell cycle-specific regulation of histone gene transcription. hpc4 is unique in that derepression occurs only in the presence of hydroxyurea but not alpha-factor, suggesting that at least one of the regulatory factors is specific to histone gene transcription after DNA replication is blocked. One of the hpc mutations (hpc2) suppresses delta insertion mutations in the HIS4 and LYS2 loci. This effect allowed the cloning and sequence analysis of HPC2, which encodes a 67.5-kDa, highly charged basic protein.","authors":"Xu, H., Kim, UJ., Schuster, T., Grunstein, M.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Mol Cell Biol","volume":"12","issue":"11","page":"5249-59","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1992-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"232466","title":"Mechanism of leukemogenesis and of target cell specificity by defective avian leukemia viruses: a hypothesis.","abstract":null,"authors":"Graf, T., von Kirchbach, A., Beug, H.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Haematol Blood Transfus","volume":"23","issue":null,"page":"429-38","pdf":null,"JrId":"30276","fulltextlink":null,"preprintlink":null,"articledate":"1980-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34856602","title":"Human blastoids model blastocyst development and implantation.","abstract":"One week after fertilization, human embryos implant into the uterus. This event requires that the embryo forms a blastocyst consisting of a sphere encircling a cavity lodging the embryo proper. Stem cells can form a blastocyst model, which we termed blastoid<sup>1<\/sup>. Here we show that naive human pluripotent stem cells (PXGL hPSCs)<sup>2<\/sup> triply inhibited for the Hippo, TGF-\u03b2, and ERK pathways efficiently (&gt;70%) form blastoids generating blastocyst-stage analogs of the 3 founding lineages (&gt;97% trophectoderm, epiblast, and primitive endoderm) according to the sequence and timing of blastocyst development. Blastoids spontaneously form the first axis and we observe that the epiblast induces the maturation of the polar trophectoderm that consequently acquires the specific capacity to attach to hormonally-stimulated endometrial cells, as during implantation. Such a human blastoid is a faithful, scalable, and ethical model to explore human implantation and development<sup>3,4<\/sup>.","authors":"Kagawa, H., Javali, A., Khoei, HH., Sommer, TM., Sestini, G., Novatchkova, M., Scholte Op Reimer, Y., Castel, G., Bruneau, A., Maenhoudt, N., Lammers, J., Loubersac, S., Freour, T., Vankelecom, H., David, L., Rivron, N.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1358441","title":"The leukaemia oncogene v-erbA: a dominant negative version of ligand dependent transcription factors that regulates red cell differentiation?","abstract":"The v-erbA oncogene of avian erythroblastosis virus alters the growth properties and arrests differentiation of chick erythroid progenitor cells. The v-erbA protein is a mutated, ligand independent version of the c-erbA\/T3R alpha chick receptor for T3, a ligand dependent transcriptional regulator. In reconstituted systems using idealized hormone responsive elements, over-expressed v-erbA acts as a dominant repressor of transcription mediated by liganded c-erbA\/T3R alpha. This property seems to account for at least part of the phenotype of AEV transformed erythroid cells and for the transcriptional repression of some erythrocyte specific genes. However, v-erbA is likely to interfere with regulatory circuits other than those directly regulated by T3 receptors. Aspects of this hypothesis are discussed in the context of available evidence for the role of T3 and other hormones in erythroid progenitor cells proliferation\/differentiation.","authors":"Ghysdael, J., Beug, H.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Cancer Surv","volume":"14","issue":null,"page":"169-80","pdf":null,"JrId":"2787","fulltextlink":null,"preprintlink":null,"articledate":"1992-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7720562","title":"Mouse embryonic germ (EG) cell lines: transmission through the germline and differences in the methylation imprint of insulin-like growth factor 2 receptor (Igf2r) gene compared with embryonic stem (ES) cell lines.","abstract":"Primordial germ cells of the mouse cultured on feeder layers with leukemia inhibitory factor, Steel factor and basic fibroblast growth factor give rise to cells that resemble undifferentiated blastocyst-derived embryonic stem cells. These primordial germ cell-derived embryonic germ cells can be induced to differentiate extensively in culture, form teratocarcinomas when injected into nude mice and contribute to chimeras when injected into host blastocysts. Here, we report the derivation of multiple embryonic germ cell lines from 8.5 days post coitum embryos of C57BL\/6 inbred mice. Four independent embryonic germ cell lines with normal male karyotypes have formed chimeras when injected into BALB\/c host blastocysts and two of these lines have transmitted coat color markers through the germline. We also show that pluripotent cell lines capable of forming teratocarcinomas and coat color chimeras can be established from primordial germ cells of 8.0 days p.c. embryos and 12.5 days p.c. genital ridges. We have examined the methylation status of the putative imprinting box of the insulin-like growth factor type 2 receptor gene (Igf2r) in these embryonic germ cell lines. No correlation was found between methylation pattern and germline competence. A significant difference was observed between embryonic stem cell and embryonic germ cell lines in their ability to maintain the methylation imprint of the Igf2r gene in culture. This may illustrate a fundamental difference between these two cell types.","authors":"Labosky, PA., Barlow, DP., Hogan, BL.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Development","volume":"120","issue":"11","page":"3197-204","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"1995-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9392515","title":"The characterization of novel Pax genes of the sea urchin and Drosophila reveal an ancient evolutionary origin of the Pax2\/5\/8 subfamily.","abstract":"The developmental control genes of the Pax family can be grouped into different subclasses according to structure and sequence homology. Here we describe the isolation and characterization of three novel Pax genes of the sea urchin for which no homologues are yet known in other animal phyla. One of these genes, suPaxB, codes for the previously characterized transcription factor TSAP which is involved in the developmental regulation of two pairs of late histone genes. Furthermore, conserved members of the Pax2\/5\/8 subfamily, which have so far been described only in vertebrates, were isolated not only from the sea urchin, but also from Drosophila and C. elegans. Hence, the Pax2\/5\/8 transcription factors constitute an ancient subfamily of highly conserved Pax proteins. During Drosophila embryogenesis, the Pax258 gene is shown to be expressed in the precursor cells of the external sensory organs, thus suggesting a role for Pax258 in the early development of the peripheral nervous system of insects.","authors":"Czerny, T., Bouchard, M., Kozmik, Z., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Mech Dev","volume":"67","issue":"2","page":"179-92","pdf":null,"JrId":"1825","fulltextlink":null,"preprintlink":null,"articledate":"1998-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1374647","title":"Analysis of a gene cluster coding for the Xenopus laevis U7 snRNA.","abstract":"A cluster of Xenopus laevis U7 snRNA genes has been isolated and sequenced. The gene structure is more compact than, but otherwise comparable to, the major U snRNA genes since the distal sequence element (DSE) is located only 4 nt upstream of the PSE. The corresponding RNA is present in the oocyte and accumulates early in oogenesis.","authors":"Phillips, SC., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Biochim Biophys Acta","volume":"1131","issue":"1","page":"95-8","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1992-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7710779","title":"Large-scale isolation of human 1p36-specific P1 clones and their use for fluorescence in situ hybridization.","abstract":"A series of 80 microclone probes derived from the chromosomal region 1p36 was used to isolate corresponding clones from the ICRF human P1 library (see Francis et al., this issue). Hybridization screenings were performed using probe pools on high-density filter grids. A total of 87 P1 clones specific for 1p36 were isolated. This large-scale approach allowed a detailed evaluation of the complexity, quality, and utility of this library. The isolated P1 clones were used both for size determination by pulsed-field gel electrophoresis and as probes for fluorescence in situ hybridization (FISH) analysis. FISH of P1 clones is shown to be both easy and efficient to perform on metaphase chromosomes and interphase nuclei. This observation is expected to reveal new avenues for diagnosis of disease-related chromosomal changes. The use of P1 clones as a tool in clinical and tumor interphase cytogenetics is discussed and compared with FISH data of other long insert clones such as cosmids and YAC clones.","authors":"Lengauer, C., Henn, T., Onyango, P., Francis, F., Lehrach, H., Weith, A.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Genet Anal Tech Appl","volume":"11","issue":"5-6","page":"140-7","pdf":null,"JrId":"1642","fulltextlink":null,"preprintlink":null,"articledate":"1995-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9323022","title":"Cloning, purification, crystallization, and preliminary X-ray diffraction analysis of cystathionine gamma-synthase from E. coli.","abstract":"The Escherichia coli metB gene has been PCR-extracted from genomic DNA and placed under the control of a tac and a T7 promoter in plasmids pCYB1 and pET22b(+), respectively, to produce overexpressing bacterial strains for the gene product, cystathionine gamma-synthase. Efficient purification procedures have been developed for a C-terminally intein-tagged version and the wild-type target protein, yielding the product in a quantity and homogeneity amenable to high-resolution single-crystal X-ray analysis. Crystals have been obtained in space group P1 with unit cell constants a=82.2 A, b=84.2 A, c=116.2 A, alpha=107.0 degrees, beta=96.3 degrees, gamma=108.0 degrees, suggesting eight monomers per asymmetric unit (V[M]=2.23 A3\/Da). Crystals diffract to beyond 2.6 A resolution and a data set complete to 2.8 A resolution has been collected using a rotating anode X-ray source. A cryogenic buffer system has been developed to allow synchrotron data collection. Patterson self rotation searches reveal the presence of two independent tetramers with local 222 symmetry in an asymmetric unit. The crystallographic results corroborate and extend previous solution studies regarding the quaternary organization of the enzyme.","authors":"Wahl, MC., Huber, R., Prade, L., Marinkovic, S., Messerschmidt, A., Clausen, T.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"FEBS Lett","volume":"414","issue":"3","page":"492-6","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7698643","title":"Mice lacking ADPRT and poly(ADP-ribosyl)ation develop normally but are susceptible to skin disease.","abstract":"Poly(ADP-ribosyl)ation is catalyzed by NAD+: protein(ADP-ribosyl) transferase (ADPRT), a chromatin-associated enzyme which, in the presence of DNA breaks, transfers ADP-ribose from NAD+ to nuclear proteins. This post-translational modification has been implicated in many fundamental processes, like DNA repair, chromatin stability, cell proliferation, and cell death. To elucidate the biological function of ADPRT and poly(ADP-ribosyl)ation in vivo the gene was inactivated in the mouse germ line. Mice homozygous for the ADPRT mutation are healthy and fertile. Analysis of mutant tissues and fibroblasts isolated from mutant fetuses revealed the absence of ADPRT enzymatic activity and poly(ADP-ribose), implying that no poly(ADP-ribosyl)ated proteins are present. Mutant embryonic fibroblasts were able to efficiently repair DNA damaged by UV and alkylating agents. However, proliferation of mutant primary fibroblasts as well as thymocytes following gamma-radiation in vivo was impaired. Moreover, mutant mice are susceptible to the spontaneous development of skin disease as approximately 30% of older mice develop epidermal hyperplasia. The generation of viable ADPRT-\/-mice negates an essential role for this enzyme in normal chromatin function, but the impaired proliferation and the onset of skin lesions in older mice suggest a function for ADPRT in response to environmental stress.","authors":"Wang, ZQ., Auer, B., Stingl, L., Berghammer, H., Haidacher, D., Schweiger, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Genes Dev","volume":"9","issue":"5","page":"509-20","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1995-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34875224","title":"20 years of Developmental Cell: Looking forward.","abstract":"In our 20th anniversary year, we reflect on how fields have changed since our first issue and here look to the future. In this collection of Voices, our writers speculate on the future: in terms of philosophy, cell states, cell processes, and then how to model cell systems.","authors":"Hiiragi, T., Gladfelter, AS., Miguel-Aliaga, I., Coller, HA., Lau, OS., McBride, HM., Aoki, K., Linkermann, A., Santaguida, S., Wasteneys, G., Rivron, NC., Shahbazi, MN., Ebisuya, M., Lancaster, MA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Dev Cell","volume":"56","issue":"23","page":"3185-3191","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7687522","title":"Self-renewal and differentiation of normal avian erythroid progenitor cells: regulatory roles of the TGF alpha\/c-ErbB and SCF\/c-kit receptors.","abstract":"The c-kit proto-oncogene product is a major regulator of early hematopoiesis in mice. We show here that the avian c-Kit protein, together with the c-erbB protooncogene product, regulates self-renewal and differentiation in two types of normal chick erythroid progenitors. A relatively frequent progenitor expressing only c-Kit transiently proliferated in response to avian c-Kit ligand (stem cell factor [SCF]). A second, rare progenitor coexpressed c-Kit and c-ErbB and was induced to long-term self-renewal by SCF or transforming growth factor alpha (TGF alpha), a c-ErbB ligand. In the absence of SFC or TGF alpha, both progenitors underwent erythropoietin (Epo)-dependent terminal differentiation with indistinguishable kinetics. Interestingly, Epo induced differentiation in the SCF progenitors even when SCF was present. In contrast, the c-ErbB-expressing, TGF alpha-induced progenitors continued to self-renew when treated with Epo plus the growth factors SCF, TGF alpha, or both. Expression of c-ErbB thus may be a dominant determinant for the sustained self-renewal of committed erythroid progenitors.","authors":"Hayman, MJ., Meyer, S., Martin, F., Steinlein, P., Beug, H.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Cell","volume":"74","issue":"1","page":"157-69","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1993-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9260928","title":"Dynamics of cell cycle regulators: artifact-free analysis by recultivation of cells synchronized by centrifugal elutriation.","abstract":"Studies on the molecular properties of cell cycle regulators in animal cells require cell preparations highly enriched in particular cell cycle phases. Centrifugal elutriation is frequently used to synchronize cells because this technique was thought to cause only minimal distortions in protein expression or metabolic functions. However, in primary chicken erythroblasts, we consistently observed artefacts in mitotic cyclin mRNA expression and p70 S6 kinase activity, which were clearly caused by the elutriation procedure. Therefore, we modified the standard protocol by reseeding various elutriated fractions into preconditioned medium, a process termed recultivation, and harvesting after an appropriate amount of time. This avoided the pleiotropic effects caused by stress and lack of growth factor supply during elutriation. Using this recultivation procedure, highly synchronous progression starting from any given cell cycle phase could be achieved for a variety of cell types, including primary, factor-dependent cells of hematopoietic origin. Mitotic cyclin expression and S6 kinase activity was found to be normal again in recultivated cultures, as opposed to elutriated ones. Finally, monitoring of mitosis-specific cyclin A degradation in recultivated G2 phase cells showed that recultivation provided an excellent tool to follow cells through M phase into G1 without the requirement for a chemical cell cycle block.","authors":"Mikulits, W., Dolznig, H., Edelmann, H., Sauer, T., Deiner, EM., Ballou, L., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"DNA Cell Biol","volume":"16","issue":"7","page":"849-59","pdf":null,"JrId":"1412","fulltextlink":null,"preprintlink":null,"articledate":"1997-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"189521","title":"Expression of virus specific morphological cell transformation induced in enucleated cells.","abstract":"Chick embryo fibroblasts infected by a temperature sensitive mutant of Rous sarcoma virus were enucleated with Cytochalasin B. The cytoplasts were still able to transform morphologically when shifted from nonpermissive to permissive temperature, and to revert ot normal morphology when shifted from permissive to nonpermissive temperature. This indicates that the viral gene product responsible for transformation acts primarily on cytoplasmic or membrane components and not on the nucleus.","authors":"Beug, H., Peters, JH., Graf, T.","publication_status":"ppublish","journalpubyear":"1976","journaltitle":"Z Naturforsch C Biosci","volume":"31","issue":"11-12","page":"766-8","pdf":null,"JrId":"8159","fulltextlink":null,"preprintlink":null,"articledate":"1977-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"188724","title":"Target cells for transformation with avian leukosis viruses.","abstract":null,"authors":"Graf, T., Royer-Pokora, B., Beug, H.","publication_status":"ppublish","journalpubyear":"1976","journaltitle":"Hamatol Bluttransfus","volume":"19","issue":null,"page":"169-76","pdf":null,"JrId":"3936","fulltextlink":null,"preprintlink":null,"articledate":"1977-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34624221","title":"Cohesin mediates DNA loop extrusion by a \"swing and clamp\" mechanism.","abstract":"Structural maintenance of chromosomes (SMC) complexes organize genome topology in all kingdoms of life and have been proposed to perform this function by DNA loop extrusion. How this process works is unknown. Here, we have analyzed how loop extrusion is mediated by human cohesin-NIPBL complexes, which enable chromatin folding in interphase cells. We have identified DNA binding sites and large-scale conformational changes that are required for loop extrusion and have determined how these are coordinated. Our results suggest that DNA is translocated by a spontaneous 50\u00a0nm-swing of cohesin's hinge, which hands DNA over to the ATPase head of SMC3, where upon binding of ATP, DNA is clamped by NIPBL. During this process, NIPBL \"jumps ship\" from the hinge toward the SMC3 head and might thereby couple the spontaneous hinge swing to ATP-dependent DNA clamping. These results reveal mechanistic principles of how cohesin-NIPBL and possibly other SMC complexes mediate loop extrusion.","authors":"Bauer, BW., Davidson, IF., Canena, D., Wutz, G., Tang, W., Litos, G., Horn, S., Hinterdorfer, P., Peters, JM.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell","volume":"184","issue":"21","page":"5448-5464.e22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7641697","title":"Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae.","abstract":"S phase entry depends on cyclin-dependent kinases whose activation during late G1 due partly to the synthesis of unstable cyclin subunits. We identify here a second type of unstable protein, Cdc6, whose synthesis during G1 is important for initiation of DNA replication. The CDC6 gene is normally transcribed at the end of mitosis, but in cells with a prolonged G1 phase there is a second burst of transcription in late G1. The former is due to Swi5, while the latter is due to MBF or SBF transcription factors. Small G1 cells that cannot synthesize Cdc6 in late G1 progress through S phase very slowly. Cells that transcribe CDC6 neither at the end of mitosis nor in late G1 fail to replicate DNA but, despite this, undergo mitosis and produce daughter cells with fractional DNA contents. This 'reductional' anaphase occurs with almost wild-type kinetics and depends on the activity of G2 cyclins. Thus, cells that fail to duplicate chromosomes due to a cdc6 defect cannot prevent the onset of mitosis, unlike other mutants with replication defects. We show, by fluorescence in situ hybridization, that chromosomes which remain unduplicated due to a lack of Cdc6 synthesis are segregated intact to spindle poles during the 'reductional' anaphase.","authors":"Piatti, S., Lengauer, C., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"EMBO J","volume":"14","issue":"15","page":"3788-99","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1995-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7624132","title":"In vitro growth of factor-dependent multipotential hematopoietic cells is induced by the nuclear oncoprotein v-Ski.","abstract":"Understanding how self renewal, commitment and differentiation are regulated in normal, multipotent hematopoietic progenitors is important for our understanding of underlying mechanisms involved in leukemogenesis. In addition, knowledge of progenitor cell biology is critical if these cells are to be used for gene therapy. In this communication, we demonstrate that the oncogenic transcription factor v-Ski, together with the ligand activated receptor tyrosine kinase c-Kit, induces the continuous in vitro self renewal of primary avian multipotent progenitors. These cells have an in vitro life span of &gt; 100 generations. In addition they spontaneously differentiate into cells of the erythroid, monocytic and granulocytic lineages. If clonal strains of these multipotent progenitors are exposed to specific mixtures of growth factors and hormones, they develop into committed cells of either the erythroid or myeloid lineages. These committed cells underwent efficient terminal differentiation when they were treated with the relevant lineage-specific growth\/differentiation factors, but underwent apoptosis when exposed to the incorrect factors for the respective lineage. While the committed cells coexpress marker proteins from different lineages, expression of the 'wrong' lineage marker is repressed during terminal differentiation. Our results indicate that a combination of v-Ski and activated c-Kit induces long-term self renewal in primary multipotent progenitors, which can be induced to commit and differentiate along specific lineages under different, defined conditions. Our data also suggest that growth factors and steroid hormones control terminal differentiation by a combined induction of commitment, growth and apoptosis, a process likely to be affected in stem cell leukemias.","authors":"Beug, H., Dahl, R., Steinlein, P., Meyer, S., Deiner, EM., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Oncogene","volume":"11","issue":"1","page":"59-72","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1995-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34711951","title":"AKIRIN2 controls the nuclear import of proteasomes in vertebrates.","abstract":"Protein expression and turnover are controlled through a complex interplay of transcriptional, post-transcriptional and post-translational mechanisms to enable spatial and temporal regulation of cellular processes. To systematically elucidate such gene regulatory networks, we developed a CRISPR screening assay based on time-controlled Cas9 mutagenesis, intracellular immunostaining and fluorescence-activated cell sorting that enables the identification of regulatory factors independent of their effects on cellular fitness. We pioneered this approach by systematically probing the regulation of the transcription factor MYC, a master regulator of cell growth<sup>1-3<\/sup>. Our screens uncover a highly conserved protein, AKIRIN2, that is essentially required for nuclear protein degradation. We found that AKIRIN2 forms homodimers that directly bind to fully assembled 20S proteasomes to mediate their nuclear import. During mitosis, proteasomes are excluded from condensing chromatin and re-imported into newly formed daughter nuclei in a highly dynamic, AKIRIN2-dependent process. Cells undergoing mitosis in the absence of AKIRIN2 become devoid of nuclear proteasomes, rapidly causing accumulation of MYC and other nuclear proteins. Collectively, our study reveals a dedicated pathway controlling the nuclear import of proteasomes in vertebrates and establishes a scalable approach to decipher regulators in essential cellular processes.","authors":"de Almeida, M., Hinterndorfer, M., Brunner, H., Grishkovskaya, I., Singh, K., Schleiffer, A., Jude, J., Deswal, S., Kalis, R., Vunjak, M., Lendl, T., Imre, R., Roitinger, E., Neumann, T., Kandolf, S., Schutzbier, M., Mechtler, K., Versteeg, GA., Haselbach, D., Zuber, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature","volume":"599","issue":"7885","page":"491-496","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1310933","title":"Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein.","abstract":"Repression of transcription from densely methylated genes can be mediated by the methyl-CpG binding protein MeCP-1 (Boyes and Bird, 1991). Here we have investigated the effect of methylation on genes with a low density of methyl-CpG. We found that sparse methylation could repress transfected genes completely, but the inhibition was fully overcome by the presence in cis of an SV40 enhancer. Densely methylated genes, however, could not be reactivated by the enhancer. In vitro studies showed that the sparsely methylated genes bound weakly to MeCP-1 and that binding interfered with transcription. In the absence of available MeCP-1, methylation had minimal effects on transcription. From these and other results we propose that sparsely methylated genes form an unstable complex with MeCP-1 which prevents transcription when the promoter is weak. This complex can be disrupted by a strong promoter, thereby allowing the methylated gene to be transcribed.","authors":"Boyes, J., Bird, A.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"EMBO J","volume":"11","issue":"1","page":"327-33","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1992-03-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1340117","title":"Transferrinfection: a highly efficient way to express gene constructs in eukaryotic cells.","abstract":null,"authors":"Zatloukal, K., Wagner, E., Cotten, M., Phillips, S., Plank, C., Steinlein, P., Curiel, DT., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Ann N Y Acad Sci","volume":"660","issue":null,"page":"136-53","pdf":null,"JrId":"611","fulltextlink":null,"preprintlink":null,"articledate":"1993-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1316144","title":"Expression of human foamy virus is differentially regulated during development in transgenic mice.","abstract":"The human foamy virus (HFV) is a recently characterized member of the spumavirus family. Although no diseases have been unequivocally associated with HFV infection, expression of HFV regulatory genes in transgenic mice induces a characteristic acute neurodegenerative disease and a myopathy. To better characterize the sequence of events leading to disease, and to gain a better understanding of the underlying pathogenetic mechanisms, we have analyzed in detail the transgene expression pattern during development. Transcription of a construct containing all regulatory elements and ancillary genes of HFV was analyzed by in situ hybridization and was shown to occur in two distinct phases. At midgestation, low but widespread expression was first detected in cells of extraembryonic tissues. Later, various tissues originating from embryonic mesoderm, neuroectoderm, and neural crest transcribed the transgene at moderate levels. However, expression decreased dramatically during late gestation and was suppressed shortly after birth. After a latency period of up to 5 weeks, transcription of the transgene resumed in single cells distributed irregularly in the central nervous system and in the skeletal muscle. By the age of 8 weeks, an increasing number of cells displayed much higher expression levels than in embryonic life and eventually underwent severe degenerative changes. These findings demonstrate that HFV transgene expression is differentially regulated in development and that HFV cytotoxicity may be dose-dependent. Such biphasic pattern of expression differs from that of murine retroviruses and may be explained by the specificity of HFV regulatory elements in combination with cellular factors. Future studies of this model system should, therefore, provide novel insights in the mechanisms controlling retroviral latency.","authors":"Aguzzi, A., Bothe, K., Anhauser, I., Horak, I., Rethwilm, A., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"New Biol","volume":"4","issue":"3","page":"225-37","pdf":null,"JrId":"1880","fulltextlink":null,"preprintlink":null,"articledate":"1992-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34652942","title":"miR-1 sustains muscle physiology by controlling V-ATPase complex assembly.","abstract":"[Figure: see text].","authors":"Guti\u00e9rrez-P\u00e9rez, P., Santill\u00e1n, EM., Lendl, T., Wang, J., Schrempf, A., Steinacker, TL., Asparuhova, M., Brandstetter, M., Haselbach, D., Cochella, L.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Sci Adv","volume":"7","issue":"42","page":"eabh1434","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"499384","title":"5-methylcytosine content of DNA during differentiation in mouse teratocarcinoma cells.","abstract":null,"authors":"Fabricant, JD., Wagner, EF., Auer, B., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Exp Cell Res","volume":"124","issue":"1","page":"25-9","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1980-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1297653","title":"SWI6 is a regulatory subunit of two different cell cycle START-dependent transcription factors in Saccharomyces cerevisiae.","abstract":"Most genes involved in DNA replication in the yeast Saccharomyces cerevisiae are transcribed transiently during late G1 as cells undergo START. Their promoters all contain one or more versions of an 8-base pair motif (ACGCGTNA) called the MluI cell cycle box (MCB). MCBs have been shown to be both necessary and sufficient for the late G1-specific transcription of the TMP1 thymidylate synthase and POLI DNA polymerase genes. A different late G1-specific transcription element called the SCB (CACGAAAA) is bound by a factor containing the SWI4 and SWI6 proteins. We describe here the formation in vitro of complexes on TMP1 MCBs that contain the SWI6 protein and, we suggest, a 120 kDa protein that is distinct from SWI4. Transcription due to SCBs and MCBs occurs in the absence of SWI6 but it is no longer correctly cell cycle regulated. We suggest that SWI6 is an essential regulatory subunit of two different START-dependent transcription factors. One factor (SBF) contains SWI4 and binds to SCBs whereas the other (MBF) contains p120 and binds MCBs.","authors":"Moll, T., Dirick, L., Auer, H., Bonkovsky, J., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"J Cell Sci Suppl","volume":"16","issue":null,"page":"87-96","pdf":null,"JrId":"4591","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"493132","title":"A regulatory sequence near the 3' end of sea urchin histone genes.","abstract":"The 3' flanking sequences of all five histone genes have been sequenced in the histone DNA clone h19 of the sea urchin Psammechinus miliaris. A large (23 bp) and a small (10 bp) conserved sequence was found by sequence comparison, some 29-40 bp downstream from the termination codon. 12 bases of the larger homology block show a dyad symmetry. The available sequences of clone h22 of the same species and those of the histone clones pSp2 and pSp17 of Strongylocentrotus purpuratus, another sea urchin species, fit well into this comparison. Two types of sequences are involved in the dyad symmetry; one is H1, H3 and H4 specific, the other is H2A and H2B specific. If these conserved sequences are transcribed, a hairpin loop could form in the RNA molecules. This secondary structure might serve as a recognition signal for a regulatory protein.","authors":"Busslinger, M., Portmann, R., Birnsteil, ML.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Nucleic Acids Res","volume":"6","issue":"9","page":"2997-3008","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1979-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1297649","title":"cis and trans regulation of tissue-specific transcription.","abstract":"Analysis of both the cis-regulatory sequences which control globin gene switching as well as the trans-acting factors which bind to these sequences to elicit a differential, developmentally regulated response has lent insight into the general mechanisms responsible for tissue-specific gene regulation. We show here that the chicken adult beta-globin gene promoter sequences are intimately involved in competitive interaction with the beta\/epsilon-globin enhancer to regulate differentially epsilon- versus beta-globin gene transcription. Secondly, we show that the family of GATA transcription factors directs gene regulation in a variety of discrete cell types, and describe potential cellular target genes for each member of the GATA factor family, as well as potential mechanisms whereby multiple GATA factors expressed in a single cell might be used to elicit differential transcriptional activities.","authors":"Engel, JD., Beug, H., LaVail, JH., Zenke, MW., Mayo, K., Leonard, MW., Foley, KP., Yang, Z., Kornhauser, JM., Ko, LJ.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"J Cell Sci Suppl","volume":"16","issue":null,"page":"21-31","pdf":null,"JrId":"4591","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2824281","title":"Reversibility of differentiation and proliferative capacity in avian myelomonocytic cells transformed by tsE26 leukemia virus.","abstract":"Chicken hematopoietic cells infected with E26 leukemia virus can be transformed into growth factor-dependent, rapidly proliferating cells that exhibit properties of immature myelomonocytic cells. Cells infected with a mutant of E26 that carries a temperature-sensitive lesion, presumably residing in the myb oncogene, differentiate into resting, macrophage-like cells when shifted from 37 degrees to 42 degrees C (Beug et al. 1984). Here we show that differentiated tsE26 cells gradually reacquire an immature phenotype and proliferative capacity when shifted back to 37 degrees C, provided that they are kept at 42 degrees C no longer than 4-8 days. We also show that DNA synthesis inhibitors do not prevent terminal differentiation at 42 degrees C but inhibit the complete reexpression of the immature phenotype in downshift experiments. Our results suggest that the reactivation of the E26 protein function can both induce a \"retro-differentiation\" and cell proliferation in myelomonocytic target cells.","authors":"Beug, H., Blundell, PA., Graf, T.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Genes Dev","volume":"1","issue":"3","page":"277-86","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1988-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"319341","title":"Development of E.coli virus T1: the pattern of gene expression.","abstract":"T1 infected bacteria exhibit a distinct pattern of gene expression. The control of this expression is accessible to biochemical analysis. T1 induces the synthesis of 31 proteins in E. coli. The virion contains 15 proteins. By means of T1 amber mutants, 10 gene products have been assigned to specific T1 genes. Three classes of T1 proteins are defined by the kinetics of their syntheses: early, early-late and late proteins. The regulation of protein synthesis involes at least three mechanisms: for cessation of host gene expression, for discontinuation of the early class during the late phase and for induction of the late T1 proteins. The positive control of late gene expression is not coupled to replication. The host RNA-polymerase transcribes the viral genome throughout the infectious cycle. No virus coded RNA-polymerase is induced.","authors":"Wagner, EF., Ponta, H., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1977","journaltitle":"Mol Gen Genet","volume":"150","issue":"1","page":"21-8","pdf":null,"JrId":"5910","fulltextlink":null,"preprintlink":null,"articledate":"1977-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34562374","title":"Structure of the peripheral arm of a minimalistic respiratory complex I.","abstract":"Respiratory complex I drives proton translocation across energy-transducing membranes by NADH oxidation coupled with (ubi)quinone reduction. In humans, its dysfunction is associated with neurodegenerative diseases. The Escherichia coli complex represents the structural minimal form of an energy-converting NADH:ubiquinone oxidoreductase. Here, we report the structure of the peripheral arm of the E.\u00a0coli complex I consisting of six subunits, the FMN cofactor, and nine iron-sulfur clusters at 2.7\u00a0\u00c5 resolution obtained by cryo electron microscopy. While the cofactors are in equivalent positions as in the complex from other species, individual subunits are adapted to the absence of supernumerary proteins to guarantee structural stability. The catalytically important subunits NuoC and D are fused resulting in a specific architecture of functional importance. Striking features of the E.\u00a0coli complex are scrutinized by mutagenesis and biochemical characterization of the variants. Moreover, the arrangement of the subunits sheds light on the unknown assembly of the complex.","authors":"Schimpf, J., Oppermann, S., Gerasimova, T., Santos Seica, AF., Hellwig, P., Grishkovskaya, I., Wohlwend, D., Haselbach, D., Friedrich, T.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Structure","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7578427","title":"On the biological role of the nuclear polymerizing NAD+: protein(ADP-ribosyl) transferase (ADPRT): ADPRT from Dictyostelium discoideum and inactivation of the ADPRT gene in the mouse.","abstract":"Two approaches have been used to elucidate the role of the nuclear polymerizing NAD+:protein(ADP-ribosyl)-transferase (ADPRT): i) comparison of the primary structure of Dictyostelium discoideum ADPRT derived from a 2 kb, partial cDNA sequence with the mammalian, fish, amphibian and insect counterparts revealed an overall homology of 25%. Whereas the automodification domain was not conserved at all, the NAD+ binding domain (aa 859-908) showed more than 70% identical amino acids in all species. Together with the similar enzymatic properties of the ADPRTs the genetic conservation underlined the notion that ADPRT plays a major role in various cellular processes; and ii) inactivation of the ADPRT gene in murine embryonic stem cells by homologous recombination led to mouse strains with a complete lack of nuclear poly(ADP-ribosyl)ation. These ADPRT mutant mice were viable and fertile indicating that ADPRT is dispensable in mouse development. Moreover, repair of UV and MNNG induced DNA damage was not affected in ADPRT\/3T3 like fibroblasts, as measured by reactivation of in vitro damaged reporter plasmids and unscheduled DNA synthesis. However, about 30% of the ADPRT mutant mice developed pathological skin aberrations on a mixed 129\/Sv x C57B1\/6 genetic background. These mice will be extremely useful to define the precise biological role of poly(ADP-ribosyl)ation.","authors":"Auer, B., Flick, K., Wang, ZQ., Haidacher, D., J\u00e4ger, S., Berghammer, H., Kofler, B., Schweiger, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Biochimie","volume":"77","issue":"6","page":"444-9","pdf":null,"JrId":"1043","fulltextlink":null,"preprintlink":null,"articledate":"1995-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9224716","title":"Genetic analysis reveals that PAX6 is required for normal transcription of pancreatic hormone genes and islet development.","abstract":"We present genetic and biochemical evidence that PAX6 is a key regulator of pancreatic islet hormone gene transcription and is required for normal islet development. In embryos homozygous for a mutant allele of the Pax6 gene, Small eye (Sey(Neu)), the numbers of all four types of endocrine cells in the pancreas are decreased significantly, and islet morphology is abnormal. In the remaining islet cells, hormone production, particularly glucagon production, is markedly reduced because of decreased gene transcription. These effects appear to result from a lack of PAX6 protein in the mutant embryos. Biochemical studies identify wild-type PAX6 protein as the transcription factor that binds to a common element in the glucagon, insulin, and somatostatin promoters, and show that PAX6 transactivates the glucagon and insulin promoters.","authors":"Sander, M., Neub\u00fcser, A., Kalamaras, J., Ee, HC., Martin, GR., German, MS.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Genes Dev","volume":"11","issue":"13","page":"1662-73","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1997-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"390303","title":"Radiation sensitivity of messenger RNA.","abstract":"Messenger RNA function is inactivated by irradiation with ultraviolet light. A unit length mRNA (in bases) is 2-3 times more sensitive than a unit length of DNA (in base pairs) with respect to the inactivation of template function. These data stem from four experimental systems all of which do not repair DNA: the translation of E. coli mRNA in rifampicin-treated cells, of T7 mRNA in infected E. coli, of f2 phage RNA in vivo, and of stable mRNA in chromosomeless minicells. The comparison of relative sensitivities to UV is relevant to the technique of UV mapping of transcription units which enjoys increasing popularity in pro- and eukaryotic genetic research.","authors":"Ponta, H., Pfennig-Yeh, ML., Wagner, EF., Schweiger, M., Herrlich, P.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Mol Gen Genet","volume":"175","issue":"1","page":"13-7","pdf":null,"JrId":"5910","fulltextlink":null,"preprintlink":null,"articledate":"1980-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"376871","title":"Development of Escherichia coli virus T1: escape from host restriction.","abstract":"The bacterial virus T1 grows interchangeably on different Escherichia coli strains (C, B, and K). This implies that T1 has an efficient mechanism to overcome the host restriction barrier. The DNA of T1 was found to be methylated independently of the hosts. The percentage of N6-methyladenine varied from 1.6 to 1.8, and the 5-methylcytosine content varied from 0.1 to 0.4%. In contrast, the range in percentage of N6-methyladenine and 5-methylcytosine found in the hosts was 0.7 to 2.4 and 0.0 to 1.1, respectively.","authors":"Wagner, EF., Auer, B., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"J Virol","volume":"29","issue":"3","page":"1229-31","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1979-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"215208","title":"Avian leukemia viruses: interaction with their target cells in vivo and in vitro.","abstract":null,"authors":"Graf, T., Beug, H.","publication_status":"ppublish","journalpubyear":"1978","journaltitle":"Biochim Biophys Acta","volume":"516","issue":"3","page":"269-99","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1979-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34817859","title":"Targeting CD56 with an antibody-drug conjugate in Merkel cell carcinoma.","abstract":null,"authors":"Leiendecker, L., Jung, PS., Obenauf, AC.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Br J Dermatol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"202847","title":"Tumor specificity of acute avian leukemia viruses reflected by their transformation target cell specificity in vitro.","abstract":null,"authors":"Graf, T., Royer-Pokora, B., Meyer-Glauner, W., Beug, H.","publication_status":"ppublish","journalpubyear":"1977","journaltitle":"Med Microbiol Immunol","volume":"164","issue":"1-3","page":"139-53","pdf":null,"JrId":"5638","fulltextlink":null,"preprintlink":null,"articledate":"1978-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7566172","title":"Asymmetric segregation of Numb and Prospero during cell division.","abstract":"A cell can divide asymmetrically by specifically segregating a determinant into one of its daughter cells. The Numb protein is a candidate for such a determinant in the asymmetric cell divisions of the developing Drosophila nervous system. Numb is a membrane-associated protein that localizes asymmetrically during cell division and segregates into one daughter cell, where it is required for the specification of the correct cell fate. Here we show that a nuclear protein, Prospero, translocates to the membrane at the beginning of cell division and colocalizes with Numb throughout mitosis, suggesting a common mechanism for asymmetric segregation. Numb and Prospero localization is coupled to mitosis and tightly correlated with the position of one of the two centrosomes. In contrast to centrosome positioning, however, Numb and Prospero localization is independent of microtubules. Cytochalasin D treatment suggests that the process is also independent of actin. We propose that there is an organizer of asymmetric cell division which provides positional information for both the orientation of the mitotic spindle and asymmetric localization of Numb and Prospero.","authors":"Knoblich, JA., Jan, LY., Jan, YN.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Nature","volume":"377","issue":"6550","page":"624-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1995-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18724273","title":"PR-SET7 and SUV4-20H regulate H4 lysine-20 methylation at imprinting control regions in the mouse.","abstract":"Imprinted genes are important in development and their allelic expression is mediated by imprinting control regions (ICRs). On their DNA-methylated allele, ICRs are marked by trimethylation at H3 Lys 9 (H3K9me3) and H4 Lys 20 (H4K20me3), similar to pericentric heterochromatin. Here, we investigate which histone methyltransferases control this methylation of histone at ICRs. We found that inactivation of SUV4-20H leads to the loss of H4K20me3 and increased levels of its substrate, H4K20me1. H4K20me1 is controlled by PR-SET7 and is detected on both parental alleles. The disruption of SUV4-20H or PR-SET7 does not affect methylation of DNA at ICRs but influences precipitation of H3K9me3, which is suggestive of a trans-histone change. Unlike at pericentric heterochromatin, however, H3K9me3 at ICRs does not depend on SUV39H. Our data show not only new similarities but also differences between ICRs and heterochromatin, both of which show constitutive maintenance of methylation of DNA in somatic cells.","authors":"Pannetier, M., Julien, E., Schotta, G., Tardat, M., Sardet, C., Jenuwein, T., Feil, R.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO Rep","volume":"9","issue":"10","page":"998-1005","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25146755","title":"A video protocol of retroviral infection in primary intestinal organoid culture.","abstract":"Lgr5-positive stem cells can be supplemented with the essential growth factors Egf, Noggin, and R-Spondin, which allows us to culture ever-expanding primary 3D epithelial structures in vitro. Both the architecture and physiological properties of these 'mini-guts', also called organoids, closely resemble their in vivo counterparts. This makes them an attractive model system for the small intestinal epithelium. Using retroviral transduction, functional genetics can now be performed by conditional gene overexpression or knockdown. This video demonstrates the procedure of organoid culture, the generation of retroviruses, and the retroviral transduction of organoids to assist phenotypic analysis of the small intestinal epithelium in vitro. This novel organotypic model system in combination with retroviral mediated gene expression provides a valuable tool for rapid analysis of gene function in vitro without the need of costly and time-consuming generation for transgenic animals.","authors":"Andersson-Rolf, A., Fink, J., Mustata, RC., Koo, BK.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"J Vis Exp","volume":null,"issue":"90","page":"e51765","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18694996","title":"Stat5 regulates cellular iron uptake of erythroid cells via IRP-2 and TfR-1.","abstract":"Erythropoiesis strictly depends on signal transduction through the erythropoietin receptor (EpoR)-Janus kinase 2 (Jak2)-signal transducer and activator of transcription 5 (Stat5) axis, regulating proliferation, differentiation, and survival. The exact role of the transcription factor Stat5 in erythropoiesis remained puzzling, however, since the first Stat5-deficient mice carried a hypomorphic Stat5 allele, impeding full phenotypical analysis. Using mice completely lacking Stat5--displaying early lethality--we demonstrate that these animals suffer from microcytic anemia due to reduced expression of the antiapoptotic proteins Bcl-x(L) and Mcl-1 followed by enhanced apoptosis. Moreover, transferrin receptor-1 (TfR-1) cell surface levels on erythroid cells were decreased more than 2-fold on erythroid cells of Stat5(-\/-) animals. This reduction could be attributed to reduced transcription of TfR-1 mRNA and iron regulatory protein 2 (IRP-2), the major translational regulator of TfR-1 mRNA stability in erythroid cells. Both genes were demonstrated to be direct transcriptional targets of Stat5. This establishes an unexpected mechanistic link between EpoR\/Jak\/Stat signaling and iron metabolism, processes absolutely essential for erythropoiesis and life.","authors":"Kerenyi, MA., Grebien, F., Gehart, H., Schifrer, M., Artaker, M., Kovacic, B., Beug, H., Moriggl, R., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Blood","volume":"112","issue":"9","page":"3878-88","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18157137","title":"GraFix: sample preparation for single-particle electron cryomicroscopy.","abstract":"We developed a method, named GraFix, that considerably improves sample quality for structure determination by single-particle electron cryomicroscopy (cryo-EM). GraFix uses a glycerol gradient centrifugation step in which the complexes are centrifuged into an increasing concentration of a chemical fixation reagent to prevent aggregation and to stabilize individual macromolecules. The method can be used to prepare samples for negative-stain, cryo-negative-stain and, particularly, unstained cryo-EM.","authors":"Kastner, B., Fischer, N., Golas, MM., Sander, B., Dube, P., Boehringer, D., Hartmuth, K., Deckert, J., Hauer, F., Wolf, E., Uchtenhagen, H., Urlaub, H., Herzog, F., Peters, JM., Poerschke, D., L\u00fchrmann, R., Stark, H.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Methods","volume":"5","issue":"1","page":"53-5","pdf":null,"JrId":"32338","fulltextlink":null,"preprintlink":null,"articledate":"2008-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"187337","title":"Oncornavirus-induced sarcoma formation obscured by rapid development of lethal leukemia.","abstract":"Injection i.v. of avian erythroblastosis virus (AEV) strain ES4 causes a high incidence of leukemia and the death of most of the inoculated chicks within 2 weeks. As found earlier, the virus is defective for replication and transforms bone marrow cultures in vitro, and surprisingly, also chick embryo fibroblasts. Inoculation of transformed AEV cells negative for virus production into newborn chicks induced the formation of sarcomas only, whereas cells superinfected with helper virus induced the formation of erythroblastosis in addition to sarcomas. The helper virus alone caused neither sarcomas nor erythroblastosis during the experimental period. These findings were explained by the hypothesis that AEV-induced erythroblastosis develops more rapidly than do AEV-induced sarcomas and that animals receiving i.v. injections die of the leukemia before sarcomas become detectable. The observation that animals receiving i.m. injections of AEV developed sarcomas at the site of injection strongly supports this concept. Most of the animals that received i.m. injections also developed an erythroblastosis that was delayed, however, in comparison to the animals receiving i.v. injections. Our data also suggest that the erythroblastosis induced by AEV does not suppress the formation of sarcomas in the same animal.","authors":"Graf, T., Fink, D., Beug, H., Royer-Pokora, B.","publication_status":"ppublish","journalpubyear":"1977","journaltitle":"Cancer Res","volume":"37","issue":"1","page":"59-63","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"1977-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7525597","title":"Degeneration of neural cells in the central nervous system of mice deficient in the gene for the adhesion molecule on Glia, the beta 2 subunit of murine Na,K-ATPase.","abstract":"We generated mice, null mutant in the adhesion molecule on glia (AMOG), the beta 2 subunit of the murine Na,K-ATPase gene. These mice exhibit motor incoordination at 15 d of age, subsequently tremor and paralysis of extremities, and die at 17-18 d after birth. At these ages, the mutants have enlarged ventricles, degenerating photoreceptor cells, and swelling and degeneration of astrocytic endfeet, leading to vacuoles adjoining capillaries of brain stem, thalamus, striatum, and spinal cord. In tissue homogenates from entire brains of 16-17-d-old mutants, Na,K-ATPase activity and expression of the beta 1 subunit of the Na,K-ATPase and of the neural adhesion molecules L1, N-CAM, and MAG appear normal. We suggest that the mutant phenotype can be related primarily to reduced pump activity, with neural degeneration as a possible consequence of osmotic imbalance.","authors":"Magyar, JP., Bartsch, U., Wang, ZQ., Howells, N., Aguzzi, A., Wagner, EF., Schachner, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"J Cell Biol","volume":"127","issue":"3","page":"835-45","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1994-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18660448","title":"Angiotensin converting enzyme-2 confers endothelial protection and attenuates atherosclerosis.","abstract":"The endothelium plays a central role in the maintenance of vascular homeostasis. One of the main effectors of endothelial dysfunction is ANG II, and pharmacological approaches to limit ANG II bioactivity remain the cornerstone of cardiovascular therapeutics. Angiotensin converting enzyme-2 (ACE2) has been identified as a critical negative modulator of ANG II bioactivity, counterbalancing the effects of ACE in determining net tissue ANG II levels; however, the role of ACE2 in the vasculature remains unknown. In the present study, we hypothesized that ACE2 is a novel target to limit endothelial dysfunction and atherosclerosis. To this aim, we performed in vitro gain and loss of function experiments in endothelial cells and evaluated in vivo angiogenesis and atherosclerosis in apolipoprotein E-knockout mice treated with AdACE2. ACE2-deficient mice exhibited impaired endothelium-dependent relaxation. Overexpression of ACE2 in human endothelial cells stimulated endothelial cell migration and tube formation, and limited monocyte and cellular adhesion molecule expression; effects that were reversed in ACE2 gene silenced and endothelial cells isolated from ACE2-deficient animals. ACE2 attenuated ANG II-induced reactive oxygen species production in part through decreasing the expression of p22phox. The effects of ACE2 on endothelial activation were attenuated by pharmacological blockade of ANG-(1-7) with A779. ACE2 promoted capillary formation and neovessel maturation in vivo and reduced atherosclerosis in apolipoprotein E-knockout mice These data indicate that ACE2, in an ANG-(1-7)-dependent fashion, functions to improve endothelial homeostasis via a mechanism that may involve attenuation of NADPHox-induced reactive oxygen species production. ACE2-based treatment approaches may be a novel approach to limit aberrant vascular responses and atherothrombosis.","authors":"Lovren, F., Pan, Y., Quan, A., Teoh, H., Wang, G., Shukla, PC., Levitt, KS., Oudit, GY., Al-Omran, M., Stewart, DJ., Slutsky, AS., Peterson, MD., Backx, PH., Penninger, JM., Verma, S.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Am J Physiol Heart Circ Physiol","volume":"295","issue":"4","page":"H1377-84","pdf":null,"JrId":"21619","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7491774","title":"The adenovirus protease is required for virus entry into host cells.","abstract":"We have analyzed the mechanisms used by adenovirus to gain entry into the host cell. Using both virus infection and the ability of adenovirus particles to enhance polylysine\/DNA uptake as a measure of virus entry, we have demonstrated that the adenovirus-encoded 23K protease is required for two functions in the infection process. A proteolytic processing of the capsid is required to generate a virus capsid that can increase membrane interactions at pH 5. We have found that forms of adenovirus capsid that have not undergone the processing reactions (immature capsids) are deficient in their ability to disrupt membranes at pH 5 and are unable to enhance the entry of polylysine\/DNA complexes. A second role of the protease was revealed by experiments using inhibitors of the protease. Mature virus capsids lose their ability to enhance gene delivery and become noninfectious after exposure to inhibitors of the protease (1 microM N-ethylmaleimide, 100-300 microM copper chloride, 1 microM MDL28170, or anti-protease antiserum), suggesting that the viral protease activity is required during the cellular entry process.","authors":"Cotten, M., Weber, JM.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Virology","volume":"213","issue":"2","page":"494-502","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1996-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34521022","title":"The cellular and signaling dynamics of salamander limb regeneration.","abstract":"Limb amputation in salamanders yields a wound response that ultimately leads to replacement of the missing part. This unique-among-tetrapod trait involves the migration and recruitment of multiple cell types including epithelium, immune cells, axonal growth cones, and connective tissue cells to build the blastema which contains the proliferating stem and progenitor cells to rebuild the limb tissues. A number of the signaling and cell biological events have been defined. They point to the intimate coordination of physical events such as osmotic pressure, cell migration, and cell-cell communication with changes in cell identity such as dedifferentiation into embryonic-like epithelial and mesenchymal cells.","authors":"Bassat, E., Tanaka, EM.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Curr Opin Cell Biol","volume":"73","issue":null,"page":"117-123","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-3","title":"Biomolecular Mechanisms with Computational Biology","abstract":null,"authors":"Eisenhaber F.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"","volume":null,"issue":null,"page":null,"pdf":null,"JrId":"21933","fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-140","title":"Using MATLAB to Achieve Nanoscale Optical Sectioning in the Vicinity of Metamaterial Substrates by Simulating Emitter-Substrate Interactions","abstract":null,"authors":"Elsayad, K., Suplata, M., Heinze, KG.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Engineering Education and Research Using MATLAB","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":"http:\/\/www.intechopen.com\/articles\/show\/title\/using-matlab-to-achieve-nanoscale-optical-sectioning-in-the-vicinity-of-metamaterial-substrates-by-s","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24204693","title":"Generation of BAC transgenic epithelial organoids.","abstract":"Under previously developed culture conditions, mouse and human intestinal epithelia can be cultured and expanded over long periods. These so-called organoids recapitulate the three-dimensional architecture of the gut epithelium, and consist of all major intestinal cell types. One key advantage of these ex vivo cultures is their accessibility to live imaging. So far the establishment of transgenic fluorescent reporter organoids has required the generation of transgenic mice, a laborious and time-consuming process, which cannot be extended to human cultures. Here we present a transfection protocol that enables the generation of recombinant mouse and human reporter organoids using BAC (bacterial artificial chromosome) technology.","authors":"Schwank, G., Andersson-Rolf, A., Koo, BK., Sasaki, N., Clevers, H.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"PLoS One","volume":"8","issue":"10","page":"e76871","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18775482","title":"High efficiency transformation of Tetrahymena using a codon-optimized neomycin resistance gene.","abstract":"Tetrahymena thermophila is a useful model for the study of eukaryotic biology. A neomycin resistance gene (neo) has been developed that was optimized for the codon usage of T. thermophila. Using this codon-optimized neo gene (neoTet), a new drug resistance marker cassette, neo4, has been constructed. The neo4 cassette resulted in about ten times more drug resistant transformants than a cassette containing the non-codon-optimized original neo gene. The new cassette enables transgenic Tetrahymena strains to be created with high efficiency. This study also emphasizes the importance of codon optimization in transgene expression in Tetrahymena.","authors":"Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Gene","volume":"425","issue":"1-2","page":"79-83","pdf":null,"JrId":"3886","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18216279","title":"Disruption of c-Jun reduces cellular migration and invasion through inhibition of c-Src and hyperactivation of ROCK II kinase.","abstract":"The spread of metastatic tumors to different organs is associated with poor prognosis. The metastatic process requires migration and cellular invasion. The protooncogene c-jun encodes the founding member of the activator protein-1 family and is required for cellular proliferation and DNA synthesis in response to oncogenic signals and plays an essential role in chemical carcinogenesis. The role of c-Jun in cellular invasion remains to be defined. Genetic deletion of c-Jun in transgenic mice is embryonic lethal; therefore, transgenic mice encoding a c-Jun gene flanked by LoxP sites (c-jun(f\/f)) were used. c-jun gene deletion reduced c-Src expression, hyperactivated ROCK II signaling, and reduced cellular polarity, migration, and invasiveness. c-Jun increased c-Src mRNA abundance and c-Src promoter activity involving an AP-1 site in the c-Src promoter. Transduction of c-jun(-\/-) cells with either c-Jun or c-Src retroviral expression systems restored the defective cellular migration of c-jun(-\/-) cells. As c-Src is a critical component of pathways regulating proliferation, survival, and metastasis, the induction of c-Src abundance, by c-Jun, provides a novel mechanism of cooperative signaling in cellular invasion.","authors":"Jiao, X., Katiyar, S., Liu, M., Mueller, SC., Lisanti, MP., Li, A., Pestell, TG., Wu, K., Ju, X., Li, Z., Wagner, EF., Takeya, T., Wang, C., Pestell, RG.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Mol Biol Cell","volume":"19","issue":"4","page":"1378-90","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17989365","title":"Identification of an axonal kinesin-3 motor for fast anterograde vesicle transport that facilitates retrograde transport of neuropeptides.","abstract":"A screen for genes required in Drosophila eye development identified an UNC-104\/Kif1 related kinesin-3 microtubule motor. Analysis of mutants suggested that Drosophila Unc-104 has neuronal functions that are distinct from those of the classic anterograde axonal motor, kinesin-1. In particular, unc-104 mutations did not cause the distal paralysis and focal axonal swellings characteristic of kinesin-1 (Khc) mutations. However, like Khc mutations, unc-104 mutations caused motoneuron terminal atrophy. The distributions and transport behaviors of green fluorescent protein-tagged organelles in motor axons indicate that Unc-104 is a major contributor to the anterograde fast transport of neuropeptide-filled vesicles, that it also contributes to anterograde transport of synaptotagmin-bearing vesicles, and that it contributes little or nothing to anterograde transport of mitochondria, which are transported primarily by Khc. Remarkably, unc-104 mutations inhibited retrograde runs by neurosecretory vesicles but not by the other two organelles. This suggests that Unc-104, a member of an anterograde kinesin subfamily, contributes to an organelle-specific dynein-driven retrograde transport mechanism.","authors":"Barkus, RV., Klyachko, O., Horiuchi, D., Dickson, BJ., Saxton, WM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Mol Biol Cell","volume":"19","issue":"1","page":"274-83","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17957136","title":"p38alpha: a suppressor of cell proliferation and tumorigenesis.","abstract":"The mitogen-activated protein kinase (MAPK) p38alpha is involved in numerous biological processes and is a drug target for inflammation-associated diseases. Genetic analysis in mice demonstrated that fetuses lacking p38alpha are embryonic lethal owing to impaired placental development. The function of p38alpha in mice after birth remained unclear until conditional alleles of p38alpha were used. It was found that p38alpha is essential for lung function in both neonatal and adult mice. Increased proliferation and impaired differentiation are the hallmarks of p38alpha-deficient cells. Moreover, mice deficient in p38alpha are prone to cancer development using carcinogen or oncogene-induced cancer models. p38alpha can suppress cell proliferation by antagonizing the JNK\/c-Jun pathway, which is an important regulator of proliferation and apoptosis. These findings suggest that therapeutic inhibition of p38 might lead to unwanted proliferation. Therefore, a combined inhibition of p38 and other pathways, such as the JNK pathway, should be considered for targeting cancer inflammation.","authors":"Hui, L., Bakiri, L., Stepniak, E., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell Cycle","volume":"6","issue":"20","page":"2429-33","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2008-10-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18923426","title":"Clustering of VASP actively drives processive, WH2 domain-mediated actin filament elongation.","abstract":"Vasodilator-stimulated phosphoprotein (VASP) is a key regulator of dynamic actin structures like filopodia and lamellipodia, but its precise function in their formation is controversial. Using in vitro TIRF microscopy, we show for the first time that both human and Dictyostelium VASP are directly involved in accelerating filament elongation by delivering monomeric actin to the growing barbed end. In solution, DdVASP markedly accelerated actin filament elongation in a concentration-dependent manner but was inhibited by low concentrations of capping protein (CP). In striking contrast, VASP clustered on functionalized beads switched to processive filament elongation that became insensitive even to very high concentrations of CP. Supplemented with the in vivo analysis of VASP mutants and an EM structure of the protein, we propose a mechanism by which membrane-associated VASP oligomers use their WH2 domains to effect both the tethering of actin filaments and their processive elongation in sites of active actin assembly.","authors":"Breitsprecher, D., Kiesewetter, AK., Linkner, J., Urbanke, C., Resch, GP., Small, JV., Faix, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO J","volume":"27","issue":"22","page":"2943-54","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"66","title":"Partial purification and properties of a phenobarbital-induced aldehyde dehydrogenase of rat liver.","abstract":"Properties of the phenobarbital induced cytoplasmic aldehyde dehydrogenase (EC 1.2.1.3) have been studied in rat liver. 7-12-Fold higher levels were seen in the cytoplasmic activities after phenobarbital treatment in reactor compared to non-reactor animals with high concentrations of acetaldehyde (18 mM) and propionaldehyde (9 mM). No difference was found with 0.12 mM acetaldehyde, 2 mM glycolaldehyde, 6 mM formaldehyde or 0.5 mM betaine aldehyde. The reactor group also had slightly higher activity in the mitochondrial fraction with the high acetaldehyde and propionaldehyde concentrations. In the microsomal fraction, the activities showed no differences at any substrate concentration. An induced aldehyde dehydrogenase was purified 70-fold by chromatographic techniques. It had different molecular and enzymic properties than the main high-Km enzyme normally present in rat liver cytoplasm. The pI of the induced enzyme was about 7.0 as measured by isoelectric focusing. It was active with several aliphatic and aromatic aldehydes but not with formaldehyde, glycolaldehyde or D-glyceraldehyde. The Km-values for propionaldehyde and acetaldehyde were in the millimolar range. Millimolar concentrations of aromatic aldehydes caused a strong substrate inhibition. The enzyme was inhibited by submicromolar concentrations of disulfiram. Estrone, deoxycorticosterone, progesterone and diethylstilbestrol also affected the enzyme activity.","authors":"Koivula, T., Koivusalo, M.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"1-11","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8831789","title":"Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A.","abstract":"Cystathionine beta-lyase (CBL) is a member of the gamma-family of PLP-dependent enzymes, that cleaves C beta-S bonds of a broad variety of substrates. The crystal structure of CBL from E. coli has been solved using MIR phases in combination with density modification. The structure has been refined to an R-factor of 15.2% at 1.83 A resolution using synchroton radiation diffraction data. The asymmetric unit of the crystal cell (space group C222(1)) contains two monomers related by 2-fold symmetry. A homotetramer with 222 symmetry is built up by crystallographic and non-crystallographic symmetry. Each monomer of CBL can be described in terms of three spatially and functionally different domains. The N-terminal domain (residues 1 to 60) consists of three alpha-helices and one beta-strand. It contributes to tetramer formation and is part of the active site of the adjacent subunit. The second domain (residues 61 to 256) harbors PLP and has an alpha\/beta-structure with a seven-stranded beta-sheet as the central part. The remaining C-terminal domain (residues 257 to 395), connected by a long alpha-helix to the PLP-binding domain, consists of four helices packed on the solvent-accessible side of an antiparallel four-stranded beta-sheet. The fold of the C-terminal and the PLP-binding domain and the location of the active site are similar to aminotransferases. Most of the residues in the active site are strongly conserved among the enzymes of the transsulfuration pathway. Additionally, CBL is homologous to the mal gamma gene product indicating an evolutionary relationship between alpha and gamma-family of PLP-dependent enzymes. The structure of the beta, beta, beta-trifluoroalanine inactivated CBL has been refined at 2.3 A resolution to an R-factor of 16.2%. It suggests that Lys210, the PLP-binding residue, mediates the proton transfer between C alpha and S gamma.","authors":"Clausen, T., Huber, R., Laber, B., Pohlenz, HD., Messerschmidt, A.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"J Mol Biol","volume":"262","issue":"2","page":"202-24","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1996-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18812090","title":"SHOC1, an XPF endonuclease-related protein, is essential for the formation of class I meiotic crossovers.","abstract":"Crossovers (COs) are essential for the completion of meiosis in most species and lead to new allelic combinations in gametes. Two pathways of meiotic crossover formation have been distinguished. Class I COs, which are the major class of CO in budding yeast, mammals, Caenorhabditis elegans, and Arabidopsis, depend on a group of proteins called ZMM and rely on specific DNA structure intermediates that are processed to form COs. We identified a novel gene, SHOC1, involved in meiosis in Arabidopsis. Shoc1 mutants showed a striking reduction in the number of COs produced, a similar phenotype to the previously described Arabidopsis zmm mutants. The early steps of recombination, revealed by DMC1 foci, and completion of synapsis are not affected in shoc1 mutants. Double mutant analysis showed that SHOC1 acts in the same pathway as AtMSH5, a conserved member of the ZMM group. SHOC1 is thus a novel gene required for class I CO formation in Arabidopsis. Sequence similarity studies detected putative SHOC1 homologs in a large range of eukaryotes including human. SHOC1 appears to be related to the XPF endonuclease protein family, which suggests that it is directly involved in the maturation of DNA intermediates that lead to COs.","authors":"Macaisne, N., Novatchkova, M., Peirera, L., Vezon, D., Jolivet, S., Froger, N., Chelysheva, L., Grelon, M., Mercier, R.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Biol","volume":"18","issue":"18","page":"1432-7","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34426690","title":"Regulatory T cells function in established systemic inflammation and reverse fatal autoimmunity.","abstract":"The immunosuppressive function of regulatory T (T<sub>reg<\/sub>) cells is dependent on continuous expression of the transcription factor Foxp3. Foxp3 loss of function or induced ablation of T<sub>reg<\/sub> cells results in a fatal autoimmune disease featuring all known types of inflammatory responses with every manifestation stemming from T<sub>reg<\/sub> cell paucity, highlighting a vital function of T<sub>reg<\/sub> cells in preventing fatal autoimmune inflammation. However, a major question remains whether T<sub>reg<\/sub> cells can persist and effectively exert their function in a disease state, where a broad spectrum of inflammatory mediators can either inactivate T<sub>reg<\/sub> cells or render innate and adaptive pro-inflammatory effector cells insensitive to suppression. By reinstating Foxp3 protein expression and suppressor function in cells expressing a reversible Foxp3 null allele in severely diseased mice, we found that the resulting single pool of rescued T<sub>reg<\/sub> cells normalized immune activation, quelled severe tissue inflammation, reversed fatal autoimmune disease and provided long-term protection against them. Thus, T<sub>reg<\/sub> cells are functional in settings of established broad-spectrum systemic inflammation and are capable of affording sustained reset of immune homeostasis.","authors":"Hu, W., Wang, ZM., Feng, Y., Schizas, M., Hoyos, BE., van der Veeken, J., Verter, JG., Bou-Puerto, R., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Immunol","volume":"22","issue":"9","page":"1163-1174","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18989380","title":"Proliferation of human HCC cells and chemically induced mouse liver cancers requires JNK1-dependent p21 downregulation.","abstract":"JNK proteins have been shown to be involved in liver carcinogenesis in mice, but the extent of their involvement in the development of human liver cancers is unknown. Here, we show that activation of JNK1 but not JNK2 was increased in human primary hepatocellular carcinomas (HCCs). Further, JNK1 was required for human HCC cell proliferation in vitro and tumorigenesis after xenotransplantation. Importantly, mice lacking JNK1 displayed decreased tumor cell proliferation in a mouse model of liver carcinogenesis and decreased hepatocyte proliferation in a mouse model of liver regeneration. In both cases, impaired proliferation was caused by increased expression of p21, a cell-cycle inhibitor, and reduced expression of c-Myc, a negative regulator of p21. Genetic inactivation of p21 in JNK1(-\/-) mice restored hepatocyte proliferation in models of both liver carcinogenesis and liver regeneration, and overexpression of c-Myc increased proliferation of JNK1(-\/-) liver cells. Similarly, JNK1 was found to control the proliferation of human HCC cells by affecting p21 and c-Myc expression. Pharmacologic inhibition of JNK reduced the growth of both xenografted human HCC cells and chemically induced mouse liver cancers. These findings provide a mechanistic link between JNK activity and liver cell proliferation via p21 and c-Myc and suggest JNK targeting can be considered as a new therapeutic approach for HCC treatment.","authors":"Hui, L., Zatloukal, K., Scheuch, H., Stepniak, E., Wagner, EF.","publication_status":"aheadofprint","journalpubyear":"2008","journaltitle":"J Clin Invest","volume":null,"issue":null,"page":null,"pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18799149","title":"The tumor necrosis factor family receptors RANK and CD40 cooperatively establish the thymic medullary microenvironment and self-tolerance.","abstract":"Medullary thymic epithelial cells (mTECs) establish T cell self-tolerance through the expression of autoimmune regulator (Aire) and peripheral tissue-specific self-antigens. However, signals underlying mTEC development remain largely unclear. Here, we demonstrate crucial regulation of mTEC development by receptor activator of NF-kappaB (RANK) and CD40 signals. Whereas only RANK signaling was essential for mTEC development during embryogenesis, in postnatal mice, cooperation between CD40 and RANK signals was required for mTEC development to successfully establish the medullary microenvironment. Ligation of RANK or CD40 on fetal thymic stroma in vitro induced mTEC development in a tumor necrosis factor-associated factor 6 (TRAF6)-, NF-kappaB inducing kinase (NIK)-, and IkappaB kinase beta (IKKbeta)-dependent manner. These results show that developmental-stage-dependent cooperation between RANK and CD40 promotes mTEC development, thereby establishing self-tolerance.","authors":"Akiyama, T., Shimo, Y., Yanai, H., Qin, J., Ohshima, D., Maruyama, Y., Asaumi, Y., Kitazawa, J., Takayanagi, H., Penninger, JM., Matsumoto, M., Nitta, T., Takahama, Y., Inoue, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Immunity","volume":"29","issue":"3","page":"423-37","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2008-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6580963","title":"Prenatal lethalities in mice homozygous for human growth hormone gene sequences integrated in the germ line.","abstract":"The mutagenic potential of recombinant DNA in the germ line was investigated in the descendants of mice obtained from eggs injected with the human growth-hormone gene in a pBR322 vector. Six positive animals (including one mosaic) were produced and had 1-20 copies of the donor sequences in unique and often complex integration patterns indicative of a single or an interrupted insertion. All were heterozygotes and transmitted the foreign insert to their progeny, forming six new HUGH strains. Matings between heterozygotes yielded viable healthy homozygotes in four of the strains. However, in the HUGH\/3 and HUGH\/4 strains, no postnatal homozygotes were found and litter sizes at birth were small. These two independent cases of mutation, both homozygous recessive prenatal lethals, are attributable to disruption of native sequences by alien ones. They constitute the first instances of insertional mutagenesis due to integration of recombinant DNA in the germ line of the mouse. The mutants provide new possibilities for molecular identification of gene functions necessary for normal development.","authors":"Wagner, EF., Covarrubias, L., Stewart, TA., Mintz, B.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Cell","volume":"35","issue":"3 Pt 2","page":"647-55","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1984-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11933019","title":"Transferrin\/transferrin receptor-mediated drug delivery.","abstract":"Since transferrin was discovered more than half a century ago, a considerable effort has been made towards understanding tranferrin-mediated iron uptake. However, it was not until recently with the identification and characterization of several new genes related to iron homeostasis, such as the hemochromatosis protein HFE and the iron transporter DMT1, that our knowledge has been advanced dramatically. A major pathway for cellular iron uptake is through internalization of the complex of iron-bound transferrin and the transferrin receptor, which is negatively modulated by HFE, a protein related to hereditary hemochromatosis. Iron is released from transferrin as the result of the acidic pH in endosome and then is transported to the cytosol by DMT1. The iron is then utilized as a cofactor by heme and ribonucleotide reductase or stored in ferritin. Apart from iron, many other metal ions of therapeutic and diagnostic interests can also bind to transferrin at the iron sites and their transferrin complexes can be recognized by many cells. Therefore, transferrin has been thought as a \"delivery system\" for many beneficial and harmful metal ions into the cells. Transferrin has also be widely applied as a targeting ligand in the active targeting of anticancer agents, proteins, and genes to primary proliferating malignant cells that overexpress transferrin receptors. This is achieved by conjugation of transferrin with drugs, proteins, hybride systems with marcomolecules and as liposomal-coated systems. Conjugates of anticancer drugs with transferrin can significantly improve the selectivity and toxicity and overcome drug resistance, thereby leading to a better treatment. The coupling of DNA to transferrin via a polycation such as polylysine or via cationic liposomes can target and transfer of the extrogenous DNA particularly into proliferating cells through receptor-mediated endocytosis. These kinds of non-viral vectors are potential alternatives to viral vectors for gene therapy, if the transfection efficiency can be improved. Moreover, transferrin receptors have shown potentials in delivery of therapeutic drugs or genes into the brain across blood-brain barrier.","authors":"Li, H., Qian, ZM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Med Res Rev","volume":"22","issue":"3","page":"225-50","pdf":null,"JrId":"5606","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23028068","title":"Preparation of small RNA libraries for high-throughput sequencing.","abstract":"This protocol details the process of small RNA cloning for sequencing on the Illumina\/Solexa sequencing platform, but it can be easily modified for use on other next-generation platforms (e.g., SOLiD, 454). This procedure is designed to clone canonical small RNA molecules with 5'-monophosphate and 3'-hydroxyl termini. Modifications, such as the presence of a 2'-O-methyl group, can reduce efficiency, although not sufficiently to negate the utility of the approach. Other termini modifications, such as a 5' triphosphate or a 3' phosphate, can be altered by enzymatic treatment before cloning.","authors":"Malone, C., Brennecke, J., Czech, B., Aravin, A., Hannon, GJ.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Cold Spring Harb Protoc","volume":"2012","issue":"10","page":"1067-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22813735","title":"The Drosophila female aphrodisiac pheromone activates ppk23(+) sensory neurons to elicit male courtship behavior.","abstract":"Females of many animal species emit chemical signals that attract and arouse males for mating. For example, the major aphrodisiac pheromone of Drosophila melanogaster females, 7,11-heptacosadiene (7,11-HD), is a potent inducer of male-specific courtship and copulatory behaviors. Here, we demonstrate that a set of gustatory sensory neurons on the male foreleg, defined by expression of the ppk23 marker, respond to 7,11-HD. Activity of these neurons is required for males to robustly court females or to court males perfumed with 7,11-HD. Artificial activation of these ppk23(+) neurons stimulates male-male courtship even without 7,11-HD perfuming. These data identify the ppk23(+) sensory neurons as the primary targets for female sex pheromones in Drosophila.","authors":"Toda, H., Zhao, X., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Rep","volume":"1","issue":"6","page":"599-607","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6297784","title":"Transforming capacities of avian erythroblastosis virus mutants deleted in the erbA or erbB oncogenes.","abstract":"Mutants of avian erythroblastosis virus (AEV) were constructed by deleting large nucleotide segments in each of the viral oncogenes termed v-erbA and v-erbB. Mutants in erbA (erbA -B +) retained the ability to transform fibroblasts in vitro, and these cells exhibited most of the transformation characteristics that typify wild-type AEV-transformed fibroblasts. In addition, the mutants induced small erythroid colonies upon infection of bone marrow cells in culture. Chickens inoculated with erbA -B + virus or with erbA -B +-transformed cells developed sarcomas or atypical erythroid leukemias. The erythroid cells transformed in vivo or in vitro by the erbA -B + viruses appeared not to be as tightly blocked in differentiation as wild-type transformed cells. In contrast, fibroblasts infected with the erbA +B - mutant resembled normal cells in all transformation parameters tested, and no bone marrow cell transformation was observed with the mutant. The results indicate that the main transforming properties of AEV are encoded in erbB and that its effects are enhanced by erbA.","authors":"Frykberg, L., Palmieri, S., Beug, H., Graf, T., Hayman, MJ., Vennstr\u00f6m, B.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Cell","volume":"32","issue":"1","page":"227-38","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1983-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6293903","title":"Expression of embryonic haemoglobin in tsAEV-transformed embryonic erythroid cells during temperature-induced differentiation.","abstract":"Cells prepared from 1-day-old chick blastoderms were infected with a temperature-sensitive mutant of avian erythroblastosis virus (tsAEV). Clonal strains of transformed erythroblasts were isolated from the infected blastoderm cells. By shift to the nonpermissive temperature, these cells could be induced to differentiate into erythrocyte-like cells which expressed embryonic haemoglobins. Embryonic haemoglobins could not be detected in tsAEV-transformed erythroblasts from adult bone marrow when induced to differentiate under the same conditions. In contrast to normal primitive erythrocytes, tsAEV-infected embryonic erythroblasts differentiated in vitro expressed also adult haemoglobin. These results suggest an influence of the haematopoietic environment on the switch from embryonic to adult erythrocytes.","authors":"Freudenstein, C., Beug, H., Palmieri, S., Graf, T.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Differentiation","volume":"22","issue":"3","page":"231-4","pdf":null,"JrId":"3402","fulltextlink":null,"preprintlink":null,"articledate":"1983-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6274754","title":"Characterization of the hematopoietic target cells of defective avian leukemia viruses by velocity sedimentation and density gradient centrifugation analyses.","abstract":null,"authors":"Graf, T., Royer-Pokora, B., Korzeniewska, E., Grieser, S., Beug, H.","publication_status":"ppublish","journalpubyear":"1981","journaltitle":"Haematol Blood Transfus","volume":"26","issue":null,"page":"417-23","pdf":null,"JrId":"30276","fulltextlink":null,"preprintlink":null,"articledate":"1982-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19269368","title":"The TRIM-NHL protein TRIM32 activates microRNAs and prevents self-renewal in mouse neural progenitors.","abstract":"In the mouse neocortex, neural progenitor cells generate both differentiating neurons and daughter cells that maintain progenitor fate. Here, we show that the TRIM-NHL protein TRIM32 regulates protein degradation and microRNA activity to control the balance between those two daughter cell types. In both horizontally and vertically dividing progenitors, TRIM32 becomes polarized in mitosis and is concentrated in one of the two daughter cells. TRIM32 overexpression induces neuronal differentiation while inhibition of TRIM32 causes both daughter cells to retain progenitor cell fate. TRIM32 ubiquitinates and degrades the transcription factor c-Myc but also binds Argonaute-1 and thereby increases the activity of specific microRNAs. We show that Let-7 is one of the TRIM32 targets and is required and sufficient for neuronal differentiation. TRIM32 is the mouse ortholog of Drosophila Brat and Mei-P26 and might be part of a protein family that regulates the balance between differentiation and proliferation in stem cell lineages.","authors":"Schwamborn, JC., Berezikov, E., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"136","issue":"5","page":"913-25","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6256754","title":"Mutant of avian erythroblastosis virus defective for erythroblast transformation: deletion in the erb portion of p75 suggests function of the protein in leukemogenesis.","abstract":"Previous studies have shown that td359 AEV, a mutant of avian erythroblastosis virus (AEV), is unable to transform erythroblasts in vitro or in vivo but is capable of transforming fibroblasts in vitro and of causing sarcomas in chicks. In this paper we show that the mutant synthesizes a gag-gene related protein (delta p75) which is about 1000 daltons smaller than the protein, p75, induced by wild-type AEV. The mutant protein lacks 3 of the approximately 53 lysine-arginine tryptic peptides resolved in p75 and also contains an additional peptide. By cleavage of delta p75 with p15 protease and analysis of the fragments for size and peptide composition, the deletion in delta p75 could be located in the non-gag region of the molecule. In contrast, with p40 AEV, a second AEV-specific protein synthesized in in vitro translation experiments, there is no change in size of translation products obtained from td359 AEV RNA. Our data provide direct evidence that p75 is required for erythroblast transformation.","authors":"Beug, H., Kitchener, G., Doederlein, G., Graf, T., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"Proc Natl Acad Sci U S A","volume":"77","issue":"11","page":"6683-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1981-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22535953","title":"Human high temperature requirement serine protease A1 (HTRA1) degrades tau protein aggregates.","abstract":"Protective proteases are key elements of protein quality control pathways that are up-regulated, for example, under various protein folding stresses. These proteases are employed to prevent the accumulation and aggregation of misfolded proteins that can impose severe damage to cells. The high temperature requirement A (HtrA) family of serine proteases has evolved to perform important aspects of ATP-independent protein quality control. So far, however, no HtrA protease is known that degrades protein aggregates. We show here that human HTRA1 degrades aggregated and fibrillar tau, a protein that is critically involved in various neurological disorders. Neuronal cells and patient brains accumulate less tau, neurofibrillary tangles, and neuritic plaques, respectively, when HTRA1 is expressed at elevated levels. Furthermore, HTRA1 mRNA and HTRA1 activity are up-regulated in response to elevated tau concentrations. These data suggest that HTRA1 is performing regulated proteolysis during protein quality control, the implications of which are discussed.","authors":"Tennstaedt, A., P\u00f6psel, S., Truebestein, L., Hauske, P., Brockmann, A., Schmidt, N., Irle, I., Sacca, B., Niemeyer, CM., Brandt, R., Ksiezak-Reding, H., Tirniceriu, AL., Egensperger, R., Baldi, A., Dehmelt, L., Kaiser, M., Huber, R., Clausen, T., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Biol Chem","volume":"287","issue":"25","page":"20931-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6244556","title":"Target cell specificity of defective avian leukemia viruses: hematopoietic target cells for a given virus type can be infected but not transformed by strains of a different type.","abstract":"Defective avian leukemia viruses of the avian erythroblastosis (AEV), avian myelocytomatosis (MC29), and avian myeloblastosis (AMV) type induce the proliferation of leukemic cells with properties of erythroblasts, macrophages, and myeloblasts, respectively. Their target cells can be separated and have properties of cells of the erythroid (AEV) and myeloid lineage (MC29 and AMV), respectively. In the present study we have shown that this target cell specificity is not due to the ability of the different strains to infect only certain types of hematopoietic cells. Instead, AEV was found to replicate in macrophages and to induce the expression of p75 AEV, its presumptive transforming protein. Likewise, MC29 was found to replicate in AEV-infected erythroblasts as well as in AMV-infected myeloblasts and to express the p110 MC29 protein in these cells. Superinfection with MC29 or AMV of ts34 AEV-infected erythroblasts did not impair their capacity to accumulate hemoglobin after shift to nonpermissive temperature. Our results support a model in which the transforming proteins of AEV, MC29, and MAV block the differentiation of their target cells by competitively inhibiting the action of a hypothetical homologous cellular differentiation protein synthesized in the corresponding target cells only.","authors":"Graf, T., Beug, H., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"Proc Natl Acad Sci U S A","volume":"77","issue":"1","page":"389-93","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1980-05-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6190135","title":"The sequence GGCmCGG is resistant to MspI cleavage.","abstract":"MspI essentially fails to cut the sequence GGCmCGG at enzyme concentrations which give total digestion of CCGG, CmCGG and GGCCGG sites. This result explains why certain sites in mammalian DNA are resistant to both MspI and HpaII and shows that this results from an idiosynchracy of MspI rather than a novel form of DNA methylation at this site in mammalian cells.","authors":"Busslinger, M., deBoer, E., Wright, S., Grosveld, FG., Flavell, RA.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Nucleic Acids Res","volume":"11","issue":"11","page":"3559-69","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1983-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6151703","title":"Gene transfer into the germ line of mice and into embryonal carcinoma stem cells.","abstract":"Recombinant genes can be introduced into the germ line of mice by microinjection into the fertilized egg or via embryonal carcinoma stem cells. A regulated, cell-type specific expression of the newly introduced gene following microinjection is usually not found. However, in one series of experiments the insertion of human growth hormone genes in the germ line led to prenatal recessive lethal mutations. Alternatively, embryonal carcinoma stem cells can be used to introduce and express genes in mice, for example after infection with selectable retroviral vectors. In addition, these cells are useful for differentiation studies in vitro following DNA-mediated gene transfer.","authors":"Wagner, EF.","publication_status":"ppublish","journalpubyear":"1984","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"307","issue":"1132","page":"313-7","pdf":null,"JrId":"8277","fulltextlink":null,"preprintlink":null,"articledate":"1985-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8507400","title":"CD4, CD8 and tyrosine kinases in thymic selection.","abstract":"Analysis of T-cell development in transgenic and gene-deficient mice suggests that the co-receptor function of CD8 is essential for positive selection. Recent data also demonstrate that the requirement for CD4 and CD8 in negative selection of T cells is not absolute and may be regulated by T-cell receptor affinity for the deleting ligand, an interpretation consistent with the affinity model of thymic selection. In addition to its association with CD4 and CD8, it appears that p56lck is also important during the early stages of thymic development.","authors":"Wallace, VA., Penninger, J., Mak, TW.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Curr Opin Immunol","volume":"5","issue":"2","page":"235-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1993-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9950424","title":"OPGL is a key regulator of osteoclastogenesis, lymphocyte development and lymph-node organogenesis.","abstract":"The tumour-necrosis-factor-family molecule osteoprotegerin ligand (OPGL; also known as TRANCE, RANKL and ODF) has been identified as a potential osteoclast differentiation factor and regulator of interactions between T cells and dendritic cells in vitro. Mice with a disrupted opgl gene show severe osteopetrosis and a defect in tooth eruption, and completely lack osteoclasts as a result of an inability of osteoblasts to support osteoclastogenesis. Although dendritic cells appear normal, opgl-deficient mice exhibit defects in early differentiation of T and B lymphocytes. Surprisingly, opgl-deficient mice lack all lymph nodes but have normal splenic structure and Peyer's patches. Thus OPGL is a new regulator of lymph-node organogenesis and lymphocyte development and is an essential osteoclast differentiation factor in vivo.","authors":"Kong, YY., Yoshida, H., Sarosi, I., Tan, HL., Timms, E., Capparelli, C., Morony, S., Oliveira-dos-Santos, AJ., Van, G., Itie, A., Khoo, W., Wakeham, A., Dunstan, CR., Lacey, DL., Mak, TW., Boyle, WJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nature","volume":"397","issue":"6717","page":"315-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19295516","title":"Directional Delta and Notch trafficking in Sara endosomes during asymmetric cell division.","abstract":"Endocytosis has a crucial role during Notch signalling after the asymmetric division of fly sensory organ precursors (SOPs): directional signalling is mediated by differential endocytosis of the ligand Delta and the Notch effector Sanpodo in one of the SOP daughters, pIIb. Here we show a new mechanism of directional signalling on the basis of the trafficking of Delta and Notch molecules already internalized in the SOP and subsequently targeted to the other daughter cell, pIIa. Internalized Delta and Notch traffic to an endosome marked by the protein Sara. During SOP mitosis, Sara endosomes containing Notch and Delta move to the central spindle and then to pIIa. Subsequently, in pIIa (but not in pIIb) Notch appears cleaved in Sara endosomes in a gamma-secretase- and Delta internalization-dependent manner, indicating that the release of the intracellular Notch tail to activate Notch target genes has occurred. We thus uncover a new mechanism to bias signalling even before asymmetric endocytosis of Sanpodo and Delta takes place in the daughter cells: already during SOP mitosis, asymmetric targeting of Delta and Notch-containing Sara endosomes will increase Notch signalling in pIIa and decrease it in pIIb.","authors":"Coumailleau, F., F\u00fcrthauer, M., Knoblich, JA., Gonz\u00e1lez-Gait\u00e1n, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nature","volume":"458","issue":"7241","page":"1051-5","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34778127","title":"Results of WICOVIR Gargle Pool PCR Testing in German Schools Based on the First 100,000 Tests.","abstract":"<b>Background:<\/b> Opening schools and keeping children safe from SARS-CoV-2 infections at the same time is urgently needed to protect children from direct and indirect consequences of the COVID-19 pandemic. To achieve this goal, a safe, efficient, and cost-effective SARS-CoV-2 testing system for schools in addition to standard hygiene measures is necessary. <b>Methods:<\/b> We implemented the screening WICOVIR concept for schools in the southeast of Germany, which is based on gargling at home, pooling of samples in schools, and assessment of SARS-CoV-2 by pool rRT-PCR, performed decentralized in numerous participating laboratories. Depooling was performed if pools were positive, and results were transmitted with software specifically developed for the project within a day. Here, we report the results after the first 13 weeks in the project. <b>Findings:<\/b> We developed and implemented the proof-of-concept test system within a pilot phase of 7 weeks based on almost 17,000 participants. After 6 weeks in the main phase of the project, we performed &gt;100,000 tests in total, analyzed in 7,896 pools, identifying 19 cases in &gt;100 participating schools. On average, positive children showed an individual CT value of 31 when identified in the pools. Up to 30 samples were pooled (mean 13) in general, based on school classes and attached school staff. All three participating laboratories detected positive samples reliably with their previously established rRT-PCR standard protocols. When self-administered antigen tests were performed concomitantly in positive cases, only one of these eight tests was positive, and when antigen tests performed after positive pool rRT-PCR results were already known were included, 3 out of 11 truly positive tests were also identified by antigen testing. After 3 weeks of repetitive WICOVIR testing twice weekly, the detection rate of positive children in that cohort decreased significantly from 0.042 to 0.012 (<i>p<\/i> = 0.008). <b>Interpretation:<\/b> Repeated gargle pool rRT-PCR testing can be implemented quickly in schools. It is an effective, valid, and well-received test system for schools, superior to antigen tests in sensitivity, acceptance, and costs.","authors":"Kheiroddin, P., Sch\u00f6berl, P., Althammer, M., Cibali, E., W\u00fcrfel, T., Wein, H., Kulawik, B., Buntrock-D\u00f6pke, H., Weigl, E., Gran, S., Gr\u00fcndl, M., Langguth, J., Lampl, B., Judex, G., Niggel, J., Pagel, P., Schratzenstaller, T., Schneider-Brachert, W., Gastiger, S., Bodenschatz, M., Konrad, M., Levchuk, A., Roth, C., Sch\u00f6ner, D., Schneebauer, F., Rohrmanstorfer, R., Dekens, MP., Brandstetter, S., Zuber, J., Wallerstorfer, D., Burkovski, A., Ambrosch, A., Wagner, T., Kabesch, M.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Front Pediatr","volume":"9","issue":null,"page":"721518","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21914793","title":"Keeping the soma free of transposons: programmed DNA elimination in ciliates.","abstract":"Many transposon-related sequences are removed from the somatic macronucleus of ciliates during sexual reproduction. In the ciliate Tetrahymena, an RNAi-related mechanism produces small noncoding RNAs that induce heterochromatin formation, which is followed by DNA elimination. Because RNAi-related mechanisms repress transposon activities in a variety of eukaryotes, the DNA elimination mechanism of ciliates might have evolved from these types of transposon-silencing mechanisms. Nuclear dimorphism allows ciliates to identify any DNA that has invaded the germ-line micronucleus using small RNAs and a whole genome comparison of the micronucleus and the somatic macronucleus.","authors":"Schoeberl, UE., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Biol Chem","volume":"286","issue":"43","page":"37045-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18789384","title":"Identification of the human homolog of the imprinted mouse Air non-coding RNA.","abstract":"Genomic imprinting is widely conserved amongst placental mammals. Imprinted expression of IGF2R, however, differs between mice and humans. In mice, Igf2r imprinted expression is seen in all fetal and adult tissues. In humans, adult tissues lack IGF2R imprinted expression, but it is found in fetal tissues and Wilms' tumors where it is polymorphic and only seen in a small proportion of tested samples. Mouse Igf2r imprinted expression is controlled by the Air (Airn) ncRNA whose promoter lies in an intronic maternally-methylated CpG island. The human IGF2R gene carries a homologous intronic maternally-methylated CpG island of unknown function. Here, we use transfection and transgenic studies to show that the human IGF2R intronic CpG island is a ncRNA promoter. We also identify the same ncRNA at the endogenous human locus in 16-40% of Wilms' tumors. Thus, the human IGF2R gene shows evolutionary conservation of key features that control imprinted expression in the mouse.","authors":"Yotova, IY., Vlatkovic, IM., Pauler, FM., Warczok, KE., Ambros, PF., Oshimura, M., Theussl, HC., Gessler, M., Wagner, EF., Barlow, DP.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genomics","volume":"92","issue":"6","page":"464-73","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19363474","title":"Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi.","abstract":"Genome-wide RNA interference (RNAi) screens have identified near-complete sets of genes involved in cellular processes. However, this methodology has not yet been used to study complex developmental processes in a tissue-specific manner. Here we report the use of a library of Drosophila strains expressing inducible hairpin RNAi constructs to study the Notch signalling pathway during external sensory organ development. We assigned putative loss-of-function phenotypes to 21.2% of the protein-coding Drosophila genes. Using secondary assays, we identified 6 new genes involved in asymmetric cell division and 23 novel genes regulating the Notch signalling pathway. By integrating our phenotypic results with protein interaction data, we constructed a genome-wide, functionally validated interaction network governing Notch signalling and asymmetric cell division. We used clustering algorithms to identify nuclear import pathways and the COP9 signallosome as Notch regulators. Our results show that complex developmental processes can be analysed on a genome-wide level and provide a unique resource for functional annotation of the Drosophila genome.","authors":"Mummery-Widmer, JL., Yamazaki, M., Stoeger, T., Novatchkova, M., Bhalerao, S., Chen, D., Dietzl, G., Dickson, BJ., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nature","volume":"458","issue":"7241","page":"987-92","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26453572","title":"The quest for mammalian Polycomb response elements: are we there yet?","abstract":"A long-standing mystery in the field of Polycomb and Trithorax regulation is how these proteins, which are highly conserved between flies and mammals, can regulate several hundred equally highly conserved target genes, but recognise these targets via cis-regulatory elements that appear to show no conservation in their DNA sequence. These elements, termed Polycomb\/Trithorax response elements (PRE\/TREs or PREs), are relatively well characterised in flies, but their mammalian counterparts have proved to be extremely difficult to identify. Recent progress in this endeavour has generated a wealth of data and raised several intriguing questions. Here, we ask why and to what extent mammalian PREs are so different to those of the fly. We review recent advances, evaluate current models and identify open questions in the quest for mammalian PREs.","authors":"Bauer, M., Trupke, J., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Chromosoma","volume":"125","issue":"3","page":"471-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19029837","title":"Experimental testing of predicted myristoylation targets involved in asymmetric cell division and calcium-dependent signalling.","abstract":"Evolutionary conservation of N-terminal N-myristoylation within protein families indicates significant functional impact of this lipid posttranslational modification for function. In the MYRbase study (Maurer-Stroh et al., (2004) Genome Biology 5, R21), protein families with relevance to asymmetric cell division in animals and the group of plant calcium-dependent protein kinases (CPKs) have surfaced with many predicted myristoylated members. Here, we describe experimental in vitro verification of predicted myristoylation and explore its impact on subcellular localization for these targets in vivo. Our results confirm that, indeed, Numb isoform A, Neuralized isoforms C and D from Drosophila melanogaster and two Neuralized-like homologues from Mus musculus have the capability for N-terminal myristoylation in vitro and in vivo (in fly tissue and in mouse 3T3 cells respectively) whereas other isoforms such as Neuralized A and B have not. The latter two cases are an examples of different potential of various isoforms for posttranslational modifications. Additionally, the Arabidopsis thaliana CDPKs CPK6, CPK9 and CPK13 are shown to be substrates for myristoylation in vitro, which also affects their subcellular localization (in Arabidopsis protoplasts and tobacco leaves). At the same time, CPK6 and CPK13 do not appear to be substrates of a NMT1-like enzyme; the reasons for differing substrate specificities of NMT homologues in plants are derived from the evolutionary divergence of their N-myristoyl transferase sequences. As a methodical advance, we describe a fast and very sensitive technique (compared to traditional autoradiography) for in vitro testing of myristoylation based on thin layer chromatography read-out of the incorporated radioactive myristoyl anchor with subsequent Western blotting detection for protein yield determination using the same membrane.","authors":"Benetka, W., Mehlmer, N., Maurer-Stroh, S., Sammer, M., Koranda, M., Neum\u00fcller, R., Betschinger, J., Knoblich, JA., Teige, M., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell Cycle","volume":"7","issue":"23","page":"3709-19","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6084590","title":"The cDNA sequences of the sea urchin U7 small nuclear RNA suggest specific contacts between histone mRNA precursor and U7 RNA during RNA processing.","abstract":"3' Processing of sea urchin H3 histone pre-mRNA depends on a small nuclear RNP which contains an RNA of nominally 60 nucleotide length, referred to below as U7 RNA. The U7 RNA can be enriched by precipitation of sea urchin U-snRNPs with human systematic lupus erythematosus antiserum of the Sm serotype. We have prepared cDNA clones of U7 RNA and determined by hybridization techniques that this RNA is present in sea urchin eggs at 30-fold lower molar concentration than U1 RNA. The RNA sequences derived from an analysis of eight U7 cDNA clones show neither homologies nor complementarities to any other know U-RNAs. The 3' portion of the presumptive RNA sequence can be folded into a stem-loop structure. The 5'-terminal sequences would be largely unstructured as free RNA. Their most striking feature is their base complementarity to the 3' conserved sequences of histone pre-mRNAs. Six out of nine bases of the conserved CAAGAAAGA sequence of the histone mRNA precursor and 13 out of 16 nucleotides from the conserved palindrome can be base paired with presumptive U7 RNA sequence, suggesting a unique hybrid structure for a processing intermediate formed from histone precursor and U7 RNA.","authors":"Strub, K., Galli, G., Busslinger, M., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1984","journaltitle":"EMBO J","volume":"3","issue":"12","page":"2801-7","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1985-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"180670","title":"A novel type of cellular variant with altered expression of virus-induced cell transformation.","abstract":null,"authors":"Graf, T., Beug, H.","publication_status":"ppublish","journalpubyear":"1976","journaltitle":"Virology","volume":"72","issue":"1","page":"283-6","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1976-09-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8096184","title":"In situ analyses of in ovo graft-vs.-host reaction induced by thymic nurse cell lymphocytes.","abstract":"In both mammalian and avian systems, thymic nurse cells (TNC) have been shown to harbor a heterogeneous population of T lymphocytes (TNC-L) some of which exhibit a postselectional phenotype. By transplanting micromanipulated single chicken TNC onto the chorionallantoic membrane (CAM) of major histocompatibility complex (MHC)-disparate embryos, an experimental system which allows for the detection of lymphocytes with graft-vs.-host (GVH) reactivity, we demonstrate here that TNC enclose lymphocytes that can develop into both CD4+ single-positive (sp) and CD8+ sp, T cell receptor (TcR) alpha beta+, or TcR gamma delta+ cells. This finding was additionally confirmed by serial transfer of primary expanded alloreactive T cells onto the CAM of secondary hosts. All donor TNC-L expressed MHC class II molecules and the interleukin-2 receptor alpha chain in primary and secondary GVH reactions. Furthermore, we observed selective accumulation of CD8+ and TcR gamma delta+ host lymphocytes in the CAM upon the induction of a local GVH reaction, most probably as a consequence of the pathological alteration of the epithelium.","authors":"Rieker, T., Penninger, J., Hala, K., Cooper, MD., Wick, G.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Eur J Immunol","volume":"23","issue":"4","page":"904-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1993-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19276654","title":"Non-coding RNA: a bridge between small RNA and DNA.","abstract":"Small RNAs are not only involved in post-transcriptional gene silencing in the cytoplasm, but also modulate activities of the nuclear genome. Although silencing of mRNAs involves RNA-RNA base-pairing, it remains unclear whether the RNAi machinery responsible for chromatin or DNA modification interacts with DNA or RNA. The identification of an RNA helicase required for chromatin-Argonaute protein interaction as well as the presence of Argonaute-associated long non-coding transcripts in Tetrahymena suggest the presence of RNA-RNA interactions prior to small RNA-induced heterochromatin formation in ciliates.","authors":"Kurth, HM., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"RNA Biol","volume":"6","issue":"2","page":"138-40","pdf":null,"JrId":"32563","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36272088","title":"Baculovirus Production and Infection in Axolotls.","abstract":"Salamanders have served as an excellent model for developmental and tissue regeneration studies. While transgenic approaches are available for various salamander species, their long generation time and expensive maintenance have driven the development of alternative gene delivery methods for functional studies. We have previously developed pseudotyped baculovirus (BV) as a tool for gene delivery in the axolotl (Oliveira et al. Dev Biol 433(2):262-275, 2018). Since its initial conception, we have refined our protocol of BV production and usage in salamander models. In this chapter, we describe a detailed and versatile protocol for BV-mediated transduction in urodeles.","authors":"Murawala, P., Oliveira, CR., Okulski, H., Yun, MH., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Methods Mol Biol","volume":"2562","issue":null,"page":"369-387","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19247375","title":"miR-29a suppresses tristetraprolin, which is a regulator of epithelial polarity and metastasis.","abstract":"Several microRNAs (miRNAs) have recently been described as crucial regulators of epithelial-to-mesenchymal transition (EMT) and metastasis. By comparing the expression profiles of miRNAs, we found upregulation of miR-29a in mesenchymal, metastatic RasXT cells relative to epithelial EpRas cells. Overexpression of miR-29a suppressed the expression of tristetraprolin (TTP), a protein involved in the degradation of messenger RNAs with AU-rich 3'-untranslated regions, and led to EMT and metastasis in cooperation with oncogenic Ras signalling. We also observed enhanced miR-29a and reduced TTP levels in breast cancer patient samples, indicating relevance for human disease. Previously, miR-29 family members were shown to have tumour-suppressive effects in haematopoietic, cholangiocytic and lung tumours. Therefore, miRNAs can act as either oncogenes or tumour suppressors, depending on the context.","authors":"Gebeshuber, CA., Zatloukal, K., Martinez, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"EMBO Rep","volume":"10","issue":"4","page":"400-5","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19240163","title":"2'-O-methylation stabilizes Piwi-associated small RNAs and ensures DNA elimination in Tetrahymena.","abstract":"Small RNAs approximately 20-30 nucleotides (nt) in length regulate gene expression at the transcriptional and post-transcriptional levels. In the plant Arabidopsis, all small RNAs are 3'-terminal 2'-O-methylated by HEN1, whereas only a subset of small RNAs carry this modification in metazoans. This methylation is known to stabilize small RNAs, but its biological significance remains unclear. In the ciliated protozoan Tetrahymena thermophila, two classes of small RNAs have been identified: RNAs approximately 28-29 nt long (scnRNAs) that are expressed only during sexual reproduction, and constitutively expressed approximately 23-24 nt siRNAs. In this study, we demonstrate that scnRNAs, but not siRNAs, are 2'-O-methylated at their 3' ends. The Tetrahymena HEN1 homolog Hen1p is responsible for scnRNA 2'-O-methylation. Loss of Hen1p causes a gradual reduction in the level and length of scnRNAs, defects in programmed DNA elimination, and inefficient production of sexual progeny. Therefore, Hen1p-mediated 2'-O-methylation stabilizes scnRNA and ensures DNA elimination in Tetrahymena. This study clearly shows that 3'-terminal 2'-O-methylation on a selected class of small RNAs regulates the function of a specific RNAi pathway.","authors":"Kurth, HM., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"RNA","volume":"15","issue":"4","page":"675-85","pdf":null,"JrId":"8792","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6895866","title":"Beta + thalassemia: aberrant splicing results from a single point mutation in an intron.","abstract":"We have analyzed the molecular basis of beta + thalassemia by studying the expression of a cloned beta-globin gene in HeLa cells. This beta-globin gene was isolated from a beta + thalassemic patient and differs from the normal beta-globin genes by only a single point mutation within the first intron. The beta + thalassemic and the normal beta-globin genes were cloned into an SV40-pBR328 vector and introduced into HeLa cells by calcium phosphate coprecipitation. We assayed the RNA from these transfected HeLa cells by S1 nuclease mapping and cDNA sequencing to detect the nature of the defect in beta-globin gene expression. While the transcripts of the normal beta-globin gene are processed correctly, the first intron of the beta + thalassemic beta-globin gene is incorrectly spliced in about 90% of the mRNA because of an additional 3; splice site that has been created by the point mutation. This incorrectly spliced mRNA is effectively exported to the cytoplasm, where it would conceivably be translated to give a truncated globin chain of 35 amino acids. The remaining 10% of the mRNA transcribed from the beta+ thalassemic globin gene is correctly spliced and can therefore be translated to give normal beta-globin. In addition to the incorrect splicing of the first intron, the splicing of both introns is retarded, which results in the accumulation of unspliced pre-mRNA. This suggests that removal of the first intron might facilitate splicing of the second intron.","authors":"Busslinger, M., Moschonas, N., Flavell, RA.","publication_status":"ppublish","journalpubyear":"1981","journaltitle":"Cell","volume":"27","issue":"2 Pt 1","page":"289-98","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1982-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19373242","title":"Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes.","abstract":"Cell death is essential for a plethora of physiological processes, and its deregulation characterizes numerous human diseases. Thus, the in-depth investigation of cell death and its mechanisms constitutes a formidable challenge for fundamental and applied biomedical research, and has tremendous implications for the development of novel therapeutic strategies. It is, therefore, of utmost importance to standardize the experimental procedures that identify dying and dead cells in cell cultures and\/or in tissues, from model organisms and\/or humans, in healthy and\/or pathological scenarios. Thus far, dozens of methods have been proposed to quantify cell death-related parameters. However, no guidelines exist regarding their use and interpretation, and nobody has thoroughly annotated the experimental settings for which each of these techniques is most appropriate. Here, we provide a nonexhaustive comparison of methods to detect cell death with apoptotic or nonapoptotic morphologies, their advantages and pitfalls. These guidelines are intended for investigators who study cell death, as well as for reviewers who need to constructively critique scientific reports that deal with cellular demise. Given the difficulties in determining the exact number of cells that have passed the point-of-no-return of the signaling cascades leading to cell death, we emphasize the importance of performing multiple, methodologically unrelated assays to quantify dying and dead cells.","authors":"Galluzzi, L., Aaronson, SA., Abrams, J., Alnemri, ES., Andrews, DW., Baehrecke, EH., Bazan, NG., Blagosklonny, MV., Blomgren, K., Borner, C., Bredesen, DE., Brenner, C., Castedo, M., Cidlowski, JA., Ciechanover, A., Cohen, GM., De Laurenzi, V., De Maria, R., Deshmukh, M., Dynlacht, BD., El-Deiry, WS., Flavell, RA., Fulda, S., Garrido, C., Golstein, P., Gougeon, ML., Green, DR., Gronemeyer, H., Hajn\u00f3czky, G., Hardwick, JM., Hengartner, MO., Ichijo, H., J\u00e4\u00e4ttel\u00e4, M., Kepp, O., Kimchi, A., Klionsky, DJ., Knight, RA., Kornbluth, S., Kumar, S., Levine, B., Lipton, SA., Lugli, E., Madeo, F., Malomi, W., Marine, JC., Martin, SJ., Medema, JP., Mehlen, P., Melino, G., Moll, UM., Morselli, E., Nagata, S., Nicholson, DW., Nicotera, P., Nu\u00f1ez, G., Oren, M., Penninger, J., Pervaiz, S., Peter, ME., Piacentini, M., Prehn, JH., Puthalakath, H., Rabinovich, GA., Rizzuto, R., Rodrigues, CM., Rubinsztein, DC., Rudel, T., Scorrano, L., Simon, HU., Steller, H., Tschopp, J., Tsujimoto, Y., Vandenabeele, P., Vitale, I., Vousden, KH., Youle, RJ., Yuan, J., Zhivotovsky, B., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell Death Differ","volume":"16","issue":"8","page":"1093-107","pdf":null,"JrId":"20326","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22138822","title":"Controlled gene expression in primary Lgr5 organoid cultures.","abstract":"The study of gene function in endodermal epithelia such as of stomach, small intestine and colon relies heavily on transgenic approaches. Establishing such animal models is laborious, expensive and time-consuming. We present here a method based on Cre recombinase-inducible retrovirus vectors that allows the conditional manipulation of gene expression in primary mouse organoid culture systems.","authors":"Koo, BK., Stange, DE., Sato, T., Karthaus, W., Farin, HF., Huch, M., van Es, JH., Clevers, H.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Methods","volume":"9","issue":"1","page":"81-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19228756","title":"The role of ACE2 in pulmonary diseases--relevance for the nephrologist.","abstract":null,"authors":"Oudit, GY., Imai, Y., Kuba, K., Scholey, JW., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nephrol Dial Transplant","volume":"24","issue":"5","page":"1362-5","pdf":null,"JrId":"5843","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34448449","title":"Sensitivity and specificity of the antigen-based anterior nasal self-testing programme for detecting SARS-CoV-2 infection in schools, Austria, March 2021.","abstract":"This study evaluates the performance of the antigen-based anterior nasal screening programme implemented in all Austrian schools to detect SARS-CoV-2 infections. We combined nationwide antigen-based screening data obtained in March 2021 from 5,370 schools (Grade 1-8) with an RT-qPCR-based prospective cohort study comprising a representative sample of 244 schools. Considering a range of assumptions, only a subset of infected individuals are detected with the programme (low to moderate sensitivity) and non-infected individuals mainly tested negative (very high specificity).","authors":"Willeit, P., Bernar, B., Zurl, C., Al-Rawi, M., Berghold, A., Bernhard, D., Borena, W., Doppler, C., Kerbl, R., K\u00f6hler, A., Krause, R., Lamprecht, B., Pr\u00f6ll, J., Schmidt, H., Steinmetz, I., Stelzl, E., Stoiber, H., von Laer, D., Zuber, J., M\u00fcller, T., Strenger, V., Wagner, M.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Euro Surveill","volume":"26","issue":"34","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9754575","title":"Thymic heterotypic cellular complexes in gene-targeted mice with defined blocks in T cell development and adhesion molecule expression.","abstract":"Thymocytes form unique multicellular complexes with epithelial cells (thymic nurse cells, TNC) and rosettes (ROS) with macrophages, epithelial cells and dendritic cells. To investigate the role of differentiation checkpoints in the formation of the thymic heterotypic complexes in vivo, we used mutant mice which have genetically defined blocks at early and late stages of T cell development. We show that RAG-1-\/-, TCRbeta-\/- , and p56lck-\/- mice lack thymocyte ROS formation with epithelial cells, macrophages, or dendritic cells. TNC formation was not affected by TCRbeta and p56lck gene mutations but partially decreased in RAG-1-\/- mice, indicating that TNC are the earliest thymocyte-stromal cell complexes formed in development, whereas ROS only appear after thymocytes have rearranged and expressed a functional TCRbeta chain. Genetic blocks in CD8 lineage commitment (CD8-\/- and IFN regulatory factor-1-\/- mice) and positive and negative T cell selection (CD45-\/-, TCRalpha-\/-, and CD30-\/- mice) did not affect thymocyte-stromal cell complexes. Surprisingly, CD4-\/- mice, but not MHC class II-\/- mice, had significantly reduced numbers of TNC and ROS, in particular, a severe defect in ROS formation with thymic dendritic cells. The CD4-\/- block in ROS and TNC formation was rescued by the introduction of a human CD4 transgene. Moreover, we show that the adhesion receptors CD44 and LFA-1 cooperate in the formation of the thymic microenvironment. These results provide genetic evidence on the role of defined stages in T cell development and adhesion molecules on thymocyte\/stromal cell interactions in vitro.","authors":"Oliveira-dos-Santos, AJ., Penninger, JM., Rieker-Geley, T., Matsumoto, G., Mak, TM., Wick, G.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Eur J Immunol","volume":"28","issue":"9","page":"2882-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-10-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34663789","title":"Inhibition of CBP synergizes with the RNA-dependent mechanisms of Azacitidine by limiting protein synthesis.","abstract":"The nucleotide analogue azacitidine (AZA) is currently the best treatment option for patients with high-risk myelodysplastic syndromes (MDS). However, only half of treated patients respond and of these almost all eventually relapse. New treatment options are urgently needed to improve the clinical management of these patients. Here, we perform a loss-of-function shRNA screen and identify the histone acetyl transferase and transcriptional co-activator, CREB binding protein (CBP), as a major regulator of AZA sensitivity. Compounds inhibiting the activity of CBP and the closely related p300 synergistically reduce viability of MDS-derived AML cell lines when combined with AZA. Importantly, this effect is specific for the RNA-dependent functions of AZA and not observed with the related compound decitabine that is only incorporated into DNA. The identification of immediate target genes leads us to the unexpected finding that the effect of CBP\/p300 inhibition is mediated by globally down regulating protein synthesis.","authors":"Diesch, J., Le Pann\u00e9rer, MM., Winkler, R., Casquero, R., Muhar, M., van der Garde, M., Maher, M., Herr\u00e1ez, CM., Bech-Serra, JJ., Fellner, M., Rathert, P., Brooks, N., Zamora, L., Gentilella, A., de la Torre, C., Zuber, J., G\u00f6tze, KS., Buschbeck, M.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"6060","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19270511","title":"Non-coding RNAs in polycomb\/trithorax regulation.","abstract":"The Polycomb (PcG) and Trithorax (TrxG) proteins are epigenetic regulators that maintain correct expression patterns of several hundred developmentally important genes by binding to DNA regulatory elements called Polycomb\/Trithorax Response Elements (PRE\/TREs). Many PRE\/TREs are transcribed into long non-coding RNAs. Furthermore, many PcG and TrxG proteins bind to RNA, and recent evidence suggests that these RNA interactions are essential for targeting both groups of proteins to specific sites, and modulating their effects on gene expression. We discuss current evidence for the molecular mechanisms by which non-coding RNAs may recruit PcG and TrxG proteins, switch gene expression states, and maintain epigenetic memory.","authors":"Hekimoglu, B., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"RNA Biol","volume":"6","issue":"2","page":"129-37","pdf":null,"JrId":"32563","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"4006902","title":"Transfer of genes into embryonal carcinoma cells by retrovirus infection: efficient expression from an internal promoter.","abstract":"The expression of retroviral genomes after infection of embryonal carcinoma (EC) cells is usually restricted. We have constructed a retroviral vector which has the potential to express efficiently in EC cells an inserted sequence, the selectable neomycin (neo) gene, from an internal thymidine kinase promoter. A second retrovirus vector contained in addition a v-myc oncogene, which in NIH 3T3 cells could be expressed from the viral long terminal repeat (LTR) through a subgenomic mRNA. 10-100% of the EC cells infected with recombinant virus gave rise to neo-resistant colonies following drug selection. The neo gene was expressed in both the non-permissive EC and the permissive NIH 3T3 cells at similar levels, and transcription of neo-specific RNA was initiated at the proper site in the thymidine kinase promoter. In contrast, v-myc mRNA was produced only in the NIH 3T3 cells and not in EC cells, even after induction of differentiation. Thus, genes inserted into retrovirus constructs can easily be introduced into EC cells by virus infection, even without drug selection, and they can be efficiently expressed when transcribed from promoters other than the viral LTRs.","authors":"Wagner, EF., Vanek, M., Vennstr\u00f6m, B.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"EMBO J","volume":"4","issue":"3","page":"663-6","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1985-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19106158","title":"Blockage by SP600125 of Fcepsilon receptor-induced degranulation and cytokine gene expression in mast cells is mediated through inhibition of phosphatidylinositol 3-kinase signalling pathway.","abstract":"SP600125 is used as a specific inhibitor of c-Jun N-terminal kinase (JNK). We initially aimed to examine physiological roles of JNK in mast cells that play a central role in inflammatory and immediate allergic responses. We found that Fc receptor for IgE (FcepsilonRI)-induced degranulation (serotonin release) and cytokine gene expression [interleukin (IL)-6, tumour necrosis factor-alpha and IL-13] in bone marrow-derived mast cells, were almost completely inhibited by SP600125. However, the time course of FcepsilonRI-induced JNK activation did not correlate with that of serotonin release. Furthermore, FcepsilonRI-induced degranulation and cytokine gene expression were not impaired in a JNK activator, MKK7-deficient mast cells, in which JNK activation was lost. These results indicate that the inhibitory effects by SP600125 are not due to impaired JNK activation. Instead, we found that SP600125 markedly inhibited the FcepsilonRI-induced activation of phosphatidylinositol 3-kinase (PI3K) and Akt, the same as a PI3K inhibitor, wortmannin. Finally, we found that SP600125 specifically inhibits delta form of p110 catalytic subunit (p110delta) of PI3K. Thus, SP600125 exerts its influence on mast cell functions by inhibiting the kinase activity of PI3K, but not JNK.","authors":"Tanemura, S., Momose, H., Shimizu, N., Kitagawa, D., Seo, J., Yamasaki, T., Nakagawa, K., Kajiho, H., Penninger, JM., Katada, T., Nishina, H.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Biochem","volume":"145","issue":"3","page":"345-54","pdf":null,"JrId":"4552","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3896777","title":"Analysis of the differentiation-promoting potential of inducible c-fos genes introduced into embryonal carcinoma cells.","abstract":"To investigate the differentiation-promoting potential of c-fos in embryonal carcinoma cells (EC cells) we have designed various human metallothionein promoter-mouse-c-fos gene constructs containing also the selectable SV40 promoter-driven neo gene. Upon transfection into F9 EC cells and selection for neo resistance, the following results were obtained. (i) With each of the constructs, colonies of morphologically altered and differentiated (i.e., TROMA-1 and TROMA-3 expressing) cells were identified. (ii) Expression of c-fos was required to affect the differentiation state of F9 cells to a significant extent, but a low level was sufficient; no enhancement of differentiation was noticeable even after 100-fold induction of c-fos expression by cadmium. (iii) F9 cell clones were isolated which, in spite of very high levels of exogenous c-fos expression, had stem cell morphology. These cells, however, continuously generated morphologically altered and differentiated cells upon subculturing. (iv) In other EC cell lines, which resemble stem cells more closely than the 'partially differentiated' F9 cells, c-fos expression showed either a less pronounced (P19 cells) or no differentiation-promoting effect at all (PC13 cells). Our results suggest that the c-fos gene product acts in concert with other, probably 'spontaneously' occurring events to promote differentiation of certain EC cell lines.","authors":"R\u00fcther, U., Wagner, EF., M\u00fcller, R.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"EMBO J","volume":"4","issue":"7","page":"1775-81","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1985-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19389726","title":"ANNIE: integrated de novo protein sequence annotation.","abstract":"Function prediction of proteins with computational sequence analysis requires the use of dozens of prediction tools with a bewildering range of input and output formats. Each of these tools focuses on a narrow aspect and researchers are having difficulty obtaining an integrated picture. ANNIE is the result of years of close interaction between computational biologists and computer scientists and automates an essential part of this sequence analytic process. It brings together over 20 function prediction algorithms that have proven sufficiently reliable and indispensable in daily sequence analytic work and are meant to give scientists a quick overview of possible functional assignments of sequence segments in the query proteins. The results are displayed in an integrated manner using an innovative AJAX-based sequence viewer. ANNIE is available online at: http:\/\/annie.bii.a-star.edu.sg. This website is free and open to all users and there is no login requirement.","authors":"Ooi, HS., Kwo, CY., Wildpaner, M., Sirota, FL., Eisenhaber, B., Maurer-Stroh, S., Wong, WC., Schleiffer, A., Eisenhaber, F., Schneider, G.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nucleic Acids Res","volume":"37","issue":"Web Server issue","page":"W435-40","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19379014","title":"An innovative method to study target protein-drug interactions by mass spectrometry.","abstract":"We report the combination of chemical cross-linking and high-resolution mass spectrometry for analyzing conformational changes in target proteins that are induced by drug binding. With this approach conformational changes in the peroxisome proliferator-activated receptor alpha (PPARalpha) upon binding of low-molecular weight compounds were readily detected, proving that the strategy provides a basis to efficiently characterize target protein-drug interactions.","authors":"M\u00fcller, MQ., de Koning, LJ., Schmidt, A., Ihling, C., Syha, Y., Rau, O., Mechtler, K., Schubert-Zsilavecz, M., Sinz, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Med Chem","volume":"52","issue":"9","page":"2875-9","pdf":null,"JrId":"4938","fulltextlink":"http:\/\/pubs.acs.org\/doi\/full\/10.1021\/jm9000665?cookieSet=1","preprintlink":null,"articledate":"2009-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19277198","title":"F- and G-actin concentrations in lamellipodia of moving cells.","abstract":"Cells protrude by polymerizing monomeric (G) into polymeric (F) actin at the tip of the lamellipodium. Actin filaments are depolymerized towards the rear of the lamellipodium in a treadmilling process, thereby supplementing a G-actin pool for a new round of polymerization. In this scenario the concentrations of F- and G-actin are principal parameters, but have hitherto not been directly determined. By comparing fluorescence intensities of bleached and unbleached regions of lamellipodia in B16-F1 mouse melanoma cells expressing EGFP-actin, before and after extraction with Triton X-100, we show that the ratio of F- to G-actin is 3.2+\/-0.9. Using electron microscopy to determine the F-actin content, this ratio translates into F- and G-actin concentrations in lamellipodia of approximately 500 microM and 150 microM, respectively. The excess of G-actin, at several orders of magnitude above the critical concentrations at filament ends indicates that the polymerization rate is not limited by diffusion and is tightly controlled by polymerization\/depolymerization modulators.","authors":"Koestler, SA., Rottner, K., Lai, F., Block, J., Vinzenz, M., Small, JV.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS One","volume":"4","issue":"3","page":"e4810","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34396360","title":"Prevalence of RT-qPCR-detected SARS-CoV-2 infection at schools: First results from the Austrian School-SARS-CoV-2 prospective cohort study.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">34396360<\/PMID><DateRevised><Year>2021<\/Year><Month>09<\/Month><Day>23<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">2666-7762<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>5<\/Volume><PubDate><Year>2021<\/Year><Month>Jun<\/Month><\/PubDate><\/JournalIssue><Title>The Lancet regional health. Europe<\/Title><ISOAbbreviation>Lancet Reg Health Eur<\/ISOAbbreviation><\/Journal><ArticleTitle>Prevalence of RT-qPCR-detected SARS-CoV-2 infection at schools: First results from the Austrian School-SARS-CoV-2 prospective cohort study.<\/ArticleTitle><Pagination><MedlinePgn>100086<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.lanepe.2021.100086<\/ELocationID><Abstract><AbstractText Label=\"Background\" NlmCategory=\"UNASSIGNED\">The role of schools in the SARS-CoV-2 pandemic is much debated. We aimed to quantify reliably the prevalence of SARS-CoV-2 infections at schools detected with reverse-transcription quantitative polymerase-chain-reaction (RT-qPCR).","authors":"Willeit, P., Krause, R., Lamprecht, B., Berghold, A., Hanson, B., Stelzl, E., Stoiber, H., Zuber, J., Heinen, R., K\u00f6hler, A., Bernhard, D., Borena, W., Doppler, C., von Laer, D., Schmidt, H., Pr\u00f6ll, J., Steinmetz, I., Wagner, M.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Lancet Reg Health Eur","volume":"5","issue":null,"page":"100086","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19345119","title":"Stepwise activation of enhancer and promoter regions of the B cell commitment gene Pax5 in early lymphopoiesis.","abstract":"Pax5 is an essential regulator of B cell identity and function. Here, we used transgenesis and deletion mapping to identify a potent enhancer in intron 5 of the Pax5 locus. This enhancer in combination with the promoter region was sufficient to recapitulate the B lymphoid expression of Pax5. The enhancer was silenced by DNA methylation in embryonic stem cells, but became activated in multipotent hematopoietic progenitors. It contained functional binding sites for the transcription factors PU.1, IRF4, IRF8, and NF-kappaB, suggesting that these regulators contribute to sequential enhancer activation in hematopoietic progenitors and during B cell development. In contrast, the promoter region was repressed by Polycomb group proteins in non-B cells and was activated only at the onset of pro-B cell development through induction of chromatin remodeling by the transcription factor EBF1. These experiments demonstrate a stepwise activation of Pax5 in early lymphopoiesis and provide mechanistic insights into the process of B cell commitment.","authors":"Decker, T., Pasca di Magliano, M., McManus, S., Sun, Q., Bonifer, C., Tagoh, H., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Immunity","volume":"30","issue":"4","page":"508-20","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19015638","title":"ILEI requires oncogenic Ras for the epithelial to mesenchymal transition of hepatocytes and liver carcinoma progression.","abstract":"In human hepatocellular carcinoma (HCC), epithelial to mesenchymal transition (EMT) correlates with aggressiveness of tumors and poor survival. We employed a model of EMT based on immortalized p19(ARF) null hepatocytes (MIM), which display tumor growth upon expression of oncogenic Ras and undergo EMT through the synergism of Ras and transforming growth factor (TGF)-beta. Here, we show that the interleukin-related protein interleukin-like EMT inducer (ILEI), a novel EMT-, tumor- and metastasis-inducing protein, cooperates with oncogenic Ras to cause TGF-beta-independent EMT. Ras-transformed MIM hepatocytes overexpressing ILEI showed cytoplasmic E-cadherin, loss of ZO-1 and induction of alpha-smooth muscle actin as well as platelet-derived growth factor (PDGF)\/PDGF-R isoforms. As shown by dominant-negative PDGF-R expression in these cells, ILEI-induced PDGF signaling was required for enhanced cell migration, nuclear accumulation of beta-catenin, nuclear pY-Stat3 and accelerated growth of lung metastases. In MIM hepatocytes expressing the Ras mutant V12-C40, ILEI collaborated with PI3K signaling resulting in tumor formation without EMT. Clinically, human HCC samples showed granular or cytoplasmic localization of ILEI correlating with well and poorly differentiated tumors, respectively. In conclusion, these data indicate that ILEI requires cooperation with oncogenic Ras to govern hepatocellular EMT through mechanisms involving PDGF-R\/beta-catenin and PDGF-R\/Stat3 signaling.","authors":"Lahsnig, C., Mikula, M., Petz, M., Zulehner, G., Schneller, D., van Zijl, F., Huber, H., Csiszar, A., Beug, H., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Oncogene","volume":"28","issue":"5","page":"638-50","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12952528","title":"Towards a complete description of the microRNA complement of animal genomes.","abstract":"Recent cloning and computational studies have sought to catalog all the microRNA genes encoded in animal genomes. Here, we highlight recent advances in identifying Caenorhabditis elegans and Drosophila melanogaster microRNAs.","authors":"Brennecke, J., Cohen, SM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Genome Biol","volume":"4","issue":"9","page":"228","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2706312","title":"Hydration of B-DNA: comparison between the water network around poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) on the basis of Monte Carlo computations.","abstract":"A computational method is elaborated for studying the water environment around regular polynucleotide duplexes; it allows rigorous structural information on the hydration shell of DNA to be obtained. The crucial aspect of this Monte Carlo simulation is the use of periodical boundary conditions. The output data consists of local maxima of water density in the space near the DNA molecule and the properties of one- and two-membered water bridges as function of pairs of polar groups of DNA. In the present paper the results for poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) are presented. The differences in their hydration shells are of a purely structural nature and are caused by the symmetry of the polar groups of the polymers under study, the symmetry being reflected by the hydration shell. The homopolymer duplex hydration shell mirrors the mononucleotide repeat. The water molecules contacting the polynucleotide in the minor groove are located nearly in the plane midway between the planes of successive base pairs. One water molecule per base pair forms a water bridge facing two polar groups of bases from adjacent base pairs and on different strands making a \"spine\"-like structure. In contrast, the major groove hydration is stabilized exclusively by two-membered water bridges; the water molecules deepest in the groove are concentrated near the plane of the corresponding base pair. The alternating polymer is characterized by a marked dyad symmetry of the hydration shell corresponding to the axis between two successive base pairs. The minor groove hydration of the dCpdG step resembles the characteristic features of the homopolymer, but the bridge between the O2 oxygens of the other base-stacking type is formed by two water molecules. The major groove hydration is characterized by high probability of one-membered water bridges and by localization of a water molecule on the dyad axis of the dGpdC step. The found structural elements are discussed as reasonable invariants of a dynamic hydration shell.","authors":"Eisenhaber, F., Tumanyan, VG., Eisenmenger, F., Gunia, W.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Biopolymers","volume":"28","issue":"3","page":"741-61","pdf":null,"JrId":"1181","fulltextlink":null,"preprintlink":null,"articledate":"1989-05-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9095363","title":"Influence of membrane-active peptides on lipospermine\/DNA complex mediated gene transfer.","abstract":"To explore whether endosomal release presents a major barrier to lipospermine-mediated gene delivery, acidic membrane-active peptides derived from influenza virus or artificial sequences were incorporated into DNA\/dioctadecylamidoglycylspermine (= Transfectam) complexes. Depending on the cell line used, gene expression levels are approximately 3-30-fold higher than those obtained by applying DNA complexed to optimal amounts of Transfectam alone. In addition, gene transfer efficiency of DNA complexes with lower amounts of Transfectam (1.5-2 charge equiv) is increased by a factor of up to 1000 by peptides INF6 (influenza virus derived sequence) and INF10 (artificial sequence). The helper lipids 1,2-dioleoylphosphatidylethanolamine, egg phosphatidylethanolamine, and 1,2-dioleoyl-racglycerol also can enhance the gene transfer. Thus, endosomal escape seems to be only a moderate barrier for optimized, positively charged DNA\/Transfectam complexes, but a substantial bottleneck for less positively charged complexes.","authors":"Kichler, A., Mechtler, K., Behr, JP., Wagner, E.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Bioconjug Chem","volume":"8","issue":"2","page":"213-21","pdf":null,"JrId":"1061","fulltextlink":null,"preprintlink":null,"articledate":"1997-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3034588","title":"Expression of retroviral vectors in transgenic mice obtained by embryo infection.","abstract":"Pre-implantation embryos were infected with the retroviral vector MMCV-neo, which carries the neomycin resistance (neo) gene and the v-myc gene. Three transgenic substrains (M-TKneo 1-3) were derived which stably transmit a single intact copy of the vector. In all of the substrains, expression of the neo gene from the internal thymidine kinase (TK) promoter was detected, with two of the substrains expressing the gene in all tissues analysed. In the third substrain, the vector had integrated on the X chromosome and neo expression varied between different tissues. A second series of transgenic mice were obtained with the retroviral vector SAX, in which the human adenosine deaminase cDNA (ADA) is under the control of an internal SV40 promoter. Four substrains (M-SAX 1-4) were analysed; however, no expression of the ADA cDNA was detected. In all mice, no expression was found of the genes under the control of the viral 5' long terminal repeats (LTRs). In the M-TKneo substrains the vector was hypomethylated irrespective of its expression whereas in the M-SAX mice the vector was hypermethylated. These results demonstrate for the first time that the TK promoter can apparently express a gene in all tissues of adult mice and that retroviral vectors with internal promoters may provide an alternative to DNA injection for the efficient expression of genes in transgenic mice.","authors":"Stewart, CL., Schuetze, S., Vanek, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"EMBO J","volume":"6","issue":"2","page":"383-8","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1987-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18793650","title":"Architecture and flexibility of the yeast Ndc80 kinetochore complex.","abstract":"Kinetochores mediate microtubule-chromosome attachment and ensure accurate segregation of sister chromatids. The highly conserved Ndc80 kinetochore complex makes direct contacts with the microtubule and is essential for spindle checkpoint signaling. It contains a long coiled-coil region with globular domains at each end involved in kinetochore localization and microtubule binding, respectively. We have directly visualized the architecture of the yeast Ndc80 complex and found a dramatic kink within the 560-A coiled-coil rod located about 160 A from the larger globular head. Comparison of our electron microscopy images to the structure of the human Ndc80 complex allowed us to position the kink proximal to the microtubule-binding end and to define the conformational range of the complex. The position of the kink coincides with a coiled-coil breaking region conserved across eukaryotes. We hypothesize that the kink in Ndc80 is essential for correct kinetochore geometry and could be part of a tension-sensing mechanism at the kinetochore.","authors":"Wang, HW., Long, S., Ciferri, C., Westermann, S., Drubin, D., Barnes, G., Nogales, E.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Mol Biol","volume":"383","issue":"4","page":"894-903","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3017698","title":"Temperature-sensitive mutants of MH2 avian leukemia virus that map in the v-mil and the v-myc oncogene respectively.","abstract":"MH2 is an avian retrovirus that contains the v-mil and v-myc oncogenes. In vitro it transforms chick macrophages that are capable of proliferation in the absence of growth factor. Earlier work showed that v-myc induces macrophage transformation and that v-mil induces the production of chicken myelomonocytic growth factor (cMGF), thus generating an autocrine system. We describe the isolation of temperature-sensitive (ts) mutants of MH2 virus. As suggested by marker rescue experiments, one mutant bears a ts lesion in v-mil, whereas the other carries a mutation in v-myc. Ts v-mil MH2-transformed macrophages become factor-dependent at the non-permissive temperature (42 degrees C), while ts-v-myc MH2-transformed macrophages cease growing and acquire a more normal macrophage phenotype at 42 degrees C irrespective of the presence of cMGF. Both phenotypes can be reversed by backshift to the permissive temperature. These results suggest that the gene products of v-mil and v-myc function independently of each other and that v-mil is necessary for the maintenance of autocrine growth, whereas v-myc is required to maintain the transformed phenotype.","authors":"von Weizs\u00e4cker, F., Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"EMBO J","volume":"5","issue":"7","page":"1521-7","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1986-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3007187","title":"Primitive series embryonic chick erythrocytes express the transferrin receptor.","abstract":"A monoclonal antibody specific for the chicken transferrin receptor was used to study receptor expression on circulating red cells from chick embryos of different ages. The use of indirect immunofluorescence with this antibody showed that all circulating immature reticulocytes and primitive series erythrocytes--but not erythrocytes from the definitive series--expressed the receptor. In all cells, the protein was synthesized as a 90-95-kD form. The retention of the transferrin receptor (and another proliferation-dependent cell surface protein) contrasted with the behaviour of a series of other developmentally regulated antigens which are lost during maturation of both primitive and definitive series erythroid cells.","authors":"Schmidt, JA., Marshall, J., Hayman, MJ., Beug, H.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Exp Cell Res","volume":"164","issue":"1","page":"71-8","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1986-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19308701","title":"How cohesin and CTCF cooperate in regulating gene expression.","abstract":"Cohesin is a DNA-binding protein complex that is essential for sister chromatid cohesion and facilitates the repair of damaged DNA. In addition, cohesin has important roles in regulating gene expression, but the molecular mechanisms of this function are poorly understood. Recent experiments have revealed that cohesin binds to the same sites in mammalian genomes as the zinc finger transcription factor CTCF. At a few loci CTCF has been shown to function as an enhancer-blocking transcriptional insulator, and recent observations indicate that this function depends on cohesin. Here we review what is known about the roles of cohesin and CTCF in regulating gene expression in mammalian cells, and we discuss how cohesin might mediate the insulator function of CTCF.","authors":"Wendt, KS., Peters, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Chromosome Res","volume":"17","issue":"2","page":"201-14","pdf":null,"JrId":"8478","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18936163","title":"Weak but uniform enrichment of the histone variant macroH2A1 along the inactive X chromosome.","abstract":"We studied the enrichment and distribution of the histone variant mH2A1 in the condensed inactive X (Xi) chromosome. By using highly specific antibodies against mH2A1 and stable HEK 293 cell lines expressing either green fluorescent protein (GFP)-mH2A1 or GFP-H2A, we found that the Xi chromosome contains approximately 1.5-fold more mH2A1 than the autosomes. To determine the in vivo distribution of mH2A1 along the X chromosome, we used a native chromatin immunoprecipitation-on-chip technique. DNA isolated from mH2A1-immunoprecipitated nucleosomes from either male or female mouse liver were hybridized to tiling microarrays covering 5 kb around most promoters or the entire X chromosome. The data show that mH2A1 is uniformly distributed across the entire Xi chromosome. Interestingly, a stronger mH2A1 enrichment along the pseudoautosomal X chromosome region was observed in both sexes. Our results indicate a potential role for macroH2A in large-scale chromosome structure and genome stability.","authors":"Mietton, F., Sengupta, AK., Molla, A., Picchi, G., Barral, S., Heliot, L., Grange, T., Wutz, A., Dimitrov, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Cell Biol","volume":"29","issue":"1","page":"150-6","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18988843","title":"Wired for sex: the neurobiology of Drosophila mating decisions.","abstract":"Decisions about whom to mate with can sometimes be difficult, but making the right choice is critical for an animal's reproductive success. The ubiquitous fruit fly, Drosophila, is clearly very good at making these decisions. Upon encountering another fly, a male may or may not choose to court. He estimates his chances of success primarily on the basis of pheromone signals and previous courtship experience. The female decides whether to accept or reject the male, depending on her perception of his pheromone and acoustic signals, as well as her own readiness to mate. This simple and genetically tractable system provides an excellent model to explore the neurobiology of decision making.","authors":"Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Science","volume":"322","issue":"5903","page":"904-9","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2985286","title":"Extended life span and tumorigenicity of nonestablished mouse connective tissue cells transformed by the fos oncogene of FBR-MuSV.","abstract":"We have analyzed the transforming potential of two fos oncogene products in nonestablished cultures of mouse connective tissue cells: p55fos of FBJ-MuSV and p75gag-fos of FBR-MuSV. Although both proteins induced morphological transformation and colony formation at low cell density in a G418 resistance selection assay, p75gag-fos exhibited more pronounced transforming potential than p55fos. In addition, p75gag-fos-transformed cells overcame crisis with a high probability and were tumorigenic in syngenic mice. These properties of the FBR-MuSV appear to be linked to structural alterations in the p75gag-fos oncogene product. Polyoma virus large T protein complemented the transforming potential of fos, in that it not only increased the probability of establishment of fos-transformed cells but also enhanced fos-induced morphological transformation. Our results suggest that different oncogenes affect morphological transformation, low cell density growth, establishment, and tumorigenicity to various degrees.","authors":"Jenuwein, T., M\u00fcller, D., Curran, T., M\u00fcller, R.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Cell","volume":"41","issue":"2","page":"629-37","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1985-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19246991","title":"X chromosome inactivation sparked by non-coding RNAs.","abstract":"Non-coding RNAs regulate dosage compensation in mammals by controlling transcriptional silencing of one of the two X chromosomes in females. The two major transcripts involved in this process are Xist and its antisense counterpart Tsix. Expression of Xist and Tsix from the X inactivation center is mutually exclusive. Xist expression triggers chromosome wide silencing of the X chromosome from which it is transcribed. Tsix is a repressor of Xist and is specifically expressed from the other X chromosome, maintaining its activity. Here, we review non-coding RNAs that have been implicated in X chromosome inactivation. Focusing on the best studied transcripts Xist and Tsix we portray a current perspective on chromosome wide gene regulation by non-coding RNAs.","authors":"Leeb, M., Steffen, PA., Wutz, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"RNA Biol","volume":"6","issue":"2","page":"94-9","pdf":null,"JrId":"32563","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34359703","title":"Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development.","abstract":"Epithelial ovarian cancer (EOC) is the most lethal disease of the female reproductive tract, and although most patients respond to the initial treatment with platinum (cPt)-based compounds, relapse is very common. We investigated the role of epigenetic changes in cPt-sensitive and -resistant EOC cell lines and found distinct differences in their enhancer landscape. Clinical data revealed that two genes (JAK1 and FGF10), which gained large enhancer clusters in resistant EOC cell lines, could provide novel biomarkers for early patient stratification with statistical independence for JAK1. To modulate the enhancer remodeling process and prevent the acquisition of cPt resistance in EOC cells, we performed a chromatin-focused RNAi screen in the presence of cPt. We identified subunits of the Nucleosome Remodeling and Deacetylase (NuRD) complex as critical factors sensitizing the EOC cell line A2780 to platinum treatment. Suppression of the Methyl-CpG Binding Domain Protein 3 (MBD3) sensitized cells and prevented the establishment of resistance under prolonged cPt exposure through alterations of H3K27ac at enhancer regions, which are differentially regulated in cPt-resistant cells, leading to a less aggressive phenotype. Our work establishes JAK1 as an independent prognostic marker and the NuRD complex as a potential target for combinational therapy.","authors":"Bauer, TL., Collmar, K., Kaltofen, T., Loeffler, AK., Decker, L., Mueller, J., Pinter, S., Eisler, SA., Mahner, S., Fraungruber, P., Kommoss, S., Staebler, A., Francis, L., Conlan, RS., Zuber, J., Jeschke, U., Trillsch, F., Rathert, P.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Cancers (Basel)","volume":"13","issue":"15","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34010414","title":"Core-binding factor leukemia hijacks the T-cell-prone PU.1 antisense promoter.","abstract":"The blood system serves as a key model for cell differentiation and cancer. It is orchestrated by precise spatiotemporal expression of crucial transcription factors. One of the key master regulators in the hematopoietic systems is PU.1. Reduced levels of PU.1 are characteristic for human acute myeloid leukemia (AML) and are known to induce AML in mouse models. Here, we show that transcriptional downregulation of PU.1 is an active process involving an alternative promoter in intron 3 that is induced by RUNX transcription factors driving noncoding antisense transcription. Core-binding factor (CBF) fusions RUNX1-ETO and CBF\u03b2-MYH11 in t(8;21) and inv(16) AML, respectively, activate the PU.1 antisense promoter that results in a shift from sense toward antisense transcription and myeloid differentiation blockade. In patients with CBF-AML, we found that an elevated antisense\/sense transcript and promoter accessibility ratio represents a hallmark compared with normal karyotype AML or healthy CD34+ cells. Competitive interaction of an enhancer with the proximal or the antisense promoter forms a binary on\/off switch for either myeloid or T-cell development. Leukemic CBF fusions thus use a physiological mechanism used by T cells to decrease sense transcription. Our study is the first example of a sense\/antisense promoter competition as a crucial functional switch for gene expression perturbation by oncogenes. Hence, this disease mechanism reveals a previously unknown Achilles heel for future precise therapeutic targeting of oncogene-induced chromatin remodeling.","authors":"van der Kouwe, E., Heller, G., Czibere, A., Pulikkan, JA., Agreiter, C., Castilla, LH., Delwel, R., Di Ruscio, A., Ebralidze, AK., Forte, M., Grebien, F., Heyes, E., Kazianka, L., Klinger, J., Kornauth, C., Le, T., Lind, K., Barbosa, IAM., Pemovska, T., Pichler, A., Schmolke, AS., Schweicker, CM., Sill, H., Sperr, WR., Spittler, A., Surapally, S., Trinh, BQ., Valent, P., Vanura, K., Welner, RS., Zuber, J., Tenen, DG., Staber, PB.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Blood","volume":"138","issue":"15","page":"1345-1358","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19034303","title":"Decreased glomerular and tubular expression of ACE2 in patients with type 2 diabetes and kidney disease.","abstract":"Angiotensin converting enzyme (ACE) generates angiotensin II from angiotensin I, which plays a critical role in the pathophysiology of diabetic nephropathy. However, ACE2 generates angiotensin 1-7, which may protect the kidney by attenuating the effects of angiotensin II, since deletion of the Ace2 gene leads to glomerulosclerosis in mice, and pharmacologic inhibition of ACE2 exacerbates experimental diabetic nephropathy. We measured ACE2 and ACE expression in renal biopsies of patients with kidney disease due to type 2 diabetes to determine if the expression pattern is specific to diabetic nephropathy. ACE2 and ACE mRNA levels were measured by real-time PCR in laser microdissected renal biopsies from 13 diabetic and 8 control patients. ACE2 mRNA was significantly reduced by more than half in both the glomeruli and proximal tubules of the diabetic patients compared to controls, but ACE mRNA was increased in both compartments. There was a significant parallel decrease in ACE2 protein expression, determined by immunohistochemistry, in proximal tubules, a pattern not found in 12 patients with focal glomerulosclerosis or 10 patients with chronic allograft nephropathy. Our results suggest that the kidney disease of patients with type 2 diabetes is associated with a reduction in ACE2 gene and protein expression and this may contribute to the progression of renal injury.","authors":"Reich, HN., Oudit, GY., Penninger, JM., Scholey, JW., Herzenberg, AM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Kidney Int","volume":"74","issue":"12","page":"1610-6","pdf":null,"JrId":"5428","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2852341","title":"A point mutation in the DNA binding domain of the v-myb oncogene of E26 virus confers temperature sensitivity for transformation of myelomonocytic cells.","abstract":"We have molecularly cloned a mutant of the v-myb, ets-containing E26 avian leukemia virus which is temperature sensitive for the transformation of myeloid cells. Cells infected with this mutant, ts21E26, are immature at 37 degrees C and can be induced to differentiate into resting, macrophage-like cells when shifted to 42 degrees C. The sequence of ts21E26 reveals a single relevant nucleotide alteration resulting in a threonine to arginine change in the highly conserved, putative DNA binding v-myb portion of the p135gag-myb-ets protein. Surprisingly, a ts21E26 viral construct in which the v-ets gene domain was deleted was only weakly temperature sensitive, although temperature sensitivity was largely restored in another v-ets deletion mutant whose 3' terminal sequences were replaced with those from the AMV v-myb gene. These results suggest that the temperature sensitive lesion in v-myb of ts21E26 alters the DNA binding capacity of p135 at 42 degrees C and that the primary structure of the C-terminus of this protein has an influence on the activity of sequences that are further upstream.","authors":"Frykberg, L., Metz, T., Brady, G., Introna, M., Beug, H., Vennstr\u00f6m, B., Graf, T.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Oncogene Res","volume":"3","issue":"4","page":"313-22","pdf":null,"JrId":"6326","fulltextlink":null,"preprintlink":null,"articledate":"1989-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-122","title":"PI3Kgamma AKTing during myocardial ischemia and reperfusion.","abstract":null,"authors":"Haubner, B. J., Neely, G., Pachinger, O., Penninger, J. M., Metzler, B.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Wiener Klin. Wochenschrift","volume":"","issue":"15","page":"95-97","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-123","title":"RANK(L) as a key target for controlling bone loss.","abstract":null,"authors":"Leibbrandt, A., Penninger, J. M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"In: Therapeutic Targets of the TNF Superfamily. Ed. I. Grewal. Landes Bioscience\/Eurekah.com","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-125","title":"The Role of the E3 ubiquitin ligase Cbl-b in T-cells signalling and tolerance.","abstract":null,"authors":"Loeser, S., Penninger, J.M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"In: CBL Proteins. Ed. A. Tsygankov. Nova Science Publishers Inc","volume":"","issue":"","page":"Chapter 9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-124","title":"The role of RANKL in cancer.","abstract":null,"authors":"Leibbrandt, A., Penninger, J. M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"In: Encyclopedia of Cancer. Ed. Schwab, M. Springer","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-120","title":"Role of Growth factors in Bone development and differentiation.","abstract":null,"authors":"Fujimori, S., Kostanova Poliakova, D., Hartmann C.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"In: The Skeletal System. Ed. Pourquie, O. Cold Spring Harbor Laboratory Press, New York","volume":"Chapter","issue":"","page":"8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-126","title":"Regulation of T cell anergy and escape from regulatory T cells suppression by Cbl-b.","abstract":null,"authors":"Loeser, S., Penninger, J.M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"In: The Epigenetics of Autoimmune disease. Ed. N. Zouali","volume":"","issue":"","page":"pp. 75-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18295731","title":"Ubiquitination system and autoimmunity: the bridge towards the modulation of the immune response.","abstract":"The ubiquitination system comprises a highly specific and regulated post-translational mechanism by which the immune response can be modulated, setting the balance between immunity and tolerance. Proteolysis dependent and independent mechanisms have been implicated. Particularly, the role of ubiquitin ligases as modulators of central and peripheral tolerance has brought attention to this system as one of the key elements of a complex regulatory network designed to maintain an active surveillance system. Cbl-b, GRAIL and Itch are the main E3 ligases, considered as negative regulators of the immune response as part of the genetic program induced by the calcium\/calcineurin pathway. Other key signaling pathways for the immune response, such as the NF-kappaB and TGF-beta signaling are prone to be modulated by these ubiquitin ligases. Diverse mechanisms have been implicated in the development of anergy associated to E3 ligases, among these, the setting for TCR responsiveness and repression of cytokine transcription are best well characterized. Also, a role as inductors of regulatory T cells has been evidenced for Cbl-b and GRAIL. The defective expression of some of these E3 ligases has been related to the development of autoimmune disease, in experimental murine and human models, remarking its possible pathogenic role.","authors":"G\u00f3mez-Mart\u00edn, D., D\u00edaz-Zamudio, M., Alcocer-Varela, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Autoimmun Rev","volume":"7","issue":"4","page":"284-90","pdf":null,"JrId":"30408","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2835659","title":"Functional analysis of the sea urchin U7 small nuclear RNA.","abstract":"U7 small nuclear RNA (snRNA) is an essential component of the RNA-processing machinery which generates the 3' end of mature histone mRNA in the sea urchin. The U7 small nuclear ribonucleoprotein particle (snRNP) is classified as a member of the Sm-type U snRNP family by virtue of its recognition by both anti-trimethylguanosine and anti-Sm antibodies. We analyzed the function-structure relationship of the U7 snRNP by mutagenesis experiments. These suggested that the U7 snRNP of the sea urchin is composed of three important domains. The first domain encompasses the 5'-terminal sequences, up to about nucleotides 7, which are accessible to micrococcal nuclease, while the remainder of the RNA is highly protected and hence presumably bound by proteins. This region contains the sequence complementarities between the U7 snRNA and the histone pre-mRNA which have previously been shown to be required for 3' processing (F. Schaufele, G. M. Gilmartin, W. Bannwarth, and M. L. Birnstiel, Nature [London] 323:777-781, 1986). Nucleotides 9 to 20 constitute a second domain which includes sequences for Sm protein binding. The complementarities between the U7 snRNA sequences in this region and the terminal palindrome of the histone mRNA appear to be fortuitous and play only a secondary, if any, role in 3' processing. The third domain is composed of the terminal palindrome of U7 snRNA, the secondary structure of which must be maintained for the U7 snRNP to function, but its sequence can be drastically altered without any observable effect on snRNP assembly or 3' processing.","authors":"Gilmartin, GM., Schaufele, F., Schaffner, G., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Mol Cell Biol","volume":"8","issue":"3","page":"1076-84","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1988-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11316610","title":"Molecular controls of antigen receptor clustering and autoimmunity.","abstract":"Cellular organization of the cytoskeleton, assembly of intracellular signaling complexes and movement of membrane receptors into supramolecular activation complexes (SMACs) are crucial prerequisites for lymphocyte activation and function. Full T-cell activation requires costimulatory signals in addition to antigen-mediated signals. Costimulatory signals facilitate T-cell activation by inducing SMAC formation, resulting in sustained signal transduction, cell-cycle progression and cytokine production. The guanine nucleotide exchange factor Vav1 and the Wiscott-Aldrich syndrome protein (WASP) regulate the actin cytoskeleton in T cells and also regulate SMAC formation. In mice lacking the E3 ubiquitin ligase Cbl-b, the Vav-WASP signaling pathway is active in the absence of costimulation resulting in deregulated cytoskeletal reorganization, enhanced priming and expansion of autoreactive T cells, and the development of autoimmunity. This review discusses the role of Cbl-b, Vav and WASP in the regulation of SMAC formation and the implications for the maintenance of tolerance and the development of autoimmunity.","authors":"Krawczyk, C., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Trends Cell Biol","volume":"11","issue":"5","page":"212-20","pdf":null,"JrId":"21041","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33980539","title":"Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia.","abstract":"In acute myeloid leukemia (AML) with inv(3)(q21;q26) or t(3;3)(q21;q26), a translocated <i>GATA2<\/i> enhancer drives oncogenic expression of <i>EVI1<\/i>. We generated an EVI1-GFP AML model and applied an unbiased CRISPR\/Cas9 enhancer scan to uncover sequence motifs essential for <i>EVI1<\/i> transcription. Using this approach, we pinpointed a single regulatory element in the translocated <i>GATA2<\/i> enhancer that is critically required for aberrant <i>EVI1<\/i> expression. This element contained a DNA-binding motif for the transcription factor MYB, which specifically occupied this site at the translocated allele and was dispensable for <i>GATA2<\/i> expression. <i>MYB<\/i> knockout as well as peptidomimetic blockade of CBP\/p300-dependent MYB functions resulted in downregulation of EVI1 but not of GATA2. Targeting MYB or mutating its DNA-binding motif within the <i>GATA2<\/i> enhancer resulted in myeloid differentiation and cell death, suggesting that interference with MYB-driven <i>EVI1<\/i> transcription provides a potential entry point for therapy of inv(3)\/t(3;3) AMLs. SIGNIFICANCE: We show a novel paradigm in which chromosomal aberrations reveal critical regulatory elements that are nonfunctional at their endogenous locus. This knowledge provides a rationale to develop new compounds to selectively interfere with oncogenic enhancer activity.<i>This article is highlighted in the In This Issue feature, p. 2659<\/i>.","authors":"Smeenk, L., Ottema, S., Mulet-Lazaro, R., Ebert, A., Havermans, M., Varea, AA., Fellner, M., Pastoors, D., van Herk, S., Erpelinck-Verschueren, C., Grob, T., Hoogenboezem, RM., Kavelaars, FG., Matson, DR., Bresnick, EH., Bindels, EM., Kentsis, A., Zuber, J., Delwel, R.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cancer Discov","volume":"11","issue":"11","page":"2868-2883","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15032575","title":"Ubiquitin ligases and the immune response.","abstract":"Ubiquitin (Ub)-protein conjugation represents a novel means of posttranscriptional modification in a proteolysis-dependent or -independent manner. E3 Ub ligases play a key role in governing the cascade of Ub transfer reactions by recognizing and catalyzing Ub conjugation to specific protein substrates. The E3s, which can be generally classified into HECT-type and RING-type families, are involved in the regulation of many aspects of the immune system, including the development, activation, and differentiation of lymphocytes, T cell-tolerance induction, antigen presentation, immune evasion, and virus budding. E3-promoted ubiquitination affects a wide array of biological processes, such as receptor downmodulation, signal transduction, protein processing or translocation, protein-protein interaction, and gene transcription, in addition to proteasome-mediated degradation. Deficiency or mutation of some of the E3s like Cbl, Cbl-b, or Itch, causes abnormal immune responses such as autoimmunity, malignancy, and inflammation. This review discusses our current understanding of E3 Ub ligases in both innate and adaptive immunity. Such knowledge may facilitate the development of novel therapeutic approaches for immunological diseases.","authors":"Liu, YC.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Annu Rev Immunol","volume":"22","issue":"","page":"81-127","pdf":null,"JrId":"1564","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9036857","title":"APC-mediated proteolysis of Ase1 and the morphogenesis of the mitotic spindle.","abstract":"The molecular mechanisms that link cell-cycle controls to the mitotic apparatus are poorly understood. A component of the Saccharomyces cerevisiae spindle, Ase1, was observed to undergo cell cycle-specific degradation mediated by the cyclosome, or anaphase promoting complex (APC). Ase1 was degraded when cells exited from mitosis and entered G1. Inappropriate expression of stable Ase1 during G1 produced a spindle defect that is sensed by the spindle assembly checkpoint. In addition, loss of ASE1 function destabilized telophase spindles, and expression of a nondegradable Ase1 mutant delayed spindle disassembly. APC-mediated proteolysis therefore appears to regulate both spindle assembly and disassembly.","authors":"Juang, YL., Huang, J., Peters, JM., McLaughlin, ME., Tai, CY., Pellman, D.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Science","volume":"275","issue":"5304","page":"1311-4","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19185505","title":"Role of RANKL in bone diseases.","abstract":"Bone remodeling is a tightly regulated process of osteoclast-mediated bone resorption, balanced by osteoblast-mediated bone formation. Disruption of this balance can lead to increased bone turnover, resulting in excessive bone loss or extra bone formation and consequent skeletal disease. The receptor activator of nuclear factor kappaB ligand (RANKL) (along with its receptor), the receptor activator of nuclear factor kappaB and its natural decoy receptor, osteoprotegerin, are the final effector proteins of osteoclastic bone resorption. Here, I provide an overview of recent studies that highlight the key role of RANKL in the pathophysiology of several bone diseases and discuss the novel therapeutic approaches afforded by the modulation of RANKL.","authors":"Anandarajah, AP.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Trends Endocrinol Metab","volume":"20","issue":"2","page":"88-94","pdf":null,"JrId":"21213","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19428330","title":"Mechanisms of interferon-beta effects on bone homeostasis.","abstract":"Restoration of dysregulated bone homeostasis is a therapeutic goal in many diseases including osteoporosis, rheumatoid arthritis and metastatic cancer. The molecular pathways regulating bone remodeling are major therapeutic targets, and studies continue to reveal endogenous factors that may be pathologically up- or down-regulated and lead to an uncoupling of bone formation and resorption. The purpose of this commentary is to highlight new mechanisms of bone homeostatic regulation mediated through the induction of endogenous interferon-beta (IFN-beta). The receptor activator of nuclear factor-kappaB (RANK) ligand (RANKL) is an important factor in the bone resorption cascade, and the RANK-RANKL interaction has been shown to induce IFN-beta and osteoclastogenesis via induction of the c-fos gene. Subsequent binding of IFN-beta to its biological receptor initiates a signal transduction cascade through the classic JAK\/STAT pathway, causing an inhibition of c-fos protein production and osteoclast proliferation and differentiation (negative feedback). Another mechanism pertinent to the anti-resorptive effect of IFN-beta is the induction of nitric oxide which has been shown to inhibit osteoclast formation. The role of IFN-beta in bone metabolism could warrant its systematic evaluation as a potential adjunct to therapeutic regimens of osteolytic diseases. Here we also provide discussion of the potential challenges to optimizing IFN-beta pharmacotherapy for such purposes.","authors":"Abraham, AK., Ramanathan, M., Weinstock-Guttman, B., Mager, DE.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Biochem Pharmacol","volume":"77","issue":"12","page":"1757-62","pdf":null,"JrId":"1015","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19201081","title":"Mechanism of bone metastasis: the role of osteoprotegerin and of the host-tissue microenvironment-related survival factors.","abstract":"Osteoprotegerin (OPG), member of tumor necrosis factor (TNF) receptor superfamily, has various biological functions including bone remodeling. OPG binds to receptor activator of nuclear factor-kB ligand (RANKL) and prevents osteoclastic bone resorption. Recently, OPG has gained more clinical interest as its role in cancer-mediated bone destruction and the potential of RANKL inhibition could act as a novel treatment in tumor-induced bone disease. OPG protects prostate cancer cells from apoptotic effects of TRAIL and therefore provides tumor cells producing OPG with survival advantages. Additionally, the increased RANKL\/OPG ratio in metastatic breast cancer results in severe osteolysis. Thus, bone formation and resorption are the crux of cancer metastasis, resulting in bone pain and pathological fractures. This review provides an overview of the role of OPG in cancer-induced bone disease.","authors":"Fili, S., Karalaki, M., Schaller, B.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cancer Lett","volume":"283","issue":"1","page":"10-9","pdf":null,"JrId":"2780","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19323506","title":"Suppression of the kinase activity of receptor tyrosine kinases by anthocyanin-rich mixtures extracted from bilberries and grapes.","abstract":"Two standardized anthocyanin-rich mixtures were investigated for their ability to inhibit the receptor tyrosine kinases (RTKs) EGFR, ErbB2, ErbB3, VEGFR-2, and VEGFR-3. Both mixtures reduced the kinase activity of recombinant kinase domains of each RTK at concentrations &lt;or=12.9 microg\/mL, with preferential inhibition of VEGFR-2 and EGFR (&lt;or=3.4 microg\/mL). Similarly, ligand-induced autophosphorylation of these RTKs in human vulva carcinoma or porcine aortic endothelial cells was suppressed by both mixtures, with ErbB3 and VEGFR-3 being preferentially inhibited. Anthocyanin-rich extracts completely abrogated VEGFR-3 phosphorylation at concentrations of &gt;or=50 microg\/mL. These results indicate that anthocyanin-rich mixtures can inhibit RTKs with low specificity. The rank order of inhibitory efficacy against the tested RTKs in intact cells was VEGFR-3 &gt;&gt; VEGFR-2 &gt; ErbB3 &gt; EGFR &gt; ErbB2. Considering the important role of RTKs in carcinogenesis, their inhibition by anthocyanin-rich mixtures suggests that they may serve as biomarkers of the pharmacological efficacy of anthocyanins in future chemoprevention experiments and in clinical intervention studies.","authors":"Teller, N., Thiele, W., Marczylo, TH., Gescher, AJ., Boettler, U., Sleeman, J., Marko, D.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Agric Food Chem","volume":"57","issue":"8","page":"3094-101","pdf":null,"JrId":"4421","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18991786","title":"Novel anti-cancer strategy in bone tumors by targeting molecular and cellular modulators of bone resorption.","abstract":"Tumor cells alter the balanced process of bone formation and bone resorption mediated respectively by osteoblasts and osteoclasts, leading to the disruption of the normal equilibrium and resulting in a spectrum of osteolytic to osteoblastic lesions. This review will summarize research on molecules that play direct and essential roles in the differentiation and activity of osteoclasts, and the role of these molecules in bone destruction caused by cancer. Results from experimental models suggest that the Receptor Activator of NF-kB Ligand (RANKL), a member of the TNF superfamily is a common effector of bony lesions in osteolysis caused by primary and secondary bone tumors. Therefore, osteoclast represents an attractive target across a broad range of tumors that develop in bone. Elucidation of the mechanisms of RANKL interactions with its activator (RANK) and decoy (osteoprotegerin: OPG) receptors has enable the development of pharmacological inhibitors of RANKL (and of its signalling pathway) which have been recently patented, with potential for the treatment of cancer-induced bone disease. Blocking bone resorption by specific other drugs such as bisphosphonates, inhibitors of cathepsin K (the main enzyme involved in bone resorption mechanisms) or signalling pathways regulating osteoclast differentiation and activation is also a promising target for the treatment of osteolysis associated to bone tumors.","authors":"Brounais, B., Ruiz, C., Rousseau, J., Lamoureux, F., Blanchard, F., Heymann, D., Redini, F.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Recent Pat Anticancer Drug Discov","volume":"3","issue":"3","page":"178-86","pdf":null,"JrId":"33786","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2807488","title":"Tumour induction in fetal brain transplants exposed to the viral oncogenes polyoma middle T and v-src.","abstract":"Using a neural transplantation model, we have studied the effect of polyoma virus middle T antigen and of the viral src oncogene on the developing rat brain. For this purpose, single-cell suspensions of fetal rat brain were prepared on day 14 of gestation (E14), infected with a replication-defective retroviral vector which carries the middle T oncogene driven by an internal thymidine kinase promoter, and stereotaxically injected into the caudoputamen of adult host rats. With mock-infected donor cells, the transplants developed into an organotypically differentiated population of neurons, astrocytes, oligodendrocytes and other central nervous system cell types and expressed marker proteins of mature neuroectodermal cells, including neuron-specific enolase, synaptophysin, neurofilament protein, glial fibrillary acidic protein and S-100 protein. A high percentage of rats carrying transplants infected with the middle T-encoding vector died within two to six weeks from massive haemorrhage into the transplant. Upon microscopic examination, gross abnormalities of the microvasculature were seen, with formation of large blood-filled spaces lined by a thin layer of proliferating endothelial cells. This effect of middle T was apparently cell type-specific, since the differentiation of neuroectodermal cells within the graft proceeded in a regular fashion. In order to assess further the cell-specificity of the oncogene, analogous experiments were carried out with a retroviral construct in which the middle T cDNA had been replaced by the viral src gene (v-src). Transplants infected with the v-src vector developed astrocytomas, but no vascular abnormalities.(ABSTRACT TRUNCATED AT 250 WORDS)","authors":"Wiestler, OD., Aguzzi, A., Williams, RL., Wagner, EF., Boulter, CA., Kleihues, P.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"IARC Sci Publ","volume":null,"issue":"96","page":"267-74","pdf":null,"JrId":"22092","fulltextlink":null,"preprintlink":null,"articledate":"1989-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21750572","title":"Phosphatases: providing safe passage through mitotic exit.","abstract":"The mitosis-to-interphase transition involves dramatic cellular reorganization from a state that supports chromosome segregation to a state that complies with all functions of an interphase cell. This process, termed mitotic exit, depends on the removal of mitotic phosphorylations from a broad range of substrates. Mitotic exit regulation involves inactivation of mitotic kinases and activation of counteracting protein phosphatases. The key mitotic exit phosphatase in budding yeast, Cdc14, is now well understood. By contrast, in animal cells, it is now emerging that mitotic exit relies on distinct regulatory networks, including the protein phosphatases PP1 and PP2A.","authors":"Wurzenberger, C., Gerlich, DW.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Rev Mol Cell Biol","volume":"12","issue":"8","page":"469-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2734288","title":"Conserved terminal hairpin sequences of histone mRNA precursors are not involved in duplex formation with the U7 RNA but act as a target site for a distinct processing factor.","abstract":"The hairpin loop structure and the downstream spacer element of histone mRNA precursors are both needed for efficient 3' end formation in vivo and in vitro. Though generally considered as a single processing signal, these two motifs are involved in different types of interaction with the processing machinery. Whereas RNA duplex formation between the downstream spacer element and the U7 small nuclear RNA is essential for processing, we show here that base pairing between the histone stem-loop structure and the U7 RNA is not relevant. Our experiments demonstrate that a processing factor other than the U7 RNA makes contact with the highly conserved hairpin structure of the histone precursor. The recognition of the target site by the processing factor is structure and sequence specific. Prevention of this interaction results in an 80% decrease of 3' cleavage efficiency in vitro. The hairpin binding factor is Sm-precipitable and can be partially separated from the U7 small nuclear ribonucleoprotein particle on a Mono Q column.","authors":"Vasserot, AP., Schaufele, FJ., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Proc Natl Acad Sci U S A","volume":"86","issue":"12","page":"4345-9","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1989-07-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20385584","title":"Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes.","abstract":"Polycomb group (PcG) proteins are transcriptional repressors, which regulate proliferation and cell fate decisions during development, and their deregulated expression is a frequent event in human tumours. The Polycomb repressive complex 2 (PRC2) catalyzes trimethylation (me3) of histone H3 lysine 27 (K27), and it is believed that this activity mediates transcriptional repression. Despite the recent progress in understanding PcG function, the molecular mechanisms by which the PcG proteins repress transcription, as well as the mechanisms that lead to the activation of PcG target genes are poorly understood. To gain insight into these mechanisms, we have determined the global changes in histone modifications in embryonic stem (ES) cells lacking the PcG protein Suz12 that is essential for PRC2 activity. We show that loss of PRC2 activity results in a global increase in H3K27 acetylation. The methylation to acetylation switch correlates with the transcriptional activation of PcG target genes, both during ES cell differentiation and in MLL-AF9-transduced hematopoietic stem cells. Moreover, we provide evidence that the acetylation of H3K27 is catalyzed by the acetyltransferases p300 and CBP. Based on these data, we propose that the PcG proteins in part repress transcription by preventing the binding of acetyltransferases to PcG target genes.","authors":"Pasini, D., Malatesta, M., Jung, HR., Walfridsson, J., Willer, A., Olsson, L., Skotte, J., Wutz, A., Porse, B., Jensen, ON., Helin, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nucleic Acids Res","volume":"38","issue":"15","page":"4958-69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34893784","title":"Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis.","abstract":null,"authors":"Kawahara, R., Chernykh, A., Alagesan, K., Bern, M., Cao, W., Chalkley, RJ., Cheng, K., Choo, MS., Edwards, N., Goldman, R., Hoffmann, M., Hu, Y., Huang, Y., Kim, JY., Kletter, D., Liquet, B., Liu, M., Mechref, Y., Meng, B., Neelamegham, S., Nguyen-Khuong, T., Nilsson, J., Pap, A., Park, GW., Parker, BL., Pegg, CL., Penninger, JM., Phung, TK., Pioch, M., Rapp, E., Sakalli, E., Sanda, M., Schulz, BL., Scott, NE., Sofronov, G., Stadlmann, J., Vakhrushev, SY., Woo, CM., Wu, HY., Yang, P., Ying, W., Zhang, H., Zhang, Y., Zhao, J., Zaia, J., Haslam, SM., Palmisano, G., Yoo, JS., Larson, G., Khoo, KH., Medzihradszky, KF., Kolarich, D., Packer, NH., Thaysen-Andersen, M.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Nat Methods","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18000378","title":"MicroRNAs in carcinogenesis.","abstract":"MicroRNAs are an abundant class of noncoding RNAs, typically 20-23 nucleotides in length that are often evolutionarily conserved in metazoans and expressed in a cell and tissue specific manner. MicroRNAs exert their gene regulatory activity primarily by imperfectly base pairing to the 3' UTR of their target mRNAs, leading to mRNA degradation or translational inhibition. In cancer, microRNAs are often dysregulated with their expression patterns being correlated with clinically relevant tumor characteristics. Recently, microRNAs were shown to be directly involved in cancer initiation and progression. This review focuses primarily on emerging developments in the microRNA field that impact our understanding of how these molecules contribute to carcinogenesis.","authors":"Hagan, JP., Croce, CM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cytogenet Genome Res","volume":"118","issue":"2-4","page":"252-9","pdf":null,"JrId":"29987","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18988671","title":"Strain-specific differences in the mechanisms of progesterone regulation of murine mammary gland development.","abstract":"Progesterone (P) is required for normal mammary gland development, and is implicated in the etiology of mammary cancer in rodents and humans. We analyzed mammary gland developmental responses to P and estrogen (E) in two strains of mice (BALB\/c and C57BL\/6) that exhibit differences in ductal development at sexual maturity and alveologenesis during pregnancy. C57BL\/6 mice exhibited reduced proliferative and morphological responses to P. Analysis of known mediators of sidebranching and alveologenesis revealed that reduced P-induced expression of P receptor isoform B and receptor activator of nuclear factor-kappaB ligand (RANKL), as well as altered expression and regulation of cyclin D1, CCAAT\/enhancer binding protein beta, and the downstream effectors of RANKL, nuclear Id2 and p21, contribute significantly to the reduced P responsiveness of the C57BL\/6 mammary gland. In contrast, E responsiveness was greater in C57BL\/6 than in BALB\/c glands. E may play a compensatory role in C57BL\/6 alveologenesis through its effect on the induction and activation of signal transducer and activator of transcription 5a, a known regulator of RANKL. These observations suggest that in human populations with heterogeneous genetic backgrounds, individuals may respond differentially to the same hormone. Thus, genetic diversity may have a role in determining the effects of P in normal mammary development and tumorigenesis.","authors":"Aupperlee, MD., Drolet, AA., Durairaj, S., Wang, W., Schwartz, RC., Haslam, SZ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Endocrinology","volume":"150","issue":"3","page":"1485-94","pdf":null,"JrId":"3530","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19011755","title":"Role of full-length osteoprotegerin in tumor cell biology.","abstract":"Osteoprotegerin (OPG) is a soluble tumor necrosis factor receptor family member, which potently inhibits RANKL-mediated osteoclastogenesis. Numerous constructs have been created for therapeutic purposes in which the heparin-binding and death homology domains of OPG were removed and the remaining peptide (amino acids 22-194) was fused to the Fc domain of human IgG1 (OPG-Fc). The administration of OPG-Fc efficiently counteracted bone loss in a variety of preclinical models of cancers. However, several in vitro studies have shown that native or recombinant full-length OPG not only neuralizes RANKL, but also the death-inducing ligand TRAIL, suggesting that OPG might potentially counteract the anti-tumor activity of TRAIL. Additional evidence suggests that full-length OPG possesses RANKL- and TRAIL-independent biological properties, mainly related to the promotion of endothelial cell survival and angiogenesis. Finally, breast tumor cells overexpressing OPG have shown increased bone metastatic potential in vivo. The relevance of these apparently conflicting findings in tumor cell biology is highlighted.","authors":"Zauli, G., Melloni, E., Capitani, S., Secchiero, P.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell Mol Life Sci","volume":"66","issue":"5","page":"841-51","pdf":null,"JrId":"20436","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21179009","title":"MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression.","abstract":"Recombinant adeno-associated viruses (rAAVs) that can cross the blood-brain-barrier and achieve efficient and stable transvascular gene transfer to the central nervous system (CNS) hold significant promise for treating CNS disorders. However, following intravascular delivery, these vectors also target liver, heart, skeletal muscle, and other tissues, which may cause untoward effects. To circumvent this, we used tissue-specific, endogenous microRNAs (miRNAs) to repress rAAV expression outside the CNS, by engineering perfectly complementary miRNA-binding sites into the rAAV9 genome. This approach allowed simultaneous multi-tissue regulation and CNS-directed stable transgene expression without detectably perturbing the endogenous miRNA pathway. Regulation of rAAV expression by miRNA was primarily via site-specific cleavage of the transgene mRNA, generating specific 5' and 3' mRNA fragments. Our findings promise to facilitate the development of miRNA-regulated rAAV for CNS-targeted gene delivery and other applications.","authors":"Xie, J., Xie, Q., Zhang, H., Ameres, SL., Hung, JH., Su, Q., He, R., Mu, X., Seher Ahmed, S., Park, S., Kato, H., Li, C., Mueller, C., Mello, CC., Weng, Z., Flotte, TR., Zamore, PD., Gao, G.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mol Ther","volume":"19","issue":"3","page":"526-35","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18707795","title":"Pathophysiological roles of osteoprotegerin (OPG).","abstract":"Osteoprotegerin (OPG) is a secreted glycoprotein central to bone turnover via its role as a decoy receptor for the receptor activator of nuclear factor kappaB ligand (RANKL) and has traditionally been linked to a number of bone-related diseases. However, there is additional evidence that OPG can promote cell survival by inhibiting TNF-related apoptosis-inducing ligand (TRAIL)-induced apoptosis. As a result, a number of in vitro, in vivo and clinical studies have been performed assessing the role of OPG in tumourigenesis. Similar studies have been performed regarding vascular pathologies, resulting from observations of expression and regulation of OPG in the vasculature. This review aims to provide an update on this area and assess the potential protective or detrimental role of OPG in both vascular pathologies and tumourigenesis.","authors":"Reid, P., Holen, I.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Eur J Cell Biol","volume":"88","issue":"1","page":"1-17","pdf":null,"JrId":"3585","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24581498","title":"Serpins promote cancer cell survival and vascular co-option in brain metastasis.","abstract":"Brain metastasis is an ominous complication of cancer, yet most cancer cells that infiltrate the brain die of unknown causes. Here, we identify plasmin from the reactive brain stroma as a defense against metastatic invasion, and plasminogen activator (PA) inhibitory serpins in cancer cells as a shield against this defense. Plasmin suppresses brain metastasis in two ways: by converting membrane-bound astrocytic FasL into a paracrine death signal for cancer cells, and by inactivating the axon pathfinding molecule L1CAM, which metastatic cells express for spreading along brain capillaries and for metastatic outgrowth. Brain metastatic cells from lung cancer and breast cancer express high levels of anti-PA serpins, including neuroserpin and serpin B2, to prevent plasmin generation and its metastasis-suppressive effects. By protecting cancer cells from death signals and fostering vascular co-option, anti-PA serpins provide a unifying mechanism for the initiation of brain metastasis in lung and breast cancers.","authors":"Valiente, M., Obenauf, AC., Jin, X., Chen, Q., Zhang, XH., Lee, DJ., Chaft, JE., Kris, MG., Huse, JT., Brogi, E., Massagu\u00e9, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell","volume":"156","issue":"5","page":"1002-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-121","title":"MicroRNAs and their impact on tumor initiation and progression.","abstract":null,"authors":"Gebeshuber, C., Salv\u00e1 Gir\u00f3, A., Martinez, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"In: Human Epithelial Tumor Cell Plasticity: Implications for Cancer Progression and Metastasis. Ed. Paul J. Higgins","volume":"p","issue":"","page":"103","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-127","title":"Do genes dream?","abstract":null,"authors":"Penninger, J.M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"In: Identitaet(en). Ed. GLOBArt. Springer","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":"","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36272083","title":"Navigation and Use of Custom Tracks within the Axolotl Genome Browser.","abstract":"The availability of the chromosome-scale axolotl genome sequences has made it possible to explore genome evolution, perform cross-species comparisons, and use additional sequencing data to analyze both genome-wide features and individual genes. Here, we will focus on the UCSC genome browser and demonstrate in a step-by-step manner how to use it to integrate different data to approach a broad question of the Fgf8 locus evolution and analyze the neighborhood of a gene that was reported missing in axolotl - Pax3.","authors":"Nowoshilow, S., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Methods Mol Biol","volume":"2562","issue":null,"page":"273-289","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2685555","title":"Mating-type control in Saccharomyces cerevisiae: isolation and characterization of mutants defective in repression by a1-alpha 2.","abstract":"The alpha 2 protein, the product of the MAT alpha 2 cistron, represses various genes specific to the a mating type (alpha 2 repression), and when combined with the MATa1 gene product, it represses MAT alpha 1 and various haploid-specific genes (a1-alpha 2 repression). One target of a1-alpha 2 repression is RME1, which is a negative regulator of a\/alpha-specific genes. We have isolated 13 recessive mutants whose a1-alpha 2 repression is defective but which retain alpha 2 repression in a genetic background of ho MATa HML alpha HMRa sir3 or ho MAT alpha HMRa HMRa sir3. These mutations can be divided into three different classes. One class contains a missense mutation, designated hml alpha 2-102, in the alpha 2 cistron of HML, and another class contains two mat alpha 2-202, in the MAT alpha locus. These three mutants each have an amino acid substitution of tyrosine or acid substitution of tyrosine or phenylalanine for cysteine at the 33rd codon from the translation initiation codon in the alpha 2 cistron of HML alpha or MAT alpha. The remaining 10 mutants make up the third class and form a single complementation group, having mutations designated aar1 (a1-alpha 2 repression), at a gene other than MAT, HML, HMR, RME1, or the four SIR genes. Although a diploid cell homozygous for the aarl and sir3 mutations and for the MATa, HML alpha, and HMRa alleles showed alpha mating type, it could sporulate and gave rise to asci containing four alpha mating-type spores. These facts indicate that the domain for alpha2 repression is separable from that for a1-alpha2 protein interaction or complex formation in the alpha2 protein and that an additional regulation gene, AAR1, is associated with the a1-alpha2 repression of the alpha1 cistron and haploid-specific genes.","authors":"Harashima, S., Miller, AM., Tanaka, K., Kusumoto, K., Tanaka, K., Mukai, Y., Nasmyth, K., Oshima, Y.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Mol Cell Biol","volume":"9","issue":"10","page":"4523-30","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1989-12-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21106652","title":"Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins.","abstract":"In flies, 22-23-nucleotide (nt) microRNA duplexes typically contain mismatches and begin with uridine, so they bind Argonaute1 (Ago1), whereas 21-nt siRNA duplexes are perfectly paired and begin with cytidine, promoting their loading into Ago2. A subset of Drosophila endogenous siRNAs-the hairpin-derived hp-esiRNAs-are born as mismatched duplexes that often begin with uridine. These would be predicted to load into Ago1, yet accumulate at steady-state bound to Ago2. In vitro, such hp-esiRNA duplexes assemble into Ago1. In vivo, they encounter complementary target mRNAs that trigger their tailing and trimming, causing Ago1-loaded hp-esiRNAs to be degraded. In contrast, Ago2-associated hp-esiRNAs are 2'-O-methyl modified at their 3' ends, protecting them from tailing and trimming. Consequently, the steady-state distribution of esiRNAs reflects not only their initial sorting between Ago1 and Ago2 according to their duplex structure, length, and first nucleotide, but also the targeted destruction of the single-stranded small RNAs after their loading into an Argonaute protein.","authors":"Ameres, SL., Hung, JH., Xu, J., Weng, Z., Zamore, PD.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"RNA","volume":"17","issue":"1","page":"54-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19357790","title":"Pharmacologic inhibition of the TGF-beta type I receptor kinase has anabolic and anti-catabolic effects on bone.","abstract":"During development, growth factors and hormones cooperate to establish the unique sizes, shapes and material properties of individual bones. Among these, TGF-beta has been shown to developmentally regulate bone mass and bone matrix properties. However, the mechanisms that control postnatal skeletal integrity in a dynamic biological and mechanical environment are distinct from those that regulate bone development. In addition, despite advances in understanding the roles of TGF-beta signaling in osteoblasts and osteoclasts, the net effects of altered postnatal TGF-beta signaling on bone remain unclear. To examine the role of TGF-beta in the maintenance of the postnatal skeleton, we evaluated the effects of pharmacological inhibition of the TGF-beta type I receptor (TbetaRI) kinase on bone mass, architecture and material properties. Inhibition of TbetaRI function increased bone mass and multiple aspects of bone quality, including trabecular bone architecture and macro-mechanical behavior of vertebral bone. TbetaRI inhibitors achieved these effects by increasing osteoblast differentiation and bone formation, while reducing osteoclast differentiation and bone resorption. Furthermore, they induced the expression of Runx2 and EphB4, which promote osteoblast differentiation, and ephrinB2, which antagonizes osteoclast differentiation. Through these anabolic and anti-catabolic effects, TbetaRI inhibitors coordinate changes in multiple bone parameters, including bone mass, architecture, matrix mineral concentration and material properties, that collectively increase bone fracture resistance. Therefore, TbetaRI inhibitors may be effective in treating conditions of skeletal fragility.","authors":"Mohammad, KS., Chen, CG., Balooch, G., Stebbins, E., McKenna, CR., Davis, H., Niewolna, M., Peng, XH., Nguyen, DH., Ionova-Martin, SS., Bracey, JW., Hogue, WR., Wong, DH., Ritchie, RO., Suva, LJ., Derynck, R., Guise, TA., Alliston, T.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS One","volume":"4","issue":"4","page":"e5275","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8812138","title":"Expression of avian Pax1 and Pax9 is intrinsically regulated in the pharyngeal endoderm, but depends on environmental influences in the paraxial mesoderm.","abstract":"Pax1 and Pax9 represent a subfamily of paired-box-containing genes. In vertebrates, Pax1 and Pax9 transcripts have been found specifically in mesodermal tissues and the pharyngeal endoderm. Pax1 expression in the sclerotomes has been shown to be indispensable for proper formation of the axial skeleton, but expression of Pax1 in the endoderm has not been studied in detail. We have cloned the chick homologue of the murine Pax9 gene. Our results show that transcripts of Pax1 and Pax9 are first detectable in the prospective foregut endoderm of headfold-stage avian embryos. Endodermal expression correlates with the highly proliferative zones of the folding foregut and evaginating pharyngeal pouches. In later stages, Pax1 and Pax9 are expressed in overlapping but distinct patterns within the developing sclerotomes and limb buds. From grafting experiments we conclude that activation of pharyngeal Pax1 and Pax9 expression is an intrinsic property of the endoderm, not requiring midline structures or head mesoderm. In contrast, notochord is required to induce Pax1 in competent sclerotomes. Here we show that in vitro there is a cranio-caudal gradient of inductive capacity in the notochord. This coincides with the graded expression of Pax1 and Pax9 along the cranio-caudal axis in 2- to 3-day-old embryos. Furthermore, paraxial head mesoderm shows no competence to express Pax1. Finally, in vitro we find counteracting influences on notochord signaling by lateral tissues (lateral plate, intermediate mesoderm), leading to an inhibition of Sonic hedgehog (Shh) expression in notochord and floor plate, as well as Pax1 and Pax9 expression in sclerotomes. Taken together, our results demonstrate that different mechanisms regulate expression of Pax1 and Pax9 in foregut and sclerotome, but suggest a common function for both genes in the two tissues that is promoting proliferation and preventing fusion of neighboring blastemas.","authors":"M\u00fcller, TS., Ebensperger, C., Neub\u00fcser, A., Koseki, H., Balling, R., Christ, B., Wilting, J.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Dev Biol","volume":"178","issue":"2","page":"403-17","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19442193","title":"In or out stemness: comparing growth factor signalling in mouse embryonic stem cells and primordial germ cells.","abstract":"Embryonic stem (ES) cells do not exist in nature but, usually produced from the inner cell mass (ICM) of the blastocyst, are considered equivalent to ICM cells captured during a short period of transient self-renewal and pluripotency capability. Although, artificial, ES cells represent a formidable model to investigate fundamental aspects of cell stemness and early embryo development. ES cells are indeed the only stem cell type able to indefinite self-renewal and to differentiate into cellular derivates of ectodermal, mesodermal and endodermal lineages. Recent extensive studies have revealed that ES cells maintain self-renewal and pluripotency because of a self-organizing network of transcription factors and intracellular pathways activated by extracellular signalling that together prevent their differentiation and promote their proliferation, and because of epigenetic processes that maintain the chromatin in a plastic differentiation status. Primordial germ cells (PGCs), the embryonic precursors of gametes, because of their unique ability to retain true developmental totipotency, are considered the mother of all stem cells. Despite several similarities with ES cells, they display only transient self-renewal capability and distinct lineage-specific characteristics. In fact, in normal condition PGCs are believed to differentiate into germ cells only, oogonia\/oocytes in the female, and prospermatogonia in the male which ultimately produce eggs and sperm, respectively. It is not until the fertilization of the egg or parthenogenesis that the intrinsic germ cell totipotency program is revealed. Many aspects of the extrinsic factors and signalling required for ES cell self-renewal and pluripotency have been identified and dissected. On the other hand, several extrinsic factors controlling PGC development have been identified, but the underlying molecular signalling remains little defined. In the present review, by comparing the available information about signalling elicited by four growth factors such as leukaemia inhibitory factor (LIF), bone morphogenic protein 4 (BMP4), fibroblast growth factor 2 (FGF2) and kit ligand (KL) in mouse ES cells and PGCs, on which most of such studies have been performed, we aimed to give clues for the molecular understanding of the similarities and differences between these two unique cell types and to explain how apparent contradictory properties such as lineage-specific characteristics and pluripotency may coexist within PGCs. The first two growth factors have been demonstrated to control key aspects of the self-renewal and pluripotency of ES cells. BMP4 and KL are known for their crucial role in regulating various process of PGC development in the embryo from the formation of PGC precursors and PGC specification (BMP4) to their survival, proliferation and migration (KL). Moreover, the combined action of LIF, FGF2 and KL is necessary and sufficient for PGC transformation into ES-like cells termed embryonic germ (EG) cells.","authors":"De Felici, M., Farini, D., Dolci, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Stem Cell Res Ther","volume":"4","issue":"2","page":"87-97","pdf":null,"JrId":"33892","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19348043","title":"Wnt therapy for bone loss: golden goose or Trojan horse?","abstract":"The Wnt pathway has been found to play a role in the development of many tissues and to spur growth and differentiation of adult osteoblasts, sparking interest in its potential clinical application for bone growth. However, when deregulated, this pathway can be oncogenic in some tissues. In this issue of the JCI, Kansara and colleagues reveal that Wnt inhibitory factor 1 is epigenetically silenced in human osteosarcomas and that its absence augments osteosarcoma formation in mice (see the related article beginning on page 837). These observations suggest the need for caution in stimulating the Wnt pathway for therapeutic bone growth.","authors":"Enders, GH.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Clin Invest","volume":"119","issue":"4","page":"758-60","pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8791397","title":"Cell differentiation.","abstract":null,"authors":"Derynck, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Curr Opin Cell Biol","volume":"7","issue":"6","page":"843-4","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"1995-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"39556024","title":"Alternative lengthening of telomere-based immortalization renders H3G34R-mutant diffuse hemispheric glioma hypersensitive to PARP inhibitor combination regimens.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">39556024<\/PMID><DateCompleted><Year>2025<\/Year><Month>03<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2025<\/Year><Month>03<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1523-5866<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>27<\/Volume><Issue>3<\/Issue><PubDate><Year>2025<\/Year><Month>Mar<\/Month><Day>07<\/Day><\/PubDate><\/JournalIssue><Title>Neuro-oncology<\/Title><ISOAbbreviation>Neuro Oncol<\/ISOAbbreviation><\/Journal><ArticleTitle>Alternative lengthening of telomere-based immortalization renders H3G34R-mutant diffuse hemispheric glioma hypersensitive to PARP inhibitor combination regimens.<\/ArticleTitle><Pagination><StartPage>811<\/StartPage><EndPage>827<\/EndPage><MedlinePgn>811-827<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/neuonc\/noae228<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Diffuse hemispheric glioma, H3 G34R\/V-mutant (DHG-H3G34) is characterized by poor prognosis and lack of effective treatment options. DHG-H3G34R further harbor deactivation of alpha-thalassemia\/mental retardation syndrome X-linked protein (ATRX; DHG-H3G34R_ATRX) suggesting a unique interaction of these 2 oncogenic alterations. In this study, we dissect their cell biological interplay, investigate the impact on telomere stabilization, and consequently validate a targeted therapy approach.","authors":"Laemmerer, A., Lehmann, C., Mayr, L., Bruckner, K., Gabler, L., Senfter, D., Meyer, P., Balber, T., Pirker, C., Jaunecker, CN., Kirchhofer, D., Vician, P., Griesser, M., Spiegl-Kreinecker, S., Schmook, MT., Traub-Weidinger, T., Kuess, P., Eckert, F., Federico, A., Madlener, S., Stepien, N., Robl, B., Baumgartner, A., Hainfellner, JA., Dieckmann, K., Dorfer, C., Roessler, K., Corsini, NS., Holzmann, K., Schmidt, WM., Peyrl, A., Azizi, AA., Haberler, C., Beck, A., Pfister, SM., Schueler, J., L\u00f6tsch-Gojo, D., Knoblich, JA., Berger, W., Gojo, J.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Neuro Oncol","volume":"27","issue":"3","page":"811-827","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-03-08","doi":"10.1093\/neuonc\/noae228","first_author":null,"corresponding_authors":null},{"pmid":"22693558","title":"The BMP ligand Gdf6 prevents differentiation of coronal suture mesenchyme in early cranial development.","abstract":"Growth Differentiation Factor-6 (Gdf6) is a member of the Bone Morphogenetic Protein (BMP) family of secreted signaling molecules. Previous studies have shown that Gdf6 plays a role in formation of a diverse subset of skeletal joints. In mice, loss of Gdf6 results in fusion of the coronal suture, the intramembranous joint that separates the frontal and parietal bones. Although the role of GDFs in the development of cartilaginous limb joints has been studied, limb joints are developmentally quite distinct from cranial sutures and how Gdf6 controls suture formation has remained unclear. In this study we show that coronal suture fusion in the Gdf6-\/- mouse is due to accelerated differentiation of suture mesenchyme, prior to the onset of calvarial ossification. Gdf6 is expressed in the mouse frontal bone primordia from embryonic day (E) 10.5 through 12.5. In the Gdf6-\/- embryo, the coronal suture fuses prematurely and concurrently with the initiation of osteogenesis in the cranial bones. Alkaline phosphatase (ALP) activity and Runx2 expression assays both showed that the suture width is reduced in Gdf6+\/- embryos and is completely absent in Gdf6-\/- embryos by E12.5. ALP activity is also increased in the suture mesenchyme of Gdf6+\/- embryos compared to wild-type. This suggests Gdf6 delays differentiation of the mesenchyme occupying the suture, prior to the onset of ossification. Therefore, although BMPs are known to promote bone formation, Gdf6 plays an inhibitory role to prevent the osteogenic differentiation of the coronal suture mesenchyme.","authors":"Clendenning, DE., Mortlock, DP.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"5","page":"e36789","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8921939","title":"Tumor cells expressing a recall antigen are powerful cancer vaccines.","abstract":"Tumor cells were engineered to express a specific recall antigen molecule to serve as a target for the host's existing memory response, and then used as immunogens as a novel form of cancer vaccine. As recall antigen, the efficiently expressible hybrid protein Heat1 was employed, that contains an antigenic fragment of the Mycobacterium bovis 65-kDa heat shock protein (hsp65), and thus can be recognized in mice immunized with live Bacillus Calmette-Gu\u00e9rin (BCG) or its derivatives. Mouse M-3 melanoma cells were transfected to express Heat1, irradiated, and used as anti-melanoma vaccines. Vaccination elicited anti-tumor immunity in mice, i.e. a subsequent challenge with the parental wild-type M-3 melanoma cells was rejected. Successful vaccination was dependent on the correct recognition of the recall antigen, since vaccination failed to prevent outgrowth of the challenge in mice possessing no memory response against the recall antigen. The results indicate that expression of a recall antigen can turn tumor cells into powerful vaccines. By using the Heat1 protein or other appropriate antigens, this general concept may be applied for human therapy.","authors":"Schweighoffer, T.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Eur J Immunol","volume":"26","issue":"11","page":"2559-64","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"1997-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8790871","title":"Normal brainstem auditory evoked potentials in Pax5-deficient mice despite morphologic alterations in the auditory midbrain region.","abstract":"The inferior colliculus in the auditory midbrain region is underdeveloped near the midline in mice lacking the transcription factor Pax5. We have now tested whether hearing deficiencies occur in these mice by measuring auditory evoked brainstem responses. However, the responses and audiograms obtained in homozygous Pax5 mutants did not differ from those of control mice, suggesting that the observed morphologic alterations of the inferior colliculus do not affect hearing, as judged by auditory evoked potential recordings. The only detectable effect of the Pax5 mutation was a delay in the development of the auditory sensitivity and response latency that correlates with the general growth retardation observed in these mice.","authors":"Reimer, K., Urb\u00e1nek, P., Busslinger, M., Ehret, G.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Audiology","volume":"35","issue":"1","page":"55-61","pdf":null,"JrId":"909","fulltextlink":null,"preprintlink":null,"articledate":"1996-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8844203","title":"Activation of the complement system by synthetic DNA complexes: a potential barrier for intravenous gene delivery.","abstract":"We have examined the complement-activating properties of synthetic cationic molecules and their complexes with DNA. Commonly used gene delivery vehicles include complexes of DNA with polylysine of various chain lengths, transferrin-polylysine, a fifth-generation poly(amidoamine) (PAMAM) dendrimer, poly(ethyleneimine), and several cationic lipids (DOTAP, DC-Chol\/DOPE, DOGS\/DOPE, and DOTMA\/DOPE). These agents activate the complement system to varying extents. Strong complement activation is seen with long-chain polylysines, the dendrimer, poly(ethyleneimine), and DOGS (half-maximal at about 3 microM amine content in the assay used). Compared to these compounds, the other cationic lipids (in liposome formulations) are weak activators of the complement system (half-maximal approximately 50-100 microM positive charge in assay). Complement activation by polylysine is strongly dependent on the chain length. Short-chain oligolysines are comparable to cationic lipids in their activation of complement. Incubation of these compounds with DNA to form complexes reduces complement activation in virtually all cases. The degree of complement activation by DNA complexes is strongly dependent on the ratio of polycation and DNA (expressed as the charge ratio) for polylysine, dendrimer, poly(ethyleneimine), and DOGS. To a lesser degree, charge ratio also influences complement activation by monovalent cationic lipid-DNA complexes. For polylysine-DNA complexes, complement activation can be considerably reduced by modifying the surface of preformed DNA complexes with polyethyleneglycol (half-maximal approximately 20 microM amine content). The data suggests that, by appropriate formulation of DNA complexes, complement activation can be minimized or even avoided. These findings should facilitate the search for DNA complex formulations appropriate for reproducible intravenous gene delivery.","authors":"Plank, C., Mechtler, K., Szoka, FC., Wagner, E.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Hum Gene Ther","volume":"7","issue":"12","page":"1437-46","pdf":null,"JrId":"1041","fulltextlink":null,"preprintlink":null,"articledate":"1997-01-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18229681","title":"Analysis of large-scale sequencing of small RNAs.","abstract":"The advent of large-scale sequencing has opened up new areas of research, such as the study of Piwi-interacting small RNAs (piRNAs). piRNAs are longer than miRNAs, close to 30 nucleotides in length, involved in various functions, such as the suppression of transposons in germline. Since a large number of them (many tens of thousands) are generated from a wide range of positions in the genome, large-scale sequencing is the only way to study them. The key to understanding their genesis and biological roles is efficient analysis, which is complicated by the large volumes of sequence data. Taking account of the underlying biology is also important. We describe here novel analyses techniques and tools applied to small RNAs from germ cells in D. melanogaster, that allowed us to infer mechanism and biological function.","authors":"Olson, AJ., Brennecke, J., Aravin, AA., Hannon, GJ., Sachidanandam, R.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Pac Symp Biocomput","volume":null,"issue":null,"page":"126-36","pdf":null,"JrId":"20660","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40208986","title":"Rules of engagement for condensins and cohesins guide mitotic chromosome formation.","abstract":"We used Hi-C, imaging, proteomics, and polymer modeling to define rules of engagement for SMC (structural maintenance of chromosomes) complexes as cells refold interphase chromatin into rod-shaped mitotic chromosomes. First, condensin disassembles interphase chromatin loop organization by evicting or displacing extrusive cohesin. Second, condensin bypasses cohesive cohesins, thereby maintaining sister chromatid cohesion as sisters separate. Studies of mitotic chromosomes formed by cohesin, condensin II, and condensin I alone or in combination lead to refined models of mitotic chromosome conformation. In these models, loops are consecutive and not overlapping, implying that condensins stall upon encountering each other. The dynamics of Hi-C interactions and chromosome morphology reveal that during prophase, loops are extruded in vivo at &#x223c;1 to 3 kilobases per second by condensins as they form a disordered discontinuous helical scaffold within individual chromatids.","authors":"Samejima, K., Gibcus, JH., Abraham, S., Cisneros-Soberanis, F., Samejima, I., Beckett, AJ., Pu\u01ce\u010dekov\u00e1, N., Abad, MA., Spanos, C., Medina-Pritchard, B., Paulson, JR., Xie, L., Jeyaprakash, AA., Prior, IA., Mirny, LA., Dekker, J., Goloborodko, A., Earnshaw, WC.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Science","volume":"388","issue":"6743","page":"eadq1709","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-10","doi":"10.1126\/science.adq1709","first_author":null,"corresponding_authors":null},{"pmid":"34967612","title":"Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics.","abstract":"Single-cell proteomics workflows have considerably improved in sensitivity and reproducibility to characterize as-yet unknown biological phenomena. With the emergence of multiplexed single-cell proteomics, studies increasingly present single-cell measurements in conjunction with an abundant congruent carrier to improve the precursor selection and enhance identifications. While these extreme carrier spikes are often &gt;100\u00d7 more abundant than the investigated samples, the total ion current undoubtably increases but the quantitative accuracy possibly is affected. We here focus on narrowly titrated carrier spikes (i.e., &lt;20\u00d7) and assess their elimination for a comparable sensitivity with superior accuracy. We find that subtle changes in the carrier ratio can severely impact the measurement variability and describe alternative multiplexing strategies to evaluate data quality. Lastly, we demonstrate elevated replicate overlap while preserving acquisition throughput at an improved quantitative accuracy with DIA-TMT and discuss optimized experimental designs for multiplexed proteomics of trace samples. This comprehensive benchmarking gives an overview of currently available techniques and guides the conceptualization of the optimal single-cell proteomics experiment.","authors":"Ctortecka, C., Stejskal, K., Kr\u0161\u0161\u00e1kov\u00e1, G., Mendjan, S., Mechtler, K.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Anal Chem","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8875231","title":"Depletion of naive T cells of the peripheral lymph nodes abrogates systemic antitumor protection conferred by IL-2 secreting cancer vaccines.","abstract":"It has been postulated that IL-2 secreting cancer vaccines establish antitumor immunity because the cytokine acting in a paracrine fashion would deliver a helper signal directly to the T cells making contact with the modified tumor cells at the site of vaccination. However, patterns of lymphocyte recirculation cannot be reconciled with the above direct interaction model: only primed memory T cells rather than naive T lymphocytes patrol the periphery, while naive T cells travel to the peripheral lymph nodes, where priming occurs. We have found that in vivo treatment of mice with the antibody MEL-14 directed against L-selectin, which is a molecule expressed at high levels on naive T cells, can completely abrogate protection against a mouse melanoma conferred by an IL-2 secreting vaccine. Since mouse memory CD4 and CD8 T cells are L-selectin-low, only migration of naive T cells is perturbed by the in vivo antibody blockade. Thus, priming of naive T cells in the draining lymph node is a critical step for the successful vaccination by IL-2 secreting cancer vaccines. Such priming is performed most efficiently by professional antigen presenting cells; consequently, these data also imply that allogeneic origin of tumor vaccines may not exclude successful vaccination.","authors":"Schweighoffer, T., Schmidt, W., Buschle, M., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Gene Ther","volume":"3","issue":"9","page":"819-24","pdf":null,"JrId":"8603","fulltextlink":null,"preprintlink":null,"articledate":"1997-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19281760","title":"The contribution of different cell lineages to bone repair: exploring a role for muscle stem cells.","abstract":"An anabolic response driven by osteoblasts is critical for the process of bone healing. Current evidence suggests that these osteoblasts may arise from multiple tissue types and cell lineages. Stem cells present in the bone marrow, periosteum, local soft tissues, vasculature, and\/or circulation have been shown to have osteogenic potential. Transplanted cells from these sources have also been shown to incorporate into induced ectopic bone or repaired bone. While these experiments demonstrate the latent capacity of different lineages to assume an osteoblastic phenotype under pro-osteogenic conditions, the actual contribution of the different lineages to various repair situations in vivo remains unclear. This review explores the data arising from different bone formation and repair models. We propose a model suggesting that cells arising from the local tissues, particularly muscle cells, may play an important role in fracture repair under situations where the periosteal and\/or bone marrow progenitor populations are depleted.","authors":"Schindeler, A., Liu, R., Little, DG.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Differentiation","volume":"77","issue":"1","page":"12-8","pdf":null,"JrId":"3402","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8854860","title":"The Lx1 gene maps to mouse chromosome 17 and codes for a protein that is homologous to glucose and polyspecific transmembrane transporters.","abstract":"A novel mouse gene, provisionally named Lx1, has been cloned and sequenced. Lx1 most likely represents the mouse homolog of the rat gene OCT1, which encodes a polyspecific transmembrane transporter that is possibly involved in drug elimination. The LX1 predicted protein is highly hydrophobic, possesses twelve putative transmembrane domains, and also shares significant homology with members of the sugar transporter family, particularly the novel liver-specific transporter NLT. Lx1 mRNA is expressed at high levels in mouse liver, kidney, and intestine, and at low levels in the adrenals and in lactating mammary glands. The Lx1 gene maps very close to the imprinted Igf2r\/Mpr300 gene on mouse Chromosome (Chr) 17, in a region that is syntenic to human Chr 6q. Chr 6q has been previously associated with transient neonatal diabetes mellitus and breast cancer.","authors":"Schweifer, N., Barlow, DP.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Mamm Genome","volume":"7","issue":"10","page":"735-40","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"1997-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15650749","title":"Inducible DNA-loop formation blocks transcriptional activation by an SV40 enhancer.","abstract":"It is well established that gene expression in eukaryotes is controlled by sequence-dependent binding of trans-acting proteins to regulatory elements like promoters, enhancers or silencers. A less well understood level of gene regulation is governed by the various structural and functional states of chromatin, which have been ascribed to changes in covalent modification of core histone proteins. And, much on how topological domains in the genome take part in establishing and maintaining distinct gene expression patterns is still unknown. Here we present a set of regulatory proteins that allow to reversibly alter the DNA structure in vivo and in vitro by adding low molecular weight effectors that control their oligomerization and DNA binding. Using this approach, we completely regulate the activity of an SV40 enhancer in HeLa cells by reversible loop formation to topologically separate it from the promoter. This result establishes a new mechanism for DNA-structure-dependent gene regulation in vivo and provides evidence supporting the structural model of insulator function.","authors":"Ameres, SL., Drueppel, L., Pfleiderer, K., Schmidt, A., Hillen, W., Berens, C.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"EMBO J","volume":"24","issue":"2","page":"358-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10201986","title":"CD28 costimulation is crucial for the development of spontaneous autoimmune encephalomyelitis.","abstract":"Multiple sclerosis (MS) is a severe central nervous system disease. Experimental autoimmune encephalomyelitis (EAE) mimics MS in mice. We report that spontaneous development of EAE in RAG-1-deficient mice transgenic for a myelin basic protein (MBP)-specific TCR (TgMBP+\/RAG-1-\/-) requires expression of the T cell costimulatory molecule CD28. Surprisingly, T cells from CD28-\/-TgMBP+\/RAG-1-\/- mice proliferate and produce IL-2 in response to MBP1-17 peptide in vitro, excluding clonal anergy as the mechanism of CD28-regulated pathogenesis. Proliferation of autoaggressive T cells was dependent on the concentration of the MBP peptide, as was the development of MBP-induced EAE in CD28-deficient PL\/J mice. These results provide the first genetic evidence that CD28 costimulation is crucial for MBP-specific T cell activation in vivo and the initiation of spontaneous EAE.","authors":"Oliveira-dos-Santos, AJ., Ho, A., Tada, Y., Lafaille, JJ., Tonegawa, S., Mak, TW., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Immunol","volume":"162","issue":"8","page":"4490-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8816483","title":"The transcription factor Swi5 regulates expression of the cyclin kinase inhibitor p40SIC1.","abstract":"DNA replication in budding yeast cells depends on the activation of the Cdc28 kinase (Cdk1 of Saccharomyces cerevisiae) associated with B-type cyclins Clb1 to Clb6. Activation of the kinase depends on proteolysis of the Cdk inhibitor p40SIC1 in late G1, which is mediated by the ubiquitin-conjugating enzyme Cdc34 and two other proteins, Cdc4 and Cdc53. Inactivation of any one of these three proteins prevents p40SIC1 degradation and causes cells to arrest in G1 with active Cln kinases but no Clb-associated Cdc28 kinase activity. Deletion of SIC1 allows these mutants to replicate. p40SIC1 disappears at the G1\/S transition and reappears only after nuclear division. Cell cycle-regulated proteolysis seems largely responsible for this pattern, but transcriptional control could also contribute; SIC1 RNA accumulates to high levels as cells exit M phase. To identify additional factors necessary for the inhibition of the Cdk1\/Cdc28 kinase in G1, we isolated mutants that can replicate DNA in the absence of Cdc4 function. Mutations in three loci (SIC1, SWI5, and RIC3) were identified. We have shown that high SIC1 transcript levels at late M phase depend on Swi5. Swi5 accumulates in the cytoplasm during S, G2, and M phases of the cell cycle but enters the nuclei at late anaphase. Our data suggest that cell cycle-regulated nuclear accumulation of Swi5 is responsible for the burst of SIC1 transcription at the end of anaphase. This transcriptional control may be important for inactivation of the Clb\/Cdk1 kinase in G2\/M transition and during the subsequent G1 period.","authors":"Knapp, D., Bhoite, L., Stillman, DJ., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Mol Cell Biol","volume":"16","issue":"10","page":"5701-7","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1996-11-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19246338","title":"Novel function for interleukin-7 in dendritic cell development.","abstract":"Interleukin-7 (IL-7) is crucial for the development of T and B lymphocytes from common lymphoid progenitors (CLPs) and for the maintenance of mature T lymphocytes. Its in vivo role for dendritic cells (DCs) has been poorly defined. Here, we investigated whether IL-7 is important for the development or maintenance of different DC types. Bone marrow-derived DCs expressed the IL-7 receptor (IL-7R) and survived significantly longer in the presence of IL-7. Migratory DCs (migDCs) isolated from lymph nodes also expressed IL-7R. Surprisingly, IL-7R was not required for their maintenance but indirectly for their development. Conventional DCs (cDCs) and plasmacytoid DCs (pDCs) resident in lymph nodes and spleen were IL-7R(-). Using mixed bone marrow chimeras, we observed an intrinsic requirement for IL-7R signals in their development. As the number of CLPs but not myeloid progenitors was reduced in the absence of IL-7 signals, we propose that a large fraction of cDCs and pDCs derives from CLPs and shares not only the lymphoid origin but also the IL-7 requirement with lymphocyte precursors.","authors":"Vogt, TK., Link, A., Perrin, J., Finke, D., Luther, SA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Blood","volume":"113","issue":"17","page":"3961-8","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22609551","title":"The smooth muscle microRNA miR-145 regulates gut epithelial development via a paracrine mechanism.","abstract":"MicroRNAs are potent modulators of cellular differentiation. miR-145 is expressed in, and promotes the differentiation of vascular and visceral smooth muscle cells (SMCs). Interestingly, we have observed that miR-145 also promotes differentiation of the gut epithelium in the developing zebrafish, a cell type where it is not expressed. Here we identify that a paracrine pathway involving the morphogens Sonic hedgehog (Shh) in epithelium and bone morphogenic protein 4 (Bmp4) in SMCs is modulated by miR-145. We show that expression of miR-145 in visceral SMCs normally represses the expression of the morphogen bmp4, as loss of miR-145 leads to upregulation of bmp4 in SMCs. We show that bmp4 in turn controls expression of Shh in the visceral epithelium. Conversely, in miR-145 morphants where bmp4 expression is increased, expression of sonic hedgehog a (shha) is strongly increased in gut epithelium. We show that expression of bmp4 is modulated by the miR-145 direct target gata6 but not a second potential direct target, klf5a. Thus although miR-145 is a tissue-restricted microRNA, it plays an essential role in promoting the patterning of both gut layers during gut development via a paracrine mechanism.","authors":"Zeng, L., Childs, SJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Dev Biol","volume":"367","issue":"2","page":"178-86","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35003058","title":"Angiotensin-Converting Enzyme 2 (ACE2) in the Pathogenesis of ARDS in COVID-19.","abstract":"Seventeen years after the epidemic of SARS coronavirus, a novel coronavirus SARS-CoV-2-emerged resulting in an unprecedented pandemic. Angiotensin-converting enzyme 2 (ACE2) is an essential receptor for cell entry of SARS-CoV-2 as well as the SARS coronavirus. Despite many similarities to SARS coronavirus, SARS-CoV-2 exhibits a higher affinity to ACE2 and shows higher infectivity and transmissibility, resulting in explosive increase of infected people and COVID-19 patients. Emergence of the variants harboring mutations in the receptor-binding domain of the Spike protein has drawn critical attention to the interaction between ACE2 and Spike and the efficacies of vaccines and neutralizing antibodies. ACE2 is a carboxypeptidase which degrades angiotensin II, B1-bradykinin, or apelin, and thereby is a critical regulator of cardiovascular physiology and pathology. In addition, the enzymatic activity of ACE2 is protective against acute respiratory distress syndrome (ARDS) caused by viral and non-viral pneumonias, aspiration, or sepsis. Upon infection, both SARS-CoV-2 and SARS coronaviruses downregulates ACE2 expression, likely associated with the pathogenesis of ARDS. Thus, ACE2 is not only the SARS-CoV-2 receptor but might also play an important role in multiple aspects of COVID-19 pathogenesis and possibly post-COVID-19 syndromes. Soluble forms of recombinant ACE2 are currently utilized as a pan-variant decoy to neutralize SARS-CoV-2 and a supplementation of ACE2 carboxypeptidase activity. Here, we review the role of ACE2 in the pathology of ARDS in COVID-19 and the potential application of recombinant ACE2 protein for treating COVID-19.","authors":"Kuba, K., Yamaguchi, T., Penninger, JM.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Front Immunol","volume":"12","issue":null,"page":"732690","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18463631","title":"An endogenous small interfering RNA pathway in Drosophila.","abstract":"Drosophila endogenous small RNAs are categorized according to their mechanisms of biogenesis and the Argonaute protein to which they bind. MicroRNAs are a class of ubiquitously expressed RNAs of approximately 22 nucleotides in length, which arise from structured precursors through the action of Drosha-Pasha and Dicer-1-Loquacious complexes. These join Argonaute-1 to regulate gene expression. A second endogenous small RNA class, the Piwi-interacting RNAs, bind Piwi proteins and suppress transposons. Piwi-interacting RNAs are restricted to the gonad, and at least a subset of these arises by Piwi-catalysed cleavage of single-stranded RNAs. Here we show that Drosophila generates a third small RNA class, endogenous small interfering RNAs, in both gonadal and somatic tissues. Production of these RNAs requires Dicer-2, but a subset depends preferentially on Loquacious rather than the canonical Dicer-2 partner, R2D2 (ref. 14). Endogenous small interfering RNAs arise both from convergent transcription units and from structured genomic loci in a tissue-specific fashion. They predominantly join Argonaute-2 and have the capacity, as a class, to target both protein-coding genes and mobile elements. These observations expand the repertoire of small RNAs in Drosophila, adding a class that blurs distinctions based on known biogenesis mechanisms and functional roles.","authors":"Czech, B., Malone, CD., Zhou, R., Stark, A., Schlingeheyde, C., Dus, M., Perrimon, N., Kellis, M., Wohlschlegel, JA., Sachidanandam, R., Hannon, GJ., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"453","issue":"7196","page":"798-802","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8790404","title":"Transloading of tumor cells with foreign major histocompatibility complex class I peptide ligand: a novel general strategy for the generation of potent cancer vaccines.","abstract":"The major hurdle to be cleared in active immunotherapy of cancer is the poor immunogenicity of cancer cells. In previous attempts to overcome this problem, whole tumor cells have been used as vaccines, either admixed with adjuvant(s) or genetically engineered to express nonself proteins or immunomodulatory factors before application. We have developed a novel approach to generate an immunogeneic, highly effective vaccine: major histocompatibility complex (MHC) class I-positive cancer cells are administered together with MHC class I-matched peptide ligands of foreign, nonself origin, generated by a procedure we term transloading. Murine tumor lines of the H2-Kd or the H2-Db haplotype, melanoma M-3 and B16-F10, respectively, as well as colon carcinoma CT-26 (H2-Kd), were transloaded with MHC-matched influenza virus-derived peptides and applied as irradiated vaccines. Mice bearing a deposit of live M-3 melanoma cells were efficiently cured by this treatment. In the CT-26 colon carcinoma and the B16-F10 melanoma, high efficacies were obtained against tumor challenge, suggesting the universal applicability of this new type of vaccine. With foreign peptide ligands adapted to the requirements of a desired MHC class I haplotype, this concept may be used for the treatment of human cancers.","authors":"Schmidt, W., Steinlein, P., Buschle, M., Schweighoffer, T., Herbst, E., Mechtler, K., Kirlappos, H., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Proc Natl Acad Sci U S A","volume":"93","issue":"18","page":"9759-63","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1996-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-141","title":"Mechanistische Analyse des humanen RNA-Interferenz-Effektor-Komplexes","abstract":null,"authors":"Ameres, S.L.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"BioSpektrum","volume":"","issue":"7","page":"756","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19039138","title":"An epigenetic role for maternally inherited piRNAs in transposon silencing.","abstract":"In plants and mammals, small RNAs indirectly mediate epigenetic inheritance by specifying cytosine methylation. We found that small RNAs themselves serve as vectors for epigenetic information. Crosses between Drosophila strains that differ in the presence of a particular transposon can produce sterile progeny, a phenomenon called hybrid dysgenesis. This phenotype manifests itself only if the transposon is paternally inherited, suggesting maternal transmission of a factor that maintains fertility. In both P- and I-element-mediated hybrid dysgenesis models, daughters show a markedly different content of Piwi-interacting RNAs (piRNAs) targeting each element, depending on their parents of origin. Such differences persist from fertilization through adulthood. This indicates that maternally deposited piRNAs are important for mounting an effective silencing response and that a lack of maternal piRNA inheritance underlies hybrid dysgenesis.","authors":"Brennecke, J., Malone, CD., Aravin, AA., Sachidanandam, R., Stark, A., Hannon, GJ.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Science","volume":"322","issue":"5906","page":"1387-92","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22592126","title":"BMP activity is required for tooth development from the lamina to bud stage.","abstract":"Several Bmp genes are expressed in the developing mouse tooth germ from the initiation to the late-differentiation stages, and play pivotal roles in multiple steps of tooth development. In this study, we investigated the requirement of BMP activity in early tooth development by transgenic overexpression of the extracellular BMP antagonist Noggin. We show that overexpression of Noggin in the dental epithelium at the tooth initiation stage arrests tooth development at the lamina\/early-bud stage. This phenotype is coupled with a significantly reduced level of cell proliferation rate and a down-regulation of Cyclin-D1 expression, specifically in the dental epithelium. Despite unaltered expression of genes known to be implicated in early tooth development in the dental mesenchyme and dental epithelium of transgenic embryos, the expression of Pitx2, a molecular marker for the dental epithelium, became down-regulated, suggesting the loss of odontogenic fate in the transgenic dental epithelium. Our results reveal a novel role for BMP signaling in the progression of tooth development from the lamina stage to the bud stage by regulating cell proliferation and by maintaining odontogenic fate of the dental epithelium.","authors":"Wang, Y., Li, L., Zheng, Y., Yuan, G., Yang, G., He, F., Chen, Y.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Dent Res","volume":"91","issue":"7","page":"690-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19465913","title":"Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile.","abstract":"Piwi proteins and their associated Piwi-interacting RNAs (piRNAs) are implicated in transposon silencing in the mouse germ line. There is currently little information on additional proteins in the murine Piwi complex and how they might regulate the entry of transcripts that accumulate as piRNAs in the Piwi ribonucleoprotein (piRNP). We isolated Mili-containing complexes from adult mouse testes and identified Tudor domain-containing protein-1 (Tdrd1) as a factor specifically associated with the Mili piRNP throughout spermatogenesis. Complex formation is promoted by the recognition of symmetrically dimethylated arginines at the N terminus of Mili by the tudor domains of Tdrd1. Similar to a Mili mutant, mice lacking Tdrd1 show derepression of L1 transposons accompanied by a loss of DNA methylation at their regulatory elements and delocalization of Miwi2 from the nucleus to the cytoplasm. Finally, we show that Mili piRNPs devoid of Tdrd1 accept the entry of abundant cellular transcripts into the piRNA pathway and accumulate piRNAs with a profile that is drastically different from that of the wild type. Our data suggest that Tdrd1 ensures the entry of correct transcripts into the normal piRNA pool.","authors":"Reuter, M., Chuma, S., Tanaka, T., Franz, T., Stark, A., Pillai, RS.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Struct Mol Biol","volume":"16","issue":"6","page":"639-46","pdf":null,"JrId":"31761","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19395010","title":"Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary.","abstract":"In Drosophila gonads, Piwi proteins and associated piRNAs collaborate with additional factors to form a small RNA-based immune system that silences mobile elements. Here, we analyzed nine Drosophila piRNA pathway mutants for their impacts on both small RNA populations and the subcellular localization patterns of Piwi proteins. We find that distinct piRNA pathways with differing components function in ovarian germ and somatic cells. In the soma, Piwi acts singularly with the conserved flamenco piRNA cluster to enforce silencing of retroviral elements that may propagate by infecting neighboring germ cells. In the germline, silencing programs encoded within piRNA clusters are optimized via a slicer-dependent amplification loop to suppress a broad spectrum of elements. The classes of transposons targeted by germline and somatic piRNA clusters, though not the precise elements, are conserved among Drosophilids, demonstrating that the architecture of piRNA clusters has coevolved with the transposons that they are tasked to control.","authors":"Malone, CD., Brennecke, J., Dus, M., Stark, A., McCombie, WR., Sachidanandam, R., Hannon, GJ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"137","issue":"3","page":"522-35","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8105804","title":"Genetically modified animals and immunodeficiency.","abstract":"Mouse strains with defined genetic defects engineered by the method of targeted gene disruption and homologous recombination have furthered our understanding of immune functions at the single gene level. More importantly, these mutant 'gene knockout' mice are powerful in vivo tools to dissect the complex mechanisms of lymphocyte development and function, complementing our broadening knowledge of congenital and acquired human immunodeficiencies.","authors":"Yeung, RS., Penninger, J., Mak, TW.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Curr Opin Immunol","volume":"5","issue":"4","page":"585-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1993-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34995498","title":"RNF43\/ZNRF3 negatively regulates taste tissue homeostasis and positively regulates dorsal lingual epithelial tissue homeostasis.","abstract":"Taste bud cells are renewed throughout life in a process requiring innervation. Recently, we reported that R-spondin substitutes for neuronal input for taste cell regeneration. R-spondin amplifies WNT signaling by interacting with stem-cell-expressed E3 ubiquitin ligases RNF43\/ZNRF3 (negative regulators of WNT signaling) and G-protein-coupled receptors LGR4\/5\/6 (positive regulators of WNT signaling). Therefore, we hypothesized that RNF43\/ZNRF3 may serve as a brake, controlled by gustatory neuron-produced R-spondin, for regulating taste tissue homeostasis. Here, we show that mice deficient for Rnf43\/Znrf3 in KRT5-expressing epithelial stem\/progenitor cells (RZ dKO) exhibited taste cell hyperplasia; in stark contrast, epithelial tissue on the tongue degenerated. WNT signaling blockade substantially reversed all these effects in RZ dKO mice. Furthermore, innervation becomes dispensable for taste cell renewal in RZ dKO mice. We thus demonstrate important but distinct functions of RNF43\/ZNRF3 in regulating taste versus lingual epithelial tissue homeostasis.","authors":"Lu, C., Lin, X., Yamashita, J., Xi, R., Zhou, M., Zhang, YV., Wang, H., Margolskee, RF., Koo, BK., Clevers, H., Matsumoto, I., Jiang, P.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Stem Cell Reports","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8779714","title":"Role of inscuteable in orienting asymmetric cell divisions in Drosophila.","abstract":"Drosophila neuroblasts and epithelial cells in the procephalic neurogenic region divide perpendicular to the surface, and segregate the proteins Numb and Prospero into the basal daughter cell. We demonstrate here that orientation of the mitotic spindle and correct localization of Numb and Prospero in these cells require the inscuteable gene. Moreover, ectopic expression of inscuteable in other epithelial cells leads to spindle reorientation. The Inscuteable protein localizes to the apical cell cortex before mitosis, suggesting that Inscuteable functions in establishing polarity for asymmetric cell division.","authors":"Kraut, R., Chia, W., Jan, LY., Jan, YN., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Nature","volume":"383","issue":"6595","page":"50-5","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1996-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19295514","title":"Histone modifications at human enhancers reflect global cell-type-specific gene expression.","abstract":"The human body is composed of diverse cell types with distinct functions. Although it is known that lineage specification depends on cell-specific gene expression, which in turn is driven by promoters, enhancers, insulators and other cis-regulatory DNA sequences for each gene, the relative roles of these regulatory elements in this process are not clear. We have previously developed a chromatin-immunoprecipitation-based microarray method (ChIP-chip) to locate promoters, enhancers and insulators in the human genome. Here we use the same approach to identify these elements in multiple cell types and investigate their roles in cell-type-specific gene expression. We observed that the chromatin state at promoters and CTCF-binding at insulators is largely invariant across diverse cell types. In contrast, enhancers are marked with highly cell-type-specific histone modification patterns, strongly correlate to cell-type-specific gene expression programs on a global scale, and are functionally active in a cell-type-specific manner. Our results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression.","authors":"Heintzman, ND., Hon, GC., Hawkins, RD., Kheradpour, P., Stark, A., Harp, LF., Ye, Z., Lee, LK., Stuart, RK., Ching, CW., Ching, KA., Antosiewicz-Bourget, JE., Liu, H., Zhang, X., Green, RD., Lobanenkov, VV., Stewart, R., Thomson, JA., Crawford, GE., Kellis, M., Ren, B.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nature","volume":"459","issue":"7243","page":"108-12","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22589745","title":"Bmps and id2a act upstream of Twist1 to restrict ectomesenchyme potential of the cranial neural crest.","abstract":"Cranial neural crest cells (CNCCs) have the remarkable capacity to generate both the non-ectomesenchyme derivatives of the peripheral nervous system and the ectomesenchyme precursors of the vertebrate head skeleton, yet how these divergent lineages are specified is not well understood. Whereas studies in mouse have indicated that the Twist1 transcription factor is important for ectomesenchyme development, its role and regulation during CNCC lineage decisions have remained unclear. Here we show that two Twist1 genes play an essential role in promoting ectomesenchyme at the expense of non-ectomesenchyme gene expression in zebrafish. Twist1 does so by promoting Fgf signaling, as well as potentially directly activating fli1a expression through a conserved ectomesenchyme-specific enhancer. We also show that Id2a restricts Twist1 activity to the ectomesenchyme lineage, with Bmp activity preferentially inducing id2a expression in non-ectomesenchyme precursors. We therefore propose that the ventral migration of CNCCs away from a source of Bmps in the dorsal ectoderm promotes ectomesenchyme development by relieving Id2a-dependent repression of Twist1 function. Together our model shows how the integration of Bmp inhibition at its origin and Fgf activation along its migratory route would confer temporal and spatial specificity to the generation of ectomesenchyme from the neural crest.","authors":"Das, A., Crump, JG.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"5","page":"e1002710","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8723350","title":"Identification of a novel ubiquitin-conjugating enzyme involved in mitotic cyclin degradation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">8723350<\/PMID><DateCompleted><Year>1997<\/Year><Month>03<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>6<\/Volume><Issue>4<\/Issue><PubDate><Year>1996<\/Year><Month>Apr<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Identification of a novel ubiquitin-conjugating enzyme involved in mitotic cyclin degradation.<\/ArticleTitle><Pagination><MedlinePgn>455-66<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The destruction of cyclin B is required for exit from mitosis, and is mediated by the ubiquitin pathway. Recently, a 20S complex, termed the anaphase-promoting complex (APC) or the cyclosome, has been genetically and biochemically identified as the cyclin-specific ubiquitin ligase (E3). In addition, a ubiquitin-conjugating enzyme (E2), UBC4, was shown to be involved in cyclin ubiquitination in Xenopus egg extracts. Another E2 activity, designated UBCx, can independently support cyclin ubiquitination in Xenopus. A similar activity (E2-C) has also been observed in clams. However, the molecular identity of Xenopus UBCx or clam E2-C has not been established.","authors":"Yu, H., King, RW., Peters, JM., Kirschner, MW.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Curr Biol","volume":"6","issue":"4","page":"455-66","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22586700","title":"Absence of bone sialoprotein (BSP) impairs primary bone formation and resorption: the marrow ablation model under PTH challenge.","abstract":"Bone sialoprotein (BSP) is highly expressed in early bone deposition and may play a part in primary bone mineralization. We previously showed that while BSP\u2212\/\u2212 mice have a mild secondary bone phenotype and are responsive to mechanical (unloading) and hormonal (ovariectomy, parathyroid hormone (PTH)) challenges, repair of a cortical bone defect, which involves primary bone deposition is significantly delayed in these mice. In the present study, we investigated the role of BSP in a pure model of primary bone modeling. Bone marrow was ablated by trans-epiphysis aspiration in the femora of BSP+\/+ and BSP\u2212\/\u2212 mice, and 7 days post surgery \u03bcCT analysis showed vigorous new bone formation in the shaft of BSP+\/+ animals but much less in BSP\u2212\/\u2212 mice. After 14 days, the volume of medullary bone was significantly decreased as expected in BSP+\/+ mice, while it remained stable in the BSP\u2212\/\u2212. Osteoid thickness and surface were higher in BSP\u2212\/\u2212 at day 7, suggesting delayed mineralization, while osteoclast surface and number were significantly lower at day 14, a stage of high medullary bone resorption. At day 7, mRNA expression of early osteoblast marker genes (RUNX2, osterix, alkaline phosphatase, osteopontin) did not differ between the two genotypes, while markers of terminal differentiation (MEPE, DMP1, osteocalcin) as well as receptor activator of NF-kappaB ligand (RANKL) and tartrate-resistant acid phosphatase (TRAP) were significantly lower in BSP\u2212\/\u2212 than in BSP+\/+ mice. PTH treatment maintained the volume of medullary bone up to 12 days after ablation in BSP+\/+ mice, but failed to do so in BSP\u2212\/\u2212 mice. PTH significantly increased bone formation rate in both genotype, while it reduced osteoclast number and surface in BSP+\/+, but not in BSP\u2212\/\u2212 medullary bone. In summary, medullary bone formation after marrow ablation is blunted in BSP\u2212\/\u2212 mice, with delayed resorption and impaired response to PTH. These findings confirm the hypothesis of a crucial role for BSP in primary ossification, which has long been suspected for mineralization, but here extends to bone deposition and turnover.","authors":"Wade-Gueye, NM., Boudiffa, M., Vanden-Bossche, A., Laroche, N., Aubin, JE., Vico, L., Lafage-Proust, MH., Malaval, L.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Bone","volume":"50","issue":"5","page":"1064-73","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19498169","title":"McsB is a protein arginine kinase that phosphorylates and inhibits the heat-shock regulator CtsR.","abstract":"All living organisms face a variety of environmental stresses that cause the misfolding and aggregation of proteins. To eliminate damaged proteins, cells developed highly efficient stress response and protein quality control systems. We performed a biochemical and structural analysis of the bacterial CtsR\/McsB stress response. The crystal structure of the CtsR repressor, in complex with DNA, pinpointed key residues important for high-affinity binding to the promoter regions of heat-shock genes. Moreover, biochemical characterization of McsB revealed that McsB specifically phosphorylates arginine residues in the DNA binding domain of CtsR, thereby impairing its function as a repressor of stress response genes. Identification of the CtsR\/McsB arginine phospho-switch expands the repertoire of possible protein modifications involved in prokaryotic and eukaryotic transcriptional regulation.","authors":"Fuhrmann, J., Schmidt, A., Spiess, S., Lehner, A., Turgay, K., Mechtler, K., Charpentier, E., Clausen, T.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Science","volume":"324","issue":"5932","page":"1323-7","pdf":null,"JrId":"7473","fulltextlink":"http:\/\/www.sciencemag.org\/cgi\/content\/full\/324\/5932\/1323?ijkey=dKnxR.QIAABWo&keytype=ref&siteid=sci","preprintlink":null,"articledate":"2009-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19488057","title":"Wicked views on stem cell news.","abstract":null,"authors":"Neum\u00fcller, RA., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Cell Biol","volume":"11","issue":"6","page":"678-9","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18199681","title":"A pachygyria-causing alpha-tubulin mutation results in inefficient cycling with CCT and a deficient interaction with TBCB.","abstract":"The agyria (lissencephaly)\/pachygyria phenotypes are catastrophic developmental diseases characterized by abnormal folds on the surface of the brain and disorganized cortical layering. In addition to mutations in at least four genes--LIS1, DCX, ARX and RELN--mutations in a human alpha-tubulin gene, TUBA1A, have recently been identified that cause these diseases. Here, we show that one such mutation, R264C, leads to a diminished capacity of de novo tubulin heterodimer formation. We identify the mechanisms that contribute to this defect. First, there is a reduced efficiency whereby quasinative alpha-tubulin folding intermediates are generated via ATP-dependent interaction with the cytosolic chaperonin CCT. Second, there is a failure of CCT-generated folding intermediates to stably interact with TBCB, one of the five tubulin chaperones (TBCA-E) that participate in the pathway leading to the de novo assembly of the tubulin heterodimer. We describe the behavior of the R264C mutation in terms of its effect on the structural integrity of alpha-tubulin and its interaction with TBCB. In spite of its compromised folding efficiency, R264C molecules that do productively assemble into heterodimers are capable of copolymerizing into dynamic microtubules in vivo. The diminished production of TUBA1A tubulin in R264C individuals is consistent with haploinsufficiency as a cause of the disease phenotype.","authors":"Tian, G., Kong, XP., Jaglin, XH., Chelly, J., Keays, D., Cowan, NJ.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Mol Biol Cell","volume":"19","issue":"3","page":"1152-61","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8334701","title":"Normal B lymphocyte development but impaired T cell maturation in CD45-exon6 protein tyrosine phosphatase-deficient mice.","abstract":"The transmembrane tyrosine phosphatase CD45 is expressed in multiple isoforms on all nucleated hematopoietic cells, resulting from alternative splicing of variable exons. We generated mice with a mutation in the variable CD45 exon 6, using homologous recombination. In mice homozygous for the CD45-exon6 mutation, B cells and most T cells did not express CD45. Development of B cells appeared normal, although Ig mu-induced proliferation was completely abrogated. Thymocyte maturation was blocked at the transitional stage from immature CD4+CD8+ to mature CD4+ or CD8+ cells, and only a few T cells could be detected in peripheral lymphoid organs. Clonal deletion of superantigen-reactive T cells still occurred. Cytotoxic T cell responses to lymphocytic choriomeningitis virus were absent in CD45-exon6-\/- mice. These data imply that CD45 is differentially required for the development and function of B and T lymphocytes.","authors":"Kishihara, K., Penninger, J., Wallace, VA., K\u00fcndig, TM., Kawai, K., Wakeham, A., Timms, E., Pfeffer, K., Ohashi, PS., Thomas, ML.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Cell","volume":"74","issue":"1","page":"143-56","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1993-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40355754","title":"Metabolic mapping of the human solute carrier superfamily.","abstract":"Solute carrier (SLC) transporters govern most of the chemical exchange across cellular membranes and are integral to metabolic regulation, which in turn is linked to cellular function and identity. Despite their key role, individual functions of the SLC superfamily members were not evaluated systematically. We determined the metabolic and transcriptional profiles upon SLC overexpression in knock-out or wild-type isogenic cell backgrounds for 378 SLCs and 441 SLCs, respectively. Targeted metabolomics provided a fingerprint of 189 intracellular metabolites, while transcriptomics offered insights into cellular programs modulated by SLC expression. Beyond the metabolic profiles of 102 SLCs directly related to their known substrates, we identified putative substrates or metabolic pathway connections for 71 SLCs without previously annotated bona fide substrates, including SLC45A4 as a new polyamine transporter. By comparing the molecular profiles, we identified functionally related SLC groups, including some with distinct impacts on osmolyte balancing and glycosylation. The assessment of functionally related human genes presented here may serve as a blueprint for other systematic studies and supports future investigations into the functional roles of SLCs.","authors":"Wiedmer, T., Teoh, ST., Christodoulaki, E., Wolf, G., Tian, C., Sedlyarov, V., Jarret, A., Leippe, P., Frommelt, F., Ingles-Prieto, A., Lindinger, S., Barbosa, BMG., Onstein, S., Klimek, C., Garcia, J., Serrano, I., Reil, D., Santacruz, D., Piotrowski, M., Noell, S., Bueschl, C., Li, H., Chi, G., Mereiter, S., Oliveira, T., Penninger, JM., Sauer, DB., Steppan, CM., Viollet, C., Klavins, K., Hannich, JT., Goldmann, U., Superti-Furga, G.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Mol Syst Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-13","doi":"10.1038\/s44320-025-00106-4","first_author":null,"corresponding_authors":null},{"pmid":"19383908","title":"B-MYB is required for recovery from the DNA damage-induced G2 checkpoint in p53 mutant cells.","abstract":"In response to DNA damage, several signaling pathways that arrest the cell cycle in G(1) and G(2) are activated. The down-regulation of mitotic genes contributes to the stable maintenance of the G(2) arrest. The human LINC or DREAM complex, together with the B-MYB transcription factor, plays an essential role in the expression of G(2)-M genes. Here, we show that DNA damage results in the p53-dependent binding of p130 and E2F4 to LINC and the dissociation of B-MYB from LINC. We find that B-MYB fails to dissociate from LINC in p53 mutant cells, that this contributes to increased G(2)-M gene expression in response to DNA damage in these cells, and, importantly, that B-MYB is required for recovery from the G(2) DNA damage checkpoint in p53-negative cells. Reanalysis of microarray expression data sets revealed that high levels of B-MYB correlate with a p53 mutant status and an advanced tumor stage in primary human breast cancer. Taken together, these data suggest that B-MYB\/LINC plays an important role in the DNA damage response downstream of p53.","authors":"Mannefeld, M., Klassen, E., Gaubatz, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cancer Res","volume":"69","issue":"9","page":"4073-80","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22586496","title":"Extracellular matrix mineralization promotes E11\/gp38 glycoprotein expression and drives osteocytic differentiation.","abstract":"Osteocytes are terminally differentiated osteoblasts which reside in a mineralized extracellular matrix (ECM). The factors that regulate this differentiation process are unknown. We have investigated whether ECM mineralization could promote osteocyte formation. To do this we have utilised MLO-A5 pre-osteocyte-like cells and western blotting and comparative RT-PCR to examine whether the expression of osteocyte-selective markers is elevated concurrently with the onset of ECM mineralization. Secondly, if mineralization of the ECM is indeed a driver of osteocyte formation, we reasoned that impairment of ECM mineralization would result in a reversible inhibition of osteocyte formation. Supplementation of MLO-A5 cell cultures with ascorbic acid and phosphate promoted progressive ECM mineralization as well as temporally associated increases in expression of the osteocyte-selective markers, E11\/gp38 glycoprotein and sclerostin. Consistent with a primary role for ECM mineralization in osteocyte formation, we also found that inhibition of ECM mineralization, by omitting phosphate or adding sodium pyrophosphate, a recognized inhibitor of hydroxyapatite formation, resulted in a 15-fold decrease in mineral deposition that was closely accompanied by lower expression of E11 and other osteocyte markers such as Dmp1, Cd44 and Sost whilst expression of osteoblast markers Ocn and Col1a increased. To rule out the possibility that such restriction of ECM mineralization may produce an irreversible modification in osteoblast behaviour to limit E11 expression and osteocytogenesis, we also measured the capacity of MLO-A5 cells to re-enter the osteocyte differentiation programme. We found that the mineralisation process was re-initiated and closely allied to increased expression of E11 protein after re-administration of phosphate or omission of sodium pyrophosphate, indicating an ECM mineralization-induced restoration in osteocyte formation. These results emphasise the importance of cell-ECM interactions in regulating osteoblast behaviour and, more importantly, suggest that ECM mineralization exerts pivotal control during terminal osteoblast differentiation and acquisition of the osteocyte phenotype.","authors":"Prideaux, M., Loveridge, N., Pitsillides, AA., Farquharson, C.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"5","page":"e36786","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8666235","title":"Activation of S-phase-promoting CDKs in late G1 defines a \"point of no return\" after which Cdc6 synthesis cannot promote DNA replication in yeast.","abstract":"In eukaryotic cells, DNA replication is confined to a discrete period of the cell cycle and does not usually recur until after anaphase. In the budding yeast Saccharomyces cerevisiae, assembly of pre-replication complexes (pre-RCs) at future origins as cells exit mitosis (or later during G1 is necessary for subsequent initiation of DNA replication triggered by activation in late G1 of Cdc28\/Cdk1 kinases associated with B-type cyclins Clb1-Clb6. The absence of pre-RCs during G2 and M phases could explain why origins of DNA replication fire only once during the cell cycle, even though S-phase-promoting Cdks remain active from the beginning of S phase through the end of M phase. Formation of pre-RCs and their maintenance during G1 depend on the synthesis and activity of an unstable protein encoded by CDC6. We find that Cdc6 synthesis can only promote DNA replication in a restricted window of the cell cycle: between destruction of Clbs after anaphase and activation of Clb5\/ and Clb6\/Cdk1 in late G1. The latter corresponds to a \"point of no return,\" after which Cdc6 synthesis can no longer promote DNA replication. Cdc6 protein can be made throughout the cell cycle and, in certain circumstances, can accumulate within the nuclei of G2 and M phase cells without inducing re-replication. Thus, control over Cdc6 degradation and\/or nuclear localization is not crucial for preventing origin re-firing. Our data are consistent with the notion that cells can no longer incorporate de novo synthesized Cdc6 into pre-RCs once C1b\/Cdk1 kinases have been activated. We show that Cdc6p associates with Clb\/Cdk1 kinases from late G1 until late anaphase, which might be important for inhibiting pre-RC assembly during S, G2, and M phases. Inhibition of pre-RC assembly by the same kinases that trigger initiation explains how origins are prevented from re-firing until Clb kinases are destroyed after anaphase.","authors":"Piatti, S., B\u00f6hm, T., Cocker, JH., Diffley, JF., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Genes Dev","volume":"10","issue":"12","page":"1516-31","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1996-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17625558","title":"A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila.","abstract":"Forward genetic screens in model organisms have provided important insights into numerous aspects of development, physiology and pathology. With the availability of complete genome sequences and the introduction of RNA-mediated gene interference (RNAi), systematic reverse genetic screens are now also possible. Until now, such genome-wide RNAi screens have mostly been restricted to cultured cells and ubiquitous gene inactivation in Caenorhabditis elegans. This powerful approach has not yet been applied in a tissue-specific manner. Here we report the generation and validation of a genome-wide library of Drosophila melanogaster RNAi transgenes, enabling the conditional inactivation of gene function in specific tissues of the intact organism. Our RNAi transgenes consist of short gene fragments cloned as inverted repeats and expressed using the binary GAL4\/UAS system. We generated 22,270 transgenic lines, covering 88% of the predicted protein-coding genes in the Drosophila genome. Molecular and phenotypic assays indicate that the majority of these transgenes are functional. Our transgenic RNAi library thus opens up the prospect of systematically analysing gene functions in any tissue and at any stage of the Drosophila lifespan.","authors":"Dietzl, G., Chen, D., Schnorrer, F., Su, KC., Barinova, Y., Fellner, M., Gasser, B., Kinsey, K., Oppel, S., Scheiblauer, S., Couto, A., Marra, V., Keleman, K., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"448","issue":"7150","page":"151-6","pdf":null,"JrId":"6012","fulltextlink":"http:\/\/futurezone.orf.at\/stories\/1610676\/","preprintlink":null,"articledate":"2007-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18847425","title":"[Advances in diabetes mellitus, diabetic nephropathy, metabolic syndrome and cardio-vascular-renal risk].","abstract":"1. Epidemiological aspects: There is evidence that the pandemic of DM is entering a stabilization phase, with a slight downturn in the rates of ESRD attributed to DM in the United States. 2. New pathogenic and progression mechanisms of renal disease are proposed: 1) Intraglomerular hyperpressure with phenotypical cell changes, inducing TGF-beta activation; 2) Genetic polymorphisms, with candidate genes in chromosomes 18q, 3q, 7p and others; 3) Endothelial dysfunction as an injury initiating mechanism, demonstrated in the eNOS knockout rat; 4) Isoforms of PKC molecules that favor progression of nephropathy. 3. Importance of metabolic syndrome as a progression factor of chronic renal disease. 4. Increased CV risk in patients treated with thiazolidinediones (glitazones) -Hydrosaline retention and heart failure. 5. Recent studies: ADVANCE study: Combined treatment with an ACE inhibitor (perindropil) and a diuretic (indapamide) in fixed doses helps to reduce CV risk and overall mortality.DREAM study: Ramipril does not reduce the occurrence of DM2, but does improve reversion to normoglycemia. AVOID study: Direct renin inhibitors add greater antihypertensive and antiproteinuric efficacy. 6. New therapeutic targets: Antifibrotic, anti-inflammatory and antiproteinuric effects of sulodexide, isosorbide mononitrate, PKC inhibitors and others. 7. The most effective strategy continues to be intensive, multifactorial and multidisciplinary management of the type 2 diabetic patient, as shown by long-term follow-up in the Steno-2 study.","authors":"Mart\u00ednez Castelao, A.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nefrologia","volume":"28 Suppl 5","issue":"","page":"79-84","pdf":null,"JrId":"21675","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22547442","title":"Aldosterone inhibits antifibrotic factors in mouse hypertensive heart.","abstract":"The renin-angiotensin-aldosterone system is involved in the arterial hypertension-associated cardiovascular remodeling. In this context, the development of cardiac fibrosis results from an imbalance between profibrotic and antifibrotic pathways, in which the role of aldosterone is yet not established. To determine the role of intracardiac aldosterone in the development of myocardial fibrosis during hypertension, we used a double transgenic model (AS-Ren) of cardiac hyperaldosteronism (AS) and systemic hypertension (Ren). The 9-month-old hypertensive mice had cardiac fibrosis, and hyperaldosteronism enhanced the fibrotic level. The mRNA levels of connective tissue growth factor and transforming growth factor-\u03b21 were similarly increased in Ren and AS-Ren mice compared with wild-type and AS mice, respectively. Hyperaldosteronism combined with hypertension favored the macrophage infiltration (CD68(+) cells) in heart, and enhanced the mRNA level of monocyte chemoattractant protein 1, osteopontin, and galectin 3. Interestingly, in AS-Ren mice the hypertension-induced increase in bone morphogenetic protein 4 mRNA and protein levels was significantly inhibited, and B-type natriuretic peptide expression was blunted. The mineralocorticoid receptor antagonist eplerenone restored B-type natriuretic peptide and bone morphogenetic protein 4 levels and decreased CD68 and galectin 3 levels in AS-Ren mice. Finally, when hypertension was induced by angiotensin II infusion in wild-type and AS mice, the mRNA profiles did not differ from those observed in Ren and AS-Ren mice, respectively. The aldosterone-induced inhibition of B-type natriuretic peptide and bone morphogenetic protein 4 expression was confirmed in vitro in neonatal mouse cardiomyocytes. Altogether, we demonstrate that, at the cardiac level, hyperaldosteronism worsens hypertension-induced fibrosis through 2 mineralocorticoid receptor-dependent mechanisms, activation of inflammation\/galectin 3-induced fibrosis and inhibition of antifibrotic factors (B-type natriuretic peptide and bone morphogenetic protein 4).","authors":"Azibani, F., Benard, L., Schlossarek, S., Merval, R., Tournoux, F., Fazal, L., Polidano, E., Launay, JM., Carrier, L., Chatziantoniou, C., Samuel, JL., Delcayre, C.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Hypertension","volume":"59","issue":"6","page":"1179-87","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8742062","title":"Avian stem cell factor (SCF): production and characterization of the recombinant His-tagged SCF of chicken and its neutralizing antibody.","abstract":"Recombinant chicken stem cell factor (SCF) was produced in bacteria as a histidine-tagged protein (His delta SCF) and purified by affinity chromatography on an Ni(2+)-NTA agarose column. His delta SCF is devoid of signal peptide and transmembrane domains and therefore mimics a soluble form of SCF. We demonstrate that the factor is biologically fully active in supporting sustained proliferation of SCF-dependent red blood progenitor cells of chicken in vitro. Polyclonal SCF-specific antibodies were raised in rabbits and shown to display potent SCF-neutralizing activity. Thus, recombinant chicken His delta SCF together with the SCF-specific antibody provide valuable tools for studying the role of SCF and c-kit receptor in development, growth and differentiation of avian haematopoietic cells.","authors":"Bart\u016fn\u0115k, P., Pichl\u00edkov\u00e1, L., Stengl, G., Boehmelt, G., Martin, FH., Beug, H., Dvor\u00e1k, M., Zenke, M.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Cytokine","volume":"8","issue":"1","page":"14-20","pdf":null,"JrId":"1149","fulltextlink":null,"preprintlink":null,"articledate":"1996-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18579744","title":"DREAM mediates cAMP-dependent, Ca2+-induced stimulation of GFAP gene expression and regulates cortical astrogliogenesis.","abstract":"In the developing mouse brain, once the generation of neurons is mostly completed during the prenatal period, precisely coordinated signals act on competent neural precursors to direct their differentiation into astrocytes, which occurs mostly after birth. Among these signals, those provided by neurotrophic cytokines and bone morphogenetic proteins appear to have a key role in triggering the neurogenic to gliogenic switch and in regulating astrocyte numbers. In addition, we have reported previously that the neurotrophic peptide pituitary adenylate cyclase-activating polypeptide (PACAP) is able to promote astrocyte differentiation of cortical precursors via activation of a cAMP-dependent pathway. Signals acting on progenitor cells of the developing cortex to generate astrocytes activate glial fibrillary acidic protein (GFAP) gene expression, but the transcriptional mechanisms that regulate this activation are unclear. Here, we identify the previously known transcriptional repressor downstream regulatory element antagonist modulator (DREAM) as an activator of GFAP gene expression. We found that DREAM occupies specific sites on the GFAP promoter before and after differentiation is initiated by exposure of cortical progenitor cells to PACAP. PACAP raises intracellular calcium concentration via a mechanism that requires cAMP, and DREAM-mediated transactivation of the GFAP gene requires the integrity of calcium-binding domains. Cortical progenitor cells from dream(-\/-) mice fail to express GFAP in response to PACAP. Moreover, the neonatal cortex of dream(-\/-) mice exhibits a reduced number of astrocytes and increased number of neurons. These results identify the PACAP-cAMP-Ca(2+)-DREAM cascade as a new pathway to activate GFAP gene expression during astrocyte differentiation.","authors":"Cebolla, B., Fern\u00e1ndez-P\u00e9rez, A., Perea, G., Araque, A., Vallejo, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Neurosci","volume":"28","issue":"26","page":"6703-13","pdf":null,"JrId":"5035","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18430168","title":"Retrospective on reverse genetics in mice around the world and in Japan.","abstract":"The 2007 Nobel Prize for Physiology or Medicine was awarded to Mario R. Capecchi, Martin J. Evans and Oliver Smithies for their contribution in generating mutant mice by gene targeting in embryonic stem (ES) cells. Although there are many experimental animals, it is yet only in mouse that one can genetically examine functions of genes at will. It was merely a dream in the early 1980s that genetic studies with mutants would one day become a reality in mammals. The story began with tetratocarcinoma\/embryonal carcinoma cells. Now, through the successes of cloning in mammals, somatic cells such as our skin cells will shortly be transformed into ES-like (induced pluripotent stem) cells by the proper activation of endogenous genes such as Oct4 and Sox2 with chemicals. How have times changed?","authors":"Aizawa, S.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Dev Growth Differ","volume":"50 Suppl 1","issue":"","page":"S29-34","pdf":null,"JrId":"3391","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8627769","title":"The complete DNA sequence and genomic organization of the avian adenovirus CELO.","abstract":"The complete DNA sequence of the avian adenovirus chicken embryo lethal orphan (CELO) virus (FAV-1) is reported here. The genome was found to be 43,804 bp in length, approximately 8 kb longer than those of the human subgenus C adenoviruses (Ad2 and Ad5). This length is supported by pulsed-field gel electrophoresis analysis of genomes isolated from several related FAV-1 isolates (Indiana C and OTE). The genes for major viral structural proteins (Illa, penton base, hexon, pVI, and pVIII), as well as the 52,000-molecular-weight (52K) and 100K proteins and the early-region 2 genes and IVa2, are present in the expected locations in the genome. CELO virus encodes two fiber proteins and a different set of the DNA-packaging core proteins, which may be important in condensing the longer CELO virus genome. No pV or pIX genes are present. Most surprisingly, CELO virus possesses no identifiable E1, E3, and E4 regions. There is 5 kb at the left end of the CELO virus genome and 15 kb at the right end with no homology to Ad2. The sequences are rich in open reading frames, and it is likely that these encode functions that replace the missing El, E3, and E4 functions.","authors":"Chiocca, S., Kurzbauer, R., Schaffner, G., Baker, A., Mautner, V., Cotten, M.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"J Virol","volume":"70","issue":"5","page":"2939-49","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1996-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21896737","title":"Neural-specific elongation of 3' UTRs during Drosophila development.","abstract":"The 3' termini of eukaryotic mRNAs influence transcript stability, translation efficiency, and subcellular localization. Here we report that a subset of developmental regulatory genes, enriched in critical RNA-processing factors, exhibits synchronous lengthening of their 3' UTRs during embryogenesis. The resulting UTRs are up to 20-fold longer than those found on typical Drosophila mRNAs. The large mRNAs emerge shortly after the onset of zygotic transcription, with several of these genes acquiring additional, phased UTR extensions later in embryogenesis. We show that these extended 3' UTR sequences are selectively expressed in neural tissues and contain putative recognition motifs for the translational repressor, Pumilio, which also exhibits the 3' lengthening phenomenon documented in this study. These findings suggest a previously unknown mode of posttranscriptional regulation that may contribute to the complexity of neurogenesis or neural function.","authors":"Hilgers, V., Perry, MW., Hendrix, D., Stark, A., Levine, M., Haley, B.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Proc Natl Acad Sci U S A","volume":"108","issue":"38","page":"15864-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18201103","title":"NMR structure of DREAM: Implications for Ca(2+)-dependent DNA binding and protein dimerization.","abstract":"DREAM (calsenilin\/KChIP3) is an EF-hand calcium-binding protein that binds to specific DNA sequences and regulates Ca2+-induced transcription of prodynorphin and c-fos genes. Here, we present the atomic-resolution structure of Ca2+-bound DREAM in solution determined by nuclear magnetic resonance (NMR) spectroscopy. Pulsed-field gradient NMR diffusion experiments and 15N NMR relaxation analysis indicate that Ca2+-bound DREAM forms a stable dimer in solution. The structure of the first 77 residues from the N-terminus could not be determined by our NMR analysis. The C-terminal DREAM structure (residues 78-256) contains four EF-hand motifs arranged in a tandem linear array, similar to that seen in KChIP1, recoverin, and other structures of the neuronal calcium sensor (NCS) branch of the calmodulin superfamily. Mg2+ is bound at the second EF-hand, whereas Ca2+ is bound functionally at the third and fourth sites. The first and second EF-hands form an exposed hydrophobic groove on the protein surface lined by side-chain atoms of L96, F100, F114, I117, Y118, F121, F122, Y151, L155, L158, and L159 that are highly conserved in all NCS proteins. An exposed leucine near the C-terminus (L251) is suggested to form intermolecular contacts with leucine residues in the hydrophobic groove (L155, L158, and L159). Positively charged side chains of Arg and Lys (Lys87, Lys90, Lys91, Arg98, Lys101, Arg160, and Lys166) are clustered on one side of the protein surface and may mediate electrostatic contacts with DNA targets. We propose that Ca2+-induced dimerization of DREAM may partially block the putative DNA-binding site, which may suggest as to how Ca2+ abolishes DREAM binding to DNA to activate the transcription of prodynorphin and other downstream genes in pain control.","authors":"Lusin, JD., Vanarotti, M., Li, C., Valiveti, A., Ames, JB.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Biochemistry","volume":"47","issue":"8","page":"2252-64","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8585994","title":"Spatiotemporal relationships between a novel Drosophila stripe expressing gene and known segmentation genes by simultaneous visualization of transcript patterns.","abstract":"We describe the cloning of the Drosophila transcription unit odd-striped (ost), which maps close to the P-element insertion site of the enhancer-trap line 05279. In order rapidly to gain information on its chromosomal localization, and to determine the spatial and temporal expression patterns of ost in whole-mount embryos, we established a double-label in situ hybridization protocol to localize two different DNA or RNA sequences simultaneously. The double-label in situ hybridization method involves digoxigenin- and biotin-labeled DNA probes that are processed to result in blue alkaline phosphatase and brown peroxidase reaction products, respectively. Using reference probes as internal standards, we show that the ost transcription unit is located within the cytogenetic band interval 89A1,2 on the right arm of the third chromosome, and that it exerts diagnostic segmentation gene expression patterns in the embryo. The ost transcripts are initially expressed in an anterior cap at the blastoderm stage, followed by a transient pair-rule gene expression pattern, which eventually changes into a segmental polarity gene pattern at gastrulation. Our results establish detailed spatial and temporal relationships between ost expression and the known patterns of the segmentation genes fushi tarazu and wingless, and demonstrate the potential of the double-label method with differently tagged DNA probes.","authors":"Hartmann, C., J\u00e4ckle, H.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Chromosoma","volume":"104","issue":"2","page":"84-91","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18041812","title":"Yin-yang ways of controlling gene expression are now in our hands.","abstract":"Molecular biologists have long dreamed of switching genes on and off at will in any part of the body during embryonic development. Their dream is now coming true thanks to the transparency of the embryonic body of the zebrafish ( Danio rerio), which has made gene manipulation by photoillumination possible.","authors":"Okamoto, H.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"ACS Chem Biol","volume":"2","issue":"10","page":"646-8","pdf":null,"JrId":"33137","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10197978","title":"SHIP is a negative regulator of growth factor receptor-mediated PKB\/Akt activation and myeloid cell survival.","abstract":"SHIP is an inositol 5' phosphatase that hydrolyzes the PI3'K product PI(3,4,5)P3. We show that SHIP-deficient mice exhibit dramatic chronic hyperplasia of myeloid cells resulting in splenomegaly, lymphadenopathy, and myeloid infiltration of vital organs. Neutrophils and bone marrow-derived mast cells from SHIP-\/- mice are less susceptible to programmed cell death induced by various apoptotic stimuli or by growth factor withdrawal. Engagement of IL3-R and GM-CSF-R in these cells leads to increased and prolonged PI3'K-dependent PI(3,4,5)P3 accumulation and PKB activation. These data indicate that SHIP is a negative regulator of growth factor-mediated PKB activation and myeloid cell survival.","authors":"Liu, Q., Sasaki, T., Kozieradzki, I., Wakeham, A., Itie, A., Dumont, DJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Genes Dev","volume":"13","issue":"7","page":"786-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8282313","title":"The role of p56lck and p59fyn tyrosine kinases and CD45 protein tyrosine phosphatase in T-cell development and clonal selection.","abstract":null,"authors":"Penninger, JM., Wallace, VA., Kishihara, K., Mak, TW.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Immunol Rev","volume":"135","issue":null,"page":"183-214","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1994-02-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22073976","title":"Universal and confident phosphorylation site localization using phosphoRS.","abstract":"An algorithm for the assignment of phosphorylation sites in peptides is described. The program uses tandem mass spectrometry data in conjunction with the respective peptide sequences to calculate site probabilities for all potential phosphorylation sites. Tandem mass spectra from synthetic phosphopeptides were used for optimization of the scoring parameters employing all commonly used fragmentation techniques. Calculation of probabilities was adapted to the different fragmentation methods and to the maximum mass deviation of the analysis. The software includes a novel approach to peak extraction, required for matching experimental data to the theoretical values of all isoforms, by defining individual peak depths for the different regions of the tandem mass spectrum. Mixtures of synthetic phosphopeptides were used to validate the program by calculation of its false localization rate versus site probability cutoff characteristic. Notably, the empirical obtained precision was higher than indicated by the applied probability cutoff. In addition, the performance of the algorithm was compared to existing approaches to site localization such as Ascore. In order to assess the practical applicability of the algorithm to large data sets, phosphopeptides from a biological sample were analyzed, localizing more than 3000 nonredundant phosphorylation sites. Finally, the results obtained for the different fragmentation methods and localization tools were compared and discussed.","authors":"Taus, T., K\u00f6cher, T., Pichler, P., Paschke, C., Schmidt, A., Henrich, C., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Proteome Res","volume":"10","issue":"12","page":"5354-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2352943","title":"The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model.","abstract":"The CpG dinucleotide is present at approximately 20% of its expected frequency in vertebrate genomes, a deficiency thought due to a high mutation rate from the methylated form of CpG to TpG and CpA. We examine the hypothesis that the 20% frequency represents an equilibrium between rate of creation of new CpGs and accelerated rate of CpG loss from methylation. Using this model, we calculate the expected reduction in the equilibrium frequency of the CpG dinucleotide and find that the observed CpG deficiency can be explained by mutation from methylated CpG to TpG\/CpA at approximately 12 times the normal transition rate, the exact rate depending on the ratio of transitions to transversions. The observed rate of CpG dinucleotide loss in a human alpha-globin nonprocessed pseudogene, psi alpha 1, and the apparent replenishment of the CpG pool in this sequence by new mutations, agree with the above parameters. These calculations indicate that it would take 25 million years or less, a small fraction of the time for vertebrate evolution, for CpG frequency to be reduced from undepleted levels to the current depleted levels.","authors":"Sved, J., Bird, A.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Proc Natl Acad Sci U S A","volume":"87","issue":"12","page":"4692-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1990-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6396086","title":"Purification and characterization of cMGF, a novel chicken myelomonocytic growth factor.","abstract":"We describe the purification of a novel hematopoietic growth factor from conditioned medium of a transformed macrophage cell line. The factor, termed chicken myelomonocytic growth factor (cMGF) stimulates the growth of chicken myeloblasts transformed by myb oncogene-containing retroviruses and induces the formation of macrophage colonies in uninfected chick bone marrow cultures. The biological activity of the factor is destroyed by trypsin and by reducing reagents but not by SDS. Analysis of crude conditioned medium on non-reducing SDS gels reveals two active species of cMGF with mol. wts. of 23 and 27 kd. Incubation of radioiodinated partially purified cMGF with myeloblasts demonstrates the specific binding of 23- and 27-kd components under non-reducing, and 25- and 29-kd components under reducing conditions. Glycosylation inhibition experiments indicate that the larger molecules represent glycosylated forms of a single protein moiety. The 27-kd species has been purified to homogeneity (80 000-fold enrichment) and exerts its half maximal activity at 2 X 10(-12) M and its maximal activity at 3 X 10(-11) M. Antibodies prepared to purified cMGF completely neutralize the growth-stimulating activity of the factor.","authors":"Leutz, A., Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1984","journaltitle":"EMBO J","volume":"3","issue":"13","page":"3191-7","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1985-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6323030","title":"Temperature-sensitive mutants of avian erythroblastosis virus: surface expression of the erbB product correlates with transformation.","abstract":"The v-erbB gene of avian erythroblastosis virus (AEV) codes for an integral plasma membrane glycoprotein, gp74erbB. Expression of gp74erbB and its intracellular precursors, gp66erbB and gp68erbB, has been studied in cells transformed by two temperature-sensitive mutants of AEV. After shift to 42 degrees C, the processing of gp68erbB is blocked in tsAEV-transformed, but not in wtAEV-transformed, erythroblasts and fibroblasts. In addition, gp74erbB disappears from the surface of tsAEV cells within 12 hr after shift. Thus tsAEV mutants probably bear a lesion in v-erbB that affects the maturation and subcellular localization of gp74erbB. The tsAEV erythroblasts, when \"committed\" to differentiation by a pulse-shift to 42 degrees C, reexpress gp74erbB during terminal differentiation at 36 degrees C. This suggests that tsAEV erythroblasts become insensitive to the transforming functions of gp74erbB at a certain stage of differentiation.","authors":"Beug, H., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1984","journaltitle":"Cell","volume":"36","issue":"4","page":"963-72","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1984-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19563751","title":"Fly stem cell research gets infectious.","abstract":"To maintain tissue homeostasis, stem cells need to increase their proliferation rate to repair tissue damage caused by stress or infection. In this issue, Jiang et al. (2009) describe a regulatory feedback mechanism involving the Jak\/Stat signaling pathway that enables stem cells of the fly midgut to accomplish this task.","authors":"Conder, R., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"137","issue":"7","page":"1185-7","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19504061","title":"Transgenesis in Drosophila melanogaster.","abstract":"Transgenesis in Drosophila melanogaster relies upon direct microinjection of embryos and subsequent crossing of surviving adults. The necessity of crossing single flies to screen for transgenic events limits the range of useful transgenesis techniques to those that have a very high frequency of integration, so that about 1 in 10 to 1 in 100 surviving adult flies carry a transgene. Until recently, only random P-element transgenesis fulfilled these criteria. However, recent advances have brought homologous recombination and site-directed integration up to and beyond this level of efficiency. For all transgenesis techniques in Drosophila melanogaster, microinjection of embryos is the central procedure. This chapter gives a detailed protocol for microinjection, and aims to enable the reader to use it for both site-directed integration and for P-element transgenesis.","authors":"Ringrose, L.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Methods Mol Biol","volume":"561","issue":null,"page":"3-19","pdf":null,"JrId":"2488","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17975059","title":"The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race.","abstract":"Increasingly complex networks of small RNAs act through RNA-interference (RNAi) pathways to regulate gene expression, to mediate antiviral responses, to organize chromosomal domains, and to restrain the spread of selfish genetic elements. Historically, RNAi has been defined as a response to double-stranded RNA. However, some small RNA species may not arise from double-stranded RNA precursors. Yet, like microRNAs and small interfering RNAs, such species guide Argonaute proteins to silencing targets through complementary base-pairing. Silencing can be achieved by corecruitment of accessory factors or through the activity of Argonaute itself, which often has endonucleolytic activity. As a specific and adaptive regulatory system, RNAi is used throughout eukarya, which indicates a long evolutionary history. A likely function of RNAi throughout that history is to protect the genome from both pathogenic and parasitic invaders.","authors":"Aravin, AA., Hannon, GJ., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Science","volume":"318","issue":"5851","page":"761-4","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2361155","title":"Structural principles of B-DNA grooves hydration in fibers as revealed by Monte Carlo simulations and X-ray diffraction.","abstract":"Being interested in possible effects of sequence-dependent hydration of B-DNA with mixed sequence in fibers, we performed a series of Monte Carlo calculations of hydration of polydeoxyribonucleotides in B form, considering all sequences with dinucleotide repeat. The computational results allow the ten base-stacking types to be classified in accordance with their primary hydration in the minor groove. As a rule, the minor groove is occupied by two water molecules per base pair in the depth of the groove, which are located nearly midway between the planes of successive base pairs and symmetrically according to the dyad there. The primary hydration of the major groove depends on the type of the given base pair. The coordinates of 3 water molecules per base pair in the depth of the major groove are determined by the type of this pair together with its position and orientation in the helix, and are practically independent on the adjacent base pairs. A\/T-homopolymer tracts do not fit into this hydration pattern; the base pair edges are hydrated autonomously in both grooves. Analysis of the Li-B-DNA x-ray diffraction intensities reveals those two water positions in the minor groove. In the major groove, no electronic density peaks in sufficient distance from the base edges were found, thus confirming the absence of any helical invariance of primary hydration in this region. With the help of the rules proposed in this paper it is possible to position the water molecules of the first hydration shell in the grooves of canonical B-DNA for any given sequence.","authors":"Eisenhaber, F., Mannik, JH., Tumanyan, VG.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Biopolymers","volume":"29","issue":"10-11","page":"1453-64","pdf":null,"JrId":"1181","fulltextlink":null,"preprintlink":null,"articledate":"1990-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"132","title":"Cardiac output response to altered acid-base status during diethyl ether anaesthesia.","abstract":"The effects of acid-base changes on cardiac output during diethyl ether anaesthesia were studied in 25 mongrel dogs prepared by surgically implanting a plastic encased non-ferrous core electromagnetic probe on the ascending aorta. The findings are: (1) Metabolic acidaemia produced only slight decrease in cardiac output but a more marked fall became evident with decreasing pH(2) Respiratory acidaemia led to a slight rise in cardiac output. (3) Respiratory alkalaemia decreased cardiac output. (4) Metabolic alkalaemia also produced a decline in cardiac output.","authors":"Sodipo, JO., Lee, DC., Morris, LE.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can Anaesth Soc J","volume":"22","issue":"6","page":"673-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17346786","title":"Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila.","abstract":"Drosophila Piwi-family proteins have been implicated in transposon control. Here, we examine piwi-interacting RNAs (piRNAs) associated with each Drosophila Piwi protein and find that Piwi and Aubergine bind RNAs that are predominantly antisense to transposons, whereas Ago3 complexes contain predominantly sense piRNAs. As in mammals, the majority of Drosophila piRNAs are derived from discrete genomic loci. These loci comprise mainly defective transposon sequences, and some have previously been identified as master regulators of transposon activity. Our data suggest that heterochromatic piRNA loci interact with potentially active, euchromatic transposons to form an adaptive system for transposon control. Complementary relationships between sense and antisense piRNA populations suggest an amplification loop wherein each piRNA-directed cleavage event generates the 5' end of a new piRNA. Thus, sense piRNAs, formed following cleavage of transposon mRNAs may enhance production of antisense piRNAs, complementary to active elements, by directing cleavage of transcripts from master control loci.","authors":"Brennecke, J., Aravin, AA., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., Hannon, GJ.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell","volume":"128","issue":"6","page":"1089-103","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2007-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-142","title":"Vibrational excitons in ionophores: experimental probes for quantum coherence-assisted ion transport and selectivity in ion channels","abstract":null,"authors":"Ganim, Z., Tokmakoff, A., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"New J. Phys.","volume":"13","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":"http:\/\/iopscience.iop.org\/1367-2630\/13\/11\/113030\/","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17994019","title":"RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.","abstract":"It is widely assumed that the key rate-limiting step in gene activation is the recruitment of RNA polymerase II (Pol II) to the core promoter. Although there are well-documented examples in which Pol II is recruited to a gene but stalls, a general role for Pol II stalling in development has not been established. We have carried out comprehensive Pol II chromatin immunoprecipitation microarray (ChIP-chip) assays in Drosophila embryos and identified three distinct Pol II binding behaviors: active (uniform binding across the entire transcription unit), no binding, and stalled (binding at the transcription start site). The notable feature of the approximately 10% genes that are stalled is that they are highly enriched for developmental control genes, which are either repressed or poised for activation during later stages of embryogenesis. We propose that Pol II stalling facilitates rapid temporal and spatial changes in gene activity during development.","authors":"Zeitlinger, J., Stark, A., Kellis, M., Hong, JW., Nechaev, S., Adelman, K., Levine, M., Young, RA.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Genet","volume":"39","issue":"12","page":"1512-6","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2265229","title":"Structure of the hydration shells of oligo(dA-dT).oligo(dA-dT) and oligo(dA).oligo(dT) tracts in B-type conformation on the basis of Monte Carlo calculations.","abstract":"Monte Carlo simulations [(N, V, T)-ensemble] were performed for the hydration shell of poly(dA-dT).poly(dA-dT) in canonical B form and for the hydration shell of poly(dA).poly(dT) in canonical B conformation and in a conformation with narrow minor groove, highly inclined bases, but with a nearly zero-inclined base pair plane (B' conformation). We introduced helical periodic boundary conditions with a rather small unit cell and a limited number of water molecules to reduce the dimensionality of the configuration space. The coordinates of local maxima of water density and the properties of one- and two-membered water bridges between polar groups of the DNA were obtained. The AT-alternating duplex hydration mirrors the dyad symmetry of polar group distribution. At the dApdT step, a water bridge between the two carbonyl oxygens O2 of thymines is formed as in the central base-pair step of Dickerson's dodecamer. In the major groove, 5-membered water chains along the tetranucleotide pattern d(TATA).d(TATA) are observed. The hydration geometry of poly(dA).poly(dT) in canonical B conformation is distinguished by autonomous primary hydration of the base-pair edges in both grooves. When this polymer adopts a conformation with highly inclined bases and narrow minor groove, the water density distribution in the minor groove is in excellent agreement with Dickerson's spine model. One local maximum per base pair of the first layer is located near the dyad axis between adjacent base pairs, and one local maximum per base pair in the second shell lies near the dyad axis of the base pair itself. The water bridge between the two strands formed within the first layer was observed with high probability. But the water molecules of the second layer do not have a statistically favored orientation necessary for bridging first layer waters. In the major groove, the hydration geometry of the (A.T) base-pair edge resembles the main features of the AT-pair hydration derived from other sequences for the canonical B form. The preference of the B' conformation for oligo(dA).oligo(dT) tracts may express the tendency to common hydration of base-pair edges of successive base pairs in the grooves of B-type DNA. The mean potential energy of hydration of canonical B-DNA was estimated to be -60 to -80 kJ\/mole nucleotides in dependence on the (G.C) contents. Because of the small system size, this estimation is preliminary.","authors":"Eisenhaber, F., Tumanyan, VG., Abagyan, RA.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Biopolymers","volume":"30","issue":"5-6","page":"563-81","pdf":null,"JrId":"1181","fulltextlink":null,"preprintlink":null,"articledate":"1991-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2179502","title":"Mitogenic effect of interleukin-2 on unstimulated human T cells: an editorial review.","abstract":"The most salient feature of the lymphokine interleukin-2 (IL-2), a hormone-like protein, is its ability to sustain the proliferation of immunocompetent T cells. Results of initial studies characterizing IL-2 in vitro led investigators to conclude that IL-2 had no known effects on lymphocytes that had not been previously activated by exposure to a mitogen or antigen. Several groups postulated that T cell growth required two signals. The first signal, delivered by a mitogen or antigen, induced T cell activation. Resting T cells, which were thought to lack the membrane receptor for interleukin-2 (IL-2R), progressed from the G0-G1 phase to the S phase, during which time they converted from IL-2R- to IL-2R+ cells. Thereafter, the second signal, served by IL-2, induced T cell proliferation of the IL-2R+ cells. Recently, a number of investigators have demonstrated that highly purified preparations of both natural and recombinant IL-2 induced high levels of T cell proliferation in the absence of any known mitogens or antigens. Presented herein is a review of these studies and an overview of the hypotheses of the mechanisms whereby IL-2 alone induces T cell activation and proliferation.","authors":"Mookerjee, BK., Pauly, JL.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"J Clin Lab Anal","volume":"4","issue":"2","page":"138-49","pdf":null,"JrId":"5120","fulltextlink":null,"preprintlink":null,"articledate":"1990-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19286556","title":"Structure of the anaphase-promoting complex\/cyclosome interacting with a mitotic checkpoint complex.","abstract":"Once all chromosomes are connected to the mitotic spindle (bioriented), anaphase is initiated by the protein ubiquitylation activity of the anaphase-promoting complex\/cyclosome (APC\/C) and its coactivator Cdc20 (APC\/C(Cdc20)). Before chromosome biorientation, anaphase is delayed by a mitotic checkpoint complex (MCC) that inhibits APC\/C(Cdc20). We used single-particle electron microscopy to obtain three-dimensional models of human APC\/C in various functional states: bound to MCC, to Cdc20, or to neither (apo-APC\/C). These experiments revealed that MCC associates with the Cdc20 binding site on APC\/C, locks the otherwise flexible APC\/C in a \"closed\" state, and prevents binding and ubiquitylation of a wide range of different APC\/C substrates. These observations clarify the structural basis for the inhibition of APC\/C by spindle checkpoint proteins.","authors":"Herzog, F., Primorac, I., Dube, P., Lenart, P., Sander, B., Mechtler, K., Stark, H., Peters, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Science","volume":"323","issue":"5920","page":"1477-81","pdf":null,"JrId":"7473","fulltextlink":"http:\/\/www.sciencemag.org\/cgi\/content\/full\/323\/5920\/1477","preprintlink":null,"articledate":"2009-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40401474","title":"In preprints: retinoic acid degradation and tissue stiffness coordinate axolotl limb regeneration.","abstract":null,"authors":"Masselink, W.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Development","volume":"152","issue":"10","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-22","doi":"10.1242\/dev.204891","first_author":null,"corresponding_authors":null},{"pmid":"17322397","title":"Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.","abstract":"Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determined the genome-wide occupancy of the dorsoventral (DV) determinants Dorsal, Twist, and Snail in the Drosophila embryo using chromatin immunoprecipitation coupled with microarray analysis (ChIP-chip). The in vivo binding of these proteins correlate tightly with the limits of known enhancers. Our analysis predicts substantially more target genes than previous estimates, and includes Dpp signaling components and anteroposterior (AP) segmentation determinants. Thus, the ChIP-chip data uncover a much larger than expected regulatory network, which integrates diverse patterning processes during development.","authors":"Zeitlinger, J., Zinzen, RP., Stark, A., Kellis, M., Zhang, H., Young, RA., Levine, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genes Dev","volume":"21","issue":"4","page":"385-90","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17043305","title":"Denoising feedback loops by thresholding--a new role for microRNAs.","abstract":null,"authors":"Cohen, SM., Brennecke, J., Stark, A.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Genes Dev","volume":"20","issue":"20","page":"2769-72","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2006-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19494123","title":"Shifting views on the leading role of the lamellipodium in cell migration: speckle tracking revisited.","abstract":null,"authors":"Vallotton, P., Small, JV.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Sci","volume":"122","issue":"Pt 12","page":"1955-8","pdf":null,"JrId":"4592","fulltextlink":"http:\/\/jcs.biologists.org\/cgi\/reprint\/122\/12\/1955","preprintlink":null,"articledate":"2009-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16337999","title":"Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution.","abstract":"MicroRNAs are small noncoding RNAs that serve as posttranscriptional regulators of gene expression in higher eukaryotes. Their widespread and important role in animals is highlighted by recent estimates that 20%-30% of all genes are microRNA targets. Here, we report that a large set of genes involved in basic cellular processes avoid microRNA regulation due to short 3'UTRs that are specifically depleted of microRNA binding sites. For individual microRNAs, we find that coexpressed genes avoid microRNA sites, whereas target genes and microRNAs are preferentially expressed in neighboring tissues. This mutually exclusive expression argues that microRNAs confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions.","authors":"Stark, A., Brennecke, J., Bushati, N., Russell, RB., Cohen, SM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell","volume":"123","issue":"6","page":"1133-46","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2006-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20495554","title":"RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila.","abstract":"Human immune cells have to penetrate an endothelial barrier during their beneficial pursuit of infection and their destructive infiltration of tissues in autoimmune diseases. This transmigration requires Rap1 GTPase to activate integrin affinity. We define a new model system for this process by demonstrating, with live imaging and genetics, that during embryonic development Drosophila melanogaster immune cells penetrate an epithelial, Drosophila E-cadherin (DE-cadherin)-based tissue barrier. A mutant in RhoL, a GTPase homologue that is specifically expressed in haemocytes, blocks this invasive step but not other aspects of guided migration. RhoL mediates integrin adhesion caused by Drosophila Rap1 overexpression and moves Rap1 away from a concentration in the cytoplasm to the leading edge during invasive migration. These findings indicate that a programmed migratory step during Drosophila development bears striking molecular similarities to vertebrate immune cell transmigration during inflammation, and identify RhoL as a new regulator of invasion, adhesion and Rap1 localization. Our work establishes the utility of Drosophila for identifying novel components of immune cell transmigration and for understanding the in vivo interplay of immune cells with the barriers they penetrate.","authors":"Siekhaus, D., Haesemeyer, M., Moffitt, O., Lehmann, R.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Cell Biol","volume":"12","issue":"6","page":"605-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2167175","title":"The identification of a second cell cycle control on the HO promoter in yeast: cell cycle regulation of SW15 nuclear entry.","abstract":"HO encodes a site-specific endonuclease that initiates mating type switching in S. cerevisiae. It is expressed only transiently during the cell cycle of mother cells, as they undergo Start, but not in daughter cells. Since SWI5 appears to be the only HO transcription factor missing when daughter cells undergo Start, we were interested in the intracellular distribution of SWI5 at cell division. We discovered that SWI5 is found equally concentrated in the nuclei of both mother and daughter cells at the end of anaphase, suggesting that its subsequent fate must somehow differ. Prior to the end of anaphase, SWI5 accumulates in the cytoplasm and only moves into the nucleus when cells enter G1. A version of the HO promoter that has lost its dependence on Start is nevertheless still strongly cell cycle regulated and is activated when SWI5 moves into the nucleus.","authors":"Nasmyth, K., Adolf, G., Lydall, D., Seddon, A.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Cell","volume":"62","issue":"4","page":"631-47","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1990-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16815998","title":"mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.","abstract":"MicroRNAs (miRNAs) silence the expression of target genes post-transcriptionally. Their function is mediated by the Argonaute proteins (AGOs), which colocalize to P-bodies with mRNA degradation enzymes. Mammalian P-bodies are also marked by the GW182 protein, which interacts with the AGOs and is required for miRNA function. We show that depletion of GW182 leads to changes in mRNA expression profiles strikingly similar to those observed in cells depleted of the essential Drosophila miRNA effector AGO1, indicating that GW182 functions in the miRNA pathway. When GW182 is bound to a reporter transcript, it silences its expression, bypassing the requirement for AGO1. Silencing by GW182 is effected by changes in protein expression and mRNA stability. Similarly, miRNAs silence gene expression by repressing protein expression and\/or by promoting mRNA decay, and both mechanisms require GW182. mRNA degradation, but not translational repression, by GW182 or miRNAs is inhibited in cells depleted of CAF1, NOT1, or the decapping DCP1:DCP2 complex. We further show that the N-terminal GW repeats of GW182 interact with the PIWI domain of AGO1. Our findings indicate that GW182 links the miRNA pathway to mRNA degradation by interacting with AGO1 and promoting decay of at least a subset of miRNA targets.","authors":"Behm-Ansmant, I., Rehwinkel, J., Doerks, T., Stark, A., Bork, P., Izaurralde, E.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Genes Dev","volume":"20","issue":"14","page":"1885-98","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-128","title":"Evolution of Genes and Genomes on the Drosophila Phylogeny.","abstract":null,"authors":"Drosophila 12 Genomes Consortium.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"450","issue":"7167","page":"203-18","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19285745","title":"Evolution of the achaete-scute complex in insects: convergent duplication of proneural genes.","abstract":"Proneural genes encode transcriptional activators of the basic Helix-loop-helix class that are involved in neuronal specification and differentiation. We have used the recent availability of genome sequences of multiple distant insect species to study the evolution of a family of proneural genes, the achaete-scute genes, and to examine their genomic organization and evolution. We document independent evolution of multiple copies of achaete-scute homologues and argue that this might have contributed to morphological diversity in Diptera and Lepidoptera.","authors":"Negre, B., Simpson, P.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Trends Genet","volume":"25","issue":"4","page":"147-52","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22129557","title":"Exome sequencing can detect pathogenic mosaic mutations present at low allele frequencies.","abstract":"The development of next generation sequencing (NGS) has radically transformed the scientific landscape, making it possible to sequence the exome of any given individual in a cost-effective way. The power of this approach has been demonstrated by a number of groups who have identified pathogenic mutations in small pedigrees that have been resistant to traditional genetic mapping. Recently it has become clear that exome sequencing has great potential with respect to sporadic disease and the identification of de novo mutations. This is highlighted by studies reporting whole-exome sequencing of patient-parental trios affected by learning disability, autism and schizophrenia. It is widely anticipated that the introduction of this technique into a clinical setting will revolutionise genetic diagnosis. However, the sensitivity of NGS exome sequencing is currently unclear. Here, we describe the exome sequencing of DNA samples from a patient with double cortex syndrome and her parents, resulting in the detection of a mosaic splicing mutation in LIS1. This variant was found at an allele frequency of just 18%, demonstrating that NGS methods have the capacity to identify pathogenic mosaic mutations present at a low level.","authors":"Pagnamenta, AT., Lise, S., Harrison, V., Stewart, H., Jayawant, S., Quaghebeur, G., Deng, AT., Murphy, VE., Sadighi Akha, E., Rimmer, A., Mathieson, I., Knight, SJ., Kini, U., Taylor, JC., Keays, DA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Hum Genet","volume":"57","issue":"1","page":"70-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16601183","title":"Developmental biology. Mixed messages in early development.","abstract":null,"authors":"Cohen, SM., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Science","volume":"312","issue":"5770","page":"65-6","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16204177","title":"Not miR-ly muscular: microRNAs and muscle development.","abstract":null,"authors":"Brennecke, J., Stark, A., Cohen, SM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Genes Dev","volume":"19","issue":"19","page":"2261-4","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8575752","title":"Determination and regional assignment of grouped sets of microclones in chromosome 1pter-p35.","abstract":"In an approach to mapping physically the most distal 30 Mb of human chromosome 1p, region-specific clone libraries were generated by microdissection and microcloning. PFGE blot hybridization of single or low-copy microclones against rare-cutter digests of genomic DNA revealed physical linkage for groups of markers. Supplementary PFGE analysis of 31 1p36-p35-specific probes for genetically mapped loci established a total of 15 grouped sets, consisting of altogether 69 markers. Twelve of the grouped sets were located in 1pter-p36.12, as revealed by microcell hybrid mapping; the remaining three were localized proximal to 1p36.12. Regional assignment and ordering of most grouped sets was achieved either by evaluating the included genetic markers or by fluorescence in situ hybridization of representative probes. The genomic extent of individual grouped sets encompassed between 1100 and 2100 kb, covering a total of approximately 22 Mb of the distal chromosome 1p region. One particular grouped set was shown to contain seven polymorphic marker loci that were previously suggested to be distributed across the entire 1pter-p35 region. The increase in the number of hybridization marker probes in 1p36 and their physical mapping is expected to facilitate positional cloning experiments in this region; in particular, the construction of clone contigs may be greatly facilitated.","authors":"Barnas, CM., Onyango, P., Ellmeier, W., Lengauer, C., Kleiner, E., Henn, T., Brunner, C., Stapleton, P., Weith, A.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Genomics","volume":"29","issue":"3","page":"607-15","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19490875","title":"Long range clustering of oligonucleotides containing the CG signal.","abstract":"The distance distributions between successive occurrences of the same oligonucleotides in chromosomal DNA are studied, in different classes of higher eucaryotic organisms. A two-parameter modeling is undertaken and applied on the distance distribution of quintuplets (sequences of size five bps) and hexaplets (sequences of size six bps); the first parameter k refers to the short range exponential decay of the distributions, whereas the second parameter m refers to the power law behavior. A two-dimensional scatter plot representing the model equation demonstrates that the points corresponding to the distance distribution of oligonucleotides containing the CG consensus sequence (promoter of the RNA polymerase II) cluster together (group alpha), apart from all other oligonucleotides (group beta). This is shown for the available chordata Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, Gallus gallus and Danio rerio. This clustering is less evident in lower Animalia and plants, such as Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. Moreover, in all organisms the oligonucleotides which contain any consensus sequence are found to be described by long range distributions, whereas all others have a stronger influence of short range decay. Various measures are introduced and evaluated, to numerically characterize the clustering of the two groups. The one which most clearly discriminates the two classes is shown to be the proximity factor.","authors":"Katsaloulis, P., Theoharis, T., Provata, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Theor Biol","volume":"258","issue":"1","page":"18-26","pdf":null,"JrId":"5295","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8228830","title":"The induction of experimental autoimmune myocarditis in mice lacking CD4 or CD8 molecules [corrected].","abstract":"Experimental induction of most autoimmune diseases appears to depend on the activation of CD4+ T helper cells, while CD8+ lymphocytes may have a role in disease progression. To study the role of CD4+ and CD8+ T cell subsets in T cell-dependent autoimmunity, mice lacking CD4 or CD8 molecules after gene targeting were injected with cardiac myosin to induce organ specific autoimmune myocarditis. Mice homozygous for the CD8 mutation (CD8-\/-) developed significantly more severe disease as compared to CD4+\/-CD8+\/- controls. Surprisingly, CD4-\/- mice developed autoimmune myocarditis with infiltration of TCR alpha beta +CD4-CD8- T cells in the heart tissue and appearance of autoantibodies. These data demonstrate that the lack of CD4+ or CD8+ T cells has no significant influence on the initiation of autoimmune myocarditis. CD4+ and CD8+ cells regulate disease severity and these results may explain the occurrence of autoimmunity in CD4 immunodeficiencies.","authors":"Penninger, JM., Neu, N., Timms, E., Wallace, VA., Koh, DR., Kishihara, K., Pummerer, C., Mak, TW.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Exp Med","volume":"178","issue":"5","page":"1837-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1993-11-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19407921","title":"The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: a consequence of dosage compensation?","abstract":"In Drosophila, there is a consistent deficit of male-biased genes on the X chromosome. It has been suggested that male-biased genes may evolve from initially unbiased genes as a result of increased expression levels in males. If transcription rates are limited, a large increase in expression in the testis may be harder to achieve for single-copy X-linked genes than for autosomal genes, because they are already hypertranscribed due to dosage compensation. This hypothesis predicts that the larger the increase in expression required to make a male-biased gene, the lower the chance of this being achievable if it is located on the X chromosome. Consequently, highly expressed male-biased genes should be located on the X chromosome less often than lowly expressed male-biased genes. This pattern is observed in our analysis of publicly available data, where microarray data or EST data are used to detect male-biased genes in D. melanogaster and to measure their expression levels. This is consistent with the idea that limitations in transcription rates may prevent male-biased genes from accumulating on the X chromosome.","authors":"Vicoso, B., Charlesworth, B.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Mol Evol","volume":"68","issue":"5","page":"576-83","pdf":null,"JrId":"4969","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8566238","title":"Cloning, purification, and crystallization of Escherichia coli cystathionine beta-lyase.","abstract":"The metC gene coding for cystathionine beta-lyase of Escherichia coli has been cloned and used to construct an overproducing E. coli strain. An efficient purification scheme has been developed and the purified enzyme has been crystallized by the hanging drop vapour diffusion method using either ammonium sulfate or polyethyleneglycol 400 as precipitating agent. The crystals belong to the orthorombic space group C222. Their unit cell parameters are a = 60.9 A, b = 154.7 A and c = 152.7 A. Consideration of the possible values of VM accounts for the presence of one dimer per asymmetric unit. The crystals are suitable for X-ray analysis and a complete native date set to 1.83 A resolution has been collected using synchrotron radiation.","authors":"Laber, B., Clausen, T., Huber, R., Messerschmidt, A., Egner, U., M\u00fcller-Fahrnow, A., Pohlenz, HD.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"FEBS Lett","volume":"379","issue":"1","page":"94-6","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2140770","title":"An abundant and ubiquitous homo-oligomeric ring-shaped ATPase particle related to the putative vesicle fusion proteins Sec18p and NSF.","abstract":"We have discovered a ring-shaped particle of 12.5 nm diameter, 14.5S and apparent molecular weight of approximately 570,000 that displays 6-fold radial symmetry and is composed of a single kind of an acidic (pI approximately 5.5) polypeptide of Mr 97,000 (p97). Using antibodies to this protein we have detected its occurrence in a wide range of cells and tissues of diverse species from frog to man, including highly specialized cells such as mammalian erythrocytes and spermatozoa. In Xenopus laevis oocytes, the particle is found in both isolated nuclei and in manually enucleated ooplasms, which corresponds to immunofluorescence staining dispersed over both nucleoplasm and cytoplasm. The particle has a N-ethylmaleimide (NEM)-inhibitable Mg2(+)-ATPase activity, and its amino acid sequence, as deduced from cDNA clones, displays considerable homology to the mammalian NEM-sensitive fusion protein (NSF) and yeast Sec18p believed to be essential for vesicle fusion in secretory processes, indicating that these three proteins belong to the same multigene family.","authors":"Peters, JM., Walsh, MJ., Franke, WW.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"EMBO J","volume":"9","issue":"6","page":"1757-67","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1990-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2147872","title":"Cyclin activation of p34cdc2.","abstract":"The gradual accumulation of cyclin in the frog egg induces an abrupt and concerted activation of p34cdc2 that initiates mitosis. Activation is delayed even after the accumulation of cyclin to a critical threshold concentration. We have reproduced these unusual kinetic properties of p34cdc2 activation in vitro using bacterially expressed cyclin proteins and extracts derived from Xenopus eggs. Abrupt activation follows a lag period, the length of which is independent of the concentration of cyclin. The threshold concentration of cyclin and the length of the lag period are regulated by INH, an inhibitor of MPF activation in oocytes recently identified as a type 2A protein phosphatase. Binding to cyclin induces both tyrosine and threonine phosphorylation of the previously unphosphorylated p34cdc2, rendering it inactivated. The concerted transition into mitosis involves both a reduction in the rate of p34cdc2 phosphorylation on tyrosine and an increase in its rate of dephosphorylation.","authors":"Solomon, MJ., Glotzer, M., Lee, TH., Philippe, M., Kirschner, MW.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Cell","volume":"63","issue":"5","page":"1013-24","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1991-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26490398","title":"Reconciling randomness and precision.","abstract":null,"authors":"Ringrose, L.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Rev Mol Cell Biol","volume":"16","issue":"11","page":"642","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2129545","title":"A regular pattern of two types of 100-residue motif in the sequence of titin.","abstract":"Titin is the largest polypeptide yet described (relative molecular mass approximately 3 x 10(6); refs 1, 2) and an abundant protein of striated muscle. Its molecules are string-like and in vivo span from the M to Z-lines. I-band regions of titin are thought to make elastic connections between the thick filament and the Z-line, thereby forming a third type of sarcomere filament. These would centre the A-band in the sarcomere and provide structural continuity in relaxed myofibrils. The A-band region of titin seems to be bound to the thick filament, where it has been proposed to act as a 'molecular ruler' regulating filament length and assembly. Here, we show that partial titin complementary DNAs encode a regular pattern of two types of 100-residue motif, each of which probably folds into a separate domain type. Such motifs are present in several evolutionarily divergent muscle proteins, all of which are likely to interact with myosin. One or both of the domain types is therefore likely to bind to myosin.","authors":"Labeit, S., Barlow, DP., Gautel, M., Gibson, T., Holt, J., Hsieh, CL., Francke, U., Leonard, K., Wardale, J., Whiting, A.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Nature","volume":"345","issue":"6272","page":"273-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1990-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22068587","title":"A RANKL G278R mutation causing osteopetrosis identifies a functional amino acid essential for trimer assembly in RANKL and TNF.","abstract":"Receptor activator of nuclear factor-\u03baB ligand (RANKL), a trimeric tumor necrosis factor (TNF) superfamily member, is the central mediator of osteoclast formation and bone resorption. Functional mutations in RANKL lead to human autosomal recessive osteopetrosis (ARO), whereas RANKL overexpression has been implicated in the pathogenesis of bone degenerative diseases such as osteoporosis. Following a forward genetics approach using N-ethyl-N-nitrosourea (ENU)-mediated random mutagenesis, we generated a novel mouse model of ARO caused by a new loss-of-function allele of Rankl with a glycine-to-arginine mutation at codon 278 (G278R) at the extracellular inner hydrophobic F \u03b2-strand of RANKL. Mutant mice develop severe osteopetrosis similar to Rankl-deficient mice, whereas exogenous administration of recombinant RANKL restores osteoclast formation in vivo. We show that RANKL(G278R) monomers fail to assemble into homotrimers, are unable to bind and activate the RANK receptor and interact with wild-type RANKL exerting a dominant-negative effect on its trimerization and function in vitro. Since G278 is highly conserved within the TNF superfamily, we identified that a similar substitution in TNF, G122R, also abrogated trimerization, binding to TNF receptor and consequently impaired TNF biological activity. Notably, SPD304, a potent small-molecule inhibitor of TNF trimerization that interacts with G122, also inhibited RANKL activity, suggesting analogous inhibitory mechanisms. Our results provide a new disease model for ARO and identify a functional amino acid in the TNF-like core domain essential for trimer formation both in RANKL and in TNF that could be considered a novel potential target for inhibiting their biological activities.","authors":"Douni, E., Rinotas, V., Makrinou, E., Zwerina, J., Penninger, JM., Eliopoulos, E., Schett, G., Kollias, G.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Hum Mol Genet","volume":"21","issue":"4","page":"784-98","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19520911","title":"Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection.","abstract":"Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved in susceptibility or resistance to intestinal infection with the bacterium Serratia marcescens. We first employed whole-organism gene suppression, followed by tissue-specific silencing in gut epithelium or hemocytes to identify several hundred genes involved in intestinal antibacterial immunity. Among the pathways identified, we showed that the JAK-STAT signaling pathway controls host defense in the gut by regulating stem cell proliferation and thus epithelial cell homeostasis. Therefore, we revealed multiple genes involved in antibacterial defense and the regulation of innate immunity.","authors":"Cronin, SJ., Nehme, NT., Limmer, S., Liegeois, S., Pospisilik, JA., Schramek, D., Leibbrandt, A., Simoes, Rde M., Gruber, S., Puc, U., Ebersberger, I., Zoranovic, T., Neely, GG., von Haeseler, A., Ferrandon, D., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Science","volume":"325","issue":"5938","page":"340-3","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8562472","title":"Terminal differentiation of normal chicken erythroid progenitors: shortening of G1 correlates with loss of D-cyclin\/cdk4 expression and altered cell size control.","abstract":"Detailed knowledge is available about the molecular makeup of the cell cycle clock in dividing cells. However, comparatively little is known about cell cycle regulation during terminal differentiation. Here we describe a primary cell system in which this question can be addressed. Normal avian erythroid progenitors undergo continuous self-renewal in suspension culture in the presence of growth factors and hormones, allowing us to obtain large cell numbers (10(10)-10(11)). By replacing these \"self-renewal factors\" with erythropoietin and insulin, the cells can be induced to synchronous, terminal differentiation. During the first 72 h, the cells undergo five cell divisions. Thereafter, they arrest in G1 and complete their maturation into RBC without further divisions. Sixteen to 24 h after induction of differentiation, the cell cycle length decreased from about 20 to 12 h. This shortened doubling time was due to a drastic reduction of G1 (from 12 to 5 h), while S- and G2-phase lengths were not affected. At the same time, the differentiating cells underwent an extensive and concerted switch in their gene expression pattern. During the subsequent four cell divisions, the cell volume decreased from about 300 to less than 70 femtoliters, but the rate of protein synthesis normalized to cell volume remained constant. Interestingly, the shortening of G1 was accompanied by a rapid down-regulation of D-type cyclins and their partner, cyclin-dependent kinase type 4 (cdk4), while expression of S- and G2-M-associated cell cycle regulators (cyclin A and cdk1\/cdc2) remained high until the cells arrested in G1 72-96 h after differentiation induction. We conclude that concerted reprogramming of progenitor gene expression during erythroid differentiation is accompanied by profoundly altered cell cycle progression involving the loss or alteration of cell size control at the restriction point.","authors":"Dolznig, H., Bartunek, P., Nasmyth, K., M\u00fcllner, EW., Beug, H.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell Growth Differ","volume":"6","issue":"11","page":"1341-52","pdf":null,"JrId":"1848","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21747402","title":"Determinants and dynamics of genome accessibility.","abstract":"In eukaryotes, all DNA-templated reactions occur in the context of chromatin. Nucleosome packaging inherently restricts DNA accessibility for regulatory proteins but also provides an opportunity to regulate DNA-based processes through modulating nucleosome positions and local chromatin structure. Recent advances in genome-scale methods are yielding increasingly detailed profiles of the genomic distribution of nucleosomes, their modifications and their modifiers. The picture now emerging is one in which the dynamic control of genome accessibility is governed by contributions from DNA sequence, ATP-dependent chromatin remodelling and nucleosome modifications. Here we discuss the interplay of these processes by reviewing our current understanding of how chromatin access contributes to the regulation of transcription, replication and repair.","authors":"Bell, O., Tiwari, VK., Thom\u00e4, NH., Sch\u00fcbeler, D.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Rev Genet","volume":"12","issue":"8","page":"554-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19307313","title":"Molecular evolution and functional diversification of fatty acid desaturases after recurrent gene duplication in Drosophila.","abstract":"Frequent gene duplications in the genome incessantly supply new genetic materials for functional innovation presumably driven by positive Darwinian selection. This mechanism in the desaturase gene family has been proposed to be important in triggering the pheromonal diversification in insects. With the recent completion of a dozen Drosophila genomes, a genome-wide perspective is possible. In this study, we first identified homologs of desaturase genes in 12 Drosophila species and noted that while gene duplication events are relatively frequent, gene losses are not scarce, especially in the desat1-desat2-desatF clade. By reconciling the gene tree with species phylogeny and the chromosomal synteny of the sequenced Drosophila genomes, at least one gene loss in desat2 and a minimum of six gene gains (resulting in seven desatF homologs, alpha-eta), three gene losses and one relocation in desatF were inferred. Upon branching off the ancestral desat1 lineage, both desat2 and desatF gained novel functions through accelerating protein evolution. The amino acid residues under positive selection located near the catalytic sites and the C-terminal region might be responsible for altered substrate selectivity between closely related species. The association between the expression pattern of desatF-alpha and the chemical composition of cuticular hydrocarbons implies that the ancestral function of desatF-alpha is the second desaturation at the four carbons after the first double bond in diene synthesis, and the shift from bisexual to female-specific expression in desatF-alpha occurred in the ancestral lineage of Drosophila melanogaster subgroup. A relationship between the number of expressed desatF homologs and the diene diversification has also been observed. These results suggest that the molecular diversification of fatty acid desaturases after recurrent gene duplication plays an important role in pheromonal diversity in Drosophila.","authors":"Fang, S., Ting, CT., Lee, CR., Chu, KH., Wang, CC., Tsaur, SC.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Biol Evol","volume":"26","issue":"7","page":"1447-56","pdf":null,"JrId":"5749","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2111020","title":"Lesion-induced increase in nerve growth factor mRNA is mediated by c-fos.","abstract":"Lesion of the sciatic nerve caused a rapid increase in c-fos and c-jun mRNA that was followed about 2 hr later by an increase in nerve growth factor (NGF) mRNA. To evaluate whether the initial increase in c-fos mRNA is causally related to the subsequent increase in NGF mRNA, we performed experiments with fibroblasts of transgenic mice carrying an exogenous c-fos gene under the control of a metallothionein promoter. In primary cultures of these fibroblasts, CdCl2 evoked a rapid increase in exogenous c-fos mRNA, followed immediately by an increase in endogenous c-jun mRNA and with a slight delay by an increase in NGF mRNA. In fibroblasts of C3H control mice, CdCl2 had no effect on the mRNA levels of the protooncogenes c-fos and c-jun or of NGF. Additional evidence for a causal relationship between c-fos induction and the subsequent increase in NGF mRNA was obtained in cotransfection experiments. Fibroblasts of C3H control mice were cotransfected with a metallothionein-promoter-driven c-fos expression vector and a NGF promoter-chloramphenicol acetyltransferase reporter gene construct. Induction of the exogenous c-fos by CdCl2 resulted in increased activity of the NGF promoter. DNase I footprint experiments demonstrated that a binding site for transcription factor AP-1 (Fos\/Jun heterodimer) in the first intron of the NGF gene was protected following c-fos induction. That this protected AP-1 site indeed was functional in the regulation of NGF expression was verified by deletion experiments and by a point mutation in the corresponding AP-1 binding region in the NGF promoter-chloramphenicol acetyltransferase reporter construct.","authors":"Hengerer, B., Lindholm, D., Heumann, R., R\u00fcther, U., Wagner, EF., Thoenen, H.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Proc Natl Acad Sci U S A","volume":"87","issue":"10","page":"3899-903","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1990-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22606938","title":"Activity-based probe for histidine kinase signaling.","abstract":"Bacterial two-component systems (TCSs) are signaling pathways composed of two proteins: a histidine kinase (HK) and a response regulator (RR). Upon stimulation, the HK autophosphorylates at a conserved histidine. The phosphoryl group is subsequently transferred to an aspartate on an RR, eliciting an adaptive response, often up- or downregulation of gene expression. TCS signaling controls many functions in bacteria, including development, virulence, and antibiotic resistance, making the proteins involved in these systems potential therapeutic targets. Efficient methods for the profiling of HKs are currently lacking. For direct readout of HK activity, we sought to design a probe that enables detection of the phosphotransfer event; however, analysis of the phosphohistidine species is made difficult by the instability of the P-N bond. We anticipated that use of a \u03b3-thiophosphorylated ATP analogue, which would yield a thiophosphorylated histidine intermediate, could overcome this challenge. We determined that the fluorophore-conjugated probe, BODIPY-FL-ATP\u03b3S, labels active HK proteins and is competitive for the ATP binding site. This activity-based probe provides a new strategy for analysis of TCSs and other HK-mediated processes and will facilitate both functional studies and inhibitor identification.","authors":"Wilke, KE., Francis, S., Carlson, EE.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Am Chem Soc","volume":"134","issue":"22","page":"9150-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19285146","title":"Molecular phylogeny of the Drosophila tripunctata and closely related species groups (Diptera: Drosophilidae).","abstract":"We suggest a new phylogenetic hypothesis for the tripunctata radiation based on sequences of mitochondrial genes. Phylogenetic trees were reconstructed by parsimony, maximum likelihood and Bayesian methods. We performed tests for hypotheses of monophyly for taxonomic groups and other specific hypotheses. Results reject the monophyly for the tripunctata group whereas monophyly is not rejected for the tripunctata radiation and other specific groups within the radiation. Although most of the basal nodes were unresolved we were able to identify four clusters within the tripunctata radiation. These results suggest the collection of additional data before a proper taxonomic revision could be proposed.","authors":"Hatadani, LM., McInerney, JO., de Medeiros, HF., Junqueira, AC., de Azeredo-Espin, AM., Klaczko, LB.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Phylogenet Evol","volume":"51","issue":"3","page":"595-600","pdf":null,"JrId":"2616","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19478081","title":"Orphan transporter SLC6A18 is renal neutral amino acid transporter B0AT3.","abstract":"The orphan transporter Slc6a18 (XT2) is highly expressed at the luminal membrane of kidney proximal tubules and displays approximately 50% identity with Slc6a19 (B(0)AT1), which is the main neutral amino acid transporter in both kidney and small intestine. As yet, the amino acid transport function of XT2 has only been experimentally supported by the urinary glycine loss observed in xt2 null mice. We report here that in Xenopus laevis oocytes, co-expressed ACE2 (angiotensin-converting enzyme 2) associates with XT2 and reveals its function as a Na(+)- and Cl(-)-de pend ent neutral amino acid transporter. In contrast to its association with ACE2 observed in Xenopus laevis oocytes, our experiments with ace2 and collectrin null mice demonstrate that in vivo it is Collectrin, a smaller homologue of ACE2, that is required for functional expression of XT2 in kidney. To assess the function of XT2 in vivo, we reanalyzed its knock-out mouse model after more than 10 generations of backcrossing into C57BL\/6 background. In addition to the previously published glycinuria, we observed a urinary loss of several other amino acids, in particular beta-branched and small neutral ones. Using telemetry, we confirmed the previously described link of XT2 absence with hypertension but only in physically restrained animals. Taken together, our data indicate that the formerly orphan transporter XT2 functions as a sodium and chloride-de pend ent neutral amino acid transporter that we propose to rename B(0)AT3.","authors":"Singer, D., Camargo, SM., Huggel, K., Romeo, E., Danilczyk, U., Kuba, K., Chesnov, S., Caron, MG., Penninger, JM., Verrey, F.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Biol Chem","volume":"284","issue":"30","page":"19953-60","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19458196","title":"Cortactin promotes migration and platelet-derived growth factor-induced actin reorganization by signaling to Rho-GTPases.","abstract":"Dynamic actin rearrangements are initiated and maintained by actin filament nucleators, including the Arp2\/3-complex. This protein assembly is activated in vitro by distinct nucleation-promoting factors such as Wiskott-Aldrich syndrome protein\/Scar family proteins or cortactin, but the relative in vivo functions of each of them remain controversial. Here, we report the conditional genetic disruption of murine cortactin, implicated previously in dynamic actin reorganizations driving lamellipodium protrusion and endocytosis. Unexpectedly, cortactin-deficient cells showed little changes in overall cell morphology and growth. Ultrastructural analyses and live-cell imaging studies revealed unimpaired lamellipodial architecture, Rac-induced protrusion, and actin network turnover, although actin assembly rates in the lamellipodium were modestly increased. In contrast, platelet-derived growth factor-induced actin reorganization and Rac activation were impaired in cortactin null cells. In addition, cortactin deficiency caused reduction of Cdc42 activity and defects in random and directed cell migration. Reduced migration of cortactin null cells could be restored, at least in part, by active Rac and Cdc42 variants. Finally, cortactin removal did not affect the efficiency of receptor-mediated endocytosis. Together, we conclude that cortactin is fully dispensable for Arp2\/3-complex activation during lamellipodia protrusion or clathrin pit endocytosis. Furthermore, we propose that cortactin promotes cell migration indirectly, through contributing to activation of selected Rho-GTPases.","authors":"Lai, FP., Szczodrak, M., Oelkers, JM., Ladwein, M., Acconcia, F., Benesch, S., Auinger, S., Faix, J., Small, JV., Polo, S., Stradal, TE., Rottner, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Biol Cell","volume":"20","issue":"14","page":"3209-23","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2099346","title":"Increased expression of high-affinity low-density lipoprotein receptors on human T-blasts.","abstract":"Like all cells, lymphocytes need cholesterol for proper function, a requirement met by a finely tuned homeostasis between intracellular synthesis and uptake from the environment via low-density lipoproteins (LDL). We used flow cytometry to analyze the receptor activity of resting cells and T blasts incubated\/activated in serum-free culture medium, or in medium supplemented with 25-5,000 micrograms\/ml LDL. Dioctadecyl-indocarbocyanine has proved to be a useful fluorescent probe for investigating the LDL receptor activity of lymphocytes. The results show the receptor activity of day-3 resting T cells to be reduced more than 50% by 50 microgram LDL\/ml, whereas 100-fold higher concentrations are necessary to achieve the same level of reduction in day-3 PHA blasts. The LDL receptor activities of individual blood donors' resting T cells, in vitro cholesterol-deprived resting T cells, and activated T blasts, were compared using two analytical techniques: spectrofluorometric analysis of detergent-solubilized cell suspensions and flow cytometric analysis of single living cells. Receptor affinity was determined by Scatchard analysis of spectrofluorometric binding curves, and by Line-weaver-Burke plots of flow cytometric data. Both methods yielded essentially identical dissociation constants (Kd) for cholesterol-deprived resting T cells and mitogen-activated T blasts, which fell in the expected range for the high-affinity LDL receptor (4.1-8.9 nM). In addition, spectrofluorometric analysis, but not flow cytometry, permitted quantification of LDL uptake.(ABSTRACT TRUNCATED AT 250 WORDS)","authors":"Huber, LA., B\u00f6ck, G., J\u00fcrgens, G., Traill, KN., Sch\u00f6nitzer, D., Wick, G.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Int Arch Allergy Appl Immunol","volume":"93","issue":"2-3","page":"205-11","pdf":null,"JrId":"4261","fulltextlink":null,"preprintlink":null,"articledate":"1991-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-143","title":"Reply: Visualizing branched actin filaments in lamellipodia by electron tomography","abstract":null,"authors":"Small, J.V., Winkler, C., Vinzenz, M. and Schmeiser, S","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nature Cell Biology","volume":"doi:10.1038\/ncb2322","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"79","title":"Studies on electron transfer between mercury electrode and hemoprotein.","abstract":"The electrochemical behaviour of ferricytochrome c, metmyoglobin and methemoglobin was studied using d.c., a.c. and differential pulse polarography, and controlled potential electrolysis. 1. The three hemoproteins yield d.c. polarographic steps, and peaks in differential pulse polarograms, the height of which is proportional to concentration. The charge transfer is influenced by strong adsorption. 2. The concentration dependence of the a.c. polarograms indicates structural changes in the adsorbed molecules. 3. The reduction products of controlled potential electrolysis of metmyoglobin and methemoglobin have absorption spectra identical with the native control samples. The affinity for oxygen and the cooperativity in hemoglobin are not affected by the reaction at the electrode. 4. The charge transfer proceeds via adsorbed, already reduced, molecules to freely diffusible proteins.","authors":"Scheller, F., J\u00e4nchen, M., Lampe, J., Pr\u00fcmke, HJ., Blanck, J., Palecek, E.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"1","page":"157-67","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19465924","title":"A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis.","abstract":"The microRNA pathway has been implicated in the regulation of synaptic protein synthesis and ultimately in dendritic spine morphogenesis, a phenomenon associated with long-lasting forms of memory. However, the particular microRNAs (miRNAs) involved are largely unknown. Here we identify specific miRNAs that function at synapses to control dendritic spine structure by performing a functional screen. One of the identified miRNAs, miR-138, is highly enriched in the brain, localized within dendrites and negatively regulates the size of dendritic spines in rat hippocampal neurons. miR-138 controls the expression of acyl protein thioesterase 1 (APT1), an enzyme regulating the palmitoylation status of proteins that are known to function at the synapse, including the alpha(13) subunits of G proteins (Galpha(13)). RNA-interference-mediated knockdown of APT1 and the expression of membrane-localized Galpha(13) both suppress spine enlargement caused by inhibition of miR-138, suggesting that APT1-regulated depalmitoylation of Galpha(13) might be an important downstream event of miR-138 function. Our results uncover a previously unknown miRNA-dependent mechanism in neurons and demonstrate a previously unrecognized complexity of miRNA-dependent control of dendritic spine morphogenesis.","authors":"Siegel, G., Obernosterer, G., Fiore, R., Oehmen, M., Bicker, S., Christensen, M., Khudayberdiev, S., Leuschner, PF., Busch, CJ., Kane, C., H\u00fcbel, K., Dekker, F., Hedberg, C., Rengarajan, B., Drepper, C., Waldmann, H., Kauppinen, S., Greenberg, ME., Draguhn, A., Rehmsmeier, M., Martinez, J., Schratt, GM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Cell Biol","volume":"11","issue":"6","page":"705-16","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8649372","title":"The Saccharomyces cerevisiae Start-specific transcription factor Swi4 interacts through the ankyrin repeats with the mitotic Clb2\/Cdc28 kinase and through its conserved carboxy terminus with Swi6.","abstract":"At a point in late G1 termed Start, yeast cells enter S phase, duplicate their spindle pole bodies, and form buds. These events require activation of Cdc28 kinase by G1 cyclins. Swi4 associates with Swi6 to form the SCB-binding factor complex which activates G1 cyclin genes CLN1 and CLN2 in late G1. In G2 and M phases, the transcriptional activity of SCB-binding factor is repressed by the mitotic Clb2\/Cdc28 kinase. Mbp1, a transcription factor related to Swi4, forms the MCB-binding factor complex with Swi6, which activates DNA synthesis genes and S-phase cyclin genes CLB5 and CLB6 in late G1. Clb2\/Cdc28 kinase is not required for the repression of MCB-binding factor transcriptional activity in G2 and M phase. We show here that the Swi4 carboxy terminus is sufficient for interaction with Swi6 in vitro. A carboxy-terminal domain of Swi6 is required and sufficient for interaction with Swi4. The carboxy terminus of Mbp1 is sufficient for interaction with Swi6, and the carboxy terminus of Swi6 is required for interaction with Mbp1. By coimmunoprecipitation, we show that Swi4 but not Mbp1 interacts with Clb2\/Cdc28 kinase in vivo during the G2 and M phases of the cell cycle. We demonstrate that the ankyrin repeats of Swi4 mediate the interaction with Clb2\/Cdc28 kinase. The ankyrin repeats constitute a domain by which a cell cycle-specific transcription factor can interact with cyclin-dependent kinase complexes, thus enabling it to link its transcriptional activity to cell cycle progression.","authors":"Siegmund, RF., Nasmyth, KA.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Mol Cell Biol","volume":"16","issue":"6","page":"2647-55","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1996-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19444102","title":"Giant cell tumour of bone.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19444102<\/PMID><DateCompleted><Year>2009<\/Year><Month>07<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2015<\/Year><Month>11<\/Month><Day>19<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1531-703X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>21<\/Volume><Issue>4<\/Issue><PubDate><Year>2009<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>Current opinion in oncology<\/Title><ISOAbbreviation>Curr Opin Oncol<\/ISOAbbreviation><\/Journal><ArticleTitle>Giant cell tumour of bone.<\/ArticleTitle><Pagination><MedlinePgn>338-44<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1097\/CCO.0b013e32832c951d<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE OF REVIEW\" NlmCategory=\"OBJECTIVE\">Giant cell tumour of bone (GCT) is the most common benign bone tumour and afflicts a young population. Treatment options for patients with unresectable disease have remained fairly static for the past three decades.","authors":"Thomas, DM., Skubitz, KM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Opin Oncol","volume":"21","issue":"4","page":"338-44","pdf":null,"JrId":"1063","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29078019","title":"Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis.","abstract":"During meiosis, the formation of crossovers (COs) generates genetic variation and provides physical links that are essential for accurate chromosome segregation. COs occur in the context of a proteinaceous chromosome axis. The transcriptomes and proteomes of anthers and meiocytes comprise several thousand genes and proteins, but because of the level of complexity relatively few have been functionally characterized. Our understanding of the physical and functional interactions between meiotic proteins is also limited. Here we use affinity proteomics to analyse the proteins that are associated with the meiotic chromosome axis protein, ASY1, in Brassica oleracea anthers and meiocytes. We show that during prophase\u00a0I ASY1 and its interacting partner, ASY3, are extensively phosphorylated, and we precisely assign phosphorylation sites. We identify 589 proteins that co-immunoprecipitate with ASY1. These correspond to 492 Arabidopsis orthologues, over 90% of which form a coherent protein-protein interaction (PPI) network containing known and candidate meiotic proteins, including proteins more usually associated with other cellular processes such as DNA replication and proteolysis. Mutant analysis confirms that affinity proteomics is a viable strategy for revealing previously unknown meiotic proteins, and we show how the PPI network can be used to prioritise candidates for analysis. Finally, we identify another axis-associated protein with a role in meiotic recombination. Data are available via ProteomeXchange with identifier PXD006042.","authors":"Osman, K., Yang, J., Roitinger, E., Lambing, C., Heckmann, S., Howell, E., Cuacos, M., Imre, R., D\u00fcrnberger, G., Mechtler, K., Armstrong, S., Franklin, FCH.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Plant J","volume":"93","issue":"1","page":"17-33","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2684648","title":"Ribozyme mediated destruction of RNA in vivo.","abstract":"Previous studies have demonstrated that high ribozyme to substrate ratios are required for ribozyme inhibitory function in nuclear extracts. To obtain high intracellular levels of ribozymes, tRNA genes, known to be highly expressed in most tissues, have been modified for use as ribozyme expression cassettes. Ribozyme coding sequences were placed between the A and the B box, internal promoter sequences of a Xenopus tRNAMet gene. When injected into the nucleus of frog oocytes, the ribozyme tRNA gene (ribtDNA) produces 'hammerhead' ribozymes which cleave the 5' sequences of U7snRNA, its target substrate, with high efficiency in vitro. Oocytes were coinjected with ribtDNA, U7snRNA and control substrate RNA devoid of a cleavage sequence. It was found that the ribtRNA remained localized mainly in the nucleus, whereas the substrate and the control RNA exited rapidly into the cytoplasm. However, sufficient ribtRNA migrated into the cytoplasm to cleave, and destroy, the U7snRNA. Thus, the action of targeted 'hammerhead' ribozymes in vivo is demonstrated.","authors":"Cotten, M., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"EMBO J","volume":"8","issue":"12","page":"3861-6","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1990-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8617244","title":"C-terminal activating and inhibitory domains determine the transactivation potential of BSAP (Pax-5), Pax-2 and Pax-8.","abstract":"Pax-5 encodes the transcription factor BSAP which plays an essential role in early B cell development and midbrain patterning. In this study we have analysed the structural requirements for transcriptional activation by BSAP. In vitro mutagenesis and transient transfection experiments indicate that the C-terminal serine\/threonine\/proline-rich region of BSAP contains a potent transactivation domain of 55 amino acids which is active from promoter and enhancer positions. This transactivation domain was found to be inactivated by a naturally occurring frameshift mutation in one PAX-5 allele of the acute lymphoblastic leukemia cell line REH. The function of the transactivation domain is negatively regulated by adjacent sequences from the extreme C-terminus. The activating and inhibitory domains function together as an independent regulatory module in different cell types as shown by fusion to the GAL4 DNA binding domain. The same arrangement of positively and negatively acting sequences has been conserved in the mammalian Pax-2 and Pax-8, the zebrafish Pax-b as well as the sea urchin Pax-258 proteins. These data demonstrate that the transcriptional competence of a subfamily of Pax proteins is determined by a C-terminal regulatory module composed of activating and inhibitory sequences.","authors":"D\u00f6rfler, P., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"EMBO J","volume":"15","issue":"8","page":"1971-82","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1996-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8011213","title":"T-cell development and function in gene-knockout mice.","abstract":"The use of mice with defined genetic defects engineered by homologous recombination in embryonic stem cells has greatly enhanced our understanding of immune functions at the single-gene level. The complex molecular interactions involved in T-cell development and antigen recognition have been especially targeted for detailed analysis via knockout technology.","authors":"Yeung, RS., Penninger, J., Mak, TW.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Curr Opin Immunol","volume":"6","issue":"2","page":"298-307","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1994-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"217186","title":"Studies of simian sarcoma and simian sarcoma-associated virus. I. Analysis of viral structural proteins, and preparation and characterization of antiserum specific for viral envelope components.","abstract":null,"authors":"Deinhardt, F., Bergholz, C., Hunsmann, G., Schneider, J., Thiel, HJ., Beug, H., Sch\u00e4fer, W.","publication_status":"ppublish","journalpubyear":"1978","journaltitle":"Z Naturforsch C Biosci","volume":"33","issue":"11-12","page":"969-80","pdf":null,"JrId":"8159","fulltextlink":null,"preprintlink":null,"articledate":"1979-04-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"180661","title":"Evidence for the multiple oncogenic potential of cloned leukemia virus: in vitro and in vitro studies with avian erythroblastosis virus.","abstract":null,"authors":"Graf, T., Royer-Pokora, B., Schubert, GE., Beug, H.","publication_status":"ppublish","journalpubyear":"1976","journaltitle":"Virology","volume":"71","issue":"2","page":"423-33","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1976-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1","title":"Formate assay in body fluids: application in methanol poisoning.","abstract":"","authors":"Makar, AB., McMartin, KE., Palese, M., Tephly, TR.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Med","volume":"13","issue":"2","page":"117-26","pdf":null,"JrId":"1012","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"83052","title":"Studies of simian sarcoma and simian sarcoma-associated virus. II. Isolation of the major viral glycoprotein, properties of this component and its specific antiserum.","abstract":null,"authors":"Thiel, HJ., Beug, H., Graf, T., Schwarz, H., Sch\u00e4fer, W., Bergholz, C., Deinhardt, F.","publication_status":"ppublish","journalpubyear":"1978","journaltitle":"Virology","volume":"90","issue":"2","page":"360-5","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1979-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26076","title":"Aspects of the regulation of histone genes.","abstract":"Sequencing of cloned histone DNA of the sea urchin Psammechinus miliaris has confirmed the map of the histone genes obtained earlier by rather less refined techniques. Sequencing of spacer has revealed that it is unlikely to code for protein. Some interesting sequences in the prelude regions to the structural genes have been found. The technique of injecting DNA into the germinal vesicle of the Xenopus oocyte has been greatly simplified, so that now many of the parameters governing the transcription of the injected genes can be investigated. Some mRNA-like molecules appear when circular histone DNA is inserted into the oocyte nucleus. We are cautiously optimistic that the technique can be further developed and will provide a useful tool for the study of the molecular mechanisms governing the expression of structural genes coding for proteins.","authors":"Birnstiel, ML., Kressmann, A., Schaffner, W., Portmann, R., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1978","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"283","issue":"997","page":"319-24","pdf":null,"JrId":"8277","fulltextlink":null,"preprintlink":null,"articledate":"1978-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19124606","title":"RNA-regulated interaction of transportin-1 and exportin-5 with the double-stranded RNA-binding domain regulates nucleocytoplasmic shuttling of ADAR1.","abstract":"Double-stranded RNA (dsRNA)-binding proteins interact with substrate RNAs via dsRNA-binding domains (dsRBDs). Several proteins harboring these domains exhibit nucleocytoplasmic shuttling and possibly remain associated with their substrate RNAs bound in the nucleus during nuclear export. In the human RNA-editing enzyme ADAR1-c, the nuclear localization signal overlaps the third dsRBD, while the corresponding import factor is unknown. The protein also lacks a clear nuclear export signal but shuttles between the nucleus and the cytoplasm. Here we identify transportin-1 as the import receptor for ADAR1. Interestingly, dsRNA binding interferes with transportin-1 binding. At the same time, each of the dsRBDs in ADAR1 interacts with the export factor exportin-5. RNA binding stimulates this interaction but is not a prerequisite. Thus, our data demonstrate a role for some dsRBDs as RNA-sensitive nucleocytoplasmic transport signals. dsRBD3 in ADAR1 can mediate nuclear import, while interaction of all dsRBDs might control nuclear export. This finding may have implications for other proteins containing dsRBDs and suggests a selective nuclear export mechanism for substrates interacting with these proteins.","authors":"Fritz, J., Strehblow, A., Taschner, A., Schopoff, S., Pasierbek, P., Jantsch, MF.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Cell Biol","volume":"29","issue":"6","page":"1487-97","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-129","title":"Improving Phosphopeptide\/Protein Identification Using a New Data Mining Framework for MS\/MS Spectra Preprocessing","abstract":null,"authors":"Cerqueira, FR., Morandell, S., Ascher, S., Mechtler, K., Huber, LA., Pfeifer, B., Graber, A., Tilg, B., Baumgartner, C.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Proteomics Bioinform","volume":"2","issue":"","page":"150-164","pdf":null,"JrId":"34911","fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19309262","title":"Novel role of NADPH oxidase in angiogenesis and stem\/progenitor cell function.","abstract":"Neovascularization is involved in normal development and wound repair as well as ischemic heart disease and peripheral artery disease. Both angiogenesis and vasculogenesis [de novo new vessel formation through mobilization of stem\/progenitor cells from bone marrow (BM) and their homing to the ischemic sites] contribute to the formation of new blood vessels after tissue ischemia. Angiogenesis is dependent on cell proliferation, migration, and capillary tube formation in endothelial cells (ECs). Stem\/progenitor cells have been used for cell-based therapy to promote revascularization after peripheral or myocardial ischemia. Excess amounts of reactive oxygen species (ROS) are involved in senescence and apoptosis of ECs and stem\/progenitor cells, causing defective neovascularization. ROS at low levels function as signaling molecules to mediate cell proliferation, migration, differentiation, and gene expression. NADPH oxidase is one of the major sources of ROS in ECs and stem\/progenitor cells, and is activated by various growth factors, cytokines, hypoxia, and ischemia. ROS derived from NADPH oxidase play an important role in redox signaling linked to angiogenesis ECs, as well as stem\/progenitor cell mobilization, homing, and differentiation, thereby promoting neovascularization. Understanding these mechanisms may provide insight into NADPH oxidase and its mediators as potential therapeutic targets for ischemic heart and limb disease.","authors":"Ushio-Fukai, M., Urao, N.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Antioxid Redox Signal","volume":"11","issue":"10","page":"2517-33","pdf":null,"JrId":"22011","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20944002","title":"An intrinsic mechanism predisposes Foxp3-expressing regulatory T cells to Th2 conversion in vivo.","abstract":"Naturally occurring regulatory T (nTreg) cells express Foxp3 and were originally discovered as immune suppressors critical for self-tolerance and immune homeostasis. Through yet-to-be-defined mechanisms, nTreg cells were recently shown to convert into proinflammatory cells. Particularly, attenuation of Foxp3 expression led to Th2 conversion of nTreg cells in vivo. In this paper, we demonstrated an nTreg-specific mechanism controlling their Th2 conversion. We found that wild-type nTreg cells expressing reduced levels of Foxp3 but not those expressing no Foxp3 produced the Th2 cytokine IL-4. Intriguingly, IL-4 production by converted nTreg cells is required for Th2 differentiation of coexisting naive CD4 T cells in vivo, suggesting that Th2 conversion of nTreg cells might be critical for directing Th2 immune responses. Th2 conversion of nTreg cells was not due to their inability to become Th1 cells, because IFN-\u03b3 was produced by Foxp3-low-expressing cells when IL-4\/STAT-6 signaling was abrogated. Surprisingly, however, unlike naive CD4 T cells whose IL-4 production is dependent on STAT-6, Foxp3-low-expressing cells generated IL-4 independent of STAT-6, indicating an intrinsic mechanism that favors nTreg-to-Th2 differentiation. Indeed, compared with naive CD4 T cells, nTreg expressed elevated levels of GATA-3 independent of STAT-6. And GATA-3 was required for nTreg-to-Th2 conversion. Foxp3 may account for this GATA-3 upregulation in nTreg cells, because ectopic expression of Foxp3 preferentially promoted GATA-3 but not T-bet expression. Thus, we have identified an intrinsic mechanism that imposes a Th2\/Th1 imbalance and predisposes Foxp3-expressing cells to IL-4 production independent of STAT-6 signaling.","authors":"Wang, Y., Souabni, A., Flavell, RA., Wan, YY.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Immunol","volume":"185","issue":"10","page":"5983-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19718050","title":"Hepatic tumor-stroma crosstalk guides epithelial to mesenchymal transition at the tumor edge.","abstract":"The tumor-stroma crosstalk is a dynamic process fundamental in tumor development. In hepatocellular carcinoma (HCC), the progression of malignant hepatocytes frequently depends on transforming growth factor (TGF)-beta provided by stromal cells. TGF-beta induces an epithelial to mesenchymal transition (EMT) of oncogenic Ras-transformed hepatocytes and an upregulation of platelet-derived growth factor (PDGF) signaling. To analyse the influence of the hepatic tumor-stroma crosstalk onto tumor growth and progression, we co-injected malignant hepatocytes and myofibroblasts (MFBs). For this, we either used in vitro-activated p19(ARF) MFBs or in vivo-activated MFBs derived from physiologically inflamed livers of Mdr2\/p19(ARF) double-null mice. We show that co-transplantation of MFBs with Ras-transformed hepatocytes strongly enhances tumor growth. Genetic interference with the PDGF signaling decreases tumor cell growth and maintains plasma membrane-located E-cadherin and beta-catenin at the tumor-host border, indicating a blockade of hepatocellular EMT. We further generated a collagen gel-based three dimensional HCC model in vitro to monitor the MFB-induced invasion of micro-organoid HCC spheroids. This invasion was diminished after inhibition of TGF-beta or PDGF signaling. These data suggest that the TGF-beta\/PDGF axis is crucial during hepatic tumor-stroma crosstalk, regulating both tumor growth and cancer progression.","authors":"van Zijl, F., Mair, M., Csiszar, A., Schneller, D., Zulehner, G., Huber, H., Eferl, R., Beug, H., Dolznig, H., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Oncogene","volume":"28","issue":"45","page":"4022-33","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19667128","title":"Phosphoregulation of the budding yeast EB1 homologue Bim1p by Aurora\/Ipl1p.","abstract":"EB1 (end binding 1) proteins have emerged as central regulators of microtubule (MT) plus ends in all eukaryotes, but molecular mechanisms controlling the activity of these proteins are poorly understood. In this study, we show that the budding yeast EB1 protein Bim1p is regulated by Aurora B\/Ipl1p-mediated multisite phosphorylation. Bim1p forms a stable complex with Ipl1p and is phosphorylated on a cluster of six Ser residues in the flexible linker connecting the calponin homology (CH) and EB1 domains. Using reconstitution of plus end tracking in vitro and total internal reflection fluorescence microscopy, we show that dimerization of Bim1p and the presence of the linker domain are both required for efficient tip tracking and that linker phosphorylation removes Bim1p from static and dynamic MTs. Bim1 phosphorylation occurs during anaphase in vivo, and it is required for normal spindle elongation kinetics and an efficient disassembly of the spindle midzone. Our results define a mechanism for the use and regulation of CH domains in an EB1 protein.","authors":"Zimniak, T., Stengl, K., Mechtler, K., Westermann, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Biol","volume":"186","issue":"3","page":"379-91","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19537771","title":"Preventing carryover of peptides and proteins in nano LC-MS separations.","abstract":"Sample carryover is a significant problem that occurs in high-performance liquid chromatography (HPLC) analysis. Carryover effects cannot be tolerated in any high-performance liquid chromatography-mass spectroscopy (HPLC-MS) separation system, and proteomics analysis must be performed in a separation system with virtually no carryover. Several procedures have been tested for effective and fast removal of interfering peptides and proteins originating from previous analyses in the HPLC system. We have developed and optimized a cleaning method for eliminating carryover caused by the autosampler and the trap column. The new washing method uses an injection of trifluoroethanol into the injection path and onto the trap column to remove strongly bound peptides and proteins, and it includes trifluoroethanol as an additional solvent in the chromatographic mobile phase for enhanced cleaning of the separation column. By application of this method, a significant reduction in carryover was achieved without any loss in the amount of proteins and peptides identified by MS.","authors":"Mitulovi\u0107, G., Stingl, C., Steinmacher, I., Hudecz, O., Hutchins, JR., Peters, JM., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Anal Chem","volume":"81","issue":"14","page":"5955-60","pdf":null,"JrId":"519","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18996479","title":"Cell division, growth and death.","abstract":null,"authors":"Barral, Y., Knoblich, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Opin Cell Biol","volume":"20","issue":"6","page":"647-9","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19551900","title":"The TLR-independent DNA recognition pathway in murine macrophages: Ligand features and molecular signature.","abstract":"Recognition of foreign DNA by cytosolic innate immune receptors triggers the production of IFN-beta. However, it is unclear whether different types of DNA ligands are recognized by similar receptors and whether the resulting response is distinct from the endosomal TLR response. To address these questions, we compared the two most commonly used types of DNA ligands (IFN-stimulatory DNA (ISD) and poly(dAdT)) and assessed the minimal structural requirements for stimulatory capacity in RAW264.7 cells. Gene expression signatures and competition experiments suggest that ISD and poly(dAdT) are qualitatively indistinguishable and differ from the CpG-containing oligonucleotides triggering the TLR9 pathway. Structure - activity relationship analyses revealed that a minimal length of two helical turns is sufficient for ISD-mediated IFN-beta induction, while phosphorylation at the 5'-end is dispensable. Altogether, our data suggest that, in murine macrophages, only one major cytosolic DNA recognition pathway is operational.","authors":"Karayel, E., B\u00fcrckst\u00fcmmer, T., Bilban, M., D\u00fcrnberger, G., Weitzer, S., Martinez, J., Superti-Furga, G.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Eur J Immunol","volume":"39","issue":"7","page":"1929-36","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2040202","title":"Polymorphic HSRs in chromosome 1 of the two semispecies Mus musculus musculus and M. m. domesticus have a common origin in an ancestral population.","abstract":"HSRs (homogeneously staining regions) are the cytological correlates of DNA amplification. In the house mouse, Mus musculus, many populations are polymorphic for the presence or absence of HSRs on chromosome 1. In the semispecies M. m. domesticus the amplified DNA is present within one HSR, whereas in M. m. musculus chromosomes 1 with two HSRs are found. Hybridization of HSR-specific probes to Southern blots of HSR-carrying genomic DNAs from different localities and semispecies revealed similar complex band patterns. The remaining variation is restricted to sequences with a low degree of amplification. Variation is higher between semispecies than within one semispecies. It is assumed that HSRs are derived from one original amplification event and that unequal recombination is the mechanism underlying the length variation of HSRs present today in both semispecies. Evidence from G-banding and in situ hybridization shows that the two HSRs of M. m. musculus originated from a single HSR by means of a paracentric inversion, where one break-point was located within the single HSR and the second outside the HSR. As a consequence of the paracentric inversion the two HSRs of M. m. musculus are permanently linked together. Since exchange of genes between the two semispecies is restricted to a narrow hybrid zone the amplification that gave rise to the HSR most probably occurred prior to the divergence into the semispecies M. m. domesticus and M. m. musculus about 1 million years ago.","authors":"Winking, H., Weith, A., Boldyreff, B., Moriwaki, K., Fredga, K., Traut, W.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Chromosoma","volume":"100","issue":"3","page":"147-51","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"1991-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19695325","title":"Structure, function and regulation of the conserved serine proteases DegP and DegS of Escherichia coli.","abstract":"Two members of the widely conserved HtrA family of serine proteases, DegP and DegS, are key players in extracytoplasmic protein quality control. The underlying mechanisms of their main functions in stress sensing, regulation and protection during the unfolded protein response are discussed.","authors":"Meltzer, M., Hasenbein, S., Mamant, N., Merdanovic, M., Poepsel, S., Hauske, P., Kaiser, M., Huber, R., Krojer, T., Clausen, T., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Res Microbiol","volume":"160","issue":"9","page":"660-6","pdf":null,"JrId":"6914","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19668863","title":"Peptidic small molecule activators of the stress sensor DegS.","abstract":"Bacterial DegS is a regulatory protease that acts as a molecular stress sensor and initiates a periplasmic stress response pathway. Upon binding of misfolded proteins to its PDZ domain, the protease domain of DegS is allosterically activated, thereby initiating a signal cascade that results in the elevated expression of protein quality control factors. Although the structural basis of this activation mode has been elucidated previously, it is not yet fully understood if binding to the PDZ domain is sufficient for protease domain activation or if secondary interactions with the protease domain are required. Here, we demonstrate that tripeptidic small molecule activators which only bind to the PDZ domain are sufficient to trigger DegS activation. Furthermore, we show that the hydrophobicity of the peptidic small molecule activators is a critical determinant for efficient activation.","authors":"Hauske, P., Mamant, N., Hasenbein, S., Nickel, S., Ottmann, C., Clausen, T., Ehrmann, M., Kaiser, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Biosyst","volume":"5","issue":"9","page":"980-5","pdf":null,"JrId":"33015","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19660473","title":"Structural basis of substrate specificity of plant 12-oxophytodienoate reductases.","abstract":"12-Oxophytodienoate reductase 3 (OPR3) is a FMN-dependent oxidoreductase that catalyzes the reduction of the cyclopentenone (9S,13S)-12-oxophytodienoate [(9S,13S)-OPDA] to the corresponding cyclopentanone in the biosynthesis of the plant hormone jasmonic acid. In vitro, however, OPR3 reduces the jasmonic acid precursor (9S,13S)-OPDA as well as the enantiomeric (9R,13R)-OPDA, while its isozyme OPR1 is highly selective, accepting only (9R,13R)-OPDA as a substrate. To uncover the molecular determinants of this remarkable enantioselectivity, we determined the crystal structures of OPR1 and OPR3 in complex with the ligand p-hydroxybenzaldehyde. Structural comparison with the OPR1:(9R,13R)-OPDA complex and further biochemical and mutational analyses revealed that two active-site residues, Tyr78 and Tyr246 in OPR1 and Phe74 and His244 in OPR3, are critical for substrate filtering. The relatively smaller OPR3 residues allow formation of a wider substrate binding pocket that is less enantio-restrictive. Substitution of Phe74 and His244 by the corresponding OPR1 tyrosines resulted in an OPR3 mutant showing enhanced, OPR1-like substrate selectivity. Moreover, sequence analysis of the OPR family supports the filtering function of Tyr78 and Tyr246 and allows predictions with respect to substrate specificity and biological function of thus far uncharacterized OPR isozymes. The discovered structural features may also be relevant for other stereoselective proteins and guide the rational design of stereospecific enzymes for biotechnological applications.","authors":"Breithaupt, C., Kurzbauer, R., Schaller, F., Stintzi, A., Schaller, A., Huber, R., Macheroux, P., Clausen, T.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Mol Biol","volume":"392","issue":"5","page":"1266-77","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19647941","title":"Automated monitoring to reduce electron microscope downtime.","abstract":"High-end transmission electron microscopes are complex and sensitive instruments. Failure of one of the external supplies, malfunction of the microscope hardware or maloperation are typical reasons for subsystems to fail. Especially if undiscovered for a longer period of time, this can cause unnecessary downtime, compromising user access and increasing operating costs. Utilizing the software introduced in this article (\"MoniTEM\"), we have succeeded to reduce downtime of an FEI Tecnai Polara by coupling constant monitoring of critical subsystems with automatic, remote feedback to the system supervisor, ensuring immediate problem solving. The software described here is freely available from http:\/\/www.imba.oeaw.ac.at\/monitem\/ and can be readily adapted for use with other FEI transmission electron microscopes.","authors":"Brunner, MJ., Resch, GP.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Ultramicroscopy","volume":"109","issue":"11","page":"1389-92","pdf":null,"JrId":"7881","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8220470","title":"BPF-1, a pathogen-induced DNA-binding protein involved in the plant defense response.","abstract":"The mechanisms by which plants restrict the growth of pathogens include transient activation of numerous defense-related genes. Box P is a putative cis-acting element of a distinct group of such genes, including those encoding the enzyme phenylalanine ammonialyase (PAL). A DNA-binding activity to Box P was identified in nuclear extracts from cultured parsley cells and a cDNA encoding the protein BPF-1 (Box P-binding Factor) partially characterized. BPF-1 binds to this element with specificity similar to that of the binding activity in nuclear extracts. BPF-1 mRNA accumulates rapidly in elicitor-treated parsley cells and around fungal infection sites on parsley leaves. This accumulation is, at least partly, due to a rapid and transient increase in the transcription rate of BPF-1. Moreover, tight correlation between the relative amounts of BPF-1 and PAL mRNAs was observed in different organs of a parsley plant. These results are consistent with the hypothesis that BPF-1 is involved in disease resistance by modulating plant defense gene expression.","authors":"da Costa e Silva, O., Klein, L., Schmelzer, E., Trezzini, GF., Hahlbrock, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Plant J","volume":"4","issue":"1","page":"125-35","pdf":null,"JrId":"2425","fulltextlink":null,"preprintlink":null,"articledate":"1993-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8197198","title":"In vivo production of human factor VII in mice after intrasplenic implantation of primary fibroblasts transfected by receptor-mediated, adenovirus-augmented gene delivery.","abstract":"Hemophilia A is caused by defects in the factor VIII gene. This results in life-threatening hemorrhages and severe arthropathies. Today, hemophiliacs are treated with human blood-derived factor VIII. In the future, it may be possible to use gene therapy to avoid long-term complications of conventional therapy and to improve the quality of life. However, initial gene therapy models using retroviral vectors and nonviral gene transfer techniques to introduce factor VIII gene constructs have been hampered by low expression levels of factor VIII. We show here that high expression levels of the B-domain-deleted human factor VIII in primary mouse fibroblasts and myoblasts are obtained by using receptor-mediated, adenovirus-augmented gene delivery (transferrinfection). We demonstrate that, presumably owing to the high molecular weight of factor VIII or its metabolic instability, secretion into the blood and attainment of therapeutic in vivo levels of factor VIII is achieved only if transfected autologous primary fibroblasts or myoblasts are delivered to the liver or spleen, but not if myoblasts are implanted into muscle, a strategy known to be successful for factor IX delivery.","authors":"Zatloukal, K., Cotten, M., Berger, M., Schmidt, W., Wagner, E., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Proc Natl Acad Sci U S A","volume":"91","issue":"11","page":"5148-52","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"101","title":"Ehlers-Danlos type V (X-linked form): a lysyl oxidase deficiency.","abstract":"","authors":"Di Ferrante, N., Leachman, RD., Angelini, P., Donnelly, PV., Francis, G., Almazan, A., Segni, G., Franzblau, C., Jordan, RE.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Birth Defects Orig Artic Ser","volume":"11","issue":"6","page":"31-7","pdf":null,"JrId":"1208","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34","title":"Determinants of intracellular pH in the erythrocyte.","abstract":"","authors":"Warth, J., Desforges, JF.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Haematol","volume":"29","issue":"3","page":"369-72","pdf":null,"JrId":"1822","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19647510","title":"MicroRNAs cross the line: the battle for mRNA stability enters the coding sequence.","abstract":"A study in this issue of Molecular Cell (Elcheva et al., 2009) shows the inherent instability of the betaTrCP1 mRNA to be caused by microRNA-183 targeting the coding sequence; interestingly, this action is directly opposed by the RNA-binding protein CRD-BP.","authors":"Nielsen, AF., Gloggnitzer, J., Martinez, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Cell","volume":"35","issue":"2","page":"139-40","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19632172","title":"Ars2 and the Cap-Binding Complex Team up for Silencing.","abstract":"In this issue, Sabin et al. (2009) and Gruber et al. (2009) reveal the protein Ars2 as a versatile regulator of RNA silencing. They show that Ars2 stimulates microRNA processing, contributes to antiviral resistance in flies, and is important for cell proliferation in mammals.","authors":"Nielsen, AF., Gloggnitzer, J., Martinez, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"138","issue":"2","page":"224-6","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8152791","title":"Retroviral capture of c-erbB proto-oncogene sequences: rapid evolution of distinct viral genomes carrying mutant v-erbB genes with different transforming capacities.","abstract":"The evolution of oncogene-transducing retroviruses was followed by studying the genomes of five new, erbB carrying retroviruses. These viruses, isolated from cells of one chicken infected with Rous Associated virus 1 (RAV-1), had captured c-erbB sequences as a consequence of RAV-1 integration into the host genome. Their genome structures were distinct; however, their v-erbB genes had sustained identical 5' and 3' deletions and the v-erbB-env junctions were identical at the nucleotide level. The results therefore strongly suggest that all five viruses originate from the same capture event. Sequence analyses of the v-erbB genes from three of these viruses revealed that one of them had undergone no further mutation and lacked detectable capacity to transform cells, therefore probably representing an 'early' form of transducing virus. The two other v-erbB genes contained distinct mutations and differed in their potential to induce fibroblast- and erythroblast transformation; they therefore probably represent later derivatives of the virus that captured the erbB oncogene. The data suggest that the initial retrovirus rapidly underwent many alterations after capture of c-erbB sequences, already in the RAV-1 infected bird as well as during subsequent in vitro isolation procedures. The changes involve both major rearrangements of the genome as well as point mutations that activated the erbB oncogene.","authors":"Vennstr\u00f6m, B., Raynoscheck, C., Jansson, L., Doederlein, G., Lhotak, V., Johnsson, A., Beug, H.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Oncogene","volume":"9","issue":"5","page":"1307-20","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1994-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19734303","title":"PI3Kgamma regulates cartilage damage in chronic inflammatory arthritis.","abstract":"The gamma isoform of phosphoinositide 3-kinase (PI3Kgamma) has been viewed as restricted to leukocytes mediating the regulation of chemokine-induced migration and recruitment of neutrophils, monocytes, and macrophages. In line with the observation that PI3Kgamma-deficient mice display defects in adaptive immunity, inhibition of PI3Kgamma reduces synovial inflammation in the collagen-induced arthritis mouse model of inflammatory arthritis [rheumatoid arthritis (RA)], which has been attributed to reduced influx of inflammatory cells. Challenging the concept of leukocyte-restricted PI3Kgamma function, we report here a novel, nonredundant function of PI3Kgamma as an important regulator of fibroblast-induced cartilage destruction during chronic destructive arthritis. We show that in human tumor necrosis factor transgenic mice, the loss of PI3Kgamma leads to a milder inflammatory arthritis. Interestingly, PI3Kgamma deficiency does not alter the recruitment of inflammatory cells, but significantly reduces cartilage damage through reduced expression of matrix metalloproteinases in fibroblasts and chondrocytes. In vitro analyses demonstrate that the decreased invasiveness of fibroblasts is mediated by reduced phosphorylation of Akt and extracellular signal-regulated kinase. Using a PI3Kgamma specific inhibitor, these data are confirmed in human synovial fibroblasts from patients with RA who exhibit a disease-specific up-regulation of PI3Kgamma. Our data indicate that in addition to mediating the recruitment of inflammatory cells, PI3Kgamma is an important regulator of fibroblast-mediated joint destruction in RA and suggest that specific inhibitors of PI3Kgamma will interfere with the activation of RA synovial fibroblasts and reduce cartilage destruction in RA.","authors":"Hayer, S., Pundt, N., Peters, MA., Wunrau, C., K\u00fchnel, I., Neugebauer, K., Strietholt, S., Zwerina, J., Korb, A., Penninger, J., Joosten, LA., Gay, S., R\u00fcckle, T., Schett, G., Pap, T.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"FASEB J","volume":"23","issue":"12","page":"4288-98","pdf":null,"JrId":"3815","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16476668","title":"Transient and selective overexpression of dopamine D2 receptors in the striatum causes persistent abnormalities in prefrontal cortex functioning.","abstract":"Increased activity of D2 receptors (D2Rs) in the striatum has been linked to the pathophysiology of schizophrenia. To determine directly the behavioral and physiological consequences of increased D2R function in the striatum, we generated mice with reversibly increased levels of D2Rs restricted to the striatum. D2 transgenic mice exhibit selective cognitive impairments in working memory tasks and behavioral flexibility without more general cognitive deficits. The deficit in the working memory task persists even after the transgene has been switched off, indicating that it results not from continued overexpression of D2Rs but from excess expression during development. To determine the effects that may mediate the observed cognitive deficits, we analyzed the prefrontal cortex, the brain structure mainly associated with working memory. We found that D2R overexpression in the striatum impacts dopamine levels, rates of dopamine turnover, and activation of D1 receptors in the prefrontal cortex, measures that are critical for working memory.","authors":"Kellendonk, C., Simpson, EH., Polan, HJ., Malleret, G., Vronskaya, S., Winiger, V., Moore, H., Kandel, ER.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Neuron","volume":"49","issue":"4","page":"603-15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19760071","title":"RANK(L) as a key target for controlling bone loss.","abstract":"Bone-related diseases, such as osteoporosis or rheumatoid arthritis, affect hundreds of millions of people worldwide and pose a tremendous burden to health care. By deepening our understanding of the molecular mechanisms of bone metabolism and bone turnover, it became possible over the past years to devise new and promising strategies for treating such diseases. In particular, three molecules, the receptor activator of NF-kappaB(RANK), its ligand RANKL and the decoy receptor of RANKL, osteoprotegerin (OPG), attracted the attention of scientists and pharmaceutical companies alike. Genetic experiments evolving around these molecules established their pivotal role as central regulators of osteoclast function. RANK-RANKL signaling not only activates a variety of downstream signaling pathways required for osteoclast development, but crosstalk with other signaling pathways also fine-tunes bone homeostasis both in normal physiology and disease. Consequently, novel drugs specifically targeting RANK-RANKL and their signaling pathways in osteoclasts are expected to revolutionize the treatment of various ailments associated with bone loss, such as arthritis, cancer metastases, or osteoporosis.","authors":"Leibbrandt, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Adv Exp Med Biol","volume":"647","issue":null,"page":"130-45","pdf":null,"JrId":"280","fulltextlink":null,"preprintlink":null,"articledate":"2010-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19714573","title":"E3 ubiquitin ligases in T-cell tolerance.","abstract":"The immune system uses several mechanisms of central and peripheral tolerance in order to prevent the activation of T lymphocytes toward self-antigens. Although the importance of immune self-tolerance has been established for a long time, some essential cellular and molecular mechanisms of T-cell tolerance have only been recently revealed. Once thought to be a recycling system, protein ubiquitylation by E3 ligases has now emerged as a regulated and crucial modulator of immune responses, and more importantly as a key signaling pathway involved in T-cell tolerance. In this review, we highlight our current understanding of the transcriptional and molecular signaling mechanisms involved in ubiquitylation-mediated T-cell tolerance.","authors":"Paolino, M., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Eur J Immunol","volume":"39","issue":"9","page":"2337-44","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1979159","title":"The v-erb A oncogene causes repression of erythrocyte-specific genes and an immature, aberrant differentiation phenotype in normal erythroid progenitors.","abstract":"We have compared the effects of the v-erb A oncogene on proliferation and differentiation of normal erythroid progenitors with those of tyrosine kinase oncogenes, e.g. v-sea. For this, a v-erb A retrovirus containing the neomycin resistance gene as a selectable marker or, alternatively, a v-erb A-ts v-sea retrovirus were used to infect normal bone marrow cells. V-erb A induced the outgrowth of immature, erythropoietin(EPO)-dependent erythroid cells from infected bone marrow which ceased to proliferate and disintegrated after 9 to 18 divisions. In contrast, ts-v-sea erythroblasts grew for the expected 25 to 40 population doublings in the absence of EPO. Transcription of the erythrocyte genes carbonic anhydrase II and erythrocyte anion transporter was significantly inhibited in v-erb A infected erythroblasts, indicating that v-erb A alone was sufficient for the repression of the erythrocyte-specific genes observed in AEV-transformed leukemic cells. A detailed analysis of the differentiation phenotype induced by v-erb A in erythroblasts (in the presence or absence of a temperature-inactivated ts sea oncogene) indicates that v-erb A-erythroblasts express a partially mature, aberrant phenotype characterized by the coexpression of mature and immature differentiation antigens. This phenotype clearly differs from that induced by tyrosine kinase oncogenes in erythroid cells.","authors":"Schroeder, C., Raynoschek, C., Fuhrmann, U., Damm, K., Vennstr\u00f6m, B., Beug, H.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Oncogene","volume":"5","issue":"10","page":"1445-53","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1991-01-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2005907","title":"Transcripts from amplified sequences of an inherited homogeneously staining region in chromosome 1 of the house mouse (Mus musculus).","abstract":"Several populations of the house mouse, Mus musculus, are polymorphic for the presence or absence of an inherited homogeneously staining region (HSR) in chromosome 1. The HSR consists of highly amplified DNA sequences, present in low copy numbers in the HSR- genome. A cloned HSR-derived genomic sequence detected transcripts of about 1.3 and 4.5 kb on blots of poly(A)+ RNA from liver of HSR+ mice but not from that of HSR- mice. A cDNA library was established from RNA of HSR+ mice and screened with the HSR-derived genomic clone. Positive clones were isolated and shown to be complementary to the 1.3-kb RNA species and to amplified DNA sequences in the HSR+ genome. The combined sequence of four overlapping cloned cDNAs is 959 nucleotides long and includes an open reading frame encoding a putative protein of 208 amino acids. The pertinent gene is unidentified. No homologous sequence is stored in the EMBL data base. A stretch of 109 nucleotides at the 3' end of the 1.3-kb RNA homology region in the same genomic fragment, as indicated by hybridization data and sequence motifs resembling promoter elements. Thus, our data suggest that at least two genes or gene families are encoded in the HSR.","authors":"Eckert, WA., Plass, C., Weith, A., Traut, W., Winking, H.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Mol Cell Biol","volume":"11","issue":"4","page":"2229-35","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1991-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"124","title":"Haemoglobin Rahere (beta Lys-Thr): A new high affinity haemoglobin associated with decreased 2, 3-diphosphoglycerate binding and relative polycythaemia.","abstract":"A new haemoglobin with increased oxygen affinity, beta82 (EF6) lysine leads to threonine (Hb Rahere), was found during the investigation of a patient who was found to have a raised haemoglobin concentration after a routine blood count. The substitution affects one of the 2, 3-diphosphoglycerate binding sites, resulting in an increased affinity for oxygen, but both the haem-haem interaction and the alkaline Bohr effect are normal in the haemolysate. This variant had the same mobility as haemoglobin A on electrophoresis at alkaline pH but was detected by measuring the whole blood oxygen affinity; it could be separated from haemoglobin A, however, by electrophoresis in agar at acid pH. The raised haemoglobin concentration was mainly due to a reduction in plasma volume (a relative polycythaemia) and was associated with a persistently raised white blood count. This case emphasises the need to measure the oxygen affinity of haemoglobin in all patients with absolute or relative polycythaemia when some obvious cause is not evident.","authors":"Lorkin, PA., Stephens, AD., Beard, ME., Wrigley, PF., Adams, L., Lehmann, H.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br Med J","volume":"4","issue":"5990","page":"200-2","pdf":null,"JrId":"1912","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18784187","title":"FLYSNPdb: a high-density SNP database of Drosophila melanogaster.","abstract":"FLYSNPdb provides high-resolution single nucleotide polymorphism (SNP) data of Drosophila melanogaster. The database currently contains 27,367 polymorphisms, including &gt;3700 indels (insertions\/deletions), covering all major chromsomes. These SNPs are clustered into 2238 markers, which are evenly distributed with an average density of one marker every 50.3 kb or 6.6 genes. SNPs were identified automatically, filtered for high quality and partly manually curated. The database provides detailed information on the SNP data including molecular and cytological locations (genome Releases 3-5), alleles of up to five commonly used laboratory stocks, flanking sequences, SNP marker amplification primers, quality scores and genotyping assays. Data specific for a certain region, particular stocks or a certain genome assembly version are easily retrievable through the interface of a publicly accessible website (http:\/\/flysnp.imp.ac.at\/flysnpdb.php).","authors":"Chen, D., Berger, J., Fellner, M., Suzuki, T.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nucleic Acids Res","volume":"37","issue":"Database issue","page":"D567-70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"59","title":"Regulation of nitrogen fixation. Nitrogenase-derepressed mutants of Klebsiella pneumoniae.","abstract":"1. A new procedure is described for selecting nitrogenase-derepressed mutants based on the method of Brenchley et al. (Brenchley, J.E., Prival, M.J. and Magasanik, B. (1973) J. Biol. Chem. 248, 6122-6128) for isolating histidase-constitutive mutants of a non-N2-fixing bacterium. 2. Nitrogenase levels of the new mutants in the presence of NH4+ were as high as 100% of the nitrogenase activity detected in the absence of NH4+. 3. Biochemical characterization of these nitrogen fixation (nif) derepressed mutants reveals that they fall into three classes. Three mutants (strains SK-24, 28 and 29), requiring glutamate for growth, synthesize nitrogenase and glutamine synthetase constitutively (in the presence of NH4+). A second class of mutants (strains SK-27 and 37) requiring glutamine for growth produces derepressed levels of nitrogenase activity and synthesized catalytically inactive glutamine synthetase protein, as determined immunologically. A third class of glutamine-requiring, nitrogenase-derepressed mutants (strain SK-25 and 26) synthesizes neither a catalytically active glutamine synthetase enzyme nor an immunologically cross-reactive glutamine synthetase protein. 4. F-prime complementation analysis reveals that the mutant strains SK-25, 26, 27, 37 map in a segment of the Klebsiella chromosome corresponding to the region coding for glutamine synthetase. Since the mutant strains SK-27 and SK-37 produce inactive glutamine synthetase protein, it is concluded that these mutations map within the glutamine synthetase structural gene.","authors":"Shanmugam, KT., Chan, I., Morandi, C.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"408","issue":"2","page":"101-11","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"123","title":"The importance of an innervated and intact antrum and pylorus in preventing postoperative duodenogastric reflux and gastritis.","abstract":"This study has investigated the relationship between duodenogastric reflux, gastritis and certain symptoms 6-12 months after three operations for uncomplicated duodenal ulcer. The operations studied were proximal gastric vagotomy (PGV, 20 cases), truncal vagotomy and pyloroplasty (TV+P, 22 cases) and truncal vagotomy and antrectomy (TV+A, 21 cases). Duodenogastric reflux was assessed both by a radiological technique and by measuring the concentration of bilirubin in the gastric aspirate before and after operation. Incidence and severity of postoperative gastritis were determined by endoscopic biopsy. Symptoms were assessed by symptomatic score and Visick grading. There was a significant correlation between duodenal reflux and histological evidence of both severe superficial gastritis and glandular atrophy (P less than 0-01). There was also a close association between the degree of reflux and the presence of severe heartburn, epigastric pain and bile vomiting after operation. The amount of reflux did not differ before operation. There was significantly less reflux following PGV than after either TV+P (P less than 0-025) or TV+A (P less than 0-001). The results indicate that an operation which preserves an innervated and intact antrum and pylorus will protect against postoperative duodenogastric reflux, gastritis and symptoms.","authors":"Keighley, MR., Asquith, P., Edwards, JA., Alexander-Williams, J.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Surg","volume":"62","issue":"10","page":"845-9","pdf":null,"JrId":"1907","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19755491","title":"Wif-1 is expressed at cartilage-mesenchyme interfaces and impedes Wnt3a-mediated inhibition of chondrogenesis.","abstract":"Wnt factors are involved in the regulation of all steps of cartilage development. The activity of Wnt factors is generally regulated at the extracellular level by factors like the Dkk family, sFRPs, Cerberus and Wnt inhibitory factor 1 (Wif-1). Here we report that Wif-1 is highly expressed at cartilage-mesenchyme interfaces of the early developing skeleton. In fetal and postnatal skeletal development, Wif-1 is expressed in a sharply restricted zone in the upper hyaline layer of epiphyseal and articular cartilage and in trabecular bone. Coimmunoprecipitation and pull-down assays using recombinant Wif-1 and Wnt factors show specific binding of Wif-1 to Wnt3a, Wnt4, Wnt5a, Wnt7a, Wnt9a and Wnt11. Moreover, Wif-1 was able to block Wnt3a-mediated activation of the canonical Wnt signalling pathway. Consequently, Wif-1 impaired growth of mesenchymal precursor cells and neutralised Wnt3a-mediated inhibition of chondrogenesis in micromass cultures of embryonic chick limb-bud cells. These results identify Wif-1 as a novel extracellular Wnt modulator in cartilage biology.","authors":"Surmann-Schmitt, C., Widmann, N., Dietz, U., Saeger, B., Eitzinger, N., Nakamura, Y., Rattel, M., Latham, R., Hartmann, C., von der Mark, H., Schett, G., von der Mark, K., Stock, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Sci","volume":"122","issue":"Pt 20","page":"3627-37","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1968657","title":"A nuclear protein that binds preferentially to methylated DNA in vitro may play a role in the inaccessibility of methylated CpGs in mammalian nuclei.","abstract":"The effects of DNA methylation on gene expression and chromatin structure suggest the existence of a mechanism in the nucleus capable of distinguishing methylated and non-methylated sequences. We report the finding of a nuclear protein in several vertebrate tissues and cell lines that binds preferentially to methylated DNA in vitro. Its lack of sequence-specific requirements makes it potentially capable of binding to any methylated sequence in mammalian nuclei. An in vivo counterpart of these results is that methylated CpGs are inaccessible to nucleases within nuclei. In contrast, non-methylated CpG sites, located mainly at CpG islands, and restriction sites not containing this dinucleotide, are relatively accessible. The possibility that DNA methylation acts through binding to specific proteins that could alter chromatin structure is discussed.","authors":"Meehan, R., Antequera, F., Lewis, J., MacLeod, D., McKay, S., Kleiner, E., Bird, AP.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"326","issue":"1235","page":"199-205","pdf":null,"JrId":"8277","fulltextlink":null,"preprintlink":null,"articledate":"1990-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8144891","title":"The transcription factor BSAP (NF-HB) is essential for immunoglobulin germ-line epsilon transcription.","abstract":"Treatment of murine splenic B lymphocytes and certain B-lineage cell lines with mitogen (LPS) and the lymphokine IL-4 has been shown to induce expression of germ-line epsilon transcripts (l epsilon transcripts) and class switching to the C epsilon gene. Three protein complexes, one of which (complex 3) is constitutively expressed, have been shown to bind to a 179-base pair LPS\/IL-4-responsive l epsilon promoter (Rothman, P., S. C. Li, B. Gorham, L. Glimcher, F. W. Alt, and M. Boothby. 1991. Mol. Cell. Biol. 11:5551). Complex 3 is indispensable for this inducible promoter activity. In this report, we have used electrophoretic mobility shift assays (EMSA) to demonstrate that the early B cell-specific transcription factor (BSAP) is involved in the formation of complex 3. In addition, BSAP is implicated functionally in l epsilon transcription because a BSAP binding site either from a sea urchin histone promoter (H2A-2.2) or from 5' of murine immunoglobulin S gamma 2a can substitute for the epsilon-associated site (epsilon(foot), as assayed by transient transfection assays of the l epsilon:CAT reporter constructs into the M12.4.1 B cell line. Like the sea urchin histone BSAP site, the complex 3 binding site (epsilon(foot)) functions as an upstream promoter element when assayed in the OVEC vector. These results indicate that BSAP is an essential protein required for LPS\/IL-4 induction of the l epsilon promoter. In addition, experiments showing that a BSAP binding site from 5' of S gamma 2a also functions as an upstream promoter element in OVEC suggest a potential role for BSAP in regulation of the IgG2a isotype.","authors":"Liao, F., Birshtein, BK., Busslinger, M., Rothman, P.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"J Immunol","volume":"152","issue":"6","page":"2904-11","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"1994-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15207239","title":"Chromatin acetylation, memory, and LTP are impaired in CBP+\/- mice: a model for the cognitive deficit in Rubinstein-Taybi syndrome and its amelioration.","abstract":"We studied a mouse model of the haploinsufficiency form of Rubinstein-Taybi syndrome (RTS), an inheritable disorder caused by mutations in the gene encoding the CREB binding protein (CBP) and characterized by mental retardation and skeletal abnormalities. In these mice, chromatin acetylation, some forms of long-term memory, and the late phase of hippocampal long-term potentiation (L-LTP) were impaired. We ameliorated the L-LTP deficit in two ways: (1) by enhancing the expression of CREB-dependent genes, and (2) by inhibiting histone deacetyltransferase activity (HDAC), the molecular counterpart of the histone acetylation function of CBP. Inhibition of HDAC also reversed the memory defect observed in fear conditioning. These findings suggest that some of the cognitive and physiological deficits observed on RTS are not simply due to the reduction of CBP during development but may also result from the continued requirement throughout life for both the CREB co-activation and the histone acetylation function of CBP.","authors":"Alarc\u00f3n, JM., Malleret, G., Touzani, K., Vronskaya, S., Ishii, S., Kandel, ER., Barco, A.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Neuron","volume":"42","issue":"6","page":"947-59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12876470","title":"Altered processing of novel information in N-CAM-deficient mice.","abstract":"N-CAM-deficient mice display anatomical and electrophysiological abnormalities in the CNS and behavioral deficits. Here, we address the question whether information processing is altered in these mice by analysis of the expression of c-fos and arg 3.1\/arc in N-CAM-deficient mice after presentation of saccharin as novel or familiar and water as neutral gustatory stimulus. When compared to their wild-type control littermates, increased expression of c-fos mRNA in the amygdala after the novel taste and of arg 3.1\/arc mRNA in the dentate gyrus 4.5 h after the neutral taste was detected in the absence of N-CAM. Furthermore, the novelty-induced increase in arg 3.1\/arc expression in the cingulate cortex 4.5 h after the novel taste was not observed in N-CAM-deficient mice. These data suggest that information processing mediated by immediate-early gene expression is altered in N-CAM-deficient mice.","authors":"Montag-Sallaz, M., Montag, D., Schachner, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Neuroreport","volume":"14","issue":"10","page":"1343-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1936990","title":"Changes in a SWI4,6-DNA-binding complex occur at the time of HO gene activation in yeast.","abstract":"The yeast HO gene is transcribed transiently during G1 as cells undergo START. START-specific HO activation requires two proteins, SWI4 and SWI6, which act via a motif (CACGA4) repeated up to 10 times within the URS2 region of the HO promoter. We identified a DNA-binding activity containing SWI4 and SWI6 that recognizes the CACGA4 sequences within URS2. Two forms of SWI4,6-DNA complexes called L and U can be distinguished by their electrophoretic mobility. L complexes can be detected at all stages of the cell cycle, but U complexes are only detected in cells that have undergone START. The formation of U complexes may be the trigger of HO activation. The SWI6 protein is concentrated in the nucleus throughout G1, but at some point in S or G2 significant amounts accumulate in the cytoplasm. This change in cellular location of the SWI6 protein might contribute to the turnoff of HO transcription after cells have undergone START.","authors":"Taba, MR., Muroff, I., Lydall, D., Tebb, G., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Genes Dev","volume":"5","issue":"11","page":"2000-13","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1991-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1936121","title":"Correlation of lymphocyte lipid composition membrane microviscosity and mitogen response in the aged.","abstract":"Healthy aged and young blood donors were investigated for the role of membrane lipid composition in the age-related increase in membrane microviscosity and decline of mitogen responsiveness. Membrane microviscosity was shown to correlate positively with membrane cholesterol\/phospholipid molar ratios, which were significantly elevated in the elderly. A positive correlation also was confirmed between lymphocyte membrane microviscosity, which was measured using the probe 1,6-diphenyl 1,3,5-hexatriene, and phytohemagglutinin responsiveness of cells from the same donor. Using stepwise regression statistical analysis, the variables age, cholesterol, cholesterol\/total phospholipid and phosphatidyl ethanolamine\/phosphatidyl choline molar ratios were all shown to have a significant positive influence on membrane microviscosity, whereas total phospholipids had a negative effect. No statistically significant difference was seen in content of any single saturated or unsaturated fatty acid between young and old donors. After pooling, however, the proportion of all unsaturated fatty acids was significantly higher in cells from the elderly as a consequence of an increase of n-6 and n-3 polyunsaturated fatty acids. Changes in lipid composition and physical properties of lymphocyte plasma membranes may, therefore, be responsible (at least partially) for the diminution of immune reactivity in old age.","authors":"Huber, LA., Xu, QB., J\u00fcrgens, G., B\u00f6ck, G., B\u00fchler, E., Gey, KF., Sch\u00f6nitzer, D., Traill, KN., Wick, G.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Eur J Immunol","volume":"21","issue":"11","page":"2761-5","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"1991-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1914514","title":"Thymic nurse cells: a site for positive selection and differentiation of T cells.","abstract":null,"authors":"Wick, G., Rieker, T., Penninger, J.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Curr Top Microbiol Immunol","volume":"173","issue":null,"page":"99-105","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1991-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11266467","title":"A novel 14-kilodalton protein interacts with the mitogen-activated protein kinase scaffold mp1 on a late endosomal\/lysosomal compartment.","abstract":"We have identified a novel, highly conserved protein of 14 kD copurifying with late endosomes\/lysosomes on density gradients. The protein, now termed p14, is peripherally associated with the cytoplasmic face of late endosomes\/lysosomes in a variety of different cell types. In a two-hybrid screen with p14 as a bait, we identified the mitogen-activated protein kinase (MAPK) scaffolding protein MAPK\/extracellular signal-regulated kinase (ERK) kinase (MEK) partner 1 (MP1) as an interacting protein. We confirmed the specificity of this interaction in vitro by glutathione S-transferase pull-down assays and by coimmunoprecipitation, cosedimentation on glycerol gradients, and colocalization. Moreover, expression of a plasma membrane-targeted p14 causes mislocalization of coexpressed MP1. In addition, we could reconstitute protein complexes containing the p14-MP1 complex associated with ERK and MEK in vitro.The interaction between p14 and MP1 suggests a MAPK scaffolding activity localized to the cytoplasmic surface of late endosomes\/lysosomes, thereby combining catalytic scaffolding and subcellular compartmentalization as means to modulate MAPK signaling within a cell.","authors":"Wunderlich, W., Fialka, I., Teis, D., Alpi, A., Pfeifer, A., Parton, RG., Lottspeich, F., Huber, LA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Cell Biol","volume":"152","issue":"4","page":"765-76","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19513101","title":"Turning meiosis into mitosis.","abstract":"Apomixis, or asexual clonal reproduction through seeds, is of immense interest due to its potential application in agriculture. One key element of apomixis is apomeiosis, a deregulation of meiosis that results in a mitotic-like division. We isolated and characterised a novel gene that is directly involved in controlling entry into the second meiotic division. By combining a mutation in this gene with two others that affect key meiotic processes, we created a genotype called MiMe in which meiosis is totally replaced by mitosis. The obtained plants produce functional diploid gametes that are genetically identical to their mother. The creation of the MiMe genotype and apomeiosis phenotype is an important step towards understanding and engineering apomixis.","authors":"d'Erfurth, I., Jolivet, S., Froger, N., Catrice, O., Novatchkova, M., Mercier, R.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS Biol","volume":"7","issue":"6","page":"e1000124","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6246522","title":"Introduction of a viral thymidine kinase gene and the human beta-globin gene into developmentally multipotential mouse teratocarcinoma cells.","abstract":"Teratocarcinoma (TCC) stem cells provide unique prospects for the introduction of specific genes into mice, by virtue of their dual capacity for propagation in vitro and for normal differentiation in embryos. In this study, we have demonstrated that foreign genes amenable to selection in culture can be transferred into the stem cells and expressed. These cells maintain expression of the gene for long periods during differentiation in tumors in vivo in the absence of selective pressure. The cells also integrate an unlinked nonselectable gene at high frequency. Addition of the cloned herpes simplex virus (HSV) thymidine kinase (tk; ATP:thymidine 5'-phosphotransferase, EC 2.7.1.21) gene to cultures of tk(-)TCC cells yielded tk(+) colonies at a frequency of one colony per 4 mug of plasmid DNA. This transformation efficiency, although appreciably lower than for mouse L tk(-) cells, permits the isolation of many transformants. The HSV provenance of the transformed phenotype was verified by the characteristic electrophoretic mobility of the tk protein and by neutralization of the tk activity with specific antiserum. Moreover, blot hybridization tests revealed at least one intact copy of the viral tk gene integrated into the DNA of transformed cells. When injected into syngeneic mice, the cells formed solid tumors with various differentiating tissues. From blot hybridization comparisons with their cell lines of origin, seven of nine tumors examined had maintained the HSV tk gene without significant loss or rearrangement. Viral tk enzyme activity could also be demonstrated in at least some of the tumors. Cotransfer of the cloned human beta-globin gene along with the unlinked HSV tk gene was successful in 2 of 10 tk(+) transformants. Thus, defined genes can be stably introduced into TCC cells in culture and maintained in vivo in a form in which they are transcribed and translated to produce a functional protein.","authors":"Pellicer, A., Wagner, EF., el-Kareh, A., Dewey, MJ., Reuser, AJ., Silverstein, S., Axel, R., Mintz, B.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"Proc Natl Acad Sci U S A","volume":"77","issue":"4","page":"2098-102","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1980-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19648946","title":"Oct4 to count 2.","abstract":null,"authors":"Wutz, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell Res","volume":"19","issue":"8","page":"917-9","pdf":null,"JrId":"20515","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11955007","title":"N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences.","abstract":"N-terminal N-myristoylation is a lipid anchor modification of eukaryotic and viral proteins targeting them to membrane locations, thus changing the cellular function of modified proteins. Protein myristoylation is critical in many pathways; e.g. in signal transduction, apoptosis, or alternative extracellular protein export. The myristoyl-CoA:protein N-myristoyltransferase (NMT) recognizes the sequence motif of appropriate substrate proteins at the N terminus and attaches the lipid moiety to the absolutely required N-terminal glycine residue. Reliable recognition of capacity for N-terminal myristoylation from the substrate protein sequence alone is desirable for proteome-wide function annotation projects but the existing PROSITE motif is not practical, since it produces huge numbers of false positive and even some false negative predictions. As a first step towards a new prediction method, it is necessary to refine the sequence motif coding for N-terminal N-myristoylation. Relying on the in-depth study of the amino acid sequence variability of substrate proteins, on binding site analyses in X-ray structures or 3D homology models for NMTs from various taxa, and on consideration of biochemical data extracted from the scientific literature, we found indications that, at least within a complete substrate protein, the N-terminal 17 protein residues experience different types of variability restrictions. We identified three motif regions: region 1 (positions 1-6) fitting the binding pocket; region 2 (positions 7-10) interacting with the NMT's surface at the mouth of the catalytic cavity; and region 3 (positions 11-17) comprising a hydrophilic linker. Each region was characterized by physical requirements to single sequence positions or groups of positions regarding volume, polarity, backbone flexibility and other typical properties of amino acids (http:\/\/mendel.imp.univie.ac.at\/myristate\/). These specificity differences are confined partly to taxonomic ranges and are proposed for the design of NMT inhibitors in pathogenic fungal and protozoan systems including Aspergillus fumigatus, Leishmania major, Trypanosoma cruzi, Trypanosoma brucei, Giardia intestinalis, Entamoeba histolytica, Pneumocystis carinii, Strongyloides stercoralis and Schistosoma mansoni. An exhaustive search for NMT-homologues led to the discovery of two putative entomopoxviral NMTs.","authors":"Maurer-Stroh, S., Eisenhaber, B., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Mol Biol","volume":"317","issue":"4","page":"523-40","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19815084","title":"X inactivation and disease.","abstract":"X inactivation is the mechanism by which mammals adjust the X-linked gene dosage between the sexes. The dosage difference between XX females and XY males is functionally equalized by silencing one of the two X chromosomes in female cells. This dosage-compensation mechanism is based on the long functional Xist RNA. Here, we review our understanding of dosage compensation and Xist function in the context of disease.","authors":"Agrelo, R., Wutz, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Semin Cell Dev Biol","volume":"21","issue":"2","page":"194-200","pdf":null,"JrId":"20707","fulltextlink":null,"preprintlink":null,"articledate":"2010-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17516553","title":"Bone morphogenetic protein 4 induces epithelial-mesenchymal transition through MSX2 induction on pancreatic cancer cell line.","abstract":"In our study, we found that bone morphogenetic protein 4 (BMP4) has a novel effect as an inducer of epithelial-mesenchymal transition (EMT) on Panc-1 cells, a human pancreatic carcinoma cell line. BMP4-treated Panc-1 cells showed loose cell contacts and a scattered, fibroblast-like appearance along with E-cadherin downregulation, Vimentin upregulation and enhanced cell migration, which are characteristic of EMT. BMP4 treatment also induced homeobox gene MSX2 expression, which we previously showed to be associated with EMT in pancreatic carcinoma cells. BMP4 treatment activated the Smad signaling pathway, and extracellular signal-related kinase (ERK) and p38 mitogen-activated kinase (MAPK) pathways in these cells. MSX2 was markedly induced by BMP4 through the ERK and p38 MAPK pathways in collaboration with the Smad signaling pathway. The repression of E-cadherin, induction of Vimentin and enhanced cell migration disappeared when siRNA-based MSX2 downregulated pancreatic cancer cells were treated with BMP4. These findings indicate that BMP4 may be involved in pancreatic carcinoma development through the promotion of EMT and that MSX2 is indispensable to this process.","authors":"Hamada, S., Satoh, K., Hirota, M., Kimura, K., Kanno, A., Masamune, A., Shimosegawa, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Cell Physiol","volume":"213","issue":"3","page":"768-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19834226","title":"BrainGazer--visual queries for neurobiology research.","abstract":"Neurobiology investigates how anatomical and physiological relationships in the nervous system mediate behavior. Molecular genetic techniques, applied to species such as the common fruit fly Drosophila melanogaster, have proven to be an important tool in this research. Large databases of transgenic specimens are being built and need to be analyzed to establish models of neural information processing. In this paper we present an approach for the exploration and analysis of neural circuits based on such a database. We have designed and implemented BrainGazer, a system which integrates visualization techniques for volume data acquired through confocal microscopy as well as annotated anatomical structures with an intuitive approach for accessing the available information. We focus on the ability to visually query the data based on semantic as well as spatial relationships. Additionally, we present visualization techniques for the concurrent depiction of neurobiological volume data and geometric objects which aim to reduce visual clutter. The described system is the result of an ongoing interdisciplinary collaboration between neurobiologists and visualization researchers.","authors":"Bruckner, S., Solt\u00e9szov\u00e1, V., Gr\u00f6ller, ME., Hlad\u016fvka, J., B\u00fchler, K., Yu, JY., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"IEEE Trans Vis Comput Graph","volume":"15","issue":"6","page":"1497-504","pdf":null,"JrId":"31980","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19801973","title":"Induction of autophagy by spermidine promotes longevity.","abstract":"Ageing results from complex genetically and epigenetically programmed processes that are elicited in part by noxious or stressful events that cause programmed cell death. Here, we report that administration of spermidine, a natural polyamine whose intracellular concentration declines during human ageing, markedly extended the lifespan of yeast, flies and worms, and human immune cells. In addition, spermidine administration potently inhibited oxidative stress in ageing mice. In ageing yeast, spermidine treatment triggered epigenetic deacetylation of histone H3 through inhibition of histone acetyltransferases (HAT), suppressing oxidative stress and necrosis. Conversely, depletion of endogenous polyamines led to hyperacetylation, generation of reactive oxygen species, early necrotic death and decreased lifespan. The altered acetylation status of the chromatin led to significant upregulation of various autophagy-related transcripts, triggering autophagy in yeast, flies, worms and human cells. Finally, we found that enhanced autophagy is crucial for polyamine-induced suppression of necrosis and enhanced longevity.","authors":"Eisenberg, T., Knauer, H., Schauer, A., B\u00fcttner, S., Ruckenstuhl, C., Carmona-Gutierrez, D., Ring, J., Schroeder, S., Magnes, C., Antonacci, L., Fussi, H., Deszcz, L., Hartl, R., Schraml, E., Criollo, A., Megalou, E., Weiskopf, D., Laun, P., Heeren, G., Breitenbach, M., Grubeck-Loebenstein, B., Herker, E., Fahrenkrog, B., Fr\u00f6hlich, KU., Sinner, F., Tavernarakis, N., Minois, N., Kroemer, G., Madeo, F.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Cell Biol","volume":"11","issue":"11","page":"1305-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"87","title":"Some physicochemical properties of hemoglobin-manitoba (alpha2 102Ser replaced by Arg (G9) beta2).","abstract":"Hb-Manitoba was discovered in 1970 [1] in a Canadian family of British origin. Recently we observed the same variant in a second family, and found that the oxy-derivative of Hb-Manitoba is slightly unstable at 65 degrees C, dissociates less readily at alkaline pH than does Hb-A, and forms asymmetric hybrids with other hemoglobins which are readily detectable by electrophoresis.","authors":"Wrightstone, RN., Smith, LL., Wilson, JB., Vella, F., Huisman, TH.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"2","page":"283-7","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"83","title":"Mechanical precipitation of hemoglobin k\u00f6ln.","abstract":"Hb K\u00f6ln (beta 98 Val leads to Met) was found to precipitate rapidly during mechanical shaking. The rate of precipitation of Hb K\u00f6ln is 5-6 times faster than that of Hb S. The kinetics of precipitation of the patient's hemolysate, which is a mixture of Hb K\u00f6ln and Hb A, showed a biphasic curve indicating that Hb K\u00f6ln precipitates independently from Hb A. The instability of Hb K\u00f6ln may be attributed to the conformational change in the vicinity of heme. The mechanical shaking may be used as a new method for detection and quantitation of hemoglobin K\u00f6ln and other unstable hemoglobins.","authors":"Asakura, T., Adachi, K., Shapiro, M., Friedman, S., Schwartz, E.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"2","page":"197-201","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19913403","title":"Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information.","abstract":"We recently witnessed a tremendous increase in genomics studies on gene regulation and in entirely sequenced genomes from closely related species. This has triggered analyses that suggest a wide range of evolutionary dynamics of gene regulation, from rapid turnover of transcription-factor binding sites to conservation of enhancer function across large evolutionary distances. Many examples show that enhancers can evolve beyond recognizable sequence similarity while retaining function. However, bioinformatics approaches are increasingly able to detect conserved regulatory elements through characteristic evolutionary sequence signatures. Cis-regulatory changes are also a major source of morphological evolution, which might be facilitated by many biochemically functional elements that are selectively neutral and by the buffering function of redundant enhancers and 'shadow' enhancers.","authors":"Meireles-Filho, AC., Stark, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Opin Genet Dev","volume":"19","issue":"6","page":"565-70","pdf":null,"JrId":"2199","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18","title":"Inhibition of aldehyde reductase isoenzymes in human and rat brain.","abstract":"","authors":"Ris, MM., Deitrich, RA., Von Wartburg, JP.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"20","page":"1865-9","pdf":null,"JrId":"1015","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"13","title":"Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the presence of valinomycin.","abstract":"","authors":"J\u00e4rvisalo, J., Saris, NE.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"18","page":"1701-5","pdf":null,"JrId":"1015","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-118","title":"Identification of new targets using expression profiling.","abstract":null,"authors":"Burkard, TR., Trajanoski, Z., Novatchkova, M., Hackl, H., Eisenhaber, F. ","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"In Antiangiogenic cancer therapy (Davis, D.R., Herbst, R.S., & Abbruzzese, J.L., eds.); CRC Press Taylor & Francis Group, Boca Raton London New York.","volume":"","issue":"","page":"415-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19836226","title":"Transcriptional networks controlling skeletal development.","abstract":"The formation of the vertebrate skeletal elements relies on the differentiation of the required cell types, chondrocytes and osteoblasts, which are derived from a common mesenchymal precursor. Furthermore it requires coordination between maturation of chondrocytes and osteoblasts to enable proper growth and development of skeletal elements. Over the past years various transcription factors have been identified on the basis of in vivo and in vitro studies that play important roles for skeletal formation being either active in chondrocytes or osteoblasts or even in both cell types. In this article their mode of action in skeletal development and how their activity is controlled are reviewed.","authors":"Hartmann, C.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Opin Genet Dev","volume":"19","issue":"5","page":"437-43","pdf":null,"JrId":"2199","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17297450","title":"Dissecting the role of TGF-beta type I receptor\/ALK5 in pancreatic ductal adenocarcinoma: Smad activation is crucial for both the tumor suppressive and prometastatic function.","abstract":"In the present study, we have analysed the effects of transforming growth factor-beta (TGF-beta) signaling on the growth behavior of pancreatic carcinoma cells in vitro and on their tumorigenicity in vivo. Ectopic expression of dominant-negative mutants of the TGF-beta type II receptor or type I receptor\/activin receptor-like kinase 5 (ALK5) in TGF-beta-sensitive pancreatic ductal adenocarcinoma PANC-1 cells prevented the TGF-beta-induced activation of transfected Smad-responsive reporter genes and growth arrest. The growth-inhibitory effect was mimicked by stable expression of kinase-active ALK5 (ALK5-T204D), and was dependent on ALK5's ability to activate Smad signaling, as a ALK5-derived mutant with an intact kinase domain but deficient in its ability to activate Smads (RImL45) failed to suppress proliferation in the absence of added TGF-beta. Moreover, this mutant often displayed opposite effects to those of ALK5-TD and blocked various ligand-induced responses in vitro, indicating that it acts in a dominant-negative fashion to inhibit endogenous wild-type receptors. ALK5-TD-, but not RImL45-TD-transduced cells underwent epithelial-to-mesenchymal transition, exhibited a higher ratio of thrombospondin-1 to vascular endothelial growth factor-A expression and upregulated various metastasis-associated genes. Upon orthotopic transplantation of PANC-1 clones into immunodeficient mice, ALK5-TD, but not RImL45-TD, greatly reduced tumor size and induced the formation of liver metastases in otherwise non-metastatic PANC-1 cells. These results suggest a causal, dominant role for the endogenous Smad2\/3 signaling pathway in the tumor suppressor and prometastatic activities of TGF-beta in pancreatic tumor cells.","authors":"Schniewind, B., Groth, S., Sebens M\u00fcerk\u00f6ster, S., Sipos, B., Sch\u00e4fer, H., Kalthoff, H., F\u00e4ndrich, F., Ungefroren, H.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Oncogene","volume":"26","issue":"33","page":"4850-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7894157","title":"Fine genetic mapping defines the genetic order of Pax9, Tcf3a, and Acrodysplasia (Adp).","abstract":"We present here the fine genetic mapping of the proximal part of mouse Chromosome (Chr) 12 between D12Mit54 and D12Mit4. This chromosomal region contains three loci, Pax9, Tcf3a, and Acrodysplasia (Adp), which seem to play an important role in pattern formation during mouse embryogenesis. The Adp mutation, which was created by transgene integration, causes skull, paw, and tail deformities. Pax9, which is expressed in the face, paws, and tail, once qualified as a possible candidate for the Adp locus. We analyzed 997 interspecific backcross progeny for recombination between the markers D12Mit54 and D12Mit4; we recovered 117 recombinants, which were further typed for Pax9, Tcf3a, Adp, D12Mit88, D12Nds1, D12Mit36, and D12Mit34. This study represents the first instance in which all the above loci have been included in a single analysis, thereby allowing unambiguous determination of the genetic order and distance between D12Mit54 and D12Mit4. From our results, we conclude that the Adp locus is distinct from either Pax9 or Tcf3a.","authors":"Watanabe, T., Tarttelin, E., Neub\u00fcser, A., Kimura, M., Solter, D.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Mamm Genome","volume":"5","issue":"12","page":"768-70","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"1995-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8058727","title":"Mapping of Ras-related GTP-binding proteins by GTP overlay following two-dimensional gel electrophoresis.","abstract":"For identification of Rab, Rac, Rho, Ral, Rap, and Arf proteins on two-dimensional polyacrylamide gels, we have expressed full-length cDNAs of members of these protein families with the T7 RNA polymerase-recombinant vaccinia virus expression system. Membrane preparations from cells expressing the cDNAs were subjected to high-resolution two-dimensional polyacrylamide gel electrophoresis followed by [alpha-32P]GTP ligand blotting. We have mapped 28 small GTP-binding proteins relative to their isoelectric points and according to their molecular weights and by immunoblotting with specific antibodies. Rab and Rho proteins could be specifically identified by extraction of streptolysin O-permeabilized Madin-Darby canine kidney (MDCK) cells with Rab- and Rho-GDP dissociation inhibitor. We applied the reference mapping to analyze the GTP-binding patterns of synaptosome fractions from rat brain. The purified synaptosomes exhibited specific enrichment of Rab3a, Rab5a, Ral, and several other GTPases. This approach and the map we have produced should provide a useful aid for the analysis of the expression and localization of members of all families of small GTP-binding proteins in various cell types and subcellular fractions.","authors":"Huber, LA., Ullrich, O., Takai, Y., L\u00fctcke, A., Dupree, P., Olkkonen, V., Virta, H., de Hoop, MJ., Alexandrov, K., Peter, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Proc Natl Acad Sci U S A","volume":"91","issue":"17","page":"7874-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1994-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10603348","title":"Regulation of mouse lens fiber cell development and differentiation by the Maf gene.","abstract":"Maf is a basic domain\/leucine zipper domain protein originally identified as a proto-oncogene whose consensus target site in vitro, the T-MARE, is an extended version of an AP-1 site normally recognized by Fos and Jun. Maf and the closely related family members Neural retina leucine zipper (Nrl), L-Maf, and Krml1\/MafB have been implicated in a wide variety of developmental and physiologic roles; however, mutations in vivo have been described only for Krml1\/MafB, in which a loss-of-function causes abnormalities in hindbrain development due to failure to activate the Hoxa3 and Hoxb3 genes. We have used gene targeting to replace Maf coding sequences with those of lacZ, and have carried out a comprehensive analysis of embryonic expression and the homozygous mutant phenotype in the eye. Maf is expressed in the lens vesicle after invagination, and becomes highly upregulated in the equatorial zone, the site at which self-renewing anterior epithelial cells withdraw from the cell cycle and terminally differentiate into posterior fiber cells. Posterior lens cells in Maf(lacZ) mutant mice exhibit failure of elongation at embryonic day 11.5, do not express (&amp;agr;)A- and all of the (beta)-crystallin genes, and display inappropriately high levels of DNA synthesis. This phenotype partially overlaps with those reported for gene targeting of Prox1 and Sox1; however, expression of these genes is grossly normal, as is expression of Eya1, Eya2, Pax6, and Sox2. Recombinant Maf protein binds to T-MARE sites in the (alpha)A-, (beta)B2-, and (beta)A4-crystallin promoters but fails to bind to a point mutation in the (alpha)A-crystallin promoter that has been shown previously to be required for promoter function. Our results indicate that Maf directly activates many if not all of the (beta)-crystallin genes, and suggest a model for coordinating cell cycle withdrawal with terminal differentiation.","authors":"Ring, BZ., Cordes, SP., Overbeek, PA., Barsh, GS.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Development","volume":"127","issue":"2","page":"307-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19779746","title":"Universal species concept: pipe dream or a step toward unifying  biology?","abstract":"The Universal Tree of Life, which is based on phylogenetic analysis of the RNA sequence from the small ribosomal subunit, was a breakthrough in understanding the relatedness among all living organisms. The result has had a major impact on taxonomy by separating life into three domains: Eukarya, Bacteria, and Archaea. Indeed, microbiologists have used the 16S ribosomal RNA (rRNA) of the small ribosomal subunit to construct the hierarchical classification of Bacteria and Archaea from the level of domain to genus. However, the 16S rRNA of the Bacteria and Archaea and the corresponding 18S rRNA of the Eukarya are too highly conserved to be useful phylogenetically at the species level. For this reason, I propose that biologists adopt a phylogenomic species concept that utilizes both phylogenetic analyses of less highly conserved genes and proteins as well as genomic analyses for the circumscription of species. If biologists adopt a phylogenomic concept for species, the classification of all living organisms from domain to species could be completed. Furthermore, this universal species concept could help provide a more equitable circumscription among all species, as well as aid in the unification of biologists and biology.","authors":"Staley, JT.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Ind Microbiol Biotechnol","volume":"36","issue":"11","page":"1331-6","pdf":null,"JrId":"20546","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"129","title":"The involvement of lysophosphoglycerides in neurotransmitter release; the composition and turnover of phospholipids of synaptic vesicles of guinea-pig cerebral cortex and Torpedo electric organ and the effect of stimulation.","abstract":"(1) Crude synaptosomal fractions (P2) derived from guinea-pig cerebral cortex were incubated in the presence of 50 mM KCl in a Krebs-glucose medium. Torpedo marmorata electric organs were stimulated electrically in vivo at 5 pulses\/sec for 30 min by electrodes placed on the electric lobe. Synaptic vesicles were isolated from each source and the phospholipid compositions analysed and compared with vesicles  from unstimulated controls. (2) Lysophosphatidylcholine was the only lysophosphoglyceride demonstrable in the synaptic vesicles from either source and its low levels did not increase as a result of chemical or electircal stimulation. In each case there was a close similarity of the phospholipid distributions in the vesicles taken from control and stimulated samples. (3) Control experiments indicated extensive decreases in the acetylcholine content of the vesicles from the stimulated electric organ and smaller decreases in the acetylcholine content of the synaptic vesicles from stimulated crude synaptosomal fractions. These fractions were found to respire linearly in the presence of 10 mM glucose and the vesicle fractions were shown to have low levels of contaiminating membranes as judged by marker enzyme analyses. (4) Crude synaptosomal fractions from guinea-pig cerebral cortex were incubated in a Krebs-glucose medium with labelled fatty acids and [3H]glucose in the presence or absence of 50 mM KCl. Subsynaptosomal fractionation was carried out and specific radioactivities of phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine and phosphatidylinositol were determined in fractions D (synaptic vesicles), E (microsomes) and H (disrupted synaptosomes). The release of neurotransmitter did not significantly enhance the labelling of phospholipids in any of the fractions studied as compared with phospholipids from unstimulated fractions. This was found after two incubation times and using [14C]oleate, [14C]arachidonate, [3H]palmitate and [3H]glucose.","authors":"Baker, RR., Dowdall, MJ., Whittaker, VP.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Brain Res","volume":"100","issue":"3","page":"629-44","pdf":null,"JrId":"1920","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10523817","title":"Genetic alteration of the alpha2-adrenoceptor subtype c in mice affects the development of behavioral despair and stress-induced increases in plasma corticosterone levels.","abstract":"alpha2-Adrenoceptors (alpha2-AR) modulate many central nervous system functions, such as regulation of sympathetic tone, vigilance, attention, and reactivity to environmental stressors. Three alpha2-AR subtypes (alpha2A, alpha2B, and alpha2C) with distinct tissue-distribution patterns are known to exist, but the functional significance of each subtype is not clear. Since specific, alpha2-AR subtype-selective pharmacological probes are not available, mice with genetically altered alpha2C-AR expression were studied in order to investigate the possible involvement of the alpha2C-AR in physiological and behavioral responses to acute and repeated stress. A modified version of Porsolt's forced swimming test was used to assess the possible effects of altered alpha2C-AR expression on the development of behavioral despair. alpha2C-Overexpression increased and the lack of alpha2C-AR (alpha2C-KO) decreased the immobility of mice in the forced swimming test, ie alpha2C-AR expression appeared to promote the development of behavioral despair. In addition, alpha2C-KO was associated with attenuated elevation of plasma corticosterone after different stressors, and overexpression of alpha2C-ARs was linked with increased corticosterone levels after repeated stress. Moreover, the brain dopamine and serotonin balance, but not norepinephrine turnover, was dependent on alpha2C-AR expression, and the expression of c-fos and junB mRNA was increased in alpha2C-KO mice. Since alpha2C-KO produced stress-protective effects, and alpha2C-AR overexpression seemed to promote the development of changes related to depression, it is suggested that a yet-to-be developed subtype-selective alpha2C-AR antagonist might have therapeutic value in the treatment of stress-related neuropsychiatric disorders.","authors":"Sallinen, J., Haapalinna, A., MacDonald, E., Viitamaa, T., L\u00e4hdesm\u00e4ki, J., Rybnikova, E., Pelto-Huikko, M., Kobilka, BK., Scheinin, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Mol Psychiatry","volume":"4","issue":"5","page":"443-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19619530","title":"Deletion of the p107\/p130-binding domain of Mip130\/LIN-9 bypasses the requirement for CDK4 activity for the dissociation of Mip130\/LIN-9 from p107\/p130-E2F4 complex.","abstract":"Mip130\/LIN-9 is part of a large complex that includes homologs of the Drosophila dREAM (drosophila RB-like, E2F, and Myb) and C. elegans DRM complexes. This complex also includes proteins such as Mip40\/LIN-37, Mip120\/LIN-54, and LIN-52. In mammalian cells, Mip130\/LIN-9 specifically associates with the p107\/p130-E2F4 repressor complex in G0\/G1 and with B-Myb in S-phase. However, little is known about how the transition occurs and whether Mip130\/LIN-9 contributes to the repressor effect of p107\/p130. In this report, we demonstrate that Mip130\/LIN-9, Mip40\/LIN-37, Mip120\/LIN-54, and Sin3b form a core complex, the Mip Core Complex or LIN Complex (MCC\/LINC), which is detectable in all phases of the cell cycle. This complex specifically recruits transcriptional repressors such as p107, p130, E2F4 and HDAC1 in G0\/G1, and B-Myb in S-phase. Importantly, we provide strong evidence that the transition between repressors and activators of transcription is mediated by CDK4, through the phosphorylation of the pocket proteins, p107 and p130. The requirement for CDK4 activity is bypassed by the deletion of the first 84 amino acids (Mip130\/LIN-9(Delta84)), since this mutant is unable to interact with p107\/p130 in G0\/G1, while maintaining its association with B-Myb. Importantly, the Mip130\/LIN-9(Delta84) allele rescues the low expression of G1\/S genes observed in CDK4(-\/-) MEFs demonstrating that Mip130\/LIN-9 contributes to the repression of these E2F-regulated genes in G0\/G1.","authors":"Sandoval, R., Pilkinton, M., Colamonici, OR.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Exp Cell Res","volume":"315","issue":"17","page":"2914-20","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19369220","title":"Towards programming languages for genetic engineering of living cells.","abstract":"Synthetic biology aims at producing novel biological systems to carry out some desired and well-defined functions. An ultimate dream is to design these systems at a high level of abstraction using engineering-based tools and programming languages, press a button, and have the design translated to DNA sequences that can be synthesized and put to work in living cells. We introduce such a programming language, which allows logical interactions between potentially undetermined proteins and genes to be expressed in a modular manner. Programs can be translated by a compiler into sequences of standard biological parts, a process that relies on logic programming and prototype databases that contain known biological parts and protein interactions. Programs can also be translated to reactions, allowing simulations to be carried out. While current limitations on available data prevent full use of the language in practical applications, the language can be used to develop formal models of synthetic systems, which are otherwise often presented by informal notations. The language can also serve as a concrete proposal on which future language designs can be discussed, and can help to guide the emerging standard of biological parts which so far has focused on biological, rather than logical, properties of parts.","authors":"Pedersen, M., Phillips, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J R Soc Interface","volume":"6 Suppl 4","issue":"","page":"S437-50","pdf":null,"JrId":"32845","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19725879","title":"LIN54 is an essential core subunit of the DREAM\/LINC complex that binds to the cdc2 promoter in a sequence-specific manner.","abstract":"Recently, the conserved human LINC\/DREAM complex has been described as an important regulator of cell cycle genes. LINC consists of a core module that dynamically associates with E2F transcription factors, p130 and the B-MYB transcription factor in a cell cycle-dependent manner. In this study, we analyzed the evolutionary conserved LIN54 subunit of LINC. We found that LIN54 is required for cell cycle progression. Protein interaction studies demonstrated that a predicted helix-coil-helix motif is required for the interaction of LIN54 with p130 and B-MYB. In addition, we found that the cysteine-rich CXC domain of LIN54 is a novel DNA-binding domain that binds to the cdc2 promoter in a sequence-specific manner. We identified two binding sites for LIN54 in the cdc2 promoter, one of which overlaps with the cell cycle homology region at the transcriptional start site. Gel shift assays suggested that, in quiescent cells, the binding of LIN54 at the cell cycle homology region is stabilized by the binding of E2F4 to the adjacent cell cycle-dependent element. Our data demonstrate that LIN54 is an important and integral subunit of LINC.","authors":"Schmit, F., Cremer, S., Gaubatz, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"FEBS J","volume":"276","issue":"19","page":"5703-16","pdf":null,"JrId":"32231","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19942373","title":"[Epigenetics and pseudohypoparathyroidism].","abstract":"Parental imprinting and the type of the genetic alteration play a determinant role in the phenotype expression of GNAS locus associated to pseudohypoparathyroidism (PHP). This imprint is tissue-specific, mainly localized in the kidney and the thyroid. Only the maternal allele is expressed at this level. An alteration in the coding sequence of the gene leads to an haplo-insufficiency and a dysmorphic phenotype (Albright's syndrome). If the alteration is on the maternal allele, there is a hormonal resistance to the PTH at the kidney level and to the TSH at the thyroid level. The phenotype is known as a PHP1a. If the alteration is on the paternal allele, there are few clinical signs with no hormonal resistance and the phenotype is known as pseudo-pseudo-hypoparathyroidism (PPHP). Methylation anomalies of GNAS locus, in particular of exon 1A, are responsible for a lack of expression of G\u03b1s at kidney and thyroid levels only. If these anomalies concern the maternal allele (the only one expressed) with a paternal pattern, there is no haplo-insufficiency and no dysmorphic syndrome. The hormonal resistance is yet again limited to PTH and TSH. The phenotype is known as PHP1b. In the familial forms, these methylation anomalies are associated with a deletion of the syntaxine 16 gene in the maternal allele. This gene contains probably the imprinting center of the locus.","authors":"Richard, N., Ab\u00e9guil\u00e9, G., Coudray, N., Kottler, ML.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Pathol Biol (Paris)","volume":"58","issue":"5","page":"367-71","pdf":null,"JrId":"6376","fulltextlink":null,"preprintlink":null,"articledate":"2011-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19934649","title":"Epigenetic regulation of developmental timing in floral stem cells.","abstract":"In mammalian stem cells, expression of differentiation genes is repressed by Polycomb Repressive group protein Complexes PRC1 and PRC2, which are associated with the trimethylated histone H3 lys27 (H3K27me3) repressive mark. This repression is transmitted through DNA replication to maintain pluripotency, and at the same time, it is reversible under appropriate conditions that promote differentiation. Recent studies of plant stem cells suggest that the H3K27me3 mark is also involved in stem cell differentiation and proliferation in Arabidopsis flowers. In flower development, stem cell activity is terminated by a feedback loop of transcriptional regulators only after the proper number of organ primordia is created. One transcriptional repressor in the feedback loop plays a key role in balancing proliferation and differentiation of floral stem cells, and the status of H3K27me3 at the locus is involved in controlling the timing of induction during development. This review will summarize and discuss recent work on PRC-mediated temporal regulation of stem cell differentiation in flower development.","authors":"Ito, T., Sun, B.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Epigenetics","volume":"4","issue":"8","page":"564-7","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19939367","title":"Epigenetics in polycystic ovary syndrome: a pilot study of global DNA methylation.","abstract":"The percent global methylation of peripheral blood DNA was not significantly altered in 20 women with polycystic ovary syndrome (PCOS) compared with 20 controls. The study of specific tissues and target genomic regions will be required to further determine whether epigenetic alteration influences the development of PCOS.","authors":"Xu, N., Azziz, R., Goodarzi, MO.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Fertil Steril","volume":"94","issue":"2","page":"781-3.e1","pdf":null,"JrId":"3705","fulltextlink":null,"preprintlink":null,"articledate":"2010-07-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19934651","title":"Unlocking the Arabidopsis epigenome.","abstract":"The patterns of DNA methylation, referred to as the \"methylome,\" must be faithfully propagated for proper development of plants and mammals. However, it has been unclear to which extent transgenerational epigenetic inheritance will be affected after DNA methylation distribution has been altered. Recently, three reports have addressed this issue in the model plant Arabidopsis thaliana. Here we revisit the results of these experiments addressing the stability of epigenetic inheritance within two populations of epigenetic recombinant inbred lines (epiRILs), in which mosaic epigenomes were subjected to inbreeding for multiple generations. The manner in which the epigenetic variation was induced differed between the two populations, one by adversely affecting chromatin remodeling and the second by impairing the maintenance of DNA methylation, yet the comparison of the results provides a broader view of transgenerational epigenetic inheritance that may find parallels in other organisms.","authors":"Reinders, J., Paszkowski, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Epigenetics","volume":"4","issue":"8","page":"557-63","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19940235","title":"Epigenetics: a molecular link between environmental factors and type 2 diabetes.","abstract":"","authors":"Ling, C., Groop, L.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Diabetes","volume":"58","issue":"12","page":"2718-25","pdf":null,"JrId":"3397","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29863353","title":"CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction.","abstract":"Coeluting peptides are still a major challenge for the identification and validation of MS\/MS spectra, but carry great potential. To tackle these problems, we have developed the here presented CharmeRT workflow, combining a chimeric spectra identification strategy implemented as part of the MS Amanda algorithm with the validation system Elutator, which incorporates a highly accurate retention time prediction algorithm. For high-resolution data sets this workflow identifies 38-64% chimeric spectra, which results in up to 63% more unique peptides compared to a conventional single search strategy.","authors":"Dorfer, V., Maltsev, S., Winkler, S., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"J Proteome Res","volume":"17","issue":"8","page":"2581-2589","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19941173","title":"Staging neurological disorders: expressions of cognitive and motor disorder.","abstract":"In neurologic disorders, there are progressive losses in regional brain structural integrity, circuitry, and neuronal process that threaten individuals' ability to express functional capacity at several levels of severity. The classification of (a) patients on the basis of diagnosis, risk prognosis, and intervention outcome forms the basis of clinical staging and (b) laboratory animals on the basis of animal model of brain disorder, extent of insult and dysfunctional expression, provides the components for the clinical staging and preclinical staging, respectively, of the disease state with certain associated epidemiological, biological, and genetic characteristics. The investigation of epigenetics and biomarkers is intrinsic to any analysis of the progressive nature of the neurogenerative disorders, in the present account disorders relating to Alzheimer's disease, Parkinson's disease, depression, and diabetes.","authors":"Archer, T., Kostrzewa, RM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Neurotox Res","volume":"18","issue":"2","page":"107-11","pdf":null,"JrId":"30332","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19924914","title":"Key environmental epigenetics paper challenged.","abstract":"","authors":"Renner, R.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Environ Sci Technol","volume":"43","issue":"21","page":"8009-10","pdf":null,"JrId":"21768","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19923920","title":"Epigenetic regulation of vertebrate Hox genes: a dynamic equilibrium.","abstract":"Temporal and spatial control of Hox gene expression is essential for correct patterning of many animals. In both Drosophila and vertebrates, Polycomb and Trithorax group complexes control the maintenance of Hox gene expression in appropriate domains. In vertebrates, dynamic changes in chromatin modifications are also observed during the sequential activation of Hox genes in the embryo, suggesting that progressive epigenetic modifications could regulate collinear gene activation.","authors":"Soshnikova, N., Duboule, D.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Epigenetics","volume":"4","issue":"8","page":"537-40","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21700422","title":"Coronin 1A is an essential regulator of the TGF\u03b2 receptor\/SMAD3 signaling pathway in Th17 CD4(+) T cells.","abstract":"Transforming growth factor \u03b2 (TGF\u03b2) plays a central role in maintaining immune homeostasis by regulating the initiation and termination of immune responses and thus preventing the development of autoimmune diseases. In this study, we describe an essential mechanism by which the actin regulatory protein Coronin 1A (Coro1A) ensures the proper response of Th17 CD4(+) T cells to TGF\u03b2. Coro1A has been established as a key player in T cell survival, migration, activation, and Ca(2+) regulation in naive T cells. We show that mice lacking Coro1a developed less severe experimental autoimmune encephalomyelitis (EAE). Unexpectedly, upon the re-induction of EAE, Coro1a(-\/-) mice exhibited enhanced EAE signs that correlated with increased numbers of IL-17 producing CD4(+) cells in the central nervous system (CNS) compared to wild-type mice. In vitro differentiated Coro1a(-\/-) Th17 CD4(+) T cells consistently produced more IL-17 than wild-type cells and displayed a Th17\/Th1-like phenotype in regard to the expression of the Th1 markers T-bet and IFN\u03b3. Mechanistically, the Coro1a(-\/-) Th17 cell phenotype correlated with a severe defect in TGF\u03b2R-mediated SMAD3 activation. Taken together, these data provide experimental evidence of a non-redundant role of Coro1A in the regulation of Th17 CD4(+) cell effector functions and, subsequently, in the development of autoimmunity.","authors":"Kaminski, S., Hermann-Kleiter, N., Meisel, M., Thuille, N., Cronin, S., Hara, H., Fresser, F., Penninger, JM., Baier, G.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Autoimmun","volume":"37","issue":"3","page":"198-208","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40632047","title":"Unlocking Immunity Within: Inflammatory Monocytes Stimulate T Cells at Immune Hubs in the Tumor Microenvironment.","abstract":null,"authors":"Estivill, G., Elewaut, A., Obenauf, AC.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"J Invest Dermatol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-07-09","doi":"10.1016\/j.jid.2025.05.037","first_author":null,"corresponding_authors":null},{"pmid":"19923908","title":"The epigenome: archive of the prenatal environment.","abstract":"World-wide, research initiatives are in progress to establish the role of the epigenome in human disease. Empirical data are still scarce, but particularly studies investigating how the epigenome links early developmental and adult disease may rapidly change this situation. Recently, several reports showed that prenatal environmental conditions are associated with persistent changes of the human epigenome. The evaluation of candidate loci among individuals prenatally exposed to the Dutch Famine indicates that such changes may be common but individually relatively small and may greatly depend on the timing of the exposure during gestation. These findings suggest that the epigenomic contribution to disease risk may entail the combination of multiple changes especially when adaptive responses are involved to cope with environmental conditions. Well-designed epigenome-wide studies will be crucial in creating a catalog of epigenomic regions that are sensitive to the prenatal environment to evaluate developmental influences on common human disease.","authors":"Heijmans, BT., Tobi, EW., Lumey, LH., Slagboom, PE.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Epigenetics","volume":"4","issue":"8","page":"526-31","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19923895","title":"Early environmental effects on epigenetic regulation in humans.","abstract":"","authors":"Waterland, RA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Epigenetics","volume":"4","issue":"8","page":"523-5","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19947505","title":"[Epigenetics and cancer].","abstract":"Epigenetic modifications, including DNA methylation, histone modifications, RNA epigenetics and nucleosome remodeling, are important for gene transcription, but such modifications do not change the coding sequence of the gene. Although these events are heritable, they are potentially reversible, thus opening up opportunities for the therapy of cancer. So epigenetic modifications have been thrusted into the forefront of new drug discoveries. Current knowledge suggests that the agents that intervene epigenetics by \"turning back on\" silenced genes may represent a significant advancement in treating many forms of cancer. In this review, we summarized the research progress of epigenetic gene regulation and the proteins which could read epigenetic codes. And the relationship between epigenetics and cancer was discussed comprehensively.","authors":"Xue, C., Yu, J., Liu, H., Chen, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Sheng Wu Yi Xue Gong Cheng Xue Za Zhi","volume":"26","issue":"5","page":"1133-6","pdf":null,"JrId":"21127","fulltextlink":null,"preprintlink":null,"articledate":"2011-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19923898","title":"Cancer progenitors and epigenetic contexts: an Xisting connection.","abstract":"In mammals, silencing of one of the two X chromosomes is necessary to achieve dosage compensation. The non coding RNA Xist triggers X inactivation. Gene silencing by Xist is only possible in certain developmental contexts that only exist in cells of the early embryo and specific hematopoietic progenitors. Critical silencing factors may only be present in these contexts giving an explanation of why Xist is not operative outside these contexts. It has been demonstrated that Xist is functional in tumor cells, where SATB1 was identified as the first silencing factor for Xist mediated chromosome silencing.","authors":"Agrelo, R., Wutz, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Epigenetics","volume":"4","issue":"8","page":"568-70","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22789543","title":"The ALK(F1174L) mutation potentiates the oncogenic activity of MYCN in neuroblastoma.","abstract":"The ALK(F1174L) mutation is associated with intrinsic and acquired resistance to crizotinib and cosegregates with MYCN in neuroblastoma. In this study, we generated a mouse model overexpressing ALK(F1174L) in the neural crest. Compared to ALK(F1174L) and MYCN alone, co-expression of these two oncogenes led to the development of neuroblastomas with earlier onset, higher penetrance, and enhanced lethality. ALK(F1174L)\/MYCN tumors exhibited increased MYCN dosage due to ALK(F1174L)-induced activation of the PI3K\/AKT\/mTOR and MAPK pathways, coupled with suppression of MYCN pro-apoptotic effects. Combined treatment with the ATP-competitive mTOR inhibitor Torin2 overcame the resistance of ALK(F1174L)\/MYCN tumors to crizotinib. Our findings demonstrate a pathogenic role for ALK(F1174L) in neuroblastomas overexpressing MYCN and suggest a strategy for improving targeted therapy for ALK-positive neuroblastoma.","authors":"Berry, T., Luther, W., Bhatnagar, N., Jamin, Y., Poon, E., Sanda, T., Pei, D., Sharma, B., Vetharoy, WR., Hallsworth, A., Ahmad, Z., Barker, K., Moreau, L., Webber, H., Wang, W., Liu, Q., Perez-Atayde, A., Rodig, S., Cheung, NK., Raynaud, F., Hallberg, B., Robinson, SP., Gray, NS., Pearson, AD., Eccles, SA., Chesler, L., George, RE.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cancer Cell","volume":"22","issue":"1","page":"117-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19949925","title":"Epigenetic regulation of multidrug resistance 1 gene expression: profiling CpG methylation status using bisulphite sequencing.","abstract":"Methylation of CpG dinucleotides is one of the major epigenetic processes involved in the regulation of gene expression. Catalyzed by DNA methyltransferases, hypermethylation of CpG islands in promoter regions is typically associated with gene silencing. DNA methylation plays an important role in normal differentiation, development, and maintenance of genomic stability, with aberrant CpG methylation being linked with a number of disease states. Three CpG islands within a 1.15- kb region characterize the chromatin landscape surrounding the transcriptional start site of the multidrug resistance 1 (MDR1) gene. We and others have demonstrated that hypermethylation of this region is correlated with MDR1 gene silencing and the inability of chemotherapeutic agents to activate MDR1 transcription. The bisulphite sequencing and cloning method allows a precise interpretation of the methylation status of each individual CpG dinucleotide in the MDR1 region.","authors":"Baker, EK., El-Osta, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Methods Mol Biol","volume":"596","issue":"","page":"183-98","pdf":null,"JrId":"2488","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19933087","title":"[Epigenetics: advances of non-coding RNAs regulation in mammalian cells].","abstract":"Epigenetics is the study of meiotically and mitotically heritable changes in gene expression that are not coded for in the underlying DNA sequence. The term epigenetics is derived from epi- (meaning upon) and genetics. Epigenetic regulation of mammalian gene expression has profound effects in controlling cell growth, differentiation and cancer development. The important epigenetic mechanisms include DNA cytosine methylation, histone modifications and the more recently discovered non-coding RNAs. Non-coding RNAs are functional RNA molecules that are not translated into proteins. The main classes of regulatory non-coding RNAs include siRNA, miRNA, piRNA and long non-coding RNAs. There is growing evidence that regulatory non-coding RNAs play essential roles in the regulation of gene expression and are impor-tant in mammalian development and disease processes. Here, we review current research efforts aimed at understanding non-coding RNAs and their mechanisms of function in mammalian cells.","authors":"YU, H.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Yi Chuan","volume":"31","issue":"11","page":"1077-86","pdf":null,"JrId":"25477","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19920348","title":"Epigenetic learning in non-neural organisms.","abstract":"Learning involves a usually adaptive response to an input (an external stimulus or the organism's own behaviour) in which the input-response relation is memorized; some physical traces of the relation persist and can later be the basis of a more effective response. Using toy models we show that this characterization applies not only to the paradigmatic case of neural learning, but also to cellular responses that are based on epigenetic mechanisms of cell memory. The models suggest that the research agenda of epigenetics needs to be expanded.","authors":"Ginsburg, S., Jablonka, E.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Biosci","volume":"34","issue":"4","page":"633-46","pdf":null,"JrId":"8648","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1860820","title":"Importance of the position of TYR R boxes for repression and activation of the tyrP and aroF genes in Escherichia coli.","abstract":"Tyrosine-mediated repression of aroF and tyrP was studied by inserting DNA sequences between the two adjacent TYR R boxes which, in each case, overlap the respective RNA polymerase binding sites of these genes. In both cases, repression was greatest when homologous regions of these two TYR R boxes were on the same face of the DNA helix and the boxes were directly adjacent. An insertion of 3 bases was sufficient to abolish repression, which was reestablished as the boxes became separated by one full turn of the helix. These observations, coupled with the results of in vitro DNase I protection studies, supported the hypothesis that the binding of TyrR protein to the downstream boxes required cooperative interaction with TyrR protein already bound to the upstream boxes. In the case of tyrP, moving the upstream box also affected activation. Maximal activation was observed when the box was moved 3 or 12 to 14 residues upstream. Practically no activation was seen at intermediate positions, such as +7 and -4. It is hypothesized that these results indicate positions allowing maximal interaction between TyrR protein bound to the upstream box and RNA polymerase bound to the RNA polymerase binding site.","authors":"Andrews, AE., Dickson, B., Lawley, B., Cobbett, C., Pittard, AJ.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"J Bacteriol","volume":"173","issue":"16","page":"5079-85","pdf":null,"JrId":"4540","fulltextlink":null,"preprintlink":null,"articledate":"1991-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1845916","title":"The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus.","abstract":"T-associated maternal effect (Tme) is the only known maternal-effect mutation in the mouse. The defect is nuclear-encoded and embryos that inherit a deletion of the Tme locus from their mother die at day 15 of gestation. There are many genomically imprinted regions known in the mouse genome but so far no imprinted genes have been cloned. The Tme locus is absent in two chromosome-17 deletion mutants, Thp and the tLub2, and its position has been localized using these deletions to a 1-cM region. We report here that the genes for insulin-like growth factor type-2 receptor (Igf2r) and mitochondrial superoxide dismutase-2 (Sod-2) are absent from both deletions. Probes for these genes and for plasminogen (Plg) and T-complex peptide 1 (Tcp-1) were used in pulsed-field gel mapping to show that Tme must lie within a region of 800-1,100 kb. We also demonstrate that embryos express Igf2r only from the maternal chromosome, and that Tcp-1, Plg and Sod-2 are expressed from both chromosomes. Therefore Igf2r is imprinted and closely linked or identical to Tme.","authors":"Barlow, DP., St\u00f6ger, R., Herrmann, BG., Saito, K., Schweifer, N.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Nature","volume":"349","issue":"6304","page":"84-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1991-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520219","title":"Reversal of chlorpyrifos neurobehavioral teratogenicity in mice by allographic transplantation of adult subventricular zone-derived neural stem cells.","abstract":"Neurobehavioral teratogenicity can be reversed with transplantation of neural stem cells. However, the usefulness of this therapy would be greatly enhanced by employing adult stem cells. In pursuit of this this goal, we developed a model that uses subventricular zone (SVZ) cells. HS\/Ibg mice were exposed prenatally to chlorpyrifos on gestational days 9-18 (3 mg\/kg\/day, SC) in order to induce deficits in their performance in the Morris water maze test. Both the control and the exposed offspring were transplanted with SVZ cells (or vehicle) on postnatal day 35; this actually represents an allogenic transplantation, because the HS\/Ibg strain is a heterogeneous stock. The transplanted cells were later observed in the host brain by DiI tracing, and their initial differentiation to cholinergic neurons and astrocytes was ascertained. On postnatal day 80, animals that had been exposed prenatally to chlorpyrifos displayed impaired Morris water maze performance, requiring more time to reach the platform. Transplantation of adult SVZ-derived neural stem cells (NSC) reversed the deficits. Applying autologous transplantation provides an important demonstration that the methodological obstacles of immunological rejection and the ethical concerns related to using embryonic stem cells may be successfully bypassed in developing stem cell therapies for neurodevelopmental disorders.","authors":"Turgeman, G., Pinkas, A., Slotkin, TA., Tfilin, M., Langford, R., Yanai, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Neurosci Res","volume":"89","issue":"8","page":"1185-93","pdf":null,"JrId":"5310","fulltextlink":null,"preprintlink":null,"articledate":"2011-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19956766","title":"Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus.","abstract":"Cohesin is a chromatin-associated protein complex that mediates sister chromatid cohesion by connecting replicated DNA molecules. Cohesin also has important roles in gene regulation, but the mechanistic basis of this function is poorly understood. In mammalian genomes, cohesin co-localizes with CCCTC binding factor (CTCF), a zinc finger protein implicated in multiple gene regulatory events. At the imprinted IGF2-H19 locus, CTCF plays an important role in organizing allele-specific higher-order chromatin conformation and functions as an enhancer blocking transcriptional insulator. Here we have used chromosome conformation capture (3C) assays and RNAi-mediated depletion of cohesin to address whether cohesin affects higher order chromatin conformation at the IGF2-H19 locus in human cells. Our data show that cohesin has a critical role in maintaining CTCF-mediated chromatin conformation at the locus and that disruption of this conformation coincides with changes in IGF2 expression. We show that the cohesin-dependent, higher-order chromatin conformation of the locus exists in both G1 and G2 phases of the cell cycle and is therefore independent of cohesin's function in sister chromatid cohesion. We propose that cohesin can mediate interactions between DNA molecules in cis to insulate genes through the formation of chromatin loops, analogous to the cohesin mediated interaction with sister chromatids in trans to establish cohesion.","authors":"Nativio, R., Wendt, KS., Ito, Y., Huddleston, JE., Uribe-Lewis, S., Woodfine, K., Krueger, C., Reik, W., Peters, JM., Murrell, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS Genet","volume":"5","issue":"11","page":"e1000739","pdf":null,"JrId":"32385","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20015680","title":"Type III secretion systems shape up as they ship out.","abstract":"Virulence associated protein type III secretion systems (T3SSs) are intricately structured organic nanosyringes that achieve the translocation of bacterial proteins from the prokaryotic cytoplasm across three membranes into the host cytosol. The substrates for these systems number in the hundreds, with remarkably diverse biological activities, modulating host cell biology for the benefit of the pathogen. Although there has been tremendous progress on the structure and function of the T3SS substrates, there has been comparatively little progress on the much more highly conserved secretion apparatus itself. This review summarizes recent advances in the field of structural microbiology that have begun to address this shortcoming, finally bringing to bear the power of structural biology to this central virulence system of Gram-negative bacterial pathogens.","authors":"Marlovits, TC., Stebbins, CE.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Curr Opin Microbiol","volume":"13","issue":"1","page":"47-52","pdf":null,"JrId":"21196","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20059948","title":"The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline.","abstract":"Host-defense mechanisms against transposable elements are critical to protect the genome information. Here we show that tudor-domain containing 9 (Tdrd9) is essential for silencing Line-1 retrotransposon in the mouse male germline. Tdrd9 encodes an ATPase\/DExH-type helicase, and its mutation causes male sterility showing meiotic failure. In Tdrd9 mutants, Line-1 was highly activated and piwi-interacting small RNAs (piRNAs) corresponding to Line-1 were increased, suggesting that feedforward amplification operates in the mutant. In fetal testes, Tdrd9 mutation causes Line-1 desilencing and an aberrant piRNA profile in prospermatogonia, followed by cognate DNA demethylation. TDRD9 complexes with MIWI2 with distinct compartmentalization in processing bodies, and this TDRD9-MIWI2 localization is regulated by MILI and TDRD1 residing at intermitochondrial cement. Our results identify TDRD9 as a functional partner of MIWI2 and indicate that the tudor-piwi association is a conserved feature, while two separate axes, TDRD9-MIWI2 and TDRD1-MILI, cooperate nonredundantly in the piwi-small RNA pathway in the mouse male germline.","authors":"Shoji, M., Tanaka, T., Hosokawa, M., Reuter, M., Stark, A., Kato, Y., Kondoh, G., Okawa, K., Chujo, T., Suzuki, T., Hata, K., Martin, SL., Noce, T., Kuramochi-Miyagawa, S., Nakano, T., Sasaki, H., Pillai, RS., Nakatsuji, N., Chuma, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Dev Cell","volume":"17","issue":"6","page":"775-87","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22689981","title":"Expression of MALT1 oncogene in hematopoietic stem\/progenitor cells recapitulates the pathogenesis of human lymphoma in mice.","abstract":"Chromosomal translocations involving the MALT1 gene are hallmarks of mucosa-associated lymphoid tissue (MALT) lymphoma. To date, targeting these translocations to mouse B cells has failed to reproduce human disease. Here, we induced MALT1 expression in mouse Sca1(+)Lin(-) hematopoietic stem\/progenitor cells, which showed NF-\u03baB activation and early lymphoid priming, being selectively skewed toward B-cell differentiation. These cells accumulated in extranodal tissues and gave rise to clonal tumors recapitulating the principal clinical, biological, and molecular genetic features of MALT lymphoma. Deletion of p53 gene accelerated tumor onset and induced transformation of MALT lymphoma to activated B-cell diffuse large-cell lymphoma (ABC-DLBCL). Treatment of MALT1-induced lymphomas with a specific inhibitor of MALT1 proteolytic activity decreased cell viability, indicating that endogenous Malt1 signaling was required for tumor cell survival. Our study shows that human-like lymphomas can be modeled in mice by targeting MALT1 expression to hematopoietic stem\/progenitor cells, demonstrating the oncogenic role of MALT1 in lymphomagenesis. Furthermore, this work establishes a molecular link between MALT lymphoma and ABC-DLBCL, and provides mouse models to test MALT1 inhibitors. Finally, our results suggest that hematopoietic stem\/progenitor cells may be involved in the pathogenesis of human mature B-cell lymphomas.","authors":"Vicente-Due\u00f1as, C., Font\u00e1n, L., Gonzalez-Herrero, I., Romero-Camarero, I., Segura, V., Aznar, MA., Alonso-Escudero, E., Campos-Sanchez, E., Ruiz-Roca, L., Barajas-Diego, M., Sagardoy, A., Martinez-Ferrandis, JI., Abollo-Jimenez, F., Bertolo, C., Pe\u00f1uelas, I., Garcia-Criado, FJ., Garc\u00eda-Cenador, MB., Tousseyn, T., Agirre, X., Prosper, F., Garcia-Bragado, F., McPhail, ED., Lossos, IS., Du, MQ., Flores, T., Hernandez-Rivas, JM., Gonzalez, M., Salar, A., Bellosillo, B., Conde, E., Siebert, R., Sagaert, X., Cobaleda, C., Sanchez-Garcia, I., Martinez-Climent, JA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Proc Natl Acad Sci U S A","volume":"109","issue":"26","page":"10534-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21481027","title":"GMI1, a structural-maintenance-of-chromosomes-hinge domain-containing protein, is involved in somatic homologous recombination in Arabidopsis.","abstract":"DNA double-strand breaks (DSBs) pose one of the most severe threats to genome integrity, potentially leading to cell death. After detection of a DSB, the DNA damage and repair response is initiated and the DSB is repaired by non-homologous end joining and\/or homologous recombination. Many components of these processes are still unknown in Arabidopsis thaliana. In this work, we characterized \u03b3-irradiation and mitomycin C induced 1 (GMI1), a member of the SMC-hinge domain-containing protein family. RT-PCR analysis and promoter-GUS fusion studies showed that \u03b3-irradiation, the radio-mimetic drug bleocin, and the DNA cross-linking agent mitomycin C strongly enhance GMI1 expression particularly in meristematic tissues. The induction of GMI1 by \u03b3-irradiation depends on the signalling kinase Ataxia telangiectasia-mutated (ATM) but not on ATM and Rad3-related (ATR). Epistasis analysis of single and double mutants demonstrated that ATM acts upstream of GMI1 while the atr gmi1-2 double mutant was more sensitive than the respective single mutants. Comet assay revealed a reduced rate of DNA double-strand break repair in gmi1 mutants during the early recovery phase after exposure to bleocin. Moreover, the rate of homologous recombination of a reporter construct was strongly reduced in gmi1 mutant plants upon exposure to bleocin or mitomycin C. GMI1 is the first member of its protein family known to be involved in DNA repair.","authors":"B\u00f6hmdorfer, G., Schleiffer, A., Brunmeir, R., Ferscha, S., Nizhynska, V., Koz\u00e1k, J., Angelis, KJ., Kreil, DP., Schweizer, D.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Plant J","volume":"67","issue":"3","page":"420-33","pdf":null,"JrId":"2425","fulltextlink":null,"preprintlink":null,"articledate":"2011-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16988814","title":"Lessons from SARS: control of acute lung failure by the SARS receptor ACE2.","abstract":"Angiotensin-converting enzyme 2 (ACE2), a second angiotensin-converting enzyme (ACE), regulates the renin-angiotensin system by counterbalancing ACE activity. Accumulating evidence in recent years has demonstrated a physiological and pathological role of ACE2 in the cardiovascular systems. Recently, it has been shown that severe acute respiratory syndrome (SARS) coronavirus, the cause of SARS, utilizes ACE2 as an essential receptor for cell fusion and in vivo infections in mice. Intriguingly, ACE2 acts as a protective factor in various experimental models of acute lung failure and, therefore, acts not only as a key determinant for SARS virus entry into cells but also contributes to SARS pathogenesis. Here we review the role of ACE2 in disease pathogenesis, including lung diseases and cardiovascular diseases.","authors":"Kuba, K., Imai, Y., Rao, S., Jiang, C., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Mol Med (Berl)","volume":"84","issue":"10","page":"814-20","pdf":null,"JrId":"8748","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19946273","title":"Role of STAT5 in controlling cell survival and immunoglobulin gene recombination during pro-B cell development.","abstract":"STAT5 and interleukin 7 (IL-7) signaling are thought to control B lymphopoiesis by regulating the expression of key transcription factors and by activating variable (V(H)) gene segments at the immunoglobulin heavy-chain (Igh) locus. Using conditional mutagenesis to delete the gene encoding the transcription factor STAT5, we demonstrate that the development of pro-B cells was restored by transgenic expression of the prosurvival protein Bcl-2, which compensated for loss of the antiapoptotic protein Mcl-1. Expression of the genes encoding the B cell-specification factor EBF1 and the B cell-commitment protein Pax5 as well as V(H) gene recombination were normal in STAT5- or IL-7 receptor alpha-chain (IL-7Ralpha)-deficient pro-B cells rescued by Bcl-2. STAT5-expressing pro-B cells contained little or no active chromatin at most V(H) genes. In contrast, rearrangements of the immunoglobulin-kappa light-chain locus (Igk) were more abundant in STAT5- or IL-7Ralpha-deficient pro-B cells. Hence, STAT5 and IL-7 signaling control cell survival and the developmental ordering of immunoglobulin gene rearrangements by suppressing premature Igk recombination in pro-B cells.","authors":"Malin, S., McManus, S., Cobaleda, C., Novatchkova, M., Delogu, A., Bouillet, P., Strasser, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Immunol","volume":"11","issue":"2","page":"171-9","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19944134","title":"Experimental identification of microRNA targets.","abstract":"microRNAs are small RNAs that regulate protein synthesis post-transcriptionally. Animal microRNAs recognize their targets by incomplete base pairing to sequence motifs most often present in the 3' untranslated region of their target mRNAs. This partial complementarity vastly expands the repertoire of potential targets and constitutes a problem for computational target prediction. Although computational analyses have shed light on important aspects of microRNA target recognition, several questions remain regarding how microRNAs can recognize and regulate their targets. Forward experimental approaches allow for an unbiased study of microRNA target recognition and may unveil novel, rare or uncommon target binding patterns. In this review we focus on animal microRNAs and the experimental approaches that have been described for identification of their targets.","authors":"\u00d8rom, UA., Lund, AH.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Gene","volume":"451","issue":"1-2","page":"1-5","pdf":null,"JrId":"3886","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20044575","title":"The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer.","abstract":"The Tasmanian devil, a marsupial carnivore, is endangered because of the emergence of a transmissible cancer known as devil facial tumor disease (DFTD). This fatal cancer is clonally derived and is an allograft transmitted between devils by biting. We performed a large-scale genetic analysis of DFTD with microsatellite genotyping, a mitochondrial genome analysis, and deep sequencing of the DFTD transcriptome and microRNAs. These studies confirm that DFTD is a monophyletic clonally transmissible tumor and suggest that the disease is of Schwann cell origin. On the basis of these results, we have generated a diagnostic marker for DFTD and identify a suite of genes relevant to DFTD pathology and transmission. We provide a genomic data set for the Tasmanian devil that is applicable to cancer diagnosis, disease evolution, and conservation biology.","authors":"Murchison, EP., Tovar, C., Hsu, A., Bender, HS., Kheradpour, P., Rebbeck, CA., Obendorf, D., Conlan, C., Bahlo, M., Blizzard, CA., Pyecroft, S., Kreiss, A., Kellis, M., Stark, A., Harkins, TT., Marshall Graves, JA., Woods, GM., Hannon, GJ., Papenfuss, AT.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Science","volume":"327","issue":"5961","page":"84-7","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29","title":"Lorazepam in sexual disorders.","abstract":"","authors":"Maneksha, S., Harry, TV.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Clin Pract","volume":"29","issue":"7","page":"175-6","pdf":null,"JrId":"1778","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26934225","title":"MARCKS-like protein is an initiating molecule in axolotl appendage regeneration.","abstract":"Identifying key molecules that launch regeneration has been a long-sought goal. Multiple regenerative animals show an initial wound-associated proliferative response that transits into sustained proliferation if a considerable portion of the body part has been removed. In the axolotl, appendage amputation initiates a round of wound-associated cell cycle induction followed by continued proliferation that is dependent on nerve-derived signals. A wound-associated molecule that triggers the initial proliferative response to launch regeneration has remained obscure. Here, using an expression cloning strategy followed by in vivo gain- and loss-of-function assays, we identified axolotl MARCKS-like protein (MLP) as an extracellularly released factor that induces the initial cell cycle response during axolotl appendage regeneration. The identification of a regeneration-initiating molecule opens the possibility of understanding how to elicit regeneration in other animals.","authors":"Sugiura, T., Wang, H., Barsacchi, R., Simon, A., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nature","volume":"531","issue":"7593","page":"237-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10804172","title":"brakeless is required for lamina targeting of R1-R6 axons in the Drosophila visual system.","abstract":"Photoreceptors in the Drosophila eye project their axons retinotopically to targets in the optic lobe of the brain. The axons of photoreceptor cells R1-R6 terminate in the first optic ganglion, the lamina, while R7 and R8 axons project through the lamina to terminate in distinct layers of the second ganglion, the medulla. Here we report the identification of the gene brakeless (bks) and show that its function is required in the developing eye specifically for the lamina targeting of R1-R6 axons. In mosaic animals lacking bks function in the eye, R1-R6 axons project through the lamina to terminate in the medulla. Other aspects of visual system development appear completely normal: photoreceptor and lamina cell fates are correctly specified, R7 axons correctly target the medulla, and both correctly targeted R7 axons and mistargeted R1-R6 axons maintain their retinotopic order with respect to both anteroposterior and dorsoventral axes. bks encodes two unusually hydrophilic nuclear protein isoforms, one of which contains a putative C(2)H(2) zinc finger domain. Transgenic expression of either Bks isoform is sufficient to restore the lamina targeting of R1-R6 axons in bks mosaics, but not to retarget R7 or R8 axons to the lamina. These data demonstrate the existence of a lamina-specific targeting mechanism for R1-R6 axons in the Drosophila visual system, and provide the first entry point in the molecular characterization of this process.","authors":"Senti, K., Keleman, K., Eisenhaber, F., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Development","volume":"127","issue":"11","page":"2291-301","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2000-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12","title":"The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.","abstract":"","authors":"Stein, JM.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"18","page":"1659-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1752436","title":"A new role for MCM1 in yeast: cell cycle regulation of SW15 transcription.","abstract":"In the yeast Saccharomyces cerevisiae cell cycle-regulated SW15 transcription is essential for ensuring that mother and not daughter cells switch mating type. We have identified a 55-bp promoter sequence that appears to be responsible for restricting transcription to the late S, G2, and M phases of the cell cycle. Two proteins, MCM1, a transcription factor described previously, and SFF (SWI five factor, a newly identified factor) bind this sequence in vitro. MCM1 binds the DNA tightly on its own, but SFF will only bind as part of a ternary complex with MCM1. We observe a strong correlation between the ability of mutated SWI5 promoter sequences to form a ternary MCM1-SFF-containing complex in vitro and to activate transcription in vivo, which suggests that efficient transcription requires that both proteins bind DNA. Through its interactions with cell type-specific coactivators and corepressors, MCM1 controls cell type-specific expression of pheromone and receptor genes. By analogy, we propose that SFF enables MCM1 to function as a part of a cell cycle-regulated transcription complex.","authors":"Lydall, D., Ammerer, G., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Genes Dev","volume":"5","issue":"12B","page":"2405-19","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1992-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28439859","title":"Genome-Wide Profiling of Histone Modifications and Histone Variants in Arabidopsis thaliana and Marchantia polymorpha.","abstract":"Histone modifications and histone variants barcode the genome and play major roles in epigenetic regulations. Chromatin immunoprecipitation (ChIP) coupled with next-generation sequencing (NGS) is a well-established method to investigate the landscape of epigenetic marks at a genomic level. Here, we describe procedures for conducting ChIP, subsequent NGS library construction, and data analysis on histone modifications and histone variants in Arabidopsis thaliana. We also describe an optimized nuclear isolation procedure to prepare chromatin for ChIP in the liverwort, Marchantia polymorpha, which is the emerging model plant ideal for evolutionary studies.","authors":"Yelagandula, R., Osakabe, A., Axelsson, E., Berger, F., Kawashima, T.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Methods Mol Biol","volume":"1610","issue":null,"page":"93-106","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20220848","title":"Systematic genetic analysis of muscle morphogenesis and function in Drosophila.","abstract":"Systematic genetic approaches have provided deep insight into the molecular and cellular mechanisms that operate in simple unicellular organisms. For multicellular organisms, however, the pleiotropy of gene function has largely restricted such approaches to the study of early embryogenesis. With the availability of genome-wide transgenic RNA interference (RNAi) libraries in Drosophila, it is now possible to perform a systematic genetic dissection of any cell or tissue type at any stage of the lifespan. Here we apply these methods to define the genetic basis for formation and function of the Drosophila muscle. We identify a role in muscle for 2,785 genes, many of which we assign to specific functions in the organization of muscles, myofibrils or sarcomeres. Many of these genes are phylogenetically conserved, including genes implicated in mammalian sarcomere organization and human muscle diseases.","authors":"Schnorrer, F., Sch\u00f6nbauer, C., Langer, CC., Dietzl, G., Novatchkova, M., Schernhuber, K., Fellner, M., Azaryan, A., Radolf, M., Stark, A., Keleman, K., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nature","volume":"464","issue":"7286","page":"287-91","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24","title":"Influence of a new virostatic compound on the induction of enzymes in rat liver.","abstract":"The virostatic compound N,N-diethyl-4-[2-(2-oxo-3-tetradecyl-1-imidazolidinyl)-ethyl]-1-piperazinecarboxamide-hydrochloride (5531) was analyzed as to its effect on the induction of tryptophan-pyrrolase and tyrosineaminotransferase in rat liver. 1. The basic activity of the enzymes was not influenced by the substance either in normal or in adrenalectomized animals. 2. The induction of the enzymes by cortisone increased in the presence of the compound whereas the substrate induction remained unchanged. 3. The induction of tyrosine-aminotransferase by dexamethasonephosphate in tissue culture is inhibited if the dose of compound 5531 is higher than 5 mug\/ml.","authors":"Kr\u00f6ger, H., Donner, I., Skiello, G.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Arzneimittelforschung","volume":"25","issue":"9","page":"1426-9","pdf":null,"JrId":"884","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"93","title":"[Structure formation in interphase adsorption layers of lysozyme at liquid boundaries].","abstract":"In connection with the modelling of biomembranes regularities of the formation and development of interphase adsorption layers of lysozyme at liquid borders under different conditions and depending on the nature of carbohydrate phase were investigated by the determination of mechanical characteristics of such layers. The investigations carried out showed that the most solid layers appeared under the conditions which assured the formation of the maximum number of intermolecular bonds (which in a common case is performed with maximum disorderlinesss of the macromolecules which get at the interphase).","authors":"Alekseeva, IG., Lapina, GP., Tulovskaia, ZD., Izma\u012dlova, VN.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biofizika","volume":"20","issue":"4","page":"566-9","pdf":null,"JrId":"1060","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"82","title":"The behavior of holo- and apo-forms of bovine superoxide dismutase at low pH.","abstract":"1. Holo-superoxide dismutase from bovine erythrocytes has been shown to undergo a reversible structural modification in the pH 3-5 range. 2. The spectral alterations observed on changing from neutrality to pH 2 were: a slight attenuation of the 680 nm absorbance; the loss of the 450 nm shoulder, apparent in the optical spectrum of the native protein; and a new band appeared at 330 nm. The circular dichroism at 600 nm was essentially lost while a weak negative band appeared at approx. 380 nm and a positive band at 310 nm. 3. The EPR spectrum was also modified on changing from the native to the low pH form: A parallel increased from approximately 130 to approximately 150 G, g parallel remained unchanged at approximately 2.27, and gm decreased from approximately 2.09 to approximately 2.08. The apparent linewidth remained essentially constant. 4. High resolution (220 MHz) PMR spectra of holo- and apoproteins revealed that the metals influence the three-dimensional structure of the protein. 5. PMR studies indicated that at pH 3 the apoprotein existed almost entirely in a random coil form and that it assumed a compact well-ordered structure on returning to neutral pH. The holoprotein maintained a compact, apparently dimeric, structure even at pH 3.","authors":"Fee, JA., Phillips, WD.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"1","page":"26-38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-157","title":"Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signalling","abstract":null,"authors":"Finger, F., Ottens, F., Springhorn, A., Drexel, T., Proksch, L., Metz, S., Cochella, L., Hoppe, T.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nature Metabolism","volume":"1","issue":"","page":"350\u2013359","pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.nature.com\/articles\/s42255-019-0033-z","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22592113","title":"Mantle cell lymphoma-like lymphomas in c-myc-3'RR\/p53+\/- mice and c-myc-3'RR\/Cdk4R24C mice: differential oncogenic mechanisms but similar cellular origin.","abstract":"Mantle cell lymphoma (MCL) is a malignant lymphoproliferative B-cell disorder that does not occur spontaneously in mice but experimental mice model have been developed. Recently two different mice models prone to develop MCL-like lymphomas were generated: c-myc-3'RR\/Cdk4(R24C) mice and c-myc-3'RR\/p53+\/- mice. Comparison of their gene expression profiles does not highlight specific differences other than those in relation with their specific mutational status (i.e., Cdk4(R24C) mutation or p53 mutations). We propose that similarly to typical human MCL and its blastoid or cyclin-D1 variants that correspond to the same genetic entity, MCL-like lymphomas of c-myc-3'RR\/ p53+\/- mice and c-myc-3'RR\/Cdk4(R24C) mice represent a spectrum of the same entity.","authors":"Rouaud, P., Fiancette, R., Vincent-Fabert, C., Magnone, V., Cogn\u00e9, M., Dubus, P., Denizot, Y.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Oncotarget","volume":"3","issue":"5","page":"586-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33122427","title":"A human tissue screen identifies a regulator of ER secretion as a brain-size determinant.","abstract":"Loss-of-function (LOF) screens provide a powerful approach to identify regulators in biological processes. Pioneered in laboratory animals, LOF screens of human genes are currently restricted to two-dimensional cell cultures, which hinders the testing of gene functions requiring tissue context. Here, we present CRISPR-lineage tracing at cellular resolution in heterogeneous tissue (CRISPR-LICHT), which enables parallel LOF studies in human cerebral organoid tissue. We used CRISPR-LICHT to test 173 microcephaly candidate genes, revealing 25 to be involved in known and uncharacterized microcephaly-associated pathways. We characterized <i>IER3IP1<\/i>, which regulates the endoplasmic reticulum (ER) function and extracellular matrix protein secretion crucial for tissue integrity, the dysregulation of which results in microcephaly. Our human tissue screening technology identifies microcephaly genes and mechanisms involved in brain-size control.","authors":"Esk, C., Lindenhofer, D., Haendeler, S., Wester, RA., Pflug, F., Schroeder, B., Bagley, JA., Elling, U., Zuber, J., von Haeseler, A., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Science","volume":"370","issue":"6519","page":"935-941","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40163300","title":"Functional Lineage Tracing Using CaTCH.","abstract":"CaTCH is a functional lineage tracing tool using genetic barcodes to label and follow million of cell clones in a selection experiment. Furthermore, CaTCH allows to isolate specific cell clones from heterogeneous populations by their barcode. Thus, founding clones of a phenotype of interest can be retrospectively isolated alive using FACS (fluorescence-activated cell sorting), allowing to perform functional experiments. Example applications of this method are investigating the evolutionary selection of resistance to therapies or other evolutionary pressures.","authors":"Umkehrer, C., Obenauf, A.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Methods Mol Biol","volume":"2905","issue":null,"page":"95-120","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-15","doi":"10.1007\/978-1-0716-4418-8_6","first_author":null,"corresponding_authors":null},{"pmid":"21935921","title":"High-resolution analyses of copy number changes in disseminated tumor cells of patients with breast cancer.","abstract":"The presence of disseminated tumor cells (DTCs) in bone marrow (BM) identifies breast cancer patients with less favorable outcome. Furthermore, molecular characterization is required to investigate the malignant potential of these cells. This study presents a single-cell array comparative genomic hybridization (SCaCGH) method providing molecular analysis of immunomorphologically detected DTCs. The resolution limit of the method was estimated using the cancer cell line SK-BR-3 on 44 and 244k arrays. The technique was further tested on 28 circulating tumor cells and four hematopoietic cells (HCs) from peripheral blood (n = 8 patients). The SCaCGH method was finally applied to 24 DTCs, three immunopositive cells morphologically classified as probable HCs from breast cancer patients and five HC controls from BM (n = 7 patients plus n = 1 healthy donor). The frequency of copy number changes of the DTCs revealed similarities with primary breast tumor samples. Three of the patients had available profiles for DTCs and the corresponding tumor tissue from primary surgery. More than two-third of the analyzed DTCs disclosed equivalent changes, both to each other and to the corresponding primary disease, whereas the rest of the cells showed balanced profiles. The probable HCs revealed either balanced profiles (n = 2) or changes comparable to the tumor tissue and DTCs (n = 1), indicating morphological overlap between HCs and DTCs. Similar aberration patterns were visible in DTCs collected at diagnosis and at 3 years relapse-free follow-up. SCaCGH may be a powerful tool for the molecular characterization of DTCs.","authors":"Mathiesen, RR., Fjelldal, R., Liest\u00f8l, K., Due, EU., Geigl, JB., Riethdorf, S., Borgen, E., Rye, IH., Schneider, IJ., Obenauf, AC., Mauermann, O., Nilsen, G., Christian Lingjaerde, O., B\u00f8rresen-Dale, AL., Pantel, K., Speicher, MR., Naume, B., Baumbusch, LO.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Int J Cancer","volume":"131","issue":"4","page":"E405-15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8507488","title":"Control of the yeast cell cycle by the Cdc28 protein kinase.","abstract":"It is becoming increasingly apparent that the diverse functions of Cdc28 during the yeast cell cycle are performed by forms of the kinase that are distinguished by their cyclin subunits. Entry into the cell cycle at START involves the Cln cyclins. S phase needs Clb5 or Clb6 B-type cyclins. Bipolar mitotic spindle formation involves Clb1-4 B-type cyclins. Much of the order and timing of the cell cycle events may involve the progressive activation of Cdc28 kinase activities associated with different cyclins, whose periodicity during the cycle is determined by both transcriptional and post-transcriptional controls.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Curr Opin Cell Biol","volume":"5","issue":"2","page":"166-79","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"1993-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1728587","title":"Constitutive myc expression impairs hypertrophy and calcification in cartilage.","abstract":"The myc oncogene is expressed by proliferating quail embryo chondrocytes (QEC) grown as adherent cells and is repressed in QEC maintained in suspension culture. To investigate the interference of myc expression during chondrocyte differentiation, QEC were infected with a retrovirus carrying the v-myc oncogene (QEC-v-myc). Uninfected or helper virus-infected QEC were used as control. In adherent culture, QEC-v-myc displayed a chondrocytic phenotype and synthesized type II collagen and Ch21 protein, while control chondrocytes synthesized type I and type II collagen with no Ch21 protein detected as long as the attachment to the plastic was kept. In suspension culture, QEC-v-myc readily aggregated and within 1 week the cell aggregates released small single cells; still they secreted only type II collagen and Ch21 protein. In the same conditions control cell aggregates released hypertrophic chondrocytes producing type II and type X collagens and Ch21 protein. In the appropriate culture conditions, QEC-v-myc reconstituted a tissue defined as nonhypertrophic, noncalcifying cartilage by the high cellularity, the low levels of alkaline phosphatase enzymatic activity, and the absence of type X collagen synthesis and of calcium deposition. We conclude that the constitutive expression of the v-myc oncogene keeps chondrocytes in stage I (active proliferation and synthesis of type II collagen) and prevents these cells from reconstituting hypertrophic calcifying cartilage.","authors":"Quarto, R., Dozin, B., Tacchetti, C., Robino, G., Zenke, M., Campanile, G., Cancedda, R.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Dev Biol","volume":"149","issue":"1","page":"168-76","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"1992-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20188538","title":"Molecular transformers in the cell: lessons learned from the DegP protease-chaperone.","abstract":"Structure-function analysis of DegP revealed a novel mechanism for protease and chaperone regulation. Binding of unfolded proteins induces the oligomer reassembly from the resting hexamer (DegP6) into the functional protease-chaperone DegP12\/24. The newly formed cage exhibits the characteristics of a proteolytic folding chamber, shredding those proteins that are severely misfolded while stabilizing and protecting proteins present in their native state. Isolation of native DegP complexes with folded outer membrane proteins (OMPs) highlights the importance of DegP in OMP biogenesis. The encapsulated OMP beta-barrel is significantly stabilized in the hydrophobic chamber of DegP12\/24 and thus DegP seems to employ a reciprocal mechanism to those chaperones assisting the folding of water soluble proteins via polar interactions. In addition, we discuss in this review similarities to other complex proteolytic machines that, like DegP, are under control of a substrate-induced or stress-induced oligomer conversion.","authors":"Sawa, J., Heuck, A., Ehrmann, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Curr Opin Struct Biol","volume":"20","issue":"2","page":"253-8","pdf":null,"JrId":"8602","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20154139","title":"A novel conserved phosphotyrosine motif in the Drosophila fibroblast growth factor signaling adaptor Dof with a redundant role in signal transmission.","abstract":"The fibroblast growth factor receptor (FGFR) signals through adaptors constitutively associated with the receptor. In Drosophila melanogaster, the FGFR-specific adaptor protein Downstream-of-FGFR (Dof) becomes phosphorylated upon receptor activation at several tyrosine residues, one of which recruits Corkscrew (Csw), the Drosophila homolog of SHP2, which provides a molecular link to mitogen-activated protein kinase (MAPK) activation. However, the Csw pathway is not the only link from Dof to MAPK. In this study, we identify a novel phosphotyrosine motif present in four copies in Dof and also found in other insect and vertebrate signaling molecules. We show that these motifs are phosphorylated and contribute to FGF signal transduction. They constitute one of three sets of phosphotyrosines that act redundantly in signal transmission: (i) a Csw binding site, (ii) four consensus Grb2 recognition sites, and (iii) four novel tyrosine motifs. We show that Src64B binds to Dof and that Src kinases contribute to FGFR-dependent MAPK activation. Phosphorylation of the novel tyrosine motifs is required for the interaction of Dof with Src64B. Thus, Src64B recruitment to Dof through the novel phosphosites can provide a new link to MAPK activation and other cellular responses. This may give a molecular explanation for the involvement of Src kinases in FGF-dependent developmental events.","authors":"Csiszar, A., Vogelsang, E., Beug, H., Leptin, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Mol Cell Biol","volume":"30","issue":"8","page":"2017-27","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18192061","title":"Defining 'chromosomal instability'.","abstract":"Most scientists agree that the majority of human solid malignant tumors are characterized by chromosomal instability (CIN) involving gain or loss of whole chromosomes or fractions of chromosomes. CIN is thought to be an early event during tumorigenesis and might therefore be involved in tumor initiation. Despite its frequent occurrence in tumors and its potential importance in tumor evolution, CIN is poorly defined and is used inconsistently and imprecisely. Here, we provide criteria to define CIN and argue that few experimental approaches are capable of assessing the presence of CIN. Accurate assessment of CIN is crucial to elucidate whether CIN is a driving force for tumorigenesis and whether a chromosomally unstable genome is necessary for tumor progression.","authors":"Geigl, JB., Obenauf, AC., Schwarzbraun, T., Speicher, MR.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Trends Genet","volume":"24","issue":"2","page":"64-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8408204","title":"Protein transport to the dendritic plasma membrane of cultured neurons is regulated by rab8p.","abstract":"In the companion paper (Huber, L. A., S. W. Pimplikar, R. G. Parton, H. Virta, M. Zerial, and K. Simons. J. Cell Biol. 123:35-45) we reported that the small GTPase rab8p is involved in transport from the TGN to the basolateral plasma membrane in epithelia. In the present work we investigated the localization and function of rab8p in polarized hippocampal neurons. By immunofluorescence microscopy we found that rab8p localized preferentially in the somatodendritic domain, and was excluded from the axon. Double-labeling immunofluorescence showed that some of the rab8p co-localized in the dendrites with the Semliki Forest Virus glycoprotein E2 (SFV-E2). An antisense oligonucleotide approach was used to investigate the role of rab8p in dendritic transport of newly synthesized viral glycoproteins. Antisense oligonucleotides corresponding to the initiation region of the rab8 coding sequence were added to the cultured neurons for four days. This treatment resulted in a significant decrease in cellular levels of rab8p and transport of SFV-E2 from the cell body to the dendrites was significantly reduced. However, no effect was observed on axonal transport of influenza HA. From these results we conclude that rab8p is involved in transport of proteins to the dendritic surface in neurons.","authors":"Huber, LA., de Hoop, MJ., Dupree, P., Zerial, M., Simons, K., Dotti, C.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Cell Biol","volume":"123","issue":"1","page":"47-55","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1993-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"62","title":"Light-induced changes of absorbance and electron spin resonance in small photosystem II particles.","abstract":"Photosystem II reaction center components have been studied in small system II particles prepared with digitonin. Upon illumination the reduction of the primary acceptor was indicated by absorbance changes due to the reduction of a plastoquinone to the semiquinone anion and by a small blue shifts of absorption bands near 545 nm (C550) and 685 nm. The semiquinone to chlorophyll ratio was between 1\/20 and 1\/70 in various preparations. The terminal electron donor in this reaction did not cause large absorbance changes but its oxidized form was revealed by a hitherto unknown electron spin resonance (ESR) signal, which had some properties of the well-known signal II but a linewidth and g-value much nearer to those of signal I. Upon darkening absorbance and ESR changes decayed together in a cyclic or back reaction which was stimulated by 3-(3,4 dichlorophenyl)-1,1-dimethylurea. The donor could be oxidized by ferricyanide in the dark. Illumination in the presence of ferricyanide induced absorbance and ESR changes, rapidly reversed upon darkening, which may be ascribed to the oxidation of a chlorophyll a dimer, possibly the primary electron donor of photosystem II. In addition an ESR signal with 15 to 20 gauss linewidth and a slower dark decay was observed, which may have been caused by a secondary donor.","authors":"Van Gorkom, HJ., Pulles, MP., Wessels, JS.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"408","issue":"3","page":"331-9","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20130060","title":"Human rhinovirus 14 enters rhabdomyosarcoma cells expressing icam-1 by a clathrin-, caveolin-, and flotillin-independent pathway.","abstract":"Intercellular adhesion molecule 1 (ICAM-1) mediates binding and entry of major group human rhinoviruses (HRVs). Whereas the entry pathway of minor group HRVs has been studied in detail and is comparatively well understood, the pathway taken by major group HRVs is largely unknown. Use of immunofluorescence microscopy, colocalization with specific endocytic markers, dominant negative mutants, and pharmacological inhibitors allowed us to demonstrate that the major group virus HRV14 enters rhabdomyosarcoma cells transfected to express human ICAM-1 in a clathrin-, caveolin-, and flotillin-independent manner. Electron microscopy revealed that many virions accumulated in long tubular structures, easily distinguishable from clathrin-coated pits and caveolae. Virus entry was strongly sensitive to the Na(+)\/H(+) ion exchange inhibitor amiloride and moderately sensitive to cytochalasin D. Thus, cellular uptake of HRV14 occurs via a pathway exhibiting some, but not all, characteristics of macropinocytosis and is similar to that recently described for adenovirus 3 entry via alpha(v) integrin\/CD46 in HeLa cells.","authors":"Khan, AG., Pickl-Herk, A., Gajdzik, L., Marlovits, TC., Fuchs, R., Blaas, D.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Virol","volume":"84","issue":"8","page":"3984-92","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25533954","title":"Cell division: Hold on and let go.","abstract":null,"authors":"Tachibana-Konwalski, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nature","volume":"517","issue":"7535","page":"441-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21875651","title":"Cytoarchitectural disruption of the superior colliculus and an enlarged acoustic startle response in the Tuba1a mutant mouse.","abstract":"The Jenna mutant mouse harbours an S140G mutation in Tuba1a that impairs tubulin heterodimer formation resulting in defective neuronal migration during development. The consequence of decreased neuronal motility is a fractured pyramidal cell layer in the hippocampus and wave-like perturbations in the cerebral cortex. Here, we extend our characterisation of this mouse investigating the laminar architecture of the superior colliculus (SC). Our results reveal that the structure of the SC in mutant animals is intact; however, it is significantly thinner with an apparent fusion of the intermediate grey and white layers. Birthdate labelling at E12.5 and E13.5 showed that the S140G mutation impairs the radial migration of neurons in the SC. A quantitative assessment of neuronal number in adulthood reveals a massive reduction in postmitotic neurons in mutant animals, which we attribute to increased apoptotic cell death. Consistent with the role of the SC in modulating sensorimotor gating, and the circuitry that modulates this behaviour, we find that Jenna mutants exhibit an exaggerated acoustic startle response. Our results highlight the importance of Tuba1a for correct neuronal migration and implicate postnatal apoptotic cell death in the pathophysiological mechanisms underlying the tubulinopathies.","authors":"Edwards, A., Treiber, CD., Breuss, M., Pidsley, R., Huang, GJ., Cleak, J., Oliver, PL., Flint, J., Keays, DA.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Neuroscience","volume":"195","issue":null,"page":"191-200","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20176924","title":"A Syd-1 homologue regulates pre- and postsynaptic maturation in Drosophila.","abstract":"Active zones (AZs) are presynaptic membrane domains mediating synaptic vesicle fusion opposite postsynaptic densities (PSDs). At the Drosophila neuromuscular junction, the ELKS family member Bruchpilot (BRP) is essential for dense body formation and functional maturation of AZs. Using a proteomics approach, we identified Drosophila Syd-1 (DSyd-1) as a BRP binding partner. In vivo imaging shows that DSyd-1 arrives early at nascent AZs together with DLiprin-alpha, and both proteins localize to the AZ edge as the AZ matures. Mutants in dsyd-1 form smaller terminals with fewer release sites, and release less neurotransmitter. The remaining AZs are often large and misshapen, and ectopic, electron-dense accumulations of BRP form in boutons and axons. Furthermore, glutamate receptor content at PSDs increases because of excessive DGluRIIA accumulation. The AZ protein DSyd-1 is needed to properly localize DLiprin-alpha at AZs, and seems to control effective nucleation of newly forming AZs together with DLiprin-alpha. DSyd-1 also organizes trans-synaptic signaling to control maturation of PSD composition independently of DLiprin-alpha.","authors":"Owald, D., Fouquet, W., Schmidt, M., Wichmann, C., Mertel, S., Depner, H., Christiansen, F., Zube, C., Quentin, C., K\u00f6rner, J., Urlaub, H., Mechtler, K., Sigrist, SJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Cell Biol","volume":"188","issue":"4","page":"565-79","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20123906","title":"Polycomb complexes act redundantly to repress genomic repeats and genes.","abstract":"Polycomb complexes establish chromatin modifications for maintaining gene repression and are essential for embryonic development in mice. Here we use pluripotent embryonic stem (ES) cells to demonstrate an unexpected redundancy between Polycomb-repressive complex 1 (PRC1) and PRC2 during the formation of differentiated cells. ES cells lacking the function of either PRC1 or PRC2 can differentiate into cells of the three germ layers, whereas simultaneous loss of PRC1 and PRC2 abrogates differentiation. On the molecular level, the differentiation defect is caused by the derepression of a set of genes that is redundantly repressed by PRC1 and PRC2 in ES cells. Furthermore, we find that genomic repeats are Polycomb targets and show that, in the absence of Polycomb complexes, endogenous murine leukemia virus elements can mobilize. This indicates a contribution of the Polycomb group system to the defense against parasitic DNA, and a potential role of genomic repeats in Polycomb-mediated gene regulation.","authors":"Leeb, M., Pasini, D., Novatchkova, M., Jaritz, M., Helin, K., Wutz, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Genes Dev","volume":"24","issue":"3","page":"265-76","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20217869","title":"QIKS--Quantitative identification of kinase substrates.","abstract":"Signaling networks regulate cellular responses to external stimuli through post-translational modifications such as protein phosphorylation. Phosphoproteomics facilitate the large-scale identification of kinase substrates. Yet, the characterization of critical connections within these networks and the identification of respective kinases remain the major analytical challenge. To address this problem, we present a novel approach for the identification of direct kinase substrates using chemical genetics in combination with quantitative phosphoproteomics. Quantitative identification of kinase substrates (QIKS) is a novel-screening platform developed for the proteome-wide substrate-analysis of specific kinases. Here, we aimed to identify substrates of mitogen-activated protein kinase\/Erk kinase (Mek1), an essential kinase in the mitogen-activated protein kinase cascade. An ATP analog-sensitive mutant of Mek1 (Mek1-as) was incubated with a cell extract from Mek1 deficient cells. Phosphorylated proteins were analyzed by LC-MS\/MS of IMAC-enriched phosphopeptides, labeled differentially for relative quantification. The identification of extracellular regulated kinase 1\/2 as the sole cytoplasmic substrates of MEK1 validates the applicability of this approach and suggests that QIKS could be used to identify substrates of a wide variety of kinases.","authors":"Morandell, S., Grosstessner-Hain, K., Roitinger, E., Hudecz, O., Lindhorst, T., Teis, D., Wrulich, OA., Mazanek, M., Taus, T., Ueberall, F., Mechtler, K., Huber, LA.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proteomics","volume":"10","issue":"10","page":"2015-25","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22566683","title":"Kruppel-like factor 1 (KLF1), KLF2, and Myc control a regulatory network essential for embryonic erythropoiesis.","abstract":"The Kr\u00fcppel-like factor 1 (KLF1) and KLF2 positively regulate embryonic \u03b2-globin expression and have additional overlapping roles in embryonic (primitive) erythropoiesis. KLF1(-\/-) KLF2(-\/-) double knockout mice are anemic at embryonic day 10.5 (E10.5) and die by E11.5, in contrast to single knockouts. To investigate the combined roles of KLF1 and KLF2 in primitive erythropoiesis, expression profiling of E9.5 erythroid cells was performed. A limited number of genes had a significantly decreasing trend of expression in wild-type, KLF1(-\/-), and KLF1(-\/-) KLF2(-\/-) mice. Among these, the gene for Myc (c-Myc) emerged as a central node in the most significant gene network. The expression of the Myc gene is synergistically regulated by KLF1 and KLF2, and both factors bind the Myc promoters. To characterize the role of Myc in primitive erythropoiesis, ablation was performed specifically in mouse embryonic proerythroblast cells. After E9.5, these embryos exhibit an arrest in the normal expansion of circulating red cells and develop anemia, analogous to KLF1(-\/-) KLF2(-\/-) embryos. In the absence of Myc, circulating erythroid cells do not show the normal increase in \u03b1- and \u03b2-like globin gene expression but, interestingly, have accelerated erythroid cell maturation between E9.5 and E11.5. This study reveals a novel regulatory network by which KLF1 and KLF2 regulate Myc to control the primitive erythropoietic program.","authors":"Pang, CJ., Lemsaddek, W., Alhashem, YN., Bondzi, C., Redmond, LC., Ah-Son, N., Dumur, CI., Archer, KJ., Haar, JL., Lloyd, JA., Trudel, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Mol Cell Biol","volume":"32","issue":"13","page":"2628-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20074523","title":"Drosophila genome-wide obesity screen reveals hedgehog as a determinant of brown versus white adipose cell fate.","abstract":"Over 1 billion people are estimated to be overweight, placing them at risk for diabetes, cardiovascular disease, and cancer. We performed a systems-level genetic dissection of adiposity regulation using genome-wide RNAi screening in adult Drosophila. As a follow-up, the resulting approximately 500 candidate obesity genes were functionally classified using muscle-, oenocyte-, fat-body-, and neuronal-specific knockdown in vivo and revealed hedgehog signaling as the top-scoring fat-body-specific pathway. To extrapolate these findings into mammals, we generated fat-specific hedgehog-activation mutant mice. Intriguingly, these mice displayed near total loss of white, but not brown, fat compartments. Mechanistically, activation of hedgehog signaling irreversibly blocked differentiation of white adipocytes through direct, coordinate modulation of early adipogenic factors. These findings identify a role for hedgehog signaling in white\/brown adipocyte determination and link in vivo RNAi-based scanning of the Drosophila genome to regulation of adipocyte cell fate in mammals.","authors":"Pospisilik, JA., Schramek, D., Schnidar, H., Cronin, SJ., Nehme, NT., Zhang, X., Knauf, C., Cani, PD., Aumayr, K., Todoric, J., Bayer, M., Haschemi, A., Puviindran, V., Tar, K., Orthofer, M., Neely, GG., Dietzl, G., Manoukian, A., Funovics, M., Prager, G., Wagner, O., Ferrandon, D., Aberger, F., Hui, CC., Esterbauer, H., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell","volume":"140","issue":"1","page":"148-60","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1711219","title":"Hormone-dependent transcriptional regulation and cellular transformation by Fos-steroid receptor fusion proteins.","abstract":"The protooncogene c-fos has been implicated in the control of proliferation and transformation of fibroblasts, and its protein product is an essential component of transcription factor AP1. The important target genes and, hence, the molecular mechanism of Fos function are, however, still unknown, partly due to the lack of a tightly regulated Fos-induction system. Here we show that different activities of the Fos protein can be controlled hormonally by fusing the mouse c-Fos protein to the ligand-binding domain of either the rat glucocorticoid or the human estrogen receptor. These fusion proteins stimulate AP1-dependent transcription and repress endogenous fos mRNA synthesis in a strictly hormone-dependent manner. Expression of these chimeric proteins in rat fibroblasts results in fast, reversible, and tightly controlled transformation in response to hormone. A Fos-estrogen receptor expressing cell line was used to isolate Fos-responsive genes by subtractive cDNA cloning. Run-on analysis of one of these genes showed that its transcription is rapidly and directly regulated by the hormone-activated Fos-estrogen receptor protein, demonstrating the potential of this induction system for identifying Fos target genes.","authors":"Superti-Furga, G., Bergers, G., Picard, D., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Proc Natl Acad Sci U S A","volume":"88","issue":"12","page":"5114-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1991-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19913286","title":"Meiotic chromosome homology search involves modifications of the nuclear envelope protein Matefin\/SUN-1.","abstract":"Genome haploidization during meiosis depends on recognition and association of parental homologous chromosomes. The C. elegans SUN\/KASH domain proteins Matefin\/SUN-1 and ZYG-12 have a conserved role in this process. They bridge the nuclear envelope, connecting the cytoplasm and the nucleoplasm to transmit forces that allow chromosome movement and homolog pairing and prevent nonhomologous synapsis. Here, we show that Matefin\/SUN-1 forms rapidly moving aggregates at putative chromosomal attachment sites in the meiotic transition zone (TZ). We analyzed requirements for aggregate formation and identified multiple phosphotarget residues in the nucleoplasmic domain of Matefin\/SUN-1. These CHK-2 dependent phosphorylations occur in leptotene\/zygotene, diminish during pachytene and are involved in pairing. Mimicking phosphorylation causes an extended TZ and univalents at diakinesis. Our data suggest that the properties of the nuclear envelope are altered during the time window when homologs are sorted and Matefin\/SUN-1 aggregates form, thereby controling the movement, homologous pairing and interhomolog recombination of chromosomes.","authors":"Penkner, AM., Fridkin, A., Gloggnitzer, J., Baudrimont, A., Machacek, T., Woglar, A., Csaszar, E., Pasierbek, P., Ammerer, G., Gruenbaum, Y., Jantsch, V.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"139","issue":"5","page":"920-33","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25595124","title":null,"abstract":null,"authors":"","publication_status":null,"journalpubyear":null,"journaltitle":null,"volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20184896","title":"Conversion of a regulatory into a degradative protease.","abstract":"The PDZ protease DegS senses mislocalized outer membrane proteins and initiates the sigmaE pathway in the bacterial periplasm. This unfolded protein response pathway is activated by processing of the anti-sigma factor RseA by DegS and other proteases acting downstream of DegS. DegS mediates the rate-limiting step of sigma E induction and its activity must be highly specific and tightly regulated. While DegS is structurally and biochemically well studied, the determinants of its pronounced substrate specificity are unknown. We therefore performed swapping experiments by introducing elements of the homologous but unspecific PDZ protease DegP. Introduction of loop L2 of DegP into DegS converted the enzyme into a non-specific protease, while swapping of PDZ domains did not. Therefore, loop L2 of the protease domain is a key determinant of substrate specificity. Interestingly, swapping of loop L2 did not affect the tight regulation of DegS. In addition, the combined introduction of loop L2 and PDZ domain 1 of DegP into DegS converted DegS even further into a DegP-like protease. These and other data suggest that homologous enzymes with distinct activities and regulatory features can be converted by simple genetic modifications.","authors":"Hasenbein, S., Meltzer, M., Hauske, P., Kaiser, M., Huber, R., Clausen, T., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Mol Biol","volume":"397","issue":"4","page":"957-66","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20227268","title":"STAT5 in B cell development and leukemia.","abstract":"Early B cell development depends on a network of transcription factors, whereby E2A and EBF1 regulate B cell specification and Pax5 controls B-lineage commitment. In contrast, activation of the transcription factor STAT5 in response to IL-7R signaling promotes cell survival by activating the prosurvival gene Mcl1 and orders immunoglobulin gene rearrangement by repressing Igk recombination in pro-B cells. Subsequently, it cooperates with the pre-B cell receptor to facilitate pre-B cell expansion. STAT5 also plays a key role in the generation of B cell precursor acute lymphoblastic leukemia, whereby the BCR-ABL1 translocation or the collaboration of JAK2 mutations with overexpression of the thymic stromal lymphopoietin receptor CRLF2 results in constitutive STAT5 activation leading to cytokine-independent survival and growth of leukemic cells.","authors":"Malin, S., McManus, S., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Curr Opin Immunol","volume":"22","issue":"2","page":"168-76","pdf":null,"JrId":"1461","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1702881","title":"MAP2 kinase and 70K S6 kinase lie on distinct signalling pathways.","abstract":"Activation of protein synthesis is required for quiescent cells to transit the cell cycle, and seems to be mediated in part by phosphorylation of the 40S ribosomal protein, S6. A mitogen-activated S6 kinase of relative molecular mass 70,000 (70K) has been isolated from mouse fibroblasts as well as from avian, rat and rabbit tissues. Comparison of complementary DNA sequences shows that this enzyme is distinct from S6 kinase II (92K) found in Xenopus eggs and fibroblasts. Both kinases are activated by serine\/threonine phosphorylation, suggesting that at least one serine\/threonine kinase links receptor tyrosine kinases with S6 kinases. A candidate for this link is MAP2 kinase, which is rapidly activated by tyrosine\/threonine phosphorylation following mitogenic stimulation. Incubation of MAP2 kinase from insulin-treated 3T3-L1 adipocytes with phosphatase-inactivated S6 kinase II from Xenopus leads to partial reactivation and phosphorylation of the enzyme. These and other findings have led to the suggestion that MAP2 kinase also activates the 70K S6 kinase. Here we refute this idea by showing that the two kinases lie on distinct signalling pathways.","authors":"Ballou, LM., Luther, H., Thomas, G.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Nature","volume":"349","issue":"6307","page":"348-50","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1991-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"102","title":"Urinary alpha-L-fucosidase.","abstract":"","authors":"Ng, WG., Donnell, GN., Koch, R., Bergren, WR.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Birth Defects Orig Artic Ser","volume":"11","issue":"6","page":"335-9","pdf":null,"JrId":"1208","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8384702","title":"MAP kinase-related FUS3 from S. cerevisiae is activated by STE7 in vitro.","abstract":"Pheromone-stimulated haploid yeast cells undergo a differentiation process that allows them to mate. Transmission of the intracellular signal involves threonine and tyrosine phosphorylation of the redundant FUS3 and KSS1 kinases, which are members of the MAP kinase family. FUS3\/KSS1 phosphorylation depends on two additional kinases, STE11 and STE7 (refs 2, 5, 6). Genetic analyses predict an ordered pathway where STE11 acts before STE7 and FUS3\/KSS1 (refs 2, 7). Here we report that STE7 is a dual-specificity kinase that modifies FUS3 at the appropriate sites and stimulates its catalytic activity in vitro. From these data and previous genetic results, we argue that STE7 is the physiological activator of FUS3. Recent indications that MAP kinase activators are related to STE7 suggest that signal transduction pathways in many, if not all, eukaryotic organisms use homologous kinase cascades.","authors":"Errede, B., Gartner, A., Zhou, Z., Nasmyth, K., Ammerer, G.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Nature","volume":"362","issue":"6417","page":"261-4","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1993-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19285466","title":"Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors.","abstract":"Most heritable behavioral traits have a complex genetic basis, but few multigenic traits are understood at a molecular level. Here we show that the C. elegans strains N2 and CB4856 have opposite behavioral responses to simultaneous changes in environmental O(2) and CO(2). We identify two quantitative trait loci (QTL) that affect this trait and map each QTL to a single-gene polymorphism. One gene, npr-1, encodes a previously described neuropeptide receptor whose high activity in N2 promotes CO(2) avoidance. The second gene, glb-5, encodes a neuronal globin domain protein whose high activity in CB4856 modifies behavioral responses to O(2) and combined O(2)\/CO(2) stimuli. glb-5 acts in O(2)-sensing neurons to increase O(2)-evoked calcium signals, implicating globins in sensory signaling. An analysis of wild C. elegans strains indicates that the N2 alleles of npr-1 and glb-5 arose recently in the same strain background, possibly as an adaptation to laboratory conditions.","authors":"McGrath, PT., Rockman, MV., Zimmer, M., Jang, H., Macosko, EZ., Kruglyak, L., Bargmann, CI.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Neuron","volume":"61","issue":"5","page":"692-9","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8371760","title":"c-jun is essential for normal mouse development and hepatogenesis.","abstract":"The proto-oncogene c-jun is the cellular homologue of v-jun, the transforming oncogene of the avian sarcoma virus 17 (ref. 1). c-jun encodes one major component of the AP-1 transcription factor complex and is expressed in many organs during mouse development and in the adult. Because of its rapid induction in cells following growth stimulation and the presence of AP-1 binding sites in the promoter regions of many genes, the c-Jun protein is thought to have important functions in cell proliferation and differentiation. But embryonic stem (ES) cells lacking c-Jun are viable and have a normal in vitro differentiation capacity, although c-Jun appears to be important for growth of teratocarcinomas in vivo. To define the function of c-jun better, targeted ES cells were used to generate mice lacking c-Jun. Here we report that heterozygous mutant mice appear normal, but embryos lacking c-Jun die at mid- to late-gestation and exhibit impaired hepatogenesis, altered fetal liver erythropoiesis and generalized oedema. Interestingly, c-jun-\/- ES cells can participate efficiently in the development of all somatic cells in chimaeric mice except liver cells, further suggesting an essential function of c-Jun in hepatogenesis.","authors":"Hilberg, F., Aguzzi, A., Howells, N., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Nature","volume":"365","issue":"6442","page":"179-81","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1993-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22522502","title":"Why are epididymal tumours so rare?","abstract":"Epididymal tumour incidence is at most 0.03% of all male cancers. It is an enigma why the human epididymis does not often succumb to cancer, when it expresses markers of stem and cancer cells, and constitutively expresses oncogenes, pro-proliferative and pro-angiogenic factors that allow tumour cells to escape immunosurveillance in cancer-prone tissues. The privileged position of the human epididymis in evading tumourigenicity is reflected in transgenic mouse models in which induction of tumours in other organs is not accompanied by epididymal neoplasia. The epididymis appears to: (i) prevent tumour initiation (it probably lacks stem cells and has strong anti-oxidative mechanisms, active tumour suppressors and inactive oncogene products); (ii) foster tumour monitoring and destruction (by strong immuno-surveillance and -eradication, and cellular senescence); (iii) avert proliferation and angiogenesis (with persistent tight junctions, the presence of anti-angiogenic factors and misplaced pro-angiogenic factors), which together (iv) promote dormancy and restrict dividing cells to hyperplasia. Epididymal cells may be rendered non-responsive to oncogenic stimuli by the constitutive expression of factors generally inducible in tumours, and resistant to the normal epididymal environment, which mimics that of a tumour niche promoting tumour growth. The threshold for tumour initiation may thus be higher in the epididymis than in other organs. Several anti-tumour mechanisms are those that maintain spermatozoa quiescent and immunologically silent, so the low incidence of cancer in the epididymis may be a consequence of its role in sperm maturation and storage. Understanding these mechanisms may throw light on cancer prevention and therapy in general.","authors":"Yeung, CH., Wang, K., Cooper, TG.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Asian J Androl","volume":"14","issue":"3","page":"465-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19948116","title":"Multiscale analysis of dynamics and interactions of heterochromatin protein 1 by fluorescence fluctuation microscopy.","abstract":"Heterochromatin protein 1 (HP1) is a central factor in establishing and maintaining the repressive heterochromatin state. To elucidate its mobility and interactions, we conducted a comprehensive analysis on different time and length scales by fluorescence fluctuation microscopy in mouse cell lines. The local mobility of HP1alpha and HP1beta was investigated in densely packed pericentric heterochromatin foci and compared with other bona fide euchromatin regions of the nucleus by fluorescence bleaching and correlation methods. A quantitative description of HP1alpha\/beta in terms of its concentration, diffusion coefficient, kinetic binding, and dissociation rate constants was derived. Three distinct classes of chromatin-binding sites with average residence times t(res) &lt;or= 0.2 s (class I, dominant in euchromatin), 7 s (class II, dominant in heterochromatin), and approximately 2 min (class III, only in heterochromatin) were identified. HP1 was present at low micromolar concentrations at heterochromatin foci, and required histone H3 lysine 9 methylases Suv39h1\/2 for two- to fourfold enrichment at these sites. These findings impose a number of constraints for the mechanism by which HP1 is able to maintain a heterochromatin state.","authors":"M\u00fcller, KP., Erdel, F., Caudron-Herger, M., Marth, C., Fodor, BD., Richter, M., Scaranaro, M., Beaudouin, J., Wachsmuth, M., Rippe, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Biophys J","volume":"97","issue":"11","page":"2876-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8322518","title":"Identification of a gene encoding a novel zinc finger protein in Saccharomyces cerevisiae.","abstract":"In the course of a comprehensive genomic screen for cell cycle regulated genes in the yeast Saccharomyces cerevisiae (Price et al., 1991) we identified and characterized a transcriptional unit encoding a putative zinc finger protein named FZF1 (EMBL accession number: X67787). This gene encodes a protein containing five zinc fingers of the Cys2His2 class, three of which are positioned in tandem at the N-terminus. The fourth and fifth finger follow after an interruption of 61 and 66 amino acids, respectively. While FZF1 is constitutively expressed at a very low level, its deletion is not essential for growth. Its similarity with known transcription factors, however, suggests that the FZF1 gene product may serve as a transcription factor in yeast.","authors":"Breitwieser, W., Price, C., Schuster, T.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Yeast","volume":"9","issue":"5","page":"551-6","pdf":null,"JrId":"8252","fulltextlink":null,"preprintlink":null,"articledate":"1993-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19950018","title":"Novel functions of RANK(L) signaling in the immune system.","abstract":"The TNF family members RANKL and its receptor RANK have initially been described as factors expressed on T cells and dendritic cells (DCs), respectively, and have been shown to augment the ability of DCs to stimulate naive T cell proliferation and enhance DC survival. Since another, yet soluble receptor for RANKL, namely OPG, was initially characterized as a factor inhibiting osteoclast development and bone resorption, it was somewhat enigmatic at first why one and the same genes would be essential both for the immune system and bone development - two processes that on first sight do not have much in common. However, in a series of experiments it was conclusively shown that RANKL-expressing T cells can also activate RANK-expressing osteoclasts, and thereby in principal mimicking RANKL-expressing osteoblasts. These findings lead to a paradigm shift and helped to coin the term osteoimmunology in order to account for the crosstalk of immune cells and bone. More importantly was that these findings also provided a rationale for the bone loss observed in patients with a chronically activated immune system such as in rheumatoid arthritis, leukemias, or the like, arguing that T cells, which were activated during the course of the disease to fight it off, also express RANKL, which induces osteoclastogenesis and thereby shifts the intricate balance of bone deposition and resorption in favor of the latter. Through knockout mice it became also clear that the RANKL-RANK-OPG system is involved in other processes such as in controlling autoimmunity or immune responses in the skin. We will briefly summarize the role of RANK(L) signaling in the immune system before we discuss some of the recent data we and others have obtained on the role of RANK(L) in controlling autoimmunity and immune responses in the skin.","authors":"Leibbrandt, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Adv Exp Med Biol","volume":"658","issue":null,"page":"77-94","pdf":null,"JrId":"280","fulltextlink":null,"preprintlink":null,"articledate":"2011-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8306970","title":"The N-terminal domain of a rab protein is involved in membrane-membrane recognition and\/or fusion.","abstract":"Proteins of the YPT1\/SEC4\/rab family are well documented to be involved in the regulation of membrane transport. We have previously reported that rab5 regulates endosome-endosome recognition and\/or fusion in vitro. Here, we show that this process depends on the rab5 N-terminal domain. Treatment of early endosomal membranes at a low trypsin concentration essentially abolished fusion and cleaved rab5 to a 1 kDa smaller polypeptide. Two-dimensional gel analysis suggested that rab5 is one of the few, if not the only, polypeptides cleaved by trypsin under these conditions. Whereas endosome fusion could be stimulated by cytosol prepared from cells overexpressing rab5 (and thus containing high amounts of the protein), this stimulation was abolished by trypsin-treatment of the cytosol. Trypsin-treated cytosol prepared from mock-transfected cells, which contains very low amounts of rab5, showed no inhibitory activity indicating that rab5 is the target of trypsin in these experiments. Purified rab5 prepared after expression in Escherichia coli was treated with trypsin, which cleaved the protein at the N-terminus. A synthetic peptide of rab5 N-terminal domain inhibited endosome fusion in our cell-free assay. A version of the same peptide truncated at the N-terminus or a peptide of rab3 N-terminal domain were without effects. Altogether, these observations suggest that the N-terminal domain of rab5 is involved in the process of early endosome recognition and\/or fusion, presumably because it interacts with another component of the transport machinery.","authors":"Steele-Mortimer, O., Clague, MJ., Huber, LA., Chavrier, P., Gruenberg, J., Gorvel, JP.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"EMBO J","volume":"13","issue":"1","page":"34-41","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1994-03-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23032091","title":"Van der Waals interactions in advanced materials, in memory of David C Langreth.","abstract":"","authors":"Hyldgaard, P., Rahman, TS.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Phys Condens Matter","volume":"24","issue":"42","page":"420201","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20007453","title":"Tumor necrosis factor induces matrix metalloproteinases in cardiomyocytes and cardiofibroblasts differentially via superoxide production in a PI3Kgamma-dependent manner.","abstract":"Tumor necrosis factor (TNF) is an inflammatory cytokine that is upregulated in a number of cardiomyopathies. Adverse cardiac remodeling and dilation result from degradation of the extracellular matrix by matrix metalloproteinases (MMPs). We investigated whether TNF can directly trigger expression and activation of MMPs in cardiac cells. We compared MMP expression profile and activities between primary cultures of mouse neonatal cardiomyocytes and cardiofibroblasts and in cellular and extracellular compartments. In response to recombinant TNF (rTNF, 20 ng\/ml), cardiomyocytes exhibited faster and more pronounced superoxide production compared with cardiofibroblasts, concomitant with increased expression of several MMPs. MMP9 levels increased more rapidly and about twofold more in cardiomyocytes than in cardiofibroblasts. TNF did not induce MMP2 expression. Expression of collagenases (MMP8, MMP12, MMP13, and MMP14) increased significantly, while total collagenase activity increased to a greater degree in conditioned medium of cardiomyocytes than in cardiofibroblasts. rTNF-mediated MMP expression and activation were dependent on superoxide production and were blocked by apocynin, an NADPH oxidase inhibitor. We identified phosphatidylinositol 3-kinase (PI3K)gamma as a key factor in TNF-mediated events since TNF-induced superoxide production, MMP expression, and activity were significantly suppressed in cardiomyocytes and cardiofibroblasts deficient in PI3Kgamma. We further demonstrated that the TNF-superoxide-MMP axis of events is in fact activated in heart disease in vivo. Wild-type and TNF(-\/-) mice subjected to cardiac pressure overload revealed that TNF deficiency resulted in reduced superoxide levels, collagenase activities, PI3K activity, and fibrosis leading to attenuated cardiac dilation and dysfunction. Our study demonstrates that TNF triggers expression and activation of MMPs faster and stronger in cardiomyocytes than in cardiofibroblasts in a superoxide-dependent manner and via activation of PI3Kgamma, thereby contributing to adverse myocardial remodeling in disease.","authors":"Awad, AE., Kandalam, V., Chakrabarti, S., Wang, X., Penninger, JM., Davidge, ST., Oudit, GY., Kassiri, Z.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Am J Physiol Cell Physiol","volume":"298","issue":"3","page":"C679-92","pdf":null,"JrId":"21623","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9778245","title":"Negative regulation of PKB\/Akt-dependent cell survival by the tumor suppressor PTEN.","abstract":"PTEN is a tumor suppressor with sequence homology to protein tyrosine phosphatases and the cytoskeletal protein tensin. mPTEN-mutant mouse embryos display regions of increased proliferation. In contrast, mPTEN-deficient immortalized mouse embryonic fibroblasts exhibit decreased sensitivity to cell death in response to a number of apoptotic stimuli, accompanied by constitutively elevated activity and phosphorylation of protein kinase B\/Akt, a crucial regulator of cell survival. Expression of exogenous PTEN in mutant cells restores both their sensitivity to agonist-induced apoptosis and normal pattern of PKB\/Akt phosphorylation. Furthermore, PTEN negatively regulates intracellular levels of phosphatidylinositol (3,4,5) trisphosphate in cells and dephosphorylates it in vitro. Our results show that PTEN may exert its role as a tumor suppressor by negatively regulating the PI3'K\/PKB\/Akt signaling pathway.","authors":"Stambolic, V., Suzuki, A., de la Pompa, JL., Brothers, GM., Mirtsos, C., Sasaki, T., Ruland, J., Penninger, JM., Siderovski, DP., Mak, TW.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Cell","volume":"95","issue":"1","page":"29-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9759859","title":"Impaired TCR-mediated apoptosis and Bcl-XL expression in T cells lacking the stress kinase activator SEK1\/MKK4.","abstract":"The dual specificity kinase SEK1 (MKK4) is a direct activator of stress-activated protein kinases (SAPK\/JNK) in response to environmental stresses or mitogenic factors. We show in Sek1(-\/-)Rag(-\/-) chimeric mice that a Sek1 null mutation augments the susceptibility of peripheral T cells to TCR\/CD3 religation-induced apoptosis. Sek1(-\/-) T cells failed to induce expression of the death suppressor Bcl-XL in response to Ag receptor activation. The Sek1 mutation did not alter the induction of apoptosis in response to etoposide, cisplatinum, Adriamycin, and gamma-irradiation. Moreover, we show that CD3epsilon activation alone leads to SEK1 activation in Sek1(+\/+) T cells. These results suggest that SEK1 transduces cellular survival signals during T cell stimulation.","authors":"Nishina, H., Radvanyi, L., Raju, K., Sasaki, T., Kozieradzki, I., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Immunol","volume":"161","issue":"7","page":"3416-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9736711","title":"Transformation of hematopoietic cells by the Ski oncoprotein involves repression of retinoic acid receptor signaling.","abstract":"The Ski oncogene has dramatic effects on the differentiation of several different cell types. It induces the differentiation of quail embryo cells into myoblasts and arrests the differentiation of chicken hematopoietic cells. The mechanism that Ski uses to carry out these disparate biological activities is unknown. However, we were struck by the similarity of these effects to those of certain members of the nuclear hormone receptor family. Both Ski and the thyroid hormone receptor-derived oncogene v-ErbA can arrest the differentiation of avian erythroblasts, and v-Ski-transformed avian multipotent progenitor cells resemble murine hematopoietic cells that express a dominant-negative form of the retinoic acid receptor, RARalpha. In this paper, we have tested the hypothesis that v-Ski and its cellular homologue c-Ski exert their effects by interfering with nuclear hormone receptor-induced transcription. We demonstrate that Ski associates with the RAR complex and can repress transcription from a retinoic acid response element. The physiological significance of this finding is demonstrated by the ability of high concentrations of a RARalpha-specific ligand to abolish v-Ski-induced transformation of the multipotent progenitors. These results strongly suggest that the ability of Ski to alter cell differentiation is caused in part by the modulation of RAR signaling pathways.","authors":"Dahl, R., Kieslinger, M., Beug, H., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Proc Natl Acad Sci U S A","volume":"95","issue":"19","page":"11187-92","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1998-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19948988","title":"Targeting the degradation of angiotensin II with recombinant angiotensin-converting enzyme 2: prevention of angiotensin II-dependent hypertension.","abstract":"Angiotensin (Ang)-converting enzyme 2 (ACE2) cleaves Ang II to form Ang-(1-7). Here we examined whether soluble human recombinant ACE2 (rACE2) can efficiently lower Ang II and increase Ang-(1-7) and whether rACE2 can prevent hypertension caused by Ang II infusion as a result of systemic versus local mechanisms of ACE2 activity amplification. rACE2 was infused via osmotic minipumps for 3 days in conscious mice or acutely in anesthetized mice. rACE2 caused a dose-dependent increase in serum ACE2 activity but had no effect on kidney or cardiac ACE2 activity. After Ang II infusion (40 pmol\/min), rACE2 (1 mg\/kg per day) resulted in normalization of systolic blood pressure and plasma Ang II. In acute studies, rACE2 (1 mg\/kg) prevented the rapid hypertensive effect of Ang II (0.2 mg\/kg), and this was associated with both a decrease in Ang II and an increase in Ang-(1-7) in plasma. Moreover, during infusion of Ang II, the effect of rACE2 on blood pressure was unaffected by a specific Ang-(1-7) receptor blocker, A779 (0.2 mg\/kg), and infusing supraphysiologic levels of Ang-(1-7) (0.2 mg\/kg) had no effect on blood pressure. We conclude that, during Ang II infusion, rACE2 effectively degrades Ang II and, in the process, normalizes blood pressure. The mechanism of rACE2 action results from an increase in systemic, not tissue, ACE2 activity and the lowering of plasma Ang II rather than the attendant increase in Ang-(1-7). Increasing ACE2 activity may provide a new therapeutic target in states of Ang II overactivity by enhancing its degradation, an approach that differs from the current focus on blocking Ang II formation and action.","authors":"Wysocki, J., Ye, M., Rodriguez, E., Gonz\u00e1lez-Pacheco, FR., Barrios, C., Evora, K., Schuster, M., Loibner, H., Brosnihan, KB., Ferrario, CM., Penninger, JM., Batlle, D.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Hypertension","volume":"55","issue":"1","page":"90-8","pdf":null,"JrId":"4217","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20466094","title":"Tuba8 is expressed at low levels in the developing mouse and human brain.","abstract":null,"authors":"Braun, A., Breuss, M., Salzer, MC., Flint, J., Cowan, NJ., Keays, DA.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Am J Hum Genet","volume":"86","issue":"5","page":"819-22; author reply 822-3","pdf":null,"JrId":"428","fulltextlink":null,"preprintlink":null,"articledate":"2010-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20422424","title":"MRE11 and COM1\/SAE2 are required for double-strand break repair and efficient chromosome pairing during meiosis of the protist Tetrahymena.","abstract":"Programmed DNA double-strand breaks (DSBs) are generated during meiosis to initiate homologous recombination. Various aspects of DSB formation, signaling, and repair are accomplished or governed by Mre11, a component of the MRN\/MRX complex, partially in cooperation with Com1\/Sae2\/CtIP. We used Tetrahymena to study evolutionarily conserved and changed functions of Mre11 and Com1. There is a difference between organisms with respect to the dependency of meiotic DSB formation on Mre11. By cytology and an electrophoresis-based assay for DSBs, we found that in Tetrahymena Mre11p is not required for the formation and ATR-dependent signaling of DSBs. Its dispensability is also reflected by wild-type-like DSB-dependent reorganization of the meiotic nucleus and by the phosphorylation of H2A.X in mre11\u2206 mutant. However, mre11\u2206 and com1\u2206 mutants are unable to repair DSBs, and chromosome pairing is reduced. It is concluded that, while MRE11 has no universal role in DNA damage signaling, its requirement for DSB repair is conserved between evolutionarily distant organisms. Moreover, reduced chromosome pairing in repair-deficient mutants reveals the existence of two complementing pairing processes, one by the rough parallel arrangement of chromosomes imposed by the tubular shape of the meiotic nucleus and the other by repair-dependent precise sequence matching.","authors":"Lukaszewicz, A., Howard-Till, RA., Novatchkova, M., Mochizuki, K., Loidl, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Chromosoma","volume":"119","issue":"5","page":"505-18","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20357003","title":"A domesticated piggyBac transposase plays key roles in heterochromatin dynamics and DNA cleavage during programmed DNA deletion in Tetrahymena thermophila.","abstract":"Transposons comprise large fractions of eukaryotic genomes and provide genetic reservoirs for the evolution of new cellular functions. We identified TPB2, a homolog of the piggyBac transposase gene that is required for programmed DNA deletion in Tetrahymena. TPB2 was expressed exclusively during the time of DNA excision, and its encoded protein Tpb2p was localized in DNA elimination heterochromatin structures. Notably, silencing of TPB2 by RNAi disrupts the final assembly of these heterochromatin structures and prevents DNA deletion to occur. In vitro studies revealed that Tpb2p is an endonuclease that produces double-strand breaks with four-base 5' protruding ends, similar to the ends generated during DNA deletion. These findings suggest that Tpb2p plays a key role in the assembly of specialized DNA elimination chromatin architectures and is likely responsible for the DNA cleavage step of programmed DNA deletion.","authors":"Cheng, CY., Vogt, A., Mochizuki, K., Yao, MC.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Mol Biol Cell","volume":"21","issue":"10","page":"1753-62","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-130","title":"Multifrequency parallelized near-field optical imaging with anistropic metal-dielectric stacks","abstract":null,"authors":"Elsayad, K., Heinze, KG.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Physical Review A","volume":"81","issue":"5","page":"","pdf":null,"JrId":null,"fulltextlink":"http:\/\/pra.aps.org\/abstract\/PRA\/v81\/i5\/e053840","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10781064","title":"The in vitro and in vivo phosphotyrosine map of activated MuSK.","abstract":"The muscle-specific receptor tyrosine kinase MuSK plays a crucial role in neuromuscular synapse formation. Activation of MuSK is induced by agrin leading to clustering of several proteins, including acetylcholine receptors, at synaptic sites. In a first step to elucidate the signal transduction cascade following MuSK activation and leading to clustering of synaptic proteins, we sought to identify the tyrosine residues that are phosphorylated in activated MuSK. We mapped the tyrosine residues that are phosphorylated in vitro and in vivo using methods that provide high sensitivity and do not require radioactive tracers. We expressed MuSK in insect cells by using a baculovirus expression vector and mapped the tyrosines that are phosphorylated in MuSK in an in vitro kinase assay using matrix-assisted laser desorption ionization MS to sequence tryptic peptides fractionated by HPLC. In addition, we isolated MuSK from Torpedo electric organ and used nanoelectrospray tandem mass spectrometry and parent ion scanning to identify the tyrosine residues that are phosphorylated in activated, endogenous MuSK in vivo. We found that six of the nineteen intracellular tyrosine residues in MuSK are phosphorylated in activated MuSK: the juxtamembrane tyrosine (Y553), the tyrosines within the activation loop (Y750, Y754, and Y755), a tyrosine near the beginning of the kinase domain (Y576), and a tyrosine (Y812) within the C-terminal lobe of the kinase domain. Our biochemical data are consistent with results from functional experiments and establish a good correlation between tyrosine residues that are phosphorylated in activated MuSK and tyrosines that are required for MuSK signaling.","authors":"Watty, A., Neubauer, G., Dreger, M., Zimmer, M., Wilm, M., Burden, SJ.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Proc Natl Acad Sci U S A","volume":"97","issue":"9","page":"4585-90","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2000-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20866433","title":"Internal dissipation of a polymer.","abstract":"The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics of a single chain in the absence of solvent to characterize the nature of this internal friction. We model the chains as freely hinged but with localized bond angles and threefold symmetric dihedral angles. We show that the damping is close but not identical to Kelvin damping, which depends on the first temporal and second spatial derivative of monomer position. With no internal potential between monomers, the magnitude of the damping is small for long wavelengths and weakly damped oscillatory time dependent behavior is seen for a large range of spatial modes. When the size of the internal potential is increased, such oscillations persist, but the damping becomes larger. However underdamped motion is present even with quite strong dihedral barriers for long enough wavelengths.","authors":"Deutsch, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Phys Rev E Stat Nonlin Soft Matter Phys","volume":"81","issue":"6 Pt 1","page":"061804","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1656369","title":"Expression of v-rel in a replication competent virus: transformation and biochemical characterization.","abstract":"The avian reticuloendotheliosis virus strain T (REV-T) transforms bone marrow cells and may cause phenotypic changes in fibroblasts. Both events are thought to result from expression of the v-rel oncoprotein, a member of the NF-kappa B family of transcription factors. Most REV stocks contain a cytopathic and immunosuppressive helper virus (REV-A) unrelated to standard avian retroviruses, and thus the degree to which v-rel expression alone contributes to the transformed phenotype in bone marrow cells and fibroblasts is complicated by helper virus expression. To gain a more accurate picture of how v-rel contributes to transformation, we have cloned the v-rel gene into a replication-competent avian retrovirus vector (RCAS) and have expressed it in both chick embryo fibroblasts (CEF) and bone marrow cells. Transfection of RCAS-rel into CEF readily produced a partially transformed phenotype, demonstrating that expression of the v-rel protein is sufficient for fibroblast transformation. The RCAS-rel virus also transformed bone marrow cells in vitro, but required culture conditions different from those normally required for transformation by REV-T. The v-rel protein expressed in transformed CEF was biochemically indistinguishable from that expressed in transformed bone marrow cells, being localized to the cytoplasm and the nucleus, and forming a complex with cellular proteins. We also demonstrate that the RCAS-rel-transformed hematopoietic cells exhibited a distinct differentiation phenotype.","authors":"Morrison, LE., Boehmelt, G., Beug, H., Enrietto, PJ.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Oncogene","volume":"6","issue":"9","page":"1657-66","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1991-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12973358","title":"EphB-ephrinB bi-directional endocytosis terminates adhesion allowing contact mediated repulsion.","abstract":"Eph receptors and their membrane-associated ephrin ligands mediate cell-cell repulsion to guide migrating cells and axons. Repulsion requires that the ligand-receptor complex be removed from the cell surface, for example by proteolytic processing of the ephrin ectodomain. Here we show that cell contact-induced EphB-ephrinB complexes are rapidly endocytosed during the retraction of cells and neuronal growth cones. Endocytosis occurs in a bi-directional manner that comprises of full-length receptor and ligand complexes. Endocytosis is sufficient to promote cell detachment and seems necessary for axon withdrawal during growth cone collapse. Here, we show a mechanism for the termination of adhesion and the promotion of cell repulsion after intercellular (trans) interaction between two transmembrane proteins.","authors":"Zimmer, M., Palmer, A., K\u00f6hler, J., Klein, R.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nat Cell Biol","volume":"5","issue":"10","page":"869-78","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2003-11-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21210653","title":"Molecular properties from conformational ensembles. 1. Dipole moments of molecules with multiple internal rotations.","abstract":"We present a novel method for constructing the stable conformational space of small molecules with many rotatable bonds that uses our iterative stochastic elimination (ISE) algorithm, a robust stochastic search method capable of finding ensembles of best solutions for large combinatorial problems. To validate the method, we show that ISE reproduces the best conformers found in a fully exhaustive search, as well as compare computed dipole moments to experimental values, based on molecular ensembles and their Boltzmann distributions. Results were also compared to the alternative molecular dynamics and simulated annealing methods. Our results clarify that many low energy conformations may be required to reproduce molecular properties, while single low energy conformers or ensembles of low energy conformers cannot account for the experimental properties of flexible molecules. Whereas ISE well reproduces conformations that are not separated by very large energy barriers, it has not been successful in reproducing conformations of strained molecules.","authors":"Lavy, T., Harries, D., Goldblum, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Phys Chem A","volume":"115","issue":"23","page":"5794-809","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20350779","title":"NF-kappaB promotes epithelial-mesenchymal transition, migration and invasion of pancreatic carcinoma cells.","abstract":"The transcription factor NF-kappaB is constitutively active in pancreatic adenocarcinoma. Here we explore the contribution of NF-kappaB to the malignant phenotype of pancreatic cancer cells in addition to its anti-apoptotic role. Block of NF-kappaB signalling by non-destructible IkappaBalpha rendered cells resistant to TGF-beta-induced epithelial-mesenchymal transition (EMT). In contrast, NF-kappaB activation by TNF-alpha or expression of constitutively active IKK2 induced an EMT-phenotype with up-regulation of vimentin and ZEB1, and down-regulation of E-cadherin. EMT could also be induced in cells with defective TGF-beta signalling. Functional assays demonstrated reduced or strongly enhanced migration and invasion upon NF-kappaB inhibition or activation, respectively.","authors":"Maier, HJ., Schmidt-Strassburger, U., Huber, MA., Wiedemann, EM., Beug, H., Wirth, T.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cancer Lett","volume":"295","issue":"2","page":"214-28","pdf":null,"JrId":"2780","fulltextlink":null,"preprintlink":null,"articledate":"2010-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20471268","title":"Sex peptide receptor and neuronal TOR\/S6K signaling modulate nutrient balancing in Drosophila.","abstract":"Animals often decide between alternative actions according to their current needs, and hence the value they assign to each of the competing options. This process is of special relevance during nutrient balancing, in which animals choose between different food sources according to their current nutritional state. How such value-based decision making is implemented at the molecular and neuronal level in the brain is not well understood. Here we describe Drosophila melanogaster food choice as a genetically tractable model to study value-based decision making in the context of nutrient balancing. When faced with a choice between yeast and an alternative food source, flies deprived of protein prefer the yeast. We show here that mating status is a critical modulator of this decision-making process in females and that it relies on the action of the sex peptide receptor in internal ppk(+) sensory neurons. Neuronal TOR\/S6K function is another critical input to this decision, possibly signaling the fly's current nutritional status. We propose that the brain uses these internal states to assign value to external sensory information from potential food sources, thereby guiding food choice and ensuring nutrient homeostasis.","authors":"Ribeiro, C., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Curr Biol","volume":"20","issue":"11","page":"1000-5","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20941426","title":"Internal dynamics in complexes of water with organic molecules. Details of the internal motions in tert-butylalcohol-water.","abstract":"The peculiar propensity of water to have a high internal dynamic activity in its molecular complexes with organic molecules is described in this paper. Often, the corresponding large amplitude motions are reflected in the tunnelling splittings of the rotational transitions which, in turn, provide information for the determination of the potential energy surfaces and of the noncovalent interactions of water with a variety of atoms and\/or functional groups. A classification of this kind of molecular complexes is given, also in relation to the tunnelling features of the rotational spectra. As a specific example, the rotational spectrum of tert-butylalcohol-water, investigated by Fourier transform microwave spectroscopy, is reported. Details are given of the large amplitude motions which take place in the adduct, the internal rotation of the hydroxyl group and the oscillations of the water molecule, by interpreting the experimental data with a flexible model.","authors":"Evangelisti, L., Caminati, W.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Phys Chem Chem Phys","volume":"12","issue":"43","page":"14433-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20360735","title":"Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes.","abstract":"Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life. To start to fill this gap we developed a high-throughput phenotypic screening platform combining potent gene silencing by RNA interference, time-lapse microscopy and computational image processing. We carried out a genome-wide phenotypic profiling of each of the approximately 21,000 human protein-coding genes by two-day live imaging of fluorescently labelled chromosomes. Phenotypes were scored quantitatively by computational image processing, which allowed us to identify hundreds of human genes involved in diverse biological functions including cell division, migration and survival. As part of the Mitocheck consortium, this study provides an in-depth analysis of cell division phenotypes and makes the entire high-content data set available as a resource to the community.","authors":"Neumann, B., Walter, T., H\u00e9rich\u00e9, JK., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U., Cetin, C., Sieckmann, F., Pau, G., Kabbe, R., W\u00fcnsche, A., Satagopam, V., Schmitz, MH., Chapuis, C., Gerlich, DW., Schneider, R., Eils, R., Huber, W., Peters, JM., Hyman, AA., Durbin, R., Pepperkok, R., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nature","volume":"464","issue":"7289","page":"721-7","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2010-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20479465","title":"The Dam1 complex confers microtubule plus end-tracking activity to the Ndc80 kinetochore complex.","abstract":"Kinetochores must remain associated with microtubule ends, as they undergo rapid transitions between growth and shrinkage. The molecular basis for this essential activity that ensures correct chromosome segregation is unclear. In this study, we have used reconstitution of dynamic microtubules and total internal reflection fluorescence microscopy to define the functional relationship between two important budding yeast kinetochore complexes. We find that the Dam1 complex is an autonomous plus end-tracking complex. The Ndc80 complex, despite being structurally related to the general tip tracker EB1, fails to recognize growing ends efficiently. Dam1 oligomers are necessary and sufficient to recruit Ndc80 to dynamic microtubule ends, where both complexes remain continuously associated. The interaction occurs specifically in the presence of microtubules and is subject to regulation by Ipl1 phosphorylation. These findings can explain how the force harvested by Dam1 is transmitted to the rest of the kinetochore via the Ndc80 complex.","authors":"Lampert, F., Hornung, P., Westermann, S.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Cell Biol","volume":"189","issue":"4","page":"641-9","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2010-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8188742","title":"ADP ribosylation factor and a 14-kD polypeptide are associated with heparan sulfate-carrying post-trans-Golgi network secretory vesicles in rat hepatocytes.","abstract":"Constitutive secretory vesicles carrying heparan sulfate proteoglycan (HSPG) were identified in isolated rat hepatocytes by pulse-chase experiments with [35S]sulfate and purified by velocity-controlled sucrose gradient centrifugation followed by equilibrium density centrifugation in Nycodenz. Using this procedure, the vesicles were separated from plasma membranes, Golgi, trans-Golgi network (TGN), ER, endosomes, lysosomes, transcytotic vesicles, and mitochondria. The diameter of these vesicles was approximately 100-200 nm as determined by electron microscopy. A typical coat structure as described for intra-Golgi transport vesicles or clathrin-coated vesicles could not be seen, and the vesicles were not associated with the coat protein beta-COP. Furthermore, the vesicles appear to represent a low density compartment (1.05-1.06 g\/ml). Other constitutively secreted proteins (rat serum albumin, apolipoprotein E, and fibrinogen) could not be detected in purified HSPG-carrying vesicles, but banded in the denser fractions of the Nycodenz gradient. Moreover, during pulse-chase labeling with [35S]methionine, labeled albumin did not appear in the post-TGN vesicle fraction carrying HSPGs. These findings indicate sorting of HSPGs and albumin into different types of constitutive secretory vesicles in hepatocytes. Two proteins were found to be tightly associated with the membranes of the HSPG carrying vesicles: a member of the ADP ribosylation factor family of small guanine nucleotide-binding proteins and an unknown 14-kD peripheral membrane protein (VAPP14). Concerning the secretory pathway, we conclude from these results that ADP ribosylation factor proteins are not only involved in vesicular transport from the ER via the Golgi to the TGN, but also in vesicular transport from the TGN to the plasma membrane.","authors":"Nickel, W., Huber, LA., Kahn, RA., Kipper, N., Barthel, A., Fasshauer, D., S\u00f6ling, HD.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"J Cell Biol","volume":"125","issue":"4","page":"721-32","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20545842","title":"Raman microspectroscopy reveals long-term extracellular activity of Chlamydiae.","abstract":"The phylum Chlamydiae consists exclusively of obligate intracellular bacteria. Some of them are formidable pathogens of humans, while others occur as symbionts of amoebae. These genetically intractable bacteria possess a developmental cycle consisting of replicative reticulate bodies and infectious elementary bodies, which are believed to be physiologically inactive. Confocal Raman microspectroscopy was applied to differentiate between reticulate bodies and elementary bodies of Protochlamydia amoebophila and to demonstrate in situ the labelling of this amoeba symbiont after addition of isotope-labelled phenylalanine. Unexpectedly, uptake of this amino acid was also observed for both developmental stages for up to 3 weeks, if incubated extracellularly with labelled phenylalanine, and P. amoebophila remained infective during this period. Furthermore, P. amoebophila energizes its membrane and performs protein synthesis outside of its host. Importantly, amino acid uptake and protein synthesis after extended extracellular incubation could also be demonstrated for the human pathogen Chlamydia trachomatis, which synthesizes stress-related proteins under these conditions as shown by 2-D gel electrophoresis and MALDI-TOF\/TOF mass spectrometry. These findings change our perception of chlamydial biology and reveal that host-free analyses possess a previously not recognized potential for direct experimental access to these elusive microorganisms.","authors":"Haider, S., Wagner, M., Schmid, MC., Sixt, BS., Christian, JG., H\u00e4cker, G., Pichler, P., Mechtler, K., M\u00fcller, A., Baranyi, C., Toenshoff, ER., Montanaro, J., Horn, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Mol Microbiol","volume":"77","issue":"3","page":"687-700","pdf":null,"JrId":"5753","fulltextlink":null,"preprintlink":null,"articledate":"2010-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20461749","title":"Methods and tools for the prediction of hydrodynamic coefficients and other solution properties of flexible macromolecules in solution. A tutorial minireview.","abstract":"The calculation of solution properties of flexible macromolecules and other nanoparticles requires, in addition to the hydrodynamic formalisms needed for the sedimentation coefficient and other transport properties, the consideration of the conformational statistics and internal dynamics. The latter aspects can be handled with simulation methods like Monte Carlo and Brownian dynamics. An example of a Monte Carlo simulation for a model specific of DNA is illustrated with results for the several solution properties over an extremely wide range of molecular weight. The convenience of having computational tools of a quite general applicability has prompted us to implement the simulation and hydrodynamic treatments in software packages, MONTEHYDRO for Monte Carlo, and SIMUFLEX for Brownian dynamics which-with a scope similar to the HYDRO suite for rigid particles-can handle a variety of situations. As an application of the new methodology to a yet unclear problem in analytical ultracentrifugation, in a simple application of the SIMUFLEX software, we present a simulation of the so-called anomalous sedimentation of very long DNA molecules, obtaining results for the experimentally observable rotor-speed-dependence of the sedimentation coefficient.","authors":"Garc\u00eda de la Torre, J., Ortega, A., Amor\u00f3s, D., Rodr\u00edguez Schmidt, R., Hern\u00e1ndez Cifre, JG.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Macromol Biosci","volume":"10","issue":"7","page":"721-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8188220","title":"Characterization of a region-specific library of microclones in the vicinity of the Bcg and splotch loci on mouse chromosome 1.","abstract":"The proximal portion of mouse chromosome 1 harbors a variety of mutant loci that have yet to be characterized at the molecular level. We have constructed a library of genomic DNA fragments from the proximal portion of mouse chromosome 1 by microdissection and microcloning techniques, with the aim of generating genetic markers in close proximity to some of these mutant loci. To facilitate the genetic mapping of 27 microclones from this library, we divided a 56-cM segment of chromosome 1 between the Col3a1 and Ren 1,2 genes into eight intervals defined by anchor loci. Restriction fragment length polymorphisms were determined for each of the microclones and their segregation with the anchor loci was followed in informative animals from a panel of 252 interspecific backcross mice (C57BL\/6J x Mus spretus) x C57BL\/6J. We were able to assign 26 of 27 (96%) randomly selected microclones to each of the defined chromosome 1 intervals. A total of eight microclones mapped within the large interstitial deletion found in the Spr mouse mutant. Two of these clones were found to be tightly linked to the host resistance locus Bcg and at least one was found to be linked to the neural tube defect mutant splotch. Other clones mapped to intervals containing several other mouse mutants. These novel DNA markers should aid in positional cloning strategies presently employed to identify these mutant loci. These clones should also be useful in the creation of both physical and YAC contiguous maps of the proximal portion of mouse chromosome 1.","authors":"Epstein, DJ., Bardeesy, N., Vidal, S., Malo, D., Weith, A., Vekemans, M., Gros, P.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Genomics","volume":"19","issue":"1","page":"163-6","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20515094","title":"Dynamics simulation of N(2) scattering onto W(100,110) surfaces: A stringent test for the recently developed flexible periodic London-Eyring-Polanyi-Sato potential energy surface.","abstract":"An efficient method to construct the six dimensional global potential energy surface (PES) for two atoms interacting with a periodic rigid surface, the flexible periodic London-Eyring-Polanyi-Sato model, has been proposed recently. The main advantages of this model, compared to state-of-the-art interpolated ab initio PESs developed in the past, reside in its global nature along with the small number of electronic structure calculations required for its construction. In this work, we investigate to which extent this global representation is able to reproduce the fine details of the scattering dynamics of N(2) onto W(100,110) surfaces reported in previous dynamics simulations based on locally interpolated PESs. The N(2)\/W(100) and N(2)\/W(110) systems are chosen as benchmarks as they exhibit very unusual and distinct dissociative adsorption dynamics although chemically similar. The reaction pathways as well as the role of dynamic trapping are scrutinized. Besides, elastic\/inelastic scattering dynamics including internal state and angular distributions of reflected molecules are also investigated. The results are shown to be in fair agreement with previous theoretical predictions.","authors":"Martin-Gondre, L., Crespos, C., Larregaray, P., Rayez, JC., van Ootegem, B., Conte, D.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Chem Phys","volume":"132","issue":"20","page":"204501","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20404563","title":"High-throughput knockout screen in Schizosaccharomyces pombe identifies a novel gene required for efficient homolog disjunction during meiosis I.","abstract":"Meiosis is the process which produces haploid gametes from diploid precursor cells. This reduction of chromosome number is achieved by two successive divisions. Whereas homologs segregate during meiosis I, sister chromatids segregate during meiosis II. To identify novel proteins required for proper segregation of chromosomes during meiosis, we applied a high-throughput knockout technique to delete 87 S. pombe genes whose expression is upregulated during meiosis and analyzed the mutant phenotypes. Using this approach, we identified a new protein, Dil1, which is required to prevent meiosis I homolog non-disjunction. We show that Dil1 acts in the dynein pathway to promote oscillatory nuclear movement during meiosis.","authors":"Rumpf, C., Cipak, L., Novatchkova, M., Li, Z., Polakova, S., Dudas, A., Kovacikova, I., Miadokova, E., Ammerer, G., Gregan, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell Cycle","volume":"9","issue":"9","page":"1802-8","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8179929","title":"Recombinant murine erythropoietin receptor expressed in avian erythroid progenitors mediates terminal erythroid differentiation in vitro.","abstract":"The biological activity of the recombinant murine erythropoietin receptor (muEpoR) has so far been ascertained only in nonerythroid, established cell lines ectopically expressing the exogenous receptor. Here we show that the regulation of proliferation and differentiation by the muEpoR can be studied in chicken erythroid cells capable of terminal differentiation. The cloned muEpoR was introduced into primary and immortalized chicken erythroblast clones transformed by conditional oncogenes, using retroviral gene transfer. After turning off oncoprotein function, these cells terminally differentiated in response to human erythropoietin (rhu-Epo), similar to cells treated with chicken anemic serum containing avian Epo. Control vector-containing erythroblasts were totally unresponsive to rhu-Epo, but differentiated normally in presence of avian Epo. The avian erythroblasts expressed biologically active muEpoR at physiological levels and bound rhu-Epo with similar high affinity as mammalian erythroblasts expressing endogenous EpoR. Finally, rhu-Epo synergized with insulin in these cells similar to avian Epo. Our results demonstrate that the exogenous muEpoR is able to mediate normal, terminal differentiation in avian erythroid progenitors.","authors":"Steinlein, P., Deiner, E., Leutz, A., Beug, H.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Growth Factors","volume":"10","issue":"1","page":"1-16","pdf":null,"JrId":"1632","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20018716","title":"Navigating molecular worms inside chemical labyrinths.","abstract":"Predicting whether a molecule can traverse chemical labyrinths of channels, tunnels, and buried cavities usually requires performing computationally intensive molecular dynamics simulations. Often one wants to screen molecules to identify ones that can pass through a given chemical labyrinth or screen chemical labyrinths to identify those that allow a given molecule to pass. Because it is impractical to test each molecule\/labyrinth pair using computationally expensive methods, faster, approximate methods are used to prune possibilities, \"triaging\" the ability of a proposed molecule to pass through the given chemical labyrinth. Most pruning methods estimate chemical accessibility solely on geometry, treating atoms or groups of atoms as hard spheres with appropriate radii. Here, we explore geometric configurations for a moving \"molecular worm,\" which replaces spherical probes and is assembled from solid blocks connected by flexible links. The key is to extend the fast marching method, which is an ordered upwind one-pass Dijkstra-like method to compute optimal paths by efficiently solving an associated Eikonal equation for the cost function. First, we build a suitable cost function associated with each possible configuration, and second, we construct an algorithm that works in ensuing high-dimensional configuration space: at least seven dimensions are required to account for translational, rotational, and internal degrees of freedom. We demonstrate the algorithm to study shortest paths, compute accessible volume, and derive information on topology of the accessible part of a chemical labyrinth. As a model example, we consider an alkane molecule in a porous material, which is relevant to designing catalysts for oil processing.","authors":"Haranczyk, M., Sethian, JA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Proc Natl Acad Sci U S A","volume":"106","issue":"51","page":"21472-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8181521","title":"Maternal transfer of infectious mouse mammary tumor retroviruses does not depend on clonal deletion of superantigen-reactive V beta 14+ T cells.","abstract":"Female C3H\/HeJ mice maternally transmit through their milk an infectious mouse mammary tumor retrovirus (MMTV) which causes clonal deletion of T cell receptor (TcR)V beta 14+ T cells reactive to the retroviral superantigen (SAG). To test whether CD4+ or CD8+ T cells are crucial for intestinal infection and maternal transfer of exogenous retroviruses, newborn mice lacking CD4 or CD8 molecules after gene targetting were raised by surrogate C3H\/HeJ mothers. In CD8-\/- mice, clonal deletion of TcRV beta 14+ cells reactive to the SAG from this exogenous MMTV occurred with delayed kinetics. Deletion of TcRV beta 14+ cells was not observed in CD4-\/- mice up to 12 months after exposure to the retrovirus. In both CD4-\/- and CD8-\/- mice TcRV beta 5+ and TcRV beta 11+ T cells were deleted in the presence of genomically integrated endogenous MMTV (Mtv), indicating that the lack of SAG-induced clonal deletion was not due to a general defect in these mutant mouse strains. Although TcRV beta 14+ T cells were not deleted in CD4-\/- mice, female CD4-\/- mice nursed on C3H\/HeJ milk maternally transmitted the retrovirus to their offspring, albeit with delayed kinetics. These data demonstrate that CD4+ and CD8+ lymphocytes influence clonal deletion events and that the mechanisms responsible for clonal deletion of SAG-reactive TcRV beta 14+ T cells may be different from mechanisms which allow the mammary tumor virus to enter the mammary gland and complete its infectious cycle.","authors":"Penninger, JM., Wallace, VA., Timms, E., Mak, TW.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Eur J Immunol","volume":"24","issue":"5","page":"1102-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1994-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19723031","title":"AIF: not just an apoptosis-inducing factor.","abstract":"Since its discovery nearly a decade ago, apoptosis-inducing factor (AIF) has had anything but a staid and uneventful existence. AIF was originally described as a mitochondrial intermembrane protein that, after apoptosis induction, can translocate to the nucleus and trigger chromatin condensation and DNA fragmentation. Over the years, an AIF-mediated caspase-independent cell death pathway has been defined. Rather than functioning as a general component of the cell death machinery, AIF is required for specific cell death pathways, including lethal responses to excitotoxins such as N-methyl-D-aspartate and glutamate, the DNA-alkylating agent N-methyl-N'-nitro-N-nitroso-guanidine, hypoxia-ischemia, or growth factor deprivation. Also, important roles of AIF in mitochondrial metabolism and redox control, and more recently in obesity and diabetes, have been discovered. Much of our knowledge has come from studies of AIF orthologs in model organisms, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and mice, which have also highlighted the importance of AIF in animal physiology and human pathology. Here, we discuss the manifold nature of AIF in cell life and death, with particular emphasis of its roles in vivo.","authors":"Joza, N., Pospisilik, JA., Hangen, E., Hanada, T., Modjtahedi, N., Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Ann N Y Acad Sci","volume":"1171","issue":null,"page":"2-11","pdf":null,"JrId":"611","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19533212","title":"Comparative genomics of Drosophila mtDNA: Novel features of conservation and change across functional domains and lineages.","abstract":"To gain insight on mitochondrial DNA (mtDNA) evolution, we assembled and analyzed the mitochondrial genomes of Drosophila erecta, D. ananassae, D. persimilis, D. willistoni, D. mojavensis, D. virilis and D. grimshawi together with the sequenced mtDNAs of the melanogaster subgroup. Genomic comparisons across the well-defined Drosophila phylogeny impart power for detecting conserved mtDNA regions that maintain metabolic function and regions that evolve uniquely on lineages. Evolutionary rate varies across intergenic regions of the mtDNA. Rapidly evolving intergenic regions harbor the majority of mitochondrial indel divergence. In contrast, patterns of nearly perfect conservation within intergenic regions reveal a refined set of nucleotides underlying the binding of transcription termination factors. Sequencing of 5' cDNA ends indicates that cytochrome C oxidase I (CoI) has a novel (T\/C)CG start codon and that perfectly conserved regions upstream of two NADH dehydrogenase (ND) genes are transcribed and likely extend these protein sequences. Substitutions at synonymous sites in the Drosophila mitochondrial proteomes reflect a mutation process that is biased toward A and T nucleotides and differs between mtDNA strands. Differences in codon usage bias across genes reveal that weak selection at silent sites may offset the mutation bias. The mutation-selection balance at synonymous sites has also diverged between the Drosophila and Sophophora lineages. Rates of evolution are highly heterogeneous across the mitochondrial proteome, with ND accumulating many more amino acid substitutions than CO. These oxidative phosphorylation complex-specific rates of evolution vary across lineages and may reflect physiological and ecological change across the Drosophila phylogeny.","authors":"Montooth, KL., Abt, DN., Hofmann, JW., Rand, DM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Mol Evol","volume":"69","issue":"1","page":"94-114","pdf":null,"JrId":"4969","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19490888","title":"With Happyhour, everyone's under the table.","abstract":"The molecular and cellular targets that mediate alcohol intoxication are poorly understood. In this issue, Corl et al. (2009) now implicate a new Ste20 family kinase (Happyhour) and the EGFR\/ERK signaling pathway it antagonizes in alcohol intoxication in flies.","authors":"Palfreyman, MT.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"137","issue":"5","page":"802-4","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23082280","title":"\u010cerenkov radiation emission and excited luminescence (CREL) sensitivity during external beam radiation therapy: Monte Carlo and tissue oxygenation phantom studies.","abstract":"Radiotherapy generates \u010cerenkov radiation emission in tissue, and spectral absorption features appearing in the emission spectrum can be used to quantify blood oxygen saturation (S(t)O(2)) from the known absorptions of hemoglobin. Additionally, the \u010cerenkov light can be used to excite oxygen-sensitive phosphorescence of probe PtG4, whose emission lifetime directly reports on tissue oxygen partial pressure (pO(2)). Thus, it is feasible to probe both hemoglobin S(t)O(2) and pO(2) using external radiation therapy beam to create as an internal light source in tumor tissue. In this study, the sensitivity and spatial origins of these two signals were examined. Emission was detected using a fiber-optic coupled intensifier-gated CCD camera interfaced to a spectrometer. The phosphorescence lifetimes were quantified and compared with S(t)O(2) changes previously measured. Monte Carlo simulations of the linear accelerator beam were used together with tracking of the optical signals, to predict the spatial distribution and zone sensitivity within the phantom. As the fiber-to-beam distance (FBD) varied from 0 to 30 mm, i.e. the distance from the fiber tip to the nearest side of the radiotherapy beam, the effective sampling depth for CR emission changed from 4 to 29 mm for the wavelengths in the range of 600-1000 nm. For the secondary emission (phosphorescence) the effective sampling depth was determined to be in the range of 9 to 19 mm. These results indicate that sampling of S(t)O(2) and pO(2) in tissue should be feasible during radiation therapy, and that the radiation beam and fiber sampling geometry can be set up to acquire signals that originate as deep as a few centimeters in the tissue.","authors":"Zhang, R., Glaser, A., Esipova, TV., Kanick, SC., Davis, SC., Vinogradov, S., Gladstone, D., Pogue, BW.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Biomed Opt Express","volume":"3","issue":"10","page":"2381-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23082236","title":"Event perception.","abstract":"Events are central elements of human experience. Formally, they can be individuated in terms of the entities that compose them, the features of those entities, and the relations amongst entities. Psychologically, representations of events capture their spatiotemporal location, the people and objects involved, and the relations between these elements. Here, we present an account of the nature of psychological representations of events and how they are constructed and updated. Event representations are like images in that they are isomorphic to the situations they represent. However, they are like models or language in that they are constructed of components rather than being holistic. Also, they are partial representations that leave out some elements and abstract others. Representations of individual events are informed by schematic knowledge about general classes of events. Event representations are constructed in a process that segments continuous activity into discrete events. The construction of a series of event representations forms a basis for predicting the future, planning for that future, and imagining alternatives. WIREs Cogni Sci 2011 2 608-620 DOI: 10.1002\/wcs.133 This article is categorized under: Psychology &gt; Memory.","authors":"Radvansky, GA., Zacks, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Wiley Interdiscip Rev Cogn Sci","volume":"2","issue":"6","page":"608-620","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19373566","title":"Serum bone turnover markers may be involved in the metastatic potential of lung cancer patients.","abstract":"The aim of this study was to investigate several bone markers in Non-Small Cell Lung (NSCLC) and Small Cell Lung (SCLC) patients experiencing or not secondary bony disease. Fasting serum levels of bone formation, bone resorption, and osteoclastogenesis markers were determined in 22 NSCLC patients with bone metastases, 18 without bone metastasis, and 28 SCLC patients. A total of 29 healthy volunteers were also included in the study. Decreased osteocalcin (OC) serum levels and increased osteopontin and ligand of the receptor of nuclear factor kB (RANKL) serum levels were detected in NCSLC patients with bone metastases while increased C-terminal cross-linking telopeptide of type I collagen and increased RANKL\/OPG (osteoprotegerin) ratio were detected in SCLC patients. Increased serum levels of OPG were observed in all lung cancer patients. OPG may be actively involved in the development of lung cancer metastasis. Furthermore, OC, OPN, and RANKL in NSCLC and CTX and RANKL in SCLC patients may also have a broader role in the pathogenesis and spread of lung cancer. They also provide useful information in identifying the group of patients that may benefit from a more rigorous treatment.","authors":"Karapanagiotou, EM., Terpos, E., Dilana, KD., Alamara, C., Gkiozos, I., Polyzos, A., Syrigos, KN.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Med Oncol","volume":"27","issue":"2","page":"332-8","pdf":null,"JrId":"8582","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1646986","title":"Abnormalities of chromosome 1 and loss of heterozygosity on 1p in primary hepatomas.","abstract":"Cytogenetic analysis of eight human hepatoma-derived cell lines and one primary hepatocellular carcinoma biopsy revealed multiple chromosome abnormalities; however, only chromosome 1 was consistently affected by rearrangements. Pseudopolysomy 1 as well as chromosome 1 deletions and\/or translocations that resulted in loss of the distal 1p region from at least one copy of chromosome 1 were observed in all but one of the cell lines analysed. Molecular analyses of tumor-derived and normal genomic DNA from six cases of hepatocellular carcinoma and from two of hepatoblastoma, using a panel of chromosome 1p-specific DNA probes indicated allelic loss in the distal 1p region in five of the six hepatocellular carcinomas but not in either hepatoblastoma. These results suggest the location of a gene in the distal 1p region whose functional loss may be involved in hepatocellular carcinogenesis.","authors":"Simon, D., Knowles, BB., Weith, A.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Oncogene","volume":"6","issue":"5","page":"765-70","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1991-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7835148","title":"Embryonic germ cell lines and their derivation from mouse primordial germ cells.","abstract":"When primordial germ cells of the mouse are cultured on feeder layers with the addition of the polypeptide signalling molecules leukaemia inhibitory factor, Steel factor and basic fibroblast growth factor they give rise to cells that resemble undifferentiated blastocyst-derived embryonic stem cells. These primordial germ cell-derived embryonic germ cells (EG cells) can be induced to differentiate extensively in culture and also form teratocarcinomas when injected into nude mice. Additionally, they contribute to chimeras when injected into host blastocysts. We have derived multiple EG cell lines from 8.5 days post coitum (dpc) embryos of C57BL\/6 inbred mice. Four independent EG cell lines with normal male karyotypes have formed chimeras (up to 70% coat colour chimerism) when injected into BALB\/c host blastocysts. Chimeric mice from all four cell lines are fertile, but only those from one line have transmitted coat colour markers through the germline. Studies have also been carried out to determine whether gonadal primordial germ cells can give rise to pluripotent EG cells. Germ cells from gonads of 15.5 dpc C57BL\/6 embryos and newborn mice failed to produce EG cell lines. EG cell lines capable of forming teratocarcinomas and coat colour chimeras have been established from primordial germ cells of 12.5 dpc genital ridges. We are currently testing the genomic imprinting status of the insulin-like growth factor type 2 receptor gene (Igf2r) in our different EG cell lines.","authors":"Labosky, PA., Barlow, DP., Hogan, BL.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Ciba Found Symp","volume":"182","issue":null,"page":"157-68; discussion 168-78","pdf":null,"JrId":"2951","fulltextlink":null,"preprintlink":null,"articledate":"1995-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31036636","title":"Tinbergen's challenge for the neuroscience of behavior.","abstract":"Nobel laureate Nikolaas Tinbergen provided clear criteria for declaring a neuroscience problem solved, criteria which despite the passage of more than 50 years and vastly expanded neuroscience tool kits remain applicable today. Tinbergen said for neuroscientists to claim that a behavior is understood, they must correspondingly understand its (<i>i<\/i>) development and its (<i>ii<\/i>) mechanisms and its (<i>iii<\/i>) function and its (<i>iv<\/i>) evolution. Now, all four of these domains represent hotbeds of current experimental work, each using arrays of new techniques which overlap only partly. Thus, as new methodologies come online, from single-nerve-cell RNA sequencing, for example, to smart FISH, large-scale calcium imaging from cortex and deep brain structures, computational ethology, and so on, one person, however smart, cannot master everything. Our response to the likely \"fracturing\" of neuroscience recognizes the value of ever larger consortia. This response suggests new kinds of problems for (<i>i<\/i>) funding and (<i>ii<\/i>) the fair distribution of credit, especially for younger scientists.","authors":"Pfaff, D., Tabansky, I., Haubensak, W.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Proc Natl Acad Sci U S A","volume":"116","issue":"20","page":"9704-9710","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20597996","title":"Mapping of balanced chromosome translocation breakpoints to the basepair level from microdissected chromosomes.","abstract":"The analysis of structural variants associated with specific phenotypic features is promising for the elucidation of the function of involved genes. There is, however, at present no approach allowing the rapid mapping of chromosomal translocation breakpoints to the basepair level from a single chromosome. Here we demonstrate that we have advanced both the microdissection and the subsequent unbiased amplification to an extent that breakpoint mapping to the basepair level has become possible. As a case in point we analysed the two breakpoints of a t(7;13) translocation observed in a patient with split hand\/foot malformation (SHFM1). The amplification products of the der(7) and of the der(13) were hybridized to custom-made arrays, enabling us to define primers at flanking breakpoint regions and thus to fine-map the breakpoints to the basepair level. Consequently, our results will also contribute to a further delineation of causative mechanisms underlying SHFM1 which are currently unknown.","authors":"Obenauf, AC., Schwarzbraun, T., Auer, M., Hoffmann, EM., Waldispuehl-Geigl, J., Ulz, P., G\u00fcnther, B., Duba, HC., Speicher, MR., Geigl, JB.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Cell Mol Med","volume":"14","issue":"8","page":"2078-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17875663","title":"The origins of oncomice: a history of the first transgenic mice genetically engineered to develop cancer.","abstract":"This perspective describes the concurrent development in the 1980s of the first transgenic mice genetically engineered to express dominant oncogenes, involving independent researchers who were largely unaware of each other's strategies and progress. We relate the experimental designs, the pitfalls and challenges encountered, and the eventual success in developing distinctive mouse models of cancer, wherein tumors arose heritably in various organs. These early oncomice have produced a wealth of new knowledge, become topics of intellectual property, and spawned a vibrant field of cancer research that is revealing mechanisms of tumorigenesis and suggesting new therapeutic strategies for treating the human disease.","authors":"Hanahan, D., Wagner, EF., Palmiter, RD.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genes Dev","volume":"21","issue":"18","page":"2258-70","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2007-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18782654","title":"Genospirituality: genetic engineering for spiritual and religious enhancement.","abstract":"The most frequently discussed role for genetic engineering is in relation to medicine, and a second area which provokes discussion is the use of genetic engineering as an enhancement technology. But one neglected area is the potential use of genetic engineering to increase human spiritual and religious experience - or genospirituality. If technologies are devised which can conveniently and safely engineer genes causal of spiritual and religious behaviours, then people may become able to choose their degree of religiosity or spiritual sensitivity. For instance, it may become possible to increase the likelihood of direct religious experience - i.e. 'revelation': the subjective experience of communication from the deity. Or, people may be able to engineer 'animistic' thinking, a mode of cognition in which the significant features of the world - such as large animals, trees, distinctive landscape features - are regarded as sentient and intentional beings; so that the individual experiences a personal relationship with the world. Another potentially popular spiritual ability would probably be shamanism; in which states of altered consciousness (e.g. trances, delirium or dreams) are induced and the shaman may undergo the experience of transformations, 'soul journeys' and contact with a spirit realm. Ideally, shamanistic consciousness could be modulated such that trances were self-induced only when wanted and when it was safe and convenient; and then switched-off again completely when full alertness and concentration are necessary. It seems likely that there will be trade-offs for increased spirituality; such as people becoming less 'driven' to seek status and monetary rewards - as a result of being more spiritually fulfilled people might work less hard and take more leisure. On the other hand, it is also possible that highly moral, altruistic, peaceable and principled behaviours might become more prevalent; and the energy and joyousness of the best churches might spread and be strengthened. Overall, genospirituality would probably be used by people who were unable to have the kind of spiritual or religious experiences which they wanted (or perhaps even needed) in order to lead the kind of life to which they aspired.","authors":"Charlton, BG.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Med Hypotheses","volume":"71","issue":"6","page":"825-8","pdf":null,"JrId":"5617","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18701890","title":"Autophagy in thymic epithelium shapes the T-cell repertoire and is essential for tolerance.","abstract":"Recognition of self-antigen-derived epitopes presented by major histocompatibility complex class II (MHC II) molecules on thymic epithelial cells (TECs) is critical for the generation of a functional and self-tolerant CD4 T-cell repertoire. Whereas haematopoietic antigen-presenting cells generate MHC-II-peptide complexes predominantly through the processing of endocytosed polypeptides, it remains unknown if and how TECs use unconventional pathways of antigen presentation. Here we address the role of macroautophagy, a process that has recently been shown to allow for endogenous MHC II loading, in T-cell repertoire selection in the mouse thymus. In contrast to most other tissues, TECs had a high constitutive level of autophagy. Genetic interference with autophagy specifically in TECs led to altered selection of certain MHC-II-restricted T-cell specificities and resulted in severe colitis and multi-organ inflammation. Our findings indicate that autophagy focuses the MHC-II-peptide repertoire of TECs on their intracellular milieu, which notably comprises a wide array of otherwise strictly 'tissue-specific' self antigens. In doing so, it contributes to T-cell selection and is essential for the generation of a self-tolerant T-cell repertoire.","authors":"Nedjic, J., Aichinger, M., Emmerich, J., Mizushima, N., Klein, L.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"455","issue":"7211","page":"396-400","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2008-10-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-158","title":"BrainTrawler: A visual analytics framework for iterative exploration of heterogeneous big brain data","abstract":null,"authors":"Ganglberger, F., Swoboda, N., Frauenstein, L.,  Kaczanowska, J., Haubensak, W., Buehle,r K.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Computer & Graphics","volume":"82","issue":"","page":"304-320","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18548006","title":"Osteoclast size is controlled by Fra-2 through LIF\/LIF-receptor signalling and hypoxia.","abstract":"Osteoclasts are multinucleated haematopoietic cells that resorb bone. Increased osteoclast activity causes osteoporosis, a disorder resulting in a low bone mass and a high risk of fractures. Increased osteoclast size and numbers are also a hallmark of other disorders, such as Paget's disease and multiple myeloma. The protein c-Fos, a component of the AP-1 transcription factor complex, is essential for osteoclast differentiation. Here we show that the Fos-related protein Fra-2 controls osteoclast survival and size. The bones of Fra-2-deficient newborn mice have giant osteoclasts, and signalling through leukaemia inhibitory factor (LIF) and its receptor is impaired. Similarly, newborn animals lacking LIF have giant osteoclasts, and we show that LIF is a direct transcriptional target of Fra-2 and c-Jun. Moreover, bones deficient in Fra-2 and LIF are hypoxic and express increased levels of hypoxia-induced factor 1alpha (HIF1alpha) and Bcl-2. Overexpression of Bcl-2 is sufficient to induce giant osteoclasts in vivo, whereas Fra-2 and LIF affect HIF1alpha through transcriptional modulation of the HIF prolyl hydroxylase PHD2. This pathway is operative in the placenta, because specific inactivation of Fra-2 in the embryo alone does not cause hypoxia or the giant osteoclast phenotype. Thus placenta-induced hypoxia during embryogenesis leads to the formation of giant osteoclasts in young pups. These findings offer potential targets for the treatment of syndromes associated with increased osteoclastogenesis.","authors":"Bozec, A., Bakiri, L., Hoebertz, A., Eferl, R., Schilling, AF., Komnenovic, V., Scheuch, H., Priemel, M., Stewart, CL., Amling, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"454","issue":"7201","page":"221-5","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18309324","title":"No death without life: vital functions of apoptotic effectors.","abstract":"As a result of the genetic experiments performed in Caenorhabditis elegans, it has been tacitly assumed that the core proteins of the 'apoptotic machinery' (CED-3, -4, -9 and EGL-1) would be solely involved in cell death regulation\/execution and would not exert any functions outside of the cell death realm. However, multiple studies indicate that the mammalian orthologs of these C. elegans proteins (i.e. caspases, Apaf-1 and multidomain proteins of the Bcl-2 family) participate in cell death-unrelated processes. Similarly, loss-of-function mutations of ced-4 compromise the mitotic arrest of DNA-damaged germline cells from adult nematodes, even in a context in which the apoptotic machinery is inoperative (for instance due to mutations of egl-1 or ced-3). Moreover, EGL-1 is required for the activation of autophagy in starved nematodes. Finally, the depletion of caspase-independent death effectors, such as apoptosis-inducing factor (AIF) and endonuclease G, provokes cell death-independent consequences, both in mammals and in yeast (Saccharomyces cerevisiae). These results corroborate the conjecture that any kind of protein that has previously been specifically implicated in apoptosis might have a phylogenetically conserved apoptosis-unrelated function, most likely as part of an adaptive response to cellular stress.","authors":"Galluzzi, L., Joza, N., Tasdemir, E., Maiuri, MC., Hengartner, M., Abrams, JM., Tavernarakis, N., Penninger, J., Madeo, F., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell Death Differ","volume":"15","issue":"7","page":"1113-23","pdf":null,"JrId":"20326","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8625408","title":"Asymmetric accumulation of Ash1p in postanaphase nuclei depends on a myosin and restricts yeast mating-type switching to mother cells.","abstract":"Cell division in haploid yeast gives rise to a \"mother\" cell capable of mating-type switching and a \"daughter\" cell that is not. Switching is initiated by the HO endonuclease, whose gene is only transcribed in cells that have previously given birth to a bud (mother cells). HO expression depends on a minimyosin, She1p\/Myo4p, which accumulates preferentially in growing buds. We describe a gene, ASH1, that is necessary to repress HO in daughters. ASH1 encodes a zinc finger protein whose preferential accumulation in daughter cell nuclei at the end of anaphase depends on She1p\/Myo4p. The greater abundance of Ash1p in daughter cells is responsible for restricting HO expression to mother cells.","authors":"Bobola, N., Jansen, RP., Shin, TH., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Cell","volume":"84","issue":"5","page":"699-709","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1996-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19688741","title":"The protein tyrosine kinase Tec regulates mast cell function.","abstract":"Mast cells play crucial roles in a variety of normal and pathophysiological processes and their activation has to be tightly controlled. Here, we demonstrate that the protein tyrosine kinase Tec is a crucial regulator of murine mast cell function. Tec was activated upon Fc epsilon RI stimulation of BM-derived mast cells (BMMC). The release of histamine in the absence of Tec was normal in vitro and in vivo; however, leukotriene C(4) levels were reduced in Tec(-) (\/) (-) BMMC. Furthermore, the production of IL-4 was severely impaired, and GM-CSF, TNF-alpha and IL-13 levels were also diminished. Finally, a comparison of WT, Tec(-) (\/) (-), Btk(-) (\/) (-) and Tec(-) (\/) (-)Btk(-) (\/) (-) BMMC revealed a negative role for Btk in the regulation of IL-4 production, while for the efficient production of TNF-alpha, IL-13 and GM-CSF, both Tec and Btk were required. Our results demonstrate a crucial role for Tec in mast cells, which is partially different to the function of the well-characterized family member Btk.","authors":"Schmidt, U., Abramova, A., Boucheron, N., Eckelhart, E., Schebesta, A., Bilic, I., Kneidinger, M., Unger, B., Hammer, M., Sibilia, M., Valent, P., Ellmeier, W.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Eur J Immunol","volume":"39","issue":"11","page":"3228-38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18235444","title":"Cohesin mediates transcriptional insulation by CCCTC-binding factor.","abstract":"Cohesin complexes mediate sister-chromatid cohesion in dividing cells but may also contribute to gene regulation in postmitotic cells. How cohesin regulates gene expression is not known. Here we describe cohesin-binding sites in the human genome and show that most of these are associated with the CCCTC-binding factor (CTCF), a zinc-finger protein required for transcriptional insulation. CTCF is dispensable for cohesin loading onto DNA, but is needed to enrich cohesin at specific binding sites. Cohesin enables CTCF to insulate promoters from distant enhancers and controls transcription at the H19\/IGF2 (insulin-like growth factor 2) locus. This role of cohesin seems to be independent of its role in cohesion. We propose that cohesin functions as a transcriptional insulator, and speculate that subtle deficiencies in this function contribute to 'cohesinopathies' such as Cornelia de Lange syndrome.","authors":"Wendt, KS., Yoshida, K., Itoh, T., Bando, M., Koch, B., Schirghuber, E., Tsutsumi, S., Nagae, G., Ishihara, K., Mishiro, T., Yahata, K., Imamoto, F., Aburatani, H., Nakao, M., Imamoto, N., Maeshima, K., Shirahige, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"451","issue":"7180","page":"796-801","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8125997","title":"Distinct 19 S and 20 S subcomplexes of the 26 S proteasome and their distribution in the nucleus and the cytoplasm.","abstract":"The 26 S proteolytic complex (\"26 S proteasome\") is a macromolecular assembly thought to be involved in ATP- and ubiquitin-dependent protein degradation in the cytoplasm of higher eukaryotic cells. This complex is composed of one 20 S cylinder particle (multicatalytic proteinase, 20 S proteasome) and two cap-shaped 19 S particles comprising a set of polypeptides in the M(r) range of 35,000-110,000. Here we show that cell supernatant fractions contain both these two subunit complexes as distinct particles as well as assembled to 26 S proteasomes. We have separated and purified all three forms from Xenopus laevis oocytes and have determined their peptidase and protease activities. Using various antibodies specific for either a constitutive p52 polypeptide of the 19 S cap complex or for proteins of the 20 S cylinder particle, we have immunolocalized these complexes in both the cytoplasm and the nucleus of diverse species and cell types. The occurrence of all three forms, the 26 S proteasome, the 20 S cylinder particle, and the 19 S cap complex in the nucleoplasm has also been demonstrated in analyses of isolated giant nuclei from Xenopus oocytes. In addition, we show that the 19 S and 20 S subcomplexes can be released from 26 S proteasomes by ATP depletion and that readdition of ATP to 19 S and 20 S particles in cell extracts leads to the reformation of 26 S proteasomes. We discuss that all three particles (19 S, 20 S, and 26 S) exist in a dynamic equilibrium in both cell compartments and serve cytoplasmic as well as nucleus-specific functions.","authors":"Peters, JM., Franke, WW., Kleinschmidt, JA.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"J Biol Chem","volume":"269","issue":"10","page":"7709-18","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1994-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17989251","title":"Reliable prediction of regulator targets using 12 Drosophila genomes.","abstract":"Gene expression is regulated pre- and post-transcriptionally via cis-regulatory DNA and RNA motifs. Identification of individual functional instances of such motifs in genome sequences is a major goal for inferring regulatory networks yet has been hampered due to the motifs' short lengths that lead to many chance matches and poor signal-to-noise ratios. In this paper, we develop a general methodology for the comparative identification of functional motif instances across many related species, using a phylogenetic framework that accounts for the evolutionary relationships between species, allows for motif movements, and is robust against missing data due to artifacts in sequencing, assembly, or alignment. We also provide a robust statistical framework for evaluating motif confidence, which enables us to translate evolutionary conservation into a confidence measure for each motif instance, correcting for varying motif length, composition, and background conservation of the target regions. We predict targets of fly transcription factors and miRNAs in alignments of 12 recently sequenced Drosophila species. When compared to extensive genome-wide experimental data, predicted targets are of high quality, matching and surpassing ChIP-chip microarrays and recovering miRNA targets with high sensitivity. The resulting regulatory network suggests significant redundancy between pre- and post-transcriptional regulation of gene expression.","authors":"Kheradpour, P., Stark, A., Roy, S., Kellis, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genome Res","volume":"17","issue":"12","page":"1919-31","pdf":null,"JrId":"8754","fulltextlink":null,"preprintlink":null,"articledate":"2008-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17694067","title":"The E3 ligase HACE1 is a critical chromosome 6q21 tumor suppressor involved in multiple cancers.","abstract":"Transformation and cancer growth are regulated by the coordinate actions of oncogenes and tumor suppressors. Here, we show that the novel E3 ubiquitin ligase HACE1 is frequently downregulated in human tumors and maps to a region of chromosome 6q21 implicated in multiple human cancers. Genetic inactivation of HACE1 in mice results in the development of spontaneous, late-onset cancer. A second hit from either environmental triggers or genetic heterozygosity of another tumor suppressor, p53, markedly increased tumor incidence in a Hace1-deficient background. Re-expression of HACE1 in human tumor cells directly abrogates in vitro and in vivo tumor growth, whereas downregulation of HACE1 via siRNA allows non-tumorigenic human cells to form tumors in vivo. Mechanistically, the tumor-suppressor function of HACE1 is dependent on its E3 ligase activity and HACE1 controls adhesion-dependent growth and cell cycle progression during cell stress through degradation of cyclin D1. Thus, HACE1 is a candidate chromosome 6q21 tumor-suppressor gene involved in multiple cancers.","authors":"Zhang, L., Anglesio, MS., O'Sullivan, M., Zhang, F., Yang, G., Sarao, R., Mai, PN., Cronin, S., Hara, H., Melnyk, N., Li, L., Wada, T., Liu, PP., Farrar, J., Arceci, RJ., Sorensen, PH., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Med","volume":"13","issue":"9","page":"1060-9","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34302268","title":"Correction to: Cross-Modality Imaging of Murine Tumor Vasculature-a Feasibility Study.","abstract":null,"authors":"Zopf, LM., Heimel, P., Geyer, SH., Kavirayani, A., Reier, S., Fr\u00f6hlich, V., Stiglbauer-Tscholakoff, A., Chen, Z., Nics, L., Zinnanti, J., Drexler, W., Mitterhauser, M., Helbich, T., Weninger, WJ., Slezak, P., Obenauf, A., B\u00fchler, K., Walter, A.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Mol Imaging Biol","volume":"23","issue":"6","page":"894","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-01","doi":"10.1007\/s11307-021-01625-w","first_author":null,"corresponding_authors":null},{"pmid":"17971781","title":"Fluorescence correlation spectroscopy in living cells.","abstract":"Fluorescence correlation spectroscopy (FCS) is an ideal analytical tool for studying concentrations, propagation, interactions and internal dynamics of molecules at nanomolar concentrations in living cells. FCS analyzes minute fluorescence-intensity fluctuations about the equilibrium of a small ensemble (&lt;10(3)) of molecules. These fluctuations act like a 'fingerprint' of a molecular species detected when entering and leaving a femtoliter-sized optically defined observation volume created by a focused laser beam. In FCS the fluorescence fluctuations are recorded as a function of time and then statistically analyzed by autocorrelation analysis. The resulting autocorrelation curve yields a measure of self-similarity of the system after a certain time delay, and its amplitude describes the normalized variance of the fluorescence fluctuations. By fitting the curves to an appropriate physical model, this method provides precise information about a multitude of measurement parameters, including diffusion coefficients, local concentration, states of aggregation and molecular interactions. FCS operates in real time with diffraction-limited spatial and sub-microsecond temporal resolution. Assessing diverse molecular dynamics within the living cell is a challenge well met by FCS because of its single-molecule sensitivity and high dynamic resolution. For these same reasons, however, intracellular FCS measurements also harbor the large risk of collecting artifacts and thus producing erroneous data. Here we provide a step-by-step guide to the application of FCS to cellular systems, including methods for minimizing artifacts, optimizing measurement conditions and obtaining parameter values in the face of diverse and complex conditions of the living cell. A discussion of advantages and disadvantages of one-photon versus two-photon excitation for FCS is available in Supplementary Methods online.","authors":"Kim, SA., Heinze, KG., Schwille, P.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Methods","volume":"4","issue":"11","page":"963-73","pdf":null,"JrId":"32338","fulltextlink":null,"preprintlink":null,"articledate":"2008-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17704783","title":"Microfluidics for in vivo imaging of neuronal and behavioral activity in Caenorhabditis elegans.","abstract":"The nematode C. elegans is an excellent model organism for studying behavior at the neuronal level. Because of the organism's small size, it is challenging to deliver stimuli to C. elegans and monitor neuronal activity in a controlled environment. To address this problem, we developed two microfluidic chips, the 'behavior' chip and the 'olfactory' chip for imaging of neuronal and behavioral responses in C. elegans. We used the behavior chip to correlate the activity of AVA command interneurons with the worm locomotion pattern. We used the olfactory chip to record responses from ASH sensory neurons exposed to high-osmotic-strength stimulus. Observation of neuronal responses in these devices revealed previously unknown properties of AVA and ASH neurons. The use of these chips can be extended to correlate the activity of sensory neurons, interneurons and motor neurons with the worm's behavior.","authors":"Chronis, N., Zimmer, M., Bargmann, CI.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Methods","volume":"4","issue":"9","page":"727-31","pdf":null,"JrId":"32338","fulltextlink":null,"preprintlink":null,"articledate":"2007-10-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17643123","title":"Architecture of the Dam1 kinetochore ring complex and implications for microtubule-driven assembly and force-coupling mechanisms.","abstract":"The Dam1 kinetochore complex is essential for chromosome segregation in budding yeast. This ten-protein complex self-assembles around microtubules, forming ring-like structures that move with depolymerizing microtubule ends, a mechanism with implications for cellular function. Here we used EM-based single-particle and helical analyses to define the architecture of the Dam1 complex at 30-A resolution and the self-assembly mechanism. Ring oligomerization seems to be facilitated by a conformational change upon binding to microtubules, suggesting that the Dam1 ring is not preformed, but self-assembles around kinetochore microtubules. The C terminus of the Dam1p protein, where most of the Aurora kinase Ipl1 phosphorylation sites reside, is in a strategic location to affect oligomerization and interactions with the microtubule. One of Ipl1's roles might be to fine-tune the coupling of the microtubule interaction with the conformational change required for oligomerization, with phosphorylation resulting in ring breakdown.","authors":"Wang, HW., Ramey, VH., Westermann, S., Leschziner, AE., Welburn, JP., Nakajima, Y., Drubin, DG., Barnes, G., Nogales, E.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Struct Mol Biol","volume":"14","issue":"8","page":"721-6","pdf":null,"JrId":"31761","fulltextlink":null,"preprintlink":null,"articledate":"2007-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1608451","title":"A central role for SWI6 in modulating cell cycle Start-specific transcription in yeast.","abstract":"Most genes involved in DNA replication in the yeast Saccharomyces cerevisiae are transcribed transiently during late G1 as cells become committed to a new cell cycle at Start. Their promoters all contain one or more versions of an 8-base-pair motif (ACGCGTNA) containing an MluI restriction enzyme site and called the MluI cell-cycle box (MCB). MCBs are both necessary and sufficient for the late G1-specific transcription of the TMP1 thymidylate synthase and POL1 DNA polymerase genes. A different late G1-specific 8-base-pair transcription element called the SCB (CACGAAAA; ref. 5) is bound by a factor containing the Swi4 and Swi6 proteins. We describe here the formation in vitro of complexes on TMP1 MCBs that contain the Swi6 protein and, we suggest, a protein of relative molecular mass 120,000 (p120) that is distinct from Swi4. Transcription due to SCBs and MCBs occurs in the absence of Swi6 but it is no longer correctly regulated in the cell cycle. We suggest that Swi6 is an essential regulatory subunit of two different Start-dependent transcription factors. One factor (SBF) contains Swi4 and binds to SCBs, whereas the other (MBF) contains the protein p120 and binds MCBs.","authors":"Dirick, L., Moll, T., Auer, H., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Nature","volume":"357","issue":"6378","page":"508-13","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1992-07-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17367545","title":"The ring between ring fingers (RBR) protein family.","abstract":"Proteins of the ring between ring fingers (RBR)-domain family are characterized by three groups of specifically clustered (typically eight) cysteine and histidine residues. Whereas the amino-terminal ring domain (N-RING) binds two zinc ions and folds into a classical cross-brace ring finger, the carboxy-terminal ring domain (C-RING) involves only one zinc ion. The three-dimensional structure of the central ring domain, the IBR domain, is still unsolved. About 400 genes coding for RBR proteins have been identified in the genomes of uni- and multicellular eukaryotes and some of their viruses, but the family has not been found in archaea or bacteria. The RBR proteins are classified into 15 major subfamilies (besides some orphan cases) by the phylogenetic relationships of the RBR segments and the conservation of their sequence architecture. The RBR domain mediates protein-protein interactions and a subset of RBR proteins has been shown to function as E3 ubiquitin ligases. RBR proteins have attracted interest because of their involvement in diseases such as parkinsonism, dementia with Lewy bodies, and Alzheimer's disease, and in susceptibility to some intracellular bacterial pathogens. Here, we present an overview of the RBR-domain containing proteins and their subcellular localization, additional domains, function, specificity, and regulation.","authors":"Eisenhaber, B., Chumak, N., Eisenhaber, F., Hauser, MT.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genome Biol","volume":"8","issue":"3","page":"209","pdf":null,"JrId":"21904","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36272071","title":"Ethyl Cinnamate-Based Tissue Clearing Strategies.","abstract":"Tissue clearing turns otherwise turbid and opaque tissue transparent, enabling imaging deep within tissues. The nontransparent nature of most tissues is due to the refractive index mismatch between its three major constituent components (lipids, proteins, and water). All tissue clearing methods rectify this mismatch by homogenizing the refractive index within the tissue and carefully matching it to the surrounding media. Here we describe a detailed protocol to clear a wide range of salamander tissues. We also include several optional steps such as depigmentation, antibody staining, and tissue mounting. These steps are optional, and do not change anything in the steps needed for tissue clearing. Depending on the fluorescent signal and optics employed, images up to several millimeters inside of the tissue can be acquired.","authors":"Masselink, W., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Methods Mol Biol","volume":"2562","issue":null,"page":"123-133","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17486093","title":"The adaptor protein CARD9 is essential for the activation of myeloid cells through ITAM-associated and Toll-like receptors.","abstract":"Immunoreceptor tyrosine-based activation motifs (ITAMs) are crucial in antigen receptor signaling in acquired immunity. Although receptors associated with the ITAM-bearing adaptors FcRgamma and DAP12 on myeloid cells have been suggested to activate innate immune responses, the mechanism coupling those receptors to 'downstream' signaling events is unclear. The CARMA1-Bcl-10-MALT1 complex is critical for the activation of transcription factor NF-kappaB in lymphocytes but has an unclear function in myeloid cells. Here we report that deletion of the gene encoding the Bcl-10 adaptor-binding partner CARD9 resulted in impaired myeloid cell activation of NF-kappaB signaling by several ITAM-associated receptors. Moreover, CARD9 was required for Toll-like receptor-induced activation of dendritic cells through the activation of mitogen-activated protein kinases. Although Bcl10-\/- and Card9-\/- mice had similar signaling impairment in myeloid cells, Card11-\/- (CARMA1-deficient) myeloid cell responses were normal, and although Card11-\/- lymphocytes were defective in antigen receptor-mediated activation, Card9-\/- lymphocytes were not. Thus, the activation of lymphoid and myeloid cells through ITAM-associated receptors or Toll-like receptors is regulated by CARMA1-Bcl-10 and CARD9-Bcl-10, respectively.","authors":"Hara, H., Ishihara, C., Takeuchi, A., Imanishi, T., Xue, L., Morris, SW., Inui, M., Takai, T., Shibuya, A., Saijo, S., Iwakura, Y., Ohno, N., Koseki, H., Yoshida, H., Penninger, JM., Saito, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Immunol","volume":"8","issue":"6","page":"619-29","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17352656","title":"Dendritic cells at the osteo-immune interface: implications for inflammation-induced bone loss.","abstract":"Within the past decade, the critical roles of T cells and T cell-mediated immunity in inflammation-induced osteoclastogenesis and subsequent bone loss have been extensively studied, thereby establishing the new paradigm of osteoimmunology. Therefore, dendritic cells (DCs), the most potent antigen-presenting cells, responsible for activation of na\u00efve T cells and orchestration of the immune response, became critically situated at the osteo-immune interface. Today, emerging new evidence suggests that DC may be directly involved in inflammation-induced osteoclastogenesis and bone loss, by acting as osteoclast (OC) precursors that can further develop into DC-derived OCs (DDOC) under inflammatory conditions. These findings have tremendous implications, because in addition to DC's important roles in regulating innate and adaptive immunity, a direct contribution by these cells to inflammation-induced bone loss may provide a promising therapeutic target not only for controlling inflammation but also for modulating bone destruction.","authors":"Alnaeeli, M., Park, J., Mahamed, D., Penninger, JM., Teng, YT.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Bone Miner Res","volume":"22","issue":"6","page":"775-80","pdf":null,"JrId":"104","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17322887","title":"Selection of Foxp3+ regulatory T cells specific for self antigen expressed and presented by Aire+ medullary thymic epithelial cells.","abstract":"The parameters specifying whether autoreactive CD4(+) thymocytes are deleted (recessive tolerance) or differentiate into regulatory T cells (dominant tolerance) remain unresolved. Dendritic cells directly delete thymocytes, partly through cross-presentation of peripheral antigens 'promiscuously' expressed in medullary thymic epithelial cells (mTECs) positive for the autoimmune regulator Aire. It is unclear if and how mTECs themselves act as antigen-presenting cells during tolerance induction. Here we found that an absence of major histocompatibility class II molecules on mTECs resulted in fewer polyclonal regulatory T cells. Furthermore, targeting of a model antigen to Aire(+) mTECs led to the generation of specific regulatory T cells independently of antigen transfer to dendritic cells. Thus, 'routing' of mTEC-derived self antigens may determine whether specific thymocytes are deleted or enter the regulatory T cell lineage.","authors":"Aschenbrenner, K., D'Cruz, LM., Vollmann, EH., Hinterberger, M., Emmerich, J., Swee, LK., Rolink, A., Klein, L.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Immunol","volume":"8","issue":"4","page":"351-8","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2007-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17211412","title":"A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing.","abstract":"Adult cancers may derive from stem or early progenitor cells. Epigenetic modulation of gene expression is essential for normal function of these early cells but is highly abnormal in cancers, which often show aberrant promoter CpG island hypermethylation and transcriptional silencing of tumor suppressor genes and pro-differentiation factors. We find that for such genes, both normal and malignant embryonic cells generally lack the hypermethylation of DNA found in adult cancers. In embryonic stem cells, these genes are held in a 'transcription-ready' state mediated by a 'bivalent' promoter chromatin pattern consisting of the repressive mark, histone H3 methylated at Lys27 (H3K27) by Polycomb group proteins, plus the active mark, methylated H3K4. However, embryonic carcinoma cells add two key repressive marks, dimethylated H3K9 and trimethylated H3K9, both associated with DNA hypermethylation in adult cancers. We hypothesize that cell chromatin patterns and transient silencing of these important regulatory genes in stem or progenitor cells may leave these genes vulnerable to aberrant DNA hypermethylation and heritable gene silencing during tumor initiation and progression.","authors":"Ohm, JE., McGarvey, KM., Yu, X., Cheng, L., Schuebel, KE., Cope, L., Mohammad, HP., Chen, W., Daniel, VC., Yu, W., Berman, DM., Jenuwein, T., Pruitt, K., Sharkis, SJ., Watkins, DN., Herman, JG., Baylin, SB.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Genet","volume":"39","issue":"2","page":"237-42","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1594245","title":"Mutations in the rel-homology domain alter the biochemical properties of v-rel and render it transformation defective in chicken embryo fibroblasts.","abstract":"Sequential deletions of approximately 100 base pairs were made in the rel-homology domain of the viral rel protein. Each deletion mutant was cloned into a replication-competent viral vector and assayed in chicken embryo fibroblasts (CEFs). The deleted v-rel proteins were analysed for localization, complex formation and ability to induce transformation. In vitro-translated mutant proteins were assayed for binding to a NF-kappa B consensus sequence. All the deletion mutants between nucleotides 37 and 798 in v-rel were transformation defective. Each of the mutants localized predominantly in the cytoplasm, whereas wild-type v-rel localizes predominantly in the nucleus of CEFs. Any disruption of the rel-homology domain reduced binding of the mutant v-rel proteins to the cellular protein, p36, while the requirements for binding to p68c-rel, p115 and p124 appeared to be more complicated. The binding of these three proteins to v-rel appeared to be linked and mediated through c-rel, suggesting that v-rel disrupts normal c-rel function. None of the deletion mutants in this region were able to bind to the NF-kappa B site. However, mutants which lie outside the rel-homology domain retained the ability to transform CEFs, localize to the nucleus, complex with p36, p115, p124 and p68c-rel and bind to the NK-kappa B site. These results suggest that transformation by v-rel requires an intact rel-homology domain and that the biochemical properties of v-rel are linked and dependent upon higher order protein structure for full function.","authors":"Morrison, LE., Boehmelt, G., Enrietto, PJ.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Oncogene","volume":"7","issue":"6","page":"1137-47","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1992-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1518816","title":"Influenza virus hemagglutinin HA-2 N-terminal fusogenic peptides augment gene transfer by transferrin-polylysine-DNA complexes: toward a synthetic virus-like gene-transfer vehicle.","abstract":"Complexes containing plasmid DNA, transferrin-polylysine conjugates, and polylysine-conjugated peptides derived from the N-terminal sequence of the influenza virus hemagglutinin subunit HA-2 have been used for the transfer of luciferase or beta-galactosidase marker genes to K562 cells, HeLa cells, and BNL CL.2 hepatocytes. These DNA complexes mimic the entry of viruses into cells, as they contain functions for (i) the packaging of the nucleic acid with polylysine, (ii) the attachment to the cell and receptor-mediated endocytosis with transferrin as a ligand, and (iii) the release from endosomes by using membrane-disrupting influenza peptides. The presence of these influenza peptide conjugates in the DNA complexes renders the complexes active in membrane disruption in a liposome leakage assay and results in a substantial augmentation of the transferrin-polylysine-mediated gene transfer.","authors":"Wagner, E., Plank, C., Zatloukal, K., Cotten, M., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Proc Natl Acad Sci U S A","volume":"89","issue":"17","page":"7934-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1992-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1461284","title":"Raf functions downstream of Ras1 in the Sevenless signal transduction pathway.","abstract":"Specification of the R7 cell fate in the developing Drosophila eye requires activation of the Sevenless (Sev) receptor tyrosine kinase, located on the surface of the R7 precursor cell, by its interaction with the Boss protein, expressed on the surface of the neighbouring R8 cell. Four genes that participate in the intracellular transmission of this signal have so far been identified and molecularly characterized: Ras1, Sos, Gap1 and sina (refs 4-8). The Drosophila homologue of the mammalian Raf-1 serine\/threonine kinase, which has been implicated in signal transduction pathways activated by many receptor tyrosine kinases (reviewed in refs 9 and 10), is encoded by the raf locus (also known as l(1)polehole, Draf-1 or Draf). Here we show that the Drosophila Raf serine\/threonine kinase also plays a crucial role in the R7 pathway: the response to Sev activity is dependent on raf function, and a constitutively activated Raf protein can induce R7 cell development in the absence of sev function. We also present genetic evidence suggesting that Raf acts downstream of Ras1 and upstream of Sina in this signal transduction cascade.","authors":"Dickson, B., Sprenger, F., Morrison, D., Hafen, E.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Nature","volume":"360","issue":"6404","page":"600-3","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1993-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16585178","title":"Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state.","abstract":"Histone H3 lysine 9 (H3K9) and lysine 27 (H3K27) trimethylation are properties of stably silenced heterochromatin whereas H3K9 dimethylation (H3K9me2) is important for euchromatic gene repression. In colorectal cancer cells, all of these marks, as well as the key enzymes which establish them, surround the hMLH1 promoter when it is DNA hypermethylated and aberrantly silenced, but are absent when the gene is unmethylated and fully expressed in a euchromatic state. When the aberrantly silenced gene is DNA demethylated and reexpressed following 5-aza-2'-deoxycytidine treatment, H3K9me1 and H3K9me2 are the only silencing marks that are lost. A series of other silenced and DNA hypermethylated gene promoters behave identically even when the genes are chronically DNA demethylated and reexpressed after genetic knockout of DNA methyltransferases. Our data indicate that when transcription of DNA hypermethylated genes is activated in cancer cells, their promoters remain in an environment with certain heterochromatic characteristics. This finding has important implications for the translational goal of reactivating aberrantly silenced cancer genes as a therapeutic maneuver.","authors":"McGarvey, KM., Fahrner, JA., Greene, E., Martens, J., Jenuwein, T., Baylin, SB.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cancer Res","volume":"66","issue":"7","page":"3541-9","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16572175","title":"Regulation of cancer cell migration and bone metastasis by RANKL.","abstract":"Bone metastases are a frequent complication of many cancers that result in severe disease burden and pain. Since the late nineteenth century, it has been thought that the microenvironment of the local host tissue actively participates in the propensity of certain cancers to metastasize to specific organs, and that bone provides an especially fertile 'soil'. In the case of breast cancers, the local chemokine milieu is now emerging as an explanation for why these tumours preferentially metastasize to certain organs. However, as the inhibition of chemokine receptors in vivo only partially blocks metastatic behaviour, other factors must exist that regulate the preferential metastasis of breast cancer cells. Here we show that the cytokine RANKL (receptor activator of NF-kappaB ligand) triggers migration of human epithelial cancer cells and melanoma cells that express the receptor RANK. RANK is expressed on cancer cell lines and breast cancer cells in patients. In a mouse model of melanoma metastasis, in vivo neutralization of RANKL by osteoprotegerin results in complete protection from paralysis and a marked reduction in tumour burden in bones but not in other organs. Our data show that local differentiation factors such as RANKL have an important role in cell migration and the tissue-specific metastatic behaviour of cancer cells.","authors":"Jones, DH., Nakashima, T., Sanchez, OH., Kozieradzki, I., Komarova, SV., Sarosi, I., Morony, S., Rubin, E., Sarao, R., Hojilla, CV., Komnenovic, V., Kong, YY., Schreiber, M., Dixon, SJ., Sims, SM., Khokha, R., Wada, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nature","volume":"440","issue":"7084","page":"692-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1429906","title":"Characterization of early and late endocytic compartments of the transferrin cycle. Transferrin receptor antibody blocks erythroid differentiation by trapping the receptor in the early endosome.","abstract":"We describe a detailed morphological characterization of the endocytic pathway in differentiating chicken erythroblasts transformed by a temperature-sensitive mutant of avian erythroblastosis virus (AEV). These cells express high levels of transferrin receptors (TfR) when induced to differentiate at 42 degrees C. Biochemical analysis showed that most (approximately 90%) of the internalized 125I-Tf recycled within approximately 30 min while a smaller fraction of 125I-Tf required up to 2 h for recycling. By immunocytochemistry, the bulk of Tf and TfR was localized at the plasma membrane and in tubuloreticular early endosomes. This structure contained coated buds that labelled with an antibody specific for the clathrin light chain. Decreasing amounts of both Tf and TfR were detected in two distal compartments, spherical endosome vesicles resembling multivesicular bodies and the prelysosomal compartment (PLC) enriched in cation-independent mannose 6-phosphate receptor. As shown by fluorescent (FITC-Tf) labelling of living cells, the movement of Tf\/TfR complex into these late structures was accompanied by a significant drop in pH from about 6, the value displayed by early endosomes, to values below pH 5.0. Since no detectable 125I-Tf degradation was observed during a 4 h period we believe that the Tf\/TfR detected in these late endocytic structures avoids degradation and recycles back to the cell surface. The addition of an anti-TfR monoclonal antibody to the culture medium of these cells blocks their differentiation. Under this condition the antibody-TfR complex was trapped in an early endosome compartment that enlarged to more than twice its normal size. However, this condition did not affect the transport kinetics of horseradish peroxidase from the medium to the PLC.","authors":"Killisch, I., Steinlein, P., R\u00f6misch, K., Hollinshead, R., Beug, H., Griffiths, G.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"J Cell Sci","volume":"103 ( Pt 1)","issue":null,"page":"211-32","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"1992-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16439995","title":"Cleavage of the siRNA passenger strand during RISC assembly in human cells.","abstract":"A crucial step in the RNA interference (RNAi) pathway involves the assembly of RISC, the RNA-induced silencing complex. RISC initially recognizes a double-stranded short interfering RNA (siRNA), but only one strand is finally retained in the functional ribonucleoprotein complex. The non-incorporated strand, or 'passenger' strand, is removed during the assembly process and most probably degraded thereafter. In this report, we show that the passenger strand is cleaved during the course of RISC assembly following the same rules established for the siRNA-guided cleavage of a target RNA. Chemical modifications impairing the cleavage of the passenger strand also impair the cleavage of a target RNA in vitro as well as the silencing of a reporter gene in vivo, suggesting that passenger strand removal is facilitated by its cleavage during RISC assembly. Interestingly, target RNA cleavage can be rescued if an otherwise non-cleavable passenger strand shows a nick at the scissile phosphodiester bond, which further indicates that the cleavage event per se is not essential.","authors":"Leuschner, PJ., Ameres, SL., Kueng, S., Martinez, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"EMBO Rep","volume":"7","issue":"3","page":"314-20","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2006-06-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34101107","title":"Cross-Modality Imaging of Murine Tumor Vasculature-a Feasibility Study.","abstract":"Tumor vasculature and angiogenesis play a crucial role in tumor progression. Their visualization is therefore of utmost importance to the community. In this proof-of-principle study, we have established a novel cross-modality imaging (CMI) pipeline to characterize exactly the same murine tumors across scales and penetration depths, using orthotopic models of melanoma cancer. This allowed the acquisition of a comprehensive set of vascular parameters for a single tumor. The workflow visualizes capillaries at different length scales, puts them into the context of the overall tumor vessel network and allows quantification and comparison of vessel densities and morphologies by different modalities. The workflow adds information about hypoxia and blood flow rates. The CMI approach includes well-established technologies such as magnetic resonance imaging (MRI), positron emission tomography (PET), computed tomography (CT), and ultrasound (US), and modalities that are recent entrants into preclinical discovery such as optical coherence tomography (OCT) and high-resolution episcopic microscopy (HREM). This novel CMI platform establishes the feasibility of combining these technologies using an extensive image processing pipeline. Despite the challenges pertaining to the integration of microscopic and macroscopic data across spatial resolutions, we also established an open-source pipeline for the semi-automated co-registration of the diverse multiscale datasets, which enables truly correlative vascular imaging. Although focused on tumor vasculature, our CMI platform can be used to tackle a multitude of research questions in cancer biology.","authors":"Zopf, LM., Heimel, P., Geyer, SH., Kavirayani, A., Reier, S., Fr\u00f6hlich, V., Stiglbauer-Tscholakoff, A., Chen, Z., Nics, L., Zinnanti, J., Drexler, W., Mitterhauser, M., Helbich, T., Weninger, WJ., Slezak, P., Obenauf, A., B\u00fchler, K., Walter, A.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Mol Imaging Biol","volume":"23","issue":"6","page":"874-893","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-04","doi":"10.1007\/s11307-021-01615-y","first_author":null,"corresponding_authors":null},{"pmid":"16415853","title":"The Dam1 kinetochore ring complex moves processively on depolymerizing microtubule ends.","abstract":"Chromosomes interact through their kinetochores with microtubule plus ends and they are segregated to the spindle poles as the kinetochore microtubules shorten during anaphase A of mitosis. The molecular natures and identities of coupling proteins that allow microtubule depolymerization to pull chromosomes to poles during anaphase have long remained elusive. In budding yeast, the ten-protein Dam1 complex is a critical microtubule-binding component of the kinetochore that oligomerizes into a 50-nm ring around a microtubule in vitro. Here we show, with the use of a real-time, two-colour fluorescence microscopy assay, that the ring complex moves processively for several micrometres at the ends of depolymerizing microtubules without detaching from the lattice. Electron microscopic analysis of 'end-on views' revealed a 16-fold symmetry of the kinetochore rings. This out-of-register arrangement with respect to the 13-fold microtubule symmetry is consistent with a sliding mechanism based on an electrostatically coupled ring-microtubule interface. The Dam1 ring complex is a molecular device that can translate the force generated by microtubule depolymerization into movement along the lattice to facilitate chromosome segregation.","authors":"Westermann, S., Wang, HW., Avila-Sakar, A., Drubin, DG., Nogales, E., Barnes, G.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nature","volume":"440","issue":"7083","page":"565-9","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16343932","title":"Methods to measure ubiquitin-dependent proteolysis mediated by the anaphase-promoting complex.","abstract":"The anaphase-promoting complex (APC) or cyclosome is a multi-subunit ubiquitin ligase that controls progression through mitosis and the G1-phase of the cell cycle. The APC ubiquitinates regulatory proteins such as securin and cyclin B and thereby targets them for destruction by the 26S proteasome. Activation of the APC depends on the activator proteins Cdc20 and Cdh1, which are thought to recruit substrates to the APC. In vitro, APC's RING finger subunit Apc11 alone can also function as a ubiquitin ligase. Here, we review different methods that have been used to measure the ubiquitination activity of the APC in vitro and to analyze APC-mediated degradation reactions either in vitro or in vivo. We describe procedures to isolate the APC from human cells or from Xenopus eggs, to activate purified APC with recombinant Cdc20 or Cdh1 and to measure the ubiquitination activity of the resulting APC(Cdc20) and APC(Cdh1) complexes. We also describe procedures to analyze the ubiquitination activity associated with recombinant Apc11.","authors":"Kraft, C., Gmachl, M., Peters, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Methods","volume":"38","issue":"1","page":"39-51","pdf":null,"JrId":"20385","fulltextlink":null,"preprintlink":null,"articledate":"2006-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16227983","title":"Development and function of agonist-induced CD25+Foxp3+ regulatory T cells in the absence of interleukin 2 signaling.","abstract":"Interleukin 2 signaling is believed to be critically involved in several aspects of CD25(+) CD4(+) regulatory T cell biology, such as intrathymic development, peripheral survival and suppressive function. Here we have analyzed the effects of interleukin 2 or CD25 deficiency on agonist-driven thymic development and the peripheral homeostasis of an antigen-specific population of regulatory T cells positive for forkhead family transcription factor Foxp3 and have correlated our observations with polyclonal suppressor populations. We found that the differentiation, acquisition of functional capacity and formation of a sizeable pool of suppressor T cells in the thymus was independent of interleukin 2 signaling, but that interleukin 2 was essential for the survival of mature Foxp3(+) regulatory T cells.","authors":"D'Cruz, LM., Klein, L.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Immunol","volume":"6","issue":"11","page":"1152-9","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16222244","title":"Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin.","abstract":"Histones are subject to numerous post-translational modifications. Some of these 'epigenetic' marks recruit proteins that modulate chromatin structure. For example, heterochromatin protein 1 (HP1) binds to histone H3 when its lysine 9 residue has been tri-methylated by the methyltransferase Suv39h (refs 2-6). During mitosis, H3 is also phosphorylated by the kinase Aurora B. Although H3 phosphorylation is a hallmark of mitosis, its function remains mysterious. It has been proposed that histone phosphorylation controls the binding of proteins to chromatin, but any such mechanisms are unknown. Here we show that antibodies against mitotic chromosomal antigens that are associated with human autoimmune diseases specifically recognize H3 molecules that are modified by both tri-methylation of lysine 9 and phosphorylation of serine 10 (H3K9me3S10ph). The generation of H3K9me3S10ph depends on Suv39h and Aurora B, and occurs at pericentric heterochromatin during mitosis in different eukaryotes. Most HP1 typically dissociates from chromosomes during mitosis, but if phosphorylation of H3 serine 10 is inhibited, HP1 remains chromosome-bound throughout mitosis. H3 phosphorylation by Aurora B is therefore part of a 'methyl\/phos switch' mechanism that displaces HP1 and perhaps other proteins from mitotic heterochromatin.","authors":"Hirota, T., Lipp, JJ., Toh, BH., Peters, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nature","volume":"438","issue":"7071","page":"1176-80","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1386897","title":"Anatomy of a transcription factor important for the start of the cell cycle in Saccharomyces cerevisiae.","abstract":"Entry of yeast cells into the mitotic cell cycle (Start) involves a form of the CDC28 kinase that associates with G1-specific cyclins encoded by CLN1 and CLN2 (ref. 1). The onset of Start may be triggered by the activation of CLN1 and CLN2 transcription in late G1 (ref. 2). SWI4 and SWI6 are components of a factor (SBF) that binds the CACGAAAA (SCB) promoter elements responsible for activation in late G1 of the HO endonuclease, CLN1 and CLN2 genes. A related factor (MBF) containing SWI6 and a 120K protein binds to the ACGCGTNA (MCB) promoter elements responsible for late G1-specific transcription of DNA replication genes. Nothing is known about how these heteromeric proteins bind DNA. We show here that SWI4 contains a novel DNA-binding domain at its N terminus that alone binds specifically to SCBs and a C-terminal domain that binds to SWI6. SWI4's DNA-binding domain is similar to an N-terminal domain of the cdc10 protein that is a component of an MBF-like factor from Schizosaccharomyces pombe and is required for Start. An involvement of this kind of DNA-binding domain in transcriptional controls at Start may therefore be a conserved feature of eukaryotic cells.","authors":"Primig, M., Sockanathan, S., Auer, H., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Nature","volume":"358","issue":"6387","page":"593-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1992-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16179255","title":"A topological interaction between cohesin rings and a circular minichromosome.","abstract":"Sister chromatid cohesion depends on a multiprotein cohesin complex containing two SMC subunits, Smc1 and Smc3, that dimerize to form V-shaped molecules with ABC-like ATPase heads at the tips of their two arms. Cohesin's Smc1 and Smc3 \"heads\" are connected by an alpha kleisin subunit called Scc1, forming a tripartite ring with a diameter around 40 nm. We show here that some cohesin remains tightly bound to circular minichromosomes after their purification from yeast cells and that cleavage either of cohesin's ring or of the minichromosome's DNA destroys their association. This suggests that the stable association between cohesin and chromatin detected here is topological rather than physical, which is consistent with the notion that DNA is trapped inside cohesin rings.","authors":"Ivanov, D., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell","volume":"122","issue":"6","page":"849-60","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15855271","title":"Implications of the serine protease HtrA1 in amyloid precursor protein processing.","abstract":"The defining features of the widely conserved HtrA (high temperature requirement) family of serine proteases are the combination of a catalytic protease domain with one or more C-terminal PDZ domains and reversible zymogen activation. Even though HtrAs have previously been implicated in protein quality control and various diseases, including cancer, arthritis, and neuromuscular disorder, the biology of the human family members is not well understood. Our data suggest that HtrA1 is directly involved in the beta-amyloid pathway as it degrades various fragments of amyloid precursor protein while an HtrA1 inhibitor causes accumulation of Abeta in astrocyte cell culture supernatants. Furthermore, HtrA1 colocalizes with beta-amyloid deposits in human brain samples. Potential implications in Alzheimer's disease are discussed.","authors":"Grau, S., Baldi, A., Bussani, R., Tian, X., Stefanescu, R., Przybylski, M., Richards, P., Jones, SA., Shridhar, V., Clausen, T., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Proc Natl Acad Sci U S A","volume":"102","issue":"17","page":"6021-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15952899","title":"The structure and function of SMC and kleisin complexes.","abstract":"Protein complexes consisting of structural maintenance of chromosomes (SMC) and kleisin subunits are crucial for the faithful segregation of chromosomes during cell proliferation in prokaryotes and eukaryotes. Two of the best-studied SMC complexes are cohesin and condensin. Cohesin is required to hold sister chromatids together, which allows their bio-orientation on the mitotic spindle. Cleavage of cohesin's kleisin subunit by the separase protease then triggers the movement of sister chromatids into opposite halves of the cell during anaphase. Condensin is required to organize mitotic chromosomes into coherent structures that prevent them from getting tangled up during segregation. Here we describe the discovery of SMC complexes and discuss recent advances in determining how members of this ancient protein family may function at a mechanistic level.","authors":"Nasmyth, K., Haering, CH.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Annu Rev Biochem","volume":"74","issue":null,"page":"595-648","pdf":null,"JrId":"665","fulltextlink":null,"preprintlink":null,"articledate":"2005-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15737064","title":"Shugoshin prevents dissociation of cohesin from centromeres during mitosis in vertebrate cells.","abstract":"Cohesion between sister chromatids is essential for their bi-orientation on mitotic spindles. It is mediated by a multisubunit complex called cohesin. In yeast, proteolytic cleavage of cohesin's alpha kleisin subunit at the onset of anaphase removes cohesin from both centromeres and chromosome arms and thus triggers sister chromatid separation. In animal cells, most cohesin is removed from chromosome arms during prophase via a separase-independent pathway involving phosphorylation of its Scc3-SA1\/2 subunits. Cohesin at centromeres is refractory to this process and persists until metaphase, whereupon its alpha kleisin subunit is cleaved by separase, which is thought to trigger anaphase. What protects centromeric cohesin from the prophase pathway? Potential candidates are proteins, known as shugoshins, that are homologous to Drosophila MEI-S332 and yeast Sgo1 proteins, which prevent removal of meiotic cohesin complexes from centromeres at the first meiotic division. A vertebrate shugoshin-like protein associates with centromeres during prophase and disappears at the onset of anaphase. Its depletion by RNA interference causes HeLa cells to arrest in mitosis. Most chromosomes bi-orient on a metaphase plate, but precocious loss of centromeric cohesin from chromosomes is accompanied by loss of all sister chromatid cohesion, the departure of individual chromatids from the metaphase plate, and a permanent cell cycle arrest, presumably due to activation of the spindle checkpoint. Remarkably, expression of a version of Scc3-SA2 whose mitotic phosphorylation sites have been mutated to alanine alleviates the precocious loss of sister chromatid cohesion and the mitotic arrest of cells lacking shugoshin. These data suggest that shugoshin prevents phosphorylation of cohesin's Scc3-SA2 subunit at centromeres during mitosis. This ensures that cohesin persists at centromeres until activation of separase causes cleavage of its alpha kleisin subunit. Centromeric cohesion is one of the hallmarks of mitotic chromosomes. Our results imply that it is not an intrinsically stable property, because it can easily be destroyed by mitotic kinases, which are kept in check by shugoshin.","authors":"McGuinness, BE., Hirota, T., Kudo, NR., Peters, JM., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"PLoS Biol","volume":"3","issue":"3","page":"e86","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15916961","title":"The WD40 propeller domain of Cdh1 functions as a destruction box receptor for APC\/C substrates.","abstract":"Activation of the anaphase-promoting complex\/cyclosome (APC\/C) by Cdc20 and Cdh1 leads to ubiquitin-dependent degradation of securin and cyclin B and thereby promotes the initiation of anaphase and exit from mitosis. Cyclin B and securin ubiquitination depend on a destruction box (D box) sequence in these proteins, but how APC\/C bound to Cdc20 or Cdh1 recognizes the D box is poorly understood. By using site-specific photocrosslinking in combination with mutational analyses, we show that the D box directly interacts with an evolutionarily conserved surface on the predicted WD40 propeller structure of Cdh1 and that this interaction is essential for processive substrate ubiquitination. We further show that Cdh1 specifically crosslinks to the APC\/C subunit Cdc27 and that Cdh1 binding to APC\/C depends on the presence of Cdc27. Our data imply that APC\/C is activated by the association of Cdh1 with Cdc27, which enables APC\/C to recognize the D box of substrates via Cdh1's propeller domain.","authors":"Kraft, C., Vodermaier, HC., Maurer-Stroh, S., Eisenhaber, F., Peters, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Mol Cell","volume":"18","issue":"5","page":"543-53","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8009222","title":"Involvement of the IRF-1 transcription factor in antiviral responses to interferons.","abstract":"The mechanisms underlying interferon (IFN)-induced antiviral states are not well understood. Interferon regulatory factor-1 (IRF-1) is an IFN-inducible transcriptional activator, whereas IRF-2 suppresses IRF-1 action. The inhibition of encephalomyocarditis virus (EMCV) replication by IFN-alpha and especially by IFN-gamma was impaired in cells from mice with a null mutation in the IRF-1 gene (IRF-1-\/- mice). The IRF-1-\/- mice were less resistant than normal mice to EMCV infection, as revealed by accelerated mortality and a larger virus titer in target organs. The absence of IRF-1 did not clearly affect replication of two other types of viruses. Thus, IRF-1 is necessary for the antiviral action of IFNs against some viruses, but IFNs activate multiple activation pathways through diverse target genes to induce the antiviral state.","authors":"Kimura, T., Nakayama, K., Penninger, J., Kitagawa, M., Harada, H., Matsuyama, T., Tanaka, N., Kamijo, R., Vilcek, J., Mak, TW.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Science","volume":"264","issue":"5167","page":"1921-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1994-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15678104","title":"The profile of repeat-associated histone lysine methylation states in the mouse epigenome.","abstract":"Histone lysine methylation has been shown to index silenced chromatin regions at, for example, pericentric heterochromatin or of the inactive X chromosome. Here, we examined the distribution of repressive histone lysine methylation states over the entire family of DNA repeats in the mouse genome. Using chromatin immunoprecipitation in a cluster analysis representing repetitive elements, our data demonstrate the selective enrichment of distinct H3-K9, H3-K27 and H4-K20 methylation marks across tandem repeats (e.g. major and minor satellites), DNA transposons, retrotransposons, long interspersed nucleotide elements and short interspersed nucleotide elements. Tandem repeats, but not the other repetitive elements, give rise to double-stranded (ds) RNAs that are further elevated in embryonic stem (ES) cells lacking the H3-K9-specific Suv39h histone methyltransferases. Importantly, although H3-K9 tri- and H4-K20 trimethylation appear stable at the satellite repeats, many of the other repeat-associated repressive marks vary in chromatin of differentiated ES cells or of embryonic trophoblasts and fibroblasts. Our data define a profile of repressive histone lysine methylation states for the repetitive complement of four distinct mouse epigenomes and suggest tandem repeats and dsRNA as primary triggers for more stable chromatin imprints.","authors":"Martens, JH., O'Sullivan, RJ., Braunschweig, U., Opravil, S., Radolf, M., Steinlein, P., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"EMBO J","volume":"24","issue":"4","page":"800-12","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15580273","title":"Locus 'decontraction' and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene.","abstract":"Allelic exclusion of immunoglobulin genes ensures the expression of a single antibody molecule in B cells through mostly unknown mechanisms. Large-scale contraction of the immunoglobulin heavy-chain (Igh) locus facilitates rearrangements between Igh variable (V(H)) and diversity gene segments in pro-B cells. Here we show that these long-range interactions are mediated by 'looping' of individual Igh subdomains. The Igk locus also underwent contraction by looping in small pre-B and immature B cells, demonstrating that immunoglobulin loci are in a contracted state in rearranging cells. Successful Igh recombination induced the rapid reversal of locus contraction in response to pre-B cell receptor signaling, which physically separated the distal V(H) genes from the proximal Igh domain, thus preventing further rearrangements. In the absence of locus contraction, only the four most proximal V(H) genes escaped allelic exclusion in immature mu-transgenic B lymphocytes. Pre-B cell receptor signaling also led to rapid repositioning of one Igh allele to repressive centromeric domains in response to downregulation of interleukin 7 signaling. These data link both locus 'decontraction' and centromeric recruitment to the establishment of allelic exclusion at the Igh locus.","authors":"Rold\u00e1n, E., Fuxa, M., Chong, W., Martinez, D., Novatchkova, M., Busslinger, M., Skok, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Immunol","volume":"6","issue":"1","page":"31-41","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15340062","title":"Targeted gene knockout reveals a role in meiotic recombination for ZHP-3, a Zip3-related protein in Caenorhabditis elegans.","abstract":"The meiotically expressed Zip3 protein is found conserved from Saccharomyces cerevisiae to humans. In baker's yeast, Zip3p has been implicated in synaptonemal complex (SC) formation, while little is known about the protein's function in multicellular organisms. We report here the successful targeted gene disruption of zhp-3 (K02B12.8), the ZIP3 homolog in the nematode Caenorhabditis elegans. Homozygous zhp-3 knockout worms show normal homologue pairing and SC formation. Also, the timing of appearance and the nuclear localization of the recombination protein Rad-51 seem normal in these animals, suggesting proper initiation of meiotic recombination by DNA double-strand breaks. However, the occurrence of univalents during diplotene indicates that C. elegans ZHP-3 protein is essential for reciprocal recombination between homologous chromosomes and thus chiasma formation. In the absence of ZHP-3, reciprocal recombination is abolished and double-strand breaks seem to be repaired via alternative pathways, leading to achiasmatic chromosomes and the occurrence of univalents during meiosis I. Green fluorescent protein-tagged C. elegans ZHP-3 forms lines between synapsed chromosomes and requires the SC for its proper localization.","authors":"Jantsch, V., Pasierbek, P., Mueller, MM., Schweizer, D., Jantsch, M., Loidl, J.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Mol Cell Biol","volume":"24","issue":"18","page":"7998-8006","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15358620","title":"Different steroids co-regulate long-term expansion versus terminal differentiation in primary human erythroid progenitors.","abstract":"Outgrowth, long-term self-renewal, and terminal maturation of human erythroid progenitors derived from umbilical cord blood in serum-free medium can be modulated by steroid hormones. Homogeneous erythroid cultures, as characterized by flow cytometry and dependence on a specific mixture of physiologic proliferation factors, were obtained within 8 days from a starting population of mature and immature mononuclear cells. Due to previous results in mouse and chicken erythroblasts, the proliferation-promoting effect of glucocorticoids was not unexpected. Surprisingly, however, androgen had a positive effect on the sustained expansion of human female but not male erythroid progenitors. Under optimal conditions, sustained proliferation of erythroid progenitors resulted in a more than 10(9)-fold expansion within 60 days. Terminal erythroid maturation was significantly improved by adding human serum and thyroid hormone (3,5,3'-triiodothyronine [T3]) to the differentiation medium. This resulted in highly synchronous differentiation of the cells toward enucleated erythrocytes within 6 days, accompanied by massive size decrease and hemoglobin accumulation to levels comparable to those in peripheral blood erythrocytes. Thus, obviously, different ligand-activated nuclear hormone receptors massively influence the decision between self-renewal and terminal maturation in the human erythroid compartment.","authors":"Leberbauer, C., Boulm\u00e9, F., Unfried, G., Huber, J., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Blood","volume":"105","issue":"1","page":"85-94","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7916298","title":"Experimental allergic encephalomyelitis (EAE) in mice lacking CD4+ T cells.","abstract":"Like most experimental autoimmune disease experimental allergic encephalomyelitis (EAE) has been shown to be mediated by CD4+ helper T cells. In vivo antibody blocking studies with anti-CD4 and adoptive transfer of activated CD4+ T cells indicate the importance of CD4+ cells in disease induction. Fourth backcross generation mutant CD4-\/-PL\/J mice were immunized with myelin basic protein. Despite the lack CD4+ T cells some of these mice developed EAE, albeit, at a considerably reduced frequency and with variable severity. Furthermore, antigen-specific T cell proliferation can be demonstrated, indicating some residual helper activity that is major histocompatibility complex class II restricted. This demonstrated that, although the CD4+ T cell is the prime effector cell in EAE, in mice developmentally lacking in CD4, the expanded double-negative T cells may subserve helper and effector functions.","authors":"Koh, DR., Ho, A., Rahemtulla, A., Penninger, J., Mak, TW.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Eur J Immunol","volume":"24","issue":"9","page":"2250-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1994-10-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7698796","title":"Signal transduction, mitotic catastrophes, and death in T-cell development.","abstract":null,"authors":"Penninger, JM., Mak, TW.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Immunol Rev","volume":"142","issue":null,"page":"231-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1995-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15254422","title":"Control of erythropoiesis by erythropoietin and stem cell factor: a novel role for Bruton's tyrosine kinase.","abstract":"Erythropoietin (Epo) and stem cell factor (SCF) are essential factors in the control of survival, expansion and differentiation of erythroid progenitors. Upon activation, their receptors, the EpoR and c-Kit, initiate multiple signalling pathways that control many cellular processes. To control erythropoiesis, the strength, duration and specificity of signalling must be tightly controlled. Negative feed-back regulation is extensively studied, but positive feed-forward control is relatively little studied. The cytoplasmic tyrosine kinase Bruton's tyrosine kinase (Btk) was found to be phosphorylated by Jak2 in response to Epo and appeared to be required for fast and efficient phosphorylation of Epo-induced targets including the EpoR itself and downstream targets such as PLCgamma and Stat5. Erythroid progenitors deficient in Btk fail to undergo renewal divisions and differentiate instead at low, physiologic concentrations of Epo and SCF. In addition, Btk is phosphorylated by SCF, which causes association of Btk with TRAIL-receptor1. In absence of Btk, erythroid progenitors are hypersensitive to TRAIL. Thus, Btk modulates signalling in erythroid progenitors to enhance expansion of erythroid progenitors. The complexity of signalling by the EpoR\/c-Kit signalosome and its control by Btk is discussed with respect to normal and aberrant erythropoiesis.","authors":"von Lindern, M., Schmidt, U., Beug, H.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell Cycle","volume":"3","issue":"7","page":"876-9","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7688930","title":"Stable murine chondrogenic cell lines derived from c-fos-induced cartilage tumors.","abstract":"This study describes the detailed characterization of four murine chondrogenic cell lines (wT2-1, wT2-7, wT2-8, and wT2-9) that were isolated from a cartilage tumor induced by the protooncogene c-fos in chimeric mice. All cell lines are clonal and display a fibroblastic morphology with a doubling time of 1-2 days. Northern blot analysis demonstrated that in addition to expressing high levels of exogenous c-fos, all clones express varying levels of the cartilage marker gene type II collagen in addition to type I collagen. The clones also expressed high levels of the AP-1 genes c-jun and fra-1. The doubling times of these clones did not change over a period of 14 months in culture. Most importantly, however, expression of type II collagen was maintained in all cell lines for 8 months in culture, and two cell lines maintained type II collagen expression when analyzed after 14 months. Interestingly, type I collagen expression was lost after long-term culture. Following injection into syngeneic and nude mice, all cell lines formed tumors containing areas with the morphologic appearance of hyaline cartilage, indicating that these cell lines are chondrogenic. Thus, these stable murine chondrogenic cell lines provide a useful tool for studying the transcriptional control of cartilage-specific gene expression, as well as the growth control of chondrogenic cells.","authors":"Wang, ZQ., Grigoriadis, AE., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"J Bone Miner Res","volume":"8","issue":"7","page":"839-47","pdf":null,"JrId":"104","fulltextlink":null,"preprintlink":null,"articledate":"1993-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15226378","title":"Sister-chromatid cohesion mediated by the alternative RF-CCtf18\/Dcc1\/Ctf8, the helicase Chl1 and the polymerase-alpha-associated protein Ctf4 is essential for chromatid disjunction during meiosis II.","abstract":"Cohesion between sister chromatids mediated by a multisubunit complex called cohesin is established during DNA replication and is essential for the orderly segregation of chromatids during anaphase. In budding yeast, a specialized replication factor C called RF-C(Ctf18\/Dcc1\/Ctf8) and the DNA-polymerase-alpha-associated protein Ctf4 are required to maintain sister-chromatid cohesion in cells arrested for long periods in mitosis. We show here that CTF8, CTF4 and a helicase encoded by CHL1 are required for efficient sister chromatid cohesion in unperturbed mitotic cells, and provide evidence that Chl1 functions during S-phase. We also show that, in contrast to mitosis, RF-C(Ctf18\/Dcc1\/Cft8), Ctf4 and Chl1 are essential for chromosome segregation during meiosis and for the viability of meiotic products. Our finding that cells deleted for CTF8, CTF4 or CHL1 undergo massive meiosis II non-disjunction suggests that the second meiotic division is particularly sensitive to cohesion defects. Using a functional as well as a cytological assay, we demonstrate that CTF8, CHL1 and CTF4 are essential for cohesion between sister centromeres during meiosis but dispensable for cohesin's association with centromeric DNA. Our finding that mutants in fission yeast ctf18 and dcc1 have similar defects suggests that the involvement of the alternative RF-C(Ctf18\/Dcc1\/Ctf8) complex in sister chromatid cohesion might be highly conserved.","authors":"Petronczki, M., Chwalla, B., Siomos, MF., Yokobayashi, S., Helmhart, W., Deutschbauer, AM., Davis, RW., Watanabe, Y., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Cell Sci","volume":"117","issue":"Pt 16","page":"3547-59","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15105377","title":"RISC is a 5' phosphomonoester-producing RNA endonuclease.","abstract":"Gene silencing in the process of RNA interference is mediated by a ribonucleoprotein complex referred to as RNA-induced silencing complex (RISC). Here we describe the molecular mechanism of target RNA cleavage using affinity-purified minimal RISC from human cells. Cleavage proceeds via hydrolysis and the release of a 3'-hydroxyl and a 5'-phosphate terminus. Substitution of the 2'-hydroxyl group at the cleavage site by 2'-deoxy had no significant effect, suggesting that product release and\/or a conformational transition rather than a chemical step is rate-limiting. Substitution by 2'-O-methyl at the cleavage site substantially reduced cleavage, which is presumably due to steric interference. Mutational analysis of the target RNA revealed that mismatches across from the 5' or the 3' end of the siRNA had little effect and that substrate RNAs as short as 15 nucleotides were cleaved by RISC.","authors":"Martinez, J., Tuschl, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genes Dev","volume":"18","issue":"9","page":"975-80","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15007095","title":"Btk is required for an efficient response to erythropoietin and for SCF-controlled protection against TRAIL in erythroid progenitors.","abstract":"Regulation of survival, expansion, and differentiation of erythroid progenitors requires the well-controlled activity of signaling pathways induced by erythropoietin (Epo) and stem cell factor (SCF). In addition to qualitative regulation of signaling pathways, quantitative control may be essential to control appropriate cell numbers in peripheral blood. We demonstrate that Bruton's tyrosine kinase (Btk) is able to associate with the Epo receptor (EpoR) and Jak2, and is a substrate of Jak2. Deficiency of Btk results in reduced and delayed phosphorylation of the EpoR, Jak2, and downstream signaling molecules such as Stat5 and PLCgamma1 as well as in decreased responsiveness to Epo. As a result, expansion of erythroid progenitors lacking Btk is impaired at limiting concentrations of Epo and SCF. In addition, we show that SCF induces Btk to interact with TNF-related apoptosis-inducing ligand (TRAIL)-receptor 1 and that lack of Btk results in increased sensitivity to TRAIL-induced apoptosis. Together, our results indicate that Btk is a novel, quantitative regulator of Epo\/SCF-dependent expansion and survival in erythropoiesis.","authors":"Schmidt, U., van den Akker, E., Parren-van Amelsvoort, M., Litos, G., de Bruijn, M., Guti\u00e9rrez, L., Hendriks, RW., Ellmeier, W., L\u00f6wenberg, B., Beug, H., von Lindern, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Exp Med","volume":"199","issue":"6","page":"785-95","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7615496","title":"Cyclin-dependent kinase site-regulated signal-dependent nuclear localization of the SW15 yeast transcription factor in mammalian cells.","abstract":"Control over the nuclear transport of transcription factors (TFs) represents a level of gene regulation integral to cellular processes such as differentiation, transformation and signal transduction. The Saccharomyces cerevisiae TF SWI5 is excluded from the nucleus in a cell cycle-dependent fashion, mediated by phosphorylation by the cyclin-dependent kinase (cdk) CDC28. Nuclear entry occurs in G1. beta-galactosidase fusion proteins carrying SWI5 amino acids 633-682, including the nuclear localization sequence (NLS: Lys-Lys-Tyr-Glu-Asn-Val-Val-Ile-Lys-Arg-Ser-Pro-Arg-Lys-Arg-Gly-Arg-Pro- Arg-Lys655) were analyzed for subcellular localization in appropriate temperature-sensitive yeast strains blocked in G1 or G2\/M using indirect immunofluorescence, and for nuclear import kinetics in living rat hepatoma or Vero African green monkey kidney cells microinjected with fluorescently labeled bacterially expressed protein and quantitative confocal laser microscopy. Cell cycle-dependent nuclear localization in yeast was both NLS and cdk site-dependent, whereby mutation of the cdk site serines (Ser646 and Ser664) to alanine resulted in constitutive nuclear localization. In mammalian cells, the SWI5 fusion proteins were similarly transported to the nucleus in an NLS-dependent fashion, while the mutation to Ala of the cdk site serines increased the maximal level of nuclear accumulation from about 1- to over 8-fold. We suggest that phosphorylation at the cdk sites inhibits nuclear transport of SWI5, consistent with our previous observations for the inhibition of SV40 large tumor antigen nuclear transport by phosphorylation by the cdk cdc2. The results indicate for the first time that a yeast NLS and, fascinatingly, its regulatory mechanisms are functional in higher eukaryotes, implying the universal nature of regulatory signals for protein transport to the nucleus.","authors":"Jans, DA., Moll, T., Nasmyth, K., Jans, P.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Biol Chem","volume":"270","issue":"29","page":"17064-7","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1995-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14702045","title":"Epigenetic regulation of telomere length in mammalian cells by the Suv39h1 and Suv39h2 histone methyltransferases.","abstract":"Telomeres are capping structures at the ends of eukaryotic chromosomes composed of TTAGGG repeats bound to an array of specialized proteins. Telomeres are heterochromatic regions. Yeast and flies with defects in activities that modify the state of chromatin also have abnormal telomere function, but the putative role of chromatin-modifying activities in regulating telomeres in mammals is unknown. Here we report on telomere length and function in mice null with respect to both the histone methyltransferases (HMTases) Suv39h1 and Suv39h2 (called SUV39DN mice). Suv39h1 and Suv39h2 govern methylation of histone H3 Lys9 (H3-Lys9) in heterochromatic regions. We show that primary cells derived from SUV39DN mice have abnormally long telomeres relative to wild-type controls. Using chromatin immunoprecipitation (ChIP) analysis, we found that telomeres were enriched in di- and trimethylated H3-Lys9 but that telomeres of SUV39DN cells had less dimethylated and trimethylated H3-Lys9 but more monomethylated H3-Lys9. Concomitant with the decrease in H3-Lys9 methylation, telomeres in SUV39DN cells had reduced binding of the chromobox proteins Cbx1, Cbx3 and Cbx5, homologs of Drosophila melanogaster heterochromatin protein 1 (HP1). These findings indicate substantial changes in the state of telomeric heterochromatin in SUV39DN cells, which are associated with abnormal telomere elongation. Taken together, the results indicate epigenetic regulation of telomere length in mammals by Suv39h1 and Suv39h2.","authors":"Garc\u00eda-Cao, M., O'Sullivan, R., Peters, AH., Jenuwein, T., Blasco, MA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nat Genet","volume":"36","issue":"1","page":"94-9","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7592886","title":"Activation of p70 S6 kinase and erk-encoded mitogen-activated protein kinases is resistant to high cyclic nucleotide levels in Swiss 3T3 fibroblasts.","abstract":"Treatment of Swiss mouse 3T3 fibroblasts with certain cyclic nucleotide phosphodiesterase inhibitors (theophylline, SQ 20,006, and MY-5445) prevents the activation of the M(r) 70,000 S6 kinase (p70S6k) induced by a variety of external stimuli. Concentrations giving half-maximal inhibition were 800, 50, and 25 microM, respectively. Western blot analysis and immunocomplex kinase assays showed that these compounds inhibit the phosphorylation and activation of p70S6k without affecting the erk-encoded mitogen-activated protein (MAP) kinases or the rsk-encoded S6 kinase (p90rsk). A distinct collection of cAMP and cGMP agonists and analogues did not suppress p70S6k activation, indicating that 1) high intracellular cyclic nucleotide concentrations do not antagonize the p70S6k pathway and 2) phosphodiesterase inhibitors block p70S6k activation by a mechanism that is independent of cAMP or cGMP production. The effect of theophylline and SQ 20,006, but not MY-5445, on p70S6k signaling may be due in part to the inhibition of a phosphatidylinositol 3-kinase that acts upstream of p70S6k. Finally, in contrast to many other cell types, cAMP and cGMP were also found to have no inhibitory effect on the MAP kinase\/p90rsk signaling pathway in Swiss 3T3 fibroblasts.","authors":"Petritsch, C., Woscholski, R., Edelmann, HM., Ballou, LM.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Biol Chem","volume":"270","issue":"44","page":"26619-25","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1995-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14657206","title":"Functions of lipoprotein receptors in neurons.","abstract":"The LDL receptor (LDLR) family is comprised of several multifunctional cell surface proteins that bind and endocytose ligands with diverse biological functions. One ligand common to all LDLR family members is apolipoprotein E (apoE), a lipid transport protein that also plays a central role in the pathogenesis of neurodegeneration in Alzheimer's disease. This review discusses the role of apoE and its receptors in the central nervous system and, in particular, the signaling mechanisms by which two members of the LDLR gene family, apoE receptor-2 and VLDL receptor, control brain development, normal neuronal positioning, and neurotransmission in the adult brain.","authors":"Beffert, U., Stolt, PC., Herz, J.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Lipid Res","volume":"45","issue":"3","page":"403-9","pdf":null,"JrId":"4914","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14690609","title":"Partitioning and plasticity of repressive histone methylation states in mammalian chromatin.","abstract":"Methylation of position-specific lysine residues in histone N termini is a central modification for regulating epigenetic transitions in chromatin. Each methylatable lysine residue can exist in a mono-, di-, or trimethylated state, thereby extending the indexing potential of this particular modification. Here, we examine all possible methylation states for histone H3 lysine 9 (H3-K9) and lysine 27 (H3-K27) in mammalian chromatin. Using highly specific antibodies together with quantitative mass spectrometry, we demonstrate that pericentric heterochromatin is selectively enriched for H3-K27 monomethylation and H3-K9 trimethylation. This heterochromatic methylation profile is dependent on the Suv39h histone methyltransferases (HMTases) but independent of the euchromatic G9a HMTase. In Suv39h double null cells, pericentric heterochromatin is converted to alternative methylation imprints and accumulates H3-K27 trimethylation and H3-K9 monomethylation. Our data underscore the selective presence of distinct histone lysine methylation states in partitioning chromosomal subdomains but also reveal a surprising plasticity in propagating methylation patterns in eukaryotic chromatin.","authors":"Peters, AH., Kubicek, S., Mechtler, K., O'Sullivan, RJ., Derijck, AA., Perez-Burgos, L., Kohlmaier, A., Opravil, S., Tachibana, M., Shinkai, Y., Martens, JH., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Mol Cell","volume":"12","issue":"6","page":"1577-89","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-154","title":"Direct comparison of ischemic- vs. cryoinjury in the neonatal mouse heart. ","abstract":null,"authors":"Schuetz T, Kuehn B, Penninger JM, Haubner BJ","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Wiener Klinische Wochenschrift","volume":"","issue":"127","page":"9-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12818158","title":"The MAGUK family protein CARD11 is essential for lymphocyte activation.","abstract":"Members of the MAGUK family proteins cluster receptors and intracellular signaling molecules at the neuronal synapse. We report that genetic inactivation of the MAGUK family protein CARD11\/Carma1\/Bimp3 results in a complete block in T and B cell immunity. CARD11 is essential for antigen receptor- and PKC-mediated proliferation and cytokine production in T and B cells due to a selective defect in JNK and NFkappaB activation. Moreover, B cell proliferation and JNK activation were impaired upon stimulation of TLR4 with lipopolysaccharide, indicating that CARD11 is involved in both the innate and adaptive immune systems. Our results show that the same family of molecules are critical regulators of neuronal synapses and immune receptor signaling.","authors":"Hara, H., Wada, T., Bakal, C., Kozieradzki, I., Suzuki, S., Suzuki, N., Nghiem, M., Griffiths, EK., Krawczyk, C., Bauer, B., D'Acquisto, F., Ghosh, S., Yeh, WC., Baier, G., Rottapel, R., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Immunity","volume":"18","issue":"6","page":"763-75","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33896069","title":"Gene and transgenics nomenclature for the laboratory axolotl-Ambystoma mexicanum.","abstract":"The laboratory axolotl (Ambystoma mexicanum) is widely used in biological research. Recent advancements in genetic and molecular toolkits are greatly accelerating the work using axolotl, especially in the area of tissue regeneration. At this juncture, there is a critical need to establish gene and transgenic nomenclature to ensure uniformity in axolotl research. Here, we propose guidelines for genetic nomenclature when working with the axolotl.","authors":"Nowoshilow, S., Fei, JF., Voss, SR., Tanaka, EM., Murawala, P.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Dev Dyn","volume":"251","issue":"6","page":"913-921","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25142875","title":"CLP1 as a novel player in linking tRNA splicing to neurodegenerative disorders.","abstract":"Defects in RNA metabolic pathways are well-established causes for neurodegenerative disorders. Several mutations in genes involved in pre-messenger RNA (pre-mRNA) and tRNA metabolism, RNA stability and protein translation have been linked to motor neuron diseases. Our study on a mouse carrying a catalytically inactive version of the RNA kinase CLP1, a component of the tRNA splicing endonuclease complex, revealed a neurological disorder characterized by progressive loss of lower spinal motor neurons. Surprisingly, mutant mice accumulate a novel class of tRNA-derived fragments. In addition, patients with homozygous missense mutations in CLP1 (R140H) were recently identified who suffer from severe motor-sensory defects, cortical dysgenesis and microcephaly, and exhibit alterations in transfer RNA (tRNA) splicing. Here, we review functions of CLP1 in different RNA pathways and provide hypotheses on the role of the tRNA splicing machinery in the generation of tRNA fragments and the molecular links to neurodegenerative disorders. We further immerse the biology of tRNA splicing into topics of (t)RNA metabolism and oxidative stress, putting forward the idea that defects in tRNA processing leading to tRNA fragment accumulation might trigger the development of neurodegenerative diseases.","authors":"Weitzer, S., Hanada, T., Penninger, JM., Martinez, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Wiley Interdiscip Rev RNA","volume":"6","issue":"1","page":"47-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1370202","title":"Factor-dependent erythroid cell lines derived from mice transplanted with hematopoietic cells expressing the v-src oncogene.","abstract":"Transplantation of spleen cells from primary reconstituted mice expressing the v-src oncogene to secondary and tertiary irradiated recipients resulted in the emergence of erythroid precursors with a transformed phenotype. When cultured in methyl cellulose, these precursors generated colonies of undifferentiated cells that could be expanded into continuously growing factor-dependent cell lines in liquid culture. All lines tested had a similar phenotype and expressed the v-src oncogene. In addition they responded to factors that regulate normal erythroid development, namely erythropoietin (Epo), interleukin-3 (IL-3), and mast cell growth factor (MGF), the ligand to the c-kit encoded receptor. When cells from one of the lines were maintained in the absence of factor, a \"factor independent\" subpopulation emerged that appeared to grow in an autocrine fashion. Conditioned medium from these cells stimulated their own growth as well as the growth of broad spectrum of normal precursors. Studies with neutralizing antibodies indicated that the predominant colony-stimulating factor produced by these cells is IL-3.","authors":"Kennedy, M., Beug, H., Wagner, EF., Keller, G.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Blood","volume":"79","issue":"1","page":"180-90","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"1992-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12853483","title":"JNK phosphorylation relieves HDAC3-dependent suppression of the transcriptional activity of c-Jun.","abstract":"The AP-1 transcription factor c-Jun is a prototypical nuclear effector of the JNK signal transduction pathway. The integrity of JNK phosphorylation sites at serines 63\/73 and at threonines 91\/93 in c-Jun is essential for signal-dependent target gene activation. We show that c-Jun phosphorylation mediates dissociation of an inhibitory complex, which is associated with histone deacetylase 3 (HDAC3). The subsequent events that ultimately cause increased mRNA synthesis are independent of c-Jun phosphorylation and its interaction with JNK. These findings provide an 'activation by de-repression' model as an explanation for the stimulatory function of JNK on c-Jun.","authors":"Weiss, C., Schneider, S., Wagner, EF., Zhang, X., Seto, E., Bohmann, D.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"EMBO J","volume":"22","issue":"14","page":"3686-95","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2003-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12575993","title":"The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains.","abstract":"We have identified a family of 'Agenet' domains that are plant-specific homologs of Tudor domains. This finding has been extended, using a combination of sequence- and structure-dependent approaches, to show that the three beta-stranded core regions of Tudor, PWWP, chromatin-binding (Chromo) and MBT domains are homologous because they originate from a common ancestor. In addition, we have revealed pairs of tandem repeats in the fragile X mental retardation protein (FMRP) family that are also members of this Tudor domain 'Royal Family'.","authors":"Maurer-Stroh, S., Dickens, NJ., Hughes-Davies, L., Kouzarides, T., Eisenhaber, F., Ponting, CP.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Trends Biochem Sci","volume":"28","issue":"2","page":"69-74","pdf":null,"JrId":"7837","fulltextlink":null,"preprintlink":null,"articledate":"2003-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12618753","title":"Activation of ERK1\/2 by deltaRaf-1:ER* represses Bim expression independently of the JNK or PI3K pathways.","abstract":"CC139 fibroblasts are one of several model systems in which the Raf --&gt; MEK --&gt; ERK1\/2 pathway can inhibit apoptosis independently of the PI3K pathway; however, the precise mechanism for this protective effect is not known. Serum withdrawal from CC139 fibroblasts resulted in the rapid onset of apoptosis, which was prevented by actinomycin D or cycloheximide. Serum withdrawal promoted the rapid, de novo accumulation of Bim(EL), a proapoptotic 'BH3-only' member of the Bcl-2 protein family. Bim(EL) expression was an early event, occurring several hours prior to caspase activation. In contrast to studies in neurons, activation of the JNK --&gt; c-Jun pathway was neither necessary nor sufficient to induce Bim(EL) expression. Selective inhibition of either the ERK pathway (with U0126) or the PI3K pathway (with LY294002) caused an increase in the expression of Bim(EL). Furthermore, selective activation of the ERK1\/2 pathway by deltaRaf-1:ER* substantially reduced Bim(EL) expression, abolished conformational changes in Bax and blocked the appearance of apoptotic cells. The ability of deltaRaf-1:ER* to repress Bim(EL) expression required the ERK pathway but was independent of the PI3K --&gt; PDK --&gt; PKB pathway. Thus, serum withdrawal-induced expression of Bim(EL) occurs independently of the JNK --&gt; c-Jun pathway and can be repressed by the ERK pathway independently of the PI3K pathway. This may contribute to Raf- and Ras-induced cell survival at low serum concentrations.","authors":"Weston, CR., Balmanno, K., Chalmers, C., Hadfield, K., Molton, SA., Ley, R., Wagner, EF., Cook, SJ.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Oncogene","volume":"22","issue":"9","page":"1281-93","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2003-04-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1352882","title":"High-efficiency receptor-mediated delivery of small and large (48 kilobase gene constructs using the endosome-disruption activity of defective or chemically inactivated adenovirus particles.","abstract":"One limit to successful receptor-mediated gene delivery is the exit of the endocytosed material from the endosome. We demonstrate here the delivery of marker genes to tissue culture cells using a modification of the receptor-mediated gene delivery technique that exploits the endosomolytic activity of defective adenovirus particles. In particular, greater than 90% of the transfected-cell population is found to express a beta-galactosidase gene, and, most importantly, this high level of expression can be obtained with psoralen-inactivated virus particles. Furthermore, because the delivered gene is not carried within the genome of the adenovirus particle, the size constraints are relieved, and we can, therefore, show the delivery of a 48-kilobase cosmid DNA molecule.","authors":"Cotten, M., Wagner, E., Zatloukal, K., Phillips, S., Curiel, DT., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Proc Natl Acad Sci U S A","volume":"89","issue":"13","page":"6094-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1992-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12678844","title":"CD45 regulated signaling pathways.","abstract":"CD45 is expressed on all nucleated haematopoietic cells and was originally identified as the first and prototypic transmembrane protein tyrosine phosphatase (PTPase). CD45 has been extensively studied for over two decades as a PTPase that functions in antigen receptor signaling by dephosphorylation of Src-kinases. CD45 can operate as a positive as well negative regulator of Src-family kinases. In CD45 mutant cell lines, CD45-deficient mice, and CD45-deficient human SCID patients, CD45 is required for signal transduction through antigen receptors. Our group has recently shown that CD45 can also function as a Janus kinase (JAK) tyrosine phosphatase that negatively regulates cytokine receptor signaling involved in the differentiation, proliferation, and antiviral immunity of haematopoietic cells. Moreover, a point mutation in CD45, implicated in affecting CD45 dimerization, and a genetic polymorphism that affects alternative CD45 splicing have been implicated in autoimmunity in mice and humans. CD45 is expressed in multiple isoforms and modulation of specific CD45 splice variants with antibodies can prevent transplant rejections. Moreover, loss of CD45 can affect microglia activation in a mouse model for Alzheimer's disease. Modulation of CD45 splice variants and CD45 activity might provide a unique opportunity to design drugs that turn off or turn-on antigen and cytokine receptor signaling in cancer, allergy, transplantation, or autoimmunity.","authors":"Irie-Sasaki, J., Sasaki, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Top Med Chem","volume":"3","issue":"7","page":"783-96","pdf":null,"JrId":"27009","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12386155","title":"Snapshots of the cystine lyase C-DES during catalysis. Studies in solution and in the crystalline state.","abstract":"The cystine lyase (C-DES) of Synechocystis is a pyridoxal-5'-phosphate-dependent enzyme distantly related to the family of NifS-like proteins. The crystal structure of an N-terminal modified variant has recently been determined. Herein, the reactivity of this enzyme variant was investigated spectroscopically in solution and in the crystalline state to follow the course of the reaction and to determine the catalytic mechanism on a molecular level. Using the stopped-flow technique, the reaction with the preferred substrate cystine was found to follow biphasic kinetics leading to the formation of absorbing species at 338 and 470 nm, attributed to the external aldimine and the alpha-aminoacrylate; the reaction with cysteine also exhibited biphasic behavior but only the external aldimine accumulated. The same reaction intermediates were formed in crystals as seen by polarized absorption microspectrophotometry, thus indicating that C-DES is catalytically competent in the crystalline state. The three-dimensional structure of the catalytically inactive mutant C-DES(K223A) in the presence of cystine showed the formation of an external aldimine species, in which two alternate conformations of the substrate were observed. The combined results allow a catalytic mechanism to be proposed involving interactions between cystine and the active site residues Arg-360, Arg-369, and Trp-251*; these residues reorient during the beta-elimination reaction, leading to the formation of a hydrophobic pocket that stabilizes the enolimine tautomer of the aminoacrylate and the cysteine persulfide product.","authors":"Kaiser, JT., Bruno, S., Clausen, T., Huber, R., Schiaretti, F., Mozzarelli, A., Kessler, D.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Biol Chem","volume":"278","issue":"1","page":"357-65","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2003-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1354613","title":"Transcriptional repression of band 3 and CAII in v-erbA transformed erythroblasts accounts for an important part of the leukaemic phenotype.","abstract":"The v-erbA oncogene confers two prominent properties on transformed erythroblasts: a block of spontaneous differentiation and tolerance to wide variations in the pH or ionic strength of culture medium. V-erbA acts as a constitutive repressor of erythrocyte-specific gene transcription, arresting the expression of at least three different erythroid genes: the erythrocyte anion transporter (band 3), carbonic anhydrase II (CAII) and delta-aminolevulinate synthase (ALA-S). To test whether or not the v-erbA induced repression of these genes is causally related to the v-erbA induced leukaemic phenotype, we have reintroduced the genes for band 3 or CAII into transformed erythroblasts via retrovirus vectors. We show here that such erythroblasts, expressing v-erbA, require the same narrow range of medium pH and ion concentration for growth as do transformed erythroblasts lacking v-erbA, i.e. the v-erbA induced tolerance to pH variation was abrogated. The v-erbA induced differentiation block, however, remained unaffected by the re-expression of band 3 and was only slightly affected by the re-expression of CAII. Our experiments show that the two v-erbA-related 'erythroblast transformation parameters' are separable: suppression of band 3 and CAII accounts for one parameter (pH\/ion tolerance), while the second parameter (differentiation block) must involve v-erbA regulation of a different set of target genes.","authors":"Fuerstenberg, S., Leitner, I., Schroeder, C., Schwarz, H., Vennstr\u00f6m, B., Beug, H.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"EMBO J","volume":"11","issue":"9","page":"3355-65","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1992-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12119031","title":"Spectroscopic and kinetic analyses reveal the pyridoxal 5'-phosphate binding mode and the catalytic features of Treponema denticola cystalysin.","abstract":"To obtain insight into the functional properties of Treponema denticola cystalysin, we have analyzed the pH- and ligand-induced spectral transitions, the pH dependence of the kinetic parameters, and the substrate specificity of the purified enzyme. The absorption spectrum of cystalysin has maxima at 418 and 320 nm. The 320 nm band increases at high pH, while the 418 nm band decreases; the apparent pK(spec) of this spectral transition is about 8.4. Cystalysin emitted fluorescence at 367 and 504 nm upon excitation at 320 and 418 nm, respectively. The pH profile for the 367 nm emission intensity increases above a single pK of approximately 8.4. On this basis, the 418 and 320 nm absorbances have been attributed to the ketoenamine and substituted aldamine, respectively. The pH dependence of both log k(cat) and log k(cat)\/K(m) for alpha,beta-elimination reaction indicates that a single ionizing group with a pK value of approximately 6.6 must be unprotonated to achieve maximum velocity. This implies that cystalysin is more catalytically competent in alkaline solution where a remarkable portion of its coenzyme exists as inactive aldamine structure. Binding of substrates or substrate analogues to the enzyme over the pH range 6-9.5 converts both the 418 and 320 nm bands into an absorbing band at 429 nm, assigned to the external aldimine in the ketoenamine form. All these data suggest that the equilibrium from the inactive aldamine form of the coenzyme shifts to the active ketoenamine form on substrate binding. In addition, reinvestigation of the substrate spectrum of alpha,beta-elimination indicates that cystalysin is a cyst(e)ine C-S lyase rather than a cysteine desulfhydrase as claimed previously.","authors":"Bertoldi, M., Cellini, B., Clausen, T., Voltattorni, CB.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Biochemistry","volume":"41","issue":"29","page":"9153-64","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36480208","title":"Correction: Biallelic PAX5 mutations cause hypogammaglobulinemia, sensorimotor deficits, and autism spectrum disorder.","abstract":null,"authors":"Kaiser, FMP., Gruenbacher, S., Oyaga, MR., Nio, E., Jaritz, M., Sun, Q., van der Zwaag, W., Kreidl, E., Zopf, LM., Dalm, VASH., Pel, J., Gaiser, C., van der Vliet, R., Wahl, L., Rietman, A., Hill, L., Leca, I., Driessen, G., Laffeber, C., Brooks, A., Katsikis, PD., Lebbink, JHG., Tachibana, K., van der Burg, M., De Zeeuw, CI., Badura, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"J Exp Med","volume":"220","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12032080","title":"Essential function of histone deacetylase 1 in proliferation control and CDK inhibitor repression.","abstract":"Histone deacetylases (HDACs) modulate chromatin structure and transcription, but little is known about their function in mammalian development. HDAC1 was implicated previously in the repression of genes required for cell proliferation and differentiation. Here we show that targeted disruption of both HDAC1 alleles results in embryonic lethality before E10.5 due to severe proliferation defects and retardation in development. HDAC1-deficient embryonic stem cells show reduced proliferation rates, which correlate with decreased cyclin-associated kinase activities and elevated levels of the cyclin-dependent kinase inhibitors p21(WAF1\/CIP1) and p27(KIP1). Similarly, expression of p21 and p27 is up-regulated in HDAC1-null embryos. In addition, loss of HDAC1 leads to significantly reduced overall deacetylase activity, hyperacetylation of a subset of histones H3 and H4 and concomitant changes in other histone modifications. The expression of HDAC2 and HDAC3 is induced in HDAC1-deficient cells, but cannot compensate for loss of the enzyme, suggesting a unique function for HDAC1. Our study provides the first evidence that a histone deacetylase is essential for unrestricted cell proliferation by repressing the expression of selective cell cycle inhibitors.","authors":"Lagger, G., O'Carroll, D., Rembold, M., Khier, H., Tischler, J., Weitzer, G., Schuettengruber, B., Hauser, C., Brunmeir, R., Jenuwein, T., Seiser, C.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"EMBO J","volume":"21","issue":"11","page":"2672-81","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9708736","title":"Differential requirement for caspase 9 in apoptotic pathways in vivo.","abstract":"Mutation of Caspase 9 (Casp9) results in embryonic lethality and defective brain development associated with decreased apoptosis. Casp9-\/- embryonic stem cells and embryonic fibroblasts are resistant to several apoptotic stimuli, including UV and gamma irradiation. Casp9-\/- thymocytes are also resistant to dexamethasone- and gamma irradiation-induced apoptosis, but are surprisingly sensitive to apoptosis induced by UV irradiation or anti-CD95. Resistance to apoptosis is accompanied by retention of the mitochondrial membrane potential in mutant cells. In addition, cytochrome c is translocated to the cytosol of Casp9-\/- ES cells upon UV stimulation, suggesting that Casp9 acts downstream of cytochrome c. Caspase processing is inhibited in Casp9-\/- ES cells but not in thymocytes or splenocytes. Comparison of the requirement for Casp9 and Casp3 in different apoptotic settings indicates the existence of at least four different apoptotic pathways in mammalian cells.","authors":"Hakem, R., Hakem, A., Duncan, GS., Henderson, JT., Woo, M., Soengas, MS., Elia, A., de la Pompa, JL., Kagi, D., Khoo, W., Potter, J., Yoshida, R., Kaufman, SA., Lowe, SW., Penninger, JM., Mak, TW.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Cell","volume":"94","issue":"3","page":"339-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7492595","title":"The ATPase activity of purified CDC48p from Saccharomyces cerevisiae shows complex dependence on ATP-, ADP-, and NADH-concentrations and is completely inhibited by NEM.","abstract":"The cell cycle protein CDC48p from Saccharomyces cerevisiae is a member of a protein superfamily (AAA superfamily) characterized by a common region of approximately 200 amino-acid residues including an ATP binding consensus. CDC48p purified to homogeneity showed considerable ATPase activity which could be completely abolished by preincubation with NEM in the absence of ATP. ATP protects the protein from NEM and stabilizes the otherwise labile enzyme. The ATPase activity is reversibly inhibited by NADH and shows cooperativity with its substrate ATP. The application of the in vitro ATPase activity to the identification of physiologically interacting molecules is discussed. By electron microscopy, the enzyme was shown to consist of hexameric ring structures similar to its vertebrate homologue.","authors":"Fr\u00f6hlich, KU., Fries, HW., Peters, JM., Mecke, D.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Biochim Biophys Acta","volume":"1253","issue":"1","page":"25-32","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1996-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11484059","title":"Rb targets histone H3 methylation and HP1 to promoters.","abstract":"In eukaryotic cells the histone methylase SUV39H1 and the methyl-lysine binding protein HP1 functionally interact to repress transcription at heterochromatic sites. Lysine 9 of histone H3 is methylated by SUV39H1 (ref. 2), creating a binding site for the chromo domain of HP1 (refs 3, 4). Here we show that SUV39H1 and HP1 are both involved in the repressive functions of the retinoblastoma (Rb) protein. Rb associates with SUV39H1 and HP1 in vivo by means of its pocket domain. SUV39H1 cooperates with Rb to repress the cyclin E promoter, and in fibroblasts that are disrupted for SUV39, the activity of the cyclin E and cyclin A2 genes are specifically elevated. Chromatin immunoprecipitations show that Rb is necessary to direct methylation of histone H3, and is necessary for binding of HP1 to the cyclin E promoter. These results indicate that the SUV39H1-HP1 complex is not only involved in heterochromatic silencing but also has a role in repression of euchromatic genes by Rb and perhaps other co-repressor proteins.","authors":"Nielsen, SJ., Schneider, R., Bauer, UM., Bannister, AJ., Morrison, A., O'Carroll, D., Firestein, R., Cleary, M., Jenuwein, T., Herrera, RE., Kouzarides, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nature","volume":"412","issue":"6846","page":"561-5","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11740497","title":"Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin.","abstract":"Post-translational modifications of histone amino termini are an important regulatory mechanism that induce transitions in chromatin structure, thereby contributing to epigenetic gene control and the assembly of specialized chromosomal subdomains. Methylation of histone H3 at lysine 9 (H3-Lys9) by site-specific histone methyltransferases (Suv39h HMTases) marks constitutive heterochromatin. Here, we show that H3-Lys9 methylation also occurs in facultative heterochromatin of the inactive X chromosome (Xi) in female mammals. H3-Lys9 methylation is retained through mitosis, indicating that it might provide an epigenetic imprint for the maintenance of the inactive state. Disruption of the two mouse Suv39h HMTases abolishes H3-Lys9 methylation of constitutive heterochromatin but not that of the Xi. In addition, HP1 proteins, which normally associate with heterochromatin, do not accumulate with the Xi. These observations suggest the existence of an Suv39h-HP1-independent pathway regulating H3-Lys9 methylation of facultative heterochromatin.","authors":"Peters, AH., Mermoud, JE., O'Carroll, D., Pagani, M., Schweizer, D., Brockdorff, N., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nat Genet","volume":"30","issue":"1","page":"77-80","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10802648","title":"The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1.","abstract":"The gene encoding the insulin-like growth-factor type-2 receptor (Igf2r) is maternally expressed and imprinted. A CpG island in Igf2r intron 2 that carries a maternal-specific methylation imprint was shown in a transgenic model to be essential for Igf2r imprinting and for the production of an antisense RNA from the paternal allele. We report here that the endogenous region2 is the promoter for this antisense RNA (named Air, for antisense Igf2r RNA) and that the 3' end lies 107,796 bp distant in an intron of the flanking, but non-imprinted, gene Mas1.","authors":"Lyle, R., Watanabe, D., te Vruchte, D., Lerchner, W., Smrzka, OW., Wutz, A., Schageman, J., Hahner, L., Davies, C., Barlow, DP.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nat Genet","volume":"25","issue":"1","page":"19-21","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2000-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36522499","title":"Reply to: Assessment of 3D MINFLUX data for quantitative structural biology in cells.","abstract":null,"authors":"Gwosch, KC., Balzarotti, F., Pape, JK., Hoess, P., Ellenberg, J., Ries, J., Matti, U., Schmidt, R., Sahl, SJ., Hell, SW.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Methods","volume":"20","issue":"1","page":"52-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1347914","title":"Modulation of normal erythroid differentiation by the endogenous thyroid hormone and retinoic acid receptors: a possible target for v-erbA oncogene action.","abstract":"The v-erbA oncogene, a mutated version of the thyroid hormone receptor alpha (c-erbA\/TR-alpha), inhibits erythroid differentiation and constitutively represses transcription of certain erythrocyte genes, suggesting a normal function of the proto-oncogene c-erbA in erythropoiesis. Here we demonstrate that the endogenous thyroid hormone receptor alpha (c-erbA\/TR-alpha) and the closely related retinoic acid receptor alpha (RAR-alpha) play a role in the regulation of normal erythroid differentiation. Retinoic acid (RA) distinctly modulated the erythroid differentiation program of normal erythroid progenitors and erythroblasts reversibly transformed by a conditional tyrosine kinase oncogene. When added pulsewise to immature cells, differentiation was accelerated while more mature cells underwent premature cell death. Thyroid hormone (T3) alone caused similar but weaker effects. Interestingly, T3 strongly enhanced the action of RA, suggesting cooperative action of the two receptors in modulating erythroid differentiation. Expression of the human RAR-alpha in receptor-negative erythroblasts conferred RA-induced regulation of differentiation to the otherwise unresponsive cells, thus showing that the RAR-alpha is essential for the RA effect. Likewise, enhanced expression of exogenous c-erbA\/TR-alpha in erythroblasts rendered them susceptible to modulation of differentiation by T3, suggesting a similar function of both receptors.","authors":"Schroeder, C., Gibson, L., Zenke, M., Beug, H.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Oncogene","volume":"7","issue":"2","page":"217-27","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1992-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11377202","title":"X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11377202<\/PMID><DateCompleted><Year>2001<\/Year><Month>11<\/Month><Day>01<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>09<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0969-2126<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>9<\/Volume><Issue>5<\/Issue><PubDate><Year>2001<\/Year><Month>May<\/Month><Day>09<\/Day><\/PubDate><\/JournalIssue><Title>Structure (London, England : 1993)<\/Title><ISOAbbreviation>Structure<\/ISOAbbreviation><\/Journal><ArticleTitle>X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE.<\/ArticleTitle><Pagination><MedlinePgn>419-29<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">12-Oxophytodienoate reductase (OPR) is a flavin mononucleotide (FMN)-dependent oxidoreductase in plants that belongs to the family of Old Yellow Enzyme (OYE). It was initially characterized as an enzyme involved in the biosynthesis of the plant hormone jasmonic acid, where it catalyzes the reduction of the cyclic fatty acid derivative 9S,13S-12-oxophytodienoate (9S,13S-OPDA) to 1S,2S-3-oxo-2(2'[Z]-pentenyl)-cyclopentane-1-octanoate. Several isozymes of OPR are now known that show different stereoselectivities with regard to the four stereoisomers of OPDA.","authors":"Breithaupt, C., Strassner, J., Breitinger, U., Huber, R., Macheroux, P., Schaller, A., Clausen, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Structure","volume":"9","issue":"5","page":"419-29","pdf":null,"JrId":"22305","fulltextlink":null,"preprintlink":null,"articledate":"2001-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11356363","title":"Re-SET-ting heterochromatin by histone methyltransferases.","abstract":"Histone methylation was first described more than 35 years ago, but its role has remained enigmatic. Proposed functions range from transcriptional regulation to the higher-order packaging of chromatin in preparation for mitotic condensation. Histone methylation can occur on Arg or Lys residues, with an exquisite site selectivity for Lys methylation at specific positions in the N-termini of histones H3 and H4. Thus, Lys methylation joins acetylation and phosphorylation as a third component of a 'histone code' that modifies the underlying chromatin structure of the genetic information. Notably, in contrast to acetylation and phosphorylation, Lys methylation appears to be a relatively stable histone modification, thereby providing an ideal epigenetic mark for more long-term maintenance of chromatin states. The recent discovery of the first histone Lys methyltransferase has allowed the identification of a molecular mechanism in which the specific methylation of histone H3 at Lys9 generates a binding site for heterochromatin-associated proteins. These findings have broad implications for the overall functional organization of chromosome structure at constitutive heterochromatin (e.g. centromeres) and for chromatin-dependent inheritance of gene expression patterns. This review discusses how understanding this methylation system should address some of the long-standing mysteries of heterochromatin.","authors":"Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Trends Cell Biol","volume":"11","issue":"6","page":"266-73","pdf":null,"JrId":"21041","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11462210","title":"Remembering silence.","abstract":"Polycomb response elements (PREs) are regulatory switch elements that can direct the genes that they control to be either active or silenced. Once decided, this on or off state is maintained through subsequent cell divisions. We do not know how the switching works, or how it is copied to newly replicated chromosomes. Experiments that switch a silenced PRE to an active state have provided insights into both questions. A PRE switched experimentally can remember its previously silenced state and return to it after several cell divisions. In the most recent study of this phenomen on, the data show that several distinct variables affect the ability of PREs to \"remember\" and restore their previous state. The authors' interpretation of these results is discussed here.","authors":"Ringrose, L., Paro, R.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Bioessays","volume":"23","issue":"7","page":"566-70","pdf":null,"JrId":"1014","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25415977","title":"Arabidopsis PIAL1 and 2 promote SUMO chain formation as E4-type SUMO ligases and are involved in stress responses and sulfur metabolism.","abstract":"The Arabidopsis thaliana genes PROTEIN INHIBITOR OF ACTIVATED STAT LIKE1 (PIAL1) and PIAL2 encode proteins with SP-RING domains, which occur in many ligases of the small ubiquitin-related modifier (SUMO) conjugation pathway. We show that PIAL1 and PIAL2 function as SUMO ligases capable of SUMO chain formation and require the SUMO-modified SUMO-conjugating enzyme SCE1 for optimal activity. Mutant analysis indicates a role for PIAL1 and 2 in salt stress and osmotic stress responses, whereas under standard conditions, the mutants show close to normal growth. Mutations in PIAL1 and 2 also lead to altered sulfur metabolism. We propose that, together with SUMO chain binding ubiquitin ligases, these enzymes establish a pathway for proteolytic removal of sumoylation substrates.","authors":"Tomanov, K., Zeschmann, A., Hermkes, R., Eifler, K., Ziba, I., Grieco, M., Novatchkova, M., Hofmann, K., Hesse, H., Bachmair, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Plant Cell","volume":"26","issue":"11","page":"4547-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10882066","title":"Cohesin's binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins.","abstract":"Cohesion between sister chromatids depends on a multisubunit cohesin complex that binds to chromosomes around DNA replication and dissociates from them at the onset of anaphase. Scc2p, though not a cohesin subunit, is also required for sister chromatid cohesion. We show here that Scc2p forms a complex with a novel protein, Scc4p, which is also necessary for sister cohesion. In scc2 or scc4 mutants, cohesin complexes form normally but fail to bind both to centromeres and to chromosome arms. Our data suggest that a major role for the Scc2p\/Scc4p complex is to facilitate the loading of cohesin complexes onto chromosomes.","authors":"Ciosk, R., Shirayama, M., Shevchenko, A., Tanaka, T., Toth, A., Shevchenko, A., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Cell","volume":"5","issue":"2","page":"243-54","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2000-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7094019","title":"Temperature-sensitive changes in the structure of globin chromatin in lines of red cell precursors transformed by ts-AEV.","abstract":"Chicken bone marrow cells infected in vitro with a temperature-sensitive avian erythroblastosis virus fall to produce hemoglobin at 36 degrees C. When the product or products of the transforming gene (erb) are inactivated by a temperature shift to 42 degrees C in culture, several different cloned lines of cells infected with the temperature-sensitive avian erythroblastosis virus begin to make hemoglobin. This shift in phenotype correlates with an increase in hemoglobin mRNA specific to both adult and embryonic alpha and beta globin. The switch is accompanied by the acquisition of DNAase I-hypersensitive sites in one cell line (clone 2); however, a hypothetically more mature line (clone 3) has already acquired globin DNAase-hypersensitive sites but does not express hemoglobin until the temperature shift. Several (but not all) specific restriction sites associated with both the alpha and beta domains become unmethylated after the switch from 36 degrees C to 42 degrees C. The magnitude of these methylation switches is small compared with changes that occur in these genes during normal avian erythropoiesis. The results suggest that changes in chromosomal structure precede transcription and are not a consequence of transcription. Since (presumptive) precursor cloned lines can be established with some, but not all, of the structural properties of active globin chromatin, it is likely that many of these properties can be independently established and are not obligatorily related.","authors":"Weintraub, H., Beug, H., Groudine, M., Graf, T.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Cell","volume":"28","issue":"4","page":"931-40","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1982-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6328316","title":"Identification of a form of the avian erythroblastosis virus erb-B gene product at the cell surface.","abstract":"Avian erythroblastosis virus (AEV) induces both erythroblastosis and fibrosarcoma in chickens. The viral oncogene responsible for these diseases, erb, is divided into two regions, erb-A and erb-B, although recent evidence suggests that it is primarily the erb-B gene product that is responsible for the transforming activity. The erb-B gene product has been reported previously to be a membrane glycoprotein of 68,000 molecular weight (MW), gp68erb -B. However, we show here that gp68erb -B is an intracellular precursor which is modified further to a 74,000 MW protein, gp74erb -B. By the criteria of resistance to digestion with endoglycosidase H, subcellular fractionation and inhibition of biosynthesis by the ionophore monensin, gp74erb -B appears to be located at the cell surface. Recently, a comparison of the erb-B sequence with that of the epidermal growth factor (EGF) receptor has shown that these two genes are highly homologous, and that erb-B appears to represent a truncated form of this growth factor. In light of these data the identification of gp74erb -B at the plasma membrane suggests that this may be the functionally important form of the erb-B gene product.","authors":"Hayman, MJ., Beug, H.","publication_status":"ppublish","journalpubyear":"1984","journaltitle":"Nature","volume":"309","issue":"5967","page":"460-2","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1984-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6299767","title":"Detection of avian hematopoietic cell surface antigens with monoclonal antibodies to myeloid cells. Their distribution on normal and leukemic cells of various lineages.","abstract":"The isolation and characterization of monoclonal antibodies reacting with cell surface antigenic determinants of normal and leukemic avian hematopoietic cells is described. The antibodies were produced by immunizing mice with normal macrophages, as well as with myeloid cells transformed with the avian acute leukemia viruses MC29, AMV and E26. Eleven antibodies were characterized for their reactivity with a variety of normal and leukemic cells of the myeloid, B- and T-lymphoid and of the erythroid cell lineage. Using several methods, they could be subdivided into five distinct types: I. Four antibodies were specific for the myeloid lineage, predominantly reacting with immature myeloid cells. II. One antibody reacted with mature and immature myeloid cells as well as with T-lymphoid cells. III. Four antibodies reacted with myeloid, erythroid and T-lymphoid cells. IV. One antibody reacted with myeloid as well as with T- and B-lymphoid cells. V. One antibody reacted with all kinds of chicken hematopoietic cells except erythrocytes. The first type of antibodies detected glycoproteins with MWs of 170 and 130 kD. The pattern of antigens precipitated varied with the different monoclonal antibodies of this group. The antibody of the fourth type precipitated a 30 kD polypeptide from extracts of myeloid and lymphoid cells. None of the other antibodies precipitated any detectable proteins.","authors":"Kornfeld, S., Beug, H., Doederlein, G., Graf, T.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Exp Cell Res","volume":"143","issue":"2","page":"383-94","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1983-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6297801","title":"Identification and characterization of the avian erythroblastosis virus erbB gene product as a membrane glycoprotein.","abstract":"Avian erythroblastosis virus causes erythroid leukemia and sarcomas in chickens. The viral oncogene responsible for these diseases, erb, is divided into two regions known as erbA and erbB, and recent evidence suggests that it is the erbB gene that is responsible for the transforming activity. From rats bearing avian erythroblastosis virus-induced sarcomas, we have obtained antisera which are specific for the erb gene products. Using such antisera, we have been able to characterize the erbB gene product as a 68,000 molecular weight protein. Pulse-chase and cell-free in vitro translation experiments show that the initial product is a 62,500 dalton protein which is initially modified to a 66,000 dalton protein, and then further modified to a 68,000 dalton form. These modifications could be shown to be associated with glycosylation and phosphorylation. Cell fractionation experiments revealed that the 66,000 and 68,000 dalton proteins were located in cell membrane fractions, and immunofluorescence results showed the erbB gene product to be expressed on the cell surface.","authors":"Hayman, MJ., Ramsay, GM., Savin, K., Kitchener, G., Graf, T., Beug, H.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Cell","volume":"32","issue":"2","page":"579-88","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1983-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10595588","title":"Cloning, purification and characterisation of cystathionine gamma-synthase from Nicotiana tabacum.","abstract":"Cystathionine gamma-synthase, the enzyme catalysing the first reaction specific for methionine biosynthesis, has been cloned from Nicotiana tabacum, overexpressed in Escherichia coli and purified to homogeneity. The recombinant cystathionine gamma-synthase catalyses the pyridoxal 5'-phosphate dependent formation of L-cystathionine from L-homoserine phosphate and L-cysteine with apparent Km-values of 7.1+\/-3.1 mM and of 0.23+\/-0.07 mM, respectively. The enzyme was irreversibly inhibited by DL-propargylglycine (Ki = 18 microM, k(inact) = 0.56 min(-1)), while the homoserine phosphate analogues 3-(phosphonomethyl)pyridine-2-carboxylic acid, 4-(phosphonomethyl)pyridine-2-carboxylic acid, Z-3-(2-phosphonoethen-1-yl)pyridine-2-carboxylic acid, and DL-E-2-amino-5-phosphono-3-pentenoic acid acted as reversible competitive inhibitors with Ki values of 0.20, 0.30, 0.45, and 0.027 mM, respectively. In combination these results suggest a ping-pong mechanism for the cystathionine gamma-synthase reaction, with homoserine phosphate binding to the enzyme first. Large single crystals of cystathionine gamma-synthase diffracting to beyond 2.7 A resolution were obtained by the sitting drop vapour diffusion method. The crystals belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell constants a = 120.0 A, b = 129.5 A, c = 309.8 A, corresponding to two tetramers per asymmetric unit.","authors":"Clausen, T., Wahl, MC., Messerschmidt, A., Huber, R., Fuhrmann, JC., Laber, B., Streber, W., Steegborn, C.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Biol Chem","volume":"380","issue":"10","page":"1237-42","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"2000-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1341948","title":"Human foamy virus: an underestimated neuropathogen?","abstract":"Human foamy virus (HFV) is a recently characterized retrovirus which was originally isolated from patients with various neoplastic and degenerative diseases. However, until today it has not been possible to identify HFV as the causative agent of any disease and little is known about its prevalence in human populations. Like HTLV and HIV, HFV encodes the three structural retroviral genes, gag, pol and env, and an additional region containing three open reading frames, bel-1 to bel-3. Bel-1 activates transcription of the long terminal repeat of HFV and HIV. In order to study the consequences of expressing HFV regulatory genes and to investigate a possible pathogenic potential of HFV, we have introduced parts of the HFV genome into the germ line of mice. Our studies with transgenic mice demonstrate that HFV transgenes encompassing the bel region are transiently transcribed between midgestation and birth at moderate levels in various tissues. Expression is then suppressed, but resumes after a latency of several weeks in a restricted range of tissues and leads to extensive accumulation of HFV transcripts in single cells. This is associated with a progressive degenerative disease of the central nervous system and of striated muscle. These findings provide the first evidence of a disease induced by HFV and suggest that HFV might also act as a human pathogen in neurological diseases. Moreover, the transgenic mouse model will be useful for studying the molecular basis of HFV-induced neurotoxicity, the role of individual disease-associated HFV genes and the regulation of retroviral latency.","authors":"Aguzzi, A., Bothe, K., Wagner, EF., Rethwilm, A., Horak, I.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Brain Pathol","volume":"2","issue":"1","page":"61-9","pdf":null,"JrId":"2602","fulltextlink":null,"preprintlink":null,"articledate":"1994-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25345765","title":"Identifying (non-)coding RNAs and small peptides: challenges and opportunities.","abstract":"Over the past decade, high-throughput studies have identified many novel transcripts. While their existence is undisputed, their coding potential and functionality have remained controversial. Recent computational approaches guided by ribosome profiling have indicated that translation is far more pervasive than anticipated and takes place on many transcripts previously assumed to be non-coding. Some of these newly discovered translated transcripts encode short, functional proteins that had been missed in prior screens. Other transcripts are translated, but it might be the process of translation rather than the resulting peptides that serves a function. Here, we review annotation studies in zebrafish to discuss the challenges of placing RNAs onto the continuum that ranges from functional protein-encoding mRNAs to potentially non-functional peptide-producing RNAs to non-coding RNAs. As highlighted by the discovery of the novel signaling peptide Apela\/ELABELA\/Toddler, accurate annotations can give rise to exciting opportunities to identify the functions of previously uncharacterized transcripts.","authors":"Pauli, A., Valen, E., Schier, AF.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Bioessays","volume":"37","issue":"1","page":"103-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10463584","title":"An insulin-like growth factor-mediated, phosphatidylinositol 3' kinase-independent survival signaling pathway in beta tumor cells.","abstract":"Hyperproliferation of tumor cells usually coincides with increased tumor cell apoptosis. To overcome apoptosis, tumor cells frequently induce the expression of growth factors that mediate cell survival. In nontransformed cells, including fibroblasts and neurons, survival factor-mediated signal transduction involves the activation of phosphatidylinositol 3' kinase (PI-3K) and protein kinase B\/c-Akt (PKB). Here we demonstrate that tumor cell lines derived from a transgenic mouse model of pancreatic beta cell carcinogenesis use insulin-like growth factors to repress apoptosis independently of PI-3K and PKB. The results indicate that tumor cells can use additional survival signal transduction pathways.","authors":"Burtscher, I., Compagni, A., Lamm, GM., Christofori, G.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cancer Res","volume":"59","issue":"16","page":"3923-6","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"1999-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3856569","title":"Protein synthesis in differentiating normal and leukemic erythroid cells.","abstract":"Erythroleukemic cells transformed by the AEV or S13 strains of avian erythroblastosis virus differentiate in vitro either spontaneously (S13) or following a temperature induction (temperature-sensitive mutants of AEV). To study differentiation in these cells at the molecular level, homogeneous fractions of maturing cells at discrete stages of differentiation were prepared by Percoll density-gradient centrifugation. This method was also used for the fractionation of differentiating normal erythroid cells separated from total bone marrow by an immunological \"panning\" technique. Total protein synthesis in these cells was then analyzed by two-dimensional gel electrophoresis. The expression of several proteins was altered in differentiating leukemic cells but not in their normal counterparts. However, in general, the normal and leukemic cells from comparable stages of maturity showed closely related protein synthetic patterns. Similar early and late changes in the synthesis of a number of polypeptides were detected during maturation from early erythroid precursors to terminally differentiated erythrocytes. Further, the leukemic as well as the normal cells appeared to undergo a major switch in total protein synthetic pattern during late differentiation. These results demonstrate that normal and erythroleukemic cells differentiate along similar pathways.","authors":"Adkins, B., Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"J Cell Physiol","volume":"123","issue":"2","page":"269-76","pdf":null,"JrId":"4586","fulltextlink":null,"preprintlink":null,"articledate":"1985-05-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10319811","title":"Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter.","abstract":"Gene activation in eukaryotes requires chromatin remodeling complexes like Swi\/Snf and histone acetylases like SAGA. How these factors are recruited to promoters is not yet understood. Using CHIP, we measured recruitment of Swi\/Snf, SAGA, the repressor Ash1p, and transcription factors Swi5p and SBF to the HO endonuclease promoter as cells progress through the yeast cell cycle. Swi5p's entry into nuclei at the end of anaphase recruits Swi\/Snf, which then recruits SAGA. These two factors then facilitate SBF's binding. Ash1p, which only accumulates in daughter cell nuclei, binds to HO soon after Swi5p and aborts recruitment of Swi\/Snf, SAGA, and SBF. Swi5p remains at HO for only 5 min. Swi\/Snf's and SAGA's subsequent persistence at HO is self sustaining and constitutes an \"epigenetic memory\" of HO's transient interaction with Swi5p.","authors":"Cosma, MP., Tanaka, T., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cell","volume":"97","issue":"3","page":"299-311","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1999-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3498933","title":"The human alpha-1-antitrypsin gene is efficiently expressed from two tissue-specific promotors in transgenic mice.","abstract":"Alpha 1-antitrypsin (alpha 1AT) present in large amounts in human serum and synthesized predominantly in hepatocytes, is the most abundant protease inhibitor and alpha 1AT mutant proteins are associated with hereditary disorders. To investigate the regulation of the normal human alpha 1AT gene, we have microinjected fertilized mouse eggs with a 17.5 kb DNA fragment containing the entire gene with 7 kb 5' and 0.3 kb 3' flanking sequences. We show that this DNA fragment contains all the information for efficient, accurate and tissue-specific expression. High serum concentration of the human protein was found in three independent transgenic mouse lines. The human alpha 1AT RNA is transcribed efficiently in liver, kidney and macrophages and we demonstrate that two different promoters are used for the expression in liver and macrophages of the transgenic mice.","authors":"R\u00fcther, U., Tripodi, M., Cortese, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Nucleic Acids Res","volume":"15","issue":"18","page":"7519-29","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1987-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"4631665","title":"Dynamics of antigenic membrane sites relating to cell aggregation in Dictyostelium discoideum.","abstract":"Membrane interaction in aggregating cells of Dictyostelium discoideum can be blocked by univalent antibodies directed against specific membrane sites. Using a quantitative technique for measuring cell association, two classes of target sites for blocking antibodies were distinguished and their developmental dynamics studied. One class of these sites is specific for aggregation-competent cells, their quantity rising from virtually 0-level during growth, with a steep increase shortly before cell aggregation. The serological activity of these structures is species specific; they are not detectable in a nonaggregating mutant, but present in a revertant undergoing normal morphogenesis. Patterns of cell assembly in the presence of antibodies show that selective blockage of these membrane sites abolishes the preference for end-to-end association which is typical for aggregating cells. A second class of target sites is present in comparable quantities in particle fractions from both growth-phase and aggregation-competent cells. Blockage of these sites leads to aggregation patterns in which the side-by-side contacts of aggregating cells are abolished. The target sites of aggregation-inhibiting antibodies are suggested to be identical or associated with the molecular units of the cell membrane that mediate cell-to-cell contacts during aggregation. The results indicate that in one cell, two independent classes of contact sites can be simultaneously active.","authors":"Beug, H., Katz, FE., Gerisch, G.","publication_status":"ppublish","journalpubyear":"1973","journaltitle":"J Cell Biol","volume":"56","issue":"3","page":"647-58","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1973-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10327136","title":"The use of in vitro expanded erythroid cells in a model system for the isolation of fetal cells from maternal blood.","abstract":"The development of a non-invasive prenatal diagnostic test using fetal nucleated red blood cells (NRBCs) isolated from the maternal circulation is hampered by the low frequency of these cells in maternal blood, requiring extensive enrichment procedures before any analytical procedure can be performed. In order to improve and simplify these procedures, we have used in vitro expanded erythroid cells derived from male umbilical cord blood in a model system for the isolation of fetal NRBCs from maternal blood. Erythroblast cells were expanded in vitro to high cell numbers and were immunophenotypically identical to fetal NRBCs isolated from maternal blood. Magnetic activated cell sorting (MACS) isolation procedures were optimized using in vitro expanded male NRBCs diluted up to 1 in 400,000 with female peripheral blood mononucleated cells. The number of recovered male cells was determined using two-colour fluorescence in situ hybridization with X and Y chromosomal probes. Using this model system, an NRBC isolation technique is described. It is based on a one-step MACS enrichment protocol for CD71 positive cells, which showed a significant (Wilcoxon signed ranks test, p&lt;0.05) two-fold higher yield of male NRBCs than previously described MACS methodologies, in which CD71 positive cells were enriched after depletion of other cell types. Application of these isolation strategies to maternal blood samples resulted in a similar improved enrichment of male fetal cells after the direct enrichment of CD71 positive cells.","authors":"Jansen, MW., von Lindern, M., Beug, H., Brandenburg, H., Wildschut, HI., Wladimiroff, JW., In 't Veld, PA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Prenat Diagn","volume":"19","issue":"4","page":"323-9","pdf":null,"JrId":"6583","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7481803","title":"Lymphoproliferative disorders with early lethality in mice deficient in Ctla-4.","abstract":"The role of the cell-surface molecule CTLA-4 in the regulation of T cell activation has been controversial. Here, lymph nodes and spleens of CTLA-4-deficient mice accumulated T cell blasts with up-regulated activation markers. These blast cells also infiltrated liver, heart, lung, and pancreas tissue, and amounts of serum immunoglobulin were elevated. The mice invariably became moribund by 3 to 4 weeks of age. Although CTLA-4-deficient T cells proliferated spontaneously and strongly when stimulated through the T cell receptor, they were sensitive to cell death induced by cross-linking of the Fas receptor and by gamma irradiation. Thus, CTLA-4 acts as a negative regulator of T cell activation and is vital for the control of lymphocyte homeostasis.","authors":"Waterhouse, P., Penninger, JM., Timms, E., Wakeham, A., Shahinian, A., Lee, KP., Thompson, CB., Griesser, H., Mak, TW.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Science","volume":"270","issue":"5238","page":"985-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1995-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9808580","title":"Deregulated PAX-5 transcription from a translocated IgH promoter in marginal zone lymphoma.","abstract":"The PAX-5 gene codes for the transcription factor BSAP, which is expressed throughout B-cell development. Although loss-of-function mutation in the mouse showed an essential role for Pax-5 in early B lymphopoiesis, gain-of-function mutations have implicated the human PAX-5 gene in the control of late B-cell differentiation. PAX-5 (on 9p13) has been involved together with the immunoglobulin heavy-chain (IgH) gene (on 14q32) in the recurring t(9;14)(p13;q32) translocation that is characteristic of small lymphocytic lymphoma with plasmacytoid differentiation. Here we have characterized a complex t(2;9;14)(p12;p13;q32) translocation present in a closely related non-Hodgkin's lymphoma referred to as splenic marginal zone lymphoma (MZL). In this MZL-1 translocation, the two promoters of PAX-5 were replaced on the derivative chromosome 14 by an immunoglobulin switch Smicro promoter that was linked to the structural PAX-5 gene upstream of its translation initiation codon in exon 1B. Expression analyses confirmed that PAX-5 transcription was upregulated due to efficient initiation at the Smicro promoter in the malignant B lymphocytes of patient MZL-1. For comparison we have analyzed PAX-5 expression in another B-cell lymphoma, KIS-1, indicating that transcription from the distal PAX-5 promoter was increased in this tumor in agreement with the previously characterized translocation of the immunoglobulin Emicro; enhancer adjacent to PAX-5 exon 1A. In both lymphomas, the J-chain gene, which is thought to be under negative control by BSAP, was not expressed, whereas transcription of the putative target gene p53 was unaffected by PAX-5 overexpression. Together these data indicate that the t(9;14)(p13;q32) translocation contributes to lymphoma formation as a regulatory mutation that leads to increased PAX-5 expression in late B-cell differentiation due to promoter replacement or enhancer insertion.","authors":"Morrison, AM., J\u00e4ger, U., Chott, A., Schebesta, M., Haas, OA., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Blood","volume":"92","issue":"10","page":"3865-78","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"1998-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9724654","title":"Association of RPA with chromosomal replication origins requires an Mcm protein, and is regulated by Rad53, and cyclin- and Dbf4-dependent kinases.","abstract":"Eukaryotic cells use multiple replication origins to replicate their large genomes. Some origins fire early during S phase whereas others fire late. In Saccharomyces cerevisiae, initiator sequences (ARSs) are bound by the origin recognition complex (ORC). Cdc6p synthesized at the end of mitosis joins ORC and facilitates recruitment of Mcm proteins, which renders origins competent to fire. However, origins fire only upon the subsequent activation of S phase cyclin-dependent kinases (S-CDKs) and Dbf4\/Cdc7 at the G1\/S boundary. We have used a chromatin immunoprecipitation assay to measure the association with ARS sequences of DNA primase and the single-stranded DNA binding replication protein A (RPA) when fork movement is inhibited by hydroxyurea (HU). RPA's association with origins requires S-CDKs, Dbf4\/Cdc7 kinase and an Mcm protein. The recruitment of DNA primase depends on RPA. Furthermore, early- and late-firing origins differ not in the timing of their recruitment of an Mcm protein, but in the timing of RPA's recruitment. RPA is recruited to early but not to late origins in HU. We also show that Rad53 kinase is required to prevent RPA association with a late origin in HU. Our data suggest that the origin unwinding accompanied by RPA association is a key step, regulated by S-CDKs, Dbf4\/Cdc7 and Rad53p. Thus, in the presence of active S-CDKs and Dbf4\/Cdc7, Mcms may open origins and thereby facilitate the loading of RPA.","authors":"Tanaka, T., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"EMBO J","volume":"17","issue":"17","page":"5182-91","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1998-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3537125","title":"Immunolocalization and partial characterization of a nucleolar autoantigen (PM-Scl) associated with polymyositis\/scleroderma overlap syndromes.","abstract":"Precipitating anti-PM-Scl antibodies are present in sera from patients with polymyositis, scleroderma, and polymyositis\/scleroderma overlap syndromes. By indirect immunofluorescence microscopy, anti-PM-Scl antibodies stained the nucleolus in cells of different tissues and species, suggesting that the antigen is highly conserved. By electron microscopy, anti-PM-Scl antibodies reacted primarily with the granular component of the nucleolus. Drugs that inhibit rRNA synthesis had a marked effect on the expression of PM-Scl antigen. In actinomycin D-treated cells, immunofluorescence staining by anti-PM-Scl was significantly reduced with residual staining restricted to the granular regions of nucleoli. Treatment with 5,6-dichloro-beta-D-ribofuranosylbenzimidazole (DRB) also selectively reduced nucleolar staining. On a molecular level, anti-PM-Scl antibodies precipitated 11 polypeptides with molecular weights (Mr) ranging from 110,000 to 20,000. The Mr 80,000 and 20,000 polypeptides were phosphorylated. Evidence suggests that the PM-Scl antigen complex may be related to a preribosomal particle.","authors":"Reimer, G., Scheer, U., Peters, JM., Tan, EM.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"J Immunol","volume":"137","issue":"12","page":"3802-8","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"1987-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1334023","title":"Prepattern in the developing Drosophila eye revealed by an activated torso--sevenless chimeric receptor.","abstract":"Induction of the R7 photoreceptor cell fate in the developing eye of Drosophila depends on the activation of the sevenless receptor tyrosine kinase in the R7 precursor cell. The sevenless protein is expressed transiently in 8 of the 20 precursors of an ommatidium. Activation of the sevenless kinase in these eight cells indicates that six of them are competent to become R7 cells. To test the competence of all 20 ommatidial precursors in a temporally unrestricted manner we have used a constitutively activated sevenless kinase created by fusing the extracellular domain of a mutant torso protein, another Drosophila receptor tyrosine kinase, to the sevenless kinase. Our results show that competence to develop as neuronal cells in response to sevenless activity is spatially and temporally limited to the cells expressing sevenless. Therefore, the expression of sevenless marks a preexisting pattern of developmental potential in the disc epithelium.","authors":"Dickson, B., Sprenger, F., Hafen, E.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Genes Dev","volume":"6","issue":"12A","page":"2327-39","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1993-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9384703","title":"Adenovirus-enhanced receptor-mediated transferrinfection for the generation of tumor vaccines.","abstract":"Cancer vaccines are genetically modified tumor cells that, by cytokine secretion or by expression of costimulatory molecules, are capable of mobilizing the host's immune system to destroy tumor cells. We have used adenovirus-enhanced transferrinfection (AVET) for the generation of cancer vaccines. This is a highly efficient method to deliver various genes into a large proportion of tumor cells, making further selection unnecessary. We found in the mouse M-3 melanoma model that two consecutive vaccinations with transfected cells secreting IL-2 protect animals from tumor development by a subsequent challenge, and result in long-lasting tumor-specific immunity dependent on both CD4+ and CD8+ T cells. Patterns of lymphocyte recirculation and the need for CD4+ T cells indicated that the role of IL-2 is not merely local 'replacement of help', as has been proposed before. Instead, our findings suggest a three-stage process for the generation of effector T cells after vaccination with IL-2 secreting tumor cells: (1) tumor antigen uptake and processing at the site of injection by APCs, (2) migration of APCs into the regional draining lymph nodes where T-cell priming occurs, and (3) recirculation of activated cytotoxic T cells, that recognize and eliminate distant tumor cells. This model also implies that allogeneic tumor cells or synthetic tumor antigens may be used with success in future cancer vaccines.","authors":"Schweighoffer, T., Berger, M., Buschle, M., Schmidt, W., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Cytokines Mol Ther","volume":"2","issue":"3","page":"185-91","pdf":null,"JrId":"20747","fulltextlink":null,"preprintlink":null,"articledate":"1997-12-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8617399","title":"Chicken thymic nurse cells: an overview.","abstract":"Thymic nurse cells are multicellular complexes located in the subcortical area of the thymus of all avian, mammalian and amphibian species investigated so far. Since their first description in 1980 many studies have been carried out to characterize their morphological and functional properties. The purpose of this review is to summarize recent morphological as well a functional analyses of chicken thymic nurse cells which suggest a role of these cell complexes in T cell selection.","authors":"Rieker, T., Penninger, J., Romani, N., Wick, G.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Dev Comp Immunol","volume":"19","issue":"4","page":"281-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1996-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8125257","title":"Elucidation of the role of breathless, a Drosophila FGF receptor homolog, in tracheal cell migration.","abstract":"DFGF-R1 (breathless), a Drosophila FGF receptor homolog, is required for the migration of tracheal cells and the posterior midline glial cells during embryonic development. To define the role of this receptor in cell migration, we have monitored the biological effects of a deregulated receptor containing the extracellular and transmembrane regions of the torso dominant allele and the cytoplasmic domain of DFGF-R1. Ubiquitous expression of the chimeric receptor at the time of tracheal cell migration did not disrupt migration in wild-type embryos. However, induction of the chimeric receptor corrected the tracheal defects of breathless (btl) mutant embryos, allowing the tracheal cells to migrate along their normal tracts. This result indicates that the normal activity of DFGF-R1 in promoting cell migration does not require spatially restricted cues. Late inductions of the chimeric construct, after the normal initiation of tracheal migration, allowed the definition of a broad time window during which the external signals guiding migration persist and the tracheal cells retain the capacity to respond to these cues. Rescue of tracheal migration in btl mutant embryos by the chimeric construct provides a sensitive biological assay for the activity of other Drosophila receptor tyrosine kinases (RTKs). Deregulated receptors containing the cytoplasmic domains of DFGF-R2, DER, torso, and sevenless were all able to partially rescue the migration defects. Consistent with the notion that these RTKs share a common signaling pathway, constructs containing the activated downstream elements Dras1 and Draf were also able to rescue tracheal migration, demonstrating that these two proteins are key players in the DFGF-R1 signaling pathway.","authors":"Reichman-Fried, M., Dickson, B., Hafen, E., Shilo, BZ.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Genes Dev","volume":"8","issue":"4","page":"428-39","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1994-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3443100","title":"Inducible and tissue-specific expression of human C-reactive protein in transgenic mice.","abstract":"C-reactive protein (CRP) is a major acute phase reactant in man but not in mouse. It is synthesized in abundant quantities by human hepatocytes during the course of several diseases, mainly acute inflammations. To investigate the regulation of CRP expression, the human CRP gene was introduced into fertilized eggs by microinjection and transgenic mouse lines were derived. The CRP gene is exclusively transcribed in the liver and expression is strictly dependent on experimental inflammation. The kinetics of induction both for RNA and protein synthesis is very fast; RNA is first detectable after 2 h in the liver, the protein after 6 h in the serum. Human CRP levels in the sera of transgenic mice are comparable to those observed in human diseases. Nuclear run-on experiments indicate that regulation is primarily at the transcriptional level.","authors":"Ciliberto, G., Arcone, R., Wagner, EF., R\u00fcther, U.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"EMBO J","volume":"6","issue":"13","page":"4017-22","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1988-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1319831","title":"Oncogene complementation in fetal brain transplants.","abstract":"Using a neural transplantation model and retrovirus-mediated gene transfer, we have introduced the oncogenes v-Ha-ras and v-myc into the developing rat brain. Upon insertion of a construct encoding v-Ha-ras and the Escherichia coli beta-galactosidase marker gene, the retroviral vector was found to be expressed in neurons, astrocytes, and endothelial cells of the graft. After latency periods of several months, fascicular neoplasms with expression of S-100 protein were observed in 50% of the transplants. The foreign genes were shown to be highly expressed in the tumors and in intact donor cells, by 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside histochemistry, indicating that an activated Ha-ras oncogene has the potential to initiate neoplastic transformation of glial cells. Introduction of the v-myc oncogene into 15 grafts resulted in only a single primitive neuroectodermal tumor. However, simultaneous expression of the v-Ha-ras and v-myc genes yielded highly malignant, polyclonal neoplasms in all recipient animals, as early as 13 days after transplantation, from which cell lines could be easily derived. In addition, neoplastic transformation was also observed in vitro following introduction of ras and myc into embryonic forebrain cultures and into newborn cerebellar cultures. These data indicate a powerful complementary transforming effect of ras and myc on neural progenitors in vivo and in vitro. Coexpression of ras and myc may, therefore, provide a highly efficient tool for transforming neural precursor cells in distinct segments of the central nervous system at different stages of development.","authors":"Wiestler, OD., Aguzzi, A., Schneemann, M., Eibl, R., von Deimling, A., Kleihues, P.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Cancer Res","volume":"52","issue":"13","page":"3760-7","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"1992-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8390761","title":"Identification of pol-related gene products of human foamy virus.","abstract":"Human foamy virus pol gene fragments were molecularly cloned into a procaryotic expression vector. The expression pattern of the cloned fragments and nucleotide sequence analysis of the 5' pol gene region revealed that in HFV the protease (PR) is located in the pol open reading frame. Purified recombinant proteins were used to generate antibodies in rats. In immunoblot assay, using infected cells as antigen, a precursor protein with an apparent molecular mass (M(r)) of 127K was identified by antibodies directed against the reverse transcriptase (RT), RNaseH, or integrase (IN) domains of pol. With concentrated virus as antigen, the RT and RNaseH antibodies recognized a protein of 80K, the IN antiserum recognized a protein of 40K, and the PR antiserum detected a protein of approximately 10K.","authors":"Netzer, KO., Schliephake, A., Maurer, B., Watanabe, R., Aguzzi, A., Rethwilm, A.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Virology","volume":"192","issue":"1","page":"336-8","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1993-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8406007","title":"DNA sequence recognition by Pax proteins: bipartite structure of the paired domain and its binding site.","abstract":"Previous DNA-binding studies indicated that an intact paired domain is required for interaction of the transcription factor BSAP (Pax-5) with DNA. We have now identified a subset of BSAP recognition sequences that also bind to a truncated BSAP peptide lacking 36 carboxy-terminal amino acids of the paired domain. Sequence comparison of this class of BSAP-binding sites made it possible to unequivocally align all known BSAP-binding sites and to deduce a consensus sequence consisting of two distinct half sites. We propose here a model for the paired domain--DNA interaction in which the paired domain is composed of two subdomains that bind to the two half-sites in adjacent major grooves on the same side of the DNA helix. The existence of these half sites and of the two paired domain subregions was directly demonstrated by methylation interference analysis and by in vitro mutagenesis of both the paired domain and its recognition sequence. Both half-sites contribute to the overall affinity of a given BSAP-binding site according to their match with the consensus sequence. However, none of the naturally occurring BSAP-binding sites completely conform to the consensus sequence. Instead, they contain compensatory base changes in their half-sites that explain the versatile and seemingly degenerate DNA sequence recognition of Pax proteins. Domain swap experiments between BSAP and Pax-1 demonstrated that the sequence specificity of the BSAP paired domain is determined by both its amino- and carboxy-terminal subdomains. Moreover, mutations affecting only one of the two subdomains restricted the sequence specificity of the paired domain. Such mutations have been shown previously to be the cause of mouse developmental mutants (undulated, Splotch, and Small eye) and human syndromes (Waardenburg's syndrome and aniridia) and may thus differentially affect the regulation of target genes by the mutated Pax protein.","authors":"Czerny, T., Schaffner, G., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Genes Dev","volume":"7","issue":"10","page":"2048-61","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1993-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8504254","title":"Regulating the HO endonuclease in yeast.","abstract":"The pedigree of mating-type switching in yeast is determined by the transcription pattern of the HO endonuclease gene, which is expressed during late G1 in mother cells but not at all in daughter cells. The late-G1 specificity of HO transcription depends on a heteromeric factor, SBF, which is composed of the Swi4 and Swi6 proteins. Mother-cell specificity involves a second site-specific DNA-binding factor, Swi5, which is synthesized in the G2 and M phases and only enters the nucleus at the end of mitosis. Swi5 enters mother and daughter nuclei in equal amounts and most is then rapidly degraded. It has been suggested that in mothers but not in daughters some Swi5 protein escapes degradation and persists until SBF is activated in late G1. This subset of Swi5 molecules may constitute a mother cell's memory.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Curr Opin Genet Dev","volume":"3","issue":"2","page":"286-94","pdf":null,"JrId":"2199","fulltextlink":null,"preprintlink":null,"articledate":"1993-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3360325","title":"Temperature-sensitive v-sea transformed erythroblasts: a model system to study gene expression during erythroid differentiation.","abstract":"The isolation and characterization of a temperature-sensitive mutant (ts1 S13) of the avian erythroblastosis virus, S13, is described. The temperature-sensitive lesion in ts1 S13 was identified as affecting the tyrosine kinase activity but not the plasma membrane localization of the ts1 S13 v-sea gene product. Erythroblasts transformed by ts1 S13 can be induced to synchronously differentiate into erythrocytes in an erythropoietin (EPO)-dependent fashion. Analysis of erythrocyte-specific gene expression in ts1 S13 erythroblasts reveals that the transformed, self-renewing erythroblasts obtained at permissive temperature already express all erythrocyte genes tested for, although at a low level. Upon differentiation induction, expression of erythrocyte-specific genes is not coordinately regulated but rather involves complex regulatory mechanisms that appear to be specific for the individual genes.","authors":"Knight, J., Zenke, M., Disela, C., Kowenz, E., Vogt, P., Engel, JD., Hayman, MJ., Beug, H.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Genes Dev","volume":"2","issue":"2","page":"247-58","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1988-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3279026","title":"Hematopoietic growth factor glycosylation. Multiple forms of chicken myelomonocytic growth factor.","abstract":"The production of chicken myelomonocytic growth factor (cMGF) can be rapidly induced by bacterial lipopolysaccharide from the macrophage cell line HD11. Immunoprecipitation analysis of lipopolysaccharide-induced HD11 cells labeled with various radioactive precursors showed the secretion of a variety of cMGF forms. The precursor-product relationships of the different cMGF forms were studied by pulse-chase experiments, by long-term metabolic labeling in the presence or absence of glycosylation- and oligosaccharide-processing inhibitors, as well as by glycosidase treatment of immunoprecipitates. Our results show that the half-time for intracellular processing\/secretion is less than 10 min, making cMGF one of the most rapidly processed proteins. The different forms of the factor are generated from a 24-kDa polypeptide precursor by co- and post-translational acquisition of one or two N-linked oligosaccharides and by O-linked glycosylation. In addition, a fraction of cMGF is modified by long chain, chondroitinase-sensitive, sulfated glycans. This modification is tunicamycin-sensitive, suggesting that the sulfated glycans are attached to N-linked rather than to O-linked oligosaccharides.","authors":"Leutz, A., Beug, H., Walter, C., Graf, T.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"J Biol Chem","volume":"263","issue":"8","page":"3905-11","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1988-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8577838","title":"Evolution of the cell cycle.","abstract":"Cell proliferation involves duplication of all cell constituents and their more-or-less equal segregation to daughter cells. It seems probable that the performance of primitive cell-like structures would have been dogged by poor duplication and segregation fidelity, and by parasitism. This favoured evolution of the genome and with it the distinction between 'genomic' components like chromosomes whose synthesis is periodic and most other 'functional' components whose synthesis is continuous. Eukaryotic cells evolved from bacterial ancestors whose fused genome was replicated from a single origin and whose means of segregating sister chromatids depended on fixing their identity at replication. Evolution of an endo- or cytoskeleton, initially as means of consuming other bacteria, eventually enabled evolution of the mitotic spindle and a new means of segregating sister chromatids whose replication could be initiated from multiple origins. In this primitive eukaryotic cell, S and M phases might have been triggered by activation of a single cyclin-dependent kinase whose destruction along with that of other proteins would have triggered anaphase. Mitotic non-disjunction would have greatly facilitated genomic expansion, now possible due to multiple origins, and thereby accelerated the tempo of evolution when permitted by environmental conditions.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"349","issue":"1329","page":"271-81","pdf":null,"JrId":"8277","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3332012","title":"Two new retroviral onc genes, sea and jun.","abstract":"Avian leukemia virus S13 induces erythroblastosis, granulocytic leukemia, fibrosarcoma, anemia, and endothelial neoplasia. It transforms chick embryo fibroblasts and primitive erythroid cells in culture and is defective in replication. Its onc gene, sea, is expressed as transformation specific env-sea fusion glycoprotein of 155 kDa. Gp155 is proteolytically processed into gp85env and gp70env-sea. The latter shows tyrosine specific protein kinase activity. Avian sarcoma virus 17 induces fibrosarcoma and transforms chick embryo fibroblasts in culture. Its cell derived onc gene, jun, is not related to known onc genes and appears to be expressed as a gag-jun fusion protein of 55 kDa. The amino acid sequence of jun shows homology in its C-terminal region to the C-terminal DNA binding region of the yeast regulatory protein GCN4, suggesting that the jun protein may bind to DNA.","authors":"Bos, TJ., Beug, H., Graf, T., Hayman, M., Maki, Y., Uckert, W., Vogt, PK.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Princess Takamatsu Symp","volume":"17","issue":null,"page":"23-30","pdf":null,"JrId":"4543","fulltextlink":null,"preprintlink":null,"articledate":"1988-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"391565","title":"A novel ATP-driven glucose transport system in Escherichia coli.","abstract":"In Escherichia coli wild-type cells and in ATPase-deficient cells (unc mutants), glucose was found to be transported mainly by an ATP-driven system. The evidence is based on experiments involving interference at different sites of energy metabolism with the use of uncouplers, arsenate, and starved cells. Furthermore, addition of succinate to starved cells increased glucose uptake only in the wild-type cells, where ATP could be regenerated. Glucose transport was also ATP-dependent in cells deficient in methyl-beta-galactoside transport (a system that carries glucose specificity). It was found to be shock-sensitive in all strains tested. The NOVEL ATP-driven glucose transport is a high-affinity (Km 3-10 microM) and high-capacity (V 240-330 Mmol . min-1 . mg cell protein-1) uptake system.","authors":"Wagner, EF., Fabricant, JD., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Eur J Biochem","volume":"102","issue":"1","page":"231-6","pdf":null,"JrId":"3607","fulltextlink":null,"preprintlink":null,"articledate":"1980-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25414306","title":"Characterization of a DNA exit gate in the human cohesin ring.","abstract":"Chromosome segregation depends on sister chromatid cohesion mediated by cohesin. The cohesin subunits Smc1, Smc3, and Scc1 form tripartite rings that are thought to open at distinct sites to allow entry and exit of DNA. However, direct evidence for the existence of open forms of cohesin is lacking. We found that cohesin's proposed DNA exit gate is formed by interactions between Scc1 and the coiled-coil region of Smc3. Mutation of this interface abolished cohesin's ability to stably associate with chromatin and to mediate cohesion. Electron microscopy revealed that weakening of the Smc3-Scc1 interface resulted in opening of cohesin rings, as did proteolytic cleavage of Scc1. These open forms may resemble intermediate states of cohesin normally generated by the release factor Wapl and the protease separase, respectively.","authors":"Huis in 't Veld, PJ., Herzog, F., Ladurner, R., Davidson, IF., Piric, S., Kreidl, E., Bhaskara, V., Aebersold, R., Peters, JM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Science","volume":"346","issue":"6212","page":"968-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8175790","title":"NK-kappa B subunit-specific regulation of the I kappa B alpha promoter.","abstract":"Stimulation of endothelial cells by cytokines and bacterial lipopolysaccharide leads to activation of the transcription factor NF-kappa B. NF-kappa B in turn regulates the expression of several genes involved in the inflammatory reaction, including cell adhesion molecules, interleukins, and transcription factors. One of these induced genes encodes an inhibitor of NF-kappa B, ECI-6\/I kappa B alpha, that contains in its 5' regulatory region six consensus binding sites for NF-kappa B. We demonstrate here that these sites display striking differences in their ability in vitro to bind to various NF-kappa B subunits. In vivo, all six sites contribute, though to varying degrees, to transcription from the ECI-6\/I kappa B alpha promoter, as demonstrated by deletion and mutation analysis. Among the NF-kappa B subunits tested p65, the p65\/p50 heterodimer and, to a lesser extent, c-Rel, are able to activate transcription, whereas p50 or p50\/Re1B were inactive. Since many genes regulated by NF-kappa B contain only one or two DNA-binding sites for this transcription factor, the presence of six functional NF-kappa B-binding sites in the ECI-6\/I kappa B alpha promoter represents a unique feature of this gene.","authors":"Cheng, Q., Cant, CA., Moll, T., Hofer-Warbinek, R., Wagner, E., Birnstiel, ML., Bach, FH., de Martin, R.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"J Biol Chem","volume":"269","issue":"18","page":"13551-7","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7689725","title":"Induction of tumor formation and cell transformation by polyoma middle T antigen in the absence of Src.","abstract":"In polyomavirus-transformed cells, middle T antigen binds to and activates the protein tyrosine kinase, Src. To determine whether this interaction is critical for middle T transformation, we examined the ability of middle T to transform cells that lack endogenous Src (because of a targeted disruption of both Src alleles). Infection of newborn or 2-week-old Src-negative mice with a retrovirus encoding middle T led to the induction of visceral hemangiomas that were indistinguishable from tumors in wild-type mice with respect to their morphology, frequency or latency period. In addition, middle T was able to induce foci formation on cell monolayers and colony formation in soft agar in Src-negative immortalized fibroblasts. These results indicated that Src is not essential for middle T-induced transformation of the cells targeted in these assays. To examine the protein tyrosine kinases that interact with middle T in the absence of Src, we compared the level of middle T phosphorylation in immune complex kinase assays from Src-negative and Src-positive cell lysates, and identified the middle T-associated kinases in these cells. In Src-positive cell lysates, there was a similar level of middle T phosphorylation in Src and Yes immunoprecipitates, suggesting that middle T can bind to Src and Yes to a similar extent in this cell type. Fyn immunoprecipitates displayed fourfold lower levels of middle T phosphorylation than that detected in the Src and Yes immunoprecipitates. In Src-negative cells, the level of middle T phosphorylation in Yes and Fyn immunoprecipitates was not significantly different from that detected in the Src-positive cells, suggesting that the absence of Src does not lead to a compensating increase in the proportion of middle T associated with these kinases. The level of middle T-associated phosphatidylinositol 3'-kinase was also examined since this kinase is known to interact with middle T-kinase complexes. Phosphatidylinositol 3'-kinase activity associated with middle T was reduced 30-60% in Src-negative cells, suggesting that Src contributes at least one-third of the total middle T associated in wild-type cells. Taken together, these results indicate that Src is not required for middle T-induced hemangiomas in mice or for focus induction in immortalized fibroblasts, and that the residual level of Yes, Fyn and phosphatidylinositol kinase activity associated with middle T in Src-negative cells may compensate for the absence of Src.","authors":"Thomas, JE., Aguzzi, A., Soriano, P., Wagner, EF., Brugge, JS.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Oncogene","volume":"8","issue":"9","page":"2521-9","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1993-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7545687","title":"Caenorhabditis elegans cyclin A- and B-type genes: a cyclin A multigene family, an ancestral cyclin B3 and differential germline expression.","abstract":"We have cloned cDNAs for Caenorhabditis elegans cyclins A1, B and B3. While cyclins A1 and B are most closely related to either A- or B-type cyclins of other species, cyclin B3 is less related to these cyclins. However, this cyclin is most similar to the recently identified chicken cyclin B3. Our identification of a Caenorhabditis homolog demonstrates that cyclin B3 has been conserved in evolution. Cyclin A1 is a member of an A-type multigene family; however the cyclin A1 cDNA only recognizes a single band on northern blots. A single-sized RNA is also observed for the cyclin B3 cDNA. In contrast, three different transcripts are observed for the cyclin B cDNA. Based on our analyses using RNAs from germline-defective mutants and from populations enriched for males, one cyclin B transcript is specific to the paternal germline. The two other cyclin B transcripts, as well as the cyclin A1 and cyclin B3 transcripts, are most abundant in the maternal germline and are only present at low levels in other tissues. Moreover, the 3' untranslated regions of each Caenorhabditis cyclin cDNA possess several copies of potential translational control elements shown in Xenopus and Drosophila maternal cyclin mRNAs to function during oogenesis and early embryogenesis.","authors":"Kreutzer, MA., Richards, JP., De Silva-Udawatta, MN., Temenak, JJ., Knoblich, JA., Lehner, CF., Bennett, KL.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Cell Sci","volume":"108 ( Pt 6)","issue":null,"page":"2415-24","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"1995-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3127777","title":"The effects of v-src expression on the differentiation of embryonal carcinoma cells.","abstract":"We have used replication-defective selectable retroviruses to express inducibly or constitutively the v-src gene in the embryonal carcinoma (EC) cell lines F9, PC13 and P19. High v-src expression in F9 and PC13 cells does not induce or disrupt their differentiation. In contrast, P19 cells expressing high levels of v-src have a 'differentiated' morphology and are unable to respond to signals that normally induce differentiation along the neural or muscle pathways. Regulation of v-src transcription from the inducible human metallothionein (MT) promoter has shown that v-src expression above a threshold level induces differentiation of these cells, as defined by loss of the stem cell marker ECMA-7. These results suggest that v-src expression may be compatible with differentiation events occurring early in embryogenesis, represented by F9 and PC13 cell differentiation, but might disrupt the differentiation of cell types present at later developmental stages.","authors":"Boulter, CA., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Oncogene","volume":"2","issue":"3","page":"207-14","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1988-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3005614","title":"Rous-associated virus 1-induced erythroleukemic cells exhibit a weakly transformed phenotype in vitro and release c-erbB-containing retroviruses unable to transform fibroblasts.","abstract":"Avian leukosis viruses induce erythroblastosis in chicks by integrating into the c-erbB gene and thus activating c-erbB transcription. We characterized Rous-associated virus 1-induced leukemic erythroblasts in vitro and showed that they mostly resemble erythropoietin-independent but otherwise normal erythroid progenitors. Some leukemic cells, however, were able to both differentiate and proliferate extensively in vitro. All 14 leukemias studied expressed high levels of erbB-related proteins that were 5 to 10 kilodaltons larger but otherwise very similar to the gp74erbB protein of avian erythroblastosis virus ES4 with respect to biosynthesis, glycosylation, and cell surface expression. Two leukemias contained and released retroviruses that transduced erbB. Chicken embryo fibroblasts fully infected with these viruses expressed high levels of erbB RNA and protein but retained a normal phenotype. Our results suggest that certain forms of c-erbB, activated by long terminal repeat insertion or viral transduction, are capable of inducing erythroleukemia but unable to transform fibroblasts.","authors":"Beug, H., Hayman, MJ., Raines, MB., Kung, HJ., Vennstr\u00f6m, B.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"J Virol","volume":"57","issue":"3","page":"1127-38","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1986-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6883509","title":"DNA methylation and the regulation of globin gene expression.","abstract":"We have studied the effect of DNA methylation on human gamma-globin gene expression, using a novel in vitro DNA methylation technique. With this method we have methylated specific segments of the gamma-globin gene and its 5'-flanking region, which were cloned for this purpose in the bacteriophage vector M13mp8. The vitro methylated DNA was introduced into mouse L-cells by cotransfer using the herpes simplex virus thymidine kinase gene as a selective marker. Transformed cell lines were isolated to examine the inheritance of the segmental methylation pattern and its effect on the expression of the gamma-globin gene. Cells transformed with DNA methylated throughout the M13 vector and gamma-globin DNA sequences do not express the gamma-globin gene. Methyl-C residues in either the M13 DNA sequences or the gamma-globin structural gene have, however, no inhibitory effect on globin transcription. In contrast, methylation in the 5' region of the gamma-globin gene (from nucleotides -760 to +100) prevents transcription. These data indicate that DNA methylation in the 5' region of a gene might play a direct role in the regulation of gene expression.","authors":"Busslinger, M., Hurst, J., Flavell, RA.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Cell","volume":"34","issue":"1","page":"197-206","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1983-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10662641","title":"Pax2 and homeodomain proteins cooperatively regulate a 435 bp enhancer of the mouse Pax5 gene at the midbrain-hindbrain boundary.","abstract":"Pax and homeodomain transcription factors are essential for the formation of an organizing center at the midbrain-hindbrain boundary (mhb) which controls the genesis of the midbrain and cerebellum in the vertebrate embryo. Pax2 and Pax5 are sequentially activated in this brain region, with Pax2 expression preceding that of Pax5. Using a transgenic reporter assay, we have now identified a conserved 435 bp enhancer in the 5' flanking region of mammalian Pax5 genes which directs lacZ expression in the correct temporal and spatial pattern at the mhb. This minimal enhancer is composed of two distinct elements, as shown by protein-binding assays with mhb-specific extracts. The proximal element contains overlapping consensus binding sites for members of the Pax2\/5\/8 and POU protein families, whereas a distal element is bound by homeodomain and zinc finger transcription factors. Expression analysis of transgenes carrying specific mutations in these recognition motifs identified the Pax- and homeodomain-binding sites as functional elements which cooperatively control the activity of the mhb enhancer. lacZ genes under the control of either the minimal enhancer or the endogenous Pax5 locus were normally expressed at the mhb in Pax5 mutant embryos, indicating that this enhancer does not depend on autoregulation by Pax5. In Pax2 mutant embryos, expression of the endogenous Pax5 gene was, however, delayed and severely reduced in lateral aspects of the neural plate which, on neural tube closure, becomes the dorsal mhb region. This cross-regulation by Pax2 is mediated by the Pax-binding site of the minimal enhancer which, upon specific mutation, resulted in severely reduced transgene expression in the dorsal part of the mhb. Together these data indicate that Pax2 and homeodomain proteins directly bind to and cooperatively regulate the mhb enhancer of Pax5.","authors":"Pfeffer, PL., Bouchard, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Development","volume":"127","issue":"5","page":"1017-28","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2000-04-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41025354","title":"Pathway to Independence: a forecast for the future of developmental biology.","abstract":"In 2022, Development launched its Pathway to Independence (PI) programme, aimed at supporting postdocs as they transition to their first independent position. In 2025, we welcome our third cohort of eight talented PI fellows. In this article, each fellow discusses their perspective on the future of their field and how their work will contribute to this exciting new era.","authors":"Ewe, CK., Farnworth, MS., Miller, A., Navajas Acedo, J., Oomen, ME., Paci, G., Widen, SA., Yamada, T.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Development","volume":"152","issue":"19","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-09-30","doi":"10.1242\/dev.205224","first_author":null,"corresponding_authors":null},{"pmid":"2897102","title":"Common site of mutation in the erbB gene of avian erythroblastosis virus mutants that are temperature sensitive for transformation.","abstract":"The genome of the avian erythroblastosis virus temperature sensitive mutant ts34 was cloned from a cell line that was shown to contain a single integrated copy of the virus. The mutation was localized to the v-erbB gene by making chimeric viruses between the mutant genome and that of wildtype. Sequencing of the mutant v-erbB gene revealed a single amino acid change of a histidine to an aspartate residue at a position equivalent to amino-acid 826 of the human epidermal growth factor receptor. Interestingly this is the identical mutation to that recently reported for another temperature sensitive mutant ts167, indicating that this may be a hot spot for mutations in the v-erbB gene that give rise to ts transformation mutants. In addition, the different biological phenotypes of ts34 and ts167 are suggested to be due to an additional mutation in v-erbA in ts167.","authors":"Scotting, P., Vennstrom, B., Jansen, M., Graf, T., Beug, H., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Oncogene Res","volume":"1","issue":"3","page":"265-78","pdf":null,"JrId":"6326","fulltextlink":null,"preprintlink":null,"articledate":"1988-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11343123","title":"ICOS is essential for effective T-helper-cell responses.","abstract":"The outcome of T-cell responses after T-cell encounter with specific antigens is modulated by co-stimulatory signals, which are required for both lymphocyte activation and development of adaptive immunity. ICOS, an inducible co-stimulator with homology to CD28, is expressed on activated, but not resting T cells, and shows T-cell co-stimulatory function in vitro. ICOS binds specifically to its counter-receptor B7RP-1 (refs 5,6,7), but not to B7-1 or B7-2. Here we provide in vivo genetic evidence that ICOS delivers a co-stimulatory signal that is essential both for efficient interaction between T and B cells and for normal antibody responses to T-cell-dependent antigens. To determine the physiological function of ICOS, we generated and characterized gene-targeted ICOS-deficient mice. In vivo, a lack of ICOS results in severely deficient T-cell-dependent B-cell responses. Germinal centre formation is impaired and immunoglobulin class switching, including production of allergy-mediating IgE, is defective. ICOS-deficient T cells primed in in vivo and restimulated in vitro with specific antigen produce only low levels of interleukin-4, but remain fully competent to produce interferon-gamma.","authors":"Tafuri, A., Shahinian, A., Bladt, F., Yoshinaga, SK., Jordana, M., Wakeham, A., Boucher, LM., Bouchard, D., Chan, VS., Duncan, G., Odermatt, B., Ho, A., Itie, A., Horan, T., Whoriskey, JS., Pawson, T., Penninger, JM., Ohashi, PS., Mak, TW.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nature","volume":"409","issue":"6816","page":"105-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3360326","title":"Expression of human alpha 1-acid glycoprotein genes in cultured cells and in transgenic mice.","abstract":"The human genome contains three alpha 1-glycoprotein genes (AGP-A, AGP-B, and AGP-B') encoding for slightly different forms of the protein. The major component of human alpha 1-acid glycoprotein found in plasma is coded by AGP-A, which is expressed in liver and in hepatoma cell lines and is induced by inflammatory stimuli. We have studied the regulation of the cloned AGP-A gene by transfection into cell lines of hepatic and nonhepatic origin. Unlike any other liver-specific gene investigated so far, every AGP construct tested was expressed with comparable efficiency in hepatoma and HeLa cells. In contrast, identical constructs in transgenic mice are expressed in a tissue-specific manner and are regulated by acute-phase stimuli. Transgenic mice carrying the cluster of three AGP genes secrete the human protein in the serum, and the corresponding mRNA is mainly derived from the AGP-A gene. The mRNA is liver specific, and its concentration increases several fold following experimentally induced inflammation. Additional transgenic lines carrying only the AGP-A gene showed that sufficient information for tissue-specific and regulated expression is contained within a 6.6-kb segment comprising the whole coding region plus 1.2-kb 5'-flanking and 2-kb 3'-flanking DNA.","authors":"Dente, L., R\u00fcther, U., Tripodi, M., Wagner, EF., Cortese, R.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Genes Dev","volume":"2","issue":"2","page":"259-66","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1988-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2830578","title":"Defective v-erbB genes can be complemented by v-erbA in erythroblast and fibroblast transformation.","abstract":"We have introduced 3'-terminal deletions of increasing size in the v-erbB oncogene and analysed the effects of these mutations on the transformation of fibroblasts and erythroblasts. The results show that the transforming activity of the mutants is gradually diminished, and completely abolished in those mutants that do not produce stable v-erbB proteins. The capacity to transform erythroblasts is lost before fibroblast transformation is severely affected, suggesting that a larger part of the C-terminal domain is required for mitogenic signalling in erythroid cells than in fibroblasts. In addition, the v-erbA oncogene was found to cooperate with v-erbB not only in erythroblast but also in fibroblast transformation, inducing a fully transformed phenotype in fibroblasts partially transformed by a mutant erbB oncogene.","authors":"Jansson, M., Beug, H., Gray, C., Graf, T., Vennstr\u00f6m, B.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Oncogene","volume":"1","issue":"2","page":"167-73","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1988-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2831463","title":"Zinc-finger motifs expressed in E. coli and folded in vitro direct specific binding to DNA.","abstract":"The short sequence motif named 'zinc finger', first recognized repeated in tandem in the Xenopus transcription factor IIIA (TFIIIA), is also found in the yeast transcriptional activator SWI5 (ref. 3) and many other regulator proteins. Embedded in the 709-amino-acid polypeptide chain of SWI5 are three tandemly repeated zinc-finger motifs. Because the zinc fingers of TFIIIA are known to bind to DNA, it is probable that in the case of SWI5 these finger motifs also play an important, but not necessarily exclusive, role in the sequence-specific binding of the protein to DNA. To test this prediction we have expressed the 89-amino-acid sequence of the domain containing the three zinc fingers of SWI5 in Escherichia coli as a cleavable fusion protein, purified under denaturing conditions and folded in vitro. This experimental approach allows us to study directly both the metal requirement and DNA-binding properties of the isolated polypeptide. We find that zinc is required for specific DNA recognition and, most significantly, DNaseI protection studies show that the isolated three-fingered domain is sufficient for sequence-specific binding to DNA.","authors":"Nagai, K., Nakaseko, Y., Nasmyth, K., Rhodes, D.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Nature","volume":"332","issue":"6161","page":"284-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1988-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2820586","title":"v-myb dominance over v-myc in doubly transformed chick myelomonocytic cells.","abstract":"Chick myelomonocytic cells transformed by the v-myc oncogene resemble mature macrophages; those transformed by v-myb or v-myb,ets exhibit an immature phenotype. We have analyzed whether these oncogenes are capable of altering the differentiation phenotype of transformed cells by introducing both v-myc plus either v-myb or v-myb,ets into the same cells. Surprisingly, the doubly transformed cells were found to be essentially indistinguishable from cells transformed by v-myb or v-myb,ets alone even when they expressed a high level of v-myc protein. These results demonstrate that v-myb is dominant over v-myc and that, while v-myc induces cell proliferation without affecting differentiation, v-myb induces in the same target cells both proliferation and a block or reversal of differentiation.","authors":"Ness, SA., Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Cell","volume":"51","issue":"1","page":"41-50","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1987-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2663360","title":"Immunodeficiency in old age.","abstract":"Aging is a multi-facetted process, but the deterioration of the immune function seems to play a central role in this context. Paradoxically, immune reactivity against exogenous antigens declines during aging while autoimmune reactivity increases. One of the aims of our investigations on the function of the senescent immune system was to define immune parameters of 'normal' aging, i.e. those not dependent on underlying diseases. Specifically, our interest was focused on the possible role of an altered lipid metabolism of cells of the immune system during aging. The known decrease of plasma membrane fluidity of lymphoid cells and monocytes in higher age may be one of the factors responsible for the nonoptimal functioning of the immune system. This property, in turn, seems to be based on an altered lipid metabolism. Specifically, we have evidence that the finely tuned balance between the transport of cholesterol to and from lymphoid cells via the environment and the intracellular cholesterol biosynthesis seems to be disturbed with increasing age. This conclusion is drawn from experiments where low-density lipoprotein (LDL) and high-density lipoprotein (HDL) receptor activity is assessed using fluorescently labeled lipoproteins in fluorescence-activated cell sorter (FACS) analyses. LDL receptor uptake is unexpectedly increased in the elderly, but LDL receptor regulation, and serum LDL composition itself seem to be normal. Preliminary data point out the possibility that the efflux of cholesterol via HDL may be insufficient. Attempts to modulate plasma membrane fluidity by means of the phospholipid mixture 'active lipid 721' (AL 721) showed that this drug, in contrast to literature reports, is not a 'membrane fluidizer' but rather exerts this effect as a nutrient for lymphocytes and monocytes.","authors":"Wick, G., Huber, LA., Offner, F., Winter, U., B\u00f6ck, G., Schauenstein, K., J\u00fcrgens, G., Traill, KN.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Curr Probl Dermatol","volume":"18","issue":null,"page":"120-30","pdf":null,"JrId":"3223","fulltextlink":null,"preprintlink":null,"articledate":"1989-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2547184","title":"c-fos expression induces bone tumors in transgenic mice.","abstract":"The proto-oncogene c-fos has been isolated as the cellular homolog of the v-fos gene found in the osteosarcoma inducing FBR- and FBJ-murine sarcoma viruses (MSV). Expression of the c-fos gene in transgenic mice leads to the development of bone lesions of which about half progress to bone tumors mainly chondrosarcomas. The tumors display a strong preference for males and have a latency with a mean of 9.5 months. However, also mice without visible lesions develop bone tumors with the same sex preference and latency. These consequences of c-fos expression are independent of the chosen promoter but dependent on a replacement of 3' noncoding sequences of c-fos by a long terminal repeat (LTR) of the FBJ-MSV virus.","authors":"R\u00fcther, U., Komitowski, D., Schubert, FR., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Oncogene","volume":"4","issue":"7","page":"861-5","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1989-09-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2419128","title":"Expression of foreign genes from retroviral vectors in mouse teratocarcinoma chimaeras.","abstract":"The formation of chimaeric mice from embryonic stem cells (EC and ES) carrying and exposing foreign genes is described. Two retroviral vectors were used to stably introduce genes, by virus infection and selection into EC and ES cells. In the first series EC cell clones were isolated that contained a single intact copy of the vector, which expressed the neomycin resistance gene (neo) from the 5' long terminal repeat (LTR). Following the formation of chimaeras with one of the clones, expression of the foreign gene was found in all chimaeric tissues examined. In the second series, a vector was used which contained the OK10 v-myc oncogene under the control of the 5' LTR as well as the neo gene expressed from an internal thymidine kinase (TK) promoter. ES cell clones were again isolated and used to form chimaeras. Although expression of the TK neo transcripts was maintained in the chimaeric tissues analysed, no expression of the v-myc transcripts from the 5' LTR was detected. These results show that genes can be introduced into mice, using clones of embryonic stem cells selected in vitro and that the expression of the genes can be maintained probably throughout development and in all tissues. The advantages this approach offers compared with DNA injection into eggs and the use of retroviruses as vectors for introducing genes into mice are discussed.","authors":"Stewart, CL., Vanek, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"EMBO J","volume":"4","issue":"13B","page":"3701-9","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1986-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2497422","title":"Expression of v-src arrests murine glial cell differentiation.","abstract":"A replication-defective retroviral vector carrying the v-src oncogene and the gene for neomycin resistance was used to infect neurone- and fibroblast-depleted embryonic mouse brain cells in vitro. Cells resistant to the antibiotic G418 were obtained and continually passaged. Several cell lines were isolated which express high levels of v-src mRNA and v-src tyrosine kinase activity. The antigenic marker profile of either the pooled cells from an individual infection or sublines isolated from individual foci showed the cells to be immature glia: most cells expressed vimentin, A2B5 antigen and\/or J1\/tenascin glycoproteins, but not fibronectin. Sublines expressed different antigen profiles suggesting that the immortalised cells were derived from glial cells of different phenotypes. The cell lines expressed the 120 and 140 but not the 180 kd components of N-CAM as well as voltage-activated potassium channels, typical for glial cells. 01 antigen-positive oligodendrocytes were never observed in the lines or sublines after long term passage (over 1 year), but some cells expressed glial fibrillary acidic protein, a marker for mature astrocytes. Thus, expression of v-src in murine glial cells appears to arrest their development and prevent their differentiation.","authors":"Trotter, J., Boulter, CA., Sontheimer, H., Schachner, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Oncogene","volume":"4","issue":"4","page":"457-64","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1989-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2027755","title":"Non-methylated islands in fish genomes are GC-poor.","abstract":"In the vertebrate genomes studied to date the 5' end of many genes are associated with distinctive sequences known as CpG islands. CpG islands have three properties: they are non-methylated; the dinucleotide CpG occurs at the frequency predicted by base composition; and they are GC-rich. Unexpectedly we have found that CpG islands in certain fish only have the first two properties; that is, their GC-content is not elevated compared to bulk genomic DNA. Based on this finding, we speculate that the GC-richness of CpG islands in vertebrates other than fish is a passive consequence of a higher mutation rate in regions of open chromatin under conditions where the nucleotide precursor pools are biased.","authors":"Cross, S., Kovarik, P., Schmidtke, J., Bird, A.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Nucleic Acids Res","volume":"19","issue":"7","page":"1469-74","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1991-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1945882","title":"A simple procedure for the preparation of protected 2'-O-methyl or 2'-O-ethyl ribonucleoside-3'-O-phosphoramidites.","abstract":"Protected 2'-O-methyl and 2'-O-ethyl ribonucleoside-3'-O-phosphoramidites were prepared via alkylation of the ribonucleosides at an early stage in the synthesis. Utilizing a strategy of minimal protection, the alkylation was performed with unprotected cytidine and adenosine, or with O6-protected guanosine and N3,5'-O-protected uridine using methyl or ethyl iodide and sodium hydride. In subsequent steps, the introduction of standard protective groups for oligonucleotide synthesis and the concomitant separation from 3'-O-alkylated isomers was accomplished. A modification of the phosphitylation procedure permitted facile isolation of the desired phosphoramidites which show high coupling efficiencies in oligomer assembly.","authors":"Wagner, E., Oberhauser, B., Holzner, A., Brunar, H., Issakides, G., Schaffner, G., Cotten, M., Knollm\u00fcller, M., Noe, CR.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Nucleic Acids Res","volume":"19","issue":"21","page":"5965-71","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1991-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2067849","title":"Localization of regulatory elements controlling human MYCN expression.","abstract":"Expression of the cellular oncogene MYCN is restricted to few cell lineages and is highest during development both in mouse and in humans. In pursuit of elucidating the mechanisms underlying MYCN regulation we introduced a human MYCN clone (pNb-9) with approximately 2.5 kbp 5'- and 6 kbp 3'-flanking genomic sequences into different murine and human cell lines as well as into mice. In all cases we found a correlation between the expression of the exogenous and the endogenous MYCN. Among cell lines, only those expressing the endogenous gene also expressed the transfected gene. In the transgenic mice transcripts of the transgene were present in proportion to the transcripts of the endogenous MYCN gene with the highest level in the brain. Therefore, the genetic information necessary for regulated expression of MYCN appears to be contained in pNb-9. To localize the DNA-regions responsible for regulated expression, we generated MYCN\/CAT hybrid genes with different portions of the putative MYCN promoter region linked to the reporter gene. Transient transfections into various murine and human cell lines identified three DNA regions apparently involved in the regulation of expression. One region about 200 bp upstream of the transcriptional start site is responsible for a basal level of MYCN expression. A second region located about 800 bp further upstream appears to be involved in cell type-specific gene activation. The third regulatory element is located at the 3' end of the first exon and\/or in the first intron and may mediate tissue-specific down regulation of gene expression.","authors":"Hiller, S., Breit, S., Wang, ZQ., Wagner, EF., Schwab, M.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Oncogene","volume":"6","issue":"6","page":"969-77","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1991-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1833188","title":"Mature mRNA 3' end formation stimulates RNA export from the nucleus.","abstract":"We have analysed nucleocytoplasmic export of mRNAs in primate cells with the aim of identifying signals promoting RNA transport. Our results demonstrate that sequences directing either histone mRNA 3' processing or cleavage\/polyadenylation of mRNA stimulate nucleocytoplasmic RNA transport. To elucidate the nature of this stimulation, we engineered test gene transcripts which could obtain a mature histone 3' end by the RNA cleaving activity of a cis-acting ribozyme, thus circumventing the cellular 3' end processing machinery. However, such transcripts were found to be transport deficient and accumulated in the nuclear compartment. Our experiments provide genetic evidence that there is a linkage between 3' end formation and the export of RNA transcripts from the nucleus. Analysis of a similar series of histone mRNAs in which the mature 3' end was generated by means of ribozyme cleavage led to the discovery of a second export mechanism which relies on features specific for mature histone RNA and which can be uncoupled from the cellular processing machinery. The presence of histone mRNA sequences and of the highly conserved histone hairpin structure, positioned close to the 3' terminus, are critical determinants for this export mechanism.","authors":"Eckner, R., Ellmeier, W., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"EMBO J","volume":"10","issue":"11","page":"3513-22","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1991-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1731251","title":"Regulation of p34CDC28 tyrosine phosphorylation is not required for entry into mitosis in S. cerevisiae.","abstract":"Progression from G2 to M phase in eukaryotes requires activation of a protein kinase composed of p34cdc2\/CDC28 associated with G1-specific cyclins. In some organisms the activation of the kinase at the G2\/M boundary is due to dephosphorylation of a highly conserved tyrosine residue at position 15 (Y15) of the cdc2 protein. Here we report that in the budding yeast Saccharomyces cerevisiae, p34CDC28 also undergoes cell-cycle regulated dephosphorylation on an equivalent tyrosine residue (Y19). However, in contrast to previous observations in S. pombe, Xenopus and mammalian cells, dephosphorylation of Y19 is not required for the activation of the CDC28\/cyclin kinase. Furthermore, mutation of this tyrosine residue does not affect dependence of mitosis on DNA synthesis nor does it abolish G2 arrest induced by DNA damage. Our data imply that regulated phosphorylation of this tyrosine residue is not the 'universal' means by which the onset of mitosis is determined. We propose that there are other unidentified controls that regulate entry into mitosis.","authors":"Amon, A., Surana, U., Muroff, I., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Nature","volume":"355","issue":"6358","page":"368-71","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1992-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1741287","title":"Effective incorporation of 2'-O-methyl-oligoribonucleotides into liposomes and enhanced cell association through modification with thiocholesterol.","abstract":"Cholesterol was linked to 2'-O-methyl-oligoribonucleotides (2'-OMe-RNA) via a disulfide bond by reacting the 3'-(pyridyldithio)-modified 2'-OMe-RNA with thiocholesterol in dichloromethane-methanol solution. This ligation reaction was made possible by a novel strategy in which the highly charged oligonucleotide was rendered soluble in nonaqueous solvent through conversion to a lipophilic amidinium salt. The biodegradable lipophilic modification of 2'-OMe-RNA resulted in a large increase in incorporation of such oligonucleotides into liposomes prepared by reversephase evaporation. Furthermore, association of these modified oligonucleotides with cultured TIB 73 cells was 100-fold higher than that seen with unmodified 2'-OMe-RNA in serum-free medium and about 10 to 30-fold higher in the presence of 10% calf serum. During incubation with cells, release of the internalized oligonucleotide from the thiocholesteryl moiety can be demonstrated.","authors":"Oberhauser, B., Wagner, E.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Nucleic Acids Res","volume":"20","issue":"3","page":"533-8","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1992-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1835087","title":"Two-step affinity purification of U7 small nuclear ribonucleoprotein particles using complementary biotinylated 2'-O-methyl oligoribonucleotides.","abstract":"U7 snRNP is a low-abundance small nuclear ribonucleoprotein particle essential for 3' processing of replication-dependent histone pre-mRNA. We have developed a two-step purification of the particle from TB21 mouse mastocytoma cell nuclear extracts, with about a 20% overall yield, using affinity binding to 2'-O-methyl oligoribonucleotides. The purified particle is homogeneous with respect to RNA content. SDS\/PAGE of the U7 snRNP proteins revealed a full complement of the standard core proteins (B, DD', E, F, and G) found in the majority of snRNPs. In addition, two U7-specific polypeptides of 14 kDa and 50 kDa were identified. Summation of the molecular masses of the identified components of the U7 particle yields a particle mass of 249 kDa, in approximate agreement with estimates from sucrose gradient sedimentation (261 kDa) and nondenaturing gradient PAGE (217 kDa).","authors":"Smith, HO., Tabiti, K., Schaffner, G., Soldati, D., Albrecht, U., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Proc Natl Acad Sci U S A","volume":"88","issue":"21","page":"9784-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1991-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"730179","title":"Deficiency of DNA ligase activity in Fanconi's anemia.","abstract":"A significant decrease in DNA ligase activity was observed in lymphocytes and fibroblasts of a patient with Fanconi's anemia (FA). This decrease is related to the observed DNA repair deficiency indicated by the delayed closing of repair DNA strands following UV irradiation. Other steps of DNA repair were analyzed in the FA fibroblasts, including endonucleolytic incision of DNA, repair DNA synthesis, and exonucleolytic removal of the photoproducts. No differences were found against control cells. The action of DNA ligase is delayed during replication in the FA cells, as seen by an accumulation of replicative intermediates.","authors":"Hirsch-Kauffmann, M., Schweiger, M., Wagner, EF., Sperling, K.","publication_status":"ppublish","journalpubyear":"1978","journaltitle":"Hum Genet","volume":"45","issue":"1","page":"25-32","pdf":null,"JrId":"4137","fulltextlink":null,"preprintlink":null,"articledate":"1979-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2479828","title":"Ribozyme, antisense RNA, and antisense DNA inhibition of U7 small nuclear ribonucleoprotein-mediated histone pre-mRNA processing in vitro.","abstract":"A comparative analysis of ribozyme, antisense RNA, and antisense DNA inhibitors of the in vitro small nuclear ribonucleoprotein U7-dependent histone pre-mRNA processing reaction was performed. RNA molecules complementary to the U7 sequence inhibited in vitro processing of histone pre-mRNA at a sixfold excess over U7. Single-stranded DNA complementary to the entire U7 sequence inhibited the reaction at a 60-fold excess over U7, while a short, 18-nucleotide DNA molecule complementary to the 5' end of U7 inhibited the processing reaction at a 600-fold excess. A targeted ribozyme was capable of specifically cleaving the U7 small nuclear ribonucleoprotein in a nuclear extract and inhibited the U7-dependent processing reaction, but in our in vitro system it required a 1,000-fold excess over U7 for complete inhibition of processing.","authors":"Cotten, M., Schaffner, G., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Mol Cell Biol","volume":"9","issue":"10","page":"4479-87","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1989-12-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2416462","title":"Clustered homeo boxes are differentially expressed during murine development.","abstract":"A murine homeo box (m6-12) known to be expressed during differentiation of embryonal carcinoma cells lies within a cluster of homeo boxes located in 30 kilobase pairs of genomic DNA. We have established the organization of the boxes within this complex, as well as the nucleotide sequence of a second box, m5-4. Similar to the m6-12 box, expression of novel m5-4 transcripts is induced upon differentiation of embryonal carcinoma cells. Transcripts of genes containing m6-12 were found in embryonic tissue during almost all stages of prenatal development studied, whereas expression of m5-4 was detected only in 12 day embryonic tissue. Finally, we have described the differential expression of these homeo-box-containing regions in various adult tissues.","authors":"Colberg-Poley, AM., Voss, SD., Chowdhury, K., Stewart, CL., Wagner, EF., Gruss, P.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Cell","volume":"43","issue":"1","page":"39-45","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1986-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"227607","title":"Chicken hematopoietic cells transformed by seven strains of defective avian leukemia viruses display three distinct phenotypes of differentiation.","abstract":"Chicken hematopoietic cells transformed in vitro and in vivo by seven strains of replication-defective avian leukemia viruses were assayed for the expression of six erythroid and five myeloid differentiation parameters, including differentiation-specific surface antigens as detected by newly developed antisera. The transformed cells were found to display three distinct phenotypes of differentiation. First, cells transformed by AEV resemble erythroblasts. They express heme, globin, carbonic anhydrase and erythrocyte cell surface antigen at low levels, and histone H5 and erythroblast cell surface antigen at high levels. Second, cells transformed by MC29, CMII, OK10 and MH2 viruses have macrophage-like properties. They strongly express Fc receptors, phagocytic capacity and macrophage cell surface antigen, but only weakly express myeloblast cell surface antigen and are negative for ATPase activity. Third, cells transformed by AMV and E26 viruses resemble myeloblasts in that they weakly express Fc receptors, phagocytic capacity and macrophage cell surface antigen but strongly express myeloblast cell surface antigen and ATPase activity. No difference was found between in vitro- and in vivo-transformed cells in the parameters tested. In light of recent genetic and biochemical evidence, we believe that these phenotypes reflect the action of three new types of viral-transforming genes, designated erb (erythroblast), mac (macrophage) and myb (myeloblast).","authors":"Beug, H., von Kirchbach, A., D\u00f6derlein, G., Conscience, JF., Graf, T.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Cell","volume":"18","issue":"2","page":"375-90","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1980-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16603183","title":"Combining pharmacological mobilization with intramyocardial delivery of bone marrow cells over-expressing VEGF is more effective for cardiac repair.","abstract":"We postulated that combining cell based hVEGF165 gene delivery with cytokine-induced mobilization of bone marrow cells (BMC) may give better prognosis in an infarcted heart. Forty-eight myoabalated female C57BL\/6J mice (20-25 g) received 1 x 10(6) BMC from transgenic GFP+ male mice. One month later, acute myocardial infarction (MI) model was developed by coronary artery ligation. Animals were grouped (N = 12) to receive intramyocardial injections of 10 microl DMEM without cells (group 1; group 2) or with 1x10(5) mesenchymal stem cells (MSC) over-expressing hVEGF165 (group 3; group 4). The animals received either cytokine therapy (group 2 and 4) or saline solution (group 1 and 3) for 7 days after MI. Hemodynamic data were obtained 4 weeks after MI using Millar's P-V system and cardiac tissue was harvested for immunohistological studies. We observed regeneration and extensive survival of BMC in and around the infarcted myocardium in groups 3 and 4. Blood vessel density was markedly enhanced in group 4 as compared with groups 1 and 2 in peri-infarct area. Fibrotic area was significantly reduced with improved LV-contractile function in group 2 and 4. LV-systolic and diastolic functions were well-preserved in group 4 as indicated by +dP\/dt, -dP\/dt and Tau (glantz). We therefore conclude that transplantation of MSC overexpressing VEGF combined with cytokine induced BMC mobilization is superior to either of the monotherapy approach for angiomyogenesis and LV-function recovery.","authors":"Wang, Y., Haider, HK., Ahmad, N., Xu, M., Ge, R., Ashraf, M.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Mol Cell Cardiol","volume":"40","issue":"5","page":"736-45","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"113","title":"Proceedings: The effects of glucagon on the hepatic arterial vasculature of the dog: an inhibition of the effects of vasoconstrictor agents.","abstract":"","authors":"Richardson, PD., Withrington, PG.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Pharmacol","volume":"55","issue":"2","page":"272P-273P","pdf":null,"JrId":"1895","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20534472","title":"Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway.","abstract":"Piwi-interacting RNAs (piRNAs) are essential for silencing of transposable elements in the germline, but their biogenesis is poorly understood. Here we demonstrate that MOV10L1, a germ cell-specific putative RNA helicase, is associated with Piwi proteins. Genetic disruption of the MOV10L1 RNA helicase domain in mice renders both MILI and MIWI2 devoid of piRNAs. Absence of a functional piRNA pathway in Mov10l1 mutant testes causes loss of DNA methylation and subsequent derepression of retrotransposons in germ cells. The Mov10l1 mutant males are sterile owing to complete meiotic arrest. This mouse mutant expresses Piwi proteins but lacks piRNAs, suggesting that MOV10L1 is required for piRNA biogenesis and\/or loading to Piwi proteins.","authors":"Zheng, K., Xiol, J., Reuter, M., Eckardt, S., Leu, NA., McLaughlin, KJ., Stark, A., Sachidanandam, R., Pillai, RS., Wang, PJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc Natl Acad Sci U S A","volume":"107","issue":"26","page":"11841-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"226888","title":"Three new types of viral oncogene of cellular origin specific for haematopoietic cell transformation.","abstract":"The RNAs of seven replication-defective leukaemia virus (DLV) strains contain three types of unique sequences, which correlate with the capacity of a given virus strain to transform erythroblasts, macrophage-like cells and myeloblasts, respectively. These sequences, termed erb, mac and myb, have their counterparts in the normal DNA of avian and mammalian species. Our results indicate that DLVs represent recombinants between a common 'vector' related to a chicken endogenous virus and one of three types of cellular gene possibly involved in haematopoietic differentiation.","authors":"Roussel, M., Saule, S., Lagrou, C., Rommens, C., Beug, H., Graf, T., Stehelin, D.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Nature","volume":"281","issue":"5731","page":"452-5","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1979-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17564582","title":"The EWS-Oct-4 fusion gene encodes a transforming gene.","abstract":"The t(6;22)(p21;q12) translocation associated with human bone and soft-tissue tumours results in a chimaeric molecule fusing the NTD (N-terminal domain) of the EWS (Ewing's sarcoma) gene to the CTD (C-terminal domain) of the Oct-4 (octamer-4) embryonic gene. Since the N-terminal domains of EWS and Oct-4 are structurally different, in the present study we have assessed the functional consequences of the EWS-Oct-4 fusion. We find that this chimaeric gene encodes a nuclear protein which binds DNA with the same sequence specificity as the parental Oct-4 protein. Comparison of the transactivation properties of EWS-Oct-4 and Oct-4 indicates that the former has higher transactivation activity for a known target reporter gene containing Oct-4 binding. Deletion analysis of the functional domains of EWS-Oct-4 indicates that the EWS (NTD), the POU domain and the CTD of EWS-Oct-4 are necessary for full transactivation potential. EWS-Oct-4 induced the expression of fgf-4 (fibroblast growth factor 4) and nanog, which are potent mitogens as well as Oct-4 downstream target genes whose promoters contain potential Oct-4-binding sites. Finally, ectopic expression of EWS-Oct-4 in Oct-4-null ZHBTc4 ES (embryonic stem) cells resulted in increased tumorigenic growth potential in nude mice. These results suggest that the oncogenic effect of the t(6;22) translocation is due to the EWS-Oct-4 chimaeric protein and that fusion of the EWS NTD to the Oct-4 DNA-binding domain produces a transforming chimaeric product.","authors":"Lee, J., Kim, JY., Kang, IY., Kim, HK., Han, YM., Kim, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Biochem J","volume":"406","issue":"3","page":"519-26","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2328927","title":"17 beta-estradiol inhibits LDL oxidation and cholesteryl ester formation in cultured macrophages.","abstract":"The effects of 17 beta estradiol, testosterone, the estradiol benzoate, and probucol on the oxidation kinetics of low density lipoprotein (LDL) in vitro in absorption presence of 10 microM Cu (II) are examined. Changes in the absorption at 234 nm (A234) and fluorescence (Ex340\/Em420) are monitored. The kinetics of the changes observed let us suggest a precursor-product relationship between dienes and fluorochromes in the oxidized LDL. The addition of 17 beta estradiol and probucol to LDL results in a prolongation of the lag phase characterized by only insignificant formation of dienes and fluorochromes. The addition of testosterone and estradiol benzoate used as control compounds has no effect on the lag phase and thus no LDL stabilizing effect. Conditioned LDL which was incubated in F-10 medium before exposure to cultured P388D.1 macrophages increases the formation of cytoplasmic lipid droplets and of cellular cholesteryl esters. The LDL stabilizing compounds beta estradiol and probucol (but not testosterone) causes a reduction of the cholesteryl ester content of the cultured macrophages. Protection of LDL particles against oxidative damage apparently results also in lowering of cytoplasmic cholesteryl ester in cultured P388D.1 cells. We conclude that the known antiatherosclerotic potency of 17 beta estradiol may in part result from its LDL stabilizing activity.","authors":"Huber, LA., Scheffler, E., Poll, T., Ziegler, R., Dresel, HA.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Free Radic Res Commun","volume":"8","issue":"3","page":"167-73","pdf":null,"JrId":"3904","fulltextlink":null,"preprintlink":null,"articledate":"1990-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"110","title":"Polypsychopharmacy.","abstract":"","authors":"Sturges, S., Brown, M.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Bull Menninger Clin","volume":"39","issue":"3","page":"274-9","pdf":null,"JrId":"2355","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8887663","title":"Myb-Ets fusion oncoprotein inhibits thyroid hormone receptor\/c-ErbA and retinoic acid receptor functions: a novel mechanism of action for leukemogenic transformation by E26 avian retrovirus.","abstract":"The E26 and avian erythroblastosis virus (AEV) avian retroviruses induce acute leukemia in chickens. E26 can block both erythroid and myeloid differentiation at an early multipotent stage. Moreover, E26 can block erythroid differentiation at the erythroid burst-forming unit\/erythroid CFU (BFU-E\/CFU-E) stage, which also corresponds to the differentiation stage blocked by AEV. AEV carries two oncogenes, v-erbA and v-erbB, whereas E26 encodes a single 135-kDa Gag-Myb-Ets fusion oncoprotein. v-ErbA is responsible for the erythroid differentiation arrest through negative interferences with both the retinoic acid receptor (RAR) and the thyroid hormone receptor (T3R\/c-ErbA). We investigated whether Myb-Ets could block erythroid differentiation in a manner similar to v-ErbA. We show here that Myb-Ets inhibits both RAR and c-ErbA activities on specific hormone response elements in transient-expression assays. Moreover, Myb-Ets abrogates the inactivation of transcription factor AP-1 by RAR and T3R, another feature shared with v-ErbA. Myb-Ets also antagonizes the biological response of erythrocytic progenitor cells to retinoic acid and T3. Analysis of a series of mutants of Myb-Ets reveals that the domains of the oncoprotein involved in these inhibitory activities are the same as those involved in oncogenic transformation of hematopoietic cells. These data demonstrate that the Myb-Ets oncoprotein shares properties with the v-ErbA oncoprotein and that inhibition of ligand-dependent RAR and c-ErbA functions by Myb-Ets is responsible for blocking the differentiation of hematopoietic progenitors.","authors":"Rascle, A., Ferrand, N., Gandrillon, O., Samarut, J.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Mol Cell Biol","volume":"16","issue":"11","page":"6338-51","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1996-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"46","title":"Purification and properties of Escherichia coli dihydrofolate reductase.","abstract":"Dihydrofolate reductase has been purified 40-fold to apparent homogeneity from a trimethoprim-resistant strain of Escherichia coli (RT 500) using a procedure that includes methotrexate affinity column chromatography. Determinations of the molecular weight of the enzyme based on its amino acid composition, sedimentation velocity, and sodium dodecyl sulfate gel electrophoresis gave values of 17680, 17470 and 18300, respectively. An aggregated form of the enzyme with a low specific activity can be separated from the monomer by gel filtration; treatment of the aggregate with mercaptoethanol or dithiothreitol results in an increase in enzymic activity and a regeneration of the monomer. Also, multiple molecular forms of the monomer have been detected by polyacrylamide gel electrophoresis. The unresolved enzyme exhibits two pH optima (pH 4.5 and pH 7.0) with dihydrofolate as a substrate. Highest activities are observed in buffers containing large organic cations. In 100 mM imidazolium chloride (pH 7), the specific activity is 47 mumol of dihydrofolate reduced per min per mg at 30 degrees. Folic acid also serves as a substrate with a single pH optimum of pH 4.5. At this pH the Km for folate is 16 muM, and the Vmax is 1\/1000 of the rate observed with dihydrofolate as the substrate. Monovalent cations (Na+, K+, Rb+, and Cs+) inhibit dihydrofolate reductase; at a given ionic strength the degree of inhibition is a function of the ionic radius of the cation. Divalent cations are more potent inhibitors; the I50 of BaCl2 is 250 muM, as compared to 125 mM for KCl. Anions neither inhibit nor activate the enzyme.","authors":"Baccanari, D., Phillips, A., Smith, S., Sinski, D., Burchall, J.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"24","page":"5267-73","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-214","title":"PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes","abstract":null,"authors":"Wutz, G., Davidson, I.F., Banigan, E.J., Kawasumi, R., Stocsits, R.R., Tang, W., Nagasaka, K., Costantino, L., Jansen, R., Hirota, K., Branzei, D., Mirny, D. and Peters, J.-M. ","publication_status":"epublish","journalpubyear":"2025","journaltitle":"bioRxiv ","volume":"673243","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2025.08.30.673243v3","preprintlink":null,"articledate":"2025-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"42","title":"A competitive labeling method for the determination of the chemical properties of solitary functional groups in proteins.","abstract":"The properties of the functional groups in a protein can be used as built-in-probes of the structure of the protein. We have developed a general procedure whereby the ionization constant and chemical reactivity of solitary functional groups in proteins may be determined. The method may be applied to the side chain of histidine, tyrosine, lysine, and cysteine, as well as to the amino terminus of the protein. The method, which is an extension of the competitive labeling technique using [3H]- and [14C]1-fluoro-2,4-dinitrobenzene (N2ph-F) in a double-labeling procedure, is rapid and sensitive. Advantage is taken of the fact that after acid hydrolysis of a dinitrophenylated protein, a derivative is obtained which must be derived from a unique position in the protein. The method has been applied to the solitary histidine residue of lysozyme, alpha-lytic protease, and Streptomyces griseus (S.G.) trypsin, as well as to the amino terminus of the latter protein. The following parameters were obtained for reaction with N2ph-F at 20 degrees C in 0.1 N KCl: the histidine of hen egg-white lysozyme, pKa of 6.4 and second-order velocity constant of 0.188 M-1 min-1; the histidine of alpha-lytic protease, pKa of 6.5 and second-order velocity constant of 0.0235 M-1 min-1; the histidine of S.G. trypsin, pKa of 6.5 and second-order velocity constant of 0.0328 M-1 min-1; the valyl amino terminus of S.G. trypsin, pKa of 8.1 and second-order velocity constant of 0.403 M-1 min-1. In addition, the results obtained provide clues as to the microenvironments of these functional groups, and indicate that the proteins studied undergo pH-dependent conformational changes which affect the microenvironment, and hence the chemical reactivity of these groups.","authors":"Duggleby, RG., Kaplan, H.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"23","page":"5168-75","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19325882","title":"Characterization of the interferon-producing cell in mice infected with Listeria monocytogenes.","abstract":"Production of type I interferons (IFN-I, mainly IFNalpha and IFNbeta) is a hallmark of innate immune responses to all classes of pathogens. When viral infection spreads to lymphoid organs, the majority of systemic IFN-I is produced by a specialized \"interferon-producing cell\" (IPC) that has been shown to belong to the lineage of plasmacytoid dendritic cells (pDC). It is unclear whether production of systemic IFN-I is generally attributable to pDC irrespective of the nature of the infecting pathogen. We have addressed this question by studying infections of mice with the intracellular bacterium Listeria monocytogenes. Protective innate immunity against this pathogen is weakened by IFN-I activity. In mice infected with L. monocytogenes, systemic IFN-I was amplified via IFN-beta, the IFN-I receptor (IFNAR), and transcription factor interferon regulatory factor 7 (IRF7), a molecular circuitry usually characteristic of non-pDC producers. Synthesis of serum IFN-I did not require TLR9. In contrast, in vitro-differentiated pDC infected with L. monocytogenes needed TLR9 to transcribe IFN-I mRNA. Consistent with the assumption that pDC are not the producers of systemic IFN-I, conditional ablation of the IFN-I receptor in mice showed that most systemic IFN-I is produced by myeloid cells. Furthermore, results obtained with FACS-purified splenic cell populations from infected mice confirmed the assumption that a cell type with surface antigens characteristic of macrophages and not of pDC is responsible for bulk IFN-I synthesis. The amount of IFN-I produced in the investigated mouse lines was inversely correlated to the resistance to lethal infection. Based on these data, we propose that the engagement of pDC, the mode of IFN-I mobilization, as well as the shaping of the antimicrobial innate immune response by IFN-I differ between intracellular pathogens.","authors":"Stockinger, S., Kastner, R., Kernbauer, E., Pilz, A., Westermayer, S., Reutterer, B., Soulat, D., Stengl, G., Vogl, C., Frenz, T., Waibler, Z., Taniguchi, T., R\u00fclicke, T., Kalinke, U., M\u00fcller, M., Decker, T.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS Pathog","volume":"5","issue":"3","page":"e1000355","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2895057","title":"Biological effects of the v-erbA oncogene in transformation of avian erythroid cells.","abstract":"","authors":"Vennstr\u00f6m, B., Beug, R., Damm, K., Engel, D., Gehring, U., Graf, T., Mu\u00f1oz, A., Sap, J., Zenke, M.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Horm Metab Res Suppl","volume":"17","issue":"","page":"14-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1988-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2178137","title":"Characterization of fos-induced osteogenic tumours and tumour-derived murine cell lines.","abstract":"Osteogenic tumours from c-fos (MT-c-fos-LTR)-transgenic mice and from mice infected with the v-fos-bearing FBR murine osteosarcoma virus (FBR MSV) showed close morphological and neoplastic similarities. Fos mRNA expression was elevated in both types of tumours, and expression of several genes characteristic of differentiated bone cells was either lower, enhanced, or not detectable in comparison to that in normal bone. Tumour-derived cell lines showed variable levels of exogenous fos expression; bone-cell-specific genes were similarly expressed in both primary tumours and tumour-derived cell lines. Upon transplantation the tumour cells formed fibrosarcomas, some of which contained areas of focal osseochondrous differentiation. Non-tumorigenic cell lines established from bone tissue of normal and MT-c-fos-LTR transgenic mice showed osteoblastic characteristics, whereas no parathyroid hormone (PTH) response was observed in transgenic tumour cell lines in spite of high alkaline phosphatase activity. These data indicate that deregulated fos expression interferes with terminal osteogenic differentiation in v-fos- and c-fos-induced bone tumours.","authors":"Goralczyk, R., Closs, EI., R\u00fcther, U., Wagner, EF., Strauss, PG., Erfle, V., Schmidt, J.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Differentiation","volume":"44","issue":"2","page":"122-31","pdf":null,"JrId":"3402","fulltextlink":null,"preprintlink":null,"articledate":"1991-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1672166","title":"Ontogeny of the v-erbA oncoprotein from the thyroid hormone receptor: an alteration in the DNA binding domain plays a role crucial for v-erbA function.","abstract":"The avian erythroblastosis virus v-erbA oncogene is imprecisely derived from a cellular gene (c-erbA) encoding a thyroid hormone receptor: the v-erbA protein has sustained both small terminal deletions and internal amino acid sequence changes relative to c-erbA. We report here that one of these missense differences between v- and c-erbA proteins, located in a zinc finger DNA binding domain, has dramatic effects on the biological activities of the encoded protein. Back mutation of the viral coding sequence to resemble c-erbA at this site severely impairs erythroid transformation and produces subtle changes in DNA binding by the encoded protein, suggesting that differences in DNA binding by the viral and cellular proteins may be involved in the activation of v-erbA as an oncogene.","authors":"Bonde, BG., Sharif, M., Privalsky, ML.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"J Virol","volume":"65","issue":"4","page":"2037-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1991-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"92","title":"Membrane-bound enzymes. III. Protease activity in leucocytes in relation to erythrocyte membranes.","abstract":"Protease activity was detected in membranes of human bovine erythrocytes prepared by the conventional procedures which include washing and removal of the  \"buffy layer\". The enzyme was extracted by 0.75 M KCNS or (NH4)2SO4 and was activated by 0.4 to 0.5 M of the same salts. Colored, particulate hide powder-azure, membrane fractions and soluble proteins such as hemoglobin, casein or albumin were susceptible to hydrolysis by the membraneous protease. Partial purification of the enzyme was accomplished through disc-gel electrophoresis on polyacrylamide in the presence of 0.25% positively charged detergents like cetyltrimethylammonium bromide. An alkaline protease (pH 7.4) with properties similar to those of the erythrocyte enzyme was found in leucocytes. The similarity between the properties of the leucocytic and erythrocytic proteases and the correlation of the activity in erythrocyte membranes with content of white cells in these preparations, suggest that enzymatic activities in the contaminating leucocytes are responsible for the activity of membraneous proteases in erythrocytes.","authors":"Heller, M., Edelstein, P., Mayer, M.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"413","issue":"3","page":"472-82","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"210958","title":"Differential expression of Rous Sarcoma virus-specific transformation parameters in enucleated cells.","abstract":"Chicken embryo fibroblasts transformed with the Ta and ts68 mutants of Rous Sarcoma virus (RSV) were enucleated and studied for their capacity to express reversibly the transformed phenotype in response to temperature changes. After shift to the permissive temperature (35 degrees C), the cytoplasts acquired a transformed morphology and displayed characteristic ruffles and microvilli at their surface. As detected by immunofluorescence, they also lost their actin filament cables and exhibited characteristic changes in the pattern of cell surface structures containing LETS protein. Expression of all these transformation parameters was reversible after shiftback to the nonpermissive temperature (41 degrees C). These results indicate that a whole set of changes characteristic for the transformed phenotype can be expressed independently of the cell nucleus. In contrast, ts mutant-infected cytoplasts were no longer able to respond to temperature shifts with changes in their hexose transport rate. Cytoplasts prepared from cells grown at 41 degrees C retained their low rate of hexose uptake after shift to 35 degrees C, whereas cytoplasts from cells grown at 35 degrees C exhibited a high rate of hexose transport even after 10 hr of shift to 41 degrees C. These results are in accordance with the hypothesis that the product of the src gene of RSV represents a multifunctional protein which acts independently on nuclear and extranuclear sites.","authors":"Beug, H., Claviez, M., Jockusch, BM., Graf, T.","publication_status":"ppublish","journalpubyear":"1978","journaltitle":"Cell","volume":"14","issue":"4","page":"843-56","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1978-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19663507","title":"High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all.","abstract":"The development of quantitative techniques in mass spectrometry has generated the ability to systematically monitor protein expression. Isobaric tags for relative and absolute quantification (iTRAQ) have become a widely used tool for the quantification of proteins. However, application of iTRAQ methodology using ion traps and hybrid mass spectrometers containing an ion trap such as the LTQ-Orbitrap was not possible until the development of pulsed Q dissociation (PQD) and higher energy C-trap dissociation (HCD). Both methods allow iTRAQ-based quantification on an LTQ-Orbitrap but are less suited for protein identification at a proteomic scale than the commonly used collisional induced dissociation (CID) fragmentation. We developed an analytical strategy combining the advantages of CID and HCD, allowing sensitive and accurate protein identification and quantitation at the same time. In a direct comparison, the novel method outperformed PQD and HCD regarding its limit of detection, the number of identified peptides and the analytical precision of quantitation. The new method was applied to study changes in protein expression in mouse hearts upon transverse aortic constriction, a model for cardiac stress.","authors":"K\u00f6cher, T., Pichler, P., Schutzbier, M., Stingl, C., Kaul, A., Teucher, N., Hasenfuss, G., Penninger, JM., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Proteome Res","volume":"8","issue":"10","page":"4743-52","pdf":null,"JrId":"30137","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-131","title":"Temperature dependence of the near-field superlensing effect for single metal layers and stacked metal-dielectric films","abstract":null,"authors":"Elsayad, K., Heinze, KG. ","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc. SPIE","volume":"7757","issue":"","page":"77573L","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-132","title":"Fast near-field imaging of spectrally broad sources using layered metallic structures","abstract":null,"authors":"Elsayad, K., Urich, A., Unterrainer, K., Heinze, KG.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc. SPIE","volume":"7757","issue":"","page":"77573M","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"159","title":"Serum lactate dehydrogenase activity ratios with different substrates.","abstract":"1. The lactate dehydrogenase activity of 89 sera from patients suffering myocardial infarction and of 55 sera from patients with hepatocellular damage was assayed under optimal conditions using pyruvate, alpha-oxobutyrate, hydroxypyruvate and glyoxylate as substrates. Activity was also measured with lactate as substrate at different pH values. 2. The ratios of activities under these different assay conditions were calculated for both series of patients. Correct differentiations for single ratios ranged from virtually nil for hydroxypyruvate\/alpha-oxobutyrate to is greater than 93 per cent for glyoxylate\/hydroxypyruvate and glyoxylate\/alpha-oxobutyrate. This was little improved by the use of multiple ratios involving up to seven separate assays. 3. The activity ratio of hydroxypyruvate to pyruvate which is consistently greater than unity was found to be inverted in a case of morphine poisoning.","authors":"Barlow, D., Naghizadeh, F., King, J.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Biochem","volume":"8","issue":"5","page":"307-15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23698349","title":"Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs.","abstract":"Large-scale genomics and computational approaches have identified thousands of putative long non-coding RNAs (lncRNAs). It has been controversial, however, as to what fraction of these RNAs is truly non-coding. Here, we combine ribosome profiling with a machine-learning approach to validate lncRNAs during zebrafish development in a high throughput manner. We find that dozens of proposed lncRNAs are protein-coding contaminants and that many lncRNAs have ribosome profiles that resemble the 5' leaders of coding RNAs. Analysis of ribosome profiling data from embryonic stem cells reveals similar properties for mammalian lncRNAs. These results clarify the annotation of developmental lncRNAs and suggest a potential role for translation in lncRNA regulation. In addition, our computational pipeline and ribosome profiling data provide a powerful resource for the identification of translated open reading frames during zebrafish development.","authors":"Chew, GL., Pauli, A., Rinn, JL., Regev, A., Schier, AF., Valen, E.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Development","volume":"140","issue":"13","page":"2828-34","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23","title":"Effect of etafenone on total and regional myocardial blood flow.","abstract":"The distribution of blood flow to the subendocardial, medium and subepicardial layers of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). Regional myocardial blood flow was determined by means of the particle distribution method. In normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a significantly higher flow rate compared with the subepicardial layers. In hypoxia induced vasodilation this transmural gradient of flow was persistent. In contrast a marked redistribution of regional flow was observed under pharmacologically induced vasodilation. The transmural gradient decreased. In contrast to some findings these experiments demonstrate that a considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by drugs. The differences observed for the intramural distribution pattern of flow under hypoxia and drug induced vasodilation support the hypothesis that this pattern reflects corresponding gradients of regional myocardial metabolism.","authors":"Flohr, H., Breull, W.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Arzneimittelforschung","volume":"25","issue":"9","page":"1400-3","pdf":null,"JrId":"884","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21","title":"[Biochemical studies on camomile components\/III. In vitro studies about the antipeptic activity of (--)-alpha-bisabolol (author's transl)].","abstract":"(--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 percent through addition of bisabolol in the ratio of 1\/0.5. The antipeptic action of bisabolol only occurs in case of direct contact. In case of a previous contact with the substrate, the inhibiting effect is lost.","authors":"Isaac, O., Thiemer, K.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Arzneimittelforschung","volume":"25","issue":"9","page":"1352-4","pdf":null,"JrId":"884","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"90","title":"Alterations in phospholipid-dependent (Na+ +K+)-ATPase activity due to lipid fluidity. Effects of cholesterol and Mg2+.","abstract":"The (Na+ +K+)-activated, Mg2+-dependent ATPase from rabbit kidney outer medulla was prepared in a partially inactivated, soluble form depleted of endogenous phospholipids, using deoxycholate. This preparation was reactivated 10 to 50-fold by sonicated liposomes of phosphatidylserine, but not by non-sonicated phosphatidylserine liposomes or sonicated phosphatidylcholine liposomes. The reconstituted enzyme resembled native membrane preparations of (Na+ +K+)-ATPase in its pH optimum being around 7.0, showing optimal activity at Mg2+:ATP mol ratios of approximately 1 and a Km value for ATP of 0.4 mM. Arrhenius plots of this reactivated activity at a constant pH of 7.0 and an Mg2+: ATP mol ratio of 1:1 showed a discontinuity (sharp change of slope) at 17 degrees C, with activation energy (Ea) values of 13-15 kcal\/mol above this temperature and 30-35 kcal below it. A further discontinuity was also found at 8.0 degrees C and the Ea below this was very high (greater than 100 kcal\/mol). Increased Mg2+ concentrations at Mg2+:ATP ratios in excess of 1:1 inhibited the (Na+ +K+)-ATPase activity and also abolished the discontinuities in the Arrhenius plots. The addition of cholesterol to phosphatidylserine at a 1:1 mol ratio partially inhibited (Na+ +K+)-ATPase reactivation. Arrhenius plots under these conditions showed a single discontinuity at 20 degrees C and Ea values of 22 and 68 kcal\/mol above and below this temperature respectively. The ouabain-insensitive Mg2+-ATPase normally showed a linear Arrhenius plot with an Ea of 8 kcal\/mol. The cholesterol-phosphatidylserine mixed liposomes stimulated the Mg2+-ATPase activity, which now also showed a discontinuity at 20 degrees C with, however, an increased value of 14 kcal\/mol above this temperature and 6 kcal\/mol below. Kinetic studies showed that cholesterol had no significant effect on the Km values for ATP. Since both cholesterol and Mg2+ are known to alter the effects of temperature on the fluidity of phospholipids, the above results are discussed in this context.","authors":"Kimelberg, HK.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"413","issue":"1","page":"143-56","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19635780","title":"Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform.","abstract":"Drosophila melanogaster expresses three classes of small RNAs, which are classified according to their mechanisms of biogenesis. MicroRNAs are approximately 22-23 nucleotides (nt), ubiquitously expressed small RNAs that are sequentially processed from hairpin-like precursors by Drosha\/Pasha and Dcr-1\/Loquacious complexes. MicroRNAs usually associate with AGO1 and regulate the expression of protein-coding genes. Piwi-interacting RNAs (piRNAs) of approximately 24-28 nt associate with Piwi-family proteins and can arise from single-stranded precursors. piRNAs function in transposon silencing and are mainly restricted to gonadal tissues. Endo-siRNAs are found in both germline and somatic tissues. These approximately 21-nt RNAs are produced by a distinct Dicer, Dcr-2, and do not depend on Drosha\/Pasha complexes. They predominantly bind to AGO2 and target both mobile elements and protein-coding genes. Surprisingly, a subset of endo-siRNAs strongly depend for their production on the dsRNA-binding protein Loquacious (Loqs), thought generally to be a partner for Dcr-1 and a cofactor for miRNA biogenesis. Endo-siRNA production depends on a specific Loqs isoform, Loqs-PD, which is distinct from the one, Loqs-PB, required for the production of microRNAs. Paralleling their roles in the biogenesis of distinct small RNA classes, Loqs-PD and Loqs-PB bind to different Dicer proteins, with Dcr-1\/Loqs-PB complexes and Dcr-2\/Loqs-PD complexes driving microRNA and endo-siRNA biogenesis, respectively.","authors":"Zhou, R., Czech, B., Brennecke, J., Sachidanandam, R., Wohlschlegel, JA., Perrimon, N., Hannon, GJ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"RNA","volume":"15","issue":"10","page":"1886-95","pdf":null,"JrId":"8792","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19629043","title":"The cohesin complex is required for the DNA damage-induced G2\/M checkpoint in mammalian cells.","abstract":"Cohesin complexes mediate sister chromatid cohesion. Cohesin also becomes enriched at DNA double-strand break sites and facilitates recombinational DNA repair. Here, we report that cohesin is essential for the DNA damage-induced G2\/M checkpoint. In contrast to cohesin's role in DNA repair, the checkpoint function of cohesin is independent of its ability to mediate cohesion. After RNAi-mediated depletion of cohesin, cells fail to properly activate the checkpoint kinase Chk2 and have defects in recruiting the mediator protein 53BP1 to DNA damage sites. Earlier work has shown that phosphorylation of the cohesin subunits Smc1 and Smc3 is required for the intra-S checkpoint, but Smc1\/Smc3 are also subunits of a distinct recombination complex, RC-1. It was, therefore, unknown whether Smc1\/Smc3 function in the intra-S checkpoint as part of cohesin. We show that Smc1\/Smc3 are phosphorylated as part of cohesin and that cohesin is required for the intra-S checkpoint. We propose that accumulation of cohesin at DNA break sites is not only needed to mediate DNA repair, but also facilitates the recruitment of checkpoint proteins, which activate the intra-S and G2\/M checkpoints.","authors":"Watrin, E., Peters, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"EMBO J","volume":"28","issue":"17","page":"2625-35","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20814424","title":"Role of the RNA\/DNA kinase Grc3 in transcription termination by RNA polymerase I.","abstract":"Transcription termination by RNA polymerase I in Saccharomyces cerevisiae is mediated by a 'torpedo' mechanism: co-transcriptional RNA cleavage by Rnt1 at the ribosomal DNA 3'-region generates a 5'-end that is recognized by the 5'-3' exonuclease Rat1; this degrades the downstream transcript and eventually causes termination. In this study, we identify Grc3 as a new factor involved in this process. We demonstrate that GRC3, an essential gene of previously unknown function, encodes a polynucleotide kinase that is required for efficient termination by RNA polymerase I. We propose that it controls the phosphorylation status of the downstream Rnt1 cleavage product and thereby regulates its accessibility to the torpedo Rat1.","authors":"Braglia, P., Heindl, K., Schleiffer, A., Martinez, J., Proudfoot, NJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"EMBO Rep","volume":"11","issue":"10","page":"758-64","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20705756","title":"Identification and functional analysis of endothelial tip cell-enriched genes.","abstract":"Sprouting of developing blood vessels is mediated by specialized motile endothelial cells localized at the tips of growing capillaries. Following behind the tip cells, endothelial stalk cells form the capillary lumen and proliferate. Expression of the Notch ligand Delta-like-4 (Dll4) in tip cells suppresses tip cell fate in neighboring stalk cells via Notch signaling. In DLL4(+\/-) mouse mutants, most retinal endothelial cells display morphologic features of tip cells. We hypothesized that these mouse mutants could be used to isolate tip cells and so to determine their genetic repertoire. Using transcriptome analysis of retinal endothelial cells isolated from DLL4(+\/-) and wild-type mice, we identified 3 clusters of tip cell-enriched genes, encoding extracellular matrix degrading enzymes, basement membrane components, and secreted molecules. Secreted molecules endothelial-specific molecule 1, angiopoietin 2, and apelin bind to cognate receptors on endothelial stalk cells. Knockout mice and zebrafish morpholino knockdown of apelin showed delayed angiogenesis and reduced proliferation of stalk cells expressing the apelin receptor APJ. Thus, tip cells may regulate angiogenesis via matrix remodeling, production of basement membrane, and release of secreted molecules, some of which regulate stalk cell behavior.","authors":"del Toro, R., Prahst, C., Mathivet, T., Siegfried, G., Kaminker, JS., Larrivee, B., Breant, C., Duarte, A., Takakura, N., Fukamizu, A., Penninger, J., Eichmann, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Blood","volume":"116","issue":"19","page":"4025-33","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-215","title":"A multivalent adaptor mechanism drives the nuclear import of proteasomes","abstract":null,"authors":"Brunner HL, Kalis RW, Grundmann L, Hod\u00e1kov\u00e1 Z, Koskova Z, Grishkovskaya I, de Almeida M, Hinterndorfer M, H\u00f6fflin S, Andersch F, Kotisch H, Dickmanns A, Cuylen-H\u00e4ring S, Zuber J, Haselbach D","publication_status":"preprint","journalpubyear":"2024","journaltitle":"625870","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.11.08.622636v2","preprintlink":null,"articledate":"2024-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29361316","title":"Structure and Conformational Dynamics of the Human Spliceosomal B<sup>act<\/sup> Complex.","abstract":"The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B<sup>act<\/sup> spliceosome at 3.4\u00a0\u00c5 resolution. In the B<sup>act<\/sup> state, the spliceosome is activated but not catalytically primed, so that it is functionally blocked prior to the first catalytic step of splicing. The spliceosomal core is similar to the yeast B<sup>act<\/sup> spliceosome; important differences include the presence of the RNA helicase aquarius and peptidyl prolyl isomerases. To examine the overall dynamic behavior of the purified spliceosome, we developed a principal component analysis-based approach. Calculating the energy landscape revealed eight major conformational states, which we refined to higher resolution. Conformational differences of the highly flexible structural components between these eight states reveal how spliceosomal components contribute to the assembly of the spliceosome, allowing it to generate a dynamic interaction network required for its subsequent catalytic activation.","authors":"Haselbach, D., Komarov, I., Agafonov, DE., Hartmuth, K., Graf, B., Dybkov, O., Urlaub, H., Kastner, B., L\u00fchrmann, R., Stark, H.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell","volume":"172","issue":"3","page":"454-464.e11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20458601","title":"Cbl-b in T-cell activation.","abstract":"Peripheral activation of antigen-specific T cells is stringently controlled to prevent immune responses against self-antigens. Only after a T cell is presented with two signals, an antigen and a co-stimulatory signal, can they be fully activated. In case antigen presentation occurs without co-stimulation, T-cell receptor (TCR) signaling pathways are regulated to prevent T-cell activation and induce T-cell tolerance. Thus, for a productive T-cell response to occur, co-stimulatory receptors need to serve the dual role of amplifying the TCR signaling while concomitantly releasing T cells from suppression. Biochemical and genetic studies during the last 10 years have documented the critical role of the E3 ubiquitin-ligase Cbl-b in this fundamental two-signal modulation of T-cell responses. In this review, we will discuss our current understanding on how Cbl-b controls T-cell activation and tolerance, its in vivo implications, as well as mechanisms for tuning T-cell-mediated immune responses by this essential E3 ligase.","authors":"Paolino, M., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Semin Immunopathol","volume":"32","issue":"2","page":"137-48","pdf":null,"JrId":"33486","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19584402","title":"Identification of cancer stem cells in a Tax-transgenic (Tax-Tg) mouse model of adult T-cell leukemia\/lymphoma.","abstract":"Adult T-cell leukemia\/lymphoma (ATL) is a malignant lymphoproliferative disorder caused by HTLV-I infection. In ATL, chemotherapeutic responses are generally poor, which has suggested the existence of chemotherapy-resistant cancer stem cells (CSCs). To identify CSC candidates in ATL, we have focused on a Tax transgenic mouse (Tax-Tg) model, which reproduces ATL-like disease both in Tax-Tg animals and also after transfer of Tax-Tg splenic lymphomatous cells (SLCs) to nonobese diabetic\/severe combined immunodeficiency (NOD\/SCID) mice. Using a limiting dilution transplantation, it was estimated that one CSC existed per 10(4) SLCs (0.01%). In agreement with this, we have successfully identified candidate CSCs in a side population (0.06%), which overlapped with a minor population of CD38(-)\/CD71(-)\/CD117(+) cells (0.03%). Whereas lymphoma did not develop after transplantation of 10(2) SLCs, 10(2) CSCs could consistently regenerate the original lymphoma. In addition, lymphoma and CSCs could also be demonstrated in the bone marrow and CD117(+) CSCs were observed in both osteoblastic and vascular niches. In the CSCs, Tax, Notch1, and Bmi1 expression was down-regulated, suggesting that the CSCs were derived from Pro-T cells or early hematopoietic progenitor cells. Taken together, our data demonstrate that CSCs certainly exist and have the potential to regenerate lymphoma in our mouse model.","authors":"Yamazaki, J., Mizukami, T., Takizawa, K., Kuramitsu, M., Momose, H., Masumi, A., Ami, Y., Hasegawa, H., Hall, WW., Tsujimoto, H., Hamaguchi, I., Yamaguchi, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Blood","volume":"114","issue":"13","page":"2709-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19515822","title":"Regulatory T cell differentiation of thymocytes does not require a dedicated antigen-presenting cell but is under T cell-intrinsic developmental control.","abstract":"The majority of regulatory T cells (T(regs)) are believed to be of thymic origin. It has been hypothesized that this may result from unique intrathymic environmental cues, possibly requiring a dedicated antigen-presenting cell (APC). However, T cell-intrinsic developmental regulation of the susceptibility to T(reg) differentiation remains a mutually non-exclusive scenario. We found that upon exposure of monoclonal T cells of sequential developmental stages to a thymic microenvironment expressing cognate antigen, the efficiency of T(reg) induction inversely correlated with progressive maturation. This inclination of immature thymocytes toward T(reg) differentiation was even seen in an APC-free in vitro system, providing only TCR stimulation and IL-2. In support of quantitative but not qualitative features of external cues being critical, thymic epithelial cells as well as different thymic dendritic cell (DC)-subtypes efficiently induced T(reg) development of immature thymocytes, albeit at strikingly different optimal doses of cognate antigen. We propose that the intrinsically high predisposition of immature thymocytes to T(reg) development may contribute to the predominantly thymic origin of the T(reg) repertoire. The underlying instructive stimulus, however, does not require unique features of a dedicated APC and can be delivered by hematopoietic as well as epithelial thymic stromal cells.","authors":"Wirnsberger, G., Mair, F., Klein, L.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Proc Natl Acad Sci U S A","volume":"106","issue":"25","page":"10278-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17406365","title":"Co-culturing human prostate carcinoma cells with hepatocytes leads to increased expression of E-cadherin.","abstract":"Metastasis is a multi-step process wherein tumour cells detach from the primary mass, migrate through barrier matrices, gain access to conduits to disseminate, and subsequently survive and proliferate in an ectopic site. During the initial invasion stage, prostate carcinoma cells undergo epithelial-mesenchymal-like transition with gain of autocrine signalling and loss of E-cadherin, hallmarks that appear to enable invasion and dissemination. However, some metastases express E-cadherin, and we found close connections between prostate carcinoma cells and hepatocytes in a liver microtissue bioreactor. We hypothesise that phenotypic plasticity occurs late in prostate cancer progression at the site of ectopic seeding. Immunofluorescence staining for E-cadherin in co-cultures of hepatocytes and DU-145 prostate cancer cells revealed E-cadherin upregulation at peripheral sites of contact by day 2 of co-culture; E-cadherin expression also increased in PC-3 cells in co-culture. These carcinoma cells bound to hepatocytes in an E-cadherin-dependent manner. Although the signals by which the hepatocytes elicited E-cadherin expression remain undetermined, it appeared related to downregulation of epidermal growth factor receptor (EGFR) signalling. Inhibition of autocrine EGFR signalling increased E-cadherin expression and cell-cell heterotypic adhesion; further, expression of a downregulation-resistant EGFR variant prevented E-cadherin upregulation. These findings were supported by finding E-cadherin and catenins but not activated EGFR in human prostate metastases to the liver. We conclude that the term epithelial-mesenchymal transition only summarises the transient downregulation of E-cadherin for invasion with re-expression of E-cadherin being a physiological consequence of metastatic seeding.","authors":"Yates, CC., Shepard, CR., Stolz, DB., Wells, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Br J Cancer","volume":"96","issue":"8","page":"1246-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20624430","title":"Modules for C-terminal epitope tagging of Tetrahymena genes.","abstract":"Although epitope tagging has been widely used for analyzing protein function in many organisms, there are few genetic tools for epitope tagging in Tetrahymena. In this study, we describe several C-terminal epitope tagging modules that can be used to express tagged proteins in Tetrahymena cells by both plasmid- and PCR-based strategies.","authors":"Kataoka, K., Schoeberl, UE., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Microbiol Methods","volume":"82","issue":"3","page":"342-6","pdf":null,"JrId":"21204","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1985022","title":"Three linked myosin heavy chain genes clustered within 370 kb of each other show independent transcriptional and post-transcriptional regulation during differentiation of a mouse muscle cell line.","abstract":"We have examined myosin heavy chain gene transcription in the mouse muscle cell line C2\/7 under different culture conditions. Gene-specific probes for embryonic (MHCemb), perinatal (MHCpn), and adult (MHCIIB) MHC sequences were used in nuclear run-on experiments, and transcriptional levels compared with cytoplasmic RNA accumulation of the transcripts during muscle cell differentiation. Transcripts are not detectable in myoblasts. These three MHC genes are physically linked within 370 kb of each other. However, they are not activated coordinately, but show independent transcriptional regulation as muscle cells differentiate into myotubes and as myotubes mature in culture. Post-transcriptional mechanisms also regulate cytoplasmic RNA accumulation of these MHC genes.","authors":"Cox, RD., Weydert, A., Barlow, D., Buckingham, ME.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Dev Biol","volume":"143","issue":"1","page":"36-43","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"1991-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9753321","title":"Apaf1 is required for mitochondrial pathways of apoptosis and brain development.","abstract":"Apoptosis is essential for the precise regulation of cellular homeostasis and development. The role in vivo of Apaf1, a mammalian homolog of C. elegans CED-4, was investigated in gene-targeted Apaf1-\/- mice. Apaf1-deficient mice exhibited reduced apoptosis in the brain and striking craniofacial abnormalities with hyperproliferation of neuronal cells. Apaf1-deficient cells were resistant to a variety of apoptotic stimuli, and the processing of Caspases 2, 3, and 8 was impaired. However, both Apaf1-\/- thymocytes and activated T lymphocytes were sensitive to Fas-induced killing, showing that Fas-mediated apoptosis in these cells is independent of Apaf1. These data indicate that Apaf1 plays a central role in the common events of mitochondria-dependent apoptosis in most death pathways and that this role is critical for normal development.","authors":"Yoshida, H., Kong, YY., Yoshida, R., Elia, AJ., Hakem, A., Hakem, R., Penninger, JM., Mak, TW.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Cell","volume":"94","issue":"6","page":"739-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-10-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20154683","title":"Active flight increases the gain of visual motion processing in Drosophila.","abstract":"We developed a technique for performing whole-cell patch-clamp recordings from genetically identified neurons in behaving Drosophila. We focused on the properties of visual interneurons during tethered flight, but this technique generalizes to different cell types and behaviors. We found that the peak-to-peak responses of a class of visual motion-processing interneurons, the vertical-system visual neurons (VS cells), doubled when flies were flying compared with when they were at rest. Thus, the gain of the VS cells is not fixed, but is instead behaviorally flexible and changes with locomotor state. Using voltage clamp, we found that the passive membrane resistance of VS cells was reduced during flight, suggesting that the elevated gain was a result of increased synaptic drive from upstream motion-sensitive inputs. The ability to perform patch-clamp recordings in behaving Drosophila promises to help unify the understanding of behavior at the gene, cell and circuit levels.","authors":"Maimon, G., Straw, AD., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Neurosci","volume":"13","issue":"3","page":"393-9","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19468067","title":"Mitotic control of kinetochore-associated dynein and spindle orientation by human Spindly.","abstract":"Mitotic spindle formation and chromosome segregation depend critically on kinetochore-microtubule (KT-MT) interactions. A new protein, termed Spindly in Drosophila and SPDL-1 in C. elegans, was recently shown to regulate KT localization of dynein, but depletion phenotypes revealed striking differences, suggesting evolutionarily diverse roles of mitotic dynein. By characterizing the function of Spindly in human cells, we identify specific functions for KT dynein. We show that localization of human Spindly (hSpindly) to KTs is controlled by the Rod\/Zw10\/Zwilch (RZZ) complex and Aurora B. hSpindly depletion results in reduced inter-KT tension, unstable KT fibers, an extensive prometaphase delay, and severe chromosome misalignment. Moreover, depletion of hSpindly induces a striking spindle rotation, which can be rescued by co-depletion of dynein. However, in contrast to Drosophila, hSpindly depletion does not abolish the removal of MAD2 and ZW10 from KTs. Collectively, our data reveal hSpindly-mediated dynein functions and highlight a critical role of KT dynein in spindle orientation.","authors":"Chan, YW., Fava, LL., Uldschmid, A., Schmitz, MH., Gerlich, DW., Nigg, EA., Santamaria, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Biol","volume":"185","issue":"5","page":"859-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-146","title":"Epithelial Plasticity of Hepatocytes During Liver Tumor Progression","abstract":null,"authors":"Mikula M., Lahsnig C., Fischer A.N.M., Proell V., Huber H., Fuchs E., Eger A., Beug H., Mikulits W. ","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Stem Cells and their Potential for Clinical Application ","volume":"","issue":"","page":"123-135 ","pdf":null,"JrId":null,"fulltextlink":"http:\/\/dx.doi.org\/10.1007\/978-1-4020-6469-2_9","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19465910","title":"Mutations in the beta-tubulin gene TUBB2B result in asymmetrical polymicrogyria.","abstract":"Polymicrogyria is a relatively common but poorly understood defect of cortical development characterized by numerous small gyri and a thick disorganized cortical plate lacking normal lamination. Here we report de novo mutations in a beta-tubulin gene, TUBB2B, in four individuals and a 27-gestational-week fetus with bilateral asymmetrical polymicrogyria. Neuropathological examination of the fetus revealed an absence of cortical lamination associated with the presence of ectopic neuronal cells in the white matter and in the leptomeningeal spaces due to breaches in the pial basement membrane. In utero RNAi-based inactivation demonstrates that TUBB2B is required for neuronal migration. We also show that two disease-associated mutations lead to impaired formation of tubulin heterodimers. These observations, together with previous data, show that disruption of microtubule-based processes underlies a large spectrum of neuronal migration disorders that includes not only lissencephaly and pachygyria, but also polymicrogyria malformations.","authors":"Jaglin, XH., Poirier, K., Saillour, Y., Buhler, E., Tian, G., Bahi-Buisson, N., Fallet-Bianco, C., Phan-Dinh-Tuy, F., Kong, XP., Bomont, P., Castelnau-Ptakhine, L., Odent, S., Loget, P., Kossorotoff, M., Snoeck, I., Plessis, G., Parent, P., Beldjord, C., Cardoso, C., Represa, A., Flint, J., Keays, DA., Cowan, NJ., Chelly, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Genet","volume":"41","issue":"6","page":"746-52","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18826944","title":"Di-methyl H4 lysine 20 targets the checkpoint protein Crb2 to sites of DNA damage.","abstract":"Histone lysine methylation is an important chromatin modification that can be catalyzed to a mono-, di-, or tri-methyl state. An ongoing challenge is to decipher how these different methyllysine histone marks can mediate distinct aspects of chromatin function. The fission yeast checkpoint protein Crb2 is rapidly targeted to sites of DNA damage after genomic insult, and this recruitment requires methylation of histone H4 lysine 20 (H4K20). Here we show that the tandem tudor domains of Crb2 preferentially bind the di-methylated H4K20 residue. Loss of this interaction by disrupting either the tudor-binding motif or the H4K20 methylating enzyme Set9\/Kmt5 ablates Crb2 localization to double-strand breaks and impairs checkpoint function. Further we show that dimethylation, but not tri-methylation, of H4K20 is required for Crb2 localization, checkpoint function, and cell survival after DNA damage. These results argue that the di-methyl H4K20 modification serves as a binding target that directs Crb2 to sites of genomic lesions and defines an important genome integrity pathway mediated by a specific methyl-lysine histone mark.","authors":"Greeson, NT., Sengupta, R., Arida, AR., Jenuwein, T., Sanders, SL.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Biol Chem","volume":"283","issue":"48","page":"33168-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18342508","title":"A simple vision-based algorithm for decision making in flying Drosophila.","abstract":"Animals must quickly recognize objects in their environment and act accordingly. Previous studies indicate that looming visual objects trigger avoidance reflexes in many species [1-5]; however, such reflexes operate over a close range and might not detect a threatening stimulus at a safe distance. We analyzed how fruit flies (Drosophila melanogaster) respond to simple visual stimuli both in free flight and in a tethered-flight simulator. Whereas Drosophila, like many other insects, are attracted toward long vertical objects [6-10], we found that smaller visual stimuli elicit not weak attraction but rather strong repulsion. Because aversion to small spots depends on the vertical size of a moving object, and not on looming, it can function at a much greater distance than expansion-dependent reflexes. The opposing responses to long stripes and small spots reflect a simple but effective object classification system. Attraction toward long stripes would lead flies toward vegetative perches or feeding sites, whereas repulsion from small spots would help them avoid aerial predators or collisions with other insects. The motion of flying Drosophila depends on a balance of these two systems, providing a foundation for studying the neural basis of behavioral choice in a genetic model organism.","authors":"Maimon, G., Straw, AD., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Biol","volume":"18","issue":"6","page":"464-70","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-147","title":"Phosphoproteomics as a tool to unravel plant regulatory mechanisms","abstract":null,"authors":"De la Fuente van Bentema S., Roitinger E., Anratherc D., Csaszarc E., Hirt H.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Physiologia Plantarum ","volume":"126","issue":"1","page":"110-119","pdf":null,"JrId":null,"fulltextlink":"http:\/\/dx.doi.org\/10.1111\/j.1399-3054.2006.00615.x","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1838695","title":"Molecular organization, ontogeny and expression of murine alpha beta and gamma delta T cell receptors.","abstract":"T lymphocytes recognize antigens via transmembrane heterodimers, their T cell receptors (TCR). T cells express either TCR alpha beta or TCR gamma delta isotypes. Several molecular mechanisms are employed to diversify the TCR repertoire. Ontogeny, transcriptional regulation, and control of TCR expression will be discussed.","authors":"Penninger, J., Wallace, VA., Kishihara, K., Molina, T., Krause, H., Mak, TW.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Exp Clin Immunogenet","volume":"8","issue":"2","page":"57-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1992-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16151841","title":"Velocity constancy and models for wide-field visual motion detection in insects.","abstract":"The tangential neurons in the lobula plate region of the flies are known to respond to visual motion across broad receptive fields in visual space. When intracellular recordings are made from tangential neurons while the intact animal is stimulated visually with moving natural imagery,we find that neural response depends upon speed of motion but is nearly invariant with respect to variations in natural scenery. We refer to this invariance as velocity constancy. It is remarkable because natural scenes, in spite of similarities in spatial structure, vary considerably in contrast, and contrast dependence is a feature of neurons in the early visual pathway as well as of most models for the elementary operations of visual motion detection. Thus, we expect that operations must be present in the processing pathway that reduce contrast dependence in order to approximate velocity constancy. We consider models for such operations, including spatial filtering, motion adaptation, saturating nonlinearities, and nonlinear spatial integration by the tangential neurons themselves, and evaluate their effects in simulations of a tangential neuron and precursor processing in response to animated natural imagery. We conclude that all such features reduce interscene variance in response, but that the model system does not approach velocity constancy as closely as the biological tangential cell.","authors":"Shoemaker, PA., O'Carroll, DC., Straw, AD.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Biol Cybern","volume":"93","issue":"4","page":"275-87","pdf":null,"JrId":"1081","fulltextlink":null,"preprintlink":null,"articledate":"2006-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-148","title":"Epigenom","abstract":null,"authors":"Jenuwein T., Almouzni G., Avner P.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"BIOFUTUR  ","volume":"","issue":"268","page":"67-69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1899479","title":"A single site mutation in a truncated Fos protein allows it to interact with the TRE in vitro.","abstract":"The Fos and Jun proteins, which are components of the transcription factor AP1, associate through the interaction of their so-called leucine zipper domains and bind strongly and specifically to DNA at phorbol ester-responsive elements. Jun also homodimerizes and binds the same element whereas Fos seems to have no specific affinity for DNA. We show that a single amino-acid change in the leucine zipper of Fos is sufficient to allow a truncated Fos protein to homodimerize and thus form a complex with DNA, even in the absence of Jun. This Fos-derived homodimer recognizes the consensus phorbol-ester responsive element specifically, in vitro. We conclude that the structural requirements for specific DNA binding are present in the Fos protein itself, with the exception of its lack of self-affinity.","authors":"Nicklin, MJ., Casari, G.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Oncogene","volume":"6","issue":"1","page":"173-9","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1991-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1721533","title":"Early fetal hematopoietic development from in vitro differentiated embryonic stem cells.","abstract":"In this report we describe the efficient hematopoietic differentiation of embryonic stem (ES) cells in vitro. When cultured in semisolid medium two of five ES cell lines efficiently generated embryoid bodies (EBs) containing blood islands in which hematopoietic cells from all six myeloid lineages could be detected. Among a variety of growth factors tested, only erythropoietin significantly increased blood island formation. We directly demonstrate the presence of hematopoietic progenitors in the EBs by employing an in vitro precursor assay. Colony-forming cells (CFC) of all myeloid lineages as well as bi- and multipotent (CFC-MIX) progenitors were readily identified, and a detailed time-course analysis of their appearance was performed. Despite a high frequency of CFC-MIX in vitro, we did not observe any spleen colony-forming cells (CFU-S) in vivo. We conclude that hematopoietic differentiation of ES cells under these conditions reflects formation of the complete range of blood cells found in the yolk sac of the early fetus. Therefore this system provides a unique model in which to study the earliest events of hematopoietic development in vitro.","authors":"Burkert, U., von R\u00fcden, T., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"New Biol","volume":"3","issue":"7","page":"698-708","pdf":null,"JrId":"1880","fulltextlink":null,"preprintlink":null,"articledate":"1992-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19448632","title":"RAG-1 and ATM coordinate monoallelic recombination   and nuclear positioning of immunoglobulin loci.","abstract":"Coordinated recombination of homologous antigen receptor loci is thought to be important for allelic exclusion. Here we show that homologous immunoglobulin alleles pair in a stage-specific way that mirrors the recombination patterns of these loci. The frequency of homologous immunoglobulin pairing was much lower in the absence of the RAG-1-RAG-2 recombinase and was restored in Rag1-\/- developing B cells with a transgene expressing a RAG-1 active-site mutant that supported DNA binding but not cleavage. The introduction of DNA breaks on one immunoglobulin allele induced ATM-dependent repositioning of the other allele to pericentromeric heterochromatin. ATM activated by the cleaved allele acts in trans on the uncleaved allele to prevent biallelic recombination and chromosome breaks or translocations.","authors":"Hewitt, SL., Yin, B., Ji, Y., Chaumeil, J., Marszalek, K., Tenthorey, J., Salvagiotto, G., Steinel, N., Ramsey, LB., Ghysdael, J., Farrar, MA., Sleckman, BP., Schatz, DG., Busslinger, M., Bassing, CH., Skok, JA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Immunol","volume":"10","issue":"6","page":"655-64","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19452197","title":"What was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor?","abstract":"Ubiquitin (Ub)-conjugating enzymes (E2) are key enzymes in ubiquitination or Ub-like modifications of proteins. We searched for all proteins belonging to the E2 enzyme super-family in seven species (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Arabidopsis thaliana) to identify families and to reconstruct each family's phylogeny. Our phylogenetic analysis of 207 genes led us to define 17 E2 families, with 37 E2 genes, in the human genome. The subdivision of E2 into four classes did not correspond to the phylogenetic tree. The sequence signature HPN (histidine-proline-asparagine), followed by a tryptophan residue at 16 (up to 29) amino acids, was highly conserved. When present, the active cysteine was found 7 to 8 amino acids from the C-terminal end of HPN. The secondary structures were characterized by a canonical alpha\/beta fold. Only family 10 deviated from the common organization because the proteins were devoid of enzymatic activity. Family 7 had an insertion between beta strands 1 and 2; families 3, 5 and 14 had an insertion between the active cysteine and the conserved tryptophan. The three-dimensional data of these proteins highlight a strong structural conservation of the core domain. Our analysis shows that the primitive eukaryote ancestor possessed a diversified set of E2 enzymes, thus emphasizing the importance of the Ub pathway. This comprehensive overview of E2 enzymes emphasizes the diversity and evolution of this superfamily and helps clarify the nomenclature and true orthologies. A better understanding of the functions of these enzymes is necessary to decipher several human diseases.","authors":"Michelle, C., Vourc'h, P., Mignon, L., Andres, CR.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Mol Evol","volume":"68","issue":"6","page":"616-28","pdf":null,"JrId":"4969","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24486161","title":"RANKL\/RANK - from bone physiology to breast cancer.","abstract":"RANK and its ligand RANKL are key molecules in bone metabolism and are critically involved in pathologic bone disorders. Deregulation of the RANK\/RANKL system is for example a main reason for the development of postmenopausal osteoporosis, which affects millions of women worldwide. Another essential function of RANK and RANKL is the development of a functional lactating mammary gland during pregnancy. Sex hormones, in particular progesterone, induce RANKL expression resulting in proliferation of mammary epithelial cells. Moreover, RANK and RANKL have been shown to regulate mammary epithelial stem cells. RANK and RANKL were also identified as critical mechanism in the development of hormone-induced breast cancer and metastatic spread to bone. In this review, we will focus on the various RANK\/RANKL functions ranging from bone physiology, immune regulation, and initiation of breast cancer.","authors":"Sigl, V., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cytokine Growth Factor Rev","volume":"25","issue":"2","page":"205-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"137","title":"Enzymatic hydrolysis of agar: purification and characterization of neoagarobiose hydrolase and p-nitrophenyl alpha-galactoside hydrolase.","abstract":"The mixture of polysaccharides in the gelling component of agar (agarose) is hydrolyzed to D-galactose and 3,6-anhydro-L-galactose by a series of hydrolytic enzymes obtained from Pseudomonas atlantica. The final degradative step in the pathway of agarose decomposition is the hydrolysis of the alpha-linkage in the dissaccharide neoagarobiose yielding D-galactose and 3,6-anhydro-L-galactose. Pseudomonas atlantica when grown on agar produces two specific enzymes, p-nitrophenyl alpha-galactose hydrolase and neoagarobiose hydrolase. The purification and partial characterization of both enzymes are presented.","authors":"Day, DF., Yaphe, W.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Microbiol","volume":"21","issue":"10","page":"1512-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-149","title":"Systematic Investigation of Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase (NNRTIs)","abstract":null,"authors":"Beyer A., Lawtrakul L., Hannongbua S., Wolschann P. ","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Chemical Monthly ","volume":"135","issue":"8","page":"1047-1059","pdf":null,"JrId":null,"fulltextlink":"http:\/\/dx.doi.org\/10.1007\/s00706-004-0173-y","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20876096","title":"Organization and coordinated assembly of the type III secretion export apparatus.","abstract":"Type III protein secretion systems are unique bacterial nanomachines with the capacity to deliver bacterial effector proteins into eukaryotic cells. These systems are critical to the biology of many pathogenic or symbiotic bacteria for insects, plants, animals, and humans. Essential components of these systems are multiprotein envelope-associated organelles known as the needle complex and a group of membrane proteins that compose the so-called export apparatus. Here, we show that components of the export apparatus associate intimately with the needle complex, forming a structure that can be visualized by cryo-electron microscopy. We also show that formation of the needle complex base is initiated at the export apparatus and that, in the absence of export apparatus components, there is a significant reduction in the levels of needle complex base assembly. Our results show a substantial coordination in the assembly of the two central elements of type III secretion machines.","authors":"Wagner, S., K\u00f6nigsmaier, L., Lara-Tejero, M., Lefebre, M., Marlovits, TC., Gal\u00e1n, JE.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc Natl Acad Sci U S A","volume":"107","issue":"41","page":"17745-50","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20573403","title":"Tracing antigen signatures in the human IgE repertoire.","abstract":"Allergen recognition by IgE antibodies is a key event in allergic inflammation. In this study, the IgE IGHV repertoires of individuals with allergy to the major birch pollen allergen, Bet v 1, were analyzed over a four years period of allergen exposure by RT-PCR and sequencing of cDNA. Approximately half of the IgE transcripts represented non-redundant sequences, which belonged to seventeen different IGHV genes. Most variable regions contained somatic mutations but also non-mutated sequences were identified. There was no evidence for relevant increases of somatic mutations over time of allergen exposure. Highly similar IgE variable regions were found after four years of allergen exposure in the same and in genetically non-related individuals. Our results indicate that allergens select and shape a limited number of similar IgE variable regions in the human IgE repertoire.","authors":"Marth, K., Novatchkova, M., Focke-Tejkl, M., Jenisch, S., J\u00e4ger, S., Kabelitz, D., Valenta, R.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Mol Immunol","volume":"47","issue":"14","page":"2323-9","pdf":null,"JrId":"5892","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18849980","title":"Loss of nucleoplasmic LAP2alpha-lamin A complexes causes erythroid and epidermal progenitor hyperproliferation.","abstract":"Lamina-associated polypeptide (LAP) 2alpha is a chromatin-associated protein that binds A-type lamins. Mutations in both LAP2alpha and A-type lamins are linked to human diseases called laminopathies, but the molecular mechanisms are poorly understood. The A-type lamin-LAP2alpha complex interacts with and regulates retinoblastoma protein (pRb), but the significance of this interaction in vivo is unknown. Here we address the function of the A-type lamin-LAP2alpha complex with the use of LAP2alpha-deficient mice. We show that LAP2alpha loss causes relocalization of nucleoplasmic A-type lamins to the nuclear envelope and impairs pRb function. This causes inefficient cell-cycle arrest in dense fibroblast cultures and hyperproliferation of epidermal and erythroid progenitor cells in vivo, leading to tissue hyperplasia. Our results support a disease-relevant model in which LAP2alpha defines A-type lamin localization in the nucleoplasm, which in turn affects pRb-mediated regulation of progenitor cell proliferation and differentiation in highly regenerative tissues.","authors":"Naetar, N., Korbei, B., Kozlov, S., Kerenyi, MA., Dorner, D., Kral, R., Gotic, I., Fuchs, P., Cohen, TV., Bittner, R., Stewart, CL., Foisner, R.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Cell Biol","volume":"10","issue":"11","page":"1341-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20593797","title":"Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap.","abstract":"Peptide labeling with isobaric tags has become a popular technique in quantitative shotgun proteomics. Using two different samples viz. a protein mixture and HeLa extracts, we show that three commercially available isobaric tags differ with regard to peptide identification rates: The number of identified proteins and peptides was largest with iTRAQ 4-plex, followed by TMT 6-plex, and smallest with iTRAQ 8-plex. In all experiments, we employed a previously described method where two scans were acquired for each precursor on an LTQ Orbitrap: A CID scan under standard settings for identification, and a HCD scan for quantification. The observed differences in identification rates were similar when data was searched with either Mascot or Sequest. We consider these findings to be the result of a combination of several factors, most notably prominent ions in CID spectra as a consequence of loss of fragments of the label tag from precursor ions. These fragment ions cannot be explained by current search engines and were observed to have a negative impact on peptide scores.","authors":"Pichler, P., K\u00f6cher, T., Holzmann, J., Mazanek, M., Taus, T., Ammerer, G., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Anal Chem","volume":"82","issue":"15","page":"6549-58","pdf":null,"JrId":"519","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-150","title":"Anomalous diffusion on dynamical networks: a model for interacting epithelial cell migration","abstract":null,"authors":"Thurner S., Wick N., Hanel R., Sedivy R., Huber L. ","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Physica A: Statistical Mechanics and its Applications","volume":"320","issue":"","page":"475-484","pdf":null,"JrId":null,"fulltextlink":"http:\/\/dx.doi.org\/10.1016\/S0378-4371(02)01598-4","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20581463","title":"Casein kinase 1 is required for efficient removal of Rec8 during meiosis I.","abstract":"Segregation of chromosomes during meiosis depends on separase cleavage of Rec8, the meiosis-specific alpha-kleisin subunit of cohesin. We mapped Rec8 phosphorylation sites by mass spectrometry and show that Rec8 phosphorylation is required for proper chromosome disjunction during meiosis. We further show that the fission yeast casein kinase 1 (CK1) delta\/epsilon isoforms Hhp1 and Hhp2 are required for full levels of Rec8 phosphorylation and for efficient removal of Rec8 at the onset of anaphase I. Our data are consistent with the model that Hhp1\/Hhp2-dependent phosphorylation of Rec8 is required for separase-mediated cleavage of Rec8 during meiosis I.","authors":"Rumpf, C., Cipak, L., Dudas, A., Benko, Z., Pozgajova, M., Riedel, CG., Ammerer, G., Mechtler, K., Gregan, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell Cycle","volume":"9","issue":"13","page":"2657-62","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1714376","title":"A novel target cell for c-fos-induced oncogenesis: development of chondrogenic tumours in embryonic stem cell chimeras.","abstract":"Embryonic stem (ES) cells were used to investigate the target cell specificity and consequences of c-fos when expressed ectopically during embryonic development. Chimeric mice generated with different ES cell clones selected for high exogenous c-fos expression were not affected during embryonic development; however, a high frequency of cartilage tumours developed as early as 3-4 weeks of age apparently independent of the extent of chimerism. The tumours originated from cartilagenous tissues and contained many chondrocytes. Expression of exogenous c-fos RNA and Fos protein was observed during development but was highest in tumour tissues, predominantly in differentiating chondrocytes. A number of primary and clonal tumour-derived cell lines were established which expressed high levels of c-fos, c-jun as well as the cartilage-specific gene type II collagen and which gave rise to cartilage tumours in vivo, some of which also contained bone. Interestingly, the levels of c-Fos and c-Jun appeared to be coordinately regulated in the cell lines as well as in chimeric tissues. Thus, we demonstrate that chondrogenic cells and earlier progenitors are specially transformed by Fos\/Jun and therefore represent a novel mesenchymal target cell for c-fos overexpression.","authors":"Wang, ZQ., Grigoriadis, AE., M\u00f6hle-Steinlein, U., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"EMBO J","volume":"10","issue":"9","page":"2437-50","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1991-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1671532","title":"EGF promotes in vivo tumorigenic growth of primary chicken embryo fibroblasts expressing v-myc and enhances in vitro transformation by the v-erbA oncogene.","abstract":"We report that the activation of the endogenous chicken EGF receptor leads to the tumorigenic growth in vivo of early passage chicken embryo fibroblasts (CEFs) that express a nonsarcomagenic oncogene, v-myc. To provide a continuous paracrine source of this growth factor in vivo, we employed irradiated Rat-1 cells which had been stably transfected with a synthetic cDNA to human EGF. Expression of another non-sarcomagenic nuclear oncogene, v-erbA, prones the CEFs to in vitro transformation by EGF, but does not cause EGF dependent tumorigenicity in vivo. The short period of incubation in the in vivo assay employed by our study (10 days), together with the genetic stability of primary chicken embryo fibroblasts, make it very likely that the reported alterations in cellular behaviour are a direct and primary effect of the expression of the relevant oncogenes and their cooperation with the EGF induced response. Dose response and ligand binding assays suggest that the EGF response is transmitted via the chicken c-erbB molecule, which by virtue of its preference for TGF-alfa is distinct from the mammalian EGF receptors studied so far. The level of expression of the endogenous chicken EGF receptor is within the same range as that reported for primary human fibroblasts (5-7 x 10(3) per cell). The cooperative effect of v-myc with chicken c-erbB probably takes place at a post receptor level, as its expression did not affect the steady state level or affinity for ligand of the chicken EGF receptor.","authors":"Khazaie, K., Panayotou, G., Aguzzi, A., Samarut, J., Gazzolo, L., Jurdic, P.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Oncogene","volume":"6","issue":"1","page":"21-8","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1991-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-151","title":"Mouse Chromosome 17 ","abstract":null,"authors":"Silver LM., Artzt K., Barlow D., Fischer-Lindahl K., Lyon MF., Klein J., Snyder L.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Mammalian Genome","volume":"3","issue":"1 Supplement","page":"S241-S260","pdf":"a4d188e0b4777e332145bce9bf4d98a6","JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8598042","title":"Impaired negative selection of T cells in Hodgkin's disease antigen CD30-deficient mice.","abstract":"CD30 is found on Reed-Sternberg cells of Hodgkin's disease and on a variety of non-Hodgkin's lymphoma cells and is up-regulated on cells after Epstein-Barr virus, human T cell leukemia virus, and HIV infections. We report here that the thymus in CD30-deficient mice contains elevated numbers of thymocytes. Activation-induced death of thymocytes after CD3 cross-linking is impaired both in vitro and in vivo. Breeding the CD30 mutation separately into alpha beta TCR-or gamma delta TCR-transgenic mice revealed a gross defect in negative but not positive selection. Thus, like TNF-receptors and Fas\/Apo-1, the CD30 receptor is involved in cell death signaling. It is also an important coreceptor that participates in thymic deletion.","authors":"Amakawa, R., Hakem, A., Kundig, TM., Matsuyama, T., Simard, JJ., Timms, E., Wakeham, A., Mittruecker, HW., Griesser, H., Takimoto, H., Schmits, R., Shahinian, A., Ohashi, P., Penninger, JM., Mak, TW.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Cell","volume":"84","issue":"4","page":"551-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1996-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40119193","title":"Author Correction: Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development.","abstract":null,"authors":"Fedl, AS., Tagoh, H., Gruenbacher, S., Sun, Q., Schenk, RL., Froussios, K., Jaritz, M., Busslinger, M., Schwickert, TA.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nat Immunol","volume":"26","issue":"5","page":"805","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-01","doi":"10.1038\/s41590-025-02139-1","first_author":null,"corresponding_authors":null},{"pmid":"11140374","title":"\"Promiscuous\" expression of tissue antigens in the thymus: a key to T-cell tolerance and autoimmunity?","abstract":"Induction and maintenance of self-tolerance in the developing and mature T cell repertoire is mediated by multiple mechanisms operating both in the thymus (\"central tolerance\") and in peripheral lymphoid and nonlymphoid organs (\"peripheral tolerance\"). The thymus is viewed as the prime site of T cell tolerance induction to ubiquitous proteins and abundant blood-borne antigens entering the thymus via the circulation. By contrast, tolerance to self-antigens that are confined to specific tissues has been ascribed to a variety of mechanisms acting on peripheral T cells. Based on the recent finding that intrathymic expression of \"tissue-specific\" antigens is a common occurrence the prevailing notion that tolerance induction in the thymus applies only to a limited set of \"abundant\" proteins may have to be revised. Interestingly, this \"promiscuous\" expression of tissue antigens in the thymus appears to be a unique property of thymic epithelial cells rather than bone marrow derived antigen-presenting cells, implying cell type specific regulation rather than basal leakiness as a mechanism of \"promiscuous\" gene transcription. We summarize recent experimental evidence supporting this novel concept and discuss implications for autoimmunity.","authors":"Klein, L., Kyewski, B.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Mol Med (Berl)","volume":"78","issue":"9","page":"483-94","pdf":null,"JrId":"8748","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18948975","title":"Positional cloning by fast-track SNP-mapping in Drosophila melanogaster.","abstract":"Positional cloning of chemically induced mutations is the rate-limiting step in forward genetic screens in Drosophila. Single-nucleotide polymorphisms (SNPs) are useful markers to locate a mutated region in the genome. Here, we provide a protocol for high-throughput, high-resolution SNP mapping that enables rapid and cost-effective positional cloning in Drosophila. In stage 1 of the protocol, we use highly multiplexed tag-array mini-sequencing assays to map mutations to an interval of 1-2 Mb. In these assays, SNPs are genotyped by primer extension using fluorescently labeled dideoxy-nucleotides. Fluorescent primers are captured and detected on a microarray. In stage 2, we selectively isolate recombinants within the identified 1-2 Mb interval for fine mapping of mutations to about 50 kb. We have previously demonstrated the applicability of this protocol by mapping 14 muscle morphogenesis mutants within 4 months, which represents a significant acceleration compared with other commonly used mapping strategies that may take years.","authors":"Schnorrer, F., Ahlford, A., Chen, D., Milani, L., Syv\u00e4nen, AC.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Protoc","volume":"3","issue":"11","page":"1751-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23400928","title":"Increased thymic development of regulatory T cells in NOD mice is functionally dissociated from type I diabetes susceptibility.","abstract":"Regulatory T (Treg) lymphocytes play a central role in the control of autoimmune pathology. Any alteration in Treg-cell biology in mouse strains used for the study of these disorders therefore raises the question of its direct link with disease susceptibility. Paradoxically, in non-obese diabetic (NOD) mice increased numbers of Treg cells develop in the thymus. In this report we identify a locus of &lt;7 Mbp that quantitatively controls Treg-cell development in the thymus of the NOD mouse. This 'Trd1' region is located centromeric to the H2 complex on chromosome 17 and does not include genes encoding classical MHC molecules. The genomic region identified here contains the Idd16 diabetes susceptibility locus and the use of congenic mouse strains allowed us to investigate the potential link between quantitatively altered thymic Treg cells and diabetes susceptibility. Hybrid mice present similar levels of thymic Treg cells as B6 animals but they developed diabetes with the same kinetics as NOD mice. Therefore, the increased Treg-cell development in NOD mice controlled by Trd1 is functionally dissociated from the susceptibility of NOD to diabetes.","authors":"Tellier, J., Andrianjaka, A., Vicente, R., Thiault, N., Enault, G., Garchon, HJ., van Meerwijk, JP., Romagnoli, P.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Eur J Immunol","volume":"43","issue":"5","page":"1356-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7918455","title":"High-level expression of various apolipoprotein(a) isoforms by \"transferrinfection\": the role of kringle IV sequences in the extracellular association with low-density lipoprotein.","abstract":"Characterization of the assembly of lipoprotein(a) [Lp(a)] is of fundamental importance to understanding the biosynthesis and metabolism of this atherogenic lipoprotein. Since no established cell lines exist that express Lp(a) or apolipoprotein(a) [apo(a)], a \"transferrinfection\" system for apo(a) was developed utilizing adenovirus receptor- and transferrin receptor-mediated DNA uptake into cells. Using this method, different apo(a) cDNA constructions of variable length, due to the presence of 3, 5, 7, 9, 15, or 18 internal kringle IV sequences, were expressed in cos-7 cells or CHO cells. All constructions contained kringle IV-36, which includes the only unpaired cysteine residue (Cys-4057) in apo(a). r-Apo(a) was synthesized as a precursor and secreted as mature apolipoprotein into the medium. When medium containing r-apo(a) with 9, 15, or 18 kringle IV repeats was mixed with normal human plasma LDL, stable complexes formed that had a bouyant density typical of Lp(a). Association was substantially decreased if Cys-4057 on r-apo(a) was replaced by Arg by site-directed mutagenesis or if Cys-4057 was chemically modified. Lack of association was also observed with r-apo(a) containing only 3, 5, or 7 kringle IV repeats without \"unique kringle IV sequences\", although Cys-4057 was present in all of these constructions. Synthesis and secretion of r-apo(a) was not dependent on its sialic acid content. r-Apo(a) was expressed even more efficiently in sialylation-defective CHO cells than in wild-type CHO cells. In transfected CHO cells defective in the addition of N-acetylglucosamine, apo(a) secretion was found to be decreased by 50%. Extracellular association with LDL was not affected by the carbohydrate moiety of r-apo(a), indicating a protein-protein interaction between r-apo(a) and apoB. These results show that, besides kringle IV-36, other kringle IV sequences are necessary for the extracellular association of r-apo(a) with LDL. Changes in the carbohydrate moiety of apo(a), however, do not affect complex formation.","authors":"Frank, S., Krasznai, K., Durovic, S., Lobentanz, EM., Dieplinger, H., Wagner, E., Zatloukal, K., Cotten, M., Utermann, G., Kostner, GM.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Biochemistry","volume":"33","issue":"40","page":"12329-39","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1994-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20081838","title":"Cohesin cleavage and Cdk inhibition trigger formation of daughter nuclei.","abstract":"The metaphase-anaphase transition is orchestrated through proteolysis of numerous proteins by a ubiquitin protein ligase called the anaphase-promoting complex or cyclosome (APC\/C). A crucial aspect of this process is sister chromatid separation, which is thought to be mediated by separase, a thiol protease activated by the APC\/C. Separase cleaves cohesin, a ring-shaped complex that entraps sister DNAs. It is a matter of debate whether cohesin-independent forces also contribute to sister chromatid cohesion. Using 4D live-cell imaging of Drosophila melanogaster syncytial embryos blocked in metaphase (via APC\/C inhibition), we show that artificial cohesin cleavage is sufficient to trigger chromosome disjunction. This is nevertheless insufficient for correct chromosome segregation. Kinetochore-microtubule attachments are rapidly destabilized by the loss of tension caused by cohesin cleavage in the presence of high Cdk1 (cyclin-dependent kinase 1) activity, as occurs when the APC\/C cannot destroy mitotic cyclins. Metaphase chromosomes undergo a bona fide anaphase when cohesin cleavage is combined with Cdk1 inhibition. We conclude that only two key events, opening of cohesin rings and downregulation of Cdk1, are sufficient to drive proper segregation of chromosomes in anaphase.","authors":"Oliveira, RA., Hamilton, RS., Pauli, A., Davis, I., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Cell Biol","volume":"12","issue":"2","page":"185-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7504231","title":"Transformation of chicken bone marrow cells by the v-ski oncogene.","abstract":"The effect of the v-ski oncogene on the transformation of chicken hematopoietic cells was examined. In initial experiments viruses encoding the v-ski oncoprotein did not transform chicken bone marrow cells. However, whereas viruses encoding the ts-v-sea oncoprotein transform solely erythroid cells, viruses encoding both the v-ski and the ts-v-sea oncogenes were found capable of transforming myeloid cells from the monocytic and\/or granulocytic lineages in addition to erythroid cells. Analysis of cell clones transformed by the v-ski\/ts-v-sea virus identified one clone that no longer expressed the v-sea protein, indicating that this protein was necessary for the initiation but not the maintenance of transformation. Subsequent experiments testing the effects of various growth factors on transformation of bone marrow cells by the v-ski oncogene product alone identified the avian c-kit ligand (stem cell factor; SCF) as being able to co-operate with the v-ski protein to cause transformation of chicken hematopoietic cells of both myeloid and erythroid lineages.","authors":"Larsen, J., Meyer, S., Steinlein, P., Beug, H., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Oncogene","volume":"8","issue":"12","page":"3221-8","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1993-12-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"136","title":"Nitrofurazone-reducing enzymes in E. coli and their role in drug activation in vivo.","abstract":"Earlier work showed that Escherichia coli contains at least two enzymes which reduce nitrofurazone and other nitrofuran derivatives. One of these enzymes is lacking in some nitrofurazone-resistant mutant strains. We now report that there are three separable nitrofuran reductases in this organism: reductase I (mol. wt. approximately 50 000, insensitive to O2), reductase IIa (mol. wt. approximately 120 000, inhibited by oxygen), reductase IIb (mol. wt. approximately 700 000, inhibited by O2). Unstable metabolites formed during the reduction of nitrofurazone by preparations containing reductases IIa and IIb produce breaks in DNA in vitro. In vivo experiments with nitrofurazone-resistant strains, which lack reductase II but contain reductases IIa and IIb, demonstrated that lethality, mutation, and DNA breakage are all greatly increased when cultures are incubated under anaerobic conditions, i.e., conditions such that reductase II is active. These results provide further evidence for the importance of reductive activation of nitrofurazone.","authors":"McCalla, DR., Olive, P., Tu, Y., Fan, ML.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Microbiol","volume":"21","issue":"10","page":"1484-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17786051","title":"hClp1: a novel kinase revitalizes RNA metabolism.","abstract":"The RNA-induced silencing complex (RISC) is the effector complex in the RNA interference (RNAi) pathway. In order to become assembled into RISC, synthetic small interfering RNAs (siRNAs) are phosphorylated at the 5' end upon transfection into cells. The enzymatic activity responsible for this phosphorylation event has so far remained elusive. Using a classical chromatographic approach, we recently identified and characterized hClp1 as the \"siRNA-kinase\" in HeLa cells. hClp1 is in fact a general RNA-kinase, and a component of the tRNA splicing endonuclease and the mRNA 3' end formation machinery. We discuss the relevance of this finding, and provide further views and perspectives for the analysis of hClp1 in tRNA splicing, mRNA cleavage and polyadenylation and other RNA metabolic processes in which hClp1 might play a role.","authors":"Weitzer, S., Martinez, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell Cycle","volume":"6","issue":"17","page":"2133-7","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2007-10-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19401336","title":"Mechanosensing in actin stress fibers revealed by a close correlation between force and protein localization.","abstract":"The mechanics of the actin cytoskeleton have a central role in the regulation of cells and tissues, but the details of how molecular sensors recognize deformations and forces are elusive. By performing cytoskeleton laser nanosurgery in cultured epithelial cells and fibroblasts, we show that the retraction of stress fibers (SFs) is restricted to the proximity of the cut and that new adhesions form at the retracting end. This suggests that SFs are attached to the substrate. A new computational model for SFs confirms this hypothesis and predicts the distribution and propagation of contractile forces along the SF. We then analyzed the dynamics of zyxin, a focal adhesion protein present in SFs. Fluorescent redistribution after laser nanosurgery and drug treatment shows a high correlation between the experimentally measured localization of zyxin and the computed localization of forces along SFs. Correlative electron microscopy reveals that zyxin is recruited very fast to intermediate substrate anchor points that are highly tensed upon SF release. A similar acute localization response is found if SFs are mechanically perturbed with the cantilever of an atomic force microscope. If actin bundles are cut by nanosurgery in living Drosophila egg chambers, we also find that zyxin redistribution dynamics correlate to force propagation and that zyxin relocates at tensed SF anchor points, demonstrating that these processes also occur in living organisms. In summary, our quantitative analysis shows that force and protein localization are closely correlated in stress fibers, suggesting a very direct force-sensing mechanism along actin bundles.","authors":"Colombelli, J., Besser, A., Kress, H., Reynaud, EG., Girard, P., Caussinus, E., Haselmann, U., Small, JV., Schwarz, US., Stelzer, EH.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Sci","volume":"122","issue":"Pt 10","page":"1665-79","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17704644","title":"The ubiquitin E3 ligase Cbl-b in T cells tolerance and tumor immunity.","abstract":"The implication of the immune system in tumor surveillance is proven and widely accepted. However, anti-cancer immunotherapy is still difficult due to insufficient activation, immune suppression and tolerance induction. The ubiquitin E3 ligase Cbl-b, is a member of the Cbl (casitas B-lineage lymphoma) protein family and was identified as a key dominant \"tolerogenic\" factor in T cells that directly regulates T-cell activation by controlling activation thresholds and the requirement for co-stimulation. Intriguingly, Cbl-b deficient mice spontaneously reject a variety of cancers including spontaneous solid tumors and hematopoietic malignancies. Mechanistically, modulation of Cbl-b in T cells controls activation of tumor-reactive cytotoxic T cells in vivo and might circumvent several limitations of T cell immunotherapy. Therefore manipulation of Cbl-b might provide us with a unique opportunity for future immune treatment of human disorders such as autoimmunity, chronic viral infections, or cancer.","authors":"Loeser, S., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell Cycle","volume":"6","issue":"20","page":"2478-85","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"211440","title":"Temperature-sensitive mutant of avian erythroblastosis virus suggests a block of differentiation as mechanism of leukaemogenesis.","abstract":"A temperature sensitive mutant has been isolated for the first time from a replication defective acute leukaemia virus, AEV. In vivo, at 41 degrees C, the mutant shows a reduced leukaemogenic potential. In vitro, in erythroblasts transformed at 35 degrees C, haemoglobin synthesis can be induced by a shift to 41 degrees C. This indicates that the continuous expression of a viral gene product is necessary to maintain the undifferentiated state of the virus-transformed leukaemia cells.","authors":"Graf, T., Ade, N., Beug, H.","publication_status":"ppublish","journalpubyear":"1978","journaltitle":"Nature","volume":"275","issue":"5680","page":"496-501","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1978-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"128","title":"Inhibitory postsynaptic actions of taurine, GABA and other amino acids on motoneurons of the isolated frog spinal cord.","abstract":"The actions of glycine, GABA, alpha-alanine, beta-alanine and taurine were studied by intracellular recordings from lumbar motoneurons of the isolated spinal cord of the frog. All amino acids tested produced a reduction in the amplitude of postsynaptic potentials, a blockade of the antidromic action potential and an increase of membrane conductance. Furthermore, membrane polarizations occurred, which were always in the same direction as the IPSP. All these effects indicate a postsynaptic inhibitory action of these amino acids. When the relative strength of different amino acids was compared, taurine had the strongest inhibitory potency, followed by beta-alanine, alpha-alanine, GABA and glycine. Topically applied strychnine and picrotoxin induced different changes of post-synaptic potentials, indicating that distinct inhibitory systems might be influenced by these two convulsants. Interactions with amino acids showed that picrotoxin seletively diminished the postsymaptic actions of GABA, while strychnine reduced the effects of taurine, glycine, alpha- and beta-alanine. But differences in the susceptibility of these amino acid actions to strychnine could be detected: the action of taurine was more sensitively blocked by strychnine compared with glycine, alpha- and beta-alanine. With regard to these results the importance of taurine and GABA as transmitters of postsynaptic inhibition on motoneurons in the spinal cord of the frog is discussed.","authors":"Sonnhof, U., Grafe, P., Krumnikl, J., Linder, M., Schindler, L.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Brain Res","volume":"100","issue":"2","page":"327-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16750914","title":"Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein\/peptide complex.","abstract":"For structural studies of proteins and their complexes, chemical cross-linking combined with mass spectrometry presents a promising strategy to obtain structural data of protein interfaces from low quantities of proteins within a short time. We explore the use of isotope-labeled cross-linkers in combination with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry for a more efficient identification of cross-linker containing species. For our studies, we chose the calcium-independent complex between calmodulin and a 25-amino acid peptide from the C-terminal region of adenylyl cyclase 8 containing an \"IQ-like motif.\" Cross-linking reactions between calmodulin and the peptide were performed in the absence of calcium using the amine-reactive, isotope-labeled (d0 and d4) cross-linkers BS3 (bis[sulfosuccinimidyl]suberate) and BS2G (bis[sulfosuccinimidyl]glutarate). Tryptic in-gel digestion of excised gel bands from covalently cross-linked complexes resulted in complicated peptide mixtures, which were analyzed by nano-HPLC\/nano-ESI-FTICR mass spectrometry. In cases where more than one reactive functional group, e.g., amine groups of lysine residues, is present in a sequence stretch, MS\/MS analysis is a prerequisite for unambiguously identifying the modified residues. MS\/MS experiments revealed two lysine residues in the central alpha-helix of calmodulin as well as three lysine residues both in the C-terminal and N-terminal lobes of calmodulin to be cross-linked with one single lysine residue of the adenylyl cyclase 8 peptide. Further cross-linking studies will have to be conducted to propose a structural model for the calmodulin\/peptide complex, which is formed in the absence of calcium. The combination of using isotope-labeled cross-linkers, determining the accurate mass of intact cross-linked products, and verifying the amino acid sequences of cross-linked species by MS\/MS presents a convenient approach that offers the perspective to obtain structural data of protein assemblies within a few days.","authors":"Ihling, C., Schmidt, A., Kalkhof, S., Schulz, DM., Stingl, C., Mechtler, K., Haack, M., Beck-Sickinger, AG., Cooper, DMF., Sinz, A.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Am Soc Mass Spectrom","volume":"17","issue":"8","page":"1100-1113","pdf":null,"JrId":"21031","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"119","title":"Proceedings: The role of dopamine in rotational behaviour produced by unilateral lesions of the locus coeruleus.","abstract":"","authors":"Donaldson, I., Dolphin, A., Jenner, P., Mardsen, CK., Pycock, C.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Pharmacol","volume":"55","issue":"2","page":"290P","pdf":null,"JrId":"1895","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"114","title":"Proceedings: Central hypertensive action of histamine in rats.","abstract":"","authors":"Finch, L., Hicks, PE.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Pharmacol","volume":"55","issue":"2","page":"274P-275P","pdf":null,"JrId":"1895","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"107","title":"Potable water quality in rural Georgetown County.","abstract":"Drinking water supplies of 161 rural communities, in Georgetown County, South Carolina, were randomly selected for sample collection. The analysis showed that most of the waters were slightly acidic. Low, but acceptable concentrations of chloride, copper, fluoride, sodium, cadmium, nitrate and phosphate were found. A few water samples showed higher then recommended levels of arsenic, mercury, zinc and lead. Although only 2% of the samples exceeded the mandatory limit of 0.05 ppm for arsenic, 72% exceeded the recommended level of 0.01 ppm. The mandatory limit for manganese was exceeded in 37% of the waters while 88% exceeded the limit for iron. The high iron content was generally responsible for the high turbidity found in 45% of the samples. The well depth and the consumer income had some bearing on water quality. Statistical evidence suggested that septic tank seepage was partially responsible for nitrate, phosphate, iron and arsenic contamination of shallow water supplies. Lead concentrations appear to vary according to the plumbing used and the pH of the waters.","authors":"Sandhu, SS., Nelson, P., Warren, WJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Bull Environ Contam Toxicol","volume":"14","issue":"4","page":"465-72","pdf":null,"JrId":"2110","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18157899","title":"Molecular basis for skeletal variation: insights from developmental genetic studies in mice.","abstract":"Skeletal variations are common in humans, and potentially are caused by genetic as well as environmental factors. We here review molecular principles in skeletal development to develop a knowledge base of possible alterations that could explain variations in skeletal element number, shape or size. Environmental agents that induce variations, such as teratogens, likely interact with the molecular pathways that regulate skeletal development.","authors":"Kappen, C., Neub\u00fcser, A., Balling, R., Finnell, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Birth Defects Res B Dev Reprod Toxicol","volume":"80","issue":"6","page":"425-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19394412","title":"The serpin gene family in Anopheles gambiae.","abstract":"Serpins (serine protease inhibitors) regulate some innate immune responses of insects by inhibiting endogenous proteases. In this study, we characterized the serpin (SRPN) gene family in the mosquito Anopheles gambiae, the major malaria vector in Sub-Saharan Africa. We identified 18 A. gambiae SRPN genes, all on chromosomes 2 and 3, through searches of genomic DNA and EST databases. In addition to SRPN10, previously documented to exhibit alternative splicing, we found three splicing isoforms of SRPN4. We completed sequencing of cDNAs for the A. gambiae serpins to obtain complete coding sequence information and to verify or improve gene predictions. The predicted SRPN9 and 15 in the initial genome annotation were determined to be a single gene (SRPN9). Sixteen of the serpins contained putative secretion signal sequences. Multiple sequence alignments showing conserved residues important in structural conformation, including the consensus pattern within the hinge region, indicated that most of the A. gambiae serpins may be inhibitory. Phylogenetic analyses confirmed that SRPN1, 2, 3, 8, 9 and 10 formed phylogenetic clusters with known inhibitory serpins from Drosophila melanogaster and Manduca sexta. Many of the A. gambiae serpins were expressed during all life stages. However, SRPN7, 8, 12, and 19 were expressed at very low levels in the adult stage. SRPN13 was expressed mostly in eggs and young larvae, whereas SRPN5 and 14 were expressed mostly in adults. Such differences in expression pattern suggest that the serpins are involved in multiple physiological processes. Determining the biological functions of the mosquito serpins will require future work to identify the proteases they inhibit in vivo.","authors":"Suwanchaichinda, C., Kanost, MR.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Gene","volume":"442","issue":"1-2","page":"47-54","pdf":null,"JrId":"3886","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1628620","title":"Mutually exclusive expression of a helix-loop-helix gene and N-myc in human neuroblastomas and in normal development.","abstract":"We have isolated a novel human gene encoding a helix-loop-helix (HLH) protein by molecularly cloning chromosome 1p36-specific CpG islands. The gene termed heir-1 was localized to the neuroblastoma consensus deletion at 1p36.2-p36.12. Its predicted protein is 95.8% identical to the mouse HLH462 protein and has clear homology to the mouse Id and Drosophila emc proteins. Heir-1 does not encode a basic DNA binding domain as found in basic HLH proteins. The gene is expressed specifically at high abundance in adult lung, kidney and adrenal medulla, but not in adult brain. Despite prominent heir-1 expression in adrenal medulla, which is a prime target for neuroblastomas, 10 out of 12 neuroblastoma-derived cell lines revealed very low levels of heir-1 mRNA. Low heir-1 expression was generally found in tumor cell lines with N-myc overexpression, whereas the two cell lines displaying high heir-1 levels did not overexpress N-myc. Mutually exclusive expression of both genes was also found by in situ hybridization in developing mouse tissues, particularly in the forebrain neuroectoderm. We conclude that heir-1 expression is reduced specifically in the majority of neuroblastomas and suggest an inverse correlation between heir-1 and N-myc expression in neuroblastoma tumors and in embryonic development.","authors":"Ellmeier, W., Aguzzi, A., Kleiner, E., Kurzbauer, R., Weith, A.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"EMBO J","volume":"11","issue":"7","page":"2563-71","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1992-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23081743","title":"Detection of loci for allergic asthma using SMXA recombinant inbred strains of mice.","abstract":"Asthma is regarded as a multifactorial inflammatory disorder arising as a result of inappropriate immune responses in genetically susceptible individuals to common environmental antigens. However, the precise molecular basis is unknown. To identify genes for susceptibility to three asthma-related traits, airway hyperresponsiveness (AHR), eosinophil infiltration, and allergen-specific serum IgE levels, we conducted a genetic analysis using SMXA recombinant inbred (RI) strains of mice. Quantitative trait locus analysis detected a significant locus for AHR on chromosome 17. For eosinophil infiltration, significant loci were detected on chromosomes 9 and 16. Although we could not detect any significant loci for allergen-specific serum IgE, analysis of consomic strains showed that chromosomes 17 and 19 carried genes that affected this trait. We detected genetic susceptibility loci that separately regulated the three asthma-related phenotypes. Our results suggested that different genetic mechanisms regulate these asthma-related phenotypes. Genetic analyses using murine RI and consomic strains enhance understanding of the molecular mechanisms of asthma in human.","authors":"Ohno, T., Okamoto, M., Hara, T., Hashimoto, N., Imaizumi, K., Matsushima, M., Nishimura, M., Shimokata, K., Hasegawa, Y., Kawabe, T.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Immunogenetics","volume":"65","issue":"1","page":"17-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"200423","title":"Development of Escherichia coli virus T1: repression of host gene expression.","abstract":"Host protein synthesis, measured either as amino acid incorporation into proteins or as enzyme synthesis, is inhibited rapidly after infection Escherichia coli with T1. Analysis of this inhibition, using a technique which distinguishes between translation and transcription, revealed that translation of host mRNA is specifically blocked. Comparison of the time course of T1-induced host repression with inhibition by the drugs rifampicin, nitrofurantoin and chloramphenicol showed that T1 affects the initiation step of host translation. Intact membranes are apparently essential for host repression, suggesting a membrane-mediated process. Concomitant viral protein synthesis is not required. The membrane-altering principle is a constituent of the viral particle.","authors":"Wagner, EF., Ponta, H., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1977","journaltitle":"Eur J Biochem","volume":"80","issue":"1","page":"255-60","pdf":null,"JrId":"3607","fulltextlink":null,"preprintlink":null,"articledate":"1978-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"171","title":"Arterial catecholamines in hypoxic exercise in man.","abstract":"1. We measured the minute ventilation and arterial blood catecholamine concentrations in four normal men standing and at two levels of moderate treadmill exercise breathing 14% oxygen or air. 2. Minute ventilation was significantly higher during hypoxic exercise than during normoxic exercise at an oxygen uptake of 1500 ml\/min. 3. Arterial plasma noradrenaline during hypoxic exercise at an oxygen uptake of 1500 ml\/min was significantly greater than at rest. 4. Arterial plasma noradrenaline during normoxic exercise at an oxygen uptake of 1500 ml\/min was not elevated above the resting concentration. 5. The results are compatible with the suggestion that increased concentrations of arterial plasma noradrenaline contribute to the hypoxic potentiation of the respiratory response to moderate exercise.","authors":"Clancy, LJ., Critchley, JA., Leitch, AG., Kirby, BJ., Ungar, A., Flenley, DC.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Sci Mol Med","volume":"49","issue":"5","page":"503-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14755052","title":"Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena.","abstract":"Genome-wide DNA elimination accompanies development of the somatic macronucleus from the germ-line micronucleus during the sexual process of conjugation in the ciliated protozoan Tetrahymena thermophila. Small RNAs, referred to as \"scan RNAs\" (scnRNAs), that accumulate only during conjugation are highly enriched in the eliminated sequences, and mutations that prevent DNA elimination also affect the accumulation of scnRNAs, suggesting that an RNA interference (RNAi)-like mechanism is involved in DNA elimination. Histone H3 that is methylated at lysine 9 (K9) is a hallmark of heterochromatin and, in Tetrahymena, is found only in developing macronuclei (anlagen) in association with chromatin containing the sequences undergoing elimination. In this article, we demonstrate that a mutation in the TWI1 gene that eliminates the accumulation of scnRNAs also abolishes H3 methylation at K9. We created mutant strains of Tetrahymena in which the only major H3 contained a K9Q mutation. These mutants accumulated scnRNAs normally during conjugation but showed dramatically reduced efficiency of DNA elimination. These results provide strong genetic evidence linking an RNAi-like pathway, H3 K9 methylation, and DNA elimination in Tetrahymena.","authors":"Liu, Y., Mochizuki, K., Gorovsky, MA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Proc Natl Acad Sci U S A","volume":"101","issue":"6","page":"1679-84","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"106","title":"[Level of nicotinamide coenzymes in the myocardium of rats during the effects of methylxanthines (theophylline, theobromine, caffeine) and catecholamines].","abstract":"It was shown in acute experiments on rats that one hour after an intraperitoneal injection of theophylline (50 mg\/kg) there was a decrease in the NAD + NADP content by 19.4%, a tendency to a fall of NAD.H2 + NADP.H2 was expressed, and the total nicotinamide coferment level was reduced. A tendency to decrease NAD + NADP and the total pyridine nucleotide level was seen after caffeine administration. The action of catecholamines and methylxanthines was compared. Theobromine produced no significant effect on the indices under study. It was shown that isadrine decreased the NAD + NADP level; adrenaline (25 mkg\/kg) increased the content of both the oxidized (by 24%) and of the reduced (by 48%) forms of pyridine nucleotides. An increase of adrenaline dose to 1000 mkg\/kg was accompanied by reduction of the oxidized forms (by 22.2%) and of the total nicotinamide coferment level (by 18%).","authors":"Frantsuzova, SB.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biull Eksp Biol Med","volume":"79","issue":"4","page":"68-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1543918","title":"The mouse plasminogen locus maps to the recombination breakpoints of the tLub2 and TtOrl partial t haplotypes but is not at the tw73 locus.","abstract":"The mouse plasminogen (Plg) locus maps to a region of chromosome (Chr) 17 which is inverted in the t haplotype Chromosomal variant. Here we investigate the genomic organization of the Plg locus in structurally variant forms of Chr 17; wild-type (+), t haplotype (t), and two partial t haplotypes TtOrl and tLub2 which arose by recombination between + and t chromosomes. Our analysis suggests that the t haplotype chromosomal variant contains extra, inverted copies of the Plg locus, and that a single locus is present in the wild-type variant. Changes in the Plg locus in TtOrl and tLub2 suggest that they arose by homologous recombination across elements in the Plg locus having the same orientation in the wild-type and t haplotype chromosomes. One hundred ten kb around the wild-type Plg genomic locus have been cloned and the proximal breakpoint of a deletion in the tLub2 chromosome has been localized to a fragment 30 kb downstream of the Plg gene. The tLub2 deletion has been shown to delete a gene named tw73 that affects blastocyst implantation, a process probably requiring proteases such as plasminogen. However, the mapping of Plg relative to the tLub2 deletion and mRNA analysis of plasminogen in tw73 heterozygotes suggests that Plg does not lie at the tw73 locus.","authors":"Schweifer, N., Barlow, DP.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Mamm Genome","volume":"2","issue":"4","page":"260-8","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"1992-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12475938","title":"Mammalian septins nomenclature.","abstract":"There are 10 known mammalian septin genes, some of which produce multiple splice variants. The current nomenclature for the genes and gene products is very confusing, with several different names having been given to the same gene product and distinct names given to splice variants of the same gene. Moreover, some names are based on those of yeast or Drosophila septins that are not the closest homologues. Therefore, we suggest that the mammalian septin field adopt a common nomenclature system, based on that adopted by the Mouse Genomic Nomenclature Committee and accepted by the Human Genome Organization Gene Nomenclature Committee. The human and mouse septin genes will be named SEPT1-SEPT10 and Sept1-Sept10, respectively. Splice variants will be designated by an underscore followed by a lowercase \"v\" and a number, e.g., SEPT4_v1.","authors":"Macara, IG., Baldarelli, R., Field, CM., Glotzer, M., Hayashi, Y., Hsu, SC., Kennedy, MB., Kinoshita, M., Longtine, M., Low, C., Maltais, LJ., McKenzie, L., Mitchison, TJ., Nishikawa, T., Noda, M., Petty, EM., Peifer, M., Pringle, JR., Robinson, PJ., Roth, D., Russell, SE., Stuhlmann, H., Tanaka, M., Tanaka, T., Trimble, WS., Ware, J., Zeleznik-Le, NJ., Zieger, B.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Biol Cell","volume":"13","issue":"12","page":"4111-3","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11926985","title":"Phosphoinositide 3-kinases in immunity: lessons from knockout mice.","abstract":"Phosphoinositide 3-kinases (PI3Ks) constitute a family of evolutionarily conserved lipid kinases that phosphorylate the D3 position of the inositol ring of phosphoinositides and produce PI(3)P, PI(3,4)P(2), and PI(3,4,5)P(3). Intense in vitro research over the last decade has unequivocally demonstrated that PI3Ks, in particular those belonging to class I, regulate a vast array of fundamental cellular responses. Given the pleiotropic roles of PI3Ks and the lipid product PI(3,4,5)P(3) in plethora of cellular responses, it is pertinent to explore the significance of PI3K signaling in vivo. In the past two or three years, the components of this signaling pathway have been genetically manipulated in mouse. This review briefly summarizes the immunological significance of PI3K signaling as revealed by the study of gene-targeted \"knockout\" mice.","authors":"Sasaki, T., Suzuki, A., Sasaki, J., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Biochem","volume":"131","issue":"4","page":"495-501","pdf":null,"JrId":"4552","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25188634","title":"Generation of cerebral organoids from human pluripotent stem cells.","abstract":"Human brain development exhibits several unique aspects, such as increased complexity and expansion of neuronal output, that have proven difficult to study in model organisms. As a result, in vitro approaches to model human brain development and disease are an intense area of research. Here we describe a recently established protocol for generating 3D brain tissue, so-called cerebral organoids, which closely mimics the endogenous developmental program. This method can easily be implemented in a standard tissue culture room and can give rise to developing cerebral cortex, ventral telencephalon, choroid plexus and retinal identities, among others, within 1-2 months. This straightforward protocol can be applied to developmental studies, as well as to the study of a variety of human brain diseases. Furthermore, as organoids can be maintained for more than 1 year in long-term culture, they also have the potential to model later events such as neuronal maturation and survival.","authors":"Lancaster, MA., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Protoc","volume":"9","issue":"10","page":"2329-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1531384","title":"A new method for the isolation of recombinant baculovirus.","abstract":"An improved method for the isolation of baculovirus recombinants is described. The method involves the replication and maintenance of the baculovirus genome in the yeast Saccharomyces cerevisiae which was accomplished by the isolation of a baculovirus recombinant containing yeast ARS and CEN sequences ensuring stable replication in yeast and a URA3 selectable marker. The viral DNA maintained its ability to replicate in insect cells. An efficient and rapid selection system was set up, to isolate viral recombinants in yeast; DNA from selected yeast colonies was transfected into insect cells to obtain recombinant virus. We demonstrate the utility of this system by isolating recombinant viruses that express two different members of the CREB\/ATF family of transcription factors.","authors":"Patel, G., Nasmyth, K., Jones, N.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Nucleic Acids Res","volume":"20","issue":"1","page":"97-104","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1992-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1473147","title":"Activation of an inducible c-FosER fusion protein causes loss of epithelial polarity and triggers epithelial-fibroblastoid cell conversion.","abstract":"As a novel approach to studying the modulation of the polarized epithelial phenotype, we have expressed c-Fos and c-Myc estrogen receptor fusion proteins (c-FosER and c-MycER) in mammary epithelial cells. The hybrid proteins could be activated by estrogen for defined time periods and after the cells had achieved their fully polarized organization. Activation of c-MycER deregulated proliferation but did not affect epithelial polarity. Short-term activation of c-FosER induced the reversible loss of morphological and functional cell polarity. In contrast, long-term stimulation of c-FosER caused the cells to depolarize irreversibly, to invade collagen gels, and to undergo epithelial-fibroblastoid cell conversion. Our data suggest that Fos proteins are important in modulating the epithelial phenotype both in normal tissue development and in invasive processes.","authors":"Reichmann, E., Schwarz, H., Deiner, EM., Leitner, I., Eilers, M., Berger, J., Busslinger, M., Beug, H.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Cell","volume":"71","issue":"7","page":"1103-16","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1993-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41038866","title":"Retinol Binding Protein 4 reactivates latent HIV-1 by triggering canonical NF-&#x3ba;B, JAK\/STAT5 and JNK signalling.","abstract":"Reactivation of the latent viral reservoirs is crucial for a cure of HIV\/AIDS. However, current latency reversing agents are inefficient, and the endogenous factors that have the potential to reactivate HIV in vivo remain poorly understood. To identify natural activators of latent HIV-1, we screened a comprehensive peptide\/protein library derived from human hemofiltrate, representing the entire blood peptidome, using J-Lat cell lines harboring transcriptionally silent HIV-1 GFP reporter viruses. Fractions potently reactivating HIV-1 from latency contained human Retinol Binding Protein 4 (RBP4), the carrier of retinol (Vitamin A). We found that retinol-bound holo-RBP4 but not retinol-free apo-RBP4 strongly reactivates HIV-1 in a variety of latently infected T cell lines. Functional analyses indicate that this reactivation involves activation of the canonical NF-&#x3ba;B pathway and is strengthened by JAK\/STAT5 and JNK signalling but does not require retinoic acid production. High levels of RBP4 were detected in plasma from both healthy individuals and people living with HIV-1. Physiological concentrations of RBP4 induced significant viral reactivation in latently infected cells from individuals on long-term antiretroviral therapy with undetectable viral loads. As a potent natural HIV-1 latency-reversing agent, RBP4 offers a novel approach to activating the latent reservoirs and bringing us closer to a cure.","authors":"Pastorio, C., Richard, K., Usmani, S., Kissmann, AK., Bolotnikov, G., Gos\u00e1lbez, G., Hayn, M., Koepke, L., Sauertnik, A., Preising, A., Preising, N., St\u00e4ndker, L., Fair, M., Morris, J., Papasavvas, E., Liu, Q., Sun, H., Rodr\u00edguez, A., Mounzer, K., Wiese, S., Tebas, P., Du, Y., Laird, GM., Jaritz, M., Rosenau, F., Gaidt, MM., Sparrer, KMJ., Montaner, LJ., Kirchhoff, F.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Signal Transduct Target Ther","volume":"10","issue":"1","page":"326","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-10-02","doi":"10.1038\/s41392-025-02424-3","first_author":null,"corresponding_authors":null},{"pmid":"9190204","title":"Topogenesis of a nucleolar protein: determination of molecular segments directing nucleolar association.","abstract":"To identify the element(s) in nucleolar proteins which determine nucleolus-specific topogenesis, we have used different kinds of cDNA constructs encoding various chimeric combinations of mutants of the constitutive nucleolar protein NO38 (B23): 1) with an amino terminally placed short \"myc tag\"; 2) with two different carboxyl terminally attached large alpha-helical coiled coil structures, the lamin A rod domain or the rod domain of vimentin; 3) with the sequence-related nucleoplasmic histone-binding protein nucleo-plasmin; and 4) with the soluble cytoplasmic protein pyruvate kinase. To avoid the problem of formation of complexes with endogenous wild-type (wt) molecules and \"piggyback\" localization, special care was taken to secure that the mutants and chimeras used did not oligomerize as is typical of protein NO38 (B23). Using microinjection and transfection of cultured cells, we found that the segment comprising the amino-terminal 123 amino acids (aa) alone was sufficient to effect nucleolar accumulation of the construct molecules, including the chimeras with the entire rod domains of lamin A and vimentin. However, when the amino-terminal 109 aa were deleted, the molecules still associated with the nucleolus. The results of further deletion experiments and of domain swaps with nucleoplasmin all point to the topogenic importance of two independent molecular regions located at both the amino- and carboxyl-terminal end. Our definition of dominant elements determining the nucleolar localization of protein NO38 (B23) as well as of diverse nonnucleolar proteins will help to identify its local binding partner(s) and functions, the construction of probes examining other proteins or sequence elements within the nucleolar microenvironment, and the generation of cells with an altered nuclear architecture.","authors":"Zirwes, RF., Kouzmenko, AP., Peters, JM., Franke, WW., Schmidt-Zachmann, MS.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Mol Biol Cell","volume":"8","issue":"2","page":"231-48","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8180136","title":"Structure and expression of the chicken retinoblastoma gene.","abstract":"The molecular cloning and initial characterization of the complementary DNA encoding the chicken homologue of the human retinoblastoma susceptibility gene product Rb are described. Chicken Rb (chRb) was found to be highly homologous to human, mouse, and Xenopus Rb in primary amino acid sequence, underlining its conserved function in cell cycle control in higher eukaryotes. The highest level of homology was found within the Rb \"pocket domains\" and at the Rb COOH terminus, whereas the extreme NH2 terminus of chRb is divergent. We also show that transcription of chRb initiates at multiple start sites within a DNA segment which represents a CpG island. ChRb is transcribed as a 4.7-kilobase (kb) mRNA species in a variety of normal chicken tissues and oncogene-transformed hematopoietic cells. However, in v-rel-transformed cell lines, a variant 3.1-kb Rb-specific mRNA was detected in addition to the 4.7-kb transcript. ChRb is expressed as a 104 kilodalton protein and is therefore slightly smaller than the mammalian Rb proteins.","authors":"Boehmelt, G., Ulrich, E., Kurzbauer, R., Mellitzer, G., Bird, A., Zenke, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Cell Growth Differ","volume":"5","issue":"2","page":"221-30","pdf":null,"JrId":"1848","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1460424","title":"CD45RA and CD45RBhigh expression induced by thymic selection events.","abstract":"CD45 is a protein tyrosine phosphatase involved in T and B cell signaling. While peripheral T cells switch CD45 isoforms upon activation, events leading to exon switching during T cell development in the thymus have not been determined. The expression of high molecular weight isoforms of CD45 was examined on thymocytes from nontransgenic and T cell receptor (TCR) transgenic mice. All thymocytes from nontransgenic mice were CD45RB+ as assessed by staining with MB23G2, an anti-CD45RB-specific monoclonal antibody. Interestingly, there was a small population (1-3%) of thymocytes that displayed a higher intensity of staining with MB23G2, CD45RBhigh. CD45RBhigh thymocytes were found in all subsets defined by CD4 and CD8 expression and were also present within the TCR-alpha\/beta high population. To analyze whether or not CD45 expression correlated with thymic selection events, expression of CD45RBhigh and a second isoform, CD45RA, was examined on thymocytes from H-Y and 2C TCR transgenic mice and found to correlate with positive and negative selection events but did not occur in nonselecting backgrounds. CD45RA and CD45RBhigh upregulation was also not observed in transgenic mice backcrossed into CD8-deficient mice, a scenario in which there is no positive selection of transgene-expressing thymocytes. These data suggest that modulation of CD45 isoform expression may be involved in thymic selection events.","authors":"Wallace, VA., Fung-Leung, WP., Timms, E., Gray, D., Kishihara, K., Loh, DY., Penninger, J., Mak, TW.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"J Exp Med","volume":"176","issue":"6","page":"1657-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1993-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17588603","title":"Dimer composition and promoter context contribute to functional cooperation between AP-1 and NFAT.","abstract":"The transcription factors activator protein 1 (AP-1) and nuclear factor of activated T-cells (NFAT) cooperate to induce the expression of cytokines during the immune response. While much is known about the signaling pathways and physical interactions between NFAT and AP-1 dimers following lymphocyte activation, few studies have addressed the role of AP-1 composition in modulating NFAT:AP-1-dependent transcription. We examined the function of specific AP-1 complexes using \"tethered\" AP-1 dimers with defined composition. We found that NFAT can functionally cooperate with all AP-1 dimers tested. Noteworthy, Jun approximately Jun-containing dimers, which are relatively inactive when tested on an AP-1-dependent promoter, are effective co-activators of an NFAT:AP-1-dependent promoter. Interestingly, specific AP-1 dimer combinations behave differently when tested on interleukin 2 (IL2) and interleukin 4 (IL4) gene regulatory regions. Moreover, the requirement for NFAT to activate each of the promoters is different. Our results suggest that higher NFAT levels are necessary to activate the IL4 promoter. Hence changes in AP-1 composition and the level of participating NFAT proteins can differentially influence cytokine gene expression, resulting in biological consequences for the modulation and dynamics of the immune response.","authors":"Wisniewska, MB., Ameyar-Zazoua, M., Bakiri, L., Kaminska, B., Yaniv, M., Weitzman, JB.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Mol Biol","volume":"371","issue":"3","page":"569-76","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2339110","title":"Receptor-mediated endocytosis of transferrin-polycation conjugates: an efficient way to introduce DNA into hematopoietic cells.","abstract":"Most current gene transfer methods function satisfactorily in specialized systems involving established cell lines but are often not applicable with nonadherent, primary hematopoietic cells, which are notoriously difficult to transfect. To approach this problem, we have investigated an alternative method of gene transfer, \"transferrinfection,\" in which DNA complexed to transferrin-polycation conjugates is introduced into cells by receptor-mediated endocytosis [Wagner, E., Zenke, M., Cotten, M., Beug, H. &amp; Birnstiel, M. L. (1990) Proc. Natl. Acad. Sci. USA 87, 3410-3414]. We show here that transferrin-polylysine and transferrin-protamine, when complexed to plasmid DNA containing a luciferase reporter gene, is efficiently bound and moved into avian erythroblasts by endocytosis. Successful transfer and expression of the luciferase reporter gene depends on specific interaction of the transferrin-polylysine-DNA complex with the transferrin receptor and occurs in a significant fraction (greater than 95%) of the cells. Gene transfer efficiency by transferrinfection is lower than with an optimized DEAE-dextran transfection method but reaches similar efficiencies when the cells are treated with chloroquine. Because the procedure in the absence of chloroquine is completely nontoxic to cells, a constant expression level of transferred genes may be maintained by repeated additions of transferrin-polylysine-DNA complex. In addition, the usefulness of transferrinfection for gene transfer into primary hematopoietic cells is demonstrated.","authors":"Zenke, M., Steinlein, P., Wagner, E., Cotten, M., Beug, H., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Proc Natl Acad Sci U S A","volume":"87","issue":"10","page":"3655-9","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1990-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2317863","title":"Alternative chromatin structure at CpG islands.","abstract":"Actively transcribed chromatin is structurally different from bulk inactive chromatin. It has been difficult to define the molecular basis of the difference, however, because purified fractions of active chromatin were not available. We have overcome this problem by releasing oligonucleosomes from the nonmethylated CpG-rich islands (CpG islands) of HeLa cell nuclei using restriction endonucleases. Since CpG islands very often include the promoters and 5' transcribed regions of genes, they represent a model for the \"active\" chromatin structure. CpG island chromatin differs in three respects from bulk chromatin prepared in the same way: histone H1 is present in very low amounts; histones H3 and H4 are highly acetylated; and nucleosome-free regions are present. Except for the latter regions, the average nucleosomal spacing is similar to that of bulk chromatin.","authors":"Tazi, J., Bird, A.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Cell","volume":"60","issue":"6","page":"909-20","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1990-05-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2349215","title":"Transferrin-polycation-mediated introduction of DNA into human leukemic cells: stimulation by agents that affect the survival of transfected DNA or modulate transferrin receptor levels.","abstract":"We have subverted a receptor-mediated endocytosis event to transport genes into human leukemic cells. By coupling the natural iron-delivery protein transferrin to the DNA-binding polycations polylysine or protamine, we have created protein conjugates that bind nucleic acids and carry them into the cell during the normal transferrin cycle [Wagner, E., Zenke, M., Cotten, M., Beug, H. &amp; Birnstiel, M. L. (1990) Proc. Natl. Acad. Sci. USA 87, 3410-3414]. We demonstrate here that this procedure is useful for a human leukemic cell line. We enhanced the rate of gene delivery by (i) increasing the transferrin receptor density through treatment of the cells with the cell-permeable iron chelator desferrioxamine, (ii) interfering with the synthesis of heme with succinyl acetone treatment, or (iii) stimulating the degradation of heme with cobalt chloride treatment. Consistent with gene delivery as an endocytosis event, we show that the subsequent expression in K-562 cells of a gene included in the transported DNA depends upon the cellular presence of the lysosomotropic agent chloroquine. By contrast, monensin blocks \"transferrinfection,\" as does incubation of the cells at 18 degrees C.","authors":"Cotten, M., L\u00e4ngle-Rouault, F., Kirlappos, H., Wagner, E., Mechtler, K., Zenke, M., Beug, H., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Proc Natl Acad Sci U S A","volume":"87","issue":"11","page":"4033-7","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1990-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"103","title":"[Combined effects of hypoxia and hypercapnia on the functional state of the respiratory center].","abstract":"Experiments were conducted on cats under nembutal anesthesia; a study was made of pulse activity of bulbar respiratory neurons, electrical activity of the diaphragm and of the intercostal muscles; pO2, pCO2, pH, arterial blood oxygen saturation were determined in combined action of hypoxia and hypercapnia. When hypoxic gaseous mixture was given for respiration the developing hypocapnia disturbed the discharge rhythmic activity of the respiratory neurons, the respiration acquiring a pathological character of the Cheyne--Stokes type. After addition to the hypoxic gaseous mixture of 2% CO2 the gaseous composition of the arterial blood approached the initial values; this addition prevented the development of hypercapnia and disturbances of rhythmic discharge activity of the respiratory neurons. Addition of 5% CO2 to the hypoxic gaseous mixture produced a negative effect: at first it intensified and then depressed the pulse activity of the respiratory neurons, caused metabolic and respiratory acidosis, and promoted asphyxia.","authors":"Kulik, AM., Kondrat'eva, LN.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biull Eksp Biol Med","volume":"79","issue":"4","page":"39-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17347895","title":"Estimating the number of coding mutations in genotypic and phenotypic driven N-ethyl-N-nitrosourea (ENU) screens: revisited.","abstract":"We recently described methods for estimating the number of N-ethyl-N-nitrosourea (ENU)-induced coding mutations in phenotypic and genotypic screens. In this article we revisit these methods, clarifying their application. In particular, we focus on the difference between unconditional and conditional probabilities. We also introduce a website to assist investigators in the application of these equations ( http:\/\/www.well.ox.ac.uk\/enuMutRat ).","authors":"Keays, DA., Clark, TG., Campbell, TG., Broxholme, J., Valdar, W.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mamm Genome","volume":"18","issue":"2","page":"123-4","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"2007-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"91","title":"Conformational and molecular responses to pH variation of the purified membrane adenosine triphosphatase of Micrococcus lysodeikticus.","abstract":"A preparation of ATPase from the membranes of Micrococcus lysodeikticus, solubilized and more than 95% pure, showed two main bands in analytical polyacrylamide gel electrophoresis. They did not correspond to isoenzymes because one band could be converted into the other by exposure to a mildly alkaline pH value. The conversion was paralleled by changes in molecular weight, circular dichroism and catalytic properties. Denaturation by pH at 25 degrees C was followed by means of circular dichroism, ultracentrifugation and polyacrylamide gel electrophoresis. A large conformational transition took place in the acid range with midpoints at about pH = 3.6 (I = 10(-4) M), 4.3 (I = 0.03 M) and 5.3 (I = 0.1 M). The transition was irreversible. Strong aggregation of the protein occurred in this range of pH. The final product was largely random coil, but even at pH 1.5 dissociation into individual subunits was not complete. However, partial dissociation took place at pH 5 (I = 0.028 M). At this pH value the enzyme was inactive, but 20-30% of the activity could be recovered when the pH was returned to 7.5. In the alkaline region the midpoint of the transition occurred near pH = 11 (I = 0.028 M). The pK of most of the tyrosine residues of the protein was about 10.9. The unfolding was irreversible and the protein was soon converted into peptide species with molecular weights lower than those determined for the subunits by gel electrophoresis in the presence of sodium dodecyl sulphate. Conventional proteolysis did not account for the transformation.","authors":"Nieto, M., Mu\u00f1oz, E., Carreira, J., Andreu, JM.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"413","issue":"3","page":"394-414","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22736430","title":"Screening for MYO15A gene mutations in autosomal recessive nonsyndromic, GJB2 negative Iranian deaf population.","abstract":"MYO15A is located at the DFNB3 locus on chromosome 17p11.2, and encodes myosin-XV, an unconventional myosin critical for the formation of stereocilia in hair cells of cochlea. Recessive mutations in this gene lead to profound autosomal recessive nonsyndromic hearing loss (ARNSHL) in humans and the shaker2 (sh2) phenotype in mice. Here, we performed a study on 140 Iranian families in order to determine mutations causing ARNSHL. The families, who were negative for mutations in GJB2, were subjected to linkage analysis. Eight of these families showed linkage to the DFNB3 locus, suggesting a MYO15A mutation frequency of 5.71% in our cohort of Iranian population. Subsequent sequencing of the MYO15A gene led to identification of 7 previously unreported mutations, including 4 missense mutations, 1 nonsense mutation, and 2 deletions in different regions of the myosin-XV protein.","authors":"Fattahi, Z., Shearer, AE., Babanejad, M., Bazazzadegan, N., Almadani, SN., Nikzat, N., Jalalvand, K., Arzhangi, S., Esteghamat, F., Abtahi, R., Azadeh, B., Smith, RJ., Kahrizi, K., Najmabadi, H.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Am J Med Genet A","volume":"158A","issue":"8","page":"1857-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22859403","title":"Genetic analysis of albuminuria in collaborative cross and multiple mouse intercross populations.","abstract":"Albuminuria is an important marker of nephropathy that increases the risk of progressive renal and chronic cardiovascular diseases. The genetic basis of kidney disease is well-established in humans and rodent models, but the causal genes remain to be identified. We applied several genetic strategies to map and refine genetic loci affecting albuminuria in mice and translated the findings to human kidney disease. First, we measured albuminuria in mice from 33 inbred strains, used the data for haplotype association mapping (HAM), and detected 10 genomic regions associated with albuminuria. Second, we performed eight F(2) intercrosses between genetically diverse strains to identify six loci underlying albuminuria, each of which was concordant to kidney disease loci in humans. Third, we used the Oak Ridge National Laboratory incipient Collaborative Cross subpopulation to detect an additional novel quantitative trait loci (QTL) underlying albuminuria. We also performed a ninth intercross, between genetically similar strains, that substantially narrowed an albuminuria QTL on Chromosome 17 to a region containing four known genes. Finally, we measured renal gene expression in inbred mice to detect pathways highly correlated with albuminuria. Expression analysis also identified Glcci1, a gene known to affect podocyte structure and function in zebrafish, as a strong candidate gene for the albuminuria QTL on Chromosome 6. Overall, these findings greatly enhance our understanding of the genetic basis of albuminuria in mice and may guide future studies into the genetic basis of kidney disease in humans.","authors":"Thaisz, J., Tsaih, SW., Feng, M., Philip, VM., Zhang, Y., Yanas, L., Sheehan, S., Xu, L., Miller, DR., Paigen, B., Chesler, EJ., Churchill, GA., Dipetrillo, K.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Am J Physiol Renal Physiol","volume":"303","issue":"7","page":"F972-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12679032","title":"bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila.","abstract":"Cell proliferation, cell death, and pattern formation are coordinated in animal development. Although many proteins that control cell proliferation and apoptosis have been identified, the means by which these effectors are linked to the patterning machinery remain poorly understood. Here, we report that the bantam gene of Drosophila encodes a 21 nucleotide microRNA that promotes tissue growth. bantam expression is temporally and spatially regulated in response to patterning cues. bantam microRNA simultaneously stimulates cell proliferation and prevents apoptosis. We identify the pro-apoptotic gene hid as a target for regulation by bantam miRNA, providing an explanation for bantam's anti-apoptotic activity.","authors":"Brennecke, J., Hipfner, DR., Stark, A., Russell, RB., Cohen, SM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cell","volume":"113","issue":"1","page":"25-36","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12779345","title":"A novel alpha-conotoxin identified by gene sequencing is active in suppressing the vascular response to selective stimulation of sensory nerves in vivo.","abstract":"We describe the identification of a conopeptide sequence in venom duct mRNA from Conus victoriae that suppresses a vascular response to pain in the rat. PCR-RACE was used to screen venom duct cDNAs for those transcripts that encode specific antagonists of vertebrate neuronal nicotinic acetylcholine receptors (nAChRs). One of these peptides, Vc1.1, was active as an antagonist of neuronal nAChRs in receptor binding and functional studies in bovine chromaffin cells. It also suppressed the vascular responses to unmyelinated sensory nerve C-fiber activation in rats. Such vascular responses are involved in pain transmission. Furthermore, its ability to suppress C-fiber function was greater than that of MVIIA, an omega-conotoxin with known analgesic activity in rats and humans. Vc1.1 has a high degree of sequence similarity to the alpha-conotoxin family of peptides and has the 4,7 loop structure characteristic of the subfamily of peptides that act on neuronal-type nAChRs. The results suggest that neuronal alpha-conotoxins should be further investigated with respect to their potential to suppress pain.","authors":"Sandall, DW., Satkunanathan, N., Keays, DA., Polidano, MA., Liping, X., Pham, V., Down, JG., Khalil, Z., Livett, BG., Gayler, KR.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Biochemistry","volume":"42","issue":"22","page":"6904-11","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17081975","title":"Evidence that loading of cohesin onto chromosomes involves opening of its SMC hinge.","abstract":"Cohesin is a multisubunit complex that mediates sister-chromatid cohesion. Its Smc1 and Smc3 subunits possess ABC-like ATPases at one end of 50 nm long coiled coils. At the other ends are pseudosymmetrical hinge domains that interact to create V-shaped Smc1\/Smc3 heterodimers. N- and C-terminal domains within cohesin's kleisin subunit Scc1 bind to Smc3 and Smc1 ATPase heads respectively, thereby creating a huge tripartite ring. It has been suggested that cohesin associates with chromosomes by trapping DNA within its ring. Opening of the ring due to cleavage of Scc1 by separase destroys sister-chromatid cohesion and triggers anaphase. We show that cohesin's hinges are not merely dimerization domains. They are essential for cohesin's association with chromosomes, which is blocked by artificially holding hinge domains together but not by preventing Scc1's dissociation from SMC ATPase heads. Our results suggest that entry of DNA into cohesin's ring requires transient dissociation of Smc1 and Smc3 hinge domains.","authors":"Gruber, S., Arumugam, P., Katou, Y., Kuglitsch, D., Helmhart, W., Shirahige, K., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell","volume":"127","issue":"3","page":"523-37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-12-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17532061","title":"Behavioural characterisation of the robotic mouse mutant.","abstract":"The ataxic mouse mutant robotic is characterised by progressive adult-onset Purkinje cell loss that occurs in a distinctive region-specific pattern. We report the first behavioural characterisation of this mutant and quantify its performance on tests of motor function, locomotor and exploratory activity over a time course that reflects specific stages of cell loss in the cerebellum. Robotic mutants are significantly impaired on the rotarod and static rod tests of coordination and their performance declined during aging. In addition, gait analysis revealed an increase in the severity of the ataxia displayed by mutants over time. Interestingly, spontaneous alternation testing in a T-maze was not significantly affected in robotic mice, unlike other ataxic mutants with more rapid and extensive cerebellar degeneration; robotic therefore provides an opportunity to investigate the necessity of specific Purkinje cell populations for various behavioural tasks.","authors":"Oliver, PL., Keays, DA., Davies, KE.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Behav Brain Res","volume":"181","issue":"2","page":"239-47","pdf":null,"JrId":"1436","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"165","title":"A clinical method for the determination of serum gamma-glutamyl transpeptidase.","abstract":"A simple, highly sensitive and reproducible method for the assay of gamma-glutamyl transpeptidase (EC 2.3.2-) activity is introduced, using gamma-glutamyl-p-nitroanilide as a substrate and glycylglycine as an acceptor in 50 g\/l of polyoxyethylene nonylphenol. Serum transpeptidase activity was assayed in 1080 healthy adults, the normal mean value being 14.8 mU\/ml. The diagnostic evaluation of the enzyme in various hepatobiliary diseases is also discussed.","authors":"Tamaoki, H., Minato, S., Takei, S., Fujisawa, K.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Chim Acta","volume":"65","issue":"1","page":"21-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"164","title":"Problems associated with the determination of arylsulfatase A and B using nitrocatechol sulfate substrate.","abstract":"","authors":"Shapira, E., Nadler, HL.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Chim Acta","volume":"65","issue":"1","page":"1-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"163","title":"Measurement of total alkaline phosphatase activity in human serum.","abstract":"","authors":"Bowers, GN., McComb, RB.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Chem","volume":"21","issue":"13","page":"1988-95","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12941964","title":"Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins.","abstract":"Fructose-1,6-bisphosphate aldolase (FBPA) catalyzes the reversible cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate in the glycolytic pathway. FBPAs from archaeal organisms have recently been identified and characterized as a divergent family of proteins. Here, we report the first crystal structure of an archaeal FBPA at 1.9-A resolution. The structure of this 280-kDa protein complex was determined using single wavelength anomalous dispersion followed by 10-fold non-crystallographic symmetry averaging and refined to an R-factor of 14.9% (Rfree 17.9%). The protein forms a dimer of pentamers, consisting of subunits adopting the ubiquitous (betaalpha)8 barrel fold. Additionally, a crystal structure of the archaeal FBPA covalently bound to dihydroxyacetone phosphate was solved at 2.1-A resolution. Comparison of the active site residues with those of classical FBPAs, which share no significant sequence identity but display the same overall fold, reveals a common ancestry between these two families of FBPAs. Structural comparisons, furthermore, establish an evolutionary link to the triosephosphate isomerases, a superfamily hitherto considered independent from the superfamily of aldolases.","authors":"Lorentzen, E., Pohl, E., Zwart, P., Stark, A., Russell, RB., Knura, T., Hensel, R., Siebers, B.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Biol Chem","volume":"278","issue":"47","page":"47253-60","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12595245","title":"A model for statistical significance of local similarities in structure.","abstract":"Structural biology can provide three-dimensional structures for proteins of unknown function. When sequence or structure comparisons fail to suggest a function, insights can come from discovery of functionally important local structural patterns. Existing methods to detect such patterns lack rigorous statistics needed for widespread application. Here, we derive a formula to calculate statistical significance of the root-mean-square deviation between atoms in such patterns. When combined with a database search method, our statistics permit true functional or structural patterns in different folds to be discerned from noise. The approach is highly complementary to fold comparison for providing functional clues for new structures, and is key for the detection of recurrences of any new pattern.","authors":"Stark, A., Sunyaev, S., Russell, RB.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Mol Biol","volume":"326","issue":"5","page":"1307-16","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2003-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22639462","title":"Definition of a critical genetic interval related to kidney abnormalities in the Potocki-Lupski syndrome.","abstract":"Potocki-Lupski syndrome is a genomic disorder caused by duplication of 17p11.2. It is characterized by failure to thrive, intellectual disability, hypotonia, and behavioral difficulties. Structural renal anomalies have been observed in &lt;10% of affected individuals. We present detailed clinical and molecular data on six patients with Potocki-Lupski syndrome, two of whom had renal abnormalities, and investigate the prevalence of kidney abnormalities in the mouse model for the syndrome. In contrast to affected humans, the mouse model does not demonstrate a renal phenotype. Comparison of the duplicated segment in patients with Potocki-Lupski syndrome and the renal phenotype and the syntenic duplicated region in the mouse model allowed us to suggest a 0.285 Mb critical region, including the FLCN gene that may be important for development of renal abnormalities in patients with this duplication.","authors":"Goh, ES., Perez, IC., Canales, CP., Ruiz, P., Agatep, R., Yoon, G., Chitayat, D., Dror, Y., Shago, M., Goobie, S., Sgro, M., Walz, K., Mendoza-Londono, R.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Am J Med Genet A","volume":"158A","issue":"7","page":"1579-88","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12453411","title":"A dynamic structural model for estrogen receptor-alpha activation by ligands, emphasizing the role of interactions between distant A and E domains.","abstract":"The functional interplay between different domains of estrogen receptor-alpha (ERalpha, NR3A1) is responsible for the overall properties of the full-length protein. We previously identified an interaction between the N-terminal A and C-terminal domains, which we demonstrate here to repress ligand-independent transactivation and transrepression abilities of ERalpha. Using targeted mutations based on ERalpha structural models, we determine the basis for this interaction that defines a regulatory interplay between ERalpha A domain, corepressors, and ERalpha Helix 12 for binding to the same C-terminal surface. We propose a dynamic model where binding of different ligands influences the A\/D-F domain interaction and results in specific functional outcomes. This model gives insights into the dynamic properties of full-length ERalpha and into the structure of unliganded ERalpha.","authors":"M\u00e9tivier, R., Stark, A., Flouriot, G., H\u00fcbner, MR., Brand, H., Penot, G., Manu, D., Denger, S., Reid, G., Kos, M., Russell, RB., Kah, O., Pakdel, F., Gannon, F.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Cell","volume":"10","issue":"5","page":"1019-32","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2003-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"89","title":"Effects of membrane ribonuclease and 3'-nucleotidase on the digestion of polyuridylic acid by rat liver plasma membrane.","abstract":"1. Fragments of isolated rat liver plasma membrane possess a ribonuclease activity which at pH 7.8 in the presence of 10 mM EDTA can digest polyuridylic acid (poly(U)) and polycytidylic acid (poly(C)) but not polyadenylic acid (poly(A)) and polyguanylic acid (poly(G)). Under these conditions, the membrane preparation does not degrade native or denatured DNA. 2. The products of the reaction with poly(U) (10 mM EDTA present) can be separated on DEAE-Sephadex into oligonucleotides of increasing chain length. Most of the products are di- to hexa-nucleotides which contain terminal 3'-phosphate groups. 3. When EDTA is not present (pH 7.8 or 8.8) the plasma membrane preparation degrades both poly(A) and poly(U). With poly(A) the product is all nucleoside while with poly(U) as substrate most of the product is nucleoside, but also some oligonucleotides are produced. 4. The ribonuclease releases acid soluble products very slowly from high concentrations of poly(U) (mg\/ml). 5. Uridine trinucleotide with and without a terminal 3'-phosphate group is degraded by rat liver plasma membrane. The trinucleotide diphosphate is rapidly hydrolyzed to nucleoside while the trinucleotide itself is slowly digested and yields intermediate products, including nucleoside.","authors":"Aronson, NN., Yannarell, A.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"413","issue":"1","page":"135-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15296734","title":"Finding functional sites in structural genomics proteins.","abstract":"Assigning function to structures is an important aspect of structural genomics projects, since they frequently provide structures for uncharacterized proteins. Similarities uncovered by structure alignment can suggest a similar function, even in the absence of sequence similarity. For proteins adopting novel folds or those with many functions, this strategy can fail, but functional clues can still come from comparison of local functional sites involving a few key residues. Here we assess the general applicability of functional site comparison through the study of 157 proteins solved by structural genomics initiatives. For 17, the method bolsters confidence in predictions made based on overall fold similarity. For another 12 with new folds, it suggests functions, including a putative phosphotyrosine binding site in the Archaeal protein Mth1187 and an active site for a ribose isomerase. The approach is applied weekly to all new structures, providing a resource for those interested in using structure to infer function.","authors":"Stark, A., Shkumatov, A., Russell, RB.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Structure","volume":"12","issue":"8","page":"1405-12","pdf":null,"JrId":"22305","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1402689","title":"CD4 expression is differentially required for deletion of MLS-1a-reactive T cells.","abstract":"Clonal deletion of thymocytes expressing potentially self-reactive T cell receptors (TCRs) occurs during thymocyte ontogeny. Mice deficient for CD4 expression provide a unique model system to study the contribution of the CD4 molecule in negative selection of T cells reactive against the major histocompatibility complex class II-associated retroviral self-superantigen, Mls-1a. In the presence of Mls-1a determinants, mature CD8+ T cells expressing V beta 6, 8.1, and 9 were deleted in CD4-deficient mice, thus demonstrating that TCR affinity for Mls-1a is sufficient for deletion and that a signal through CD4 was not required. However, in instances where the TCR affinity for Mls-1a is low, as in the case of V beta 7+ T cells, CD4 expression was required for clonal deletion. These results demonstrate that for Mls-1a-mediated clonal deletion of T cells, the requirement for the accessory or coreceptor function of CD4 depends on the affinity of the TCR.","authors":"Wallace, VA., Rahemtulla, A., Timms, E., Penninger, J., Mak, TW.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"J Exp Med","volume":"176","issue":"5","page":"1459-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1992-11-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9637685","title":"Miranda as a multidomain adapter linking apically localized Inscuteable and basally localized Staufen and Prospero during asymmetric cell division in Drosophila.","abstract":"Neuroblasts in the developing Drosophila CNS asymmetrically localize the cell fate determinants Numb and Prospero as well as prospero RNA to the basal cortex during mitosis. The localization of Prospero requires the function of inscuteable and miranda, whereas prospero RNA localization requires inscuteable and staufen function. We demonstrate that Miranda contains multiple functional domains: an amino-terminal asymmetric localization domain, which interacts with Inscuteable, a central Numb interaction domain, and a more carboxy-terminal Prospero interaction domain. We also show that Miranda and Staufen have similar subcellular localization patterns and interact in vitro. Furthermore, miranda function is required for the asymmetric localization of Staufen. Miranda localization is disrupted by the microfilament disrupting agent latrunculin A. Our results suggest that Miranda directs the basal cortical localization of multiple molecules, including Staufen and prospero RNA, in mitotic neuroblasts in an actin-dependent manner.","authors":"Shen, CP., Knoblich, JA., Chan, YM., Jiang, MM., Jan, LY., Jan, YN.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Genes Dev","volume":"12","issue":"12","page":"1837-46","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1998-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9635435","title":"An ESP1\/PDS1 complex regulates loss of sister chromatid cohesion at the metaphase to anaphase transition in yeast.","abstract":"Cohesion between sister chromatids during G2 and M phases depends on the \"cohesin\" protein Scc1p (Mcd1p). Loss of cohesion at the metaphase to anaphase transition is accompanied by Scc1p's dissociation from chromatids, which depends on proteolysis of Pds1p mediated by a ubiquitin protein ligase called the anaphase promoting complex (APC). We show that destruction of Pds1p is the APC's sole role in triggering Scc1p's dissociation from chromatids and that Pds1p forms a stable complex with a 180 kDa protein called Esp1p, which is essential for the dissociation of Scc1p from sister chromatids and for their separation. We propose that the APC promotes sister separation not by destroying cohesins but instead by liberating the \"sister-separating\" Esp1 protein from its inhibitor Pds1p.","authors":"Ciosk, R., Zachariae, W., Michaelis, C., Shevchenko, A., Mann, M., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Cell","volume":"93","issue":"6","page":"1067-76","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1998-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16949097","title":"Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions.","abstract":"Recent advances in functional genomics have helped generate large-scale high-throughput protein interaction data. Such networks, though extremely valuable towards molecular level understanding of cells, do not provide any direct information about the regions (domains) in the proteins that mediate the interaction. Here, we performed co-evolutionary analysis of domains in interacting proteins in order to understand the degree of co-evolution of interacting and non-interacting domains. Using a combination of sequence and structural analysis, we analyzed protein-protein interactions in F1-ATPase, Sec23p\/Sec24p, DNA-directed RNA polymerase and nuclear pore complexes, and found that interacting domain pair(s) for a given interaction exhibits higher level of co-evolution than the non-interacting domain pairs. Motivated by this finding, we developed a computational method to test the generality of the observed trend, and to predict large-scale domain-domain interactions. Given a protein-protein interaction, the proposed method predicts the domain pair(s) that is most likely to mediate the protein interaction. We applied this method on the yeast interactome to predict domain-domain interactions, and used known domain-domain interactions found in PDB crystal structures to validate our predictions. Our results show that the prediction accuracy of the proposed method is statistically significant. Comparison of our prediction results with those from two other methods reveals that only a fraction of predictions are shared by all the three methods, indicating that the proposed method can detect known interactions missed by other methods. We believe that the proposed method can be used with other methods to help identify previously unrecognized domain-domain interactions on a genome scale, and could potentially help reduce the search space for identifying interaction sites.","authors":"Jothi, R., Cherukuri, PF., Tasneem, A., Przytycka, TM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Mol Biol","volume":"362","issue":"4","page":"861-75","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2006-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16365314","title":"Correlation between evolutionary structural development and protein folding.","abstract":"Evolution should have played important roles in determining folding mechanisms and structures of proteins. In this article we discuss how the folding mechanisms had been affected by the early stage of evolution through which the uniqueness of structure had developed. Although the process of such early-time evolution has remained a mystery, a plausible scenario is that the evolution of proteins toward the ordered structures was guided by functional selection pressure as demonstrated in vitro and in silico. We examine the in silico functional selection of sequences and show that there is a significant correlation between two different processes toward the unique 3D structure, the evolutionary development of structure through sequence selection, and the folding process of the resultant sequence. This finding could be rephrased as protein folding recapitulates the emergence of topology in the molecular evolution. The correlation suggests a guideline for engineering foldable proteins.","authors":"Nagao, C., Terada, TP., Yomo, T., Sasai, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Proc Natl Acad Sci U S A","volume":"102","issue":"52","page":"18950-5","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2006-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1358796","title":"Identification and mapping of six microdissected genomic DNA probes to the proximal region of mouse chromosome 1.","abstract":"Six independent DNA probes, lambda Mm1C-150, lambda Mm1C-153, lambda Mm1C-156, lambda Mm1C-162, lambda Mm1C-163, and lambda Mm1C-165, have been isolated from a library of microdissected fragments from mouse chromosome 1, spanning cytogenetic bands C2 to C5. These DNA probes have been mapped by restriction fragment length polymorphism analysis with respect to 12 marker loci previously assigned to this portion of mouse chromosome 1, in a panel of 251 segregating Mus spretus x C57BL\/6J interspecific backcross mice. The gene order and intergene distances were determined by segregation analysis to be centromere- lambda Mm1C-162-11.1 cM-Col3a1-8.8 cM-Len-2-2.6 cM-lambda Mm1C-163-1.6 cM-Fn-1-1.6 cM-Tp-1-0.8 cM-lambda Mm1C-165\/Vil-0.4 cM-Inha-2.8 cM-lambda Mm1C-153-2.4 cM-lambda Mm1C-156-1.2 cM-Pax-3-5.6 cM-Akp-3-0.8 cM-Acrg-2.0 cM-Sag-0.5 cM-Col6a3-1.8 cM-lambda Mm1C-150-15.4 cM-Ren1,2. Four of these probes map within a chromosome 1 segment that is homologous to human chromosome 2q. Southern blotting analyses indicate that one of these anonymous probes, lambda Mm1C-165, detects DNA fragments highly conserved across species. These novel polymorphic probes should prove useful for linkage and physical mapping of this chromosomal region.","authors":"Vidal, SM., Epstein, DJ., Malo, D., Weith, A., Vekemans, M., Gros, P.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Genomics","volume":"14","issue":"1","page":"32-7","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"1992-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6196212","title":"The cellular oncogenes c-myc, c-myb and c-erb are transcribed in defined types of avian hematopoietic cells.","abstract":"The possible role of normal chicken cellular sequences c-erb, c-myb and c-myc, together referred to as c-onc genes and related to the oncogenes of defective avian acute leukemia retroviruses (DLVs), was investigated by determining the accumulation of c-onc RNA in different avian cells an cell lines. Levels of c-myc and in some instances c-myb RNA are elevated in immature hematopoietic cells or cell lines from various lineages but more mature hematopoietic cells, as well as non-hematopoietic cells, contain only low levels. In contrast, the level of c-erb RNA is generally low, but high in a small number of normal bone marrow cells. The results indicate that the cellular homologues of the viral oncogenes are differentially expressed during hematopoiesis. They also indicate that the hypothesis that DLV target cells express their homologous c-onc genes might hold for c-erb, but is not valid in its simple form for c-myc and c-myb.","authors":"Coll, J., Saule, S., Martin, P., Raes, MB., Lagrou, C., Graf, T., Beug, H., Simon, IE., Stehelin, D.","publication_status":"ppublish","journalpubyear":"1983","journaltitle":"Exp Cell Res","volume":"149","issue":"1","page":"151-62","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1984-01-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19355944","title":"Multiple myeloma bone marrow niche.","abstract":"\"Niche\" is defined as a specialized regulatory microenvironment, consisting of components which control the fate specification of stem and progenitor cells, as well as maintaining their development by supplying the requisite factors. Bone marrow (BM) niche has a well-organized architecture and is composed of osteoblasts, osteoclasts, bone marrow endothelial cells, stromal cells, adipocytes and extracellular matrix proteins (ECM). These elements play an essential role in the survival, growth and differentiation of diverse lineages of blood cells, but also provide optimal growth environment for multiple hematological malignancies including multiple myeloma (MM). MM is a neoplastic plasma cell disorder which not only resides in BM but also converts it into specialized neoplastic niche. This niche aids the growth and spreading of tumor cells by a complex interplay of cytokines, chemokines, proteolytic enzymes and adhesion molecules. Moreover, the MM BM microenvironment was shown to confer survival and chemoresistance of MM cells to current therapies. However, our knowledge in this field is still in infancy and many details are unknown. Therefore, there is a strong need to further dissect the MM BM niche and understand the process of how the complex interactions with BM milieu influence MM growth, survival and development of resistance to chemotherapy. A better and more detailed understanding of neoplastic MM niche will provide a guiding model for identifying and validating novel targeted therapies directed against MM. Therefore, in the present review, we have focused principally on the basic features, physical structures, and functions of the BM niche and have highlighted its interaction with MM cells.","authors":"Basak, GW., Srivastava, AS., Malhotra, R., Carrier, E.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Pharm Biotechnol","volume":"10","issue":"3","page":"345-6","pdf":null,"JrId":"22464","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20817720","title":"Functional shifts in insect microRNA evolution.","abstract":"MicroRNAs (miRNAs) are short endogenous RNA molecules that regulate gene expression at the posttranscriptional level and have been shown to play critical roles during animal development. The identification and comparison of miRNAs in metazoan species are therefore paramount for our understanding of the evolution of body plans. We have characterized 203 miRNAs from the red flour beetle Tribolium castaneum by deep sequencing of small RNA libraries. We can conclude, from a single study, that the Tribolium miRNA set is at least 15% larger than that in the model insect Drosophila melanogaster (despite tens of high-throughput sequencing experiments in the latter). The rate of birth and death of miRNAs is high in insects. Only one-third of the Tribolium miRNA sequences are conserved in D. melanogaster, and at least 18 Tribolium miRNAs are conserved in vertebrates but lost in Drosophila. More than one-fifth of miRNAs that are conserved between Tribolium and Drosophila exhibit changes in the transcription, genomic organization, and processing patterns that lead to predicted functional shifts. For example, 13% of conserved miRNAs exhibit seed shifting, and we describe arm-switching events in 11% of orthologous pairs. These shifts fundamentally change the predicted targets and therefore function of orthologous miRNAs. In general, Tribolium miRNAs are more representative of the insect ancestor than Drosophila miRNAs and are more conserved in vertebrates.","authors":"Marco, A., Hui, JH., Ronshaugen, M., Griffiths-Jones, S.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Genome Biol Evol","volume":"2","issue":"","page":"686-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17178906","title":"p14-MP1-MEK1 signaling regulates endosomal traffic and cellular proliferation during tissue homeostasis.","abstract":"The extracellular signal-regulated kinase (ERK) cascade regulates proliferation, differentiation, and survival in multicellular organisms. Scaffold proteins regulate intracellular signaling by providing critical spatial and temporal specificity. The scaffold protein MEK1 (mitogen-activated protein kinase and ERK kinase 1) partner (MP1) is localized to late endosomes by the adaptor protein p14. Using conditional gene disruption of p14 in mice, we now demonstrate that the p14-MP1-MEK1 signaling complex regulates late endosomal traffic and cellular proliferation. This function its essential for early embryogenesis and during tissue homeostasis, as revealed by epidermis-specific deletion of p14. These findings show that endosomal p14-MP1-MEK1 signaling has a specific and essential function in vivo and, therefore, indicate that regulation of late endosomal traffic by extracellular signals is required to maintain tissue homeostasis.","authors":"Teis, D., Taub, N., Kurzbauer, R., Hilber, D., de Araujo, ME., Erlacher, M., Offterdinger, M., Villunger, A., Geley, S., Bohn, G., Klein, C., Hess, MW., Huber, LA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Cell Biol","volume":"175","issue":"6","page":"861-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"84","title":"Physical properties and subunits of Haemopis grandis erythrocruorin.","abstract":"The erythrocruorin of the leech Haemopis grandis possessed an S20,w of 57 S at neutral pH, its isoelectric point at pH 6.0 and exhibited a slightly sigmoid oxygenation curve with n approximately 2.1 and P50 = 11.2 mm at pH 7.4. A minimum molecular weight of 24000 +\/- 1500 per heme group was determined from the iron and heme contents, 0.22 +\/- 0.01 and 2.73 +\/- 0.14 weight %, respectively. The subunit composition of the erythrocruorin was investigated using gel filtration in sodium dodecyl sulfate and polyacrylamide gel electrophoresis in sodium dodecyl sulfate at neutral pH. Haemopis erythrocruorin dissociated in the presence of sodium dodecyl sulfate into four subunits (1 through 4) possessing molecular weights of about 27000, 23000, 21000 and 13500, respectively. When the erythrocruorin was reduced with mercaptoethanol prior to sodium dodecyl sulfate electrophoresis, three subunits  were observed, possessing molecular weights of about 13000 (I), 16500 (II) and 28000 (III). Sodium dodecyl sulfate electrophoresis of the isolated subunits 1 through 4 showed that subunit I was provided by subunits 1 and 4, subunit II was provided by subunit 1 and subunit III was provided by both subunit 2 and subunit 3. Haemopis erythrocruorin thus appeared to consist of at least five different polypeptide chains. It is likely that not all of the constituent polypeptide chains were associated each with a heme group. The shape of the Haemopis erythrocruorin observed by electron microscopy appeared to be consistent with the two-tiered hexagonal array characteristic of annelid erythrocruorins and chlorocruorins.","authors":"Andonian, MR., Barrett, AS., Vinogradov, SN.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"2","page":"202-13","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19632183","title":"Ars2 regulates both miRNA- and siRNA- dependent silencing and suppresses RNA virus infection in Drosophila.","abstract":"Intrinsic immune responses autonomously inhibit viral replication and spread. One pathway that restricts viral infection in plants and insects is RNA interference (RNAi), which targets and degrades viral RNA to limit infection. To identify additional genes involved in intrinsic antiviral immunity, we screened Drosophila cells for modulators of viral infection using an RNAi library. We identified Ars2 as a key component of Drosophila antiviral immunity. Loss of Ars2 in cells, or in flies, increases susceptibility to RNA viruses. Consistent with its antiviral properties, we found that Ars2 physically interacts with Dcr-2, modulates its activity in vitro, and is required for siRNA-mediated silencing. Furthermore, we show that Ars2 plays an essential role in miRNA-mediated silencing, interacting with the Microprocessor and stabilizing pri-miRNAs. The identification of Ars2 as a player in these small RNA pathways provides new insight into the biogenesis of small RNAs that may be extended to other systems.","authors":"Sabin, LR., Zhou, R., Gruber, JJ., Lukinova, N., Bambina, S., Berman, A., Lau, CK., Thompson, CB., Cherry, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"138","issue":"2","page":"340-51","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18641957","title":"An overview of the identification, detection, and functional analysis of Drosophila microRNAs.","abstract":"MicroRNAs (miRNAs), small noncoding RNAs that post-transcriptionally regulate gene expression, are one of the most abundant classes of gene regulators. Yet, little is known about the roles that specific miRNAs play in the development of multicellular organisms. Drosophila provides an excellent model system to explore the in vivo activities of particular miRNAs within the context of well-defined gene-expression programs that control the development of a complex organism. This chapter reviews the various approaches currently used to identify Drosophila miRNAs, detect their expression, determine their messenger RNA targets, and study their function.","authors":"Sokol, NS.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Methods Mol Biol","volume":"420","issue":"","page":"319-34","pdf":null,"JrId":"2488","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22584052","title":"Expression screening of 17q12-21 amplicon reveals GRB7 as an ERBB2-dependent oncogene.","abstract":"Gene amplification is a major genetic alteration in human cancers. Amplicons, amplified genomic regions, are believed to contain \"driver\" genes responsible for tumorigenesis. However, the significance of co-amplified genes has not been extensively studied. We have established an integrated analysis system of amplicons using retrovirus-mediated gene transfer coupled with a human full-length cDNA set. Applying this system to 17q12-21 amplicon observed in breast cancer, we identified GRB7 as a context-dependent oncogene, which modulates the ERBB2 signaling pathway through enhanced phosphorylation of ERBB2 and Akt. Our work provides an insight into the biological significance of gene amplification in human cancers.","authors":"Saito, M., Kato, Y., Ito, E., Fujimoto, J., Ishikawa, K., Doi, A., Kumazawa, K., Matsui, A., Takebe, S., Ishida, T., Azuma, S., Mochizuki, H., Kawamura, Y., Yanagisawa, Y., Honma, R., Imai, J., Ohbayashi, H., Goshima, N., Semba, K., Watanabe, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"FEBS Lett","volume":"586","issue":"12","page":"1708-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16177575","title":"Separase is required at multiple pre-anaphase cell cycle stages in human cells.","abstract":"The yeast separase proteins Esp1 and Cut1 are required for loss of sister chromatid cohesion that occurs at the moment of anaphase onset. Circumstantial evidence has linked human separase to centromere separation at anaphase, but a direct test that the role of this enzyme is functionally conserved with the yeast proteins is lacking. Here we describe the effects of separase depletion from human cells using RNA interference. Surprisingly, HeLa cells lacking separase are delayed or arrest at the G2-M phase transition. This arrest is not likely due to the activation of a known checkpoint control, but may be a result of a failure to construct a mitotic chromosome. Without separase, cells also have a prolonged prometaphase, perhaps resulting from defects in spindle assembly or dynamics. In cells that reach mitosis, sister arm resolution and separation are perturbed, whereas in anaphase cells sister centromeres do appear to separate. These data indicate that separase function is not restricted to anaphase initiation and that its role in promoting loss of sister chromatid cohesion might be preferentially at arms but not centromeres.","authors":"Gim\u00e9nez-Abi\u00e1n, JF., D\u00edaz-Mart\u00ednez, LA., Waizenegger, IC., Gim\u00e9nez-Mart\u00edn, G., Clarke, DJ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell Cycle","volume":"4","issue":"11","page":"1576-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19351792","title":"Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila.","abstract":"Rates of single nucleotide substitution in Drosophila are highly variable within the genome, and several examples illustrate that evolutionary rates differ among Drosophila species as well. Here, we use a maximum likelihood method to quantify lineage-specific substitutional patterns and apply this method to 4-fold degenerate synonymous sites and introns from more than 8,000 genes aligned in the Drosophila melanogaster group. We find that within species, different classes of sequence evolve at different rates, with long introns evolving most slowly and short introns evolving most rapidly. Relative rates of individual single nucleotide substitutions vary approximately 3-fold among lineages, yielding patterns of substitution that are comparatively less GC-biased in the melanogaster species complex relative to Drosophila yakuba and Drosophila erecta. These results are consistent with a model coupling a mutational shift toward reduced GC content, or a shift in mutation-selection balance, in the D. melanogaster species complex, with variation in selective constraint among different classes of DNA sequence. Finally, base composition of coding and intronic sequences is not at equilibrium with respect to substitutional patterns, which primarily reflects the slow rate of the substitutional process. These results thus support the view that mutational and\/or selective processes are labile on an evolutionary timescale and that if the process is indeed selection driven, then the distribution of selective constraint is variable across the genome.","authors":"Singh, ND., Arndt, PF., Clark, AG., Aquadro, CF.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Biol Evol","volume":"26","issue":"7","page":"1591-605","pdf":null,"JrId":"5749","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19349579","title":"Canonical Wnts function as potent regulators of osteogenesis by human mesenchymal stem cells.","abstract":"Genetic evidence indicates that Wnt signaling is critically involved in bone homeostasis. In this study, we investigated the functions of canonical Wnts on differentiation of adult multipotent human mesenchymal stem cells (hMSCs) in vitro and in vivo. We observe differential sensitivities of hMSCs to Wnt inhibition of osteogenesis versus adipogenesis, which favors osteoblastic commitment under binary in vitro differentiation conditions. Wnt inhibition of osteogenesis is associated with decreased expression of osteoblastic transcription factors and inhibition of c-Jun N-terminal kinase and p38 mitogen-activated protein kinase activation, which are involved in osteogenic differentiation. An hMSC subpopulation exhibits high endogenous Wnt signaling, the inhibition of which enhances osteogenic and adipogenic differentiation in vitro. In an in vivo bone formation model, high levels of Wnt signaling inhibit de novo bone formation by hMSCs. However, hMSCs with exogenous expression of Wnt1 but not stabilized beta-catenin markedly stimulate bone formation by naive hMSCs, arguing for an important role of a canonical Wnt gradient in hMSC osteogenesis in vivo.","authors":"Liu, G., Vijayakumar, S., Grumolato, L., Arroyave, R., Qiao, H., Akiri, G., Aaronson, SA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Biol","volume":"185","issue":"1","page":"67-75","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23623555","title":"An iron-rich organelle in the cuticular plate of avian hair cells.","abstract":"Hair cells reside in specialized epithelia in the inner ear of vertebrates, mediating the detection of sound, motion, and gravity. The transduction of these stimuli into a neuronal impulse requires the deflection of stereocilia, which are stabilized by the actin-rich cuticular plate. Recent electrophysiological studies have implicated the vestibular system in pigeon magnetosensation. Here we report the discovery of a single iron-rich organelle that resides in the cuticular plate of cochlear and vestibular hair cells in the pigeon. Transmission electron microscopy, coupled with elemental analysis, has shown that this structure is composed of ferritin-like granules, is approximately 300-600 nm in diameter, is spherical, and in some instances is membrane-bound and\/or organized in a paracrystalline array. This organelle is found in hair cells in a wide variety of avian species, but not in rodents or in humans. This structure may function as (1) a store of excess iron, (2) a stabilizer of stereocilia, or (3) a mediator of magnetic detection. Given the specific subcellular location, elemental composition, and evolutionary conservation, we propose that this structure is an integral component of the sensory apparatus in birds.","authors":"Lauwers, M., Pichler, P., Edelman, NB., Resch, GP., Ushakova, L., Salzer, MC., Heyers, D., Saunders, M., Shaw, J., Keays, DA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Curr Biol","volume":"23","issue":"10","page":"924-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15637609","title":"Conditional alleles, inteins and degrons.","abstract":null,"authors":"Gregan, J.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Biotechnol","volume":"23","issue":"1","page":"18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16990141","title":"A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.","abstract":"We present rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. Rna22 does not rely upon cross-species conservation, is resilient to noise, and, unlike previous methods, it first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA. Computationally, we show that rna22 identifies most of the currently known heteroduplexes. Experimentally, with luciferase assays, we demonstrate average repressions of 30% or more for 168 of 226 tested targets. The analysis suggests that some microRNAs may have as many as a few thousand targets, and that between 74% and 92% of the gene transcripts in four model genomes are likely under microRNA control through their untranslated and amino acid coding regions. We also extended the method's key idea to a low-error microRNA-precursor-discovery scheme; our studies suggest that the number of microRNA precursors in mammalian genomes likely ranges in the tens of thousands.","authors":"Miranda, KC., Huynh, T., Tay, Y., Ang, YS., Tam, WL., Thomson, AM., Lim, B., Rigoutsos, I.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell","volume":"126","issue":"6","page":"1203-17","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2006-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15056358","title":"Conservation of DNA methylation in dipteran insects.","abstract":"DNA methylation is a central mechanism of epigenetic regulation. Whereas vertebrate DNA methylation requires at least four different DNA methyltransferases, Drosophila melanogaster only utilizes a single, Dnmt2-like enzyme. This profound difference has raised the question of the evolutionary significance of the Drosophila methylation system. We have now identified Dnmt2-like open reading frames in the genome sequences of Drosophila pseudoobscura and Anopheles gambiae. These genes represent the only candidate DNA methyltransferases in their respective genomes. Consistent with a catalytic activity of Dnmt2 proteins, we could also demonstrate low but significant levels of DNA methylation in genomic DNA from these species. Lastly, we were also able to detect highly conserved Dnmt2-like open reading frames and concomitant DNA methylation in several additional Drosophila species, which suggests that Dnmt2-mediated DNA methylation has been conserved over a considerable evolutionary distance.","authors":"Marhold, J., Rothe, N., Pauli, A., Mund, C., Kuehle, K., Brueckner, B., Lyko, F.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Insect Mol Biol","volume":"13","issue":"2","page":"117-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"80","title":"The binding of organic phosphates to human methaemoglobin A. Perturbation of the polymerization of proteins by effectors.","abstract":"Theory is presented relating to the binding of an effector to two states of a protein acceptor coexisting in equilibrium. The problem is treated in terms of the four possible cases which specify relations between numbers of binding sites and intrinsic binding constants relevant to the acceptor states. It is shown that a distinction between these cases may be possible on the basis of the form of a plot of unbound effector concentration versus the constituent equilibrium coefficient which may be calculated from the sedimentation coefficient of the protein constituent. Particularly noteworthy in this respect is the finding that a turning point may exist in this plot for defined conditions with systems in which binding sites are not conserved (and binding affinities are altered) on polymer formation. The latter type of system is exemplified by studies on methaemoglobin A in 0.25 M sodium acetate, pH 5.4. In the absence of added organic phosphate effectors, a dimer-tetramer equilibrium operates governed by an association constant of 4.15 +\/- 0.06 X 10(3) 1\/mol, determined from sedimentation equilibrium results. Correlation of sedimentation velocity and equilibrium results shows that addition of adenosine 5'-triphosphate (ATP) results in its binding to one site on each of the dimeric (alpha beta) and tetrameric (alpha beta)2 species with intrinsic binding constants 1.03-10(3)-1.20-10(3) and 1.1-10(4)-2.1-10(4) 1\/mol, respectively. It is also shown that 2,3-diphosphoglycerate perturbs the dimer-tetramer equilibrium in a similar way to ATP.","authors":"Baghurst, PA., Nichol, LW.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"1","page":"168-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"76","title":"Multiple forms of casein kinase from rabbit erythrocytes.","abstract":"Two rabbit erythrocyte casein kinases, GTP:casein kinase I and GTP:casein kinase II, have been purified 29 000- and 47 000-fold, respectively. Studies employing sucrose density gradient centrifugation indicate that kinase I has a molecular weight of about 9.5 - 10(5) (25 S) and kinase II about 1.4 - 10(6) (32 S). These enzymes can utilize either ATP or GTP as the phosphoryl donor. Among various protein substrates examined, these kinases catalyze the phosphorylation of casein greater than 50% dephosphorylated phosvitin congruent to 50% dephosphorylated casein greater than phosvitin. Histones, protamine and bovine serum albumin are poor phosphoryl acceptors. Kinetic data indicate that both enzymes are inhibited by high casein substrate concentrations which may be partially relieved by NaCl. Both phosphotransferases require Mg(2+) for activity and are optimally active at pH 9.0. The enzymes have apparent Km values of 2.5 - 10(-5) M for GTP, 2 - 10(-5) M for ATP, and 0.4--0.6 mg\/ml for casein. The incorporation of the terminal phosphate of GTP into casein as catalyzed by these enzymes is inhibited to varying degrees by ATP, ITP, ADP, and GDP but not by UTP, CTP, GMP, adenosine 3':5'-cyclic monophosphate, and guanosine 3':5'-cyclic monophosphate. In addition, NaF and 2,3-diphosphoglyceric acid are also found to inhibit the activity of both kinases. The effect of 2,3-diphosphoglycerate is interesting and suggests that this metabolite may regulate the activity of the casein kinases in the red blood cells.","authors":"Kumar, R., Tao, M.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"87-98","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19325869","title":"Accurate prediction of peptide binding sites on protein surfaces.","abstract":"Many important protein-protein interactions are mediated by the binding of a short peptide stretch in one protein to a large globular segment in another. Recent efforts have provided hundreds of examples of new peptides binding to proteins for which a three-dimensional structure is available (either known experimentally or readily modeled) but where no structure of the protein-peptide complex is known. To address this gap, we present an approach that can accurately predict peptide binding sites on protein surfaces. For peptides known to bind a particular protein, the method predicts binding sites with great accuracy, and the specificity of the approach means that it can also be used to predict whether or not a putative or predicted peptide partner will bind. We used known protein-peptide complexes to derive preferences, in the form of spatial position specific scoring matrices, which describe the binding-site environment in globular proteins for each type of amino acid in bound peptides. We then scan the surface of a putative binding protein for sites for each of the amino acids present in a peptide partner and search for combinations of high-scoring amino acid sites that satisfy constraints deduced from the peptide sequence. The method performed well in a benchmark and largely agreed with experimental data mapping binding sites for several recently discovered interactions mediated by peptides, including RG-rich proteins with SMN domains, Epstein-Barr virus LMP1 with TRADD domains, DBC1 with Sir2, and the Ago hook with Argonaute PIWI domain. The method, and associated statistics, is an excellent tool for predicting and studying binding sites for newly discovered peptides mediating critical events in biology.","authors":"Petsalaki, E., Stark, A., Garc\u00eda-Urdiales, E., Russell, RB.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS Comput Biol","volume":"5","issue":"3","page":"e1000335","pdf":null,"JrId":"32534","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24348275","title":"A domesticated PiggyBac transposase interacts with heterochromatin and catalyzes reproducible DNA elimination in Tetrahymena.","abstract":"The somatic genome of the ciliated protist Tetrahymena undergoes DNA elimination of defined sequences called internal eliminated sequences (IESs), which account for ~30% of the germline genome. During DNA elimination, IES regions are heterochromatinized and assembled into heterochromatin bodies in the developing somatic nucleus. The domesticated piggyBac transposase Tpb2p is essential for the formation of heterochromatin bodies and DNA elimination. In this study, we demonstrate that the activities of Tpb2p involved in forming heterochromatin bodies and executing DNA elimination are genetically separable. The cysteine-rich domain of Tpb2p, which interacts with the heterochromatin-specific histone modifications, is necessary for both heterochromatin body formation and DNA elimination, whereas the endonuclease activity of Tpb2p is only necessary for DNA elimination. Furthermore, we demonstrate that the endonuclease activity of Tpb2p in vitro and the endonuclease activity that executes DNA elimination in vivo have similar substrate sequence preferences. These results strongly indicate that Tpb2p is the endonuclease that directly catalyzes the excision of IESs and that the boundaries of IESs are at least partially determined by the combination of Tpb2p-heterochromatin interaction and relaxed sequence preference of the endonuclease activity of Tpb2p.","authors":"Vogt, A., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"PLoS Genet","volume":"9","issue":"12","page":"e1004032","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23580138","title":"Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant.","abstract":"The first centromeric protein identified in any species was CENP-A, a divergent member of the histone H3 family that was recognised by autoantibodies from patients with scleroderma-spectrum disease. It has recently been suggested to rename this protein CenH3. Here, we argue that the original name should be maintained both because it is the basis of a long established nomenclature for centromere proteins and because it avoids confusion due to the presence of canonical histone H3 at centromeres.","authors":"Earnshaw, WC., Allshire, RC., Black, BE., Bloom, K., Brinkley, BR., Brown, W., Cheeseman, IM., Choo, KH., Copenhaver, GP., Deluca, JG., Desai, A., Diekmann, S., Erhardt, S., Fitzgerald-Hayes, M., Foltz, D., Fukagawa, T., Gassmann, R., Gerlich, DW., Glover, DM., Gorbsky, GJ., Harrison, SC., Heun, P., Hirota, T., Jansen, LE., Karpen, G., Kops, GJ., Lampson, MA., Lens, SM., Losada, A., Luger, K., Maiato, H., Maddox, PS., Margolis, RL., Masumoto, H., McAinsh, AD., Mellone, BG., Meraldi, P., Musacchio, A., Oegema, K., O'Neill, RJ., Salmon, ED., Scott, KC., Straight, AF., Stukenberg, PT., Sullivan, BA., Sullivan, KF., Sunkel, CE., Swedlow, JR., Walczak, CE., Warburton, PE., Westermann, S., Willard, HF., Wordeman, L., Yanagida, M., Yen, TJ., Yoda, K., Cleveland, DW.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Chromosome Res","volume":"21","issue":"2","page":"101-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20133844","title":"Protein interactions and ligand binding: from protein subfamilies to functional specificity.","abstract":"The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as \"specificity determining positions\" (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.","authors":"Rausell, A., Juan, D., Pazos, F., Valencia, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc Natl Acad Sci U S A","volume":"107","issue":"5","page":"1995-2000","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18362168","title":"p23\/Sba1p protects against Hsp90 inhibitors independently of its intrinsic chaperone activity.","abstract":"The molecular chaperone Hsp90 assists a subset of cellular proteins and is essential in eukaryotes. A cohort of cochaperones contributes to and regulates the multicomponent Hsp90 machine. Unlike the biochemical activities of the cochaperone p23, its in vivo functions and the structure-function relationship remain poorly understood, even in the genetically tractable model organism Saccharomyces cerevisiae. The SBA1 gene that encodes the p23 ortholog in this species is not an essential gene. We found that in the absence of p23\/Sba1p, yeast and mammalian cells are hypersensitive to Hsp90 inhibitors. This protective function of Sba1p depends on its abilities to bind Hsp90 and to block the Hsp90 ATPase and inhibitor binding. In contrast, the protective function of Sba1p does not require the Hsp90-independent molecular chaperone activity of Sba1p. The structure-function analysis suggests that Sba1p undergoes considerable structural rearrangements upon binding Hsp90 and that the large size of the p23\/Sba1p-Hsp90 interaction surface facilitates maintenance of high affinity despite sequence divergence during evolution. The large interface may also contribute to preserving a protective function in an environment in which Hsp90 inhibitory compounds can be produced by various microorganisms.","authors":"Forafonov, F., Toogun, OA., Grad, I., Suslova, E., Freeman, BC., Picard, D.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Mol Cell Biol","volume":"28","issue":"10","page":"3446-56","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34225319","title":"Five-Year Longitudinal Cohort Study Determines the Critical Intervals for Periodic Audiometric Testing Based on 5070 Tests of Metallurgical Workers Exposed and Nonexposed to Noise.","abstract":"on Status=\"Publisher\" Owner=\"NLM\"><PMID Version=\"1\">34225319<\/PMID><DateRevised><Year>2021<\/Year><Month>07<\/Month><Day>05<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1538-4667<\/ISSN><JournalIssue CitedMedium=\"Internet\"><PubDate><Year>2021<\/Year><Month>Jul<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Ear and hearing<\/Title><ISOAbbreviation>Ear Hear<\/ISOAbbreviation><\/Journal><ArticleTitle>Five-Year Longitudinal Cohort Study Determines the Critical Intervals for Periodic Audiometric Testing Based on 5070 Tests of Metallurgical Workers Exposed and Nonexposed to Noise.<\/ArticleTitle><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1097\/AUD.0000000000001077<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\" NlmCategory=\"OBJECTIVE\">To compare the progression of 3-, 4-, and 6-kHz thresholds (pure-tone average) over 5 years and determine the most critical period for occupational risk among workers exposed and nonexposed to noise.","authors":"Silva, VAR., Guimar\u00e3es, AC., Lavinsky, J., Pauna, HF., Duarte, ASM., Castilho, AM., Chone, CT., Crespo, AN.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Ear Hear","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33744833","title":"Cephalogram synthesis and landmark detection in dental cone-beam CT systems.","abstract":"Due to the lack of a standardized 3D cephalometric analysis methodology, 2D cephalograms synthesized from 3D cone-beam computed tomography (CBCT) volumes are widely used for cephalometric analysis in dental CBCT systems. However, compared with conventional X-ray film based cephalograms, such synthetic cephalograms lack image contrast and resolution, which impairs cephalometric landmark identification. In addition, the increased radiation dose applied to acquire the scan for 3D reconstruction causes potential health risks. In this work, we propose a sigmoid-based intensity transform that uses the nonlinear optical property of X-ray films to increase image contrast of synthetic cephalograms from 3D volumes. To improve image resolution, super resolution deep learning techniques are investigated. For low dose purpose, the pixel-to-pixel generative adversarial network (pix2pixGAN) is proposed for 2D cephalogram synthesis directly from two cone-beam projections. For landmark detection in the synthetic cephalograms, an efficient automatic landmark detection method using the combination of LeNet-5 and ResNet50 is proposed. Our experiments demonstrate the efficacy of pix2pixGAN in 2D cephalogram synthesis, achieving an average peak signal-to-noise ratio (PSNR) value of 33.8 with reference to the cephalograms synthesized from 3D CBCT volumes. Pix2pixGAN also achieves the best performance in super resolution, achieving an average PSNR value of 32.5 without the introduction of checkerboard or jagging artifacts. Our proposed automatic landmark detection method achieves 86.7% successful detection rate in the 2\u00a0mm clinical acceptable range on the ISBI Test1 data, which is comparable to the state-of-the-art methods. The method trained on conventional cephalograms can be directly applied to landmark detection in the synthetic cephalograms, achieving 93.0% and 80.7% successful detection rate in 4\u00a0mm precision range for synthetic cephalograms from 3D volumes and 2D projections, respectively.","authors":"Huang, Y., Fan, F., Syben, C., Roser, P., Mill, L., Maier, A.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Med Image Anal","volume":"70","issue":"","page":"102028","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25805138","title":"Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified.","abstract":"Huang et al. (2013) recently reported that chromatin immunoprecipitation sequencing (ChIP-seq) reveals the genome-wide sites of occupancy by Piwi, a piRNA-guided Argonaute protein central to transposon silencing in Drosophila. Their study also reported that loss of Piwi causes widespread rewiring of transcriptional patterns, as evidenced by changes in RNA polymerase II occupancy across the genome. Here we reanalyze their data and report that the underlying deep-sequencing dataset does not support the authors' genome-wide conclusions.","authors":"Marinov, GK., Wang, J., Handler, D., Wold, BJ., Weng, Z., Hannon, GJ., Aravin, AA., Zamore, PD., Brennecke, J., Toth, KF.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Dev Cell","volume":"32","issue":"6","page":"765-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17495533","title":"The crystal structure of human cyclin B.","abstract":"Cyclin B is the key regulatory protein controlling mitosis in all eukaryotes, where it binds cyclin-dependent kinase, cdk1, forming a complex which initiates the mitotic program through phosphorylation of select proteins. Cyclin B regulates the activation, subcellular localization, and substrate specificity of cdk1, and destruction of cyclin B is necessary for mitotic exit. Overexpression of human cyclin B1 has been found in numerous cancers and has been associated with tumor aggressiveness. Here we report the crystal structure of human cyclin B1 to 2.9 A. Comparison of the structure with cyclin A and cyclin E reveals remarkably similar N-terminal cyclin box motifs but significant differences among the C-terminal cyclin box lobes. Divergence in sequence gives rise to unique interaction surfaces at the proposed cyclin B\/cdk1 interface as well as the 'RxL' motif substrate binding site on cyclin B. Examination of the structure provides insight into the molecular basis for differential affinities of protein based cyclin\/cdk inhibitors such as p27, substrate recognition, and cdk interaction.","authors":"Petri, ET., Errico, A., Escobedo, L., Hunt, T., Basavappa, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell Cycle","volume":"6","issue":"11","page":"1342-9","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23632858","title":"Life(span) in balance: oxygen fuels a sophisticated neural network for lifespan homeostasis in C. elegans.","abstract":null,"authors":"Skora, S., Zimmer, M.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"EMBO J","volume":"32","issue":"11","page":"1499-501","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16103226","title":"An ECT2-centralspindlin complex regulates the localization and function of RhoA.","abstract":"In anaphase, the spindle dictates the site of contractile ring assembly. Assembly and ingression of the contractile ring involves activation of myosin-II and actin polymerization, which are triggered by the GTPase RhoA. In many cells, the central spindle affects division plane positioning via unknown molecular mechanisms. Here, we dissect furrow formation in human cells and show that the RhoGEF ECT2 is required for cortical localization of RhoA and contractile ring assembly. ECT2 concentrates on the central spindle by binding to centralspindlin. Depletion of the centralspindlin component MKLP1 prevents central spindle localization of ECT2; however, RhoA, F-actin, and myosin still accumulate on the equatorial cell cortex. Depletion of the other centralspindlin component, CYK-4\/MgcRacGAP, prevents cortical accumulation of RhoA, F-actin, and myosin. CYK-4 and ECT2 interact, and this interaction is cell cycle regulated via ECT2 phosphorylation. Thus, central spindle localization of ECT2 assists division plane positioning and the CYK-4 subunit of centralspindlin acts upstream of RhoA to promote furrow assembly.","authors":"Y\u00fcce, O., Piekny, A., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Cell Biol","volume":"170","issue":"4","page":"571-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29451854","title":"Tracing Stem Cell Division in Adult Neurogenesis.","abstract":"Neural stem cells in the ventricular-subventricular zone of the adult brain continuously generate differentiated neurons without depleting the stem cell pool. In this issue of Cell Stem Cell, Obernier et\u00a0al. (2018) present the surprising finding that this occurs through mostly symmetric divisions that either generate two differentiating or two self-renewing daughter cells.","authors":"Corsini, NS., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell Stem Cell","volume":"22","issue":"2","page":"143-145","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"162","title":"Improved high-resolution high-voltage paper electrophoresis system for use in screening for aminoacidopathies.","abstract":"High-voltage paper electrophoresis of small samples of serum and urine at pH 6.0 resolves basic and acidic amino acids and separates them from the neutral amino acids. For separation and identification of the neutral amino acids, the appropriate area of the electrophoretogram is cut out, sewn onto a second sheet of paper, and rerun at pH 1.9. By this method, amino acids are rapidly resolved. It is suited for use with special procedures such as oxidation of biological fluid with performic acid and specific staining for confirmation of amino acid identification.","authors":"Spiekerman, AM., Hetherly, ME., Hall, FF.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Chem","volume":"21","issue":"13","page":"1981-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15777618","title":"MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants.","abstract":"MIKC-type proteins represent a class of MADS-domain transcription factors and are defined by a unique domain structure: in addition to the highly conserved DNA-binding MADS-domain, they have three other domains ('I', 'K' and 'C'), with the keratin-like K-domain being the most highly conserved and characteristic one. The number and functional diversity of MIKC-type proteins increased considerably during land plant evolution, culminating in higher flowering plants, where they dominate the control of reproductive development from early to late stages. We wonder how one special class of proteins became important in the control of essentially all stages of a morphogenetic process. All MADS-domain proteins appear to bind to DNA as homo- or heterodimers and may function as part of ternary transcription factor complexes involving non-MADS-domain proteins. Only MIKC-type proteins, however, generate complex intrafamily interaction networks. These are based on the special potential of MIKC-type proteins to form complexes involving more than two homologous proteins constituting transcriptional regulators. We speculate that the potential to form heteromultimers of homologous proteins was achieved by the acquisition of the K-domain during evolution. There is emerging evidence that organismal complexity arises from progressively more elaborate regulation of gene expression. We hypothesize that combinatorial multimer formation of MIKC-type MADS-domain proteins facilitated an unusually efficient and rapid functional diversification based on gene duplication, sequence divergence and fixation. This 'networking' may have enabled a more sophisticated transcriptional control of target genes which was recruited for controlling increasingly complex and diverse developmental pathways during the rapid origin and diversification of plant reproductive structures. Therefore, MIKC-type proteins may owe their evolutionary 'success' and present-day developmental importance in part to their modular domain structure. Investigating the evolution of MIKC-type genes may thus help to better understand origin and diversification of gene regulatory networks.","authors":"Kaufmann, K., Melzer, R., Theissen, G.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Gene","volume":"347","issue":"2","page":"183-98","pdf":null,"JrId":"3886","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"161","title":"Rapid kinetic measurement of lactate in plasma with a centrifugal analyzer.","abstract":"In this method, blood is collected in ammonium heparinized microhematocrit tubes and lactate is directly determined in the plasma, separated within 15 min from the erythrocytes. Lactate is assayed by mixing 10 mul of sample with NAD+ and lactate dehydrogenase in tris(hydroxymethyl)aminomethane hydrazine buffer. The rate of increase in absorbance of the NADH formed, measured at 340 nm, is proportional to lactate concentration. The assay is complete in 4 min and absorbance is linearly related to concentration from 0.625 to 15 mmol\/liter. Analytical recoveries of lactate added to plasma averaged 104% (range, 91-116%). Results compared well for plasma samples analyzed by this method with the CentrifiChem and the Du Pont aca.","authors":"Pesce, MA., Bodourian, SH., Nicholson, JF.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Chem","volume":"21","issue":"13","page":"1932-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"160","title":"Fluorometric assay for N-acetylprocainamide.","abstract":"We describe a simple, rapid fluorometric assay for separate quantitative analysis of procainamide and N-acetylprocainamide in mixtures. The effective lenear range (fluorescence vs. concentration) in serum is 0.1 to 10.0 mg\/liter, regardless of the ratio (by weight) of the two drugs from 1:10 to 10:1. Analytical recoveries by the extraction method used were 100.0 +\/- 3.0% and 98.0 +\/- 4.0%, respectively. For determination of either compound, the maximum coefficient of variation was 10%.","authors":"Matusik, E., Gibson, TP.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Chem","volume":"21","issue":"13","page":"1899-902","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33663974","title":"Is it necessary to perform occupational audiometric testing at 6-months of employment?","abstract":"on Status=\"Publisher\" Owner=\"NLM\"><PMID Version=\"1\">33663974<\/PMID><DateRevised><Year>2021<\/Year><Month>03<\/Month><Day>05<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1808-8686<\/ISSN><JournalIssue CitedMedium=\"Internet\"><PubDate><Year>2021<\/Year><Month>Jan<\/Month><Day>19<\/Day><\/PubDate><\/JournalIssue><Title>Brazilian journal of otorhinolaryngology<\/Title><ISOAbbreviation>Braz J Otorhinolaryngol<\/ISOAbbreviation><\/Journal><ArticleTitle>Is it necessary to perform occupational audiometric testing at 6-months of employment?<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S1808-8694(21)00003-3<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.bjorl.2020.12.008<\/ELocationID><Abstract><AbstractText Label=\"INTRODUCTION\" NlmCategory=\"BACKGROUND\">Current Brazilian legislation requires that all workers exposed to noise are to be given an audiogram upon hiring, after 6 months of employment (first periodic test), and annually after the first periodic test. In other countries, the regulations of hearing conservation programs do not include the requirement for audiometric testing at 6 months of employment, but only annually. There is no evidence that the periodicity adopted by Brazilian legislation is the most appropriate.","authors":"Silva, VARD., Guimar\u00e3es, AC., Duarte, ASM., Lavinsky, J., Castilho, AM., Chone, CT., Crespo, AN.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Braz J Otorhinolaryngol","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15210992","title":"Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice.","abstract":"Investigation of sequence variation in common inbred mouse strains has revealed a segmented pattern in which regions of high and low variant density are intermixed. Furthermore, it has been suggested that allelic strain distribution patterns also occur in well defined blocks and consequently could be used to map quantitative trait loci (QTL) in comparisons between inbred strains. We report a detailed analysis of polymorphism distribution in multiple inbred mouse strains over a 4.8-megabase region containing a QTL influencing anxiety. Our analysis indicates that it is only partly true that the genomes of inbred strains exist as a patchwork of segments of sequence identity and difference. We show that the definition of haplotype blocks is not robust and that methods for QTL mapping may fail if they assume a simple block-like structure.","authors":"Yalcin, B., Fullerton, J., Miller, S., Keays, DA., Brady, S., Bhomra, A., Jefferson, A., Volpi, E., Copley, RR., Flint, J., Mott, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Proc Natl Acad Sci U S A","volume":"101","issue":"26","page":"9734-9","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15201222","title":"FGF signaling is required for initiation of feather placode development.","abstract":"Morphogenesis of hairs and feathers is initiated by an as yet unknown dermal signal that induces placode formation in the overlying ectoderm. To determine whether FGF signals are required for this process we over-expressed soluble versions of FGFR1 or FGFR2 in the skin of chicken embryos. This produced a complete failure of feather formation prior to any morphological or molecular signs of placode development. We further show that Fgf10 is expressed in the dermis of nascent feather primordia, and that anti-FGF10 antibodies block feather placode development in skin explants. In addition we show that FGF10 can induce expression of positive and negative regulators of feather development and can induce its own expression under conditions of low BMP signaling. Together these results demonstrate that FGF signaling is required for the initiation of feather placode development and implicate FGF10 as an early dermal signal involved in this process.","authors":"Mandler, M., Neub\u00fcser, A.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Development","volume":"131","issue":"14","page":"3333-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"169","title":"Some pharmacologic aspects of the antihistamines. A survey of current clinical applications.","abstract":"","authors":"Zepp, EA., Thomas, JA., Knotts, GR.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Pediatr (Phila)","volume":"14","issue":"12","page":"1119-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"166","title":"[Inborn error of glycolipid metabolism].","abstract":"","authors":"Suzuki, Y.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Horumon To Rinsho","volume":"23","issue":"9","page":"885-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40780179","title":"DIY innate immune sensing: Crafting fresh DNA to detect viruses.","abstract":"The innate immune receptor cGAS is geared toward detecting DNA from pathogens. In a recent Cell publication, Lahaye et al.<sup>1<\/sup> discovered that viral infection triggers de novo synthesis of self-DNA-activating cGAS.","authors":"Valeri, E., Gaidt, MM.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Mol Cell","volume":"85","issue":"15","page":"2818-2820","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-08","doi":"10.1016\/j.molcel.2025.07.009","first_author":null,"corresponding_authors":null},{"pmid":"8792607","title":"Polydactyly in the Strong's luxoid mouse is suppressed by limb deformity alleles.","abstract":"The study of limb development has provided insight into pattern formation during vertebrate embryogenesis. Genetic approaches offer powerful ways to identify the critical molecules and their pathways of action required to execute a complex morphogenetic program. We have applied genetic analysis to the process of limb development by studying two mouse mutants, limb deformity (ld) and Strong's luxoid (lst). These mutations confer contrasting phenotypic alterations to the anteroposterior limb pattern. The six mutant ld alleles are fully recessive and result in oligosyndactyly of all four limbs. By contrast, the two mutant lst alleles result in a mirror-image polydactylous limb phenotype inherited in a semidominant fashion. Morphological and molecular analysis of embryonic limbs has shown that the ld and lst alleles affect the extent and distribution of two key signaling centers differentially: the apical ectodermal ridge and the zone of polarizing activity. Molecular characterization of the ld gene has defined a new family of evolutionarily conserved proteins termed the formins. The underlying molecular defect in the lst mutation has not been identified; however, both loci are tightly linked on mouse chromosome 2, suggesting the possibility that they may be allelic. In this study, we have used genetic analysis to examine the epistatic and allelic relationships of ld and lst. We observed that in + ld\/lst + double heterozygotes, a single mutant ld allele is able to suppress the semi-dominant polydactylous lst limb phenotype. By segregating the lst and ld loci in a backcross, we observed that these loci recombine and are separated by a genetic distance of approximately 6 cM. Therefore, while our observations demonstrate a genetic interaction between ld and lst, it is probable that ld and lst are not allelic. Instead, lst and ld may be operating either in a linear or in a parallel (bypass) genetic pathway to affect the limb signaling centers.","authors":"Vogt, TF., Leder, P.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Dev Genet","volume":"19","issue":"1","page":"33-42","pdf":null,"JrId":"3018","fulltextlink":null,"preprintlink":null,"articledate":"1997-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"170","title":"Anaerobic glycolysis in normal human erythrocytes incubated in vitro with sodium salicylate.","abstract":"1. Some effects of sodium salicylate upon anaerobic glycolysis have been studied in normal human erythrocytes incubated for up to 6 h at 37 degrees C in autologous sera. 2. Both glucose consumption and lactate production were stimulated by concentrations of salicylate up to 60 mmol\/l but at the highest concentration used (90 mmol\/l) an initial stimulus was followed by inhibition of glycolysis. 3. Losses occurred of adenosine 5'-triphosphate (ATP), adenosine 5'-diphosphate (ADP) and adenosine 5'-phosphate(AMP)at higher concentrations of salicylate and there was a concomitant increase of inorganic phosphate. 4. Other phosphate esters underwent concentration changes at higher concentrations of salicylate that reflected inadequate concentrations of ATP for glycolysis. 5. The rates of sodium efflux from, and potassium influx into, erythrocytes were unaffected by the presence of salicylate at concentrations sufficient to stimulate glycolysis.","authors":"Worathumrong, N., Grimes, AJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Clin Sci Mol Med","volume":"49","issue":"5","page":"375-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1355767","title":"Dexamethasone selectively regulates the activity of enzymatic markers of cerebral endothelial cell lines.","abstract":"Two endothelial cell lines were derived from grafts of the central nervous system using retrovirus mediated gene transfer to introduce the polyoma middle-T oncogene into fetal rat brain endothelial cells and transplantation of these cells into adult rat brain. In this report, we further characterize these cells and the effect of dexamethasone on the expression of specific enzymatic markers. These cells take up acetylated low density lipoprotein, leucine, and glucose, and express Factor VIII-related antigen, angiotensin converting enzyme, alkaline phosphatase, gamma-glutamyltranspeptidase, and as yet undescribed aminopeptidase A and B-like enzymes. When grown on semi-permeable membranes, these transformed cells do not spontaneously retain small hydrophilic molecules. In culture, one of the lines (EC 193) forms a confluent monolayer of spindle-shaped cells homogenously expressing gamma-glutamyltranspeptidase at a level comparable to primary cells. The other cell line (EC 219) grows as clusters of elongated cells, and gamma-glutamyltranspeptidase activity is expressed mainly in cells forming the clusters. This clustered pattern changes to a confluent one after culture on type-I collagen. Dexamethasone increases angiotensin-converting enzyme activity, and decreases the expression of gamma-glutamyltranspeptidase and aminopeptidase A, whereas the aminopeptidase B activity is little modified. Inhibition of aminopeptidase A activity by amastatin, potentiates angiotensin II effects on DNA synthesis. These results indicate that retrovirally transformed brain endothelial cells are a useful model for studying the blood-brain barrier in vitro and that dexamethasone, an agent with the potential to reduce brain edema, directly affects some blood-brain barrier properties in these endothelial cell lines.","authors":"Juillerat-Jeanneret, L., Aguzzi, A., Wiestler, OD., Darekar, P., Janzer, RC.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"In Vitro Cell Dev Biol","volume":"28A","issue":"7-8","page":"537-43","pdf":null,"JrId":"4515","fulltextlink":null,"preprintlink":null,"articledate":"1992-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15081122","title":"The novel mouse microphthalmia mutations Mitfmi-enu5 and Mitfmi-bcc2 produce dominant negative Mitf proteins.","abstract":"Mutations in the microphthalmia-associated transcription factor (Mitf) gene affect the development of different cell types, including melanocytes, osteoclasts, and retinal pigmented epithelial cells of the eye. Many different mutations at the locus are known and since they affect the phenotype to different extents they form an allelic series. The Mitf protein is a member of the Mitf-Tfe subfamily of basic helix-loop-helix-leucine zipper (bHLH-Zip) transcription factors and binds the 6-bp canonical CAC\/TGTG sequence (E box) as either a homodimer or a heterodimer with related proteins. The many Mitf mutations have provided important insights into the in vivo behavior of a bHLH-Zip protein. Here we describe the phenotype of two new semidominant Mitf mutations recovered in recent mutagenic screens, Mitf(mi-enu5) and Mitf(mi-bcc2); determine the molecular lesions involved; and show that the mutant proteins act in a dominant negative fashion in vitro. The novel mutations are phenotypically distinct from previously known Mitf mutations.","authors":"Hansdottir, AG., P\u00e1lsd\u00f3ttir, K., Favor, J., Neuh\u00e4user-Klaus, A., Fuchs, H., de Angelis, MH., Steingr\u00edmsson, E.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genomics","volume":"83","issue":"5","page":"932-5","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17629745","title":"Neuronal migration: unraveling the molecular pathway with humans, mice, and a fungus.","abstract":"This review highlights the utility of comparative genetics in understanding the molecular mechanisms that underlie neuronal migration. It is apparent from studies in humans, mice, and a fungus that nuclear migration is a key component of neuronal migration and that both are dependent on a dynamic microtubule network. In vertebrates regulation of this network involves a complex pathway that is dependent on extracellular guidance cues, membrane-bound receptors, intracellular signaling molecules, proteins associated with microtubules, and the components of microtubules themselves.","authors":"Keays, DA.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mamm Genome","volume":"18","issue":"6-7","page":"425-30","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15141162","title":"Asymmetric distribution of the apical plasma membrane during neurogenic divisions of mammalian neuroepithelial cells.","abstract":"At the onset of neurogenesis in the mammalian central nervous system, neuroepithelial cells switch from symmetric, proliferative to asymmetric, neurogenic divisions. In analogy to the asymmetric division of Drosophila neuroblasts, this switch of mammalian neuroepithelial cells is thought to involve a change in cleavage plane orientation from perpendicular (vertical cleavage) to parallel (horizontal cleavage) relative to the apical surface of the neuroepithelium. Here, we report, using TIS21-GFP knock-in mouse embryos to identify neurogenic neuroepithelial cells, that at the onset as well as advanced stages of neurogenesis the vast majority of neurogenic divisions, like proliferative divisions, show vertical cleavage planes. Remarkably, however, neurogenic divisions of neuroepithelial cells, but not proliferative ones, involve an asymmetric distribution to the daughter cells of the apical plasma membrane, which constitutes only a minute fraction (1-2%) of the entire neuroepithelial cell plasma membrane. Our results support a novel concept for the cell biological basis of asymmetric, neurogenic divisions of neuroepithelial cells in the mammalian central nervous system.","authors":"Kosodo, Y., R\u00f6per, K., Haubensak, W., Marzesco, AM., Corbeil, D., Huttner, WB.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"EMBO J","volume":"23","issue":"11","page":"2314-24","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17850624","title":"Lissencephaly and LIS1: insights into the molecular mechanisms of neuronal migration and development.","abstract":"Lissencephaly is a severe human neuronal migration defect characterized by a smooth cerebral surface, mental retardation and seizures. LIS1 was first gene cloned in an organism important for neuronal migration, as it was deleted or mutated in patients with lissencephaly in a heterozygous fashion. Studies in model organisms, particularly Aspergillus nidulans, as well as those in the mouse, have uncovered an evolutionarily conserved pathway that involves LIS1 and cytoplasmic dynein. This pathway codes for proteins in a complex with cytoplasmic dynein and positively regulates its conserved function in nuclear migration. This complex appears to be important for proliferation and neuronal survival as well as neuronal migration. One of the components of this complex, NDEL1, is a phosphoprotein that is a substrate for CDK5 (or CDK2 in fibroblasts) and Aurora-A, two mitotic kinases. CDK5-phosphorylated NDEL1 binds to 14-3-3epsilon, which protects it from phosphatase attack. Interestingly, 14-3-3epsilon is located 1 Mb from LIS1 and is heterozygously deleted with LIS1 in patients with a severe form of lissencephaly, Miller-Dieker syndrome. Mouse models confirm that 14-3-3epsilon plays an important role in neuronal migration, and mice that are double heterozygotes for mutations in Lis1 and 14-3-3epsilon, display more severe neuronal migration defects. The identification of LIS1 as the first lissencephaly gene, and the first gene required for neuronal migration has revealed the importance of the regulation of cytoplasmic dynein in the control of neuronal migration by modulating nuclear migration in a pathway conserved in virtually all eukaryotes.","authors":"Wynshaw-Boris, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Clin Genet","volume":"72","issue":"4","page":"296-304","pdf":null,"JrId":"3010","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-133","title":"Integrative model of Drosophila flight","abstract":null,"authors":"Dickson, W.B., Straw, A.D., Dickinson, M.H. ","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"AIAA Journal","volume":"46","issue":"9","page":"2150-2164","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15611655","title":"JNK2: a negative regulator of cellular proliferation.","abstract":"The three different c-Jun N-terminal kinases (JNKs) are activated in multiple cell types by both apoptotic and mitogenic signals, and in turn regulate the activity of transcription factors such as c-Jun. Being highly homologous and ubiquitously expressed, the JNK1 and JNK2 proteins have been thought to perform redundant functions in many physiological process. However, our data from Jnk1-\/- or Jnk2-\/- cells and mice suggest that both JNK isozymes perform distinct functions in regulating cellular proliferation via differential regulation of c-Jun, which is a critical regulator of cell-cycle progression. Absence of JNK1, the positive regulator of c-Jun, leads to decreased fibroblast proliferation. In contrast, JNK2 deficiency leads to reduced c-Jun degradation, thereby augmenting c-Jun levels and cellular proliferation. Various cell types including fibroblasts, erythroblasts and hepatocytes from Jnk2-\/- mice exhibit increased proliferation rates compared to their wild-type counterparts. These data therefore suggests that JNK2, in contrast to JNK1, is a negative regulator of cellular proliferation in multiple cell types.","authors":"Sabapathy, K., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell Cycle","volume":"3","issue":"12","page":"1520-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16518690","title":"Estimating the number of coding mutations in genotypic- and phenotypic-driven N-ethyl-N-nitrosourea (ENU) screens.","abstract":"N-ethyl-N-nitrosourea (ENU) is a widely used mutagen in genotypic and phenotypic screens aimed at elucidating gene function. The high rate at which ENU induces point mutations raises the possibility that an observed phenotype may be to the result of another unidentified linked mutation. This article presents methods for estimating the probability of additional linked coding mutations (1) in a given region of DNA using both Poisson and Bayesian models and in (2) an F(1) animal exposed to ENU that has undergone b number of backcrosses. Applying these methods to the mouse data set of Quwailid et al., we estimate that the probability that a confounding mutation is linked to a cloned mutation when the candidate region is 5 Mb is very slim (p &lt; 0.002). Where mutants are identified by genotypic methods, we show that backcrossing in the absence of marker-assisted selection is an inefficient means of eliminating linked confounding mutations.","authors":"Keays, DA., Clark, TG., Flint, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Mamm Genome","volume":"17","issue":"3","page":"230-8","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19482889","title":"Tis21 expression marks not only populations of neurogenic precursor cells but also new postmitotic neurons in adult hippocampal neurogenesis.","abstract":"During embryonic cortical development, expression of Tis21 is associated with cell cycle lengthening and neurogenic divisions of progenitor cells. We here investigated if the expression pattern of Tis21 also correlates with the generation of new neurons in the adult hippocampus. We used Tis21 knock-in mice expressing green fluorescent protein (GFP) and studied Tis21-GFP expression together with markers of adult hippocampal neurogenesis in newly generated cells. We found that Tis21-GFP 1) was absent from the radial glia-like putative stem cells (type-1 cells), 2) first appeared in transient amplifying progenitor cells (type-2 and 3 cells), 3) did not colocalize with markers of early postmitotic maturation stage, 4) was expressed again in maturing neurons, and 5) finally decreased in mature granule cells. Our data show that, in the course of adult neurogenesis, Tis21 is expressed in a phase additional to the one of the embryonic neurogenesis. This additional phase of expression might be associated with a new and different function of Tis21 than during embryonic brain development, where no Tis21 is expressed in mature neurons. We hypothesize that this function is related to the final functional integration of the newborn neurons. Tis21 can thus serve as new marker for key stages of adult neurogenesis.","authors":"Attardo, A., Fabel, K., Krebs, J., Haubensak, W., Huttner, WB., Kempermann, G.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cereb Cortex","volume":"20","issue":"2","page":"304-14","pdf":null,"JrId":"2171","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"73","title":"Radioactive labeling and location of specific thiol groups in myosin from fast, slow and cardiac muscles.","abstract":"1. Based on incorporation of radioactively labeled N-ethylmaleimide, the readily reactive thiol groups of isolated myosin (EC 3.6.1.3) from fast, slow and cardiac muscles could be classified into 3 types. All 3 myosins contain 2 thiol-1, 2 thiol-2 and a variable number of thiol-3 groups per molecule. Both thiol-1 and thiol-2 groups which are essential for functioning of the K+-stimulated ATPase, are located in the heavy chains in all 3 myosin types. 2. The variation in the incorporation pattern of N-ethylmaleimide over the 3 thiol group classes under steady-state conditions of Mg(2+) - ATP hydrolysis allowed different conformations of some reaction intermediates to be characterized. In all 3 types of myosin the hydrolytic cycle of Mg(2+) - ATP was found to be controlled by the same step at 25 degrees C. In all three cases, this rate-limiting step is changed in the same way by lowereing temperature. 3. Using the chemically determined molecular weights for myosin light chains, their stoichiometry was found on the basis of sodium dodecyl sulfate electrophoresis to be 1.2 : 2.1 : 0.8 for light chain-1: light chain-2:light chain-3 per molecule of fast myosin, 2.0 : 1.9 for light chain-1:light chain-2 per molecule of slow myosin and 1.9 : 1.9 for light chain-1:light chain-2 per molecule of cardiac myosin. This qualitative difference in light subunit composition between the fast and the two types of slow myosin is not reflected in the small variations of the characteristics exhibited by the isolated myosins, but rather seems to be connected with their respective myofibrillar ATPase activities.","authors":"Pfister, M., Schaub, MC., Watterson, JG., Knecht, M., Waser, PG.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"193-209","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34361063","title":"A Potential Role of Semaphorin 3A during Orthodontic Tooth Movement.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">34361063<\/PMID><DateCompleted><Year>2021<\/Year><Month>08<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>08<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1422-0067<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>22<\/Volume><Issue>15<\/Issue><PubDate><Year>2021<\/Year><Month>Aug<\/Month><Day>02<\/Day><\/PubDate><\/JournalIssue><Title>International journal of molecular sciences<\/Title><ISOAbbreviation>Int J Mol Sci<\/ISOAbbreviation><\/Journal><ArticleTitle>A Potential Role of Semaphorin 3A during Orthodontic Tooth Movement.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">8297<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.3390\/ijms22158297<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Induced tooth movement during orthodontic therapy requires mechano-induced bone remodeling. Besides various cytokines and growth-factors, neuronal guidance molecules gained attention for their roles in bone homeostasis and thus, potential roles during tooth movement. Several neuronal guidance molecules have been implicated in the regulation of bone remodeling. Amongst them, Semaphorin 3A is particular interesting as it concurrently induces osteoblast differentiation and disturbs osteoclast differentiation.","authors":"\u015een, S., Lux, CJ., Erber, R.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Int J Mol Sci","volume":"22","issue":"15","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14963232","title":"Neurons arise in the basal neuroepithelium of the early mammalian telencephalon: a major site of neurogenesis.","abstract":"Neurons of the mammalian CNS are thought to originate from progenitors dividing at the apical surface of the neuroepithelium. Here we use mouse embryos expressing GFP from the Tis21 locus, a gene expressed throughout the neural tube in most, if not all, neuron-generating progenitors, to specifically reveal the cell divisions that produce CNS neurons. In addition to the apical, asymmetric divisions of neuroepithelial (NE) cells that generate another NE cell and a neuron, we find, from the onset of neurogenesis, a second population of progenitors that divide in the basal region of the neuroepithelium and generate two neurons. Basal progenitors are most frequent in the telencephalon, where they outnumber the apically dividing neuron-generating NE cells. Our observations reconcile previous data on the origin and lineage of CNS neurons and show that basal, rather than apical, progenitors are the major source of the neurons of the mammalian neocortex.","authors":"Haubensak, W., Attardo, A., Denk, W., Huttner, WB.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Proc Natl Acad Sci U S A","volume":"101","issue":"9","page":"3196-201","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20940859","title":"Ultrafast widefield optical sectioning microscopy by multifocal temporal focusing.","abstract":"The need for optical sectioning in bio-imaging has amongst others led to the development of the two-photon scanning microscopy. However, this comes with some intrinsic fundamental limitations in the temporal domain as the focused spot has to be scanned mechanically in the sample plane. Hence for a large number of biological applications where imaging speed is a limiting factor, it would be significantly advantageous to generate widefield excitations with an optical sectioning comparable to the two-photon scanning microscopy. Recently by using the technique of temporal focusing it was shown that high axial resolution widefield excitation can be generated in picosecond time scales without any mechanical moving parts. However the achievable axial resolution is still well above that of a two-photon scanning microscope. Here we demonstrate a new ultrafast widefield two-photon imaging technique termed Multifocal Temporal Focusing (MUTEF) which relies on the generation of a set of diffraction limited beams produced by an Echelle grating that scan across a second tilted diffraction grating in picosecond time scale, generating a widefield excitation area with an axial resolution comparable to a two-photon scanning microscope. Using this method we have shown widefield two-photon imaging on fixed biological samples with an axial sectioning with a FWHM of ~0.85 \u03bcm.","authors":"Vaziri, A., Shank, CV.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Opt Express","volume":"18","issue":"19","page":"19645-55","pdf":null,"JrId":"29989","fulltextlink":null,"preprintlink":null,"articledate":"2011-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20639875","title":"Network mechanisms of theta related neuronal activity in hippocampal CA1 pyramidal neurons.","abstract":"Although hippocampal theta oscillations represent a prime example of temporal coding in the mammalian brain, little is known about the specific biophysical mechanisms. Intracellular recordings support a particular abstract oscillatory interference model of hippocampal theta activity, the soma-dendrite interference model. To gain insight into the cellular and circuit level mechanisms of theta activity, we implemented a similar form of interference using the actual hippocampal network in mice in vitro. We found that pairing increasing levels of phasic dendritic excitation with phasic stimulation of perisomatic projecting inhibitory interneurons induced a somatic polarization and action potential timing profile that reproduced most common features. Alterations in the temporal profile of inhibition were required to fully capture all features. These data suggest that theta-related place cell activity is generated through an interaction between a phasic dendritic excitation and a phasic perisomatic shunting inhibition delivered by interneurons, a subset of which undergo activity-dependent presynaptic modulation.","authors":"Losonczy, A., Zemelman, BV., Vaziri, A., Magee, JC.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Neurosci","volume":"13","issue":"8","page":"967-72","pdf":null,"JrId":"21092","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12734431","title":"Replication-coupled topoisomerase II templates the mitotic chromosome scaffold?","abstract":null,"authors":"Gim\u00e9nez-Abi\u00e1n, JF., Clarke, DJ.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cell Cycle","volume":"2","issue":"3","page":"230-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23830831","title":"The phosphatase PP4c controls spindle orientation to maintain proliferative symmetric divisions in the developing neocortex.","abstract":"In the developing neocortex, progenitor cells expand through symmetric division before they generate cortical neurons through multiple rounds of asymmetric cell division. Here, we show that the orientation of the mitotic spindle plays a crucial role in regulating the transition between those two division modes. We demonstrate that the protein phosphatase PP4c regulates spindle orientation in early cortical progenitor cells. Upon removing PP4c, mitotic spindles fail to orient in parallel to the neuroepithelial surface and progenitors divide with random orientation. As a result, their divisions become asymmetric and neurogenesis starts prematurely. Biochemical and genetic experiments show that PP4c acts by dephosphorylating the microtubule binding protein Ndel1, thereby enabling complex formation with Lis1 to form a functional spindle orientation complex. Our results identify a key regulator of cortical development and demonstrate that changes in the orientation\u00a0of\u00a0progenitor division are responsible for the transition between symmetric and asymmetric cell division.","authors":"Xie, Y., J\u00fcschke, C., Esk, C., Hirotsune, S., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Neuron","volume":"79","issue":"2","page":"254-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9580557","title":"BDNF-GFP containing secretory granules are localized in the vicinity of synaptic junctions of cultured cortical neurons.","abstract":"The protein family of mammalian neurotrophins, comprising nerve-growth factor (NGF), brain-derived neurotrophic factor (BDNF), neurotrophin-3 and -4\/5 (NT-3, NT-4\/5), supports the survival and the phenotype of neurons from the central as well as the peripheral nervous system (CNS, PNS). In addition, exogenous application of neurotrophins has recently been found to modulate synaptic transmission in the rodent CNS. However, to provide evidence for a role of neurotophins as endogenous fast acting modulators of synaptic transmission, the synaptic localization and secretion of neurotrophins needs to be shown. We have now constructed a fusion protein consisting of N-terminal BDNF (the most abundant neurotrophin in the rodent hippocampus and neocortex) and C-terminal green fluorescent protein (GFP) to elucidate the cellular localization of BDNF in cortical neurons. Transient expression of BDNF-GFP in COS-7 cells revealed that the cellular localization in the trans-Golgi network (TGN), the processing of precursor proteins and the secretion of mature BDNF-GFP is indistinguishable from the properties of untagged BDNF. Upon transient transfection of primary rat cortical neurons, BDNF-GFP was found in secretory granules of the regulated pathway of secretion, as indicated by colocalization with the secretory granule marker secretogranin II. BDNF-GFP vesicles were found in the neurites of transfected neurons with a pattern reminiscent of the localization of endogenous BDNF in untransfected cortical neurons. BDNF-GFP vesicles were found predominantly in the somatodendritic compartment of the neurons, whereas additional axonal localization was found less frequently. Immunocytochemical staining of synaptic terminals with synapsin I antibodies revealed that the density of BDNF-GFP vesicles is elevated in the vicinity of synaptic junctions, indicating that BDNF is localized appropriately to function as an acute modulator of synaptic transmission. These data suggest that BDNF-GFP will be a useful tool to investigate synaptic release of BDNF during physiological synaptic stimulation, and will thereby allow us to elucidate the participation of neurotrophin release in activity dependent synaptic plasticity.","authors":"Haubensak, W., Narz, F., Heumann, R., Lessmann, V.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Cell Sci","volume":"111 ( Pt 11)","issue":null,"page":"1483-93","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"1998-07-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12484932","title":"Experimental two-photon, three-dimensional entanglement for quantum communication.","abstract":"Orbital angular momentum entangled photons emitted by a down-conversion source are in higher dimensional entangled states. Here we report the experimental confirmation by demonstrating a violation of a generalized Clauser-Horne-Shimony-Holt-type Bell inequality in three dimensions by more than 18 standard deviations. Higher dimensional entangled states allow the realization of new types of quantum communication protocols. They also provide a more secure quantum cryptography scheme. Therefore our experimental results are likely to have applications in future quantum communication technology.","authors":"Vaziri, A., Weihs, G., Zeilinger, A.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Phys Rev Lett","volume":"89","issue":"24","page":"240401","pdf":null,"JrId":"21217","fulltextlink":null,"preprintlink":null,"articledate":"2003-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16712208","title":"High-order quantum resonances observed in a periodically kicked Bose-Einstein condensate.","abstract":"We have observed high-order quantum resonances in a realization of the quantum delta-kicked rotor, using Bose-condensed Na atoms subjected to a pulsed standing wave of laser light. These resonances occur for pulse intervals that are rational fractions of the Talbot time, and are characterized by ballistic momentum transfer to the atoms. The condensate's narrow momentum distribution not only permits the observation of the quantum resonances at 3\/4 and 1\/3 of the Talbot time, but also allows us to study scaling laws for the resonance width in quasimomentum and pulse interval.","authors":"Ryu, C., Andersen, MF., Vaziri, A., d'Arcy, MB., Grossman, JM., Helmerson, K., Phillips, WD.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Phys Rev Lett","volume":"96","issue":"16","page":"160403","pdf":null,"JrId":"21217","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14683274","title":"Concentration of higher dimensional entanglement: qutrits of photon orbital angular momentum.","abstract":"Enhancement of entanglement is necessary for most quantum communication protocols many of which are defined in Hilbert spaces larger than 2. In this work we present the experimental realization of entanglement concentration of orbital angular momentum entangled photons. We investigate the specific case of three dimensions and the possibility of generating different entangled states out of an initial state. The results presented here are of importance for pure states as well as for mixed states.","authors":"Vaziri, A., Pan, JW., Jennewein, T., Weihs, G., Zeilinger, A.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Phys Rev Lett","volume":"91","issue":"22","page":"227902","pdf":null,"JrId":"21217","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32643450","title":"Impact of preanalytical storage on the measurement of erythrocyte sedimentation rate using an infrared microphotometer system (TEST1).","abstract":"This study examined the influence of temperature and time on the pre-analytical stability of the erythrocyte sedimentation rate (ESR) measured on a TEST1 system. The first experiment included 102 samples stored at room temperature and the second experiment included 112 subjects and investigated refrigerated (2-8\u2009\u00b0C) storage. Our study showed a stable ESR results at room temperature (15-25\u2009\u00b0C) up to 8\u2009h (<i>p<\/i>\u2009=\u20090.512). Samples stored at 2-8\u2009\u00b0C for 24\u2009h were stable (<i>p<\/i>\u2009=\u20090.280) for 24\u2009h.","authors":"Ilardo, C., Richerd, C., Rostain, V.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Scand J Clin Lab Invest","volume":"80","issue":"6","page":"523-524","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32563857","title":"Prediction of 5-hydroxytryptamine transporter inhibitors based on machine learning.","abstract":"In patients with depression, the use of 5-HT reuptake inhibitors can improve the condition. Machine learning methods can be used in ligand-based activity prediction processes. In order to predict SERT inhibitors, the SERT inhibitor data from the ChEMBL database was screened and pre-processed. Then 4 machine learning methods (LR, SVM, RF, and KNN) and 4 molecular fingerprints (CDK, Graph, MACCS, and PubChem) were used to build 16 prediction models. The top 5 models of accuracy (Q) in the cross-validation of training set were used to build three different ensemble learning models. In the test1 set, the VOT_CLF3 model had the largest SP (0.871), Q (0.869), AUC (0.919), and MCC (0.728). In the unbalanced test2 set, VOT_CLF3 had the largest SE (0.857), SP (0.867), Q (0.865) and MCC (0.639). VOT_CLF3 was recommended for the virtual screening process of SERT inhibitors. In addition, 12 molecular structural alerts that frequently appear in SERT inhibitors were found (P &lt; 0.05), which provided important reference value for the design work of SERT inhibitors.","authors":"Kong, W., Wang, W., An, J.","publication_status":"aheadofprint","journalpubyear":"2020","journaltitle":"Comput Biol Chem","volume":"87","issue":"","page":"107303","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32504011","title":"Test1.","abstract":"","authors":"","publication_status":"aheadofprint","journalpubyear":"2019","journaltitle":"Nature","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20472826","title":"Near-isotropic 3D optical nanoscopy with photon-limited chromophores.","abstract":"Imaging approaches based on single molecule localization break the diffraction barrier of conventional fluorescence microscopy, allowing for bioimaging with nanometer resolution. It remains a challenge, however, to precisely localize photon-limited single molecules in 3D. We have developed a new localization-based imaging technique achieving almost isotropic subdiffraction resolution in 3D. A tilted mirror is used to generate a side view in addition to the front view of activated single emitters, allowing their 3D localization to be precisely determined for superresolution imaging. Because both front and side views are in focus, this method is able to efficiently collect emitted photons. The technique is simple to implement on a commercial fluorescence microscope, and especially suitable for biological samples with photon-limited chromophores such as endogenously expressed photoactivatable fluorescent proteins. Moreover, this method is relatively resistant to optical aberration, as it requires only centroid determination for localization analysis. Here we demonstrate the application of this method to 3D imaging of bacterial protein distribution and neuron dendritic morphology with subdiffraction resolution.","authors":"Tang, J., Akerboom, J., Vaziri, A., Looger, LL., Shank, CV.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc Natl Acad Sci U S A","volume":"107","issue":"22","page":"10068-73","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2010-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32154354","title":"A dataset of histograms of original and fake voice recordings (H-Voice).","abstract":"This paper presents H-Voice, a dataset of 6672 histograms of original and <i>fake<\/i> voice recordings obtained by the Imitation [1,2] and the Deep Voice [3] methods. The dataset is organized into six directories: <i>Training_fake<\/i>, <i>Training_original<\/i>, <i>Validation_fake<\/i>, <i>Validation_original<\/i>, <i>External_test1<\/i>, and <i>External_test2<\/i>. The training directories include 2088 histograms of <i>fake<\/i> voice recordings and 2020 histograms of original voice recordings. Each validation directory has 864 histograms obtained from <i>fake<\/i> voice recordings and original voice recordings. Finally, External_test1 has 760 histograms (380 from <i>fake<\/i> voice recordings obtained by the Imitation method and 380 from original voice recordings), and External_test2 has 76 histograms (72 from <i>fake<\/i> voice recordings obtained by the Deep Voice method and 4 from original voice recordings). With this dataset, the researchers can train, cross-validate and test classification models using machine learning techniques to identify <i>fake<\/i> voice recordings.","authors":"Ballesteros, DM., Rodriguez, Y., Renza, D.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Data Brief","volume":"29","issue":"","page":"105331","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-134","title":"Superpositions of the orbital angular momentum for applications in quantum experiments ","abstract":null,"authors":"Vaziri A, Weihs G., Zeilinger A.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Journal of Optics B: Quantum and Semiclassical Optics","volume":"4","issue":"2","page":"S1-S5 ","pdf":null,"JrId":null,"fulltextlink":"http:\/\/iopscience.iop.org\/1464-4266\/4\/2\/367\/","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-136","title":"Quantum coherence in ion channels: resonances, transport and verification","abstract":null,"authors":"Vaziri A., Plenio M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"New Journal of Physics","volume":"12","issue":"085001","page":"","pdf":null,"JrId":null,"fulltextlink":"http:\/\/www.vaziria.com\/pdf\/Quantum%20Resonances%20in%20ion%20channels.pdf","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-135","title":"Experimental quantum cryptography with qutrits","abstract":null,"authors":"Gr\u00f6blacher S., Jennewein T., Vaziri A., Weihs G., Zeilinger A.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"New Journal of Physics","volume":"8","issue":"75","page":"","pdf":null,"JrId":null,"fulltextlink":"http:\/\/www.vaziria.com\/pdf\/NJP%20qunit%20cryptogrphy.pdf","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15783538","title":"Experimental quantum coin tossing.","abstract":"In this Letter we present the first implementation of a quantum coin-tossing protocol. This protocol belongs to a class of \"two-party\" cryptographic problems, where the communication partners distrust each other. As with a number of such two-party protocols, the best implementation of the quantum coin tossing requires qutrits, resulting in a higher security than using qubits. In this way, we have also performed the first complete quantum communication protocol with qutrits. In our experiment the two partners succeeded to remotely toss a row of coins using photons entangled in the orbital angular momentum. We also show the experimental bounds of a possible cheater and the ways of detecting him.","authors":"Molina-Terriza, G., Vaziri, A., Ursin, R., Zeilinger, A.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Phys Rev Lett","volume":"94","issue":"4","page":"040501","pdf":null,"JrId":"21217","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"65","title":"Bile acids. XLVII. 12alpha-Hydroxylation of precursors of allo bile acids by rabbit liver microsomes.","abstract":"Rabbit liver microsomal preparations fortified with 0.1 mM NADPH effectively promote hydroxylation of [3beta-3H]- or [24-14C]allochenodeoxycholic acid or [5alpha,6alpha-3H2]5alpha-cholestane-3alpha,7alpha-diol to their respective 12alpha-hydroxyl derivatives in yields of about 25 or 65% in 60 min. Minor amounts of other products are formed from the diol. The requirements for activity of rabbit liver microsomal 12alpha-hydroxylase resemble those of rat liver microsomes. Of a number of enzyme inhibitors studied only p-chloromercuribenzoate demonstrated a marked ability to inhibit the reaction with either tritiated substrate. There was no difference in the quantity of product produced from the tritiated acid or the 14C-labeled acid. No clear sex difference was found in activity of the enzyme, nor was an appreciable difference noted in activity of the enzyme between mature and immature animals.","authors":"Ali, SS., Elliott, WH.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"409","issue":"2","page":"249-57","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17512415","title":"Snapshot: genetic mouse models of cancer.","abstract":null,"authors":"Zender, L., Zuber, J., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell","volume":"129","issue":"4","page":"838","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"61","title":"Identification of the 120 mus phase in the decay of delayed fluorescence in spinach chloroplasts and subchloroplast particles as the intrinsic back reaction. The dependence of the level of this phase on the thylakoids internal pH.","abstract":"After a 500 mus laser flash a 120 mus phase in the decay of delayed fluorescence is visible under a variety of circumstances in spinach chloroplasts and subchloroplast particles enriched in Photosystem II prepared by means of digitonin. The level of this phase is high in the case of inhibition of oxygen evolution at the donor side of Photosystem II. Comparison with the results of Babcock and Sauer (1975) Biochim. Bio-phys. Acta 376, 329-344, indicates that their EPR signal IIf which they suppose to be due to Z+, the oxidized first secondary donor of Photosystem II, is well correlated with a large amplitude of our 120 mus phase. We explain our 120 mus phase by the intrinsic back reaction of the excited reaction center in the presence of Z+, as predicted by Van Gorkom and Donze (1973) Photochem. Photobiol. 17, 333-342. The redox state of Z+ is dependent on the internal pH of the thylakoids. The results on the effect of pH in the mus region are compared with those obtained in the ms region.","authors":"Haveman, J., Lavorel, J.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"408","issue":"3","page":"269-38","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15169262","title":"Triggered qutrits for quantum communication protocols.","abstract":"A general protocol in quantum information and communication relies in the ability of producing, transmitting, and reconstructing, in general, qunits. In this Letter we show for the first time the experimental implementation of these three basic steps on a pure state in a three-dimensional space, by means of the orbital angular momentum of the photons. The reconstruction of the qutrit is performed with tomographic techniques and a maximum-likelihood estimation method. For the tomographic reconstruction we used more than 2400 different projections. In this way we also demonstrate that we can perform any transformation in the three-dimensional space.","authors":"Molina-Terriza, G., Vaziri, A., Reh\u00e1cek, J., Hradil, Z., Zeilinger, A.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Phys Rev Lett","volume":"92","issue":"16","page":"167903","pdf":null,"JrId":"21217","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20935472","title":"Laser microsurgery provides evidence for merotelic kinetochore attachments in fission yeast cells lacking Pcs1 or Clr4.","abstract":"In order to segregate chromosomes properly, the cell must prevent merotelic kinetochore attachment, an error that occurs when a single kinetochore is attached to microtubules emanating from both spindle poles. Merotelic kinetochore orientation represents a major mechanism of aneuploidy in mitotic mammalian cells and it is the primary mechanism of chromosome instability in cancer cells. Fission yeast mutants defective in putative microtubule-site clamp Pcs1\/Mde4 or Clr4\/Swi6-dependent centromeric heterochromatin display high frequencies of lagging chromosomes during anaphase. Here, we developed an assay based on laser microsurgery to show that the stretched morphology of lagging kinetochores in pcs1\u0394 and clr4\u0394 mutant cells is due to merotelic attachment. We further show that Mde4 is regulated by Cdc2 and that Cdc2 activity prevents precocious localization of Mde4 to the metaphase spindle. Finally, we show that Pcs1\/Mde4 complex shares similar features with the conserved kinetochore complex Spc24\/Spc25 suggesting that these two complexes may occupy a similar functional niche.","authors":"Rumpf, C., Cipak, L., Schleiffer, A., Pidoux, A., Mechtler, K., Toli\u0107-N\u00f8rrelykke, IM., Gregan, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell Cycle","volume":"9","issue":"19","page":"3997-4004","pdf":null,"JrId":"30098","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34294143","title":"A NOTCH1\/LSD1\/BMP2 co-regulatory network mediated by miR-137 negatively regulates osteogenesis of human adipose-derived stem cells.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Automated\" Owner=\"NLM\"><PMID Version=\"1\">34294143<\/PMID><DateCompleted><Year>2021<\/Year><Month>08<\/Month><Day>06<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>08<\/Month><Day>06<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1757-6512<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>12<\/Volume><Issue>1<\/Issue><PubDate><Year>2021<\/Year><Month>07<\/Month><Day>22<\/Day><\/PubDate><\/JournalIssue><Title>Stem cell research &amp; therapy<\/Title><ISOAbbreviation>Stem Cell Res Ther<\/ISOAbbreviation><\/Journal><ArticleTitle>A NOTCH1\/LSD1\/BMP2 co-regulatory network mediated by miR-137 negatively regulates osteogenesis of human adipose-derived stem cells.<\/ArticleTitle><Pagination><MedlinePgn>417<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13287-021-02495-3<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">MicroRNAs have been recognized as critical regulators for the osteoblastic lineage differentiation of human adipose-derived stem cells (hASCs). Previously, we have displayed that silencing of miR-137 enhances the osteoblastic differentiation potential of hASCs partly through the coordination of lysine-specific histone demethylase 1 (LSD1), bone morphogenetic protein 2 (BMP2), and mothers against decapentaplegic homolog 4 (SMAD4). However, still numerous molecules involved in the osteogenic regulation of miR-137 remain unknown. This study aimed to further elucidate the epigenetic mechanisms of miR-137 on the osteogenic differentiation of hASCs.","authors":"Fan, C., Ma, X., Wang, Y., Lv, L., Zhu, Y., Liu, H., Liu, Y.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Stem Cell Res Ther","volume":"12","issue":"1","page":"417","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15346269","title":"[Cyclosporin A-induced posterior reversible encephalopathy syndrome (PRES) in MRI].","abstract":null,"authors":"Herzog, H., Zuber, J., Stroszczynski, C.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Rofo","volume":"176","issue":"9","page":"1326-7","pdf":null,"JrId":"7048","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34265156","title":"Modeling fusion gene-associated sarcoma: Advantages for understanding sarcoma biology and pathology.","abstract":"Disease-specific gene fusions are reportedly major driver mutations in approximately 30% of bone and soft tissue sarcomas. Most fusion genes encode transcription factors or co-factors that regulate downstream target genes, altering cell growth, lineage commitment, and differentiation. Given the limitations of investigating their functions in vitro, the generation of mouse models expressing fusion genes in the appropriate cellular lineages is pivotal. Therefore, we generated a series of mouse models by introducing fusion genes into embryonic mesenchymal progenitors. This review describes mouse models of Ewing, synovial, alveolar soft part, and CIC-rearranged sarcomas. Furthermore, we describe the similarities between these models and their human counterparts. These models provide remarkable advantages to identify cells-of-origin, specific collaborators of fusion genes, angiogenesis key factors, or diagnostic biomarkers. Finally, we discuss the relationship between fusion proteins and the epigenetic background as well as the possible role of the super-enhancers.","authors":"Tanaka, M., Nakamura, T.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Pathol Int","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"58","title":"Constitution and properties of axonal membranes of crustacean nerves.","abstract":"The purification of axonal membranes of crustaceans was followed by measuring enrichment in [3H]tetrodotoxin binding capacity and in Na+, K+-ATPase activity. A characteristic of these membranes is their high content of lipids and their low content of protein as compared to other types of plasmatic membranes. The axonal membrane contains myosin-like, actin-like, tropomyosin-like, and tubulin-like proteins. It also contains Na+, K+-ATPase and acetylcholinesterase. The molecular weights of these two enzymes after solubilization are 280,000 and 270,000, respectively. The molecular weights of the catalytic subunits are 96,000 for ATPase and 71,000 for acetylcholinesterase. We confirmed the presence of a nicotine binding component in the axonal membrane of the lobster but we have been unable to find [3H]nicotine binding to crab axonal membranes. The binding to axonal membranes og of the sodium channel, has been studied in detail. The dissociation constant for the binding of [3H]tetrodotoxin to the axonal membrane receptor is 2.9 nM at pH 7.4. The concentration of the tetrodotoxin receptor in crustacean membranes is about 10 pmol\/mg of membrane protein, 7 times less than the acetylcholinesterase, 30 times less than the Na+, K+-ATPase, and 30 times less than the nicotine binding component in the lobster membrane. A reasonable estimate indicates that approximately only one peptide chain in 1000 constitutes the tetrodotoxin binding part of the sodium channel in the axonal membrane. Veratridine, which acts selectively on the resting sodium permeability, binds to the phospholipid part of the axonal membrane. [3H]Veratridine binding to membranes parallels the electrophysiological effect. Veratridine and tetrodotoxin have different receptor sites. Although tetrodotoxin can repolarize the excitable membrane of a giant axon depolarized by veratridine, veratridine does not affect the binding of [3H]tetrodotoxin to purified axonal membranes. Similarly, tetrodotoxin does not affect the binding of [3H]veratridine to axonal membranes. Scorpion neurotoxin I, a presynaptic toxin which affects both the Na+ and the K+ channels, does not interfere with the binding of [3H]tetrodotoxin or [3H]veratridine to axonal membranes. Tetrodotoxin, veratridine, and scorpion neurotoxin I, which have in common the perturbation of the normal functioning of the sodium channel, act upon three different types of receptor sites.","authors":"Balerna, M., Fosset, M., Chicheportiche, R., Romey, G., Lazdunski, M.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"25","page":"5500-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34249467","title":"DLX5 promotes osteosarcoma progression via activation of the NOTCH signaling pathway.","abstract":"The distal-less (dlx) homeobox transcription factors have been implicated roles in bone development. DLX5, in particular, was shown to play essential roles in osteoblast differentiation by targeting RUNX2, a master transcription factor for bone development. Interestingly, DLX5 has also been shown to play an oncogenic role in lung and other cancers, possibly via regulation of MYC expression. Given its dual roles in bone and cancer, this study aimed to investigate the effect of DLX5 on progression of osteosarcoma (OS), the primary bone cancer that is characterized by abnormal bone formation and osteoblast activity. Expression of DLX5 in OS cell lines was detected by quantitative real-time PCR (qRT-PCR) and western blot (WB). In vitro and in vivo assays were performed to investigate the oncogenic function of DLX5 in OS cells and xenograft models. Luciferase reporter assay was performed to determine the underlying mechanism of DLX5-mediated OS aggressiveness. The results showed that DLX5 was differentially expressed in OS cell lines, with significantly upregulated levels in HOS and MG-63 and relatively low levels in U2OS and 143B cell lines, compared with the normal bone cell line. DLX5 knockdown in HOS and MG-63 cell lines by siRNA inhibited OS cell growth and progression, and induced cell apoptosis and cell cycle changes both in vitro and in vivo. Meanwhile, DLX5 overexpression had the opposite effect on U2OS and 143B cell lines. Notably, a positive correlation between the expression patterns of NOTCH1 and DLX5 was also observed. The expression levels of NICD (NOTCH1 intracellular domain) and HES1 (classical target of NOTCH) were closely associated with DLX5 expression. Whereas knockdown of DLX5 in OS cells resulted in decreased expression of NOTCH1 and reduced cell proliferation and migration, which were rescued by overexpression of NOTCH1. We further analyzed DLX5 and NOTCH1 genes using JASPAR software and found two potential DLX5 binding sites within the <i>NOTCH1<\/i> promoter. Dual-luciferase assay demonstrated that DLX5 specifically activates the NOTCH1 promoter and controls its expression. Taken together, our results support that DLX5 plays an oncogenic role in OS development, which can at least partially, be attributed to activation of the NOTCH signaling pathway.","authors":"Zhang, X., Bian, H., Wei, W., Wang, Q., Chen, J., Hei, R., Chen, C., Wu, X., Yuan, H., Gu, J., Lu, Y., Cai, C., Zheng, Q.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Am J Cancer Res","volume":"11","issue":"6","page":"3354-3374","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21087090","title":"Physiology and pathophysiology of the RANKL\/RANK system.","abstract":"The TNF family molecule RANKL and its receptor RANK are key regulators of bone remodeling, lymph node formation, and mammary gland development during pregnancy. RANKL and RANK are also expressed in the central nervous systems (CNS). However, the functional relevance of RANKL\/RANK in the brain was entirely unknown. Recently, our group reported that the RANKL\/RANK signaling pathway has an essential role in the central regulation of body temperature via the prostaglandin axis. This review discusses novel aspects of the RANKL\/RANK system as key regulators of fever and female basal body temperature in the CNS.","authors":"Hanada, R., Hanada, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Biol Chem","volume":"391","issue":"12","page":"1365-70","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34199016","title":"Biological Mechanisms of Paeonoside in the Differentiation of Pre-Osteoblasts and the Formation of Mineralized Nodules.","abstract":"<i>Paeonia suffruticosa<\/i> is a magnificent and long-lived woody plant that has traditionally been used to treat various diseases including inflammatory, neurological, cancer, and cardiovascular diseases. In the present study, we demonstrated the biological mechanisms of paeonoside (PASI) isolated from the dried roots of <i>P. suffruticosa<\/i> in pre-osteoblasts. Herein, we found that PASI has no cytotoxic effects on pre-osteoblasts. Migration assay showed that PASI promoted wound healing and transmigration in osteoblast differentiation. PASI increased early osteoblast differentiation and mineralized nodule formation. In addition, PASI enhanced the expression of Wnt3a and bone morphogenetic protein 2 (BMP2) and activated their downstream molecules, Smad1\/5\/8 and \u03b2-catenin, leading to increases in runt-related transcription factor 2 (RUNX2) expression during osteoblast differentiation. Furthermore, PASI-mediated osteoblast differentiation was attenuated by inhibiting the BMP2 and Wnt3a pathways, which was accompanied by reduction in the expression of RUNX2 in the nucleus. Taken together, our findings provide evidence that PASI enhances osteoblast differentiation and mineralized nodules by regulating RUNX2 expression through the BMP2 and Wnt3a pathways, suggesting a potential role for PASI targeting osteoblasts to treat bone diseases including osteoporosis and periodontitis.","authors":"Park, KR., Lee, JY., Cho, M., Hong, JT., Yun, HM.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Int J Mol Sci","volume":"22","issue":"13","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12791398","title":"Dissection of signal-regulated transcriptional modules by signaling pathway interference in oncogene-transformed cells.","abstract":null,"authors":"Sch\u00e4fer, R., Tchernitsa, OI., Zuber, J., Sers, C.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Adv Enzyme Regul","volume":"43","issue":null,"page":"379-91","pdf":null,"JrId":"278","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11849205","title":"Cytoprotective function of keratinocyte growth factor in tumour therapy-induced tissue damage.","abstract":null,"authors":"Wirth, K., Mertelsmann, R.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Br J Haematol","volume":"116","issue":"3","page":"505-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19298879","title":"Optimizing the performance of tin dioxide microspheres for phosphopeptide enrichment.","abstract":"Phosphopeptide enrichment based on metal oxide affinity chromatography is one of the most powerful tools for studying protein phosphorylation on a large scale. To complement existing metal oxide sorbents, we have recently introduced tin dioxide as a promising alternative. The preparation of SnO(2) microspheres by the nanocasting technique, using silica of different morphology as a template, offers a strategy to prepare materials that vary in their particle size and their porosity. Here, we demonstrate how such stannia materials can be successfully generated and their properties fine-tuned in order to obtain an optimized phosphopeptide enrichment material. We combined data from liquid chromatography-mass spectrometry experiments and physicochemical characterization, including nitrogen physisorption and energy-dispersive X-ray spectroscopy (EDX), to explain the influence of the various experimental parameters.","authors":"Leitner, A., Sturm, M., Sm\u00e5tt, JH., J\u00e4rn, M., Lind\u00e9n, M., Mechtler, K., Lindner, W.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Anal Chim Acta","volume":"638","issue":"1","page":"51-7","pdf":null,"JrId":"520","fulltextlink":"http:\/\/www.sciencedirect.com\/science?_ob=ArticleURL&_udi=B6TF4-4VJSRY1-1&_user=4888655&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054145&_version=1&_urlVersion=0&_userid=4888655&md5=990476b869156f7726e029505d9a0724","preprintlink":null,"articledate":"2009-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27","title":"Editorial: \"Old lamps for new\".","abstract":"","authors":"Conway, CM.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Anaesth","volume":"47","issue":"8","page":"811-2","pdf":null,"JrId":"1754","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31725953","title":"Analytical validation of the iSED automated analyzer for erythrocyte sedimentation rate.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31725953<\/PMID><DateCompleted><Year>2021<\/Year><Month>02<\/Month><Day>03<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>02<\/Month><Day>03<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1751-553X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>42<\/Volume><Issue>2<\/Issue><PubDate><Year>2020<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>International journal of laboratory hematology<\/Title><ISOAbbreviation>Int J Lab Hematol<\/ISOAbbreviation><\/Journal><ArticleTitle>Analytical validation of the iSED automated analyzer for erythrocyte sedimentation rate.<\/ArticleTitle><Pagination><MedlinePgn>109-115<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/ijlh.13120<\/ELocationID><Abstract><AbstractText Label=\"INTRODUCTION\" NlmCategory=\"BACKGROUND\">iSED is an alternate automated analyzer for erythrocyte sedimentation rate (ESR) based on photometric rheology technology that estimates ESR by measuring rouleaux formation. The aim was to evaluate the analytical performance of the iSED analyzer and compare the results with the Westergren method and another alternate ESR analyzer, TEST1.","authors":"Lapi\u0107, I., Milo\u0161, M., Tosato, F., Piva, E., Zadro, R., Rogi\u0107, D., Plebani, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Int J Lab Hematol","volume":"42","issue":"2","page":"109-115","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34154572","title":"Depletion of EREG enhances the osteo\/dentinogenic differentiation ability of dental pulp stem cells via the p38 MAPK and Erk pathways in an inflammatory microenvironment.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Automated\" Owner=\"NLM\"><PMID Version=\"1\">34154572<\/PMID><DateCompleted><Year>2021<\/Year><Month>06<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>07<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1472-6831<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>21<\/Volume><Issue>1<\/Issue><PubDate><Year>2021<\/Year><Month>06<\/Month><Day>21<\/Day><\/PubDate><\/JournalIssue><Title>BMC oral health<\/Title><ISOAbbreviation>BMC Oral Health<\/ISOAbbreviation><\/Journal><ArticleTitle>Depletion of EREG enhances the osteo\/dentinogenic differentiation ability of dental pulp stem cells via the p38 MAPK and Erk pathways in an inflammatory microenvironment.<\/ArticleTitle><Pagination><MedlinePgn>314<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12903-021-01675-0<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Epiregulin (EREG) is an important component of EGF and was demonstrated to promote the osteo\/dentinogenic differentiation of stem cells from dental apical papilla (SCAPs). Whether EREG can stimulate the osteo\/dentinogenic differentiation of dental pulp stem cells (DPSCs) in inflammatory environment is not clear. The purpose of the present study is to investigate the role of EREG on the osteo\/dentinogenic differentiation ability of DPSCs in inflammatory environment.","authors":"Ran, R., Yang, H., Cao, Y., Yan, W., Jin, L., Zheng, Y.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"BMC Oral Health","volume":"21","issue":"1","page":"314","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11248250","title":"The fas locus of the phytopathogen Rhodococcus fascians affects mitosis of tobacco BY-2 cells.","abstract":"The effect of Rhodococcus fascians, the causal agent of leafy gall disease, on the mitotic behavior of synchronized tobacco Bright Yellow-2 (BY-2) cells was investigated. Incubation of aphidicolin-synchronized BY-2 cells with R. fascians cells specifically resulted in a broader mitotic index peak, an effect that was linked to an intact and expressed fas virulence locus. The obtained results pointed towards an effect of R. fascians on the prophase of mitosis. The relevance of these results to the virulence of the bacterium is discussed.","authors":"Temmerman, W., Ritsema, T., Sim\u00f3n-Mateo, C., Van Montagu, M., Mironov, V., Inz\u00e9, D., Goethals, K., Holsters, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"FEBS Lett","volume":"492","issue":"1-2","page":"127-32","pdf":null,"JrId":"3696","fulltextlink":null,"preprintlink":null,"articledate":"2001-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19718028","title":"p53 deletion impairs clearance of chromosomal-instable stem cells in aging telomere-dysfunctional mice.","abstract":"Telomere dysfunction limits the proliferative capacity of human cells and induces organismal aging by activation of p53 and p21. Although deletion of p21 elongates the lifespan of telomere-dysfunctional mice, a direct analysis of p53 in telomere-related aging has been hampered by early tumor formation in p53 knockout mice. Here we analyzed the functional consequences of conditional p53 deletion. Intestinal deletion of p53 shortened the lifespan of telomere-dysfunctional mice without inducing tumor formation. In contrast to p21 deletion, the deletion of p53 impaired the depletion of chromosomal-instable intestinal stem cells in aging telomere-dysfunctional mice. These instable stem cells contributed to epithelial regeneration leading to an accumulation of chromosomal instability, increased apoptosis, altered epithelial cell differentiation and premature intestinal failure. Together, these results provide the first experimental evidence for an organ system in which p53-dependent mechanisms prevent tissue destruction in response to telomere dysfunction by depleting genetically instable stem cells.","authors":"Begus-Nahrmann, Y., Lechel, A., Obenauf, AC., Nalapareddy, K., Peit, E., Hoffmann, E., Schlaudraff, F., Liss, B., Schirmacher, P., Kestler, H., Danenberg, E., Barker, N., Clevers, H., Speicher, MR., Rudolph, KL.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Genet","volume":"41","issue":"10","page":"1138-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21046621","title":"Proteomic analysis of endosomes from genetically modified p14\/MP1 mouse embryonic fibroblasts.","abstract":"The p14\/MP1 scaffold complex binds MEK1 and ERK1\/2 on late endosomes, thus regulating the strength, duration and intracellular location of MAPK signaling. By organelle proteomics we have compared the protein composition of endosomes purified from genetically modified p14(-\/-), p14(+\/-) and p14(rev) mouse embryonic fibroblasts. The latter ones were reconstituted retrovirally from p14(-\/-) mouse embryonic fibroblasts by reexpression of pEGFP-p14 at equimolar ratios with its physiological binding partner MP1, as shown here by absolute quantification of MP1 and p14 proteins on endosomes by quantitative MS using the Equimolarity through Equalizer Peptide strategy. A combination of subcellular fractionation, 2-D DIGE and MALDI-TOF\/TOF MS revealed 31 proteins differentially regulated in p14(-\/-) organelles, which were rescued by reexpression of pEGFP-p14 in p14(-\/-) endosomes. Regulated proteins are known to be involved in actin remodeling, endosomal signal transduction and trafficking. Identified proteins and their in silico interaction networks suggested that endosomal signaling might regulate such major cellular functions such as proliferation, differentiation, migration and survival.","authors":"Stasyk, T., Holzmann, J., Stumberger, S., Ebner, HL., Hess, MW., Bonn, GK., Mechtler, K., Huber, LA.","publication_status":"aheadofprint","journalpubyear":"2010","journaltitle":"Proteomics","volume":null,"issue":null,"page":null,"pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31355447","title":"Evaluation of healing at molar extraction sites with and without ridge preservation: A three-arm histologic analysis.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Automated\" Owner=\"NLM\"><PMID Version=\"1\">31355447<\/PMID><DateCompleted><Year>2020<\/Year><Month>07<\/Month><Day>02<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>07<\/Month><Day>02<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1943-3670<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>91<\/Volume><Issue>1<\/Issue><PubDate><Year>2020<\/Year><Month>01<\/Month><\/PubDate><\/JournalIssue><Title>Journal of periodontology<\/Title><ISOAbbreviation>J Periodontol<\/ISOAbbreviation><\/Journal><ArticleTitle>Evaluation of healing at molar extraction sites with and without ridge preservation: A three-arm histologic analysis.<\/ArticleTitle><Pagination><MedlinePgn>74-82<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/JPER.19-0237<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Little evidence is available regarding the benefit of ridge preservation (RP) at molar sites. The primary objective of this three-arm cohort study was to histologically compare the healing outcome between natural healing after molar tooth extraction and two different techniques of RP using freeze-dried bone allograft (FDBA) and a nonresorbable dense polytetrafluoroethylene (dPTFE) membrane, or an absorbable collagen sponge as a barrier.","authors":"Duong, M., Mealey, BL., Walker, C., Al-Harthi, S., Prihoda, TJ., Huynh-Ba, G.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Periodontol","volume":"91","issue":"1","page":"74-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24755934","title":"What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory.","abstract":"In any biological system with memory, the state of the system depends on its history. Epigenetic memory maintains gene expression states through cell generations without a change in DNA sequence and in the absence of initiating signals. It is immensely powerful in biological systems - it adds long-term stability to gene expression states and increases the robustness of gene regulatory networks. The Polycomb group (PcG) and Trithorax group (TrxG) proteins can confer long-term, mitotically heritable memory by sustaining silent and active gene expression states, respectively. Several recent studies have advanced our understanding of the molecular mechanisms of this epigenetic memory during DNA replication and mitosis.","authors":"Steffen, PA., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Rev Mol Cell Biol","volume":"15","issue":"5","page":"340-56","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21075115","title":"Molecular architecture and connectivity of the budding yeast Mtw1 kinetochore complex.","abstract":"Kinetochores are large multiprotein complexes that connect centromeres to spindle microtubules in all eukaryotes. Among the biochemically distinct kinetochore complexes, the conserved four-protein Mtw1 complex is a central part of the kinetochore in all organisms. Here we present the biochemical reconstitution and characterization of the budding yeast Mtw1 complex. Direct visualization by electron microscopy revealed an elongated bilobed structure with a 25-nm-long axis. The complex can be assembled from two stable heterodimers consisting of Mtw1p-Nnf1p and Dsn1p-Nsl1p, and it interacts directly with the microtubule-binding Ndc80 kinetochore complex via the centromere-proximal Spc24\/Spc25 head domain. In addition, we have reconstituted a partial Ctf19 complex and show that it directly associates with the Mtw1 complex in vitro. Ndc80 and Ctf19 complexes do not compete for binding to the Mtw1 complex, suggesting that Mtw1 can bridge the microtubule-binding components of the kinetochore to the inner centromere.","authors":"Hornung, P., Maier, M., Alushin, GM., Lander, GC., Nogales, E., Westermann, S.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Mol Biol","volume":"405","issue":"2","page":"548-59","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2011-02-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8020094","title":"Closing the cell cycle circle in yeast: G2 cyclin proteolysis initiated at mitosis persists until the activation of G1 cyclins in the next cycle.","abstract":"It is thought that DNA replication and mitosis in yeast are triggered by oscillations in the level of G1-specific (CLN1 and CLN2) and G2-specific (CLB1-CLB4) cyclins, which determine the substrate specificity of the CDC28 protein kinase. It is not understood how the time and order of appearance of different cyclin types are determined. We show here that CLB2 proteolysis, which is important for transition from mitosis to G1, is not confined to a narrow window at the end of mitosis as previously thought but continues until reactivation of CDC28 by CLN cyclins toward the end of the subsequent G1 period. Thus, cell cycle-regulated proteolysis prevents accumulation of G2-specific CLB cyclins during G1 and thereby ensures that the CLN-associated forms of the CDC28 kinase are activated without interference from CLB cyclins. Accumulation of CLN cyclins leads to inactivation of CLB cyclin proteolysis, which is a precondition for subsequent activation of G2-specific B-type cyclins.","authors":"Amon, A., Irniger, S., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Cell","volume":"77","issue":"7","page":"1037-50","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1994-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20147977","title":"SHIP-1 inhibits CD95\/APO-1\/Fas-induced apoptosis in primary T lymphocytes and T leukemic cells by promoting CD95 glycosylation independently of its phosphatase activity.","abstract":"SHIP-1 (SH2 (Src homology 2)-containing inositol 5'-phosphatase-1) functions as a negative regulator of immune responses by hydrolyzing phosphatidylinositol-3,4,5-triphosphate generated by phosphoinositide-3 (PI 3)-kinase activity. As a result, SHIP-1 deficiency in mice results in myeloproliferation and B-cell lymphoma. On the other hand, SHIP-1-deficient mice have a reduced T-cell population, but the underlying mechanisms are unknown. In this work, we hypothesized that SHIP-1 plays anti-apoptotic functions in T cells upon stimulation of the death receptor CD95\/APO-1\/Fas. Using primary T cells from SHIP-1(-\/-) mice and T leukemic cell lines, we report that SHIP-1 is a potent inhibitor of CD95-induced death. We observed that a small fraction of the SHIP-1 pool is localized to the endoplasmic reticulum (ER), in which it promotes CD95 glycosylation. This post-translational modification requires an intact SH2 domain of SHIP-1, but is independent of its phosphatase activity. The glycosylated CD95 fails to oligomerize upon stimulation, resulting in impaired death-inducing signaling complex (DISC) formation and downstream apoptotic cascade. These results uncover an unanticipated inhibitory function for SHIP-1 and emphasize the role of glycosylation in the regulation of CD95 signaling in T cells. This work may also provide a new basis for therapeutic strategies using compounds inducing apoptosis through the CD95 pathway on SHIP-1-negative leukemic T cells.","authors":"Charlier, E., Cond\u00e9, C., Zhang, J., Deneubourg, L., Di Valentin, E., Rahmouni, S., Chariot, A., Agostinis, P., Pang, PC., Haslam, SM., Dell, A., Penninger, J., Erneux, C., Piette, J., Gloire, G.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Leukemia","volume":"24","issue":"4","page":"821-32","pdf":null,"JrId":"5536","fulltextlink":null,"preprintlink":null,"articledate":"2010-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20934772","title":"The piRNA pathway: a fly's perspective on the guardian of the genome.","abstract":"Throughout the eukaryotic lineage, small RNA silencing pathways protect the genome against the deleterious influence of selfish genetic elements such as transposons. In animals an elaborate small RNA pathway centered on PIWI proteins and their interacting piRNAs silences transposons within the germline. In contrast to other small RNA silencing pathways, we lack a mechanistic understanding of this genome defense system. However, genetic and molecular studies have uncovered a fascinating conceptual framework for this pathway that is conserved from sponges to mammals. We discuss our current understanding of the piRNA pathway in Drosophila with an emphasis on origin and biogenesis of piRNAs.","authors":"Senti, KA., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Trends Genet","volume":"26","issue":"12","page":"499-509","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20300111","title":"Jun and JunD-dependent functions in cell proliferation and stress response.","abstract":"Jun is essential for fetal development, as fetuses lacking Jun die at mid-gestation with multiple cellular defects in liver and heart. Embryos expressing JunD in place of Jun (Jun(d\/d)) can develop to term with normal fetal livers, but display cardiac defects as observed in fetuses lacking Jun. Jun(d\/d) mouse embryonic fibroblasts (MEFs) exhibit early senescence, which can be rescued by EGF and HB-EGF stimulation, probably through activation of Akt signaling. Thus, JunD cannot functionally replace Jun in regulating fibroblast proliferation. In Jun(-\/-) fetal livers, increased hydrogen peroxide levels are detected and expression of Nrf1 and Nrf2 (nuclear erythroid 2-related transcription factors) is downregulated. Importantly, increased oxidative stress as well as expression of Nrf1 and Nrf2 is rescued by JunD in Jun(d\/d) fetal livers. These data show that Jun is of critical importance for cellular protection against oxidative stress in fetal livers and fibroblasts, and Jun-dependent cellular senescence can be restored by activation of the epidermal growth factor receptor pathway.","authors":"Meixner, A., Karreth, F., Kenner, L., Penninger, JM., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell Death Differ","volume":"17","issue":"9","page":"1409-19","pdf":null,"JrId":"20326","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19297526","title":"Tetrahymena meiotic nuclear reorganization is induced by a checkpoint kinase-dependent response to DNA damage.","abstract":"In the ciliate Tetrahymena, meiotic micronuclei (MICs) undergo extreme elongation, and meiotic pairing and recombination take place within these elongated nuclei (the \"crescents\"). We have previously shown that elongation does not occur in the absence of Spo11p-induced DNA double-strand breaks (DSBs). Here we show that elongation is restored in spo11Delta mutants by various DNA-damaging agents including ones that may not cause DSBs to a notable extent. MIC elongation following Spo11p-induced DSBs or artificially induced DNA lesions is probably a DNA-damage response mediated by a phosphokinase signal transduction pathway, since it is suppressed by the ATM\/ATR kinase inhibitors caffeine and wortmannin and by knocking out Tetrahymena's ATR orthologue. MIC elongation occurs concomitantly with the movement of centromeres away from the telomeric pole of the MIC. This DNA damage-dependent reorganization of the MIC helps to arrange homologous chromosomes alongside each other but is not sufficient for exact pairing. Thus, Spo11p contributes to bivalent formation in two ways: by creating a favorable spatial disposition of homologues and by stabilizing pairing by crossovers. The polarized chromosome orientation inside the crescent resembles the conserved meiotic bouquet, and crescent and bouquet also share the putative function of aiding meiotic pairing. However, they are regulated differently because in Tetrahymena, DSBs are required for entering rather than exiting this stage.","authors":"Loidl, J., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Biol Cell","volume":"20","issue":"9","page":"2428-37","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34087681","title":"The platelet derived growth factor BB promotes osteogenic differentiation of periodontal ligament stem cells via the Wnt\/\u03b2-catenin signaling pathway.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Automated\" Owner=\"NLM\"><PMID Version=\"1\">34087681<\/PMID><DateCompleted><Year>2021<\/Year><Month>08<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>08<\/Month><Day>16<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-1506<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>129<\/Volume><PubDate><Year>2021<\/Year><Month>Sep<\/Month><\/PubDate><\/JournalIssue><Title>Archives of oral biology<\/Title><ISOAbbreviation>Arch Oral Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The platelet derived growth factor BB promotes osteogenic differentiation of periodontal ligament stem cells via the Wnt\/\u03b2-catenin signaling pathway.<\/ArticleTitle><Pagination><MedlinePgn>105162<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0003-9969(21)00125-4<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.archoralbio.2021.105162<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">To determine the role of platelet derived growth factor BB in the regulation of cell cycle, migration and differentiation of stem cells.","authors":"Deng, J., Pan, J., Luo, Y., Yu, L., Zhang, W., Liu, X., Liu, Y.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Arch Oral Biol","volume":"129","issue":"","page":"105162","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40168118","title":"PHLPP2 is a pseudophosphatase that lost activity in the metazoan ancestor.","abstract":"The phosphoinositide 3-kinase (PI3K) pathway is a major regulator of cell and organismal growth. Consequently, hyperactivation of PI3K and its downstream effector kinase, Akt, is observed in many human cancers. Pleckstrin homology domain leucine-rich repeat-containing protein phosphatases (PHLPP), two paralogous members of the metal-dependent protein phosphatase family, have been reported as negative regulators of Akt signaling and, therefore, tumor suppressors. However, the stoichiometry and identity of the bound metal ion(s), mechanism of action, and enzymatic specificity of these proteins are not known. Seeking to fill these gaps in our understanding of PHLPP biology, we unexpectedly found that PHLPP2 has no catalytic activity in vitro. Instead, we found that PHLPP2 is a pseudophosphatase with a single zinc ion bound in its catalytic center. Furthermore, we found that cancer genomics data do not support the proposed role of PHLPP1 or PHLPP2 as tumor suppressors. Phylogenetic analyses revealed an ancestral phosphatase that arose more than 1,000 Mya, but that lost activity at the base of the metazoan lineage. Surface conservation indicates that while PHLPP2 has lost catalytic activity, it may have retained substrate binding. Finally, using phylogenomics, we identify coevolving genes consistent with a scaffolding role for PHLPP2 on membranes. In summary, our results provide a molecular explanation for the inconclusive results that have hampered research on PHLPP and argue for a focus on the noncatalytic roles of PHLPP1 and PHLPP2.","authors":"Husremovi\u0107, T., Meier, V., Pi\u00ebch, L., Siess, KM., Antonioli, S., Grishkovskaya, I., Kircheva, N., Angelova, SE., Wenzl, K., Brandst\u00e4tter, A., Veis, J., Mio\u010di\u0107-Sto\u0161i\u0107, F., Anrather, D., Hartl, M., Truebestein, L., Cerron-Alvan, LM., Leeb, M., \u017dagrovi\u0107, B., Hann, S., Bock, C., Ogris, E., Dudev, T., Irwin, NAT., Haselbach, D., Leonard, TA.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Proc Natl Acad Sci U S A","volume":"122","issue":"14","page":"e2417218122","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-15","doi":"10.1073\/pnas.2417218122","first_author":null,"corresponding_authors":null},{"pmid":"21063389","title":"Nol9 is a novel polynucleotide 5'-kinase involved in ribosomal RNA processing.","abstract":"In a cell, an enormous amount of energy is channelled into the biogenesis of ribosomal RNAs (rRNAs). In a multistep process involving a large variety of ribosomal and non-ribosomal proteins, mature rRNAs are generated from a long polycistronic precursor. Here, we show that the non-ribosomal protein Nol9 is a polynucleotide 5'-kinase that sediments primarily with the pre-60S ribosomal particles in HeLa nuclear extracts. Depletion of Nol9 leads to a severe impairment of ribosome biogenesis. In particular, the polynucleotide kinase activity of Nol9 is required for efficient generation of the 5.8S and 28S rRNAs from the 32S precursor. Upon Nol9 knockdown, we also observe a specific maturation defect at the 5' end of the predominant 5.8S short-form rRNA (5.8S(S)), possibly due to the Nol9 requirement for 5'&gt;3' exonucleolytic trimming. In contrast, the endonuclease-dependent generation of the 5'-extended, minor 5.8S long-form rRNA (5.8S(L)) is largely unaffected. This is the first report of a nucleolar polynucleotide kinase with a role in rRNA processing.","authors":"Heindl, K., Martinez, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"EMBO J","volume":"29","issue":"24","page":"4161-71","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30691750","title":"Therapeutic heat and cold around the elbow on the response of median neurodynamic test 1.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30691750<\/PMID><DateCompleted><Year>2019<\/Year><Month>06<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1532-9283<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>23<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>Jan<\/Month><\/PubDate><\/JournalIssue><Title>Journal of bodywork and movement therapies<\/Title><ISOAbbreviation>J Bodyw Mov Ther<\/ISOAbbreviation><\/Journal><ArticleTitle>Therapeutic heat and cold around the elbow on the response of median neurodynamic test 1.<\/ArticleTitle><Pagination><MedlinePgn>183-188<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S1360-8592(18)30061-5<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.jbmt.2018.01.012<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">To compare the effects of the application of therapeutic heat and cold on the mechanical response of the median nerve neurodynamic testing.","authors":"Gomes, WC., Vishal, K., Balthillaya, G.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Bodyw Mov Ther","volume":"23","issue":"1","page":"183-188","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10592328","title":"The MYC dualism in growth and death.","abstract":"Over-expression of the transcription factor c-Myc immortalizes primary cells and transforms in co-operation with activated ras. Therefore, c-myc is considered a proto-oncogene. Since its discovery c-Myc has been shown to render cells growth factor independent, accelerates passage through G1 of the cell cycle, inhibits differentiation and elicits apoptosis. Whereas the effects on immortalization, proliferation and inhibition of differentiation are in conceivable accordance with gain of function, as it is defined for a proto-oncogene, its pro-apoptotic activity disables a straight forward explanation of the physiological role of c-Myc and suggests a highly complex contribution during development. The recent accomplishments in c-Myc research shed some light on the difficile regulatory network which keeps check on c-Myc activity such as by binding to proteins some of which are transcription factors for non-c-Myc targets. Moreover, it was shown that genes are targeted by c-Myc depending on the sequence of flanking regions adjacent to the E-box or in dependence on the availability of binding partners which is most probably specific to the cellular context. Cdc25A and ornithine decarboxylase, both described to be c-Myc targets, have been brought forward as downstream effectors in the induction of proliferation under serum rich conditions, or in the induction of apoptosis when serum factors are limited. These genes seem to be regulated by c-Myc in a cell type-specific manner. H-ferritin, IRP2 and telomerase are the most recently discovered direct targets of c-Myc. The regulation of H-ferritin and IRP2 might explain the potential of c-Myc to promote proliferation and the regulation of telomerase could be responsible for the immortalizing properties of c-Myc. In the future, H-ferritin and telomerase have to be analyzed whether or not these genes are also Myc targets in other cell systems. Although the intense research efforts regarding the function of c-Myc last already two decades the role of this gene is still enigmatic.","authors":"Fuhrmann, G., Rosenberger, G., Grusch, M., Klein, N., Hofmann, J., Krupitza, G.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Mutat Res","volume":"437","issue":"3","page":"205-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"57","title":"The reversible reduction of horse metmyoglobin by the iron(II) complex of trans-1,2-diaminocyclohexane-N,N,N,n-tetraacetate.","abstract":"The reduction of metmyoglobin by the iron(II) complex of trans-1,2-diaminocyclohexane-N,N,N'N'-tetraacetate (FeCDTA2-) has been investigated. The equilibrium constant, measured spectrophotometrically, is 0.21 with a resulting reduction potential of 0.050 V for Mb0. The rate constant for the reduction is 28 M-1 sec-1 with a deltaH ++ of 13 kcal M-1 and deltaS ++ of -11 eu. Both CN- and OH- inhibit the reduction because of the relatively low reactivity of cyanometmyoglobin (Mb+CN-) and ionized metmyglobin (Mb+OH-). The rate constant for the reduction of Mb+CN- by FeCDTA2- is 4.0 X 10(-2) M-1 sec-1 and that for reduction of Mb+OH- is 4.8 M-1 sec-1. The nitric oxide complex of metmyoglobin is reduced with a rate constant of 10 M-1 sec-1. The kinetics of oxidation of oxymyoglobin by FeCDTA- were studied. The data are consistent with a mechanism where oxidation takes place entirely through the deoxy form. A rate constant of 1.45 X 10(2) M-1 sec-1 was calculated for the oxidation of deoxymyoglobin by FeCDTA-, in equilibrium constant and rate constant for reduction. The above data are discussed in terms of a simple outer-sphere reduction reaction.","authors":"Cassatt, JC., Marini, CP., Bender, JW.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"25","page":"5470-5","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21074052","title":"A genome-wide Drosophila screen for heat nociception identifies \u03b12\u03b43 as an evolutionarily conserved pain gene.","abstract":"Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the \u03b12\u03b4 family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (\u03b12\u03b43) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, \u03b12\u03b43 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in \u03b12\u03b43 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in \u03b12\u03b43 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing.","authors":"Neely, GG., Hess, A., Costigan, M., Keene, AC., Goulas, S., Langeslag, M., Griffin, RS., Belfer, I., Dai, F., Smith, SB., Diatchenko, L., Gupta, V., Xia, CP., Amann, S., Kreitz, S., Heindl-Erdmann, C., Wolz, S., Ly, CV., Arora, S., Sarangi, R., Dan, D., Novatchkova, M., Rosenzweig, M., Gibson, DG., Truong, D., Schramek, D., Zoranovic, T., Cronin, SJ., Angjeli, B., Brune, K., Dietzl, G., Maixner, W., Meixner, A., Thomas, W., Pospisilik, JA., Alenius, M., Kress, M., Subramaniam, S., Garrity, PA., Bellen, HJ., Woolf, CJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell","volume":"143","issue":"4","page":"628-38","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20889976","title":"Mutations in the carboxyl-terminal SEC24 binding motif of the serotonin transporter impair folding of the transporter.","abstract":"The serotonin transporter (SERT) is a member of the SLC6 family of solute carriers. SERT plays a crucial role in synaptic neurotransmission by retrieving released serotonin. The intracellular carboxyl terminus of various neurotransmitter transporters has been shown to be important for the correct delivery of SLC6 family members to the cell surface. Here we studied the importance of the C terminus in trafficking and folding of human SERT. Serial truncations followed by mutagenesis identified sequence spots (PG(601,602), RII(607-609)) within the C terminus relevant for export of SERT from the endoplasmic reticulum (ER). RI(607,608) is homologous to the RL-motif that in other SLC6 family members provides a docking site for the COPII component Sec24D. The primary defect resulting from mutation at PG(601,602) and RI(607,608) was impaired folding, because mutated transporters failed to bind the inhibitor [(3)H]imipramine. In contrast, when retained in the ER (e.g. by dominant negative Sar1) the wild type transporter bound [(3)H]imipramine with an affinity comparable to that of the surface-expressed transporter. SERT-RI(607,608)AA and SERT-RII(607-609)AAA were partially rescued by treatment of cells with the nonspecific chemical chaperone DMSO or the specific pharmacochaperone ibogaine (which binds to the inward facing conformation of SERT) but not by other classes of ligands (inhibitors, substrates, amphetamines). These observations (i) demonstrate an hitherto unappreciated role of the C terminus in the folding of SERT, (ii) indicates that the folding trajectory proceeds via an inward facing intermediate, and (iii) suggest a model where the RI-motif plays a crucial role in preventing premature Sec24-recruitment and export of incorrectly folded transporters.","authors":"El-Kasaby, A., Just, H., Malle, E., Stolt-Bergner, PC., Sitte, HH., Freissmuth, M., Kudlacek, O.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Biol Chem","volume":"285","issue":"50","page":"39201-10","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34079254","title":"Nano-Sized Hydroxyapatite Induces Apoptosis and Osteogenic Differentiation of Vascular Smooth Muscle Cells via JNK\/c-JUN Pathway.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Curated\" Owner=\"NLM\"><PMID Version=\"1\">34079254<\/PMID><DateCompleted><Year>2021<\/Year><Month>06<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>06<\/Month><Day>11<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Electronic\">1178-2013<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>16<\/Volume><PubDate><Year>2021<\/Year><\/PubDate><\/JournalIssue><Title>International journal of nanomedicine<\/Title><ISOAbbreviation>Int J Nanomedicine<\/ISOAbbreviation><\/Journal><ArticleTitle>Nano-Sized Hydroxyapatite Induces Apoptosis and Osteogenic Differentiation of Vascular Smooth Muscle Cells via JNK\/c-JUN Pathway.<\/ArticleTitle><Pagination><MedlinePgn>3633-3648<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.2147\/IJN.S303714<\/ELocationID><Abstract><AbstractText Label=\"Purpose\" NlmCategory=\"UNASSIGNED\">The deposition of hydroxyapatite (HAp) crystals plays an important role in the development of vascular calcification (VC). This study aimed to demonstrate the effects of nanosized HAp (nHAp) on vascular smooth muscle cells (VSMCs) and VC progression.","authors":"Liu, Q., Xiang, P., Chen, M., Luo, Y., Zhao, Y., Zhu, J., Jing, W., Yu, H.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Int J Nanomedicine","volume":"16","issue":"","page":"3633-3648","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29791075","title":"Erythrocyte sedimentation rate measured using microhemagglutination is not elevated in monoclonal gammopathy compared with other diseases.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">29791075<\/PMID><DateCompleted><Year>2019<\/Year><Month>02<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>26<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1751-553X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>40<\/Volume><Issue>5<\/Issue><PubDate><Year>2018<\/Year><Month>Oct<\/Month><\/PubDate><\/JournalIssue><Title>International journal of laboratory hematology<\/Title><ISOAbbreviation>Int J Lab Hematol<\/ISOAbbreviation><\/Journal><ArticleTitle>Erythrocyte sedimentation rate measured using microhemagglutination is not elevated in monoclonal gammopathy compared with other diseases.<\/ArticleTitle><Pagination><MedlinePgn>540-548<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/ijlh.12859<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The erythrocyte sedimentation rate (ESR) as measured using the Westergren method is extremely elevated in patients with monoclonal gammopathy (MG) owing to the abundance of positively charged paraproteins. However, it has not been determined if the ESR is likewise high in patients with MG when measured using alternate ESR methods.","authors":"Kim, M., Ju, YS., Lee, EJ., Lee, E., Jeon, K., Lee, J., Kang, HJ., Kim, HS., Lee, JS., Kim, HJ., Lee, YK.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Int J Lab Hematol","volume":"40","issue":"5","page":"540-548","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27573325","title":"The evaluation of i-SIDRA - a tool for intelligent feedback - in a course on the anatomy of the locomotor system.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">27573325<\/PMID><DateCompleted><Year>2017<\/Year><Month>12<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1872-8243<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>94<\/Volume><PubDate><Year>2016<\/Year><Month>10<\/Month><\/PubDate><\/JournalIssue><Title>International journal of medical informatics<\/Title><ISOAbbreviation>Int J Med Inform<\/ISOAbbreviation><\/Journal><ArticleTitle>The evaluation of i-SIDRA - a tool for intelligent feedback - in a course on the anatomy of the locomotor system.<\/ArticleTitle><Pagination><MedlinePgn>172-81<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.ijmedinf.2016.07.008<\/ELocationID><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S1386-5056(16)30159-9<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\">This paper presents an empirical study of a formative mobile-based assessment approach that can be used to provide students with intelligent diagnostic feedback to test its educational effectiveness.","authors":"Fern\u00e1ndez-Alem\u00e1n, JL., L\u00f3pez-Gonz\u00e1lez, L., Gonz\u00e1lez-Sequeros, O., Jayne, C., L\u00f3pez-Jim\u00e9nez, JJ., Toval, A.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Int J Med Inform","volume":"94","issue":"","page":"172-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"112","title":"PH changes on the surface of burns.","abstract":"","authors":"Kemble, JV.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Plast Surg","volume":"28","issue":"3","page":"181-4","pdf":null,"JrId":"1897","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34079065","title":"PP2A in LepR+ mesenchymal stem cells contributes to embryonic and postnatal endochondral ossification through Runx2 dephosphorylation.","abstract":"It has not been well studied which cells and related mechanisms contribute to endochondral ossification. Here, we fate mapped the leptin receptor-expressing (LepR<sup>+<\/sup>) mesenchymal stem cells (MSCs) in different embryonic and adult extremities using Lepr-cre; tdTomato mice and investigated the underling mechanism using Lepr-cre; Ppp2r1a<sup>fl\/fl<\/sup> mice. Tomato<sup>+<\/sup> cells appear in the primary and secondary ossification centers and express the hypertrophic markers. Ppp2r1a deletion in LepR<sup>+<\/sup> MSCs reduces the expression of Runx2, Osterix, alkaline phosphatase, collagen X, and MMP13, but increases that of the mature adipocyte marker perilipin, thereby reducing trabecular bone density and enhancing fat content. Mechanistically, PP2A dephosphorylates Runx2 and BRD4, thereby playing a major role in positively and negatively regulating osteogenesis and adipogenesis, respectively. Our data identify LepR<sup>+<\/sup> MSC as the cell origin of endochondral ossification during embryonic and postnatal bone growth and suggest that PP2A is a therapeutic target in the treatment of dysregulated bone formation.","authors":"Yen, YT., Chien, M., Wu, PY., Hung, SC.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Commun Biol","volume":"4","issue":"1","page":"658","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34069142","title":"Enhanced Osteogenic Differentiation of Pluripotent Stem Cells via \u03b3-Secretase Inhibition.","abstract":"Bone healing is a complex, well-organized process. Multiple factors regulate this process, including growth factors, hormones, cytokines, mechanical stimulation, and aging. One of the most important signaling pathways that affect bone healing is the Notch signaling pathway. It has a significant role in controlling the differentiation of bone mesenchymal stem cells and forming new bone. Interventions to enhance the healing of critical-sized bone defects are of great importance, and stem cell transplantations are eminent candidates for treating such defects. Understanding how Notch signaling impacts pluripotent stem cell differentiation can significantly enhance osteogenesis and improve the overall healing process upon transplantation. In Rancourt's lab, mouse embryonic stem cells (ESC) have been successfully differentiated to the osteogenic cell lineage. This study investigates the role of Notch signaling inhibition in the osteogenic differentiation of mouse embryonic and induced pluripotent stem cells (iPS). Our data showed that Notch inhibition greatly enhanced the differentiation of both mouse embryonic and induced pluripotent stem cells.","authors":"Helmi, SA., Rohani, L., Zaher, AR., El Hawary, YM., Rancourt, DE.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Int J Mol Sci","volume":"22","issue":"10","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21317887","title":"The stress kinase MKK7 couples oncogenic stress to p53 stability and tumor suppression.","abstract":"Most preneoplastic lesions are quiescent and do not progress to form overt tumors. It has been proposed that oncogenic stress activates the DNA damage response and the key tumor suppressor p53, which prohibits tumor growth. However, the molecular pathways by which cells sense a premalignant state in vivo are largely unknown. Here we report that tissue-specific inactivation of the stress signaling kinase MKK7 in KRas(G12D)-driven lung carcinomas and NeuT-driven mammary tumors markedly accelerates tumor onset and reduces overall survival. Mechanistically, MKK7 acts through the kinases JNK1 and JNK2, and this signaling pathway directly couples oncogenic and genotoxic stress to the stability of p53, which is required for cell cycle arrest and suppression of epithelial cancers. These results show that MKK7 functions as a major tumor suppressor in lung and mammary cancer in mouse and identify MKK7 as a vital molecular sensor to set a cellular anti-cancer barrier.","authors":"Schramek, D., Kotsinas, A., Meixner, A., Wada, T., Elling, U., Pospisilik, JA., Neely, GG., Zwick, RH., Sigl, V., Forni, G., Serrano, M., Gorgoulis, VG., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Genet","volume":"43","issue":"3","page":"212-9","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2011-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-138","title":"Elementary Cellular Processes Driven by  Actin Assembly: Lamellipodia and Filopodia","abstract":null,"authors":"Small, J.V. and Rottner, K.R","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"In \u201cActin-based Motility\u201d Ed by  M.F. Carlier, Springer Science","volume":"","issue":"","page":"pp 3-33","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34064134","title":"Regulation and Role of Transcription Factors in Osteogenesis.","abstract":"Bone is a dynamic tissue constantly responding to environmental changes such as nutritional and mechanical stress. Bone homeostasis in adult life is maintained through bone remodeling, a controlled and balanced process between bone-resorbing osteoclasts and bone-forming osteoblasts. Osteoblasts secrete matrix, with some being buried within the newly formed bone, and differentiate to osteocytes. During embryogenesis, bones are formed through intramembraneous or endochondral ossification. The former involves a direct differentiation of mesenchymal progenitor to osteoblasts, and the latter is through a cartilage template that is subsequently converted to bone. Advances in lineage tracing, cell sorting, and single-cell transcriptome studies have enabled new discoveries of gene regulation, and new populations of skeletal stem cells in multiple niches, including the cartilage growth plate, chondro-osseous junction, bone, and bone marrow, in embryonic development and postnatal life. Osteoblast differentiation is regulated by a master transcription factor RUNX2 and other factors such as OSX\/SP7 and ATF4. Developmental and environmental cues affect the transcriptional activities of osteoblasts from lineage commitment to differentiation at multiple levels, fine-tuned with the involvement of co-factors, microRNAs, epigenetics, systemic factors, circadian rhythm, and the microenvironments. In this review, we will discuss these topics in relation to transcriptional controls in osteogenesis.","authors":"Chan, WCW., Tan, Z., To, MKT., Chan, D.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Int J Mol Sci","volume":"22","issue":"11","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24526121","title":"BRD4: a BET(ter) target for the treatment of AML?","abstract":null,"authors":"Valent, P., Zuber, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell Cycle","volume":"13","issue":"5","page":"689-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21353615","title":"Functional identification of optimized RNAi triggers using a massively parallel sensor assay.","abstract":"Short hairpin RNAs (shRNAs) provide powerful experimental tools by enabling stable and regulated gene silencing through programming of endogenous microRNA pathways. Since requirements for efficient shRNA biogenesis and target suppression are largely unknown, many predicted shRNAs fail to efficiently suppress their target. To overcome this barrier, we developed a \"Sensor assay\" that enables the biological identification of effective shRNAs at large scale. By constructing and evaluating 20,000 RNAi reporters covering every possible target site in nine\u00a0mammalian transcripts, we show that our assay\u00a0reliably identifies potent shRNAs that are surprisingly rare and predominantly missed by existing algorithms. Our unbiased analyses reveal that potent shRNAs share various predicted and previously unknown features associated with specific microRNA processing steps, and suggest a model for competitive strand selection. Together, our study establishes a powerful tool for large-scale identification of highly potent shRNAs and provides insights into sequence requirements of effective RNAi.","authors":"Fellmann, C., Zuber, J., McJunkin, K., Chang, K., Malone, CD., Dickins, RA., Xu, Q., Hengartner, MO., Elledge, SJ., Hannon, GJ., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mol Cell","volume":"41","issue":"6","page":"733-46","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2011-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21217643","title":"Molecular mechanism of Ena\/VASP-mediated actin-filament elongation.","abstract":"Ena\/VASP proteins are implicated in a variety of fundamental cellular processes including axon guidance and cell migration. In vitro, they enhance elongation of actin filaments, but at rates differing in nearly an order of magnitude according to species, raising questions about the molecular determinants of rate control. Chimeras from fast and slow elongating VASP proteins were generated and their ability to promote actin polymerization and to bind G-actin was assessed. By in vitro TIRF microscopy as well as thermodynamic and kinetic analyses, we show that the velocity of VASP-mediated filament elongation depends on G-actin recruitment by the WASP homology 2 motif. Comparison of the experimentally observed elongation rates with a quantitative mathematical model moreover revealed that Ena\/VASP-mediated filament elongation displays a saturation dependence on the actin monomer concentration, implying that Ena\/VASP proteins, independent of species, are fully saturated with actin in vivo and generally act as potent filament elongators. Moreover, our data showed that spontaneous addition of monomers does not occur during processive VASP-mediated filament elongation on surfaces, suggesting that most filament formation in cells is actively controlled.","authors":"Breitsprecher, D., Kiesewetter, AK., Linkner, J., Vinzenz, M., Stradal, TE., Small, JV., Curth, U., Dickinson, RB., Faix, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"EMBO J","volume":"30","issue":"3","page":"456-67","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34058311","title":"Exposure to biomass smoke induces pulmonary Th17 cell differentiation by activating TLR2 on dendritic cells in a COPD rat model.","abstract":"Almost three billion people in developing countries are exposed to biomass smoke (BS), which predisposes them to developing chronic obstructive pulmonary disease (COPD). COPD is associated with abnormal innate and adaptive immune responses in the lungs and systemic circulation, but the mechanisms underlying BS-COPD development are uncertain. We investigated the role of dendritic cells (DCs) and interleukin (IL)-17A in BS-COPD. We investigated T helper cell responses in the BS-exposed COPD rat model by flow cytometry, quantitative PCR, and enzyme-linked immunosorbent assays. We conducted ex vivo experiments to determine which antigen-presenting cells induce Th17 cell responses. We evaluated the in vitro effects of BS-related particulate matter (BRPM) (2.5 \u03bcm) on the function of bone marrow-derived dendritic cells (BMDCs). We found that BS exposure enhanced Th17 responses in the lungs of the COPD-modelled rats, and the stimulated DCs (but not the macrophages) were sufficient to induce na\u00efve CD4 + T cells to produce IL-17A in ex vivo experiments. BRPM significantly enhanced the maturation and activation of DCs through Toll-like receptor 2 (TLR2), but not TLR4, and induced Th17 responses. Therefore, BS activated lung DCs through TLR2, which led to Th17 responses and emphysema in the rats. This process is possibly therapeutically targetable.","authors":"Pu, J., Xu, J., Chen, L., Zhou, H., Cao, W., Hao, B., Li, N., Wu, J., Zheng, J., Hong, W., Li, B., Ran, P.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Toxicol Lett","volume":"348","issue":"","page":"28-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19541849","title":"Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays.","abstract":"Clinical DNA is often available in limited quantities requiring whole-genome amplification for subsequent genome-wide assessment of copy-number variation (CNV) by array-CGH. In pre-implantation diagnosis and analysis of micrometastases, even merely single cells are available for analysis. However, procedures allowing high-resolution analyses of CNVs from single cells well below resolution limits of conventional cytogenetics are lacking. Here, we applied amplification products of single cells and of cell pools (5 or 10 cells) from patients with developmental delay, cancer cell lines and polar bodies to various oligo tiling array platforms with a median probe spacing as high as 65 bp. Our high-resolution analyses reveal that the low amounts of template DNA do not result in a completely unbiased whole genome amplification but that stochastic amplification artifacts, which become more obvious on array platforms with tiling path resolution, cause significant noise. We implemented a new evaluation algorithm specifically for the identification of small gains and losses in such very noisy ratio profiles. Our data suggest that when assessed with sufficiently sensitive methods high-resolution oligo-arrays allow a reliable identification of CNVs as small as 500 kb in cell pools (5 or 10 cells), and of 2.6-3.0 Mb in single cells.","authors":"Geigl, JB., Obenauf, AC., Waldispuehl-Geigl, J., Hoffmann, EM., Auer, M., H\u00f6rmann, M., Fischer, M., Trajanoski, Z., Schenk, MA., Baumbusch, LO., Speicher, MR.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nucleic Acids Res","volume":"37","issue":"15","page":"e105","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17060609","title":"Murine inner cell mass-derived lineages depend on Sall4 function.","abstract":"Sall4 is a mammalian Spalt transcription factor expressed by cells of the early embryo and germ cells, an expression pattern similar to that of both Oct4 and Sox2, which play essential roles during early murine development. We show that the activity of Sall4 is cell-autonomously required for the development of the epiblast and primitive endoderm from the inner cell mass. Furthermore, no embryonic or extraembryonic endoderm stem cell lines could be established from Sall4-deficient blastocysts. In contrast, neither the development of the trophoblast lineage nor the ability to generate trophoblast cell lines from murine blastocysts was impaired in the absence of Sall4. These data establish Sall4 as an essential transcription factor required for the early development of inner cell mass-derived cell lineages.","authors":"Elling, U., Klasen, C., Eisenberger, T., Anlag, K., Treier, M.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Proc Natl Acad Sci U S A","volume":"103","issue":"44","page":"16319-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21153305","title":"TNF conference 2009: beyond bones - RANKL\/RANK in the immune system.","abstract":null,"authors":"Leibbrandt, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Adv Exp Med Biol","volume":"691","issue":null,"page":"5-22","pdf":null,"JrId":"280","fulltextlink":null,"preprintlink":null,"articledate":"2011-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10026910","title":"Gene-modified dendritic cells by receptor-mediated transfection.","abstract":null,"authors":"Diebold, SS., Cotten, M., Wagner, E., Zenke, M.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Adv Exp Med Biol","volume":"451","issue":null,"page":"449-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34026818","title":"The Smad Dependent TGF-\u03b2 and BMP Signaling Pathway in Bone Remodeling and Therapies.","abstract":"Bone remodeling is a continuous process that maintains the homeostasis of the skeletal system, and it depends on the homeostasis between bone-forming osteoblasts and bone-absorbing osteoclasts. A large number of studies have confirmed that the Smad signaling pathway is essential for the regulation of osteoblastic and osteoclastic differentiation during skeletal development, bone formation and bone homeostasis, suggesting a close relationship between Smad signaling and bone remodeling. It is known that Smads proteins are pivotal intracellular effectors for the members of the transforming growth factor-\u03b2 (TGF-\u03b2) and bone morphogenetic proteins (BMP), acting as transcription factors. Smad mediates the signal transduction in TGF-\u03b2 and BMP signaling pathway that affects both osteoblast and osteoclast functions, and therefore plays a critical role in the regulation of bone remodeling. Increasing studies have demonstrated that a number of Smad signaling regulators have potential functions in bone remodeling. Therefore, targeting Smad dependent TGF-\u03b2 and BMP signaling pathway might be a novel and promising therapeutic strategy against osteoporosis. This article aims to review recent advances in this field, summarizing the influence of Smad on osteoblast and osteoclast function, together with Smad signaling regulators in bone remodeling. This will facilitate the understanding of Smad signaling pathway in bone biology and shed new light on the modulation and potential treatment for osteoporosis.","authors":"Zou, ML., Chen, ZH., Teng, YY., Liu, SY., Jia, Y., Zhang, KW., Sun, ZL., Wu, JJ., Yuan, ZD., Feng, Y., Li, X., Xu, RS., Yuan, FL.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Front Mol Biosci","volume":"8","issue":"","page":"593310","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24337297","title":"Progressive specification rather than intercalation of segments during limb regeneration.","abstract":"An amputated salamander limb regenerates the correct number of segments. Models explaining limb regeneration were largely distinct from those for limb development, despite the presence of common patterning molecules. Intercalation has been an important concept to explain salamander limb regeneration, but clear evidence supporting or refuting this model was lacking. In the intercalation model, the first blastema cells acquire fingertip identity, creating a gap in positional identity that triggers regeneration of the intervening region from the stump. We used HOXA protein analysis and transplantation assays to show that axolotl limb blastema cells acquire positional identity in a proximal-to-distal sequence. Therefore, intercalation is not the primary mechanism for segment formation during limb regeneration in this animal. Patterning in development and regeneration uses similar mechanisms.","authors":"Roensch, K., Tazaki, A., Chara, O., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Science","volume":"342","issue":"6164","page":"1375-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19289832","title":"EZH2 is a mediator of EWS\/FLI1 driven tumor growth and metastasis blocking endothelial and neuro-ectodermal differentiation.","abstract":"Ewing tumors (ET) are highly malignant, localized in bone or soft tissue, and are molecularly defined by ews\/ets translocations. DNA microarray analysis revealed a relationship of ET to both endothelium and fetal neural crest. We identified expression of histone methyltransferase enhancer of Zeste, Drosophila, Homolog 2 (EZH2) to be increased in ET. Suppressive activity of EZH2 maintains stemness in normal and malignant cells. Here, we found EWS\/FLI1 bound to the EZH2 promoter in vivo, and induced EZH2 expression in ET and mesenchymal stem cells. Down-regulation of EZH2 by RNA interference in ET suppressed oncogenic transformation by inhibiting clonogenicity in vitro. Similarly, tumor development and metastasis was suppressed in immunodeficient Rag2(-\/-)gamma(C)(-\/-) mice. EZH2-mediated gene silencing was shown to be dependent on histone deacetylase (HDAC) activity. Subsequent microarray analysis of EZH2 knock down, HDAC-inhibitor treatment and confirmation in independent assays revealed an undifferentiated phenotype maintained by EZH2 in ET. EZH2 regulated stemness genes such as nerve growth factor receptor (NGFR), as well as genes involved in neuroectodermal and endothelial differentiation (EMP1, EPHB2, GFAP, and GAP43). These data suggest that EZH2 might have a central role in ET pathology by shaping the oncogenicity and stem cell phenotype of this tumor.","authors":"Richter, GH., Plehm, S., Fasan, A., R\u00f6ssler, S., Unland, R., Bennani-Baiti, IM., Hotfilder, M., L\u00f6wel, D., von Luettichau, I., Mossbrugger, I., Quintanilla-Martinez, L., Kovar, H., Staege, MS., M\u00fcller-Tidow, C., Burdach, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Proc Natl Acad Sci U S A","volume":"106","issue":"13","page":"5324-9","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21248250","title":"Essential role of E3 ubiquitin ligase activity in Cbl-b-regulated T cell functions.","abstract":"E3 ubiquitin ligases have been placed among the essential molecules involved in the regulation of T cell functions and T cell tolerance. However, it has never been experimentally proven in vivo whether these functions indeed depend on the catalytic E3 ligase activity. The Casitas B-cell lymphoma (Cbl) family protein Cbl-b was the first E3 ubiquitin ligase directly implicated in the activation and tolerance of the peripheral T cell. In this study, we report that selective genetic inactivation of Cbl-b E3 ligase activity phenocopies the T cell responses observed when total Cbl-b is ablated, resulting in T cell hyperactivation, spontaneous autoimmunity, and impaired induction of T cell anergy in vivo. Moreover, mice carrying a Cbl-b E3 ligase-defective mutation spontaneously reject tumor cells that express human papilloma virus Ags. These data demonstrate for the first time, to our knowledge, that the catalytic function of an E3 ligase, Cbl-b, is essential for negative regulation of T cells in vivo. Thus, modulation of the E3 ligase activity of Cbl-b might be a novel modality to control T cell immunity in vaccination, cancer biology, or autoimmunity.","authors":"Paolino, M., Thien, CB., Gruber, T., Hinterleitner, R., Baier, G., Langdon, WY., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Immunol","volume":"186","issue":"4","page":"2138-47","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2011-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19273628","title":"CX3CR1+ CD115+ CD135+ common macrophage\/DC precursors and the role of CX3CR1 in their response to inflammation.","abstract":"CX(3)CR1 expression is associated with the commitment of CSF-1R(+) myeloid precursors to the macrophage\/dendritic cell (DC) lineage. However, the relationship of the CSF-1R(+) CX(3)CR1(+) macrophage\/DC precursor (MDP) with other DC precursors and the role of CX(3)CR1 in macrophage and DC development remain unclear. We show that MDPs give rise to conventional DCs (cDCs), plasmacytoid DCs (PDCs), and monocytes, including Gr1(+) inflammatory monocytes that differentiate into TipDCs during infection. CX(3)CR1 deficiency selectively impairs the recruitment of blood Gr1(+) monocytes in the spleen after transfer and during acute Listeria monocytogenes infection but does not affect the development of monocytes, cDCs, and PDCs.","authors":"Auffray, C., Fogg, DK., Narni-Mancinelli, E., Senechal, B., Trouillet, C., Saederup, N., Leemput, J., Bigot, K., Campisi, L., Abitbol, M., Molina, T., Charo, I., Hume, DA., Cumano, A., Lauvau, G., Geissmann, F.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Exp Med","volume":"206","issue":"3","page":"595-606","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20707031","title":"Allogeneic somatic cell therapy: process development challenges and future opportunities.","abstract":"Cell-replacement therapy has emerged during the past decade as a potential solution for many diseases. However, for this promise to be fulfilled, numerous process development challenges specific to these products need to be overcome. This editorial overview highlights some key observations derived from research on an allogeneic somatic cell therapy product for the treatment of Parkinson's disease.","authors":"Fawaz, FS., Hermiston, TW., Dinter, H.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Curr Opin Mol Ther","volume":"12","issue":"4","page":"383-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19321860","title":"Humanized large-scale expanded endothelial colony-forming cells function in vitro and in vivo.","abstract":"Endothelial progenitor cells are critically involved in essential biologic processes, such as vascular homeostasis, regeneration, and tumor angiogenesis. Endothelial colony-forming cells (ECFCs) are endothelial progenitor cells with robust proliferative potential. Their profound vessel-forming capacity makes them a promising tool for innovative experimental, diagnostic, and therapeutic strategies. Efficient and safe methods for their isolation and expansion are presently lacking. Based on the previously established efficacy of animal serum-free large-scale clinical-grade propagation of mesenchymal stromal cells, we hypothesized that endothelial lineage cells may also be propagated efficiently following a comparable strategy. Here we demonstrate that human ECFCs can be recovered directly from unmanipulated whole blood. A novel large-scale animal protein-free humanized expansion strategy preserves the progenitor hierarchy with sustained proliferation potential of more than 30 population doublings. By applying large-scale propagated ECFCs in various test systems, we observed vascular networks in vitro and perfused vessels in vivo. After large-scale expansion and cryopreservation phenotype, function, proliferation, and genomic stability were maintained. For the first time, proliferative, functional, and storable ECFCs propagated under humanized conditions can be explored in terms of their therapeutic applicability and risk profile.","authors":"Reinisch, A., Hofmann, NA., Obenauf, AC., Kashofer, K., Rohde, E., Schallmoser, K., Flicker, K., Lanzer, G., Linkesch, W., Speicher, MR., Strunk, D.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Blood","volume":"113","issue":"26","page":"6716-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17709014","title":"Cell biologists sort things out: Analysis and purification of intracellular organelles by flow cytometry.","abstract":"Flow cytometry was established originally for measuring DNA content and for the analysis of cell-surface markers in combination with cell sorting. During the past two decades, it has added new dimensions to various areas of immunology and medicine. Increased sensitivity and precision of flow cytometers, accompanied by the development of new fluorescent dyes and probes, has led to new applications in molecular cell biology and genetics. This article focuses on applications of flow cytometry in analysis and sorting of intracellular organelles.","authors":"B\u00f6ck, G., Steinlein, P., Huber, LA.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Trends Cell Biol","volume":"7","issue":"12","page":"499-503","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1708176","title":"Gene isolation is 25 years old this month.","abstract":null,"authors":"Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Trends Genet","volume":"6","issue":"12","page":"380-1","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1991-05-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34020531","title":"Thyroid hormone and thyroid hormone nuclear receptors: History and present state of art.","abstract":"The present review traces the road leading to discovery of L-thyroxine, thyroid hormone (3,5,3\u00b4-triiodo-L-thyronine, T<sub>3<\/sub>) and its cognate nuclear receptors. Thyroid hormone is a pleio-tropic regulator of growth, differentiation, and tissue homeostasis in higher organisms. The major site of the thyroid hormone action is predominantly a cell nucleus. T<sub>3<\/sub> specific binding sites in the cell nuclei have opened a new era in the field of the thyroid hormone receptors (TRs) discovery. T<sub>3<\/sub> actions are mediated by high affinity nuclear TRs, TRalpha and TRbeta, which function as T<sub>3<\/sub>-activated transcription factors playing an essential role as transcription-modulating proteins affecting the transcriptional responses in target genes. Discovery and characterization of nuclear retinoid X receptors (RXRs), which form with TRs a heterodimer RXR\/TR, positioned RXRs at the epicenter of molecular endocrinology. Transcriptional control via nuclear RXR\/TR heterodimer represents a direct action of thyroid hormone. T<sub>3<\/sub> plays a crucial role in the development of brain, it exerts significant effects on the cardiovascular system, skeletal muscle contractile function, bone development and growth, both female and male reproductive systems, and skin. It plays an important role in maintaining the hepatic, kidney and intestine homeostasis and in pancreas, it stimulates the beta-cell proliferation and survival. The TRs cross-talk with other signaling pathways intensifies the T<sub>3<\/sub> action at cellular level. The role of thyroid hormone in human cancers, acting via its cognate nuclear receptors, has not been fully elucidated yet. This review is aimed to describe the history of T<sub>3<\/sub> receptors, starting from discovery of T3 binding sites in the cell nuclei to revelation of T<sub>3<\/sub> receptors as T<sub>3<\/sub>-inducible transcription factors in relation to T<sub>3<\/sub> action at cellular level. It also focuses on milestones of investigation, comprising RXR\/TR dimerization, cross-talk between T<sub>3<\/sub> receptors, and other regulatory pathways within the cell and mainly on genomic action of T<sub>3<\/sub>. This review also focuses on novel directions of investigation on relationships between T<sub>3<\/sub> receptors and cancer. Based on the update of available literature and the author's experimental experience, it is devoted to clinicians and medical students.","authors":"Brtko, J.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Endocr Regul","volume":"55","issue":"2","page":"103-119","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21131983","title":"Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNAi.","abstract":"Short hairpin RNAs (shRNAs) are versatile tools for analyzing loss-of-function phenotypes in vitro and in vivo. However, their use for studying genes involved in proliferation and survival, which are potential therapeutic targets in cancer and other diseases, is confounded by the strong selective advantage of cells in which shRNA expression is inefficient. We therefore developed a toolkit that combines Tet-regulated miR30-shRNA technology, robust transactivator expression and two fluorescent reporters to track and isolate cells with potent target knockdown. We demonstrated that this system improves the study of essential genes and was sufficiently robust to eradicate aggressive cancer in mice by suppressing a single gene. Further, we applied this system for in vivo negative-selection screening with pooled shRNAs and propose a streamlined, inexpensive workflow that will facilitate the use of RNA interference (RNAi) for the identification and evaluation of essential therapeutic targets.","authors":"Zuber, J., McJunkin, K., Fellmann, C., Dow, LE., Taylor, MJ., Hannon, GJ., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Biotechnol","volume":"29","issue":"1","page":"79-83","pdf":null,"JrId":"20305","fulltextlink":null,"preprintlink":null,"articledate":"2011-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25256866","title":"The impact of diurnal sleep on the consolidation of a complex gross motor adaptation task.","abstract":"Diurnal sleep effects on consolidation of a complex, ecological valid gross motor adaptation task were examined using a bicycle with an inverse steering device. We tested 24 male subjects aged between 20 and 29 years using a between-subjects design. Participants were trained to adapt to the inverse steering bicycle during 45 min. Performance was tested before (TEST1) and after (TEST2) training, as well as after a 2 h retention interval (TEST3). During retention, participants either slept or remained awake. To assess gross motor performance, subjects had to ride the inverse steering bicycle 3 \u00d7 30 m straight-line and 3 \u00d7 30 m through a slalom. Beyond riding time, we sophisticatedly measured performance accuracy (standard deviation of steering angle) in both conditions using a rotatory potentiometer. A significant decrease of accuracy during straight-line riding after nap and wakefulness was shown. Accuracy during slalom riding remained stable after wakefulness but was reduced after sleep. We found that the duration of rapid eye movement sleep as well as sleep spindle activity are negatively related with gross motor performance changes over sleep. Together these findings suggest that the consolidation of adaptation to a new steering device does not benefit from a 2 h midday nap. We speculate that in case of strongly overlearned motor patterns such as normal cycling, diurnal sleep spindles and rapid eye movement sleep might even help to protect everyday needed skills, and to rapidly forget newly acquired, interfering and irrelevant material.","authors":"Hoedlmoser, K., Birklbauer, J., Schabus, M., Eibenberger, P., Rigler, S., Mueller, E.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Sleep Res","volume":"24","issue":"1","page":"100-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8596953","title":"Inhibition of HIV-1 replication in lymphocytes by mutants of the Rev cofactor eIF-5A.","abstract":"Eukaryotic initiation factor 5A(eIF-5A) is a cellular cofactor require d for the function of the human immunodeficiency virus type-1 (HIV-1) Rev trans-activator protein. The majority of a set of eIF-5A mutants did not support growth of yeast cells having an inactivated genomic copy of eIF-5A, indicating that the introduced mutation eliminated eIF-5A activity. Two nonfunctional mutants, eIF-5AM13 and eIF-5AM14, retained their binding capacity for the HIV-1 Rev response element:Rev complex. Both mutants were constitutively expressed in human T cells. When these T cells were infected with replication-competent HIV-1, virus replication was inhibited. The eIF-5AM13 and eIF5AM14 proteins blocked Rev trans-activation and Rev-mediated nuclear export.","authors":"Bevec, D., Jaksche, H., Oft, M., W\u00f6hl, T., Himmelspach, M., Pacher, A., Schebesta, M., Koettnitz, K., Dobrovnik, M., Csonga, R., Lottspeich, F., Hauber, J.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Science","volume":"271","issue":"5257","page":"1858-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1996-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20854846","title":"Telmisartan attenuates aortic hypertrophy in hypertensive rats by the modulation of ACE2 and profilin-1 expression.","abstract":"Profilin-1 has recently been linked to vascular hypertrophy and remodeling. Here, we assessed the hypothesis that angiotensin (Ang) II type I receptor antagonist telmisartan improves vascular hypertrophy by modulation of expression of profilin-1 and angiotensin-converting enzyme 2 (ACE2). Ten-week-old male spontaneously hypertensive rats (SHR) were received oral administration of telmisartan (5 or 10mg\/kg; daily) or saline for 10 weeks. Compared with Wistar-Kyoto (WKY) rats, there were marked increases in systolic blood pressure and profilin-1 expression and reduced ACE2 and peroxisome proliferator activated receptor-\u03b3 (PPAR\u03b3) levels in aorta of SHR, associated with elevated extracellular-signal regulated kinase 1\/2 (ERK1\/2) and c-Jun N-terminal kinase (JNK) phosphorylation signaling and aortic hypertrophy characterized with increased media thickness, which were strikingly reversed by telmisartan. In cultured human umbilical artery smooth muscle cells (HUASMCs), Ang II induced a dose-dependent increase in profilin-1 expression, along with decreased ACE2 protein expression and elevated ERK1\/2 and JNK phosphorylation. In addition, blockade of ERK1\/2 or JNK by either specific inhibitor was able to abolish Ang II-induced ACE2 downregulation and profilin-1 upregulation in HUASMCs. Importantly, treatment with telmisartan (1 or 10 \u03bcM) or recombinant human ACE2 (2mg\/ml) largely ameliorated Ang II-induced profilin-1 expression and ERK1\/2 and JNK phosphorylation and augmented PPAR\u03b3 \uf020expression in the cultured HUASMCs. In conclusion, telmisartan treatment attenuates vascular hypertrophy in SHR by the modulation of ACE2 and profilin-1 expression with a marked reversal of ERK1\/2 and JNK phosphorylation signaling pathways.","authors":"Zhong, JC., Ye, JY., Jin, HY., Yu, X., Yu, HM., Zhu, DL., Gao, PJ., Huang, DY., Shuster, M., Loibner, H., Guo, JM., Yu, XY., Xiao, BX., Gong, ZH., Penninger, JM., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Regul Pept","volume":"166","issue":"1-3","page":"90-7","pdf":null,"JrId":"6960","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29411653","title":"Cardiac regeneration in a newborn: what does this mean for future cardiac repair research?","abstract":null,"authors":"Haubner, BJ., Schuetz, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Expert Rev Cardiovasc Ther","volume":"16","issue":"3","page":"155-157","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25035496","title":"Organogenesis in a dish: modeling development and disease using organoid technologies.","abstract":"Classical experiments performed half a century ago demonstrated the immense self-organizing capacity of vertebrate cells. Even after complete dissociation, cells can reaggregate and reconstruct the original architecture of an organ. More recently, this outstanding feature was used to rebuild organ parts or even complete organs from tissue or embryonic stem cells. Such stem cell-derived three-dimensional cultures are called organoids. Because organoids can be grown from human stem cells and from patient-derived induced pluripotent stem cells, they have the potential to model human development and disease. Furthermore, they have potential for drug testing and even future organ replacement strategies. Here, we summarize this rapidly evolving field and outline the potential of organoid technology for future biomedical research.","authors":"Lancaster, MA., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Science","volume":"345","issue":"6194","page":"1247125","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19240811","title":"BMP-13 emerges as a potential inhibitor of bone formation.","abstract":"Bone morphogenetic protein-13 (BMP-13) plays an important role in skeletal development. In the light of a recent report that mutations in the BMP-13 gene are associated with spine vertebral fusion in Klippel-Feil syndrome, we hypothesized that BMP-13 signaling is crucial for regulating embryonic endochondral ossification. In this study, we found that BMP-13 inhibited the osteogenic differentiation of human bone marrow multipotent mesenchymal stromal cells (BM MSCs) in vitro. The endogenous BMP-13 gene expression in MSCs was examined under expansion conditions. The MSCs were then induced to differentiate into osteoblasts in osteo-inductive medium containing exogenous BMP-13. Gene expression was analysed by real-time PCR. Alkaline phosphatase (ALP) expression and activity, proteoglycan (PG) synthesis and matrix mineralization were assessed by cytological staining or ALP assay. Results showed that endogenous BMP-13 mRNA expression was higher than BMP-2 or -7 during MSC growth. BMP-13 supplementation strongly inhibited matrix mineralization and ALP activity of osteogenic differentiated MSCs, yet increased PG synthesis under the same conditions. In conclusion, BMP-13 inhibited osteogenic differentiation of MSCs, implying that functional mutations or deficiency of BMP-13 may allow excess bone formation. Our finding provides an insight into the molecular mechanisms and the therapeutic potential of BMP-13 in restricting pathological bone formation.","authors":"Shen, B., Bhargav, D., Wei, A., Williams, LA., Tao, H., Ma, DD., Diwan, AD.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Int J Biol Sci","volume":"5","issue":"2","page":"192-200","pdf":null,"JrId":"32196","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24503275","title":"Severe amygdala dysfunction in a MAPT transgenic mouse model of frontotemporal dementia.","abstract":"Frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17) is a neurodegenerative tauopathy caused by mutations in the tau gene (MAPT). Individuals with FTDP-17 have deficits in learning, memory, and language, in addition to personality and behavioral changes that are often characterized by a lack of social inhibition. Several transgenic mouse models expressing tau mutations have been tested extensively for memory or motor impairments, though reports of amygdala-dependent behaviors are lacking. To this end, we tested the rTg4510 mouse model on a behavioral battery that included amygdala-dependent tasks of exploration. As expected, rTg4510 mice exhibit profound impairments in hippocampal-dependent learning and memory tests, including contextual fear conditioning. However, rTg4510 mice also display an abnormal hyperexploratory phenotype in the open-field assay, elevated plus maze, light-dark exploration, and cued fear conditioning, indicative of amygdala dysfunction. Furthermore, significant tau burden is detected in the amygdala of both rTg4510 mice and human FTDP-17 patients, suggesting that the rTg4510 mouse model recapitulates the behavioral disturbances and neurodegeneration of the amygdala characteristic of FTDP-17.","authors":"Cook, C., Dunmore, JH., Murray, ME., Scheffel, K., Shukoor, N., Tong, J., Castanedes-Casey, M., Phillips, V., Rousseau, L., Penuliar, MS., Kurti, A., Dickson, DW., Petrucelli, L., Fryer, JD.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Neurobiol Aging","volume":"35","issue":"7","page":"1769-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19238593","title":"PACAP signaling to DREAM: a cAMP-dependent pathway that regulates cortical astrogliogenesis.","abstract":"Astrocytes constitute a very abundant cell type in the mammalian central nervous system and play critical roles in brain function. During development, astrocytes are generated from neural progenitor cells only after these cells have generated neurons. This so called gliogenic switch is tightly regulated by intrinsic factors that inhibit the generation of astrocytes during the neurogenic period. Once neural progenitors acquire gliogenic competence, they differentiate into astrocytes in response to specific extracellular signals. Some of these signals are delivered by neurotrophic cytokines via activation of the gp130-JAK-signal transducer and activator of transcription system, whereas others depend on the activity of pituitary adenylate cyclase-activating polypeptide (PACAP) on specific PAC1 receptors that stimulate the production of cAMP. This results in the activation of the small GTPases Rap1 and Ras, and in the cAMP-dependent entry of extracellular calcium into the cell. Calcium, in turn, stimulates the transcription factor downstream regulatory element antagonist modulator (DREAM), which is bound to specific sites of the promoter of the glial fibrillary acidic protein gene, stimulating its expression during astrocyte differentiation. Lack of DREAM in vivo results in alterations in the number of neurons and astrocytes generated during development. Thus, the PACAP-cAMP-Ca(2+)-DREAM signaling cascade constitutes an important pathway to activate glial-specific gene expression during astrocyte differentiation.","authors":"Vallejo, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Neurobiol","volume":"39","issue":"2","page":"90-100","pdf":null,"JrId":"1466","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18704105","title":"9p21 deletion in primary cutaneous large B-cell lymphoma, leg type, may escape detection by standard FISH assays.","abstract":null,"authors":"Wiesner, T., Obenauf, AC., Geigl, JB., Vallant, EM., Speicher, MR., Fink-Puches, R., Kerl, H., Cerroni, L.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Invest Dermatol","volume":"129","issue":"1","page":"238-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24469834","title":"Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy.","abstract":"In female mammals, one of the two X chromosomes is transcriptionally silenced to equalize X-linked gene dosage relative to XY males, a process termed X chromosome inactivation. Mechanistically, this is thought to occur via directed recruitment of chromatin modifying factors by the master regulator, X-inactive specific transcript (Xist) RNA, which localizes in cis along the entire length of the chromosome. A well-studied example is the recruitment of polycomb repressive complex 2 (PRC2), for which there is evidence of a direct interaction involving the PRC2 proteins Enhancer of zeste 2 (Ezh2) and Supressor of zeste 12 (Suz12) and the A-repeat region located at the 5' end of Xist RNA. In this study, we have analyzed Xist-mediated recruitment of PRC2 using two approaches, microarray-based epigenomic mapping and superresolution 3D structured illumination microscopy. Making use of an ES cell line carrying an inducible Xist transgene located on mouse chromosome 17, we show that 24 h after synchronous induction of Xist expression, acquired PRC2 binding sites map predominantly to gene-rich regions, notably within gene bodies. Paradoxically, these new sites of PRC2 deposition do not correlate with Xist-mediated gene silencing. The 3D structured illumination microscopy was performed to assess the relative localization of PRC2 proteins and Xist RNA. Unexpectedly, we observed significant spatial separation and absence of colocalization both in the inducible Xist transgene ES cell line and in normal XX somatic cells. Our observations argue against direct interaction between Xist RNA and PRC2 proteins and, as such, prompt a reappraisal of the mechanism for PRC2 recruitment in X chromosome inactivation.","authors":"Cerase, A., Smeets, D., Tang, YA., Gdula, M., Kraus, F., Spivakov, M., Moindrot, B., Leleu, M., Tattermusch, A., Demmerle, J., Nesterova, TB., Green, C., Otte, AP., Schermelleh, L., Brockdorff, N.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Proc Natl Acad Sci U S A","volume":"111","issue":"6","page":"2235-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29419816","title":"Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data.","abstract":"This protocol describes a workflow for creating structural models of proteins or protein complexes using distance restraints derived from cross-linking mass spectrometry experiments. The distance restraints are used (i) to adjust preliminary models that are calculated on the basis of a homologous template and primary sequence, and (ii) to select the model that is in best agreement with the experimental data. In the case of protein complexes, the cross-linking data are further used to dock the subunits to one another to generate models of the interacting proteins. Predicting models in such a manner has the potential to indicate multiple conformations and dynamic changes that occur in solution. This modeling protocol is compatible with many cross-linking workflows and uses open-source programs or programs that are free for academic users and do not require expertise in computational modeling. This protocol is an excellent additional application with which to use cross-linking results for building structural models of proteins. The established protocol is expected to take 6-12 d to complete, depending on the size of the proteins and the complexity of the cross-linking data.","authors":"Orb\u00e1n-N\u00e9meth, Z., Beveridge, R., Hollenstein, DM., Rampler, E., Stranzl, T., Hudecz, O., Doblmann, J., Schl\u00f6gelhofer, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Protoc","volume":"13","issue":"3","page":"478-494","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25490258","title":"Structure of an APC3-APC16 complex: insights into assembly of the anaphase-promoting complex\/cyclosome.","abstract":"The anaphase-promoting complex\/cyclosome (APC\/C) is a massive E3 ligase that controls mitosis by catalyzing ubiquitination of key cell cycle regulatory proteins. The APC\/C assembly contains two subcomplexes: the \"Platform\" centers around a cullin-RING-like E3 ligase catalytic core; the \"Arc Lamp\" is a hub that mediates transient association with regulators and ubiquitination substrates. The Arc Lamp contains the small subunits APC16, CDC26, and APC13, and tetratricopeptide repeat (TPR) proteins (APC7, APC3, APC6, and APC8) that homodimerize and stack with quasi-2-fold symmetry. Within the APC\/C complex, APC3 serves as center for regulation. APC3's TPR motifs recruit substrate-binding coactivators, CDC20 and CDH1, via their C-terminal conserved Ile-Arg (IR) tail sequences. Human APC3 also binds APC16 and APC7 and contains a &gt;200-residue loop that is heavily phosphorylated during mitosis, although the basis for APC3 interactions and whether loop phosphorylation is required for ubiquitination are unclear. Here, we map the basis for human APC3 assembly with APC16 and APC7, report crystal structures of APC3\u0394loop alone and in complex with the C-terminal domain of APC16, and test roles of APC3's loop and IR tail binding surfaces in APC\/C-catalyzed ubiquitination. The structures show how one APC16 binds asymmetrically to the symmetric APC3 dimer and, together with biochemistry and prior data, explain how APC16 recruits APC7 to APC3, show how APC3's C-terminal domain is rearranged in the full APC\/C assembly, and visualize residues in the IR tail binding cleft important for coactivator-dependent ubiquitination. Overall, the results provide insights into assembly, regulation, and interactions of TPR proteins and the APC\/C.","authors":"Yamaguchi, M., Yu, S., Qiao, R., Weissmann, F., Miller, DJ., VanderLinden, R., Brown, NG., Frye, JJ., Peters, JM., Schulman, BA.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Mol Biol","volume":"427","issue":"8","page":"1748-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7975222","title":"Psoralen treatment of adenovirus particles eliminates virus replication and transcription while maintaining the endosomolytic activity of the virus capsid.","abstract":"Adenovirus entry into its host cell transiently permeabilizes the cell allowing the coentry of reagents such as DNA. We compare here adenovirus inactivation with beta-propiolactone and several psoralen derivatives, seeking reagents that disrupt the viral genome without impairing the viral entry functions. No virus replication can be detected after 8-methoxypsoralen (8-MOP) modification. Viral transcription is not detectable by Northern analysis, and reverse transcriptase\/PCR analysis demonstrates at least a 1000-fold decrease in viral transcription after 8-MOP treatment. Using [3H]8-MOP, the psoralen is found to enter the virus capsid and react throughout the viral genome, with approximately one psoralen modification per 100 bp of viral DNA. This inactivated adenovirus allows us to deliver DNA to target cells without interference from adenovirus gene expression or replication. Furthermore, we can now study the host cell response to adenovirus entry without the complications of adenovirus gene expression.","authors":"Cotten, M., Saltik, M., Kursa, M., Wagner, E., Maass, G., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Virology","volume":"205","issue":"1","page":"254-61","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1994-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23902686","title":"Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation.","abstract":"Cell migration is commonly accompanied by protrusion of membrane ruffles and lamellipodia. In two-dimensional migration, protrusion of these thin sheets of cytoplasm is considered relevant to both exploration of new space and initiation of nascent adhesion to the substratum. Lamellipodium formation can be potently stimulated by Rho GTPases of the Rac subfamily, but also by RhoG or Cdc42. Here we describe viable fibroblast cell lines genetically deficient for Rac1 that lack detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent lamellipodia, but these structures were restored by expression of either Rac subfamily member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction in wound closure and random cell migration and a notable loss of sensitivity to a chemotactic gradient. Despite these defects, Rac-deficient cells were able to spread, formed filopodia and established focal adhesions. Spreading in these cells was achieved by the extension of filopodia followed by the advancement of cytoplasmic veils between them. The number and size of focal adhesions as well as their intensity were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased the mobility of different components in focal adhesions, potentially explaining how Rac - although not essential - can contribute to focal adhesion assembly. Together, our data demonstrate that Rac signaling is essential for lamellipodium protrusion and for efficient cell migration, but not for spreading or filopodium formation. Our findings also suggest that Rac GTPases are crucial to the establishment or maintenance of polarity in chemotactic migration.","authors":"Steffen, A., Ladwein, M., Dimchev, GA., Hein, A., Schwenkmezger, L., Arens, S., Ladwein, KI., Margit Holleboom, J., Schur, F., Victor Small, J., Schwarz, J., Gerhard, R., Faix, J., Stradal, TE., Brakebusch, C., Rottner, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Cell Sci","volume":"126","issue":"Pt 20","page":"4572-88","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25064852","title":"Central amygdala PKC-\u03b4(+) neurons mediate the influence of multiple anorexigenic signals.","abstract":"Feeding can be inhibited by multiple cues, including those associated with satiety, sickness or unpalatable food. How such anorexigenic signals inhibit feeding at the neural circuit level is not completely understood. Although some inhibitory circuits have been identified, it is not yet clear whether distinct anorexigenic influences are processed in a convergent or parallel manner. The amygdala central nucleus (CEA) has been implicated in feeding control, but its role is controversial. The lateral subdivision of CEA (CEl) contains a subpopulation of GABAergic neurons that are marked by protein kinase C-\u03b4 (PKC-\u03b4). We found that CEl PKC-\u03b4(+) neurons in mice were activated by diverse anorexigenic signals in vivo, were required for the inhibition of feeding by such signals and strongly suppressed food intake when activated. They received presynaptic inputs from anatomically distributed neurons activated by different anorexigenic agents. Our data suggest that CEl PKC-\u03b4(+) neurons constitute an important node that mediates the influence of multiple anorexigenic signals.","authors":"Cai, H., Haubensak, W., Anthony, TE., Anderson, DJ.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Neurosci","volume":"17","issue":"9","page":"1240-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40930075","title":"Trio fatale: Neutrophils, NETs, and necrosis.","abstract":"In a recent issue of Nature, Adrover et al. report a neutrophil subset that induces pleomorphic tumor necrosis through neutrophil extracellular trap (NET)-mediated vascular occlusion. This process drives epithelial-to-mesenchymal transition (EMT) and metastasis of perinecrotic cancer cells, reframing necrosis as an active process and uncovering targetable mechanisms to combat cancer dissemination.","authors":"Estivill, G., Obenauf, AC.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Immunity","volume":"58","issue":"9","page":"2154-2156","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-09-10","doi":"10.1016\/j.immuni.2025.08.010","first_author":null,"corresponding_authors":null},{"pmid":"19233659","title":"Selectivity profiling of DegP substrates and inhibitors.","abstract":"Protein quality control factors are involved in many key physiological processes and severe human diseases that are based on misfolding or amyloid formation. Prokaryotic representatives are often virulence factors of pathogenic bacteria. Therefore, protein quality control factors represent a novel class of drug targets. The bacterial serine protease DegP, belonging to the widely conserved family of HtrA proteases, exhibits unusual structural and functional plasticity that could be exploited by small molecule modulators. However, only one weak synthetic peptide substrate and no inhibitors are available to date. We report the identification of a potent heptameric pNA-substrate and chloromethyl ketone based inhibitors of DegP. In addition, specificity profiling resulted in the identification of one strong inhibitor and a potent substrate for subtilisin as well as a number of specific elastase substrates and inhibitors.","authors":"Hauske, P., Meltzer, M., Ottmann, C., Krojer, T., Clausen, T., Ehrmann, M., Kaiser, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Bioorg Med Chem","volume":"17","issue":"7","page":"2920-4","pdf":null,"JrId":"8539","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"50","title":"Circular dichroism and fluorescence studies of homogeneous antibodies to type III pneumococcal polysaccharide.","abstract":"The near-ultraviolet circular dichroism (CD) of three homogeneous anti-type III pneumococcal antibodies in the absence and the presence of the specific hexasaccharide ligand was studied. In addition recombinations and hybridizations of H and L chains derived from two of these antibodies were carried out and the CD spectra of bound and free reconstituted IgG molecules were measured. The results indicate that the CD spectra of the native antibodies in the 260-310-nm range are very similar in shape and sign and exhibit a positive band at 285 nm. The homologous reconstituted antibody molecules exhibited CD spectra very similar in shape and sign to those of the native antibody molecules although recombinant molecules are no longer stabilized by interchain disulfide bonds. Upon addition of the hexasaccharide ligand, a significant decrease in amplitude of the CD spectra (18-21%) occurred in all three native antibodies and their Fab fragments as well as in the homologous recombinant molecules. No CD spectral changes could be detected upon interaction of the hapten ligand with the heterologous recombinants. All homogeneous antibodies studied exhibited fluorescence quenching upon oligosaccharide binding and a blue shift of the emission maximum. This property allowed the determination of the binding constant of one selected antibody to be made. Taken together, CD and fluorescence spectroscopic data suggest that oligosaccharide ligands induced detectable conformational changes in the Fab fragment of the antibody.","authors":"Jaton, JC., Huser, H., Blatt, Y., Pecht, I.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"24","page":"5308-11","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24493848","title":"Long-term expression of human contextual fear and extinction memories involves amygdala, hippocampus and ventromedial prefrontal cortex: a reinstatement study in two independent samples.","abstract":"Human context conditioning studies have focused on acquisition and extinction. Subsequent long-term changes in fear behaviors not only depend on associative learning processes during those phases but also on memory consolidation processes and the later ability to retrieve and express fear and extinction memories. Clinical theories explain relapse after successful exposure-based treatment with return of fear memories and remission with stable extinction memory expression. We probed contextual fear and extinction memories 1 week (Day8) after conditioning (Day1) and subsequent extinction (Day2) by presenting conditioned contexts before (Test1) and after (Test2) a reinstatement manipulation. We find consistent activation patterns in two independent samples: activation of a subgenual part of the ventromedial prefrontal cortex before reinstatement (Test1) and (albeit with different temporal profiles between samples) of the amygdala after reinstatement (Test2) as well as up-regulation of anterior hippocampus activity after reinstatement (Test2 &gt; Test1). These areas have earlier been implicated in the expression of cued extinction and fear memories. The present results suggest a general role for these structures in defining the balance between fear and extinction memories, independent of the conditioning mode. The results are discussed in the light of hypotheses implicating the anterior hippocampus in the processing of situational ambiguity.","authors":"Lonsdorf, TB., Haaker, J., Kalisch, R.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Soc Cogn Affect Neurosci","volume":"9","issue":"12","page":"1973-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19223442","title":"Genome-wide identification of targets of the drosha-pasha\/DGCR8 complex.","abstract":"Drosha is a type III RNase, which plays a critical role in miRNA biogenesis. Drosha and its double-stranded RNA-binding partner protein Pasha\/DGCR8 likely recognize and cleave miRNA precursor RNAs or pri-miRNA hairpins cotranscriptionally. To identify RNAs processed by Drosha, we used tiling microarrays to examine transcripts after depletion of drosha mRNA with dsRNA in Drosophila Schneider S2 cells. This strategy identified 137 Drosha-regulated RNAs, including 11 putative pri-miRNAs comprising 15 annotated miRNAs. Most of the identified pri-miRNAs seem extremely large, &gt;10 kb as revealed by both the Drosha knock-down strategy and by RNA PolII chromatin IP followed by Drosophila tiling microarrays. Surprisingly, more than a hundred additional RNAs not annotated as miRNAs are under Drosha control and are likely to be direct targets of Drosha action. This is because many of them encode annotated genes, and unlike bona fide pri-miRNAs, they are not affected by depletion of the miRNA processing factor, dicer-1. Moreover, application of the evofold analysis software indicates that at least 25 of the Drosha-regulated RNAs contain evolutionarily conserved hairpins similar to those recognized by the Drosha-Pasha\/DGCR8 complex in pri-miRNAs. One of these hairpins is located in the 5' UTR of both pasha and mammalian DGCR8. These observations suggest that a negative feedback loop acting on pasha mRNA may regulate the miRNA-biogenesis pathway: i.e., excess Drosha cleaves pasha\/DGCR8 primary transcripts and leads to a reduction in pasha\/DGCR8 mRNA levels and Pasha\/DGCR8 synthesis.","authors":"Kadener, S., Rodriguez, J., Abruzzi, KC., Khodor, YL., Sugino, K., Marr, MT., Nelson, S., Rosbash, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"RNA","volume":"15","issue":"4","page":"537-45","pdf":null,"JrId":"8792","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25517091","title":"Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.","abstract":"Gene transcription in animals involves the assembly of RNA polymerase II at core promoters and its cell-type-specific activation by enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has been less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different core promoters might exhibit an intrinsic specificity to certain enhancers. This is conceivable, as various core promoter sequence elements are differentially distributed between genes of different functions, including elements that are predominantly found at either developmentally regulated or at housekeeping genes. Here we show that thousands of enhancers in Drosophila melanogaster S2 and ovarian somatic cells (OSCs) exhibit a marked specificity to one of two core promoters--one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor--and confirm the existence of these two classes for five additional core promoters from genes with diverse functions. Housekeeping enhancers are active across the two cell types, while developmental enhancers exhibit strong cell-type specificity. Both enhancer classes differ in their genomic distribution, the functions of neighbouring genes, and the core promoter elements of these neighbouring genes. In addition, we identify two transcription factors--Dref and Trl--that bind and activate housekeeping versus developmental enhancers, respectively. Our results provide evidence for a sequence-encoded enhancer-core-promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.","authors":"Zabidi, MA., Arnold, CD., Schernhuber, K., Pagani, M., Rath, M., Frank, O., Stark, A.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nature","volume":"518","issue":"7540","page":"556-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30278038","title":"Cryptochrome: The magnetosensor with a sinister side?","abstract":"Over the last three decades, evidence has emerged that low-intensity magnetic fields can influence biological systems. It is now well established that migratory birds have the capacity to detect the Earth's magnetic field; it has been reported that power lines are associated with childhood leukemia and that pulsed magnetic fields increase the production of reactive oxidative species (ROS) in cellular systems. Justifiably, studies in this field have been viewed with skepticism, as the underlying molecular mechanisms are unknown. In the accompanying paper, Sherrard and colleagues report that low-flux pulsed electromagnetic fields (PEMFs) result in aversive behavior in Drosophila larvae and ROS production in cell culture. They further report that these responses require the presence of cryptochrome, a putative magnetoreceptor. If correct, it is conceivable that carcinogenesis associated with power lines, PEMF-induced ROS generation, and animal magnetoreception share a common mechanistic basis.","authors":"Landler, L., Keays, DA.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"PLoS Biol","volume":"16","issue":"10","page":"e3000018","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25081352","title":"The exon junction complex is required for definition and excision of neighboring introns in Drosophila.","abstract":"Splicing of pre-mRNAs results in the deposition of the exon junction complex (EJC) upstream of exon-exon boundaries. The EJC plays crucial post-splicing roles in export, translation, localization, and nonsense-mediated decay of mRNAs. It also aids faithful splicing of pre-mRNAs containing large introns, albeit via an unknown mechanism. Here, we show that the core EJC plus the accessory factors RnpS1 and Acinus aid in definition and efficient splicing of neighboring introns. This requires prior deposition of the EJC in close proximity to either an upstream or downstream splicing event. If present in isolation, EJC-dependent introns are splicing-defective also in wild-type cells. Interestingly, the most affected intron belongs to the piwi locus, which explains the reported transposon desilencing in EJC-depleted Drosophila ovaries. Based on a transcriptome-wide analysis, we propose that the dependency of splicing on the EJC is exploited as a means to control the temporal order of splicing events.","authors":"Hayashi, R., Handler, D., Ish-Horowicz, D., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genes Dev","volume":"28","issue":"16","page":"1772-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19147653","title":"Cardiac regulation by phosphoinositide 3-kinases and PTEN.","abstract":"The diverse effects mediated by PI3K\/PTEN (phosphoinositide 3-kinase\/phosphatase and tensin homologue deleted on chromosome 10) signalling in the heart clearly support an important biological and pathophysiological role for this signalling cascade. PI3Ks are a family of evolutionarily conserved lipid kinases that mediate many cellular responses to physiological and pathophysiological stimuli. Class I PI3K can be activated by either receptor tyrosine kinase\/cytokine receptor activation (class IA) or G-protein-coupled receptors (class IB), leading to the generation of phosphatidyl inositol (3,4,5)P3 and recruitment and activation of Akt\/protein kinase B, 3'-phosphoinositide-dependent kinase-1 (PDK1), or monomeric G-proteins, and phosphorylation of a wide range of downstream targets including glycogen synthase kinase 3beta (GSK3beta), mTOR (mammalian target of rapamycin), p70S6 kinase, endothelial nitric oxide synthase, and several anti-apoptotic effectors. Class IA (PI3Kalpha, beta, and delta) and class IB (PI3Kgamma) PI3Ks mediate distinct phenotypes in the heart under negative control by the 3'-lipid phosphatase PTEN, which dephosphorylates PtdIns(3,4,5)P3 to generate PtdIns(4,5)P2. PI3Kalpha, PI3Kgamma, and PTEN are expressed in cardiomyocytes, fibroblasts, endothelial cells, and vascular smooth muscle cells, where they modulate cell survival, hypertrophy, contractility, metabolism, and mechanotransduction. The PI3K\/PTEN signalling pathways are involved in a wide variety of diseases including myocardial hypertrophy and contractility, heart failure, and preconditioning. In this review, we discuss the signalling pathways mediated by PI3K class I isoforms and PTEN and their roles in cardiac structure and function.","authors":"Oudit, GY., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cardiovasc Res","volume":"82","issue":"2","page":"250-60","pdf":null,"JrId":"2812","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19144645","title":"Dynamic Histone H1 Isotype 4 Methylation and Demethylation by Histone Lysine Methyltransferase G9a\/KMT1C and the Jumonji Domain-containing JMJD2\/KDM4 Proteins.","abstract":"The linker histone H1 generally participates in the establishment of chromatin structure. However, of the seven somatic H1 isotypes in humans some are also implicated in the regulation of local gene expression. Histone H1 isotype 4 (H1.4) represses transcription, and its lysine residue 26 (Lys(26)) was found to be important in this aspect. H1.4K26 is known to be methylated and acetylated in vivo, but the enzymes responsible for these post-translational modifications and the regulatory cues that promote H1.4 residence on chromatin are poorly characterized. Here we report that the euchromatic histone lysine methyltransferase G9a\/KMT1C mediates H1.4K26 mono- and dimethylation in vitro and in vivo and thereby provides a recognition surface for the chromatin-binding proteins HP1 and L3MBTL1. Moreover, we show evidence that G9a promotes H1 deposition and is required for retention of H1 on chromatin. We also identify members of the JMJD2\/KDM4 subfamily of jumonji-C type histone demethylases as being responsible for the removal of H1.4K26 methylation.","authors":"Trojer, P., Zhang, J., Yonezawa, M., Schmidt, A., Zheng, H., Jenuwein, T., Reinberg, D.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Biol Chem","volume":"284","issue":"13","page":"8395-405","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-05-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23382688","title":"Mutation of the diamond-blackfan anemia gene Rps7 in mouse results in morphological and neuroanatomical phenotypes.","abstract":"The ribosome is an evolutionarily conserved organelle essential for cellular function. Ribosome construction requires assembly of approximately 80 different ribosomal proteins (RPs) and four different species of rRNA. As RPs co-assemble into one multi-subunit complex, mutation of the genes that encode RPs might be expected to give rise to phenocopies, in which the same phenotype is associated with loss-of-function of each individual gene. However, a more complex picture is emerging in which, in addition to a group of shared phenotypes, diverse RP gene-specific phenotypes are observed. Here we report the first two mouse mutations (Rps7(Mtu) and Rps7(Zma)) of ribosomal protein S7 (Rps7), a gene that has been implicated in Diamond-Blackfan anemia. Rps7 disruption results in decreased body size, abnormal skeletal morphology, mid-ventral white spotting, and eye malformations. These phenotypes are reported in other murine RP mutants and, as demonstrated for some other RP mutations, are ameliorated by Trp53 deficiency. Interestingly, Rps7 mutants have additional overt malformations of the developing central nervous system and deficits in working memory, phenotypes that are not reported in murine or human RP gene mutants. Conversely, Rps7 mouse mutants show no anemia or hyperpigmentation, phenotypes associated with mutation of human RPS7 and other murine RPs, respectively. We provide two novel RP mouse models and expand the repertoire of potential phenotypes that should be examined in RP mutants to further explore the concept of RP gene-specific phenotypes.","authors":"Watkins-Chow, DE., Cooke, J., Pidsley, R., Edwards, A., Slotkin, R., Leeds, KE., Mullen, R., Baxter, LL., Campbell, TG., Salzer, MC., Biondini, L., Gibney, G., Phan Dinh Tuy, F., Chelly, J., Morris, HD., Riegler, J., Lythgoe, MF., Arkell, RM., Loreni, F., Flint, J., Pavan, WJ., Keays, DA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"PLoS Genet","volume":"9","issue":"1","page":"e1003094","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40393401","title":"Gastrulation: Lessons from the quail embryo.","abstract":"Early development relies on reciprocal interactions between embryonic and extraembryonic tissues, but how this interplay controls embryo shape remains unclear. New findings in quail show that divergent morphogenetic responses in embryonic and extraembryonic territories involve non-uniform force propagation.","authors":"Ventura, G., Pinheiro, D.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Curr Biol","volume":"35","issue":"10","page":"R384-R386","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-21","doi":"10.1016\/j.cub.2025.04.001","first_author":null,"corresponding_authors":null},{"pmid":"19112489","title":"Gata3 acts downstream of beta-catenin signaling to prevent ectopic metanephric kidney induction.","abstract":"Metanephric kidney induction critically depends on mesenchymal-epithelial interactions in the caudal region of the nephric (or Wolffian) duct. Central to this process, GDNF secreted from the metanephric mesenchyme induces ureter budding by activating the Ret receptor expressed in the nephric duct epithelium. A failure to regulate this pathway is believed to be responsible for a large proportion of the developmental anomalies affecting the urogenital system. Here, we show that the nephric duct-specific inactivation of the transcription factor gene Gata3 leads to massive ectopic ureter budding. This results in a spectrum of urogenital malformations including kidney adysplasia, duplex systems, and hydroureter, as well as vas deferens hyperplasia and uterine agenesis. The variability of developmental defects is reminiscent of the congenital anomalies of the kidney and urinary tract (CAKUT) observed in human. We show that Gata3 inactivation causes premature nephric duct cell differentiation and loss of Ret receptor gene expression. These changes ultimately affect nephric duct epithelium homeostasis, leading to ectopic budding of interspersed cells still expressing the Ret receptor. Importantly, the formation of these ectopic buds requires both GDNF\/Ret and Fgf signaling activities. We further identify Gata3 as a central mediator of beta-catenin function in the nephric duct and demonstrate that the beta-catenin\/Gata3 pathway prevents premature cell differentiation independently of its role in regulating Ret expression. Together, these results establish a genetic cascade in which Gata3 acts downstream of beta-catenin, but upstream of Ret, to prevent ectopic ureter budding and premature cell differentiation in the nephric duct.","authors":"Grote, D., Boualia, SK., Souabni, A., Merkel, C., Chi, X., Costantini, F., Carroll, T., Bouchard, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"PLoS Genet","volume":"4","issue":"12","page":"e1000316","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19088193","title":"Multilayer three-dimensional super resolution imaging of thick biological samples.","abstract":"Recent advances in optical microscopy have enabled biological imaging beyond the diffraction limit at nanometer resolution. A general feature of most of the techniques based on photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM) has been the use of thin biological samples in combination with total internal reflection, thus limiting the imaging depth to a fraction of an optical wavelength. However, to study whole cells or organelles that are typically up to 15 microm deep into the cell, the extension of these methods to a three-dimensional (3D) super resolution technique is required. Here, we report an advance in optical microscopy that enables imaging of protein distributions in cells with a lateral localization precision better than 50 nm at multiple imaging planes deep in biological samples. The approach is based on combining the lateral super resolution provided by PALM with two-photon temporal focusing that provides optical sectioning. We have generated super-resolution images over an axial range of approximately 10 microm in both mitochondrially labeled fixed cells, and in the membranes of living S2 Drosophila cells.","authors":"Vaziri, A., Tang, J., Shroff, H., Shank, CV.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Proc Natl Acad Sci U S A","volume":"105","issue":"51","page":"20221-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22416045","title":"Vestibular and motor contributions to mobility: limitations of seniors awaiting discharge from hospital care.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22416045<\/PMID><DateCompleted><Year>2013<\/Year><Month>05<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2012<\/Year><Month>12<\/Month><Day>11<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2865<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>17<\/Volume><Issue>4<\/Issue><PubDate><Year>2012<\/Year><Month>Dec<\/Month><\/PubDate><\/JournalIssue><Title>Physiotherapy research international : the journal for researchers and clinicians in physical therapy<\/Title><ISOAbbreviation>Physiother Res Int<\/ISOAbbreviation><\/Journal><ArticleTitle>Vestibular and motor contributions to mobility: limitations of seniors awaiting discharge from hospital care.<\/ArticleTitle><Pagination><MedlinePgn>200-7<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/pri.532<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND AND PURPOSE\" NlmCategory=\"OBJECTIVE\">Following hospitalization, seniors are at risk of impaired mobility and increased risk of falling, which can lead to injuries and re-admission. The primary purpose of this paper was to evaluate the ability of hospitalized seniors to use vestibular inputs for balance control. The secondary purpose was to examine the influence of vestibular function and lower limb muscle strength on mobility.","authors":"Golder, MD., Earl, EM., Mallery, LH.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Physiother Res Int","volume":"17","issue":"4","page":"200-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34001887","title":"TRPM7 kinase-mediated immunomodulation in macrophage plays a central role in magnesium ion-induced bone regeneration.","abstract":"Despite the widespread observations on the osteogenic effects of magnesium ion (Mg<sup>2+<\/sup>), the diverse roles of Mg<sup>2+<\/sup> during bone healing have not been systematically dissected. Here, we reveal a previously unknown, biphasic mode of action of Mg<sup>2+<\/sup> in bone repair. During the early inflammation phase, Mg<sup>2+<\/sup> contributes to an upregulated expression of transient receptor potential cation channel member 7 (TRPM7), and a TRPM7-dependent influx of Mg<sup>2+<\/sup> in the monocyte-macrophage lineage, resulting in the cleavage and nuclear accumulation of TRPM7-cleaved kinase fragments (M7CKs). This then triggers the phosphorylation of Histone H3 at serine 10, in a TRPM7-dependent manner at the promoters of inflammatory cytokines, leading to the formation of a pro-osteogenic immune microenvironment. In the later remodeling phase, however, the continued exposure of Mg<sup>2+<\/sup> not only lead to the over-activation of NF-\u03baB signaling in macrophages and increased number of osteoclastic-like cells but also decelerates bone maturation through the suppression of hydroxyapatite precipitation. Thus, the negative effects of Mg<sup>2+<\/sup> on osteogenesis can override the initial pro-osteogenic benefits of Mg<sup>2+<\/sup>. Taken together, this study establishes a paradigm shift in the understanding of the diverse and multifaceted roles of Mg<sup>2+<\/sup> in bone healing.","authors":"Qiao, W., Wong, KHM., Shen, J., Wang, W., Wu, J., Li, J., Lin, Z., Chen, Z., Matinlinna, JP., Zheng, Y., Wu, S., Liu, X., Lai, KP., Chen, Z., Lam, YW., Cheung, KMC., Yeung, KWK.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"2885","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33238118","title":"Induction of Human Trophoblast Stem Cells from Somatic Cells and Pluripotent Stem Cells.","abstract":"Human trophoblast stem cells (hTSCs) derived from blastocysts and first-trimester cytotrophoblasts offer an unprecedented opportunity to study the placenta. However, access to human embryos and first-trimester placentas is limited, thus preventing the establishment of hTSCs from diverse genetic backgrounds associated with placental disorders. Here, we show that hTSCs can be generated from numerous genetic backgrounds using post-natal cells via two alternative methods: (1) somatic cell reprogramming of adult fibroblasts with OCT4, SOX2, KLF4, MYC (OSKM) and (2) cell fate conversion of naive and extended pluripotent stem cells. The resulting induced\/converted hTSCs recapitulated hallmarks of hTSCs including long-term self-renewal, expression of specific transcription factors, transcriptomic signature, and the potential to differentiate into syncytiotrophoblast and extravillous trophoblast cells. We also clarified the developmental stage of hTSCs and show that these cells resemble day 8 cytotrophoblasts. Altogether, hTSC lines of diverse genetic origins open the possibility to model both placental development and diseases in a dish.","authors":"Castel, G., Meistermann, D., Bretin, B., Firmin, J., Blin, J., Loubersac, S., Bruneau, A., Chevolleau, S., Kilens, S., Chariau, C., Gaignerie, A., Francheteau, Q., Kagawa, H., Charpentier, E., Flippe, L., Fran\u00e7ois-Campion, V., Haider, S., Dietrich, B., Kn\u00f6fler, M., Arima, T., Bourdon, J., Rivron, N., Masson, D., Fournier, T., Okae, H., Fr\u00e9our, T., David, L.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Rep","volume":"33","issue":"8","page":"108419","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33995677","title":"The role of microRNAs in the osteogenic and chondrogenic differentiation of mesenchymal stem cells and bone pathologies.","abstract":"Mesenchymal stem cells (MSCs) have been identified in many adult tissues. MSCs can regenerate through cell division or differentiate into adipocytes, osteoblasts and chondrocytes. As a result, MSCs have become an important source of cells in tissue engineering and regenerative medicine for bone tissue and cartilage. Several epigenetic factors are believed to play a role in MSCs differentiation. Among these, microRNA (miRNA) regulation is involved in the fine modulation of gene expression during osteogenic\/chondrogenic differentiation. It has been reported that miRNAs are involved in bone homeostasis by modulating osteoblast gene expression. In addition, countless evidence has demonstrated that miRNAs dysregulation is involved in the development of osteoporosis and bone fractures. The deregulation of miRNAs expression has also been associated with several malignancies including bone cancer. In this context, bone-associated circulating miRNAs may be useful biomarkers for determining the predisposition, onset and development of osteoporosis, as well as in clinical applications to improve the diagnosis, follow-up and treatment of cancer and metastases. Overall, this review will provide an overview of how miRNAs activities participate in osteogenic\/chondrogenic differentiation, while addressing the role of miRNA regulatory effects on target genes. Finally, the role of miRNAs in pathologies and therapies will be presented.","authors":"Iaquinta, MR., Lanzillotti, C., Mazziotta, C., Bononi, I., Frontini, F., Mazzoni, E., Oton-Gonzalez, L., Rotondo, JC., Torreggiani, E., Tognon, M., Martini, F.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Theranostics","volume":"11","issue":"13","page":"6573-6591","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40","title":"Human brain and placental choline acetyltransferase: purification and properties.","abstract":"Choline acetyltransferase (EC 2.3.1.6) catalyzes the biosynthesis of acetylcholine according to the following chemical equation: acetyl-CoA + choline in equilibrium to acetylcholine + CoA. In addition to nervous tissue, primate placenta is the only other animal source which contains appreciable acetylcholine and its biosynthetic enzyme. Human brain caudate nucleus and human placental choline acetyltransferase were purified to electrophoretic homogeneity using ion-exchange and blue dextran-Sepharose affinity chromatography. The molecular weights determined by Sephadex G-150 gel filtration and sodium dodecyl sulfate gel electrophoresis are 67000 plus or minus 3000. N-Ethylmaleimide, p-chloromercuribenzoate, and dithiobis(2-nitrobenzoic acid) inhibit the enzyme. Dithiothreitol reverses the inhibition produced by the latter two reagents. The pKa of the group associated with N-ethylmaleimide inhibition is 8.6 plus or minus 0.3. A chemically competent acetyl-thioenzyme is isolable by Sephadex gel filtration. The enzymes from the brain and placenta are thus far physically and biochemically indistinguishable.","authors":"Roskoski, R., Lim, CT., Roskoski, LM.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"23","page":"5105-10","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29320478","title":"An extracellular network of Arabidopsis leucine-rich repeat receptor kinases.","abstract":"The cells of multicellular organisms receive extracellular signals using surface receptors. The extracellular domains (ECDs) of cell surface receptors function as interaction platforms, and as regulatory modules of receptor activation. Understanding how interactions between ECDs produce signal-competent receptor complexes is challenging because of their low biochemical tractability. In plants, the discovery of ECD interactions is complicated by the massive expansion of receptor families, which creates tremendous potential for changeover in receptor interactions. The largest of these families in Arabidopsis thaliana consists of 225 evolutionarily related leucine-rich repeat receptor kinases (LRR-RKs), which function in the sensing of microorganisms, cell expansion, stomata development and stem-cell maintenance. Although the principles that govern LRR-RK signalling activation are emerging, the systems-level organization of this family of proteins is unknown. Here, to address this, we investigated 40,000 potential ECD interactions using a sensitized high-throughput interaction assay, and produced an LRR-based cell surface interaction network (CSI<sup>LRR<\/sup>) that consists of 567 interactions. To demonstrate the power of CSI<sup>LRR<\/sup> for detecting biologically relevant interactions, we predicted and validated the functions of uncharacterized LRR-RKs in plant growth and immunity. In addition, we show that CSI<sup>LRR<\/sup> operates as a unified regulatory network in which the LRR-RKs most crucial for its overall structure are required to prevent the aberrant signalling of receptors that are several network-steps away. Thus, plants have evolved LRR-RK networks to process extracellular signals into carefully balanced responses.","authors":"Smakowska-Luzan, E., Mott, GA., Parys, K., Stegmann, M., Howton, TC., Layeghifard, M., Neuhold, J., Lehner, A., Kong, J., Gr\u00fcnwald, K., Weinberger, N., Satbhai, SB., Mayer, D., Busch, W., Madalinski, M., Stolt-Bergner, P., Provart, NJ., Mukhtar, MS., Zipfel, C., Desveaux, D., Guttman, DS., Belkhadir, Y.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"553","issue":"7688","page":"342-346","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23502960","title":"Focal segmental glomerulosclerosis is induced by microRNA-193a and its downregulation of WT1.","abstract":"Focal segmental glomerulosclerosis (FSGS) is a frequent and severe glomerular disease characterized by destabilization of podocyte foot processes. We report that transgenic expression of the microRNA miR-193a in mice rapidly induces FSGS with extensive podocyte foot process effacement. Mechanistically, miR-193a inhibits the expression of the Wilms' tumor protein (WT1), a transcription factor and master regulator of podocyte differentiation and homeostasis. Decreased expression levels of WT1 lead to downregulation of its target genes PODXL (podocalyxin) and NPHS1 (nephrin), as well as several other genes crucial for the architecture of podocytes, initiating a catastrophic collapse of the entire podocyte-stabilizing system. We found upregulation of miR-193a in isolated glomeruli from individuals with FSGS compared to normal kidneys or individuals with other glomerular diseases. Thus, upregulation of miR-193a provides a new pathogenic mechanism for FSGS and is a potential therapeutic target.","authors":"Gebeshuber, CA., Kornauth, C., Dong, L., Sierig, R., Seibler, J., Reiss, M., Tauber, S., Bilban, M., Wang, S., Kain, R., B\u00f6hmig, GA., Moeller, MJ., Gr\u00f6ne, HJ., Englert, C., Martinez, J., Kerjaschki, D.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Med","volume":"19","issue":"4","page":"481-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23349049","title":"GABAergic neurons regulate lateral ventricular development via transcription factor Pax5.","abstract":"Postmortem studies have revealed a downregulation of the transcription factor Pax5 in GABAergic neurons in bipolar disorder, a neurodevelopmental disorder, raising the question whether Pax5 in GABAergic neurons has a role in normal brain development. In a genetic approach to study functions of Pax5 in GABAergic neurons, Pax5 was specifically deleted in GABAergic neurons from Pax5 floxed mice using a novel Gad1-Cre transgenic mouse line expressing Cre recombinase in Gad1-positive, that is, GABAergic neurons. Surprisingly, these mice developed a marked enlargement of the lateral ventricles at approximately 7 weeks of age, which was lethal within 1-2 weeks of its appearance. This hydrocephalus phenotype was observed in mice homozygous or heterozygous for the Pax5 conditional knockout, with a gene dosage-dependent penetrance. By QTL (quantitative trait loci) mapping, a 3.5 Mb segment on mouse chromosome 4 flanked by markers D4Mit237 and D4Mit214 containing approximately 92 genes including Pax5 has previously been linked to differences in lateral ventricular size. Our findings are consistent with Pax5 being a relevant gene underlying this QTL phenotype and demonstrate that Pax5 in GABAergic neurons is essential for normal ventricular development.","authors":"Ohtsuka, N., Badurek, S., Busslinger, M., Benes, FM., Minichiello, L., Rudolph, U.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Genesis","volume":"51","issue":"4","page":"234-45","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25925253","title":"Caffeine-induced diuresis and natriuresis is independent of renal tubular NHE3.","abstract":"Caffeine is one of the most widely consumed behavioral substances. We have previously shown that caffeine- and theophylline-induced inhibition of renal reabsorption causes diuresis and natriuresis, an effect that requires functional adenosine A1 receptors. In this study, we tested the hypothesis that blocking the Gi protein-coupled adenosine A1 receptor via the nonselective adenosine receptor antagonist caffeine changes Na(+)\/H(+) exchanger isoform 3 (NHE3) localization and phosphorylation, resulting in diuresis and natriuresis. We generated tubulus-specific NHE3 knockout mice (Pax8-Cre), where NHE3 abundance in the S1, S2, and S3 segments of the proximal tubule was completely absent or severely reduced (&gt;85%) in the thick ascending limb. Consumption of fluid and food, as well as glomerular filtration rate, were comparable in control or tubulus-specific NHE3 knockout mice under basal conditions, while urinary pH was significantly more alkaline without evidence for metabolic acidosis. Caffeine self-administration increased total fluid and food intake comparably between genotypes, without significant differences in consumption of caffeinated solution. Acute caffeine application via oral gavage elicited a diuresis and natriuresis that was comparable between control and tubulus-specific NHE3 knockout mice. The diuretic and natriuretic response was independent of changes in total NHE3 expression, phosphorylation of serine-552 and serine-605, or apical plasma membrane NHE3 localization. Although caffeine had no clear effect on localization of the basolateral Na(+)\/bicarbonate cotransporter NBCe1, pretreatment with DIDS inhibited caffeine-induced diuresis and natriuresis. In summary, NHE3 is not required for caffeine-induced diuresis and natriuresis.","authors":"Fenton, RA., Poulsen, SB., de la Mora Chavez, S., Soleimani, M., Busslinger, M., Dominguez Rieg, JA., Rieg, T.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Am J Physiol Renal Physiol","volume":"308","issue":"12","page":"F1409-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19047520","title":"H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome.","abstract":"In mammals, genome-wide chromatin maps and immunofluorescence studies show that broad domains of repressive histone modifications are present on pericentromeric and telomeric repeats and on the inactive X chromosome. However, only a few autosomal loci such as silent Hox gene clusters have been shown to lie in broad domains of repressive histone modifications. Here we present a ChIP-chip analysis of the repressive H3K27me3 histone modification along chr 17 in mouse embryonic fibroblast cells using an algorithm named broad local enrichments (BLOCs), which allows the identification of broad regions of histone modifications. Our results, confirmed by BLOC analysis of a whole genome ChIP-seq data set, show that the majority of H3K27me3 modifications form BLOCs rather than focal peaks. H3K27me3 BLOCs modify silent genes of all types, plus flanking intergenic regions and their distribution indicates a negative correlation between H3K27me3 and transcription. However, we also found that some nontranscribed gene-poor regions lack H3K27me3. We therefore performed a low-resolution analysis of whole mouse chr 17, which revealed that H3K27me3 is enriched in mega-base-pair-sized domains that are also enriched for genes, short interspersed elements (SINEs) and active histone modifications. These genic H3K27me3 domains alternate with similar-sized gene-poor domains. These are deficient in active histone modifications, as well as H3K27me3, but are enriched for long interspersed elements (LINEs) and long-terminal repeat (LTR) transposons and H3K9me3 and H4K20me3. Thus, an autosome can be seen to contain alternating chromatin bands that predominantly separate genes from one retrotransposon class, which could offer unique domains for the specific regulation of genes or the silencing of autonomous retrotransposons.","authors":"Pauler, FM., Sloane, MA., Huang, R., Regha, K., Koerner, MV., Tamir, I., Sommer, A., Aszodi, A., Jenuwein, T., Barlow, DP.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genome Res","volume":"19","issue":"2","page":"221-33","pdf":null,"JrId":"8754","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32966782","title":"SFPQ Depletion Is Synthetically Lethal with BRAF<sup>V600E<\/sup> in Colorectal Cancer Cells.","abstract":"Oncoproteins such as the BRAF<sup>V600E<\/sup> kinase endow cancer cells with malignant properties, but they also create unique vulnerabilities. Targeting of BRAF<sup>V600E<\/sup>-driven cytoplasmic signaling networks has proved ineffective, as patients regularly relapse with reactivation of the targeted pathways. We identify the nuclear protein SFPQ to be synthetically lethal with BRAF<sup>V600E<\/sup> in a loss-of-function shRNA screen. SFPQ depletion decreases proliferation and specifically induces S-phase arrest and apoptosis in BRAF<sup>V600E<\/sup>-driven colorectal and melanoma cells. Mechanistically, SFPQ loss in BRAF-mutant cancer cells triggers the Chk1-dependent replication checkpoint, results in decreased numbers and reduced activities of replication factories, and increases collision between replication and transcription. We find that BRAF<sup>V600E<\/sup>-mutant cancer cells and organoids are sensitive to combinations of Chk1 inhibitors and chemically induced replication stress, pointing toward future therapeutic approaches exploiting nuclear vulnerabilities induced by BRAF<sup>V600E<\/sup>.","authors":"Klotz-Noack, K., Klinger, B., Rivera, M., Bublitz, N., Uhlitz, F., Riemer, P., L\u00fcthen, M., Sell, T., Kasack, K., Gastl, B., Ispasanie, SSS., Simon, T., Janssen, N., Schwab, M., Zuber, J., Horst, D., Bl\u00fcthgen, N., Sch\u00e4fer, R., Morkel, M., Sers, C.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Rep","volume":"32","issue":"12","page":"108184","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19043546","title":"Mutations in AtPS1 (Arabidopsis thaliana parallel spindle 1) lead to the production of diploid pollen grains.","abstract":"Polyploidy has had a considerable impact on the evolution of many eukaryotes, especially angiosperms. Indeed, most--if not all-angiosperms have experienced at least one round of polyploidy during the course of their evolution, and many important crop plants are current polyploids. The occurrence of 2n gametes (diplogametes) in diploid populations is widely recognised as the major source of polyploid formation. However, limited information is available on the genetic control of diplogamete production. Here, we describe the isolation and characterisation of the first gene, AtPS1 (Arabidopsis thaliana Parallel Spindle 1), implicated in the formation of a high frequency of diplogametes in plants. Atps1 mutants produce diploid male spores, diploid pollen grains, and spontaneous triploid plants in the next generation. Female meiosis is not affected in the mutant. We demonstrated that abnormal spindle orientation at male meiosis II leads to diplogamete formation. Most of the parent's heterozygosity is therefore conserved in the Atps1 diploid gametes, which is a key issue for plant breeding. The AtPS1 protein is conserved throughout the plant kingdom and carries domains suggestive of a regulatory function. The isolation of a gene involved in diplogamete production opens the way for new strategies in plant breeding programmes and progress in evolutionary studies.","authors":"d'Erfurth, I., Jolivet, S., Froger, N., Catrice, O., Novatchkova, M., Simon, M., Jenczewski, E., Mercier, R.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"PLoS Genet","volume":"4","issue":"11","page":"e1000274","pdf":null,"JrId":"32385","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23477864","title":"The lipid mediator protectin D1 inhibits influenza virus replication and improves severe influenza.","abstract":"Influenza A viruses are a major cause of mortality. Given the potential for future lethal pandemics, effective drugs are needed for the treatment of severe influenza such as that caused by H5N1 viruses. Using mediator lipidomics and bioactive lipid screen, we report that the omega-3 polyunsaturated fatty acid (PUFA)-derived lipid mediator protectin D1 (PD1) markedly attenuated influenza virus replication via RNA export machinery. Production of PD1 was suppressed during severe influenza and PD1 levels inversely correlated with the pathogenicity of H5N1 viruses. Suppression of PD1 was genetically mapped to 12\/15-lipoxygenase activity. Importantly, PD1 treatment improved the survival and pathology of severe influenza in mice, even under conditions where known antiviral drugs fail to protect from death. These results identify the endogenous lipid mediator PD1 as an innate suppressor of influenza virus replication that protects against lethal influenza virus infection.","authors":"Morita, M., Kuba, K., Ichikawa, A., Nakayama, M., Katahira, J., Iwamoto, R., Watanebe, T., Sakabe, S., Daidoji, T., Nakamura, S., Kadowaki, A., Ohto, T., Nakanishi, H., Taguchi, R., Nakaya, T., Murakami, M., Yoneda, Y., Arai, H., Kawaoka, Y., Penninger, JM., Arita, M., Imai, Y.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell","volume":"153","issue":"1","page":"112-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23334295","title":"A structural basis for kinetochore recruitment of the Ndc80 complex via two distinct centromere receptors.","abstract":"The Ndc80 complex is the key microtubule-binding element of the kinetochore. In contrast to the well-characterized interaction of Ndc80-Nuf2 heads with microtubules, little is known about how the Spc24-25 heterodimer connects to centromeric chromatin. Here, we present molecular details of Spc24-25 in complex with the histone-fold protein Cnn1\/CENP-T illustrating how this connection ultimately links microtubules to chromosomes. The conserved Ndc80 receptor motif of Cnn1 is bound as an \u03b1 helix in a hydrophobic cleft at the interface between Spc24 and Spc25. Point mutations that disrupt the Ndc80-Cnn1 interaction also abrogate binding to the Mtw1 complex and are lethal in yeast. We identify a Cnn1-related motif in the Dsn1 subunit of the Mtw1 complex, necessary for Ndc80 binding and essential for yeast growth. Replacing this region with the Cnn1 peptide restores viability demonstrating functionality of the Ndc80-binding module in different molecular contexts. Finally, phosphorylation of the Cnn1 N-terminus coordinates the binding of the two competing Ndc80 interaction partners. Together, our data provide structural insights into the modular binding mechanism of the Ndc80 complex to its centromere recruiters.","authors":"Malvezzi, F., Litos, G., Schleiffer, A., Heuck, A., Mechtler, K., Clausen, T., Westermann, S.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"EMBO J","volume":"32","issue":"3","page":"409-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10753746","title":"A protein complex containing Inscuteable and the Galpha-binding protein Pins orients asymmetric cell divisions in Drosophila.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">10753746<\/PMID><DateCompleted><Year>2000<\/Year><Month>05<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>10<\/Volume><Issue>7<\/Issue><PubDate><Year>2000<\/Year><Month>Apr<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>A protein complex containing Inscuteable and the Galpha-binding protein Pins orients asymmetric cell divisions in Drosophila.<\/ArticleTitle><Pagination><MedlinePgn>353-62<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">In the fruit fly Drosophila, the Inscuteable protein localises to the apical cell cortex in neuroblasts and directs both the apical-basal orientation of the mitotic spindle and the basal localisation of the protein determinants Numb and Prospero during mitosis. Asymmetric localisation of Inscuteable is initiated during neuroblast delamination by direct binding to Bazooka, an apically localised protein that contains protein-interaction motifs known as PDZ domains. How apically localised Inscuteable directs asymmetric cell divisions is unclear.","authors":"Schaefer, M., Shevchenko, A., Shevchenko, A., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Curr Biol","volume":"10","issue":"7","page":"353-62","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2000-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23462470","title":"Progesterone drives mammary secretory differentiation via RankL-mediated induction of Elf5 in luminal progenitor cells.","abstract":"Progesterone-RankL paracrine signaling has been proposed as a driver of stem cell expansion in the mammary gland, and Elf5 is essential for the differentiation of mammary epithelial progenitor cells. We demonstrate that Elf5 expression is induced by progesterone and that Elf5 and progesterone cooperate to promote alveolar development. The progesterone receptor and Elf5 are expressed in a mutually exclusive pattern, and we identify RankL as the paracrine mediator of the effects of progesterone on Elf5 expression in CD61+ progenitor cells and their consequent differentiation. Blockade of RankL action prevented progesterone-induced side branching and the expansion of Elf5(+) mature luminal cells. These findings describe a mechanism by which steroid hormones can produce the expansion of steroid hormone receptor-negative mammary epithelial cells.","authors":"Lee, HJ., Gallego-Ortega, D., Ledger, A., Schramek, D., Joshi, P., Szwarc, MM., Cho, C., Lydon, JP., Khokha, R., Penninger, JM., Ormandy, CJ.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Development","volume":"140","issue":"7","page":"1397-401","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19038005","title":"Transforming growth factor-beta signaling at the tumor-bone interface promotes mammary tumor growth and osteoclast activation.","abstract":"Understanding the cellular and molecular changes in the bone microenvironment is important for developing novel therapeutics to control breast cancer bone metastasis. Although the underlying mechanism(s) of bone metastasis has been the focus of intense investigation, relatively little is known about complex molecular interactions between malignant cells and bone stroma. Using a murine syngeneic model that mimics osteolytic changes associated with human breast cancer, we examined the role of tumor-bone interaction in tumor-induced osteolysis and malignant growth in the bone microenvironment. We identified transforming growth factor-beta receptor 1 (TGF-betaRI) as a commonly upregulated gene at the tumor-bone (TB) interface. Moreover, TGF-betaRI expression and activation, analyzed by nuclear localization of phospho-Smad2, was higher in tumor cells and osteoclasts at the TB interface as compared to the tumor-alone area. Furthermore, attenuation of TGF-beta activity by neutralizing antibody to TGF-beta or TGF-betaRI kinase inhibitor reduced mammary tumor-induced osteolysis, TGF-betaRI expression and its activation. In addition, we demonstrate a potential role of TGF-beta as an important modifier of receptor activator of NF-kappaB ligand (RANKL)-dependent osteoclast activation and osteolysis. Together, these studies demonstrate that inhibition of TGF-betaRI signaling at the TB interface will be a therapeutic target in the treatment of breast cancer-induced osteolysis.","authors":"Futakuchi, M., Nannuru, KC., Varney, ML., Sadanandam, A., Nakao, K., Asai, K., Shirai, T., Sato, SY., Singh, RK.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cancer Sci","volume":"100","issue":"1","page":"71-81","pdf":null,"JrId":"30320","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33946862","title":"Lumican Inhibits Osteoclastogenesis and Bone Resorption by Suppressing Akt Activity.","abstract":"Lumican, a ubiquitously expressed small leucine-rich proteoglycan, has been utilized in diverse biological functions. Recent experiments demonstrated that lumican stimulates preosteoblast viability and differentiation, leading to bone formation. To further understand the role of lumican in bone metabolism, we investigated its effects on osteoclast biology. Lumican inhibited both osteoclast differentiation and in vitro bone resorption in a dose-dependent manner. Consistent with this, lumican markedly decreased the expression of osteoclastogenesis markers. Moreover, the migration and fusion of preosteoclasts and the resorptive activity per osteoclast were significantly reduced in the presence of lumican, indicating that this protein affects most stages of osteoclastogenesis. Among RANKL-dependent pathways, lumican inhibited Akt but not MAP kinases such as JNK, p38, and ERK. Importantly, co-treatment with an Akt activator almost completely reversed the effect of lumican on osteoclast differentiation. Taken together, our findings revealed that lumican inhibits osteoclastogenesis by suppressing Akt activity. Thus, lumican plays an osteoprotective role by simultaneously increasing bone formation and decreasing bone resorption, suggesting that it represents a dual-action therapeutic target for osteoporosis.","authors":"Lee, JY., Kim, DA., Kim, EY., Chang, EJ., Park, SJ., Kim, BJ.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Int J Mol Sci","volume":"22","issue":"9","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40608949","title":"A tighter grip on gene expression.","abstract":"A previously unknown cofactor function stabilizes transcription factor binding across the genome.","authors":"Nem\u010dko, F., Stark, A.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Science","volume":"389","issue":"6755","page":"31-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-07-03","doi":"10.1126\/science.adz2519","first_author":null,"corresponding_authors":null},{"pmid":"25576074","title":"Efficacy and mechanism of action of volasertib, a potent and selective inhibitor of Polo-like kinases, in preclinical models of acute myeloid leukemia.","abstract":"Polo-like kinase 1 (Plk1), a member of the Polo-like kinase family of serine\/threonine kinases, is a key regulator of multiple steps in mitosis. Here we report on the pharmacological profile of volasertib, a potent and selective Plk inhibitor, in multiple preclinical models of acute myeloid leukemia (AML) including established cell lines, bone marrow samples from AML patients in short-term culture, and subcutaneous as well as disseminated in vivo models in immune-deficient mice. Our results indicate that volasertib is highly efficacious as a single agent and in combination with established and emerging AML drugs, including the antimetabolite cytarabine, hypomethylating agents (decitabine, azacitidine), and quizartinib, a signal transduction inhibitor targeting FLT3. Collectively, these preclinical data support the use of volasertib as a new therapeutic approach for the treatment of AML patients, and provide a foundation for combination approaches that may further improve and prolong clinical responses.","authors":"Rudolph, D., Impagnatiello, MA., Blaukopf, C., Sommer, C., Gerlich, DW., Roth, M., Tontsch-Grunt, U., Wernitznig, A., Savarese, F., Hofmann, MH., Albrecht, C., Geiselmann, L., Reschke, M., Garin-Chesa, P., Zuber, J., Moll, J., Adolf, GR., Kraut, N.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Pharmacol Exp Ther","volume":"352","issue":"3","page":"579-89","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29481550","title":"Cell-type specific sequencing of microRNAs from complex animal tissues.","abstract":"MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular resolution. We report microRNome by methylation-dependent sequencing (mime-seq), an in vivo enzymatic small-RNA-tagging approach that enables high-throughput sequencing of tissue- and cell-type-specific miRNAs in animals. The method combines cell-type-specific 3'-terminal 2'-O-methylation of animal miRNAs by a genetically encoded, plant-specific methyltransferase (HEN1), with chemoselective small-RNA cloning and high-throughput sequencing. We show that mime-seq uncovers the miRNomes of specific cells within Caenorhabditis elegans and Drosophila at unprecedented specificity and sensitivity, enabling miRNA profiling with single-cell resolution in whole animals. Mime-seq overcomes current challenges in cell-type-specific small-RNA profiling and provides novel entry points for understanding the function of miRNAs in spatially restricted physiological settings.","authors":"Alberti, C., Manzenreither, RA., Sowemimo, I., Burkard, TR., Wang, J., Mahofsky, K., Ameres, SL., Cochella, L.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Methods","volume":"15","issue":"4","page":"283-289","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19033664","title":"Proliferation of human HCC cells and chemically induced mouse liver cancers requires JNK1-dependent p21 downregulation.","abstract":"JNK proteins have been shown to be involved in liver carcinogenesis in mice, but the extent of their involvement in the development of human liver cancers is unknown. Here, we show that activation of JNK1 but not JNK2 was increased in human primary hepatocellular carcinomas (HCCs). Further, JNK1 was required for human HCC cell proliferation in vitro and tumorigenesis after xenotransplantation. Importantly, mice lacking JNK1 displayed decreased tumor cell proliferation in a mouse model of liver carcinogenesis and decreased hepatocyte proliferation in a mouse model of liver regeneration. In both cases, impaired proliferation was caused by increased expression of p21, a cell-cycle inhibitor, and reduced expression of c-Myc, a negative regulator of p21. Genetic inactivation of p21 in JNK1-\/- mice restored hepatocyte proliferation in models of both liver carcinogenesis and liver regeneration, and overexpression of c-Myc increased proliferation of JNK1-\/- liver cells. Similarly, JNK1 was found to control the proliferation of human HCC cells by affecting p21 and c-Myc expression. Pharmacologic inhibition of JNK reduced the growth of both xenografted human HCC cells and chemically induced mouse liver cancers. These findings provide a mechanistic link between JNK activity and liver cell proliferation via p21 and c-Myc and suggest JNK targeting can be considered as a new therapeutic approach for HCC treatment.","authors":"Hui, L., Zatloukal, K., Scheuch, H., Stepniak, E., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Clin Invest","volume":"118","issue":"12","page":"3943-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23419516","title":"Monoclonal antibody against CXCL-10\/IP-10 ameliorates influenza A (H1N1) virus induced acute lung injury.","abstract":null,"authors":"Wang, W., Yang, P., Zhong, Y., Zhao, Z., Xing, L., Zhao, Y., Zou, Z., Zhang, Y., Li, C., Li, T., Wang, C., Wang, Z., Yu, X., Cao, B., Gao, X., Penninger, JM., Wang, X., Jiang, C.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Res","volume":"23","issue":"4","page":"577-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7953508","title":"Endothelial cell transformation by polyomavirus middle T antigen in mice lacking Src-related kinases.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">7953508<\/PMID><DateCompleted><Year>1994<\/Year><Month>11<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>4<\/Volume><Issue>2<\/Issue><PubDate><Year>1994<\/Year><Month>Feb<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Endothelial cell transformation by polyomavirus middle T antigen in mice lacking Src-related kinases.<\/ArticleTitle><Pagination><MedlinePgn>100-9<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Expression of polyomavirus middle T antigen (PymT) rapidly induces endothelial tumors (hemangiomas) in mice, with an apparent single rate-limiting step. Because activation of Src-like kinases is thought to be an important component of PymT-induced transformation, we have analyzed the functional requirement for individual kinases in this process. This type of analysis has only recently become possible, with the generation of 'gene knock-out' mice lacking each of the kinase genes src, fyn and yes.","authors":"Kiefer, F., Anhauser, I., Soriano, P., Aguzzi, A., Courtneidge, SA., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Curr Biol","volume":"4","issue":"2","page":"100-9","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1994-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19030109","title":"Redundant mechanisms for regulation of midline crossing in Drosophila.","abstract":"During development, all neurons have to decide on whether to cross the longitudinal midline to project on the contralateral side of the body. In vertebrates and invertebrates regulation of crossing is achieved by interfering with Robo signalling either through sorting and degradation of the receptor, in flies, or through silencing of its repulsive activity, in vertebrates. Here I show that in Drosophila a second mechanism of regulation exists that is independent from sorting. Using in vitro and in vivo assays I mapped the region of Robo that is sufficient and required for its interaction with Comm, its sorting receptor. By modifying that region, I generated new forms of Robo that are insensitive to Comm sorting in vitro and in vivo, yet still able to normally translate repulsive activity in vivo. Using gene targeting by homologous recombination I created new conditional alleles of robo that are sorting defective (robo(SD)). Surprisingly, expression of these modified proteins results in phenotypically normal flies, unveiling a sorting independent mechanism of regulation.","authors":"Gilestro, GF.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"PLoS One","volume":"3","issue":"11","page":"e3798","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"126","title":"Phobias complicating treatment of uterine carcinoma.","abstract":"","authors":"Lloyd, G., Deakin, HG.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br Med J","volume":"4","issue":"5994","page":"440","pdf":null,"JrId":"1912","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19028989","title":"Novel insights into the flexibility of cell and positional identity during urodele limb regeneration.","abstract":"The ability of diverse metazoans to regenerate whole-body structures was first described systematically by Spallanzani in 1768 and continues to fascinate biologists today. Given the current interest in stem cell biology and its therapeutic potential, examples of vertebrate regeneration garner strong interest. Among regeneration-competent vertebrates such as the fish, frog, and salamander, the salamander is particularly impressive because it can regenerate the entire limb and tail as well as various internal organs as an adult (Goss 1969). This spectacular natural phenomenon leads us to ask what cellular properties allow regeneration and what prevents this phenomenon in other vertebrates. From this perspective, it is imperative to know whether the stem cells in regenerating limbs harbor particularly special traits such as a higher plasticity in cell fate compared to tissue stem cells in other organisms. Flexibility in cell fate needs to be considered with respect not only to tissue identity, but also to patterning because limb amputation causes cells in a particular limb segment to form more distal limb elements. How positional identity is encoded in stem cells and how it is controlled to produce only the missing portion of the limb are also questions of fundamental importance.","authors":"Kragl, M., Knapp, D., Nacu, E., Khattak, S., Schnapp, E., Epperlein, HH., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"73","issue":null,"page":"583-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"64","title":"Partial purification and properties of microsomal phosphatidate phosphohydrolase from rat liver.","abstract":"Microsomal phosphatidate phosphohydrolase (phosphatidate phosphatase EC 3.1.3.4) was solubilized and fractionated to yield at least two distinct enzymatically active fractions. One, denoted FA, was non-specific, had a relatively high Km for phosphatidic acid and was insensitive to inhibition by diacylglycerol. The second fraction, FB, was specific for phosphatidates, had a low Km, and was inhibited, non-competitively, by diacylglycerol. FA exhibited a sigmoid substrate-activity curve. The isolated FB aggregated to particles of about 10(6) in the absence of salts and could be dissociated by the addition of monovalent cations at ionic strength 0.4-0.6 to about 2-10(5) daltons and thereby doubled its activity. Dissociation was time- and temperature-dependent. F- was inhibitory. Divalent ions were not required for the activity of FA or FB and inhibited at concentrations exceeding 1 mM.","authors":"Caras, I., Shapiro, B.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"409","issue":"2","page":"201-11","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19012953","title":"An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.","abstract":"Cancers are highly heterogeneous and contain many passenger and driver mutations. To functionally identify tumor suppressor genes relevant to human cancer, we compiled pools of short hairpin RNAs (shRNAs) targeting the mouse orthologs of genes recurrently deleted in a series of human hepatocellular carcinomas and tested their ability to promote tumorigenesis in a mosaic mouse model. In contrast to randomly selected shRNA pools, many deletion-specific pools accelerated hepatocarcinogenesis in mice. Through further analysis, we identified and validated 13 tumor suppressor genes, 12 of which had not been linked to cancer before. One gene, XPO4, encodes a nuclear export protein whose substrate, EIF5A2, is amplified in human tumors, is required for proliferation of XPO4-deficient tumor cells, and promotes hepatocellular carcinoma in mice. Our results establish the feasibility of in vivo RNAi screens and illustrate how combining cancer genomics, RNA interference, and mosaic mouse models can facilitate the functional annotation of the cancer genome.","authors":"Zender, L., Xue, W., Zuber, J., Semighini, CP., Krasnitz, A., Ma, B., Zender, P., Kubicka, S., Luk, JM., Schirmacher, P., McCombie, WR., Wigler, M., Hicks, J., Hannon, GJ., Powers, S., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell","volume":"135","issue":"5","page":"852-64","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23391492","title":"Vav1 regulates MHCII expression in murine resting and activated B cells.","abstract":"Vav1 is a guanine nucleotide exchange factor (GEF) for Rho GTPases, which is exclusively expressed in cells of the hematopoietic system. In addition to its well-documented GEF activity, it was suggested to have other functions due to the presence of multiple domains and nuclear localization signals in its protein structure. Although GEF-dependent and GEF-independent functions of vav have been implicated in T-cell development and T-cell receptor signaling, the role of vav1 in antigen-presenting cells is poorly understood. We found that vav1 is an important regulator of MHCII expression and transport. Microarray analysis of unstimulated bone marrow-derived macrophages revealed a novel role of vav1 in transcriptional regulation of the MHCII locus, possibly by indirect means. Primary immune cells from vav1-deficient mice had a significantly lower constitutive surface expression of MHCII with the strongest impact observed on splenic and peritoneal B cells. Impaired MHCII expression resulted in a diminished capacity for T-cell activation. Using 6-thio-GTP, a specific inhibitor of the GEF function of vav1, we were able to show that the GEF activity is required for MHCII upregulation in B cells after stimulation with LPS. Furthermore, our data show that vav1 not only affects transcription of the MHCII locus but also is an important regulator of MHCII protein transport to the cell surface.","authors":"Jux, B., Staratschek-Jox, A., Penninger, JM., Schultze, JL., Kolanus, W.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Int Immunol","volume":"25","issue":"5","page":"307-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31837139","title":"Mouse t-complex protein 11 is important for progressive motility in sperm\u2020.","abstract":"The t-complex is defined as naturally occurring variants of the proximal third of mouse chromosome 17 and has been studied by mouse geneticists for decades. This region contains many genes involved in processes from embryogenesis to sperm function. One such gene, t-complex protein 11 (Tcp11), was identified as a testis-specific gene whose protein is present in elongating spermatids. Later work on Tcp11 localized TCP11 to the sperm surface and acrosome cap and implicated TCP11 as important for sperm capacitation through the cyclic AMP\/Protein Kinase A pathway. Here, we show that TCP11 is cytoplasmically localized to elongating spermatids and absent from sperm. In the absence of Tcp11, male mice have severely reduced fertility due to a significant decrease in progressively motile sperm; however, Tcp11-null sperm continues to undergo tyrosine phosphorylation, a hallmark of capacitation. Interestingly, null sperm displays reduced PKA activity, consistent with previous reports. Our work demonstrates that TCP11 functions in elongated spermatids to confer proper motility in mature sperm.","authors":"Castaneda, JM., Miyata, H., Archambeault, DR., Satouh, Y., Yu, Z., Ikawa, M., Matzuk, MM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Biol Reprod","volume":"102","issue":"4","page":"852-862","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18347087","title":"Micromanaging regeneration.","abstract":null,"authors":"Tanaka, EM., Weidinger, G.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genes Dev","volume":"22","issue":"6","page":"700-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520456","title":"Assessing noninferiority in a three-arm trial using the Bayesian approach.","abstract":"Non-inferiority trials, which aim to demonstrate that a test product is not worse than a competitor by more than a pre-specified small amount, are of great importance to the pharmaceutical community. As a result, methodology for designing and analyzing such trials is required, and developing new methods for such analysis is an important area of statistical research. The three-arm trial consists of a placebo, a reference and an experimental treatment, and simultaneously tests the superiority of the reference over the placebo along with comparing this reference to an experimental treatment. In this paper, we consider the analysis of non-inferiority trials using Bayesian methods which incorporate both parametric as well as semi-parametric models. The resulting testing approach is both flexible and robust. The benefit of the proposed Bayesian methods is assessed via simulation, based on a study examining home-based blood pressure interventions.","authors":"Ghosh, P., Nathoo, F., G\u00f6nen, M., Tiwari, RC.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Stat Med","volume":"30","issue":"15","page":"1795-808","pdf":null,"JrId":"7188","fulltextlink":null,"preprintlink":null,"articledate":"2011-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22","title":"[Demonstration of tumor inhibiting properties of a strongly immunostimulating low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a N-(2-cyanoethylene)-urea. Novel prophylactic possibilities].","abstract":"A report is given on the recent discovery of outstanding immunological properties in BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) However this comparison is characterized by the fact that both substances exhibit two quite different (complementary) mechanisms of action. Leucocyte counts made after application of the said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with ifosfamide, the known suppression in the post-therapeutic interval usually found with standard cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow conclusions on the immunity status. Since IF can be taken as one of the most efficient cancerostatics--there is no other chemotherapeutic known up to now that has a more significant effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, the total amount of leucocytes and lymphocytes as well as their time behaviour was determined from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained numerical values clearly show that further research work on the prophylactic use of this substance seems to be necessary and very promising.","authors":"Ardenne, M., Reitnauer, PG.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Arzneimittelforschung","volume":"25","issue":"9","page":"1369-79","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18854163","title":"Linking cell cycle to asymmetric division: Aurora-A phosphorylates the Par complex to regulate Numb localization.","abstract":"Drosophila neural precursor cells divide asymmetrically by segregating the Numb protein into one of the two daughter cells. Numb is uniformly cortical in interphase but assumes a polarized localization in mitosis. Here, we show that a phosphorylation cascade triggered by the activation of Aurora-A is responsible for the asymmetric localization of Numb in mitosis. Aurora-A phosphorylates Par-6, a regulatory subunit of atypical protein kinase C (aPKC). This activates aPKC, which initially phosphorylates Lethal (2) giant larvae (Lgl), a cytoskeletal protein that binds and inhibits aPKC during interphase. Phosphorylated Lgl is released from aPKC and thereby allows the PDZ domain protein Bazooka to enter the complex. This changes substrate specificity and allows aPKC to phosphorylate Numb and release the protein from one side of the cell cortex. Our data reveal a molecular mechanism for the asymmetric localization of Numb and show how cell polarity can be coupled to cell-cycle progression.","authors":"Wirtz-Peitz, F., Nishimura, T., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell","volume":"135","issue":"1","page":"161-73","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2008-10-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18246038","title":"Heads or tails: can Wnt tell which one is up?","abstract":null,"authors":"Tanaka, EM., Weidinger, G.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Cell Biol","volume":"10","issue":"2","page":"122-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24275887","title":"A transgenic insertion on mouse chromosome 17 inactivates a novel immunoglobulin superfamily gene potentially involved in sperm-egg fusion.","abstract":"Fertilization is the process that leads to the formation of a diploid zygote from two haploid gametes. This is achieved through a complex series of cell-to-cell interactions between a sperm and an egg. The final event of fertilization is the fusion of the gametes' membranes, which allows the delivery of the sperm genetic material into the egg cytoplasm. In vivo studies in the laboratory mouse have led to the discovery of membrane proteins that are essential for the fusion process in both the sperm and egg. Specifically, the sperm protein Izumo1 was shown to be necessary for normal fertility. Izumo1-deficient spermatozoa fail to fuse with the egg plasma membrane. Izumo1 is a member of the Immunoglobulin Superfamily of proteins, which are known to be involved in cell adhesion. Here, we describe BART97b, a new mouse line with a recessive mutation that displays a fertilization block associated with a failure of sperm fusion. BART97b mutants carry a deletion that inactivates Spaca6, a previously uncharacterized gene expressed in testis. Similar to Izumo1, Spaca6 encodes an immunoglobulin-like protein. We propose that the Spaca6 gene product may, together with Izumo1, mediate sperm fusion by binding an as yet unidentified egg membrane receptor.","authors":"Lorenzetti, D., Poirier, C., Zhao, M., Overbeek, PA., Harrison, W., Bishop, CE.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mamm Genome","volume":"25","issue":"3-4","page":"141-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520285","title":"A new diagnostic test to distinguish tremulous Parkinson's disease from advanced essential tremor.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520285<\/PMID><DateCompleted><Year>2012<\/Year><Month>02<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2011<\/Year><Month>11<\/Month><Day>04<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1531-8257<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>26<\/Volume><Issue>8<\/Issue><PubDate><Year>2011<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>Movement disorders : official journal of the Movement Disorder Society<\/Title><ISOAbbreviation>Mov Disord<\/ISOAbbreviation><\/Journal><ArticleTitle>A new diagnostic test to distinguish tremulous Parkinson's disease from advanced essential tremor.<\/ArticleTitle><Pagination><MedlinePgn>1548-52<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/mds.23672<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Clinical distinction between advanced essential tremor and tremulous Parkinson's disease can be difficult.","authors":"Muthuraman, M., Hossen, A., Heute, U., Deuschl, G., Raethjen, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mov Disord","volume":"26","issue":"8","page":"1548-52","pdf":null,"JrId":"5937","fulltextlink":null,"preprintlink":null,"articledate":"2012-02-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34386878","title":"Fast and efficient generation of a full-length balancer chromosome by a single Cre\/loxP recombination event.","abstract":"Balancer chromosomes, primarily discovered and used in Drosophila melanogaster, are valuable tools to maintain lethal mutations in a particular genomic segment. Full-length balancer chromosomes would be particularly useful because of the capacity to maintain whole genomic traits. However, murine full-length balancer chromosomes generated via a single Cre\/loxP recombination are still not demonstrated. In this study, we developed a novel mouse strain with full-length inverted chromosome 17 (Ch17<sup>Inv<\/sup> balancer) via a single Cre\/loxP recombination event in mES cells. The Ch17<sup>Inv<\/sup> balancer mice are viable and phenotypically normal. When bred with other strains, the haplotype of chromosome 17 can be stably maintained as determined by the high throughput SNPs assay. Interestingly, we found that the recombination events were efficiently reduced within the inverted region but not eliminated. The method established in this study can be applied to generate other full-length balancer chromosomes. Moreover, the Ch17<sup>Inv<\/sup> balancer strain would be a valuable resource to maintain the entire chromosome 17 from different donor strains.","authors":"Ju, C., Zhang, M., Guan, M., Li, S., Zhang, Y., Zhao, J., Gao, X.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Mamm Genome","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24218563","title":"TREM2 governs Kupffer cell activation and explains belr1 genetic resistance to malaria liver stage infection.","abstract":"Plasmodium liver stage infection is a target of interest for the treatment of and vaccination against malaria. Here we used forward genetics to search for mechanisms underlying natural host resistance to infection and identified triggering receptor expressed on myeloid cells 2 (TREM2) and MHC class II molecules as determinants of Plasmodium berghei liver stage infection in mice. Locus belr1 confers resistance to malaria liver stage infection. The use of newly derived subcongenic mouse lines allowed to map belr1 to a 4-Mb interval on mouse chromosome 17 that contains the Trem2 gene. We show that Trem2 expression in the nonparenchymal liver cells closely correlates with resistance to liver stage infection, implicating TREM2 as a mediator of the belr1 genetic effect. Trem2-deficient mice are more susceptible to liver stage infection than their WT counterparts. We found that Kupffer cells are the principle cells expressing TREM2 in the liver, and that Trem2(-\/-) Kupffer cells display altered functional activation on exposure to P. berghei sporozoites. TREM2 expression in Kupffer cells contributes to the limitation of parasite expansion in isolated hepatocytes in vitro, potentially explaining the increased susceptibility of Trem2(-\/-) mice to liver stage infection. The MHC locus was also found to control liver parasite burden, possibly owing to the expression of MHC class II molecules in hepatocytes. Our findings implicate unexpected Kupffer-hepatocyte cross-talk in the control Plasmodium liver stage infection and demonstrate that TREM2 is involved in host responses against the malaria parasite.","authors":"Gon\u00e7alves, LA., Rodrigues-Duarte, L., Rodo, J., Vieira de Moraes, L., Marques, I., Penha-Gon\u00e7alves, C.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proc Natl Acad Sci U S A","volume":"110","issue":"48","page":"19531-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17507409","title":"A clonal analysis of neural progenitors during axolotl spinal cord regeneration reveals evidence for both spatially restricted and multipotent progenitors.","abstract":"Complete regeneration of the spinal cord occurs after tail regeneration in urodele amphibians such as the axolotl. Little is known about how neural progenitor cells are recruited from the mature tail, how they populate the regenerating spinal cord, and whether the neural progenitor cells are multipotent. To address these issues we used three types of cell fate mapping. By grafting green fluorescent protein-positive (GFP(+)) spinal cord we show that a 500 microm region adjacent to the amputation plane generates the neural progenitors for regeneration. We further tracked single nuclear-GFP-labeled cells as they proliferated during regeneration, observing their spatial distribution, and ultimately their expression of the progenitor markers PAX7 and PAX6. Most progenitors generate descendents that expand along the anterior\/posterior (A\/P) axis, but remain close to the dorsal\/ventral (D\/V) location of the parent. A minority of clones spanned multiple D\/V domains, taking up differing molecular identities, indicating that cells can execute multipotency in vivo. In parallel experiments, bulk labeling of dorsally or ventrally restricted progenitor cells revealed that ventral cells at the distal end of the regenerating spinal cord switch to dorsal cell fates. Analysis of PAX7 and PAX6 expression along the regenerating spinal cord indicated that these markers are expressed in dorsal and lateral domains all along the spinal cord except at the distal terminus. These results suggest that neural progenitor identity is destabilized or altered in the terminal vesicle region, from which clear migration of cells into the surrounding blastema is also observed.","authors":"McHedlishvili, L., Epperlein, HH., Telzerow, A., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Development","volume":"134","issue":"11","page":"2083-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34359735","title":"<i>PRKAR1A<\/i> and Thyroid Tumors.","abstract":"Thyroid cancer is the most common type of endocrine malignancy and the incidence is rapidly increasing. Follicular (FTC) and papillary thyroid (PTC) carcinomas comprise the well-differentiated subtype and they are the two most common thyroid carcinomas. Multiple molecular genetic and epigenetic alterations have been identified in various types of thyroid tumors over the years. Point mutations in <i>BRAF<\/i>, <i>RAS<\/i> as well as <i>RET\/PTC<\/i> and <i>PAX8\/PPAR\u03b3<\/i> chromosomal rearrangements are common. Thyroid cancer, including both FTC and PTC, has been observed in patients with Carney Complex (CNC), a syndrome that is inherited in an autosomal dominant manner and predisposes to various tumors. CNC is caused by inactivating mutations in the tumor-suppressor gene encoding the cyclic AMP (cAMP)-dependent protein kinase A (PKA) type 1\u03b1 regulatory subunit (<i>PRKAR1A<\/i>) mapped in chromosome 17 (17q22-24). Growth of the thyroid is driven by the TSH\/cAMP\/PKA signaling pathway and it has been shown in mouse models that PKA activation through genetic ablation of the regulatory subunit <i>Prkar1a<\/i> can cause FTC. In this review, we provide an overview of the molecular mechanisms contributing to thyroid tumorigenesis associated with inactivation of the <i>RRKAR1A<\/i> gene.","authors":"Pitsava, G., Stratakis, CA., Faucz, FR.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Cancers (Basel)","volume":"13","issue":"15","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-144","title":"X Inactivation and Progenitor Cancer Cells","abstract":null,"authors":"Agrelo R.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Cancers","volume":"3(2)","issue":"","page":"2169-2175","pdf":null,"JrId":null,"fulltextlink":"http:\/\/dx.doi.org\/10.3390\/cancers3022169","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24004126","title":"Sphingolipids and susceptibility to asthma.","abstract":"","authors":"Levy, BD.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"N Engl J Med","volume":"369","issue":"10","page":"976-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36494589","title":"SCON-a Short Conditional intrON for conditional knockout with one-step zygote injection.","abstract":"The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short Conditional intrON (SCON, 189&#x2009;bp) that enables the rapid generation of conditional alleles via one-step zygote injection. In this study, a total of 13 SCON mouse lines were successfully generated by 2 different laboratories. SCON has conditional intronic functions in various vertebrate species, and its target insertion is as simple as CRISPR\/Cas9-mediated gene tagging.","authors":"Wu, SS., Lee, H., Sz\u00e9p-Bakonyi, R., Colozza, G., Boese, A., Gert, KR., Hallay, N., Lee, JH., Kim, J., Zhu, Y., Linssen, MM., Pilat-Carotta, S., Hohenstein, P., Theussl, HC., Pauli, A., Koo, BK.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Exp Mol Med","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.05.09.443220v1","articledate":"2022-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24050961","title":"Intercellular transfer of tau aggregates and spreading of tau pathology: Implications for therapeutic strategies.","abstract":"Filaments made of hyperphosphorylated tau protein are encountered in a group of neurodegenerative disorders termed tauopathies. The most prevalent tauopathy, Alzheimer's disease (AD), additionally presents with extracellular deposits of the amyloid-\u03b2 peptide (A\u03b2). Current symptomatic treatments have shown short term benefits in reducing cognitive symptoms as well as behavioral abnormalities in patients with mild to moderate AD but there is still no effective treatment to prevent or reverse AD. For decades, the amyloid cascade hypothesis of AD dominated basic research and focused pharmaceutical interest on A\u03b2. However, the existence of tauopathies that are devoid of A\u03b2 deposits, together with the discovery of mutations in the tau gene leading to frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17T), confirmed the importance of tau per se in disease. Tau became an interesting disease target in its own right. We will review here recent research on cell-to-cell propagation of tau pathology, which we believe to be central to disease progression, and discuss tau immunotherapy in the light of these findings. This article is part of the Special Issue entitled 'The Synaptic Basis of Neurodegenerative Disorders'.","authors":"Clavaguera, F., Grueninger, F., Tolnay, M.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Neuropharmacology","volume":"76 Pt A","issue":"","page":"9-15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24041763","title":"Human chromosome 21 orthologous region on mouse chromosome 17 is a major determinant of Down syndrome-related developmental cognitive deficits.","abstract":"Trisomy 21 (Down syndrome, DS) is the most common genetic cause of developmental cognitive deficits, and the so-called Down syndrome critical region (DSCR) has been proposed as a major determinant of this phenotype. The regions on human chromosome 21 (Hsa21) are syntenically conserved on mouse chromosome 10 (Mmu10), Mmu16 and Mmu17. DSCR is conserved between the Cbr1 and Fam3b genes on Mmu16. Ts65Dn mice carry three copies of \u223c100 Hsa21 gene orthologs on Mmu16 and exhibited impairments in the Morris water maze and hippocampal long-term potentiation (LTP). Converting the Cbr1-Fam3b region back to two copies in Ts65Dn mice rescued these phenotypes. In this study, we performed similar conversion of the Cbr1-Fam3b region in Dp(16)1Yey\/+ mice that is triplicated for all \u223c115 Hsa21 gene orthologs on Mmu16, which also resulted in the restoration of the wild-type phenotypes in the Morris water maze and hippocampal LTP. However, converting the Cbr1-Fam3b region back to two copies in a complete model, Dp(10)1Yey\/+;Dp(16)1Yey\/+;Dp(17)1Yey\/+, failed to yield the similar phenotypic restorations. But, surprisingly, converting both the Cbr1-Fam3b region and the Hsa21 orthologous region on Mmu17 back to two copies in the complete model did completely restore these phenotypes to the wild-type levels. Our results demonstrated that the Hsa21 orthologous region on Mmu17 is a major determinant of DS-related developmental cognitive deficits. Therefore, the inclusion of the three copies of this Hsa21 orthologous region in mouse models is necessary for unraveling the mechanism underlying DS-associated developmental cognitive deficits and for developing effective interventions for this clinical manifestation.","authors":"Zhang, L., Meng, K., Jiang, X., Liu, C., Pao, A., Belichenko, PV., Kleschevnikov, AM., Josselyn, S., Liang, P., Ye, P., Mobley, WC., Yu, YE.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Hum Mol Genet","volume":"23","issue":"3","page":"578-89","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520154","title":"A three-gene panel on urine increases PSA specificity in the detection of prostate cancer.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520154<\/PMID><DateCompleted><Year>2011<\/Year><Month>12<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1097-0045<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>71<\/Volume><Issue>16<\/Issue><PubDate><Year>2011<\/Year><Month>Dec<\/Month><\/PubDate><\/JournalIssue><Title>The Prostate<\/Title><ISOAbbreviation>Prostate<\/ISOAbbreviation><\/Journal><ArticleTitle>A three-gene panel on urine increases PSA specificity in the detection of prostate cancer.<\/ArticleTitle><Pagination><MedlinePgn>1736-45<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/pros.21390<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Several studies have demonstrated the usefulness of monitoring an RNA transcript, such as PCA3, in post-prostate massage (PM) urine for increasing the specificity of prostate-specific antigen (PSA) in the detection of prostate cancer (PCa). However, a single marker may not necessarily reflect the multifactorial nature of PCa.","authors":"Rigau, M., Ortega, I., Mir, MC., Ballesteros, C., Garcia, M., Llaurad\u00f3, M., Col\u00e1s, E., Pedrola, N., Montes, M., Sequeiros, T., Ertekin, T., Majem, B., Planas, J., Ruiz, A., Abal, M., S\u00e1nchez, A., Morote, J., Revent\u00f3s, J., Doll, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Prostate","volume":"71","issue":"16","page":"1736-45","pdf":null,"JrId":"6523","fulltextlink":null,"preprintlink":null,"articledate":"2011-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18810654","title":"A GAL4\/UAS luciferase system to identify the miRNAs target mRNAs in Drosophila S2 cells.","abstract":"MicroRNAs (miRNAs) have been shown to regulate gene expression through the sequence-specific base pairing with their target mRNAs. However, our understanding of the biological roles of miRNAs is still quite limited, and only a handful of miRNAs have been assigned by genetic analysis in part owing to the difficulty in the identification of their targets. Although computational methods have shown to be helpful in the prediction of miRNA targets, a major obstacle has been the lack of quick and efficient experimental procedures to verify these targets. In this report, we describe a UAS\/GAL4-based reporter system for this purpose. Our data indicate it an assay of miRNA-target gene interaction, with greater sensitivity over the previously reported methods, and may be useful for more efficient identification\/validation the miRNA targets in Drosophila cell lines.","authors":"Lv, W., Ding, J., Hu, J., Wang, C., Xu, L., Fang, M., Yuan, L.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Biol Rep","volume":"36","issue":"6","page":"1627-31","pdf":null,"JrId":"5917","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23948895","title":"Tauopathies and tau oligomers.","abstract":"Tauopathies are neurodegenerative diseases characterized behaviorally by dementia and neuropathologically by neurofibrillary tangles and neuronal loss. Tau gene mutations have been found in frontotemporal dementia with parkinsonism linked to chromosome 17, suggesting that mutation of tau induces tauopathy. Studies on in vitro tau aggregation show that tau forms two different intermediate aggregates--called tau oligomers and granular tau oligomers--before forming fibrils. Moreover, studies using a mouse model that expresses human tau demonstrated that the process of neurofibrillary tangle formation, rather than tangles themselves, may cause synapse loss and neuron loss. Further analyses suggest that hyperphosphorylated tau or oligomeric tau is involved in synaptic loss, whereas granular tau oligomers are responsible for neuronal loss. Thus, different forms of tau aggregates are involved in the different pathological changes that occur in tauopathies.","authors":"Takashima, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Alzheimers Dis","volume":"37","issue":"3","page":"565-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21378976","title":"The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells.","abstract":"Regulatory T cells (T(reg) cells) are required for peripheral tolerance. Evidence indicates that T(reg) cells can adopt specialized differentiation programs in the periphery that are controlled by transcription factors usually associated with helper T cell differentiation. Here we demonstrate that expression of the transcription factor Blimp-1 defined a population of T(reg) cells that localized mainly to mucosal sites and produced IL-10. Blimp-1 was required for IL-10 production by these cells and for their tissue homeostasis. We provide evidence that the transcription factor IRF4, but not the transcription factor T-bet, was essential for Blimp-1 expression and for the differentiation of all effector T(reg) cells. Thus, our study defines a differentiation pathway that leads to the acquisition of T(reg) cell effector functions and requires both IRF4 and Blimp-1.","authors":"Cretney, E., Xin, A., Shi, W., Minnich, M., Masson, F., Miasari, M., Belz, GT., Smyth, GK., Busslinger, M., Nutt, SL., Kallies, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Immunol","volume":"12","issue":"4","page":"304-11","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18785189","title":"Complications of needle electromyography: hematoma risk and correlation with anticoagulation and antiplatelet therapy.","abstract":"Electromyography (EMG) is considered a relatively safe procedure based primarily on clinical experience. Literature review reveals few reported complications from bleeding or hematoma formation. No evidence-based guidelines exist for EMG procedures in patients who are taking anticoagulant or antiplatelet medications. The purpose of this study was to determine if patients taking anticoagulant or antiplatelet agents exhibit an increased risk of hematoma formation after routine needle EMG of the tibialis anterior muscle when compared to controls. Study subjects underwent routine needle EMG of the tibialis anterior muscle followed by ultrasound examination to evaluate for the presence of hematoma formation. A mean of 30.8 min elapsed between needle insertion and ultrasound evaluation. A total of 101 patients who were taking warfarin were studied. They had International Normalized Ratio (INR) values at or above 1.5, and two were found to have small, subclinical hematomas. Of 57 patients taking clopidogrel and\/or aspirin, 1 was found to have a small, subclinical hematoma. In the control group (51 patients taking neither class of medication), no hematomas were found on ultrasound. This study suggests that hematoma formation from a standard needle EMG is rare. In addition, hematoma formation in our study group of patients on anticoagulant or antiplatelet medications was also uncommon, and no patients with documented hematomas experienced symptoms. These findings should be considered when determining the feasibility of electrodiagnostic evaluation of patients who are taking anticoagulant or antiplatelet medications.","authors":"Lynch, SL., Boon, AJ., Smith, J., Harper, CM., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Muscle Nerve","volume":"38","issue":"4","page":"1225-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21326199","title":"HTRA proteases: regulated proteolysis in protein quality control.","abstract":"Controlled proteolysis underlies a vast diversity of protective and regulatory processes that are of key importance to cell fate. The unique molecular architecture of the widely conserved high temperature requirement A (HTRA) proteases has evolved to mediate critical aspects of ATP-independent protein quality control. The simple combination of a classic Ser protease domain and a carboxy-terminal peptide-binding domain produces cellular factors of remarkable structural and functional plasticity that allow cells to rapidly respond to the presence of misfolded or mislocalized polypeptides.","authors":"Clausen, T., Kaiser, M., Huber, R., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Rev Mol Cell Biol","volume":"12","issue":"3","page":"152-62","pdf":null,"JrId":"22271","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18755717","title":"Peripheral T cell lymphoma, not otherwise specified: the stuff of genes, dreams and therapies.","abstract":"Peripheral T cell lymphomas (PTCL) account for about 12% of lymphoid tumours worldwide. Almost half show such morphological and molecular variability as to hamper any further classification, and to justify their inclusion in a waste-basket category termed \"not otherwise specified (NOS)\". The latter term is used for neoplasms with aggressive presentation, poor response to therapy and dismal prognosis. In contrast to B cell lymphomas, PTCL have been the subject of only a limited number of studies to elucidate their pathobiology and identify novel pharmacological approaches. Herewith, the authors revise the most recent contributions on the subject based on the experience they have gained in the extensive application of microarray technologies. PTCL\/NOS are characterised by erratic expression of T cell associated antigens, including CD4 and CD52, which have recently been proposed as targets for ad hoc immunotherapies. PTCL\/NOS also show variable Ki-67 marking, with rates &gt;80% heralding a worse prognosis. Gene expression profiling studies have revealed that PTCL\/NOS derive from activated T lymphocytes, more often of the CD4+ type, and bear a signature composed of 155 genes and related products that play a pivotal role in cell signalling transduction, proliferation, apoptosis and matrix remodelling. This observation seems to pave the way for the use of innovative drugs such as tyrosine kinase and histone deacetylase inhibitors whose efficacy has been proven in PTCL primary cell cultures. Gene expression profiling also allows better distinction of PTCL\/NOS from angioimmunoblastic T cell lymphoma, the latter being characterised by follicular T helper lymphocyte derivation and CXCL13, PD1 and vascular endothelial growth factor expression.","authors":"Agostinelli, C., Piccaluga, PP., Went, P., Rossi, M., Gazzola, A., Righi, S., Sista, T., Campidelli, C., Zinzani, PL., Falini, B., Pileri, SA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Clin Pathol","volume":"61","issue":"11","page":"1160-7","pdf":null,"JrId":"4642","fulltextlink":null,"preprintlink":null,"articledate":"2015-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21316249","title":"EMCD real space maps of Magnetospirillum magnetotacticum.","abstract":"In this study we combine energy loss magnetic circular dichroism (EMCD) and energy filtered transmission electron microscopy (EFTEM) to map magnetic properties of nanoparticles. We show that it is a functional tool for investigating the magnetic behaviour of bio-mineralized magnetite crystals of Magnetospirillum magnetotacticum. We find that the spatial resolution of our experimental set-up is in the range of less than 2 nm. The results are compared with EMCD studies of abiogenic magnetite.","authors":"St\u00f6ger-Pollach, M., Treiber, CD., Resch, GP., Keays, DA., Ennen, I.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Micron","volume":"42","issue":"5","page":"456-60","pdf":null,"JrId":"8531","fulltextlink":null,"preprintlink":null,"articledate":"2011-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31713617","title":"Targeted PMP22 TATA-box editing by CRISPR\/Cas9 reduces demyelinating neuropathy of Charcot-Marie-Tooth disease type 1A in mice.","abstract":"Charcot-Marie-Tooth 1A (CMT1A) is the most common inherited neuropathy without a known therapy, which is caused by a 1.4 Mb duplication on human chromosome 17, which includes the gene encoding the peripheral myelin protein of 22 kDa (PMP22). Overexpressed PMP22 protein from its gene duplication is thought to cause demyelination and subsequently axonal degeneration in the peripheral nervous system (PNS). Here, we targeted TATA-box of human PMP22 promoter to normalize overexpressed PMP22 level in C22 mice, a mouse model of CMT1A harboring multiple copies of human PMP22. Direct local intraneural delivery of CRISPR\/Cas9 designed to target TATA-box of PMP22 before the onset of disease, downregulates gene expression of PMP22 and preserves both myelin and axons. Notably, the same approach was effective in partial rescue of demyelination even after the onset of disease. Collectively, our data present a proof-of-concept that CRISPR\/Cas9-mediated targeting of TATA-box can be utilized to treat CMT1A.","authors":"Lee, JS., Lee, JY., Song, DW., Bae, HS., Doo, HM., Yu, HS., Lee, KJ., Kim, HK., Hwang, H., Kwak, G., Kim, D., Kim, S., Hong, YB., Lee, JM., Choi, BO.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nucleic Acids Res","volume":"48","issue":"1","page":"130-140","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21297635","title":"Substrate-induced remodeling of the active site regulates human HTRA1 activity.","abstract":"Crystal structures of active and inactive conformations of the human serine protease HTRA1 reveal that substrate binding to the active site is sufficient to stimulate proteolytic activity. HTRA1 attaches to liposomes, digests misfolded proteins into defined fragments and undergoes substrate-mediated oligomer conversion. In contrast to those of other serine proteases, the PDZ domain of HTRA1 is dispensable for activation or lipid attachment, indicative of different underlying mechanistic features.","authors":"Truebestein, L., Tennstaedt, A., M\u00f6nig, T., Krojer, T., Canellas, F., Kaiser, M., Clausen, T., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Struct Mol Biol","volume":"18","issue":"3","page":"386-8","pdf":null,"JrId":"31761","fulltextlink":null,"preprintlink":null,"articledate":"2011-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20422318","title":"Determination of clonal status of pulmonary sclerosing hemangioma with X-chromosome inactivation mosaicism and polymorphism of phosphoglycerate kinase and androgen receptor genes.","abstract":"It has been reported that both polygonal and cuboidal cells in pulmonary sclerosing hemangioma (PSH) are monoclonal in origin and represent a variable differentiation from a common progenitor cell. However, it remains unclear about the clonality of the entire PSH lesion composed of these two types of cells. Thus, we analyzed the clonality of 22 cases of PSH and the relationship between the entire PSH and two types of cells using laser microdissection and X-chromosomal inactivation mosaicism and polymorphism at the phosphoglycerate kinase (PGK) and androgen receptor (AR) loci in female somatic cells. The results demonstrated all 22 cases of PSH showed typical histopathologic characteristics, including characteristic round or polygonal cells within the stroma and surface cuboidal cells lining the papillary projections or cystic spaces. The rates of polymorphism were 31.8% (7\/22) and 86.3% (19\/22) for the PGK and AR gene, respectively. After digestion by Hpa II or Hha I, one of two PCR amplification bands disappeared from all the samples, while the other band was retained, indicating neoplastic characteristics. Thus, we concluded that the entire PSH lesion, polygonal and cuboidal cells were neoplastic hyperplasia and originated from a common progenitor cell.","authors":"Gong, L., Ren, KX., Li, YH., Liu, XY., Zhang, WD., Yao, L., Zhu, SJ., Han, XJ., Zhang, L., Lan, M., Zhang, W.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Med Oncol","volume":"28","issue":"3","page":"913-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34273619","title":"Modeling a human CLP1 mutation in mouse identifies an accumulation of tyrosine pre-tRNA fragments causing pontocerebellar hypoplasia type 10.","abstract":"Cleavage factor polyribonucleotide kinase subunit 1 (CLP1), an RNA kinase, plays essential roles in protein complexes involved in the 3'-end formation and polyadenylation of mRNA and the tRNA splicing endonuclease complex, which is involved in precursor tRNA splicing. The mutation R140H in human CLP1 causes pontocerebellar hypoplasia type 10 (PCH10), which is characterized by microcephaly and axonal peripheral neuropathy. Previously, we reported that RNA fragments derived from isoleucine pre-tRNA introns (Ile-introns) accumulate in fibroblasts of patients with PCH10. Therefore, it has been suggested that this intronic RNA fragment accumulation may trigger PCH10 onset. However, the molecular mechanism underlying PCH10 pathogenesis remains elusive. Thus, we generated knock-in mutant mice that harbored a CLP1 mutation consistent with R140H. As expected, these mice showed progressive loss of the upper motor neurons, resulting in impaired locomotor activity, although the phenotype was milder than that of the human variant. Mechanistically, we found that the R140H mutation causes intracellular accumulation of Ile-introns derived from isoleucine pre-tRNAs and 5' tRNA fragments derived from tyrosine pre-tRNAs, suggesting that these two types of RNA fragments were cooperatively or independently involved in the onset and progression of the disease. Taken together, the CLP1-R140H mouse model provided new insights into the pathogenesis of neurodegenerative diseases, such as PCH10, caused by genetic mutations in tRNA metabolism-related molecules.","authors":"Morisaki, I., Shiraishi, H., Fujinami, H., Shimizu, N., Hikida, T., Arai, Y., Kobayashi, T., Hanada, R., Penninger, JM., Fujiki, M., Hanada, T.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Biochem Biophys Res Commun","volume":"570","issue":null,"page":"60-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21317909","title":"Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes.","abstract":"We demonstrate three-dimensional (3D) super-resolution microscopy in whole fixed cells using photoactivated localization microscopy (PALM). The use of the bright, genetically expressed fluorescent marker photoactivatable monomeric (m)Cherry (PA-mCherry1) in combination with near diffraction-limited confinement of photoactivation using two-photon illumination and 3D localization methods allowed us to investigate a variety of cellular structures at &lt;50 nm lateral and &lt;100 nm axial resolution. Compared to existing methods, we have substantially reduced excitation and bleaching of unlocalized markers, which allows us to use 3D PALM imaging with high localization density in thick structures. Our 3D localization algorithms, which are based on cross-correlation, do not rely on idealized noise models or specific optical configurations. This allows instrument design to be flexible. By generating appropriate fusion constructs and expressing them in Cos7 cells, we could image invaginations of the nuclear membrane, vimentin fibrils, the mitochondrial network and the endoplasmic reticulum at depths of greater than 8 \u03bcm.","authors":"York, AG., Ghitani, A., Vaziri, A., Davidson, MW., Shroff, H.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Methods","volume":"8","issue":"4","page":"327-33","pdf":null,"JrId":"32338","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33951054","title":"Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation.","abstract":"The interphase nucleus is functionally organized in active and repressed territories defining the transcriptional status of the cell. However, it remains poorly understood how the nuclear architecture of neurons adapts in response to behaviorally relevant stimuli that trigger fast alterations in gene expression patterns. Imaging of fluorescently tagged nucleosomes revealed that pharmacological manipulation of neuronal activity in vitro and auditory cued fear conditioning in vivo induce nucleus-scale restructuring of chromatin within minutes. Furthermore, the acquisition of auditory fear memory is impaired after infusion of a drug into auditory cortex which blocks chromatin reorganization in vitro. We propose that active chromatin movements at the nucleus scale act together with local gene-specific modifications to enable transcriptional adaptations at fast time scales. Introducing a transgenic mouse line for photolabeling of histones, we extend the realm of systems available for imaging of chromatin dynamics to living animals.","authors":"Peter, M., Aschauer, DF., Rose, R., Sinning, A., Gr\u00f6ssl, F., Kargl, D., Kraitsy, K., Burkard, TR., Luhmann, HJ., Haubensak, W., Rumpel, S.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"PLoS One","volume":"16","issue":"5","page":"e0244038","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21186364","title":"Substrate binding on the APC\/C occurs between the coactivator Cdh1 and the processivity factor Doc1.","abstract":"The anaphase-promoting complex\/cyclosome (APC\/C) is a 22S ubiquitin ligase complex that initiates chromosome segregation and mitotic exit. We have used biochemical and electron microscopic analyses of Saccharomyces cerevisiae and human APC\/C to address how the APC\/C subunit Doc1 contributes to recruitment and processive ubiquitylation of APC\/C substrates, and to understand how APC\/C monomers interact to form a 36S dimeric form. We show that Doc1 interacts with Cdc27, Cdc16 and Apc1 and is located in the vicinity of the cullin-RING module Apc2-Apc11 in the inner cavity of the APC\/C. Substrate proteins also bind in the inner cavity, in close proximity to Doc1 and the coactivator Cdh1, and induce conformational changes in Apc2-Apc11. Our results suggest that substrates are recruited to the APC\/C by binding to a bipartite substrate receptor composed of a coactivator protein and Doc1.","authors":"Buschhorn, BA., Petzold, G., Galova, M., Dube, P., Kraft, C., Herzog, F., Stark, H., Peters, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Struct Mol Biol","volume":"18","issue":"1","page":"6-13","pdf":null,"JrId":"31761","fulltextlink":null,"preprintlink":null,"articledate":"2011-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34270961","title":"The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency.","abstract":"Transcription factors (TFs) harboring broad-complex, tramtrack, and bric-a-brac (BTB) domains play important roles in development and disease. These BTB domains are thought to recruit transcriptional modulators to target DNA regions. However, a systematic molecular understanding of the mechanism of action of this TF family is lacking. Here, we identify the zinc finger BTB-TF Zbtb2 from a genetic screen for regulators of exit from pluripotency and demonstrate that its absence perturbs embryonic stem cell differentiation and the gene expression dynamics underlying peri-implantation development. We show that ZBTB2 binds the chromatin remodeler Ep400 to mediate downstream transcription. Independently, the BTB domain directly interacts with nucleosome remodeling and deacetylase and histone chaperone histone regulator A. Nucleosome remodeling and deacetylase recruitment is a common feature of BTB TFs, and based on phylogenetic analysis, we propose that this is a conserved evolutionary property. Binding to UBN2, in contrast, is specific to ZBTB2 and requires a C-terminal extension of the BTB domain. Taken together, this study identifies a BTB-domain TF that recruits chromatin modifiers and a histone chaperone during a developmental cell state transition and defines unique and shared molecular functions of the BTB-domain TF family.","authors":"Olivieri, D., Paramanathan, S., Bardet, AF., Hess, D., Smallwood, SA., Elling, U., Betschinger, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Biol Chem","volume":"297","issue":"2","page":"100947","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21161510","title":"Altered Mascot search results by changing the m\/z range of MS\/MS spectra: analysis and potential applications.","abstract":"The Mascot search algorithm is one of the most commonly used tools for protein identification. Tandem mass spectrometry data searched against a protein sequence database is utilized for identifying peptides and proteins, each reported with a score. Higher Mascot scores are associated with lower chances of random hits. The process of peak selection performed by the search engine prior to the search is a critical aspect of the process. Here, we show that Mascot divides the MS\/MS spectrum into fixed m\/z regions for peak selection, starting at the lowest m\/z value of the peak list. Therefore, modifying the m\/z range of the peak lists by insertion of a dummy peak with low m\/z value changes the ensemble of peaks used for searching. As a consequence, Mascot peptide scores and search results are altered significantly and a different subset of the peptides present in the sample is identified after processing. We further show that the effect can be exploited and additional proteins and peptides can be identified by repeating the search with a combined set of differently processed files, even when applying identical false-positive rates.","authors":"K\u00f6cher, T., Pichler, P., Mazanek, M., Swart, R., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Anal Bioanal Chem","volume":"400","issue":"8","page":"2339-47","pdf":null,"JrId":"27057","fulltextlink":null,"preprintlink":null,"articledate":"2011-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18688045","title":"Phosphatidylinositol 3-kinase gamma is a critical mediator of myocardial ischemic and adenosine-mediated preconditioning.","abstract":"Ischemic preconditioning (IPC) is a potent cellular protective mechanism whereby brief periods of sublethal ischemia protect the myocardium from prolonged ischemia-induced injury. We demonstrate the selective role of phosphatidylinositol 3-kinase (PI3K) isoforms in IPC. Hearts from PI3Kgamma knockout mice (PI3Kgamma(-\/-)) displayed poorer functional recovery and greater tissue injury following IPC compared to wild-type and PI3Kgamma(+\/-) hearts. Examination of the cell-signaling pathways revealed restored phosphorylation levels of Akt and glycogen synthase kinase (GSK)3beta in wild-type hearts, which were abolished in PI3Kgamma(-\/-) hearts subjected to IPC. Inhibition of GSK3beta by LiCl reversed the loss in protection in PI3Kgamma(-\/-) hearts. In contrast, mice expressing a cardiac-specific kinase-deleted PI3Kalpha (PI3KalphaDN) were resistant to injury induced by 30 minutes of ischemia followed by 40 minutes of reperfusion. Furthermore, the resistance of PI3KalphaDN hearts to ischemia\/reperfusion correlated with the persistent expression of p110gamma and was blocked by the PI3K inhibitor wortmannin, suggesting the possible enhanced cell signaling through the PI3Kgamma pathway. These results demonstrate the importance of the PI3Kgamma-Akt-GSK3beta signaling pathway in IPC. Selective activation of myocardial PI3Kgamma may be an attractive target for the treatment of ischemic heart disease.","authors":"Ban, K., Cooper, AJ., Samuel, S., Bhatti, A., Patel, M., Izumo, S., Penninger, JM., Backx, PH., Oudit, GY., Tsushima, RG.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Circ Res","volume":"103","issue":"6","page":"643-53","pdf":null,"JrId":"2974","fulltextlink":null,"preprintlink":null,"articledate":"2008-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21360669","title":"Quality control in LC-MS\/MS.","abstract":"In the last 15 years, MS-based protein characterization has expanded at a rapid rate. This success is built upon constantly improving instrumentation and a variety of ingenious methods applied to numerous biological questions. However, the reproducibility of mass spectrometric results is considered by many as insufficient. In part, inadequate quality control might be responsible for the lack of reproducibility. Quality control is rarely discussed in scientific publications. Here, we briefly present measures undertaken in our laboratory to foster a general discussion of the subject.","authors":"K\u00f6cher, T., Pichler, P., Swart, R., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Proteomics","volume":"11","issue":"6","page":"1026-30","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18679426","title":"The role of the transcription factor AP-1 in colitis-associated and beta-catenin-dependent intestinal tumorigenesis in mice.","abstract":"Chronic inflammation is an important cancer risk factor but the molecular pathways linking inflammation and cancer are incompletely understood. The transcription factor c-Jun\/AP-1 (activator protein 1) is involved in inflammatory responses and tumorigenesis and has been proposed as an essential mediator of oncogenic beta-catenin signaling in the intestine. Here, we examined the functions of c-Jun in two distinct mouse models of conditional and intestine-specific activation of beta-catenin. c-Jun is strongly expressed in the small intestine of mutant mice. However, beta-catenin-dependent cell proliferation is surprisingly not affected in mice lacking c-jun in intestinal epithelium, suggesting that c-Jun is not an essential immediate target of beta-catenin signaling in the small intestine. To examine the functions of Jun and Fos proteins during inflammation and cancer in the colon, colitis-associated tumors were induced chemically in the respective knockout mice. Tumors were characterized by activated beta-catenin and strongly expressed c-Jun and JunB. However, tumorigenesis was not affected by inactivation of c-Jun in either intestinal epithelium or myeloid cells. Moreover, tumorigenesis was not altered in mice lacking junB, junD, c-fos, fra-1 or fra-2, suggesting that inhibition of c-Jun or other single AP-1 proteins is not a determining factor in colitis-associated cancer in mice.","authors":"Hasselblatt, P., Gresh, L., Kudo, H., Guinea-Viniegra, J., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Oncogene","volume":"27","issue":"47","page":"6102-9","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2008-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21078886","title":"CD14 is a coreceptor of Toll-like receptors 7 and 9.","abstract":"Recognition of pathogens by the innate immune system requires proteins that detect conserved molecular patterns. Nucleic acids are recognized by cytoplasmic sensors as well as by endosomal Toll-like receptors (TLRs). It has become evident that TLRs require additional proteins to be activated by their respective ligands. In this study, we show that CD14 (cluster of differentiation 14) constitutively interacts with the MyD88-dependent TLR7 and TLR9. CD14 was necessary for TLR7- and TLR9-dependent induction of proinflammatory cytokines in vitro and for TLR9-dependent innate immune responses in mice. CD14 associated with TLR9 stimulatory DNA in precipitation experiments and confocal imaging. The absence of CD14 led to reduced nucleic acid uptake in macrophages. Additionally, CD14 played a role in the stimulation of TLRs by viruses. Using various types of vesicular stomatitis virus, we showed that CD14 is dispensable for viral uptake but is required for the triggering of TLR-dependent cytokine responses. These data show that CD14 has a dual role in nucleic acid-mediated TLR activation: it promotes the selective uptake of nucleic acids, and it acts as a coreceptor for endosomal TLR activation.","authors":"Baumann, CL., Aspalter, IM., Sharif, O., Pichlmair, A., Bl\u00fcml, S., Grebien, F., Bruckner, M., Pasierbek, P., Aumayr, K., Planyavsky, M., Bennett, KL., Colinge, J., Knapp, S., Superti-Furga, G.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Exp Med","volume":"207","issue":"12","page":"2689-701","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-216","title":"Bouncer\u2019s receptor on sperm: Investigating sperm-egg compatibility in fish","abstract":null,"authors":"Blaha, A., Pauli, A.","publication_status":"preprint","journalpubyear":"2024","journaltitle":"bioRxiv ","volume":"2024.12.13.628393","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.12.13.628393v1","preprintlink":null,"articledate":"2024-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22216188","title":"Activation-induced cytidine deaminase expression in CD4+ T cells is associated with a unique IL-10-producing subset that increases with age.","abstract":"Activation-induced cytidine deaminase (AID), produced by the Aicda gene, is essential for the immunoglobulin gene (Ig) alterations that form immune memory. Using a Cre-mediated genetic system, we unexpectedly found CD4(+) T cells that had expressed Aicda (exAID cells) as well as B cells. ExAID cells increased with age, reaching up to 25% of the CD4(+) and B220(+) cell populations. ExAID B cells remained IgM(+), suggesting that class-switched memory B cells do not accumulate in the spleen. In T cells, AID was expressed in a subset that produced IFN-\u03b3 and IL-10 but little IL-4 or IL-17, and showed no evidence of genetic mutation. Interestingly, the endogenous Aicda expression in T cells was enhanced in the absence of B cells, indicating that the process is independent from the germinal center reaction. These results suggest that in addition to its roles in B cells, AID may have previously unappreciated roles in T-cell function or tumorigenesis.","authors":"Qin, H., Suzuki, K., Nakata, M., Chikuma, S., Izumi, N., Huong, le T., Maruya, M., Fagarasan, S., Busslinger, M., Honjo, T., Nagaoka, H.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"PLoS One","volume":"6","issue":"12","page":"e29141","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-145","title":"Epithelial-Mesenchymal Transition in Pancreatic Carcinoma","abstract":null,"authors":"Maier HJ., Wirth T., Beug H.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cancers ","volume":"2(4)","issue":"","page":"2058-2083","pdf":null,"JrId":null,"fulltextlink":"http:\/\/dx.doi.org\/10.3390\/cancers2042058","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22279045","title":"Anti-apoptotic Mcl-1 is essential for the development and sustained growth of acute myeloid leukemia.","abstract":"Acute myeloid leukemia (AML) frequently relapses after initial treatment. Drug resistance in AML has been attributed to high levels of the anti-apoptotic Bcl-2 family members Bcl-x(L) and Mcl-1. Here we report that removal of Mcl-1, but not loss or pharmacological blockade of Bcl-x(L), Bcl-2, or Bcl-w, caused the death of transformed AML and could cure disease in AML-afflicted mice. Enforced expression of selective inhibitors of prosurvival Bcl-2 family members revealed that Mcl-1 is critical for survival of human AML cells. Thus, targeting of Mcl-1 or regulators of its expression may be a useful strategy for the treatment of AML.","authors":"Glaser, SP., Lee, EF., Trounson, E., Bouillet, P., Wei, A., Fairlie, WD., Izon, DJ., Zuber, J., Rappaport, AR., Herold, MJ., Alexander, WS., Lowe, SW., Robb, L., Strasser, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genes Dev","volume":"26","issue":"2","page":"120-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22101327","title":"Cohesin acetyltransferase Esco2 is a cell viability factor and is required for cohesion in pericentric heterochromatin.","abstract":"Sister chromatid cohesion, mediated by cohesin and regulated by Sororin, is essential for chromosome segregation. In mammalian cells, cohesion establishment and Sororin recruitment to chromatin-bound cohesin depends on the acetyltransferases Esco1 and Esco2. Mutations in Esco2 cause Roberts syndrome, a developmental disease in which mitotic chromosomes have a 'railroad' track morphology. Here, we show that Esco2 deficiency leads to termination of mouse development at pre- and post-implantation stages, indicating that Esco2 functions non-redundantly with Esco1. Esco2 is transiently expressed during S-phase when it localizes to pericentric heterochromatin (PCH). In interphase, Esco2 depletion leads to a reduction in cohesin acetylation and Sororin recruitment to chromatin. In early mitosis, Esco2 deficiency causes changes in the chromosomal localization of cohesin and its protector Sgo1. Our results suggest that Esco2 is needed for cohesin acetylation in PCH and that this modification is required for the proper distribution of cohesin on mitotic chromosomes and for centromeric cohesion.","authors":"Whelan, G., Kreidl, E., Wutz, G., Egner, A., Peters, JM., Eichele, G.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"EMBO J","volume":"31","issue":"1","page":"71-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22209216","title":"Reshaping the optical dimension in optogenetics.","abstract":"Optogenetics has been revolutionizing circuit neuroscience in the last few years. Optical methods combined with genetics and molecular techniques have provided new tools for stimulation of neurons, which hold great promise to provide a solution to the circuit mapping problem and more generally provide us with the ability to artificially control the natural stimulus space. Nevertheless, until very recently almost all applications of optogenetics have been based on relatively simple optical schemes mainly used for inducing population activity in neuronal assembles. In this context, alternative optical schemes that enhance the spatial or temporal resolution of excitation and allow for flexible and arbitrary generation of light patterns have all synergetic impact on the development of new optogenetic actuators. In the following we discuss and compare the main new optical techniques that have become available in the recent years. Their respective strengths and limitations as well as their application to different biological contexts are illustrated.","authors":"Vaziri, A., Emiliani, V.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Curr Opin Neurobiol","volume":"22","issue":"1","page":"128-37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29944854","title":"A User's Guide for Phase Separation Assays with Purified Proteins.","abstract":"The formation of membrane-less organelles and compartments by protein phase separation is an important way in which cells organize their cytoplasm and nucleoplasm. In vitro phase separation assays with purified proteins have become the standard way to investigate proteins that form membrane-less compartments. By now, various proteins have been purified and tested for their ability to phase separate and form liquid condensates in vitro. However, phase-separating proteins are often aggregation-prone and difficult to purify and handle. As a consequence, the results from phase separation assays often differ between labs and are not easily reproduced. Thus, there is an urgent need for high-quality proteins, standardized procedures, and generally agreed-upon practices for protein purification and conducting phase separation assays. This paper provides protocols for protein purification and guides the user through the practicalities of in vitro protein phase separation assays, including best-practice approaches and pitfalls to avoid. We believe that this compendium of protocols and practices will provide a useful resource for scientists studying the phase behavior of proteins.","authors":"Alberti, S., Saha, S., Woodruff, JB., Franzmann, TM., Wang, J., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"J Mol Biol","volume":"430","issue":"23","page":"4806-4820","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23623375","title":"The impact of epithelial-mesenchymal transition on R1 status of the mesopancreatic resection margin after pancreaticoduodenectomy for pancreatic carcinoma: a research proposal topic.","abstract":"","authors":"Peparini, N., Chirletti, P.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Eur J Cancer","volume":"49","issue":"10","page":"2455-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22308412","title":"Auditory circuit in the Drosophila brain.","abstract":"Most animals exhibit innate auditory behaviors driven by genetically hardwired neural circuits. In Drosophila, acoustic information is relayed by Johnston organ neurons from the antenna to the antennal mechanosensory and motor center (AMMC) in the brain. Here, by using structural connectivity analysis, we identified five distinct types of auditory projection neurons (PNs) interconnecting the AMMC, inferior ventrolateral protocerebrum (IVLP), and ventrolateral protocerebrum (VLP) regions of the central brain. These auditory PNs are also functionally distinct; AMMC-B1a, AMMC-B1b, and AMMC-A2 neurons differ in their responses to sound (i.e., they are narrowly tuned or broadly tuned); one type of audioresponsive IVLP commissural PN connecting the two hemispheres is GABAergic; and one type of IVLP-VLP PN acts as a generalist responding to all tested audio frequencies. Our findings delineate an auditory processing pathway involving AMMC\u2192IVLP\u2192VLP in the Drosophila brain.","authors":"Lai, JS., Lo, SJ., Dickson, BJ., Chiang, AS.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Proc Natl Acad Sci U S A","volume":"109","issue":"7","page":"2607-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34149362","title":"Rare Opportunities for Insights Into Serotonergic Contributions to Brain and Bowel Disorders: Studies of the SERT Ala56 Mouse.","abstract":"Altered structure, expression, and regulation of the presynaptic serotonin (5-HT) transporter (SERT) have been associated with multiple neurobehavioral disorders, including mood disorders, obsessive-compulsive disorder (OCD), and autism spectrum disorder (ASD). Opportunities to investigate mechanistic links supporting these associations were spurred with the identification of multiple, rare human SERT coding variants in a study that established a male-specific linkage of ASD to a linkage marker on chromosome 17 which encompassed the location of the SERT gene (<i>SLC6A4<\/i>). We have explored the most common of these variants, SERT Ala56, <i>in vitro<\/i> and <i>in vivo<\/i>. Results support a tonic elevation of 5-HT transport activity in transfected cells and human lymphoblasts by the variant <i>in vitro<\/i> that leads to an increased 5-HT clearance rate <i>in vivo<\/i> when studied in the SERT Ala56 mouse model, along with altered sensitivity to SERT regulatory signaling pathways. Importantly, hyperserotonemia, or an elevated whole blood 5-HT, level, was found in SERT Ala56 mice, reproducing a well-replicated trait observed in a significant fraction of ASD subjects. Additionally, we found multiple biochemical, physiological, and behavioral alterations in the SERT Ala56 mice that can be analogized to those observed in ASD and its medical comorbidities. The similarity of the functional impact of the SERT Ala56 variant to the consequences of p38\u03b1 MAPK activation, ascribed to the induction of a biased conformation of the transporter toward an outward-facing conformation, has resulted in successful efforts to restore normal behavioral and bowel function <i>via<\/i> pharmacological and genetic p38\u03b1 MAPK targeting. Moreover, the ability of the inflammatory cytokine IL-1\u03b2 to enhance SERT activity <i>via<\/i> a p38\u03b1 MAPK-dependent pathway suggests that the SERT Ala56 conformation mimics that of a chronic inflammatory state, supporting findings in ASD of elevated inflammatory cytokine levels. In this report, we review studies of the SERT Ala56 variant, discussing opportunities for continued insight into how chronically altered synaptic 5-HT homeostasis can drive reversible, functional perturbations in 5-HT sensitive pathways in the brain and periphery, and how targeting the SERT regulome, particularly through activating pathways such as those involving IL-1\u03b2\/p38\u03b1 MAPK, may be of benefit for neurobehavioral disorders, including ASD.","authors":"Stilley, SE., Blakely, RD.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Front Cell Neurosci","volume":"15","issue":"","page":"677563","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28572335","title":"A genetic signature of the evolution of loss of flight in the Galapagos cormorant.","abstract":"We have a limited understanding of the genetic and molecular basis of evolutionary changes in the size and proportion of limbs. We studied wing and pectoral skeleton reduction leading to flightlessness in the Galapagos cormorant (<i>Phalacrocorax harrisi<\/i>). We sequenced and de novo assembled the genomes of four cormorant species and applied a predictive and comparative genomics approach to find candidate variants that may have contributed to the evolution of flightlessness. These analyses and cross-species experiments in <i>Caenorhabditis elegans<\/i> and in chondrogenic cell lines implicated variants in genes necessary for transcriptional regulation and function of the primary cilium. Cilia are essential for Hedgehog signaling, and humans affected by skeletal ciliopathies suffer from premature bone growth arrest, mirroring skeletal features associated with loss of flight.","authors":"Burga, A., Wang, W., Ben-David, E., Wolf, PC., Ramey, AM., Verdugo, C., Lyons, K., Parker, PG., Kruglyak, L.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Science","volume":"356","issue":"6341","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22971992","title":"EGCG inhibits growth of human pancreatic tumors orthotopically implanted in Balb C nude mice through modulation of FKHRL1\/FOXO3a and neuropilin.","abstract":"Human pancreatic cancer is currently one of the fourth leading causes of cancer-related mortality with a 5-year survival rate of less than 5 %. Since pancreatic carcinoma is largely refractory to conventional therapies, there is a strong medical need for the development of novel and innovative cancer preventive strategies. The forkhead transcription factors of the O class (FOXO) play a major role in cell proliferation, angiogenesis, metastasis, and tumorigenesis. The objectives of this study were to examine whether FKHRL1\/FOXO3a modulates antitumor activity of (-)-epigallocatechin-3-gallate (EGCG), an active ingredient in green tea, in pancreatic cancer model in vivo. PANC-1 cells were orthotopically implanted into Balb c nude mice and gavaged with EGCG after tumor formation. Cell proliferation and apoptosis were measured by Ki67 and TUNEL staining, respectively. The expression of PI3K, AKT, ERK, and FOXO3a\/FKHRL1 and its target genes were measured by the western blot analysis and\/or q-RT-PCR. FOXO-DNA binding was measured by gel shift assay. EGCG-treated mice showed significant inhibition in tumor growth which was associated with reduced phosphorylation of ERK, PI3K, AKT, and FKHRL1\/FOXO3a, and modulation of FOXO target genes. EGCG induced apoptosis by upregulating Bim and activating caspase-3. EGCG modulated markers of cell cycle (p27\/KIP1), angiogenesis (CD31, VEGF, IL-6, IL-8, SEMA3F, and HIF1\u03b1), and metastasis (MMP2 and MMP7). The inhibition of VEGF by EGCG was associated with suppression of neuropilin. EGCG inhibited epithelial-mesenchymal transition by upregulating the expression of E-cadherin and inhibiting the expression of N-cadherin and Zeb1. These data suggest that EGCG inhibits pancreatic cancer orthotopic tumor growth, angiogenesis, and metastasis which are associated with inhibition of PI3K\/AKT and ERK pathways and activation of FKHRL1\/FOXO3a. As a conclusion, EGCG can be used for the prevention and\/or treatment of pancreatic cancer.","authors":"Shankar, S., Marsh, L., Srivastava, RK.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Mol Cell Biochem","volume":"372","issue":"1-2","page":"83-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22240455","title":"ESCRT-III polymers in membrane neck constriction.","abstract":"The endosomal sorting complex required for transport (ESCRT)-III machinery contributes to membrane deformation and scission in cytokinesis, intraluminal vesicle formation, autophagy and virus budding. Recombinant ESCRT-III subunits polymerize in vitro into filaments, tubes, sheets or rings, and ESCRT-III-dependent filaments have been observed in cells at virus bud necks and at the cytokinetic abscission site. These observations have inspired speculation about how ESCRT-III could mediate constriction and fission of membrane necks. Based on the polymer structures observed in vitro and in vivo, we discuss models for ESCRT-III function and outline how emerging technologies could be used to test these models.","authors":"Guizetti, J., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Trends Cell Biol","volume":"22","issue":"3","page":"133-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18667588","title":"A sea lamprey glycoprotein hormone receptor similar with gnathostome thyrotropin hormone receptor.","abstract":"The specificity of the vertebrate hypothalamic-pituitary-gonadal and hypothalamic-pituitary-thyroid axes is explained by the evolutionary refinement of the specificity of expression and selectivity of interaction between the glycoprotein hormones GpH (FSH, LH, and TSH) and their cognate receptors GpH-R (FSH-R, LH-R, and TSH-R). These two finely tuned signaling pathways evolved by gene duplication and functional divergence from an ancestral GpH\/GpH-R pair. Comparative analysis of the protochordate and gnathostome endocrine systems suggests that this process took place prior or concomitantly with the emergence of the gnathostome lineage. Here, we report identification and characterization of a novel glycoprotein hormone receptor (lGpH-R II) in the Agnathan sea lamprey. This 781 residue protein was found approximately 43% identical with mammalian TSH-R and FSH-R representative sequences, and similarly with these two classes of mammalian receptors it is assembled from ten exons. A synthetic ligand containing the lamprey glycoprotein hormone beta-chain tethered upstream of a mammalian alpha-chain activated the lGpH-R II expressed in COS-7 cells but in a lesser extent than lGpH-R I. Molecular phylogenetic analysis of vertebrate GpH-R protein sequences suggests a closer relationship between lGpH-R II and gnathostome thyrotropin receptors. Overall, the presence and characteristics of the lamprey glycoprotein hormone receptors suggest existence of a primitive functionally overlapping glycoprotein hormone\/glycoprotein hormone receptor system in this animal.","authors":"Freamat, M., Sower, SA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Mol Endocrinol","volume":"41","issue":"4","page":"219-28","pdf":null,"JrId":"1394","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18641127","title":"Development of pulmonary fibrosis through a pathway involving the transcription factor Fra-2\/AP-1.","abstract":"Studies using genetically modified mice have revealed fundamental functions of the transcription factor Fos\/AP-1 in bone biology, inflammation, and cancer. However, the biological role of the Fos-related protein Fra-2 is not well defined in vivo. Here we report an unexpected profibrogenic function of Fra-2 in transgenic mice, in which ectopic expression of Fra-2 in various organs resulted in generalized fibrosis with predominant manifestation in the lung. The pulmonary phenotype was characterized by vascular remodeling and obliteration of pulmonary arteries, which coincided with expression of osteopontin, an AP-1 target gene involved in vascular remodeling and fibrogenesis. These alterations were followed by inflammation; release of profibrogenic factors, such as IL-4, insulin-like growth factor 1, and CXCL5; progressive fibrosis; and premature mortality. Genetic experiments and bone marrow reconstitutions suggested that fibrosis developed independently of B and T cells and was not mediated by autoimmunity despite the marked inflammation observed in transgenic lungs. Importantly, strong expression of Fra-2 was also observed in human samples of idiopathic and autoimmune-mediated pulmonary fibrosis. These findings indicate that Fra-2 expression is sufficient to cause pulmonary fibrosis in mice, possibly by linking vascular remodeling and fibrogenesis, and suggest that Fra-2 has to be considered a contributing pathogenic factor of pulmonary fibrosis in humans.","authors":"Eferl, R., Hasselblatt, P., Rath, M., Popper, H., Zenz, R., Komnenovic, V., Idarraga, MH., Kenner, L., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Proc Natl Acad Sci U S A","volume":"105","issue":"30","page":"10525-30","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22219325","title":"Development and function of murine B cells lacking RANK.","abstract":"RANKL-RANK signaling regulates numerous physiologic processes such as bone remodeling, lymph node organogenesis, central thermoregulation, and formation of a lactating mammary gland in pregnancy. Recently, a receptor activator of NF-\u03baB ligand (RANKL)-blocking Ab has been approved for human use in potentially millions of osteoporosis and cancer patients. However, germline deficiencies in RANKL or receptor activator of NF-\u03baB (RANK) also lead to strong B cell defects in mice and human patients, suggesting that RANKL-RANK inhibition could interfere with B cell physiology and thereby trigger immunologic side-effects. To address this key question--that is, whether RANKL-RANK signaling affects B cell physiology directly or the observed defects are secondary because of the severe osteopetrosis--we generated B cell-specific RANK knockout mice. We show that B cells deficient for RANK undergo normal development and do not show any obvious defects in Ab secretion, class switch recombination, or somatic hypermutation. Our data indicate that ablation of the RANKL-RANK pathway has no direct adverse effect on B cell physiology.","authors":"Perlot, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Immunol","volume":"188","issue":"3","page":"1201-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22330342","title":"Loss of angiotensin-converting enzyme 2 enhances TGF-\u03b2\/Smad-mediated renal fibrosis and NF-\u03baB-driven renal inflammation in a mouse model of obstructive nephropathy.","abstract":"It is known that angiotensin (Ang)-converting enzyme (ACE) 2 catalyzes Ang II to Ang 1-7 to prevent the detrimental effect of Ang II on blood pressure, renal fibrosis, and inflammation. However, mechanisms of renoprotective role of Ace2 remain largely unclear. The present study tested the hypothesis that deficiency of Ace2 may accelerate intrarenal Ang II-mediated fibrosis and inflammation independent of blood pressure in a model of unilateral ureteral obstructive (UUO) nephropathy induced in Ace2(+\/y) and Ace2(-\/y) mice. Results showed that both Ace2(+\/y) and Ace2(-\/y) mice had normal levels of blood pressure and plasma Ang II\/Ang 1-7. In contrast, deletion of ACE2 resulted in a fourfold increase in the ratio of intrarenal Ang II\/Ang 1-7 in the UUO nephropathy. These changes were associated with the development of more intensive tubulointerstitial fibrosis (\u03b1-SMA, collagen I) and inflammation (TNF-\u03b1, IL-1\u03b2, MCP-1, F4\/80(+) cells, and CD3(+)T cells) in Ace2(-\/y) mice at day 3 (all P&lt;0.05) after UUO, becoming more profound at day 7 (all P&lt;0.01). Enhanced renal fibrosis and inflammation in the UUO kidney of Ace2(-\/y) mice were largely attributed to a marked increase in the intrarenal Ang II signaling (AT1-ERK1\/2 mitogen-activated protein kinase), TGF-\u03b2\/Smad2\/3, and NF-\u03baB signaling pathways. Further studies revealed that enhanced TGF-\u03b2\/Smad and NF-\u03baB signaling in the UUO kidney of Ace2(-\/y) mice was associated with upregulation of an E3 ligase Smurf2 and a loss of renal Smad7. In conclusion, enhanced Ang II-mediated TGF-\u03b2\/Smad and NF-\u03baB signaling may be the mechanisms by which loss of Ace2 enhances renal fibrosis and inflammation. Smad7 ubiquitin degradation mediated by Smurf2 may be a central mechanism by which Ace2(-\/y) mice promote TGF-\u03b2\/Smad2\/3-mediated renal fibrosis and NF-\u03baB-driven renal inflammation in a mouse model of UUO nephropathy.","authors":"Liu, Z., Huang, XR., Chen, HY., Penninger, JM., Lan, HY.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Lab Invest","volume":"92","issue":"5","page":"650-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22336714","title":"Intergenic Polycomb target sites are dynamically marked by non-coding transcription during lineage commitment.","abstract":"Non-coding (nc) RNAs are involved both in recruitment of vertebrate Polycomb (PcG) proteins to chromatin, and in activation of PcG target genes. Here we investigate dynamic changes in the relationship between ncRNA transcription and recruitment of PcG proteins to chromatin during differentiation. Profiling of purified cell populations from different stages of a defined murine in vitro neural differentiation system shows that over 50% of regulated intergenic non-coding transcripts precisely correspond to PcG target sites. We designate these PcG recruiting elements as Transcribed Intergenic Polycomb (TIP) sites. The relationship between TIP transcription and PcG recruitment switches dynamically during differentiation between different states, in which transcription and PcG recruitment exclude each other, or in which both are present. Reporter assays show that transcribed TIP sites can repress a flanking gene. Knockdown experiments demonstrate that TIP ncRNAs are themselves required for repression of target genes both in cis and in trans. We propose that TIP transcription may ensure coordinated regulation of gene networks via dynamic switching and recruitment of PcG proteins both in cis and in trans during lineage commitment.","authors":"Hekimoglu-Balkan, B., Aszodi, A., Heinen, R., Jaritz, M., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"RNA Biol","volume":"9","issue":"3","page":"314-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22319460","title":"Inter-homolog crossing-over and synapsis in Arabidopsis meiosis are dependent on the chromosome axis protein AtASY3.","abstract":"In this study we have analysed AtASY3, a coiled-coil domain protein that is required for normal meiosis in Arabidopsis. Analysis of an Atasy3-1 mutant reveals that loss of the protein compromises chromosome axis formation and results in reduced numbers of meiotic crossovers (COs). Although the frequency of DNA double-strand breaks (DSBs) appears moderately reduced in Atasy3-1, the main recombination defect is a reduction in the formation of COs. Immunolocalization studies in wild-type meiocytes indicate that the HORMA protein AtASY1, which is related to Hop1 in budding yeast, forms hyper-abundant domains along the chromosomes that are spatially associated with DSBs and early recombination pathway proteins. Loss of AtASY3 disrupts the axial organization of AtASY1. Furthermore we show that the AtASY3 and AtASY1 homologs BoASY3 and BoASY1, from the closely related species Brassica oleracea, are co-immunoprecipitated from meiocyte extracts and that AtASY3 interacts with AtASY1 via residues in its predicted coiled-coil domain. Together our results suggest that AtASY3 is a functional homolog of Red1. Since studies in budding yeast indicate that Red1 and Hop1 play a key role in establishing a bias to favor inter-homolog recombination (IHR), we propose that AtASY3 and AtASY1 may have a similar role in Arabidopsis. Loss of AtASY3 also disrupts synaptonemal complex (SC) formation. In Atasy3-1 the transverse filament protein AtZYP1 forms small patches rather than a continuous SC. The few AtMLH1 foci that remain in Atasy3-1 are found in association with the AtZYP1 patches. This is sufficient to prevent the ectopic recombination observed in the absence of AtZYP1, thus emphasizing that in addition to its structural role the protein is important for CO formation.","authors":"Ferdous, M., Higgins, JD., Osman, K., Lambing, C., Roitinger, E., Mechtler, K., Armstrong, SJ., Perry, R., Pradillo, M., Cu\u00f1ado, N., Franklin, FC.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"2","page":"e1002507","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40671959","title":null,"abstract":null,"authors":"","publication_status":null,"journalpubyear":null,"journaltitle":null,"volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18625885","title":"Igbp1 is part of a positive feedback loop in stem cell factor-dependent, selective mRNA translation initiation inhibiting erythroid differentiation.","abstract":"Stem cell factor (SCF)-induced activation of phosphoinositide-3-kinase (PI3K) is required for transient amplification of the erythroblast compartment. PI3K stimulates the activation of mTOR (target of rapamycin) and subsequent release of the cap-binding translation initiation factor 4E (eIF4E) from the 4E-binding protein 4EBP, which controls the recruitment of structured mRNAs to polysomes. Enhanced expression of eIF4E renders proliferation of erythroblasts independent of PI3K. To investigate which mRNAs are selectively recruited to polysomes, we compared SCF-dependent gene expression between total and polysome-bound mRNA. This identified 111 genes primarily subject to translational regulation. For 8 of 9 genes studied in more detail, the SCF-induced polysome recruitment of transcripts exceeded 5-fold regulation and was PI3K-dependent and eIF4E-sensitive, whereas total mRNA was not affected by signal transduction. One of the targets, Immunoglobulin binding protein 1 (Igbp1), is a regulatory subunit of protein phosphatase 2A (Pp2a) sustaining mTOR signaling. Constitutive expression of Igbp1 impaired erythroid differentiation, maintained 4EBP and p70S6k phosphorylation, and enhanced polysome recruitment of multiple eIF4E-sensitive mRNAs. Thus, PI3K-dependent polysome recruitment of Igbp1 acts as a positive feedback mechanism on translation initiation underscoring the important regulatory role of selective mRNA recruitment to polysomes in the balance between proliferation and maturation of erythroblasts.","authors":"Grech, G., Bl\u00e1zquez-Domingo, M., Kolbus, A., Bakker, WJ., M\u00fcllner, EW., Beug, H., von Lindern, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Blood","volume":"112","issue":"7","page":"2750-60","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2008-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21413103","title":"Scanning electron microscopy with an ionic liquid reveals the loss of mitotic protrusions of cells during the epithelial-mesenchymal transition.","abstract":"Epithelial-mesenchymal transition (EMT) is a key event in cancer metastasis and is characterized by increase in cell motility, increase in expression of mesenchymal cell markers, loss of proteins from cell-to-cell junction complexes, and changes in cell morphology. Here, the morphological effects of a representative EMT inducer, transforming growth factor (TGF)-\u03b21, were investigated in human lung adenocarcinoma (A549) cells and pancreatic carcinoma (Panc-1) cells. TGF-\u03b21 caused morphological changes characteristic of EMT, and immunostaining showed loss of E-cadherin from cell-to-cell junction complexes in addition to the upregulation of the mesenchymal marker vimentin. During scanning electron microscopy (SEM) with an ionic liquid, we observed EMT-specific morphological changes, including the formation of various cell protrusions. Interestingly, filopodia in mitotic cells were clearly observed by SEM, and the number of these filopodia in TFG-\u03b21-treated mitotic cells was reduced significantly. We conclude that this reduction in such mitotic protrusions is a novel effect of TGF-\u03b21 and may contribute to EMT.","authors":"Ishigaki, Y., Nakamura, Y., Takehara, T., Shimasaki, T., Tatsuno, T., Takano, F., Ueda, Y., Motoo, Y., Takegami, T., Nakagawa, H., Kuwabata, S., Nemoto, N., Tomosugi, N., Miyazawa, S.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Microsc Res Tech","volume":"74","issue":"11","page":"1024-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18621046","title":"Cellular repressor of E1A-stimulated genes is a bona fide lysosomal protein which undergoes proteolytic maturation during its biosynthesis.","abstract":"Cellular repressor of E1A-stimulated genes (CREG) has been reported to be a secretory glycoprotein implicated in cellular growth and differentiation. We now show that CREG is predominantly localized within intracellular compartments. Intracellular CREG was found to lack an N-terminal peptide present in the secreted form of the protein. In contrast to normal cells, CREG is largely secreted by fibroblasts missing both mannose 6-phosphate receptors. This is not observed in cells lacking only one of them. Mass spectrometric analysis of recombinant CREG revealed that the protein contains phosphorylated oligosaccharides at either of its two N-glycosylation sites. Cellular CREG was found to cosediment with lysosomal markers upon subcellular fractionation by density-gradient centrifugation. In fibroblasts expressing a CREG-GFP fusion construct, the heterologous protein was detected in compartments containing lysosomal proteins. Immunolocalization of endogenous CREG confirmed that intracellular CREG is localized in lysosomes. Proteolytic processing of intracellular CREG involves the action of lysosomal cysteine proteinases. These results establish that CREG is a lysosomal protein that undergoes proteolytic maturation in the course of its biosynthesis, carries the mannose 6-phosphate recognition marker and depends on the interaction with mannose 6-phosphate receptors for efficient delivery to lysosomes.","authors":"Sch\u00e4hs, P., Weidinger, P., Probst, OC., Svoboda, B., Stadlmann, J., Beug, H., Waerner, T., Mach, L.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Exp Cell Res","volume":"314","issue":"16","page":"3036-47","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"2008-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33767157","title":"An ALYREF-MYCN coactivator complex drives neuroblastoma tumorigenesis through effects on USP3 and MYCN stability.","abstract":"To achieve the very high oncoprotein levels required to drive the malignant state cancer cells utilise the ubiquitin proteasome system to upregulate transcription factor levels. Here our analyses identify ALYREF, expressed from the most common genetic copy number variation in neuroblastoma, chromosome 17q21-ter gain as a key regulator of MYCN protein turnover. We show strong co-operativity between ALYREF and MYCN from transgenic models of neuroblastoma in vitro and in vivo. The two proteins form a nuclear coactivator complex which stimulates transcription of the ubiquitin specific peptidase 3, USP3. We show that increased USP3 levels reduce K-48- and K-63-linked ubiquitination of MYCN, thus driving up MYCN protein stability. In the MYCN-ALYREF-USP3 signal, ALYREF is required for MYCN effects on the malignant phenotype and that of USP3 on MYCN stability. This data defines a MYCN oncoprotein dependency state which provides a rationale for future pharmacological studies.","authors":"Nagy, Z., Seneviratne, JA., Kanikevich, M., Chang, W., Mayoh, C., Venkat, P., Du, Y., Jiang, C., Salib, A., Koach, J., Carter, DR., Mittra, R., Liu, T., Parker, MW., Cheung, BB., Marshall, GM.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"1881","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2116362","title":"A novel B-cell lineage-specific transcription factor present at early but not late stages of differentiation.","abstract":"A novel B-cell-specific transcription factor, BSAP, was identified as a mammalian homolog of the sea urchin protein TSAP, which interacts with the promoters of four tissue-specific late histone H2A-2 and H2B-2 genes. As shown by mobility-shift, methylation interference, and mutational analyses, the mammalian protein BSAP recognizes all four sea urchin binding sites in a manner indistinguishable from TSAP; however, the two proteins differ in molecular weight. BSAP is exclusively restricted to the B-cell lineage of lymphoid differentiation. Its expression appears to be activated during pro-B-cell development, is abundant at the pre-B- and mature B-cell stages, but is absent in terminally differentiated plasma cells. Moreover, BSAP is clearly a B-cell-specific transcription factor, as a wild-type but not a mutant TSAP-binding site of the sea urchin functions only in transfected B cells as an upstream promoter element. Competition experiments did not reveal any high-affinity binding site for BSAP in known regulatory regions of immunoglobulin and class II major histocompatibility (MHC) genes, suggesting that BSAP is a regulator of a different set of B-lymphoid-specific genes.","authors":"Barberis, A., Widenhorn, K., Vitelli, L., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Genes Dev","volume":"4","issue":"5","page":"849-59","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1990-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21857030","title":"Quantitative phospho-proteomics to investigate the polo-like kinase 1-dependent phospho-proteome.","abstract":"Polo-like kinase 1 (PLK1) is a key regulator of mitotic progression and cell division, and small molecule inhibitors of PLK1 are undergoing clinical trials to evaluate their utility in cancer therapy. Despite this importance, current knowledge about the identity of PLK1 substrates is limited. Here we present the results of a proteome-wide analysis of PLK1-regulated phosphorylation sites in mitotic human cells. We compared phosphorylation sites in HeLa cells that were or were not treated with the PLK1-inhibitor BI 4834, by labeling peptides via methyl esterification, fractionation of peptides by strong cation exchange chromatography, and phosphopeptide enrichment via immobilized metal affinity chromatography. Analysis by quantitative mass spectrometry identified 4070 unique mitotic phosphorylation sites on 2069 proteins. Of these, 401 proteins contained one or multiple phosphorylation sites whose abundance was decreased by PLK1 inhibition. These include proteins implicated in PLK1-regulated processes such as DNA damage, mitotic spindle formation, spindle assembly checkpoint signaling, and chromosome segregation, but also numerous proteins that were not suspected to be regulated by PLK1. Analysis of amino acid sequence motifs among phosphorylation sites down-regulated under PLK1 inhibition in this data set identified two potential novel variants of the PLK1 consensus motif.","authors":"Grosstessner-Hain, K., Hegemann, B., Novatchkova, M., Rameseder, J., Joughin, BA., Hudecz, O., Roitinger, E., Pichler, P., Kraut, N., Yaffe, MB., Peters, JM., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mol Cell Proteomics","volume":"10","issue":"11","page":"M111.008540","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2088503","title":"Sympathetic hyperplasia and neuroblastomas in transgenic mice expressing polyoma middle T antigen.","abstract":"Transgenic mice carrying a cDNA to the polyoma virus middle T (mT) antigen linked to the thymidine kinase promoter were generated to study the consequences of deregulated expression of mT-associated tyrosine kinase activity in a wide variety of tissues. Four independent transgenic founder animals were obtained, from one of which was established a transgenic line. This mouse and all its offspring developed multiple neuroblastomas between 2 and 3 months of age. Expression of the transgene (assayed by tyrosine kinase assay and in situ hybridization) was restricted to the neurons of the central and peripheral nervous tissue, probably because of a positional effect of the transgene integration. Characteristic preneoplastic lesions in the sympathetic ganglia and in the adrenal medulla were identified from which the neuroblastomas originated. The tumors arising in these mice show striking analogies to human neuroblastomas, including the sites of development of the tumors, their histological and ultrastructural appearance, and the expression of diagnostic markers, such as synaptophysin, and high expression of the N-myc oncogene. This animal model thus provides a unique tool for studying growth control in sympathetic neuroblasts and the pathogenesis of neuroblastoma.","authors":"Aguzzi, A., Wagner, EF., Williams, RL., Courtneidge, SA.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"New Biol","volume":"2","issue":"6","page":"533-43","pdf":null,"JrId":"1880","fulltextlink":null,"preprintlink":null,"articledate":"1991-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28495877","title":"A maternal-effect selfish genetic element in <i>Caenorhabditis elegans<\/i>.","abstract":"Selfish genetic elements spread in natural populations and have an important role in genome evolution. We discovered a selfish element causing embryonic lethality in crosses between wild strains of the nematode <i>Caenorhabditis elegans<\/i> The element is made up of <i>sup-35<\/i>, a maternal-effect toxin that kills developing embryos, and <i>pha-1<\/i>, its zygotically expressed antidote. <i>pha-1<\/i> has long been considered essential for pharynx development on the basis of its mutant phenotype, but this phenotype arises from a loss of suppression of <i>sup-35<\/i> toxicity. Inactive copies of the <i>sup-35\/pha-1<\/i> element show high sequence divergence from active copies, and phylogenetic reconstruction suggests that they represent ancestral stages in the evolution of the element. Our results suggest that other essential genes identified by genetic screens may turn out to be components of selfish elements.","authors":"Ben-David, E., Burga, A., Kruglyak, L.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Science","volume":"356","issue":"6342","page":"1051-1055","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33671852","title":"CRISPR Deletion of a SVA Retrotransposon Demonstrates Function as a <i>cis<\/i>-Regulatory Element at the <i>TRPV1\/TRPV3<\/i> Intergenic Region.","abstract":"SINE-VNTR-<i>Alu<\/i> (SVA) retrotransposons are a subclass of transposable elements (TEs) that exist only in primate genomes. TE insertions can be co-opted as <i>cis<\/i>-regulatory elements (CREs); however, the regulatory potential of SVAs has predominantly been demonstrated using bioinformatic approaches and reporter gene assays. The objective of this study was to demonstrate SVA <i>cis<\/i>-regulatory activity by CRISPR (clustered regularly interspaced short palindromic repeats) deletion and subsequent measurement of direct effects on local gene expression. We identified a region on chromosome 17 that was enriched with human-specific SVAs. Comparative gene expression analysis at this region revealed co-expression of <i>TRPV1<\/i> and <i>TRPV3<\/i> in multiple human tissues, which was not observed in mouse, highlighting key regulatory differences between the two species. Furthermore, the intergenic region between <i>TRPV1<\/i> and <i>TRPV3<\/i> coding sequences contained a human specific SVA insertion located upstream of the <i>TRPV3<\/i> promoter and downstream of the 3' end of <i>TRPV1<\/i>, highlighting this SVA as a candidate to study its potential <i>cis<\/i>-regulatory activity on both genes. Firstly, we generated SVA reporter gene constructs and demonstrated their transcriptional regulatory activity in HEK293 cells. We then devised a dual-targeting CRISPR strategy to facilitate the deletion of this entire SVA sequence and generated edited HEK293 clonal cell lines containing homozygous and heterozygous SVA deletions. In edited homozygous \u2206SVA clones, we observed a significant decrease in both <i>TRPV1<\/i> and <i>TRPV3<\/i> mRNA expression, compared to unedited HEK293. In addition, we also observed an increase in the variability of mRNA expression levels in heterozygous \u2206SVA clones. Overall, in edited HEK293 with SVA deletions, we observed a disruption to the co-expression of <i>TRPV1<\/i> and <i>TRPV3<\/i>. Here we provide an example of a human specific SVA with <i>cis<\/i>-regulatory activity in situ, supporting the role of SVA retrotransposons as contributors to species-specific gene expression.","authors":"Price, E., Gianfrancesco, O., Harrison, PT., Frank, B., Bubb, VJ., Quinn, JP.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Int J Mol Sci","volume":"22","issue":"4","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21187158","title":"Early phase TGF\u03b2 receptor signalling dynamics stabilised by the deubiquitinase UCH37 promotes cell migratory responses.","abstract":"TGF\u03b2 signals through serine\/threonine kinase receptors and intracellular Smad transcription factors. An important regulatory step involves ubiquitination of Smads and\/or TGF\u03b2 receptors by specific ubiquitin ligases, in a process that can be reversed by the deubiquitinating enzyme UCH37. Here, to explore the physiological role of UCH37 in TGF\u03b2 signalling we have generated stable and inducible HaCAT keratinocyte and Colo-357 pancreatic carcinoma cell lines mis-expressing UCH37. We show that UCH37 knockdown significantly inhibits the activity of a TGF\u03b2-dependent gene reporter and selectively decreases levels of some TGF\u03b2-dependent target genes, notably p21 and PAI-1, but only during the early phase of TGF\u03b2 receptor activation. Interestingly, UCH37 knockdown in Colo-357 cells had no effect on TGF\u03b2-dependent cell proliferation and epithelial-mesenchymal transition, yet significantly impaired cell migration. Collectively, our data indicate that UCH37 sustains early TGF\u03b2 pathway activation kinetics that determines threshold-specific gene expression patterns, and that opposing actions of ubiquitin ligases and deubiquitinases influences distinct biological TGF\u03b2-dependent biological responses. Moreover, we suggest that UCH37 could represent a viable target for novel and selective cancer therapeutics.","authors":"Cutts, AJ., Soond, SM., Powell, S., Chantry, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Int J Biochem Cell Biol","volume":"43","issue":"4","page":"604-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18548008","title":"A B-Myb complex containing clathrin and filamin is required for mitotic spindle function.","abstract":"B-Myb is one member of the vertebrate Myb family of transcription factors and is ubiquitously expressed. B-Myb activates transcription of a group of genes required for the G2\/M cell cycle transition by forming the dREAM\/Myb-MuvB-like complex, which was originally identified in Drosophila. Mutants of zebrafish B-myb and Drosophila myb exhibit defects in cell cycle progression and genome instability. Although the genome instability caused by a loss of B-Myb has been speculated to be due to abnormal cell cycle progression, the precise mechanism remains unknown. Here, we have purified a B-Myb complex containing clathrin and filamin (Myb-Clafi complex). This complex is required for normal localization of clathrin at the mitotic spindle, which was previously reported to stabilize kinetochore fibres. The Myb-Clafi complex is not tightly associated with the mitotic spindles, suggesting that this complex ferries clathrin to the mitotic spindles. Thus, identification of the Myb-Clafi complex reveals a previously unrecognized function of B-Myb that may contribute to its role in chromosome stability, possibly, tumour suppression.","authors":"Yamauchi, T., Ishidao, T., Nomura, T., Shinagawa, T., Tanaka, Y., Yonemura, S., Ishii, S.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO J","volume":"27","issue":"13","page":"1852-62","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28013290","title":"Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability.","abstract":"The integrity and dynamic properties of the microtubule cytoskeleton are indispensable for the development of the mammalian brain. Consequently, mutations in the genes that encode the structural component (the \u03b1\/\u03b2-tubulin heterodimer) can give rise to severe, sporadic neurodevelopmental disorders. These are commonly referred to as the tubulinopathies. Here we report the addition of recessive quadrupedalism, also known as Uner Tan syndrome (UTS), to the growing list of diseases caused by tubulin variants. Analysis of a consanguineous UTS family identified a biallelic TUBB2B mutation, resulting in a p.R390Q amino acid substitution. In addition to the identifying quadrupedal locomotion, all three patients showed severe cerebellar hypoplasia. None, however, displayed the basal ganglia malformations typically associated with TUBB2B mutations. Functional analysis of the R390Q substitution revealed that it did not affect the ability of \u03b2-tubulin to fold or become assembled into the \u03b1\/\u03b2-heterodimer, nor did it influence the incorporation of mutant-containing heterodimers into microtubule polymers. The 390Q mutation in S. cerevisiae TUB2 did not affect growth under basal conditions, but did result in increased sensitivity to microtubule-depolymerizing drugs, indicative of a mild impact of this mutation on microtubule function. The TUBB2B mutation described here represents an unusual recessive mode of inheritance for missense-mediated tubulinopathies and reinforces the sensitivity of the developing cerebellum to microtubule defects.","authors":"Breuss, MW., Nguyen, T., Srivatsan, A., Leca, I., Tian, G., Fritz, T., Hansen, AH., Musaev, D., McEvoy-Venneri, J., James, KN., Rosti, RO., Scott, E., Tan, U., Kolodner, RD., Cowan, NJ., Keays, DA., Gleeson, JG.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Hum Mol Genet","volume":"26","issue":"2","page":"258-269","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21166957","title":"Hepatocyte growth factor activator inhibitor type 1 suppresses metastatic pulmonary colonization of pancreatic carcinoma cells.","abstract":"Hepatocyte growth factor activator inhibitor type 1 (HAI-1) is a transmembrane protease inhibitor that regulates the activities of membrane-bound and extracellular serine proteases. HAI-1 has two Kunitz-type inhibitor domains with the N-terminal Kunitz domain (KD1) responsible for inhibiting known target proteases. Previously, we reported that knockdown of HAI-1 in the human pancreatic carcinoma cell line SUIT-2 resulted in epithelial to mesenchymal transition. To evaluate the role of HAI-1 in metastasis, we examined the metastatic capability of SUIT-2 cells that did or did not stably express HAI-1 short-hairpin RNA in an experimental pulmonary metastasis assay using nude mice. The extent of pulmonary metastasis was verified by histological examination and direct measurement of human cytokeratin 19 mRNA levels. One week after injecting SUIT-2 cells into mouse tail veins, apparent metastatic colonization was observed in 36% (4\/11) of mice injected with HAI-1-knockdown SUIT-2, whereas none (0\/11) of the control mice were positive for metastasis. After 2 weeks the metastasis positive ratios were 80% (4\/5) and 40% (2\/5), and after 4 weeks the ratios were 82% (9\/11) and 45% (5\/11) for HAI-1-knockdown and control SUIT-2 cells, respectively. Thus, loss of HAI-1 promoted pulmonary metastasis. Co-injection of recombinant KD1 abolished metastasis produced by HAI-1-knockdown SUIT-2 cells after 1 week. Moreover, recombinant KD1 restored E-cadherin levels in HAI-1 knockdown SUIT-2 cells and reduced their invasiveness in vitro. These data indicate that HAI-1 regulates pulmonary metastasis of SUIT-2, and KD1 may have therapeutic application for inhibiting metastatic cancer cell spreading.","authors":"Fukushima, T., Kawaguchi, M., Yamasaki, M., Tanaka, H., Yorita, K., Kataoka, H.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Cancer Sci","volume":"102","issue":"2","page":"407-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19380743","title":"Charting the molecular network of the drug target Bcr-Abl.","abstract":"The tyrosine kinase Bcr-Abl causes chronic myeloid leukemia and is the cognate target of tyrosine kinase inhibitors like imatinib. We have charted the protein-protein interaction network of Bcr-Abl by a 2-pronged approach. Using a monoclonal antibody we have first purified endogenous Bcr-Abl protein complexes from the CML K562 cell line and characterized the set of most tightly-associated interactors by MS. Nine interactors were subsequently subjected to tandem affinity purifications\/MS analysis to obtain a molecular interaction network of some hundred cellular proteins. The resulting network revealed a high degree of interconnection of 7 \"core\" components around Bcr-Abl (Grb2, Shc1, Crk-I, c-Cbl, p85, Sts-1, and SHIP-2), and their links to different signaling pathways. Quantitative proteomics analysis showed that tyrosine kinase inhibitors lead to a disruption of this network. Certain components still appear to interact with Bcr-Abl in a phosphotyrosine-independent manner. We propose that Bcr-Abl and other drug targets, rather than being considered as single polypeptides, can be considered as complex protein assemblies that remodel upon drug action.","authors":"Brehme, M., Hantschel, O., Colinge, J., Kaupe, I., Planyavsky, M., K\u00f6cher, T., Mechtler, K., Bennett, KL., Superti-Furga, G.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Proc Natl Acad Sci U S A","volume":"106","issue":"18","page":"7414-9","pdf":null,"JrId":"6653","fulltextlink":"http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?tool=pubmed&pubmedid=19380743","preprintlink":null,"articledate":"2009-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1610893","title":"Histone H4 mRNA levels are down-regulated by 3' RNA processing during terminal differentiation of myoblasts.","abstract":"The capacity for 3' processing of the histone H4 pre-mRNA is lost following differentiation of rat L6 myoblasts to myotubes. Nuclear extracts prepared from proliferating myoblasts, but not differentiated myotubes, actively process histone H4 pre-mRNA in vitro. The activity of two factors required for 3' processing, the heat-labile factor and U7 snRNP, also changes during the differentiation period, concurrent with the loss of 3' processing activity. During myotube formation, the activity of the heat-labile factor decreases significantly while the 5' sequences of the U7 snRNA become progressively resistant to micrococcal nuclease digestion. Thus, the dramatic down-shift in histone H4 mRNA levels which occurs during myoblast differentiation is controlled at both the transcriptional and posttranscriptional level.","authors":"Larson, DE., Hoffmann, I., Zahradka, P., Birnstiel, ML., Sells, BH.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Biochim Biophys Acta","volume":"1131","issue":"2","page":"139-44","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1992-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34270680","title":"Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data.","abstract":"on Status=\"Publisher\" Owner=\"NLM\"><PMID Version=\"1\">34270680<\/PMID><DateRevised><Year>2021<\/Year><Month>07<\/Month><Day>16<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1367-4811<\/ISSN><JournalIssue CitedMedium=\"Internet\"><PubDate><Year>2021<\/Year><Month>Jul<\/Month><Day>16<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">btab526<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/bioinformatics\/btab526<\/ELocationID><Abstract><AbstractText Label=\"MOTIVATION\" NlmCategory=\"BACKGROUND\">Clinical decision making is increasingly guided by accurate and recurrent determination of presence and frequency of (somatic) variants and their haplotype through panel sequencing of disease-relevant genomic regions. Haplotype calling (phasing), however, is difficult and error prone unless variants are located on the same read which limits the ability of short-read sequencing to detect, e.g., co-occurrence of drug-resistance variants. Long-read panel sequencing enables direct phasing of amplicon variants besides having multiple other benefits, however, high error rates of current technologies prevented their applicability in the past.","authors":"Popitsch, N., Preuner, S., Lion, T.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Bioinformatics","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19343204","title":"Conserved alternative splicing and expression patterns of arthropod N-cadherin.","abstract":"Metazoan development requires complex mechanisms to generate cells with diverse function. Alternative splicing of pre-mRNA not only expands proteomic diversity but also provides a means to regulate tissue-specific molecular expression. The N-Cadherin gene in Drosophila contains three pairs of mutually-exclusive alternatively-spliced exons (MEs). However, no significant differences among the resulting protein isoforms have been successfully demonstrated in vivo. Furthermore, while the N-Cadherin gene products exhibit a complex spatiotemporal expression pattern within embryos, its underlying mechanisms and significance remain unknown. Here, we present results that suggest a critical role for alternative splicing in producing a crucial and reproducible complexity in the expression pattern of arthropod N-Cadherin. We demonstrate that the arthropod N-Cadherin gene has maintained the three sets of MEs for over 400 million years using in silico and in vivo approaches. Expression of isoforms derived from these MEs receives precise spatiotemporal control critical during development. Both Drosophila and Tribolium use ME-13a and ME-13b in \"neural\" and \"mesodermal\" splice variants, respectively. As proteins, either ME-13a- or ME-13b-containing isoform can cell-autonomously rescue the embryonic lethality caused by genetic loss of N-Cadherin. Ectopic muscle expression of either isoform beyond the time it normally ceases leads to paralysis and lethality. Together, our results offer an example of well-conserved alternative splicing increasing cellular diversity in metazoans.","authors":"Hsu, SN., Yonekura, S., Ting, CY., Robertson, HM., Iwai, Y., Uemura, T., Lee, CH., Chiba, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS Genet","volume":"5","issue":"4","page":"e1000441","pdf":null,"JrId":"32385","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18528333","title":"Mei-P26 regulates microRNAs and cell growth in the Drosophila ovarian stem cell lineage.","abstract":"Drosophila neuroblasts and ovarian stem cells are well characterized models for stem cell biology. In both cell types, one daughter cell self-renews continuously while the other undergoes a limited number of divisions, stops to proliferate mitotically and differentiates. Whereas neuroblasts segregate the Trim-NHL (tripartite motif and Ncl-1, HT2A and Lin-41 domain)-containing protein Brain tumour (Brat) into one of the two daughter cells, ovarian stem cells are regulated by an extracellular signal from the surrounding stem cell niche. After division, one daughter cell looses niche contact. It undergoes 4 transit-amplifying divisions to form a cyst of 16 interconnected cells that reduce their rate of growth and stop to proliferate mitotically. Here we show that the Trim-NHL protein Mei-P26 (refs 7, 8) restricts growth and proliferation in the ovarian stem cell lineage. Mei-P26 expression is low in stem cells but is strongly induced in 16-cell cysts. In mei-P26 mutants, transit-amplifying cells are larger and proliferate indefinitely leading to the formation of an ovarian tumour. Like brat, mei-P26 regulates nucleolar size and can induce differentiation in Drosophila neuroblasts, suggesting that these genes act through the same pathway. We identify Argonaute-1, a component of the RISC complex, as a common binding partner of Brat and Mei-P26, and show that Mei-P26 acts by inhibiting the microRNA pathway. Mei-P26 and Brat have a similar domain composition that is also found in other tumour suppressors and might be a defining property of a new family of microRNA regulators that act specifically in stem cell lineages.","authors":"Neum\u00fcller, RA., Betschinger, J., Fischer, A., Bushati, N., Poernbacher, I., Mechtler, K., Cohen, SM., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"454","issue":"7201","page":"241-5","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34256217","title":"Awakening of the zygotic genome by pioneer transcription factors.","abstract":"After fertilization, the genome of the totipotent embryo is transcriptionally inactive and then initiates bursts of transcription termed zygotic genome activation (ZGA). Despite the fundamental importance of initiating an embryonic transcription program for the start of life, the essential regulators and molecular mechanisms triggering ZGA in most organisms are poorly understood. One mechanism centers on pioneer factors that function in cellular reprogramming and differentiation. Recent studies revealed that not only a single but multiple pioneer factors bind cooperatively to the genome to open chromatin, resulting in changes in epigenetic modifications and triggering ZGA. Here, we review recent insights into the functions of pioneer factors during ZGA and discuss the potential relevance to three-dimensional chromatin organization during embryonic development.","authors":"Kobayashi, W., Tachibana, K.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Curr Opin Struct Biol","volume":"71","issue":null,"page":"94-100","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19271354","title":"Modeling of the actin-cytoskeleton in symmetric  lamellipodial fragments.","abstract":"The pushing structures of cells include laminar sheets, termed lamellipodia, made up of a meshwork of actin filaments that grow at the front and depolymerise at the rear, in a treadmilling mode.We here develop a mathematical model to describe the turnover and the mechanical properties of this network.Our basic modeling assumptions are that the lamellipodium is idealised as a two-dimensional structure, and that the actin network consists of two families of possibly bent, but locally parallel filaments. Instead of dealing with individual polymers, the filaments are assumed to be continuously distributed.The model includes (de)polymerization, of the mechanical effects of cross-linking, cell-substrate adhesion, as well as of the leading edge of the membrane.In the first version presented here, the total amount of F-actin is prescribed by assuming a constant polymerisation speed at the leading edge and a fixed total number and length distribution of filaments. We assume that cross-links at filament crossing points as well as integrin linkages with the matrix break and reform in response to incremental changes in network organization. In this first treatment, the model successfully simulates the persistence of the treadmilling network in radially spread cells.","authors":"Oelz, D., Schmeiser, C., Small, JV.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell Adh Migr","volume":"2","issue":"2","page":"117-26","pdf":null,"JrId":"34790","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19110430","title":"Lack of DREAM protein enhances learning and memory and slows brain aging.","abstract":"Memory deficits in aging affect millions of people and are often disturbing to those concerned. Dissection of the molecular control of learning and memory is paramount to understand and possibly enhance cognitive functions. Old-age memory loss also has been recently linked to altered Ca(2+) homeostasis. We have previously identified DREAM (downstream regulatory element antagonistic modulator), a member of the neuronal Ca(2+) sensor superfamily of EF-hand proteins, with specific roles in different cell compartments. In the nucleus, DREAM is a Ca(2+)-dependent transcriptional repressor, binding to specific DNA signatures, or interacting with nucleoproteins regulating their transcriptional properties. Also, we and others have shown that dream mutant (dream(-\/-)) mice exhibit marked analgesia. Here we report that dream(-\/-) mice exhibit markedly enhanced learning and synaptic plasticity related to improved cognition. Mechanistically, DREAM functions as a negative regulator of the key memory factor CREB in a Ca(2+)-dependent manner, and loss of DREAM facilitates CREB-dependent transcription during learning. Intriguingly, 18-month-old dream(-\/-) mice display learning and memory capacities similar to young mice. Moreover, loss of DREAM protects from brain degeneration in aging. These data identify the Ca(2+)-regulated \"pain gene\" DREAM as a novel key regulator of memory and brain aging.","authors":"Font\u00e1n-Lozano, A., Romero-Granados, R., del-Pozo-Mart\u00edn, Y., Su\u00e1rez-Pereira, I., Delgado-Garc\u00eda, JM., Penninger, JM., Carri\u00f3n, AM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Biol","volume":"19","issue":"1","page":"54-60","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18824692","title":"The Dam1 ring binds microtubules strongly enough to be a processive as well as energy-efficient coupler for chromosome motion.","abstract":"Accurate chromosome segregation during mitotic division of budding yeast depends on the multiprotein kinetochore complex, Dam1 (also known as DASH). Purified Dam1 heterodecamers encircle microtubules (MTs) to form rings that can function as \"couplers,\" molecular devices that transduce energy from MT disassembly into the motion of a cargo. Here we show that MT depolymerization develops a force against a Dam1 ring that is sixfold larger than the force exerted on a coupler that binds only one side of an MT. Wild-type rings slow depolymerization fourfold, but rings that include a mutant Dam1p with truncated C terminus slow depolymerization less, consistent with the idea that this tail is part of a strong bond between rings and MTs. A molecular-mechanical model for Dam1-MT interaction predicts that binding between this flexible tail and the MT wall should cause a Dam1 ring to wobble, and Fourier analysis of moving, ring-attached beads corroborates this prediction. Comparison of the forces generated against wild-type and mutant complexes confirms the importance of tight Dam1-MT association for processive cargo movement under load.","authors":"Grishchuk, EL., Efremov, AK., Volkov, VA., Spiridonov, IS., Gudimchuk, N., Westermann, S., Drubin, D., Barnes, G., McIntosh, JR., Ataullakhanov, FI.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Proc Natl Acad Sci U S A","volume":"105","issue":"40","page":"15423-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19328069","title":"Building sister chromatid cohesion: smc3 acetylation counteracts an antiestablishment activity.","abstract":"Cohesin's Smc1, Smc3, and Scc1 subunits form a tripartite ring that entraps sister DNAs. Scc3, Pds5, and Rad61 (Wapl) are regulatory subunits that control this process. We describe here smc3, scc3, pds5, and rad61 mutations that permit yeast cell proliferation and entrapment of sister DNAs by cohesin rings in the absence of Eco1, an acetyl transferase normally essential for establishing sister chromatid cohesion. The smc3 mutations cluster around and include a highly conserved lysine (K113) close to Smc3's ATP-binding pocket, which, together with K112, is acetylated by Eco1. Lethality caused by mutating both residues to arginine is suppressed by the scc3, pds5, and rad61 mutants. Scc3, Pds5, and Rad61 form a complex and inhibit entrapment of sister DNAs by a process involving the \"K112\/K113\" surface on Smc3's ATPase. According to this model, Eco1 promotes sister DNA entrapment partly by relieving an antiestablishment activity associated with Scc3, Pds5, and Rad61.","authors":"Rowland, BD., Roig, MB., Nishino, T., Kurze, A., Uluocak, P., Mishra, A., Beckou\u00ebt, F., Underwood, P., Metson, J., Imre, R., Mechtler, K., Katis, VL., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Cell","volume":"33","issue":"6","page":"763-74","pdf":null,"JrId":"20730","fulltextlink":"http:\/\/www.sciencedirect.com\/science?_ob=ArticleURL&_udi=B6WSR-4VXKKXJ-D&_user=4888655&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000054145&_version=1&_urlVersion=0&_userid=4888655&md5=11a873ac0f880e6391e7e8bd72bd2be2","preprintlink":null,"articledate":"2009-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34048690","title":"Human embryo research, stem cell-derived embryo models and in\u00a0vitro gametogenesis: Considerations leading to the revised ISSCR guidelines.","abstract":"The ISSCR Guidelines for Stem Cell Research and Clinical Translation were last revised in 2016. Since then, rapid progress has been made in research areas related to in\u00a0vitro culture of human embryos, creation of stem cell-based embryo models, and in\u00a0vitro gametogenesis. Therefore, a working group of international experts was convened to review the oversight process and provide an update to the guidelines. This report captures the discussion and summarizes the major recommendations made by this working group, with a specific emphasis on updating the categories of review and engagement with the specialized scientific and ethical oversight process.","authors":"Clark, AT., Brivanlou, A., Fu, J., Kato, K., Mathews, D., Niakan, KK., Rivron, N., Saitou, M., Surani, A., Tang, F., Rossant, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Stem Cell Reports","volume":"16","issue":"6","page":"1416-1424","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17403934","title":"Spontaneous tumor rejection by cbl-b-deficient CD8+ T cells.","abstract":"The concept of tumor surveillance implies that specific and nonspecific components of the immune system eliminate tumors in the early phase of malignancy. Understanding the biochemical mechanisms of tumor immunosurveillance is of paramount significance because it might allow one to specifically modulate spontaneous antitumor activity. We report that inactivation of the E3 ligase Casitas B cell lymphoma-b (Cbl-b) confers spontaneous in vivo rejection of tumor cells that express human papilloma virus antigens. Moreover, cbl-b(-\/-) mice develop significantly fewer ultraviolet B (UVB)-induced skin malignancies and reject UVB-induced skin tumors. CD8(+) T cells were identified as key players in the spontaneous tumor rejection response. Loss of Cbl-b not only enhances antitumor reactivity of CD8(+) T cells but also occurs in the absence of CD4(+) T cells. Mechanistically, cbl-b(-\/-) CD8(+) T cells are resistant to T regulatory cell-mediated suppression and exhibit enhanced activation and rapid tumor infiltration. Importantly, therapeutic transfer of naive cbl-b(-\/-) CD8(+) T cells is sufficient to mediate rejection of established tumors. Even up to 1 yr after the first encounter with the tumor cells, cbl-b(-\/-) mice carry an \"anticancer memory.\" These data identify Cbl-b as a key signaling molecule that controls spontaneous antitumor activity of cytotoxic T cells in different cancer models. Inhibition of Cbl-b is a novel approach to stimulate long-lasting immunity against cancer.","authors":"Loeser, S., Loser, K., Bijker, MS., Rangachari, M., van der Burg, SH., Wada, T., Beissert, S., Melief, CJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Exp Med","volume":"204","issue":"4","page":"879-91","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33242397","title":"A Human Retinal Pigment Epithelium-Based Screening Platform Reveals Inducers of Photoreceptor Outer Segments Phagocytosis.","abstract":"Phagocytosis is a key function in various cells throughout the body. A deficiency in photoreceptor outer segment (POS) phagocytosis by the retinal pigment epithelium (RPE) causes vision loss in inherited retinal diseases and possibly age-related macular degeneration. To date, there are no effective therapies available aiming at recovering the lost phagocytosis function. Here, we developed a high-throughput screening assay based on RPE derived from human embryonic stem cells (hRPE) to reveal enhancers of POS phagocytosis. One of the hits, ramoplanin (RM), reproducibly enhanced POS phagocytosis and ensheathment in hRPE, and enhanced the expression of proteins known to regulate membrane dynamics and ensheathment in other cell systems. Additionally, RM rescued POS internalization defect in Mer receptor tyrosine kinase (MERTK) mutant hRPE, derived from retinitis pigmentosa patient induced pluripotent stem cells. Our platform, including a primary phenotypic screening phagocytosis assay together with orthogonal assays, establishes a basis for RPE-based therapy discovery aiming at a broad patient spectrum.","authors":"Schreiter, S., Vafia, K., Barsacchi, R., Tsang, SH., Bickle, M., Ader, M., Karl, MO., Tanaka, EM., Almedawar, S.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Stem Cell Reports","volume":"15","issue":"6","page":"1347-1361","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32848847","title":"Membrane Physiology and Biophysics-What Remains to Be Done?","abstract":null,"authors":"Fahlke, C.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Front Physiol","volume":"11","issue":null,"page":"892","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32582699","title":"MicroRNAs: From Mechanism to Organism.","abstract":"MicroRNAs (miRNAs) are short, regulatory RNAs that act as post-transcriptional repressors of gene expression in diverse biological contexts. The emergence of small RNA-mediated gene silencing preceded the onset of multicellularity and was followed by a drastic expansion of the miRNA repertoire in conjunction with the evolution of complexity in the plant and animal kingdoms. Along this process, miRNAs became an essential feature of animal development, as no higher metazoan lineage tolerated loss of miRNAs or their associated protein machinery. In fact, ablation of the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied. In this review, we summarize recent mechanistic insight into miRNA biogenesis and function, while emphasizing features that have enabled multicellular organisms to harness the potential of this broad class of repressors. We first discuss how different mechanisms of regulation of miRNA biogenesis are used, not only to generate spatio-temporal specificity of miRNA production within an animal, but also to achieve the necessary levels and dynamics of expression. We then explore how evolution of the mechanism for small RNA-mediated repression resulted in a diversity of silencing complexes that cause different molecular effects on their targets. Multicellular organisms have taken advantage of this variability in the outcome of miRNA-mediated repression, with differential use in particular cell types or even distinct subcellular compartments. Finally, we present an overview of how the animal miRNA repertoire has evolved and diversified, emphasizing the emergence of miRNA families and the biological implications of miRNA sequence diversification. Overall, focusing on selected animal models and through the lens of evolution, we highlight canonical mechanisms in miRNA biology and their variations, providing updated insight that will ultimately help us understand the contribution of miRNAs to the development and physiology of multicellular organisms.","authors":"Dexheimer, PJ., Cochella, L.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Front Cell Dev Biol","volume":"8","issue":null,"page":"409","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32361995","title":"Genome-wide DNA methylation patterns associated with sleep and mental health in children: a population-based study.","abstract":"on Status=\"In-Process\" Owner=\"NLM\"><PMID Version=\"1\">32361995<\/PMID><DateRevised><Year>2021<\/Year><Month>03<\/Month><Day>22<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1469-7610<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>61<\/Volume><Issue>10<\/Issue><PubDate><Year>2020<\/Year><Month>10<\/Month><\/PubDate><\/JournalIssue><Title>Journal of child psychology and psychiatry, and allied disciplines<\/Title><ISOAbbreviation>J Child Psychol Psychiatry<\/ISOAbbreviation><\/Journal><ArticleTitle>Genome-wide DNA methylation patterns associated with sleep and mental health in children: a population-based study.<\/ArticleTitle><Pagination><MedlinePgn>1061-1069<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/jcpp.13252<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">DNA methylation (DNAm) has been implicated in the biology of sleep. Yet, how DNAm patterns across the genome relate to different sleep outcomes, and whether these associations overlap with mental health is currently unknown. Here, we investigated associations of DNAm with sleep and mental health in a pediatric population.","authors":"Koopman-Verhoeff, ME., Mulder, RH., Saletin, JM., Reiss, I., van der Horst, GTJ., Felix, JF., Carskadon, MA., Tiemeier, H., Cecil, CAM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Child Psychol Psychiatry","volume":"61","issue":"10","page":"1061-1069","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16424395","title":"Remodeling the regulation of iron metabolism during erythroid differentiation to ensure efficient heme biosynthesis.","abstract":"Terminal erythropoiesis is accompanied by extreme demand for iron to ensure proper hemoglobinization. Thus, erythroblasts must modify the \"standard\" post-transcriptional feedback regulation, balancing expression of ferritin (Fer; iron storage) versus transferrin receptor (TfR1; iron uptake) via specific mRNA binding of iron regulatory proteins (IRPs). Although erythroid differentiation involves high levels of incoming iron, TfR1 mRNA stability must be sustained and Fer mRNA translation must not be activated because iron storage would counteract hemoglobinization. Furthermore, translation of the erythroid-specific form of aminolevulinic acid synthase (ALAS-E) mRNA, catalyzing the first step of heme biosynthesis and regulated similarly as Fer mRNA by IRPs, must be ensured. We addressed these questions using mass cultures of primary murine erythroid progenitors from fetal liver, either undergoing sustained proliferation or highly synchronous differentiation. We indeed observed strong inhibition of Fer mRNA translation and efficient ALAS-E mRNA translation in differentiating erythroblasts. Moreover, in contrast to self-renewing cells, TfR1 stability and IRP mRNA binding were no longer modulated by iron supply. These and additional data stemming from inhibition of heme synthesis with succinylacetone or from iron overload suggest that highly efficient utilization of iron in mitochondrial heme synthesis during normal erythropoiesis alters the regulation of iron metabolism via the IRE\/IRP system.","authors":"Schranzhofer, M., Schifrer, M., Cabrera, JA., Kopp, S., Chiba, P., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Blood","volume":"107","issue":"10","page":"4159-67","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2006-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32360441","title":"Stimulated emission depletion (STED) super resolution imaging of RNA- and protein-containing domains in fixed cells.","abstract":"Super resolution microscopy has changed our capability to visualize and understand spatial arrangements of RNA- and protein-containing domains in individual cells. In a previous study, we described a novel lncRNA, Tumor-associated NBL2 transcript (TNBL), which originates from a primate specific macrosatellite repeat. We aimed to describe several aspects of TNBL lncRNA, with one focus being pinpointing its precise location in the nucleus, as well as visualizing its interactions with proteins to deduce its functionality. Using a combination of STimulated Emission Depletion (STED) super resolution microscopy, single molecule RNA (smRNA) FISH against TNBL, and immunofluorescence against SAM68 perinucleolar body, we resolved the spatial complexity of the interaction between TNBL aggregates and SAM68 bodies at the perinucleolar region. Here, we describe protocols for a step-by-step optimized smRNA FISH\/IF and STED imaging, detailing parameter settings, and three-dimensional data analysis of spatial positioning of subnuclear structures. These protocols can be employed for single-cell imaging of complex nuclear RNA-protein structures.","authors":"Dumbovi\u0107, G., Sanjuan, X., Perucho, M., Forcales, SV.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Methods","volume":"187","issue":"","page":"68-76","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16093308","title":"HOXB4 enforces equivalent fates of ES-cell-derived and adult hematopoietic cells.","abstract":"Genetic manipulation of hematopoietic stem and progenitor cells is an important tool for experimental and clinical applied hematology. However, techniques that allow for gene targeting, subsequent in vitro selection, and expansion of genetically defined clones are available only for ES cells. Such molecularly defined and, hence, \"safe\" clones would be highly desirable for somatic gene therapy. Here, we demonstrate that in vitro differentiated ES cells completely recapitulate the growth and differentiation properties of adult bone marrow cells, in vitro and in vivo, when ectopically expressing HOXB4. Myeloid development was enforced and (T) lymphoid development suppressed over a wide range of expression levels, whereas only high expression levels of the transcription factor were detrimental for erythroid development. This indicates a close association between the amounts of ectopic HOXB4 present within a progenitor cell and and the decision to self renew or differentiate. Because HOXB4 mediates similar fates of ES-derived and bone marrow hematopoietic stem cells, the primitive embryonic cells can be considered a promising alternative for investigating hematopoietic reconstitution, in vivo, based on well defined clones. Provided that HOXB4 levels are kept within a certain therapeutic window, ES cells also carry the potential of efficient and safe somatic gene therapy.","authors":"Pilat, S., Carotta, S., Schiedlmeier, B., Kamino, K., Mairhofer, A., Will, E., Modlich, U., Steinlein, P., Ostertag, W., Baum, C., Beug, H., Klump, H.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Proc Natl Acad Sci U S A","volume":"102","issue":"34","page":"12101-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32360514","title":"Silencing Sirtuin 6 induces cell cycle arrest and apoptosis in non-small cell lung cancer cell lines.","abstract":"Sirtuins (SIRT1-7), are NAD-dependent deacetylases and ADP-ribosyl transferases, plays a major part in carcinogenesis. The previous report suggests that in cancer, sirtuins gained tremendous interest and critical regulators of the unusual processes. In carcinogenesis, sirtuins possess either tumor suppressor or promoter. However, in lung cancer condition the studies of sirtuins are less studied. Hence, this designed study investigates the impact of multifaceted sirtuins in NSCLC cells. We evaluated the mRNA and protein expressions of sirtuins by RTPCR and western blot. We found SIRT6 significantly overexpressed in NCI-H520, A549, and NCI-H460 compared with the normal BEAS-2B cell line. Silencing of SIRT6 by siRNA in NSCLC cells caused activation of p53\/p21 mediated inhibition of cell proliferation leading to arrest in cell cycle and apoptosis induction. Our results implied that SIRT6 is a tumor promoter in NSCLC development, progression, and regulation. The silencing of SIRT6 to be a novel therapy for lung cancer.","authors":"Krishnamoorthy, V., Vilwanathan, R.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Genomics","volume":"112","issue":"5","page":"3703-3712","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33566224","title":"Expression profile analysis of a new testis-specifically expressed gene C17ORF64 and its association with cell apoptosis in MCF-7 cells.","abstract":"With the increasing incidence of male infertility, identification and investigation the functions of new genes related to spermatogenesis are effective avenues to elucidate the decline of testicular function. In this study, a new gene, C17ORF64 (chromosome 17 open reading frame 64), was identified from mouse testes and its potential function was studied.RT-PCR and qRT-PCR assay showed that C17ORF64 mRNA was expressed exclusively in mouse testes and up-regulated from the 3-week old to 6-month old testes during postpartum development, which is consistent with C17ORF64 protein expression profile by western blotting analysis. Immunohistochemical analysis revealed that C17ORF64 protein was mainly localized in the cytoplasm of spermatogonia and spermatocytes, which is verified by GFP- labeled C17ORF64 gene expressed in GC-1 cells. C17ORF64 overexpression not only promoted cell apoptosis in MCF-7 cells, but also significantly decreased cell viability via MTT assay. Flow cytometric assay showed that C17ORF64 overexpression could inhibit cell cycle progression by arresting G1\/S transition. Western blot and qRT-PCR analysis revealed that C17ORF64 overexpression inhibited the expression of anti-apoptotic protein bcl-2 and increased the expressions of pro-apoptotic protein caspase-3, caspase-8, caspase-9, Bax, P21 and P53. Taken together, our results confirmed C17ORF64 testis-specific expression pattern and, for the first time, demonstrated that C17ORF64 could inhibit cell viability and accelerate apoptosis in MCF-7 cells through caspase-3 regulatory pathways.","authors":"Dai, Y., Nie, J., Luo, Z., Nie, D.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Mol Biol Rep","volume":"48","issue":"2","page":"1521-1529","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1652372","title":"The role of phosphorylation and the CDC28 protein kinase in cell cycle-regulated nuclear import of the S. cerevisiae transcription factor SWI5.","abstract":"The intracellular localization of the S. cerevisiae transcription factor SWI5 is cell cycle dependent. The protein is nuclear in G1 cells but cytoplasmic in S, G2, and M phase cells. We have identified SWI5's nuclear localization signal (NLS) and show that it can confer cell cycle-dependent nuclear entry to a heterologous protein. Located within or close to the NLS are three serine residues, mutation of which results in constitutive nuclear entry. These residues are phosphorylated in a cell cycle-dependent manner in vivo, being phosphorylated when SWI5 is in the cytoplasm and dephosphorylated when it is in the nucleus. As all three serines are phosphorylated by purified CDC28-dependent H1 kinase activity in vitro, we propose a model in which the CDC28 kinase acts directly to control nuclear entry of SWI5.","authors":"Moll, T., Tebb, G., Surana, U., Robitsch, H., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Cell","volume":"66","issue":"4","page":"743-58","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1991-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1628831","title":"Signal transduction in Saccharomyces cerevisiae requires tyrosine and threonine phosphorylation of FUS3 and KSS1.","abstract":"The FUS3 and KSS1 kinases are components of the pheromone-dependent signal transduction pathway in yeast. We show that FUS3 and KSS1 become rapidly phosphorylated after pheromone treatment. Similar to mammalian MAP kinases, this modification occurs at two amino acids of FUS3, threonine-180 and tyrosine-182. A mutation introduced at either position results in complete loss of function in vivo. Amino acid substitutions that destroy catalytic activity of the kinase do not prevent phosphorylation of the mutant products, a result that excludes an autocatalytic activation pathway. The modification of FUS3 is dependent on kinases encoded by the STE11 and STE7 genes. Furthermore, a hyperactive allele of STE11 causes increased phosphorylation of FUS3 in the absence of pheromone stimulation. Thus, either STE7 or STE11 could be the kinase responsible for the phosphorylation of FUS3.","authors":"Gartner, A., Nasmyth, K., Ammerer, G.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Genes Dev","volume":"6","issue":"7","page":"1280-92","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1992-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32360068","title":"Corrigendum to \"Clinical Significance and Immunobiology of IL-21 in Autoimmunity\"[J. Autoimmun. 99C (2019) p1-14].","abstract":"","authors":"Long, D., Chen, Y., Wu, H., Zhao, M., Lu, Q.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Autoimmun","volume":"111","issue":"","page":"102455","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33319852","title":"In cis TP53 and RAD51C pathogenic variants may predispose to sebaceous gland carcinomas.","abstract":"Pathogenic variants in TP53 have been classically thought to cause Li-Fraumeni syndrome (LFS), a cancer predisposition with high risks for various childhood- and adult-onset malignancies. However, increased genetic testing has lately revealed, that pathogenic variant carriers exhibit a broader range of phenotypes and that penetrance may be dependent both on variant type and modifiers. Using next generation sequencing and short tandem repeat analysis, we identified germline pathogenic variants in TP53 and RAD51C located in cis on chromosome 17 in a 43-year-old male, who has developed a rare sebaceous gland carcinoma (SGC) but so far no tumors of the LFS spectrum. This course mirrors a Trp53-Rad51c-double-mutant cis mouse-model, which similarly develops SGC, while the characteristic Trp53-associated tumor spectrum occurs with significantly lower frequency. Therefore, we propose that co-occurent pathogenic variants in RAD51C and TP53 may predispose to SGC, reminiscent of Muir-Torre syndrome. Further, this report supports the diversity of clinical presentations associated with germline TP53 alterations, and thus, the proposed expansion of LFS to heritable TP53-related cancer syndrome.","authors":"Le Duc, D., Hentschel, J., Neuser, S., Stiller, M., Meier, C., J\u00e4ger, E., Abou Jamra, R., Platzer, K., Monecke, A., Ziemer, M., Markovic, A., Bl\u00e4ker, H., Lemke, JR.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Eur J Hum Genet","volume":"29","issue":"3","page":"489-494","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14623363","title":"N-ethyl-N-nitrosourea mouse mutants in the dissection of behavioural and psychiatric disorders.","abstract":"Twin and adoption studies have consistently implicated genetics in the aetiology of psychiatric and behavioural disorders. The identification of the genes and molecular pathways that are associated with these traits using linkage studies has been difficult because psychiatric disorders are almost always non-mendelian, heterogeneous, involve multiple genetic loci and are influenced significantly by environmental factors. Mouse models that are based on intermediate signatures of psychiatric disease and pharmacological responsiveness hold promise as a complementary approach to dissecting the molecular basis of neurobehavioural disorders. This has been made possible by the development and refinement of gene targeting technologies and the use of super-efficient chemical mutagens. N-ethyl-N-nitrosourea (ENU) mutagenesis in the mouse, when coupled to a battery of sensitive behavioural screens, is an effective way of creating and identifying novel mouse behavioural mutants. Here, the concept of screening for ENU mutants is introduced while progress with two behavioural screens, an \"anxiety\" screen and a circadian screen, are presented. It is hoped that the study of mouse mutants that have arisen from these screens will provide new insights into the genetic basis of abnormal behaviour and that they might lead to the development of novel therapeutic compounds for human psychiatric disease.","authors":"Keays, DA., Nolan, PM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Eur J Pharmacol","volume":"480","issue":"1-3","page":"205-17","pdf":null,"JrId":"3614","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12689592","title":"Kinetochore recruitment of two nucleolar proteins is required for homolog segregation in meiosis I.","abstract":"Halving of the chromosome number during meiosis I depends on the segregation of maternal and paternal centromeres. This process relies on the attachment of sister centromeres to microtubules emanating from the same spindle pole. We describe here the identification of a protein complex, Csm1\/Lrs4, that is essential for monoorientation of sister kinetochores in Saccharomyces cerevisiae. Both proteins are present in vegetative cells, where they reside in the nucleolus. Only shortly before meiosis I do they leave the nucleolus and form a \"monopolin\" complex with the meiosis-specific Mam1 protein, which binds to kinetochores. Surprisingly, Csm1's homolog in Schizosaccharomyces pombe, Pcs1, is essential for accurate chromosome segregation during mitosis and meiosis II. Csm1 and Pcs1 might clamp together microtubule binding sites on the same (Pcs1) or sister (Csm1) kinetochores.","authors":"Rabitsch, KP., Petronczki, M., Javerzat, JP., Genier, S., Chwalla, B., Schleiffer, A., Tanaka, TU., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Dev Cell","volume":"4","issue":"4","page":"535-48","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14762153","title":"Silent synapses in the immature visual cortex: layer-specific developmental regulation.","abstract":"Central glutamatergic synapses are thought to initially form as immature, so-called silent synapses showing exclusively N-methyl-d-aspartate receptor-mediated synaptic transmission. Postsynaptic insertion of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors during further development leads to a conversion into functional, mature synapses. Here, we tested the hypothesis that, according to the \"inside first-outside last\" pattern of neocortical layer formation and synaptogenesis, pyramidal cells in the superficial layers might show a higher fraction of silent synapses compared with pyramidal cells in the deep layers. We performed an electrophysiological analysis of glutamatergic synapses in acute rat visual cortex slices during postnatal development. In layer VI pyramidal neurons the incidence of silent synapses was high during the first postnatal week and strongly declined during further development. Surprisingly, in superficial cortical plate pyramidal neurons (immature layers II\/III), the fraction of silent synapses was initially very low and increased up to the second postnatal week. Thereafter, a similar decline as found in layer VI pyramidal neurons was observed. Thus the developmental regulation of silent synapses was clearly different in pyramidal neurons from different neocortical layers. The almost complete absence of silent synapses at early stages in layer II\/III pyramidal neurons indicates that an initially formed subset of synapses is constitutively functional. This might be important to enable spontaneous activity and latter activity-dependent maturation of synapses.","authors":"Rumpel, S., Kattenstroth, G., Gottmann, K.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Neurophysiol","volume":"91","issue":"2","page":"1097-101","pdf":null,"JrId":"5013","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11983169","title":"Molecular architecture of SMC proteins and the yeast cohesin complex.","abstract":"Sister chromatids are held together by the multisubunit cohesin complex, which contains two SMC (Smc1 and Smc3) and two non-SMC (Scc1 and Scc3) proteins. The crystal structure of a bacterial SMC \"hinge\" region along with EM studies and biochemical experiments on yeast Smc1 and Smc3 proteins show that SMC protamers fold up individually into rod-shaped molecules. A 45 nm long intramolecular coiled coil separates the hinge region from the ATPase-containing \"head\" domain. Smc1 and Smc3 bind to each other via heterotypic interactions between their hinges to form a V-shaped heterodimer. The two heads of the V-shaped dimer are connected by different ends of the cleavable Scc1 subunit. Cohesin therefore forms a large proteinaceous loop within which sister chromatids might be entrapped after DNA replication.","authors":"Haering, CH., L\u00f6we, J., Hochwagen, A., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Cell","volume":"9","issue":"4","page":"773-88","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2002-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22174126","title":"Fitness trade-offs and environmentally induced mutation buffering in isogenic C. elegans.","abstract":"Mutations often have consequences that vary across individuals. Here, we show that the stimulation of a stress response can reduce mutation penetrance in Caenorhabditis elegans. Moreover, this induced mutation buffering varies across isogenic individuals because of interindividual differences in stress signaling. This variation has important consequences in wild-type animals, producing some individuals with higher stress resistance but lower reproductive fitness and other individuals with lower stress resistance and higher reproductive fitness. This may be beneficial in an unpredictable environment, acting as a \"bet-hedging\" strategy to diversify risk. These results illustrate how transient environmental stimuli can induce protection against mutations, how environmental responses can underlie variable mutation buffering, and how a fitness trade-off may make variation in stress signaling advantageous.","authors":"Casanueva, MO., Burga, A., Lehner, B.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Science","volume":"335","issue":"6064","page":"82-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12376594","title":"Projection of an immunological self shadow within the thymus by the aire protein.","abstract":"Humans expressing a defective form of the transcription factor AIRE (autoimmune regulator) develop multiorgan autoimmune disease. We used aire- deficient mice to test the hypothesis that this transcription factor regulates autoimmunity by promoting the ectopic expression of peripheral tissue- restricted antigens in medullary epithelial cells of the thymus. This hypothesis proved correct. The mutant animals exhibited a defined profile of autoimmune diseases that depended on the absence of aire in stromal cells of the thymus. Aire-deficient thymic medullary epithelial cells showed a specific reduction in ectopic transcription of genes encoding peripheral antigens. These findings highlight the importance of thymically imposed \"central\" tolerance in controlling autoimmunity.","authors":"Anderson, MS., Venanzi, ES., Klein, L., Chen, Z., Berzins, SP., Turley, SJ., von Boehmer, H., Bronson, R., Dierich, A., Benoist, C., Mathis, D.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Science","volume":"298","issue":"5597","page":"1395-401","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33309518","title":"Phosphatase magnesium-dependent 1 \u03b4 (PPM1D), serine\/threonine protein phosphatase and novel pharmacological target in cancer.","abstract":"Aberrations in DNA damage response genes are recognized mediators of tumorigenesis and resistance to chemo- and radiotherapy. While protein phosphatase magnesium-dependent 1 \u03b4 (PPM1D), located on the long arm of chromosome 17 at 17q22-23, is a key regulator of cellular responses to DNA damage, amplification, overexpression, or mutation of this gene is important in a wide range of pathologic processes. In this review, we describe the physiologic function of PPM1D, as well as its role in diverse processes, including fertility, development, stemness, immunity, tumorigenesis, and treatment responsiveness. We highlight both the advances and limitations of current approaches to targeting malignant processes mediated by pathogenic alterations in PPM1D with the goal of providing rationale for continued research and development of clinically viable treatment approaches for PPM1D-associated diseases.","authors":"Nahta, R., Castellino, RC.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Biochem Pharmacol","volume":"184","issue":"","page":"114362","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11340163","title":"A conserved cyclin-binding domain determines functional interplay between anaphase-promoting complex-Cdh1 and cyclin A-Cdk2 during cell cycle progression.","abstract":"Periodic activity of the anaphase-promoting complex (APC) ubiquitin ligase determines progression through multiple cell cycle transitions by targeting cell cycle regulators for destruction. At the G(1)\/S transition, phosphorylation-dependent dissociation of the Cdh1-activating subunit inhibits the APC, allowing stabilization of proteins required for subsequent cell cycle progression. Cyclin-dependent kinases (CDKs) that initiate and maintain Cdh1 phosphorylation have been identified. However, the issue of which cyclin-CDK complexes are involved has been a matter of debate, and the mechanism of how cyclin-CDKs interact with APC subunits remains unresolved. Here we substantiate the evidence that mammalian cyclin A-Cdk2 prevents unscheduled APC reactivation during S phase by demonstrating its periodic interaction with Cdh1 at the level of endogenous proteins. Moreover, we identified a conserved cyclin-binding motif within the Cdh1 WD-40 domain and show that its disruption abolished the Cdh1-cyclin A-Cdk2 interaction, eliminated Cdh1-associated histone H1 kinase activity, and impaired Cdh1 phosphorylation by cyclin A-Cdk2 in vitro and in vivo. Overexpression of cyclin binding-deficient Cdh1 stabilized the APC-Cdh1 interaction and induced prolonged cell cycle arrest at the G(1)\/S transition. Conversely, cyclin binding-deficient Cdh1 lost its capability to support APC-dependent proteolysis of cyclin A but not that of other APC substrates such as cyclin B and securin Pds1. Collectively, these data provide a mechanistic explanation for the mutual functional interplay between cyclin A-Cdk2 and APC-Cdh1 and the first evidence that Cdh1 may activate the APC by binding specific substrates.","authors":"S\u00f8rensen, CS., Lukas, C., Kramer, ER., Peters, JM., Bartek, J., Lukas, J.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Mol Cell Biol","volume":"21","issue":"11","page":"3692-703","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2001-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11701123","title":"Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability.","abstract":"Histone H3 lysine 9 methylation has been proposed to provide a major \"switch\" for the functional organization of chromosomal subdomains. Here, we show that the murine Suv39h histone methyltransferases (HMTases) govern H3-K9 methylation at pericentric heterochromatin and induce a specialized histone methylation pattern that differs from the broad H3-K9 methylation present at other chromosomal regions. Suv39h-deficient mice display severely impaired viability and chromosomal instabilities that are associated with an increased tumor risk and perturbed chromosome interactions during male meiosis. These in vivo data assign a crucial role for pericentric H3-K9 methylation in protecting genome stability, and define the Suv39h HMTases as important epigenetic regulators for mammalian development.","authors":"Peters, AH., O'Carroll, D., Scherthan, H., Mechtler, K., Sauer, S., Sch\u00f6fer, C., Weipoltshammer, K., Pagani, M., Lachner, M., Kohlmaier, A., Opravil, S., Doyle, M., Sibilia, M., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell","volume":"107","issue":"3","page":"323-37","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32010267","title":"Abnormal expression of miR-135b-5p in bone tissue of patients with osteoporosis and its role and mechanism in osteoporosis progression.","abstract":"Osteoporosis (OP) is an age-related bone disease occurring worldwide. Osteoporotic fracture is one of the leading causes of disability and death in elderly patients. MicroRNAs (miRNAs\/miRs) are key molecular regulatory factors in bone remodeling processes. The present study investigated the expression and mechanism of miR-135b-5p in patients with osteoporosis. The present results suggested that miR-135b-5p was upregulated in bone tissue fragments of patients with osteoporosis compared with the control patients. MC3T3-E1 cells were used to perform osteogenic differentiation induction. Reverse transcription-quantitative PCR and western blot assay were used to detect the mRNA and protein expression levels of the osteogenic markers osteocalcin (OC), Osterix and alkaline phosphatase (ALP). A specific kit was used for detecting ALP activity. The present results indicated that the mRNA expression levels of OC, Osterix and ALP significantly increased on the 7 and 14th day after osteogenic differentiation induction compared with the control group. Protein expression levels of OC, Osterix and ALP also increased on the 7 and 14th day after induction. ALP assay showed that ALP activity was significantly increased on the 7 and 14th day after induction. In addition, the present study found that miR-135b-5p was downregulated in MC3T3-E1 cells 7 and 14 days after osteogenic differentiation induction. The results of TargetScan analysis and dual luciferase reporter gene assay indicated that runt-related transcription factor 2 (RUNX2) was a direct target gene of miR-135b-5p. RUNX2 was upregulated in MC3T3-E1 cells on the 7 and 14th day after induction. Moreover, the present study found that compared with the osteogenic differentiation induction group, miR-135b-5p mimic significantly decreased OC, Osterix and ALP expression, and reduced ALP activity in MC3T3-E1 cells. However, these reductions were reversed following overexpression of RUNX2. The present results showed that miR-135b-5p mimic significantly reduced cell viability in MC3T3-E1 cells and induced cell apoptosis, and these effects were significantly reversed following RUNX2 overexpression. In summary, the present results suggested that miR-135-5p participated in the occurrence and development of osteoporosis via inhibition of osteogenic differentiation and osteoblast growth by targeting RUNX2. The present study suggested a novel potential target that may faciliate the treatment of osteoporosis, and further study is required to examine this possibility.","authors":"Chen, B., Yang, W., Zhao, H., Liu, K., Deng, A., Zhang, G., Pan, K.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Exp Ther Med","volume":"19","issue":"2","page":"1042-1050","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32992138","title":"The p53-inducible CLDN7 regulates colorectal tumorigenesis and has prognostic significance.","abstract":"Most colorectal cancer (CRC) are characterized by allele loss of the genes located on the short arm of chromosome 17 (17p13.1), including the tumor suppressor p53 gene. Although important, p53 is not the only driver of chromosome 17p loss. In this study, we explored the biological and prognostic significance of genes around p53 on 17p13.1 in CRC. The Cancer Genome Atlas (TCGA) were used to identify differentially expressed genes located between 1000\u202fkb upstream and downstream of p53 gene. The function of CLDN7 was evaluated by both in vitro and in vivo experiments. Quantitative real-time PCR, western blot, and promoter luciferase activity, immunohistochemistry were used to explore the molecular drivers responsible for the development and progression of CRC. The results showed that CLDN7, located between 1000\u202fkb upstream and downstream of p53 gene, were remarkably differentially expressed in tumor and normal tissues. CLDN7 expression also positively associated with p53 level in different stages of the adenoma-carcinoma sequence. Both in vitro and in vivo assays showed that CLDN7 inhibited cell proliferation in p53 wild type CRC cells, but had no effects on p53 mutant CRC cells. Mechanistically, p53 could bind to CLDN7 promoter region and regulate its expression. Clinically, high CLDN7 expression was negatively correlated with tumor size, invasion depth, lymphatic metastasis and AJCC III\/IV stage, but was positively associated with favorable prognosis of CRC patients. Collectively, our work uncovers the tumor suppressive function for CLDN7 in a p53-dependent manner, which may mediate colorectal tumorigenesis induced by p53 deletion or mutation.","authors":"Hou, Y., Hou, L., Liang, Y., Zhang, Q., Hong, X., Wang, Y., Huang, X., Zhong, T., Pang, W., Xu, C., Zhu, L., Li, L., Fang, J., Meng, X.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Neoplasia","volume":"22","issue":"11","page":"590-603","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32908304","title":"TRIM37 controls cancer-specific vulnerability to PLK4 inhibition.","abstract":"Centrosomes catalyse the formation of microtubules needed to assemble the mitotic spindle apparatus<sup>1<\/sup>. Centrosomes themselves duplicate once per cell cycle, in a process that is controlled by the serine\/threonine protein kinase PLK4 (refs. <sup>2,3<\/sup>). When PLK4 is chemically inhibited, cell division proceeds without centrosome duplication, generating centrosome-less cells that exhibit delayed, acentrosomal spindle assembly<sup>4<\/sup>. Whether PLK4 inhibitors can be leveraged as a treatment for cancer is not yet clear. Here we show that acentrosomal spindle assembly following PLK4 inhibition depends on levels of the centrosomal ubiquitin ligase TRIM37. Low TRIM37 levels accelerate acentrosomal spindle assembly and improve proliferation following PLK4 inhibition, whereas high TRIM37 levels inhibit acentrosomal spindle assembly, leading to mitotic failure and cessation of proliferation. The Chr17q region containing the TRIM37 gene is frequently amplified in neuroblastoma and in breast cancer<sup>5-8<\/sup>, rendering these cancer types highly sensitive to PLK4 inhibition. We find that inactivating TRIM37 improves acentrosomal mitosis because TRIM37 prevents PLK4 from self-assembling into centrosome-independent condensates that serve as ectopic microtubule-organizing centres. By contrast, elevated TRIM37 expression inhibits acentrosomal spindle assembly through a distinct mechanism that involves degradation of the centrosomal component CEP192. Thus, TRIM37 is an essential determinant of mitotic vulnerability to PLK4 inhibition. Linkage of TRIM37 to prevalent cancer-associated genomic changes-including 17q gain in neuroblastoma and 17q23 amplification in breast cancer-may offer an opportunity to use PLK4 inhibition to trigger selective mitotic failure and provide new avenues to treatments for these cancers.","authors":"Meitinger, F., Ohta, M., Lee, KY., Watanabe, S., Davis, RL., Anzola, JV., Kabeche, R., Jenkins, DA., Shiau, AK., Desai, A., Oegema, K.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nature","volume":"585","issue":"7825","page":"440-446","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9618759","title":"Loss- and gain-of-function mutations reveal an important role of BSAP (Pax-5) at the start and end of B cell differentiation.","abstract":"Pax-5 codes for the transcription factor BSAP which is expressed throughout B cell development except in terminally differentiated plasma cells. Gene targeting experiments in the mouse revealed a differential dependency of fetal and adult B-lymphopoiesis on this transcription factor. BSAP is required for B-lineage commitment in the fetal liver and for progression beyond an early pro-B cell stage in adult bone marrow. The characterization of Pax-5-deficient pro-B cells demonstrated an important role of BSAP in the regulation of the CD19, mb-1 (Ig alpha) and N-myc genes as well as in the developmental pathway controlling VH-to-DHJH recombination at the immunoglobulin heavy-chain (IgH) locus. The human PAX-5 gene was recently shown to participate together with the IgH locus in the chromosomal translocation t(9;14)(p13;q32). This translocation is characteristic of a small subset of non-Hodgkin lymphomas exhibiting plasmacytoid differentiation. The translocated PAX-5 gene is deregulated by the insertion of IgH regulatory elements into its 5' region, which may contribute to tumorigenesis by interfering with the shut-down of PAX-5 transcription and thus with the completion of plasma cell differentiation.","authors":"Morrison, AM., Nutt, SL., Th\u00e9venin, C., Rolink, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Semin Immunol","volume":"10","issue":"2","page":"133-42","pdf":null,"JrId":"1183","fulltextlink":null,"preprintlink":null,"articledate":"1998-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9308963","title":"PARP is important for genomic stability but dispensable in apoptosis.","abstract":"Mice lacking the gene encoding poly(ADP-ribosyl) transferase (PARP or ADPRT) display no phenotypic abnormalities, although aged mice are susceptible to epidermal hyperplasia and obesity in a mixed genetic background. Whereas embryonic fibroblasts lacking PARP exhibit normal DNA excision repair, they grow more slowly in vitro. Here we investigated the putative roles of PARP in cell proliferation, cell death, radiosensitivity, and DNA recombination, as well as chromosomal stability. We show that the proliferation deficiency in vitro and in vivo is most likely caused by a hypersensitive response to environmental stress. Although PARP is specifically cleaved during apoptosis, cells lacking this molecule apoptosed normally in response to treatment with anti-Fas, tumor neurosis factor alpha, gamma-irradiation, and dexamethasone, indicating that PARP is dispensable in apoptosis and that PARP-\/- thymocytes are not hypersensitive to ionizing radiation. Furthermore, the capacity of mutant cells to carry out immunoglobulin class switching and V(D)J recombination is normal. Finally, primary PARP mutant fibroblasts and splenocytes exhibited an elevated frequency of spontaneous sister chromatid exchanges and elevated micronuclei formation after treatment with genotoxic agents, establishing an important role for PARP in the maintenance of genomic integrity.","authors":"Wang, ZQ., Stingl, L., Morrison, C., Jantsch, M., Los, M., Schulze-Osthoff, K., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Genes Dev","volume":"11","issue":"18","page":"2347-58","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26791720","title":"Metastatic colonization by circulating tumour cells.","abstract":"Metastasis is the main cause of death in people with cancer. To colonize distant organs, circulating tumour cells must overcome many obstacles through mechanisms that we are only now starting to understand. These include infiltrating distant tissue, evading immune defences, adapting to supportive niches, surviving as latent tumour-initiating seeds and eventually breaking out to replace the host tissue. They make metastasis a highly inefficient process. However, once metastases have been established, current treatments frequently fail to provide durable responses. An improved understanding of the mechanistic determinants of such colonization is needed to better prevent and treat metastatic cancer.","authors":"Massagu\u00e9, J., Obenauf, AC.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nature","volume":"529","issue":"7586","page":"298-306","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32796024","title":"Diversity Outbred Mice Reveal the Quantitative Trait Locus and Regulatory Cells of HER2 Immunity.","abstract":"The genetic basis and mechanisms of disparate antitumor immune response was investigated in Diversity Outbred (DO) F1 mice that express human HER2. DO mouse stock samples nearly the entire genetic repertoire of the species. We crossed DO mice with syngeneic HER2 transgenic mice to study the genetics of an anti-self HER2 response in a healthy outbred population. Anti-HER2 IgG was induced by Ad\/E2TM or naked pE2TM, both encoding HER2 extracellular and transmembrane domains. The response of DO F1 HER2 transgenic mice was remarkably variable. Still, immune sera inhibited HER2+ SKBR3 cell survival in a dose-dependent fashion. Using DO quantitative trait locus (QTL) analysis, we mapped the QTL that influences both total IgG and IgG2(a\/b\/c) Ab response to either Ad\/E2TM or pE2TM. QTL from these four datasets identified a region in chromosome 17 that was responsible for regulating the response. A\/J and NOD segments of genes in this region drove elevated HER2 Ig levels. This region is rich in MHC-IB genes, several of which interact with inhibitory receptors of NK cells. (B6xA\/J)F1 and (B6xNOD)F1 HER2 transgenic mice received Ad\/E2TM after NK cell depletion, and they produced less HER2 IgG, demonstrating positive regulatory function of NK cells. Depletion of regulatory T cells enhanced response. Using DO QTL analysis, we show that MHC-IB reactive NK cells exert positive influence on the immunity, countering negative regulation by regulatory T cells. This new, to our knowledge, DO F1 platform is a powerful tool for revealing novel immune regulatory mechanisms and for testing new interventional strategies.","authors":"Wei, WZ., Gibson, HM., Jacob, JB., Frelinger, JA., Berzofsky, JA., Maeng, H., Dyson, G., Reyes, JD., Pilon-Thomas, S., Ratner, S., Wei, KC.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Immunol","volume":"205","issue":"6","page":"1554-1563","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30462292","title":"Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor.","abstract":"Non-templated 3'-uridylation of RNAs has emerged as an important mechanism for regulating the processing, stability and biological function of eukaryotic transcripts. In Drosophila, oligouridine tailing by the terminal uridylyl transferase (TUTase) Tailor of numerous RNAs induces their degradation by the exonuclease Dis3L2, which serves functional roles in RNA surveillance and mirtron RNA biogenesis. Tailor preferentially uridylates RNAs terminating in guanosine or uridine nucleotides but the structural basis underpinning its RNA substrate selectivity is unknown. Here, we report crystal structures of Tailor bound to a donor substrate analog or mono- and oligouridylated RNA products. These structures reveal specific amino acid residues involved in donor and acceptor substrate recognition, and complementary biochemical assays confirm the critical role of an active site arginine in conferring selectivity toward\u00a03'-guanosine terminated RNAs. Notably, conservation of these active site features suggests that other eukaryotic TUTases, including mammalian TUT4 and TUT7, might exhibit similar, hitherto unknown, substrate selectivity. Together, these studies provide critical insights into the specificity of 3'-uridylation in eukaryotic post-transcriptional gene regulation.","authors":"Kroupova, A., Ivascu, A., Reim\u00e3o-Pinto, MM., Ameres, SL., Jinek, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nucleic Acids Res","volume":"47","issue":"2","page":"1030-1042","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29625069","title":"Coordinated Control of mRNA and rRNA Processing Controls Embryonic Stem Cell Pluripotency and Differentiation.","abstract":"Stem cell-specific transcriptional networks are well known to control pluripotency, but constitutive cellular processes such as mRNA splicing and protein synthesis can add complex layers of regulation with poorly understood effects on cell-fate decisions. Here, we show that the RNA binding protein HTATSF1 controls embryonic stem cell differentiation by regulating multiple aspects of RNA processing during ribosome biogenesis. HTATSF1, in a complex with splicing factor SF3B1, controls intron removal from ribosomal protein transcripts and regulates ribosomal RNA transcription and processing, thereby controlling 60S ribosomal abundance and protein synthesis. HTATSF1-dependent protein synthesis is essential for naive pre-implantation epiblast to transition into post-implantation epiblast, a stage with transiently low protein synthesis, and further differentiation toward neuroectoderm. Together, these results identify coordinated regulation of ribosomal RNA and protein synthesis by HTATSF1 and show that this essential mechanism controls protein synthesis during early mammalian embryogenesis.","authors":"Corsini, NS., Peer, AM., Moeseneder, P., Roiuk, M., Burkard, TR., Theussl, HC., Moll, I., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell Stem Cell","volume":"22","issue":"4","page":"543-558.e12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11311167","title":"Non-imprinted Igf2r expression decreases growth and rescues the Tme mutation in mice.","abstract":"In the mouse the insulin-like growth factor receptor type 2 gene (Igf2r) is imprinted and maternally expressed. Igf2r encodes a trans-membrane receptor that transports mannose-6-phosphate tagged proteins and insulin-like growth factor 2 to lysosomes. During development the receptor reduces the amount of insulin-like growth factors and thereby decreases embryonic growth. The dosage of the gene is tightly regulated by genomic imprinting, leaving only the maternal copy of the gene active. Although the function of Igf2r in development is well established, the function of imprinting the gene remains elusive. Gene targeting experiments in mouse have demonstrated that the majority of genes are not sensitive to gene dosage, and mice heterozygous for mutations generally lack phenotypic alterations. To investigate whether reduction of Igf2r gene dosage by genomic imprinting has functional consequences for development we generated a non-imprinted allele (R2Delta). We restored biallelic expression to Igf2r by deleting a critical element for repression of the paternal allele (region 2) in mouse embryonic stem cells. Maternal inheritance of the R2Delta allele has no phenotype; however, paternal inheritance results in biallelic expression of Igf2r, which causes a 20% reduction in weight late in embryonic development that persists into adulthood. Paternal inheritance of the R2Delta allele rescues the lethality of a maternally inherited Igf2r null allele and a maternally inherited Tme (T-associated maternal effect) mutation. These data show that the biological function of imprinting Igf2r is to increase birth weight and they also establish Igf2r as the Tme gene.","authors":"Wutz, A., Theussl, HC., Dausman, J., Jaenisch, R., Barlow, DP., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Development","volume":"128","issue":"10","page":"1881-7","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2001-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26395140","title":"Modeling mouse and human development using organoid cultures.","abstract":"In vitro three-dimensional (3D) cultures are emerging as novel systems with which to study tissue development, organogenesis and stem cell behavior ex vivo. When grown in a 3D environment, embryonic stem cells (ESCs) self-organize into organoids and acquire the right tissue patterning to develop into several endoderm- and ectoderm-derived tissues, mimicking their in vivo counterparts. Tissue-resident adult stem cells (AdSCs) also form organoids when grown in 3D and can be propagated in vitro for long periods of time. In this Review, we discuss recent advances in the generation of pluripotent stem cell- and AdSC-derived organoids, highlighting their potential for enhancing our understanding of human development. We will also explore how this new culture system allows disease modeling and gene repair for a personalized regenerative medicine approach.","authors":"Huch, M., Koo, BK.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Development","volume":"142","issue":"18","page":"3113-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32705597","title":"Recent Advances in the Critical Role of the Sterol Efflux Transporters ABCG5\/G8 in Health and Disease.","abstract":"Cardiovascular disease is characterized by lipid accumulation, inflammatory response, cell death, and fibrosis in the arterial wall and is the leading cause of morbidity and mortality worldwide. Cholesterol gallstone disease is caused by complex genetic and environmental factors and is one of the most prevalent and costly digestive diseases in the USA and Europe. Although sitosterolemia is a rare inherited lipid storage disease, its genetic studies led to identification of the sterol efflux transporters ABCG5\/G8 that are located on chromosome 2p21 in humans and chromosome 17 in mice. Human and animal studies have clearly demonstrated that ABCG5\/G8 play a critical role in regulating hepatic secretion and intestinal absorption of cholesterol and plant sterols. Sitosterolemia is caused by a mutation in either the ABCG5 or the ABCG8 gene alone, but not in both simultaneously. Polymorphisms in the ABCG5\/G8 genes are associated with abnormal plasma cholesterol metabolism and may play a key role in the genetic determination of plasma cholesterol concentrations. Moreover, ABCG5\/G8 is a new gallstone gene, LITH9. Gallstone-associated variants in ABCG5\/G8 are involved in the pathogenesis of cholesterol gallstones in European, Asian, and South American populations. In this chapter, we summarize the latest advances in the critical role of the sterol efflux transporters ABCG5\/G8 in regulating hepatic secretion of biliary cholesterol, intestinal absorption of cholesterol and plant sterols, the classical reverse cholesterol transport, and the newly established transintestinal cholesterol excretion, as well as in the pathogenesis and pathophysiology of ABCG5\/G8-related metabolic diseases such as sitosterolemia, cardiovascular disease, and cholesterol gallstone disease.","authors":"Wang, HH., Liu, M., Portincasa, P., Wang, DQ.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Adv Exp Med Biol","volume":"1276","issue":"","page":"105-136","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11297511","title":"Ephrin-B3 is the midline barrier that prevents corticospinal tract axons from recrossing, allowing for unilateral motor control.","abstract":"Growing axons follow highly stereotypical pathways, guided by a variety of attractive and repulsive cues, before establishing specific connections with distant targets. A particularly well-known example that illustrates the complexity of axonal migration pathways involves the axonal projections of motor neurons located in the motor cortex. These projections take a complex route during which they first cross the midline, then form the corticospinal tract, and ultimately connect with motor neurons in the contralateral side of the spinal cord. These obligatory contralateral connections account for why one side of the brain controls movement on the opposing side of the body. The netrins and slits provide well-known midline signals that regulate axonal crossings at the midline. Herein we report that a member of the ephrin family, ephrin-B3, also plays a key role at the midline to regulate axonal crossing. In particular, we show that ephrin-B3 acts as the midline barrier that prevents corticospinal tract projections from recrossing when they enter the spinal gray matter. We report that in ephrin-B3(-\/-) mice, corticospinal tract projections freely recross in the spinal gray matter, such that the motor cortex on one side of the brain now provides bilateral input to the spinal cord. This neuroanatomical abnormality in ephrin-B3(-\/-) mice correlates with loss of unilateral motor control, yielding mice that simultaneously move their right and left limbs and thus have a peculiar hopping gait quite unlike the alternate step gait displayed by normal mice. The corticospinal and walking defects in ephrin-B3(-\/-) mice resemble those recently reported for mice lacking the EphA4 receptor, which binds ephrin-B3 as well as other ephrins, suggesting that the binding of EphA4-bearing axonal processes to ephrin-B3 at the midline provides the repulsive signal that prevents corticospinal tract projections from recrossing the midline in the developing spinal cord.","authors":"Kullander, K., Croll, SD., Zimmer, M., Pan, L., McClain, J., Hughes, V., Zabski, S., DeChiara, TM., Klein, R., Yancopoulos, GD., Gale, NW.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Genes Dev","volume":"15","issue":"7","page":"877-88","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33303613","title":"Protein condensates as aging Maxwell fluids.","abstract":"Protein condensates are complex fluids that can change their material properties with time. However, an appropriate rheological description of these fluids remains missing. We characterize the time-dependent material properties of in vitro protein condensates using laser tweezer-based active and microbead-based passive rheology. For different proteins, the condensates behave at all ages as viscoelastic Maxwell fluids. Their viscosity strongly increases with age while their elastic modulus varies weakly. No significant differences in structure were seen by electron microscopy at early and late ages. We conclude that protein condensates can be soft glassy materials that we call Maxwell glasses with age-dependent material properties. We discuss possible advantages of glassy behavior for modulation of cellular biochemistry.","authors":"Jawerth, L., Fischer-Friedrich, E., Saha, S., Wang, J., Franzmann, T., Zhang, X., Sachweh, J., Ruer, M., Ijavi, M., Saha, S., Mahamid, J., Hyman, AA., J\u00fclicher, F.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Science","volume":"370","issue":"6522","page":"1317-1323","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23774255","title":"Hyperexcitability and epileptic seizures in a model of frontotemporal dementia.","abstract":"Epileptic seizures are more common in patients with Alzheimer disease than in the general elderly population. Abnormal forms of hyperphosphorylated tau accumulate in Alzheimer disease and other tauopathies. Aggregates of tau are also found in patients with epilepsy and in experimental models of epilepsy. We report here the analysis of epileptic activity and neuropathological correlates of a transgenic line over-expressing human mutant tau, a model of frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17). The FTDP-17 model displays spontaneous epileptic activity and seizures with spike-wave complexes in the EEG, and a higher sensitivity to the GABAA receptor antagonist pentylenetetrazol (PTZ) when compared to age-matched controls, showing a notably increased seizure length and a shorter latency to develop severe seizures. FTDP-17 human tau mutants also display lower convulsive thresholds and higher lethality after PTZ injections. Astrocytosis and activated microglia are prominent in the hippocampus and other brain regions of young FTDP-17 mice where the human mutant tau transgene is expressed, before the appearance of hyperphosphorylated tau aggregates in these structures. FTDP-17 human mutant tau over-expression produces epilepsy and increased GABAA receptor-mediated hyperexcitability in the absence of A\u03b2 pathology. Although aggregates of hyperphosphorylated tau have been observed in patients with epilepsy and in different chemically and electrically generated models of epilepsy, the FTDP-17 tau mutant analyzed here is the first model of genetically modified tau that presents with epilepsy. This model may represent a valuable tool to assay novel treatments in order to reduce tau pathology, a potential factor which may be involved in the development of epileptic seizures in dementia and other neurodegenerative diseases.","authors":"Garc\u00eda-Cabrero, AM., Guerrero-L\u00f3pez, R., Gir\u00e1ldez, BG., Llorens-Mart\u00edn, M., Avila, J., Serratosa, JM., S\u00e1nchez, MP.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Neurobiol Dis","volume":"58","issue":"","page":"200-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33177297","title":"Diverse ubiquitin codes in the regulation of inflammatory signaling.","abstract":"Ubiquitin is a small protein used for posttranslational modification and it regulates every aspect of biological functions. Through a three-step cascade of enzymatic action, ubiquitin is conjugated to a substrate. Because ubiquitin itself can be post-translationally modified, this small protein generates various ubiquitin codes and triggers differing regulation of biological functions. For example, ubiquitin itself can be ubiquitinated, phosphorylated, acetylated, or SUMOylated. Via the type three secretion system, some bacterial effectors also modify the ubiquitin system in host cells. This review describes the general concept of the ubiquitin system as well as the fundamental functions of ubiquitin in the regulation of cellular responses during inflammation and bacterial infection.","authors":"Ikeda, F.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Proc Jpn Acad Ser B Phys Biol Sci","volume":"96","issue":"9","page":"431-439","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26406365","title":"Coordinating the human looks.","abstract":"Prescott et\u00a0al. take a step forward in studying primate morphological evolution by a cellular anthropology approach. Through epigenomic profiling of in-vitro-derived cells, the authors identify and characterize candidate cis-regulatory elements underlying divergence in facial morphology between human and chimp, shedding new light on what makes us (look) human.","authors":"Haberle, V., Stark, A.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell","volume":"163","issue":"1","page":"24-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3025611","title":"Characterization of two nonallelic pairs of late histone H2A and H2B genes of the sea urchin: differential regulation in the embryo and tissue-specific expression in the adult.","abstract":"Two nonallelic pairs of late H2A and H2B genes of the sea urchin Psammechinus miliaris were isolated on two different cosmid clones. The genes of cosmid PmL1 are separated by 11 kilobases of DNA and code for the late H2A-2 and H2B-2 variants. The genes of clone PmL2 are divergently transcribed with 1,060 base pairs of intergenic spacer DNA and code for novel variants of the H2A-2 and H2B-2 type. A comparison of the promoter sequences revealed little homology upstream of the TATA box with the exception of a 24-base-pair-long conserved sequence which is present at the same position in both late H2B promoters and part of which is identical with the \"H2B-specific\" 5' element. The mRNAs of the H2A and H2B genes of cosmid PmL1 reach their maximal levels early in the mesenchyme blastula embryo, whereas the transcripts of both genes of clone PmL2 accumulate maximally only later in the pluteus larva. In the adult sea urchin all four mRNAs are present in the tube foot but not in the intestine and lantern muscle. This pattern of differential expression in the embryo and tissue-specific expression in the adult suggests cell lineage-specific regulation of the late H2A-2 and H2B-2 genes. Another class of late histone genes represented by the H2A-3 and H2B-1 genes was shown to be expressed in all three adult tissues tested, whereas transcripts of the late H2A-1 genes could not be detected, suggesting that these genes are active exclusively during sea urchin development.","authors":"Kemler, I., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Mol Cell Biol","volume":"6","issue":"11","page":"3746-54","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1987-02-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3226163","title":"Approach to define \"normal aging\" in man. Immune function, serum lipids, lipoproteins and neopterin levels.","abstract":"In 53 healthy women with mean age 25.1 years (age range 21-34 years) and in 51 healthy women with mean age 82.1 years (age range 75-91 years), a panel of immunological and biochemical tests was performed. These tests, comprising lymphocyte mitogen responsiveness, phenotyping of lymphocytes, uptake of low density lipoprotein by T cells, serum levels of neopterin, lipids and lipoproteins, as well as routine blood chemistry, were investigated for a possible effect of age and of the classification according to the SENIEUR Protocol of admission criteria by the European Economic Community's Concerted Action Program on Aging (EURAGE). A highly significant effect of age on serum levels of neopterin, lipids and lipoproteins was found. No clear effects, however, of SENIEUR status on these variables was detected. As expected, age had a significant impact on mitogen responsiveness of T cells. Proportional numbers of helper\/inducer and cytotoxic\/suppressor T cells (as well as antigen density on these cells) were not influenced by age. SENIEUR classification did not affect these immunologic variables. Thus, most of the tested variables that are not included in the SENIEUR admission criteria appear to present information not yet covered by the SENIEUR variables. Various ways for a possible revision or extension of the SENIEUR Protocol are discussed.","authors":"Reibnegger, G., Huber, LA., J\u00fcrgens, G., Sch\u00f6nitzer, D., Werner, ER., Wachter, H., Wick, G., Traill, KN.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Mech Ageing Dev","volume":"46","issue":"1-3","page":"67-82","pdf":null,"JrId":"5571","fulltextlink":null,"preprintlink":null,"articledate":"1989-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7040433","title":"Changes in the expression of membrane antigens during the differentiation of chicken erythroblasts.","abstract":"Chicken erythroblasts can be transformed by the avian retrovirus, avian erythroblastosis virus (AEV). Earlier studies have shown that the mechanism of transformation appears to involve a \"block\" in differentiation, in that when erythroblasts are transformed by a temperature-sensitive mutant of ts34 AEV and incubated at the nonpermissive temperature, the cells start to differentiate and produce hemoglobin. We have decided to use this system to isolate pure populations of chicken erythroblasts and raise monoclonal antibodies against their cell surface proteins. Three monoclonal antibodies were isolated and tested for their ability to bind to various hematopoietic cell types; two were shown to be erythroid-specific, whereas the other antibody bound to proliferating cells but not to erythrocytes or granulocytes. Of the erythroid-specific antibodies, one precipitated a 94,000 molecular weight protein, whereas the other precipitated a 11,000 molecular weight protein that was tentatively identified as hemoglobin. The use of this system and approach to identify and evaluate changes that occur during the differentiation is discussed.","authors":"Hayman, MJ., Beug, H., Savin, KW.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"J Cell Biochem","volume":"18","issue":"3","page":"351-62","pdf":null,"JrId":"4590","fulltextlink":null,"preprintlink":null,"articledate":"1982-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"4522296","title":"Quantitation of membrane sites in aggregating Dictyostelium cells by use of tritiated univalent antibody.","abstract":"Cell-to-cell adhesion during aggregation of Dictyostelium discoideum cells is completely blocked by univalent antibody (Fab) directed against two classes of target sites: surface structures characteristic for aggregation-competent cells (\"contact sites A\") and others present also on growth-phase cells (\"contact sites B\"). 3 x 10(5) Fab molecules bound per cell are sufficient to block contact sites A completely, although the Fab fragments cover not more than 2% of the total cell surface. Up to 8-fold this value can be bound per cell when Fab fragments of another specificity are used, without affecting activity of contact sites A. Blockage of cell-to-cell adhesion therefore depends on the binding of Fab fragments to specific target sites, rather than on the total number of Fab molecules bound per cell. This conclusion is also valid for cell adhesion attributed to contact sites B. Contact sites therefore represent a special class of cell-surface sites which, in cell homogenates as well as in vivo, can be traced by Fab, and which are not identical with the bulk of cell-surface antigens present on aggregating cells.","authors":"Beug, H., Katz, FE., Stein, A., Gerisch, G.","publication_status":"ppublish","journalpubyear":"1973","journaltitle":"Proc Natl Acad Sci U S A","volume":"70","issue":"11","page":"3150-4","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1974-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2809175","title":"Use of a FACS III for fluorescence depolarization with DPH.","abstract":"We have previously demonstrated age-related differences in human lymphocyte membrane fluidity, by use of steady-state polarization measurements on bulk cell suspensions with the fluorescence probe DPH. However, for exact analysis of the possible functional importance of these changes, single-cell measurements were deemed of interest. We have now used an analog division device to measure fluorescence depolarization \"p\" of DPH in real time with a FACS III flow cytometer. The measurements are reliable, as we have been able to confirm the differences in DPH \"p\" between monocytes and lymphocytes previously shown in bulk suspension and to demonstrate the expected differences in fluidity of lipid-modulated cells. We also found significant differences in DPH \"p\" between lymphocytes of young and elderly blood donors. Lymphocyte subsets did not differ in polarization values but did differ in fluorescence intensity with Th less than Ts less than B = NK cells.","authors":"B\u00f6ck, G., Huber, LA., Wick, G., Traill, KN.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"J Histochem Cytochem","volume":"37","issue":"11","page":"1653-8","pdf":null,"JrId":"4803","fulltextlink":null,"preprintlink":null,"articledate":"1989-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26229113","title":"BIOSAFETY. Safeguarding gene drive experiments in the laboratory.","abstract":"","authors":"Akbari, OS., Bellen, HJ., Bier, E., Bullock, SL., Burt, A., Church, GM., Cook, KR., Duchek, P., Edwards, OR., Esvelt, KM., Gantz, VM., Golic, KG., Gratz, SJ., Harrison, MM., Hayes, KR., James, AA., Kaufman, TC., Knoblich, J., Malik, HS., Matthews, KA., O'Connor-Giles, KM., Parks, AL., Perrimon, N., Port, F., Russell, S., Ueda, R., Wildonger, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Science","volume":"349","issue":"6251","page":"927-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10","title":"Digitoxin metabolism by rat liver microsomes.","abstract":"","authors":"Schmoldt, A., Benthe, HF., Haberland, G.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"17","page":"1639-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27411773","title":"The Effect of Patient-centered CPR Education for Family Caregivers of Patients with Cardiovascular Diseases.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">27411773<\/PMID><DateCompleted><Year>2017<\/Year><Month>04<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">2093-758X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>46<\/Volume><Issue>3<\/Issue><PubDate><Year>2016<\/Year><Month>Jun<\/Month><\/PubDate><\/JournalIssue><Title>Journal of Korean Academy of Nursing<\/Title><ISOAbbreviation>J Korean Acad Nurs<\/ISOAbbreviation><\/Journal><ArticleTitle>The Effect of Patient-centered CPR Education for Family Caregivers of Patients with Cardiovascular Diseases.<\/ArticleTitle><Pagination><MedlinePgn>463-74<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.4040\/jkan.2016.46.3.463<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE\" NlmCategory=\"OBJECTIVE\">For cardiovascular patients, family caregivers play a vital role in daily nursing and cardiac emergencies. This study aimed to evaluate the effect of patient-centered CPR education (PCE) for family caregivers of patients with cardiovascular diseases.","authors":"Kim, HS., Kim, HJ., Suh, EE.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Korean Acad Nurs","volume":"46","issue":"3","page":"463-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27315477","title":"The Molecular and Cellular Choreography of Appendage Regeneration.","abstract":"Recent advances in limb regeneration are revealing the molecular events that integrate growth control, cell fate programming, and positional information to yield the exquisite replacement of the amputated limb. Parallel progress in several invertebrate and vertebrate models has provided a broader context for understanding the mechanisms and the evolution of regeneration. Together, these discoveries provide a foundation for describing the principles underlying regeneration of complex, multi-tissue structures. As such these findings should provide a wealth of ideas for engineers seeking to reconstitute regeneration from constituent parts or to elicit full regeneration from partial regeneration events.","authors":"Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"165","issue":"7","page":"1598-1608","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2492453","title":"The leucine repeat motif in Fos protein mediates complex formation with Jun\/AP-1 and is required for transformation.","abstract":"Cellular and viral Fos proteins form a tight complex with other nuclear proteins, including the transcription factor and proto-oncogene AP-1\/Jun. We have mapped the c-Jun binding site in Fos to a region containing regularly spaced leucine residues recently suggested to interdigitate with a similar structure in Jun. Substitution of single or multiple leucine residues or the alteration of leucine phasing by insertion of additional amino acids reduces or abolishes the binding to Jun, while the substitution of other amino acids has no noticeable effect. These results strongly suggest that the formation of a \"leucine zipper\" mediates the interaction between Fos and Jun. We also show that the differential binding of the various Fos mutants correlates with their potential to trans-activate AP-1-dependent transcription and to induce morphological transformation.","authors":"Schuermann, M., Neuberg, M., Hunter, JB., Jenuwein, T., Ryseck, RP., Bravo, R., M\u00fcller, R.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Cell","volume":"56","issue":"3","page":"507-16","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1989-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20","title":"Aggregation of blood platelets by adrenaline and its uptake.","abstract":"","authors":"Barthel, W., Markwardt, F.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"20","page":"1903-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3","title":"Metal substitutions incarbonic anhydrase: a halide ion probe study.","abstract":"","authors":"Smith, RJ., Bryant, RG.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Biophys Res Commun","volume":"66","issue":"4","page":"1281-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32838419","title":"Insoluble Tau From Human FTDP-17 Cases Exhibit Unique Transmission Properties In Vivo.","abstract":"One hallmark of neurodegenerative diseases is the intracellular accumulation of hyperphosphorylated tau protein, a neuronal microtubule-associated protein, into structures known as neurofibrillary tangles. Tauopathies are heterogeneous neurodegenerative diseases caused by the misfolding of the tau protein. It has been previously shown that the tau protein can spread from cell to cell in a prion-like manner. Tauopathies can be sporadic or familial, with the identification of pathogenic mutations in the microtubule-associated protein tau gene on chromosome 17 in the familial cases. Different frontotemporal dementia with parkinsonism-17 (FTDP-17) cases are associated with varying clinical presentations and types of neuropathology. We previously demonstrated that insoluble tau extracted from sporadic tauopathy human brains contain distinct tau strains, which underlie the heterogeneity of these diseases. Furthermore, these tau strains seeded tau aggregates that resemble human tau neuropathology in nontransgenic and 6hTau mice in vivo. Here, we show insoluble tau from human brains of FTDP-17 cases transmit different patterns of neuronal and glial tau pathology in vivo, similar to the sporadic tauopathies. This suggests that each of these tau mutations has unique properties that underlie the heterogeneity of FTDP-17 cases.","authors":"Weitzman, SA., Narasimhan, S., He, Z., Changolkar, L., McBride, JD., Zhang, B., Schellenberg, GD., Trojanowski, JQ., Lee, VMY.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Neuropathol Exp Neurol","volume":"79","issue":"9","page":"941-949","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1531366","title":"Ubiquitous soluble Mg(2+)-ATPase complex. A structural study.","abstract":"We have performed a detailed structural analysis of the soluble Mg(2+)-ATPase complex purified from Xenopus laevis ovary, which is an abundant and ubiquitous homo-oligomeric protein complex located in the nucleus and in the cytoplasm, belonging to a novel multigene-family of putative Mg(2+)-ATPases. Enzyme activity staining after non-denaturing polyacrylamide gel electrophoresis revealed that Mg(2+)-ATPase activity of the native protein is dependent on oligomerization and could not be detected in dissociated subunits. For the native protein a sedimentation coefficient of 15.3 S and a corresponding relative molecular mass of 612,000 was determined by analytical ultracentrifugation and a relative molecular mass of 590,000 was estimated from scanning transmission electron microscopy, supporting our previous conclusion that the oligomer comprises six 97,000 Mr subunits. Conventional electron microscopy of negatively stained specimens revealed the Mg(2+)-ATPase complex to be a hexagonal molecule in its favoured \"end-on\" projection and a double-banded molecule in its \"side-on\" projection (approx. 12 nm diameter; approx. 9 nm height). In addition, dimerized complexes could be observed in negatively stained specimens, yielding pronounced hexameric images and four-banded images in their end-on and side-on orientations, respectively (approx. 12 nm diameter; approx. 18.5 nm height). Two-dimensional (2D = mono-molecular) crystals have been produced from the dimerized complexes by the negative staining carbon film technique. Hexagonal crystals with a p6 plane group symmetry were obtained from molecules in their end-on orientation and longitudinal arrays with a p2 symmetry from complexes in their side-on orientation. A low-resolution molecular model of the native protein, derived from averages of these two 2D crystals, is presented. From our results we propose oligomerization as an inherent structural principle of organization for this whole newly defined Mg(2+)-ATPase multigene-family, that includes such seemingly diverse functionally defined proteins as mammalian and yeast \"vesicle fusion\" and \"peroxisome assembly\" proteins and the product of the yeast cell cycle gene CDC48.","authors":"Peters, JM., Harris, JR., Lustig, A., M\u00fcller, S., Engel, A., Volker, S., Franke, WW.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"J Mol Biol","volume":"223","issue":"2","page":"557-71","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1992-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19","title":"Antidepressant drugs affect dopamine uptake.","abstract":"","authors":"Halaris, AE., Belendiuk, KT., Freedman, DX.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"20","page":"1896-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17","title":"Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central catecholaminergic neurons of the rat.","abstract":"","authors":"Renaud, B., Buda, M., Lewis, BD., Pujol, JF.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"18","page":"1739-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2","title":"Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution.","abstract":"","authors":"Bose, KS., Sarma, RH.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Biophys Res Commun","volume":"66","issue":"4","page":"1173-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16","title":"Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines.","abstract":"","authors":"Turner, AJ., Hick, PE.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"18","page":"1731-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32496553","title":"A universal method for the rapid isolation of all known classes of functional silencing small RNAs.","abstract":"Diverse classes of silencing small (s)RNAs operate via ARGONAUTE-family proteins within RNA-induced-silencing-complexes (RISCs). Here, we have streamlined various embodiments of a Q-sepharose-based RISC-purification method that relies on conserved biochemical properties of all ARGONAUTEs. We show, in multiple benchmarking assays, that the resulting 15-min benchtop extraction procedure allows simultaneous purification of all known classes of RISC-associated sRNAs without prior knowledge of the samples-intrinsic ARGONAUTE repertoires. Optimized under a user-friendly format, the method - coined 'TraPR' for Trans-kingdom, rapid, affordable Purification of RISCs - operates irrespectively of the organism, tissue, cell type or bio-fluid of interest, and scales to minute amounts of input material. The method is highly suited for direct profiling of silencing sRNAs, with TraPR-generated sequencing libraries outperforming those obtained via gold-standard procedures that require immunoprecipitations and\/or lengthy polyacrylamide gel-selection. TraPR considerably improves the quality and consistency of silencing sRNA sample preparation including from notoriously difficult-to-handle tissues\/bio-fluids such as starchy storage roots or mammalian plasma, and regardless of RNA contaminants or RNA degradation status of samples.","authors":"Grentzinger, T., Oberlin, S., Schott, G., Handler, D., Svozil, J., Barragan-Borrero, V., Humbert, A., Duharcourt, S., Brennecke, J., Voinnet, O.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nucleic Acids Res","volume":"48","issue":"14","page":"e79","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33","title":"Effect of human erythrocyte stromata on complement activation.","abstract":"Stroma from either normal or PNH-like red cells is capable of inhibiting, to some extent, lysis in the sucrose test and enhancing lysis in the acidified-serum test. The same opposing effects are displayed by the exclusion peaks from Sephadex G-200 obtained from each stroma preparation, suggesting that the same factor could be responsible for both activities. Stromata and peaks also induce lysis of PNH-like cells in unacidified serum, indicating activation of complement through the alternate pathway. This is confirmed by immunoelectrophoretic observation. When serum previously activated through the alternate pathway is used in the sucrose test the amount of lysis is markedly reduced. This would indicate that the classical pathway activation can be controlled by the alternate pathway. The possible clinical significance of these factors in determining the haemolytic crisis in PNH patients is discussed.","authors":"Corrocher, R., Tedesco, F., Rabusin, P., De Sandre, G.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Haematol","volume":"29","issue":"2","page":"235-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31","title":"Lysosomal hydrolases of the epidermis. 2. Ester hydrolases.","abstract":"Five distinct ester hydrolases (EC 3-1) have been characterized in guinea-pig epidermis. These are carboxylic esterase, acid phosphatase, pyrophosphatase, and arylsulphatase A and B. Their properties are consistent with those of lysosomal enzymes.","authors":"Mier, PD., van den Hurk, JJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Dermatol","volume":"93","issue":"4","page":"391-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30","title":"Lysosomal hydrolases of the epidermis. I. Glycosidases.","abstract":"Seven distinct glycosidases (EC 3.2) have been characterized in guinea-pig epidermis. Their properties indicate them to be of lysosomal origin. The 'profile' of the epidermal glycosidases is significantly different from that reported for whole skin, the activities of beta-galactosidase and beta-acetylglucosaminidase being very high and those of the remaining enzymes relatively low in epidermis.","authors":"Mier, PD., van den Hurk, JJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Dermatol","volume":"93","issue":"1","page":"1-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32","title":"A serum haemagglutinating property dependent upon polycarboxyl groups.","abstract":"A serum agglutinin reactive with red cells in the presence of polycarboxyl groups is reported. It is likely that this represents an additional example of the type of agglutinin previously described as agglutinating red cells in the absence of ionized calcium. Experimental evidence is presented indicating that it is free polycarboxyl groups that potentiate agglutination and that any metal ion, such as calcium, capable of chelating with these groups will prove to be inhibitory.","authors":"Beck, ML., Freihaut, B., Henry, R., Pierce, S., Bayer, WL.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Haematol","volume":"29","issue":"1","page":"149-56","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"44","title":"The origin of the alkaline inactivation of pepsinogen.","abstract":"Above pH 8.5, pepsinogen is converted into a form which cannot be activated to pepsin on exposure to low pH. Intermediate exposure to neutral pH, however, returns the protein to a form which can be activated. Evidence is presented for a reversible, small conformational change in the molecule, distinct from the unfolding of the protein. At the same time, the molecule is converted to a form of limited solubility, which is precipitated at low pH, where activation is normally seen. The results are interpreted in terms of the peculiar structure of the pepsinogen molecule. Titration of the basic NH2-terminal region produced an open form, which can return to the native form at neutral pH, but which is maintained at low pH by neutralization of carboxylate groups in the pepsin portion.","authors":"McPhie, P.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"24","page":"5253-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33007233","title":"Introductions to the Community: Early-Career Researchers in the Time of COVID-19.","abstract":"COVID-19 has unfortunately halted lab work, conferences, and in-person networking, which is especially detrimental to researchers just starting their labs. Through social media and our reviewer networks, we met some early-career stem cell investigators impacted by the closures. Here, they introduce themselves and their research to our readers.","authors":"Tchieu, J., Urb\u00e1n, N., Soragni, A., Kawaguchi, K., Blanchard, JW., Li, L.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Stem Cell","volume":"27","issue":"4","page":"508-510","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32363966","title":"Long-term treatment effect of a modified jailed-balloon technique for de Winter syndrome: a case report.","abstract":"Timely recognition of the characteristic electrocardiographic pattern of de Winter syndrome is important for providing immediate reperfusion therapy for acute anterior myocardial infarction. In this case, an electrocardiogram showed 1- to 3-mm upsloping ST-segment depression at the J point in leads V1 to V6, with loss of R wave progression in leads V1 to V4. Urgent angiography showed occlusion of the proximal left anterior descending coronary artery and 70% stenosis in the ostial first diagonal branch (Medina type 1.1.1.). For this bifurcation lesion, we successfully performed a modified jailed-balloon technique to protect the side branch during percutaneous coronary intervention stenting. Thereafter, thrombolysis in myocardial infarction 3 flow was restored in both branches. This modified jailed-balloon technique is safe and effective in stent placement for de Winter syndrome without any loss of side branches.","authors":"Du, JB., Wang, JJ., Li, WY., Huo, XY., Li, YN., Chen, ST., Cong, HL., Wu, SY., Wei, YL.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Int Med Res","volume":"48","issue":"5","page":"300060520905488","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32359152","title":"Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum.","abstract":"Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.","authors":"Fern\u00e1ndez, R., Marcet-Houben, M., Legeai, F., Richard, G., Robin, S., Wucher, V., Pegueroles, C., Gabald\u00f3n, T., Tagu, D.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Mol Biol Evol","volume":"37","issue":"9","page":"2601-2615","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32344427","title":"CDK6 is an essential direct target of NUP98 fusion proteins in acute myeloid leukemia.","abstract":"Fusion proteins involving Nucleoporin 98 (NUP98) are recurrently found in acute myeloid leukemia (AML) and are associated with poor prognosis. Lack of mechanistic insight into NUP98-fusion-dependent oncogenic transformation has so far precluded the development of rational targeted therapies. We reasoned that different NUP98-fusion proteins deregulate a common set of transcriptional targets that might be exploitable for therapy. To decipher transcriptional programs controlled by diverse NUP98-fusion proteins, we developed mouse models for regulatable expression of NUP98\/NSD1, NUP98\/JARID1A, and NUP98\/DDX10. By integrating chromatin occupancy profiles of NUP98-fusion proteins with transcriptome profiling upon acute fusion protein inactivation in vivo, we defined the core set of direct transcriptional targets of NUP98-fusion proteins. Among those, CDK6 was highly expressed in murine and human AML samples. Loss of CDK6 severely attenuated NUP98-fusion-driven leukemogenesis, and NUP98-fusion AML was sensitive to pharmacologic CDK6 inhibition in vitro and in vivo. These findings identify CDK6 as a conserved, critical direct target of NUP98-fusion proteins, proposing CDK4\/CDK6 inhibitors as a new rational treatment option for AML patients with NUP98-fusions.","authors":"Schmoellerl, J., Barbosa, IAM., Eder, T., Brandstoetter, T., Schmidt, L., Maurer, B., Troester, S., Pham, HTT., Sagarajit, M., Ebner, J., Manhart, G., Aslan, E., Terlecki-Zaniewicz, S., Van der Veen, C., Hoermann, G., Duployez, N., Petit, A., Lapillonne, H., Puissant, A., Itzykson, R., Moriggl, R., Heuser, M., Meisel, R., Valent, P., Sexl, V., Zuber, J., Grebien, F.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Blood","volume":"136","issue":"4","page":"387-400","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"60","title":"The reaction between the superoxide anion radical and cytochrome c.","abstract":"1. The superoxide anion radical (O2-) reacts with ferricytochrome c to form ferrocytochrome c. No intermediate complexes are observable. No reaction could be detected between O2- and ferrocytochrome c. 2. At 20 degrees C the rate constant for the reaction at pH 4.7 to 6.7 is 1.4-10(6) M-1. S -1 and as the pH increases above 6.7 the rate constant steadily decreases. The dependence on pH is the same for tuna heart and horse heart cytochrome c. No reaction could be demonstrated between O2- and the form of cytochrome c which exists above pH approximately 9.2. The dependence of the rate constant on pH can be explained if cytochrome c has pKs of 7.45 and 9.2, and O2- reacts with the form present below pH 7.45 with k = 1.4-10(6) M-1 - S-1, the form above pH 7.45 with k = 3.0- 10(5) M-1 - S-1, and the form present above pH 9.2 with k = 0. 3. The reaction has an activation energy of 20 kJ mol-1 and an enthalpy of activation at 25 degrees C of 18 kJ mol-1 both above and below pH 7.45. It is suggested that O2- may reduce cytochrome c through a track composed of aromatic amino acids, and that little protein rearrangement is required for the formation of the activated complex. 4. No reduction of ferricytochrome c by HO2 radicals could be demonstrated at pH 1.2-6.2 but at pH 5.3, HO2 radicals oxidize ferrocytochrome c with a rate constant of about 5-10(5)-5-10(6) M-1 - S-1.","authors":"Butler, J., Jayson, GG., Swallow, AJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"408","issue":"3","page":"215-22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22017987","title":"Mouse inscuteable induces apical-basal spindle orientation to facilitate intermediate progenitor generation in the developing neocortex.","abstract":"Neurons in the mammalian neocortex arise from asymmetric divisions of progenitors residing in the ventricular zone. While in most progenitor divisions, the mitotic spindle is parallel to the ventricular surface, some progenitors reorient the spindle and divide in oblique orientations. Here, we use conditional deletion and overexpression of mouse Inscuteable (mInsc) to analyze the relevance of spindle reorientation in cortical progenitors. Mutating mInsc almost abolishes oblique and vertical mitotic spindles, while mInsc overexpression has the opposite effect. Our data suggest that oblique divisions are essential for generating the correct numbers of neurons in all cortical layers. Using clonal analysis, we demonstrate that spindle orientation affects the rate of indirect neurogenesis, a process where progenitors give rise to basal progenitors, which in turn divide symmetrically into two differentiating neurons. Our results indicate that the orientation of progenitor cell divisions is important for correct lineage specification in the developing mammalian brain.","authors":"Postiglione, MP., J\u00fcschke, C., Xie, Y., Haas, GA., Charalambous, C., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Neuron","volume":"72","issue":"2","page":"269-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"70","title":"Specificity studies on alpha-mannosidases using oligosaccharides from mannosidosis urine as substrates.","abstract":"Oligosaccharides containing terminal non-reducing alpha(1 leads to 2)-, alpha(1 leads to 3)-, and alpha(1 leads to 6)-linked mannose residues, isolated from human and bovine mannosidosis urines were used as substrates to test the specificities of acidic alpha-mannosidases isolated from human and bovine liver. The enzymes released all the alpha-linked mannose residues from each oligosaccharide and were most effective on the smallest substrate. Enzyme A in each case was less active on the oligosaccharides than alpha-mannosidase B2, even though the apparent Km value for the substrates was the same with each enzyme. The human acidic alpha-mannosidases were also found to be more active on substrates isolated from human rather than bovine mannosidosis urine. Human alpha-mannosidase C, which has a neutral pH optimum when assayed with a synthetic substrate, did not hydrolyse any of the oligosaccharides at neutral pH, but was found to be active at an acidic pH.","authors":"Hultberg, B., Lundblad, A., Masson, PK., Ockerman, PA.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"156-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21315261","title":"Neuronal control of Drosophila courtship song.","abstract":"The courtship song of the Drosophila male serves as a genetically tractable model for the investigation of the neural mechanisms of decision-making, action selection, and motor pattern generation. Singing has been causally linked to the activity of the set of neurons that express the sex-specific fru transcripts, but the specific neurons involved have not been identified. Here we identify five distinct classes of fru neuron that trigger or compose the song. Our data suggest that P1 and pIP10 neurons in the brain mediate the decision to sing, and to act upon this decision, while the thoracic neurons dPR1, vPR6, and vMS11 are components of a central pattern generator that times and shapes the song's pulses. These neurons are potentially connected in a functional circuit, with the descending pIP10 neuron linking the brain and thoracic song centers. Sexual dimorphisms in each of these neurons may explain why only males sing.","authors":"von Philipsborn, AC., Liu, T., Yu, JY., Masser, C., Bidaye, SS., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Neuron","volume":"69","issue":"3","page":"509-22","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2011-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21068836","title":"Genetic dissection of an amygdala microcircuit that gates conditioned fear.","abstract":"The role of different amygdala nuclei (neuroanatomical subdivisions) in processing Pavlovian conditioned fear has been studied extensively, but the function of the heterogeneous neuronal subtypes within these nuclei remains poorly understood. Here we use molecular genetic approaches to map the functional connectivity of a subpopulation of GABA-containing neurons, located in the lateral subdivision of the central amygdala (CEl), which express protein kinase C-\u03b4 (PKC-\u03b4). Channelrhodopsin-2-assisted circuit mapping in amygdala slices and cell-specific viral tracing indicate that PKC-\u03b4(+) neurons inhibit output neurons in the medial central amygdala (CEm), and also make reciprocal inhibitory synapses with PKC-\u03b4(-) neurons in CEl. Electrical silencing of PKC-\u03b4(+) neurons in vivo suggests that they correspond to physiologically identified units that are inhibited by the conditioned stimulus, called CEl(off) units. This correspondence, together with behavioural data, defines an inhibitory microcircuit in CEl that gates CEm output to control the level of conditioned freezing.","authors":"Haubensak, W., Kunwar, PS., Cai, H., Ciocchi, S., Wall, NR., Ponnusamy, R., Biag, J., Dong, HW., Deisseroth, K., Callaway, EM., Fanselow, MS., L\u00fcthi, A., Anderson, DJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nature","volume":"468","issue":"7321","page":"270-6","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"67","title":"Cholinesterases from plant tissues. VI. Preliminary characterization of enzymes from Solanum melongena L. and Zea mays L.","abstract":"Enzymes capable of hydrolyzing esters of thiocholine have been assayed in extracts of Solanum melongena L. (eggplant) and Zea Mays L. (corn). The enzymes from both species are inhibited by the anti-cholinesterases neostigmine, physostigmine, and 284c51 and by AMO-1618, a plant growth retardant and they both have pH optima near pH 8.0. The enzyme from eggplant is maximally active at a substrate concentration of 0.15 mM acetylthiocholine and is inhibited at higher substrate concentrations. On the basis of this last property, the magnitude of inhibition by the various inhibitors, and the substrate specificity, we conclude that the enzyme from eggplant, but not that from corn, is a cholinesterase.","authors":"Fluck, RA., Jaffe, MJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"130-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18606643","title":"Cell type-specific regulation of ITAM-mediated NF-kappaB activation by the adaptors, CARMA1 and CARD9.","abstract":"Activating NK cell receptors transduce signals through ITAM-containing adaptors, including FcRgamma and DAP12. Although the caspase recruitment domain (CARD)9-Bcl10 complex is essential for FcRgamma\/DAP12-mediated NF-kappaB activation in myeloid cells, its involvement in NK cell receptor signaling is unknown. Herein we show that the deficiency of CARMA1 or Bcl10, but not CARD9, resulted in severe impairment of cytokine\/chemokine production mediated by activating NK cell receptors due to a selective defect in NF-kappaB activation, whereas cytotoxicity mediated by the same receptors did not require CARMA1-Bcl10-mediated signaling. IkappaB kinase (IKK) activation by direct protein kinase C (PKC) stimulation with PMA plus ionomycin (P\/I) was abrogated in CARMA1-deficient NK cells, similar to T and B lymphocytes, whereas CARD9-deficient dendritic cells (DCs) exhibited normal P\/I-induced IKK activation. Surprisingly, CARMA1 deficiency also abrogated P\/I-induced IKK activation in DCs, indicating that CARMA1 is essential for PKC-mediated NF-kappaB activation in all cell types, although the PKC-CARMA1 axis is not used downstream of myeloid ITAM receptors. Consistently, PKC inhibition abrogated ITAM receptor-mediated activation only in NK cells but not in DCs, suggesting PKC-CARMA1-independent, CARD9-dependent ITAM receptor signaling in myeloid cells. Conversely, the overexpression of CARD9 in CARMA1-deficient cells failed to restore the PKC-mediated NF-kappaB activation. Thus, NF-kappaB activation signaling through ITAM receptors is regulated by a cell type-specific mechanism depending on the usage of adaptors CARMA1 and CARD9, which determines the PKC dependence of the signaling.","authors":"Hara, H., Ishihara, C., Takeuchi, A., Xue, L., Morris, SW., Penninger, JM., Yoshida, H., Saito, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Immunol","volume":"181","issue":"2","page":"918-30","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32145015","title":"A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals.","abstract":"In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.","authors":"Popitsch, N., Huber, CD., Buchumenski, I., Eisenberg, E., Jantsch, M., von Haeseler, A., Gallach, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Genome Biol Evol","volume":"12","issue":"4","page":"345-357","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"88","title":"The oxygen affinity of haemoglobin Tak, a variant with an elongated beta chain.","abstract":"The oxygen affinity was investigated of purified Hb Tak, a human haemoglobin variant with elongated beta-chains. A very low P50 value was found which was not influenced by the addition of 2,3 diphosphoglycerate. The n value was 1, indicating non-cooperativity. The oxygen equilibrium curve of the whole blood haemolysate containing Hbs A and Tak was close to that of Hb A at the top of the curve, while the bottom of the curve greatly deviated from the latter, indicative of small if any interaction between Hb A and Tak during oxygenation.","authors":"Imai, K., Lehmann, H.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"2","page":"288-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31863584","title":"CHC22 clathrin mediates traffic from early secretory compartments for human GLUT4 pathway biogenesis.","abstract":"Glucose transporter 4 (GLUT4) is sequestered inside muscle and fat and then released by vesicle traffic to the cell surface in response to postprandial insulin for blood glucose clearance. Here, we map the biogenesis of this GLUT4 traffic pathway in humans, which involves clathrin isoform CHC22. We observe that GLUT4 transits through the early secretory pathway more slowly than the constitutively secreted GLUT1 transporter and localize CHC22 to the ER-to-Golgi intermediate compartment (ERGIC). CHC22 functions in transport from the ERGIC, as demonstrated by an essential role in forming the replication vacuole of Legionella pneumophila bacteria, which requires ERGIC-derived membrane. CHC22 complexes with ERGIC tether p115, GLUT4, and sortilin, and downregulation of either p115 or CHC22, but not GM130 or sortilin, abrogates insulin-responsive GLUT4 release. This indicates that CHC22 traffic initiates human GLUT4 sequestration from the ERGIC and defines a role for CHC22 in addition to retrograde sorting of GLUT4 after endocytic recapture, enhancing pathways for GLUT4 sequestration in humans relative to mice, which lack CHC22.","authors":"Camus, SM., Camus, MD., Figueras-Novoa, C., Boncompain, G., Sadacca, LA., Esk, C., Bigot, A., Gould, GW., Kioumourtzoglou, D., Perez, F., Bryant, NJ., Mukherjee, S., Brodsky, FM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Cell Biol","volume":"219","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26489412","title":"[The epigenome. Target for innovative therapies in head and neck  carcinoma].","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">26489412<\/PMID><DateCompleted><Year>2016<\/Year><Month>08<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1433-0458<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>63<\/Volume><Issue>11<\/Issue><PubDate><Year>2015<\/Year><Month>Nov<\/Month><\/PubDate><\/JournalIssue><Title>HNO<\/Title><ISOAbbreviation>HNO<\/ISOAbbreviation><\/Journal><ArticleTitle>[The epigenome. Target for innovative therapies in head and neck  carcinoma].<\/ArticleTitle><Pagination><MedlinePgn>786-91<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s00106-015-0075-9<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The pathogenesis of head and neck squamous carcinoma (HNSCC) is a complex and multistage process, which is characterized by the accumulation of genetic and epigenetic aberrations. Most of our knowledge concerning the regulation of gene expression by the epigenome is based on changes in DNA methylation and post-translational histone modifications that affect the phenotypic plasticity of cells under physiological and pathological conditions.","authors":"Leipold, A., Hess, J., Zaoui, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"HNO","volume":"63","issue":"11","page":"786-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"127","title":"Editorial: Childhood poisoning: prevention and first-aid management.","abstract":"","authors":"","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br Med J","volume":"4","issue":"5995","page":"483-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"122","title":"Meso-appendicular testis.","abstract":"","authors":"Zelikovski, A., Abu-Dalu, J., Urca, I.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Urol","volume":"47","issue":"5","page":"579","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31768977","title":"Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion.","abstract":"The varying rates at which mRNAs decay are tightly coordinated with transcriptional changes to shape gene expression during development and disease. But currently available RNA sequencing approaches lack the temporal information to determine the relative contribution of RNA biogenesis, processing and turnover to the establishment of steady-state gene expression profiles.Here, we describe a protocol that combines metabolic RNA labeling with chemical nucleoside conversion by thiol-linked alkylation of 4-thiouridine to determine RNA stability in cultured cells (SLAMseq). When coupled to cost-effective mRNA 3' end sequencing approaches, SLAMseq determines the half-life of polyadenylated transcripts in a global and transcript-specific manner using untargeted or targeted cDNA library preparation protocols.We provide a step-by-step instruction for time-resolved mRNA 3' end sequencing, which augments traditional RNA-seq approaches to acquire the temporal resolution necessary to study the molecular principles that control gene expression.","authors":"Herzog, VA., Fasching, N., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Methods Mol Biol","volume":"2062","issue":null,"page":"169-189","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"118","title":"Proceedings: Comparison of the effects of selective alpha and beta-receptor agonists on intracellular cyclic AMP levels and glycogen phosphorylase activity in guinea-pig liver.","abstract":"","authors":"Osborn, D., Jenkinson, DH.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br J Pharmacol","volume":"55","issue":"2","page":"286P-287P","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"109","title":"6th International Symposium on Maritime Medicine 1974.","abstract":"","authors":"Kersten, E.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Bull Inst Marit Trop Med Gdynia","volume":"26","issue":"2","page":"131-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"108","title":"Symposium on malaria research.","abstract":"","authors":"Lachmajer, J.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Bull Inst Marit Trop Med Gdynia","volume":"26","issue":"1","page":"53-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"100","title":"Bovine mannosidosis--a model lysosomal storage disease.","abstract":"","authors":"Jolly, RD., Thompson, KG., Winchester, BG.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Birth Defects Orig Artic Ser","volume":"11","issue":"6","page":"273-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"99","title":"Mannosidosis: clinical and biochemical findings.","abstract":"","authors":"Gehler, J., Cantz, M., O'Brien, JF., Tolksdorf, M., Spranger, J.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Birth Defects Orig Artic Ser","volume":"11","issue":"6","page":"269-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"98","title":"Microbial sources of cellulase.","abstract":"","authors":"Mandels, M.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biotechnol Bioeng Symp","volume":"","issue":"5","page":"81-105","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"97","title":"Hydrogen peroxide and iron: a microbial cellulolytic system?","abstract":"","authors":"Koenigs, JW.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biotechnol Bioeng Symp","volume":"","issue":"5","page":"151-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26087165","title":"Reduction of Neuropathic and Inflammatory Pain through Inhibition of the Tetrahydrobiopterin Pathway.","abstract":"Human genetic studies have revealed an association between GTP cyclohydrolase 1 polymorphisms, which decrease tetrahydrobiopterin (BH4) levels, and reduced pain in patients. We now show that excessive BH4 is produced in mice by both axotomized sensory neurons and macrophages infiltrating damaged nerves and inflamed tissue. Constitutive BH4 overproduction in sensory neurons increases pain sensitivity, whereas blocking BH4 production only in these cells reduces nerve injury-induced hypersensitivity without affecting nociceptive pain. To minimize risk of side effects, we targeted sepiapterin reductase (SPR), whose blockade allows minimal BH4 production through the BH4 salvage pathways. Using a structure-based design, we developed a potent SPR inhibitor and show that it reduces pain hypersensitivity effectively with a concomitant decrease in BH4 levels in target tissues, acting both on sensory neurons and macrophages, with no development of tolerance or adverse effects. Finally, we demonstrate that sepiapterin accumulation is a sensitive biomarker for SPR inhibition in vivo.","authors":"Latremoliere, A., Latini, A., Andrews, N., Cronin, SJ., Fujita, M., Gorska, K., Hovius, R., Romero, C., Chuaiphichai, S., Painter, M., Miracca, G., Babaniyi, O., Remor, AP., Duong, K., Riva, P., Barrett, LB., Ferreir\u00f3s, N., Naylor, A., Penninger, JM., Tegeder, I., Zhong, J., Blagg, J., Channon, KM., Johnsson, K., Costigan, M., Woolf, CJ.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Neuron","volume":"86","issue":"6","page":"1393-406","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-09-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"134","title":"Respiratory effects of H+ and dinitrophenol injections into the brain stem subarachnoid space of fetal lambs.","abstract":"Mock cerebrospinal fluid (pH 5.37-8.38) or 2,4-dinitrophenol (DNP) (0.15-1.5 mg) was injected into the subarachnoid space of the ventral brain stem of exteriorized fetal sheep. Changes in pH on the ventral surface of the medulla did not stimulate respiratory efforts or induce significant cardiovascular changes. The respiratory response to DNP injections ranged from no response to prolonged rhythmic ventilation that was independent of the peripheral chemoreceptors or the control arterial pH and blood gas tensions. This inconsistency suggests an effector site somewhat removed from the immediate surface of the medulla. The heart rate and blood pressure were not affected. It is concluded that increased H+ concentration in the extracellular fluid of the fetal ventral medulla does not initiate respiration, and any respiratory response to metabolic inhibitors applied to this area therefore is not attributable to a secondary change in surface pH.","authors":"Jansen, AH., Russell, BJ., Chernick, V.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Physiol Pharmacol","volume":"53","issue":"5","page":"726-33","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"131","title":"Processing of tRNA precursors in higher organisms.","abstract":"","authors":"Burdon, RH.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Brookhaven Symp Biol","volume":"","issue":"26","page":"138-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"130","title":"Uptake of radiolabeled glucose analogues by organotypic pia arachnoid cultures.","abstract":"","authors":"Spatz, M., Renkawek, K., Murray, MR., Klatzo, I.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Brain Res","volume":"100","issue":"3","page":"710-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"140","title":"Regulation and properties of an invertase from Clostridium pasteurianum.","abstract":"An intracellular invertase was induced in cultures of Clostridium pasteurianum utilizing sucrose as its carbon source for growth. This enzyme synthesis could be repressed by the addition of fructose of a sucrose-growing culture. In contrast, invertase activity was not affected by the addition of glucose to sucrose-growing cells and this enzyme could be induced in a glucose-metabolizing culture by the addition of sucrose. This enzyme was purified 10.5-fold over the induced lese, EC 3.2.1.26) by substrate-specificity studies. Invertase had a pH optimum of 6.5 and an apparent Km of 79.5 mM for sucrose, and required high concentration of potassium phosphate for maximum activity. Invertase was completely inactivated by a 2-min heat treatment at 60 degrees C. This enzyme was strongly inhibited by p-hydroxymercuribenzoate (pCMB) and weakly inhibited by 5,5'-dithiobis(2-nitrobenzoic acid), while cysteine could substantially reverse pCMB) inhibition, suggesting that sulfhydryl group(s) were necessary for invertase activity.","authors":"Laishley, EJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Microbiol","volume":"21","issue":"11","page":"1711-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31750881","title":"HDAC11 deficiency disrupts oncogene-induced hematopoiesis in myeloproliferative neoplasms.","abstract":"Protein acetylation is an important contributor to cancer initiation. Histone deacetylase 6 (HDAC6) controls JAK2 translation and protein stability and has been implicated in JAK2-driven diseases best exemplified by myeloproliferative neoplasms (MPNs). By using novel classes of highly selective HDAC inhibitors and genetically deficient mouse models, we discovered that HDAC11 rather than HDAC6 is necessary for the proliferation and survival of oncogenic JAK2-driven MPN cells and patient samples. Notably, HDAC11 is variably expressed in primitive stem cells and is expressed largely upon lineage commitment. Although Hdac11is dispensable for normal homeostatic hematopoietic stem and progenitor cell differentiation based on chimeric bone marrow reconstitution, Hdac11 deficiency significantly reduced the abnormal megakaryocyte population, improved splenic architecture, reduced fibrosis, and increased survival in the MPLW515L-MPN mouse model during primary and secondary transplantation. Therefore, inhibitors of HDAC11 are an attractive therapy for treating patients with MPN. Although JAK2 inhibitor therapy provides substantial clinical benefit in MPN patients, the identification of alternative therapeutic targets is needed to reverse MPN pathogenesis and control malignant hematopoiesis. This study establishes HDAC11 as a unique type of target molecule that has therapeutic potential in MPN.","authors":"Yue, L., Sharma, V., Horvat, NP., Akuffo, AA., Beatty, MS., Murdun, C., Colin, C., Billington, JMR., Goodheart, WE., Sahakian, E., Zhang, L., Powers, JJ., Amin, NE., Lambert-Showers, QT., Darville, LN., Pinilla-Ibarz, J., Reuther, GW., Wright, KL., Conti, C., Lee, JY., Zheng, X., Ng, PY., Martin, MW., Marshall, CG., Koomen, JM., Levine, RL., Verma, A., Grimes, HL., Sotomayor, EM., Shao, Z., Epling-Burnette, PK.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Blood","volume":"135","issue":"3","page":"191-207","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"143","title":"alpha-Naphthoflavone activation of 6-hydroxymethylbenzo(alpha)pyrene synthetase.","abstract":"alpha-Naphthoflavone activates the aryl hydroxymethyl synthetase of both the microsomal membrane-bound and soluble enzymes of rat liver and rat lung. The enzyme catalyzes the hydroxymethylation of benzo(alpha)pyrene to the 6-hydroxymethyl derivative.","authors":"Sloane, NH.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Cancer Res","volume":"35","issue":"12","page":"3731-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11296228","title":"Embryonic lethality and fetal liver apoptosis in mice lacking the c-raf-1 gene.","abstract":"The Raf kinases play a key role in relaying signals elicited by mitogens or oncogenes. Here, we report that c-raf-1(-\/-) embryos are growth retarded and die at midgestation with anomalies in the placenta and in the fetal liver. Although hepatoblast proliferation does not appear to be impaired, c-raf-1(-\/-) fetal livers are hypocellular and contain numerous apoptotic cells. Similarly, the poor proliferation of Raf-1(-\/-) fibroblasts and hematopoietic cells cultivated in vitro is due to an increase in the apoptotic index of these cultures rather than to a cell cycle defect. Furthermore, Raf-1- deficient fibroblasts are more sensitive than wild- type cells to specific apoptotic stimuli, such as actinomycin D or Fas activation, but not to tumor necrosis factor-alpha. MEK\/ERK activation is normal in Raf-1-deficient cells and embryos, and is probably mediated by B-RAF. These results indicate that the essential function of Raf-1 is to counteract apoptosis rather than to promote proliferation, and that effectors distinct from the MEK\/ERK cascade must mediate the anti-apoptotic function of Raf-1.","authors":"Mikula, M., Schreiber, M., Husak, Z., Kucerova, L., R\u00fcth, J., Wieser, R., Zatloukal, K., Beug, H., Wagner, EF., Baccarini, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"EMBO J","volume":"20","issue":"8","page":"1952-62","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18505836","title":"Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins.","abstract":"Aberrant proteins represent an extreme hazard to cells. Therefore, molecular chaperones and proteases have to carry out protein quality control in each cellular compartment. In contrast to the ATP-dependent cytosolic proteases and chaperones, the molecular mechanisms of extracytosolic factors are largely unknown. To address this question, we studied the protease function of DegP, the central housekeeping protein in the bacterial envelope. Our data reveal that DegP processively degrades misfolded proteins into peptides of defined size by employing a molecular ruler comprised of the PDZ1 domain and the proteolytic site. Furthermore, peptide binding to the PDZ domain transforms the resting protease into its active state. This allosteric activation mechanism ensures the regulated and rapid elimination of misfolded proteins upon folding stress. In comparison to the cytosolic proteases, the regulatory features of DegP are established by entirely different mechanisms reflecting the convergent evolution of an extracytosolic housekeeping protease.","authors":"Krojer, T., Pangerl, K., Kurt, J., Sawa, J., Stingl, C., Mechtler, K., Huber, R., Ehrmann, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Proc Natl Acad Sci U S A","volume":"105","issue":"22","page":"7702-7","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18505817","title":"Mind bomb-1 is essential for intraembryonic hematopoiesis in the aortic endothelium and the subaortic patches.","abstract":"Intraembryonic hematopoiesis occurs at two different sites, the floor of the aorta and subaortic patches (SAPs) of the para-aortic splanchnopleura (P-Sp)\/aorta-gonad-mesonephros (AGM) region. Notch1 and RBP-jkappa are critical for the specification of hematopoietic stem cells (HSCs) in Notch signal-receiving cells. However, the mechanism by which Notch signaling is triggered from the Notch signal-sending cells to support embryonic hematopoiesis remains to be determined. We previously reported that Mind bomb-1 (Mib1) regulates Notch ligands in the Notch signal-sending cells (B. K. Koo, M. J. Yoon, K. J. Yoon, S. K. Im, Y. Y. Kim, C. H. Kim, P. G. Suh, Y. N. Jan, and Y. Y. Kong, PLoS ONE 2:e1221, 2007). Here, we show that intraembryonic hematopoietic progenitors were absent in the P-Sp of Mib1(-\/-) embryos, whereas they were partly preserved in the Tie2-cre; Mib1(f)(\/f) P-Sps, suggesting that Mib1 plays a role in the endothelium and the SAPs. Interestingly, dll1 and dll4\/Jag1 are expressed in the SAPs and the endothelium of the AGM, respectively, where mib1 is detected. Indeed, Notch signaling was activated in the nascent HSCs at both sites. In the P-Sp explant culture, the overexpression of Dll1 in OP9 stromal cells rescued the failed production of hematopoietic progenitors in the Mib1(-\/-) P-Sp, while its activity was abolished by Mib1 knockdown. These results suggest that Mib1 is important for intraembryonic hematopoiesis not only in the aortic endothelium but also in the SAPs.","authors":"Yoon, MJ., Koo, BK., Song, R., Jeong, HW., Shin, J., Kim, YW., Kong, YY., Suh, PG.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Mol Cell Biol","volume":"28","issue":"15","page":"4794-804","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22425158","title":"Centrosomes can initiate a polarity axis from any position within one-cell C. elegans embryos.","abstract":"The stereotyped asymmetry of one-cell C. elegans embryos has proven to be an important model for identifying molecular determinants of cell polarity. How polarity is initiated is less well understood. Polarity establishment depends on centrosomes, which use two molecularly distinct pathways to break symmetry. In both, the centrosome's position adjacent to the cell cortex is thought to determine where polarization starts. Defects in centrosome-cortex juxtaposition correlate with defects in polarity establishment in several mutants, suggesting that these processes may be linked, but there is no direct test of this. Here we assess how centrosome position relative to the cortex affects polarity establishment. We find that centrosomes can initiate polarity from any position within the embryo volume, but centrosome-cortex proximity decreases the time required to initiate polarity. Polarization itself brings about close centrosome-cortex proximity. Prior to polarization, cytoplasmic microtubules constrain centrosome movement near the cortex, expanding the controversial role of microtubules during polarity establishment. The ability of centrosomes to induce a single polarity axis from any position within the egg emphasizes the flexible, self-organizing properties of polarization in C. elegans embryos and contrasts the common view of C. elegans development as invariant.","authors":"Bienkowska, D., Cowan, CR.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Curr Biol","volume":"22","issue":"7","page":"583-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22226525","title":"Methods in cell biology: analysis of cell polarity in C. elegans embryos.","abstract":"Cell polarity is a fundamental principle guiding development. Early C. elegans embryos contain a diversity of polarized cell types, ranging from asymmetrically dividing stem cells to a polarized epithelium. Over the past two decades, work using C. elegans embryos has led to mechanistic understandings of many aspects of cell polarity establishment, maintenance and propagation. Here we provide basic methods for researchers interested in using C. elegans embryos to study cell polarity, emphasizing the amenability of C. elegans to quantitative molecular analysis.","authors":"Bossinger, O., Cowan, CR.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Methods Cell Biol","volume":"107","issue":null,"page":"207-38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18496527","title":"Structural basis for the regulated protease and chaperone function of DegP.","abstract":"All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases.","authors":"Krojer, T., Sawa, J., Sch\u00e4fer, E., Saibil, HR., Ehrmann, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"453","issue":"7197","page":"885-90","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26145174","title":"Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor.","abstract":"Several terminal uridyltransferases (TUTases) are known to modulate small RNA biogenesis and\/or function via diverse mechanisms. Here, we demonstrate that Drosophila splicing-derived pre-miRNAs (mirtrons) are efficiently modified by the previously uncharacterized TUTase, Tailor. Tailor is necessary and sufficient for mirtron hairpin uridylation, and this modification inhibits mirtron biogenesis. Genome-wide analyses demonstrate that mirtrons are dominant Tailor substrates, and three features contribute to substrate specificity. First, reprogramming experiments show Tailor preferentially identifies splicing-derived miRNAs. Second, in vitro tests indicate Tailor prefers substrate hairpins over mature miRNAs. Third, Tailor exhibits sequence preference for 3'-terminal AG, a defining mirtron characteristic. Our work supports the notion that Tailor preferentially suppresses biogenesis of mirtrons, an evolutionarily adventitious pre-miRNA substrate class. Moreover, we detect preferential activity of Tailor on 3'-G canonical pre-miRNAs, and specific depletion of such loci from the pool of conserved miRNAs. Thus, Tailor activity may have had collateral impact on shaping populations of canonical miRNAs.","authors":"Bortolamiol-Becet, D., Hu, F., Jee, D., Wen, J., Okamura, K., Lin, CJ., Ameres, SL., Lai, EC.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Mol Cell","volume":"59","issue":"2","page":"217-28","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24700860","title":"Neuronal control of Drosophila walking direction.","abstract":"Most land animals normally walk forward but switch to backward walking upon sensing an obstacle or danger in the path ahead. A change in walking direction is likely to be triggered by descending \"command\" neurons from the brain that act upon local motor circuits to alter the timing of leg muscle activation. Here we identify descending neurons for backward walking in Drosophila--the MDN neurons. MDN activity is required for flies to walk backward when they encounter an impassable barrier and is sufficient to trigger backward walking under conditions in which flies would otherwise walk forward. We also identify ascending neurons, MAN, that promote persistent backward walking, possibly by inhibiting forward walking. These findings provide an initial glimpse into the circuits and logic that control walking direction in Drosophila.","authors":"Bidaye, SS., Machacek, C., Wu, Y., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Science","volume":"344","issue":"6179","page":"97-101","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18472258","title":"Developmental plasticity of lymphocytes.","abstract":"Experimental perturbation of signaling or transcription factor networks has been used to study the developmental potential of lymphoid progenitors, lineage-committed precursors and mature lymphocytes. Common lymphoid progenitors and uncommitted pro-T cells can be efficiently diverted into myeloid or erythroid lineages by ectopic cytokine signaling or retroviral expression of the myeloid C\/EBPalpha or erythroid GATA1 transcription factor. Forced C\/EBPalpha expression furthermore induces direct transdifferentiation of immature thymocytes or B cells into macrophages. Notably, conditional inactivation of the B cell commitment factor Pax5 is sufficient to convert mature B cells into functional T cells via dedifferentiation to uncommitted progenitors. Together these experiments have uncovered an unanticipated developmental plasticity of lymphocytes, which may account for lineage switches observed in human malignancies.","authors":"Cobaleda, C., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Opin Immunol","volume":"20","issue":"2","page":"139-48","pdf":null,"JrId":"1461","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18464796","title":"El Sur tambi\u00e9n existe: processing RNA in the Argentine Patagonia. Meetings on 'Cell Biology, Signaling and Alternative Splicing' and 'Gene Expression and RNA Processing'.","abstract":null,"authors":"Martinez, J., Neugebauer, KM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO Rep","volume":"9","issue":"6","page":"516-20","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23007861","title":"APC15 mediates CDC20 autoubiquitylation by APC\/C(MCC) and disassembly of the mitotic checkpoint complex.","abstract":"The anaphase-promoting complex\/cyclosome (APC\/C) bound to CDC20 (APC\/C(CDC20)) initiates anaphase by ubiquitylating B-type cyclins and securin. During chromosome bi-orientation, CDC20 assembles with MAD2, BUBR1 and BUB3 into a mitotic checkpoint complex (MCC) that inhibits substrate recruitment to the APC\/C. APC\/C activation depends on MCC disassembly, which was proposed to require CDC20 autoubiquitylation. Here we characterize APC15, a human APC\/C subunit related to yeast Mnd2. APC15 is located near APC\/C's MCC binding site; it is required for APC\/C-bound MCC (APC\/C(MCC))-dependent CDC20 autoubiquitylation and degradation and for timely anaphase initiation but is dispensable for substrate ubiquitylation by APC\/C(CDC20) and APC\/C(CDH1). Our results support the model wherein MCC is continuously assembled and disassembled to enable rapid activation of APC\/C(CDC20) and CDC20 autoubiquitylation promotes MCC disassembly. We propose that APC15 and Mnd2 negatively regulate APC\/C coactivators and report generation of recombinant human APC\/C.","authors":"Uzunova, K., Dye, BT., Schutz, H., Ladurner, R., Petzold, G., Toyoda, Y., Jarvis, MA., Brown, NG., Poser, I., Novatchkova, M., Mechtler, K., Hyman, AA., Stark, H., Schulman, BA., Peters, JM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nat Struct Mol Biol","volume":"19","issue":"11","page":"1116-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22427200","title":"An insertional mutagenesis screen identifies genes that cooperate with Mll-AF9 in a murine leukemogenesis model.","abstract":"Patients with a t(9;11) translocation (MLL-AF9) develop acute myeloid leukemia (AML), and while in mice the expression of this fusion oncogene also results in the development of myeloid leukemia, it is with long latency. To identify mutations that cooperate with Mll-AF9, we infected neonatal wild-type (WT) or Mll-AF9 mice with a murine leukemia virus (MuLV). MuLV-infected Mll-AF9 mice succumbed to disease significantly faster than controls presenting predominantly with myeloid leukemia while infected WT animals developed predominantly lymphoid leukemia. We identified 88 candidate cancer genes near common sites of proviral insertion. Analysis of transcript levels revealed significantly elevated expression of Mn1, and a trend toward increased expression of Bcl11a and Fosb in Mll-AF9 murine leukemia samples with proviral insertions proximal to these genes. Accordingly, FOSB and BCL11A were also overexpressed in human AML harboring MLL gene translocations. FOSB was revealed to be essential for growth in mouse and human myeloid leukemia cells using shRNA lentiviral vectors in vitro. Importantly, MN1 cooperated with Mll-AF9 in leukemogenesis in an in vivo BM viral transduction and transplantation assay. Together, our data identified genes that define transcription factor networks and important genetic pathways acting during progression of leukemia induced by MLL fusion oncogenes.","authors":"Bergerson, RJ., Collier, LS., Sarver, AL., Been, RA., Lugthart, S., Diers, MD., Zuber, J., Rappaport, AR., Nixon, MJ., Silverstein, KA., Fan, D., Lamblin, AF., Wolff, L., Kersey, JH., Delwel, R., Lowe, SW., O'Sullivan, MG., Kogan, SC., Adams, DJ., Largaespada, DA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Blood","volume":"119","issue":"19","page":"4512-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20562853","title":"Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing.","abstract":"Histone modifications are thought to regulate gene expression in part by modulating DNA accessibility. Here, we measured genome-wide DNA accessibility in Drosophila melanogaster by combining M.SssI methylation footprinting with methylated DNA immunoprecipitation. We show that methylase accessibility demarcates differential distribution of active and repressive histone modifications as well as sites of transcription and replication initiation. DNA accessibility is increased at active promoters and chromosomal regions that are hyperacetylated at H4K16, particularly at the male X chromosome, suggesting that transcriptional dosage compensation is facilitated by permissive chromatin structure. Conversely, inactive chromosomal domains decorated with H3K27me3 are least accessible, supporting a model for Polycomb-mediated chromatin compaction. In addition, we detect higher accessibility at chromosomal regions that replicate early and at sites of replication initiation. Together, these findings indicate that differential histone-modification patterns and the organization of replication have distinct and measurable effects on the exposure of the DNA template.","authors":"Bell, O., Schwaiger, M., Oakeley, EJ., Lienert, F., Beisel, C., Stadler, MB., Sch\u00fcbeler, D.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Struct Mol Biol","volume":"17","issue":"7","page":"894-900","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26119026","title":"Silencing Nociceptor Neurons Reduces Allergic Airway Inflammation.","abstract":"Lung nociceptors initiate cough and bronchoconstriction. To elucidate if these fibers also contribute to allergic airway inflammation, we stimulated lung nociceptors with capsaicin and observed increased neuropeptide release and immune cell infiltration. In contrast, ablating Nav1.8(+) sensory neurons or silencing them with QX-314, a charged sodium channel inhibitor that enters via large-pore ion channels to specifically block nociceptors, substantially reduced ovalbumin- or house-dust-mite-induced airway inflammation and bronchial hyperresponsiveness. We also discovered that IL-5, a cytokine produced by activated immune cells, acts directly on nociceptors to induce the release of vasoactive intestinal peptide (VIP). VIP then stimulates CD4(+) and resident innate lymphoid type 2 cells, creating an inflammatory signaling loop that promotes allergic inflammation. Our results indicate that nociceptors amplify pathological adaptive immune responses and that silencing these neurons with QX-314 interrupts this neuro-immune interplay, revealing a potential new therapeutic strategy for asthma.","authors":"Talbot, S., Abdulnour, RE., Burkett, PR., Lee, S., Cronin, SJ., Pascal, MA., Laedermann, C., Foster, SL., Tran, JV., Lai, N., Chiu, IM., Ghasemlou, N., DiBiase, M., Roberson, D., Von Hehn, C., Agac, B., Haworth, O., Seki, H., Penninger, JM., Kuchroo, VK., Bean, BP., Levy, BD., Woolf, CJ.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Neuron","volume":"87","issue":"2","page":"341-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31503413","title":"STARR-seq and UMI-STARR-seq: Assessing Enhancer Activities for Genome-Wide-, High-, and Low-Complexity Candidate Libraries.","abstract":"The identification of transcriptional enhancers and the quantitative assessment of enhancer activities is essential to understanding how regulatory information for gene expression is encoded in animal and human genomes. Further, it is key to understanding how sequence variants affect enhancer function. STARR-seq enables the direct and quantitative assessment of enhancer activity for millions of candidate sequences of arbitrary length and origin in parallel, allowing the screening of entire genomes and the establishment of genome-wide enhancer activity maps. In STARR-seq, the candidate sequences are cloned downstream of the core promoter into a reporter gene's transcription unit (i.e., the 3' UTR). Candidates that function as active enhancers lead to the transcription of reporter mRNAs that harbor the candidates' sequences. This direct coupling of enhancer sequence and enhancer activity in cis enables the straightforward and efficient cloning of complex candidate libraries and the assessment of enhancer activities of millions of candidates in parallel by quantifying the reporter mRNAs by deep sequencing. This article describes how to create focused and genome-wide human STARR-seq libraries and how to perform STARR-seq screens in mammalian cells, and also describes a novel STARR-seq variant (UMI-STARR-seq) that allows the accurate counting of reporter mRNAs for STARR-seq libraries of low complexity. \u00a9 2019 The Authors. Basic Protocol 1: STARR-seq plasmid library cloning Basic Protocol 2: Mammalian STARR-seq screening protocol Alternate Protocol: UMI-STARR-seq screening protocol-unique molecular identifier integration Support Protocol: Transfection of human cells using the MaxCyte STX scalable transfection system.","authors":"Neumayr, C., Pagani, M., Stark, A., Arnold, CD.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Curr Protoc Mol Biol","volume":"128","issue":"1","page":"e105","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19640486","title":"Chromatin: sub out the replacement.","abstract":"Nucleosomes with specific histone variants are incorporated into DNA at sites of transcription and repair. The histone variant H3.3 has been linked to transcriptional regulation, but genetic tests in the fruit fly have yielded surprising results.","authors":"Bell, O., Sch\u00fcbeler, D.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Biol","volume":"19","issue":"14","page":"R545-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22704655","title":"Dynamics and memory of heterochromatin in living cells.","abstract":"Posttranslational histone modifications are important for gene regulation, yet the mode of propagation and the contribution to heritable gene expression states remains controversial. To address these questions, we developed a chromatin in vivo assay (CiA) system employing chemically induced proximity to initiate and terminate chromatin modifications in living cells. We selectively recruited HP1\u03b1 to induce H3K9me3-dependent gene silencing and describe the kinetics and extent of chromatin modifications at the Oct4 locus in fibroblasts and pluripotent cells. H3K9me3 propagated symmetrically and continuously at average rates of ~0.18 nucleosomes\/hr to produce domains of up to 10 kb. After removal of the HP1\u03b1 stimulus, heterochromatic domains were heritably transmitted, undiminished through multiple cell generations. Our data enabled quantitative modeling of reaction kinetics, which revealed that dynamic competition between histone marking and turnover, determines the boundaries and stability of H3K9me3 domains. This framework predicts the steady-state dynamics and spatial features of the majority of euchromatic H3K9me3 domains over the genome.","authors":"Hathaway, NA., Bell, O., Hodges, C., Miller, EL., Neel, DS., Crabtree, GR.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell","volume":"149","issue":"7","page":"1447-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15525537","title":"RGS14 is a mitotic spindle protein essential from the first division of the mammalian zygote.","abstract":"Heterotrimeric G protein alpha subunits, RGS proteins, and GoLoco motif proteins have been recently implicated in the control of mitotic spindle dynamics in C. elegans and D. melanogaster. Here we show that \"regulator of G protein signaling-14\" (RGS14) is expressed by the mouse embryonic genome immediately prior to the first mitosis, where it colocalizes with the anastral mitotic apparatus of the mouse zygote. Loss of Rgs14 expression in the mouse zygote results in cytofragmentation and failure to progress to the 2-cell stage. RGS14 is found in all tissues and segregates to the nucleus in interphase and to the mitotic spindle and centrioles during mitosis. Alteration of RGS14 levels in exponentially proliferating cells leads to cell growth arrest. Our results indicate that RGS14 is one of the earliest essential product of the mammalian embryonic genome yet described and has a general role in mitosis.","authors":"Martin-McCaffrey, L., Willard, FS., Oliveira-dos-Santos, AJ., Natale, DR., Snow, BE., Kimple, RJ., Pajak, A., Watson, AJ., Dagnino, L., Penninger, JM., Siderovski, DP., D'Souza, SJ.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Dev Cell","volume":"7","issue":"5","page":"763-9","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31468430","title":"Targeting Taurine Transporter (TauT) for Cancer Immunotherapy of p53 Mutation Mediated Cancers - Molecular Basis and Preclinical Implication.","abstract":"Taurine transporter (TauT) has been identified as a target gene of p53 tumor suppressor. TauT is also found to be overexpressed in variety type of human cancers, such as leukemia. This study showed that expression of TauT was upregulated by c-Myc and c-Jun oncogenes. To explore whether blocking of TauT inhibits tumor development, the RNA interference (RNAi) and immune targeting approaches were tested in tumor cells in vitro and in p53 mutant mice in vivo. Knockdown of TauT expression by RNAi resulted in cell cycle G2 arrest and suppressed human breast cancer MCF-7 cells proliferation determined by colonies production and cell migration assays. Knockdown of TauT also rendered MCF-7 cells more susceptible to chemotherapeutic drug-induced apoptosis. An antibody specifically against TauT blocked taurine uptake and induced cell cycle G2 arrest leading to cell death of variety type of tumor cells without affecting the viability of normal mammalian cells. TauT peptide vaccination significantly increased median lifespan (1.5-fold) of the p53 null mice and rescued p53+\/- mice by extending the median lifespan from 315\u00a0days to 621\u00a0days. Furthermore, single dose treatment of tumor-bearing (thymic lymphoma) p53 null mice with TauT peptide reduced tumor size by about 50% and significantly prolonged survival of these mice from average 7\u00a0days (after observing the thymic lymphoma) to 21\u00a0days. This finding demonstrates that a novel TauT peptide vaccine can delay, inhibit, and\/or treat p53 mutation related spontaneous tumorigenesis in vivo. Therefore, TauT peptide may be used as a universal cancer vaccine to prevent and\/or treat patients with p53 mutation-mediated cancers.","authors":"Han, X.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Adv Exp Med Biol","volume":"1155","issue":"","page":"543-553","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26737501","title":"A control-theoretical approach to the identification of a commitment switch in B lymphopoiesis cell fate determination.","abstract":"Cellular differentiation is continuously orchestrated by complex networks of transcription factors, signaling molecules and genetic and epigenetic events, a fundamental prerequisite for the design of strategies for reprogramming differentiated cells to immature stem\/progenitor cells is a thorough understanding of such complex regulatory machinery. Therefore, mathematical models, along with the associated analysis and control methods, are highly needed in this research field. In the present work, we provide a first model of the genetic regulatory network driving the cellular fate determination at the stage of lymphoid lineage commitment, in particular during lineage restriction of multipotent progenitors to early B-cell committed precursors.","authors":"Salerno, L., Cosentino, C., Morrone, G., Bilotta, M., Amato, F.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Annu Int Conf IEEE Eng Med Biol Soc","volume":"2015","issue":"","page":"5355-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18347056","title":"Transcription-coupled methylation of histone H3 at lysine 36 regulates dosage compensation by enhancing recruitment of the MSL complex in Drosophila melanogaster.","abstract":"In Drosophila melanogaster, dosage compensation relies on the targeting of the male-specific lethal (MSL) complex to hundreds of sites along the male X chromosome. Transcription-coupled methylation of histone H3 lysine 36 is enriched toward the 3' end of active genes, similar to the MSL proteins. Here, we have studied the link between histone H3 methylation and MSL complex targeting using RNA interference and chromatin immunoprecipitation. We show that trimethylation of histone H3 at lysine 36 (H3K36me3) relies on the histone methyltransferase Hypb and is localized promoter distal at dosage-compensated genes, similar to active genes on autosomes. However, H3K36me3 has an X-specific function, as reduction specifically decreases acetylation of histone H4 lysine 16 on the male X chromosome. This hypoacetylation is caused by compromised MSL binding and results in a failure to increase expression twofold. Thus, H3K36me3 marks the body of all active genes yet is utilized in a chromosome-specific manner to enhance histone acetylation at sites of dosage compensation.","authors":"Bell, O., Conrad, T., Kind, J., Wirbelauer, C., Akhtar, A., Sch\u00fcbeler, D.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Mol Cell Biol","volume":"28","issue":"10","page":"3401-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18007591","title":"Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila.","abstract":"Post-translational modifications of histones are involved in transcript initiation and elongation. Methylation of lysine 36 of histone H3 (H3K36me) resides promoter distal at transcribed regions in Saccharomyces cerevisiae and is thought to prevent spurious initiation through recruitment of histone-deacetylase activity. Here, we report surprising complexity in distribution, regulation and readout of H3K36me in Drosophila involving two histone methyltransferases (HMTases). Dimethylation of H3K36 peaks adjacent to promoters and requires dMes-4, whereas trimethylation accumulates toward the 3' end of genes and relies on dHypb. Reduction of H3K36me3 is lethal in Drosophila larvae and leads to elevated levels of acetylation, specifically at lysine 16 of histone H4 (H4K16ac). In contrast, reduction of both di- and trimethylation decreases lysine 16 acetylation. Thus di- and trimethylation of H3K36 have opposite effects on H4K16 acetylation, which we propose enable dynamic changes in chromatin compaction during transcript elongation.","authors":"Bell, O., Wirbelauer, C., Hild, M., Scharf, AN., Schwaiger, M., MacAlpine, DM., Zilbermann, F., van Leeuwen, F., Bell, SP., Imhof, A., Garza, D., Peters, AH., Sch\u00fcbeler, D.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"EMBO J","volume":"26","issue":"24","page":"4974-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31219577","title":"Map2k7 Haploinsufficiency Induces Brain Imaging Endophenotypes and Behavioral Phenotypes Relevant to Schizophrenia.","abstract":"c-Jun N-terminal kinase (JNK) signaling contributes to functional plasticity in the brain and cognition. Accumulating evidence implicates a role for MAP kinase kinase 7 (MAP2K7), a JNK activator encoded by the Map2k7 gene, and other JNK pathway components in schizophrenia (ScZ). Mice haploinsufficient for Map2k7 (Map2k7+\/- mice) display ScZ-relevant cognitive deficits, although the mechanisms are unclear. Here we show that Map2k7+\/- mice display translationally relevant alterations in brain function, including hippocampal and mesolimbic system hypermetabolism with a contrasting prefrontal cortex (PFC) hypometabolism, reminiscent of patients with ScZ. In addition Map2k7+\/- mice show alterations in functional brain network connectivity paralleling those reported in early ScZ, including PFC and hippocampal hyperconnectivity and compromised mesolimbic system functional connectivity. We also show that although the cerebral metabolic response to ketamine is preserved, the response to dextroamphetamine (d-amphetamine) is significantly attenuated in Map2k7+\/- mice, supporting monoamine neurotransmitter system dysfunction but not glutamate\/NMDA receptor (NMDA-R) dysfunction as a consequence of Map2k7 haploinsufficiency. These effects are mirrored behaviorally with an attenuated impact of d-amphetamine on sensorimotor gating and locomotion, whereas similar deficits produced by ketamine are preserved, in Map2k7+\/- mice. In addition, Map2k7+\/- mice show a basal hyperactivity and sensorimotor gating deficit. Overall, these data suggest that Map2k7 modifies brain and monoamine neurotransmitter system function in a manner relevant to the positive and cognitive symptoms of ScZ.","authors":"Openshaw, RL., Thomson, DM., Thompson, R., Penninger, JM., Pratt, JA., Morris, BJ., Dawson, N.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Schizophr Bull","volume":"46","issue":"1","page":"211-223","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18463306","title":"Conservation of small RNA pathways in platypus.","abstract":"Small RNA pathways play evolutionarily conserved roles in gene regulation and defense from parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout animal lineages, but specific animal clades also show variations on these recurring themes, including species-specific small RNAs. The monotremes, with only platypus and four species of echidna as extant members, represent the basal branch of the mammalian lineage. Here, we examine the small RNA pathways of monotremes by deep sequencing of six platypus and echidna tissues. We find that highly conserved microRNA species display their signature tissue-specific expression patterns. In addition, we find a large rapidly evolving cluster of microRNAs on platypus chromosome X1, which is unique to monotremes. Platypus and echidna testes contain a robust Piwi-interacting (piRNA) system, which appears to be participating in ongoing transposon defense.","authors":"Murchison, EP., Kheradpour, P., Sachidanandam, R., Smith, C., Hodges, E., Xuan, Z., Kellis, M., Gr\u00fctzner, F., Stark, A., Hannon, GJ.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genome Res","volume":"18","issue":"6","page":"995-1004","pdf":null,"JrId":"8754","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22813779","title":"Genes involved in the evolution of herbivory by a leaf-mining, Drosophilid fly.","abstract":"Herbivorous insects are among the most successful radiations of life. However, we know little about the processes underpinning the evolution of herbivory. We examined the evolution of herbivory in the fly, Scaptomyza flava, whose larvae are leaf miners on species of Brassicaceae, including the widely studied reference plant, Arabidopsis thaliana (Arabidopsis). Scaptomyza flava is phylogenetically nested within the paraphyletic genus Drosophila, and the whole genome sequences available for 12 species of Drosophila facilitated phylogenetic analysis and assembly of a transcriptome for S. flava. A time-calibrated phylogeny indicated that leaf mining in Scaptomyza evolved between 6 and 16 million years ago. Feeding assays showed that biosynthesis of glucosinolates, the major class of antiherbivore chemical defense compounds in mustard leaves, was upregulated by S. flava larval feeding. The presence of glucosinolates in wild-type (WT) Arabidopsis plants reduced S. flava larval weight gain and increased egg-adult development time relative to flies reared in glucosinolate knockout (GKO) plants. An analysis of gene expression differences in 5-day-old larvae reared on WT versus GKO plants showed a total of 341 transcripts that were differentially regulated by glucosinolate uptake in larval S. flava. Of these, approximately a third corresponded to homologs of Drosophila melanogaster genes associated with starvation, dietary toxin-, heat-, oxidation-, and aging-related stress. The upregulated transcripts exhibited elevated rates of protein evolution compared with unregulated transcripts. The remaining differentially regulated transcripts also contained a higher proportion of novel genes than the unregulated transcripts. Thus, the transition to herbivory in Scaptomyza appears to be coupled with the evolution of novel genes and the co-option of conserved stress-related genes.","authors":"Whiteman, NK., Gloss, AD., Sackton, TB., Groen, SC., Humphrey, PT., Lapoint, RT., S\u00f8nderby, IE., Halkier, BA., Kocks, C., Ausubel, FM., Pierce, NE.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genome Biol Evol","volume":"4","issue":"9","page":"900-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22782181","title":"High-throughput physical mapping of chromosomes using automated in situ hybridization.","abstract":"Projects to obtain whole-genome sequences for 10,000 vertebrate species and for 5,000 insect and related arthropod species are expected to take place over the next 5 years. For example, the sequencing of the genomes for 15 malaria mosquitospecies is currently being done using an Illumina platform. This Anopheles species cluster includes both vectors and non-vectors of malaria. When the genome assemblies become available, researchers will have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, it has proven difficult to use next-generation sequencing reads to generate high-quality de novo genome assemblies. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented. Success of comparative genomic analyses will be limited if researchers deal with numerous sequencing contigs, rather than with chromosome-based genome assemblies. Fragmented, unmapped sequences create problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. Developing high-resolution physical maps for species with newly sequenced genomes is a timely and cost-effective investment that will facilitate genome annotation, evolutionary analysis, and re-sequencing of individual genomes from natural populations. Here, we present innovative approaches to chromosome preparation, fluorescent in situ hybridization (FISH), and imaging that facilitate rapid development of physical maps. Using An. gambiae as an example, we demonstrate that the development of physical chromosome maps can potentially improve genome assemblies and, thus, the quality of genomic analyses. First, we use a high-pressure method to prepare polytene chromosome spreads. This method, originally developed for Drosophila, allows the user to visualize more details on chromosomes than the regular squashing technique. Second, a fully automated, front-end system for FISH is used for high-throughput physical genome mapping. The automated slide staining system runs multiple assays simultaneously and dramatically reduces hands-on time. Third, an automatic fluorescent imaging system, which includes a motorized slide stage, automatically scans and photographs labeled chromosomes after FISH. This system is especially useful for identifying and visualizing multiple chromosomal plates on the same slide. In addition, the scanning process captures a more uniform FISH result. Overall, the automated high-throughput physical mapping protocol is more efficient than a standard manual protocol.","authors":"George, P., Sharakhova, MV., Sharakhov, IV.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"J Vis Exp","volume":"","issue":"64","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25164742","title":"Genomics: Hiding in plain sight.","abstract":null,"authors":"Muerdter, F., Stark, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nature","volume":"512","issue":"7515","page":"374-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9527486","title":"Two-dimensional gel electrophoresis analysis of endovacuolar organelles.","abstract":"Cells perform their multiple functions with the aid of a series of distinct membrane organelles. In the last years, many of these compartments have been isolated, purified, and extensively studied. The major roles of each organelle in the cell are well understood. However, most of the molecular basis by which they perform their functions is poorly known. The recent identification and study of a handful of proteins associated with endovacuolar compartments has had a major impact on the understanding of the molecular details of organelle functions even though two-dimensional (2-D) gel analysis indicates that hundreds of proteins are typically associated with a complex organelle. This shows that many details and surprises are still to come for cell biologists. In the present study, we have analyzed and compared different organelles of the endocytic and phagocytic apparatus using 2-D gel electrophoresis.","authors":"Scianimanico, S., Pasquali, C., Lavoie, J., Huber, LA., Gorvel, JP., Desjardins, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Electrophoresis","volume":"18","issue":"14","page":"2566-72","pdf":null,"JrId":"3579","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9515965","title":"A causal role for E-cadherin in the transition from adenoma to carcinoma.","abstract":"Development of malignant tumours is in part characterized by the ability of a tumour cell to overcome cell-cell adhesion and to invade surrounding tissue. E-cadherin is the main adhesion molecule of epithelia, and it has been implicated in carcinogenesis because it is frequently lost in human epithelial cancers. Re-establishing the functional cadherin complex in tumour cell lines results in a reversion from an invasive to a benign epithelial phenotype. However, it remained unresolved whether the loss of E-cadherin-mediated cell adhesion was a cause or a consequence of tumour progression in vivo. Here we report that the loss of E-cadherin expression coincides with the transition from well differentiated adenoma to invasive carcinoma in a transgenic mouse model of pancreatic beta-cell carcinogenesis (Rip1Tag2). Intercrossing Rip1Tag2 mice with transgenic mice that maintain E-cadherin expression in beta-tumour cells results in arrest of tumour development at the adenoma stage, whereas expression of a dominant-negative form of E-cadherin induces early invasion and metastasis. The results demonstrate that loss of E-cadherin-mediated cell adhesion is one rate-limiting step in the progression from adenoma to carcinoma.","authors":"Perl, AK., Wilgenbus, P., Dahl, U., Semb, H., Christofori, G.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Nature","volume":"392","issue":"6672","page":"190-3","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18443042","title":"c-Jun controls histone modifications, NF-kappaB recruitment, and RNA polymerase II function to activate the ccl2 gene.","abstract":"Interleukin-1 (IL-1)-induced mRNA expression of ccl2 (also called MCP-1), a prototypic highly regulated inflammatory gene, is severely suppressed in cells lacking c-Jun or Jun N-terminal protein kinase 1 (JNK1)\/JNK2 genes and is only partially restored in cells expressing a c-Jun(SS63\/73AA) mutant protein. We used chromatin immunoprecipitation to identify three c-Jun-binding sites located in the far 5' region close to the transcriptional start site and in the far 3' region of murine and human ccl2 genes. Mutational analysis revealed that the latter two sites contribute to ccl2 transcription in response to the presence of IL-1 or of ectopically expressed c-Jun-ATF-2 dimers. Further experiments comparing wild-type and c-Jun-deficient cells revealed that c-Jun regulates Ser10 phosphorylation of histone H3, acetylation of histones H3 and H4, and recruitment of histone deacetylase 3 (HDAC3), NF-kappaB subunits, and RNA polymerase II across the ccl2 locus. c-Jun also coimmunoprecipitated with p65 NF-kappaB and HDAC3. Based on DNA microarray analysis, c-Jun was required for full expression of 133 out of 162 IL-1-induced genes. For inflammatory genes, these data support the idea of an activator function of c-Jun that is executed by multiple mechanisms, including phosphorylation-dependent interaction with p65 NF-kappaB and HDAC3 at the level of chromatin.","authors":"Wolter, S., Doerrie, A., Weber, A., Schneider, H., Hoffmann, E., von der Ohe, J., Bakiri, L., Wagner, EF., Resch, K., Kracht, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Mol Cell Biol","volume":"28","issue":"13","page":"4407-23","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18433157","title":"Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis.","abstract":"An estimated one-third of all proteins in higher eukaryotes are regulated by phosphorylation by protein kinases (PKs). Although plant genomes encode more than 1000 PKs, the substrates of only a small fraction of these kinases are known. By mass spectrometry of peptides from cytoplasmic- and nuclear-enriched fractions, we determined 303 in vivo phosphorylation sites in Arabidopsis proteins. Among 21 different PKs, 12 were phosphorylated in their activation loops, suggesting that they were in their active state. Immunoblotting and mutational analysis confirmed a tyrosine phosphorylation site in the activation loop of a GSK3\/shaggy-like kinase. Analysis of phosphorylation motifs in the substrates suggested links between several of these PKs and many target sites. To perform quantitative phosphorylation analysis, peptide arrays were generated with peptides corresponding to in vivo phosphorylation sites. These peptide chips were used for kinome profiling of subcellular fractions as well as H 2O 2-treated Arabidopsis cells. Different peptide phosphorylation profiles indicated the presence of overlapping but distinct PK activities in cytosolic and nuclear compartments. Among different H 2O 2-induced PK targets, a peptide of the serine\/arginine-rich (SR) splicing factor SCL30 was most strongly affected. SRPK4 (SR protein-specific kinase 4) and MAPKs (mitogen-activated PKs) were found to phosphorylate this peptide, as well as full-length SCL30. However, whereas SRPK4 was constitutively active, MAPKs were activated by H 2O 2. These results suggest that SCL30 is targeted by different PKs. Together, our data demonstrate that a combination of mass spectrometry with peptide chip phosphorylation profiling has a great potential to unravel phosphoproteome dynamics and to identify PK substrates.","authors":"de la Fuente van Bentem, S., Anrather, D., Dohnal, I., Roitinger, E., Csaszar, E., Joore, J., Buijnink, J., Carreri, A., Forzani, C., Lorkovic, ZJ., Barta, A., Lecourieux, D., Verhounig, A., Jonak, C., Hirt, H.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Proteome Res","volume":"7","issue":"6","page":"2458-70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22535494","title":"Retrogenes moved out of the z chromosome in the silkworm.","abstract":"Previous studies on organisms with well-differentiated X and Y chromosomes, such as Drosophila and mammals, consistently detected an excess of genes moving out of the X chromosome and gaining testis-biased expression. Several selective evolutionary mechanisms were shown to be associated with this nonrandom gene traffic, which contributed to the evolution of the X chromosome and autosomes. If selection drives gene traffic, such traffic should also exist in species with Z and W chromosomes, where the females are the heterogametic sex. However, no previous studies on gene traffic in species with female heterogamety have found any nonrandom chromosomal gene movement. Here, we report an excess of retrogenes moving out of the Z chromosome in an organism with the ZW sex determination system, Bombyx mori. In addition, we showed that those \"out of Z\" retrogenes tended to have ovary-biased expression, which is consistent with the pattern of non-retrogene traffic recently reported in birds and symmetrical to the retrogene movement in mammals and fruit flies out of the X chromosome evolving testis functions. These properties of gene traffic in the ZW system suggest a general role for the heterogamety of sex chromosomes in determining the chromosomal locations and the evolution of sex-biased genes.","authors":"Wang, J., Long, M., Vibranovski, MD.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Mol Evol","volume":"74","issue":"3-4","page":"113-26","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29679476","title":"Linear ubiquitin chain-binding domains.","abstract":"Ubiquitin modification (ubiquitination) of target proteins can vary with respect to chain lengths, linkage type, and chain forms, such as homologous, mixed, and branched ubiquitin chains. Thus, ubiquitination can generate multiple unique surfaces on a target protein substrate. Ubiquitin-binding domains (UBDs) recognize ubiquitinated substrates, by specifically binding to these unique surfaces, modulate the formation of cellular signaling complexes and regulate downstream signaling cascades. Among the eight different homotypic chain types, Met1-linked (also termed linear) chains are the only chains in which linkage occurs on a non-Lys residue of ubiquitin. Linear ubiquitin chains have been implicated in immune responses, cell death and autophagy, and several UBDs - specific for linear ubiquitin chains - have been identified. In this review, we describe the main principles of ubiquitin recognition by UBDs, focusing on linear ubiquitin chains and their roles in biology.","authors":"Fennell, LM., Rahighi, S., Ikeda, F.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"FEBS J","volume":"285","issue":"15","page":"2746-2761","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31034354","title":"Human organoids: a new dimension in cell biology.","abstract":"Organoids derived from stem cells or tissues in culture can develop into structures that resemble the in vivo anatomy and physiology of intact organs. Human organoid cultures provide the potential to study human development and model disease processes with the same scrutiny and depth of analysis customary for research with nonhuman model organisms. Resembling the complexity of the actual tissue or organ, patient-derived human organoid studies may accelerate medical research, creating new opportunities for tissue engineering and regenerative medicine, generating knowledge and tools for preclinical studies, including drug development and testing. Biologists are drawn to this system as a new \"model organism\" to study complex disease phenotypes and genetic variability among individuals using patient-derived tissues. The American Society for Cell Biology convened a task force to report on the potential, challenges, and limitations for human organoid research. The task force suggests ways to ease the entry for new researchers into the field and how to facilitate broader use of this new model organism within the research community. This includes guidelines for reproducibility, culturing, sharing of patient materials, patient consent, training, and communication with the public.","authors":"Lehmann, R., Lee, CM., Shugart, EC., Benedetti, M., Charo, RA., Gartner, Z., Hogan, B., Knoblich, J., Nelson, CM., Wilson, KM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mol Biol Cell","volume":"30","issue":"10","page":"1129-1137","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22509300","title":"Statistical inference of selection and divergence from a time-dependent Poisson random field model.","abstract":"We apply a recently developed time-dependent Poisson random field model to aligned DNA sequences from two related biological species to estimate selection coefficients and divergence time. We use Markov chain Monte Carlo methods to estimate species divergence time and selection coefficients for each locus. The model assumes that the selective effects of non-synonymous mutations are normally distributed across genetic loci but constant within loci, and synonymous mutations are selectively neutral. In contrast with previous models, we do not assume that the individual species are at population equilibrium after divergence. Using a data set of 91 genes in two Drosophila species, D. melanogaster and D. simulans, we estimate the species divergence time t(div) = 2.16 N(e) (or 1.68 million years, assuming the haploid effective population size N(e) = 6.45 x 10(5) years) and a mean selection coefficient per generation \u03bc(\u03b3) = 1.98\/N(e). Although the average selection coefficient is positive, the magnitude of the selection is quite small. Results from numerical simulations are also presented as an accuracy check for the time-dependent model.","authors":"Amei, A., Sawyer, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"4","page":"e34413","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22493668","title":"Inferring phylogenies from RAD sequence data.","abstract":"Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD) to sequence restriction-site associated DNA (RAD)--the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts) and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct \"known\" phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for \"total evidence\" phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively). RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in which sufficient numbers of orthologous restriction sites are retained across species.","authors":"Rubin, BE., Ree, RH., Moreau, CS.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"4","page":"e33394","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22483047","title":"A molecular phylogeny of thermophilic fungi.","abstract":"Sequences from 86 fungal genomes and from the two outgroup genomes Arabidopsis thaliana and Drosophila melanogaster were analyzed to construct a robust molecular phylogeny of thermophilic fungi, which are potentially rich sources of industrial enzymes. To provide experimental reference points, growth characteristics of 22 reported thermophilic or thermotolerant fungi, together with eight mesophilic species, were examined at four temperatures: 22\u00a0\u00b0C, 34\u00a0\u00b0C, 45\u00a0\u00b0C, and 55\u00a0\u00b0C. Based on the relative growth performances, species with a faster growth rate at 45\u00a0\u00b0C than at 34\u00a0\u00b0C were classified as thermophilic, and species with better or equally good growth at 34\u00a0\u00b0C compared to 45\u00a0\u00b0C as thermotolerant. We examined the phylogenetic relationships of a diverse range of fungi, including thermophilic and thermotolerant species, using concatenated amino acid sequences of marker genes mcm7, rpb1, and rpb2 obtained from genome sequencing projects. To further elucidate the phylogenetic relationships in the thermophile-rich orders Sordariales and Eurotiales, we used nucleotide sequences from the nuclear ribosomal small subunit (SSU), the 5.8S gene with internal transcribed spacers 1 and 2 (ITS 1 and 2), and the ribosomal large subunit (LSU) to include additional species for analysis. These phylogenetic analyses clarified the position of several thermophilic taxa. Thus, Myriococcum thermophilum and Scytalidium thermophilum fall into the Sordariales as members of the Chaetomiaceae, Thermomyces lanuginosus belongs to the Eurotiales, Malbranchea cinnamomea is a member of the Onygenales, and Calcarisporiella thermophila is assigned to the basal fungi close to the Mucorales. The mesophilic alkalophile Acremonium alcalophilum clusters with Verticillium albo-atrum and Verticillium dahliae, placing them in the recently established order Glomerellales. Taken together, these data indicate that the known thermophilic fungi are limited to the Sordariales, Eurotiales, and Onygenales in the Ascomycota and the Mucorales with possibly an additional order harbouring C. thermophila in the basal fungi. No supporting evidence was found for thermophilic species belonging to the Basidiomycota.","authors":"Morgenstern, I., Powlowski, J., Ishmael, N., Darmond, C., Marqueteau, S., Moisan, MC., Quenneville, G., Tsang, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Fungal Biol","volume":"116","issue":"4","page":"489-502","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30939112","title":"Automated measurement of the erythrocyte sedimentation rate: method validation and comparison.","abstract":"Background Development of automated analyzers for erythrocyte sedimentation rate (ESR) has imposed the need for extensive validation prior to their implementation in routine practice, to ensure comparability with the reference Westergren method. The aim of our study was to perform the analytical validation of two automated ESR analyzers, the Ves-Matic Cube 200 and the TEST1. Methods Validation was performed according to the recent International Council for Standardization in Hematology recommendations and included determination of intrarun and inter-run precision, assessment of sample carryover, hemolysis interference, sensitivity to fibrinogen, method comparison with the gold standard Westergren method and stability test. Results The highest intrarun imprecision was obtained for the low ESR range (33.5% for Ves-Matic Cube; 37.3% for TEST1) while inter-run coefficients of variation on three levels were much better for the TEST1 (0%, 2% and 1.2%) compared to the Ves-Matic Cube 200 on two levels (24.9% and 5.8%). Both Ves-Matic Cube 200 and TEST1 showed no statistically significant difference when compared with Westergren. Bland-Altman analysis yielded overall insignificant mean biases for all comparisons, but a wider dispersion of results and 95% limits of agreement for comparisons including the Ves-Matic Cube 200. Carryover was considered insignificant, while hemolysis had a negative effect on all assessed ESR methods. The highest sensitivity to fibrinogen was observed for the Ves-Matic Cube 200, followed by Westergren and the least sensitive was the TEST1. Conclusions The obtained results proved the analytical validity of the TEST1 and the Ves-Matic Cube 200, and high comparability with the gold standard Westergren method, showing obvious improvements in standardization of ESR methods.","authors":"Lapi\u0107, I., Piva, E., Spolaore, F., Tosato, F., Pelloso, M., Plebani, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Clin Chem Lab Med","volume":"57","issue":"9","page":"1364-1373","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22481521","title":"Molecular evidence to suggest the origin of a colonization: Drosophila subobscura in America.","abstract":"The recent colonization of America by Drosophila subobscura represents a great opportunity for evolutionary biology studies. Knowledge of the populations from which the colonization started would provide an understanding of how genetic composition changed during adaptation to the new environment. Thus, a 793 nucleotide fragment of the Odh (Octanol dehydrogenase) gene was sequenced in 66 chromosomal lines from Barcelona (western Mediterranean) and in 66 from Mt. Parnes (Greece, eastern Mediterranean). No sequence of Odh fragment in Barcelona or Mt. Parnes was identical to any of those previously detected in America. However, an Odh sequence from Barcelona differed in only one nucleotide from another found in American populations. In both cases, the chromosomal lines presented the same inversion: O(7), and the Odh gene was located within this inversion. This evidence suggests a possible western Mediterranean origin for the colonization. Finally, the molecular and inversion data indicate that the colonization was not characterized by multiple reintroductions.","authors":"Ara\u00faz, PA., Peris-Bondia, F., Latorre, A., Serra, L., Mestres, F.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Genetica","volume":"139","issue":"11-12","page":"1477-86","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25126791","title":"Ecdysone and mediator change energy metabolism to terminate proliferation in Drosophila neural stem cells.","abstract":"Stem cells are highly abundant during early development but become a rare population in most adult organs. The molecular mechanisms causing stem cells to exit proliferation at a specific time are not well understood. Here, we show that changes in energy metabolism induced by the steroid hormone\u00a0ecdysone and the Mediator initiate an irreversible cascade of events leading to cell-cycle exit in Drosophila neural stem cells. We show that the timely induction of oxidative phosphorylation and the mitochondrial respiratory chain are required in neuroblasts to uncouple the cell cycle from cell growth. This results in a progressive reduction in neuroblast cell size and ultimately in terminal differentiation. Brain tumor mutant neuroblasts fail to undergo this shrinkage process and continue to proliferate until adulthood. Our findings show that cell size control can be modified by systemic hormonal signaling and reveal a unique connection between metabolism and proliferation in stem cells.","authors":"Homem, CCF., Steinmann, V., Burkard, TR., Jais, A., Esterbauer, H., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell","volume":"158","issue":"4","page":"874-888","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18405978","title":"TrackFly: virtual reality for a behavioral system analysis in free-flying fruit flies.","abstract":"Modern neuroscience and the interest in biomimetic control design demand increasingly sophisticated experimental techniques that can be applied in freely moving animals under realistic behavioral conditions. To explore sensorimotor flight control mechanisms in free-flying fruit flies (Drosophila melanogaster), we equipped a wind tunnel with a Virtual Reality (VR) display system based on standard digital hardware and a 3D path tracking system. We demonstrate the experimental power of this approach by example of a 'one-parameter open loop' testing paradigm. It provided (1) a straightforward measure of transient responses in presence of open loop visual stimulation; (2) high data throughput and standardized measurement conditions from process automation; and (3) simplified data analysis due to well-defined testing conditions. Being based on standard hardware and software techniques, our methods provide an affordable, easy to replicate and general solution for a broad range of behavioral applications in freely moving animals. Particular relevance for advanced behavioral research tools originates from the need to perform detailed behavioral analyses in genetically modified organisms and animal models for disease research.","authors":"Fry, SN., Rohrseitz, N., Straw, AD., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Neurosci Methods","volume":"171","issue":"1","page":"110-7","pdf":null,"JrId":"5306","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22439002","title":"Expression and characterization of Drosophila signal peptide peptidase-like (sppL), a gene that encodes an intramembrane protease.","abstract":"Intramembrane proteases of the Signal Peptide Peptidase (SPP) family play important roles in developmental, metabolic and signaling pathways. Although vertebrates have one SPP and four SPP-like (SPPL) genes, we found that insect genomes encode one Spp and one SppL. Characterization of the Drosophila sppL gene revealed that the predicted SppL protein is a highly conserved structural homolog of the vertebrate SPPL3 proteases, with a predicted nine-transmembrane topology, an active site containing aspartyl residues within a transmembrane region, and a carboxy-terminal PAL domain. SppL protein localized to both the Golgi and ER. Whereas spp is an essential gene that is required during early larval stages and whereas spp loss-of-function reduced the unfolded protein response (UPR), sppL loss of function had no apparent phenotype. This was unexpected given that genetic knockdown phenotypes in other organisms suggested significant roles for Spp-related proteases.","authors":"Casso, DJ., Liu, S., Biehs, B., Kornberg, TB.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"3","page":"e33827","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9342245","title":"The Kw recombinase, an integrase from Kluyveromyces waltii.","abstract":"Site-specific recombinases of the integrase family share limited amino-acid-sequence similarity, but use a common reaction mechanism to recombine distinct DNA target sites. Here we report the characterisation of the Kw site-specific recombinase, encoded on the 2 mu-like plasmid pKWS1 from the yeast Kluyveromyces waltii. Using in vitro-translated Kw recombinase, we show that the protein is able to bind and to recombine its putative DNA target site. Recombination is conservative and the Kw target site has a spacer of seven base pairs. We show that Kw recombinase is able to mediate recombination in a mammalian cell line, thus, it has potential for use as a tool for genomic manipulation in heterologous systems.","authors":"Ringrose, L., Angrand, PO., Stewart, AF.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Eur J Biochem","volume":"248","issue":"3","page":"903-12","pdf":null,"JrId":"3607","fulltextlink":null,"preprintlink":null,"articledate":"1997-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26095608","title":"RANK Signaling Amplifies WNT-Responsive Mammary Progenitors through R-SPONDIN1.","abstract":"Systemic and local signals must be integrated by mammary stem and progenitor cells to regulate their cyclic growth and turnover in the adult gland. Here, we show RANK-positive luminal progenitors exhibiting WNT pathway activation are selectively expanded in the human breast during the progesterone-high menstrual phase. To investigate underlying mechanisms, we examined mouse models and found that loss of RANK prevents the proliferation of hormone receptor-negative luminal mammary progenitors and basal cells, an accompanying loss of WNT activation, and, hence, a suppression of lobuloalveologenesis. We also show that R-spondin1 is depleted in RANK-null progenitors, and that its exogenous administration rescues key aspects of RANK deficiency by reinstating a WNT response and mammary cell expansion. Our findings point to a novel role of RANK in dictating WNT responsiveness to mediate hormone-induced changes in the growth dynamics of adult mammary cells.","authors":"Joshi, PA., Waterhouse, PD., Kannan, N., Narala, S., Fang, H., Di Grappa, MA., Jackson, HW., Penninger, JM., Eaves, C., Khokha, R.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Stem Cell Reports","volume":"5","issue":"1","page":"31-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23064464","title":"PDGFR blockade is a rational and effective therapy for NPM-ALK-driven lymphomas.","abstract":"Anaplastic large cell lymphoma (ALCL) is an aggressive non-Hodgkin's lymphoma found in children and young adults. ALCLs frequently carry a chromosomal translocation that results in expression of the oncoprotein nucleophosmin-anaplastic lymphoma kinase (NPM-ALK). The key molecular downstream events required for NPM-ALK-triggered lymphoma growth have been only partly unveiled. Here we show that the activator protein 1 family members JUN and JUNB promote lymphoma development and tumor dissemination through transcriptional regulation of platelet-derived growth factor receptor-\u03b2 (PDGFRB) in a mouse model of NPM-ALK-triggered lymphomagenesis. Therapeutic inhibition of PDGFRB markedly prolonged survival of NPM-ALK transgenic mice and increased the efficacy of an ALK-specific inhibitor in transplanted NPM-ALK tumors. Notably, inhibition of PDGFRA and PDGFRB in a patient with refractory late-stage NPM-ALK(+) ALCL resulted in rapid, complete and sustained remission. Together, our data identify PDGFRB as a previously unknown JUN and JUNB target that could be a highly effective therapy for ALCL.","authors":"Laimer, D., Dolznig, H., Kollmann, K., Vesely, PW., Schlederer, M., Merkel, O., Schiefer, AI., Hassler, MR., Heider, S., Amenitsch, L., Thallinger, C., Staber, PB., Simonitsch-Klupp, I., Artaker, M., Lagger, S., Turner, SD., Pileri, S., Piccaluga, PP., Valent, P., Messana, K., Landra, I., Weichhart, T., Knapp, S., Shehata, M., Todaro, M., Sexl, V., H\u00f6fler, G., Piva, R., Medico, E., Ruggeri, BA., Cheng, M., Eferl, R., Egger, G., Penninger, JM., Jaeger, U., Moriggl, R., Inghirami, G., Kenner, L.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nat Med","volume":"18","issue":"11","page":"1699-704","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23007704","title":"Identification of recurrence-related genes by integrating microRNA and             gene expression profiling of gastric cancer.","abstract":"We previously analyzed the microRNA (miRNA) expression pattern in gastric             cancer with and without recurrence and obtained 17 differentially expressed miRNAs             with potential to predict recurrence risk for GC patients. In the present study,             we aimed to investigate recurrence-related genes which may be regulated by the             differentially expressed miRNAs identified in our prior research. Three different             miRNA target gene databases (miRanda, TargetScan and PicTar) were used for searching             the potential genes regulated by miRNAs. A combination was performed between miRNA             target genes and recurrence-related gene expression profiling. Three bioinformatics             algorithms (PAM, SVM and RF) were used to feature recurrence-related gene selection.             In addition, we validated the expression levels of the genes in GC patients using             real-time PCR. A total of 3,263 genes were identified as potential targets of             17 miRNAs. We identified 2,736 differential expressed genes using the SAM method             based on 22K oligo microarray data which included 7 recurrence and 4 without recurrence             GC samples. Combining the target genes regulated by miRNAs and the differentially             expressed genes between recurrence and non-recurrence groups, we identified 228             differential genes for further study. Finally, we identified HNRPA0 and PRDM4             as risk biomarkers of GC patients, which were regulated by hsa-miR\u2011194 and hsa-miR-373,             respectively. Our data indicated that HNRPA0 and PRDM4 may be involved in the             recurrence process of GC and have potential to act as new prognostic biomarkers             in predicting recurrence risk for gastric cancer patients.","authors":"Yan, Z., Xiong, Y., Xu, W., Li, M., Cheng, Y., Chen, F., Ding, S., Xu, H., Zheng, G.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Int J Oncol","volume":"41","issue":"6","page":"2166-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24991958","title":"Ascending SAG neurons control sexual receptivity of Drosophila females.","abstract":"Mating induces pronounced changes in female reproductive behavior, typically including a dramatic reduction in sexual receptivity. In Drosophila, postmating behavioral changes are triggered by sex peptide (SP), a male seminal fluid peptide that acts via a\u00a0receptor (SPR) expressed in sensory neurons (SPSNs) of the female reproductive tract. Here, we identify second-order neurons that mediate the behavioral changes induced by SP. These SAG neurons receive synaptic input from SPSNs in the abdominal ganglion and project to the dorsal protocerebrum. Silencing SAG neurons renders virgin females unreceptive, whereas activating them increases the receptivity of females that have already mated. Physiological experiments demonstrate that SP downregulates the excitability of the SPSNs, and hence their input onto SAG neurons. These data thus provide a physiological correlate of mating status in the female central nervous system and a key entry point into the brain circuits that control sexual receptivity.","authors":"Feng, K., Palfreyman, MT., H\u00e4semeyer, M., Talsma, A., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Neuron","volume":"83","issue":"1","page":"135-48","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18391959","title":"BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals.","abstract":"The interpretation of genome sequences requires reliable and standardized methods to assess protein function at high throughput. Here we describe a fast and reliable pipeline to study protein function in mammalian cells based on protein tagging in bacterial artificial chromosomes (BACs). The large size of the BAC transgenes ensures the presence of most, if not all, regulatory elements and results in expression that closely matches that of the endogenous gene. We show that BAC transgenes can be rapidly and reliably generated using 96-well-format recombineering. After stable transfection of these transgenes into human tissue culture cells or mouse embryonic stem cells, the localization, protein-protein and\/or protein-DNA interactions of the tagged protein are studied using generic, tag-based assays. The same high-throughput approach will be generally applicable to other model systems.","authors":"Poser, I., Sarov, M., Hutchins, JR., H\u00e9rich\u00e9, JK., Toyoda, Y., Pozniakovsky, A., Weigl, D., Nitzsche, A., Hegemann, B., Bird, AW., Pelletier, L., Kittler, R., Hua, S., Naumann, R., Augsburg, M., Sykora, MM., Hofemeister, H., Zhang, Y., Nasmyth, K., White, KP., Dietzel, S., Mechtler, K., Durbin, R., Stewart, AF., Peters, JM., Buchholz, F., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Methods","volume":"5","issue":"5","page":"409-15","pdf":null,"JrId":"32338","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7871587","title":"Impressions of imprints.","abstract":null,"authors":"Ohlsson, R., Barlow, D., Surani, A.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Trends Genet","volume":"10","issue":"12","page":"415-7","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"1995-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26436840","title":"Determinants of amyloid fibril degradation by the PDZ protease HTRA1.","abstract":"Excessive aggregation of proteins has a major impact on cell fate and is a hallmark of amyloid diseases in humans. To resolve insoluble deposits and to maintain protein homeostasis, all cells use dedicated protein disaggregation, protein folding and protein degradation factors. Despite intense recent research, the underlying mechanisms controlling this key metabolic event are not well understood. Here, we analyzed how a single factor, the highly conserved serine protease HTRA1, degrades amyloid fibrils in an ATP-independent manner. This PDZ protease solubilizes protein fibrils and disintegrates the fibrillar core structure, allowing productive interaction of aggregated polypeptides with the active site for rapid degradation. The aggregate burden in a cellular model of cytoplasmic tau aggregation is thus reduced. Mechanistic aspects of ATP-independent proteolysis and its implications in amyloid diseases are discussed.","authors":"Poepsel, S., Sprengel, A., Sacca, B., Kaschani, F., Kaiser, M., Gatsogiannis, C., Raunser, S., Clausen, T., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Chem Biol","volume":"11","issue":"11","page":"862-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30882858","title":"Immune Profiling of Thyroid Carcinomas Suggests the Existence of Two Major Phenotypes: An ATC-Like and a PDTC-Like.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30882858<\/PMID><DateCompleted><Year>2020<\/Year><Month>05<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>05<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1945-7197<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>104<\/Volume><Issue>8<\/Issue><PubDate><Year>2019<\/Year><Month>08<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>The Journal of clinical endocrinology and metabolism<\/Title><ISOAbbreviation>J Clin Endocrinol Metab<\/ISOAbbreviation><\/Journal><ArticleTitle>Immune Profiling of Thyroid Carcinomas Suggests the Existence of Two Major Phenotypes: An ATC-Like and a PDTC-Like.<\/ArticleTitle><Pagination><MedlinePgn>3557-3575<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1210\/jc.2018-01167<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\">The understanding of the mechanisms underlying thyroid cancer immune escape can lead to the identification of new molecular targets and\/or efficacy biomarkers. For this purpose, we performed immune expression profiling in thyroid cancers to obtain a comprehensive view on immune mechanisms activated during cancer progression.","authors":"Giannini, R., Moretti, S., Ugolini, C., Macerola, E., Menicali, E., Nucci, N., Morelli, S., Colella, R., Mandarano, M., Sidoni, A., Panfili, M., Basolo, F., Puxeddu, E.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Clin Endocrinol Metab","volume":"104","issue":"8","page":"3557-3575","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22899651","title":"Converging evidence that sequence variations in the novel candidate gene MAP2K7 (MKK7) are functionally associated with schizophrenia.","abstract":"Schizophrenia is a debilitating psychiatric disease with a strong genetic contribution, potentially linked to altered glutamatergic function in brain regions such as the prefrontal cortex (PFC). Here, we report converging evidence to support a functional candidate gene for schizophrenia. In post-mortem PFC from patients with schizophrenia, we detected decreased expression of MKK7\/MAP2K7-a kinase activated by glutamatergic activity. While mice lacking one copy of the Map2k7 gene were overtly normal in a variety of behavioural tests, these mice showed a schizophrenia-like cognitive phenotype of impaired working memory. Additional support for MAP2K7 as a candidate gene came from a genetic association study. A substantial effect size (odds ratios: ~1.9) was observed for a common variant in a cohort of case and control samples collected in the Glasgow area and also in a replication cohort of samples of Northern European descent (most significant P-value: 3 \u00d7 10(-4)). While some caution is warranted until these association data are further replicated, these results are the first to implicate the candidate gene MAP2K7 in genetic risk for schizophrenia. Complete sequencing of all MAP2K7 exons did not reveal any non-synonymous mutations. However, the MAP2K7 haplotype appeared to have functional effects, in that it influenced the level of expression of MAP2K7 mRNA in human PFC. Taken together, the results imply that reduced function of the MAP2K7-c-Jun N-terminal kinase (JNK) signalling cascade may underlie some of the neurochemical changes and core symptoms in schizophrenia.","authors":"Winchester, CL., Ohzeki, H., Vouyiouklis, DA., Thompson, R., Penninger, JM., Yamagami, K., Norrie, JD., Hunter, R., Pratt, JA., Morris, BJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Hum Mol Genet","volume":"21","issue":"22","page":"4910-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18379754","title":"Marker-based introduction of three quantitative-trait loci conferring resistance to Fusarium head blight into an independent elite winter wheat breeding population.","abstract":"Fusarium head blight (FHB) is one of the most important wheat diseases that causes yield and quality losses as well as contamination with deoxynivalenol (DON). This study aimed for marker-based introduction of three previously mapped QTLs from two German winter wheat resistance sources into an elite background unrelated to the mapping population. A double cross (DC) served as initial population that combined two resistance donor-QTL alleles from \"Dream\" (Qfhs.lfl-6AL, Qfhs.lfl-7BS) and one donor-QTL allele from \"G16-92\" on chromosome 2BL with two high yielding, susceptible elite winter wheats (\"Brando\", \"LP235.1\"). The initial population of 600 DC-derived F(1) lines was selected with SSR markers for the respective QTLs. After two marker-selection steps, each of eight marker classes was represented by 9-22 lines possessing the respective donor-QTL allele or all possible combinations thereof in the homozygous state. The effect of the QTLs was estimated by field tests at four locations inoculated with Fusarium culmorum. Resistance was measured as the mean of multiple FHB ratings (0-100%). Marker classes incorporating only one QTL were not significantly more resistant than the class without any QTL, the combination of two donor-QTL alleles reduced FHB significantly. On average, lines with Qfhs.lfl-6AL were significantly taller than lines without this QTL. A considerable variation for FHB resistance was found in all marker classes. Marker-based introduction of two QTLs enhanced mean FHB rating by about 40 percentage points, the selected plants, however, were, on average, significantly taller. Both findings strongly support a phenotypic selection following after marker-based introduction of effective QTLs.","authors":"Wilde, F., Sch\u00f6n, CC., Korzun, V., Ebmeyer, E., Schmolke, M., Hartl, L., Miedaner, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Theor Appl Genet","volume":"117","issue":"1","page":"29-35","pdf":null,"JrId":"8295","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22554882","title":"Spindle orientation in mammalian cerebral cortical development.","abstract":"In any mitotic cell, the orientation of the mitotic spindle determines the orientation of the cleavage plane and therefore the position of the two daughter cells. When combined with polarization of cellular components, spindle orientation is also a well-conserved means of generating daughter cells with asymmetric cell fates, such as progenitors and differentiated cell types. In the mammalian neocortex, the precise planar spindle orientation observed early during development is vital for symmetric proliferative divisions. During later stages, spindles can be oblique or even vertical but the role of this reorientation is somewhat less clear as asymmetric cell fates can arise independently of spindle orientation during this stage. Although decades of work have identified many key conserved regulators of spindle positioning, its precise role in cell fate determination in the mammalian neocortex has been enigmatic. Recent work focused on mInsc and LGN has now revealed an important role for spindle orientation in determination of specific asymmetric cell fates, namely intermediate progenitors and a new progenitor population, termed outer radial glia. In this way, spindle orientation helps determine the neurogenic outcome of asymmetric progenitor divisions, thereby influencing neuron output and cerebral cortical expansion.","authors":"Lancaster, MA., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Curr Opin Neurobiol","volume":"22","issue":"5","page":"737-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26095367","title":"Synaptic Orb2A Bridges Memory Acquisition and Late Memory Consolidation in Drosophila.","abstract":"To adapt to an ever-changing environment, animals consolidate some, but not all, learning experiences to long-term memory. In mammals, long-term memory consolidation often involves neural pathway reactivation hours after memory acquisition. It is not known whether this delayed-reactivation schema is common across the animal kingdom or how information is stored during the delay period. Here, we show that, during courtship suppression learning, Drosophila exhibits delayed long-term memory consolidation. We also show that the same class of dopaminergic neurons engaged earlier in memory acquisition is also both necessary and sufficient for delayed long-term memory consolidation. Furthermore, we present evidence that, during learning, the translational regulator Orb2A tags specific synapses of mushroom body neurons for later consolidation. Consolidation involves the subsequent recruitment of Orb2B and the activity-dependent synthesis of CaMKII. Thus, our results provide evidence for the role of a neuromodulated, synapse-restricted molecule bridging memory acquisition and long-term memory consolidation in a learning animal.","authors":"Kr\u00fcttner, S., Traunm\u00fcller, L., Dag, U., Jandrasits, K., Stepien, B., Iyer, N., Fradkin, LG., Noordermeer, JN., Mensh, BD., Keleman, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell Rep","volume":"11","issue":"12","page":"1953-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-03-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23201143","title":"Embryonic priming of a miRNA locus predetermines postmitotic neuronal left\/right asymmetry in C. elegans.","abstract":"The mechanisms by which functional left\/right asymmetry arises in morphologically symmetric nervous systems are poorly understood. Here, we provide a mechanistic framework for how functional asymmetry in a postmitotic neuron pair is specified in C. elegans. A key feature of this mechanism is a temporally separated, two-step activation of the lsy-6 miRNA locus. The lsy-6 locus is first \"primed\" by chromatin decompaction in the precursor for the left neuron, but not the right neuron, several divisions before the neurons are born. lsy-6 expression is then \"boosted\" to functionally relevant levels several divisions later in the mother of the left neuron, through the activity of a bilaterally expressed transcription factor that can only activate lsy-6 in the primed neuron. This study shows how cells can become committed during early developmental stages to execute a specific fate much later in development and provides a conceptual framework for understanding the generation of neuronal diversity.","authors":"Cochella, L., Hobert, O.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell","volume":"151","issue":"6","page":"1229-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23159368","title":"Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression.","abstract":"Eukaryotic genomes are colonized by transposons whose uncontrolled activity causes genomic instability. The piRNA pathway silences transposons in animal gonads, yet how this is achieved molecularly remains controversial. Here, we show that the HMG protein Maelstrom is essential for Piwi-mediated silencing in Drosophila. Genome-wide assays revealed highly correlated changes in RNA polymerase II recruitment, nascent RNA output, and steady-state RNA levels of transposons upon loss of Piwi or Maelstrom. Our data demonstrate piRNA-mediated trans-silencing of hundreds of transposon copies at the transcriptional level. We show that Piwi is required to establish heterochromatic H3K9me3 marks on transposons and their genomic surroundings. In contrast, loss of Maelstrom affects transposon H3K9me3 patterns only mildly yet leads to increased heterochromatin spreading, suggesting that Maelstrom acts downstream of or in parallel to H3K9me3. Our work illustrates the widespread influence of transposons and the piRNA pathway on chromatin patterns and gene expression.","authors":"Sienski, G., D\u00f6nertas, D., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell","volume":"151","issue":"5","page":"964-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23109664","title":"Fumiyo Ikeda: ubiquitin lines up for action. Interview by Caitlin Sedwick.","abstract":null,"authors":"Ikeda, F.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Cell Biol","volume":"199","issue":"3","page":"405-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23328393","title":"Genome-wide quantitative enhancer activity maps identified by STARR-seq.","abstract":"Genomic enhancers are important regulators of gene expression, but their identification is a challenge, and methods depend on indirect measures of activity. We developed a method termed STARR-seq to directly and quantitatively assess enhancer activity for millions of candidates from arbitrary sources of DNA, which enables screens across entire genomes. When applied to the Drosophila genome, STARR-seq identifies thousands of cell type-specific enhancers across a broad continuum of strengths, links differential gene expression to differences in enhancer activity, and creates a genome-wide quantitative enhancer map. This map reveals the highly complex regulation of transcription, with several independent enhancers for both developmental regulators and ubiquitously expressed genes. STARR-seq can be used to identify and quantify enhancer activity in other eukaryotes, including humans.","authors":"Arnold, CD., Gerlach, D., Stelzer, C., Bory\u0144, \u0141M., Rath, M., Stark, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Science","volume":"339","issue":"6123","page":"1074-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23332754","title":"The myosin chaperone UNC-45 is organized in tandem modules to support myofilament formation in C. elegans.","abstract":"The UCS (UNC-45\/CRO1\/She4) chaperones play an evolutionarily conserved role in promoting myosin-dependent processes, including cytokinesis, endocytosis, RNA transport, and muscle development. To investigate the protein machinery orchestrating myosin folding and assembly, we performed a comprehensive analysis of Caenorhabditis elegans UNC-45. Our structural and biochemical data demonstrate that UNC-45 forms linear protein chains that offer multiple binding sites for cooperating chaperones and client proteins. Accordingly, Hsp70 and Hsp90, which bind to the TPR domain of UNC-45, could act in concert and with defined periodicity on captured myosin molecules. In vivo analyses reveal the elongated canyon of the UCS domain as a myosin-binding site and show that multimeric UNC-45 chains support organization of sarcomeric repeats. In fact, expression of transgenes blocking UNC-45 chain formation induces dominant-negative defects in the sarcomere structure and function of wild-type worms. Together, these findings uncover a filament assembly factor that directly couples myosin folding with myofilament formation.","authors":"Gazda, L., Pokrzywa, W., Hellerschmied, D., L\u00f6we, T., Forn\u00e9, I., Mueller-Planitz, F., Hoppe, T., Clausen, T.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell","volume":"152","issue":"1-2","page":"183-95","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24075994","title":"Circadian and circalunar clock interactions in a marine annelid.","abstract":"Life is controlled by multiple rhythms. Although the interaction of the daily (circadian) clock with environmental stimuli, such as light, is well documented, its relationship to endogenous clocks with other periods is little understood. We establish that the marine worm Platynereis dumerilii possesses endogenous circadian and circalunar (monthly) clocks and characterize their interactions. The RNAs of likely core circadian oscillator genes localize to a distinct nucleus of the worm's forebrain. The worm's forebrain also harbors a circalunar clock entrained by nocturnal light. This monthly clock regulates maturation and persists even when circadian clock oscillations are disrupted by the inhibition of casein kinase 1\u03b4\/\u03b5. Both circadian and circalunar clocks converge on the regulation of transcript levels. Furthermore, the circalunar clock changes the period and power of circadian behavior, although the period length of the daily transcriptional oscillations remains unaltered. We conclude that a second endogenous noncircadian clock can influence circadian clock function.","authors":"Zantke, J., Ishikawa-Fujiwara, T., Arboleda, E., Lohs, C., Schipany, K., Hallay, N., Straw, AD., Todo, T., Tessmar-Raible, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Rep","volume":"5","issue":"1","page":"99-113","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23246003","title":"Mutations in the \u03b2-tubulin gene TUBB5 cause microcephaly with structural brain abnormalities.","abstract":"The formation of the mammalian cortex requires the generation, migration, and differentiation of neurons. The vital role that the microtubule cytoskeleton plays in these cellular processes is reflected by the discovery that mutations in various tubulin isotypes cause different neurodevelopmental diseases, including lissencephaly (TUBA1A), polymicrogyria (TUBA1A, TUBB2B, TUBB3), and an ocular motility disorder (TUBB3). Here, we show that Tubb5 is expressed in neurogenic progenitors in the mouse and that its depletion in vivo perturbs the cell cycle of progenitors and alters the position of migrating neurons. We report the occurrence of three microcephalic patients with structural brain abnormalities harboring de novo mutations in TUBB5 (M299V, V353I, and E401K). These mutant proteins, which affect the chaperone-dependent assembly of tubulin heterodimers in different ways, disrupt neurogenic division and\/or migration in vivo. Our results provide insight into the functional repertoire of the tubulin gene family, specifically implicating TUBB5 in embryonic neurogenesis and microcephaly.","authors":"Breuss, M., Heng, JI., Poirier, K., Tian, G., Jaglin, XH., Qu, Z., Braun, A., Gstrein, T., Ngo, L., Haas, M., Bahi-Buisson, N., Moutard, ML., Passemard, S., Verloes, A., Gressens, P., Xie, Y., Robson, KJ., Rani, DS., Thangaraj, K., Clausen, T., Chelly, J., Cowan, NJ., Keays, DA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Rep","volume":"2","issue":"6","page":"1554-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25239948","title":"Cellular and molecular basis of decision-making.","abstract":"People think they are in control of their own decisions: what to eat or drink, whom to marry or pick a fight with, where to live, what to buy. Behavioural economists and neurophysiologists have long studied decision-making behaviours. However, these behaviours have only recently been studied through the light of molecular genetics. Here, we review recent research in mice, Drosophila melanogaster and Caenorhabditis elegans, that analyses the molecular and cellular mechanisms underlying decision-making. These studies interrogate decision-making about food, sexual behaviour, aggression or foraging strategies, and add molecular and cell biology understanding onto the consilience of brain and decision.","authors":"Yapici, N., Zimmer, M., Domingos, AI.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"EMBO Rep","volume":"15","issue":"10","page":"1023-35","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18349132","title":"Up-regulation of MSX2 enhances the malignant phenotype and is associated with twist 1 expression in human pancreatic cancer cells.","abstract":"MSX2 is thought to be a regulator of organ development and a downstream target of the ras signaling pathway; however, little is known about the role of MSX2 in the development of pancreatic cancers, most of which harbor a K-ras gene mutation. Therefore, we examined whether the presence of MSX2 correlates with the malignant behavior of pancreatic cancer cells. BxPC3 pancreatic cancer cells that stably overexpress MSX2 showed a flattened and scattered morphology accompanied by a change in localization of E-cadherin and beta-catenin from membrane to cytoplasm. Cell proliferation rate, cell migration, and anchorage-independent cell growth were enhanced in MSX2-expressing cells. Injection of MSX2-expressing cells into the pancreas of nude mice resulted in a significant increase in liver metastases and peritoneal disseminations compared with injection of control cells. Microarray analysis revealed a significant induction of Twist 1 expression in cells that express MSX2. When MSX2 was inactivated in pancreatic cancer cells following transfection with an MSX2-specific small interfering RNA, Twist 1 was down-regulated. Immunohistochemistry of human pancreatic carcinoma tissue revealed that MSX2 was frequently expressed in cancer cells, and that increased expression of MSX2 significantly correlated with higher tumor grade, vascular invasion, and Twist 1 expression. These data indicate that MSX2 plays a crucial role in pancreatic cancer development by inducing changes consistent with epithelial to mesenchymal transition through enhanced expression of Twist 1.","authors":"Satoh, K., Hamada, S., Kimura, K., Kanno, A., Hirota, M., Umino, J., Fujibuchi, W., Masamune, A., Tanaka, N., Miura, K., Egawa, S., Motoi, F., Unno, M., Vonderhaar, BK., Shimosegawa, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Am J Pathol","volume":"172","issue":"4","page":"926-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23222517","title":"Seventy-five genetic loci influencing the human red blood cell.","abstract":"Anaemia is a chief determinant of global ill health, contributing to cognitive impairment, growth retardation and impaired physical capacity. To understand further the genetic factors influencing red blood cells, we carried out a genome-wide association study of haemoglobin concentration and related parameters in up to 135,367 individuals. Here we identify 75 independent genetic loci associated with one or more red blood cell phenotypes at P\u2009&lt;\u200910(-8), which together explain 4-9% of the phenotypic variance per trait. Using expression quantitative trait loci and bioinformatic strategies, we identify 121 candidate genes enriched in functions relevant to red blood cell biology. The candidate genes are expressed preferentially in red blood cell precursors, and 43 have haematopoietic phenotypes in Mus musculus or Drosophila melanogaster. Through open-chromatin and coding-variant analyses we identify potential causal genetic variants at 41 loci. Our findings provide extensive new insights into genetic mechanisms and biological pathways controlling red blood cell formation and function.","authors":"van der Harst, P., Zhang, W., Mateo Leach, I., Rendon, A., Verweij, N., Sehmi, J., Paul, DS., Elling, U., Allayee, H., Li, X., Radhakrishnan, A., Tan, ST., Voss, K., Weichenberger, CX., Albers, CA., Al-Hussani, A., Asselbergs, FW., Ciullo, M., Danjou, F., Dina, C., Esko, T., Evans, DM., Franke, L., G\u00f6gele, M., Hartiala, J., Hersch, M., Holm, H., Hottenga, JJ., Kanoni, S., Kleber, ME., Lagou, V., Langenberg, C., Lopez, LM., Lyytik\u00e4inen, LP., Melander, O., Murgia, F., Nolte, IM., O'Reilly, PF., Padmanabhan, S., Parsa, A., Pirastu, N., Porcu, E., Portas, L., Prokopenko, I., Ried, JS., Shin, SY., Tang, CS., Teumer, A., Traglia, M., Ulivi, S., Westra, HJ., Yang, J., Zhao, JH., Anni, F., Abdellaoui, A., Attwood, A., Balkau, B., Bandinelli, S., Bastardot, F., Benyamin, B., Boehm, BO., Cookson, WO., Das, D., de Bakker, PI., de Boer, RA., de Geus, EJ., de Moor, MH., Dimitriou, M., Domingues, FS., D\u00f6ring, A., Engstr\u00f6m, G., Eyjolfsson, GI., Ferrucci, L., Fischer, K., Galanello, R., Garner, SF., Genser, B., Gibson, QD., Girotto, G., Gudbjartsson, DF., Harris, SE., Hartikainen, AL., Hastie, CE., Hedblad, B., Illig, T., Jolley, J., K\u00e4h\u00f6nen, M., Kema, IP., Kemp, JP., Liang, L., Lloyd-Jones, H., Loos, RJ., Meacham, S., Medland, SE., Meisinger, C., Memari, Y., Mihailov, E., Miller, K., Moffatt, MF., Nauck, M., Novatchkova, M., Nutile, T., Olafsson, I., Onundarson, PT., Parracciani, D., Penninx, BW., Perseu, L., Piga, A., Pistis, G., Pouta, A., Puc, U., Raitakari, O., Ring, SM., Robino, A., Ruggiero, D., Ruokonen, A., Saint-Pierre, A., Sala, C., Salumets, A., Sambrook, J., Schepers, H., Schmidt, CO., Sillj\u00e9, HH., Sladek, R., Smit, JH., Starr, JM., Stephens, J., Sulem, P., Tanaka, T., Thorsteinsdottir, U., Tragante, V., van Gilst, WH., van Pelt, LJ., van Veldhuisen, DJ., V\u00f6lker, U., Whitfield, JB., Willemsen, G., Winkelmann, BR., Wirnsberger, G., Algra, A., Cucca, F., d'Adamo, AP., Danesh, J., Deary, IJ., Dominiczak, AF., Elliott, P., Fortina, P., Froguel, P., Gasparini, P., Greinacher, A., Hazen, SL., Jarvelin, MR., Khaw, KT., Lehtim\u00e4ki, T., Maerz, W., Martin, NG., Metspalu, A., Mitchell, BD., Montgomery, GW., Moore, C., Navis, G., Pirastu, M., Pramstaller, PP., Ramirez-Solis, R., Schadt, E., Scott, J., Shuldiner, AR., Smith, GD., Smith, JG., Snieder, H., Sorice, R., Spector, TD., Stefansson, K., Stumvoll, M., Tang, WH., Toniolo, D., T\u00f6njes, A., Visscher, PM., Vollenweider, P., Wareham, NJ., Wolffenbuttel, BH., Boomsma, DI., Beckmann, JS., Dedoussis, GV., Deloukas, P., Ferreira, MA., Sanna, S., Uda, M., Hicks, AA., Penninger, JM., Gieger, C., Kooner, JS., Ouwehand, WH., Soranzo, N., Chambers, JC.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nature","volume":"492","issue":"7429","page":"369-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9763612","title":"The inositol polyphosphate 5-phosphatase ship is a crucial negative regulator of B cell antigen receptor signaling.","abstract":"Ship is an Src homology 2 domain containing inositol polyphosphate 5-phosphatase which has been implicated as an important signaling molecule in hematopoietic cells. In B cells, Ship becomes associated with Fcgamma receptor IIB (FcgammaRIIB), a low affinity receptor for the Fc portion of immunoglobulin (Ig)G, and is rapidly tyrosine phosphorylated upon B cell antigen receptor (BCR)-FcgammaRIIB coligation. The function of Ship in lymphocytes was investigated in Ship-\/- recombination-activating gene (Rag)-\/- chimeric mice generated from gene-targeted Ship-\/- embryonic stem cells. Ship-\/-Rag-\/- chimeras showed reduced numbers of B cells and an overall increase in basal serum Ig. Ship-\/- splenic B cells displayed prolonged Ca2+ influx, increased proliferation in vitro, and enhanced mitogen-activated protein kinase (MAPK) activation in response to BCR-FcgammaRIIB coligation. These results demonstrate that Ship plays an essential role in FcgammaRIIB-mediated inhibition of BCR signaling, and that Ship is a crucial negative regulator of Ca2+ flux and MAPK activation.","authors":"Liu, Q., Oliveira-Dos-Santos, AJ., Mariathasan, S., Bouchard, D., Jones, J., Sarao, R., Kozieradzki, I., Ohashi, PS., Penninger, JM., Dumont, DJ.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Exp Med","volume":"188","issue":"7","page":"1333-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26140366","title":"Approaching the Golden Fleece a Molecule at a Time: Biophysical Insights into Argonaute-Instructed Nucleic Acid Interactions.","abstract":"Argonaute proteins act at the core of nucleic acid-guided interference pathways that regulate gene expression and defend organisms against foreign genetic elements in all domains of life. Here, we review recent biophysical studies on how Argonaute proteins instruct oligonucleotides in the process of target finding, binding, cleavage, and release, as measured at high spatiotemporal resolution by single-molecule approaches. In the context of previous structural, biochemical, and computational studies, a model emerges for how Argonaute proteins manipulate the thermodynamic rules for nucleic acid hybridization to convey efficiency and specificity to RNA- and DNA-guided regulatory processes.","authors":"Herzog, VA., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Mol Cell","volume":"59","issue":"1","page":"4-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23319583","title":"Stimulation of bone formation in cortical bone of mice treated with a receptor activator of nuclear factor-\u03baB ligand (RANKL)-binding peptide that possesses osteoclastogenesis inhibitory activity.","abstract":"To date, parathyroid hormone is the only clinically available bone anabolic drug. The major difficulty in the development of such drugs is the lack of clarification of the mechanisms regulating osteoblast differentiation and bone formation. Here, we report a peptide (W9) known to abrogate osteoclast differentiation in vivo via blocking receptor activator of nuclear factor-\u03baB ligand (RANKL)-RANK signaling that we surprisingly found exhibits a bone anabolic effect in vivo. Subcutaneous administration of W9 three times\/day for 5 days significantly augmented bone mineral density in mouse cortical bone. Histomorphometric analysis showed a decrease in osteoclastogenesis in the distal femoral metaphysis and a significant increase in bone formation in the femoral diaphysis. Our findings suggest that W9 exerts bone anabolic activity. To clarify the mechanisms involved in this activity, we investigated the effects of W9 on osteoblast differentiation\/mineralization in MC3T3-E1 (E1) cells. W9 markedly increased alkaline phosphatase (a marker enzyme of osteoblasts) activity and mineralization as shown by alizarin red staining. Gene expression of several osteogenesis-related factors was increased in W9-treated E1 cells. Addition of W9 activated p38 MAPK and Smad1\/5\/8 in E1 cells, and W9 showed osteogenesis stimulatory activity synergistically with BMP-2 in vitro and ectopic bone formation. Knockdown of RANKL expression in E1 cells reduced the effect of W9. Furthermore, W9 showed a weak effect on RANKL-deficient osteoblasts in alkaline phosphatase assay. Taken together, our findings suggest that this peptide may be useful for the treatment of bone diseases, and W9 achieves its bone anabolic activity through RANKL on osteoblasts accompanied by production of several autocrine factors.","authors":"Furuya, Y., Inagaki, A., Khan, M., Mori, K., Penninger, JM., Nakamura, M., Udagawa, N., Aoki, K., Ohya, K., Uchida, K., Yasuda, H.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Biol Chem","volume":"288","issue":"8","page":"5562-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23152561","title":"Developmentally regulated availability of RANKL and CD40 ligand reveals distinct mechanisms of fetal and adult cross-talk in the thymus medulla.","abstract":"T cell tolerance in the thymus is a key step in shaping the developing T cell repertoire. Thymic medullary epithelial cells play multiple roles in this process, including negative selection of autoreactive thymocytes, influencing thymic dendritic cell positioning, and the generation of Foxp3(+) regulatory T cells. Previous studies show that medullary thymic epithelial cell (mTEC) development involves hemopoietic cross-talk, and numerous TNFR superfamily members have been implicated in this process. Whereas CD40 and RANK represent key examples, interplay between these receptors, and the individual cell types providing their ligands at both fetal and adult stages of thymus development, remain unclear. In this study, by analysis of the cellular sources of receptor activator for NF-\u03baB ligand (RANKL) and CD40L during fetal and adult cross-talk in the mouse, we show that the innate immune cell system drives initial fetal mTEC development via expression of RANKL, but not CD40L. In contrast, cross-talk involving the adaptive immune system involves both RANKL and CD40L, with analysis of distinct subsets of intrathymic CD4(+) T cells revealing a differential contribution of CD40L by conventional, but not Foxp3(+) regulatory, T cells. We also provide evidence for a stepwise involvement of TNFRs in mTEC development, with CD40 upregulation induced by initial RANK signaling subsequently controlling proliferation within the mTEC compartment. Collectively, our findings show how multiple hemopoietic cell types regulate mTEC development through differential provision of RANKL\/CD40L during ontogeny, revealing molecular differences in fetal and adult hemopoietic cross-talk. They also suggest a stepwise process of mTEC development, in which RANK is a master player in controlling the availability of other TNFR family members.","authors":"Desanti, GE., Cowan, JE., Baik, S., Parnell, SM., White, AJ., Penninger, JM., Lane, PJ., Jenkinson, EJ., Jenkinson, WE., Anderson, G.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Immunol","volume":"189","issue":"12","page":"5519-26","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22972982","title":"A GWAS sequence variant for platelet volume marks an alternative DNM3 promoter in megakaryocytes near a MEIS1 binding site.","abstract":"We recently identified 68 genomic loci where common sequence variants are associated with platelet count and volume. Platelets are formed in the bone marrow by megakaryocytes, which are derived from hematopoietic stem cells by a process mainly controlled by transcription factors. The homeobox transcription factor MEIS1 is uniquely transcribed in megakaryocytes and not in the other lineage-committed blood cells. By ChIP-seq, we show that 5 of the 68 loci pinpoint a MEIS1 binding event within a group of 252 MK-overexpressed genes. In one such locus in DNM3, regulating platelet volume, the MEIS1 binding site falls within a region acting as an alternative promoter that is solely used in megakaryocytes, where allelic variation dictates different levels of a shorter transcript. The importance of dynamin activity to the latter stages of thrombopoiesis was confirmed by the observation that the inhibitor Dynasore reduced murine proplatelet for-mation in vitro.","authors":"N\u00fcrnberg, ST., Rendon, A., Smethurst, PA., Paul, DS., Voss, K., Thon, JN., Lloyd-Jones, H., Sambrook, JG., Tijssen, MR., Italiano, JE., Deloukas, P., Gottgens, B., Soranzo, N., Ouwehand, WH.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Blood","volume":"120","issue":"24","page":"4859-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18342847","title":"Ca2+\/Calmodulin-dependent kinase II signaling causes skeletal overgrowth and premature chondrocyte maturation.","abstract":"The long bones of vertebrate limbs originate from cartilage templates and are formed by the process of endochondral ossification. This process requires that chondrocytes undergo a progressive maturation from proliferating to postmitotic prehypertrophic to mature, hypertrophic chondrocytes. Coordinated control of proliferation and maturation regulates growth of the skeletal elements. Various signals and pathways have been implicated in orchestrating these processes, but the underlying intracellular molecular mechanisms are often not entirely known. Here we demonstrated in the chick using replication-competent retroviruses that constitutive activation of Calcium\/Calmodulin-dependent kinase II (CaMKII) in the developing wing resulted in elongation of skeletal elements associated with premature differentiation of chondrocytes. The premature maturation of chondrocytes was a cell-autonomous effect of constitutive CaMKII signaling associated with down-regulation of cell-cycle regulators and up-regulation of chondrocyte maturation markers. In contrast, the elongation of the skeletal elements resulted from a non-cell autonomous up-regulation of the Indian hedgehog responsive gene encoding Parathyroid-hormone-related peptide. Reduction of endogenous CaMKII activity by overexpressing an inhibitory peptide resulted in shortening of the skeletal elements associated with a delay in chondrocyte maturation. Thus, CaMKII is an essential component of intracellular signaling pathways regulating chondrocyte maturation.","authors":"Taschner, MJ., Rafigh, M., Lampert, F., Schnaiter, S., Hartmann, C.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Dev Biol","volume":"317","issue":"1","page":"132-46","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30836928","title":"Pharmacological Approach of Pistacia Vera Fruit to Assess Learning and Memory Potential in Chemically-Induced Memory Impairment in Mice.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30836928<\/PMID><DateCompleted><Year>2020<\/Year><Month>01<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>01<\/Month><Day>30<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1875-6166<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>19<\/Volume><Issue>2<\/Issue><PubDate><Year>2019<\/Year><\/PubDate><\/JournalIssue><Title>Central nervous system agents in medicinal chemistry<\/Title><ISOAbbreviation>Cent Nerv Syst Agents Med Chem<\/ISOAbbreviation><\/Journal><ArticleTitle>Pharmacological Approach of Pistacia Vera Fruit to Assess Learning and Memory Potential in Chemically-Induced Memory Impairment in Mice.<\/ArticleTitle><Pagination><MedlinePgn>125-132<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.2174\/1871524919666190304122927<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">The present study was designed to investigate the potential of Pistacia vera (P. vera) fruits in experimental memory impairments in mice.","authors":"Singh, S., Kulshreshtha, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cent Nerv Syst Agents Med Chem","volume":"19","issue":"2","page":"125-132","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18342578","title":"The tumor suppressors Brat and Numb regulate transit-amplifying neuroblast lineages in Drosophila.","abstract":"In both vertebrates and insects, neurons typically arise from neural stem cells or terminally dividing intermediate progenitors. Here, we describe another mode of neurogenesis where neural stem cells generate secondary precursors that undergo multiple rounds of self-renewing transit-amplifying divisions. We identify the Posterior Asense-Negative (PAN) neuroblasts, which do not express the transcription factors Asense or Prospero. PAN neuroblasts rely on the segregating determinants Numb and Brat to generate smaller, secondary neuroblasts that in turn give rise to ganglion mother cells (GMCs) and neurons throughout larval development. In brat or numb mutants, misspecified secondary neuroblasts are unable to produce differentiated progeny and initiate tumor-like overgrowth. In prospero mutants, however, tumors arise from GMCs while secondary neuroblasts are correctly specified. Our data describe a transit-amplifying lineage in the Drosophila nervous system and suggest that different vulnerabilities in intermediate cell types can affect the outcome of tumor suppressor loss in stem cell lineages.","authors":"Bowman, SK., Rolland, V., Betschinger, J., Kinsey, KA., Emery, G., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Dev Cell","volume":"14","issue":"4","page":"535-46","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18987452","title":"[Two cases of anaplastic carcinoma of the pancreas in terms of the diversity of carcinoma cells (epithelial-mesenchymal transition; EMT)].","abstract":"The first evaluated case was a 71-year-old man with melaena. A huge tumor mass was observed in the tale of the pancreas, which we diagnosed as pancreatic carcinoma. Pathological findings confirmed that it was anaplastic pancreas carcinoma (giant cell type). The second case was a 61-year-old woman with upper abdominal pain. Irregular tumors with scattered cysts were observed in the tale of the pancreas, which rapidly increased. Autopsy findings confirmed that it was anaplastic pancreas carcinoma (pleomorphic type). Both cases showed positive for epithelial marker and mesenchymal markers and decrease in stainability by E-cadherin staining, a result which suggested diversity of tumor cells in anaplastic pancreas carcinomas.","authors":"Okamoto, M., Kitajima, S., Negishi, R., Maehata, T., Kouro, T., Yamauchi, S., Takahashi, H., Katakura, Y., Watanabe, Y., Abiko, R., Nakaya, S., Inaba, H., Takano, T., Suzuki, M., Itoh, F.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nihon Shokakibyo Gakkai Zasshi","volume":"105","issue":"11","page":"1656-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-01-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18791199","title":"Redox mechanisms switch on hypoxia-dependent epithelial-mesenchymal transition in cancer cells.","abstract":"Epithelial-mesenchymal transition (EMT) and hypoxia are considered as crucial events favouring invasion and metastasis of many cancer cells. In this study, different human neoplastic cell lines of epithelial origin were exposed to hypoxic conditions in order to investigate whether hypoxia per se may trigger EMT programme as well as to mechanistically elucidate signal transduction mechanisms involved. The following human cancer cell lines were used: HepG2 (from human hepatoblastoma), PANC-1 (from pancreatic carcinoma), HT-29 (from colon carcinoma) and MCF-7 (from breast carcinoma). Cancer cells were exposed to carefully controlled hypoxic conditions and investigated for EMT changes and signal transduction by using morphological, cell and molecular biology techniques. All cancer cells responded to hypoxia within 72 h by classic EMT changes (fibroblastoid phenotype, SNAIL and beta-catenin nuclear translocation and changes in E-cadherin) and by increased migration and invasiveness. This was involving very early inhibition of glycogen synthase kinase-3beta (GSK-3beta), early SNAIL translocation as well as later and long-lasting activation of Wnt\/beta-catenin-signalling machinery. Experimental manipulation, including silencing of hypoxia-inducible factor (HIF)-1alpha and the specific inhibition of mitochondrial generation of reactive oxygen species (ROS), revealed that early EMT-related events induced by hypoxia (GSK-3beta inhibition and SNAIL translocation) were dependent on transient intracellular increased generation of ROS whereas late migration and invasiveness were sustained by HIF-1alpha- and vascular endothelial growth factor (VEGF)-dependent mechanisms. These findings indicate that in cancer cells, early redox mechanisms can switch on hypoxia-dependent EMT programme whereas increased invasiveness is sustained by late and HIF-1alpha-dependent release of VEGF.","authors":"Cannito, S., Novo, E., Compagnone, A., Valfr\u00e8 di Bonzo, L., Busletta, C., Zamara, E., Paternostro, C., Povero, D., Bandino, A., Bozzo, F., Cravanzola, C., Bravoco, V., Colombatto, S., Parola, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Carcinogenesis","volume":"29","issue":"12","page":"2267-78","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15519672","title":"Mice with a fra-1 knock-in into the c-fos locus show impaired spatial but regular contextual learning and normal LTP.","abstract":"The immediate early gene c-fos is part of the AP-1 transcription factor complex, which is involved in molecular mechanisms underlying learning and memory. Mice that lack c-Fos in the brain show impairments in spatial reference and contextual learning, and also exhibit a reduced long-term potentiation of synaptic transmission (LTP) at CA3-to-CA1 synapses. In the present study, we investigated mice in which c-fos was deleted and replaced by fra-1 (c-fos(fra-1) mice) to determine whether other members of the c-fos gene family can substitute for the functions of the c-fos gene. In c-fos(fra-1) mice, both CA3-to-CA1 LTP and contextual learning in a Pavlovian fear conditioning task were similar to wild-type littermates, indicating that Fra-1 expression restored the impairments caused by brain-specific c-Fos depletion. However, c-Fos-mediated learning deficits in a reference memory task of the Morris watermaze were also present in c-fos(fra-1) mice. These findings suggest that different c-Fos target genes are involved in LTP, contextual learning, and spatial reference memory formation.","authors":"Gass, P., Fleischmann, A., Hvalby, O., Jensen, V., Zacher, C., Strekalova, T., Kvello, A., Wagner, EF., Sprengel, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Brain Res Mol Brain Res","volume":"130","issue":"1-2","page":"16-22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27728794","title":"Gene Regulation: Activation through Space.","abstract":"A recent study visualizes nascent RNAs in live Drosophila embryos to establish a connection between enhancer strength and the frequency of transcriptional bursts. Interestingly, one enhancer can simultaneously activate two core promoters, challenging models of enhancer-core-promoter communication via direct protein-protein contacts.","authors":"Muerdter, F., Stark, A.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Curr Biol","volume":"26","issue":"19","page":"R895-R898","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23259946","title":"ADF\/cofilin-mediated actin retrograde flow directs neurite formation in the developing brain.","abstract":"Neurites are the characteristic structural element of neurons that will initiate brain connectivity and elaborate information. Early in development, neurons are spherical cells but this symmetry is broken through the initial formation of neurites. This fundamental step is thought to rely on actin and microtubule dynamics. However, it is unclear which aspects of the complex actin behavior control neuritogenesis and which molecular mechanisms are involved. Here, we demonstrate that augmented actin retrograde flow and protrusion dynamics facilitate neurite formation. Our data indicate that a single family of actin regulatory proteins, ADF\/Cofilin, provides the required control of actin retrograde flow and dynamics to form neurites. In particular, the F-actin severing activity of ADF\/Cofilin organizes space for the protrusion and bundling of microtubules, the backbone of neurites. Our data reveal how ADF\/Cofilin organizes the cytoskeleton to drive actin retrograde flow and thus break the spherical shape of neurons.","authors":"Flynn, KC., Hellal, F., Neukirchen, D., Jacob, S., Tahirovic, S., Dupraz, S., Stern, S., Garvalov, BK., Gurniak, C., Shaw, AE., Meyn, L., Wedlich-S\u00f6ldner, R., Bamburg, JR., Small, JV., Witke, W., Bradke, F.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Neuron","volume":"76","issue":"6","page":"1091-107","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18340998","title":"[Lessons from SARS: a new potential therapy for acute respiratory distress syndrome (ARDS) with angiotensin converting enzyme 2 (ACE2)].","abstract":"During several months of 2002, severe acute respiratory syndrome (SARS) caused by SARS-coronavirus (SARS-CoV) spread rapidly from China throughout the world causing more than 800 deaths due to the development of acute respiratory distress syndrome (ARDS). Interestingly, a novel homologue of angiotensin converting-enzyme (ACE), termed angiotensin converting enzyme 2 (ACE2) has been identified as a receptor for SARS-CoV. ACE and ACE2 share homology in their catalytic domain and provide different key functions in the renin-angiotensin system. ACE cleaves angiotensin I to generate angiotensin II that is a key effector peptide of the system and exerts multiple biological functions, whereas ACE2 reduces angiotensin II levels and thus is a negative regulator of the system. Importantly, our recent studies using ACE2 knockout mice have demonstrated that ACE2 protects murine lungs from ARDS. Furthermore, SARS-CoV infections and the Spike protein of the SARS-CoV reduce ACE2 expression. Notably, injection of SARS-CoV Spike into mice worsens acute lung failure in vivo that can be attenuated by blocking the renin-angiotensin pathway, suggesting the activation of pulmonary RAS influences the pathogenesis of ARDS and SARS.","authors":"Imai, Y., Kuba, K., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Masui","volume":"57","issue":"3","page":"302-10","pdf":null,"JrId":"5355","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23800994","title":"Diversifying microRNA sequence and function.","abstract":"MicroRNAs (miRNAs) regulate the expression of most genes in animals, but we are only now beginning to understand how they are generated, assembled into functional complexes and destroyed. Various mechanisms have now been identified that regulate miRNA stability and that diversify miRNA sequences to create distinct isoforms. The production of different isoforms of individual miRNAs in specific cells and tissues may have broader implications for miRNA-mediated gene expression control. Rigorously testing the many discrepant models for how miRNAs function using quantitative biochemical measurements made in vivo and in vitro remains a major challenge for the future.","authors":"Ameres, SL., Zamore, PD.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Rev Mol Cell Biol","volume":"14","issue":"8","page":"475-88","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18327265","title":"High-resolution, high-throughput SNP mapping in Drosophila melanogaster.","abstract":"Single nucleotide polymorphisms (SNPs) are useful markers for genetic mapping experiments in model organisms. Here we report the establishment of a high-density SNP map and high-throughput genotyping assays for Drosophila melanogaster. Our map comprises 27,367 SNPs in common laboratory Drosophila stocks. These SNPs were clustered within 2,238 amplifiable markers at an average density of 1 marker every 50.3 kb, or 6.3 genes. We have also constructed a set of 62 Drosophila stocks, each of which facilitates the generation of recombinants within a defined genetic interval of 1-2 Mb. For flexible, high-throughput SNP genotyping, we used fluorescent tag-array mini-sequencing (TAMS) assays. We designed and validated TAMS assays for 293 SNPs at an average resolution of 391.3 kb, and demonstrated the utility of these tools by rapidly mapping 14 mutations that disrupt embryonic muscle patterning. These resources enable high-resolution high-throughput genetic mapping in Drosophila.","authors":"Chen, D., Ahlford, A., Schnorrer, F., Kalchhauser, I., Fellner, M., Vir\u00e0gh, E., Kiss, I., Syv\u00e4nen, AC., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Methods","volume":"5","issue":"4","page":"323-9","pdf":null,"JrId":"32338","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23913922","title":"Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex.","abstract":"The PIWI-interacting RNA (piRNA) pathway is a small RNA silencing system that keeps selfish genetic elements such as transposons under control in animal gonads. Several lines of evidence indicate that nuclear PIWI family proteins guide transcriptional silencing of their targets, yet the composition of the underlying silencing complex is unknown. Here we demonstrate that the double CHHC zinc finger protein gametocyte-specific factor 1 (Gtsf1) is an essential factor for Piwi-mediated transcriptional repression in Drosophila. Cells lacking Gtsf1 contain nuclear Piwi loaded with piRNAs, yet Piwi's silencing capacity is ablated. Gtsf1 interacts directly with a small subpool of nuclear Piwi, and loss of Gtsf1 phenocopies loss of Piwi in terms of deregulation of transposons, loss of H3K9 trimethylation (H3K9me3) marks at euchromatic transposon insertions, and deregulation of genes in proximity to repressed transposons. We propose that only a small fraction of nuclear Piwi is actively engaged in target silencing and that Gtsf1 is an essential component of the underlying Piwi-centered silencing complex.","authors":"D\u00f6nertas, D., Sienski, G., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Genes Dev","volume":"27","issue":"15","page":"1693-705","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23960144","title":"Aurora B and Kif2A control microtubule length for assembly of a functional central spindle during anaphase.","abstract":"The central spindle is built during anaphase by coupling antiparallel microtubules (MTs) at a central overlap zone, which provides a signaling scaffold for the regulation of cytokinesis. The mechanisms underlying central spindle morphogenesis are still poorly understood. In this paper, we show that the MT depolymerase Kif2A controls the length and alignment of central spindle MTs through depolymerization at their minus ends. The distribution of Kif2A was limited to the distal ends of the central spindle through Aurora B-dependent phosphorylation and exclusion from the spindle midzone. Overactivation or inhibition of Kif2A affected interchromosomal MT length and disorganized the central spindle, resulting in uncoordinated cell division. Experimental data and model simulations suggest that the steady-state length of the central spindle and its symmetric position between segregating chromosomes are predominantly determined by the Aurora B activity gradient. On the basis of these results, we propose a robust self-organization mechanism for central spindle formation.","authors":"Uehara, R., Tsukada, Y., Kamasaki, T., Poser, I., Yoda, K., Gerlich, DW., Goshima, G.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Cell Biol","volume":"202","issue":"4","page":"623-36","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23770361","title":"Loading and pre-loading processes generate a distinct siRNA population in Tetrahymena.","abstract":"The various properties of small RNAs, such as length, terminal nucleotide, thermodynamic asymmetry and duplex mismatches, can impact their sorting into different Argonaute proteins in diverse eukaryotes. The developmentally regulated 26- to 32-nt siRNAs (scnRNAs) are loaded to the Argonaute protein Twi1p and display a strong bias for uracil at the 5' end. In this study, we used deep sequencing to analyze loaded and unloaded populations of scnRNAs. We show that the size of the scnRNA is determined during a pre-loading process, whereas their 5' uracil bias is attributed to both pre-loading and loading processes. We also demonstrate that scnRNAs have a strong bias for adenine at the third base from the 3' terminus, suggesting that most scnRNAs are direct Dicer products. Furthermore, we show that the thermodynamic asymmetry of the scnRNA duplex does not affect the guide and passenger strand decision. Finally, we show that scnRNAs frequently have templated uracil at the last base without a strong bias for adenine at the second base indicating non-sequential production of scnRNAs from substrates. These findings provide a biochemical basis for the varying attributes of scnRNAs, which should help improve our understanding of the production and turnover of scnRNAs in vivo.","authors":"Mochizuki, K., Kurth, HM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Biochem Biophys Res Commun","volume":"436","issue":"3","page":"497-502","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23727888","title":"The nuclear F-actin interactome of Xenopus oocytes reveals an actin-bundling kinesin that is essential for meiotic cytokinesis.","abstract":"Nuclei of Xenopus laevis oocytes grow 100\u2009000-fold larger in volume than a typical somatic nucleus and require an unusual intranuclear F-actin scaffold for mechanical stability. We now developed a method for mapping F-actin interactomes and identified a comprehensive set of F-actin binders from the oocyte nuclei. Unexpectedly, the most prominent interactor was a novel kinesin termed NabKin (Nuclear and meiotic actin-bundling Kinesin). NabKin not only binds microtubules but also F-actin structures, such as the intranuclear actin bundles in prophase and the contractile actomyosin ring during cytokinesis. The interaction between NabKin and F-actin is negatively regulated by Importin-\u03b2 and is responsive to spatial information provided by RanGTP. Disconnecting NabKin from F-actin during meiosis caused cytokinesis failure and egg polyploidy. We also found actin-bundling activity in Nabkin's somatic paralogue KIF14, which was previously shown to be essential for somatic cell division. Our data are consistent with the notion that NabKin\/KIF14 directly link microtubules with F-actin and that such link is essential for cytokinesis.","authors":"Samwer, M., Dehne, HJ., Spira, F., Kollmar, M., Gerlich, DW., Urlaub, H., G\u00f6rlich, D.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"EMBO J","volume":"32","issue":"13","page":"1886-902","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23935529","title":"Transposon domestication versus mutualism in ciliate genome rearrangements.","abstract":"Ciliated protists rearrange their genomes dramatically during nuclear development via chromosome fragmentation and DNA deletion to produce a trimmer and highly reorganized somatic genome. The deleted portion of the genome includes potentially active transposons or transposon-like sequences that reside in the germline. Three independent studies recently showed that transposase proteins of the DDE\/DDD superfamily are indispensible for DNA processing in three distantly related ciliates. In the spirotrich Oxytricha trifallax, high copy-number germline-limited transposons mediate their own excision from the somatic genome but also contribute to programmed genome rearrangement through a remarkable transposon mutualism with the host. By contrast, the genomes of two oligohymenophorean ciliates, Tetrahymena thermophila and Paramecium tetraurelia, encode homologous PiggyBac-like transposases as single-copy genes in both their germline and somatic genomes. These domesticated transposases are essential for deletion of thousands of different internal sequences in these species. This review contrasts the events underlying somatic genome reduction in three different ciliates and considers their evolutionary origins and the relationships among their distinct mechanisms for genome remodeling.","authors":"Vogt, A., Goldman, AD., Mochizuki, K., Landweber, LF.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"PLoS Genet","volume":"9","issue":"8","page":"e1003659","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30429597","title":"Application and optimization of CRISPR-Cas9-mediated genome engineering in axolotl (Ambystoma mexicanum).","abstract":"Genomic manipulation is essential to the use of model organisms to understand development, regeneration and adult physiology. The axolotl (Ambystoma mexicanum), a type of salamander, exhibits an unparalleled regenerative capability in a spectrum of complex tissues and organs, and therefore serves as a powerful animal model for dissecting mechanisms of regeneration. We describe here an optimized stepwise protocol to create genetically modified axolotls using the CRISPR-Cas9 system. The protocol, which takes 7-8 weeks to complete, describes generation of targeted gene knockouts and knock-ins and includes site-specific integration of large targeting constructs. The direct use of purified CAS9-NLS (CAS9 containing a C-terminal nuclear localization signal) protein allows the prompt formation of guide RNA (gRNA)-CAS9-NLS ribonucleoprotein (RNP) complexes, which accelerates the creation of double-strand breaks (DSBs) at targeted genomic loci in single-cell-stage axolotl eggs. With this protocol, a substantial number of F<sub>0<\/sub> individuals harboring a homozygous-type frameshift mutation can be obtained, allowing phenotype analysis in this generation. In the presence of targeting constructs, insertions of exogenous genes into targeted axolotl genomic loci can be achieved at efficiencies of up to 15% in a non-homologous end joining (NHEJ) manner. Our protocol bypasses the long generation time of axolotls and allows direct functional analysis in F<sub>0<\/sub> genetically manipulated axolotls. This protocol can be potentially applied to other animal models, especially to organisms with a well-characterized transcriptome but lacking a well-characterized genome.","authors":"Fei, JF., Lou, WP., Knapp, D., Murawala, P., Gerber, T., Taniguchi, Y., Nowoshilow, S., Khattak, S., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Protoc","volume":"13","issue":"12","page":"2908-2943","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18321860","title":"The functional role of the second NPXY motif of the LRP1 beta-chain in tissue-type plasminogen activator-mediated activation of N-methyl-D-aspartate receptors.","abstract":"The low density lipoprotein receptor-related protein 1 (LRP1) emerges to play fundamental roles in cellular signaling pathways in the brain. One of its prominent ligands is the serine proteinase tissue-type plasminogen activator (tPA), which has been shown to act as a key activator of neuronal mitogen-activated protein kinase pathways via the N-methyl-D-aspartate (NMDA) receptor. However, here we set out to examine whether LRP1 and the NMDA receptor might eventually act in a combined fashion to mediate tPA downstream signaling. By blocking tPA from binding to LRP1 using the receptor-associated protein, we were able to completely inhibit NMDA receptor activation. Additionally, inhibition of NMDA receptor calcium influx with MK-801 resulted in dramatic reduction of tPA-mediated downstream signaling. This indicates a functional interaction between the two receptors, since both experimental approaches resulted in strongly reduced calcium influx and Erk1\/2 phosphorylation. Additionally, we were able to inhibit Erk1\/2 activation by competing for the LRP1 C-terminal binding motif with a truncated PSD95 construct resembling its PDZ III domain. Furthermore, we identified the distal NPXY amino acid motif in the C terminus of LRP1 as the crucial element for LRP1-NMDA receptor interaction via the adaptor protein PSD95. These results provide new insights into the mechanism of a tPA-induced, LRP1-mediated gating mechanism for NMDA receptors.","authors":"Martin, AM., Kuhlmann, C., Trossbach, S., Jaeger, S., Waldron, E., Roebroek, A., Luhmann, HJ., Laatsch, A., Weggen, S., Lessmann, V., Pietrzik, CU.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Biol Chem","volume":"283","issue":"18","page":"12004-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24317488","title":"Structure of a pathogenic type 3 secretion system in action.","abstract":"Type 3 secretion systems use 3.5-megadalton syringe-like, membrane-embedded 'injectisomes', each containing an ~800-\u00c5-long needle complex to connect intracellular compartments of infectious bacteria and hosts. Here we identify requirements for substrate association with, transport through and exit from the injectisome of Salmonella enterica serovar Typhimurium. This guided the design of substrates that become trapped within the secretion path and enabled visualization of injectisomes in action in situ. We used cryo-EM to define the secretion path, providing a structural explanation as to why effector proteins must be unfolded during transport. Furthermore, trapping of a heterologous substrate in the needle prevents secretion of natural bacterial effectors. Together, the data reveal the path of protein secretion across multiple membranes and show that mechanisms rejecting unacceptable substrates can be undermined, and transport of bacterial effectors across an already assembled type 3 secretion system can be inhibited.","authors":"Radics, J., K\u00f6nigsmaier, L., Marlovits, TC.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Struct Mol Biol","volume":"21","issue":"1","page":"82-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18309290","title":"Arp2\/3 complex interactions and actin network turnover in lamellipodia.","abstract":"Cell migration is initiated by lamellipodia-membrane-enclosed sheets of cytoplasm containing densely packed actin filament networks. Although the molecular details of network turnover remain obscure, recent work points towards key roles in filament nucleation for Arp2\/3 complex and its activator WAVE complex. Here, we combine fluorescence recovery after photobleaching (FRAP) of different lamellipodial components with a new method of data analysis to shed light on the dynamics of actin assembly\/disassembly. We show that Arp2\/3 complex is incorporated into the network exclusively at the lamellipodium tip, like actin, at sites coincident with WAVE complex accumulation. Capping protein likewise showed a turnover similar to actin and Arp2\/3 complex, but was confined to the tip. In contrast, cortactin-another prominent Arp2\/3 complex regulator-and ADF\/cofilin-previously implicated in driving both filament nucleation and disassembly-were rapidly exchanged throughout the lamellipodium. These results suggest that Arp2\/3- and WAVE complex-driven actin filament nucleation at the lamellipodium tip is uncoupled from the activities of both cortactin and cofilin. Network turnover is additionally regulated by the spatially segregated activities of capping protein at the tip and cofilin throughout the mesh.","authors":"Lai, FP., Szczodrak, M., Block, J., Faix, J., Breitsprecher, D., Mannherz, HG., Stradal, TE., Dunn, GA., Small, JV., Rottner, K.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO J","volume":"27","issue":"7","page":"982-92","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18316477","title":"Epigenetic regulation of gene expression by Drosophila Myb and E2F2-RBF via the Myb-MuvB\/dREAM complex.","abstract":"The Drosophila Myb oncoprotein, the E2F2 transcriptional repressor, and the RBF and Mip130\/LIN-9 tumor suppressor proteins reside in a conserved Myb-MuvB (MMB)\/dREAM complex. We now show that Myb is required in vivo for the expression of Polo kinase and components of the spindle assembly checkpoint (SAC). Surprisingly, the highly conserved DNA-binding domain was not essential for assembly of Myb into MMB\/dREAM, for transcriptional regulation in vivo, or for rescue of Myb-null mutants to adult viability. E2F2, RBF, and Mip130\/LIN-9 acted in opposition to Myb by repressing the expression of Polo and SAC genes in vivo. Remarkably, the absence of both Myb and Mip130, or of both Myb and E2F2, caused variegated expression in which high or low levels of Polo were stably inherited through successive cell divisions in imaginal wing discs. Restoration of Myb resulted in a uniformly high level of Polo expression similar to that seen in wild-type tissue, whereas restoration of Mip130 or E2F2 extinguished Polo expression. Our results demonstrate epigenetic regulation of gene expression by Myb, Mip130\/LIN-9, and E2F2-RBF in vivo, and also provide an explanation for the ability of Mip130-null mutants to rescue the lethality of Myb-null mutants in vivo.","authors":"Wen, H., Andrejka, L., Ashton, J., Karess, R., Lipsick, JS.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genes Dev","volume":"22","issue":"5","page":"601-14","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23962453","title":"ACE2 - from the renin-angiotensin system to gut microbiota and malnutrition.","abstract":"The renin-angiotensin system (RAS) is a complex network that regulates blood pressure, electrolyte and fluid homeostasis, as well as the function of several organs. Angiotensin-converting enzyme 2 (ACE2) was identified as an enzyme that negatively regulates the RAS by converting Ang II, the main bioactive molecule of the RAS, to Ang 1-7. Thus, ACE2 counteracts the role of angiotensin-converting enzyme (ACE) which generates Ang II from Ang I. ACE and ACE2 have been implicated in several pathologies such as cardiovascular and renal disease or acute lung injury. In addition, ACE2 has functions independent of the RAS: ACE2 is the receptor for the SARS coronavirus and ACE2 is essential for expression of neutral amino acid transporters in the gut. In this context, ACE2 modulates innate immunity and influences the composition of the gut microbiota, which can explain diarrhea and intestinal inflammation observed in Hartnup disorder, Pellagra, or under conditions of severe malnutrition. Here we review and discuss the diverse functions of ACE2 and its relevance to human pathologies.","authors":"Perlot, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Microbes Infect","volume":"15","issue":"13","page":"866-73","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18278037","title":"Differentially oriented populations of actin filaments generated in lamellipodia collaborate in pushing and pausing at the cell front.","abstract":"Eukaryotic cells advance in phases of protrusion, pause and withdrawal. Protrusion occurs in lamellipodia, which are composed of diagonal networks of actin filaments, and withdrawal terminates with the formation of actin bundles parallel to the cell edge. Using correlated live-cell imaging and electron microscopy, we have shown that actin filaments in protruding lamellipodia subtend angles from 15-90 degrees to the front, and that transitions from protrusion to pause are associated with a proportional increase in filaments oriented more parallel to the cell edge. Microspike bundles of actin filaments also showed a wide angular distribution and correspondingly variable bilateral polymerization rates along the cell front. We propose that the angular shift of filaments in lamellipodia serves in adapting to slower protrusion rates while maintaining the filament densities required for structural support; further, we suggest that single filaments and microspike bundles contribute to the construction of the lamella behind and to the formation of the cell edge when protrusion ceases. Our findings provide an explanation for the variable turnover dynamics of actin filaments in lamellipodia observed by fluorescence speckle microscopy and are inconsistent with a current model of lamellipodia structure that features actin filaments branching at 70 degrees in a dendritic array.","authors":"Koestler, SA., Auinger, S., Vinzenz, M., Rottner, K., Small, JV.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Cell Biol","volume":"10","issue":"3","page":"306-13","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24675893","title":"MKK7 and ARF: new players in the DNA damage response scenery.","abstract":"Sensing, integrating, and processing of stressogenic signals must be followed by accurate differential response(s) for a cell to survive and avoid malignant transformation. The DNA damage response (DDR) pathway is vital in this process, as it deals with genotoxic\/oncogenic insults, having p53 as a nodal effector that performs most of the above tasks. Accumulating data reveal that other pathways are also involved in the same or similar processes, conveying also to p53. Emerging questions are if, how, and when these additional pathways communicate with the DDR axis. Two such stress response pathways, involving the MKK7 stress-activated protein kinase (SAPK) and ARF, have been shown to be interlocked with the ATM\/ATR-regulated DDR axis in a highly ordered manner. This creates a new landscape in the DDR orchestrated response to genotoxic\/oncogenic insults that is currently discussed.","authors":"Kotsinas, A., Papanagnou, P., Galanos, P., Schramek, D., Townsend, P., Penninger, JM., Bartek, J., Gorgoulis, VG.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell Cycle","volume":"13","issue":"8","page":"1227-36","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23885122","title":"Arp2\/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin.","abstract":"Lamellipodia are sheet-like protrusions formed during migration or phagocytosis and comprise a network of actin filaments. Filament formation in this network is initiated by nucleation\/branching through the actin-related protein 2\/3 (Arp2\/3) complex downstream of its activator, suppressor of cAMP receptor\/WASP-family verprolin homologous (Scar\/WAVE), but the relative relevance of Arp2\/3-mediated branching versus actin filament elongation is unknown. Here we use instantaneous interference with Arp2\/3 complex function in live fibroblasts with established lamellipodia. This allows direct examination of both the fate of elongating filaments upon instantaneous suppression of Arp2\/3 complex activity and the consequences of this treatment on the dynamics of other lamellipodial regulators. We show that Arp2\/3 complex is an essential organizer of treadmilling actin filament arrays but has little effect on the net rate of actin filament turnover at the cell periphery. In addition, Arp2\/3 complex serves as key upstream factor for the recruitment of modulators of lamellipodia formation such as capping protein or cofilin. Arp2\/3 complex is thus decisive for filament organization and geometry within the network not only by generating branches and novel filament ends, but also by directing capping or severing activities to the lamellipodium. Arp2\/3 complex is also crucial to lamellipodia-based migration of keratocytes.","authors":"Koestler, SA., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom, JM., Krupp, J., Jacob, S., Vinzenz, M., Schur, F., Schl\u00fcter, K., Gunning, PW., Winkler, C., Schmeiser, C., Faix, J., Stradal, TE., Small, JV., Rottner, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Mol Biol Cell","volume":"24","issue":"18","page":"2861-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23682739","title":"The paradox of overnutrition in aging and cognition.","abstract":"Populations of many countries are becoming increasingly overweight and obese, driven largely by excessive calorie intake and reduced physical activity; greater body mass is accompanied by epidemic levels of comorbid metabolic diseases. At the same time, individuals are living longer. The combination of aging and the increased prevalence of metabolic disease is associated with increases in aging-related comorbid diseases such as Alzheimer's disease, cerebrovascular dementia, and sarcopenia. Here, correlative and causal links between diseases of overnutrition and diseases of aging and cognition are explored.","authors":"Fielding, RA., Gunstad, J., Gustafson, DR., Heymsfield, SB., Kral, JG., Launer, LJ., Penninger, J., Phillips, DI., Scarmeas, N.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Ann N Y Acad Sci","volume":"1287","issue":null,"page":"31-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23570689","title":"Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci.","abstract":"Nearly three-quarters of the 143 genetic signals associated with platelet and erythrocyte phenotypes identified by meta-analyses of genome-wide association (GWA) studies are located at non-protein-coding regions. Here, we assessed the role of candidate regulatory variants associated with cell type-restricted, closely related hematological quantitative traits in biologically relevant hematopoietic cell types. We used formaldehyde-assisted isolation of regulatory elements followed by next-generation sequencing (FAIRE-seq) to map regions of open chromatin in three primary human blood cells of the myeloid lineage. In the precursors of platelets and erythrocytes, as well as in monocytes, we found that open chromatin signatures reflect the corresponding hematopoietic lineages of the studied cell types and associate with the cell type-specific gene expression patterns. Dependent on their signal strength, open chromatin regions showed correlation with promoter and enhancer histone marks, distance to the transcription start site, and ontology classes of nearby genes. Cell type-restricted regions of open chromatin were enriched in sequence variants associated with hematological indices. The majority (63.6%) of such candidate functional variants at platelet quantitative trait loci (QTLs) coincided with binding sites of five transcription factors key in regulating megakaryopoiesis. We experimentally tested 13 candidate regulatory variants at 10 platelet QTLs and found that 10 (76.9%) affected protein binding, suggesting that this is a frequent mechanism by which regulatory variants influence quantitative trait levels. Our findings demonstrate that combining large-scale GWA data with open chromatin profiles of relevant cell types can be a powerful means of dissecting the genetic architecture of closely related quantitative traits.","authors":"Paul, DS., Albers, CA., Rendon, A., Voss, K., Stephens, J., van der Harst, P., Chambers, JC., Soranzo, N., Ouwehand, WH., Deloukas, P.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Genome Res","volume":"23","issue":"7","page":"1130-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18241894","title":"Evidence that genetic variation in 5-HT transporter expression is linked to changes in 5-HT2A receptor function.","abstract":"Variability in expression of the 5-HT transporter (5-HTT) gene in the human population has been associated with a range of behavioural phenotypes. The underlying mechanisms are unclear but may involve changes in 5-HT receptor levels and\/or signalling. The present study used a novel 5-HTT overexpressing transgenic mouse to test the hypothesis that variability in 5-HTT expression may alter 5-HT(2A) receptor function. In wildtype mice, the 5-HT(2) receptor agonist DOI increased regional brain mRNA expression of two immediate early genes (c-fos and Arc), and induced head twitches, and both effects were abolished by pre-treatment with the 5-HT(2A) receptor antagonist MDL 100907. In 5-HTT overexpressing mice, DOI induced a greater increase in both c-fos and Arc mRNA expression in cortical brain regions, and more head twitches, compared to wildtype mice. Autoradiographic and in situ hybridisation experiments showed that 5-HT(2A) receptor binding sites and 5-HT(2A) receptor mRNA did not differ between transgenic and wildtype mice. Finally, the transgenic mice had lower regional brain 5-HT levels compared to wildtype mice. This depletion of 5-HT may underpin the increase in 5-HT(2A) receptor function because in wildtype mice 5-HT depletion using the 5-HT synthesis inhibitor, p-chlorophenylalanine, enhanced the head twitch response to DOI. These data demonstrate that elevated 5-HTT expression is accompanied by increased 5-HT(2A) receptor function, an effect possibly mediated by decreased availability of synaptic 5-HT. Variation in levels of 5-HTT expression may therefore be a source of variability in 5-HT(2A) receptor function, which may be an important modifier of 5-HTT-linked phenotypes.","authors":"Jennings, KA., Sheward, WJ., Harmar, AJ., Sharp, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Neuropharmacology","volume":"54","issue":"5","page":"776-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33130103","title":"The Role of Angiotensin Converting Enzyme 2 in Modulating Gut Microbiota, Intestinal Inflammation, and Coronavirus Infection.","abstract":"The role of angiotensin converting enzyme 2 has expanded from regulating the renin angiotensin system to regulating intestinal amino acid homeostasis and the gut microbiome. Recently, angiotensin converting enzyme 2 was identified as a primary receptor for severe acute respiratory syndrome coronaviruses 1 and 2 being expressed in multiple tissues including the luminal surface of the gut. In this brief perspective, we examine the role of angiotensin converting enzyme 2 as the receptor for severe acute respiratory syndrome coronavirus 2 and the impact of coronavirus disease 19 infection on the gut microbiome and on the gut epithelium.","authors":"Penninger, JM., Grant, MB., Sung, JJY.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Gastroenterology","volume":"160","issue":"1","page":"39-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24662567","title":"SUN proteins facilitate the removal of membranes from chromatin during nuclear envelope breakdown.","abstract":"SUN proteins reside in the inner nuclear membrane and form complexes with KASH proteins of the outer nuclear membrane that connect the nuclear envelope (NE) to the cytoskeleton. These complexes have well-established functions in nuclear anchorage and migration in interphase, but little is known about their involvement in mitotic processes. Our analysis demonstrates that simultaneous depletion of human SUN1 and SUN2 delayed removal of membranes from chromatin during NE breakdown (NEBD) and impaired the formation of prophase NE invaginations (PNEIs), similar to microtubule depolymerization or down-regulation of the dynein cofactors NudE\/EL. In addition, overexpression of dominant-negative SUN and KASH constructs reduced the occurrence of PNEI, indicating a requirement for functional SUN-KASH complexes in NE remodeling. Codepletion of SUN1\/2 slowed cell proliferation and resulted in an accumulation of morphologically defective and disoriented mitotic spindles. Quantification of mitotic timing revealed a delay between NEBD and chromatin separation, indicating a role of SUN proteins in bipolar spindle assembly and mitotic progression.","authors":"Turgay, Y., Champion, L., Balazs, C., Held, M., Toso, A., Gerlich, DW., Meraldi, P., Kutay, U.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Cell Biol","volume":"204","issue":"7","page":"1099-109","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24277837","title":"Spectrally coded optical nanosectioning (SpecON) with biocompatible metal-dielectric-coated substrates.","abstract":"Fluorescence nanosectioning within a submicron region above an interface is desirable for many disciplines in the life sciences. A drawback, however, to most current approaches is the a priori need to physically scan a sculptured point spread function in the axial dimension, which can be undesirable for optically sensitive or highly dynamic samples. Here we demonstrate a fluorescence imaging approach that can overcome the need for scanning by exploiting the position-dependent emission spectrum of fluorophores above a simple biocompatible nanostructure. To achieve this we have designed a thin metal-dielectric-coated substrate, where the spectral modification to the total measured fluorescence can be used to estimate the axial fluorophore distribution within distances of 10-150 nm above the substrate with an accuracy of up to 5-10 nm. The modeling and feasibility of the approach are verified and successfully applied to elucidate nanoscale adhesion protein and filopodia dynamics in migrating cells. It is likely that the general principle can find broader applications in, for example, single-molecule studies, biosensing, and studying fast dynamic processes.","authors":"Elsayad, K., Urich, A., Tan, PS., Nemethova, M., Small, JV., Unterrainer, K., Heinze, KG.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proc Natl Acad Sci U S A","volume":"110","issue":"50","page":"20069-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30311561","title":"A New Linkage between the Tumor Suppressor RKIP and Autophagy: Targeted Therapeutics.","abstract":"The complexities of molecular signaling in cancer cells have been hypothesized to mediate cross-network alterations of oncogenic processes such as uncontrolled cell growth, proliferation, acquisition of epithelial-to-mesenchymal transition (EMT) markers, and resistance to cytotoxic therapies. The two biochemically exclusive processes\/proteins examined in the present review are the metastasis suppressor Raf-1 kinase inhibitory protein (RKIP) and the cell-intrinsic system of macroautophagy (hereafter referred to as autophagy). RKIP is poorly expressed in human cancer tissues, and low expression levels are correlated with high incidence of tumor growth, metastasis, poor treatment efficacy, and poor prognoses in cancer patients. By comparison, autophagy is a conserved cytoprotective degradation pathway that has been shown to influence the acquisition of resistance to hypoxia and nutrient depletion as well as the regulation of chemo-immuno-resistance and apoptotic evasion. Evidently, a broad library of cancer-relevant studies exists for RKIP and autophagy, although reports of the interactions between pathways involving RKIP and autophagy have been relatively sparse. To circumvent this limitation, the coordinate regulatory and effector mechanisms were examined for both RKIP and autophagy. Here, we propose three putative pathways that demonstrate the inherent pleiotropism and relevance of RKIP and the microtubule-associated protein 1 light chain 3 (MAP1LC3, LC3) on cell growth, proliferation, senescence, and EMT, among the hallmarks of cancer. Our findings suggest that signaling modules involving p53, signal transducer and activator of transcription 3 (STAT3), nuclear factor-\u03baB (NF-\u03baB), and Snail highlight the novel roles for RKIP in the control of autophagy and vice versa. The suggested potential crosstalk mechanisms are new areas of research in which to further study RKIP and autophagy in cancer models. These should lead to novel prognostic motifs and will provide alternative therapeutic strategies for the treatment of unresponsive aggressive cancer types.","authors":"Wang, Y., Bonavida, B.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Crit Rev Oncog","volume":"23","issue":"5-6","page":"281-305","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24512713","title":"Mathematical modeling of regenerative processes.","abstract":"In many animals, regenerative processes can replace lost body parts. Organ and tissue regeneration consequently also hold great medical promise. The regulation of regenerative processes is achieved through concerted actions of multiple organizational levels of the organism, from diffusing molecules and cellular gene expression patterns up to tissue mechanics. Our intuition is usually not adapted well to this degree of complexity and the quantitative aspects of the regulation of regenerative processes remain poorly understood. One way out of this dilemma lies in the combination of experimentation and mathematical modeling within an iterative process of model development\/refinement, model predictions for novel experimental conditions, quantitative experiments testing these predictions, and subsequent model refinement. This interdisciplinary approach has already provided key insights into smaller scale processes during embryonic development and a so-far limited number of more complex regeneration processes. This review discusses selected theoretical and interdisciplinary studies and is structured along the three phases of regeneration: (1) initiation of a regeneration response, (2) tissue patterning during regenerate growth, (3) arresting the regeneration response. Moreover, we highlight the opportunities provided by extensions of mathematical models from developmental processes toward the study of related regenerative processes.","authors":"Chara, O., Tanaka, EM., Brusch, L.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Top Dev Biol","volume":"108","issue":null,"page":"283-317","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18239685","title":"Inflammatory cardiac valvulitis in TAX1BP1-deficient mice through selective NF-kappaB activation.","abstract":"Nuclear factor kappa B (NF-kappaB) is a key mediator of inflammation. Unchecked NF-kappaB signalling can engender autoimmune pathologies and cancers. Here, we show that Tax1-binding protein 1 (TAX1BP1) is a negative regulator of TNF-alpha- and IL-1beta-induced NF-kappaB activation and that binding to mono- and polyubiquitin by a ubiquitin-binding Zn finger domain in TAX1BP1 is needed for TRAF6 association and NF-kappaB inhibition. Mice genetically knocked out for TAX1BP1 are born normal, but develop age-dependent inflammatory cardiac valvulitis, die prematurely, and are hypersensitive to low doses of TNF-alpha and IL-1beta. TAX1BP1-\/- cells are more highly activated for NF-kappaB than control cells when stimulated with TNF-alpha or IL-1beta. Mechanistically, TAX1BP1 acts in NF-kappaB signalling as an essential adaptor between A20 and its targets.","authors":"Iha, H., Peloponese, JM., Verstrepen, L., Zapart, G., Ikeda, F., Smith, CD., Starost, MF., Yedavalli, V., Heyninck, K., Dikic, I., Beyaert, R., Jeang, KT.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO J","volume":"27","issue":"4","page":"629-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24042954","title":"Regulatory Genomics - Decoding Drosophila Regulatory Sequences.","abstract":null,"authors":"Stark, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Biomed Tech (Berl)","volume":"58 Suppl 1","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18212736","title":"Ubiquitin binding mediates the NF-kappaB inhibitory potential of ABIN proteins.","abstract":"Deregulated nuclear factor kappaB (NF-kappaB) activation plays an important role in inflammation and tumorigenesis. ABIN proteins have been characterized as negative regulators of NF-kappaB signaling. However, their mechanism of NF-kappaB inhibition remained unclear. With the help of a yeast two-hybrid screen, we identified ABIN proteins as novel ubiquitin-interacting proteins. The minimal ubiquitin-binding domain (UBD) corresponds to the ABIN homology domain 2 (AHD2) and is highly conserved in ABIN-1, ABIN-2 and ABIN-3. Moreover, this region is also present in NF-kappaB essential modulator\/IkappaB kinase gamma (NEMO\/IKKgamma) and the NEMO-like protein optineurin, and is therefore termed UBD in ABIN proteins and NEMO (UBAN). Nuclear magnetic resonance studies of the UBAN domain identify it as a novel type of UBD, with the binding surface on ubiquitin being significantly different from the binding surface of other UBDs. ABIN-1 specifically binds ubiquitinated NEMO via a bipartite interaction involving its UBAN and NEMO-binding domain. Mutations in the UBAN domain led to a loss of ubiquitin binding and impaired the NF-kappaB inhibitory potential of ABINs. Taken together, these data illustrate an important role for ubiquitin binding in the negative regulation of NF-kappaB signaling by ABINs and identify UBAN as a novel UBD.","authors":"Wagner, S., Carpentier, I., Rogov, V., Kreike, M., Ikeda, F., L\u00f6hr, F., Wu, CJ., Ashwell, JD., D\u00f6tsch, V., Dikic, I., Beyaert, R.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Oncogene","volume":"27","issue":"26","page":"3739-45","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18191896","title":"D-Serine\/N-methyl-D-aspartate receptor signaling decreases DNA-binding activity of the transcriptional repressor DREAM in M\u00fcller glia from the retina.","abstract":"In the adult retina, N-methyl-D-aspartate (NMDA) neurotoxicity induces M\u00fcller cell reactive gliosis which is characterized by changes in gene expression that lead to proliferation and affect retinal physiology. The amino acid D-serine is synthesized in M\u00fcller cells and modulates these processes acting as a coagonist of NMDA receptors. We have found that the transcription factor DREAM (downstream regulatory element antagonist modulator), which acts as a transcriptional repressor by binding as a tetramer to regulatory elements located in the promoter region of target genes, is expressed in these cells and that its DNA-binding activity is modulated by NMDA receptor activation. Consistently, immunocytochemical analysis demonstrates that NMDA receptor activation induces changes in the nuclear localization of this transcription factor. DREAM is a pleiotropic transcription factor capable to repress and activate genes involved in several physiological events in different tissues. These results link, for the first time, this transcription factor with NMDA-receptor activation. Given the relevance of glutamatergic transmission in the retina and the remarkable functional plasticity of M\u00fcller cells, these findings support the notion that the NMDA receptor-dependent modulation of DREAM activity could play a role in relevant physiological processes ranging from retinal response to injury to differentiation capacity of retinal progenitor cells.","authors":"Chavira-Su\u00e1rez, E., Ram\u00edrez, M., Lamas, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Neurosci Lett","volume":"432","issue":"2","page":"121-6","pdf":null,"JrId":"5844","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2429617","title":"Photoreactivation of ultraviolet-irradiated, plasmid-bearing, and plasmid-free strains of Bacillus anthracis.","abstract":"The effects of toxin- and capsule-encoding plasmids on the kinetics of UV inactivation of various strains of Bacillus anthracis were investigated. Plasmids pXO1 and pXO2 had no effect on bacterial UV sensitivity or photoreactivation. Vegetative cells were capable of photoreactivation, but photo-induced repair of UV damage was absent in B. anthracis Sterne spores.","authors":"Knudson, GB.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Appl Environ Microbiol","volume":"52","issue":"3","page":"444-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1986-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24248598","title":"Regulation of NO synthesis, local inflammation, and innate immunity to pathogens by BET family proteins.","abstract":"Transcriptional activation of the Nos2 gene, encoding inducible nitric oxide synthase (iNOS), during infection or inflammation requires coordinate assembly of an initiation complex by the transcription factors NF-\u03baB and type I interferon-activated ISGF3. Here we show that infection of macrophages with the intracellular bacterial pathogen Listeria monocytogenes caused binding of the BET proteins Brd2, Brd3, and, most prominently, Brd4 to the Nos2 promoter and that a profound reduction of Nos2 expression occurred in the presence of the BET inhibitor JQ1. RNA polymerase activity at the Nos2 gene was regulated through Brd-mediated C-terminal domain (CTD) phosphorylation at serine 5. Underscoring the critical importance of Brd for the regulation of immune responses, application of JQ1 reduced NO production in mice infected with L. monocytogenes, as well as innate resistance to L. monocytogenes and influenza virus. In a murine model of inflammatory disease, JQ1 treatment increased the colitogenic activity of dextran sodium sulfate (DSS). The data presented in our study suggest that BET protein inhibition in a clinical setting poses the risk of altering the innate immune response to infectious or inflammatory challenge.","authors":"Wienerroither, S., Rauch, I., Rosebrock, F., Jamieson, AM., Bradner, J., Muhar, M., Zuber, J., M\u00fcller, M., Decker, T.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mol Cell Biol","volume":"34","issue":"3","page":"415-27","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18075750","title":"The Suv39h-HP1 histone methylation pathway is dispensable for enrichment and protection of cohesin at centromeres in mammalian cells.","abstract":"Sister chromatids are physically connected by cohesin complexes. This sister chromatid cohesion is essential for the biorientation of chromosomes on the mitotic and meiotic spindle. In many species, cohesion between chromosome arms is partly dissolved in prophase of mitosis, whereas cohesion is protected at centromeres until the onset of anaphase. In vertebrates, the protein Sgo1, protein phosphatase 2A, and several other proteins are required for protection of centromeric cohesin in early mitosis. In fission yeast, the recruitment of heterochromatin protein Swi6\/HP1 to centromeres by the histone-methyltransferase Clr4\/Suv39h is required for enrichment of cohesin at centromeres already in interphase. We have tested if the Suv39h-HP1 histone methylation pathway is also required for enrichment and mitotic protection of cohesin at centromeres in mammalian cells. We show that cohesin and HP1 proteins partially colocalize at mitotic centromeres but that cohesin localization is not detectably altered in mouse embryonic fibroblasts that lack Suv39h genes and in which HP1 proteins can, therefore, not be properly enriched in pericentric heterochromatin. Our data indicate that the Suv39h-HP1 pathway is not essential for enrichment and mitotic protection of cohesin at centromeres in mammalian cells.","authors":"Koch, B., Kueng, S., Ruckenbauer, C., Wendt, KS., Peters, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Chromosoma","volume":"117","issue":"2","page":"199-210","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36787743","title":"Angiotensin-converting enzyme 2-at the heart of the COVID-19 pandemic.","abstract":"ACE2 is the indispensable entry receptor for SARS-CoV and SARS-CoV-2. Because of the COVID-19 pandemic, it has become one of the most therapeutically targeted human molecules in biomedicine. ACE2 serves two fundamental physiological roles: as an enzyme, it alters peptide cascade balance; as a chaperone, it controls intestinal amino acid uptake. ACE2's tissue distribution, affected by co-morbidities and sex, explains the broad tropism of coronaviruses and the clinical manifestations of SARS and COVID-19. ACE2-based therapeutics provide a universal strategy to prevent and treat SARS-CoV-2 infections, applicable to all SARS-CoV-2 variants and other emerging zoonotic coronaviruses exploiting ACE2 as their cellular receptor.","authors":"Oudit, GY., Wang, K., Viveiros, A., Kellner, MJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Cell","volume":"186","issue":"5","page":"906-922","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18007598","title":"A novel plant gene essential for meiosis is related to the human CtIP and the yeast COM1\/SAE2 gene.","abstract":"Obligatory homologous recombination (HR) is required for chiasma formation and chromosome segregation in meiosis I. Meiotic HR is initiated by DNA double-strand breaks (DSBs), generated by Spo11, a homologue of the archaebacterial topoisomerase subunit Top6A. In Saccharomyces cerevisiae, Rad50, Mre11 and Com1\/Sae2 are essential to process an intermediate of the cleavage reaction consisting of Spo11 covalently linked to the 5' termini of DNA. While Rad50 and Mre11 also confer genome stability to vegetative cells and are well conserved in evolution, Com1\/Sae2 was believed to be fungal-specific. Here, we identify COM1\/SAE2 homologues in all eukaryotic kingdoms. Arabidopsis thaliana Com1\/Sae2 mutants are sterile, accumulate AtSPO11-1 during meiotic prophase and fail to form AtRAd51 foci despite the presence of unrepaired DSBs. Furthermore, DNA fragmentation in AtCom1 is suppressed by eliminating AtSPO11-1. In addition, AtCOM1 is specifically required for mitomycin C resistance. Interestingly, we identified CtIP, an essential protein interacting with the DNA repair machinery, as the mammalian homologue of Com1\/Sae2, with important implications for the molecular role of CtIP.","authors":"Uanschou, C., Siwiec, T., Pedrosa-Harand, A., Kerzendorfer, C., Sanchez-Moran, E., Novatchkova, M., Akimcheva, S., Woglar, A., Klein, F., Schl\u00f6gelhofer, P.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"EMBO J","volume":"26","issue":"24","page":"5061-70","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24178568","title":"Analysis of Piwi-loaded small RNAs in Tetrahymena.","abstract":"Scan RNAs (scnRNAs) are developmentally regulated siRNAs of ~26-32 nucleotides in length that are involved in programmed DNA elimination in Tetrahymena. scnRNAs are loaded onto the Piwi-related protein Twi1p and 2'-O-methylated at their 3' termini. We describe two alternative strategies for analyzing the Twi1p-loaded scnRNAs: preparation of loaded scnRNAs by immuno-purification of the Twi1p-scnRNA complex and exclusion of non-methylated scnRNAs during cDNA library construction using periodate oxidation.","authors":"Noto, T., Kurth, HM., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Methods Mol Biol","volume":"1093","issue":null,"page":"209-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23160449","title":"CBL-B is required for leukemogenesis mediated by BCR-ABL through negative regulation of bone marrow homing.","abstract":"BCR-ABL induces chronic myeloid leukemia (CML) through the aberrant regulation of multiple signaling substrates. Previous research has shown that BCR-ABL mediates down-modulation of CBL-B protein levels. A murine bone marrow transplantation (BMT) study was performed to assess the contribution of Cbl-b to BCR-ABL-induced disease. The predominant phenotype in the Cbl-b(-\/-) recipients was a CML-like myeloproliferative disease (MPD) similar to that observed in the wild-type animals, but with a longer latency, diminished circulating leukocyte numbers and reduced spleen weights. Despite the decreased leukemic burden in comparison to their wild-type counterparts, the Cbl-b(-\/-) animals displayed enhanced numbers of Gr-1(+)\/Mac-1(+) spleen cells and neutrophilia. On the basis of prior evidence of CBL-B-dependent motility toward SDF-1\u03b1, we hypothesized that Cbl-b deficiency might impair bone marrow localization during transplantation. Homing experiments showed reduced migration of Cbl-b(-\/-) cells to the bone marrow. Intrafemoral transplantation of BCR-ABL-transduced Cbl-b(-\/-) cells revealed equivalent latency of disease development to the wild-type transplants, supporting the conclusion that Cbl-b deficiency diminishes homing of leukemic cells to the bone marrow, and perturbs the proliferation of BCR-ABL-expressing malignant clones during CML development.","authors":"Badger-Brown, KM., Gillis, LC., Bailey, ML., Penninger, JM., Barber, DL.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Leukemia","volume":"27","issue":"5","page":"1146-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25855803","title":"Germline recessive mutations in PI4KA are associated with perisylvian polymicrogyria, cerebellar hypoplasia and arthrogryposis.","abstract":"Polymicrogyria (PMG) is a structural brain abnormality involving the cerebral cortex that results from impaired neuronal migration and although several genes have been implicated, many cases remain unsolved. In this study, exome sequencing in a family where three fetuses had all been diagnosed with PMG and cerebellar hypoplasia allowed us to identify regions of the genome for which both chromosomes were shared identical-by-descent, reducing the search space for causative variants to 8.6% of the genome. In these regions, the only plausibly pathogenic mutations were compound heterozygous variants in PI4KA, which Sanger sequencing confirmed segregated consistent with autosomal recessive inheritance. The paternally transmitted variant predicted a premature stop mutation (c.2386C&gt;T; p.R796X), whereas the maternally transmitted variant predicted a missense substitution (c.5560G&gt;A; p.D1854N) at a conserved residue within the catalytic domain. Functional studies using expressed wild-type or mutant PI4KA enzyme confirmed the importance of p.D1854 for kinase activity. Our results emphasize the importance of phosphoinositide signalling in early brain development.","authors":"Pagnamenta, AT., Howard, MF., Wisniewski, E., Popitsch, N., Knight, SJ., Keays, DA., Quaghebeur, G., Cox, H., Cox, P., Balla, T., Taylor, JC., Kini, U.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Hum Mol Genet","volume":"24","issue":"13","page":"3732-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22926517","title":"miR-100 suppresses IGF2 and inhibits breast tumorigenesis by interfering with proliferation and survival signaling.","abstract":"Dysregulation of micro RNAs is crucially implicated in tumorigenesis. We detected downregulation of miR-100 in breast cancer cells, leading to an upregulation of the proliferation- and survival-promoting oncogene insulin-like growth factor (IGF) 2. Stable overexpression of miR-100 strongly reduced IGF2 expression and inhibited tumor growth. In invasive human breast tumors, miR-100 was reduced about fourfold as compared with benign patient samples, whereas IGF2 was strongly enhanced. MiR-100 has also been shown to suppress other proteins of the IGF\/mammalian target of rapamycin (mTOR) signaling cascade in different human tumors. Our results reveal miR-100 as a context-dependent master regulator of the IGF\/mTOR pathway and a potential target for therapeutic approaches.","authors":"Gebeshuber, CA., Martinez, J.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Oncogene","volume":"32","issue":"27","page":"3306-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24445999","title":"A dual role for autophagy in a murine model of lung cancer.","abstract":"Autophagy is a mechanism by which starving cells can control their energy requirements and metabolic states, thus facilitating the survival of cells in stressful environments, in particular in the pathogenesis of cancer. Here we report that tissue-specific inactivation of Atg5, essential for the formation of autophagosomes, markedly impairs the progression of KRas(G12D)-driven lung cancer, resulting in a significant survival advantage of tumour-bearing mice. Autophagy-defective lung cancers exhibit impaired mitochondrial energy homoeostasis, oxidative stress and a constitutively active DNA damage response. Genetic deletion of the tumour suppressor p53 reinstates cancer progression of autophagy-deficient tumours. Although there is improved survival, the onset of Atg5-mutant KRas(G12D)-driven lung tumours is markedly accelerated. Mechanistically, increased oncogenesis maps to regulatory T cells. These results demonstrate that, in KRas(G12D)-driven lung cancer, Atg5-regulated autophagy accelerates tumour progression; however, autophagy also represses early oncogenesis, suggesting a link between deregulated autophagy and regulatory T cell controlled anticancer immunity.","authors":"Rao, S., Tortola, L., Perlot, T., Wirnsberger, G., Novatchkova, M., Nitsch, R., Sykacek, P., Frank, L., Schramek, D., Komnenovic, V., Sigl, V., Aumayr, K., Schmauss, G., Fellner, N., Handschuh, S., Gl\u00f6smann, M., Pasierbek, P., Schlederer, M., Resch, GP., Ma, Y., Yang, H., Popper, H., Kenner, L., Kroemer, G., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Commun","volume":"5","issue":null,"page":"3056","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25827581","title":"Anion-exchange chromatography of phosphopeptides: weak anion exchange versus strong anion exchange and anion-exchange chromatography versus electrostatic repulsion-hydrophilic interaction chromatography.","abstract":"Most phosphoproteomics experiments rely on prefractionation of tryptic digests before online liquid chromatography-mass spectrometry. This study compares the potential and limitations of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) and anion-exchange chromatography (AEX). At a pH higher than 5, phosphopeptides have two negative charges per residue and are well-retained in AEX. However, peptides with one or two phosphate groups are not separated from peptides with multiple Asp or Glu residues, interfering with the identification of phosphopeptides. At a pH of 2, phosphate residues have just a single negative charge but Asp and Glu are uncharged. This facilitates the separation of phosphopeptides from unmodified acidic peptides. Singly phosphorylated peptides are retained weakly under these conditions, due to electrostatic repulsion, unless hydrophilic interaction is superimposed in the ERLIC mode. Weak anion-exchange (WAX) and strong anion-exchange (SAX) columns were compared, with both peptide standards and a HeLa cell tryptic digest. The SAX column exhibited greater retention at pH 6 than did the WAX column. However, only about 60% as many phosphopeptides were identified with SAX at pH 6 than via ERLIC at pH 2. In one ERLIC run, 12\u202f467 phosphopeptides were identified, including 4233 with more than one phosphate. We conclude that chromatography of phosphopeptides is best performed at low pH in the ERLIC mode. Under those conditions, the performances of the SAX and WAX materials were comparable. The data have been deposited with the ProteomeXchange with identifier PXD001333.","authors":"Alpert, AJ., Hudecz, O., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Anal Chem","volume":"87","issue":"9","page":"4704-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24508458","title":"E3 ubiquitin ligase Cbl-b suppresses proallergic T cell development and allergic airway inflammation.","abstract":"E3 ubiquitin ligase Cbl-b has emerged as a gatekeeper that controls the activation threshold of the T\u00a0cell antigen receptor and maintains the balance between tolerance and autoimmunity. Here, we report that the loss of Cbl-b facilitates T helper 2 (Th2) and Th9 cell differentiation in\u00a0vitro. In a mouse model of asthma, the absence of Cbl-b results in severe airway inflammation and stronger Th2 and Th9 responses. Mechanistically, Cbl-b selectively associates with Stat6 upon IL-4 ligation and targets Stat6 for ubiquitination and degradation. These processes are heightened in the presence of T\u00a0cell receptor (TCR)\/CD28 costimulation. Furthermore, we identify K108 and K398 as Stat6 ubiquitination sites. Intriguingly, introducing Stat6 deficiency into Cblb(-\/-) mice abrogates hyper-Th2 responses but only partially attenuates Th9 responses. Therefore, our data reveal a function for Cbl-b in the regulation of Th2 and Th9 cell differentiation.","authors":"Qiao, G., Ying, H., Zhao, Y., Liang, Y., Guo, H., Shen, H., Li, Z., Solway, J., Tao, E., Chiang, YJ., Lipkowitz, S., Penninger, JM., Langdon, WY., Zhang, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell Rep","volume":"6","issue":"4","page":"709-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24097029","title":"Nutrition and the biology of human ageing: bone health and osteoporosis \/ sarcopenia \/ immune deficiency.","abstract":null,"authors":"Offord, EA., Karagounis, LG., Vidal, K., Fielding, R., Meydani, S., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Nutr Health Aging","volume":"17","issue":"8","page":"712-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17989255","title":"Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.","abstract":"MicroRNAs (miRNAs) are short regulatory RNAs that inhibit target genes by complementary binding in 3' untranslated regions (3' UTRs). They are one of the most abundant classes of regulators, targeting a large fraction of all genes, making their comprehensive study a requirement for understanding regulation and development. Here we use 12 Drosophila genomes to define structural and evolutionary signatures of miRNA hairpins, which we use for their de novo discovery. We predict &gt;41 novel miRNA genes, which encompass many unique families, and 28 of which are validated experimentally. We also define signals for the precise start position of mature miRNAs, which suggest corrections of previously known miRNAs, often leading to drastic changes in their predicted target spectrum. We show that miRNA discovery power scales with the number and divergence of species compared, suggesting that such approaches can be successful in human as dozens of mammalian genomes become available. Interestingly, for some miRNAs sense and anti-sense hairpins score highly and mature miRNAs from both strands can indeed be found in vivo. Similarly, miRNAs with weak 5' end predictions show increased in vivo processing of multiple alternate 5' ends and have fewer predicted targets. Lastly, we show that several miRNA star sequences score highly and are likely functional. For mir-10 in particular, both arms show abundant processing, and both show highly conserved target sites in Hox genes, suggesting a possible cooperation of the two arms, and their role as a master Hox regulator.","authors":"Stark, A., Kheradpour, P., Parts, L., Brennecke, J., Hodges, E., Hannon, GJ., Kellis, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genome Res","volume":"17","issue":"12","page":"1865-79","pdf":null,"JrId":"8754","fulltextlink":null,"preprintlink":null,"articledate":"2008-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30190407","title":"The Ly6\/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization.","abstract":"Fertilization is fundamental for sexual reproduction, yet its molecular mechanisms are poorly understood. We found that an oocyte-expressed Ly6\/uPAR protein, which we call Bouncer, is a crucial fertilization factor in zebrafish. Membrane-bound Bouncer mediates sperm-egg binding and is thus essential for sperm entry into the egg. Remarkably, Bouncer not only is required for sperm-egg interaction but is also sufficient to allow cross-species fertilization between zebrafish and medaka, two fish species that diverged more than 200 million years ago. Our study thus identifies Bouncer as a key determinant of species-specific fertilization in fish. Bouncer's closest homolog in tetrapods, SPACA4, is restricted to the male germline in internally fertilizing vertebrates, which suggests that our findings in fish have relevance to human biology.","authors":"Herberg, S., Gert, KR., Schleiffer, A., Pauli, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Science","volume":"361","issue":"6406","page":"1029-1033","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29668089","title":"A new era of proactive melanoma therapy: hit hard, hit early.","abstract":null,"authors":"Haas, L., Wiesner, T., Obenauf, AC.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Br J Dermatol","volume":"178","issue":"4","page":"817-820","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24509509","title":"Stage-specific control of early B cell development by the transcription factor Ikaros.","abstract":"The transcription factor Ikaros is an essential regulator of lymphopoiesis. Here we studied its B cell-specific function by conditional inactivation of the gene encoding Ikaros (Ikzf1) in pro-B cells. B cell development was arrested at an aberrant 'pro-B cell' stage characterized by increased cell adhesion and loss of signaling via the pre-B cell signaling complex (pre-BCR). Ikaros activated genes encoding signal transducers of the pre-BCR and repressed genes involved in the downregulation of pre-BCR signaling and upregulation of the integrin signaling pathway. Unexpectedly, derepression of expression of the transcription factor Aiolos did not compensate for the loss of Ikaros in pro-B cells. Ikaros induced or suppressed active chromatin at regulatory elements of activated or repressed target genes. Notably, binding of Ikaros and expression of its target genes were dynamically regulated at distinct stages of early B lymphopoiesis.","authors":"Schwickert, TA., Tagoh, H., G\u00fcltekin, S., Dakic, A., Axelsson, E., Minnich, M., Ebert, A., Werner, B., Roth, M., Cimmino, L., Dickins, RA., Zuber, J., Jaritz, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Immunol","volume":"15","issue":"3","page":"283-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24532575","title":"Differential requirement for Nfil3 during NK cell development.","abstract":"NK cells can be grouped into distinct subsets that are localized to different organs and exhibit a different capacity to secrete cytokines and mediate cytotoxicity. Despite these hallmarks that reflect tissue-specific specialization in NK cells, little is known about the factors that control the development of these distinct subsets. The basic leucine zipper transcription factor Nfil3 (E4bp4) is essential for bone marrow-derived NK cell development, but it is not clear whether Nfil3 is equally important for all NK cell subsets or how it induces NK lineage commitment. In this article, we show that Nfil3 is required for the formation of Eomes-expressing NK cells, including conventional medullary and thymic NK cells, whereas TRAIL(+) Eomes(-) NK cells develop independently of Nfil3. Loss of Nfil3 during the development of bone marrow-derived NK cells resulted in reduced expression of Eomes and, conversely, restoration of Eomes expression in Nfil3(-\/-) progenitors rescued NK cell development and maturation. Collectively, these findings demonstrate that Nfil3 drives the formation of mature NK cells by inducing Eomes expression and reveal the differential requirements of NK cell subsets for Nfil3.","authors":"Seillet, C., Huntington, ND., Gangatirkar, P., Axelsson, E., Minnich, M., Brady, HJ., Busslinger, M., Smyth, MJ., Belz, GT., Carotta, S.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Immunol","volume":"192","issue":"6","page":"2667-76","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24449215","title":"Downregulation of RUNX1\/CBF\u03b2 by MLL fusion proteins enhances hematopoietic stem cell self-renewal.","abstract":"RUNX1\/CBF\u03b2 (core binding factor [CBF]) is a heterodimeric transcription factor complex that is frequently involved in chromosomal translocations, point mutations, or deletions in acute leukemia. The mixed lineage leukemia (MLL) gene is also frequently involved in chromosomal translocations or partial tandem duplication in acute leukemia. The MLL protein interacts with RUNX1 and prevents RUNX1 from ubiquitin-mediated degradation. RUNX1\/CBF\u03b2 recruits MLL to regulate downstream target genes. However, the functional consequence of MLL fusions on RUNX1\/CBF\u03b2 activity has not been fully understood. In this report, we show that MLL fusion proteins and the N-terminal MLL portion of MLL fusions downregulate RUNX1 and CBF\u03b2 protein expression via the MLL CXXC domain and flanking regions. We confirmed this finding in Mll-Af9 knock-in mice and human M4\/M5 acute myeloid leukemia (AML) cell lines, with or without MLL translocations, showing that MLL translocations cause a hypomorph phenotype of RUNX1\/CBF\u03b2. Overexpression of RUNX1 inhibits the development of AML in Mll-Af9 knock-in mice; conversely, further reducing Runx1\/Cbf\u03b2 levels accelerates MLL-AF9-mediated AML in bone marrow transplantation assays. These data reveal a newly defined negative regulation of RUNX1\/CBF\u03b2 by MLL fusion proteins and suggest that targeting RUNX1\/CBF\u03b2 levels may be a potential therapy for MLLs.","authors":"Zhao, X., Chen, A., Yan, X., Zhang, Y., He, F., Hayashi, Y., Dong, Y., Rao, Y., Li, B., Conway, RM., Maiques-Diaz, A., Elf, SE., Huang, N., Zuber, J., Xiao, Z., Tse, W., Tenen, DG., Wang, Q., Chen, W., Mulloy, JC., Nimer, SD., Huang, G.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Blood","volume":"123","issue":"11","page":"1729-38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29959678","title":"Analysis of 3' End Modifications in microRNAs by High-Throughput Sequencing.","abstract":"MicroRNAs are ~22\u00a0nt small, non-coding RNAs that direct posttranscriptional silencing of gene expression to regulate animal development, physiology, and disease. An emerging mechanism that controls the biogenesis of microRNAs is the addition of non-templated nucleotides, predominantly uridine, to the 3' end of precursor-microRNAs, in a process that is commonly referred to as tailing. Here, we describe methods that enable the systematic characterization of tailing events in mature microRNAs and their precursors. We report protocols for untargeted and targeted cDNA library preparation procedures, as exemplified in the context of the model organism Drosophila melanogaster and focusing on precursor-microRNAs. We also refer to a dedicated computational framework for the subsequent analysis of untemplated nucleotide additions in cDNA libraries. The described methods for the systematic characterization of posttranscriptional modifications in gene regulatory small RNAs and their precursors will be instrumental in clarifying regulatory concepts that control posttranscriptional gene silencing.","authors":"Reim\u00e3o-Pinto, MM., Rodrigues-Viana, AM., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Methods Mol Biol","volume":"1823","issue":null,"page":"115-139","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24263382","title":"Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response.","abstract":"Arginine phosphorylation is an emerging protein modification implicated in the general stress response of Gram-positive bacteria. The modification is mediated by the arginine kinase McsB, which phosphorylates and inactivates the heat shock repressor CtsR. In this study, we developed a mass spectrometric approach accounting for the peculiar chemical properties of phosphoarginine. The improved methodology was used to analyze the dynamic changes in the Bacillus subtilis arginine phosphoproteome in response to different stress situations. Quantitative analysis showed that a B. subtilis mutant lacking the YwlE arginine phosphatase accumulated a strikingly large number of arginine phosphorylations (217 sites in 134 proteins), however only a minor fraction of these sites was increasingly modified during heat shock or oxidative stress. The main targets of McsB-mediated arginine phosphorylation comprise central factors of the stress response system including the CtsR and HrcA heat shock repressors, as well as major components of the protein quality control system such as the ClpCP protease and the GroEL chaperonine. These findings highlight the impact of arginine phosphorylation in orchestrating the bacterial stress response.","authors":"Schmidt, A., Trentini, DB., Spiess, S., Fuhrmann, J., Ammerer, G., Mechtler, K., Clausen, T.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mol Cell Proteomics","volume":"13","issue":"2","page":"537-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23707064","title":"A comprehensive wiring diagram of the protocerebral bridge for visual information processing in the Drosophila brain.","abstract":"How the brain perceives sensory information and generates meaningful behavior depends critically on its underlying circuitry. The protocerebral bridge (PB) is a major part of the insect central complex (CX), a premotor center that may be analogous to the human basal ganglia. Here, by deconstructing hundreds of PB single neurons and reconstructing them into a common three-dimensional framework, we have constructed a comprehensive map of PB circuits with labeled polarity and predicted directions of information flow. Our analysis reveals a highly ordered information processing system that involves directed information flow among CX subunits through 194 distinct PB neuron types. Circuitry properties such as mirroring, convergence, divergence, tiling, reverberation, and parallel signal propagation were observed; their functional and evolutional significance is discussed. This layout of PB neuronal circuitry may provide guidelines for further investigations on transformation of sensory (e.g., visual) input into locomotor commands in fly brains.","authors":"Lin, CY., Chuang, CC., Hua, TE., Chen, CC., Dickson, BJ., Greenspan, RJ., Chiang, AS.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Rep","volume":"3","issue":"5","page":"1739-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24439110","title":"Mutations in PGAP3 impair GPI-anchor maturation, causing a subtype of hyperphosphatasia with mental retardation.","abstract":"Glycosylphophatidylinositol (GPI)-anchored proteins play important roles in many biological processes, and mutations affecting proteins involved in the synthesis of the GPI anchor are reported to cause a wide spectrum of intellectual disabilities (IDs) with characteristic additional phenotypic features. Here, we describe a total of five individuals (from three unrelated families) in whom we identified mutations in PGAP3, encoding a protein that is involved in GPI-anchor maturation. Three siblings in a consanguineous Pakistani family presented with profound developmental delay, severe ID, no speech, psychomotor delay, and postnatal microcephaly. A combination of autozygosity mapping and exome sequencing identified a 13.8 Mb region harboring a homozygous c.275G&gt;A (p.Gly92Asp) variant in PGAP3 region 17q11.2-q21.32. Subsequent testing showed elevated serum alkaline phosphatase (ALP), a GPI-anchored enzyme, in all three affected children. In two unrelated individuals in a cohort with developmental delay, ID, and elevated ALP, we identified compound-heterozygous variants c.439dupC (p.Leu147Profs(\u2217)16) and c.914A&gt;G (p.Asp305Gly) and homozygous variant c.314C&gt;G (p.Pro105Arg). The 1 bp duplication causes a frameshift and nonsense-mediated decay. Further evidence supporting pathogenicity of the missense mutations c.275G&gt;A, c.314C&gt;G, and c.914A&gt;G was provided by the absence of the variants from ethnically matched controls, phylogenetic conservation, and functional studies on Chinese hamster ovary cell lines. Taken together with recent data on PGAP2, these results confirm the importance of the later GPI-anchor remodelling steps for normal neuronal development. Impairment of PGAP3 causes a subtype of hyperphosphatasia with ID, a congenital disorder of glycosylation that is also referred to as Mabry syndrome.","authors":"Howard, MF., Murakami, Y., Pagnamenta, AT., Daumer-Haas, C., Fischer, B., Hecht, J., Keays, DA., Knight, SJ., K\u00f6lsch, U., Kr\u00fcger, U., Leiz, S., Maeda, Y., Mitchell, D., Mundlos, S., Phillips, JA., Robinson, PN., Kini, U., Taylor, JC., Horn, D., Kinoshita, T., Krawitz, PM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Am J Hum Genet","volume":"94","issue":"2","page":"278-87","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24402316","title":"A conserved role for Snail as a potentiator of active transcription.","abstract":"The transcription factors of the Snail family are key regulators of epithelial-mesenchymal transitions, cell morphogenesis, and tumor metastasis. Since its discovery in Drosophila \u223c25 years ago, Snail has been extensively studied for its role as a transcriptional repressor. Here we demonstrate that Drosophila Snail can positively modulate transcriptional activation. By combining information on in vivo occupancy with expression profiling of hand-selected, staged snail mutant embryos, we identified 106 genes that are potentially directly regulated by Snail during mesoderm development. In addition to the expected Snail-repressed genes, almost 50% of Snail targets showed an unanticipated activation. The majority of \"Snail-activated\" genes have enhancer elements cobound by Twist and are expressed in the mesoderm at the stages of Snail occupancy. Snail can potentiate Twist-mediated enhancer activation in vitro and is essential for enhancer activity in vivo. Using a machine learning approach, we show that differentially enriched motifs are sufficient to predict Snail's regulatory response. In silico mutagenesis revealed a likely causative motif, which we demonstrate is essential for enhancer activation. Taken together, these data indicate that Snail can potentiate enhancer activation by collaborating with different activators, providing a new mechanism by which Snail regulates development.","authors":"Rembold, M., Ciglar, L., Y\u00e1\u00f1ez-Cuna, JO., Zinzen, RP., Girardot, C., Jain, A., Welte, MA., Stark, A., Leptin, M., Furlong, EE.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genes Dev","volume":"28","issue":"2","page":"167-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24120136","title":"Differentiated Troy+ chief cells act as reserve stem cells to generate all lineages of the stomach epithelium.","abstract":"Proliferation of the self-renewing epithelium of the gastric corpus occurs almost exclusively in the isthmus of the glands, from where cells migrate bidirectionally toward pit and base. The isthmus is therefore generally viewed as the stem cell zone. We find that the stem cell marker Troy is expressed at the gland base by a small subpopulation of fully differentiated chief cells. By lineage tracing with a Troy-eGFP-ires-CreERT2 allele, single marked chief cells are shown to generate entirely labeled gastric units over periods of months. This phenomenon accelerates upon tissue damage. Troy(+) chief cells can be cultured to generate long-lived gastric organoids. Troy marks a specific subset of chief cells that display plasticity in that they are capable of replenishing entire gastric units, essentially serving as quiescent \"reserve\" stem cells. These observations challenge the notion that stem cell hierarchies represent a \"one-way street.\"","authors":"Stange, DE., Koo, BK., Huch, M., Sibbel, G., Basak, O., Lyubimova, A., Kujala, P., Bartfeld, S., Koster, J., Geahlen, JH., Peters, PJ., van Es, JH., van de Wetering, M., Mills, JC., Clevers, H.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell","volume":"155","issue":"2","page":"357-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17978103","title":"Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB\/dREAM complex in proliferating cells.","abstract":"Myb-MuvB (MMB)\/dREAM is a nine-subunit complex first described in Drosophila as a repressor of transcription, dependent on E2F2 and the RBFs. Myb, an integral member of MMB, curiously plays no role in the silencing of the test genes previously analyzed. Moreover, Myb plays an activating role in DNA replication in Drosophila egg chamber follicle cells. The essential functions for Myb are executed as part of MMB. This duality of function lead to the hypothesis that MMB, which contains both known activator and repressor proteins, might function as part of a switching mechanism that is dependent on DNA sites and developmental context. Here, we used proliferating Drosophila Kc tissue culture cells to explore both the network of genes regulated by MMB (employing RNA interference and microarray expression analysis) and the genomic locations of MMB following chromatin immunoprecipitation (ChIP) and tiling array analysis. MMB occupied 3538 chromosomal sites and was promoter-proximal to 32% of Drosophila genes. MMB contains multiple DNA-binding factors, and the data highlighted the combinatorial way by which the complex was targeted and utilized for regulation. Interestingly, only a subset of chromatin-bound complexes repressed genes normally expressed in a wide range of developmental pathways. At many of these sites, E2F2 was critical for repression, whereas at other nonoverlapping sites, Myb was critical for repression. We also found sites where MMB was a positive regulator of transcript levels that included genes required for mitotic functions (G2\/M), which may explain some of the chromosome instability phenotypes attributed to loss of Myb function in myb mutants.","authors":"Georlette, D., Ahn, S., MacAlpine, DM., Cheung, E., Lewis, PW., Beall, EL., Bell, SP., Speed, T., Manak, JR., Botchan, MR.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Genes Dev","volume":"21","issue":"22","page":"2880-96","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11071528","title":"Osteoprotegerin ligand: a regulator of immune responses and bone physiology.","abstract":null,"authors":"Kong, YY., Boyle, WJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Immunol Today","volume":"21","issue":"10","page":"495-502","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25822087","title":"Cooperative loss of RAS feedback regulation drives myeloid leukemogenesis.","abstract":"RAS network activation is common in human cancers, and in acute myeloid leukemia (AML) this activation is achieved mainly through gain-of-function mutations in KRAS, NRAS or the receptor tyrosine kinase FLT3. We show that in mice, premalignant myeloid cells harboring a Kras(G12D) allele retained low levels of Ras signaling owing to negative feedback involving Spry4 that prevented transformation. In humans, SPRY4 is located on chromosome 5q, a region affected by large heterozygous deletions that are associated with aggressive disease in which gain-of-function mutations in the RAS pathway are rare. These 5q deletions often co-occur with chromosome 17 alterations involving the deletion of NF1 (another RAS negative regulator) and TP53. Accordingly, combined suppression of Spry4, Nf1 and p53 produces high levels of Ras signaling and drives AML in mice. Thus, SPRY4 is a tumor suppressor at 5q whose disruption contributes to a lethal AML subtype that appears to acquire RAS pathway activation through a loss of negative regulators.","authors":"Zhao, Z., Chen, CC., Rillahan, CD., Shen, R., Kitzing, T., McNerney, ME., Diaz-Flores, E., Zuber, J., Shannon, K., Le Beau, MM., Spector, MS., Kogan, SC., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Genet","volume":"47","issue":"5","page":"539-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-152","title":"Drosophila Embryo Stage Annotation using Label Propagation","abstract":null,"authors":"Kazmar, T., Kvon EZ., Stark, A., Lampert, CH.. ","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"International Conference on Computer Vision (ICCV). Springer","volume":"Dec","issue":"","page":"1089\u20131096","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24415537","title":"Differentiation therapy for the treatment of t(8;21) acute myeloid leukemia using histone deacetylase inhibitors.","abstract":"Epigenetic modifying enzymes such as histone deacetylases (HDACs), p300, and PRMT1 are recruited by AML1\/ETO, the pathogenic protein for t(8;21) acute myeloid leukemia (AML), providing a strong molecular rationale for targeting these enzymes to treat this disease. Although early phase clinical assessment indicated that treatment with HDAC inhibitors (HDACis) may be effective in t(8;21) AML patients, rigorous preclinical studies to identify the molecular and biological events that may determine therapeutic responses have not been performed. Using an AML mouse model driven by expression of AML1\/ETO9a (A\/E9a), we demonstrated that treatment of mice bearing t(8;21) AML with the HDACi panobinostat caused a robust antileukemic response that did not require functional p53 nor activation of conventional apoptotic pathways. Panobinostat triggered terminal myeloid differentiation via proteasomal degradation of A\/E9a. Importantly, conditional A\/E9a deletion phenocopied the effects of panobinostat and other HDACis, indicating that destabilization of A\/E9a is critical for the antileukemic activity of these agents.","authors":"Bots, M., Verbrugge, I., Martin, BP., Salmon, JM., Ghisi, M., Baker, A., Stanley, K., Shortt, J., Ossenkoppele, GJ., Zuber, J., Rappaport, AR., Atadja, P., Lowe, SW., Johnstone, RW.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Blood","volume":"123","issue":"9","page":"1341-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24332856","title":"An optimized microRNA backbone for effective single-copy RNAi.","abstract":"Short hairpin RNA (shRNA) technology enables stable and regulated gene repression. For establishing experimentally versatile RNAi tools and minimizing toxicities, synthetic shRNAs can be embedded into endogenous microRNA contexts. However, due to our incomplete understanding of microRNA biogenesis, such \"shRNAmirs\" often fail to trigger potent knockdown, especially when expressed from a single genomic copy. Following recent advances in design of synthetic shRNAmir stems, here we take a systematic approach to optimize the experimental miR-30 backbone. Among several favorable features, we identify a conserved element 3' of the basal stem as critically required for optimal shRNAmir processing and implement it in an optimized backbone termed \"miR-E\", which strongly increases mature shRNA levels and knockdown efficacy. Existing miR-30 reagents can be easily converted to miR-E, and its combination with up-to-date design rules establishes a validated and accessible platform for generating effective single-copy shRNA libraries that will facilitate the functional annotation of the genome.","authors":"Fellmann, C., Hoffmann, T., Sridhar, V., Hopfgartner, B., Muhar, M., Roth, M., Lai, DY., Barbosa, IA., Kwon, JS., Guan, Y., Sinha, N., Zuber, J.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Rep","volume":"5","issue":"6","page":"1704-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29491135","title":"Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.","abstract":"Enhancers are important genomic regulatory elements directing cell type-specific transcription. They assume a key role during development and disease, and their identification and functional characterization have long been the focus of scientific interest. The advent of next-generation sequencing and clustered regularly interspaced short palindromic repeat (CRISPR)\/Cas9-based genome editing has revolutionized the means by which we study enhancer biology. In this review, we cover recent developments in the prediction of enhancers based on chromatin characteristics and their identification by functional reporter assays and endogenous DNA perturbations. We discuss that the two latter approaches provide different and complementary insights, especially in assessing enhancer sufficiency and necessity for transcription activation. Furthermore, we discuss recent insights into mechanistic aspects of enhancer function, including findings about cofactor requirements and the role of post-translational histone modifications such as monomethylation of histone H3 Lys4 (H3K4me1). Finally, we survey how these approaches advance our understanding of transcription regulation with respect to promoter specificity and transcriptional bursting and provide an outlook covering open questions and promising developments.","authors":"Catarino, RR., Stark, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Genes Dev","volume":"32","issue":"3-4","page":"202-223","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17939997","title":"Chromosome mobility during meiotic prophase in Saccharomyces cerevisiae.","abstract":"In many organisms, a synaptonemal complex (SC) intimately connects each pair of homologous chromosomes during much of the first meiotic prophase and is thought to play a role in regulating recombination. In the yeast Saccharomyces cerevisiae, the central element of each SC contains Zip1, a protein orthologous to mammalian SYCP1. To study the dynamics of SCs in living meiotic cells, a functional ZIP1::GFP fusion was introduced into yeast and analyzed by fluorescence video microscopy. During pachytene, SCs exhibited dramatic and continuous movement throughout the nucleus, traversing relatively large distances while twisting, folding, and unfolding. Chromosomal movements were accompanied by changes in the shape of the nucleus, and all movements were reversibly inhibited by the actin antagonist Latrunculin B. Normal movement required the NDJ1 gene, which encodes a meiosis-specific telomere protein needed for the attachment of telomeres to the nuclear periphery and for normal kinetics of recombination and meiosis. These results show that SC movements involve telomere attachment to the nuclear periphery and are actin-dependent and suggest these movements could facilitate completion of meiotic recombination.","authors":"Scherthan, H., Wang, H., Adelfalk, C., White, EJ., Cowan, C., Cande, WZ., Kaback, DB.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Proc Natl Acad Sci U S A","volume":"104","issue":"43","page":"16934-9","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-153","title":"Reverse Engineering Animal Vision with Virtual Reality and Genetics.","abstract":null,"authors":"Stowers, JR., Fuhrmann, A., Hofbauer, M., Streinzer, M., Schmid, A., Dickinson, MH., Straw, AD.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Computer","volume":"14","issue":"190","page":"38\u201345","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10932199","title":"\"Catching heart disease\": antigenic mimicry and bacterial infections.","abstract":null,"authors":"Bachmaier, K., Le, J., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nat Med","volume":"6","issue":"8","page":"841-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24285714","title":"Role of SWI\/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation.","abstract":"Cancer cells frequently depend on chromatin regulatory activities to maintain a malignant phenotype. Here, we show that leukemia cells require the mammalian SWI\/SNF chromatin remodeling complex for their survival and aberrant self-renewal potential. While Brg1, an ATPase subunit of SWI\/SNF, is known to suppress tumor formation in several cell types, we found that leukemia cells instead rely on Brg1 to support their oncogenic transcriptional program, which includes Myc as one of its key targets. To account for this context-specific function, we identify a cluster of lineage-specific enhancers located 1.7 Mb downstream from Myc that are occupied by SWI\/SNF as well as the BET protein Brd4. Brg1 is required at these distal elements to maintain transcription factor occupancy and for long-range chromatin looping interactions with the Myc promoter. Notably, these distal Myc enhancers coincide with a region that is focally amplified in \u223c3% of acute myeloid leukemias. Together, these findings define a leukemia maintenance function for SWI\/SNF that is linked to enhancer-mediated gene regulation, providing general insights into how cancer cells exploit transcriptional coactivators to maintain oncogenic gene expression programs.","authors":"Shi, J., Whyte, WA., Zepeda-Mendoza, CJ., Milazzo, JP., Shen, C., Roe, JS., Minder, JL., Mercan, F., Wang, E., Eckersley-Maslin, MA., Campbell, AE., Kawaoka, S., Shareef, S., Zhu, Z., Kendall, J., Muhar, M., Haslinger, C., Yu, M., Roeder, RG., Wigler, MH., Blobel, GA., Zuber, J., Spector, DL., Young, RA., Vakoc, CR.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Genes Dev","volume":"27","issue":"24","page":"2648-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28903034","title":"Piwi Is Required to Limit Exhaustion of Aging Somatic Stem Cells.","abstract":"Sophisticated mechanisms that preserve genome integrity are critical to ensure the maintenance of regenerative capacity while preventing transformation of somatic stem cells (SCs), yet little is known about mechanisms regulating genome maintenance in these cells. Here, we show that intestinal stem cells (ISCs) induce the Argonaute family protein Piwi in response to JAK\/STAT signaling during acute proliferative episodes. Piwi function is critical to ensure heterochromatin maintenance, suppress retrotransposon activation, and prevent DNA damage in homeostasis and under regenerative pressure. Accordingly, loss of Piwi results in the loss of actively dividing ISCs and their progenies by apoptosis. We further show that Piwi expression is sufficient to allay age-related retrotransposon expression, DNA damage, apoptosis, and mis-differentiation phenotypes in the ISC lineage, improving epithelial homeostasis. Our data identify a role for Piwi in the regulation of\u00a0somatic SC function, and they highlight the importance of retrotransposon control in somatic SC maintenance.","authors":"Sousa-Victor, P., Ayyaz, A., Hayashi, R., Qi, Y., Madden, DT., Lunyak, VV., Jasper, H.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Rep","volume":"20","issue":"11","page":"2527-2537","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23975099","title":"Wapl is an essential regulator of chromatin structure and chromosome segregation.","abstract":"Mammalian genomes contain several billion base pairs of DNA that are packaged in chromatin fibres. At selected gene loci, cohesin complexes have been proposed to arrange these fibres into higher-order structures, but how important this function is for determining overall chromosome architecture and how the process is regulated are not well understood. Using conditional mutagenesis in the mouse, here we show that depletion of the cohesin-associated protein Wapl stably locks cohesin on DNA, leads to clustering of cohesin in axial structures, and causes chromatin condensation in interphase chromosomes. These findings reveal that the stability of cohesin-DNA interactions is an important determinant of chromatin structure, and indicate that cohesin has an architectural role in interphase chromosome territories. Furthermore, we show that regulation of cohesin-DNA interactions by Wapl is important for embryonic development, expression of genes such as c-myc (also known as Myc), and cell cycle progression. In mitosis, Wapl-mediated release of cohesin from DNA is essential for proper chromosome segregation and protects cohesin from cleavage by the protease separase, thus enabling mitotic exit in the presence of functional cohesin complexes.","authors":"Tedeschi, A., Wutz, G., Huet, S., Jaritz, M., Wuensche, A., Schirghuber, E., Davidson, IF., Tang, W., Cisneros, DA., Bhaskara, V., Nishiyama, T., Vaziri, A., Wutz, A., Ellenberg, J., Peters, JM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nature","volume":"501","issue":"7468","page":"564-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17937504","title":"The interplay of RecA-related proteins and the MND1-HOP2 complex during meiosis in Arabidopsis thaliana.","abstract":"During meiosis, homologous chromosomes recognize each other, align, and exchange genetic information. This process requires the action of RecA-related proteins Rad51 and Dmc1 to catalyze DNA strand exchanges. The Mnd1-Hop2 complex has been shown to assist in Dmc1-dependent processes. Furthermore, higher eukaryotes possess additional RecA-related proteins, like XRCC3, which are involved in meiotic recombination. However, little is known about the functional interplay between these proteins during meiosis. We investigated the functional relationship between AtMND1, AtDMC1, AtRAD51, and AtXRCC3 during meiosis in Arabidopsis thaliana. We demonstrate the localization of AtMND1 to meiotic chromosomes, even in the absence of recombination, and show that AtMND1 loading depends exclusively on AHP2, the Arabidopsis Hop2 homolog. We provide evidence of genetic interaction between AtMND1, AtDMC1, AtRAD51, and AtXRCC3. In vitro assays suggest that this functional link is due to direct interaction of the AtMND1-AHP2 complex with AtRAD51 and AtDMC1. We show that AtDMC1 foci accumulate in the Atmnd1 mutant, but are reduced in number in Atrad51 and Atxrcc3 mutants. This study provides the first insights into the functional differences of AtRAD51 and AtXRCC3 during meiosis, demonstrating that AtXRCC3 is dispensable for AtDMC1 focus formation in an Atmnd1 mutant background, whereas AtRAD51 is not. These results clarify the functional interactions between key players in the strand exchange processes during meiotic recombination. Furthermore, they highlight a direct interaction between MND1 and RAD51 and show a functional divergence between RAD51 and XRCC3.","authors":"Vignard, J., Siwiec, T., Chelysheva, L., Vrielynck, N., Gonord, F., Armstrong, SJ., Schl\u00f6gelhofer, P., Mercier, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"PLoS Genet","volume":"3","issue":"10","page":"1894-906","pdf":null,"JrId":"32385","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17914060","title":"Caenorhabditis elegans prom-1 is required for meiotic prophase progression and homologous chromosome pairing.","abstract":"A novel gene, prom-1, was isolated in a screen for Caenorhabditis elegans mutants with increased apoptosis in the germline. prom-1 encodes an F-box protein with limited homology to the putative human tumor suppressor FBXO47. Mutations in the prom-1 locus cause a strong reduction in bivalent formation, which results in increased embryonic lethality and a Him phenotype. Furthermore, retarded and asynchronous nuclear reorganization as well as reduced homologous synapsis occur during meiotic prophase. Accumulation of recombination protein RAD-51 in meiotic nuclei suggests disturbed repair of double-stranded DNA breaks. Nuclei in prom-1 mutant gonads timely complete mitotic proliferation and premeiotic replication, but they undergo prolonged delay upon meiotic entry. We, therefore, propose that prom-1 regulates the timely progression through meiotic prophase I and that in its absence the recognition of homologous chromosomes is strongly impaired.","authors":"Jantsch, V., Tang, L., Pasierbek, P., Penkner, A., Nayak, S., Baudrimont, A., Schedl, T., Gartner, A., Loidl, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Biol Cell","volume":"18","issue":"12","page":"4911-20","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24013820","title":"Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light.","abstract":"Recent efforts in neuroscience research have been aimed at obtaining detailed anatomical neuronal wiring maps as well as information on how neurons in these networks engage in dynamic activities. Although the entire connectivity map of the nervous system of Caenorhabditis elegans has been known for more than 25 years, this knowledge has not been sufficient to predict all functional connections underlying behavior. To approach this goal, we developed a two-photon technique for brain-wide calcium imaging in C. elegans, using wide-field temporal focusing (WF-TeFo). Pivotal to our results was the use of a nuclear-localized, genetically encoded calcium indicator, NLS-GCaMP5K, that permits unambiguous discrimination of individual neurons within the densely packed head ganglia of C. elegans. We demonstrate near-simultaneous recording of activity of up to 70% of all head neurons. In combination with a lab-on-a-chip device for stimulus delivery, this method provides an enabling platform for establishing functional maps of neuronal networks.","authors":"Schr\u00f6del, T., Prevedel, R., Aumayr, K., Zimmer, M., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Methods","volume":"10","issue":"10","page":"1013-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23974957","title":"GATA-3 regulates the self-renewal of long-term hematopoietic stem cells.","abstract":"The transcription factor GATA-3 is expressed and required for differentiation and function throughout the T lymphocyte lineage. Despite evidence it may also be expressed in multipotent hematopoietic stem cells (HSCs), any role for GATA-3 in these cells has remained unclear. Here we found GATA-3 was in the cytoplasm in quiescent long-term stem cells from steady-state bone marrow but relocated to the nucleus when HSCs cycled. Relocation depended on signaling via the mitogen-activated protein kinase p38 and was associated with a diminished capacity for long-term reconstitution after transfer into irradiated mice. Deletion of Gata3 enhanced the repopulating capacity and augmented the self-renewal of long-term HSCs in cell-autonomous fashion without affecting the cell cycle. Our observations position GATA-3 as a regulator of the balance between self-renewal and differentiation in HSCs that acts downstream of the p38 signaling pathway.","authors":"Frelin, C., Herrington, R., Janmohamed, S., Barbara, M., Tran, G., Paige, CJ., Benveniste, P., Zu\u00f1iga-Pfl\u00fccker, JC., Souabni, A., Busslinger, M., Iscove, NN.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Immunol","volume":"14","issue":"10","page":"1037-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17889804","title":"Isolation of microRNA targets using biotinylated synthetic microRNAs.","abstract":"MicroRNAs are small regulatory RNAs found in multicellular organisms where they post-transcriptionally regulate gene expression. In animals, microRNAs bind mRNAs via incomplete base pairings making the identification of microRNA targets inherently difficult. Here, we present a detailed method for experimental identification of microRNA targets based on affinity purification of tagged microRNAs associated with their targets.","authors":"Orom, UA., Lund, AH.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Methods","volume":"43","issue":"2","page":"162-5","pdf":null,"JrId":"20385","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29313542","title":"A programmable platform for sub-second multichemical dynamic stimulation and neuronal functional imaging in C. elegans.","abstract":"Caenorhabditis elegans (C. elegans) is a prominent model organism in neuroscience, as its small stereotyped nervous system offers unique advantages for studying neuronal circuits at the cellular level. Characterizing temporal dynamics of neuronal circuits is essential to fully understand neuronal processing. Characterization of the temporal dynamics of chemosensory circuits requires a precise and fast method to deliver multiple stimuli and monitor the animal's neuronal activity. Microfluidic platforms have been developed that offer an improved control of chemical delivery compared to manual methods. However, stimulating an animal with multiple chemicals at high speed is still difficult. In this work, we have developed a platform that can deliver any sequence of multiple chemical reagents, at sub-second resolution and without cross-contamination. We designed a network of chemical selectors wherein the chemical selected for stimulation is determined by the set of pressures applied to the chemical reservoirs. Modulation of inlet pressures has been automated to create robust, programmable sequences of subsecond chemical pulses. We showed that stimulation with sequences of different chemicals at the second to sub-second range can generate different neuronal activity patterns in chemosensory neurons; we observed previously unseen neuronal responses to a controlled chemical stimulation. Because of the speed and versatility of stimulus generated, this platform opens new possibilities to investigate neuronal circuits.","authors":"Rouse, T., Aubry, G., Cho, Y., Zimmer, M., Lu, H.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Lab Chip","volume":"18","issue":"3","page":"505-513","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29186688","title":"Receptor Activator of NF-\u03baB Orchestrates Activation of Antiviral Memory CD8\u00a0T Cells in the Spleen Marginal Zone.","abstract":"The spleen plays an important role in protective immunity to bloodborne pathogens. Macrophages and dendritic cells (DCs) in the spleen marginal zone capture microbial antigens to trigger adaptive immune responses. Marginal zone macrophages (MZMs) can also act as a replicative niche for intracellular pathogens, providing a platform for mounting the immune response. Here, we describe a role for RANK in the coordinated function of antigen-presenting cells in the spleen marginal zone and triggering anti-viral immunity. Targeted deletion of RANK results in the selective loss of CD169<sup>+<\/sup> MZMs, which provide a niche for viral replication, while RANK signaling in DCs promotes the recruitment and activation of anti-viral memory CD8 T\u00a0cells. These studies reveal a role for the RANKL\/RANK signaling axis in the orchestration of protective immune responses in the spleen marginal zone that has important implications for the host response to viral infection and induction of acquired immunity.","authors":"Habbeddine, M., Verthuy, C., Rastoin, O., Chasson, L., Bebien, M., Bajenoff, M., Adriouch, S., den Haan, JMM., Penninger, JM., Lawrence, T.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Rep","volume":"21","issue":"9","page":"2515-2527","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30692207","title":"A ZNRF3-dependent Wnt\/\u03b2-catenin signaling gradient is required for adrenal homeostasis.","abstract":"Spatiotemporal control of Wnt signaling is essential for the development and homeostasis of many tissues. The transmembrane E3 ubiquitin ligases ZNRF3 (zinc and ring finger 3) and RNF43 (ring finger protein 43) antagonize Wnt signaling by promoting degradation of frizzled receptors. ZNRF3 and RNF43 are frequently inactivated in human cancer, but the molecular and therapeutic implications remain unclear. Here, we demonstrate that adrenocortical-specific loss of ZNRF3, but not RNF43, results in adrenal hyperplasia that depends on Porcupine-mediated Wnt ligand secretion. Furthermore, we discovered a Wnt\/\u03b2-catenin signaling gradient in the adrenal cortex that is disrupted upon loss of ZNRF3. Unlike \u03b2-catenin gain-of-function models, which induce high Wnt\/\u03b2-catenin activation and expansion of the peripheral cortex, ZNRF3 loss triggers activation of moderate-level Wnt\/\u03b2-catenin signaling that drives proliferative expansion of only the histologically and functionally distinct inner cortex. Genetically reducing \u03b2-catenin dosage significantly reverses the ZNRF3-deficient phenotype. Thus, homeostatic maintenance of the adrenal cortex is dependent on varying levels of Wnt\/\u03b2-catenin activation, which is regulated by ZNRF3.","authors":"Basham, KJ., Rodriguez, S., Turcu, AF., Lerario, AM., Logan, CY., Rysztak, MR., Gomez-Sanchez, CE., Breault, DT., Koo, BK., Clevers, H., Nusse, R., Val, P., Hammer, GD.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Genes Dev","volume":"33","issue":"3-4","page":"209-220","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23624931","title":"The chromodomain helicase Chd4 is required for Polycomb-mediated inhibition of astroglial differentiation.","abstract":"Polycomb group (PcG) proteins form transcriptional repressor complexes with well-established functions during cell-fate determination. Yet, the mechanisms underlying their regulation remain poorly understood. Here, we extend the role of Polycomb complexes in the temporal control of neural progenitor cell (NPC) commitment by demonstrating that the PcG protein Ezh2 is necessary to prevent the premature onset of gliogenesis. In addition, we identify the chromodomain helicase DNA-binding protein 4 (Chd4) as a critical interaction partner of Ezh2 required specifically for PcG-mediated suppression of the key astrogenic marker gene GFAP. Accordingly, in vivo depletion of Chd4 in the developing neocortex promotes astrogenesis. Collectively, these results demonstrate that PcG proteins operate in a highly dynamic, developmental stage-dependent fashion during neural differentiation and suggest that target gene-specific mechanisms regulate Polycomb function during sequential cell-fate decisions.","authors":"Sparmann, A., Xie, Y., Verhoeven, E., Vermeulen, M., Lancini, C., Gargiulo, G., Hulsman, D., Mann, M., Knoblich, JA., van Lohuizen, M.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"EMBO J","volume":"32","issue":"11","page":"1598-612","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23609018","title":"Lentiviral delivery of the human wild-type tau protein mediates a slow and progressive neurodegenerative tau pathology in the rat brain.","abstract":"Most models for tauopathy use a mutated form of the Tau gene, MAPT, that is found in frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17) and that leads to rapid neurofibrillary degeneration (NFD). Use of a wild-type (WT) form of human Tau protein to model the aggregation and associated neurodegenerative processes of Tau in the mouse brain has thus far been unsuccessful. In the present study, we generated an original \"sporadic tauopathy-like\" model in the rat hippocampus, encoding six Tau isoforms as found in humans, using lentiviral vectors (LVs) for the delivery of a human WT Tau. The overexpression of human WT Tau in pyramidal neurons resulted in NFD, the morphological characteristics and kinetics of which reflected the slow and sporadic neurodegenerative processes observed in sporadic tauopathies, unlike the rapid neurodegenerative processes leading to cell death and ghost tangles triggered by the FTDP-17 mutant Tau P301L. This new model highlights differences in the molecular and cellular mechanisms underlying the pathological processes induced by WT and mutant Tau and suggests that preference should be given to animal models using WT Tau in the quest to understand sporadic tauopathies.","authors":"Caillierez, R., B\u00e9gard, S., L\u00e9colle, K., Deramecourt, V., Zommer, N., Dujardin, S., Loyens, A., Dufour, N., Aur\u00e9gan, G., Winderickx, J., Hantraye, P., D\u00e9glon, N., Bu\u00e9e, L., Colin, M.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Mol Ther","volume":"21","issue":"7","page":"1358-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41490589","title":"A Robust and Reproducible Protocol for Neural Tube Organoid Generation from Single Mouse Embryonic Stem Cells.","abstract":"The development of mammals is a highly complex process, characterized by the necessity for precise concentration- and time-dependent signaling for correct pattern formation and morphogenesis. Despite considerable technological advancements and knowledge gathered, numerous aspects of mammalian development remain elusive. When examining the entire organism, it becomes challenging to disentangle the effects of individual pathways or the mechanism by which external stimuli guide the interference of surrounding tissues and factors.In addressing this complexity, three-dimensional (3D) in vitro models such as organoids have emerged as valuable tools. Organoids, derived from embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs), exhibit tissue-like features that closely resemble their in vivo counterparts in terms of expression patterns and functionality. Importantly, they offer accessibility for manipulation and extensive biological studies within a controlled experimental setting. Despite originating from pluripotent cultures, organoid systems often exhibit heterogeneity and substantial variability, limiting their utility when studying complex and intricate biological questions. Therefore, there is a pressing need for detailed protocols aimed at harmonizing procedures that result in high-quality reproducible data, reduction of materials used, and which importantly permit the investigation of convoluted phenomena. In this context, an optimized protocol for the cultivation of neural tube organoids (NTOs) in vitro is presented here. By producing stable culture conditions and offering comprehensive troubleshooting strategies, this protocol enables the reliable and reproducible generation of NTOs, which serve as an adequate model to study relevant scientific questions, including the mechanisms of neural induction, patterning, and early central nervous system development.","authors":"Krammer, T., Tanaka, EM.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"J Vis Exp","volume":null,"issue":"226","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-06","doi":"10.3791\/67883","first_author":"Krammer, T.","corresponding_authors":null},{"pmid":"17667939","title":"Targeting c-Jun and JunB proteins as potential anticancer cell therapy.","abstract":"The activating protein-1 transcription factor, in particular the Jun proteins play critical roles in the regulation of cell proliferation and tumor progression. To study the potential clinical relevance of interfering with JunB expression, we generated retroviruses expressing short hairpin RNA. Reduction of JunB levels causes increased proliferation and tumorigenicity in wild-type murine fibroblasts, whereas in c-Jun knockout cells p53-independent cell cycle arrest and apoptosis are induced. Using melanoma-derived B16-F10 cancer cells the combination of JunB knockdown and c-Jun\/JNK inactivation leads to cell cycle arrest and apoptosis-inducing factor-dependent apoptosis. Furthermore, the combined treatment extends survival of mice inoculated with the tumor cells. These results indicate that in the absence of c-Jun, JunB can act as a tumor promoter and inactivation of both, c-Jun and JunB, could provide a valuable strategy for antitumor intervention.","authors":"Gurzov, EN., Bakiri, L., Alfaro, JM., Wagner, EF., Izquierdo, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Oncogene","volume":"27","issue":"5","page":"641-52","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23578871","title":"Cell biology: Notch recycling is numbed.","abstract":"During asymmetric cell division, the Notch regulator Numb segregates unequally to establish different cell fates in the two daughter cells. Numb is thought to act as an endocytic protein. Two new studies show that Numb antagonizes Notch signaling by also regulating recycling of Sanpodo-Notch complexes via AP-1.","authors":"Reichardt, I., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Curr Biol","volume":"23","issue":"7","page":"R270-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23580551","title":"Quantitative in vivo analysis of chromatin binding of Polycomb and Trithorax group proteins reveals retention of ASH1 on mitotic chromatin.","abstract":"The Polycomb (PcG) and Trithorax (TrxG) group proteins work antagonistically on several hundred developmentally important target genes, giving stable mitotic memory, but also allowing flexibility of gene expression states. How this is achieved in quantitative terms is poorly understood. Here, we present a quantitative kinetic analysis in living Drosophila of the PcG proteins Enhancer of Zeste, (E(Z)), Pleiohomeotic (PHO) and Polycomb (PC) and the TrxG protein absent, small or homeotic discs 1 (ASH1). Fluorescence recovery after photobleaching and fluorescence correlation spectroscopy reveal highly dynamic chromatin binding behaviour for all proteins, with exchange occurring within seconds. We show that although the PcG proteins substantially dissociate from mitotic chromatin, ASH1 remains robustly associated with chromatin throughout mitosis. Finally, we show that chromatin binding by ASH1 and PC switches from an antagonistic relationship in interphase, to a cooperative one during mitosis. These results provide quantitative insights into PcG and TrxG chromatin-binding dynamics and have implications for our understanding of the molecular nature of epigenetic memory.","authors":"Steffen, PA., Fonseca, JP., G\u00e4nger, C., Dworschak, E., Kockmann, T., Beisel, C., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nucleic Acids Res","volume":"41","issue":"10","page":"5235-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23481674","title":"Family matters: structural and functional conservation of centromere-associated proteins from yeast to humans.","abstract":"Kinetochores form the fundamental link between chromosomal domains termed centromeres and spindle microtubules in all eukaryotes. This connection, provided by a large, multiprotein complex, is essential for precise chromosome segregation and thus ensures genetic stability. Here, we review recent insights into the composition and function of centromeric chromatin. Multiple approaches have converged to identify centromere-associated proteins from yeast to humans. Among them are newly characterized histone-fold family members that operate at the DNA-kinetochore interface and provide critical connections between chromosomes and microtubules. Together, these findings contribute to a unified view of how centromeric chromatin functions as a regulated scaffold for kinetochore assembly.","authors":"Westermann, S., Schleiffer, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Trends Cell Biol","volume":"23","issue":"6","page":"260-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23088386","title":"SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments.","abstract":"While the performance of liquid chromatography (LC) and mass spectrometry (MS) instrumentation continues to increase, applications such as analyses of complete or near-complete proteomes and quantitative studies require constant and optimal system performance. For this reason, research laboratories and core facilities alike are recommended to implement quality control (QC) measures as part of their routine workflows. Many laboratories perform sporadic quality control checks. However, successive and systematic longitudinal monitoring of system performance would be facilitated by dedicated automatic or semiautomatic software solutions that aid an effortless analysis and display of QC metrics over time. We present the software package SIMPATIQCO (SIMPle AuTomatIc Quality COntrol) designed for evaluation of data from LTQ Orbitrap, Q-Exactive, LTQ FT, and LTQ instruments. A centralized SIMPATIQCO server can process QC data from multiple instruments. The software calculates QC metrics supervising every step of data acquisition from LC and electrospray to MS. For each QC metric the software learns the range indicating adequate system performance from the uploaded data using robust statistics. Results are stored in a database and can be displayed in a comfortable manner from any computer in the laboratory via a web browser. QC data can be monitored for individual LC runs as well as plotted over time. SIMPATIQCO thus assists the longitudinal monitoring of important QC metrics such as peptide elution times, peak widths, intensities, total ion current (TIC) as well as sensitivity, and overall LC-MS system performance; in this way the software also helps identify potential problems. The SIMPATIQCO software package is available free of charge.","authors":"Pichler, P., Mazanek, M., Dusberger, F., Weilnb\u00f6ck, L., Huber, CG., Stingl, C., Luider, TM., Straube, WL., K\u00f6cher, T., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Proteome Res","volume":"11","issue":"11","page":"5540-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23083740","title":"Drosophila CPEB Orb2A mediates memory independent of Its RNA-binding domain.","abstract":"Long-term memory and synaptic plasticity are thought to require the synthesis of new proteins at activated synapses. The CPEB family of RNA binding proteins, including Drosophila Orb2, has been implicated in this process. The precise mechanism by which these molecules regulate memory formation is however poorly understood. We used gene targeting and site-specific transgenesis to specifically modify the endogenous orb2 gene in order to investigate its role in long-term memory formation. We show that the Orb2A and Orb2B isoforms, while both essential, have distinct functions in memory formation. These two isoforms have common glutamine-rich and RNA-binding domains, yet Orb2A uniquely requires the former and Orb2B the latter. We further show that Orb2A induces Orb2 complexes in a manner dependent upon both its glutamine-rich region and neuronal activity. We propose that Orb2B acts as a conventional CPEB to regulate transport and\/or translation of specific mRNAs, whereas Orb2A acts in an unconventional manner to form stable Orb2 complexes that are essential for memory to persist.","authors":"Kr\u00fcttner, S., Stepien, B., Noordermeer, JN., Mommaas, MA., Mechtler, K., Dickson, BJ., Keleman, K.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Neuron","volume":"76","issue":"2","page":"383-95","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21400590","title":"Thermoforming of film-based biomedical microdevices.","abstract":"For roughly ten years now, a new class of polymer micromoulding processes comes more and more into the focus both of the microtechnology and the biomedical engineering community. These processes can be subsumed under the term \"microthermoforming\". In microthermoforming, thin polymer films are heated to a softened, but still solid state and formed to thin-walled microdevices by three-dimensional stretching. The high material coherence during forming is in contrast to common polymer microreplication processes where the material is processed in a liquid or flowing state. It enables the preservation of premodifications of the film material. In this progress report, we review the still young state of the art of microthermoforming technology as well as its first applications. So far, the applications are mainly in the biomedical field. They benefit from the fact that thermoformed microdevices have unique properties resulting from their special, unusual morphology. The focus of this paper is on the impact of the new class of micromoulding processes and the processed film materials on the characteristics of the moulded microdevices and on their applications.","authors":"Truckenm\u00fcller, R., Giselbrecht, S., Rivron, N., Gottwald, E., Saile, V., van den Berg, A., Wessling, M., van Blitterswijk, C.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Adv Mater","volume":"23","issue":"11","page":"1311-29","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17617665","title":"A chemical proteomics approach to phosphatidylinositol 3-kinase signaling in macrophages.","abstract":"Prior work using lipid-based affinity matrices has been done to investigate distinct sets of lipid-binding proteins, and one series of experiments has proven successful in mammalian cells for the proteome-wide identification of lipid-binding proteins. However, most lipid-based proteomics screens require scaled up sample preparation, are often composed of multiple cell types, and are not adapted for simultaneous signal transduction studies. Herein we provide a chemical proteomics strategy that uses cleavable lipid \"baits\" with broad applicability to diverse biological samples. The novel baits were designed to avoid preparative steps to allow functional proteomics studies when the biological source is a limiting factor. Validation of the chemical baits was first confirmed by the selective isolation of several known endogenous phosphatidylinositol 3-kinase signaling proteins using primary bone marrow-derived macrophages. The use of this technique for cellular proteomics and MS\/MS analysis was then demonstrated by the identification of known and potential novel lipid-binding proteins that was confirmed in vitro for several proteins by direct lipid-protein interactions. Further to the identification, the method is also compatible with subsequent signal transduction studies, notably for protein kinase profiling of the isolated lipid-bound protein complexes. Taken together, this integration of minimal scale proteomics, lipid chemistry, and activity-based readouts provides a significant advancement in the ability to identify and study the lipid proteome of single, relevant cell types.","authors":"Pasquali, C., Bertschy-Meier, D., Chabert, C., Curchod, ML., Arod, C., Booth, R., Mechtler, K., Vilbois, F., Xenarios, I., Ferguson, CG., Prestwich, GD., Camps, M., Rommel, C.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Cell Proteomics","volume":"6","issue":"11","page":"1829-41","pdf":null,"JrId":"26755","fulltextlink":null,"preprintlink":null,"articledate":"2008-01-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23081976","title":"An investigation into the epidemiology of feline obesity in Great Britain: results of a cross-sectional study of 47 companion animal practises.","abstract":"Previous epidemiological studies of feline obesity have been restricted to small geographical areas of Great Britain. This study represents the first published description of the prevalence and risk factors for obesity from a nationally distributed population of cats. Data were gathered from 3227 cats through 47 primary companion animal veterinary practises. The\u00a0overall prevalence of overweight\/obesity was 11.5 per cent (95% confidence interval 10.4 per cent to 12.6 per cent) in cats attending the charity's clinics. Cats in Scotland appeared to have a greater age and neutered-adjusted prevalence compared with cats in England. Neutered status, being male and middle age (around 7 years), were all significant risk factors for feline overweight\/obesity, although they did not fully explain an individual cat's risk of overweight\/obesity. Breed was not found to be a statistically significant risk factor. Partial attributable fractions were calculated from each of the significant risk factors. Neutered status appeared to contribute the most to the prevalence of obesity, followed by prime\/mature lifestage (3-10 years of age). Any interpretations of these findings should take into account the multitude of biases inherent in this study. Nevertheless, weight management following neutering appears to be very important to reduce the overall prevalence of overweight\/obesity in this population of cats.","authors":"Courcier, EA., Mellor, DJ., Pendlebury, E., Evans, C., Yam, PS.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Vet Rec","volume":"171","issue":"22","page":"560","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28880281","title":"A right-handed signalling pathway drives heart looping in vertebrates.","abstract":"Most animals show external bilateral symmetry, which hinders the observation of multiple internal left-right (L\/R) asymmetries that are fundamental to organ packaging and function. In vertebrates, left identity is mediated by the left-specific Nodal-Pitx2 axis that is repressed on the right-hand side by the epithelial-mesenchymal transition (EMT) inducer Snail1 (refs 3, 4). Despite some existing evidence, it remains unclear whether an equivalent instructive pathway provides right-hand-specific information to the embryo. Here we show that, in zebrafish, BMP mediates the L\/R asymmetric activation of another EMT inducer, Prrx1a, in the lateral plate mesoderm with higher levels on the right. Prrx1a drives L\/R differential cell movements towards the midline, leading to a leftward displacement of the cardiac posterior pole through an actomyosin-dependent mechanism. Downregulation of Prrx1a prevents heart looping and leads to mesocardia. Two parallel and mutually repressed pathways, respectively driven by Nodal and BMP on the left and right lateral plate mesoderm, converge on the asymmetric activation of the transcription factors Pitx2 and Prrx1, which integrate left and right information to govern heart morphogenesis. This mechanism is conserved in the chicken embryo, and in the mouse SNAIL1 acts in a similar manner to Prrx1a in zebrafish and PRRX1 in the chick. Thus, a differential L\/R EMT produces asymmetric cell movements and forces, more prominent from the right, that drive heart laterality in vertebrates.","authors":"Oca\u00f1a, OH., Coskun, H., Minguill\u00f3n, C., Murawala, P., Tanaka, EM., Galcer\u00e1n, J., Mu\u00f1oz-Ch\u00e1puli, R., Nieto, MA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"549","issue":"7670","page":"86-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28292837","title":"The hope and the hype of organoid research.","abstract":"The recent increase in organoid research has been met with great enthusiasm, as well as expectation, from the scientific community and the public alike. There is no doubt that this technology opens up a world of possibilities for scientific discovery in developmental biology as well as in translational research, but whether organoids can truly live up to this challenge is, for some, still an open question. In this Spotlight article, Meritxell Huch and Juergen Knoblich begin by discussing the exciting promise of organoid technology and give concrete examples of how this promise is starting to be realised. In the second part, Matthias Lutolf and Alfonso Martinez-Arias offer a careful and considered view of the state of the organoid field and its current limitations, and lay out the approach they feel is necessary to maximise the potential of organoid technology.","authors":"Huch, M., Knoblich, JA., Lutolf, MP., Martinez-Arias, A.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Development","volume":"144","issue":"6","page":"938-941","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1297655","title":"Identification of Fos target genes by the use of selective induction systems.","abstract":"c-Fos is a major component of the transcription factor AP-1 which has been implicated in the control of cell proliferation and differentiation as well as in transformation. In order to identify Fos target genes involved in these processes, we have taken advantage of the regulatory properties of the hormone-binding domain of the human estrogen receptor to develop transcriptional and post-translational induction systems, both of which allow selective elevation of Fos activity within a cell. Using this approach we have searched for Fos-responsive genes in rat fibroblasts and PC12 cells. Here we describe the identification and regulation of five Fos-responsive genes encoding a transcription factor (Fra-1), a secreted protein (Fit-1), a biosynthetic enzyme (ODC) and two membrane-associated proteins (annexin II and V), respectively. The post-translational induction system was also used to study the Fos-mediated block of neuronal differentiation of PC12 cells. These experiments demonstrate that Fos activity is dominant over NGF function and interferes with the expression of late NGF-inducible genes.","authors":"Braselmann, S., Bergers, G., Wrighton, C., Graninger, P., Superti-Furga, G., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"J Cell Sci Suppl","volume":"16","issue":null,"page":"97-109","pdf":null,"JrId":"4591","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23081802","title":"Silica monoliths with hierarchical porosity obtained from porous glasses.","abstract":"This review deals with \"classical\" porous glasses which are prepared by physical phase separation of alkali borosilicate glasses of suitable composition in combination with selective leaching. The resulting materials are characterized by a controllable pore size in the nanometer range, high mechanical, thermal and chemical stability and an adjustable macroscopic shape, which enables manufacturing of glass monoliths with various geometries. As a result of their formation, porous glasses obtained from physical phase separation exhibit a monomodal pore structure. There are only a few examples in the literature for the synthesis of hierarchically porous glasses. This review covers several synthesis strategies for the introduction of hierarchy into \"classical\" porous glass monoliths, including sintering and fusion of alkali borosilicate initial glasses as well as partial or complete pseudomorphic transformation of porous glasses into zeolites or ordered mesoporous materials.","authors":"Inayat, A., Reinhardt, B., Uhlig, H., Einicke, WD., Enke, D.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Chem Soc Rev","volume":"42","issue":"9","page":"3753-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17599067","title":"Involvement of the ubiquitin-like domain of TBK1\/IKK-i kinases in regulation of IFN-inducible genes.","abstract":"TANK-binding kinase 1 (TBK1\/NAK\/T2K) and I-kappaB Kinase (IKK-i\/IKK-epsilon) play important roles in the regulation of interferon (IFN)-inducible genes during the immune response to bacterial and viral infections. Cell stimulation with ssRNA virus, dsDNA virus or gram-negative bacteria leads to activation of TBK1 or IKK-i, which in turn phosphorylates the transcription factors, IFN-regulatory factor (IRF) 3 and IRF7, promoting their translocation in the nucleus. To understand the molecular basis of activation of TBK1, we analyzed the sequence of TBK1 and IKK-i and identified a ubiquitin-like domain (ULD) adjacent to their kinase domains. Deletion or mutations of the ULD in TBK1 or IKK-i impaired activation of respective kinases, failed to induce IRF3 phosphorylation and nuclear localization and to activate IFN-beta or RANTES promoters. The importance of the ULD of TBK1 in LPS- or poly(I:C)-stimulated IFN-beta production was demonstrated by reconstitution experiments in TBK1-IKK-i-deficient cells. We propose that the ULD is a regulatory component of the TBK1\/IKK-i kinases involved in the control of the kinase activation, substrate presentation and downstream signaling pathways.","authors":"Ikeda, F., Hecker, CM., Rozenknop, A., Nordmeier, RD., Rogov, V., Hofmann, K., Akira, S., D\u00f6tsch, V., Dikic, I.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"EMBO J","volume":"26","issue":"14","page":"3451-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17592038","title":"Isolation of microRNA targets by miRNP immunopurification.","abstract":"microRNAs (miRNAs) serve as post-transcriptional regulators of gene expression, by guiding effector complexes (miRNPs) to target RNAs. Although considerable progress has been made in computational methods to identify miRNA targets, only a relatively limited assessment of their ability to function in vivo has been reported. Here we describe an alternative approach to miRNA target identification based on a biochemical method for purifying miRNP complexes with associated miRNAs and bound mRNA targets. Microarray analysis revealed a high degree of enrichment for miRNA complementary sites in the 3'UTRs of the miRNP-associated mRNAs. mRNAs specifically associated with an individual miRNA were identified by comparing the miRNP-associated mRNAs from wild-type flies and mutant flies lacking miR-1, and their regulation by the miRNA was validated. This approach provides a means to identify functional miRNA targets based on their physical interaction in vivo.","authors":"Easow, G., Teleman, AA., Cohen, SM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"RNA","volume":"13","issue":"8","page":"1198-204","pdf":null,"JrId":"8792","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17558394","title":"Maximal chromosome compaction occurs by axial shortening in anaphase and depends on Aurora kinase.","abstract":"Eukaryotic cells must first compact their chromosomes before faithfully segregating them during cell division. Failure to do so can lead to segregation defects with pathological consequences, such as aneuploidy and cancer. Duplicated interphase chromosomes are, therefore, reorganized into tight rods before being separated and directed to the newly forming daughter cells. This vital reorganization of chromatin remains poorly understood. To address the dynamics of mitotic condensation of single chromosomes in intact cells, we developed quantitative assays based on confocal time-lapse microscopy of live mammalian cells stably expressing fluorescently tagged core histones. Surprisingly, maximal compaction was not reached in metaphase, but in late anaphase, after sister chromatid segregation. We show that anaphase compaction proceeds by a mechanism of axial shortening of the chromatid arms from telomere to centromere. Chromatid axial shortening was not affected in condensin-depleted cells, but depended instead on dynamic microtubules and Aurora kinase. Acute perturbation of this compaction resulted in failure to rescue segregation defects and in multilobed daughter nuclei, suggesting functions in chromosome segregation and nuclear architecture.","authors":"Mora-Berm\u00fadez, F., Gerlich, D., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Cell Biol","volume":"9","issue":"7","page":"822-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26072434","title":"STARR-seq - principles and applications.","abstract":"Differential gene expression is the basis for cell type diversity in multicellular organisms and the driving force of development and differentiation. It is achieved by cell type-specific transcriptional enhancers, which are genomic DNA sequences that activate the transcription of their target genes. Their identification and characterization is fundamental to our understanding of gene regulation. Features that are associated with enhancer activity, such as regulatory factor binding or histone modifications can predict the location of enhancers. Nonetheless, enhancer activity can only be assessed by transcriptional reporter assays. Over the past years massively parallel reporter assays have been developed for large scale testing of enhancers. In this review we focus on the principles and applications of STARR-seq, a functional assay that quantifies enhancer strengths in complex candidate libraries and thus allows activity-based enhancer identification in entire genomes. We explain how STARR-seq works, discuss current uses and give an outlook to future applications.","authors":"Muerdter, F., Bory\u0144, \u0141M., Arnold, CD.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Genomics","volume":"106","issue":"3","page":"145-150","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23080406","title":"Effects of hydrogen sulfide on bacterial communities on the surface of galatheid crab, Shinkaia crosnieri, and in a bacterial mat cultured in rearing tanks.","abstract":"To investigate the effects of H2S on the bacterial consortia on the galatheid crab, Shinkaia crosnieri, crabs of this species were cultivated in the laboratory under two different conditions, with and without hydrogen sulfide feeding. We developed a novel rearing tank system equipped with a feedback controller using a semiconductor sensor for hydrogen sulfide feeding. H2S aqueous concentration was successfully maintained between 5 to 40 \u00b5M for 80 d with the exception of brief periods of mechanical issues. According to real-time PCR analysis, the numbers of copies of partial 16S rRNA gene of an episymbiont of the crabs with H2S feeding was three orders of magnitude larger than that without feeding. By phylogenetic analysis of partial 16S rRNA gene, we detected several clones related to symbionts of deep sea organisms in Alphaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, and Flavobacteria, from a crab with H2S feeding. The symbiont-related clones were grouped into four different groups: Gammaproteobacteria in marine epibiont group I, Sulfurovum-affiliated Epsilonproteobacteria, Osedax mucofloris endosymbiont-affiliated Epsilonproteobacteria, and Flavobacteria closely related to CFB group bacterial epibiont of Rimicaris exoculata. The other phylotypes were related to Roseobacter, and some Flavobacteria, seemed to be free-living psychrophiles. Furthermore, white biofilm occurred on the surface of the rearing tank with H2S feeding. The biofilms contained various phylotypes of Gammaproteobacteria, Epsilonproteobacteria, and Flavobacteria, as determined by phylogenetic analysis. Interestingly, major clones were related to symbionts of Alviniconcha sp. type 2 and to endosymbionts of Osedax mucofloris, in Epsilonproteobacteria.","authors":"Konishi, M., Watsuji, TO., Nakagawa, S., Hatada, Y., Takai, K., Toyofuku, T.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Microbes Environ","volume":"28","issue":"1","page":"25-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17545998","title":"Titanium dioxide as a chemo-affinity solid phase in offline phosphopeptide chromatography prior to HPLC-MS\/MS analysis.","abstract":"We have developed a new offline chromatographic approach for the selective enrichment of phosphorylated peptides that is directly compatible with subsequent analysis by online nano electrospray ionization tandem mass spectrometry. In this technique, a titanium dioxide (TiO2)-packed pipette tip is used as a phosphopeptide trap that acts as an offline first-dimension separation step in a two-dimensional chromatography system. This is followed by online nano reversed-phase high-performance liquid chromatography. Here, we present suitable methods for enrichment, optimized separately for each step: sample loading, washing and elution from the TiO2-filled tips. To increase the trapping selectivity of the TiO2 column, we used the sodium salt of 1-octanesulfonic acid combined with 2,5-dihydroxybenzoic acid as ion-pairing agents and displacers for acidic peptides. These agents also improve the binding of phosphorylated peptides and block the binding of non-phosphorylated ones. This enrichment procedure takes 30 min, followed by a 100-min HPLC program, including washing and an elution gradient.","authors":"Mazanek, M., Mituloviae, G., Herzog, F., Stingl, C., Hutchins, JR., Peters, JM., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Protoc","volume":"2","issue":"5","page":"1059-69","pdf":null,"JrId":"33047","fulltextlink":null,"preprintlink":null,"articledate":"2008-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17517772","title":"RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition.","abstract":"RNA chaperone activity is defined as the ability of proteins to either prevent RNA from misfolding or to open up misfolded RNA conformations. One-third of all large ribosomal subunit proteins from E. coli display this activity, with L1 exhibiting one of the highest activities. Here, we demonstrate via the use of in vitro trans- and cis-splicing assays that the RNA chaperone activity of L1 is conserved in all three domains of life. However, thermophilic archaeal L1 proteins do not display RNA chaperone activity under the experimental conditions tested here. Furthermore, L1 does not exhibit RNA chaperone activity when in complexes with its cognate rRNA or mRNA substrates. The evolutionary conservation of the RNA chaperone activity among L1 proteins suggests a functional requirement during ribosome assembly, at least in bacteria, mesophilic archaea and eukarya. Surprisingly, rather than facilitating catalysis, the thermophilic archaeal L1 protein from Methanococcus jannaschii (MjaL1) completely inhibits splicing of the group I thymidylate synthase intron from phage T4. Mutational analysis of MjaL1 excludes the possibility that the inhibitory effect is due to stronger RNA binding. To our knowledge, MjaL1 is the first example of a protein that inhibits group I intron splicing.","authors":"Ameres, SL., Shcherbakov, D., Nikonova, E., Piendl, W., Schroeder, R., Semrad, K.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nucleic Acids Res","volume":"35","issue":"11","page":"3752-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23065599","title":"Requirement for stromal estrogen receptor alpha in cervical neoplasia.","abstract":"The major etiological factor for cervical cancer is the high-risk human papillomavirus (HPV), which encodes E6 and E7 oncogenes. However, HPV is not sufficient, and estrogen has been proposed as an etiological cofactor for the disease. Its requirement has been demonstrated in mouse models for HPV-associated cervical cancer (e.g., K14E7 transgenic mice). Although germline knockout of estrogen receptor alpha (ER\u03b1) renders mice resistant to cervical cancer, the cell-type-specific requirement for ER\u03b1 is not known. In this study, we demonstrate that temporal deletion of stromal ER\u03b1 induced complete regression of cervical dysplasia in K14E7 mice. Our results strongly support the hypothesis that stromal ER\u03b1 is necessary for HPV-induced cervical carcinogenesis and implicate paracrine mechanisms involving ER\u03b1 signaling in the development of estrogen-dependent cervical cancers. This is the first evidence to support the importance of stromal ER\u03b1 in estrogen-dependent neoplastic disease of the female reproductive tract.","authors":"Chung, SH., Shin, MK., Korach, KS., Lambert, PF.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Horm Cancer","volume":"4","issue":"1","page":"50-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23063333","title":"The transcription factor GATA-3 controls cell fate and maintenance of type 2 innate lymphoid cells.","abstract":"Innate lymphoid cells (ILCs) reside at mucosal surfaces and control immunity to intestinal infections. Type 2 innate lymphoid cells (ILC2s) produce cytokines such as IL-5 and IL-13, are required for immune defense against helminth infections, and are involved in the pathogenesis of airway hyperreactivity. Here, we have investigated the role of the transcription factor GATA-3 for ILC2 differentiation and maintenance. We showed that ILC2s and their lineage-specified bone marrow precursors (ILC2Ps), as identified here, were characterized by continuous high expression of GATA-3. Analysis of mice with temporary deletion of GATA-3 in all ILCs showed that GATA-3 was required for the differentiation and maintenance of ILC2s but not for ROR\u03b3t(+) ILCs. Thus, our data demonstrate that GATA-3 is essential for ILC2 fate decisions and reveal similarities between the transcriptional programs controlling ILC and T helper cell fates.","authors":"Hoyler, T., Klose, CS., Souabni, A., Turqueti-Neves, A., Pfeifer, D., Rawlins, EL., Voehringer, D., Busslinger, M., Diefenbach, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Immunity","volume":"37","issue":"4","page":"634-48","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22103557","title":"Developmentally programmed, RNA-directed genome rearrangement in Tetrahymena.","abstract":"Developmentally programmed genome rearrangement has been observed in a variety of eukaryotes from vertebrates to worms to protists, and it provides an interesting exception to the general rule of the constancy of the genome. DNA elimination in the ciliated protozoan Tetrahymena is one of the most well-characterized programmed genome rearrangement events. DNA elimination in the newly formed macronucleus of Tetrahymena is epigenetically regulated by the DNA sequence of the parental macronucleus. Dicer-produced, Piwi-associated small RNAs mediate this epigenetic regulation, probably through a whole-genome comparison of the germline micronucleus to the somatic macronucleus. However, a correlation between small RNAs and programmed genome rearrangement could not be detected in the worm Ascaris suum. Therefore, different types of eukaryotes may have developed unique solutions to perform genome rearrangement.","authors":"Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Dev Growth Differ","volume":"54","issue":"1","page":"108-19","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28446710","title":"Linear ubiquitin chains: enzymes, mechanisms and biology.","abstract":"Ubiquitination is a versatile post-translational modification that regulates a multitude of cellular processes. Its versatility is based on the ability of ubiquitin to form multiple types of polyubiquitin chains, which are recognized by specific ubiquitin receptors to induce the required cellular response. Linear ubiquitin chains are linked through Met 1 and have been established as important players of inflammatory signalling and apoptotic cell death. These chains are generated by a ubiquitin E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) that is thus far the only E3 ligase capable of forming linear ubiquitin chains. The complex consists of three subunits, HOIP, HOIL-1L and SHARPIN, each of which have specific roles in the observed biological functions of LUBAC. Furthermore, LUBAC has been found to be associated with OTULIN and CYLD, deubiquitinases that disassemble linear chains and counterbalance the E3 ligase activity of LUBAC. Gene mutations in HOIP, HOIL-1L and OTULIN are found in human patients who suffer from autoimmune diseases, and HOIL-1L mutations are also found in myopathy patients. In this paper, we discuss the mechanisms of linear ubiquitin chain generation and disassembly by their respective enzymes and review our current understanding of their biological functions and association with human diseases.","authors":"Rittinger, K., Ikeda, F.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Open Biol","volume":"7","issue":"4","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17502664","title":"RANK signals from CD4(+)3(-) inducer cells regulate development of Aire-expressing epithelial cells in the thymic medulla.","abstract":"Aire-expressing medullary thymic epithelial cells (mTECs) play a key role in preventing autoimmunity by expressing tissue-restricted antigens to help purge the emerging T cell receptor repertoire of self-reactive specificities. Here we demonstrate a novel role for a CD4(+)3(-) inducer cell population, previously linked to development of organized secondary lymphoid structures and maintenance of T cell memory in the functional regulation of Aire-mediated promiscuous gene expression in the thymus. CD4(+)3(-) cells are closely associated with mTECs in adult thymus, and in fetal thymus their appearance is temporally linked with the appearance of Aire(+) mTECs. We show that RANKL signals from this cell promote the maturation of RANK-expressing CD80(-)Aire(-) mTEC progenitors into CD80(+)Aire(+) mTECs, and that transplantation of RANK-deficient thymic stroma into immunodeficient hosts induces autoimmunity. Collectively, our data reveal cellular and molecular mechanisms leading to the generation of Aire(+) mTECs and highlight a previously unrecognized role for CD4(+)3(-)RANKL(+) inducer cells in intrathymic self-tolerance.","authors":"Rossi, SW., Kim, MY., Leibbrandt, A., Parnell, SM., Jenkinson, WE., Glanville, SH., McConnell, FM., Scott, HS., Penninger, JM., Jenkinson, EJ., Lane, PJ., Anderson, G.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Exp Med","volume":"204","issue":"6","page":"1267-72","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17485464","title":"NF-kappaB p50 and p52 regulate receptor activator of NF-kappaB ligand (RANKL) and tumor necrosis factor-induced osteoclast precursor differentiation by activating c-Fos and NFATc1.","abstract":"Postmenopausal osteoporosis and rheumatoid joint destruction result from increased osteoclast formation and bone resorption induced by receptor activator of NF-kappaB ligand (RANKL) and tumor necrosis factor (TNF). Osteoclast formation induced by these cytokines requires NF-kappaB p50 and p52, c-Fos, and NFATc1 expression in osteoclast precursors. c-Fos induces NFATc1, but the relationship between NF-kappaB and these other transcription factors in osteoclastogenesis remains poorly understood. We report that RANKL and TNF can induce osteoclast formation directly from NF-kappaB p50\/p52 double knockout (dKO) osteoclast precursors when either c-Fos or NFATc1 is expressed. RANKL- or TNF-induced c-Fos up-regulation and activation are abolished in dKO cells and in wild-type cells treated with an NF-kappaB inhibitor. c-Fos expression requires concomitant RANKL or TNF treatment to induce NFATc1 activation in the dKO cells. Furthermore, c-Fos expression increases the number and resorptive capacity of wild-type osteoclasts induced by TNF in vitro. We conclude that NF-kappaB controls early osteoclast differentiation from precursors induced directly by RANKL and TNF, leading to activation of c-Fos followed by NFATc1. Inhibition of NF-kappaB should prevent RANKL- and TNF-induced bone resorption.","authors":"Yamashita, T., Yao, Z., Li, F., Zhang, Q., Badell, IR., Schwarz, EM., Takeshita, S., Wagner, EF., Noda, M., Matsuo, K., Xing, L., Boyce, BF.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Biol Chem","volume":"282","issue":"25","page":"18245-18253","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28371822","title":"ELABELA-APJ axis protects from pressure overload heart failure and angiotensin II-induced cardiac damage.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">28371822<\/PMID><DateCompleted><Year>2018<\/Year><Month>02<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>07<\/Month><Day>18<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1755-3245<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>113<\/Volume><Issue>7<\/Issue><PubDate><Year>2017<\/Year><Month>Jun<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Cardiovascular research<\/Title><ISOAbbreviation>Cardiovasc Res<\/ISOAbbreviation><\/Journal><ArticleTitle>ELABELA-APJ axis protects from pressure overload heart failure and angiotensin II-induced cardiac damage.<\/ArticleTitle><Pagination><MedlinePgn>760-769<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/cvr\/cvx061<\/ELocationID><Abstract><AbstractText Label=\"Aims\" NlmCategory=\"UNASSIGNED\">Elabela\/Toddler\/Apela (ELA) has been identified as a novel endogenous peptide ligand for APJ\/Apelin receptor\/Aplnr. ELA plays a crucial role in early cardiac development of zebrafish as well as in maintenance of self-renewal of human embryonic stem cells. Apelin was the first identified APJ ligand, and exerts positive inotropic heart effects and regulates the renin-angiotensin system. The aim of this study was to investigate the biological effects of ELA in the cardiovascular system.","authors":"Sato, T., Sato, C., Kadowaki, A., Watanabe, H., Ho, L., Ishida, J., Yamaguchi, T., Kimura, A., Fukamizu, A., Penninger, JM., Reversade, B., Ito, H., Imai, Y., Kuba, K.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cardiovasc Res","volume":"113","issue":"7","page":"760-769","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17468757","title":"p38alpha suppresses normal and cancer cell proliferation by antagonizing the JNK-c-Jun pathway.","abstract":"The mitogen-activated protein kinase (MAPK) p38alpha controls inflammatory responses and cell proliferation. Using mice carrying conditional Mapk14 (also known as p38alpha) alleles, we investigated its function in postnatal development and tumorigenesis. When we specifically deleted Mapk14 in the mouse embryo, fetuses developed to term but died shortly after birth, probably owing to lung dysfunction. Fetal hematopoietic cells and embryonic fibroblasts deficient in p38alpha showed increased proliferation resulting from sustained activation of the c-Jun N-terminal kinase (JNK)-c-Jun pathway. Notably, in chemical-induced liver cancer development, mice with liver-specific deletion of Mapk14 showed enhanced hepatocyte proliferation and tumor development that correlated with upregulation of the JNK-c-Jun pathway. Furthermore, inactivation of JNK or c-Jun suppressed the increased proliferation of Mapk14-deficient hepatocytes and tumor cells. These results demonstrate a new mechanism whereby p38alpha negatively regulates cell proliferation by antagonizing the JNK-c-Jun pathway in multiple cell types and in liver cancer development.","authors":"Hui, L., Bakiri, L., Mairhorfer, A., Schweifer, N., Haslinger, C., Kenner, L., Komnenovic, V., Scheuch, H., Beug, H., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Genet","volume":"39","issue":"6","page":"741-9","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17457055","title":"Plasticity of mammalian myotubes upon stimulation with a thrombin-activated serum factor.","abstract":"Salamanders display unique regeneration abilities among adult vertebrates. An intriguing feature of salamander regeneration is the dedifferentiation of cells, such as myofibers and myotubes at the injury site, a process that involves cell cycle reentry from the differentiated state. A thrombin-activated serum factor that is distinct from conventional growth factors is known to cause S-phase reentry in salamander myotubes. While mammalian myotubes do not reenter S-phase upon serum stimulation, an upregulation of some immediate early genes such as jun and fos has been observed. Until now, it was unknown whether this transcriptional response was stimulated by conventional growth factors or by the thrombin-activated serum factor. By measuring transcriptional activity in individually purified C2C12 mouse myotubes using quantitative reverse transcription polymerase chain reactions, we show that a set of immediate early genes are activated in response to the thrombin-activated serum factor in a distinct manner from the growth factors PDGF, FGF and EGF. A partially purified fraction of the thrombin activated serum factor elicited stronger upregulation of a broader set of genes compared to individual growth factors and additionally caused downregulation of E2F6. Despite this robust transcriptional response in mammalian myotubes, we did not detect a large-scale change in histone H3K9 di-methylation or S-phase, a feature that characterizes salamander serum-stimulated myotubes. Our results indicate that mammalian myotubes have retained responsiveness to the thrombin-activated serum factor, but full reentry into S-phase is prevented by factors downstream of the immediate early genes.","authors":"L\u00f6\u00f6f, S., Straube, WL., Drechsel, D., Tanaka, EM., Simon, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell Cycle","volume":"6","issue":"9","page":"1096-101","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-08-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22962576","title":"Identification of pro-inflammatory cytokines associated with muscle invasive bladder cancer; the roles of IL-5, IL-20, and IL-28A.","abstract":"We used gene expression profiling to identify inflammatory cytokines that correlate with bladder cancer development. Gene expression profiles of the tissue samples were investigated using cDNA microarrays that contained 103 non-muscle invasive bladder cancers (NMIBC), 62 muscle invasive bladder cancers (MIBC), 58 samples of histologically normal-looking surrounding tissues, and 10 normal, healthy subjects who served as the control cohort for comparison. We grouped the data-sets according to biological characterizations and focused on immune response genes with at least 2-fold differential expression in MIBC vs. controls. The experimental data-set identified 36 immune-related genes that were significantly altered in MIBC samples. In addition, 10 genes were up-regulated and 26 genes were down-regulated in MIBC samples compared with the normal tissues. Among the 10 up-regulated molecules examined, the capacity for both wound-healing migration and invasion was enhanced in response to IL-5, IL-20, and IL-28A in bladder cancer cell lines (253J and EJ cells), compared with untreated cells. The expression levels of IL-5, IL-20, and IL-28A were increased in patients with MIBC. All 3 cytokines and their receptors were produced in bladder cancer cell lines, as determined by real-time PCR, immunoblot analysis and confocal immunofluorescence. Up-regulation of MMP-2 and MMP-9 was found after IL-5, IL-20, and IL-28A stimulation in both cell types. Moreover, an EMSA assay showed that treatment with IL-5, IL-20, and IL-28A induced activation of the transcription factors NF-\u03baB and AP-1 that regulate the MMP-9 promoter. Finally, activation of MAPK and Jak-Stat signaling was observed after the addition of IL-5, IL-20, and IL-28A to bladder cancer cells. This study suggests the presence of specific inflammatory cytokine (IL-5, IL-20, and IL-28A)-mediated association in bladder cancer development. All 3 cytokines may be important new molecular targets for the modulation of migration and invasion in bladder cancer.","authors":"Lee, SJ., Lee, EJ., Kim, SK., Jeong, P., Cho, YH., Yun, SJ., Kim, S., Kim, GY., Choi, YH., Cha, EJ., Kim, WJ., Moon, SK.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"9","page":"e40267","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22902560","title":"A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing.","abstract":"Epigenetic silencing of transposons by Piwi-interacting RNAs (piRNAs) constitutes an RNA-based genome defense mechanism. Piwi endonuclease action amplifies the piRNA pool by generating new piRNAs from target transcripts by a poorly understood mechanism. Here, we identified mouse Fkbp6 as a factor in this biogenesis pathway delivering piRNAs to the Piwi protein Miwi2. Mice lacking Fkbp6 derepress LINE1 (L1) retrotransposon and display reduced DNA methylation due to deficient nuclear accumulation of Miwi2. Like other cochaperones, Fkbp6 associates with the molecular chaperone Hsp90 via its tetratricopeptide repeat (TPR) domain. Inhibition of the ATP-dependent Hsp90 activity in an insect cell culture model results in the accumulation of short antisense RNAs in Piwi complexes. We identify these to be byproducts of piRNA amplification that accumulate only in nuage-localized Piwi proteins. We propose that the chaperone machinery normally ejects these inhibitory RNAs, allowing turnover of Piwi complexes for their continued participation in piRNA amplification.","authors":"Xiol, J., Cora, E., Koglgruber, R., Chuma, S., Subramanian, S., Hosokawa, M., Reuter, M., Yang, Z., Berninger, P., Palencia, A., Benes, V., Penninger, J., Sachidanandam, R., Pillai, RS.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Mol Cell","volume":"47","issue":"6","page":"970-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17451744","title":"HotPatch: a statistical approach to finding biologically relevant features on protein surfaces.","abstract":"We describe a fully automated algorithm for finding functional sites on protein structures. Our method finds surface patches of unusual physicochemical properties on protein structures, and estimates the patches' probability of overlapping functional sites. Other methods for predicting the locations of specific types of functional sites exist, but in previous analyses, it has been difficult to compare methods when they are applied to different types of sites. Thus, we introduce a new statistical framework that enables rigorous comparisons of the usefulness of different physicochemical properties for predicting virtually any kind of functional site. The program's statistical models were trained for 11 individual properties (electrostatics, concavity, hydrophobicity, etc.) and for 15 neural network combination properties, all optimized and tested on 15 diverse protein functions. To simulate what to expect if the program were run on proteins of unknown function, as might arise from structural genomics, we tested it on 618 proteins of diverse mixed functions. In the higher-scoring top half of all predictions, a functional residue could typically be found within the first 1.7 residues chosen at random. The program may or may not use partial information about the protein's function type as an input, depending on which statistical model the user chooses to employ. If function type is used as an additional constraint, prediction accuracy usually increases, and is particularly good for enzymes, DNA-interacting sites, and oligomeric interfaces. The program can be accessed online (at http:\/\/hotpatch.mbi.ucla.edu).","authors":"Pettit, FK., Bare, E., Tsai, A., Bowie, JU.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Mol Biol","volume":"369","issue":"3","page":"863-79","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15905403","title":"An active role for tRNA in decoding beyond codon:anticodon pairing.","abstract":"During transfer RNA (tRNA) selection, a cognate codon:anticodon interaction triggers a series of events that ultimately results in the acceptance of that tRNA into the ribosome for peptide-bond formation. High-fidelity discrimination between the cognate tRNA and near- and noncognate ones depends both on their differential dissociation rates from the ribosome and on specific acceleration of forward rate constants by cognate species. Here we show that a mutant tRNA(Trp) carrying a single substitution in its D-arm achieves elevated levels of miscoding by accelerating these forward rate constants independent of codon:anticodon pairing in the decoding center. These data provide evidence for a direct role for tRNA in signaling its own acceptance during decoding and support its fundamental role during the evolution of protein synthesis.","authors":"Cochella, L., Green, R.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Science","volume":"308","issue":"5725","page":"1178-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26799652","title":"Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).","abstract":null,"authors":"Klionsky, DJ., Abdelmohsen, K., Abe, A., Abedin, MJ., Abeliovich, H., Acevedo Arozena, A., Adachi, H., Adams, CM., Adams, PD., Adeli, K., Adhihetty, PJ., Adler, SG., Agam, G., Agarwal, R., Aghi, MK., Agnello, M., Agostinis, P., Aguilar, PV., Aguirre-Ghiso, J., Airoldi, EM., Ait-Si-Ali, S., Akematsu, T., Akporiaye, ET., Al-Rubeai, M., Albaiceta, GM., Albanese, C., Albani, D., Albert, ML., Aldudo, J., Alg\u00fcl, H., Alirezaei, M., Alloza, I., Almasan, A., Almonte-Beceril, M., Alnemri, ES., Alonso, C., Altan-Bonnet, N., Altieri, DC., Alvarez, S., Alvarez-Erviti, L., Alves, S., Amadoro, G., Amano, A., Amantini, C., Ambrosio, S., Amelio, I., Amer, AO., Amessou, M., Amon, A., An, Z., Anania, FA., Andersen, SU., Andley, UP., Andreadi, CK., Andrieu-Abadie, N., Anel, A., Ann, DK., Anoopkumar-Dukie, S., Antonioli, M., Aoki, H., Apostolova, N., Aquila, S., Aquilano, K., Araki, K., Arama, E., Aranda, A., Araya, J., Arcaro, A., Arias, E., Arimoto, H., Ariosa, AR., Armstrong, JL., Arnould, T., Arsov, I., Asanuma, K., Askanas, V., Asselin, E., Atarashi, R., Atherton, SS., Atkin, JD., Attardi, LD., Auberger, P., Auburger, G., Aurelian, L., Autelli, R., Avagliano, L., Avantaggiati, ML., Avrahami, L., Awale, S., Azad, N., Bachetti, T., Backer, JM., Bae, DH., Bae, JS., Bae, ON., Bae, SH., Baehrecke, EH., Baek, SH., Baghdiguian, S., Bagniewska-Zadworna, A., Bai, H., Bai, J., Bai, XY., Bailly, Y., Balaji, KN., Balduini, W., Ballabio, A., Balzan, R., Banerjee, R., B\u00e1nhegyi, G., Bao, H., Barbeau, B., Barrachina, MD., Barreiro, E., Bartel, B., Bartolom\u00e9, A., Bassham, DC., Bassi, MT., Bast, RC., Basu, A., Batista, MT., Batoko, H., Battino, M., Bauckman, K., Baumgarner, BL., Bayer, KU., Beale, R., Beaulieu, JF., Beck, GR., Becker, C., Beckham, JD., B\u00e9dard, PA., Bednarski, PJ., Begley, TJ., Behl, C., Behrends, C., Behrens, GM., Behrns, KE., Bejarano, E., Belaid, A., Belleudi, F., B\u00e9nard, G., Berchem, G., Bergamaschi, D., Bergami, M., Berkhout, B., Berliocchi, L., Bernard, A., Bernard, M., Bernassola, F., Bertolotti, A., Bess, AS., Besteiro, S., Bettuzzi, S., Bhalla, S., Bhattacharyya, S., Bhutia, SK., Biagosch, C., Bianchi, MW., Biard-Piechaczyk, M., Billes, V., Bincoletto, C., Bingol, B., Bird, SW., Bitoun, M., Bjedov, I., Blackstone, C., Blanc, L., Blanco, GA., Blomhoff, HK., Boada-Romero, E., B\u00f6ckler, S., Boes, M., Boesze-Battaglia, K., Boise, LH., Bolino, A., Boman, A., Bonaldo, P., Bordi, M., Bosch, J., Botana, LM., Botti, J., Bou, G., Bouch\u00e9, M., Bouchecareilh, M., Boucher, MJ., Boulton, ME., Bouret, SG., Boya, P., Boyer-Guittaut, M., Bozhkov, PV., Brady, N., Braga, VM., Brancolini, C., Braus, GH., Bravo-San Pedro, JM., Brennan, LA., Bresnick, EH., Brest, P., Bridges, D., Bringer, MA., Brini, M., Brito, GC., Brodin, B., Brookes, PS., Brown, EJ., Brown, K., Broxmeyer, HE., Bruhat, A., Brum, PC., Brumell, JH., Brunetti-Pierri, N., Bryson-Richardson, RJ., Buch, S., Buchan, AM., Budak, H., Bulavin, DV., Bultman, SJ., Bultynck, G., Bumbasirevic, V., Burelle, Y., Burke, RE., Burmeister, M., B\u00fctikofer, P., Caberlotto, L., Cadwell, K., Cahova, M., Cai, D., Cai, J., Cai, Q., Calatayud, S., Camougrand, N., Campanella, M., Campbell, GR., Campbell, M., Campello, S., Candau, R., Caniggia, I., Cantoni, L., Cao, L., Caplan, AB., Caraglia, M., Cardinali, C., Cardoso, SM., Carew, JS., Carleton, LA., Carlin, CR., Carloni, S., Carlsson, SR., Carmona-Gutierrez, D., Carneiro, LA., Carnevali, O., Carra, S., Carrier, A., Carroll, B., Casas, C., Casas, J., Cassinelli, G., Castets, P., Castro-Obregon, S., Cavallini, G., Ceccherini, I., Cecconi, F., Cederbaum, AI., Ce\u00f1a, V., Cenci, S., Cerella, C., Cervia, D., Cetrullo, S., Chaachouay, H., Chae, HJ., Chagin, AS., Chai, CY., Chakrabarti, G., Chamilos, G., Chan, EY., Chan, MT., Chandra, D., Chandra, P., Chang, CP., Chang, RC., Chang, TY., Chatham, JC., Chatterjee, S., Chauhan, S., Che, Y., Cheetham, ME., Cheluvappa, R., Chen, CJ., Chen, G., Chen, GC., Chen, G., Chen, H., Chen, JW., Chen, JK., Chen, M., Chen, M., Chen, P., Chen, Q., Chen, Q., Chen, SD., Chen, S., Chen, SS., Chen, W., Chen, WJ., Chen, WQ., Chen, W., Chen, X., Chen, YH., Chen, YG., Chen, Y., Chen, Y., Chen, Y., Chen, YJ., Chen, YQ., Chen, Y., Chen, Z., Chen, Z., Cheng, A., Cheng, CH., Cheng, H., Cheong, H., Cherry, S., Chesney, J., Cheung, CH., Chevet, E., Chi, HC., Chi, SG., Chiacchiera, F., Chiang, HL., Chiarelli, R., Chiariello, M., Chieppa, M., Chin, LS., Chiong, M., Chiu, GN., Cho, DH., Cho, SG., Cho, WC., Cho, YY., Cho, YS., Choi, AM., Choi, EJ., Choi, EK., Choi, J., Choi, ME., Choi, SI., Chou, TF., Chouaib, S., Choubey, D., Choubey, V., Chow, KC., Chowdhury, K., Chu, CT., Chuang, TH., Chun, T., Chung, H., Chung, T., Chung, YL., Chwae, YJ., Cianfanelli, V., Ciarcia, R., Ciechomska, IA., Ciriolo, MR., Cirone, M., Claerhout, S., Clague, MJ., Cl\u00e0ria, J., Clarke, PG., Clarke, R., Clementi, E., Cleyrat, C., Cnop, M., Coccia, EM., Cocco, T., Codogno, P., Coers, J., Cohen, EE., Colecchia, D., Coletto, L., Coll, NS., Colucci-Guyon, E., Comincini, S., Condello, M., Cook, KL., Coombs, GH., Cooper, CD., Cooper, JM., Coppens, I., Corasaniti, MT., Corazzari, M., Corbalan, R., Corcelle-Termeau, E., Cordero, MD., Corral-Ramos, C., Corti, O., Cossarizza, A., Costelli, P., Costes, S., Cotman, SL., Coto-Montes, A., Cottet, S., Couve, E., Covey, LR., Cowart, LA., Cox, JS., Coxon, FP., Coyne, CB., Cragg, MS., Craven, RJ., Crepaldi, T., Crespo, JL., Criollo, A., Crippa, V., Cruz, MT., Cuervo, AM., Cuezva, JM., Cui, T., Cutillas, PR., Czaja, MJ., Czyzyk-Krzeska, MF., Dagda, RK., Dahmen, U., Dai, C., Dai, W., Dai, Y., Dalby, KN., Dalla Valle, L., Dalmasso, G., D'Amelio, M., Damme, M., Darfeuille-Michaud, A., Dargemont, C., Darley-Usmar, VM., Dasarathy, S., Dasgupta, B., Dash, S., Dass, CR., Davey, HM., Davids, LM., D\u00e1vila, D., Davis, RJ., Dawson, TM., Dawson, VL., Daza, P., de Belleroche, J., de Figueiredo, P., de Figueiredo, RC., de la Fuente, J., De Martino, L., De Matteis, A., De Meyer, GR., De Milito, A., De Santi, M., de Souza, W., De Tata, V., De Zio, D., Debnath, J., Dechant, R., Decuypere, JP., Deegan, S., Dehay, B., Del Bello, B., Del Re, DP., Delage-Mourroux, R., Delbridge, LM., Deldicque, L., Delorme-Axford, E., Deng, Y., Dengjel, J., Denizot, M., Dent, P., Der, CJ., Deretic, V., Derrien, B., Deutsch, E., Devarenne, TP., Devenish, RJ., Di Bartolomeo, S., Di Daniele, N., Di Domenico, F., Di Nardo, A., Di Paola, S., Di Pietro, A., Di Renzo, L., DiAntonio, A., D\u00edaz-Araya, G., D\u00edaz-Laviada, I., Diaz-Meco, MT., Diaz-Nido, J., Dickey, CA., Dickson, RC., Diederich, M., Digard, P., Dikic, I., Dinesh-Kumar, SP., Ding, C., Ding, WX., Ding, Z., Dini, L., Distler, JH., Diwan, A., Djavaheri-Mergny, M., Dmytruk, K., Dobson, RC., Doetsch, V., Dokladny, K., Dokudovskaya, S., Donadelli, M., Dong, XC., Dong, X., Dong, Z., Donohue, TM., Doran, KS., D'Orazi, G., Dorn, GW., Dosenko, V., Dridi, S., Drucker, L., Du, J., Du, LL., Du, L., du Toit, A., Dua, P., Duan, L., Duann, P., Dubey, VK., Duchen, MR., Duchosal, MA., Duez, H., Dugail, I., Dumit, VI., Duncan, MC., Dunlop, EA., Dunn, WA., Dupont, N., Dupuis, L., Dur\u00e1n, RV., Durcan, TM., Duvezin-Caubet, S., Duvvuri, U., Eapen, V., Ebrahimi-Fakhari, D., Echard, A., Eckhart, L., Edelstein, CL., Edinger, AL., Eichinger, L., Eisenberg, 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Pe\u00f1a, FJ., Pe\u00f1alva, MA., Pende, M., Peng, J., Penna, F., Penninger, JM., Pensalfini, A., Pepe, S., Pereira, GJ., Pereira, PC., P\u00e9rez-de la Cruz, V., P\u00e9rez-P\u00e9rez, ME., P\u00e9rez-Rodr\u00edguez, D., P\u00e9rez-Sala, D., Perier, C., Perl, A., Perlmutter, DH., Perrotta, I., Pervaiz, S., Pesonen, M., Pessin, JE., Peters, GJ., Petersen, M., Petrache, I., Petrof, BJ., Petrovski, G., Phang, JM., Piacentini, M., Pierdominici, M., Pierre, P., Pierrefite-Carle, V., Pietrocola, F., Pimentel-Mui\u00f1os, FX., Pinar, M., Pineda, B., Pinkas-Kramarski, R., Pinti, M., Pinton, P., Piperdi, B., Piret, JM., Platanias, LC., Platta, HW., Plowey, ED., P\u00f6ggeler, S., Poirot, M., Pol\u010dic, P., Poletti, A., Poon, AH., Popelka, H., Popova, B., Poprawa, I., Poulose, SM., Poulton, J., Powers, SK., Powers, T., Pozuelo-Rubio, M., Prak, K., Prange, R., Prescott, M., Priault, M., Prince, S., Proia, RL., Proikas-Cezanne, T., Prokisch, H., Promponas, VJ., Przyklenk, K., Puertollano, R., Pugazhenthi, S., Puglielli, L., Pujol, A., Puyal, J., Pyeon, D., Qi, X., Qian, WB., Qin, ZH., Qiu, Y., Qu, Z., Quadrilatero, J., Quinn, F., Raben, N., Rabinowich, H., Radogna, F., Ragusa, MJ., Rahmani, M., Raina, K., Ramanadham, S., Ramesh, R., Rami, A., Randall-Demllo, S., Randow, F., Rao, H., Rao, VA., Rasmussen, BB., Rasse, TM., Ratovitski, EA., Rautou, PE., Ray, SK., Razani, B., Reed, BH., Reggiori, F., Rehm, M., Reichert, AS., Rein, T., Reiner, DJ., Reits, E., Ren, J., Ren, X., Renna, M., Reusch, JE., Revuelta, JL., Reyes, L., Rezaie, AR., Richards, RI., Richardson, DR., Richetta, C., Riehle, MA., Rihn, BH., Rikihisa, Y., Riley, BE., Rimbach, G., Rippo, MR., Ritis, K., Rizzi, F., Rizzo, E., Roach, PJ., Robbins, J., Roberge, M., Roca, G., Roccheri, MC., Rocha, S., Rodrigues, CM., Rodr\u00edguez, CI., de Cordoba, SR., Rodriguez-Muela, N., Roelofs, J., Rogov, VV., Rohn, TT., Rohrer, B., Romanelli, D., Romani, L., Romano, PS., Roncero, MI., Rosa, JL., Rosello, A., Rosen, KV., Rosenstiel, P., Rost-Roszkowska, M., Roth, KA., Rou\u00e9, G., Rouis, M., Rouschop, KM., Ruan, DT., Ruano, D., Rubinsztein, DC., Rucker, EB., Rudich, A., Rudolf, E., Rudolf, R., Ruegg, MA., Ruiz-Roldan, C., Ruparelia, AA., Rusmini, P., Russ, DW., Russo, GL., Russo, G., Russo, R., Rusten, TE., Ryabovol, V., Ryan, KM., Ryter, SW., Sabatini, DM., Sacher, M., Sachse, C., Sack, MN., Sadoshima, J., Saftig, P., Sagi-Eisenberg, R., Sahni, S., Saikumar, P., Saito, T., Saitoh, T., Sakakura, K., Sakoh-Nakatogawa, M., Sakuraba, Y., Salazar-Roa, M., Salomoni, P., Saluja, AK., Salvaterra, PM., Salvioli, R., Samali, A., Sanchez, AM., S\u00e1nchez-Alc\u00e1zar, JA., Sanchez-Prieto, R., Sandri, M., Sanjuan, MA., Santaguida, S., Santambrogio, L., Santoni, G., Dos Santos, CN., Saran, S., Sardiello, M., Sargent, G., Sarkar, P., Sarkar, S., Sarrias, MR., Sarwal, MM., Sasakawa, C., Sasaki, M., Sass, M., Sato, K., Sato, M., Satriano, J., Savaraj, N., Saveljeva, S., Schaefer, L., Schaible, UE., Scharl, M., Schatzl, HM., Schekman, R., Scheper, W., Schiavi, A., Schipper, HM., Schmeisser, H., Schmidt, J., Schmitz, I., Schneider, BE., Schneider, EM., Schneider, JL., Schon, EA., Sch\u00f6nenberger, MJ., Sch\u00f6nthal, AH., Schorderet, DF., Schr\u00f6der, B., Schuck, S., Schulze, RJ., Schwarten, M., Schwarz, TL., Sciarretta, S., Scotto, K., Scovassi, AI., Screaton, RA., Screen, M., Seca, H., Sedej, S., Segatori, L., Segev, N., Seglen, PO., Segu\u00ed-Simarro, JM., Segura-Aguilar, J., Seki, E., Sell, C., Seiliez, I., Semenkovich, CF., Semenza, GL., Sen, U., Serra, AL., Serrano-Puebla, A., Sesaki, H., Setoguchi, T., Settembre, C., Shacka, JJ., Shajahan-Haq, AN., Shapiro, IM., Sharma, S., She, H., Shen, CK., Shen, CC., Shen, HM., Shen, S., Shen, W., Sheng, R., Sheng, X., Sheng, ZH., Shepherd, TG., Shi, J., Shi, Q., Shi, Q., Shi, Y., Shibutani, S., Shibuya, K., Shidoji, Y., Shieh, JJ., Shih, CM., Shimada, Y., Shimizu, S., Shin, DW., Shinohara, ML., Shintani, M., Shintani, T., Shioi, T., Shirabe, K., Shiri-Sverdlov, R., Shirihai, O., Shore, GC., Shu, CW., Shukla, D., Sibirny, AA., Sica, V., Sigurdson, CJ., Sigurdsson, EM., Sijwali, PS., Sikorska, B., Silveira, WA., Silvente-Poirot, S., Silverman, GA., Simak, J., Simmet, T., Simon, AK., Simon, HU., Simone, C., Simons, M., Simonsen, A., Singh, R., Singh, SV., Singh, SK., Sinha, D., Sinha, S., Sinicrope, FA., Sirko, A., Sirohi, K., Sishi, BJ., Sittler, A., Siu, PM., Sivridis, E., Skwarska, A., Slack, R., Slaninov\u00e1, I., Slavov, N., Smaili, SS., Smalley, KS., Smith, DR., Soenen, SJ., Soleimanpour, SA., Solhaug, A., Somasundaram, K., Son, JH., Sonawane, A., Song, C., Song, F., Song, HK., Song, JX., Song, W., Soo, KY., Sood, AK., Soong, TW., Soontornniyomkij, V., Sorice, M., Sotgia, F., Soto-Pantoja, DR., Sotthibundhu, A., Sousa, MJ., Spaink, HP., Span, PN., Spang, A., Sparks, JD., Speck, PG., Spector, SA., Spies, CD., Springer, W., Clair, DS., Stacchiotti, A., Staels, B., Stang, MT., Starczynowski, DT., Starokadomskyy, P., Steegborn, C., Steele, JW., Stefanis, L., Steffan, J., Stellrecht, CM., Stenmark, H., Stepkowski, TM., Stern, ST., Stevens, C., Stockwell, BR., Stoka, V., Storchova, Z., Stork, B., Stratoulias, V., Stravopodis, DJ., Strnad, P., Strohecker, AM., Str\u00f6m, AL., Stromhaug, P., Stulik, J., Su, YX., Su, Z., Subauste, CS., Subramaniam, S., Sue, CM., Suh, SW., Sui, X., Sukseree, S., Sulzer, D., Sun, FL., Sun, J., Sun, J., Sun, SY., Sun, Y., Sun, Y., Sun, Y., Sundaramoorthy, V., Sung, J., Suzuki, H., Suzuki, K., Suzuki, N., Suzuki, T., Suzuki, YJ., Swanson, MS., Swanton, C., Sw\u00e4rd, K., Swarup, G., Sweeney, ST., Sylvester, PW., Szatmari, Z., Szegezdi, E., Szlosarek, PW., Taegtmeyer, H., Tafani, M., Taillebourg, E., Tait, SW., Takacs-Vellai, K., Takahashi, Y., Tak\u00e1ts, S., Takemura, G., Takigawa, N., Talbot, NJ., Tamagno, E., Tamburini, J., Tan, CP., Tan, L., Tan, ML., Tan, M., Tan, YJ., Tanaka, K., Tanaka, M., Tang, D., Tang, D., Tang, G., Tanida, I., Tanji, K., Tannous, BA., Tapia, JA., Tasset-Cuevas, I., Tatar, M., Tavassoly, I., Tavernarakis, N., Taylor, A., Taylor, GS., Taylor, GA., Taylor, JP., Taylor, MJ., Tchetina, EV., Tee, AR., Teixeira-Clerc, F., Telang, S., Tencomnao, T., Teng, BB., Teng, RJ., Terro, F., Tettamanti, G., Theiss, AL., Theron, AE., Thomas, KJ., Thom\u00e9, MP., Thomes, PG., Thorburn, A., Thorner, J., Thum, T., Thumm, M., Thurston, TL., Tian, L., Till, A., Ting, JP., Titorenko, VI., Toker, L., Toldo, S., Tooze, SA., Topisirovic, I., Torgersen, ML., Torosantucci, L., Torriglia, A., Torrisi, MR., Tournier, C., Towns, R., Trajkovic, V., Travassos, LH., Triola, G., Tripathi, DN., Trisciuoglio, D., Troncoso, R., Trougakos, IP., Truttmann, AC., Tsai, KJ., Tschan, MP., Tseng, YH., Tsukuba, T., Tsung, A., Tsvetkov, AS., Tu, S., Tuan, HY., Tucci, M., Tumbarello, DA., Turk, B., Turk, V., Turner, RF., Tveita, AA., Tyagi, SC., Ubukata, M., Uchiyama, Y., Udelnow, A., Ueno, T., Umekawa, M., Umemiya-Shirafuji, R., Underwood, BR., Ungermann, C., Ureshino, RP., Ushioda, R., Uversky, VN., Uzc\u00e1tegui, NL., Vaccari, T., Vaccaro, MI., V\u00e1chov\u00e1, L., Vakifahmetoglu-Norberg, H., Valdor, R., Valente, EM., Vallette, F., Valverde, AM., Van den Berghe, G., Van Den Bosch, L., van den Brink, GR., van der Goot, FG., van der Klei, IJ., van der Laan, LJ., van Doorn, WG., van Egmond, M., van Golen, KL., Van Kaer, L., van Lookeren Campagne, M., Vandenabeele, P., Vandenberghe, W., Vanhorebeek, I., Varela-Nieto, I., Vasconcelos, MH., Vasko, R., Vavvas, DG., Vega-Naredo, I., Velasco, G., Velentzas, AD., Velentzas, PD., Vellai, T., Vellenga, E., Vendelbo, MH., Venkatachalam, K., Ventura, N., Ventura, S., Veras, PS., Verdier, M., Vertessy, BG., Viale, A., Vidal, M., Vieira, HL., Vierstra, RD., Vigneswaran, N., Vij, N., Vila, M., Villar, M., Villar, VH., Villarroya, J., Vindis, C., Viola, G., Viscomi, MT., Vitale, G., Vogl, DT., Voitsekhovskaja, OV., von Haefen, C., von Schwarzenberg, K., Voth, DE., Vouret-Craviari, V., Vuori, K., Vyas, JM., Waeber, C., Walker, CL., Walker, MJ., Walter, J., Wan, L., Wan, X., Wang, B., Wang, C., Wang, CY., Wang, C., Wang, C., Wang, C., Wang, D., Wang, F., Wang, F., Wang, G., Wang, HJ., Wang, H., Wang, HG., Wang, H., Wang, HD., Wang, J., Wang, J., Wang, M., Wang, MQ., Wang, PY., Wang, P., Wang, RC., Wang, S., Wang, TF., Wang, X., Wang, XJ., Wang, XW., Wang, X., Wang, X., Wang, Y., Wang, Y., Wang, Y., Wang, YJ., Wang, Y., Wang, Y., Wang, YT., Wang, Y., Wang, ZN., Wappner, P., Ward, C., Ward, DM., Warnes, G., Watada, H., Watanabe, Y., Watase, K., Weaver, TE., Weekes, CD., Wei, J., Weide, T., Weihl, CC., Weindl, G., Weis, SN., Wen, L., Wen, X., Wen, Y., Westermann, B., Weyand, CM., White, AR., White, E., Whitton, JL., Whitworth, AJ., Wiels, J., Wild, F., Wildenberg, ME., Wileman, T., Wilkinson, DS., Wilkinson, S., Willbold, D., Williams, C., Williams, K., Williamson, PR., Winklhofer, KF., Witkin, SS., Wohlgemuth, SE., Wollert, T., Wolvetang, EJ., Wong, E., Wong, GW., Wong, RW., Wong, VK., Woodcock, EA., Wright, KL., Wu, C., Wu, D., Wu, GS., Wu, J., Wu, J., Wu, M., Wu, M., Wu, S., Wu, WK., Wu, Y., Wu, Z., Xavier, CP., Xavier, RJ., Xia, GX., Xia, T., Xia, W., Xia, Y., Xiao, H., Xiao, J., Xiao, S., Xiao, W., Xie, CM., Xie, Z., Xie, Z., Xilouri, M., Xiong, Y., Xu, C., Xu, C., Xu, F., Xu, H., Xu, H., Xu, J., Xu, J., Xu, J., Xu, L., Xu, X., Xu, Y., Xu, Y., Xu, ZX., Xu, Z., Xue, Y., Yamada, T., Yamamoto, A., Yamanaka, K., Yamashina, S., Yamashiro, S., Yan, B., Yan, B., Yan, X., Yan, Z., Yanagi, Y., Yang, DS., Yang, JM., Yang, L., Yang, M., Yang, PM., Yang, P., Yang, Q., Yang, W., Yang, WY., Yang, X., Yang, Y., Yang, Y., Yang, Z., Yang, Z., Yao, MC., Yao, PJ., Yao, X., Yao, Z., Yao, Z., Yasui, LS., Ye, M., Yedvobnick, B., Yeganeh, B., Yeh, ES., Yeyati, PL., Yi, F., Yi, L., Yin, XM., Yip, CK., Yoo, YM., Yoo, YH., Yoon, SY., Yoshida, K., Yoshimori, T., Young, KH., Yu, H., Yu, JJ., Yu, JT., Yu, J., Yu, L., Yu, WH., Yu, XF., Yu, Z., Yuan, J., Yuan, ZM., Yue, BY., Yue, J., Yue, Z., Zacks, DN., Zacksenhaus, E., Zaffaroni, N., Zaglia, T., Zakeri, Z., Zecchini, V., Zeng, J., Zeng, M., Zeng, Q., Zervos, AS., Zhang, DD., Zhang, F., Zhang, G., Zhang, GC., Zhang, H., Zhang, H., Zhang, H., Zhang, H., Zhang, J., Zhang, J., Zhang, J., Zhang, J., Zhang, JP., Zhang, L., Zhang, L., Zhang, L., Zhang, L., Zhang, MY., Zhang, X., Zhang, XD., Zhang, Y., Zhang, Y., Zhang, Y., Zhang, Y., Zhang, Y., Zhao, M., Zhao, WL., Zhao, X., Zhao, YG., Zhao, Y., Zhao, Y., Zhao, YX., Zhao, Z., Zhao, ZJ., Zheng, D., Zheng, XL., Zheng, X., Zhivotovsky, B., Zhong, Q., Zhou, GZ., Zhou, G., Zhou, H., Zhou, SF., Zhou, XJ., Zhu, H., Zhu, H., Zhu, WG., Zhu, W., Zhu, XF., Zhu, Y., Zhuang, SM., Zhuang, X., Ziparo, E., Zois, CE., Zoladek, T., Zong, WX., Zorzano, A., Zughaier, SM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Autophagy","volume":"12","issue":"1","page":"1-222","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22790597","title":"Defective intestinal amino acid absorption in Ace2 null mice.","abstract":"Mutations in the main intestinal and kidney luminal neutral amino acid transporter B(0)AT1 (Slc6a19) lead to Hartnup disorder, a condition that is characterized by neutral aminoaciduria and in some cases pellagra-like symptoms. These latter symptoms caused by low-niacin are thought to result from defective intestinal absorption of its precursor L-tryptophan. Since Ace2 is necessary for intestinal B(0)AT1 expression, we tested the impact of intestinal B(0)AT1 absence in ace2 null mice. Their weight gain following weaning was decreased, and Na(+)-dependent uptake of B(0)AT1 substrates measured in everted intestinal rings was defective. Additionally, high-affinity Na(+)-dependent transport of L-proline, presumably via SIT1 (Slc6a20), was absent, whereas glucose uptake via SGLT1 (Slc5a1) was not affected. Measurements of small intestine luminal amino acid content following gavage showed that more L-tryptophan than other B(0)AT1 substrates reach the ileum in wild-type mice, which is in line with its known lower apparent affinity. In ace2 null mice, the absorption defect was confirmed by a severalfold increase of L-tryptophan and of other neutral amino acids reaching the ileum lumen. Furthermore, plasma and muscle levels of glycine and L-tryptophan were significantly decreased in ace2 null mice, with other neutral amino acids displaying a similar trend. A low-protein\/low-niacin diet challenge led to differential changes in plasma amino acid levels in both wild-type and ace2 null mice, but only in ace2 null mice to a stop in weight gain. Despite the combination of low-niacin with a low-protein diet, plasma niacin concentrations remained normal in ace2 null mice and no pellagra symptoms, such as photosensitive skin rash or ataxia, were observed. In summary, mice lacking Ace2-dependent intestinal amino acid transport display no total niacin deficiency nor clear pellagra symptoms, even under a low-protein and low-niacin diet, despite gross amino acid homeostasis alterations.","authors":"Singer, D., Camargo, SM., Ramadan, T., Sch\u00e4fer, M., Mariotta, L., Herzog, B., Huggel, K., Wolfer, D., Werner, S., Penninger, JM., Verrey, F.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Am J Physiol Gastrointest Liver Physiol","volume":"303","issue":"6","page":"G686-95","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22732840","title":"Mps1 promotes rapid centromere accumulation of Aurora B.","abstract":"Aurora B localization to mitotic centromeres, which is required for proper chromosome alignment during mitosis, relies on Haspin-dependent histone H3 phosphorylation and on Bub1-dependent histone H2A phosphorylation--which interacts with Borealin through a Shugoshin (Sgo) intermediate. We demonstrate that Mps1 stimulates the latter recruitment axis. Mps1 activity enhances H2A-T120ph and is critical for Sgo1 recruitment to centromeres, thereby promoting Aurora B centromere recruitment in early mitosis. Importantly, chromosome biorientation defects caused by Mps1 inhibition are improved by restoring Aurora B centromere recruitment. As Mps1 kinetochore localization reciprocally depends on Aurora B, we propose that this Aurora B-Mps1 recruitment circuitry cooperates with the Aurora B-Haspin feedback loop to ensure rapid centromere accumulation of Aurora B at the onset of mitosis.","authors":"van der Waal, MS., Saurin, AT., Vromans, MJ., Vleugel, M., Wurzenberger, C., Gerlich, DW., Medema, RH., Kops, GJ., Lens, SM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"EMBO Rep","volume":"13","issue":"9","page":"847-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22653784","title":"MicroRNAs are universal regulators of differentiation, activation, and polarization of microglia and macrophages in normal and diseased CNS.","abstract":"MicroRNAs (miRNAs) are a class of small (\u223c22 nucleotides) noncoding RNAs involved in the regulation of gene expression at the post-translational level. It is estimated that 30-90% of human genes are regulated by miRNAs, which makes these molecules of great importance for cell growth, activation, and differentiation. Microglia is CNS-resident cells of a myeloid lineage that play an important role in immune surveillance and are actively involved in many neurologic pathologies. Although the exact origin of microglia remains enigmatic, it is established that primitive macrophages from a yolk sac populate the brain and spinal cord in normal conditions throughout development. During various pathological events such as neuroinflammation, bone marrow derived myeloid cells also migrate into the CNS. Within the CNS, both primitive macrophages from the yolk sac and bone marrow derived myeloid cells acquire a specific phenotype upon interaction with other cell types within the CNS microenvironment. The factors that drive differentiation of progenitors into microglia and control the state of activation of microglia and bone marrow-derived myeloid cells within the CNS are not well understood. In this review we will summarize the role of miRNAs during activation and differentiation of myeloid cells. The role of miR-124 in the adaptation of microglia and macrophages to the CNS microenvironment will be further discussed. We will also summarize the role of miRNAs as modulators of activation of microglia and microphages. Finally, we will describe the role of miR-155 and miR-124 in the polarization of macrophages towards classically and alternatively activated phenotypes.","authors":"Ponomarev, ED., Veremeyko, T., Weiner, HL.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Glia","volume":"61","issue":"1","page":"91-103","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15376260","title":"Geminin predicts adverse clinical outcome in breast cancer by reflecting cell-cycle progression.","abstract":"Geminin inhibits DNA replication by preventing Cdt1 from loading minichromosome maintenance (MCM) proteins onto DNA. The present study has investigated whether the frequency of geminin expression predicts clinical outcome in breast cancer. Immunohistochemistry was used first to examine geminin expression in normal and malignant breast tissue (n = 67). Correlations with cell-cycle parameters, pathological features, and clinical outcome were then determined using an invasive breast carcinoma tissue microarray (n = 165). Breast carcinomas were scanned for mutations (n = 61) and copy number imbalances (n = 241) of the geminin gene. Finally, the cell cycle distribution of geminin in breast cancer cells was investigated in vivo and in vitro. Despite a putative tumour suppressor function, it was found that increased geminin expression is a powerful independent indicator of adverse prognosis in invasive breast cancer. Both poor overall survival (p = 0.0002) and the development of distant metastases (p = 0.005) are predicted by high geminin expression, which performs better in this patient cohort than traditional factors currently used to determine prognosis and appropriate therapy. No mutations or deletions of the geminin gene and no evidence that a high frequency of protein expression is related to gene amplification were found. It is shown that geminin is expressed from S to M phase in breast carcinoma tissue and cell lines, disappearing at the metaphase--anaphase transition. While MCM proteins identify all non-quiescent cells, geminin identifies the sub-fraction that have entered S phase, but not exited mitosis, thereby indicating the rate of cell-cycle progression. It is suggested that this explains its unexpected value as a prognostic marker in breast cancer.","authors":"Gonzalez, MA., Tachibana, KE., Chin, SF., Callagy, G., Madine, MA., Vowler, SL., Pinder, SE., Laskey, RA., Coleman, N.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Pathol","volume":"204","issue":"2","page":"121-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-03-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25512519","title":"Epigenetic targeting of activation-induced cytidine deaminase.","abstract":"Activation-induced cytidine deaminase (AID) initiates class switch recombination (CSR) and somatic hypermutation (SHM) by deaminating cytosine residues in immunoglobulin genes (Igh, Ig\u03ba, and Ig\u03bb). At a lower frequency, AID also causes collateral DNA damage at non-Ig loci, including genes that are rearranged or mutated in B-cell lymphoma. Precisely how AID is recruited to these off-target sites is not entirely understood. To gain further insight into how AID selects its targets, we compared AID-mediated translocations in two different cell types, B cells and mouse embryonic fibroblasts (MEFs). AID targets a distinct set of hotspots in the two cell types. In both cases, hotspots are concentrated in highly transcribed but stalled genes. However, transcription alone is insufficient to recruit AID activity. Comparison of genes similarly transcribed in B cells and MEFs but targeted in only one of the two cell types reveals a common set of epigenetic features associated with AID recruitment in both cells. AID target genes are enriched in chromatin modifications associated with active enhancers (such as H3K27Ac) and marks of active transcription (such as H3K36me3) in both fibroblasts and B cells, indicating that these features are universal mediators of AID recruitment.","authors":"Wang, Q., Oliveira, T., Jankovic, M., Silva, IT., Hakim, O., Yao, K., Gazumyan, A., Mayer, CT., Pavri, R., Casellas, R., Nussenzweig, MC., Robbiani, DF.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Proc Natl Acad Sci U S A","volume":"111","issue":"52","page":"18667-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22643706","title":"T-cell receptor diversity prevents T-cell lymphoma development.","abstract":"Mature T-cell lymphomas (MTCLs) have an extremely poor prognosis and are much less frequent than immature T-cell leukemias. This suggests that malignant outgrowth of mature T lymphocytes is well controlled. Indeed, in a previous study we found that mature T cells are resistant to transformation with known T-cell oncogenes. Here, however, we observed that T-cell receptor (TCR) mono-\/oligoclonal mature T cells from TCR transgenic (tg) mice (OT-I, P14) expressing the oncogenes NPM\/ALK or \u0394TrkA readily developed MTCLs in T-cell-deficient recipients. Analysis of cell surface markers largely ruled out that TCR tg lymphomas were derived from T-cell precursors. Furthermore, cotransplanted non-modified TCR polyclonal T cells suppressed malignant outgrowth of oncogene expressing TCR tg T lymphocytes. A dominant role of an anti-leukemic immune response or Tregs in the control of MTCLs seems unlikely as na\u00efve T cells derived from oncogene expressing stem cells, which should be tolerant to leukemic antigens, as well as purified CD4 and CD8 were resistant to transformation. However, our results are in line with a model in which homeostatic mechanisms that stabilize the diversity of the normal T-cell repertoire, for example, clonal competition, also control the outgrowth of potentially malignant T-cell clones. This study introduces a new innate mechanism of lymphoma control.","authors":"Newrzela, S., Al-Ghaili, N., Heinrich, T., Petkova, M., Hartmann, S., Rengstl, B., Kumar, A., J\u00e4ck, HM., Gerdes, S., Roeder, I., Hansmann, ML., von Laer, D.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Leukemia","volume":"26","issue":"12","page":"2499-507","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22614755","title":"The non-redundant function of cohesin acetyltransferase Esco2: some answers and new questions.","abstract":"Cohesin and cohesin regulatory proteins function in an essential pathway enabling proper cohesion and segregation of sister chromatids. Additionally, these proteins are involved in double-strand break (DSB) repair and transcriptional regulation. Mutations in Establishment of cohesion 1 homolog 2 (Esco2), an evolutionary conserved cohesin acetyltransferase, are the cause of Roberts syndrome (RBS), a human congenital disorder. To explore the mechanism by which the deficiency in Esco2 affects cohesin's functions, we generated a mouse harboring a conditional Esco2 allele. To our surprise and in marked contrast to RBS, mouse Esco2 turns out to be a cell viability factor, the absence of which results in severe chromosome segregation defects and apoptosis. We found that the acetylation of the cohesin subunit Smc3 is significantly reduced in Esco2-deficient cells resulting in a marked reduction of Sororin recruitment to several, but not all cohesin bound loci. Here, we provide evidence that Esco2 is also required for DSB repair, which is consistent with previous studies in RBS cells.","authors":"Whelan, G., Kreidl, E., Peters, JM., Eichele, G.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nucleus","volume":"3","issue":"4","page":"330-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22606359","title":"Temporal dissection of K-ras(G12D) mutant in vitro and in vivo using a regulatable K-ras(G12D) mouse allele.","abstract":"Animal models which allow the temporal regulation of gene activities are valuable for dissecting gene function in tumorigenesis. Here we have constructed a conditional inducible estrogen receptor-K-ras(G12D) (ER-K-ras(G12D)) knock-in mice allele that allows us to temporally switch on or off the activity of K-ras oncogenic mutant through tamoxifen administration. In vitro studies using mice embryonic fibroblast (MEF) showed that a dose of tamoxifen at 0.05 \u00b5M works optimally for activation of ER-K-ras(G12D) independent of the gender status. Furthermore, tamoxifen-inducible activation of K-ras(G12D) promotes cell proliferation, anchor-independent growth, transformation as well as invasion, potentially via activation of downstream MAPK pathway and cell cycle progression. Continuous activation of K-ras(G12D) in vivo by tamoxifen treatment is sufficient to drive the neoplastic transformation of normal lung epithelial cells in mice. Tamoxifen withdrawal after the tumor formation results in apoptosis and tumor regression in mouse lungs. Taken together, these data have convincingly demonstrated that K-ras mutant is essential for neoplastic transformation and this animal model may provide an ideal platform for further detailed characterization of the role of K-ras oncogenic mutant during different stages of lung tumorigenesis.","authors":"Wang, Z., Feng, Y., Bardeesy, N., Bardessy, N., Wong, KK., Liu, XY., Ji, H.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"5","page":"e37308","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17434130","title":"Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homolog SU(VAR)3-3.","abstract":"Epigenetic indexing of chromatin domains by histone lysine methylation requires the balanced coordination of methyltransferase and demethylase activities. Here, we show that SU(VAR)3-3, the Drosophila homolog of the human LSD1 amine oxidase, demethylates H3K4me2 and H3K4me1 and facilitates subsequent H3K9 methylation by SU(VAR)3-9. Su(var)3-3 mutations suppress heterochromatic gene silencing, display elevated levels of H3K4me2, and prevent extension of H3K9me2 at pericentric heterochromatin. SU(VAR)3-3 colocalizes with H3K4me2 in interband regions and is abundant during embryogenesis and in syncytial blastoderm, where it appears concentrated at prospective heterochromatin during cycle 14. In embryos of Su(var)3-3\/+ females, H3K4me2 accumulates in primordial germ cells, and the deregulated expansion of H3K4me2 antagonizes heterochromatic H3K9me2 in blastoderm cells. Our data indicate an early developmental function for the SU(VAR)3-3 demethylase in controlling euchromatic and heterochromatic domains and reveal a hierarchy in which SU(VAR)3-3-mediated removal of activating histone marks is a prerequisite for subsequent heterochromatin formation by H3K9 methylation.","authors":"Rudolph, T., Yonezawa, M., Lein, S., Heidrich, K., Kubicek, S., Sch\u00e4fer, C., Phalke, S., Walther, M., Schmidt, A., Jenuwein, T., Reuter, G.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Cell","volume":"26","issue":"1","page":"103-15","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2007-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17401373","title":"Potent effect of target structure on microRNA function.","abstract":"MicroRNAs (miRNAs) are small noncoding RNAs that repress protein synthesis by binding to target messenger RNAs. We investigated the effect of target secondary structure on the efficacy of repression by miRNAs. Using structures predicted by the Sfold program, we model the interaction between an miRNA and a target as a two-step hybridization reaction: nucleation at an accessible target site followed by hybrid elongation to disrupt local target secondary structure and form the complete miRNA-target duplex. This model accurately accounts for the sensitivity to repression by let-7 of various mutant forms of the Caenorhabditis elegans lin-41 3' untranslated region and for other experimentally tested miRNA-target interactions in C. elegans and Drosophila melanogaster. These findings indicate a potent effect of target structure on target recognition by miRNAs and establish a structure-based framework for genome-wide identification of animal miRNA targets.","authors":"Long, D., Lee, R., Williams, P., Chan, CY., Ambros, V., Ding, Y.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Struct Mol Biol","volume":"14","issue":"4","page":"287-94","pdf":null,"JrId":"31761","fulltextlink":null,"preprintlink":null,"articledate":"2007-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22491011","title":"The many functions of cohesin--different rings to rule them all?","abstract":null,"authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"EMBO J","volume":"31","issue":"9","page":"2061-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19332065","title":"Notch signaling promotes the generation of EphrinB1-positive intestinal epithelial cells.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19332065<\/PMID><DateCompleted><Year>2009<\/Year><Month>07<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2016<\/Year><Month>11<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1528-0012<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>137<\/Volume><Issue>1<\/Issue><PubDate><Year>2009<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>Gastroenterology<\/Title><ISOAbbreviation>Gastroenterology<\/ISOAbbreviation><\/Journal><ArticleTitle>Notch signaling promotes the generation of EphrinB1-positive intestinal epithelial cells.<\/ArticleTitle><Pagination><MedlinePgn>145-55, 155.e1-3<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1053\/j.gastro.2009.03.046<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\" NlmCategory=\"OBJECTIVE\">The intestinal epithelium consists of EphB2-positive proliferative basal cryptic cells and EphrinB1-positive, postmitotic differentiated cells. We investigated the effects of Notch signaling on formation of the EphB2-EphrinB1 boundary using mouse and tissue culture models.","authors":"Koo, BK., Lim, HS., Chang, HJ., Yoon, MJ., Choi, Y., Kong, MP., Kim, CH., Kim, JM., Park, JG., Kong, YY.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Gastroenterology","volume":"137","issue":"1","page":"145-55, 155.e1-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31398345","title":"A Heterochromatin-Specific RNA Export Pathway Facilitates piRNA Production.","abstract":"PIWI-interacting RNAs (piRNAs) guide transposon silencing in animals. The 22-30 nt piRNAs are processed in the cytoplasm from long non-coding RNAs that often lack RNA processing hallmarks of\u00a0export-competent transcripts. By studying how these transcripts achieve nuclear export, we uncover an RNA export pathway specific for piRNA precursors in the Drosophila germline. This pathway requires Nxf3-Nxt1, a variant of the hetero-dimeric mRNA export receptor Nxf1-Nxt1. Nxf3 interacts with UAP56, a nuclear RNA helicase essential for mRNA export, and CG13741\/Bootlegger, which recruits Nxf3-Nxt1 and UAP56 to heterochromatic piRNA source loci. Upon RNA cargo binding, Nxf3 achieves nuclear export via the exportin Crm1 and accumulates together with Bootlegger in peri-nuclear nuage, suggesting that after export, Nxf3-Bootlegger delivers precursor transcripts to the piRNA processing sites. These findings indicate that the piRNA pathway bypasses nuclear RNA surveillance systems to export unprocessed transcripts to the cytoplasm, a strategy also exploited by retroviruses.","authors":"ElMaghraby, MF., Andersen, PR., P\u00fchringer, F., Hohmann, U., Meixner, K., Lendl, T., Tirian, L., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell","volume":"178","issue":"4","page":"964-979.e20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22469984","title":"The Polycomb complex PRC2 supports aberrant self-renewal in a mouse model of MLL-AF9;Nras(G12D) acute myeloid leukemia.","abstract":"The Trithorax and Polycomb groups of chromatin regulators are critical for cell-lineage specification during normal development; functions that often become deregulated during tumorigenesis. As an example, oncogenic fusions of the Trithorax-related protein mixed lineage leukemia (MLL) can initiate aggressive leukemias by altering the transcriptional circuitry governing hematopoietic cell differentiation, a process that requires multiple epigenetic pathways to implement. Here we used shRNA screening to identify chromatin regulators uniquely required in a mouse model of MLL-fusion acute myeloid leukemia, which revealed a role for the Polycomb repressive complex 2 (PRC2) in maintenance of this disease. shRNA-mediated suppression of PRC2 subunits Eed, Suz12 or Ezh1\/Ezh2 led to proliferation arrest and differentiation of leukemia cells, with a minimal impact on growth of several non-transformed hematopoietic cell lines. The requirement for PRC2 in leukemia is partly because of its role in direct transcriptional repression of genes that limit the self-renewal potential of hematopoietic cells, including Cdkn2a. In addition to implicating a role for PRC2 in the pathogenesis of MLL-fusion leukemia, our results suggest, more generally, that Trithorax and Polycomb group proteins can cooperate with one another to maintain aberrant lineage programs in cancer.","authors":"Shi, J., Wang, E., Zuber, J., Rappaport, A., Taylor, M., Johns, C., Lowe, SW., Vakoc, CR.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Oncogene","volume":"32","issue":"7","page":"930-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25483777","title":"B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity.","abstract":"The antibody gene mutator activation-induced cytidine deaminase (AID) promiscuously damages oncogenes, leading to chromosomal translocations and\u00a0tumorigenesis. Why nonimmunoglobulin loci are susceptible to AID activity is unknown. Here, we study AID-mediated lesions in the context of nuclear architecture and the B cell regulome. We show that AID targets are not randomly distributed across the\u00a0genome but are predominantly grouped within super-enhancers and regulatory clusters. Unexpectedly, in these domains, AID deaminates active promoters and eRNA(+) enhancers interconnected in some instances over megabases of linear chromatin. Using genome editing, we demonstrate that 3D-linked targets cooperate to recruit AID-mediated breaks. Furthermore, a comparison of hypermutation in mouse B cells, AID-induced kataegis in human lymphomas, and translocations in MEFs reveals that AID damages different genes in different cell types. Yet, in all cases, the targets are predominantly associated with topological complex, highly transcribed super-enhancers, demonstrating that these compartments are key mediators of AID recruitment.","authors":"Qian, J., Wang, Q., Dose, M., Pruett, N., Kieffer-Kwon, KR., Resch, W., Liang, G., Tang, Z., Math\u00e9, E., Benner, C., Dubois, W., Nelson, S., Vian, L., Oliveira, TY., Jankovic, M., Hakim, O., Gazumyan, A., Pavri, R., Awasthi, P., Song, B., Liu, G., Chen, L., Zhu, S., Feigenbaum, L., Staudt, L., Murre, C., Ruan, Y., Robbiani, DF., Pan-Hammarstr\u00f6m, Q., Nussenzweig, MC., Casellas, R.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell","volume":"159","issue":"7","page":"1524-37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27261530","title":"Molecular functions of the transcription factors E2A and E2-2 in controlling germinal center B cell and plasma cell development.","abstract":"E2A is an essential regulator of early B cell development. Here, we have demonstrated that E2A together with E2-2 controlled germinal center (GC) B cell and plasma cell development. As shown by the identification of regulated E2A,E2-2 target genes in activated B cells, these E-proteins directly activated genes with important functions in GC B cells and plasma cells by inducing and maintaining DNase I hypersensitive sites. Through binding to multiple enhancers in the Igh 3' regulatory region and Aicda locus, E-proteins regulated class switch recombination by inducing both Igh germline transcription and AID expression. By regulating 3' Igk and Igh enhancers and a distal element at the Prdm1 (Blimp1) locus, E-proteins contributed to Igk, Igh, and Prdm1 activation in plasmablasts. Together, these data identified E2A and E2-2 as central regulators of B cell immunity.","authors":"W\u00f6hner, M., Tagoh, H., Bilic, I., Jaritz, M., Poliakova, DK., Fischer, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Exp Med","volume":"213","issue":"7","page":"1201-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23059793","title":"Regeneration: the ultimate example of wound healing.","abstract":"The outcome of wound repair in mammals is often characterized by fibrotic scaring. Vertebrates such as zebrafish, frogs, and salamanders not only heal scarlessly, but also can regenerate lost appendages. Decades of study on the process of animal regeneration has produced key insights into the mechanisms of how complex tissue is restored. By examining our current knowledge of regeneration, we can draw parallels with mammalian wound healing to identify the molecular determinants that produce such differing outcomes.","authors":"Murawala, P., Tanaka, EM., Currie, JD.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Semin Cell Dev Biol","volume":"23","issue":"9","page":"954-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22109880","title":"Status of genomic imprinting in epigenetically distinct pluripotent stem cells.","abstract":"Mouse epiblast stem cells (EpiSCs) derived from postimplantation embryos are developmentally and functionally different from embryonic stem cells (ESCs) generated from blastocysts. EpiSCs require Activin A and FGF2 signaling for self-renewal, similar to human ESCs (hESCs), while mouse ESCs require LIF and BMP4. Unlike ESCs, EpiSCs have undergone X-inactivation, similar to the tendency of hESCs. The shared self-renewal and X-inactivation properties of EpiSCs and hESCs suggest that they have an epigenetic state distinct from ESCs. This hypothesis predicts that EpiSCs would have monoallelic expression of most imprinted genes, like that observed in hESCs. Here, we confirm this prediction. By contrast, we find that mouse induced pluripotent stem cells (iPSCs) tend to lose imprinting similar to mouse ESCs. These findings reveal that iPSCs have an epigenetic status associated with their pluripotent state rather than their developmental origin. Our results also reinforce the view that hESCs and EpiSCs are in vitro counterparts, sharing an epigenetic status distinct from ESCs and iPSCs.","authors":"Sun, B., Ito, M., Mendjan, S., Ito, Y., Brons, IG., Murrell, A., Vallier, L., Ferguson-Smith, AC., Pedersen, RA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Stem Cells","volume":"30","issue":"2","page":"161-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25454785","title":"Asymmetric processing of visual motion for simultaneous object and background responses.","abstract":"Visual object fixation and figure-ground discrimination in Drosophila are robust behaviors requiring sophisticated computation by the visual system, yet the neural substrates remain unknown. Recent experiments in walking flies revealed object fixation behavior mediated by circuitry independent from the motion-sensitive T4-T5 cells required for wide-field motion responses. In tethered flight experiments under closed-loop conditions, we found similar results for one feedback gain, whereas intact T4-T5 cells were necessary for robust object fixation at a higher feedback gain and in figure-ground discrimination tasks. We implemented dynamical models (available at http:\/\/strawlab.org\/asymmetric-motion\/) based on neurons downstream of T4-T5 cells\u2014one a simple phenomenological model and another, physiologically more realistic model\u2014and found that both predict key features of stripe fixation and figure-ground discrimination and are consistent with a classical formulation. Fundamental to both models is motion asymmetry in the responses of model neurons, whereby front-to-back motion elicits stronger responses than back-to-front motion. When a bilateral pair of such model neurons, based on well-understood horizontal system cells, downstream of T4-T5, is coupled to turning behavior, asymmetry leads to object fixation and figure-ground discrimination in the presence of noise. Furthermore, the models also predict fixation in front of a moving background, a behavior previously suggested to require an additional pathway. Thus, the models predict several aspects of object responses on the basis of neurons that are also thought to serve a key role in background stabilization.","authors":"Fenk, LM., Poehlmann, A., Straw, AD.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Biol","volume":"24","issue":"24","page":"2913-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520208","title":"Interleukin 2 receptor antagonists for liver transplant recipients: a systematic review and meta-analysis of controlled studies.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520208<\/PMID><DateCompleted><Year>2011<\/Year><Month>09<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>12<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1527-3350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>54<\/Volume><Issue>2<\/Issue><PubDate><Year>2011<\/Year><Month>Aug<\/Month><\/PubDate><\/JournalIssue><Title>Hepatology (Baltimore, Md.)<\/Title><ISOAbbreviation>Hepatology<\/ISOAbbreviation><\/Journal><ArticleTitle>Interleukin 2 receptor antagonists for liver transplant recipients: a systematic review and meta-analysis of controlled studies.<\/ArticleTitle><Pagination><MedlinePgn>541-54<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/hep.24385<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Interleukin 2 receptor antagonists (IL-2Ra) are frequently used as induction therapy in liver transplant recipients to decrease the risk of acute rejection while allowing the reduction of concomitant immunosuppression. We conducted a systematic review of prospective, controlled studies to test the hypothesis that the use of IL-2Ra is associated with a decrease in acute rejection and\/or a decrease in the side effects of concomitant medication. We performed a search of all major databases and secondary sources from inception to December 2010. Random effects models were used to assess the incidence of acute rejection, graft loss, patient death, and adverse side effects, with or without IL-2Ra. Subgroup analysis and meta-regression were used to explore differences in effect and sources of heterogeneity. Eighteen studies (13 randomized and 5 nonrandomized) met the inclusion and exclusion criteria. Acute rejection at 12 months or later favored the use of IL-2Ra (relative risk [RR] 0.83; 95% confidence interval [CI] 0.76-0.94) and steroid-resistant rejection was also less frequent in patients receiving IL-2Ra (RR 0.66; CI 0.48-0.91). Graft loss and patient death did not differ significantly between treatments. Patients who received IL-2Ra in addition to reduced or delayed calcineurin inhibitors had better renal function (mean difference of estimated glomerular filtration rate: 6.29 mL\/min; CI 1.66-10.91) and a lower incidence of renal dysfunction (RR 0.46; CI 0.27-0.78). The use of IL-2Ra was also associated with a lower incidence of posttransplant diabetes mellitus, whereas the incidence of other adverse events was similar.","authors":"Goralczyk, AD., Hauke, N., Bari, N., Tsui, TY., Lorf, T., Obed, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Hepatology","volume":"54","issue":"2","page":"541-54","pdf":null,"JrId":"4093","fulltextlink":null,"preprintlink":null,"articledate":"2011-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31395224","title":"Diagnostic Performance of Nonhyperemic Pressure Ratios Assessed by <sup>13<\/sup>N-Ammonium Positron Emission Tomography.","abstract":null,"authors":"Lee, JM., Hwang, D., Choi, KH., Kim, CH., Bang, JI., Suh, M., Paeng, JC., Cheon, GJ., Koo, BK.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"JACC Cardiovasc Interv","volume":"12","issue":"15","page":"1517-1518","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17356064","title":"Aurora B controls the association of condensin I but not condensin II with mitotic chromosomes.","abstract":"The assembly of mitotic chromosomes is controlled by condensin complexes. In vertebrates, condensin I binds to chromatin in prometaphase, confers rigidity to chromosomes and enables the release of cohesin complexes from chromosome arms, whereas condensin II associates with chromosomes in prophase and promotes their condensation. Both complexes are essential for chromosome segregation in anaphase. Although the association of condensins with chromatin is important for the assembly and segregation of mitotic chromosomes, it is poorly understood how this process is controlled. Here we show that the mitotic kinase Aurora B regulates the association of condensin I, but not the interaction of condensin II with chromatin. Quantitative time-lapse imaging of cells expressing GFP-tagged condensin subunits revealed that Aurora B is required for efficient loading of condensin I onto chromosomes in prometaphase and for maintenance of the complex on chromosomes in later stages of mitosis. The three non-SMC subunits of condensin I are Aurora B substrates in vitro and their mitosis-specific phosphorylation depends on Aurora B in vivo. Our data indicate that Aurora B contributes to chromosome rigidity and segregation by promoting the binding of condensin I to chromatin. We have also addressed how Aurora B might mediate the dissociation of cohesin from chromosome arms.","authors":"Lipp, JJ., Hirota, T., Poser, I., Peters, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Cell Sci","volume":"120","issue":"Pt 7","page":"1245-55","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37214360","title":"Authorship in Scientific Manuscripts.","abstract":"Authorship in scientific manuscripts indicates intellectual contribution of individuals to a research project and authors play a key role in the research and dissemination of&#xa0;results of a research project. It is important for authors to follow guidelines on authorship and submission of manuscripts and to agree on the order of authorship before beginning the project. Criteria for authorship, roles and responsibilities of authors, author metrics and misconduct of authors and their consequences are discussed in this editorial. Properly assigning authorship ensures transparency, accountability, and fairness in the scientific community.","authors":"Kambhampati, SBS., Maini, L.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Indian J Orthop","volume":"57","issue":"6","page":"783-788","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-05-03","doi":"10.1007\/s43465-023-00896-5","first_author":"Kambhampati, SBS.","corresponding_authors":null},{"pmid":"25387881","title":"A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis.","abstract":"Chromatin is a major determinant in the regulation of virtually all DNA-dependent processes. Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. The evolutionarily conserved DEK domain-containing protein is implicated in important chromatin-related processes in animals, but little is known about its DNA targets and protein interaction partners. In plants, the role of DEK has remained elusive. In this work, we identified DEK3 as a chromatin-associated protein in Arabidopsis thaliana. DEK3 specifically binds histones H3 and H4. Purification of other proteins associated with nuclear DEK3 also established DNA topoisomerase 1\u03b1 and proteins of the cohesion complex as in vivo interaction partners. Genome-wide mapping of DEK3 binding sites by chromatin immunoprecipitation followed by deep sequencing revealed enrichment of DEK3 at protein-coding genes throughout the genome. Using DEK3 knockout and overexpressor lines, we show that DEK3 affects nucleosome occupancy and chromatin accessibility and modulates the expression of DEK3 target genes. Furthermore, functional levels of DEK3 are crucial for stress tolerance. Overall, data indicate that DEK3 contributes to modulation of Arabidopsis chromatin structure and function.","authors":"Waidmann, S., Kusenda, B., Mayerhofer, J., Mechtler, K., Jonak, C.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Plant Cell","volume":"26","issue":"11","page":"4328-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27152988","title":"The BTB domains of the potassium channel tetramerization domain proteins prevalently assume pentameric states.","abstract":"Potassium channel tetramerization domain-containing (KCTD) proteins are involved in fundamental physio-pathological processes. Here, we report an analysis of the oligomeric state of the Bric-\u00e0-brack, Tram-track, Broad complex (BTB) domains of seven distinct KCTDs belonging to five major clades of the family evolution tree. Despite their functional and sequence variability, present electron microscopy data highlight the occurrence of well-defined pentameric states for all domains. Our data also show that these states coexist with alternative forms which include open pentamers. Thermal denaturation analyses conducted using KCTD1 as a model suggest that, in these proteins, different domains cooperate to their overall stability. Finally, negative-stain electron micrographs of KCTD6(BTB) in complex with Cullin3 show the presence of assemblies with a five-pointed pinwheel shape.","authors":"Smaldone, G., Pirone, L., Pedone, E., Marlovits, T., Vitagliano, L., Ciccarelli, L.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"FEBS Lett","volume":"590","issue":"11","page":"1663-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29605925","title":"Expressing Multi-subunit Complexes Using biGBac.","abstract":"The reconstitution of recombinant protein complexes is facilitated by methods that allow coexpression of their subunits from a single vector. Here we describe a detailed step-by-step protocol for the biGBac cloning method which can be used to generate baculoviral transfer vectors coding for up to 25 subunits of a protein complex (Weissmann et al., Proc Natl Acad Sci U S A 113(19):E2564-E2569, 2016). biGBac is based on Gibson assembly reactions, optimized DNA linker sequences, and uses a hierarchical two-step assembly procedure. In the first assembly step, up to five expression cassettes are combined to generate a polygene cassette. In the second step, up to five polygene cassettes can then be combined to generate transfer vectors coding for up to 25 subunits.","authors":"Weissmann, F., Peters, JM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Methods Mol Biol","volume":"1764","issue":null,"page":"329-343","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18824586","title":"Mind bomb 1 in the lymphopoietic niches is essential for T and marginal zone B cell development.","abstract":"Notch signaling regulates lineage decisions at multiple stages of lymphocyte development, and Notch activation requires the endocytosis of Notch ligands in the signal-sending cells. Four E3 ubiquitin ligases, Mind bomb (Mib) 1, Mib2, Neuralized (Neur) 1, and Neur2, regulate the Notch ligands to activate Notch signaling, but their roles in lymphocyte development have not been defined. We show that Mib1 regulates T and marginal zone B (MZB) cell development in the lymphopoietic niches. Inactivation of the Mib1 gene, but not the other E3 ligases, Mib2, Neur1, and Neur2, abrogated T and MZB cell development. Reciprocal bone marrow (BM) transplantation experiments revealed that Mib1 in the thymic and splenic niches is essential for T and MZB cell development. Interestingly, when BM cells from transgenic Notch reporter mice were transplanted into Mib1-null mice, the Notch signaling was abolished in the double-negative thymocytes. In addition, the endocytosis of Dll1 was impaired in the Mib1-null microenvironment. Moreover, the block in T cell development and the failure of Dll1 endocytosis were also observed in coculture system by Mib1 knockdown. Our study reveals that Mib1 is the essential E3 ligase in T and MZB cell development, through the regulation of Notch ligands in the thymic and splenic microenvironments.","authors":"Song, R., Kim, YW., Koo, BK., Jeong, HW., Yoon, MJ., Yoon, KJ., Jun, DJ., Im, SK., Shin, J., Kong, MP., Kim, KT., Yoon, K., Kong, YY.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Exp Med","volume":"205","issue":"11","page":"2525-36","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15733667","title":"Proximodistal patterning during limb regeneration.","abstract":"Regeneration is an ability that has been observed extensively throughout metazoan phylogeny. Amongst vertebrates, the urodele amphibians stand out for their exceptional capacity to regenerate body parts such as the limb. During this process, only the missing portion of the limb is precisely replaced--amputation in the upper arm results in regeneration of the entire limb, while amputation at the wrist produces a hand. Limb regeneration occurs through the formation of a local proliferative zone called the blastema. Here, we examine how proximodistal identity is established in the blastema. Using cell marking and transplantation experiments, we show that distal identities have already been established in the earliest stages of blastemas examined. Transplantation of cells into new environments is not sufficient to respecify cell identity. However, overexpression of the CD59, a cell surface molecule previously implicated in proximodistal identity during limb regeneration, causes distal blastema cells to translocate to a more proximal location and causes defects in the patterning of the distal elements of the regenerate. We suggest a model for the limb regeneration blastema where by 4 days post-amputation the blastema is already divided into distinct growth zones; the cells of each zone are already specified to give rise to upper arm, lower arm, and hand.","authors":"Echeverri, K., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Dev Biol","volume":"279","issue":"2","page":"391-401","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22986706","title":"Profiling of ileal carcinoids.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22986706<\/PMID><DateCompleted><Year>2014<\/Year><Month>05<\/Month><Day>28<\/Day><\/DateCompleted><DateRevised><Year>2013<\/Year><Month>02<\/Month><Day>14<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1423-0194<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>97<\/Volume><Issue>1<\/Issue><PubDate><Year>2013<\/Year><\/PubDate><\/JournalIssue><Title>Neuroendocrinology<\/Title><ISOAbbreviation>Neuroendocrinology<\/ISOAbbreviation><\/Journal><ArticleTitle>Profiling of ileal carcinoids.<\/ArticleTitle><Pagination><MedlinePgn>7-18<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1159\/000343232<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Identification of common molecular mechanisms is needed to facilitate the development of new treatment options for patients with ileal carcinoids.","authors":"Nilsson, O.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Neuroendocrinology","volume":"97","issue":"1","page":"7-18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33342665","title":"Mapping Sister Chromatid Conformation in Replicated Chromosomes.","abstract":null,"authors":"Mitter, M., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Trends Biochem Sci","volume":"46","issue":"2","page":"169-170","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27749819","title":"Arginine phosphorylation marks proteins for degradation by a Clp protease.","abstract":"Protein turnover is a tightly controlled process that is crucial for the removal of aberrant polypeptides and for cellular signalling. Whereas ubiquitin marks eukaryotic proteins for proteasomal degradation, a general tagging system for the equivalent bacterial Clp proteases is not known. Here we describe the targeting mechanism of the ClpC-ClpP proteolytic complex from Bacillus subtilis. Quantitative affinity proteomics using a ClpP-trapping mutant show that proteins phosphorylated on arginine residues are selectively targeted to ClpC-ClpP. In vitro reconstitution experiments demonstrate that arginine phosphorylation by the McsB kinase is required and sufficient for the degradation of substrate proteins. The docking site for phosphoarginine is located in the amino-terminal domain of the ClpC ATPase, as resolved at high resolution in a co-crystal structure. Together, our data demonstrate that phosphoarginine functions as a bona fide degradation tag for the ClpC-ClpP protease. This system, which is widely distributed across Gram-positive bacteria, is functionally analogous to the eukaryotic ubiquitin-proteasome system.","authors":"Trentini, DB., Suskiewicz, MJ., Heuck, A., Kurzbauer, R., Deszcz, L., Mechtler, K., Clausen, T.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nature","volume":"539","issue":"7627","page":"48-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15314694","title":"NF-kappaB is essential for epithelial-mesenchymal transition and metastasis in a model of breast cancer progression.","abstract":"The transcription factor NF-kappaB is activated in a range of human cancers and is thought to promote tumorigenesis, mainly due to its ability to protect transformed cells from apoptosis. To investigate the role of NF-kappaB in epithelial plasticity and metastasis, we utilized a well-characterized in vitro\/in vivo model of mammary carcinogenesis that depends on the collaboration of the Ha-Ras oncoprotein and TGF-beta. We show here that the IKK-2\/IkappaBalpha\/NF-kappaB pathway is required for the induction and maintenance of epithelial-mesenchymal transition (EMT). Inhibition of NF-kappaB signaling prevented EMT in Ras-transformed epithelial cells, while activation of this pathway promoted the transition to a mesenchymal phenotype even in the absence of TGF-beta. Furthermore, inhibition of NF-kappaB activity in mesenchymal cells caused a reversal of EMT, suggesting that NF-kappaB is essential for both the induction and maintenance of EMT. In line with the importance of EMT for invasion, blocking of NF-kappaB activity abrogated the metastatic potential of mammary epithelial cells in a mouse model system. Collectively, these data provide evidence of an essential role for NF-kappaB during distinct steps of breast cancer progression and suggest that the cooperation of Ras- and TGF-beta-dependent signaling pathways in late-stage tumorigenesis depends critically on NF-kappaB activity.","authors":"Huber, MA., Azoitei, N., Baumann, B., Gr\u00fcnert, S., Sommer, A., Pehamberger, H., Kraut, N., Beug, H., Wirth, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Clin Invest","volume":"114","issue":"4","page":"569-81","pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20679547","title":"Angiotensin-converting enzyme 2 suppresses pathological hypertrophy, myocardial fibrosis, and cardiac dysfunction.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20679547<\/PMID><DateCompleted><Year>2010<\/Year><Month>09<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4539<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>122<\/Volume><Issue>7<\/Issue><PubDate><Year>2010<\/Year><Month>Aug<\/Month><Day>17<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>Angiotensin-converting enzyme 2 suppresses pathological hypertrophy, myocardial fibrosis, and cardiac dysfunction.<\/ArticleTitle><Pagination><MedlinePgn>717-28, 18 p following 728<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/CIRCULATIONAHA.110.955369<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Angiotensin-converting enzyme 2 (ACE2) is a pleiotropic monocarboxypeptidase capable of metabolizing several peptide substrates. We hypothesized that ACE2 is a negative regulator of angiotensin II (Ang II)-mediated signaling and its adverse effects on the cardiovascular system.","authors":"Zhong, J., Basu, R., Guo, D., Chow, FL., Byrns, S., Schuster, M., Loibner, H., Wang, XH., Penninger, JM., Kassiri, Z., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Circulation","volume":"122","issue":"7","page":"717-28, 18 p following 728","pdf":null,"JrId":"2979","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25342715","title":"CDK6 as a key regulator of hematopoietic and leukemic stem cell activation.","abstract":"The cyclin-dependent kinase 6 (CDK6) and CDK4 have redundant functions in regulating cell-cycle progression. We describe a novel role for CDK6 in hematopoietic and leukemic stem cells (hematopoietic stem cells [HSCs] and leukemic stem cells [LSCs]) that exceeds its function as a cell-cycle regulator. Although hematopoiesis appears normal under steady-state conditions, Cdk6(-\/-) HSCs do not efficiently repopulate upon competitive transplantation, and Cdk6-deficient mice are significantly more susceptible to 5-fluorouracil treatment. We find that activation of HSCs requires CDK6, which interferes with the transcription of key regulators, including Egr1. Transcriptional profiling of HSCs is consistent with the central role of Egr1. The impaired repopulation capacity extends to BCR-ABL(p210+) LSCs. Transplantation with BCR-ABL(p210+)-infected bone marrow from Cdk6(-\/-) mice fails to induce disease, although recipient mice do harbor LSCs. Egr1 knock-down in Cdk6(-\/-) BCR-ABL(p210+) LSKs significantly enhances the potential to form colonies, underlining the importance of the CDK6-Egr1 axis. Our findings define CDK6 as an important regulator of stem cell activation and an essential component of a transcriptional complex that suppresses Egr1 in HSCs and LSCs.","authors":"Scheicher, R., Hoelbl-Kovacic, A., Bellutti, F., Tigan, AS., Prchal-Murphy, M., Heller, G., Schneckenleithner, C., Salazar-Roa, M., Z\u00f6chbauer-M\u00fcller, S., Zuber, J., Malumbres, M., Kollmann, K., Sexl, V.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Blood","volume":"125","issue":"1","page":"90-101","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20832315","title":"Cellular organization of the neural circuit that drives Drosophila courtship behavior.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20832315<\/PMID><DateCompleted><Year>2011<\/Year><Month>01<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2017<\/Year><Month>09<\/Month><Day>22<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>20<\/Volume><Issue>18<\/Issue><PubDate><Year>2010<\/Year><Month>Sep<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Cellular organization of the neural circuit that drives Drosophila courtship behavior.<\/ArticleTitle><Pagination><MedlinePgn>1602-14<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2010.08.025<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Courtship behavior in Drosophila has been causally linked to the activity of the heterogeneous set of \u223c1500 neurons that express the sex-specific transcripts of the fruitless (fru) gene, but we currently lack an appreciation of the cellular diversity within this population, the extent to which these cells are sexually dimorphic, and how they might be organized into functional circuits.","authors":"Yu, JY., Kanai, MI., Demir, E., Jefferis, GS., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Curr Biol","volume":"20","issue":"18","page":"1602-14","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18818392","title":"Defective Notch activation in microenvironment leads to myeloproliferative disease.","abstract":"Despite the great importance of nonhematopoietic cells constituting the microenvironment for normal hematopoiesis, the cellular interactions between nonhematopoietic cells themselves are largely unknown. Using the Cre-loxP system in mice to inactivate Mind bomb-1 (Mib1), an essential component for Notch ligand endocytosis, here we show that the development of an MPD is dependent on defective Notch activation in the microenvironment. Our 2 independent Mib1 conditional knockout (CKO) mouse lines each developed a myeloproliferative disease (MPD), with gradual accumulations of immature granulocytes. The mutant mice showed hepatosplenomegaly, anemia, granulocytosis, and leukocyte infiltration in multiple organs and finally died at approximately 20 weeks of age. We were surprised to find that the transplantation of wild-type bone marrow cells into the Mib1-null microenvironment resulted in a de novo MPD. Moreover, by introducing the constitutively active intracellular domain of Notch1 in the Mib1-null background, we show that active Notch1 expression in the Mib1-null microenvironment significantly suppressed the disease progression, suggesting that the MPD development in the Mib1 CKO mice is due to defective Notch activation in the nonhematopoietic cells. These findings demonstrate that normal hematopoiesis absolutely requires Notch activation through the Notch ligand-receptor interaction between microenvironmental cells themselves and shed light on the microenvironment that fosters hematopoietic disorders.","authors":"Kim, YW., Koo, BK., Jeong, HW., Yoon, MJ., Song, R., Shin, J., Jeong, DC., Kim, SH., Kong, YY.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Blood","volume":"112","issue":"12","page":"4628-38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28361309","title":"Reconstitution of a Patterned Neural Tube from Single Mouse Embryonic Stem Cells.","abstract":"The recapitulation of tissue development and patterning in three-dimensional (3D) culture is an important dimension of stem cell research. Here, we describe a 3D culture protocol in which single mouse ES cells embedded in Matrigel under neural induction conditions clonally form a lumen containing, oval-shaped epithelial structure within 3 days. By Day 7 an apicobasally polarized neuroepithelium with uniformly dorsal cell identity forms. Treatment with retinoic acid at Day 2 results in posteriorization and self-organization of dorsal-ventral neural tube patterning. Neural tube organoid growth is also supported by pure laminin gels as well as poly(ethylene glycol) (PEG)-based artificial extracellular matrix hydrogels, which can be fine-tuned for key microenvironment characteristics. The rapid generation of a simple, patterned tissue in well-defined culture conditions makes the neural tube organoid a tractable model for studying neural stem cell self-organization.","authors":"Ishihara, K., Ranga, A., Lutolf, MP., Tanaka, EM., Meinhardt, A.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Methods Mol Biol","volume":"1597","issue":null,"page":"43-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28350991","title":"Serum Proteases Potentiate BMP-Induced Cell Cycle Re-entry of Dedifferentiating Muscle Cells during Newt Limb Regeneration.","abstract":"Limb amputation in the newt induces myofibers to dedifferentiate and re-enter the cell cycle to generate proliferative myogenic precursors in the regeneration blastema. Here we show that bone morphogenetic proteins (BMPs) and mature BMPs that have been further cleaved by serum proteases induce cell cycle entry by dedifferentiating newt muscle cells. Protease-activated BMP4\/7 heterodimers that are present in serum strongly induced myotube cell cycle re-entry\u00a0with protease cleavage yielding a 30-fold potency increase of BMP4\/7 compared with canonical BMP4\/7. Inhibition of BMP signaling via muscle-specific\u00a0dominant-negative receptor expression reduced cell cycle entry in\u00a0vitro and in\u00a0vivo. In\u00a0vivo inhibition of serine protease activity depressed cell cycle re-entry, which in turn was rescued by cleaved-mimic BMP. This work identifies a mechanism of BMP activation that generates blastema cells from differentiated muscle.","authors":"Wagner, I., Wang, H., Weissert, PM., Straube, WL., Shevchenko, A., Gentzel, M., Brito, G., Tazaki, A., Oliveira, C., Sugiura, T., Shevchenko, A., Simon, A., Drechsel, DN., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Dev Cell","volume":"40","issue":"6","page":"608-617.e6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25306923","title":"Mechanism of polyubiquitination by human anaphase-promoting complex: RING repurposing for ubiquitin chain assembly.","abstract":"Polyubiquitination by E2 and E3 enzymes is a predominant mechanism regulating protein function. Some RING E3s, including anaphase-promoting complex\/cyclosome (APC), catalyze polyubiquitination by sequential reactions with two different E2s. An initiating E2 ligates ubiquitin to an E3-bound substrate. Another E2 grows a polyubiquitin chain on the ubiquitin-primed substrate through poorly defined mechanisms. Here we show that human APC's RING domain is repurposed for dual functions in polyubiquitination. The canonical RING surface activates an initiating E2-ubiquitin intermediate for substrate modification. However, APC engages and activates its specialized ubiquitin chain-elongating E2 UBE2S in ways that differ from current paradigms. During chain assembly, a distinct APC11 RING surface helps deliver a substrate-linked ubiquitin to accept another ubiquitin from UBE2S. Our data define mechanisms of APC\/UBE2S-mediated polyubiquitination, reveal diverse functions of RING E3s and E2s, and provide a framework for understanding distinctive RING E3 features specifying ubiquitin chain elongation.","authors":"Brown, NG., Watson, ER., Weissmann, F., Jarvis, MA., VanderLinden, R., Grace, CRR., Frye, JJ., Qiao, R., Dube, P., Petzold, G., Cho, SE., Alsharif, O., Bao, J., Davidson, IF., Zheng, JJ., Nourse, A., Kurinov, I., Peters, JM., Stark, H., Schulman, BA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mol Cell","volume":"56","issue":"2","page":"246-260","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20012301","title":"Functional analysis of LOXL2 in pancreatic carcinoma.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20012301<\/PMID><DateCompleted><Year>2010<\/Year><Month>04<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1432-1262<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>25<\/Volume><Issue>3<\/Issue><PubDate><Year>2010<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>International journal of colorectal disease<\/Title><ISOAbbreviation>Int J Colorectal Dis<\/ISOAbbreviation><\/Journal><ArticleTitle>Functional analysis of LOXL2 in pancreatic carcinoma.<\/ArticleTitle><Pagination><MedlinePgn>303-11<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s00384-009-0853-5<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\" NlmCategory=\"OBJECTIVE\">Lysyl oxidase-like 2 (LOXL2) plays a part in epithelial-mesenchymal transition (EMT) by stabilizing the transcription factor SNAI1. Previous studies showed that LOXL2 is one of the most highly and specifically upregulated genes in pancreatic cancer. LOXL2 was also found to be strongly upregulated in the secretome of established pancreatic cancer cell lines. To get more insight into the aggressive growth and infiltrating nature of pancreatic cancer, we evaluated the functional role of LOXL2 in pancreatic cancer cells.","authors":"R\u00fcckert, F., Joensson, P., Saeger, HD., Gr\u00fctzmann, R., Pilarsky, C.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Int J Colorectal Dis","volume":"25","issue":"3","page":"303-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21935291","title":"Near-IR Imaging of Thermal Changes in Enamel during Laser Ablation.","abstract":"The objective of this work was to observe the various thermal-induced optical changes that occur in the near-infrared (NIR) during drilling in dentin and enamel with the laser and the high-speed dental handpiece. Tooth sections of ~ 3 mm-thickness were prepared from extracted human incisors (N=60). Samples were ablated with a mechanically scanned CO(2) laser operating at a wavelength of 9.3-\u00b5m, a 300-Hz laser pulse repetition rate, and a laser pulse duration of 10-20 \u00b5s. An InGaAs imaging camera was used to acquire real-time NIR images at 1300-nm of thermal and mechanical changes (cracks). Enamel was rapidly removed by the CO(2) laser without peripheral thermal damage by mechanically scanning the laser beam while a water spray was used to cool the sample. Comparison of the peripheral thermal and mechanical changes produced while cutting with the laser and the high-speed hand-piece suggest that enamel and dentin can be removed at high speed by the CO(2) laser without excessive peripheral thermal or mechanical damage. Only 2 of the 15 samples ablated with the laser showed the formation of small cracks while 9 out of 15 samples exhibited crack formation with the dental hand-piece. The first indication of thermal change is a decrease in transparency due to loss of the mobile water from pores in the enamel which increase light-scattering. To test the hypothesis that peripheral thermal changes were caused by loss of mobile water in the enamel, thermal changes were intentionally induced by heating the surface. The mean attenuation coefficient of enamel increased significantly from 2.12 \u00b1 0.82 to 5.08 \u00b1 0.98 with loss of mobile water due to heating.","authors":"Maung, LH., Lee, C., Fried, D.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc SPIE Int Soc Opt Eng","volume":"7546","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17347653","title":"Fra-1 promotes growth and survival in RAS-transformed thyroid cells by controlling cyclin A transcription.","abstract":"Fra-1 is frequently overexpressed in epithelial cancers and implicated in invasiveness. We previously showed that Fra-1 plays crucial roles in RAS transformation in rat thyroid cells and mouse fibroblasts. Here, we report a novel role for Fra-1 as a regulator of mitotic progression in RAS-transformed thyroid cells. Fra-1 expression and phosphorylation are regulated during the cell cycle, peaking at G2\/M. Knockdown of Fra-1 caused a proliferative block and apoptosis. Although most Fra-1-knockdown cells accumulated in G2, a fraction of cells entering M-phase underwent abortive cell division and exhibited hallmarks of genomic instability (micronuclei, lagging chromosomes and anaphase bridges). Furthermore, we established a link between Fra-1 and the cell-cycle machinery by identifying cyclin A as a novel transcriptional target of Fra-1. During the cell cycle, Fra-1 was recruited to the cyclin A gene (ccna2) promoter, binding to previously unidentified AP-1 sites and the CRE. Fra-1 also induced the expression of JunB, which in turn interacts with the cyclin A promoter. Hence, Fra-1 induction is important in thyroid tumorigenesis, critically regulating cyclin expression and cell-cycle progression.","authors":"Casalino, L., Bakiri, L., Talotta, F., Weitzman, JB., Fusco, A., Yaniv, M., Verde, P.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"EMBO J","volume":"26","issue":"7","page":"1878-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17304211","title":"Genetic analysis of p38 MAP kinases in myogenesis: fundamental role of p38alpha in abrogating myoblast proliferation.","abstract":"The p38 mitogen-activated protein kinase (MAPK) pathway plays a critical role in skeletal muscle differentiation. However, the relative contribution of the four p38 MAPKs (p38alpha, p38beta, p38gamma and p38delta) to this process is unknown. Here we show that myoblasts lacking p38alpha, but not those lacking p38beta or p38delta, are unable to differentiate and form multinucleated myotubes, whereas p38gamma-deficient myoblasts exhibit an attenuated fusion capacity. The defective myogenesis in the absence of p38alpha is caused by delayed cell-cycle exit and continuous proliferation in differentiation-promoting conditions. Indeed, activation of JNK\/cJun was enhanced in p38alpha-deficient myoblasts leading to increased cyclin D1 transcription, whereas inhibition of JNK activity rescued the proliferation phenotype. Thus, p38alpha controls myogenesis by antagonizing the activation of the JNK proliferation-promoting pathway, before its direct effect on muscle differentiation-specific gene transcription. More importantly, in agreement with the defective myogenesis of cultured p38alpha(Delta\/Delta) myoblasts, neonatal muscle deficient in p38alpha shows cellular hyperproliferation and delayed maturation. This study provides novel evidence of a fundamental role of p38alpha in muscle formation in vitro and in vivo.","authors":"Perdiguero, E., Ruiz-Bonilla, V., Gresh, L., Hui, L., Ballestar, E., Sousa-Victor, P., Baeza-Raja, B., Jard\u00ed, M., Bosch-Comas, A., Esteller, M., Caelles, C., Serrano, AL., Wagner, EF., Mu\u00f1oz-C\u00e1noves, P.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"EMBO J","volume":"26","issue":"5","page":"1245-56","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19808375","title":"Loss of angiotensin-converting enzyme 2 accelerates maladaptive left ventricular remodeling in response to myocardial infarction.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19808375<\/PMID><DateCompleted><Year>2009<\/Year><Month>10<\/Month><Day>27<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1941-3297<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>2<\/Volume><Issue>5<\/Issue><PubDate><Year>2009<\/Year><Month>Sep<\/Month><\/PubDate><\/JournalIssue><Title>Circulation. Heart failure<\/Title><ISOAbbreviation>Circ Heart Fail<\/ISOAbbreviation><\/Journal><ArticleTitle>Loss of angiotensin-converting enzyme 2 accelerates maladaptive left ventricular remodeling in response to myocardial infarction.<\/ArticleTitle><Pagination><MedlinePgn>446-55<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/CIRCHEARTFAILURE.108.840124<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Angiotensin-converting enzyme 2 (ACE2) is a monocarboxypeptidase that metabolizes Ang II into Ang 1-7, thereby functioning as a negative regulator of the renin-angiotensin system. We hypothesized that ACE2 deficiency may compromise the cardiac response to myocardial infarction (MI).","authors":"Kassiri, Z., Zhong, J., Guo, D., Basu, R., Wang, X., Liu, PP., Scholey, JW., Penninger, JM., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Circ Heart Fail","volume":"2","issue":"5","page":"446-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26851380","title":"Mediator Architecture and RNA Polymerase II Interaction.","abstract":"Integrated structural biology recently elucidated the architecture of Mediator and its position on RNA polymerase II. Here we summarize these achievements and list open questions on Mediator structure and mechanism.","authors":"Plaschka, C., Nozawa, K., Cramer, P.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Mol Biol","volume":"428","issue":"12","page":"2569-2574","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21801016","title":"Limb regeneration: a new development?","abstract":"Salamander limb regeneration is a classical model of tissue morphogenesis and patterning. Through recent advances in cell labeling and molecular analysis, a more precise, mechanistic understanding of this process has started to emerge. Long-standing questions include to what extent limb regeneration recapitulates the events observed in mammalian limb development and to what extent are adult- or salamander- specific aspects deployed. Historically, researchers studying limb development and limb regeneration have proposed different models of pattern formation. Here we discuss recent data on limb regeneration and limb development to argue that although patterning mechanisms are likely to be similar, cell plasticity and signaling from nerves play regeneration-specific roles.","authors":"Nacu, E., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Annu Rev Cell Dev Biol","volume":"27","issue":null,"page":"409-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-02-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17286599","title":"In vitro differentiation of murine embryonic stem cells toward a renal lineage.","abstract":"Embryonic stem (ES) cells have the capacity to differentiate into all cells of the developing embryo and may provide a renewable resource for future cell replacement therapies. The addition of bone morphogenetic protein 4 (BMP4) to serum-free ES cell culture has previously been shown to induce transcription factors, signaling molecules, and cell adhesion proteins expressed during mesoderm specification of the embryo. Here, we show the dynamics of primitive streak mesoderm differentiation in ES cells is comparable between serum and serum-free embryoid body (EB) cultures, supplemented with BMP4. Furthermore, we show a delayed wave of expression of a cohort of genes (Pax2, WT1, podocalyxin, pod-1, and nephrin), which play important roles during embryonic kidney development. The paired box transcription factor, Pax2, is one of the earliest genes expressed during kidney organogenesis and is required for normal urogenital development. ES cell lines containing either a modified Pax2 promoter-lacZ or bacterial artificial chromosome-green fluorescent protein (GFP) transgene were generated, which enabled the quantitative analysis of kidney rather than neuronal Pax2 expression within EBs. Both beta-galactosidase activity and GFP expression were detected by immunohistochemical and flow cytometric analysis following 16 days of EB culture, which correlated with an increase in Pax2 transcript levels. Together, these results suggest a spontaneous kidney gene expression program develops in mature EBs grown in both serum and serum-free conditions, when supplemented with BMP4. Further, the recombinant growth factors BMP2, BMP4, and BMP7 strongly influence gene expression within mesoderm induced EBs. BMP4 promotes ventral (blood) and intermediate (kidney) mesoderm gene expression, whereas BMP2 and BMP7 promote kidney outcomes at the expense of hematopoietic commitment. This induction assay and these unique ES cell lines will be useful for the generation of mesoderm-derived cell populations with implications for future cell therapeutic\/integration assays.","authors":"Bruce, SJ., Rea, RW., Steptoe, AL., Busslinger, M., Bertram, JF., Perkins, AC.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Differentiation","volume":"75","issue":"5","page":"337-49","pdf":null,"JrId":"3402","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17234739","title":"HOXA10 is a critical regulator for hematopoietic stem cells and erythroid\/megakaryocyte development.","abstract":"The Homeobox (Hox) transcription factors are important regulators of normal and malignant hematopoiesis because they control proliferation, differentiation, and self-renewal of hematopoietic cells at different levels of the hematopoietic hierarchy. In transgenic mice we show that the expression of HOXA10 is tightly regulated by doxycycline. Intermediate concentrations of HOXA10 induced a 15-fold increase in the repopulating capacity of hematopoietic stem cells (HSCs) after 13 days of in vitro culture. Notably, the proliferation induction of HSC by HOXA10 was dependent on the HOXA10 concentration, because high levels of HOXA10 had no effect on HSC proliferation. Furthermore, high levels of HOXA10 blocked erythroid and megakaryocyte development, demonstrating that tight regulation of HOXA10 is critical for normal development of the erythroid and megakaryocytic lineages. The HOXA10-mediated effects on hematopoietic cells were associated with altered expression of genes that govern stem-cell self-renewal and lineage commitment (eg, hepatic leukemia factor [HlF], Dickkopf-1 [Dkk-1], growth factor independent-1 [Gfi-1], and Gata-1). Interestingly, binding sites for HOXA10 were found in HLF, Dkk-1, and Gata-1, and Dkk-1 and Gfi-1 were transcriptionally activated by HOXA10. These findings reveal novel molecular pathways that act downstream of HOXA10 and identify HOXA10 as a master regulator of postnatal hematopoietic development.","authors":"Magnusson, M., Brun, AC., Miyake, N., Larsson, J., Ehinger, M., Bjornsson, JM., Wutz, A., Sigvardsson, M., Karlsson, S.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Blood","volume":"109","issue":"9","page":"3687-96","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15580632","title":"Quantitative evaluation of morpholino-mediated protein knockdown of GFP, MSX1, and PAX7 during tail regeneration in Ambystoma mexicanum.","abstract":"Vertebrate regeneration is a fascinating but poorly understood biological phenomena. Urodele amphibians such as Ambystoma mexicanum (the axolotl) can functionally regenerate complex body structures such as the limb and tail, including the spinal cord, throughout life. So far, molecular studies on regeneration have been limited due to the paucity of tools for knocking-down gene and protein function. In this article, we quantitatively assessed the ability of morpholinos to specifically down-regulate protein expression in both cultured urodele cells and in vivo. We focused on the down-regulation of green fluorescent protein and two axolotl proteins, MSX1 and PAX7. Our data show that the expression of these proteins can be efficiently reduced by morpholinos. MSX1 has been hypothesized to be involved in muscle dedifferentiation based on experiments using cultured myotubes. Our studies in in vivo muscle fibers so far have shown no influence of overexpressing or down-regulating MSX1 on the dedifferentiation process.","authors":"Schnapp, E., Tanaka, EM., Tamaka, EM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Dev Dyn","volume":"232","issue":"1","page":"162-70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27505678","title":"A Kinase-Independent Function of CDK6 Links the Cell Cycle to Tumor Angiogenesis.","abstract":null,"authors":"Kollmann, K., Heller, G., Schneckenleithner, C., Warsch, W., Scheicher, R., Ott, RG., Sch\u00e4fer, M., Fajmann, S., Schlederer, M., Schiefer, AI., Reichart, U., Mayerhofer, M., Hoeller, C., Z\u00f6chbauer-M\u00fcller, S., Kerjaschki, D., Bock, C., Kenner, L., Hoefler, G., Freissmuth, M., Green, AR., Moriggl, R., Busslinger, M., Malumbres, M., Sexl, V.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cancer Cell","volume":"30","issue":"2","page":"359-360","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25652824","title":"Architecture of the RNA polymerase II-Mediator core initiation complex.","abstract":"The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7\u00a0\u00c5 resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.","authors":"Plaschka, C., Larivi\u00e8re, L., Wenzeck, L., Seizl, M., Hemann, M., Tegunov, D., Petrotchenko, EV., Borchers, CH., Baumeister, W., Herzog, F., Villa, E., Cramer, P.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nature","volume":"518","issue":"7539","page":"376-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17167413","title":"Essential role for collectrin in renal amino acid transport.","abstract":"Angiotensin -converting enzyme 2 (ACE2) is a regulator of the renin angiotensin system involved in acute lung failure, cardiovascular functions and severe acute respiratory syndrome (SARS) infections in mammals. A gene encoding a homologue to ACE2, termed collectrin (Tmem27), has been identified in immediate proximity to the ace2 locus. The in vivo function of collectrin was unclear. Here we report that targeted disruption of collectrin in mice results in a severe defect in renal amino acid uptake owing to downregulation of apical amino acid transporters in the kidney. Collectrin associates with multiple apical transporters and defines a novel group of renal amino acid transporters. Expression of collectrin in Xenopus oocytes and Madin-Darby canine kidney (MDCK) cells enhances amino acid transport by the transporter B(0)AT1. These data identify collectrin as a key regulator of renal amino acid uptake.","authors":"Danilczyk, U., Sarao, R., Remy, C., Benabbas, C., Stange, G., Richter, A., Arya, S., Pospisilik, JA., Singer, D., Camargo, SM., Makrides, V., Ramadan, T., Verrey, F., Wagner, CA., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nature","volume":"444","issue":"7122","page":"1088-91","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2007-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19427217","title":"HAUS, the 8-subunit human Augmin complex, regulates centrosome and spindle integrity.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19427217<\/PMID><DateCompleted><Year>2009<\/Year><Month>08<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>19<\/Volume><Issue>10<\/Issue><PubDate><Year>2009<\/Year><Month>May<\/Month><Day>26<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>HAUS, the 8-subunit human Augmin complex, regulates centrosome and spindle integrity.<\/ArticleTitle><Pagination><MedlinePgn>816-26<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2009.04.033<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The assembly of a robust microtubule-based mitotic spindle is a prerequisite for the accurate segregation of chromosomes to progeny. Spindle assembly relies on the concerted action of centrosomes, spindle microtubules, molecular motors, and nonmotor spindle proteins.","authors":"Lawo, S., Bashkurov, M., Mullin, M., Ferreria, MG., Kittler, R., Habermann, B., Tagliaferro, A., Poser, I., Hutchins, JR., Hegemann, B., Pinchev, D., Buchholz, F., Peters, JM., Hyman, AA., Gingras, AC., Pelletier, L.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Biol","volume":"19","issue":"10","page":"816-26","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17189721","title":"Role of heterodimerization of c-Fos and Fra1 proteins in osteoclast differentiation.","abstract":"Bone resorbing osteoclasts are specialized macrophages that cannot differentiate in the absence of c-Fos, a member of the dimeric transcription factor AP-1 (activator protein-1). However, osteoclast differentiation in the absence of c-Fos can be rescued in vitro and in vivo by Fra1, a Fos-like protein and transcriptional target of c-Fos. To enable AP-1 proteins binding to DNA, c-Fos or Fra1 must heterodimerize with a partner such as c-Jun, JunB and JunD. In this study, we investigated the dimerization partners of c-Fos and Fra1 required for osteoclast differentiation using synthetic \"single-chain\" AP-1 dimers in which c-Fos or Fra1 is tethered via a linker to Jun proteins. When c-Fos was analyzed in combination with any Jun protein, including a c-Jun mutant lacking major phosphorylation sites for c-Jun amino-terminal kinase (JNK), osteoclasts were efficiently formed from c-Fos-deficient hematopoietic precursors. However, Fra1 in combination with any Jun protein could not rescue osteoclastogenesis. The ability to rescue was compared to transcriptional activity measured in transient transfection assays using promoters driven by consensus AP-1 sites or a composite AP-1\/NFAT binding site. These data show that a single Jun\/c-Fos dimer is sufficient for osteoclast differentiation, likely due to its transactivation ability for a broader range of promoters, in particular consensus AP-1 sites. We propose that Fra1 together with a dimerization partner different from Jun proteins can rescue osteoclast differentiation in c-Fos-deficient precursors.","authors":"Bakiri, L., Takada, Y., Radolf, M., Eferl, R., Yaniv, M., Wagner, EF., Matsuo, K.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Bone","volume":"40","issue":"4","page":"867-75","pdf":null,"JrId":"1710","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23939621","title":"Model of the Mediator middle module based on protein cross-linking.","abstract":"The essential core of the transcription coactivator Mediator consists of two conserved multiprotein modules, the head and middle modules. Whereas the structure of the head module is known, the structure of the middle module is lacking. Here we report a 3D model of a 6-subunit Mediator middle module. The model was obtained by arranging crystal structures and homology models of parts of the module based on lysine-lysine cross-links obtained by mass spectrometric analysis. The model contains a central tetramer formed by the heterodimers Med4\/Med9 and Med7\/Med21. The Med7\/Med21 heterodimer is flanked by subunits Med10 and Med31. The model is highly extended, suggests that the middle module is flexible and contributes to a molecular basis for detailed structure-function studies of RNA polymerase II regulation.","authors":"Larivi\u00e8re, L., Plaschka, C., Seizl, M., Petrotchenko, EV., Wenzeck, L., Borchers, CH., Cramer, P.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nucleic Acids Res","volume":"41","issue":"20","page":"9266-73","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17189697","title":"LET-99, GOA-1\/GPA-16, and GPR-1\/2 are required for aster-positioned cytokinesis.","abstract":"At anaphase, the mitotic spindle positions the cytokinesis furrow [1]. Two populations of spindle microtubules are implicated in cytokinesis: radial microtubule arrays called asters and bundled nonkinetochore microtubules called the spindle midzone [2-4]. In C. elegans embryos, these two populations of microtubules provide two consecutive signals that position the cytokinesis furrow: The first signal is positioned midway between the microtubule asters; the second signal is positioned over the spindle midzone [5]. Evidence for two cytokinesis signals came from the identification of molecules that block midzone-positioned cytokinesis [5-7]. However, no molecules that are only required for, and thus define, the molecular pathway of aster-positioned cytokinesis have been identified. With RNAi screening, we identify LET-99 and the heterotrimeric G proteins GOA-1\/GPA-16 and their regulator GPR-1\/2 [10-12] in aster-positioned cytokinesis. By using mechanical spindle displacement, we show that the anaphase spindle positions cortical LET-99, at the site of the presumptive cytokinesis furrow. LET-99 enrichment at the furrow depends on the G proteins. GPR-1 is locally reduced at the site of cytokinesis-furrow formation by LET-99, which prevents accumulation of GPR-1 at this site. We conclude that LET-99 and the G proteins define a molecular pathway required for aster-positioned cytokinesis.","authors":"Bringmann, H., Cowan, CR., Kong, J., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Curr Biol","volume":"17","issue":"2","page":"185-91","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28030800","title":"The role of miR-17-92 in the miRegulatory landscape of Ewing sarcoma.","abstract":"MicroRNAs serve to fine-tune gene expression and play an important regulatory role in tissue specific gene networks. The identification and validation of miRNA target genes in a tissue still poses a significant problem since the presence of a seed sequence in the 3'UTR of an mRNA and its expression modulation upon ectopic expression of the miRNA do not reliably predict regulation under physiological conditions. The chimeric oncoprotein EWS-FLI1 is the driving pathogenic force in Ewing sarcoma. MiR-17-92, one of the most potent oncogenic miRNAs, was recently reported to be among the top EWS-FLI1 activated miRNAs. Using a combination of AGO2 pull-down experiments by PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) and of RNAseq upon miRNA depletion by ectopic sponge expression, we aimed to identify the targetome of miR-17-92 in Ewing sarcoma. Intersecting both datasets we found an enrichment of PAR-CLIP hits for members of the miR-17-92 cluster in the 3'UTRs of genes up-regulated in response to mir-17-92 specific sponge expression. Strikingly, approximately a quarter of these genes annotate to the TGFB\/BMP pathway, the majority mapping downstream of SMAD signaling. Testing for SMAD phosphorylation, we identify quiet but activatable TGFB signaling and cell autonomous activity of the BMP pathway resulting in the activation of the stemness regulatory transcriptional repressors ID1 and ID3. Taken together, our findings shed light on the complex miRegulatory landscape of Ewing Sarcoma pointing miR-17-92 as a key node connected to TGFB\/BMP pathway.","authors":"Schwentner, R., Herrero-Martin, D., Kauer, MO., Mutz, CN., Katschnig, AM., Sienski, G., Alonso, J., Aryee, DN., Kovar, H.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Oncotarget","volume":"8","issue":"7","page":"10980-10993","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17159993","title":"Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome.","abstract":"Accurate discrimination between cognate and near-cognate aminoacyl-tRNAs during translation relies on the specific acceleration of forward rate constants for cognate tRNAs. Such specific rate enhancement correlates with conformational changes in the tRNA and small ribosomal subunit that depend on an RNA-specific type of interaction, the A-minor motif, between universally conserved 16S ribosomal RNA nucleotides and the cognate codon-anticodon helix. We show that perturbations of these two components of the A-minor motif, the conserved rRNA bases and the codon-anticodon helix, result in distinct outcomes. Although both cause decreases in the rates of tRNA selection that are rescued by aminoglycoside antibiotics, only disruption of the codon-anticodon helix is overcome by a miscoding tRNA variant. On this basis, we propose that two independent molecular requirements must be met to allow tRNAs to proceed through the selection pathway, providing a mechanism for exquisite control of fidelity during this step in gene expression.","authors":"Cochella, L., Brunelle, JL., Green, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Struct Mol Biol","volume":"14","issue":"1","page":"30-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17145782","title":"Somatic excision demonstrates that c-Jun induces cellular migration and invasion through induction of stem cell factor.","abstract":"Cancer cells arise through sequential acquisition of mutations in tumor suppressors and oncogenes. c-Jun, a critical component of the AP-1 complex, is frequently overexpressed in diverse tumor types and has been implicated in promoting cellular proliferation, migration, and angiogenesis. Functional analysis of candidate genetic targets using germ line deletion in murine models can be compromised through compensatory mechanisms. As germ line deletion of c-jun induces embryonic lethality, somatic deletion of the c-jun gene was conducted using floxed c-jun (c-jun(f\/f)) conditional knockout mice. c-jun-deleted cells showed increased cellular adhesion, stress fiber formation, and reduced cellular migration. The reduced migratory velocity and migratory directionality was rescued by either c-Jun reintroduction or addition of secreted factors from wild-type cells. An unbiased analysis of cytokines and growth factors, differentially expressed and showing loss of secretion upon c-jun deletion, identified stem cell factor (SCF) as a c-Jun target gene. Immunoneutralizing antibody to SCF reduced migration of wild-type cells. SCF addition rescued the defect in cellular adhesion, cellular velocity, directional migration, transwell migration, and cellular invasion of c-jun(-\/-) cells. c-Jun induced SCF protein, mRNA, and promoter activity. Induction of the SCF promoter required the c-Jun DNA-binding domain. c-Jun bound to the SCF promoter in chromatin immunoprecipitation assays. Mutation of the c-Jun binding site abolished c-Jun-mediated induction of the SCF promoter. These studies demonstrate an essential role of c-Jun in cellular migration through induction of SCF.","authors":"Katiyar, S., Jiao, X., Wagner, E., Lisanti, MP., Pestell, RG.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Cell Biol","volume":"27","issue":"4","page":"1356-69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-03-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25241901","title":"Hyperactivation of mTORC1 and mTORC2 by multiple oncogenic events causes addiction to eIF4E-dependent mRNA translation in T-cell leukemia.","abstract":"High activation of the PI3K-AKT-mTOR pathway is characteristic for T-cell acute lymphoblastic leukemia (T-ALL). The activity of the master regulator of this pathway, PTEN, is often impaired in T-ALL. However, experimental evidence suggests that input from receptor tyrosine kinases (RTKs) is required for sustained mTOR activation, even in the absence of PTEN. We previously reported the expression of Neurotrophin receptor tyrosine kinases (TRKs) and their respective ligands in primary human leukemia samples. In the present study we aimed to dissect the downstream signaling cascades of TRK-induced T-ALL in a murine model and show that T-ALLs induced by deregulated receptor tyrosine kinase signaling acquire activating mutations in Notch1 and lose PTEN during clonal evolution. Some clones additionally lost one allele of the homeodomain transcription factor Cux1. All events independently led to a gradual hyperactivation of both mTORC1 and mTORC2 signaling. We dissected the role of the individual mTOR complexes by shRNA knockdown and found that the separate depletion of mTORC1 or mTORC2 reduced the growth of T-ALL blasts, but was not sufficient to induce apoptosis. In contrast, knockdown of the mTOR downstream effector eIF4E caused a striking cytotoxic effect, demonstrating a critical addiction to cap-dependent mRNA-translation. Although high mTORC2-AKT activation is commonly associated with drug-resistance, we demonstrate that T-ALL displaying a strong mTORC2-AKT activation were specifically susceptible to 4EGI-1, an inhibitor of the eIF4E-eIF4G interaction. To decipher the mechanism of 4EGI-1, we performed a genome-wide analysis of mRNAs that are translationally regulated by 4EGI-1 in T-ALL. 4EGI-1 effectively reduced the ribosomal occupancy of mRNAs that were strongly upregulated in T-ALL blasts compared with normal thymocytes including transcripts important for translation, mitochondria and cell cycle progression, such as cyclins and ribosomal proteins. These data suggest that disrupting the eIF4E-eIF4G interaction constitutes a promising therapy strategy in mTOR-deregulated T-cell leukemia.","authors":"Schwarzer, A., Holtmann, H., Brugman, M., Meyer, J., Schauerte, C., Zuber, J., Steinemann, D., Schlegelberger, B., Li, Z., Baum, C.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Oncogene","volume":"34","issue":"27","page":"3593-604","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23859941","title":"Taste dysfunction in BTBR mice due to a mutation of Itpr3, the inositol triphosphate receptor 3 gene.","abstract":"The BTBR T+ tf\/J (BTBR) mouse strain is indifferent to exemplars of sweet, Polycose, umami, bitter, and calcium tastes, which share in common transduction by G protein-coupled receptors (GPCRs). To investigate the genetic basis for this taste dysfunction, we screened 610 BTBR\u00d7NZW\/LacJ F2 hybrids, identified a potent QTL on chromosome 17, and isolated this in a congenic strain. Mice carrying the BTBR\/BTBR haplotype in the 0.8-Mb (21-gene) congenic region were indifferent to sweet, Polycose, umami, bitter, and calcium tastes. To assess the contribution of a likely causative culprit, Itpr3, the inositol triphosphate receptor 3 gene, we produced and tested Itpr3 knockout mice. These were also indifferent to GPCR-mediated taste compounds. Sequencing the BTBR form of Itpr3 revealed a unique 12 bp deletion in Exon 23 (Chr 17: 27238069; Build 37). We conclude that a spontaneous mutation of Itpr3 in a progenitor of the BTBR strain produced a heretofore unrecognized dysfunction of GPCR-mediated taste transduction.","authors":"Tordoff, MG., Ellis, HT.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Physiol Genomics","volume":"45","issue":"18","page":"834-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19249208","title":"Regulation of APC\/C activity in oocytes by a Bub1-dependent spindle assembly checkpoint.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19249208<\/PMID><DateCompleted><Year>2009<\/Year><Month>06<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2017<\/Year><Month>09<\/Month><Day>22<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>19<\/Volume><Issue>5<\/Issue><PubDate><Year>2009<\/Year><Month>Mar<\/Month><Day>10<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Regulation of APC\/C activity in oocytes by a Bub1-dependent spindle assembly checkpoint.<\/ArticleTitle><Pagination><MedlinePgn>369-80<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2009.01.064<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Missegregation of chromosomes during meiosis in human females causes aneuploidy, including trisomy 21, and is thought also to be the major cause of age-related infertility. Most errors are thought to occur at the first meiotic division. The high frequency of errors raises questions as to whether the surveillance mechanism known as the spindle assembly checkpoint (SAC) that controls the anaphase-promoting complex or cyclosome (APC\/C) operates effectively in oocytes. Experimental approaches hitherto used to inactivate the SAC in oocytes suffer from a number of drawbacks.","authors":"McGuinness, BE., Anger, M., Kouznetsova, A., Gil-Bernab\u00e9, AM., Helmhart, W., Kudo, NR., Wuensche, A., Taylor, S., Hoog, C., Novak, B., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Biol","volume":"19","issue":"5","page":"369-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17291761","title":"The small-molecule inhibitor BI 2536 reveals novel insights into mitotic roles of polo-like kinase 1.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">17291761<\/PMID><DateCompleted><Year>2007<\/Year><Month>04<\/Month><Day>04<\/Day><\/DateCompleted><DateRevised><Year>2013<\/Year><Month>11<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>17<\/Volume><Issue>4<\/Issue><PubDate><Year>2007<\/Year><Month>Feb<\/Month><Day>20<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The small-molecule inhibitor BI 2536 reveals novel insights into mitotic roles of polo-like kinase 1.<\/ArticleTitle><Pagination><MedlinePgn>304-15<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The mitotic kinases, Cdk1, Aurora A\/B, and Polo-like kinase 1 (Plk1) have been characterized extensively to further understanding of mitotic mechanisms and as potential targets for cancer therapy. Cdk1 and Aurora kinase studies have been facilitated by small-molecule inhibitors, but few if any potent Plk1 inhibitors have been identified.","authors":"L\u00e9n\u00e1rt, P., Petronczki, M., Steegmaier, M., Di Fiore, B., Lipp, JJ., Hoffmann, M., Rettig, WJ., Kraut, N., Peters, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Curr Biol","volume":"17","issue":"4","page":"304-15","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28006062","title":"Association Between Benign Breast Disease in African American and White American Women and Subsequent Triple-Negative Breast Cancer.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">28006062<\/PMID><DateCompleted><Year>2017<\/Year><Month>09<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">2374-2445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>3<\/Volume><Issue>8<\/Issue><PubDate><Year>2017<\/Year><Month>Aug<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>JAMA oncology<\/Title><ISOAbbreviation>JAMA Oncol<\/ISOAbbreviation><\/Journal><ArticleTitle>Association Between Benign Breast Disease in African American and White American Women and Subsequent Triple-Negative Breast Cancer.<\/ArticleTitle><Pagination><MedlinePgn>1102-1106<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1001\/jamaoncol.2016.5598<\/ELocationID><Abstract><AbstractText Label=\"Importance\" NlmCategory=\"UNASSIGNED\">Compared with white American (WA) women, African American (AA) women have a 2-fold higher incidence of breast cancers that are negative for estrogen receptor, progesterone receptor, and ERBB2 (triple-negative breast cancer [TNBC]). Triple-negative breast cancer, compared with non-TNBC, likely arises from different pathogenetic pathways, and benign breast disease (BBD) predicts future non-TNBC.","authors":"Newman, LA., Stark, A., Chitale, D., Pepe, M., Longton, G., Worsham, MJ., Nathanson, SD., Miller, P., Bensenhaver, JM., Proctor, E., Swain, M., Patriotis, C., Engstrom, PF.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"JAMA Oncol","volume":"3","issue":"8","page":"1102-1106","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27974207","title":"DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner.","abstract":"Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division.","authors":"Wiedemann, EM., Peycheva, M., Pavri, R.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Rep","volume":"17","issue":"11","page":"2927-2942","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19185582","title":"Tissue-specific amino acid transporter partners ACE2 and collectrin differentially interact with hartnup mutations.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19185582<\/PMID><DateCompleted><Year>2009<\/Year><Month>04<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1528-0012<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>136<\/Volume><Issue>3<\/Issue><PubDate><Year>2009<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>Gastroenterology<\/Title><ISOAbbreviation>Gastroenterology<\/ISOAbbreviation><\/Journal><ArticleTitle>Tissue-specific amino acid transporter partners ACE2 and collectrin differentially interact with hartnup mutations.<\/ArticleTitle><Pagination><MedlinePgn>872-82<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1053\/j.gastro.2008.10.055<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\" NlmCategory=\"OBJECTIVE\">Hartnup amino acid transporter B(0)AT1 (SLC6A19) is the major luminal sodium-dependent neutral amino acid transporter of small intestine and kidney proximal tubule. The expression of B(0)AT1 in kidney was recently shown to depend on its association with collectrin (Tmem27), a protein homologous to the membrane-anchoring domain of angiotensin-converting enzyme (ACE) 2.","authors":"Camargo, SM., Singer, D., Makrides, V., Huggel, K., Pos, KM., Wagner, CA., Kuba, K., Danilczyk, U., Skovby, F., Kleta, R., Penninger, JM., Verrey, F.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Gastroenterology","volume":"136","issue":"3","page":"872-82","pdf":null,"JrId":"3841","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17130832","title":"PDGF essentially links TGF-beta signaling to nuclear beta-catenin accumulation in hepatocellular carcinoma progression.","abstract":"The cooperation of Ras - extracellular signal-regulated kinase\/mitogen-activated protein kinase and transforming growth factor (TGF)-beta signaling provokes an epithelial to mesenchymal transition (EMT) of differentiated p19(ARF) null hepatocytes, which is accompanied by a shift in malignancy and gain of metastatic properties. Upon EMT, TGF-beta induces the secretion and autocrine regulation of platelet-derived growth factor (PDGF) by upregulation of PDGF-A and both PDGF receptors. Here, we demonstrate by loss-of-function analyses that PDGF provides adhesive and migratory properties in vitro as well as proliferative stimuli during tumor formation. PDGF signaling resulted in the activation of phosphatidylinositol-3 kinase, and furthermore associated with nuclear beta-catenin accumulation upon EMT. Hepatocytes expressing constitutively active beta-catenin or its negative regulator Axin were employed to study the impact of nuclear beta-catenin. Unexpectedly, active beta-catenin failed to accelerate proliferation during tumor formation, but in contrast, correlated with growth arrest. Nuclear localization of beta-catenin was accompanied by strong expression of the Cdk inhibitor p16(INK4A) and the concomitant induction of the beta-catenin target genes cyclin D1 and c-myc. In addition, active beta-catenin revealed protection of malignant hepatocytes against anoikis, which provides a prerequisite for the dissemination of carcinoma. From these data, we conclude that TGF-beta acts tumor progressive by induction of PDGF signaling and subsequent activation of beta-catenin, which endows a subpopulation of neoplastic hepatocytes with features of cancer stem cells..","authors":"Fischer, AN., Fuchs, E., Mikula, M., Huber, H., Beug, H., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Oncogene","volume":"26","issue":"23","page":"3395-405","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27716509","title":"A Force-Induced Directional Switch of a Molecular Motor Enables Parallel Microtubule Bundle Formation.","abstract":"Microtubule-organizing centers (MTOCs) nucleate microtubules that can grow autonomously in any direction. To generate bundles of parallel microtubules originating from a single MTOC, the growth of multiple microtubules needs to coordinated, but the underlying mechanism is unknown. Here, we show that a conserved two-component system consisting of the plus-end tracker EB1 and the minus-end-directed molecular motor Kinesin-14 is sufficient to promote parallel microtubule growth. The underlying mechanism relies on the ability of Kinesin-14 to guide growing plus ends along existing microtubules. The generality of this finding is supported by yeast, Drosophila, and human EB1\/Kinesin-14 pairs. We demonstrate that plus-end guiding involves a directional switch of the motor due to a force applied via a growing microtubule end. The described mechanism can account for the generation of parallel microtubule networks required for a broad range of cellular functions such as spindle assembly or cell polarization.","authors":"Molodtsov, MI., Mieck, C., Dobbelaere, J., Dammermann, A., Westermann, S., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"167","issue":"2","page":"539-552.e14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29256496","title":"Resolving systematic errors in widely used enhancer activity assays in human cells.","abstract":"The identification of transcriptional enhancers in the human genome is a prime goal in biology. Enhancers are typically predicted via chromatin marks, yet their function is primarily assessed with plasmid-based reporter assays. Here, we show that such assays are rendered unreliable by two previously reported phenomena relating to plasmid transfection into human cells: (i) the bacterial plasmid origin of replication (ORI) functions as a conflicting core promoter and (ii) a type I interferon (IFN-I) response is activated. These cause confounding false positives and negatives in luciferase assays and STARR-seq screens. We overcome both problems by employing the ORI as core promoter and by inhibiting two IFN-I-inducing kinases, enabling genome-wide STARR-seq screens in human cells. In HeLa-S3 cells, we uncover strong enhancers, IFN-I-induced enhancers, and enhancers endogenously silenced at the chromatin level. Our findings apply to all episomal enhancer activity assays in mammalian cells and are key to the characterization of human enhancers.","authors":"Muerdter, F., Bory\u0144, \u0141M., Woodfin, AR., Neumayr, C., Rath, M., Zabidi, MA., Pagani, M., Haberle, V., Kazmar, T., Catarino, RR., Schernhuber, K., Arnold, CD., Stark, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Methods","volume":"15","issue":"2","page":"141-149","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11286891","title":"Structural basis for the function of pyridoxine 5'-phosphate synthase.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11286891<\/PMID><DateCompleted><Year>2001<\/Year><Month>09<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>09<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0969-2126<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>9<\/Volume><Issue>3<\/Issue><PubDate><Year>2001<\/Year><Month>Mar<\/Month><Day>07<\/Day><\/PubDate><\/JournalIssue><Title>Structure (London, England : 1993)<\/Title><ISOAbbreviation>Structure<\/ISOAbbreviation><\/Journal><ArticleTitle>Structural basis for the function of pyridoxine 5'-phosphate synthase.<\/ArticleTitle><Pagination><MedlinePgn>245-53<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Pyridoxal 5'-phosphate is the active form of vitamin B(6) that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In Escherichia coli, the pathway of the de novo biosynthesis of vitamin B(6) results in the formation of pyridoxine 5'-phosphate (PNP), which can be regarded as the first synthesized B(6) vitamer. PNP synthase (commonly referred to as PdxJ) is a homooctameric enzyme that catalyzes the final step in this pathway, a complex intramolecular condensation reaction between 1-deoxy-D-xylulose-5'-phosphate and 1-amino-acetone-3-phosphate.","authors":"Franco, MG., Laber, B., Huber, R., Clausen, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Structure","volume":"9","issue":"3","page":"245-53","pdf":null,"JrId":"22305","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29700249","title":"Regenerating tissues.","abstract":null,"authors":"Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Science","volume":"360","issue":"6387","page":"374-375","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21762814","title":"AID targeting in antibody diversity.","abstract":"Antibody maturation requires class switch recombination (CSR) and somatic hypermutation (SHM), both of which are initiated by activation-induced cytidine deaminase (AID). AID deaminates cytosine residues resulting in mismatches that are differentially processed to produce double-strand breaks in Ig switch (S) regions that lead to CSR, or to point mutations in variable (V) exons resulting in SHM. Although AID was first thought to be Ig-specific, recent work indicates that it also targets a diverse group of non-Ig loci, including genes such as Bcl6 and c-myc, whose modification by AID results in lymphoma-associated mutations and translocations. Here, we review the recent literature on AID targeting and the role for transcriptional stalling in recruitment of this enzyme to Ig and non-Ig loci. We propose a model for AID recruitment based on transcriptional stalling, which reconciles several of the key features of SHM, CSR, and lymphoma-associated translocation.","authors":"Pavri, R., Nussenzweig, MC.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Adv Immunol","volume":"110","issue":null,"page":"1-26","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-11-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18281373","title":"Loss of PTEN attenuates the development of pathological hypertrophy and heart failure in response to biomechanical stress.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18281373<\/PMID><DateCompleted><Year>2008<\/Year><Month>09<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2016<\/Year><Month>11<\/Month><Day>24<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Print\">0008-6363<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>78<\/Volume><Issue>3<\/Issue><PubDate><Year>2008<\/Year><Month>Jun<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Cardiovascular research<\/Title><ISOAbbreviation>Cardiovasc Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Loss of PTEN attenuates the development of pathological hypertrophy and heart failure in response to biomechanical stress.<\/ArticleTitle><Pagination><MedlinePgn>505-14<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/cvr\/cvn041<\/ELocationID><Abstract><AbstractText Label=\"AIMS\" NlmCategory=\"OBJECTIVE\">The maladaptive response to biomechanical stress is a fundamental response in heart disease. Loss of the 3'-lipid phosphatase, phosphatase and tensin homolog deleted on chromosome ten (PTEN), is associated with increased phosphorylation of Akt\/protein kinase B and glycogen synthase kinase-beta. We hypothesize that these key changes will halt the development of pathological hypertrophy and the progression to heart failure in response to pressure overload.","authors":"Oudit, GY., Kassiri, Z., Zhou, J., Liu, QC., Liu, PP., Backx, PH., Dawood, F., Crackower, MA., Scholey, JW., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cardiovasc Res","volume":"78","issue":"3","page":"505-14","pdf":null,"JrId":"2812","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21222207","title":"Vertebrates that regenerate as models for guiding stem cels.","abstract":"There are several animal model organisms that have the ability to regenerate severe injuries by stimulating local cells to restore damaged and lost organs and appendages. In this chapter, we will describe how various vertebrate animals regenerate different structures (central nervous system, heart and appendages) as well as detail specific cellular and molecular features concerning the regeneration of these structures.","authors":"Antos, CL., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Adv Exp Med Biol","volume":"695","issue":null,"page":"184-214","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27672263","title":"MicroRNA biomarkers predicting risk, initiation and progression of colorectal cancer.","abstract":"Colorectal cancer is a major global cause of morbidity and mortality. Current strategies employed to increase detection of early, curable stages of this disease are contributing to a reduction of the negative health impact from it. While there is a genetic component to the risk of disease, diet and environment are known to have major effects on the risk of an individual for developing the disease. However, there is the potential to reduce the impact of this disease further by preventing disease development. Biomarkers which can either predict the risk for or early stages of colorectal cancer could allow intervention at a time when prospects could be modified by environmental factors, including lifestyle and diet choices. Thus, such biomarkers could be used to identify high risk individuals who would benefit from lifestyle and dietary interventions to prevent this disease. This review will give an overview on one type of biomarker in the form of microRNAs, which have the potential to predict an individual's risk for colorectal cancer, as well as providing a highly sensitive and non-invasive warning of disease presence and\/or progression. MicroRNA biomarkers which have been studied and whose levels look promising for this purpose include MiR-18a, MiR-21, MiR-92a, MiR-135b, MiR-760, MiR-601. Not only have several individual microRNAs appeared promising as biomarkers, but panels of these may be even more useful. Furthermore, understanding dietary sources and ways of dietary modulation of these microRNAs might be fruitful in reducing the incidence and slowing the progression of colorectal cancer.","authors":"Lee, K., Ferguson, LR.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"World J Gastroenterol","volume":"22","issue":"33","page":"7389-401","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17101802","title":"Distinct promoters mediate the regulation of Ebf1 gene expression by interleukin-7 and Pax5.","abstract":"Early differentiation of B lymphocytes requires the function of multiple transcription factors that regulate the specification and commitment of the lineage. Loss- and gain-of-function experiments have provided important insight into the transcriptional control of B lymphopoiesis, whereby E2A was suggested to act upstream of EBF1 and Pax5 downstream of EBF1. However, this simple hierarchy cannot account for all observations, and our understanding of a presumed regulatory network, in which transcription factors and signaling pathways operate, is limited. Here, we show that the expression of the Ebf1 gene involves two promoters that are differentially regulated and generate distinct protein isoforms. We find that interleukin-7 signaling, E2A, and EBF1 activate the distal Ebf1 promoter, whereas Pax5, together with Ets1 and Pu.1, regulates the stronger proximal promoter. In the absence of Pax5, the function of the proximal Ebf1 promoter and accumulation of EBF1 protein are impaired and the replication timing and subcellular localization of the Ebf1 locus are altered. Taken together, these data suggest that the regulation of Ebf1 via distinct promoters allows for the generation of several feedback loops and the coordination of multiple determinants of B lymphopoiesis in a regulatory network.","authors":"Roessler, S., Gy\u00f6ry, I., Imhof, S., Spivakov, M., Williams, RR., Busslinger, M., Fisher, AG., Grosschedl, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Cell Biol","volume":"27","issue":"2","page":"579-94","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33545075","title":"Taking Heart Development to the Next Level.","abstract":"Current in\u00a0vitro systems are powerful tools for studying early heart specification but lack the ability to model morphological events. Reporting in this issue of Cell Stem Cell, Rossi et\u00a0al. (2021) present a patterned embryonic organoid model (gastruloid) that mimics aspects of early cardiogenesis.","authors":"Jahnel, SM., Mendjan, S.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell Stem Cell","volume":"28","issue":"2","page":"180-181","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15345051","title":"An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15345051<\/PMID><DateCompleted><Year>2005<\/Year><Month>05<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>5<\/Volume><Issue>9<\/Issue><PubDate><Year>2004<\/Year><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries.<\/ArticleTitle><Pagination><MedlinePgn>R67<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum.","authors":"Habermann, B., Bebin, AG., Herklotz, S., Volkmer, M., Eckelt, K., Pehlke, K., Epperlein, HH., Schackert, HK., Wiebe, G., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genome Biol","volume":"5","issue":"9","page":"R67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27659466","title":"52 Genetic Loci Influencing Myocardial\u00a0Mass.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">27659466<\/PMID><DateCompleted><Year>2017<\/Year><Month>06<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>06<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1558-3597<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>68<\/Volume><Issue>13<\/Issue><PubDate><Year>2016<\/Year><Month>09<\/Month><Day>27<\/Day><\/PubDate><\/JournalIssue><Title>Journal of the American College of Cardiology<\/Title><ISOAbbreviation>J Am Coll Cardiol<\/ISOAbbreviation><\/Journal><ArticleTitle>52 Genetic Loci Influencing Myocardial\u00a0Mass.<\/ArticleTitle><Pagination><MedlinePgn>1435-1448<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0735-1097(16)34664-2<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.jacc.2016.07.729<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Myocardial mass is a key determinant of cardiac muscle function and hypertrophy. Myocardial depolarization leading to cardiac muscle contraction is reflected by the amplitude and duration of the QRS complex on the electrocardiogram (ECG). Abnormal QRS amplitude or duration reflect changes in myocardial mass and conduction, and are associated with increased risk of heart failure and death.","authors":"van der Harst, P., van Setten, J., Verweij, N., Vogler, G., Franke, L., Maurano, MT., Wang, X., Mateo Leach, I., Eijgelsheim, M., Sotoodehnia, N., Hayward, C., Sorice, R., Meirelles, O., Lyytik\u00e4inen, LP., Pola\u0161ek, O., Tanaka, T., Arking, DE., Ulivi, S., Trompet, S., M\u00fcller-Nurasyid, M., Smith, AV., D\u00f6rr, M., Kerr, KF., Magnani, JW., Del Greco M, F., Zhang, W., Nolte, IM., Silva, CT., Padmanabhan, S., Tragante, V., Esko, T., Abecasis, GR., Adriaens, ME., Andersen, K., Barnett, P., Bis, JC., Bodmer, R., Buckley, BM., Campbell, H., Cannon, MV., Chakravarti, A., Chen, LY., Delitala, A., Devereux, RB., Doevendans, PA., Dominiczak, AF., Ferrucci, L., Ford, I., Gieger, C., Harris, TB., Haugen, E., Heinig, M., Hernandez, DG., Hillege, HL., Hirschhorn, JN., Hofman, A., Hubner, N., Hwang, SJ., Iorio, A., K\u00e4h\u00f6nen, M., Kellis, M., Kolcic, I., Kooner, IK., Kooner, JS., Kors, JA., Lakatta, EG., Lage, K., Launer, LJ., Levy, D., Lundby, A., Macfarlane, PW., May, D., Meitinger, T., Metspalu, A., Nappo, S., Naitza, S., Neph, S., Nord, AS., Nutile, T., Okin, PM., Olsen, JV., Oostra, BA., Penninger, JM., Pennacchio, LA., Pers, TH., Perz, S., Peters, A., Pinto, YM., Pfeufer, A., Pilia, MG., Pramstaller, PP., Prins, BP., Raitakari, OT., Raychaudhuri, S., Rice, KM., Rossin, EJ., Rotter, JI., Schafer, S., Schlessinger, D., Schmidt, CO., Sehmi, J., Sillj\u00e9, HHW., Sinagra, G., Sinner, MF., Slowikowski, K., Soliman, EZ., Spector, TD., Spiering, W., Stamatoyannopoulos, JA., Stolk, RP., Strauch, K., Tan, ST., Tarasov, KV., Trinh, B., Uitterlinden, AG., van den Boogaard, M., van Duijn, CM., van Gilst, WH., Viikari, JS., Visscher, PM., Vitart, V., V\u00f6lker, U., Waldenberger, M., Weichenberger, CX., Westra, HJ., Wijmenga, C., Wolffenbuttel, BH., Yang, J., Bezzina, CR., Munroe, PB., Snieder, H., Wright, AF., Rudan, I., Boyer, LA., Asselbergs, FW., van Veldhuisen, DJ., Stricker, BH., Psaty, BM., Ciullo, M., Sanna, S., Lehtim\u00e4ki, T., Wilson, JF., Bandinelli, S., Alonso, A., Gasparini, P., Jukema, JW., K\u00e4\u00e4b, S., Gudnason, V., Felix, SB., Heckbert, SR., de Boer, RA., Newton-Cheh, C., Hicks, AA., Chambers, JC., Jamshidi, Y., Visel, A., Christoffels, VM., Isaacs, A., Samani, NJ., de Bakker, PIW.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Am Coll Cardiol","volume":"68","issue":"13","page":"1435-1448","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18477449","title":"Polo on the Rise-from Mitotic Entry to Cytokinesis with Plk1.","abstract":"Polo-like kinase 1 (Plk1) is a key regulator of cell division in eukaryotic cells. New techniques, including the application of small-molecule inhibitors, have greatly expanded our knowledge of the functions, targets, and regulation of this key mitotic enzyme. In this review, we focus on how Plk1 is recruited to centrosomes, kinetochores, and the spindle midzone and what the specific tasks of Plk1 at these distinct subcellular structures might be. In particular, we highlight new work on the role of Plk1 in cytokinesis in human cells. Finally, we describe how better understanding of Plk1 functions allows critical evaluation of Plk1 as a potential drug target for cancer therapy.","authors":"Petronczki, M., L\u00e9n\u00e1rt, P., Peters, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Dev Cell","volume":"14","issue":"5","page":"646-59","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31980633","title":"Genetic screening identifies a SUMO protease dynamically maintaining centromeric chromatin.","abstract":"Centromeres are defined by a self-propagating chromatin structure based on stable inheritance of CENP-A containing nucleosomes. Here, we present a genetic screen coupled to pulse-chase labeling that allow us to identify proteins selectively involved in deposition of nascent CENP-A or in long-term transmission of chromatin-bound CENP-A. These include factors with known roles in DNA replication, repair, chromatin modification, and transcription, revealing a broad set of chromatin regulators that impact on CENP-A dynamics. We further identify the SUMO-protease SENP6 as a key factor, not only controlling CENP-A stability but virtually the entire centromere and kinetochore. Loss of SENP6 results in hyper-SUMOylation of CENP-C and CENP-I but not CENP-A itself. SENP6 activity is required throughout the cell cycle, suggesting that a dynamic SUMO cycle underlies a continuous surveillance of the centromere complex that in turn ensures stable transmission of CENP-A chromatin.","authors":"Mitra, S., Bodor, DL., David, AF., Abdul-Zani, I., Mata, JF., Neumann, B., Reither, S., Tischer, C., Jansen, LET.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"501","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27447986","title":"An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx\/MLL\/COMPASS.","abstract":"Polycomb response elements (PREs) are specific DNA sequences that stably maintain the developmental pattern of gene expression. Drosophila PREs are well characterized, whereas the existence of PREs in mammals remains debated. Accumulating evidence supports a model in which CpG islands recruit Polycomb group (PcG) complexes; however, which subset of CGIs is selected to serve as PREs is unclear. Trithorax (Trx) positively regulates gene expression in Drosophila and co-occupies PREs to\u00a0antagonize Polycomb-dependent silencing. Here we\u00a0demonstrate that Trx-dependent H3K4 dimethylation (H3K4me2) marks Drosophila PREs and maintains the developmental expression pattern of nearby genes. Similarly, the mammalian Trx homolog, MLL1, deposits H3K4me2 at CpG-dense regions that could\u00a0serve as PREs. In the absence of MLL1 and H3K4me2, H3K27me3 levels, a mark of Polycomb repressive complex 2 (PRC2), increase at these loci. By inhibiting PRC2-dependent H3K27me3 in the absence of MLL1, we can rescue expression of these loci, demonstrating a functional balance between MLL1 and PRC2 activities at these sites. Thus, our study provides rules for identifying cell-type-specific\u00a0functional mammalian PREs within the human genome.","authors":"Rickels, R., Hu, D., Collings, CK., Woodfin, AR., Piunti, A., Mohan, M., Herz, HM., Kvon, E., Shilatifard, A.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Mol Cell","volume":"63","issue":"2","page":"318-328","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27259151","title":"Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC\/C.","abstract":"Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of polyubiquitination: multiubiquitination of several sites and elongation of linkage-specific UB chains. Here, cryo-EM and biochemistry show that the human E3 anaphase-promoting complex\/cyclosome (APC\/C) and its two partner E2s, UBE2C (aka UBCH10) and UBE2S, adopt specialized catalytic architectures for these two distinct forms of polyubiquitination. The APC\/C RING constrains UBE2C proximal to a substrate and simultaneously binds a substrate-linked UB to drive processive multiubiquitination. Alternatively, during UB chain elongation, the RING does not bind UBE2S but rather lures an evolving substrate-linked UB to UBE2S positioned through a cullin interaction to generate a Lys11-linked chain. Our findings define mechanisms of APC\/C regulation, and establish principles by which specialized E3-E2-substrate-UB architectures control different forms of polyubiquitination.","authors":"Brown, NG., VanderLinden, R., Watson, ER., Weissmann, F., Ordureau, A., Wu, KP., Zhang, W., Yu, S., Mercredi, PY., Harrison, JS., Davidson, IF., Qiao, R., Lu, Y., Dube, P., Brunner, MR., Grace, CRR., Miller, DJ., Haselbach, D., Jarvis, MA., Yamaguchi, M., Yanishevski, D., Petzold, G., Sidhu, SS., Kuhlman, B., Kirschner, MW., Harper, JW., Peters, JM., Stark, H., Schulman, BA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"165","issue":"6","page":"1440-1453","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33533917","title":"Niche-specific MHC II and PD-L1 regulate CD4+CD8\u03b1\u03b1+ intraepithelial lymphocyte differentiation.","abstract":"Conventional CD4+ T cells are differentiated into CD4+CD8\u03b1\u03b1+ intraepithelial lymphocytes (IELs) in the intestine; however, the roles of intestinal epithelial cells (IECs) are poorly understood. Here, we showed that IECs expressed MHC class II (MHC II) and programmed death-ligand 1 (PD-L1) induced by the microbiota and IFN-\u03b3 in the distal part of the small intestine, where CD4+ T cells were transformed into CD4+CD8\u03b1\u03b1+ IELs. Therefore, IEC-specific deletion of MHC II and PD-L1 hindered the development of CD4+CD8\u03b1\u03b1+ IELs. Intracellularly, PD-1 signals supported the acquisition of CD8\u03b1\u03b1 by down-regulating the CD4-lineage transcription factor, T helper-inducing POZ\/Kr\u00fcppel-like factor (ThPOK), via the Src homology 2 domain-containing tyrosine phosphatase (SHP) pathway. Our results demonstrate that noncanonical antigen presentation with cosignals from IECs constitutes niche adaptation signals to develop tissue-resident CD4+CD8\u03b1\u03b1+ IELs.","authors":"Moon, S., Park, Y., Hyeon, S., Kim, YM., Kim, JH., Kim, H., Park, S., Lee, KJ., Koo, BK., Ha, SJ., Lee, SW.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Exp Med","volume":"218","issue":"4","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15337699","title":"Synergistic effect of bone marrow mobilization and vascular endothelial growth factor-2 gene therapy in myocardial ischemia.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15337699<\/PMID><DateCompleted><Year>2005<\/Year><Month>04<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4539<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>110<\/Volume><Issue>11<\/Issue><PubDate><Year>2004<\/Year><Month>Sep<\/Month><Day>14<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>Synergistic effect of bone marrow mobilization and vascular endothelial growth factor-2 gene therapy in myocardial ischemia.<\/ArticleTitle><Pagination><MedlinePgn>1398-405<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">We performed a series of investigations to test the hypothesis that combining angiogenic gene therapy and cytokine (CK)-induced endothelial progenitor cell mobilization would be superior to either strategy alone for treatment of chronic myocardial ischemia.","authors":"Kawamoto, A., Murayama, T., Kusano, K., Ii, M., Tkebuchava, T., Shintani, S., Iwakura, A., Johnson, I., von Samson, P., Hanley, A., Gavin, M., Curry, C., Silver, M., Ma, H., Kearney, M., Losordo, DW.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Circulation","volume":"110","issue":"11","page":"1398-405","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28667121","title":"RNA gets in phase.","abstract":"Several neurological disorders are linked to tandem nucleotide repeat expansion in the mutated gene. Jain and Vale (2017. <i>Nature.<\/i> https:\/\/doi.org\/10.1038\/nature22386) show that, above a pathological threshold repeat number, base pairing interactions drive phase separation of RNA into membrane-less gels, suggesting that RNA can scaffold the assembly of phase-separated compartments that sequester proteins\/RNAs causing toxicity.","authors":"Saha, S., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"J Cell Biol","volume":"216","issue":"8","page":"2235-2237","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20147242","title":"Grafting axolotl (Ambystoma mexicanum) limb skin and cartilage from GFP+ donors to normal hosts.","abstract":null,"authors":"Kragl, M., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cold Spring Harb Protoc","volume":"2009","issue":"8","page":"pdb.prot5266","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27120163","title":"FGF8 and SHH substitute for anterior-posterior tissue interactions to induce limb regeneration.","abstract":"In salamanders, grafting of a left limb blastema onto a right limb stump yields regeneration of three limbs, the normal limb and two 'supernumerary' limbs. This experiment and other research have shown that the juxtaposition of anterior and posterior limb tissue plus innervation are necessary and sufficient to induce complete limb regeneration in salamanders. However, the cellular and molecular basis of the requirement for anterior-posterior tissue interactions were unknown. Here we have clarified the molecular basis of the requirement for both anterior and posterior tissue during limb regeneration and supernumerary limb formation in axolotls (Ambystoma mexicanum). We show that the two tissues provide complementary cross-inductive signals that are required for limb outgrowth. A blastema composed solely of anterior tissue normally regresses rather than forming a limb, but activation of hedgehog (HH) signalling was sufficient to drive regeneration of an anterior blastema to completion owing to its ability to maintain fibroblast growth factor (FGF) expression, the key signalling activity responsible for blastema outgrowth. In blastemas composed solely of posterior tissue, HH signalling was not sufficient to drive regeneration; however, ectopic expression of FGF8 together with endogenous HH signalling was sufficient. In axolotls, FGF8 is expressed only in the anterior mesenchyme and maintenance of its expression depends on sonic hedgehog (SHH) signalling from posterior tissue. Together, our findings identify key anteriorly and posteriorly localized signals that promote limb regeneration and show that these single factors are sufficient to drive non-regenerating blastemas to complete regeneration with full elaboration of skeletal elements.","authors":"Nacu, E., Gromberg, E., Oliveira, CR., Drechsel, D., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nature","volume":"533","issue":"7603","page":"407-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21619533","title":"Transforming growth factor beta in pancreatic cancer.","abstract":"Pancreatic cancer has high incidence and mortality rates, and effective treatment remains a clinical challenge. As deregulation of the cytokine transforming growth factor beta (TGF-\u03b2) contributes to the progression of pancreatic carcinoma, the TGF-\u03b2 pathway has been targeted using various strategies, including small molecule inhibitors of TGF-\u03b2RI, TGF-\u03b2-specific neutralizing antibodies and antisense compounds. As increased TGF-\u03b22 levels in serum or tumor tissue of patients with pancreatic cancer correlated with poor prognosis, inhibition of TGF-\u03b22 synthesis via the antisense oligonucleotide trabedersen (AP 12009) is a promising approach.","authors":"Hilbig, A., Oettle, H.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Curr Pharm Biotechnol","volume":"12","issue":"12","page":"2158-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12963636","title":"Phosphoinositide 3-kinase gamma-deficient mice are protected from isoproterenol-induced heart failure.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">12963636<\/PMID><DateCompleted><Year>2003<\/Year><Month>11<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2013<\/Year><Month>11<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4539<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>108<\/Volume><Issue>17<\/Issue><PubDate><Year>2003<\/Year><Month>Oct<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>Phosphoinositide 3-kinase gamma-deficient mice are protected from isoproterenol-induced heart failure.<\/ArticleTitle><Pagination><MedlinePgn>2147-52<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">We have recently shown that genetic inactivation of phosphoinositide 3-kinase gamma (PI3Kgamma), the isoform linked to G-protein-coupled receptors, results in increased cardiac contractility with no effect on basal cell size. Signaling via the G-protein-coupled beta-adrenergic receptors has been implicated in cardiac hypertrophy and heart failure, suggesting that PI3Kgamma might play a role in the pathogenesis of heart disease.","authors":"Oudit, GY., Crackower, MA., Eriksson, U., Sarao, R., Kozieradzki, I., Sasaki, T., Irie-Sasaki, J., Gidrewicz, D., Rybin, VO., Wada, T., Steinberg, SF., Backx, PH., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Circulation","volume":"108","issue":"17","page":"2147-52","pdf":null,"JrId":"2979","fulltextlink":null,"preprintlink":null,"articledate":"2003-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29491412","title":"The novel BET bromodomain inhibitor BI 894999 represses super-enhancer-associated transcription and synergizes with CDK9 inhibition in AML.","abstract":"Bromodomain and extra-terminal (BET) protein inhibitors have been reported as treatment options for acute myeloid leukemia (AML) in preclinical models and are currently being evaluated in clinical trials. This work presents a novel potent and selective BET inhibitor (BI 894999), which has recently entered clinical trials (NCT02516553). In preclinical studies, this compound is highly active in AML cell lines, primary patient samples, and xenografts. HEXIM1 is described as an excellent pharmacodynamic biomarker for target engagement in tumors as well as in blood. Mechanistic studies show that BI 894999 targets super-enhancer-regulated oncogenes and other lineage-specific factors, which are involved in the maintenance of the disease state. BI 894999 is active as monotherapy in AML xenografts, and in addition leads to strongly enhanced antitumor effects in combination with CDK9 inhibitors. This treatment combination results in a marked decrease of global p-Ser2 RNA polymerase II levels and leads to rapid induction of apoptosis in vitro and in vivo. Together, these data provide a strong rationale for the clinical evaluation of BI 894999 in AML.","authors":"Gerlach, D., Tontsch-Grunt, U., Baum, A., Popow, J., Scharn, D., Hofmann, MH., Engelhardt, H., Kaya, O., Beck, J., Schweifer, N., Gerstberger, T., Zuber, J., Savarese, F., Kraut, N.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Oncogene","volume":"37","issue":"20","page":"2687-2701","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17060369","title":"Activity-structure correlations in divergent lectin evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16.","abstract":"Gene duplication and sequence divergence are driving forces toward establishing protein families. To examine how sequence changes affect carbohydrate specificity, the two closely related proto-type chicken galectins CG-14 and CG-16 were selected as models. Binding properties were analyzed using a highly sensitive solid-phase assay. We tested 56 free saccharides and 34 well-defined glycoproteins. The two galectins share preference for the II (Galbeta1-4GlcNAc) versus I (Galbeta1-3GlcNAc) version of beta-galactosides. A pronounced difference is found owing to the reactivity of CG-14 with histo-blood group ABH active oligosaccharides and A\/B active glycoproteins. These experimental results prompted to determine activity-structure correlations by modeling. Computational analysis included consideration of the flexibility of binding partners and the presence of water molecules. It provided a comparative description of complete carbohydrate recognition domains, which had so far not been characterized in animal galectins. The structural models assigned II, I selectivity to a region downstream of the central Trp moiety. Docking revealed that the tetrasaccharides can be accommodated in their free-state low-energy conformations. CG-14's preference for A versus B epitopes could be attributed to a contact between His124 and the N-acetyl group of GalNAc. Regarding intergalectin comparison, the Ala53\/Cys51 exchange affects the interaction potential of His54\/His52. Close inspection of simulated dynamic interplay revealed reorientation of His124 at the site of the His124\/Glu123 substitution, with potential impact on ligand dissociation. In summary, this study identifies activity differences and provides information on their relation to structural divergence, epitomizing the value of this combined approach beyond galectins.","authors":"Wu, AM., Singh, T., Liu, JH., Krzeminski, M., Russwurm, R., Siebert, HC., Bonvin, AM., Andr\u00e9, S., Gabius, HJ.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Glycobiology","volume":"17","issue":"2","page":"165-84","pdf":null,"JrId":"2078","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16957776","title":"Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27.","abstract":"The plant Polycomb-group (Pc-G) protein CURLY LEAF (CLF) is required to repress targets such as AGAMOUS (AG) and SHOOTMERISTEMLESS (STM). Using chromatin immunoprecipitation, we identify AG and STM as direct targets for CLF and show that they carry a characteristic epigenetic signature of dispersed histone H3 lysine 27 trimethylation (H3K27me3) and localised H3K27me2 methylation. H3K27 methylation is present throughout leaf development and consistent with this, CLF is required persistently to silence AG. However, CLF is not itself an epigenetic mark as it is lost during mitosis. We suggest a model in which Pc-G proteins are recruited to localised regions of targets and then mediate dispersed H3K27me3. Analysis of transgenes carrying AG regulatory sequences confirms that H3K27me3 can spread to novel sequences in a CLF-dependent manner and further shows that H3K27me3 methylation is not sufficient for silencing of targets. We suggest that the spread of H3K27me3 contributes to the mitotic heritability of Pc-G silencing, and that the loss of silencing caused by transposon insertions at plant Pc-G targets reflects impaired spreading.","authors":"Schubert, D., Primavesi, L., Bishopp, A., Roberts, G., Doonan, J., Jenuwein, T., Goodrich, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"EMBO J","volume":"25","issue":"19","page":"4638-49","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2006-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26982367","title":"Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability.","abstract":"Microsatellite instability in colorectal cancer predicts favorable outcomes. However, the mechanistic relationship between microsatellite instability, tumor-infiltrating immune cells, Immunoscore, and their impact on patient survival remains to be elucidated. We found significant differences in mutational patterns, chromosomal instability, and gene expression that correlated with patient microsatellite instability status. A prominent immune gene expression was observed in microsatellite-instable (MSI) tumors, as well as in a subgroup of microsatellite-stable (MSS) tumors. MSI tumors had increased frameshift mutations, showed genetic evidence of immunoediting, had higher densities of Th1, effector-memory T cells, in situ proliferating T cells, and inhibitory PD1-PDL1 cells, had high Immunoscores, and were infiltrated with mutation-specific cytotoxic T cells. Multivariate analysis revealed that Immunoscore was superior to microsatellite instability in predicting patients' disease-specific recurrence and survival. These findings indicate that assessment of the immune status via Immunoscore provides a potent indicator of tumor recurrence beyond microsatellite-instability staging that could be an important guide for immunotherapy strategies.","authors":"Mlecnik, B., Bindea, G., Angell, HK., Maby, P., Angelova, M., Tougeron, D., Church, SE., Lafontaine, L., Fischer, M., Fredriksen, T., Sasso, M., Bilocq, AM., Kirilovsky, A., Obenauf, AC., Hamieh, M., Berger, A., Bruneval, P., Tuech, JJ., Sabourin, JC., Le Pessot, F., Mauillon, J., Rafii, A., Laurent-Puig, P., Speicher, MR., Trajanoski, Z., Michel, P., Sesbo\u00fce, R., Frebourg, T., Pag\u00e8s, F., Valge-Archer, V., Latouche, JB., Galon, J.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Immunity","volume":"44","issue":"3","page":"698-711","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27594427","title":"Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism.","abstract":"P granules are non-membrane-bound RNA-protein compartments that are involved in germline development in C.\u00a0elegans. They are liquids that condense at one end of the embryo by localized phase separation, driven by gradients of polarity proteins such as the mRNA-binding protein MEX-5. To probe how polarity proteins regulate phase separation, we combined biochemistry and theoretical modeling. We reconstitute P granule-like droplets in\u00a0vitro using a single protein PGL-3. By combining in\u00a0vitro reconstitution with measurements of intracellular concentrations, we show that competition between PGL-3 and\u00a0MEX-5 for mRNA can regulate the formation of PGL-3 droplets. Using theory, we show that, in a MEX-5 gradient, this mRNA competition mechanism can drive a gradient of P granule assembly with similar spatial and temporal characteristics to P granule assembly in\u00a0vivo. We conclude that gradients of polarity proteins can position RNP granules during development by using RNA competition to regulate local phase separation.","authors":"Saha, S., Weber, CA., Nousch, M., Adame-Arana, O., Hoege, C., Hein, MY., Osborne-Nishimura, E., Mahamid, J., Jahnel, M., Jawerth, L., Pozniakovski, A., Eckmann, CR., J\u00fclicher, F., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"166","issue":"6","page":"1572-1584.e16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12787496","title":"Regeneration: if they can do it, why can't we?","abstract":"The therapeutic potential of stem cells and nuclear cloning has led to renewed interest in classical models of regeneration. This longstanding problem is undergoing a renaissance spurred by the availability of new techniques that finally allow analysis on the cellular and molecular level.","authors":"Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cell","volume":"113","issue":"5","page":"559-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29325442","title":"Pooled Generation of Lentiviral Tetracycline-Regulated microRNA Embedded Short Hairpin RNA Libraries.","abstract":"Short hairpin RNA (shRNA) screens are powerful tools to probe genetic dependencies in loss-of-function studies, such as the identification of therapeutic targets in cancer research. Lentivirally delivered shRNAs embedded in endogenous microRNA contexts (shRNAmiRs) mediate efficient long-term suppression of target genes suitable for numerous experimental contexts and clinical applications. Here, an easy-to-use laboratory protocol is described, covering the design and pooled assembly of focused shRNAmiR libraries into an optimized, Tet-inducible all-in-one lentiviral vector, packaging of viral particles, followed by retrieval and quantification of hairpin sequences after cellular DNA-recovery. Starting from a gene list to the identification of hits, the protocol enables shRNA screens within 6 weeks.","authors":"Adams, FF., Hoffmann, T., Zuber, J., Heckl, D., Schambach, A., Schwarzer, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Hum Gene Ther Methods","volume":"29","issue":"1","page":"16-29","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11728305","title":"Separase is required for chromosome segregation during meiosis I in Caenorhabditis elegans.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11728305<\/PMID><DateCompleted><Year>2002<\/Year><Month>02<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>11<\/Volume><Issue>23<\/Issue><PubDate><Year>2001<\/Year><Month>Nov<\/Month><Day>27<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Separase is required for chromosome segregation during meiosis I in Caenorhabditis elegans.<\/ArticleTitle><Pagination><MedlinePgn>1825-35<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Chromosome segregation during mitosis and meiosis is triggered by dissolution of sister chromatid cohesion, which is mediated by the cohesin complex. Mitotic sister chromatid disjunction requires that cohesion be lost along the entire length of chromosomes, whereas homolog segregation at meiosis I only requires loss of cohesion along chromosome arms. During animal cell mitosis, cohesin is lost in two steps. A nonproteolytic mechanism removes cohesin along chromosome arms during prophase, while the proteolytic cleavage of cohesin's Scc1 subunit by separase removes centromeric cohesin at anaphase. In Saccharomyces cerevisiae and Caenorhabditis elegans, meiotic sister chromatid cohesion is mediated by Rec8, a meiosis-specific variant of cohesin's Scc1 subunit. Homolog segregation in S. cerevisiae is triggered by separase-mediated cleavage of Rec8 along chromosome arms. In principle, chiasmata could be resolved proteolytically by separase or nonproteolytically using a mechanism similar to the mitotic \"prophase pathway.\"","authors":"Siomos, MF., Badrinath, A., Pasierbek, P., Livingstone, D., White, J., Glotzer, M., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Curr Biol","volume":"11","issue":"23","page":"1825-35","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22918954","title":"Characterization of structural and functional domains of the anillin-related protein Mid1p that contribute to cytokinesis in fission yeast.","abstract":"Fission yeast cells depend on the anillin-related protein Mid1p for reliable cytokinesis. Insolubility limits the purification of full-length Mid1p for biophysical analysis, and lack of knowledge about the structural domains of Mid1p limits functional analysis. We addressed these limitations by identifying in a bacterial expression screen of random Mid1p fragments five soluble segments that can be purified and one insoluble segment. Using complementation experiments in \u0394mid1 cells, we tested the biological functions of these six putative domains that account for full-length Mid1p. The N-terminal domain (residues 1-149) is essential for correct positioning and orientation of septa. The third domain (residues 309-452) allows the construct composed of the first three domains (residues 1-452) to form hydrodynamically well-behaved octamers. Constructs consisting of residues 1-452 or 1-578 carry out most functions of full-length Mid1p, including concentration at the equatorial cortex in nodes that accumulate myosin-II and other contractile ring proteins during mitosis. However, cells depending on these constructs without the insoluble domain (residues 579-797) form equatorially located rings slowly from strands rather than by direct condensation of nodes. We conclude that residues 1-578 assemble node components myosin-II, Rng2p, and Cdc15p, and the insoluble domain facilitates the normal, efficient condensation of nodes into rings.","authors":"Saha, S., Pollard, TD.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Mol Biol Cell","volume":"23","issue":"20","page":"3993-4007","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26967245","title":"Exploring the role of sphingolipid machinery during the epithelial to mesenchymal transition program using an integrative approach.","abstract":"The epithelial to mesenchymal transition (EMT) program is activated in epithelial cancer cells and facilitates their ability to metastasize based on enhanced migratory, proliferative, anti-apoptotic, and pluripotent capacities. Given the fundamental impact of sphingolipid machinery to each individual process, the sphingolipid-related mechanisms might be considered among the most prominent drivers\/players of EMT; yet, there is still limited knowledge. Given the complexity of the interconnected sphingolipid system, which includes distinct sphingolipid mediators, their synthesizing enzymes, receptors and transporters, we herein apply an integrative approach for assessment of the sphingolipid-associated mechanisms underlying EMT program. We created the sphingolipid-\/EMT-relevant 41-gene\/23-gene signatures which were applied to denote transcriptional events in a lung cancer cell-based EMT model. Based on defined 35-gene sphingolipid\/EMT-attributed signature of regulated genes, we show close associations between EMT markers, genes comprising the sphingolipid network at multiple levels and encoding sphingosine 1-phosphate (S1P)-\/ceramide-metabolizing enzymes, S1P and lysophosphatidic acid (LPA) receptors and S1P transporters, pluripotency genes and inflammation-related molecules, and demonstrate the underlying biological pathways and regulators. Mass spectrometry-based sphingolipid analysis revealed an EMT-attributed shift towards increased S1P and LPA accompanied by reduced ceramide levels. Notably, using transcriptomics data across various cell-based perturbations and neoplastic tissues (24193 arrays), we identified the sphingolipid\/EMT signature primarily in lung adenocarcinoma tissues; besides, bladder, colorectal and prostate cancers were among the top-ranked. The findings also highlight novel regulatory associations between influenza virus and the sphingolipid\/EMT-associated mechanisms. In sum, data propose the multidimensional contribution of sphingolipid machinery to pathological EMT and may yield new biomarkers and therapeutic targets.","authors":"Meshcheryakova, A., Svoboda, M., Tahir, A., K\u00f6feler, HC., Triebl, A., Mungenast, F., Heinze, G., Gerner, C., Zimmermann, P., Jaritz, M., Mechtcheriakova, D.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Oncotarget","volume":"7","issue":"16","page":"22295-323","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12479824","title":"Pax5 promotes B lymphopoiesis and blocks T cell development by repressing Notch1.","abstract":"The B lineage commitment factor Pax5 (BSAP) is exclusively expressed in B lymphocytes of the blood system. To study the effect of Pax5 on the development of other hematopoietic lineages, we generated a heterozygous knockin mouse carrying a Pax5 minigene under the control of the Ikaros locus. Conditional and constitutive activation of the Ik(Pax5) allele demonstrated that precocious Pax5 expression in hematopoietic stem cells and progenitors failed to interfere with myeloid development and only weakly affected erythroblast formation. Instead, pan-hematopoietic Pax5 expression strongly promoted B cell development at the expense of T lymphopoiesis. Pax5 thereby interfered with T lineage commitment and early thymocyte development by repressing the transcription of the T cell specification gene Notch1.","authors":"Souabni, A., Cobaleda, C., Schebesta, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Immunity","volume":"17","issue":"6","page":"781-93","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2003-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12479806","title":"Localization of the MP1-MAPK scaffold complex to endosomes is mediated by p14 and required for signal transduction.","abstract":"Eukaryotic cells use the extracellular signal regulated kinase (ERK) cascade to connect cell-surface receptors to intracellular targets. Although various signals are routed through the ERK pathway, cells respond accordingly to a given stimulus. To regulate proper signal transduction, scaffolds and adaptors are employed to organize specific signaling units. The scaffold protein MP1 (MEK1 partner) assembles a scaffold complex in the ERK cascade. We show that p14 functions as an adaptor protein, which is required and sufficient to localize MP1 to endosomes. Reduction of MP1 or p14 protein levels by siRNAi results in defective signal transduction. Therefore, our results suggest that the endosomal localization of the p14\/MP1-MAPK scaffold complex is crucial for signal transduction.","authors":"Teis, D., Wunderlich, W., Huber, LA.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Dev Cell","volume":"3","issue":"6","page":"803-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"147","title":"Cytotoxic interaction between gorgonian explants: mode of action.","abstract":"","authors":"Theodor, JL., Senelar, R.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Cell Immunol","volume":"19","issue":"2","page":"194-200","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"146","title":"[Influence of beta-blocking agents on experimental atherosclerosis of cocks (author's transl)].","abstract":"","authors":"Reinis, Z., Lojda, Z., Heyrovsk\u00fd, A., Hor\u00e1kov\u00e1, D., Reisenauer, R.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Cas Lek Cesk","volume":"114","issue":"43","page":"1320-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"145","title":"Prophylactic antiarrhythmic drug therapy in acute myocardial infarction.","abstract":"","authors":"Binnion, PF., Das Gupta, R.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Cardiovasc Clin","volume":"7","issue":"2","page":"203-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"144","title":"Isolation and characterization of an unsubstituted 2,3-unsaturated sugar, trans-2,3-dideoxy-D-glycero-pent-2-enose, produced by thermal dehydration of 2-deoxy-D-erythro-pentose.","abstract":"","authors":"Esterbauer, H., Sanders, EB., Schubert, J.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Carbohydr Res","volume":"44","issue":"1","page":"126-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26933192","title":"An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client.","abstract":"Tandem affinity purification-mass spectrometry (TAP-MS) is a popular strategy for the identification of protein-protein interactions, characterization of protein complexes, and entire networks. Its employment in cellular settings best fitting the relevant physiology is limited by convenient expression vector systems. We developed an easy-to-handle, inducible, dually selectable retroviral expression vector allowing dose- and time-dependent control of bait proteins bearing the efficient streptavidin-hemagglutinin (SH)-tag at their N- or C termini. Concomitant expression of a reporter fluorophore allows to monitor bait-expressing cells by flow cytometry or microscopy and enables high-throughput phenotypic assays. We used the system to successfully characterize the interactome of the neuroblastoma RAS viral oncogene homolog (NRAS) Gly12Asp (G12D) mutant and exploited the advantage of reporter fluorophore expression by tracking cytokine-independent cell growth using flow cytometry. Moreover, we tested the feasibility of studying cytotoxicity-mediating proteins with the vector system on the cell death-inducing mixed lineage kinase domain-like protein (MLKL) Ser358Asp (S358D) mutant. Interaction proteomics analysis of MLKL Ser358Asp (S358D) identified heat shock protein 90 (HSP90) as a high-confidence interacting protein. Further phenotypic characterization established MLKL as a novel HSP90 client. In summary, this novel inducible expression system enables SH-tag-based interaction studies in the cell line proficient for the respective phenotypic or signaling context and constitutes a valuable tool for experimental approaches requiring inducible or traceable protein expression.","authors":"Bigenzahn, JW., Fauster, A., Rebsamen, M., Kandasamy, RK., Scorzoni, S., Vladimer, GI., M\u00fcller, AC., Gstaiger, M., Zuber, J., Bennett, KL., Superti-Furga, G.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Mol Cell Proteomics","volume":"15","issue":"3","page":"1139-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17026573","title":"Reversibility of the differentiated state: regeneration in amphibians.","abstract":"In contrast to mammals, some fish and amphibians have retained the ability to regenerate complex body structures or organs, such as the limb, tail, eye lens, or even parts of the heart. One major difference in the response to injury is the appearance of a mesenchymal growth zone or blastema in these regenerative species instead of the scarring seen in mammals. This blastema is thought to largely derive from the dedifferentiation of various functional cell types, such as skeletal muscle, dermis, and cartilage. In the case of multinucleated skeletal muscle fibers, cell cycle reentry into S-phase as well as fragmentation into mononucleated progenitors is observed both in vitro and in vivo.","authors":"Straube, WL., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Artif Organs","volume":"30","issue":"10","page":"743-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26912905","title":"The tumor microenvironment and Immunoscore are critical determinants of dissemination to distant metastasis.","abstract":"Although distant metastases account for most of the deaths in cancer patients, fundamental questions regarding mechanisms that promote or inhibit metastasis remain unanswered. We show the impact of mutations, genomic instability, lymphatic and blood vascularization, and the immune contexture of the tumor microenvironment on synchronous metastases in large cohorts of colorectal cancer patients. We observed large genetic heterogeneity among primary tumors, but no major differences in chromosomal instability or key cancer-associated mutations. Similar patterns of cancer-related gene expression levels were observed between patients. No cancer-associated genes or pathways were associated with M stage. Instead, mutations of FBXW7 were associated with the absence of metastasis and correlated with increased expression of T cell proliferation and antigen presentation functions. Analyzing the tumor microenvironment, we observed two hallmarks of the metastatic process: decreased presence of lymphatic vessels and reduced immune cytotoxicity. These events could be the initiating factors driving both synchronous and metachronous metastases. Our data demonstrate the protective impact of the Immunoscore, a cytotoxic immune signature, and increased marginal lymphatic vessels, against the generation of distant metastases, regardless of genomic instability.","authors":"Mlecnik, B., Bindea, G., Kirilovsky, A., Angell, HK., Obenauf, AC., Tosolini, M., Church, SE., Maby, P., Vasaturo, A., Angelova, M., Fredriksen, T., Mauger, S., Waldner, M., Berger, A., Speicher, MR., Pag\u00e8s, F., Valge-Archer, V., Galon, J.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Sci Transl Med","volume":"8","issue":"327","page":"327ra26","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26888028","title":"Oxygen-induced social behaviours in Pristionchus pacificus have a distinct evolutionary history and genetic regulation from Caenorhabditis elegans.","abstract":"Wild isolates of the nematode Caenorhabditis elegans perform social behaviours, namely clumping and bordering, to avoid hyperoxia under laboratory conditions. In contrast, the laboratory reference strain N2 has acquired a solitary behaviour in the laboratory, related to a gain-of-function variant in the neuropeptide Y-like receptor NPR-1. Here, we study the evolution and natural variation of clumping and bordering behaviours in Pristionchus pacificus nematodes in a natural context, using strains collected from 22 to 2400 metres above sea level on La R\u00e9union Island. Through the analysis of 106 wild isolates, we show that the majority of strains display a solitary behaviour similar to C. elegans N2, whereas social behaviours are predominantly seen in strains that inhabit high-altitude locations. We show experimentally that P. pacificus social strains perform clumping and bordering to avoid hyperoxic conditions in the laboratory, suggesting that social strains may have adapted to or evolved a preference for the lower relative oxygen levels available at high altitude in nature. In contrast to C. elegans, clumping and bordering in P. pacificus do not correlate with locomotive behaviours in response to changes in oxygen conditions. Furthermore, QTL analysis indicates clumping and bordering to represent complex quantitative traits. Thus, clumping and bordering behaviours represent an example of phenotypic convergence with a different evolutionary history and distinct genetic control in both nematode species.","authors":"Moreno, E., McGaughran, A., R\u00f6delsperger, C., Zimmer, M., Sommer, RJ.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Proc Biol Sci","volume":"283","issue":"1825","page":"20152263","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16930543","title":"Identification and characterization of two mature isoforms of retinoschisin in murine retina.","abstract":"Retinoschisin (RS) is a 24 kDa secreted protein expressed in retina and is required for the structural and functional integrity of the retina. RS has been predicted to serve as an adhesive protein but the precise molecular mechanism by which it functions in retina is not yet known. During investigations on structural and functional aspects of RS in murine retina using proteomic tools, we identified two isoforms of RS that differed in mass by 200 Da with no apparent change in charge. Mass spectra and amino acid sequence analysis of the tryptic peptides revealed that these isoforms differed by two amino acids at the N-terminus which suggested processing of RS signal sequence at two cleavage sites by signal peptidase as the basic mechanism underlying the occurrence of two mature RS isoforms in retina. Bioinformatic analysis identified two potential cleavage sites (between amino acids 21-22 and 23-24) in RS signal sequence. The flexibility of the signal peptidase to cleave at two sites is correlated to the amino acid composition of the RS signal sequence. This finding represents a rare example of a naturally occurring signal sequence cleavage at more than one site in vivo.","authors":"Vijayasarathy, C., Gawinowicz, MA., Zeng, Y., Takada, Y., Bush, RA., Sieving, PA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Biochem Biophys Res Commun","volume":"349","issue":"1","page":"99-105","pdf":null,"JrId":"1008","fulltextlink":null,"preprintlink":null,"articledate":"2006-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21311021","title":"HSPC117 is the essential subunit of a human tRNA splicing ligase complex.","abstract":"Splicing of mammalian precursor transfer RNA (tRNA) molecules involves two enzymatic steps. First, intron removal by the tRNA splicing endonuclease generates separate 5' and 3' exons. In animals, the second step predominantly entails direct exon ligation by an elusive RNA ligase. Using activity-guided purification of tRNA ligase from HeLa cell extracts, we identified HSPC117, a member of the UPF0027 (RtcB) family, as the essential subunit of a tRNA ligase complex. RNA interference-mediated depletion of HSPC117 inhibited maturation of intron-containing pre-tRNA both in vitro and in living cells. The high sequence conservation of HSPC117\/RtcB proteins is suggestive of RNA ligase roles of this protein family in various organisms.","authors":"Popow, J., Englert, M., Weitzer, S., Schleiffer, A., Mierzwa, B., Mechtler, K., Trowitzsch, S., Will, CL., L\u00fchrmann, R., S\u00f6ll, D., Martinez, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Science","volume":"331","issue":"6018","page":"760-4","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29031501","title":"DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel\u00a0Diseases Differentiate Disease Subtypes and Associate With Outcome.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">29031501<\/PMID><DateCompleted><Year>2018<\/Year><Month>05<\/Month><Day>03<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>02<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1528-0012<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>154<\/Volume><Issue>3<\/Issue><PubDate><Year>2018<\/Year><Month>02<\/Month><\/PubDate><\/JournalIssue><Title>Gastroenterology<\/Title><ISOAbbreviation>Gastroenterology<\/ISOAbbreviation><\/Journal><ArticleTitle>DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel\u00a0Diseases Differentiate Disease Subtypes and Associate With Outcome.<\/ArticleTitle><Pagination><MedlinePgn>585-598<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0016-5085(17)36241-8<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1053\/j.gastro.2017.10.007<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\">We analyzed DNA methylation patterns and transcriptomes of primary intestinal epithelial cells (IEC) of children newly diagnosed with inflammatory bowel diseases (IBD) to learn more about pathogenesis.","authors":"Howell, KJ., Kraiczy, J., Nayak, KM., Gasparetto, M., Ross, A., Lee, C., Mak, TN., Koo, BK., Kumar, N., Lawley, T., Sinha, A., Rosenstiel, P., Heuschkel, R., Stegle, O., Zilbauer, M.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Gastroenterology","volume":"154","issue":"3","page":"585-598","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22918943","title":"Anillin-related protein Mid1p coordinates the assembly of the cytokinetic contractile ring in fission yeast.","abstract":"In fission yeast cells cortical nodes containing the protein Blt1p and several kinases appear early in G2, mature into cytokinetic nodes by adding anillin Mid1p, myosin-II, formin Cdc12p, and other proteins, and condense into a contractile ring by movements that depend on actin and myosin-II. Previous studies concluded that cells without Mid1p lack cytokinetic nodes and assemble rings unreliably from myosin-II strands but left open questions. Why do strands form outside the equatorial region? Why is ring assembly unreliable without Mid1p? We found in \u0394mid1 cells that Cdc12p accumulates in cytokinetic nodes scattered in the cortex and produces actin filaments that associate with myosin-II, Rng2p, and Cdc15p to form strands located between the nodes. Strands incorporate nodes, and in ~67% of cells, strands slowly close into rings that constrict without the normal ~25-min maturation period. Ring assembly is unreliable and slow without Mid1p because the scattered Cdc12p nodes generate strands spread widely beyond the equator, and growing strands depend on random encounters to merge with other strands into a ring. We conclude that orderly assembly of the contractile ring in wild-type cells depends on Mid1p to recruit myosin-II, Rng2p, and Cdc15p to nodes and to place cytokinetic nodes around the cell equator.","authors":"Saha, S., Pollard, TD.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Mol Biol Cell","volume":"23","issue":"20","page":"3982-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20595231","title":"p53 loss promotes acute myeloid leukemia by enabling aberrant self-renewal.","abstract":"The p53 tumor suppressor limits proliferation in response to cellular stress through several mechanisms. Here, we test whether the recently described ability of p53 to limit stem cell self-renewal suppresses tumorigenesis in acute myeloid leukemia (AML), an aggressive cancer in which p53 mutations are associated with drug resistance and adverse outcome. Our approach combined mosaic mouse models, Cre-lox technology, and in vivo RNAi to disable p53 and simultaneously activate endogenous Kras(G12D)-a common AML lesion that promotes proliferation but not self-renewal. We show that p53 inactivation strongly cooperates with oncogenic Kras(G12D) to induce aggressive AML, while both lesions on their own induce T-cell malignancies with long latency. This synergy is based on a pivotal role of p53 in limiting aberrant self-renewal of myeloid progenitor cells, such that loss of p53 counters the deleterious effects of oncogenic Kras on these cells and enables them to self-renew indefinitely. Consequently, myeloid progenitor cells expressing oncogenic Kras and lacking p53 become leukemia-initiating cells, resembling cancer stem cells capable of maintaining AML in vivo. Our results establish an efficient new strategy for interrogating oncogene cooperation, and provide strong evidence that the ability of p53 to limit aberrant self-renewal contributes to its tumor suppressor activity.","authors":"Zhao, Z., Zuber, J., Diaz-Flores, E., Lintault, L., Kogan, SC., Shannon, K., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Genes Dev","volume":"24","issue":"13","page":"1389-402","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2010-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26085218","title":"Linear ubiquitination signals in adaptive immune responses.","abstract":"Ubiquitin can form eight different linkage types of chains using the intrinsic Met 1 residue or one of the seven intrinsic Lys residues. Each linkage type of ubiquitin chain has a distinct three-dimensional topology, functioning as a tag to attract specific signaling molecules, which are so-called ubiquitin readers, and regulates various biological functions. Ubiquitin chains linked via Met 1 in a head-to-tail manner are called linear ubiquitin chains. Linear ubiquitination plays an important role in the regulation of cellular signaling, including the best-characterized tumor necrosis factor (TNF)-induced canonical nuclear factor-\u03baB (NF-\u03baB) pathway. Linear ubiquitin chains are specifically generated by an E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) and hydrolyzed by a deubiquitinase (DUB) called ovarian tumor (OTU) DUB with linear linkage specificity (OTULIN). LUBAC linearly ubiquitinates critical molecules in the TNF pathway, such as NEMO and RIPK1. The linear ubiquitin chains are then recognized by the ubiquitin readers, including NEMO, which control the TNF pathway. Accumulating evidence indicates an importance of the LUBAC complex in the regulation of apoptosis, development, and inflammation in mice. In this article, I focus on the role of linear ubiquitin chains in adaptive immune responses with an emphasis on the TNF-induced signaling pathways.","authors":"Ikeda, F.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Immunol Rev","volume":"266","issue":"1","page":"222-36","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31951813","title":"Toward Guidelines for Research on Human Embryo Models Formed from Stem Cells.","abstract":"Over the past few years, a number of research groups have reported striking progress on the generation of in\u00a0vitro models from mouse and human stem cells that replicate aspects of early embryonic development. Not only do these models reproduce some key cell fate decisions but, especially in the mouse system, they also mimic the spatiotemporal arrangements of embryonic and extraembryonic tissues that are required for developmental patterning and implantation in the uterus. If such models could be developed for the early human embryo, they would have great potential benefits for understanding early human development, for biomedical science, and for reducing the use of animals and human embryos in research. However, guidelines for the ethical conduct of this line of work are at present not well defined. In this Forum article, we discuss some key aspects of this emerging area of research and provide some recommendations for its ethical oversight.","authors":"Hyun, I., Munsie, M., Pera, MF., Rivron, NC., Rossant, J.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Stem Cell Reports","volume":"14","issue":"2","page":"169-174","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31130485","title":"Structural and Functional Analyses of the Human PDH Complex Suggest a \"Division-of-Labor\" Mechanism by Local E1 and E3 Clusters.","abstract":"The pseudo-atomic structural model of human pyruvate dehydrogenase complex (PDHc) core composed of full-length E2 and E3BP components, calculated from our cryoelectron microscopy-derived density maps at 6-\u00c5 resolution, is similar to those of prokaryotic E2 structures. The spatial organization of human PDHc components as evidenced by negative-staining electron microscopy and native mass spectrometry\u00a0is not homogeneous, and entails the unanticipated formation of local clusters of E1:E2 and E3BP:E3 complexes. Such uneven, clustered organization translates into specific duties for E1-E2 clusters (oxidative decarboxylation and acetyl transfer) and E3BP-E3 clusters (regeneration of reduced lipoamide) corresponding to half-reactions of the PDHc catalytic cycle. The addition of substrate coenzyme A modulates the conformational landscape of PDHc, in particular of the lipoyl domains, extending the postulated multiple random coupling mechanism. The conformational and associated chemical landscapes of PDHc are thus not determined entirely stochastically, but are restrained and channeled through an asymmetric architecture and further modulated by substrate binding.","authors":"Prajapati, S., Haselbach, D., Wittig, S., Patel, MS., Chari, A., Schmidt, C., Stark, H., Tittmann, K.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Structure","volume":"27","issue":"7","page":"1124-1136.e4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25834111","title":"Neuregulin stimulation of cardiomyocyte regeneration in mice and human myocardium reveals a therapeutic window.","abstract":"Therapies developed for adult patients with heart failure have been shown to be ineffective in pediatric clinical trials, leading to the recognition that new pediatric-specific therapies for heart failure must be developed. Administration of the recombinant growth factor neuregulin-1 (rNRG1) stimulates regeneration of heart muscle cells (cardiomyocytes) in adult mice. Because proliferation-competent cardiomyocytes are more abundant in growing mammals, we hypothesized that administration of rNRG1 during the neonatal period might be more effective than in adulthood. If so, neonatal rNRG1 delivery could be a new therapeutic strategy for treating heart failure in pediatric patients. To evaluate the effectiveness of rNRG1 administration in cardiac regeneration, newborn mice were subjected to cryoinjury, which induced myocardial dysfunction and scar formation and decreased cardiomyocyte cell cycle activity. Early administration of rNRG1 to mice from birth to 34 days of age improved myocardial function and reduced the prevalence of transmural scars. In contrast, administration of rNRG1 from 4 to 34 days of age only transiently improved myocardial function. The mechanisms of early administration involved cardiomyocyte protection (38%) and proliferation (62%). We also assessed the ability of rNRG1 to stimulate cardiomyocyte proliferation in intact cultured myocardium from pediatric patients. rNRG1 induced cardiomyocyte proliferation in myocardium from infants with heart disease who were less than 6 months of age. Our results identify an effective time period within which to execute rNRG1 clinical trials in pediatric patients for the stimulation of cardiomyocyte regeneration.","authors":"Polizzotti, BD., Ganapathy, B., Walsh, S., Choudhury, S., Ammanamanchi, N., Bennett, DG., dos Remedios, CG., Haubner, BJ., Penninger, JM., K\u00fchn, B.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Sci Transl Med","volume":"7","issue":"281","page":"281ra45","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16890155","title":"Mitotic activation of the kinase Aurora-A requires its binding partner Bora.","abstract":"The protein kinase Aurora-A is required for centrosome maturation, spindle assembly, and asymmetric protein localization during mitosis. Here, we describe the identification of Bora, a conserved protein that is required for the activation of Aurora-A at the onset of mitosis. In the Drosophila peripheral nervous system, bora mutants have defects during asymmetric cell division identical to those observed in aurora-A. Furthermore, overexpression of bora can rescue defects caused by mutations in aurora-A. Bora is conserved in vertebrates, and both Drosophila and human Bora can bind to Aurora-A and activate the kinase in vitro. In interphase cells, Bora is a nuclear protein, but upon entry into mitosis, Bora is excluded from the nucleus and translocates into the cytoplasm in a Cdc2-dependent manner. We propose a model in which activation of Cdc2 initiates the release of Bora into the cytoplasm where it can bind and activate Aurora-A.","authors":"Hutterer, A., Berdnik, D., Wirtz-Peitz, F., Zigman, M., Schleiffer, A., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Dev Cell","volume":"11","issue":"2","page":"147-57","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22934970","title":"Beyond genotype to phenotype: why the phenotype of an individual cannot always be predicted from their genome sequence and the environment that they experience.","abstract":"One promise of personalized medicine is that it will be possible to make useful predictions about the phenotypes of individuals from their complete genome sequences (e.g. concerning their susceptibility to disease). However, to what extent is knowledge about an individual's genotype, together with information about the environment that they have experienced, sufficient to predict phenotypic variation? In the present review, we argue that, although the 'typical' phenotypic outcome of an individual's genome can be predicted, it is much more difficult to predict the actual outcome for a particular individual. We highlight three reasons for this. First, the outcome of mutations can be influenced by random (stochastic) processes. Second, genetic variation present in one generation can influence phenotypic traits in the next generation, even if individuals do not inherit this variation. Third, the environment experienced by one generation can influence phenotypic variation in the next generation. These contributions to phenotypic variation have long been appreciated by quantitative geneticists, although they have only recently been studied at the molecular level. Taken together, they mean that, in many cases, the genotypes of individuals and the environment that they experience may not be sufficient to determine their phenotypes. A more comprehensive genotype-to-phenotype model will be required to make accurate predictions about the biology of individuals.","authors":"Burga, A., Lehner, B.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"FEBS J","volume":"279","issue":"20","page":"3765-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16888000","title":"Activation of NFAT signal in vivo leads to osteopenia associated with increased osteoclastogenesis and bone-resorbing activity.","abstract":"The transcription factor family member NFAT plays an important role in the regulation of osteoclast differentiation. However, the role of NFAT in osteoclasts in vivo is still not fully understood. Thus, we generated transgenic mice in which constitutively active-NFAT1\/NFATc2 (CA-NFAT1) is specifically expressed in the osteoclast lineage, using the tartrate-resistant acid phosphatase gene promoter. Both x-ray and histological analyses demonstrated an osteopenic bone phenotype in the CA-NFAT1 transgenic mice, whereas the number of tartrate-resistant acid phosphatase-positive osteoclasts was markedly higher in the long bones of these mice. Furthermore, the bone-resorbing activity of mature osteoclasts derived from the transgenic mice was much higher than that of wild-type mice. Interestingly, the introduction of CA-NFAT1 into osteoclasts or RAW264 cells increased the expression and activity of c-Src and stimulated actin ring formation. In contrast, CA-NFAT1 or GFP-tagged VIVIT peptide, a specific inhibitor of NFAT, did not affect the survival of mature osteoclasts. Collectively, our data indicate that NFAT controls bone resorption in vivo by stimulating the differentiation and functioning of osteoclasts but not their survival.","authors":"Ikeda, F., Nishimura, R., Matsubara, T., Hata, K., Reddy, SV., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Immunol","volume":"177","issue":"4","page":"2384-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23383048","title":"Brain-derived neurotrophic factor promotes vasculature-associated migration of neuronal precursors toward the ischemic striatum.","abstract":"Stroke induces the recruitment of neuronal precursors from the subventricular zone (SVZ) into the ischemic striatum. In injured areas, de-routed neuroblasts use blood vessels as a physical scaffold to their migration, in a process that resembles the constitutive migration seen in the rostral migratory stream (RMS). The molecular mechanism underlying injury-induced vasculature-mediated migration of neuroblasts in the post-stroke striatum remains, however, elusive. Using adult mice we now demonstrate that endothelial cells in the ischemic striatum produce brain-derived neurotrophic factor (BDNF), a neurotrophin that promotes the vasculature-mediated migration of neuronal precursors in the RMS, and that recruited neuroblasts maintain expression of p75NTR, a low-affinity receptor for BDNF. Reactive astrocytes, which are widespread throughout the damaged area, ensheath blood vessels and express TrkB, a high-affinity receptor for BDNF. Despite the absence of BDNF mRNA, we observed strong BDNF immunolabeling in astrocytes, suggesting that these glial cells trap extracellular BDNF. Importantly, this pattern of expression is reminiscent of the adult RMS, where TrkB-expressing astrocytes bind and sequester vasculature-derived BDNF, leading to the entry of migrating cells into the stationary phase. Real-time imaging of cell migration in acute brain slices revealed a direct role for BDNF in promoting the migration of neuroblasts to ischemic areas. We also demonstrated that cells migrating in the ischemic striatum display higher exploratory behavior and longer stationary periods than cells migrating in the RMS. Our findings suggest that the mechanisms involved in the injury-induced vasculature-mediated migration of neuroblasts recapitulate, at least partially, those observed during constitutive migration in the RMS.","authors":"Grade, S., Weng, YC., Snapyan, M., Kriz, J., Malva, JO., Saghatelyan, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"PLoS One","volume":"8","issue":"1","page":"e55039","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-217","title":"Improved myelin clearance and cognitive outcomes after TBI in female mice are mediated by ovarian steroids and sex chromosomes","abstract":null,"authors":"Daniel Pinto-Benito, Carmen Paradela-Leal, Nuria Cano-Adamuz, Daniela Grassi, I\u00f1igo Azcoitia, Sofia Grade, Maria-Angeles Arevalo","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"BioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.01.28.702273v1","preprintlink":"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.01.28.702273v1","articledate":"2026-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7838527","title":"Immediate effects of reversible HTLV-1 tax function: T-cell activation and apoptosis.","abstract":"The tax protein of Human T-cell leukemia virus type 1 (HTLV-1) is important for the transforming properties of this virus in vitro and is considered to be responsible for the early stages of leukemogenesis in infected hosts. To address the early consequences of HTLV-1 tax function, we have constructed fusion proteins containing tax sequence either aminoterminal (taxER) or carboxy-terminal (ERtax) of the hormone binding domain of the human estrogen receptor (ER). Addition of estrogen or the antagonist hydroxytamoxifen to Jurkat T-cells expressing these constructs led to the trans-activation or responsive promoters and upregulation of cell surface markers CD28, CD69 and CD5 but not CD25 (IL2R-alpha subunit) or B7 (ligand for CD28). Additional stimulation of the T-cell receptor CD3 complex, led to the upregulation of CD25. B7 was upregulated by concomittent activation of ERtax and CD3 or CD28 pathways. These events were in part reversible upon withdrawal of hormone and inactivation of ERtax. Severe inhibition of proliferation, and apoptosis was observed with cells which had been subjected to short term (3 days) activation of the tax fusion proteins and the CD3 complex. Induction of ERtax activity for longer than 3 days promoted cell death independently of CD3 stimulation. Co-stimulation through the CD28 cell surface molecule did not suppress induction of apoptosis.","authors":"Chlichlia, K., Moldenhauer, G., Daniel, PT., Busslinger, M., Gazzolo, L., Schirrmacher, V., Khazaie, K.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Oncogene","volume":"10","issue":"2","page":"269-77","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1995-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20564202","title":"Negative regulation of wnt11 expression by Jnk signaling during zebrafish gastrulation.","abstract":"Stress-induced Sapk\/Jnk signaling is involved in cell survival and apoptosis. Recent studies have increased our understanding of the physiological roles of Jnk signaling in embryonic development. However, still unclear is the precise function of Jnk signaling during gastrulation, a critical step in the establishment of the vertebrate body plan. Here we use morpholino-mediated knockdown of the zebrafish orthologs of the Jnk activators Mkk4 and Mkk7 to examine the effect of Jnk signaling abrogation on early vertebrate embryogenesis. Depletion of zebrafish Mkk4b led to abnormal convergent extension (CE) during gastrulation, whereas Mkk7 morphants exhibited defective somitogenesis. Surprisingly, Mkk4b morphants displayed marked upregulation of wnt11, which is the triggering ligand of CE and stimulates Jnk activation via the non-canonical Wnt pathway. Conversely, ectopic activation of Jnk signaling by overexpression of an active form of Mkk4b led to wnt11 downregulation. Mosaic lineage tracing studies revealed that Mkk4b-Jnk signaling suppressed wnt11 expression in a non-cell-autonomous manner. These findings provide the first evidence that wnt11 itself is a downstream target of the Jnk cascade in the non-canonical Wnt pathway. Our work demonstrates that Jnk activation is indispensable for multiple steps during vertebrate body plan formation. Furthermore, non-canonical Wnt signaling may coordinate vertebrate CE movements by triggering Jnk activation that represses the expression of the CE-triggering ligand wnt11.","authors":"Seo, J., Asaoka, Y., Nagai, Y., Hirayama, J., Yamasaki, T., Namae, M., Ohata, S., Shimizu, N., Negishi, T., Kitagawa, D., Kondoh, H., Furutani-Seiki, M., Penninger, JM., Katada, T., Nishina, H.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Cell Biochem","volume":"110","issue":"4","page":"1022-37","pdf":null,"JrId":"4590","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23081759","title":"High temporal resolution in vivo blood oximetry via projection-based T2 measurement.","abstract":"Measuring venous oxygen saturation (HbO2) in large blood vessels can provide important information about oxygen delivery and its consumption in vital organs. Quantification of blood's T2 value via MR can be utilized to determine HbO2 noninvasively. We propose a fast method for in vivo blood T2 quantification via computing the complex difference of velocity-encoded projections. As blood flows continuously, its signal can be robustly isolated from the surrounding tissue by computing the complex difference of two central k-space lines with different velocity encodings. This resultant signal can then be measured as a function of echo time for rapidly quantifying T2 of blood. We applied the method to quantify HbO2 in three cerebral veins at rest and in one of the veins in response to hypercapnia. Average HbO2 measurements in superior sagittal sinus (SSS), straight sinus and internal jugular vein in the group were 63 \u00b1 3%, 68 \u00b1 4% and 65 \u00b1 4%, respectively. Average HbO2 values in SSS during baseline, hypercapnia, and recovery were 63 \u00b1 2%, 79 \u00b1 5%, and 61 \u00b1 3%, respectively. When compared with standard T2 quantification techniques, the proposed method is fast, reliable, and robust against partial volume effects.","authors":"Jain, V., Magland, J., Langham, M., Wehrli, FW.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Magn Reson Med","volume":"70","issue":"3","page":"785-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23082152","title":"An MRI study of symptomatic adhesive capsulitis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23082152<\/PMID><DateCompleted><Year>2013<\/Year><Month>04<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><Issue>10<\/Issue><PubDate><Year>2012<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>An MRI study of symptomatic adhesive capsulitis.<\/ArticleTitle><Pagination><MedlinePgn>e47277<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0047277<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Appilication of MR imaging to diagnose Adhesive Capsulitis (AC) has previously been described. However, there is insufficient information available for the MRI analysis of AC. This study is to describe and evaluate the pathomorphology of the shoulder in Asian patients with AC compared to healthy volunteers.","authors":"Zhao, W., Zheng, X., Liu, Y., Yang, W., Amirbekian, V., Diaz, LE., Huang, X.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"10","page":"e47277","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23080315","title":"Terminology and classification of muscle injuries in sport: the Munich consensus statement.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23080315<\/PMID><DateCompleted><Year>2013<\/Year><Month>09<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1473-0480<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>47<\/Volume><Issue>6<\/Issue><PubDate><Year>2013<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>British journal of sports medicine<\/Title><ISOAbbreviation>Br J Sports Med<\/ISOAbbreviation><\/Journal><ArticleTitle>Terminology and classification of muscle injuries in sport: the Munich consensus statement.<\/ArticleTitle><Pagination><MedlinePgn>342-50<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1136\/bjsports-2012-091448<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">To provide a clear terminology and classification of muscle injuries in order to facilitate effective communication among medical practitioners and development of systematic treatment strategies.","authors":"Mueller-Wohlfahrt, HW., Haensel, L., Mithoefer, K., Ekstrand, J., English, B., McNally, S., Orchard, J., van Dijk, CN., Kerkhoffs, GM., Schamasch, P., Blottner, D., Swaerd, L., Goedhart, E., Ueblacker, P.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Br J Sports Med","volume":"47","issue":"6","page":"342-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16880257","title":"T-bet negatively regulates autoimmune myocarditis by suppressing local production of interleukin 17.","abstract":"Experimental autoimmune myocarditis (EAM) appears after infectious heart disease, the most common cause of dilated cardiomyopathy in humans. Here we report that mice lacking T-bet, a T-box transcription factor required for T helper (Th)1 cell differentiation and interferon (IFN)-gamma production, develop severe autoimmune heart disease compared to T-bet+\/+ control mice. Experiments in T-bet-\/- IL-4-\/- and T-bet-\/- IL-4Ralpha-\/- mice, as well as transfer of heart-specific Th1 and Th2 cell lines, showed that autoimmune heart disease develops independently of Th1 or Th2 polarization. Analysis of T-bet-\/- IL-12Rbeta1-\/- and T-bet-\/- IL-12p35-\/- mice then identified interleukin (IL)-23 as critical for EAM pathogenesis. In addition, T-bet-\/- mice showed a marked increase in production of the IL-23-dependent cytokine IL-17 by heart-infiltrating lymphocytes, and in vivo IL-17 depletion markedly reduced EAM severity in T-bet-\/- mice. Heart-infiltrating T-bet-\/- CD8+ but not CD8- T cells secrete IFN-gamma, which inhibits IL-17 production and protects against severe EAM. In contrast, T-bet-\/- CD8+ lymphocytes completely lost their capacity to release IFN-gamma within the heart. Collectively, these data show that severe IL-17-mediated EAM can develop in the absence of T-bet, and that T-bet can regulate autoimmunity via the control of nonspecific CD8+ T cell bystander functions in the inflamed target organ.","authors":"Rangachari, M., Mauermann, N., Marty, RR., Dirnhofer, S., Kurrer, MO., Komnenovic, V., Penninger, JM., Eriksson, U.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Exp Med","volume":"203","issue":"8","page":"2009-19","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31053593","title":"Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast.","abstract":"Signaling pathways can regulate biological responses by the transcriptional regulation of target genes. In yeast, multiple signaling pathways control filamentous growth, a morphogenetic response that occurs in many species including fungal pathogens. Here, we examine the role of signaling pathways that control filamentous growth in regulating adhesion-dependent surface responses, including mat formation and colony patterning. Expression profiling and mutant phenotype analysis showed that the major pathways that regulate filamentous growth [filamentous growth MAPK (fMAPK), RAS, retrograde (RTG), RIM101, RPD3, ELP, SNF1, and PHO85] also regulated mat formation and colony patterning. The chromatin remodeling complex, SAGA, also regulated these responses. We also show that the RAS and RTG pathways coregulated a common set of target genes, and that SAGA regulated target genes known to be controlled by the fMAPK, RAS, and RTG pathways. Analysis of surface growth-specific targets identified genes that respond to low oxygen, high temperature, and desiccation stresses. We also explore the question of why cells make adhesive contacts in colonies. Cell adhesion contacts mediated by the coregulated target and adhesion molecule, Flo11p, deterred entry into colonies by macroscopic predators and impacted colony temperature regulation. The identification of new regulators (<i>e.g.<\/i>, SAGA), and targets of surface growth in yeast may provide insights into fungal pathogenesis in settings where surface growth and adhesion contributes to virulence.","authors":"Chow, J., Starr, I., Jamalzadeh, S., Muniz, O., Kumar, A., Gokcumen, O., Ferkey, DM., Cullen, PJ.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Genetics","volume":"212","issue":"3","page":"667-690","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22899815","title":"A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22899815<\/PMID><DateCompleted><Year>2013<\/Year><Month>01<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>13<\/Volume><PubDate><Year>2012<\/Year><Month>Aug<\/Month><Day>16<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8.<\/ArticleTitle><Pagination><MedlinePgn>393<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-13-393<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Nephronophthisis (NPHP) as a cause of cystic kidney disease is the most common genetic cause of progressive renal failure in children and young adults. NPHP is characterized by abnormal and\/or loss of function of proteins associated with primary cilia. Previously, we characterized an autosomal recessive phenotype of cystic kidney disease in the Lewis Polycystic Kidney (LPK) rat.","authors":"McCooke, JK., Appels, R., Barrero, RA., Ding, A., Ozimek-Kulik, JE., Bellgard, MI., Morahan, G., Phillips, JK.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"BMC Genomics","volume":"13","issue":"","page":"393","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20558712","title":"Target RNA-directed trimming and tailing of small silencing RNAs.","abstract":"In Drosophila, microRNAs (miRNAs) typically guide Argonaute1 to repress messenger RNA (mRNA), whereas small interfering RNAs (siRNAs) guide Argonaute2 to destroy viral and transposon RNA. Unlike siRNAs, miRNAs rarely form extensive numbers of base pairs to the mRNAs they regulate. We find that extensive complementarity between a target RNA and an Argonaute1-bound miRNA triggers miRNA tailing and 3'-to-5' trimming. In flies, Argonaute2-bound small RNAs--but not those bound to Argonaute1--bear a 2'-O-methyl group at their 3' ends. This modification blocks target-directed small RNA remodeling: In flies lacking Hen1, the enzyme that adds the 2'-O-methyl group, Argonaute2-associated siRNAs are tailed and trimmed. Target complementarity also affects small RNA stability in human cells. These results provide an explanation for the partial complementarity between animal miRNAs and their targets.","authors":"Ameres, SL., Horwich, MD., Hung, JH., Xu, J., Ghildiyal, M., Weng, Z., Zamore, PD.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Science","volume":"328","issue":"5985","page":"1534-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30768270","title":"Targeting the MKK7-JNK (Mitogen-Activated Protein Kinase Kinase 7-c-Jun N-Terminal Kinase) Pathway with Covalent Inhibitors.","abstract":"The protein kinase MKK7 is linked to neuronal development and the onset of cancer. The field, however, lacks high-quality functional probes that would allow for the dissection of its detailed functions. Against this background, we describe an effective covalent inhibitor of MKK7 based on the pyrazolopyrimidine scaffold.","authors":"Wolle, P., Hardick, J., Cronin, SJF., Engel, J., Baumann, M., Lategahn, J., Penninger, JM., Rauh, D.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Med Chem","volume":"62","issue":"5","page":"2843-2848","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25490264","title":"Cytokinetic abscission: molecular mechanisms and temporal control.","abstract":"Cytokinesis mediates the physical separation of dividing cells after chromosome segregation. In animal cell cytokinesis, a contractile ring, mainly composed of actin and myosin filaments, ingresses a cleavage furrow midway between the two spindle poles. A distinct machinery, involving the endosomal sorting complex required for transport III (ESCRT-III), subsequently splits the plasma membrane of nascent daughter cells in a process termed abscission. Here, we provide a brief overview of early cytokinesis events in animal cells and then cover in depth recently emerging models for the assembly and function of the abscission machinery and its temporal coordination with chromosome segregation.","authors":"Mierzwa, B., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Dev Cell","volume":"31","issue":"5","page":"525-38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29959232","title":"Time-resolved transcriptomics in neural stem cells identifies a v-ATPase\/Notch regulatory loop.","abstract":"<i>Drosophila melanogaster<\/i> neural stem cells (neuroblasts [NBs]) divide asymmetrically by differentially segregating protein determinants into their daughter cells. Although the machinery for asymmetric protein segregation is well understood, the events that reprogram one of the two daughter cells toward terminal differentiation are less clear. In this study, we use time-resolved transcriptional profiling to identify the earliest transcriptional differences between the daughter cells on their way toward distinct fates. By screening for coregulated protein complexes, we identify vacuolar-type H<sup>+<\/sup>-ATPase (v-ATPase) among the first and most significantly down-regulated complexes in differentiating daughter cells. We show that v-ATPase is essential for NB growth and persistent activity of the Notch signaling pathway. Our data suggest that v-ATPase and Notch form a regulatory loop that acts in multiple stem cell lineages both during nervous system development and in the adult gut. We provide a unique resource for investigating neural stem cell biology and demonstrate that cell fate changes can be induced by transcriptional regulation of basic, cell-essential pathways.","authors":"Wissel, S., Harzer, H., Bonnay, F., Burkard, TR., Neum\u00fcller, RA., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"J Cell Biol","volume":"217","issue":"9","page":"3285-3300","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30764600","title":"Lineage Tracing: Computational Reconstruction Goes Beyond the Limit of Imaging.","abstract":"Tracking the fate of individual cells and their progeny through lineage tracing has been widely used to investigate various biological processes including embryonic development, homeostatic tissue turnover, and stem cell function in regeneration and disease. Conventional lineage tracing involves the marking of cells either with dyes or nucleoside analogues or genetic marking with fluorescent and\/or colorimetric protein reporters. Both are imaging-based approaches that have played a crucial role in the field of developmental biology as well as adult stem cell biology. However, imaging-based lineage tracing approaches are limited by their scalability and the lack of molecular information underlying fate transitions. Recently, computational biology approaches have been combined with diverse tracing methods to overcome these limitations and so provide high-order scalability and a wealth of molecular information. In this review, we will introduce such novel computational methods, starting from single-cell RNA sequencing-based lineage analysis to DNA barcoding or genetic scar analysis. These novel approaches are complementary to conventional imaging-based approaches and enable us to study the lineage relationships of numerous cell types during vertebrate, and in particular human, development and disease.","authors":"Wu, SS., Lee, JH., Koo, BK.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mol Cells","volume":"42","issue":"2","page":"104-112","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7827404","title":"Carbohydrate receptor-mediated gene transfer to human T leukaemic cells.","abstract":"The mucin-type carbohydrate Tn cryptantigen (GalNAc alpha 1-O-Ser\/Thr, where GalNAc is N-acetyl-D-galactosamine) is expressed in many carcinomas, in haemopoietic disorders including the Tn syndrome, and on human immunodeficiency virus (HIV) coat glycoproteins, but is not expressed on normal, differentiated cells because of the expression of a Tn-processing galactosyltransferase. Using Jurkat T leukaemic cells which express high levels of Tn antigen due to deficient Tn galactosylation, we have established the Tn antigen-mediated gene transfer and demonstrate the considerable efficiency of this approach. We used poly(L-lysine) conjugates of the monoclonal antibody 1E3 directed against the Tn antigen to deliver the luciferase and beta-galactosidase reporter genes to Jurkat cells by receptor-mediated endocytosis. Addition of unconjugated 1E3 reduced transfection efficiency in a concentration-dependent manner and incubation with free GalNAc abolished DNA transfer completely, indicating that gene delivery is indeed mediated by the Tn antigen. Pre-treatment of Jurkat cells with Vibrio cholerae sialidase, which uncovers additional Tn antigens, resulted in an improvement of gene transfection. Both human and chicken adenovirus particles attached to the DNA\/polylysine complex strongly augmented transgene expression. When the beta-galactosidase (lacZ) gene was delivered to Jurkat cells by Tn-mediated endocytosis, up to 60% of the cells were positive in the cytochemical stain using 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-gal) as a chromogenic substrate. The efficiency of the transferrin receptor-mediated DNA uptake into Jurkat cells was comparatively low, although these cells were shown to express considerable amounts of transferrin receptor. We show here that a mucin-type carbohydrate antigen mediates highly efficient DNA uptake by endocytosis into Jurkat T cells. This method represents a 50-fold improvement of Jurkat cell transfection efficiency over other physical gene transfer techniques. Specific gene delivery to primary cancer cells exhibiting Tn epitopes may especially be desirable in immunotherapy protocols.","authors":"Thurnher, M., Wagner, E., Clausen, H., Mechtler, K., Rusconi, S., Dinter, A., Birnstiel, ML., Berger, EG., Cotten, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Glycobiology","volume":"4","issue":"4","page":"429-35","pdf":null,"JrId":"2078","fulltextlink":null,"preprintlink":null,"articledate":"1995-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23340483","title":"Oligodendrogenesis from neural stem cells: perspectives for remyelinating strategies.","abstract":"Mobilization of remyelinating cells spontaneously occurs in the adult brain. These cellular resources are specially active after demyelinating episodes in early phases of multiple sclerosis (MS). Indeed, oligodendrocyte precursor cells (OPCs) actively proliferate, migrate to and repopulate the lesioned areas. Ultimately, efficient remyelination is accomplished when new oligodendrocytes reinvest nude neuronal axons, restoring the normal properties of impulse conduction. As the disease progresses this fundamental process fails. Multiple causes seem to contribute to such transient decline, including the failure of OPCs to differentiate and enwrap the vulnerable neuronal axons. Regenerative medicine for MS has been mainly centered on the recruitment of endogenous self-repair mechanisms, or on transplantation approaches. The latter commonly involves grafting of neural precursor cells (NPCs) or neural stem cells (NSCs), with myelinogenic potential, in the injured areas. Both strategies require further understanding of the biology of oligodendrocyte differentiation and remyelination. Indeed, the success of transplantation largely depends on the pre-commitment of transplanted NPCs or NSCs into oligodendroglial cell type, while the endogenous differentiation of OPCs needs to be boosted in chronic stages of the disease. Thus, much effort has been focused on finding molecular targets that drive oligodendrocytes commitment and development. The present review explores several aspects of remyelination that must be considered in the design of a cell-based therapy for MS, and explores more deeply the challenge of fostering oligodendrogenesis. In this regard, we discuss herein a tool developed in our research group useful to search novel oligodendrogenic factors and to study oligodendrocyte differentiation in a time- and cost-saving manner.","authors":"Grade, S., Bernardino, L., Malva, JO.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Int J Dev Neurosci","volume":"31","issue":"7","page":"692-700","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9115398","title":"Cytoplasmic flows localize injected oskar RNA in Drosophila oocytes.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9115398<\/PMID><DateCompleted><Year>1997<\/Year><Month>06<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>7<\/Volume><Issue>5<\/Issue><PubDate><Year>1997<\/Year><Month>May<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Cytoplasmic flows localize injected oskar RNA in Drosophila oocytes.<\/ArticleTitle><Pagination><MedlinePgn>326-37<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The oskar (osk) gene encodes a determinant of posterior identity in Drosophila, and the localization of osk RNA to the pole plasm at the posterior pole of the oocyte is essential for development of the embryo. The mechanisms by which osk RNA is localized are unknown.","authors":"Glotzer, JB., Saffrich, R., Glotzer, M., Ephrussi, A.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Curr Biol","volume":"7","issue":"5","page":"326-37","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7746326","title":"Spontaneous resistance to acute T-cell leukaemias in TCRV gamma 1.1J gamma 4C gamma 4 transgenic mice.","abstract":"The concept of tumour surveillance implies that specific and non-specific components of the immune system eliminate tumours in the early phase of malignancy. The immunological mechanisms that control growth of preneoplastic cells are, however, not known. T cells expressing gamma delta T-cell receptors (TCR) were first described as lymphocytes with reactivity against various tumour cells, which suggests that gamma delta T cells could mediate tumour surveillance. Here we show that TCRV gamma 1.1J gamma 4C gamma 4 transgenic mice are spontaneously resistant to acute T-cell leukaemias but cannot reject non-haematopoietic tumours. TCRV gamma 1.1J gamma 4C gamma 4+ hybridomas isolated from these mice react in vitro against almost all haematopoietic tumour cell lines tested. Recognition of tumour cells depends on the gamma delta TCR but is independent of major histocompatibility complex (MHC) class I, MHC class II, or TAP-2 peptide transporter expression. Ligand recognition is influenced by the murine Nromp gene, which confers resistance or susceptibility to tuberculosis, lepra and leishmaniasis. These data indicate that TCRV gamma 1.1+ T cells confer spontaneous immunity against haematopoietic tumours in vivo and link innate resistance to bacterial infections with tissue-specific tumour surveillance by gamma delta+ T cells.","authors":"Penninger, JM., Wen, T., Timms, E., Potter, J., Wallace, VA., Matsuyama, T., Ferrick, D., Sydora, B., Kronenberg, M., Mak, TW.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Nature","volume":"375","issue":"6528","page":"241-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1995-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16818445","title":"Wnt9a signaling is required for joint integrity and regulation of Ihh during chondrogenesis.","abstract":"Joints, which separate skeleton elements, serve as important signaling centers that regulate the growth of adjacent cartilage elements by controlling proliferation and maturation of chondrocytes. Accurate chondrocyte maturation is crucial for endochondral ossification and for the ultimate size of skeletal elements, as premature or delayed maturation results predominantly in shortened elements. Wnt9a has previously been implicated as being a player in joint induction, based on gain-of function experiments in chicken and mouse. We show that loss of Wnt9a does not affect joint induction, but results to synovial chondroid metaplasia in some joints. This phenotype can be enhanced by removal of an additional Wnt gene, Wnt4, suggesting that Wnts are playing a crucial role in directing bi-potential chondro-synovioprogenitors to become synovial connective tissue, by actively suppressing their chondrogenic potential. Furthermore, we show that Wnt9a is a temporal and spatial regulator of Indian hedgehog (Ihh), a central player of skeletogenesis. Loss of Wnt9a activity results in transient downregulation of Ihh and reduced Ihh-signaling activity at E12.5-E13.5. The canonical Wnt\/beta-catenin pathway probably mediates regulation of Ihh expression in prehypertrophic chondrocytes by Wnt9a, because embryos double-heterozygous for Wnt9a and beta-catenin show reduced Ihh expression, and in vivo chromatin immunoprecipitation demonstrates a direct interaction between the beta-catenin\/Lef1 complex and the Ihh promoter.","authors":"Sp\u00e4ter, D., Hill, TP., O'sullivan, RJ., Gruber, M., Conner, DA., Hartmann, C.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Development","volume":"133","issue":"15","page":"3039-49","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16738054","title":"Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging.","abstract":"The premature aging disease Hutchinson-Gilford Progeria Syndrome (HGPS) is caused by a mutant lamin A (LADelta50). Nuclei in cells expressing LADelta50 are abnormally shaped and display a loss of heterochromatin. To determine the mechanisms responsible for the loss of heterochromatin, epigenetic marks regulating either facultative or constitutive heterochromatin were examined. In cells from a female HGPS patient, histone H3 trimethylated on lysine 27 (H3K27me3), a mark for facultative heterochromatin, is lost on the inactive X chromosome (Xi). The methyltransferase responsible for this mark, EZH2, is also down-regulated. These alterations are detectable before the changes in nuclear shape that are considered to be the pathological hallmarks of HGPS cells. The results also show a down-regulation of the pericentric constitutive heterochromatin mark, histone H3 trimethylated on lysine 9, and an altered association of this mark with heterochromatin protein 1alpha (Hp1alpha) and the CREST antigen. This loss of constitutive heterochromatin is accompanied by an up-regulation of pericentric satellite III repeat transcripts. In contrast to these decreases in histone H3 methylation states, there is an increase in the trimethylation of histone H4K20, an epigenetic mark for constitutive heterochromatin. Expression of LADelta50 in normal cells induces changes in histone methylation patterns similar to those seen in HGPS cells. The epigenetic changes described most likely represent molecular mechanisms responsible for the rapid progression of premature aging in HGPS patients.","authors":"Shumaker, DK., Dechat, T., Kohlmaier, A., Adam, SA., Bozovsky, MR., Erdos, MR., Eriksson, M., Goldman, AE., Khuon, S., Collins, FS., Jenuwein, T., Goldman, RD.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Proc Natl Acad Sci U S A","volume":"103","issue":"23","page":"8703-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16725309","title":"Modulation of lipoprotein receptor functions by intracellular adaptor proteins.","abstract":"Members of the low density lipoprotein (LDL) receptor gene family are critically involved in a wide range of physiological processes including lipid and vitamin homeostasis, cellular migration, neurodevelopment, and synaptic plasticity, to name a few. Lipoprotein receptors exert these diverse biological functions by acting as cellular uptake receptors or by inducing intracellular signaling cascades. It was discovered that a short sequence in the intracellular region of all lipoprotein receptors, Asn-Pro-X-Tyr (NPXY) is important for mediating either endocytosis or signal transduction events, and that this motif serves as a binding site for phosphotyrosine-binding (PTB) domain containing scaffold proteins. These molecular adaptors connect the transmembrane receptors with the endocytosis machinery and regulate cellular trafficking, or function as assembly sites for dynamic multi-protein signaling complexes. Whereas the LDL receptor represents the archetype of an endocytic lipoprotein receptor, the structurally closely related apolipoprotein E receptor 2 (apoER2) and very low density lipoprotein (VLDL) receptor activate a kinase-dependent intracellular signaling cascade after binding to the neuronal signaling molecule Reelin. This review focuses on two related PTB domain containing adaptor proteins that mediate these divergent lipoprotein receptor responses, ARH (autosomal recessive hypercholesterolemia protein) and Dab1 (disabled-1), and discusses the structural and molecular basis of this different behaviour.","authors":"Stolt, PC., Bock, HH.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell Signal","volume":"18","issue":"10","page":"1560-71","pdf":null,"JrId":"1769","fulltextlink":null,"preprintlink":null,"articledate":"2006-11-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36930647","title":"Protocol for capturing trophectoderm stem cells reflecting the blastocyst stage.","abstract":"Classically, culturing mouse blastocysts with FGF4\/TGF-&#x3b2;1, two epiblast-secreted inducers, allows for deriving trophoblast stem cells that comprise fluctuating subpopulations reflecting both pre- and post-implantation stages. However, a more complete combination of inducers (adding LPA, IL11, BMP7, Activin A, 8-Br-cAMP) captures trophectoderm stem cells with enhanced transcriptomic similarity to the blastocyst trophectoderm and self-renewal, reduced differentiation. Also, the complete combination of inducers increased potential to form blastoids and to instruct decidualization in utero, thus better reflecting the blastocyst. For complete details on the use and execution of this protocol, please refer to Seong et&#xa0;al.<sup>1<\/sup>.","authors":"Seong, J., Rivron, NC.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"STAR Protoc","volume":"4","issue":"2","page":"102151","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24714811","title":"Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.","abstract":"Gene expression is determined by genomic elements called enhancers, which contain short motifs bound by different transcription factors (TFs). However, how enhancer sequences and TF motifs relate to enhancer activity is unknown, and general sequence requirements for enhancers or comprehensive sets of important enhancer sequence elements have remained elusive. Here, we computationally dissect thousands of functional enhancer sequences from three different Drosophila cell lines. We find that the enhancers display distinct cis-regulatory sequence signatures, which are predictive of the enhancers' cell type-specific or broad activities. These signatures contain transcription factor motifs and a novel class of enhancer sequence elements, dinucleotide repeat motifs (DRMs). DRMs are highly enriched in enhancers, particularly in enhancers that are broadly active across different cell types. We experimentally validate the importance of the identified TF motifs and DRMs for enhancer function and show that they can be sufficient to create an active enhancer de novo from a nonfunctional sequence. The function of DRMs as a novel class of general enhancer features that are also enriched in human regulatory regions might explain their implication in several diseases and provides important insights into gene regulation.","authors":"Y\u00e1\u00f1ez-Cuna, JO., Arnold, CD., Stampfel, G., Bory\u0144, LM., Gerlach, D., Rath, M., Stark, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genome Res","volume":"24","issue":"7","page":"1147-56","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25297111","title":"The TRIM-NHL protein Brat promotes axon maintenance by repressing src64B expression.","abstract":"The morphology and the connectivity of neuronal structures formed during early development must be actively maintained as the brain matures. Although impaired axon stability is associated with the progression of various neurological diseases, relatively little is known about the factors controlling this process. We identified Brain tumor (Brat), a conserved member of the TRIM-NHL family of proteins, as a new regulator of axon maintenance in Drosophila CNS. Brat function is dispensable for the initial growth of Mushroom Body axons, but is required for the stabilization of axon bundles. We found that Brat represses the translation of src64B, an upstream regulator of a conserved Rho-dependent pathway previously shown to promote axon retraction. Furthermore, brat phenotypes are phenocopied by src64B overexpression, and partially suppressed by reducing the levels of src64B or components of the Rho pathway, suggesting that brat promotes axon maintenance by downregulating the levels of Src64B. Finally, Brat regulates brain connectivity via its NHL domain, but independently of its previously described partners Nanos, Pumilio, and d4EHP. Thus, our results uncover a novel post-transcriptional regulatory mechanism that controls the maintenance of neuronal architecture by tuning the levels of a conserved rho-dependent signaling pathway.","authors":"Marchetti, G., Reichardt, I., Knoblich, JA., Besse, F.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Neurosci","volume":"34","issue":"41","page":"13855-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20201032","title":"Stat5 is indispensable for the maintenance of bcr\/abl-positive leukaemia.","abstract":"Tumourigenesis caused by the Bcr\/Abl oncoprotein is a multi-step process proceeding from initial to tumour-maintaining events and finally results in a complex tumour-supporting network. A key to successful cancer therapy is the identification of critical functional nodes in an oncogenic network required for disease maintenance. So far, the transcription factors Stat3 and Stat5a\/b have been implicated in bcr\/abl-induced initial transformation. However, to qualify as a potential drug target, a signalling pathway must be required for the maintenance of the leukaemic state. Data on the roles of Stat3 or Stat5a\/b in leukaemia maintenance are elusive. Here, we show that both, Stat3 and Stat5 are necessary for initial transformation. However, Stat5- but not Stat3-deletion induces G(0)\/G(1) cell cycle arrest and apoptosis of imatinib-sensitive and imatinib-resistant stable leukaemic cells in vitro. Accordingly, Stat5-abrogation led to effective elimination of myeloid and lymphoid leukaemia maintenance in vivo. Hence, we identified Stat5 as a vulnerable point in the oncogenic network downstream of Bcr\/Abl representing a case of non-oncogene addiction (NOA).","authors":"Hoelbl, A., Schuster, C., Kovacic, B., Zhu, B., Wickre, M., Hoelzl, MA., Fajmann, S., Grebien, F., Warsch, W., Stengl, G., Hennighausen, L., Poli, V., Beug, H., Moriggl, R., Sexl, V.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"EMBO Mol Med","volume":"2","issue":"3","page":"98-110","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28130172","title":"Brain-specific knockin of the pathogenic Tubb5 E401K allele causes defects in motor coordination and prepulse inhibition.","abstract":"The generation, migration, and differentiation of neurons requires the functional integrity of the microtubule cytoskeleton. Mutations in the tubulin gene family are known to cause various neurological diseases including lissencephaly, ocular motor disorders, polymicrogyria and amyotrophic lateral sclerosis. We have previously reported that mutations in TUBB5 cause microcephaly that is accompanied by severe intellectual impairment and motor delay. Here we present the characterization of a Tubb5 mouse model that allows for the conditional expression of the pathogenic E401K mutation. Homozygous knockin animals exhibit a severe reduction in brain size and in body weight. These animals do not show any significant impairment in general activity, anxiety, or in the acoustic startle response, however, present with notable defects in motor coordination. When assessed on the static rod apparatus mice took longer to orient and often lost their balance completely. Interestingly, mutant animals also showed defects in prepulse inhibition, a phenotype associated with sensorimotor gating and considered an endophenotype for schizophrenia. This study provides insight into the behavioral consequences of tubulin gene mutations.","authors":"Breuss, MW., Hansen, AH., Landler, L., Keays, DA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Behav Brain Res","volume":"323","issue":null,"page":"47-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16648823","title":"Histone modification patterns associated with the human X chromosome.","abstract":"X inactivation is associated with chromosome-wide establishment of inactive chromatin. Although this is classically regarded as facultative heterochromatin that is uniform in nature, the exact distribution of associated epigenetic marks is not well defined. Here we have analysed histone modifications in human somatic cells within two selected regions of the X chromosome. Intergenic, coding and promoter regions are segregated into differentially marked chromatin. H3K27me3 is most prominent in intergenic and silenced coding regions, but is associated with some active coding regions as well. Histone H3\/H4 acetylation and H3K4me3 are locally enriched at promoter regions but do not necessarily mark continuing transcription. Remarkably, H3K9me3 is predominant in coding regions of active genes, a phenomenon that is not restricted to the X chromosome. These results argue against the exclusiveness of individual marks to heterochromatin or euchromatin, but rather suggest that composite patterns of interdependent or mutually exclusive modifications together signal the gene expression status.","authors":"Brinkman, AB., Roelofsen, T., Pennings, SW., Martens, JH., Jenuwein, T., Stunnenberg, HG.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"EMBO Rep","volume":"7","issue":"6","page":"628-34","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16597702","title":"Filopodia formation in the absence of functional WAVE- and Arp2\/3-complexes.","abstract":"Cell migration is initiated by plasma membrane protrusions, in the form of lamellipodia and filopodia. The latter rod-like projections may exert sensory functions and are found in organisms as distant in evolution as mammals and amoeba such as Dictyostelium discoideum. In mammals, lamellipodia protrusion downstream of the small GTPase Rac1 requires a multimeric protein assembly, the WAVE-complex, which activates Arp2\/3-mediated actin filament nucleation and actin network assembly. A current model of filopodia formation postulates that these structures arise from a dendritic network of lamellipodial actin filaments by selective elongation and bundling. Here, we have analyzed filopodia formation in mammalian cells abrogated in expression of essential components of the lamellipodial actin polymerization machinery. Cells depleted of the WAVE-complex component Nck-associated protein 1 (Nap1), and, in consequence, of lamellipodia, exhibited normal filopodia protrusion. Likewise, the Arp2\/3-complex, which is essential for lamellipodia protrusion, is dispensable for filopodia formation. Moreover, genetic disruption of nap1 or the WAVE-orthologue suppressor of cAMP receptor (scar) in Dictyostelium was also ineffective in preventing filopodia protrusion. These data suggest that the molecular mechanism of filopodia formation is conserved throughout evolution from Dictyostelium to mammals and show that lamellipodia and filopodia formation are functionally separable.","authors":"Steffen, A., Faix, J., Resch, GP., Linkner, J., Wehland, J., Small, JV., Rottner, K., Stradal, TE.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Mol Biol Cell","volume":"17","issue":"6","page":"2581-91","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30498131","title":"Precocious expression of Blimp1 in B cells causes autoimmune disease with increased self-reactive plasma cells.","abstract":"The transcription factor Blimp1 is not only an essential regulator of plasma cells, but also a risk factor for the development of autoimmune disease in humans. Here, we demonstrate in the mouse that the <i>Prdm1<\/i> (Blimp1) gene was partially activated at the chromatin and transcription level in early B cell development, although mature <i>Prdm1<\/i> mRNA did not accumulate due to posttranscriptional regulation. By analyzing a mouse model that facilitated ectopic Blimp1 protein expression throughout B lymphopoiesis, we could demonstrate that Blimp1 impaired B cell development by interfering with the B cell gene expression program, while leading to an increased abundance of plasma cells by promoting premature plasmablast differentiation of immature and mature B cells. With progressing age, these mice developed an autoimmune disease characterized by the presence of autoantibodies and glomerulonephritis. Hence, these data identified ectopic Blimp1 expression as a novel mechanism, through which Blimp1 can act as a risk factor in the development of autoimmune disease.","authors":"B\u00f6nelt, P., W\u00f6hner, M., Minnich, M., Tagoh, H., Fischer, M., Jaritz, M., Kavirayani, A., Garimella, M., Karlsson, MC., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"EMBO J","volume":"38","issue":"2","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24782245","title":"Diversity and wiring variability of visual local neurons in the Drosophila medulla M6 stratum.","abstract":"Local neurons in the vertebrate retina are instrumental in transforming visual inputs to extract contrast, motion, and color information and in shaping bipolar-to-ganglion cell transmission to the brain. In Drosophila, UV vision is represented by R7 inner photoreceptor neurons that project to the medulla M6 stratum, with relatively little known of this downstream substrate. Here, using R7 terminals as references, we generated a 3D volume model of the M6 stratum, which revealed a retinotopic map for UV representations. Using this volume model as a common 3D framework, we compiled and analyzed the spatial distributions of more than 200 single M6-specific local neurons (M6-LNs). Based on the segregation of putative dendrites and axons, these local neurons were classified into two families, directional and nondirectional. Neurotransmitter immunostaining suggested a signal routing model in which some visual information is relayed by directional M6-LNs from the anterior to the posterior M6 and all visual information is inhibited by a diverse population of nondirectional M6-LNs covering the entire M6 stratum. Our findings suggest that the Drosophila medulla M6 stratum contains diverse LNs that form repeating functional modules similar to those found in the vertebrate inner plexiform layer.","authors":"Chin, AL., Lin, CY., Fu, TF., Dickson, BJ., Chiang, AS.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Comp Neurol","volume":"522","issue":"17","page":"3795-816","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25248984","title":"Whole-blood gene-expression profiles of cows infected with Mycobacterium avium subsp. paratuberculosis reveal changes in immune response and lipid metabolism.","abstract":"Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic debilitating disease affecting ruminants worldwide. In the present study, we aimed to determine the major gene networks and pathways underlying the immune response to MAP infection using whole-blood cells, as well as provide the potential transcriptional markers for identifying the status of MAP infection. We analyzed the transcriptional profiles of whole-blood cells of cattle identified and grouped according to the presence of MAP-specific antibodies and the MAP shed by them. The grouping was based on the results obtained by ELISA and PCR analyses as follows: i) Test1 group: MAP-negative results obtained by ELISA and positive results obtained by PCR; ii) Test2 group: MAP-positive results obtained by ELISA and negative results obtained by PCR; iii) Test3 group: MAP-positive results obtained by ELISA and positive results obtained by PCR; iv) uninfected control: MAP-negative results obtained both by ELISA and PCR analysis. The results showed down-regulated production and metabolism of reactive oxygen species in the Test1 group, activation of pathways related to the host-defense response against MAP (LXR\/RXR activation and complement system) in the Test2 and Test3 groups, and anti-inflammatory response (activation of IL-10 signaling pathway) only in the Test3 group. Our data indicate a balanced response that serves the immune-limiting mechanism while the host-defense responses are progressing.","authors":"Shin, MK., Park, HT., Shin, SW., Jung, M., Im, YB., Park, HE., Cho, YI., Yoo, HS.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Microbiol Biotechnol","volume":"25","issue":"2","page":"255-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16488867","title":"Condensin I stabilizes chromosomes mechanically through a dynamic interaction in live cells.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">16488867<\/PMID><DateCompleted><Year>2006<\/Year><Month>05<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2006<\/Year><Month>11<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>16<\/Volume><Issue>4<\/Issue><PubDate><Year>2006<\/Year><Month>Feb<\/Month><Day>21<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Condensin I stabilizes chromosomes mechanically through a dynamic interaction in live cells.<\/ArticleTitle><Pagination><MedlinePgn>333-44<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Restructuring chromatin into morphologically distinct chromosomes is essential for cell division, but the molecular mechanisms underlying this process are poorly understood. Condensin complexes have been proposed as key factors, although controversial conclusions about their contribution to chromosome structure were reached by different experimental approaches in fixed cells or cell extracts. Their function under physiological conditions still needs to be defined.","authors":"Gerlich, D., Hirota, T., Koch, B., Peters, JM., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr Biol","volume":"16","issue":"4","page":"333-44","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16541024","title":"Protein phosphatase 2A protects centromeric sister chromatid cohesion during meiosis I.","abstract":"Segregation of homologous maternal and paternal centromeres to opposite poles during meiosis I depends on post-replicative crossing over between homologous non-sister chromatids, which creates chiasmata and therefore bivalent chromosomes. Destruction of sister chromatid cohesion along chromosome arms due to proteolytic cleavage of cohesin's Rec8 subunit by separase resolves chiasmata and thereby triggers the first meiotic division. This produces univalent chromosomes, the chromatids of which are held together by centromeric cohesin that has been protected from separase by shugoshin (Sgo1\/MEI-S332) proteins. Here we show in both fission and budding yeast that Sgo1 recruits to centromeres a specific form of protein phosphatase 2A (PP2A). Its inactivation causes loss of centromeric cohesin at anaphase I and random segregation of sister centromeres at the second meiotic division. Artificial recruitment of PP2A to chromosome arms prevents Rec8 phosphorylation and hinders resolution of chiasmata. Our data are consistent with the notion that efficient cleavage of Rec8 requires phosphorylation of cohesin and that this is blocked by PP2A at meiosis I centromeres.","authors":"Riedel, CG., Katis, VL., Katou, Y., Mori, S., Itoh, T., Helmhart, W., G\u00e1lov\u00e1, M., Petronczki, M., Gregan, J., Cetin, B., Mudrak, I., Ogris, E., Mechtler, K., Pelletier, L., Buchholz, F., Shirahige, K., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Nature","volume":"441","issue":"7089","page":"53-61","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16495310","title":"Multiple roles of mesenchymal beta-catenin during murine limb patterning.","abstract":"Recently canonical Wnt signaling in the ectoderm has been shown to be required for maintenance of the apical ectodermal ridge (AER) and for dorsoventral signaling. Using conditional gain- and loss-of-function beta-catenin alleles, we have studied the role of mesenchymal beta-catenin activity during limb development. Here, we show that loss of beta-catenin results in limb truncations due to a defect in AER maintenance. Stabilization of beta-catenin also results in truncated limbs, caused by a premature regression of the AER. Concomitantly, in these limbs, the expression of Bmp2, Bmp4 and Bmp7, and of the Bmp target genes Msx1, Msx2 and gremlin, is expanded in the mesenchyme. Furthermore, we found that the expression of Lmx1b, a gene exclusively expressed in the dorsal limb mesenchyme and involved in dorsoventral patterning, is reduced upon loss of beta-catenin activity and is expanded ventrally in gain-of-function limbs. However, the known ectodermal regulators Wnt7a and engrailed 1 are expressed normally. This suggests that Lmx1b is also regulated, in part, by a beta-catenin-mediated Wnt signal, independent of the non-canoncial Wnt7a signaling pathway. In addition, loss of beta-catenin results in a severe agenesis of the scapula. Concurrently, the expression of two genes, Pax1 and Emx2, which have been implicated in scapula development, is lost in beta-catenin loss-of-function limbs; however, only Emx2 is upregulated in gain-of-function limbs. Mesenchymal beta-catenin activity is therefore required for AER maintenance, and for normal expression of Lmx1b and Emx2.","authors":"Hill, TP., Taketo, MM., Birchmeier, W., Hartmann, C.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Development","volume":"133","issue":"7","page":"1219-29","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33131609","title":"Human recombinant soluble ACE2 in severe COVID-19.","abstract":null,"authors":"Zoufaly, A., Poglitsch, M., Aberle, JH., Hoepler, W., Seitz, T., Traugott, M., Grieb, A., Pawelka, E., Laferl, H., Wenisch, C., Neuhold, S., Haider, D., Stiasny, K., Bergthaler, A., Puchhammer-Stoeckl, E., Mirazimi, A., Montserrat, N., Zhang, H., Slutsky, AS., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Lancet Respir Med","volume":"8","issue":"11","page":"1154-1158","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24794707","title":"MLL3 is a haploinsufficient 7q tumor suppressor in acute myeloid leukemia.","abstract":"Recurring deletions of chromosome 7 and 7q [-7\/del(7q)] occur in myelodysplastic syndromes and acute myeloid leukemia (AML) and are associated with poor prognosis. However, the identity of functionally relevant tumor suppressors on 7q remains unclear. Using RNAi and CRISPR\/Cas9 approaches, we show that an \u223c50% reduction in gene dosage of the mixed lineage leukemia 3 (MLL3) gene, located on 7q36.1, cooperates with other events occurring in -7\/del(7q) AMLs to promote leukemogenesis. Mll3 suppression impairs the differentiation of HSPC. Interestingly, Mll3-suppressed leukemias, like human -7\/del(7q) AMLs, are refractory to conventional chemotherapy but sensitive to the BET inhibitor JQ1. Thus, our mouse model functionally validates MLL3 as a haploinsufficient 7q tumor suppressor and suggests a therapeutic option for this aggressive disease.","authors":"Chen, C., Liu, Y., Rappaport, AR., Kitzing, T., Schultz, N., Zhao, Z., Shroff, AS., Dickins, RA., Vakoc, CR., Bradner, JE., Stock, W., LeBeau, MM., Shannon, KM., Kogan, S., Zuber, J., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cancer Cell","volume":"25","issue":"5","page":"652-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16423552","title":"Jun signalling in the epidermis: From developmental defects to psoriasis and skin tumors.","abstract":"The Jun proteins Jun, JunB and JunD are core members of activator protein-1 (AP-1), a dimeric transcription factor complex consisting of homo- and heterodimers of the Jun, Fos, activating transcription factor (ATF) and musculoaponeurotic fibrosarcoma (Maf) families. Growth factors, hormones and a variety of environmental stresses activate mitogen activated protein kinase (MAPK) cascades that enhance Jun\/AP-1 activity, e.g. through phosphorylation thereby regulating cell proliferation, differentiation, transformation and\/or apoptosis. Embryonic lethality of various AP-1 knock-outs, e.g. for Jun, JunB, Fra-1 and Fra-2 largely prevented functional studies in vivo. Therefore, conditional knock-out strategies, in particular for the epidermis, have become an important model to study the regulation and function of AP-1 subunits in physiological and pathological processes in vivo. Jun is regarded as a positive regulator of keratinocyte proliferation\/differentiation during development and in skin cancer through its direct transcriptional effect on epidermal growth factor receptor (EGFR) expression. In contrast, JunB can antagonize proliferation of keratinocytes and hematopoietic stem cells. Furthermore, it has been demonstrated in patient's samples and an inducible mouse model that down-regulation of JunB\/AP-1 in keratinocytes is one initiating event in the aetiology of psoriasis which is characterized by increased cell proliferation and deregulated cytokine expression.","authors":"Zenz, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Int J Biochem Cell Biol","volume":"38","issue":"7","page":"1043-9","pdf":null,"JrId":"8630","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30982596","title":"Volumetric Ca<sup>2+<\/sup> Imaging in the Mouse Brain Using Hybrid Multiplexed Sculpted Light Microscopy.","abstract":"Calcium imaging using two-photon scanning microscopy has become an essential tool in neuroscience. However, in its typical implementation, the tradeoffs between fields of view, acquisition speeds, and depth restrictions in scattering brain tissue pose severe limitations. Here, using an integrated systems-wide optimization approach combined with multiple technical innovations, we introduce a new design paradigm for optical microscopy based on maximizing biological information while maintaining the fidelity of obtained neuron signals. Our modular design utilizes hybrid multi-photon acquisition and allows volumetric recording of neuroactivity at single-cell resolution within up to 1\u00a0\u00d7 1\u00a0\u00d7 1.22\u00a0mm volumes at up to 17\u00a0Hz in awake behaving mice. We establish the capabilities and potential of the different configurations of our imaging system at depth and across brain regions by applying it to in\u00a0vivo recording of up to 12,000 neurons in mouse auditory cortex, posterior parietal cortex, and hippocampus.","authors":"Weisenburger, S., Tejera, F., Demas, J., Chen, B., Manley, J., Sparks, FT., Mart\u00ednez Traub, F., Daigle, T., Zeng, H., Losonczy, A., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell","volume":"177","issue":"4","page":"1050-1066.e14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24760958","title":"qcML: an exchange format for quality control metrics from mass spectrometry experiments.","abstract":"Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http:\/\/code.google.com\/p\/qcml.","authors":"Walzer, M., Pernas, LE., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., van den Toorn, HW., Staes, A., Vandenbussche, J., Mazanek, M., Taus, T., Scheltema, RA., Kelstrup, CD., Gatto, L., van Breukelen, B., Aiche, S., Valkenborg, D., Laukens, K., Lilley, KS., Olsen, JV., Heck, AJ., Mechtler, K., Aebersold, R., Gevaert, K., Vizca\u00edno, JA., Hermjakob, H., Kohlbacher, O., Martens, L.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mol Cell Proteomics","volume":"13","issue":"8","page":"1905-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16456832","title":"Microscopy of the Drosophila facet eye: vademecum for standardized fixation, embedding, and sectioning.","abstract":"We describe here a standardized method for histological processing of the Drosophila compound eye. Primary fixation with 2.5% glutaraldehyde, obligatorily supplemented with 0.1% household detergent regularly yielded the best structural preservation, as compared with that of other, more complicated fixation protocols tested. Notably, it proved indispensable not only to cut off the fly's head to facilitate the penetration of the reagents but also to open the chitinous head capsule. For this, we locally pierced the cuticle between the eyes, leaving the head structurally almost intact, a prerequisite for precisely aligning the head for microtomy. We developed a two-step re-embedding procedure allowing for exact and reproducible orientation of the fly heads. Thus, highly comparable series of cross sections through a representative number of ommatidia were obtained. The feasibility of our embedding and sectioning approach is finally demonstrated by three-dimensional reconstructions of the middle segments of the R1, R7, and R8 photoreceptor cells. We present reconstructions from structurally modified ommatidia, as seen after RNAi-mediated depletion of the endosomal adaptor protein p14, and from normal ommatidia corresponding to the wildtype.","authors":"Hess, MW., Pfaller, K., Hamp\u00f6lz, B., Longato, S., Teis, D., Fl\u00f6rl, A., Gutleben, K., Huber, LA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Microsc Res Tech","volume":"69","issue":"2","page":"93-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25144871","title":"Measuring the functional organization of the neocortex at large and small scales.","abstract":"Sensory cortices are commonly structured topographically; however, the extent to which this organization principle is preserved at the microcircuit level is debated. In this issue of Neuron, Issa et\u00a0al. (2014) revisit this question by combining calcium imaging in awake mice at large scales encompassing the whole auditory cortex and small scales providing single-cell resolution.","authors":"Aschauer, DF., Rumpel, S.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Neuron","volume":"83","issue":"4","page":"756-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16387293","title":"A germline GFP transgenic axolotl and its use to track cell fate: dual origin of the fin mesenchyme during development and the fate of blood cells during regeneration.","abstract":"The development of transgenesis in axolotls is crucial for studying development and regeneration as it would allow for long-term cell fate tracing as well as gene expression analysis. We demonstrate here that plasmid injection into the one-cell stage axolotl embryo generates mosaic transgenic animals that display germline transmission of the transgene. The inclusion of SceI meganuclease in the injections (Thermes, V., Grabher, C., Ristoratore, F., Bourrat, F., Choulika, A., Wittbrodt, J., Joly, J.S., 2002. I-SceI meganuclease mediates highly efficient transgenesis in fish. Mech. Dev. 118, 91-98) resulted in a higher percentage of F0 animals displaying strong expression throughout the body. This represents the first demonstration in the axolotl of germline transmission of a transgene. Using this technique we have generated a germline transgenic animal expressing GFP ubiquitously in all tissues examined. We have used this animal to study cell fate in the dorsal fin during development. We have uncovered a contribution of somite cells to dorsal fin mesenchyme in the axolotl, which was previously assumed to derive solely from neural crest. We have also studied the role of blood during tail regeneration by transplanting the ventral blood-forming region from GFP+ embryos into unlabeled hosts. During tail regeneration, we do not observe GFP+ cells contributing to muscle or nerve, suggesting that during tail regeneration blood stem cells do not undergo significant plasticity.","authors":"Sobkow, L., Epperlein, HH., Herklotz, S., Straube, WL., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Dev Biol","volume":"290","issue":"2","page":"386-97","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28340914","title":"Editorial overview: Cell reprogramming, regeneration and repair.","abstract":null,"authors":"Reddien, PW., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Curr Opin Genet Dev","volume":"40","issue":null,"page":"iv-vi","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16356770","title":"RANKL-RANK signaling in osteoclastogenesis and bone disease.","abstract":"Hundreds of millions of people worldwide are affected by bone-related diseases, such as osteoporosis and rheumatoid arthritis. Understanding the molecular mechanisms of bone metabolism is crucial for developing novel drugs for treating such diseases. In particular, genetic experiments showing that the receptor activator of NF-kappaB (RANK), its ligand RANKL, and the decoy receptor OPG are essential, central regulators of osteoclast development and osteoclast function were significant turning points in our understanding of bone diseases. RANKL-RANK signaling activates a variety of downstream signaling pathways required for osteoclast development. Moreover, molecular cross-talk between RANKL-RANK and other ligand-receptor systems fine-tunes bone homeostasis in normal physiology and disease. Designing novel drugs that target RANKL-RANK and their signaling pathways in osteoclasts could potentially revolutionize the treatment of many diseases associated with bone loss such as arthritis, tooth loss, cancer metastases or osteoporosis.","authors":"Wada, T., Nakashima, T., Hiroshi, N., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Trends Mol Med","volume":"12","issue":"1","page":"17-25","pdf":null,"JrId":"22040","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30870096","title":"Spindle mechanics and chromosome segregation.","abstract":null,"authors":"Toli\u0107, IM., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mol Biol Cell","volume":"30","issue":"6","page":"735-736","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25100604","title":"ZPK\/DLK and MKK4 form the critical gateway to axotomy-induced motoneuron death in neonates.","abstract":"Motoneuron death after transection of the axons (axotomy) in neonates is believed to share the same mechanistic bases as naturally occurring programmed cell death during development. The c-Jun N-terminal kinase pathway is activated in both forms of motoneuron death, but it remains unknown to what extent these two forms of motoneuron death depend on this pathway and which upstream kinases are involved. We found that numbers of facial motoneurons are doubled in neonatal mice deficient in either ZPK\/DLK (zipper protein kinase, also known as dual leucine zipper kinase), a mitogen-activated protein kinase kinase kinase, or in MKK4\/MAP2K4, a mitogen-activated protein kinase kinase directly downstream of ZPK\/DLK, and that the facial motoneurons in those mutant mice are completely resistant to axotomy-induced death. Conditional deletion of MKK4\/MAP2K4 in neurons further suggested that ZPK\/DLK and MKK4\/MAP2K4-dependent mechanisms underlying axotomy-induced death are motoneuron autonomous. Nevertheless, quantitative analysis of facial motoneurons during embryogenesis revealed that both ZPK\/DLK and MKK4\/MAP2K4-dependent and -independent mechanisms contribute to developmental elimination of excess motoneurons. In contrast to MKK4\/MAP2K4, mice lacking MKK7\/MAP2K7, another mitogen-activated protein kinase kinase directly downstream of ZPK\/DLK, conditionally in neurons did not have excess facial motoneurons. However, some MKK7\/MAP2K7-deficient facial motoneurons were resistant to axotomy-induced death, indicating a synergistic effect of MKK7\/MAP2K7 on axotomy-induced death of these facial motoneurons. Together, our study provides compelling evidence for the pivotal roles of the ZPK\/DLK and MKK4\/MAP2K4-dependent mechanism in axotomy-induced motoneuron death in neonates and also demonstrates that axotomy-induced motoneuron death is not identical to developmental motoneuron death with respect to the involvement of ZPK\/DLK, MKK4\/MAP2K4 and MKK7\/MAP2K7.","authors":"Itoh, T., Horiuchi, M., Ikeda, RH., Xu, J., Bannerman, P., Pleasure, D., Penninger, JM., Tournier, C., Itoh, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Neurosci","volume":"34","issue":"32","page":"10729-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16301171","title":"Mammalian inscuteable regulates spindle orientation and cell fate in the developing retina.","abstract":"During mammalian neurogenesis, progenitor cells can divide with the mitotic spindle oriented parallel or perpendicular to the surface of the neuroepithelium. Perpendicular divisions are more likely to be asymmetric and generate one progenitor and one neuronal precursor. Whether the orientation of the mitotic spindle actually determines their asymmetric outcome is unclear. Here, we characterize a mammalian homolog of Inscuteable (mInsc), a key regulator of spindle orientation in Drosophila. mInsc is expressed temporally and spatially in a manner that suggests a role in orienting the mitotic spindle in the developing nervous system. Using retroviral RNAi in rat retinal explants, we show that downregulation of mInsc inhibits vertical divisions. This results in enhanced proliferation, consistent with a higher frequency of symmetric divisions generating two proliferating cells. Our results suggest that the orientation of neural progenitor divisions is important for cell fate specification in the retina and determines their symmetric or asymmetric outcome.","authors":"Zigman, M., Cayouette, M., Charalambous, C., Schleiffer, A., Hoeller, O., Dunican, D., McCudden, CR., Firnberg, N., Barres, BA., Siderovski, DP., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Neuron","volume":"48","issue":"4","page":"539-45","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30304679","title":"Mild Impairment of Mitochondrial OXPHOS Promotes Fatty Acid Utilization in POMC Neurons and Improves Glucose Homeostasis in Obesity.","abstract":"Mitochondrial oxidative phosphorylation (OXPHOS) and substrate utilization critically regulate the function of hypothalamic proopiomelanocortin (POMC)-expressing neurons. Here, we demonstrate that inactivation of apoptosis-inducing factor (AIF) in POMC neurons mildly impairs mitochondrial respiration and decreases firing of POMC neurons in lean mice. In contrast, under diet-induced obese conditions, POMC-Cre-specific inactivation of AIF prevents obesity-induced silencing of POMC neurons, translating into improved glucose metabolism, improved leptin, and insulin sensitivity, as well as increased energy expenditure in AIF<sup>\u0394POMC<\/sup> mice. On a cellular level, AIF deficiency improves mitochondrial morphology, facilitates the utilization of\u00a0fatty acids for mitochondrial respiration, and increases reactive oxygen species (ROS) formation\u00a0in POMC neurons from obese mice, ultimately leading to restored POMC firing upon HFD feeding. Collectively, partial impairment of mitochondrial function shifts substrate utilization of POMC neurons from glucose to fatty acid metabolism and restores their firing properties, resulting in improved\u00a0systemic glucose and energy metabolism in obesity.","authors":"Timper, K., Paeger, L., S\u00e1nchez-Lasheras, C., Varela, L., Jais, A., Nolte, H., Vogt, MC., Hausen, AC., Heilinger, C., Evers, N., Pospisilik, JA., Penninger, JM., Taylor, EB., Horvath, TL., Kloppenburg, P., Br\u00fcning, JC.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell Rep","volume":"25","issue":"2","page":"383-397.e10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8621795","title":"Identification of cardiac myosin peptides capable of inducing autoimmune myocarditis in BALB\/c mice.","abstract":"Immunization with cardiac myosin induces T cell-mediated myocarditis in genetically predisposed mice and serves as a model for autoimmune heart disease. This study was undertaken to identify pathogenic epitopes on the myosin molecule. Our approach was based on the comparison of the pathogenicity between cardiac (alpha-)myosin and soleus muscle (beta-)myosin. We show that alpha-myosin is the immunodominant isoform and induces myocarditis at high severity and prevalence whereas beta-myosin induces little disease. Therefore the immunodominant epitopes of alpha-myosin must reside in regions of different amino acid sequence between alpha- and beta-myosin isoforms. Cardiac myosin peptides corresponding to these regions of difference were synthesized and tested for their ability to induce inflammatory heart disease. Three pathogenic peptides were identified. One peptide that is located in the head portion of the molecule induced severe myocarditis, whereas two others that reside in the rod portion possessed only minor pathogenicity. The identification of pathogenic epitopes on the cardiac myosin molecule will allow detailed studies on the recognition of this antigen by the immune system and might be used to downmodulate ongoing heart disease.","authors":"Pummerer, CL., Luze, K., Gr\u00e4ssl, G., Bachmaier, K., Offner, F., Burrell, SK., Lenz, DM., Zamborelli, TJ., Penninger, JM., Neu, N.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"J Clin Invest","volume":"97","issue":"9","page":"2057-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1996-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31202577","title":"Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity.","abstract":"Topoisomerase II (TOP2) relieves torsional stress by forming transient cleavage complex intermediates (TOP2ccs) that contain TOP2-linked DNA breaks (DSBs). While TOP2ccs are normally reversible, they can be \"trapped\" by chemotherapeutic drugs such as etoposide and subsequently converted into irreversible TOP2-linked DSBs. Here, we have quantified etoposide-induced trapping of TOP2ccs, their conversion into irreversible TOP2-linked DSBs, and their processing during DNA repair genome-wide, as a function of time. We find that while TOP2 chromatin localization and trapping is independent of transcription, it requires pre-existing binding of cohesin to DNA. In contrast, the conversion of trapped TOP2ccs to irreversible DSBs during DNA repair is accelerated 2-fold at transcribed loci relative to non-transcribed loci. This conversion is dependent on proteasomal degradation and TDP2 phosphodiesterase activity. Quantitative modeling shows that only two features of pre-existing chromatin structure-namely, cohesin binding and transcriptional activity-can be used to predict the kinetics of TOP2-induced DSBs.","authors":"Canela, A., Maman, Y., Huang, SN., Wutz, G., Tang, W., Zagnoli-Vieira, G., Callen, E., Wong, N., Day, A., Peters, JM., Caldecott, KW., Pommier, Y., Nussenzweig, A.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mol Cell","volume":"75","issue":"2","page":"252-266.e8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7552164","title":"Limb development. The budding role of FGF.","abstract":"Implantation of beads soaked in fibroblast growth factor into the flank of a chick embryo causes extra limbs to be formed, suggesting that FGF is important in initiating limb buds.","authors":"Tanaka, EM., Gann, AF.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Curr Biol","volume":"5","issue":"6","page":"594-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1995-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19934006","title":"Human recombinant ACE2 reduces the progression of diabetic nephropathy.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19934006<\/PMID><DateCompleted><Year>2010<\/Year><Month>02<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1939-327X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>59<\/Volume><Issue>2<\/Issue><PubDate><Year>2010<\/Year><Month>Feb<\/Month><\/PubDate><\/JournalIssue><Title>Diabetes<\/Title><ISOAbbreviation>Diabetes<\/ISOAbbreviation><\/Journal><ArticleTitle>Human recombinant ACE2 reduces the progression of diabetic nephropathy.<\/ArticleTitle><Pagination><MedlinePgn>529-38<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.2337\/db09-1218<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">Diabetic nephropathy is one of the most common causes of end-stage renal failure. Inhibition of ACE2 function accelerates diabetic kidney injury, whereas renal ACE2 is downregulated in diabetic nephropathy. We examined the ability of human recombinant ACE2 (hrACE2) to slow the progression of diabetic kidney injury.","authors":"Oudit, GY., Liu, GC., Zhong, J., Basu, R., Chow, FL., Zhou, J., Loibner, H., Janzek, E., Schuster, M., Penninger, JM., Herzenberg, AM., Kassiri, Z., Scholey, JW.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Diabetes","volume":"59","issue":"2","page":"529-38","pdf":null,"JrId":"3397","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19416522","title":"Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19416522<\/PMID><DateCompleted><Year>2009<\/Year><Month>08<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>10<\/Volume><Issue>5<\/Issue><PubDate><Year>2009<\/Year><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila.<\/ArticleTitle><Pagination><MedlinePgn>R49<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/gb-2009-10-5-r49<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Most arthropods contain R1 and R2 retrotransposons that specifically insert into the 28S rRNA genes. Here, the sequencing reads from 12 Drosophila genomes have been used to address two questions concerning these elements. First, to what extent is the evolution of these elements subject to the concerted evolution process that is responsible for sequence homogeneity among the different copies of rRNA genes? Second, how precise are the target DNA cleavages and priming of DNA synthesis used by these elements?","authors":"Stage, DE., Eickbush, TH.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genome Biol","volume":"10","issue":"5","page":"R49","pdf":null,"JrId":"21904","fulltextlink":null,"preprintlink":null,"articledate":"2009-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19358738","title":"Evolutionary rates and centrality in the yeast gene regulatory network.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19358738<\/PMID><DateCompleted><Year>2009<\/Year><Month>09<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>10<\/Volume><Issue>4<\/Issue><PubDate><Year>2009<\/Year><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Evolutionary rates and centrality in the yeast gene regulatory network.<\/ArticleTitle><Pagination><MedlinePgn>R35<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/gb-2009-10-4-r35<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Transcription factors play a fundamental role in regulating physiological responses and developmental processes. Here we examine the evolution of the yeast transcription factors in the context of the structure of the gene regulatory network.","authors":"Jovelin, R., Phillips, PC.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genome Biol","volume":"10","issue":"4","page":"R35","pdf":null,"JrId":"21904","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24939936","title":"Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia.","abstract":"Loss-of-function mutations in hematopoietic transcription factors including PAX5 occur in most cases of B-progenitor acute lymphoblastic leukemia (B-ALL), a disease characterized by the accumulation of undifferentiated lymphoblasts. Although PAX5 mutation is a critical driver of B-ALL development in mice and humans, it remains unclear how its loss contributes to leukemogenesis and whether ongoing PAX5 deficiency is required for B-ALL maintenance. Here we used transgenic RNAi to reversibly suppress endogenous Pax5 expression in the hematopoietic compartment of mice, which cooperates with activated signal transducer and activator of transcription 5 (STAT5) to induce B-ALL. In this model, restoring endogenous Pax5 expression in established B-ALL triggers immunophenotypic maturation and durable disease remission by engaging a transcriptional program reminiscent of normal B-cell differentiation. Notably, even brief Pax5 restoration in B-ALL cells causes rapid cell cycle exit and disables their leukemia-initiating capacity. These and similar findings in human B-ALL cell lines establish that Pax5 hypomorphism promotes B-ALL self-renewal by impairing a differentiation program that can be re-engaged despite the presence of additional oncogenic lesions. Our results establish a causal relationship between the hallmark genetic and phenotypic features of B-ALL and suggest that engaging the latent differentiation potential of B-ALL cells may provide new therapeutic entry points.","authors":"Liu, GJ., Cimmino, L., Jude, JG., Hu, Y., Witkowski, MT., McKenzie, MD., Kartal-Kaess, M., Best, SA., Tuohey, L., Liao, Y., Shi, W., Mullighan, CG., Farrar, MA., Nutt, SL., Smyth, GK., Zuber, J., Dickins, RA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genes Dev","volume":"28","issue":"12","page":"1337-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8642780","title":"Cardiac myosin-induced myocarditis: target recognition by autoreactive T cells requires prior activation of cardiac interstitial cells.","abstract":"Immunization with cardiac myosin causes T cell-mediated myocarditis in genetically predisposed mice and serves as a model for autoimmune heart disease. The normal heart is not susceptible to T cells autoreactive with cardiac myosin; therefore, we investigated the conditions that are required to facilitate recognition of the target tissue. A.SW mice were immunized with cardiac myosin on Days 0 and 7. Major histocompatibility antigen (MHC Ag) and intercellular adhesion molecule-1 (ICAM-1) expression in the heart tissue was investigated by immunohistochemical techniques shortly before disease onset (ie, on Day 9). At this time point, cardiac interstitial cells expressing class II but not class I MHC Ag were significantly increased. In addition, endothelial ICAM-1 expression was strongly up-regulated. Myofibers did not show expression of these markers, and T cells were virtually absent. Because lipopolysaccaride (LPS) induced a similar distribution of class II MHC Ag and ICAM-1 in the myocardial tissue and because these molecules could be crucial to disease onset, we determined whether treatment with this immunomodulator renders the heart susceptible to passively transferred myosin-reactive T cells. We found that concanavalin A-activated spleen cells from myosin-immunized donors induced myocarditis in LPS-primed recipients, whereas normal mice were resistant to the injection of such cells. Increased class II MHC Ag expression after LPS-treatment was mediated by TNF because LPS-primed mice genetically lacking the TNF receptor failed to increase class II MHC Ag expression in the heart tissue. In summary, these results suggest that in cardiac myosin-induced myocarditis, expression of interstitial class II MHC Ag and\/or endothelial ICAM-1 is a prerequisite for target organ recognition by autoreactive T cells.","authors":"Pummerer, CL., Gr\u00e4ssl, G., Sailer, M., Bachmaier, KW., Penninger, JM., Neu, N.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Lab Invest","volume":"74","issue":"5","page":"845-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1996-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19190755","title":"Liver cancer-derived hepatitis C virus core proteins shift TGF-beta responses from tumor suppression to epithelial-mesenchymal transition.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19190755<\/PMID><DateCompleted><Year>2009<\/Year><Month>07<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>4<\/Volume><Issue>2<\/Issue><PubDate><Year>2009<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Liver cancer-derived hepatitis C virus core proteins shift TGF-beta responses from tumor suppression to epithelial-mesenchymal transition.<\/ArticleTitle><Pagination><MedlinePgn>e4355<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0004355<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Chronic hepatitis C virus (HCV) infection and associated liver cirrhosis represent a major risk factor for hepatocellular carcinoma (HCC) development. TGF-beta is an important driver of liver fibrogenesis and cancer; however, its actual impact in human cancer progression is still poorly known. The aim of this study was to investigate the role of HCC-derived HCV core natural variants on cancer progression through their impact on TGF-beta signaling.","authors":"Battaglia, S., Benzoubir, N., Nobilet, S., Charneau, P., Samuel, D., Zignego, AL., Atfi, A., Br\u00e9chot, C., Bourgeade, MF.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS One","volume":"4","issue":"2","page":"e4355","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28143932","title":"Dissection of neuronal gap junction circuits that regulate social behavior in <i>Caenorhabditis elegans<\/i>.","abstract":"A hub-and-spoke circuit of neurons connected by gap junctions controls aggregation behavior and related behavioral responses to oxygen, pheromones, and food in <i>Caenorhabditis elegans<\/i> The molecular composition of the gap junctions connecting RMG hub neurons with sensory spoke neurons is unknown. We show here that the innexin gene <i>unc-9<\/i> is required in RMG hub neurons to drive aggregation and related behaviors, indicating that UNC-9-containing gap junctions mediate RMG signaling. To dissect the circuit in detail, we developed methods to inhibit <i>unc-9<\/i>-based gap junctions with dominant-negative <i>unc-1<\/i> transgenes. <i>unc-1(dn)<\/i> alters a stomatin-like protein that regulates <i>unc-9<\/i> electrical signaling; its disruptive effects can be rescued by a constitutively active UNC-9::GFP protein, demonstrating specificity. Expression of <i>unc-1(dn)<\/i> in RMG hub neurons, ADL or ASK pheromone-sensing neurons, or URX oxygen-sensing neurons disrupts specific elements of aggregation-related behaviors. In ADL, <i>unc-1(dn)<\/i> has effects opposite to those of tetanus toxin light chain, separating the roles of ADL electrical and chemical synapses. These results reveal roles of gap junctions in a complex behavior at cellular resolution and provide a tool for similar exploration of other gap junction circuits.","authors":"Jang, H., Levy, S., Flavell, SW., Mende, F., Latham, R., Zimmer, M., Bargmann, CI.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Proc Natl Acad Sci U S A","volume":"114","issue":"7","page":"E1263-E1272","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24906153","title":"The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila.","abstract":"Argonaute proteins of the PIWI clade are central to transposon silencing in animal gonads. Their target specificity is defined by 23-30 nt PIWI interacting RNAs (piRNAs), which mostly originate from discrete genomic loci termed piRNA clusters. Here, we show that a complex composed of Rhino, Deadlock, and Cutoff (RDC) defines dual-strand piRNA clusters genome-wide in Drosophila ovaries. The RDC is anchored to H3K9me3-marked chromatin in part via Rhino's chromodomain. Depletion of Piwi results in loss of the RDC and small RNAs at a subset of piRNA clusters, demonstrating a feedback loop between Piwi and piRNA source loci. Intriguingly, profiles of RNA polymerase II occupancy, nascent transcription, and steady-state RNA levels reveal that the RDC licenses noncanonical transcription of dual-strand piRNA clusters. Likely, this process involves 5' end protection of nascent RNAs and suppression of transcription termination. Our data provide key insight into the regulation and evolution of piRNA clusters.","authors":"Mohn, F., Sienski, G., Handler, D., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell","volume":"157","issue":"6","page":"1364-1379","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24648340","title":"Functional network pipeline reveals genetic determinants associated with in situ lymphocyte proliferation and survival of cancer patients.","abstract":"The tumor microenvironment is host to a complex network of cytokines that contribute to shaping the intratumoral immune reaction. Chromosomal gains and losses, coupled with expression analysis, of 59 cytokines and receptors and their functional networks were investigated in colorectal cancers. Changes in local expression for 13 cytokines were shown. Metastatic patients exhibited an increased frequency of deletions of cytokines from chromosome 4. Interleukin 15 (IL15) deletion corresponded with decreased IL15 expression, a higher risk of tumor recurrence, and reduced patient survival. Decreased IL15 expression affected the local proliferation of B and T lymphocytes. Patients with proliferating B and T cells at the invasive margin and within the tumor center had significantly prolonged disease-free survival. These results delineate chromosomal instability as a mechanism of modulating local cytokine expression in human tumors and underline the major role of IL15. Our data provide further mechanisms resulting in changes of specific immune cell densities within the tumor, and the importance of local active lymphocyte proliferation for patient survival.","authors":"Mlecnik, B., Bindea, G., Angell, HK., Sasso, MS., Obenauf, AC., Fredriksen, T., Lafontaine, L., Bilocq, AM., Kirilovsky, A., Tosolini, M., Waldner, M., Berger, A., Fridman, WH., Rafii, A., Valge-Archer, V., Pag\u00e8s, F., Speicher, MR., Galon, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Sci Transl Med","volume":"6","issue":"228","page":"228ra37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30696984","title":"Publisher Correction: Application and optimization of CRISPR-Cas9-mediated genome engineering in axolotl (Ambystoma mexicanum).","abstract":"In the version of this protocol originally published, the recipe for CAS9 buffer was incorrectly identified as a recipe for sodium acetate solution, and vice versa. These errors have been corrected in the PDF and HTML versions of the paper.","authors":"Fei, JF., Lou, WP., Knapp, D., Murawala, P., Gerber, T., Taniguchi, Y., Nowoshilow, S., Khattak, S., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Protoc","volume":"14","issue":"8","page":"2597","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26779600","title":"Blimp-1 controls plasma cell function through the regulation of immunoglobulin secretion and the unfolded protein response.","abstract":"Plasma cell differentiation requires silencing of B cell transcription, while it establishes antibody-secretory function and long-term survival. The transcription factors Blimp-1 and IRF4 are essential for the generation of plasma cells; however, their function in mature plasma cells has remained elusive. We found that while IRF4 was essential for the survival of plasma cells, Blimp-1 was dispensable for this. Blimp-1-deficient plasma cells retained their transcriptional identity but lost the ability to secrete antibody. Blimp-1 regulated many components of the unfolded protein response (UPR), including XBP-1 and ATF6. The overlap in the functions of Blimp-1 and XBP-1 was restricted to that response, with Blimp-1 uniquely regulating activity of the kinase mTOR and the size of plasma cells. Thus, Blimp-1 was required for the unique physiological ability of plasma cells that enables the secretion of protective antibody.","authors":"Tellier, J., Shi, W., Minnich, M., Liao, Y., Crawford, S., Smyth, GK., Kallies, A., Busslinger, M., Nutt, SL.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Immunol","volume":"17","issue":"3","page":"323-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16279839","title":"Systematic discovery of new recognition peptides mediating protein interaction networks.","abstract":"Many aspects of cell signalling, trafficking, and targeting are governed by interactions between globular protein domains and short peptide segments. These domains often bind multiple peptides that share a common sequence pattern, or \"linear motif\" (e.g., SH3 binding to PxxP). Many domains are known, though comparatively few linear motifs have been discovered. Their short length (three to eight residues), and the fact that they often reside in disordered regions in proteins makes them difficult to detect through sequence comparison or experiment. Nevertheless, each new motif provides critical molecular details of how interaction networks are constructed, and can explain how one protein is able to bind to very different partners. Here we show that binding motifs can be detected using data from genome-scale interaction studies, and thus avoid the normally slow discovery process. Our approach based on motif over-representation in non-homologous sequences, rediscovers known motifs and predicts dozens of others. Direct binding experiments reveal that two predicted motifs are indeed protein-binding modules: a DxxDxxxD protein phosphatase 1 binding motif with a KD of 22 microM and a VxxxRxYS motif that binds Translin with a KD of 43 microM. We estimate that there are dozens or even hundreds of linear motifs yet to be discovered that will give molecular insight into protein networks and greatly illuminate cellular processes.","authors":"Neduva, V., Linding, R., Su-Angrand, I., Stark, A., de Masi, F., Gibson, TJ., Lewis, J., Serrano, L., Russell, RB.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"PLoS Biol","volume":"3","issue":"12","page":"e405","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2006-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24379967","title":"Effect of Physical Activity on Symptoms of Morphine Addiction in Rats, after and before of Lesion of the mPFC Area.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24379967<\/PMID><DateCompleted><Year>2013<\/Year><Month>12<\/Month><Day>31<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>10<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">2008-3866<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>16<\/Volume><Issue>10<\/Issue><PubDate><Year>2013<\/Year><Month>Oct<\/Month><\/PubDate><\/JournalIssue><Title>Iranian journal of basic medical sciences<\/Title><ISOAbbreviation>Iran J Basic Med Sci<\/ISOAbbreviation><\/Journal><ArticleTitle>Effect of Physical Activity on Symptoms of Morphine Addiction in Rats, after and before of Lesion of the mPFC Area.<\/ArticleTitle><Pagination><MedlinePgn>1091-9<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"OBJECTIVE(S)\" NlmCategory=\"OBJECTIVE\">Drug addiction is one of the fastest growing social problems that researchers, for many years, have been trying to find proper strategies for its prevention and treatment. Short-term physical activity is considered as acceptable for the treatment and prevention of addiction. On the other hand, prefrontal cortex is known to be responsible for many of the complex behavioral responses, especially those relevant to addiction and drug abuse. In this study, the effects of short-term physical activity (treadmill running) on withdrawal symptoms in rats, with or without medial Prefrontal Cortex (mPFC) area was evaluated.","authors":"Saedi Marghmaleki, V., Alaei, HA., Azizi Malekabadi, H., Pilehvarian, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Iran J Basic Med Sci","volume":"16","issue":"10","page":"1091-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28263295","title":"Prediction of potent shRNAs with a sequential classification algorithm.","abstract":"We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel data sets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a given gene. Combined with an optimized miR-E backbone, &gt;90% of high-scoring SplashRNA predictions trigger &gt;85% protein knockdown when expressed from a single genomic integration. SplashRNA can significantly improve the accuracy of loss-of-function genetics studies and facilitates the generation of compact shRNA libraries.","authors":"Pelossof, R., Fairchild, L., Huang, CH., Widmer, C., Sreedharan, VT., Sinha, N., Lai, DY., Guan, Y., Premsrirut, PK., Tschaharganeh, DF., Hoffmann, T., Thapar, V., Xiang, Q., Garippa, RJ., R\u00e4tsch, G., Zuber, J., Lowe, SW., Leslie, CS., Fellmann, C.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Biotechnol","volume":"35","issue":"4","page":"350-353","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1281302","title":"Embryonic stem (ES) cells lacking functional c-jun: consequences for growth and differentiation, AP-1 activity and tumorigenicity.","abstract":"The proto-oncogene c-jun encodes the major component of the transcription factor AP-1 and is thought to have important functions in cell proliferation and differentiation as well as in the cellular response to a variety of external stimuli. To investigate directly the role of c-jun in growth, differentiation and tumorigenicity we generated mouse embryonic stem (ES) cell lines in which both copies of the c-jun gene have been inactivated by homologous recombination. The disruption of both copies of the c-jun gene had no apparent effect on ES cell viability, growth rate and in vitro differentiation potential. Transcriptional activation of the c-jun, junB and c-fos genes following TPA\/serum induction was unaffected and efficient transactivation of AP-1 reporter constructs was demonstrated in these cells. Remarkably, subcutaneous injection of ES cells lacking c-Jun into syngeneic mice led to a drastic reduction in the formation of teratocarcinomas. We propose that whereas most of the functions of c-Jun in ES cells appear to be complemented by other Jun proteins in vitro, functional c-Jun protein is essential for efficient tumor growth in vivo.","authors":"Hilberg, F., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Oncogene","volume":"7","issue":"12","page":"2371-80","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1993-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16420668","title":"Molecular processes during fat cell development revealed by gene expression profiling and functional annotation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">16420668<\/PMID><DateCompleted><Year>2006<\/Year><Month>07<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>6<\/Volume><Issue>13<\/Issue><PubDate><Year>2005<\/Year><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Molecular processes during fat cell development revealed by gene expression profiling and functional annotation.<\/ArticleTitle><Pagination><MedlinePgn>R108<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. Detailed characterization of the sequences of identified gene products has not been done and global mechanisms have not been investigated. We evaluated the extent to which molecular processes can be revealed by expression profiling and functional annotation of genes that are differentially expressed during fat cell development.","authors":"Hackl, H., Burkard, TR., Sturn, A., Rubio, R., Schleiffer, A., Tian, S., Quackenbush, J., Eisenhaber, F., Trajanoski, Z.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Genome Biol","volume":"6","issue":"13","page":"R108","pdf":null,"JrId":"21904","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28249162","title":"BET-Bromodomain Inhibitors Engage the Host Immune System and Regulate Expression of the Immune Checkpoint Ligand PD-L1.","abstract":"BET inhibitors (BETi) target bromodomain-containing proteins and are currently being evaluated as anti-cancer agents. We find that maximal therapeutic effects of BETi in a Myc-driven B cell lymphoma model required an intact host immune system. Genome-wide analysis of the BETi-induced transcriptional response identified the immune checkpoint ligand Cd274 (Pd-l1) as a Myc-independent, BETi target-gene. BETi directly repressed constitutively expressed and interferon-gamma (IFN-\u03b3) induced CD274 expression across different human and mouse tumor cell lines and primary patient samples. Mechanistically, BETi decreased Brd4 occupancy at the Cd274 locus without any change in Myc occupancy, resulting in transcriptional pausing and rapid loss of Cd274 mRNA production. Finally, targeted inhibition of the PD-1\/PD-L1 axis by combining anti-PD-1 antibodies and the BETi JQ1 caused synergistic responses in mice bearing Myc-driven lymphomas. Our data uncover an interaction between BETi and the PD-1\/PD-L1 immune-checkpoint and provide mechanistic insight into the transcriptional regulation of CD274.","authors":"Hogg, SJ., Vervoort, SJ., Deswal, S., Ott, CJ., Li, J., Cluse, LA., Beavis, PA., Darcy, PK., Martin, BP., Spencer, A., Traunbauer, AK., Sadovnik, I., Bauer, K., Valent, P., Bradner, JE., Zuber, J., Shortt, J., Johnstone, RW.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Rep","volume":"18","issue":"9","page":"2162-2174","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10086975","title":"Tissue expression and immunolocalization of tumor necrosis factor-alpha in postinfarction dysfunctional myocardium.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">10086975<\/PMID><DateCompleted><Year>1999<\/Year><Month>04<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>23<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0009-7322<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>99<\/Volume><Issue>11<\/Issue><PubDate><Year>1999<\/Year><Month>Mar<\/Month><Day>23<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>Tissue expression and immunolocalization of tumor necrosis factor-alpha in postinfarction dysfunctional myocardium.<\/ArticleTitle><Pagination><MedlinePgn>1492-8<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Tumor necrosis factor-alpha (TNF-alpha) is markedly elevated in advanced heart failure. It is not known whether tissue TNF-alpha is elevated in the common setting of myocardial infarction leading to heart failure and what the source of TNF-alpha is. To determine this, we studied the expression and protein localization of TNF-alpha and its 2 main receptors (TNF-R1\/R2) in a rat model of large infarction.","authors":"Irwin, MW., Mak, S., Mann, DL., Qu, R., Penninger, JM., Yan, A., Dawood, F., Wen, WH., Shou, Z., Liu, P.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Circulation","volume":"99","issue":"11","page":"1492-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24138885","title":"Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer.","abstract":"The complex interactions between tumors and their\u00a0microenvironment remain to be elucidated. Combining large-scale approaches, we examined the spatio-temporal dynamics of 28 different immune cell types (immunome) infiltrating tumors. We found that the immune infiltrate composition changed at each tumor stage and that particular cells had a major impact on survival. Densities of T follicular helper (Tfh) cells and innate cells increased, whereas most T\u00a0cell densities decreased along with tumor progression. The number of B cells, which are key players in the core immune network and are associated with prolonged survival, increased at a late stage and showed a dual effect on recurrence and tumor progression. The immune control relevance was demonstrated in three endoscopic orthotopic colon-cancer mouse models. Genomic instability of the chemokine CXCL13 was a mechanism associated with Tfh and B cell infiltration. CXCL13 and IL21 were pivotal factors for the Tfh\/B cell axis correlating with survival. This integrative study reveals the immune landscape in human colorectal cancer and the major hallmarks of the microenvironment associated with tumor progression and recurrence.","authors":"Bindea, G., Mlecnik, B., Tosolini, M., Kirilovsky, A., Waldner, M., Obenauf, AC., Angell, H., Fredriksen, T., Lafontaine, L., Berger, A., Bruneval, P., Fridman, WH., Becker, C., Pag\u00e8s, F., Speicher, MR., Trajanoski, Z., Galon, J.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Immunity","volume":"39","issue":"4","page":"782-95","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27600500","title":"Mast cells are not associated with systemic insulin resistance.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">27600500<\/PMID><DateCompleted><Year>2017<\/Year><Month>05<\/Month><Day>01<\/Day><\/DateCompleted><DateRevised><Year>2017<\/Year><Month>05<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1365-2362<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>46<\/Volume><Issue>11<\/Issue><PubDate><Year>2016<\/Year><Month>Nov<\/Month><\/PubDate><\/JournalIssue><Title>European journal of clinical investigation<\/Title><ISOAbbreviation>Eur J Clin Invest<\/ISOAbbreviation><\/Journal><ArticleTitle>Mast cells are not associated with systemic insulin resistance.<\/ArticleTitle><Pagination><MedlinePgn>911-919<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/eci.12675<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Infiltration of white adipose tissue (WAT) by inflammatory cells in obesity is considered to be a key event in the development of insulin resistance. Recently, mast cells (MCs) have been identified as new players in the pathogenesis of obesity. We aimed to investigate the relationship between MCs and various inflammatory markers in serum and WAT and to determine the role of MCs in the aetiology of insulin resistance.","authors":"Einwallner, E., Kiefer, FW., Di Caro, G., Orthofer, M., Witzeneder, N., H\u00f6rmann, G., Itariu, B., Zeyda, M., Penninger, JM., Stulnig, TM., Esterbauer, H., Todoric, J.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Eur J Clin Invest","volume":"46","issue":"11","page":"911-919","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23948297","title":"A kinase-independent function of CDK6 links the cell cycle to tumor angiogenesis.","abstract":"In contrast to its close homolog CDK4, the cell cycle kinase CDK6 is expressed at high levels in lymphoid malignancies. In a model for p185BCR-ABL+ B-acute lymphoid leukemia, we show that CDK6 is part of a transcription complex that induces the expression of the tumor suppressor p16INK4a and the pro-angiogenic factor VEGF-A. This function is independent of CDK6's kinase activity. High CDK6 expression thus suppresses proliferation by upregulating p16INK4a, providing an internal safeguard. However, in the absence of p16INK4a, CDK6 can exert its full tumor-promoting function by enhancing proliferation and stimulating angiogenesis. The finding that CDK6 connects cell-cycle progression to angiogenesis confirms CDK6's central role in hematopoietic malignancies and could underlie the selection pressure to upregulate CDK6 and silence p16INK4a.","authors":"Kollmann, K., Heller, G., Schneckenleithner, C., Warsch, W., Scheicher, R., Ott, RG., Sch\u00e4fer, M., Fajmann, S., Schlederer, M., Schiefer, AI., Reichart, U., Mayerhofer, M., Hoeller, C., Z\u00f6chbauer-M\u00fcller, S., Kerjaschki, D., Bock, C., Kenner, L., Hoefler, G., Freissmuth, M., Green, AR., Moriggl, R., Busslinger, M., Malumbres, M., Sexl, V.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cancer Cell","volume":"24","issue":"2","page":"167-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26932576","title":"PU.1 cooperates with IRF4 and IRF8 to suppress pre-B-cell leukemia.","abstract":"The Ets family transcription factor PU.1 and the interferon regulatory factor (IRF)4 and IRF8 regulate gene expression by binding to composite DNA sequences known as Ets\/interferon consensus elements. Although all three factors are expressed from the onset of B-cell development, single deficiency of these factors in B-cell progenitors only mildly impacts on bone marrow B lymphopoiesis. Here we tested whether PU.1 cooperates with IRF factors in regulating early B-cell development. Lack of PU.1 and IRF4 resulted in a partial block in development the pre-B-cell stage. The combined deletion of PU.1 and IRF8 reduced recirculating B-cell numbers. Strikingly, all PU.1\/IRF4 and ~50% of PU.1\/IRF8 double deficient mice developed pre-B-cell acute lymphoblastic leukemia (B-ALL) associated with reduced expression of the established B-lineage tumor suppressor genes, Ikaros and Spi-B. These genes are directly regulated by PU.1\/IRF4\/IRF8, and restoration of Ikaros or Spi-B expression inhibited leukemic cell growth. In summary, we demonstrate that PU.1, IRF4 and IRF8 cooperate to regulate early B-cell development and to prevent pre-B-ALL formation.","authors":"Pang, SH., Minnich, M., Gangatirkar, P., Zheng, Z., Ebert, A., Song, G., Dickins, RA., Corcoran, LM., Mullighan, CG., Busslinger, M., Huntington, ND., Nutt, SL., Carotta, S.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Leukemia","volume":"30","issue":"6","page":"1375-87","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16172205","title":"Aurora A phosphorylation of TACC3\/maskin is required for centrosome-dependent microtubule assembly in mitosis.","abstract":"Centrosomes act as sites of microtubule growth, but little is known about how the number and stability of microtubules emanating from a centrosome are controlled during the cell cycle. We studied the role of the TACC3-XMAP215 complex in this process by using purified proteins and Xenopus laevis egg extracts. We show that TACC3 forms a one-to-one complex with and enhances the microtubule-stabilizing activity of XMAP215 in vitro. TACC3 enhances the number of microtubules emanating from mitotic centrosomes, and its targeting to centrosomes is regulated by Aurora A-dependent phosphorylation. We propose that Aurora A regulation of TACC3 activity defines a centrosome-specific mechanism for regulation of microtubule polymerization in mitosis.","authors":"Kinoshita, K., Noetzel, TL., Pelletier, L., Mechtler, K., Drechsel, DN., Schwager, A., Lee, M., Raff, JW., Hyman, AA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Cell Biol","volume":"170","issue":"7","page":"1047-55","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2005-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11295554","title":"Translation control: bridging the gap between genomics and proteomics?","abstract":"mRNA profiling enables the expression levels of thousands of transcripts in a cell to be monitored simultaneously. Nevertheless, analyses in yeast and mammalian cells have demonstrated that mRNA levels alone are unreliable indicators of the corresponding protein abundances. This discrepancy between mRNA and protein levels argues for the relevance of additional control mechanisms besides transcription. As translational control is a major mechanism regulating gene expression, the use of translated mRNA in profiling experiments might depict the proteome more closely than does the use of total mRNA. This would combine the technical potential of genomics with the physiological relevance of proteomics.","authors":"Pradet-Balade, B., Boulm\u00e9, F., Beug, H., M\u00fcllner, EW., Garcia-Sanz, JA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Trends Biochem Sci","volume":"26","issue":"4","page":"225-9","pdf":null,"JrId":"7837","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19933155","title":"TNFalpha shedding and epidermal inflammation are controlled by Jun proteins.","abstract":"Inducible epidermal deletion of JunB and c-Jun in adult mice causes a psoriasis-like inflammatory skin disease. Increased levels of the proinflammatory cytokine TNFalpha play a major role in this phenotype. Here we define the underlying molecular mechanism using genetic mouse models. We show that Jun proteins control TNFalpha shedding in the epidermis by direct transcriptional activation of tissue inhibitor of metalloproteinase-3 (TIMP-3), an inhibitor of the TNFalpha-converting enzyme (TACE). TIMP-3 is down-regulated and TACE activity is specifically increased, leading to massive, cell-autonomous TNFalpha shedding upon loss of both JunB and c-Jun. Consequently, a prominent TNFalpha-dependent cytokine cascade is initiated in the epidermis, inducing severe skin inflammation and perinatal death of newborns from exhaustion of energy reservoirs such as glycogen and lipids. Importantly, this metabolic \"cachectic\" phenotype can be genetically rescued in a TNFR1-deficient background or by epidermis-specific re-expression of TIMP-3. These findings reveal that Jun proteins are essential physiological regulators of TNFalpha shedding by controlling the TIMP-3\/TACE pathway. This novel mechanism describing how Jun proteins control skin inflammation offers potential targets for the treatment of skin pathologies associated with increased TNFalpha levels.","authors":"Guinea-Viniegra, J., Zenz, R., Scheuch, H., Hnisz, D., Holcmann, M., Bakiri, L., Schonthaler, HB., Sibilia, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genes Dev","volume":"23","issue":"22","page":"2663-74","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28524749","title":"Ubiquitin enzymes in the regulation of immune responses.","abstract":"Ubiquitination plays a central role in the regulation of various biological functions including immune responses. Ubiquitination is induced by a cascade of enzymatic reactions by E1 ubiquitin activating enzyme, E2 ubiquitin conjugating enzyme, and E3 ubiquitin ligase, and reversed by deubiquitinases. Depending on the enzymes, specific linkage types of ubiquitin chains are generated or hydrolyzed. Because different linkage types of ubiquitin chains control the fate of the substrate, understanding the regulatory mechanisms of ubiquitin enzymes is central. In this review, we highlight the most recent knowledge of ubiquitination in the immune signaling cascades including the T cell and B cell signaling cascades as well as the TNF signaling cascade regulated by various ubiquitin enzymes. Furthermore, we highlight the TRIM ubiquitin ligase family as one of the examples of critical E3 ubiquitin ligases in the regulation of immune responses.","authors":"Ebner, P., Versteeg, GA., Ikeda, F.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Crit Rev Biochem Mol Biol","volume":"52","issue":"4","page":"425-460","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16179614","title":"TGF-beta-induced apoptosis in endothelial cells mediated by M6P\/IGFII-R and mini-plasminogen.","abstract":"Transforming growth factor-beta (TGF-beta), a key modulator of endothelial cell apoptosis, must be activated from the latent form (LTGF-beta) to induce biological responses. In the present study, we report activation of TGF-beta by functional and physical co-operation of the mannose-6-phosphate\/insulin-like-growth-factor-II receptor (CD222) and the urokinase-type plasminogen activator receptor (CD87). We show that endothelial cells express CD222 and CD87 in a membrane complex and demonstrate that the association of these two receptors is essential for the release of active TGF-beta in the transduced mouse fibroblast used as model cells. By contrast, smooth-muscle cells, which express CD222 and CD87 at similar density to endothelial cells but not in complexed form, do not activate TGF-beta. We also have found that mini-plasminogen is a high-affinity ligand for CD222 and is essential for the activation of TGF-beta by the CD87-CD222 complex to induce apoptosis in endothelial cells. This specific mechanism of TGF-beta-mediated apoptosis in endothelial cells is thus a potential novel target to be considered for treatment of pathological vascular disorders (e.g. tumor angiogenesis).","authors":"Leksa, V., Godar, S., Schiller, HB., Fuertbauer, E., Muhammad, A., Slezakova, K., Horejsi, V., Steinlein, P., Weidle, UH., Binder, BR., Stockinger, H.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Cell Sci","volume":"118","issue":"Pt 19","page":"4577-86","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25805847","title":"Activin\/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark.","abstract":"Stem cells can self-renew and differentiate into multiple cell types. These characteristics are maintained by the combination of specific signaling pathways and transcription factors that cooperate to establish a unique epigenetic state. Despite the broad interest of these mechanisms, the precise molecular controls by which extracellular signals organize epigenetic marks to confer multipotency remain to be uncovered. Here, we use human embryonic stem cells (hESCs) to show that the Activin-SMAD2\/3 signaling pathway cooperates with the core pluripotency factor NANOG to recruit the DPY30-COMPASS histone modifiers onto key developmental genes. Functional studies demonstrate the importance of these interactions for correct histone 3 Lys4 trimethylation and also self-renewal and differentiation. Finally, genetic studies in mice show that Dpy30 is also necessary to maintain pluripotency in the pregastrulation embryo, thereby confirming the existence of similar regulations in vivo during early embryonic development. Our results reveal the mechanisms by which extracellular factors coordinate chromatin status and cell fate decisions in hESCs.","authors":"Bertero, A., Madrigal, P., Galli, A., Hubner, NC., Moreno, I., Burks, D., Brown, S., Pedersen, RA., Gaffney, D., Mendjan, S., Pauklin, S., Vallier, L.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Genes Dev","volume":"29","issue":"7","page":"702-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11456451","title":"In vivo imaging indicates muscle fiber dedifferentiation is a major contributor to the regenerating tail blastema.","abstract":"During tail regeneration in urodele amphibians such as axolotls, all of the tissue types, including muscle, dermis, spinal cord, and cartilage, are regenerated. It is not known how this diversity of cell types is reformed with such precision. In particular, the number and variety of mature cell types in the remaining stump that contribute to the blastema is unclear. Using Nomarski imaging, we followed the process of regeneration in the larval axolotl tail. Combining this with in vivo fluorescent labeling of single muscle fibers, we show that mature muscle dedifferentiates. Muscle dedifferentiation occurs by the synchronous fragmentation of the multinucleate muscle fiber into mononucleate cells followed by rapid cell proliferation and the extension of cell processes. We further show that direct clipping of the muscle fiber and severe tissue damage around the fiber are both required to initiate dedifferentiation. Our observations also make it possible to estimate for the first time how many of the blastema cells arise specifically from muscle dedifferentiation. Calculations based on our data suggest that up to 29% of nondermal-derived cells in the blastema come from dedifferentiation of mature muscle fibers. Overall, these results show that endogenous multinucleate muscle fibers can dedifferentiate into mononucleate cells and contribute significantly to the blastema.","authors":"Echeverri, K., Clarke, JD., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Dev Biol","volume":"236","issue":"1","page":"151-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9120275","title":"Alterations in the level of CD45 surface expression affect the outcome of thymic selection.","abstract":"CD45 is a receptor protein tyrosine phosphatase whose activity is required for thymocyte development and TCR-mediated signal transduction. Here we show that positive selection of TCR-alphabeta transgenic thymocytes is completely blocked in CD45 exon 6 -\/- gene-deficient (CD45 -\/-) mice that express the P14 TCR specific for the lymphocytic choriomeningitis virus. Thymocytes from mice heterozygous for the targeted disruption of the CD45 gene (CD45 +\/-) displayed a reduction in both CD45 surface intensity and enzymatic CD45 protein tyrosine phosphatase activity. Surprisingly, positive thymocyte selection was enhanced in CD45 +\/- mice as characterized by an up-regulation of the P14 TCR on thymocytes and increased numbers of transgenic T cells. Using a variant of lymphocytic choriomeningitis virus that is impaired in the induction of negative selection of P14 thymocytes, we also show that the reduction of CD45 surface expression in CD45 +\/- mice rendered P14 transgene thymocytes susceptible to negative selection. These data demonstrate that changes in the expression level of the receptor protein tyrosine phosphatase CD45 can alter thymic selection.","authors":"Wallace, VA., Penninger, JM., Kishihara, K., Timms, E., Shahinian, A., Pircher, H., K\u00fcndig, TM., Ohashi, PS., Mak, TW.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Immunol","volume":"158","issue":"7","page":"3205-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11287675","title":"Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes.","abstract":"To investigate the occurrence of glycosylphosphatidylinositol (GPI) lipid anchor modification in various taxonomic ranges, potential substrate proteins have been searched for in completely sequenced genomes. We applied the big-pi predictor for the recognition of propeptide cleavage and anchor attachment sites with a new, generalized analytical form of the extreme-value distribution for evaluating false-positive prediction rates. (i) We find that GPI modification is present among lower and higher Eukaryota (approximately 0.5% of all proteins) but it seems absent in all eubacterial and three archaeobacterial species studied. Four other archaean genomes appear to encode such a fraction of substrate proteins (in the range of eukaryots) that they cannot be explained as false-positive predictions. This result supports the possible existence of GPI anchor modification in an archaean subgroup. (ii) The frequency of GPI-modified proteins on various chromosomes of a given eukaryotic species is different. (iii) Lists of potentially GPI-modified proteins in complete genomes with their predicted cleavage sites are available at http:\/\/mendel.imp.univie.ac.at\/gpi\/gpi_genomes.html. (iv) Orthologues of known transamidase subunits have been found only for EUKARYA: Inconsistencies in domain structure among homologues some of which may indicate sequencing errors are described. We present a refined model of the transamidase complex.","authors":"Eisenhaber, B., Bork, P., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Protein Eng","volume":"14","issue":"1","page":"17-25","pdf":null,"JrId":"6619","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11279485","title":"Essential role of the mitochondrial apoptosis-inducing factor in programmed cell death.","abstract":"Programmed cell death is a fundamental requirement for embryogenesis, organ metamorphosis and tissue homeostasis. In mammals, release of mitochondrial cytochrome c leads to the cytosolic assembly of the apoptosome-a caspase activation complex involving Apaf1 and caspase-9 that induces hallmarks of apoptosis. There are, however, mitochondrially regulated cell death pathways that are independent of Apaf1\/caspase-9. We have previously cloned a molecule associated with programmed cell death called apoptosis-inducing factor (AIF). Like cytochrome c, AIF is localized to mitochondria and released in response to death stimuli. Here we show that genetic inactivation of AIF renders embryonic stem cells resistant to cell death after serum deprivation. Moreover, AIF is essential for programmed cell death during cavitation of embryoid bodies-the very first wave of cell death indispensable for mouse morphogenesis. AIF-dependent cell death displays structural features of apoptosis, and can be genetically uncoupled from Apaf1 and caspase-9 expression. Our data provide genetic evidence for a caspase-independent pathway of programmed cell death that controls early morphogenesis.","authors":"Joza, N., Susin, SA., Daugas, E., Stanford, WL., Cho, SK., Li, CY., Sasaki, T., Elia, AJ., Cheng, HY., Ravagnan, L., Ferri, KF., Zamzami, N., Wakeham, A., Hakem, R., Yoshida, H., Kong, YY., Mak, TW., Z\u00fa\u00f1iga-Pfl\u00fccker, JC., Kroemer, G., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nature","volume":"410","issue":"6828","page":"549-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25042702","title":"NANOG and CDX2 pattern distinct subtypes of human mesoderm during exit from pluripotency.","abstract":"Mesoderm is induced at the primitive streak (PS) and patterns subsequently into mesodermal subtypes and organ precursors. It is unclear whether mesoderm induction generates a multipotent PS progenitor or several distinct ones with restricted subtype potentials. We induced mesoderm in human pluripotent stem cells with ACTIVIN and BMP or with GSK3-\u03b2 inhibition. Both approaches induced BRACHYURY(+) mesoderm of distinct PS-like identities, which had differing patterning potential. ACTIVIN and BMP-induced mesoderm patterned into cardiac but not somitic subtypes. Conversely, PS precursors induced by GSK3-\u03b2 inhibition did not generate lateral\u00a0plate and cardiac mesoderm and favored instead somitic differentiation. The mechanism of these\u00a0cell fate decisions involved mutual repression of\u00a0NANOG and CDX2. Although NANOG was required for cardiac specification but blocked somitic subtypes, CDX2 was required for somitic mesoderm but blocked cardiac differentiation. In sum, rather than forming a common PS progenitor, separate induction mechanisms distinguish human mesoderm subtypes.","authors":"Mendjan, S., Mascetti, VL., Ortmann, D., Ortiz, M., Karjosukarso, DW., Ng, Y., Moreau, T., Pedersen, RA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell Stem Cell","volume":"15","issue":"3","page":"310-325","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11269950","title":"Generation of mononucleate cells from post-mitotic myotubes proceeds in the absence of cell cycle progression.","abstract":"The remarkable regenerative ability of adult urodele amphibians depends in part of the plasticity of differentiated cells at the site of injury. Limb regeneration proceeds by formation of a mesenchymal growth zone or blastema under the wound epidermis at the end of the stump. Previous work has shown that when cultured post-mitotic newt myotubes are introduced into the blastema, they re-enter the cell cycle and undergo conversion to mononucleate cells which divide and contribute to the regenerate [11, 13]. In order to investigate the interdependence of these two aspects of plasticity, we have blocked cell cycle progression of the myotubes either by X-irradiation or by transfection of the CDK4\/6 inhibitor p16. In each case, the efficacy of the block was evaluated in culture after activation of S phase re-entry by serum stimulation. The experimental myotubes were implanted into limb blastemas along with a differentially labelled control population of myotubes containing an equivalent number of nuclei. X-irradiated myotubes gave rise to mononucleate cells in the limb blastema, and the progeny were blocked in respect of S phase entry. Comparable results were obtained with the p16-expressing myotubes. We conclude that progression through S or M phase is not required for generation of mononucleate cells and suggest that such cells may arise by budding from the muscle syncytium.","authors":"Velloso, CP., Kumar, A., Tanaka, EM., Brockes, JP.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Differentiation","volume":"66","issue":"4-5","page":"239-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23931319","title":"Protein-mediated transformation of lipid vesicles into tubular networks.","abstract":"Key cellular processes are frequently accompanied by protein-facilitated shape changes in the plasma membrane. N-BAR-domain protein modules generate curvature by means of complex interactions with the membrane surface. The way they assemble and the mechanism by which they operate are largely dependent on their binding density. Although the mechanism at lower densities has recently begun to emerge, how membrane scaffolds form at high densities remains unclear. By combining electron microscopy and multiscale simulations, we show that N-BAR proteins at high densities can transform a lipid vesicle into a 3D tubular network. We show that this process is a consequence of excess adhesive energy combined with the local stiffening of the membrane, which occurs in a narrow range of mechanical properties of both the membrane and the protein. We show that lipid diffusion is significantly reduced by protein binding at this density regime and even more in areas of high Gaussian curvature, indicating a potential effect on molecular transport in cells. Finally, we reveal that the breaking of the bilayer topology is accompanied by the nematic arrangement of the protein on the surface, a structural motif that likely drives the formation of reticular structures in living cells.","authors":"Simunovic, M., Mim, C., Marlovits, TC., Resch, G., Unger, VM., Voth, GA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Biophys J","volume":"105","issue":"3","page":"711-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23863140","title":"Intron excision from precursor tRNA molecules in mammalian cells requires ATP hydrolysis and phosphorylation of tRNA-splicing endonuclease components.","abstract":"The process of tRNA splicing entails removal of an intron by TSEN (tRNA-splicing endonuclease) and ligation of the resulting exon halves to generate functional tRNAs. In mammalian cells, the RNA kinase CLP1 (cleavage and polyadenylation factor I subunit) associates with TSEN and phosphorylates the 3' exon at the 5' end in\u00a0vitro, suggesting a role for CLP1 in tRNA splicing. Interestingly, recent data suggest that the ATP-binding and\/or hydrolysis capacity of CLP1 is required to enhance pre-tRNA cleavage. In\u00a0vivo, the lack of CLP1 kinase activity leads to progressive motor neuron loss and accumulation of novel 5' leader-5' exon tRNA fragments. We have extended the investigation of the biochemical requirements in pre-tRNA splicing and found that \u03b2-\u03b3-hydrolysable ATP is crucial for the productive generation of exon halves. In addition, we provide evidence that phosphorylation of the TSEN complex components supports efficient pre-tRNA cleavage. Taken together, our data improve the mechanistic understanding of mammalian pre-tRNA processing and its regulation.","authors":"Mair, B., Popow, J., Mechtler, K., Weitzer, S., Martinez, J.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Biochem Soc Trans","volume":"41","issue":"4","page":"831-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18369314","title":"A crucial role of WW45 in developing epithelial tissues in the mouse.","abstract":"The role and molecular mechanisms of a new Hippo signalling pathway are not fully understood in mammals. Here, we generated mice that lack WW45 and revealed a crucial role for WW45 in cell-cycle exit and epithelial terminal differentiation. Many organs in the mutant mouse embryos displayed hyperplasia accompanied by defects in terminal differentiation of epithelial progenitor cells owing to impaired proliferation arrest rather than intrinsic acceleration of proliferation during differentiation. Importantly, the MST1 signalling pathway is specifically activated in differentiating epithelial cells. Moreover, WW45 is required for MST1 activation and translocation to the nucleus for subsequent LATS1\/2 activation upon differentiation signal. LATS1\/2 phosphorylates YAP, which, in turn, translocates from the nucleus into the cytoplasm, resulting in cell-cycle exit and terminal differentiation of epithelial progenitor cells. Collectively, these data provide compelling evidence that WW45 is a key mediator of MST1 signalling in the coordinate coupling of proliferation arrest with terminal differentiation for proper epithelial tissue development in mammals.","authors":"Lee, JH., Kim, TS., Yang, TH., Koo, BK., Oh, SP., Lee, KP., Oh, HJ., Lee, SH., Kong, YY., Kim, JM., Lim, DS.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO J","volume":"27","issue":"8","page":"1231-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22704499","title":"Synthetic organs for regenerative medicine.","abstract":"Differentiating tissue stem cells can self-assemble into structures that strikingly resemble functional organ subunits. Translating this insight to regenerative medicine presents several challenges.","authors":"Pedersen, RA., Mascetti, V., Mendjan, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Stem Cell","volume":"10","issue":"6","page":"646-647","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11285280","title":"Anaphase-promoting complex\/cyclosome-dependent proteolysis of human cyclin A starts at the beginning of mitosis and is not subject to the spindle assembly checkpoint.","abstract":"Cyclin A is a stable protein in S and G2 phases, but is destabilized when cells enter mitosis and is almost completely degraded before the metaphase to anaphase transition. Microinjection of antibodies against subunits of the anaphase-promoting complex\/cyclosome (APC\/C) or against human Cdc20 (fizzy) arrested cells at metaphase and stabilized both cyclins A and B1. Cyclin A was efficiently polyubiquitylated by Cdc20 or Cdh1-activated APC\/C in vitro, but in contrast to cyclin B1, the proteolysis of cyclin A was not delayed by the spindle assembly checkpoint. The degradation of cyclin B1 was accelerated by inhibition of the spindle assembly checkpoint. These data suggest that the APC\/C is activated as cells enter mitosis and immediately targets cyclin A for degradation, whereas the spindle assembly checkpoint delays the degradation of cyclin B1 until the metaphase to anaphase transition. The \"destruction box\" (D-box) of cyclin A is 10-20 residues longer than that of cyclin B. Overexpression of wild-type cyclin A delayed the metaphase to anaphase transition, whereas expression of cyclin A mutants lacking a D-box arrested cells in anaphase.","authors":"Geley, S., Kramer, E., Gieffers, C., Gannon, J., Peters, JM., Hunt, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Cell Biol","volume":"153","issue":"1","page":"137-48","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11266463","title":"A specific role of phosphatidylinositol 3-kinase gamma. A regulation of autonomic Ca(2)+ oscillations in cardiac cells.","abstract":"Purinergic stimulation of cardiomyocytes turns on a Src family tyrosine kinase-dependent pathway that stimulates PLCgamma and generates IP(3), a breakdown product of phosphatidylinositol 4,5-bisphosphate (PIP2). This signaling pathway closely regulates cardiac cell autonomic activity (i.e., spontaneous cell Ca(2+) spiking). PIP2 is phosphorylated on 3' by phosphoinositide 3-kinases (PI3Ks) that belong to a broad family of kinase isoforms. The product of PI3K, phosphatidylinositol 3,4,5-trisphosphate, regulates activity of PLCgamma. PI3Ks have emerged as crucial regulators of many cell functions including cell division, cell migration, cell secretion, and, via PLCgamma, Ca(2+) homeostasis. However, although PI3Kalpha and -beta have been shown to mediate specific cell functions in nonhematopoietic cells, such a role has not been found yet for PI3Kgamma. We report that neonatal rat cardiac cells in culture express PI3Kalpha, -beta, and -gamma. The purinergic agonist predominantly activates PI3Kgamma. Both wortmannin and LY294002 prevent tyrosine phosphorylation, and membrane translocation of PLCgamma as well as IP(3) generation in ATP-stimulated cells. Furthermore, an anti-PI3Kgamma, but not an anti-PI3Kbeta, injected in the cells prevents the effect of ATP on cell Ca(2+) spiking. A dominant negative mutant of PI3Kgamma transfected in the cells also exerts the same action. The effect of ATP was observed on spontaneous Ca(2+) spiking of wild-type but not of PI3Kgamma(2\/2) embryonic stem cell-derived cardiomyocytes. ATP activates the Btk tyrosine kinase, Tec, and induces its association with PLCgamma. A dominant negative mutant of Tec blocks the purinergic effect on cell Ca(2+) spiking. Tec is translocated to the T-tubes upon ATP stimulation of cardiac cells. Both an anti-PI3Kgamma antibody and a dominant negative mutant of PI3Kgamma injected or transfected into cells prevent the latter event. We conclude that PI3Kgamma activation is a crucial step in the purinergic regulation of cardiac cell spontaneous Ca(2+) spiking. Our data further suggest that Tec works in concert with a Src family kinase and PI3Kgamma to fully activate PLCgamma in ATP-stimulated cardiac cells. This cluster of kinases provides the cardiomyocyte with a tight regulation of IP(3) generation and thus cardiac autonomic activity.","authors":"Bony, C., Roche, S., Shuichi, U., Sasaki, T., Crackower, MA., Penninger, J., Mano, H., Puc\u00e9at, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Cell Biol","volume":"152","issue":"4","page":"717-28","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11247842","title":"Enhanced central response to dehydration in mice lacking angiotensin AT(1a) receptors.","abstract":"The objective was to determine the central nervous system (CNS) responses to dehydration (c-Fos and vasopressin mRNA) in mice lacking the ANG AT(1a) receptor [ANG AT(1a) knockout (KO)]. Control and AT(1a) KO mice were dehydrated for 24 or 48 h. Baseline plasma vasopressin (VP) was not different between the groups; however, the response to dehydration was attenuated in AT(1a) KO (24 +\/- 11 vs. 10.6 +\/- 2.7 pg\/ml). Dehydration produced similar increases in plasma osmolality and depletion of posterior pituitary VP content. Neuronal activation was observed as increases in c-Fos protein and VP mRNA. The supraoptic responses were not different between groups. In the paraventricular nucleus (PVN), c-Fos-positive neurons (57.4 +\/- 10.7 vs. 98.4 +\/- 7.4 c-Fos cells\/PVN, control vs. AT(1a) KO) and VP mRNA levels (1.0 +\/- 0.1 vs. 1.4 +\/- 0.1 microCi, control vs. AT(1a) KO) were increased with greater responses in AT(1a) KO. A comparison of 1- to 2-day water deprivation showed that plasma VP, brain c-Fos, and VP mRNA returned toward control on day 2, although plasma osmolality remained high. Data demonstrate that AT(1a) KO mice show a dichotomous response to dehydration, reduced for plasma VP and enhanced for PVN c-Fos protein and VP mRNA. The results illustrate the importance of ANG AT(1a) receptors in the regulation of osmotic and endocrine balance.","authors":"Morris, M., Means, S., Oliverio, MI., Coffman, TM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Am J Physiol Regul Integr Comp Physiol","volume":"280","issue":"4","page":"R1177-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26659182","title":"The histone chaperone CAF-1 safeguards somatic cell identity.","abstract":"Cellular differentiation involves profound remodelling of chromatic landscapes, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood. To further elucidate regulatory pathways that safeguard the somatic state, we performed two comprehensive RNA interference (RNAi) screens targeting chromatin factors during transcription-factor-mediated reprogramming of mouse fibroblasts to induced pluripotent stem cells (iPS cells). Subunits of the chromatin assembly factor-1 (CAF-1) complex, including Chaf1a and Chaf1b, emerged as the most prominent hits from both screens, followed by modulators of lysine sumoylation and heterochromatin maintenance. Optimal modulation of both CAF-1 and transcription factor levels increased reprogramming efficiency by several orders of magnitude and facilitated iPS cell formation in as little as 4 days. Mechanistically, CAF-1 suppression led to a more accessible chromatin structure at enhancer elements early during reprogramming. These changes were accompanied by a decrease in somatic heterochromatin domains, increased binding of Sox2 to pluripotency-specific targets and activation of associated genes. Notably, suppression of CAF-1 also enhanced the direct conversion of B cells into macrophages and fibroblasts into neurons. Together, our findings reveal the histone chaperone CAF-1 to be a novel regulator of somatic cell identity during transcription-factor-induced cell-fate transitions and provide a potential strategy to modulate cellular plasticity in a regenerative setting.","authors":"Cheloufi, S., Elling, U., Hopfgartner, B., Jung, YL., Murn, J., Ninova, M., Hubmann, M., Badeaux, AI., Euong Ang, C., Tenen, D., Wesche, DJ., Abazova, N., Hogue, M., Tasdemir, N., Brumbaugh, J., Rathert, P., Jude, J., Ferrari, F., Blanco, A., Fellner, M., Wenzel, D., Zinner, M., Vidal, SE., Bell, O., Stadtfeld, M., Chang, HY., Almouzni, G., Lowe, SW., Rinn, J., Wernig, M., Aravin, A., Shi, Y., Park, PJ., Penninger, JM., Zuber, J., Hochedlinger, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nature","volume":"528","issue":"7581","page":"218-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9824556","title":"A target of thrombin activation promotes cell cycle re-entry by urodele muscle cells.","abstract":"A key early event of newt limb regeneration is the local dedifferentiation of cells to form dividing progenitor cells. This involves the plasticity of differentiation and the ability to re-enter the cell cycle. In culture, differentiated newt myotubes are able to re-enter S-phase in response to serum stimulation. Here, we analyzed the intracellular and extracellular requirements for this process. Cell cycle re-entry depends on the phosphorylation of the retinoblastoma protein, which is a key regulator of the G1-S transition. This is in contrast to mammalian myotubes, which are refractory to serum stimulation and cannot phosphorylate retinoblastoma protein in response to serum. The serum factor responsible for this phosphorylation appears to be distinct from common polypeptide growth factors and is enriched in crude preparations of bovine thrombin. Fractionation and analysis of this preparation indicate that the factor is regulated by thrombin and plasmin proteolysis. These results indicate that factors involved in acute responses to wounding such as clotting may be important initiators of the regenerative response.","authors":"Tanaka, EM., Brockes, JP.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Wound Repair Regen","volume":"6","issue":"4","page":"371-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11242053","title":"Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins.","abstract":"Distinct modifications of histone amino termini, such as acetylation, phosphorylation and methylation, have been proposed to underlie a chromatin-based regulatory mechanism that modulates the accessibility of genetic information. In addition to histone modifications that facilitate gene activity, it is of similar importance to restrict inappropriate gene expression if cellular and developmental programmes are to proceed unperturbed. Here we show that mammalian methyltransferases that selectively methylate histone H3 on lysine 9 (Suv39h HMTases) generate a binding site for HP1 proteins--a family of heterochromatic adaptor molecules implicated in both gene silencing and supra-nucleosomal chromatin structure. High-affinity in vitro recognition of a methylated histone H3 peptide by HP1 requires a functional chromo domain; thus, the HP1 chromo domain is a specific interaction motif for the methyl epitope on lysine9 of histone H3. In vivo, heterochromatin association of HP1 proteins is lost in Suv39h double-null primary mouse fibroblasts but is restored after the re-introduction of a catalytically active SWUV39H1 HMTase. Our data define a molecular mechanism through which the SUV39H-HP1 methylation system can contribute to the propagation of heterochromatic subdomains in native chromatin.","authors":"Lachner, M., O'Carroll, D., Rea, S., Mechtler, K., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nature","volume":"410","issue":"6824","page":"116-20","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23681967","title":"Pharmacokinetics and pharmacodynamics of recombinant human angiotensin-converting enzyme 2 in healthy human subjects.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23681967<\/PMID><DateCompleted><Year>2014<\/Year><Month>03<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1179-1926<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>52<\/Volume><Issue>9<\/Issue><PubDate><Year>2013<\/Year><Month>Sep<\/Month><\/PubDate><\/JournalIssue><Title>Clinical pharmacokinetics<\/Title><ISOAbbreviation>Clin Pharmacokinet<\/ISOAbbreviation><\/Journal><ArticleTitle>Pharmacokinetics and pharmacodynamics of recombinant human angiotensin-converting enzyme 2 in healthy human subjects.<\/ArticleTitle><Pagination><MedlinePgn>783-92<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s40262-013-0072-7<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND AND OBJECTIVES\" NlmCategory=\"OBJECTIVE\">Angiotensin-converting enzyme 2 (ACE2) converts angiotensin II (Ang1-8) to angiotensin 1-7 (Ang1-7), a functional antagonist of Ang1-8, with vasodilatory, antiproliferative, antiangiogenic, and anti-inflammatory properties. In conditions with an unbalanced renin-angiotensin-aldosterone system with elevated Ang1-8, administration of ACE2 has shown promising effects in a variety of animal models. Enhancing ACE2 activity by exogenous administration of ACE2 might also be beneficial in human diseases with pathologically elevated Ang1-8. As a first step we performed a first-in-man study to determine pharmacokinetics, pharmacodynamics, safety, and tolerability of recombinant ACE2 in healthy volunteers.","authors":"Haschke, M., Schuster, M., Poglitsch, M., Loibner, H., Salzberg, M., Bruggisser, M., Penninger, J., Kr\u00e4henb\u00fchl, S.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Clin Pharmacokinet","volume":"52","issue":"9","page":"783-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33157046","title":"Introductions to the Community: Early-Career Researchers in the Time of COVID-19.","abstract":"COVID-19 has unfortunately halted lab work, conferences, and in-person networking, which is especially detrimental to researchers just starting their labs. Through social media and our reviewer networks, we met some early-career stem cell investigators impacted by the closures. Here, they introduce themselves and their research to our readers.","authors":"Smith, Q., McKinley, KL., Chan, CJ., Sikandar, S., Xiang, Y., Passaro, D.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Stem Cell","volume":"27","issue":"5","page":"702-704","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19279133","title":"Activin\/Nodal signalling maintains pluripotency by controlling Nanog expression.","abstract":"The pluripotent status of embryonic stem cells (ESCs) confers upon them the capacity to differentiate into the three primary germ layers, ectoderm, mesoderm and endoderm, from which all the cells of the adult body are derived. An understanding of the mechanisms controlling pluripotency is thus essential for driving the differentiation of human pluripotent cells into cell types useful for clinical applications. The Activin\/Nodal signalling pathway is necessary to maintain pluripotency in human ESCs and in mouse epiblast stem cells (EpiSCs), but the molecular mechanisms by which it achieves this effect remain obscure. Here, we demonstrate that Activin\/Nodal signalling controls expression of the key pluripotency factor Nanog in human ESCs and in mouse EpiSCs. Nanog in turn prevents neuroectoderm differentiation induced by FGF signalling and limits the transcriptional activity of the Smad2\/3 cascade, blocking progression along the endoderm lineage. This negative-feedback loop imposes stasis in neuroectoderm and mesendoderm differentiation, thereby maintaining the pluripotent status of human ESCs and mouse EpiSCs.","authors":"Vallier, L., Mendjan, S., Brown, S., Chng, Z., Teo, A., Smithers, LE., Trotter, MW., Cho, CH., Martinez, A., Rugg-Gunn, P., Brons, G., Pedersen, RA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Development","volume":"136","issue":"8","page":"1339-49","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23486400","title":"Signal transduction and signaling networks.","abstract":null,"authors":"Ikeda, F., Lahav, G.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Mol Biol Cell","volume":"24","issue":"6","page":"676","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9008710","title":"Newt myotubes reenter the cell cycle by phosphorylation of the retinoblastoma protein.","abstract":"Withdrawal from the cell cycle is an essential aspect of vertebrate muscle differentiation and requires the retinoblastoma (Rb) protein that inhibits expression of genes needed for cell cycle entry. It was shown recently that cultured myotubes derived from the Rb-\/- mouse reenter the cell cycle after serum stimulation (Schneider, J.W., W. Gu, L. Zhu, V. Mahdavi, and B. Nadal-Ginard. 1994. Science (Wash. DC). 264:1467-1471). In contrast with other vertebrates, adult urodele amphibians such as the newt can regenerate their limbs, a process involving cell cycle reentry and local reversal of differentiation. Here we show that myotubes formed in culture from newt limb cells are refractory to several growth factors, but they undergo S phase after serum stimulation and accumulate 4N nuclei. This response to serum is inhibited by contact with mononucleate cells. Despite the phenotypic parallel with Rb-\/- mouse myotubes, Rb is expressed in the newt myotubes, and its phosphorylation via cyclin-dependent kinase 4\/6 is required for cell cycle reentry. Thus, the postmitotic arrest of urodele myotubes, although intact in certain respects, can be undermined by a pathway that is inactive in other vertebrates. This may be important for the regenerative ability of these animals.","authors":"Tanaka, EM., Gann, AA., Gates, PB., Brockes, JP.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Cell Biol","volume":"136","issue":"1","page":"155-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21949345","title":null,"abstract":null,"authors":"","publication_status":null,"journalpubyear":null,"journaltitle":null,"volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30912012","title":"Using Functional Genetics in Haploid Cells for Drug Target Identification.","abstract":"Pooled genetic screens are a powerful tool to identify targets for drug development as well as chemogenetic interactions. Various complementary methods for mutagenesis are available to generate highly complex cell populations, including mRNA knockdown, directed genome editing, as well as random genome mutagenesis. With the availability of a growing number of haploid mammalian cell lines, random mutagenesis is becoming increasingly powerful and represents an attractive alternative, e.g., to CRISPR-based screening. This chapter provides a step-by-step protocol for performing haploid gene trap screens.","authors":"Volz, JC., Schuller, N., Elling, U.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Methods Mol Biol","volume":"1953","issue":null,"page":"3-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23249862","title":"Small-molecule inhibition of BRD4 as a new potent approach to eliminate leukemic stem- and progenitor cells in acute myeloid leukemia AML.","abstract":"Acute myeloid leukemia (AML) is a life-threatening stem cell disease characterized by uncontrolled proliferation and accumulation of myeloblasts. Using an advanced RNAi screen-approach in an AML mouse model we have recently identified the epigenetic 'reader' BRD4 as a promising target in AML. In the current study, we asked whether inhibition of BRD4 by a small-molecule inhibitor, JQ1, leads to growth-inhibition and apoptosis in primary human AML stem- and progenitor cells. Primary cell samples were obtained from 37 patients with freshly diagnosed AML (n=23) or refractory AML (n=14). BRD4 was found to be expressed at the mRNA and protein level in unfractionated AML cells as well as in highly enriched CD34\u207a\/CD38\u207b and CD34\u207a\/CD38\u207a stem- and progenitor cells in all patients examined. In unfractionated leukemic cells, submicromolar concentrations of JQ1 induced major growth-inhibitory effects (IC\u2085\u2080 0.05-0.5 \u00b5M) in most samples, including cells derived from relapsed or refractory patients. In addition, JQ1 was found to induce apoptosis in CD34+\/CD38\u207b and CD34\u207a\/CD38\u207a stem- and progenitor cells in all donors examined as evidenced by combined surface\/Annexin-V staining. Moreover, we were able to show that JQ1 synergizes with ARA-C in inducing growth inhibition in AML cells. Together, the BRD4-targeting drug JQ1 exerts major anti-leukemic effects in a broad range of human AML subtypes, including relapsed and refractory patients and all relevant stem- and progenitor cell compartments, including CD34\u207a\/CD38\u207b and CD34\u207a\/CD38\u207a AML cells. These results characterize BRD4-inhibition as a promising new therapeutic approach in AML which should be further investigated in clinical trials.","authors":"Herrmann, H., Blatt, K., Shi, J., Gleixner, KV., Cerny-Reiterer, S., M\u00fcllauer, L., Vakoc, CR., Sperr, WR., Horny, HP., Bradner, JE., Zuber, J., Valent, P.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Oncotarget","volume":"3","issue":"12","page":"1588-99","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23061677","title":"Understanding and targeting osteoclastic activity in prostate cancer bone metastases.","abstract":"Bone metastasis is a debilitating side effect of advanced prostatic carcinoma impacting nearly all of the men developing this disease. Even though a majority of these lesions are considered osteoblastic, it is believed that there is an underlying osteolytic component. Lytic processes are governed primarily by osteoclasts, the primary bone resorptive cell. Osteolysis has been implicated in tumor cell seeding and nourishment of tumor growth via development of pro-tumorigenic changes in the microenvironment. Herein, we provide a current view of the processes involved in regulating osteolysis in the presence of prostate cancer bone metastases. Several factors have been implicated in the division, differentiation, and activation of osteoclasts, including, but not limited to, interleukin-6, receptor activator of nuclear factor kappa B ligand (RANKL), osteoprotegerin (OPG), and parathyroid hormone-related protein (PTHrP). Effector molecules in bone resorption play a significant role, such as matrix metalloproteinases (MMPs), cathepsins, and acid secretion. The primary method for treating skeletal events associated with prostate cancer bone metastases has been bisphosphonates. However, a new therapeutic, denosumab, a monoclonal antibody that inhibits RANKL in a mechanism similar to that attributed to the endogenous mediator OPG, has received approval for treatment of skeletally associated metastases. Additional novel targets are continuously being developed for bone metastases. In this review, we describe the processes involved in osteolysis of the prostate cancer bone microenvironment, and introduce therapeutics that may play a role in inhibiting tumor growth leading to increased survival and quality of life.","authors":"Sottnik, JL., Keller, ET.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Curr Mol Med","volume":"13","issue":"4","page":"626-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26205990","title":"Targeted Gene Disruption by Ectopic Induction of DNA Elimination in Tetrahymena.","abstract":"Tetrahymena is a useful eukaryotic model for biochemistry and molecular cell biology studies. We previously demonstrated that targeted ectopic DNA elimination, also called co-Deletion (coDel), can be induced by the introduction of an internal eliminated sequence (IES)-target DNA chimeric construct. In this study, we demonstrate that coDel occurs at most of the loci tested and can be used for the production of somatic gene KO strains. We also showed that coDel at two loci can be simultaneously induced by a single transformation; thus, coDel can be used to disrupt multiple gene loci in a single cell. Therefore, coDel is a useful tool for functional genetics in Tetrahymena and further extends the usefulness of this model organism.","authors":"Hayashi, A., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Genetics","volume":"201","issue":"1","page":"55-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23059888","title":"Expression and localization of VEGF receptors in human fetal skeletal tissues.","abstract":"During development the vertebrate skeleton is the product of deriving cells from distinct embryonic lineages. The craniofacial skeleton is formed by migrating cranial neural crest cells, whereas the axial and limb skeletons are derived from mesodermal cells.   The Vascular Endothelial Growth Factors (VEGFs) \/ receptors (VEGFRs) system plays an important role in angiogenesis, as well as osteogenesis, during bone development, growth, and remodeling, attracting endothelial cells and osteoclasts and stimulating osteoblast differentiation. Recent evidence has shown that during development VEGFR-3 is also expressed in neural and glial precursors of forebrain and cerebellum, as well as in the eye.   In this study, we found that VEGFR-1, VEGFR-2 and VEGFR-3 are expressed in human bone both in fetal and adult life. The gene expression levels were significantly higher in fetal samples especially in mandibles. In addition, higher levels of VEGFR-3 in orofacial district were confirmed by western blotting analysis. We also observed that in fetal mandibular samples VEGFRs colocalized in several osteoblasts, osteoclasts and osteoprogenitor cells. Furthermore, some cells coexpressed VEGFR-3 and ET-1, a marker of neural crest cells. The results demonstrated different expression of VEGFRs in human mandibular and femoral bones which could be correlated to their different structure, function and development during organogenesis. VEGFR-3 might represent a specific signal for ectomesenchymal lineage differentiation during early human development.","authors":"Marini, M., Sarchielli, E., Toce, M., Acocella, A., Bertolai, R., Ciulli, C., Orlando, C., Sgambati, E., Vannelli, GB.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Histol Histopathol","volume":"27","issue":"12","page":"1579-87","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17124606","title":"The right dose for every sex.","abstract":"Sex chromosomes in different organisms are studied as model systems for chromatin regulation of transcription and epigenetics. Similar to the female X in mammals, the male X chromosome in Drosophila is involved in the process of dosage compensation. However, in contrast to one of the mammalian female X chromosomes undergoing inactivation, the Drosophila male X is transcriptionally upregulated by approximately twofold. The Drosophila male X is a remarkable example for a specialized, transcriptionally hyperactive chromatin domain that facilitates the study of chromatin regulation in the context of transcription, nuclear architecture, and chromatin remodeling. In addition, the rich phenomenology of dosage compensation in Drosophila provides an opportunity to explore the complexities of gene regulation through epigenetic chromatin configurations, histone modifications, and noncoding RNAs. Male-specific lethal (MSL) factors constitute the MSL complex or dosage compensation complex and are important for transcription regulation of X-linked genes. Recent biochemical studies have identified a number of interesting factors that associate with the MSL complex including components of the nuclear pore complex and exosome subunits. Furthermore, global analysis of MSL complex binding showed that MSL complexes are enriched on genes with preferential binding to 3' end of genes. Taken together, these findings suggest a role of the MSL complex in transcription elongation, RNA processing, and\/or nuclear organization.","authors":"Mendjan, S., Akhtar, A.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Chromosoma","volume":"116","issue":"2","page":"95-106","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28604678","title":"Dynamic subunit turnover in ESCRT-III assemblies is regulated by Vps4 to mediate membrane remodelling during cytokinesis.","abstract":"The endosomal sorting complex required for transport (ESCRT)-III mediates membrane fission in fundamental cellular processes, including cytokinesis. ESCRT-III is thought to form persistent filaments that over time increase their curvature to constrict membranes. Unexpectedly, we found that ESCRT-III at the midbody of human cells rapidly turns over subunits with cytoplasmic pools while gradually forming larger assemblies. ESCRT-III turnover depended on the ATPase VPS4, which accumulated at the midbody simultaneously with ESCRT-III subunits, and was required for assembly of functional ESCRT-III structures. In vitro, the Vps2\/Vps24 subunits of ESCRT-III formed side-by-side filaments with Snf7 and inhibited further polymerization, but the growth inhibition was alleviated by the addition of Vps4 and ATP. High-speed atomic force microscopy further revealed highly dynamic arrays of growing and shrinking ESCRT-III spirals in the presence of Vps4. Continuous ESCRT-III remodelling by subunit turnover might facilitate shape adaptions to variable membrane geometries, with broad implications for diverse cellular processes.","authors":"Mierzwa, BE., Chiaruttini, N., Redondo-Morata, L., von Filseck, JM., K\u00f6nig, J., Larios, J., Poser, I., M\u00fcller-Reichert, T., Scheuring, S., Roux, A., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Cell Biol","volume":"19","issue":"7","page":"787-798","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26688337","title":"Phosphorylation of an HP1-like Protein Regulates Heterochromatin Body Assembly for DNA Elimination.","abstract":"Heterochromatic loci are often assembled into higher-order heterochromatin bodies in diverse eukaryotes. However, the formation and biological roles of heterochromatin bodies are poorly understood. In the ciliated protozoan Tetrahymena, de novo heterochromatin body formation is accompanied by programmed DNA elimination. Here, we show that the heterochromatin body component Jub1p promotes heterochromatin body formation and dephosphorylation of the Heterochromatin Protein 1-like protein Pdd1p. Through the mutagenesis of the phosphorylated residues of Pdd1p, we demonstrate that Pdd1p dephosphorylation promotes the electrostatic interaction between Pdd1p and RNA in vitro and heterochromatin body formation in vivo. We therefore propose that heterochromatin body is assembled by the Pdd1p-RNA interaction. Pdd1p dephosphorylation and Jub1p are required for heterochromatin body formation and DNA elimination but not for local heterochromatin assembly, indicating that heterochromatin body plays an essential role in DNA elimination.","authors":"Kataoka, K., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Dev Cell","volume":"35","issue":"6","page":"775-88","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23019653","title":"An immunosurveillance mechanism controls cancer cell ploidy.","abstract":"Cancer cells accommodate multiple genetic and epigenetic alterations that initially activate intrinsic (cell-autonomous) and extrinsic (immune-mediated) oncosuppressive mechanisms. Only once these barriers to oncogenesis have been overcome can malignant growth proceed unrestrained. Tetraploidization can contribute to oncogenesis because hyperploid cells are genomically unstable. We report that hyperploid cancer cells become immunogenic because of a constitutive endoplasmic reticulum stress response resulting in the aberrant cell surface exposure of calreticulin. Hyperploid, calreticulin-exposing cancer cells readily proliferated in immunodeficient mice and conserved their increased DNA content. In contrast, hyperploid cells injected into immunocompetent mice generated tumors only after a delay, and such tumors exhibited reduced DNA content, endoplasmic reticulum stress, and calreticulin exposure. Our results unveil an immunosurveillance system that imposes immunoselection against hyperploidy in carcinogen- and oncogene-induced cancers.","authors":"Senovilla, L., Vitale, I., Martins, I., Tailler, M., Pailleret, C., Michaud, M., Galluzzi, L., Adjemian, S., Kepp, O., Niso-Santano, M., Shen, S., Mari\u00f1o, G., Criollo, A., Boil\u00e8ve, A., Job, B., Ladoire, S., Ghiringhelli, F., Sistigu, A., Yamazaki, T., Rello-Varona, S., Locher, C., Poirier-Colame, V., Talbot, M., Valent, A., Berardinelli, F., Antoccia, A., Ciccosanti, F., Fimia, GM., Piacentini, M., Fueyo, A., Messina, NL., Li, M., Chan, CJ., Sigl, V., Pourcher, G., Ruckenstuhl, C., Carmona-Gutierrez, D., Lazar, V., Penninger, JM., Madeo, F., L\u00f3pez-Ot\u00edn, C., Smyth, MJ., Zitvogel, L., Castedo, M., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Science","volume":"337","issue":"6102","page":"1678-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11040215","title":"Raf induces TGFbeta production while blocking its apoptotic but not invasive responses: a mechanism leading to increased malignancy in epithelial cells.","abstract":"c-Raf-1 is a major effector of Ras proteins, responsible for activation of the ERK MAP kinase pathway and a critical regulator of both normal growth and oncogenic transformation. Using an inducible form of Raf in MDCK cells, we have shown that sustained activation of Raf alone is able to induce the transition from an epithelial to a mesenchymal phenotype. Raf promoted invasive growth in collagen gels, a characteristic of malignant cells; this was dependent on the operation of an autocrine loop involving TGFbeta, whose secretion was induced by Raf. TGFbeta induced growth inhibition and apoptosis in normal MDCK cells: Activation of Raf led to inhibition of the ability of TGFbeta to induce apoptosis but not growth retardation. ERK has been reported previously to inhibit TGFbeta signaling via phosphorylation of the linker region of Smads, which prevents their translocation to the nucleus. However, we found no evidence in this system that ERK can significantly influence the function of Smad2, Smad3, and Smad4 at the level of nuclear translocation, DNA binding, or transcriptional activation. Instead, strong activation of Raf caused a broad protection of these cells from various apoptotic stimuli, allowing them to respond to TGFbeta with increased invasiveness while avoiding cell death. The Raf-MAP kinase pathway thus synergizes with TGFbeta in promoting malignancy but does not directly impair TGFbeta-induced Smad signaling.","authors":"Lehmann, K., Janda, E., Pierreux, CE., Ryt\u00f6maa, M., Schulze, A., McMahon, M., Hill, CS., Beug, H., Downward, J.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Genes Dev","volume":"14","issue":"20","page":"2610-22","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2000-11-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26680207","title":"Inhibition of the TNF Family Cytokine RANKL Prevents Autoimmune Inflammation in the Central Nervous System.","abstract":"The central nervous system (CNS) is an immunologically privileged site protected from uncontrolled access of T cells by the blood-brain barrier (BBB), which is breached upon autoimmune inflammation. Here we have shown that receptor activator of nuclear factor-\u03baB (NF-\u03baB) ligand (RANKL) on T cells regulates C-C type chemokine ligand 20 (CCL20) production by astrocytes and T cell localization in the CNS. Importantly, mice specifically lacking RANKL in T cells were resistant to experimental autoimmune encephalomyelitis (EAE) due to altered T cell trafficking. Pharmacological inhibition of RANKL prevented the development of EAE without affecting the peripheral immune response, indicating that RANKL is a potential therapeutic target for treating autoimmune diseases in the CNS.","authors":"Guerrini, MM., Okamoto, K., Komatsu, N., Sawa, S., Danks, L., Penninger, JM., Nakashima, T., Takayanagi, H.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Immunity","volume":"43","issue":"6","page":"1174-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1918145","title":"Microtubule behavior in the growth cones of living neurons during axon elongation.","abstract":"To understand how microtubules are generated in the growth cone, we have imaged fluorescently tagged microtubules in living frog embryonic neurons. The neurons were labeled by injecting rhodamine-labeled tubulin into the fertilized egg and explanting the neurons from the neural tube. Microtubules extend deep into the growth cone periphery and adopt three characteristic distributions: (a) dispersed and splayed throughout much of the growth cone; (b) looped and apparently contorted by compression; and (c) bundled into tight arrays. These distributions interconvert on a time scale of several minutes and these interconversions are correlated with the behavior of the growth cone. We observed microtubule growth and shrinkage in growth cones, but are unable to determine their contribution to net assembly. However, translocation of polymer form the axon appears to be a major mechanism of generating new polymer in the growth cone, while bundling of microtubules in the growth cone appears to be the critical step in generating new axon. Neurons that were about to turn spontaneously generated microtubules in the future direction of growth, suggesting that orientation of microtubules might be an important early step in neuronal pathfinding.","authors":"Tanaka, EM., Kirschner, MW.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"J Cell Biol","volume":"115","issue":"2","page":"345-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1991-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18200042","title":"Crif1 is a novel transcriptional coactivator of STAT3.","abstract":"Signal transducer and activator of transcription 3 (STAT3) is a transcriptional factor that performs a broad spectrum of biological functions in response to various stimuli. However, no specific coactivator that regulates the transcriptional activity of STAT3 has been identified. Here we report that CR6-interacting factor 1 (Crif1) is a specific transcriptional coactivator of STAT3, but not of STAT1 or STAT5a. Crif1 interacts with STAT3 and positively regulates its transcriptional activity. Crif1-\/- embryos were lethal around embryonic day 6.5, and manifested developmental arrest accompanied with defective proliferation and massive apoptosis. The expression of STAT3 target genes was markedly reduced in a Crif1-\/- blastocyst culture and in Oncostatin M-stimulated Crif1-deficient MEFs. Importantly, the key activities of constitutively active STAT3-C, such as transcription, DNA binding, and cellular transformation, were abolished in the Crif1-null MEFs, suggesting the essential role of Crif1 in the transcriptional activity of STAT3. Our results reveal that Crif1 is a novel and essential transcriptional coactivator of STAT3 that modulates its DNA binding ability, and shed light on the regulation of oncogenic STAT3.","authors":"Kwon, MC., Koo, BK., Moon, JS., Kim, YY., Park, KC., Kim, NS., Kwon, MY., Kong, MP., Yoon, KJ., Im, SK., Ghim, J., Han, YM., Jang, SK., Shong, M., Kong, YY.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"EMBO J","volume":"27","issue":"4","page":"642-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28615312","title":"Stem Cells in Repair of Gastrointestinal Epithelia.","abstract":"Among the endodermal tissues of adult mammals, the gastrointestinal (GI) epithelium exhibits the highest turnover rate. As the ingested food moves along the GI tract, gastric acid, digestive enzymes, and gut resident microbes aid digestion as well as nutrient and mineral absorption. Due to the harsh luminal environment, replenishment of new epithelial cells is essential to maintain organ structure and function during routine turnover and injury repair. Tissue-specific adult stem cells in the GI tract serve as a continuous source for this immense regenerative activity. Tissue homeostasis is achieved by a delicate balance between gain and loss of cells. In homeostasis, temporal tissue damage is rapidly restored by well-balanced tissue regeneration, whereas prolonged imbalance may result in diverse pathologies of homeostasis and injury repair. Starting with a summary of the current knowledge of GI tract homeostasis, we continue with providing models of acute injury and chronic diseases. Finally, we will discuss how primary organoid cultures allow new insights into the mechanisms of homeostasis, injury repair, and disease, and how this novel 3D culture system has the potential to translate into the clinic.","authors":"Andersson-Rolf, A., Zilbauer, M., Koo, BK., Clevers, H.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Physiology (Bethesda)","volume":"32","issue":"4","page":"278-289","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10362357","title":"cbl-3: a new mammalian cbl family protein.","abstract":"We have cloned a new human gene, cbl-3, which encodes a protein with marked homology to the cbl family of proteins. The predicted protein encoded by this gene retains the conserved phosphotyrosine binding domain (PTB) in the N-terminal and the zinc finger but is significantly shorter (MW 52.5 kDa) than the other mammalian cbl proteins. The protein lacks the extensive proline rich domain and leucine zipper seen in c-cbl and cbl-b and structurally most resembles the C. elegans and Drosophila cbl proteins. The gene is ubiquitously expressed with highest expression in the aerodigestive tract, prostate, adrenal gland, and salivary gland. The protein is phosphorylated and recruited to the EGFR upon EGF stimulation and inhibits EGF stimulated MAP kinase activation. In comparison to the other mammalian cbl proteins (e.g. cbl-b), cbl-3 interacts with a restricted range of proteins containing Src Homology 3 regions. An alternatively spliced form of the cbl-3 protein was also identified which deletes a critical region of the PTB domain and which does not interact with the EGFR nor inhibit EGF stimulated MAP kinase activation. These data demonstrate that cbl-3, a novel mammalian cbl protein, is a regulator of EGFR mediated signal transduction.","authors":"Keane, MM., Ettenberg, SA., Nau, MM., Banerjee, P., Cuello, M., Penninger, J., Lipkowitz, S.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Oncogene","volume":"18","issue":"22","page":"3365-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16144844","title":"A novel role for GADD45beta as a mediator of MMP-13 gene expression during chondrocyte terminal differentiation.","abstract":"The growth arrest and DNA damage-inducible 45beta (GADD45beta) gene product has been implicated in the stress response, cell cycle arrest, and apoptosis. Here we demonstrated the unexpected expression of GADD45beta in the embryonic growth plate and uncovered its novel role as an essential mediator of matrix metalloproteinase-13 (MMP-13) expression during terminal chondrocyte differentiation. We identified GADD45beta as a prominent early response gene induced by bone morphogenetic protein-2 (BMP-2) through a Smad1\/Runx2-dependent pathway. Because this pathway is involved in skeletal development, we examined mouse embryonic growth plates, and we observed expression of Gadd45beta mRNA coincident with Runx2 protein in pre-hypertrophic chondrocytes, whereas GADD45beta protein was localized prominently in the nucleus in late stage hypertrophic chondrocytes where Mmp-13 mRNA was expressed. In Gadd45beta(-\/-) mouse embryos, defective mineralization and decreased bone growth accompanied deficient Mmp-13 and Col10a1 gene expression in the hypertrophic zone. Transduction of small interfering RNA-GADD45beta in epiphyseal chondrocytes in vitro blocked terminal differentiation and the associated expression of Mmp-13 and Col10a1 mRNA in vitro. Finally, GADD45beta stimulated MMP-13 promoter activity in chondrocytes through the JNK-mediated phosphorylation of JunD, partnered with Fra2, in synergy with Runx2. These observations indicated that GADD45beta plays an essential role during chondrocyte terminal differentiation.","authors":"Ijiri, K., Zerbini, LF., Peng, H., Correa, RG., Lu, B., Walsh, N., Zhao, Y., Taniguchi, N., Huang, XL., Otu, H., Wang, H., Wang, JF., Komiya, S., Ducy, P., Rahman, MU., Flavell, RA., Gravallese, EM., Oettgen, P., Libermann, TA., Goldring, MB.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Biol Chem","volume":"280","issue":"46","page":"38544-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16139215","title":"Localization-dependent and -independent roles of numb contribute to cell-fate specification in Drosophila.","abstract":"During asymmetric cell division, protein determinants are segregated into one of the two daughter cells. The Numb protein acts as a segregating determinant during both mouse and Drosophila development. In flies, Numb localizes asymmetrically and is required for cell-fate specification in the central and peripheral nervous systems, as well as during muscle and heart development. Whether its asymmetric segregation is important to the performance of these functions is not firmly established. Here, we demonstrate that Numb acts both in a localization-dependent and in a localization-independent manner. We have generated numb mutants that affect only the asymmetric localization of the protein during mitosis. We demonstrate that asymmetric segregation of Numb into one of the two daughter cells is absolutely essential for cell-fate specification in the Drosophila peripheral nervous system. Numb localization is also essential in MP2 neuroblasts in the central nervous system and during muscle development. Surprisingly, in dividing ganglion mother cells or during heart development, Numb function is independent of its ability to segregate asymmetrically in mitosis. Our results suggest that two classes of asymmetric cell division exist, each with different requirements for asymmetric inheritance of cell-fate determinants.","authors":"Bhalerao, S., Berdnik, D., T\u00f6r\u00f6k, T., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"17","page":"1583-90","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26550828","title":"Transcriptional regulators form diverse groups with context-dependent regulatory functions.","abstract":"One of the most important questions in biology is how transcription factors (TFs) and cofactors control enhancer function and thus gene expression. Enhancer activation usually requires combinations of several TFs, indicating that TFs function synergistically and combinatorially. However, while TF binding has been extensively studied, little is known about how combinations of TFs and cofactors control enhancer function once they are bound. It is typically unclear which TFs participate in combinatorial enhancer activation, whether different TFs form functionally distinct groups, or if certain TFs might substitute for each other in defined enhancer contexts. Here we assess the potential regulatory contributions of TFs and cofactors to combinatorial enhancer control with enhancer complementation assays. We recruited GAL4-DNA-binding-domain fusions of 812 Drosophila TFs and cofactors to 24 enhancer contexts and measured enhancer activities by 82,752 luciferase assays in S2 cells. Most factors were functional in at least one context, yet their contributions differed between contexts and varied from repression to activation (up to 289-fold) for individual factors. Based on functional similarities across contexts, we define 15 groups of TFs that differ in developmental functions and protein sequence features. Similar TFs can substitute for each other, enabling enhancer re-engineering by exchanging TF motifs, and TF-cofactor pairs cooperate during enhancer control and interact physically. Overall, we show that activators and repressors can have diverse regulatory functions that typically depend on the enhancer context. The systematic functional characterization of TFs and cofactors should further our understanding of combinatorial enhancer control and gene regulation.","authors":"Stampfel, G., Kazmar, T., Frank, O., Wienerroither, S., Reiter, F., Stark, A.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nature","volume":"528","issue":"7580","page":"147-51","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27742791","title":"Neural tube morphogenesis in synthetic 3D microenvironments.","abstract":"Three-dimensional organoid constructs serve as increasingly widespread in vitro models for development and disease modeling. Current approaches to recreate morphogenetic processes in vitro rely on poorly controllable and ill-defined matrices, thereby largely overlooking the contribution of biochemical and biophysical extracellular matrix (ECM) factors in promoting multicellular growth and reorganization. Here, we show how defined synthetic matrices can be used to explore the role of the ECM in the development of complex 3D neuroepithelial cysts that recapitulate key steps in early neurogenesis. We demonstrate how key ECM parameters are involved in specifying cytoskeleton-mediated symmetry-breaking events that ultimately lead to neural tube-like patterning along the dorsal-ventral (DV) axis. Such synthetic materials serve as valuable tools for studying the discrete action of extrinsic factors in organogenesis, and allow for the discovery of relationships between cytoskeletal mechanobiology and morphogenesis.","authors":"Ranga, A., Girgin, M., Meinhardt, A., Eberle, D., Caiazzo, M., Tanaka, EM., Lutolf, MP.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Proc Natl Acad Sci U S A","volume":"113","issue":"44","page":"E6831-E6839","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22938334","title":"High pressure sample cell for total internal reflection fluorescence spectroscopy at pressures up to 2500 bar.","abstract":"Total internal reflection fluorescence (TIRF) spectroscopy is a surface sensitive technique that is widely used to characterize the structure and dynamics of molecules at planar liquid-solid interfaces. In particular, biomolecular systems, such as protein adsorbates and lipid membranes can easily be studied by TIRF spectroscopy. Applying pressure to molecular systems offers access to all kinds of volume changes occurring during assembly of molecules, phase transitions, and chemical reactions. So far, most of these volume changes have been characterized in bulk solution, only. Here, we describe the design and performance of a high pressure sample cell that allows for TIRF spectroscopy under high pressures up to 2500 bar (2.5 \u00d7 10(8) Pa), in order to expand the understanding of volume effects from the bulk phase to liquid-solid interfaces. The new sample cell is based on a cylindrical body made of Nimonic 90 alloy and incorporates a pressure transmitting sample cuvette. This cuvette is composed of a fused silica prism and a flexible rubber gasket. It contains the sample solution and ensures a complete separation of the sample from the liquid pressure medium. The sample solution is in contact with the inner wall of the prism forming the interface under study, where fluorescent molecules are immobilized. In this way, the new high pressure TIRF sample cell is very useful for studying any biomolecular layer that can be deposited at a planar water-silica interface. As examples, high pressure TIRF data of adsorbed lysozyme and two phospholipid membranes are presented.","authors":"Koo, J., Czeslik, C.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Rev Sci Instrum","volume":"83","issue":"8","page":"085109","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16107473","title":"Proximodistal identity during vertebrate limb regeneration is regulated by Meis homeodomain proteins.","abstract":"The mechanisms by which cells obtain instructions to precisely re-create the missing parts of an organ remain an unresolved question in regenerative biology. Urodele limb regeneration is a powerful model in which to study these mechanisms. Following limb amputation, blastema cells interpret the proximal-most positional identity in the stump to reproduce missing parts faithfully. Classical experiments showed the ability of retinoic acid (RA) to proximalize blastema positional values. Meis homeobox genes are involved in RA-dependent specification of proximal cell identity during limb development. To understand the molecular basis for specifying proximal positional identities during regeneration, we isolated the axolotl Meis homeobox family. Axolotl Meis genes are RA-regulated during both regeneration and embryonic limb development. During limb regeneration, Meis overexpression relocates distal blastema cells to more proximal locations, whereas Meis knockdown inhibits RA proximalization of limb blastemas. Meis genes are thus crucial targets of RA proximalizing activity on blastema cells.","authors":"Mercader, N., Tanaka, EM., Torres, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Development","volume":"132","issue":"18","page":"4131-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28504681","title":"Fused cerebral organoids model interactions between brain regions.","abstract":"Human brain development involves complex interactions between different regions, including long-distance neuronal migration or formation of major axonal tracts. Different brain regions can be cultured in vitro within 3D cerebral organoids, but the random arrangement of regional identities limits the reliable analysis of complex phenotypes. Here, we describe a coculture method combining brain regions of choice within one organoid tissue. By fusing organoids of dorsal and ventral forebrain identities, we generate a dorsal-ventral axis. Using fluorescent reporters, we demonstrate CXCR4-dependent GABAergic interneuron migration from ventral to dorsal forebrain and describe methodology for time-lapse imaging of human interneuron migration. Our results demonstrate that cerebral organoid fusion cultures can model complex interactions between different brain regions. Combined with reprogramming technology, fusions should offer researchers the possibility to analyze complex neurodevelopmental defects using cells from neurological disease patients and to test potential therapeutic compounds.","authors":"Bagley, JA., Reumann, D., Bian, S., L\u00e9vi-Strauss, J., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Methods","volume":"14","issue":"7","page":"743-751","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26478179","title":"Global brain dynamics embed the motor command sequence of Caenorhabditis elegans.","abstract":"While isolated motor actions can be correlated with activities of neuronal networks, an unresolved problem is how the brain assembles these activities into organized behaviors like action sequences. Using brain-wide calcium imaging in Caenorhabditis elegans, we show that a large proportion of neurons across the brain share information by engaging in coordinated, dynamical network activity. This brain state evolves on a cycle, each segment of which recruits the activities of different neuronal sub-populations and can be explicitly mapped, on a single trial basis, to the animals' major motor commands. This organization defines the assembly of motor commands into a string of run-and-turn action sequence cycles, including decisions between alternative behaviors. These dynamics serve as a robust scaffold for action selection in response to sensory input. This study shows that the coordination of neuronal activity patterns into global brain dynamics underlies the high-level organization of behavior.","authors":"Kato, S., Kaplan, HS., Schr\u00f6del, T., Skora, S., Lindsay, TH., Yemini, E., Lockery, S., Zimmer, M.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell","volume":"163","issue":"3","page":"656-69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28104841","title":"Human tissues in a dish: The research and ethical implications of organoid technology.","abstract":"The ability to generate human tissues in vitro from stem cells has raised enormous expectations among the biomedical research community, patients, and the general public. These organoids enable studies of normal development and disease and allow the testing of compounds directly on human tissue. Organoids hold the promise to influence the entire innovation cycle in biomedical research. They affect fields that have been subjects of intense ethical debate, ranging from animal experiments and the use of embryonic or fetal human tissues to precision medicine, organoid transplantation, and gene therapy. However, organoid research also raises additional ethical questions that require reexamination and potential recalibration of ethical and legal policies. In this Review, we describe the current state of research and discuss the ethical implications of organoid technology.","authors":"Bredenoord, AL., Clevers, H., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Science","volume":"355","issue":"6322","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17003037","title":"Neuralized-2 regulates a Notch ligand in cooperation with Mind bomb-1.","abstract":"Mutations in Drosophila neuralized (Dneur) result in a variety of developmental defects that closely resemble those of Notch mutants and other Notch pathway mutants. However, mice with disrupted neur1 do not show any aberrant cell fate specifications in neurogenesis and somitogenesis. Thus, we speculated that other vertebrate neur homolog(s) might compensate for loss of the neur gene. Here, we report the paralog of mouse Neur1, named Neuralized-2 (Neur2), which is a ubiquitin-protein isopeptide ligase (E3) that interacts with and ubiquitinates Delta. Both murine Neur1 and Neur2 have similar degrees of homology to DNeur, and neur2 is expressed in patterns similar to those of neur1 in embryos, suggesting potential functional redundancy. Interestingly, two distinct classes of E3 ligases, Mind bomb-1 (Mib1) and Neur2, have cooperative but distinct roles in Delta endocytosis to Hrs-positive vesicles, i.e. Mib1 functions in the initial step of Delta endocytosis, and Neur2 is required for targeting endocytosed Delta to Hrs-positive vesicles. Thus, our study provides a new insight into how distinct E3 ligases work together in the endocytic pathways for Notch signaling.","authors":"Song, R., Koo, BK., Yoon, KJ., Yoon, MJ., Yoo, KW., Kim, HT., Oh, HJ., Kim, YY., Han, JK., Kim, CH., Kong, YY.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Biol Chem","volume":"281","issue":"47","page":"36391-400","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25740493","title":"Transgenesis in axolotl (Ambystoma mexicanum).","abstract":"Transgenic animals have been indispensable in elucidating and deciphering mechanisms underlying various biological phenomena. In regeneration, transgenic animals expressing fluorescent protein genes have been crucial for identifying the source cells for regeneration and the mechanism of blastema formation. Animals are usually generated by manipulating their genome using various techniques at\/in one cell embryo\/fertilized egg stage. Here, we describe the generation of germline transgenic axolotls (Ambystoma mexicanum) using the I-SceI meganuclease and Tol2 transposase.","authors":"Khattak, S., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Methods Mol Biol","volume":"1290","issue":null,"page":"269-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22914942","title":"Reconstitution of the central nervous system during salamander tail regeneration from the implanted neurospheres.","abstract":"Urodele amphibians such as axolotl are well known for their regenerative potential of the damaged central nervous system structures. Upon tail amputation, neural stem cells behind the amputation plane undergo self-renewing divisions and contribute to the functional spinal cord in the newly formed regenerate. The neural stem cells, harboring this potential, can be isolated from the animal and cultured under the suspension conditions. After 2-3 weeks in vitro they will proliferate and form the floating aggregates of the spherical shape, so-called neurospheres. Reimplanted back into the animal, the neurospheres can efficiently integrate in the spinal cord lesion and contribute to the following spinal cord regeneration events. Here we demonstrate the unique method of the axolotl tail spinal cord regeneration from the implanted neurosphere.","authors":"McHedlishvili, L., Mazurov, V., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Methods Mol Biol","volume":"916","issue":null,"page":"197-202","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27816209","title":"Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors.","abstract":"Gene expression is regulated by genomic enhancers that recruit transcription factors and cofactors to activate transcription from target core promoters. Over the past years, thousands of enhancers and core promoters in animal genomes have been annotated, and we have learned much about the domain structure in which regulatory genomes are organized in animals. Enhancer-core-promoter targeting occurs at several levels, including regulatory domains, DNA accessibility, and sequence-encoded core-promoter specificities that are likely mediated by different regulatory proteins. We review here current knowledge about enhancer-core-promoter targeting, regulatory communication between enhancers and core promoters, and the protein factors involved. We conclude with an outlook on open questions that we find particularly interesting and that will likely lead to additional insights in the upcoming years.","authors":"Zabidi, MA., Stark, A.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Trends Genet","volume":"32","issue":"12","page":"801-814","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22903568","title":"Systems biology approach for new target and biomarker identification.","abstract":"The pharmaceutical industry is spending increasingly large amounts of money on the discovery and development of novel medicines, but this investment is not adequately paying off in an increased rate of newly approved drugs by the FDA. The post-genomic era has provided a wealth of novel approaches for generating large, high-dimensional genetic and transcriptomic data sets from large cohorts of preclinical species as well as normal and diseased individuals. This systems biology approach to understanding disease-related biology is revolutionizing our understanding of the cellular pathways and gene networks underlying the onset of disease, and the mechanisms of pharmacological treatments that ameliorate disease phenotypes. In this article, we review a number of approaches being used by pharmaceutical and biotechnology companies, e.g., high-throughput DNA genotyping, sequencing, and genome-wide gene expression profiling, to enable drug discovery and development through the identification of new drug targets and biomarkers of disease progression, drug pharmacodynamics, and predictive markers for selecting the patients most likely to respond to therapy.","authors":"Wang, IM., Stone, DJ., Nickle, D., Loboda, A., Puig, O., Roberts, C.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Curr Top Microbiol Immunol","volume":"363","issue":"","page":"169-99","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16857196","title":"Snx5, as a Mind bomb-binding protein, is expressed in hematopoietic and endothelial precursor cells in zebrafish.","abstract":"Notch signaling has an evolutionarily conserved function for cell fate determination and stem cell maintenance. Previously, we identified a novel component of the Notch signaling pathway in zebrafish, mind bomb, which encodes an E3 ubiquitin ligase essential for Notch signal activation. Further studies showed that Mind bomb(-\/-) mouse embryos exhibited pan-Notch phenotypes in various tissues, suggesting that Mind bomb function is conserved in mammals. Therefore we sought to understand the various molecular partners of Mind bomb using yeast two-hybrid screening. In this search we identified Sorting nexin 5 (Snx5) as a novel interacting partner of Mind bomb. Furthermore we demonstrated that Snx5 colocalizes with Mind bomb in early endosomal compartments, suggesting that Snx5 is important for Mind bomb trafficking. In addition, we identified zebrafish orthologue of Snx5 and showed that snx5 is predominantly expressed in hematopoietic and endothelial precursor cells in zebrafish. We also found defects in hematopoiesis and blood vessel development in snx5 morpholino-injected embryos. Taken together, we show that Snx5, a novel interacting partner of Mind bomb, may have an essential role for cell fate determination in early development.","authors":"Yoo, KW., Kim, EH., Jung, SH., Rhee, M., Koo, BK., Yoon, KJ., Kong, YY., Kim, CH.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"FEBS Lett","volume":"580","issue":"18","page":"4409-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28004710","title":"Lab-Built Brains.","abstract":null,"authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Sci Am","volume":"316","issue":"1","page":"26-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10215628","title":"TRAF6 deficiency results in osteopetrosis and defective interleukin-1, CD40, and LPS signaling.","abstract":"Bone resorption and remodeling is an intricately controlled, physiological process that requires the function of osteoclasts. The processes governing both the differentiation and activation of osteoclasts involve signals induced by osteoprotegerin ligand (OPGL), a member of tumor necrosis factor (TNF) superfamily, and its cognate receptor RANK. The molecular mechanisms of the intracellular signal transduction remain to be elucidated. Here we report that mice deficient in TNF receptor-associated factor 6 (TRAF6) are osteopetrotic with defects in bone remodeling and tooth eruption due to impaired osteoclast function. Using in vitro assays, we demonstrate that TRAF6 is crucial not only in IL-1 and CD40 signaling but also, surprisingly, in LPS signaling. Furthermore, like TRAF2 and TRAF3, TRAF6 is essential for perinatal and postnatal survival. These findings establish unexpectedly diverse and critical roles for TRAF6 in perinatal and postnatal survival, bone metabolism, LPS, and cytokine signaling.","authors":"Lomaga, MA., Yeh, WC., Sarosi, I., Duncan, GS., Furlonger, C., Ho, A., Morony, S., Capparelli, C., Van, G., Kaufman, S., van der Heiden, A., Itie, A., Wakeham, A., Khoo, W., Sasaki, T., Cao, Z., Penninger, JM., Paige, CJ., Lacey, DL., Dunstan, CR., Boyle, WJ., Goeddel, DV., Mak, TW.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Genes Dev","volume":"13","issue":"8","page":"1015-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25740481","title":"High-efficiency electroporation of the spinal cord in larval axolotl.","abstract":"Axolotls are well known for their remarkable ability to regenerate complex body parts and structures throughout life, including the entire limb and tail. Particularly fascinating is their ability to regenerate a fully functional spinal cord after losing the tail. Electroporation of DNA plasmids or morpholinos is a valuable tool to gain mechanistic insight into the cellular and molecular basis of regeneration. It provides among other advantages a simple and fast method to test gene function in a temporally and spatially controlled manner. Some classic drawbacks of the method, such as low transfection efficiency and damage to the tissue, had hindered our understanding of the contribution of different signaling pathways to regeneration. Here, we describe a comprehensive protocol for electroporation of the axolotl spinal cord that overcomes this limitations using a combination of high-voltage and short-length pulses followed by lower-voltage and longer-length pulses. Our approach yields highly efficient transfection of spinal cord cells with minimal tissue damage, which now allows the molecular dissection of spinal cord regeneration.","authors":"Rodrigo Albors, A., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Methods Mol Biol","volume":"1290","issue":null,"page":"115-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27774567","title":"Mice haploinsufficient for Map2k7, a gene involved in neurodevelopment and risk for schizophrenia, show impaired attention, a vigilance decrement deficit and unstable cognitive processing in an attentional task: impact of minocycline.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Curated\" Owner=\"NLM\"><PMID Version=\"1\">27774567<\/PMID><DateCompleted><Year>2017<\/Year><Month>12<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>03<\/Month><Day>18<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1432-2072<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>234<\/Volume><Issue>2<\/Issue><PubDate><Year>2017<\/Year><Month>Jan<\/Month><\/PubDate><\/JournalIssue><Title>Psychopharmacology<\/Title><ISOAbbreviation>Psychopharmacology (Berl)<\/ISOAbbreviation><\/Journal><ArticleTitle>Mice haploinsufficient for Map2k7, a gene involved in neurodevelopment and risk for schizophrenia, show impaired attention, a vigilance decrement deficit and unstable cognitive processing in an attentional task: impact of minocycline.<\/ArticleTitle><Pagination><MedlinePgn>293-305<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s00213-016-4463-y<\/ELocationID><Abstract><AbstractText Label=\"RATIONALE\">Members of the c-Jun N-terminal kinase (JNK) family of mitogen-activated protein (MAP) kinases, and the upstream kinase MKK7, have all been strongly linked with synaptic plasticity and with the development of the neocortex. However, the impact of disruption of this pathway on cognitive function is unclear.","authors":"Openshaw, RL., Thomson, DM., Penninger, JM., Pratt, JA., Morris, BJ.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Psychopharmacology (Berl)","volume":"234","issue":"2","page":"293-305","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10883659","title":"Recent advances in research on multistage tumorigenesis.","abstract":"Tumour development is a multi-step process during which genetic and epigenetic events determine the transition from a normal to a malignant cellular state. In the past decade, extensive effort has been made not only to define the molecular mechanisms underlying progression to malignancy but also to predict the development of the disease and to identify possible molecular targets for therapy. Common to most tumours, several regulatory circuits are altered during multistage tumour progression, most importantly, the control of proliferation, the balance between cell survival and programmed cell death (apoptosis), the communication with neighbouring cells and the extracellular matrix, the induction of tumour neovascularization (angiogenesis) and, finally, tumour cell migration, invasion and metastatic dissemination. De-regulation of each of these processes represents a rate-limiting step for tumour development and, hence, has to be achieved by tumour cells in a highly selective manner during tumour progression. In this review we summarize recent advances in cancer research that have provided new insights in the molecular mechanisms underlying the transition between one tumour stage and the next and into their concerted action during tumour progression. Cultured human tumour cell lines as well as transgenic and knock-out mouse models of tumorigenesis have been instrumental in these experimental approaches.","authors":"Compagni, A., Christofori, G.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Br J Cancer","volume":"83","issue":"1","page":"1-5","pdf":null,"JrId":"1765","fulltextlink":null,"preprintlink":null,"articledate":"2000-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23080075","title":"A comparative study to distinguish the vineyard of origin by NIRS using entire grapes, skins and seeds.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23080075<\/PMID><DateCompleted><Year>2013<\/Year><Month>08<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2013<\/Year><Month>02<\/Month><Day>18<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1097-0010<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>93<\/Volume><Issue>4<\/Issue><PubDate><Year>2013<\/Year><Month>Mar<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Journal of the science of food and agriculture<\/Title><ISOAbbreviation>J Sci Food Agric<\/ISOAbbreviation><\/Journal><ArticleTitle>A comparative study to distinguish the vineyard of origin by NIRS using entire grapes, skins and seeds.<\/ArticleTitle><Pagination><MedlinePgn>967-72<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/jsfa.5842<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Interest in high-quality products with a clear geographical origin is increasing. For the wine industry and market sector, identity preservation is of fundamental importance owing to the large number of geographical classifications. Nowadays, there is a growing demand for analytical methods for tracing grapes and wines. In the oenological sector, infrared spectroscopy is becoming an attractive tool allowing simultaneous measurement of several analytical parameters and enabling real-time decision making.","authors":"Ferrer-Gallego, R., Hern\u00e1ndez-Hierro, JM., Rivas-Gonzalo, JC., Escribano-Bail\u00f3n, MT.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Sci Food Agric","volume":"93","issue":"4","page":"967-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23064749","title":"Evolutionary dynamism of the primate LRRC37 gene family.","abstract":"Core duplicons in the human genome represent ancestral duplication modules shared by the majority of intrachromosomal duplication blocks within a given chromosome. These cores are associated with the emergence of novel gene families in the hominoid lineage, but their genomic organization and gene characterization among other primates are largely unknown. Here, we investigate the genomic organization and expression of the core duplicon on chromosome 17 that led to the expansion of LRRC37 during primate evolution. A comparison of the LRRC37 gene family organization in human, orangutan, macaque, marmoset, and lemur genomes shows the presence of both orthologous and species-specific gene copies in all primate lineages. Expression profiling in mouse, macaque, and human tissues reveals that the ancestral expression of LRRC37 was restricted to the testis. In the hominid lineage, the pattern of LRRC37 became increasingly ubiquitous, with significantly higher levels of expression in the cerebellum and thymus, and showed a remarkable diversity of alternative splice forms. Transfection studies in HeLa cells indicate that the human FLAG-tagged recombinant LRRC37 protein is secreted after cleavage of a transmembrane precursor and its overexpression can induce filipodia formation.","authors":"Giannuzzi, G., Siswara, P., Malig, M., Marques-Bonet, T., Mullikin, JC., Ventura, M., Eichler, EE.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Genome Res","volume":"23","issue":"1","page":"46-59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10952727","title":"Two distinct pathways leading to nuclear apoptosis.","abstract":"Apaf-1(-\/-) or caspase-3(-\/-) cells treated with a variety of apoptosis inducers manifest apoptosis-associated alterations including the translocation of apoptosis-inducing factor (AIF) from mitochondria to nuclei, large scale DNA fragmentation, and initial chromatin condensation (stage I). However, when compared with normal control cells, Apaf-1(-\/-) or caspase-3(-\/-) cells fail to exhibit oligonucleosomal chromatin digestion and a more advanced pattern of chromatin condensation (stage II). Microinjection of such cells with recombinant AIF only causes peripheral chromatin condensation (stage I), whereas microinjection with activated caspase-3 or its downstream target caspase-activated DNAse (CAD) causes a more pronounced type of chromatin condensation (stage II). Similarly, when added to purified HeLa nuclei, AIF causes stage I chromatin condensation and large-scale DNA fragmentation, whereas CAD induces stage II chromatin condensation and oligonucleosomal DNA degradation. Furthermore, in a cell-free system, concomitant neutralization of AIF and CAD is required to suppress the nuclear DNA loss caused by cytoplasmic extracts from apoptotic wild-type cells. In contrast, AIF depletion alone suffices to suppress the nuclear DNA loss contained in extracts from apoptotic Apaf-1(-\/-) or caspase-3(-\/-) cells. As a result, at least two redundant parallel pathways may lead to chromatin processing during apoptosis. One of these pathways involves Apaf-1 and caspases, as well as CAD, and leads to oligonucleosomal DNA fragmentation and advanced chromatin condensation. The other pathway, which is caspase-independent, involves AIF and leads to large-scale DNA fragmentation and peripheral chromatin condensation.","authors":"Susin, SA., Daugas, E., Ravagnan, L., Samejima, K., Zamzami, N., Loeffler, M., Costantini, P., Ferri, KF., Irinopoulou, T., Pr\u00e9vost, MC., Brothers, G., Mak, TW., Penninger, J., Earnshaw, WC., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Exp Med","volume":"192","issue":"4","page":"571-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22902500","title":"Dopamine neurons modulate pheromone responses in Drosophila courtship learning.","abstract":"Learning through trial-and-error interactions allows animals to adapt innate behavioural \u2018rules of thumb\u2019 to the local environment, improving their prospects for survival and reproduction. Naive Drosophila melanogaster males, for example, court both virgin and mated females, but learn through experience to selectively suppress futile courtship towards females that have already mated. Here we show that courtship learning reflects an enhanced response to the male pheromone cis-vaccenyl acetate (cVA), which is deposited on females during mating and thus distinguishes mated females from virgins. Dissociation experiments suggest a simple learning rule in which unsuccessful courtship enhances sensitivity to cVA. The learning experience can be mimicked by artificial activation of dopaminergic neurons, and we identify a specific class of dopaminergic neuron that is critical for courtship learning. These neurons provide input to the mushroom body (MB) \u03b3 lobe, and the DopR1 dopamine receptor is required in MB\u03b3 neurons for both natural and artificial courtship learning. Our work thus reveals critical behavioural, cellular and molecular components of the learning rule by which Drosophila adjusts its innate mating strategy according to experience.","authors":"Keleman, K., Vrontou, E., Kr\u00fcttner, S., Yu, JY., Kurtovic-Kozaric, A., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nature","volume":"489","issue":"7414","page":"145-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26764096","title":"Augmin shapes the anaphase spindle for efficient cytokinetic furrow ingression and abscission.","abstract":"During anaphase, distinct populations of microtubules (MTs) form by either centrosome-dependent or augmin-dependent nucleation. It remains largely unknown whether these different MT populations contribute distinct functions to cytokinesis. Here we show that augmin-dependent MTs are required for the progression of both furrow ingression and abscission. Augmin depletion reduced the accumulation of anillin, a contractile ring regulator at the cell equator, yet centrosomal MTs were sufficient to mediate RhoA activation at the furrow. This defect in contractile ring organization, combined with incomplete spindle pole separation during anaphase, led to impaired furrow ingression. During the late stages of cytokinesis, astral MTs formed bundles in the intercellular bridge, but these failed to assemble a focused midbody structure and did not establish tight linkage to the plasma membrane, resulting in furrow regression. Thus augmin-dependent acentrosomal MTs and centrosomal MTs contribute to nonredundant targeting mechanisms of different cytokinesis factors, which are required for the formation of a functional contractile ring and midbody.","authors":"Uehara, R., Kamasaki, T., Hiruma, S., Poser, I., Yoda, K., Yajima, J., Gerlich, DW., Goshima, G.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Mol Biol Cell","volume":"27","issue":"5","page":"812-27","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10646608","title":"Negative regulation of lymphocyte activation and autoimmunity by the molecular adaptor Cbl-b.","abstract":"The signalling thresholds of antigen receptors and co-stimulatory receptors determine immunity or tolerance to self molecules. Changes in co-stimulatory pathways can lead to enhanced activation of lymphocytes and autoimmunity, or the induction of clonal anergy. The molecular mechanisms that maintain immunotolerance in vivo and integrate co-stimulatory signals with antigen receptor signals in T and B lymphocytes are poorly understood. Members of the Cbl\/Sli family of molecular adaptors function downstream from growth factor and antigen receptors. Here we show that gene-targeted mice lacking the adaptor Cbl-b develop spontaneous autoimmunity characterized by auto-antibody production, infiltration of activated T and B lymphocytes into multiple organs, and parenchymal damage. Resting cbl-b(-\/-) lymphocytes hyperproliferate upon antigen receptor stimulation, and cbl-b(-\/-) T cells display specific hyperproduction of the T-cell growth factor interleukin-2, but not interferon-gamma or tumour necrosis factor-alpha. Mutation of Cbl-b uncouples T-cell proliferation, interleukin-2 production and phosphorylation of the GDP\/GTP exchange factor Vav1 from the requirement for CD28 co-stimulation. Cbl-b is thus a key regulator of activation thresholds in mature lymphocytes and immunological tolerance and autoimmunity.","authors":"Bachmaier, K., Krawczyk, C., Kozieradzki, I., Kong, YY., Sasaki, T., Oliveira-dos-Santos, A., Mariathasan, S., Bouchard, D., Wakeham, A., Itie, A., Le, J., Ohashi, PS., Sarosi, I., Nishina, H., Lipkowitz, S., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Nature","volume":"403","issue":"6766","page":"211-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25033469","title":"Modeling human development in 3D culture.","abstract":"Recently human embryonic stem cell research has taken on a new dimension - the third dimension. Capitalizing on increasing knowledge on directing pluripotent cells along different lineages, combined with ECM supported three-dimensional culture conditions, it has become possible to generate highly organized tissues of the central nervous system, gut, liver and kidney. Each system has been used to study different aspects of organogenesis and function including physical forces underlying optic cup morphogenesis, the function of disease related genes in progenitor cell control, as well as interaction of the generated tissues with host tissue upon transplantation. Pluripotent stem cell derived organoids represent powerful systems for the study of how cells self-organize to generate tissues with a given shape, pattern and form.","authors":"Ader, M., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Opin Cell Biol","volume":"31","issue":null,"page":"23-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22895187","title":"Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors.","abstract":"LGR5+ stem cells reside at crypt bottoms, intermingled with Paneth cells that provide Wnt, Notch and epidermal growth factor signals. Here we find that the related RNF43 and ZNRF3 transmembrane E3 ubiquitin ligases are uniquely expressed in LGR5+ stem cells. Simultaneous deletion of the two genes encoding these proteins in the intestinal epithelium of mice induces rapidly growing adenomas containing high numbers of Paneth and LGR5+ stem cells. In vitro, growth of organoids derived from these adenomas is arrested when Wnt secretion is inhibited, indicating a dependence of the adenoma stem cells on Wnt produced by adenoma Paneth cells. In the HEK293T human cancer cell line, expression of RNF43 blocks Wnt responses and targets surface-expressed frizzled receptors to lysosomes. In the RNF43-mutant colorectal cancer cell line HCT116, reconstitution of RNF43 expression removes its response to exogenous Wnt. We conclude that RNF43 and ZNRF3 reduce Wnt signals by selectively ubiquitinating frizzled receptors, thereby targeting these Wnt receptors for degradation.","authors":"Koo, BK., Spit, M., Jordens, I., Low, TY., Stange, DE., van de Wetering, M., van Es, JH., Mohammed, S., Heck, AJ., Maurice, MM., Clevers, H.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nature","volume":"488","issue":"7413","page":"665-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20479215","title":"Expression of an ASCL2 related stem cell signature and IGF2 in colorectal cancer liver metastases with 11p15.5 gain.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20479215<\/PMID><DateCompleted><Year>2010<\/Year><Month>10<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2011<\/Year><Month>11<\/Month><Day>07<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1468-3288<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>59<\/Volume><Issue>9<\/Issue><PubDate><Year>2010<\/Year><Month>Sep<\/Month><\/PubDate><\/JournalIssue><Title>Gut<\/Title><ISOAbbreviation>Gut<\/ISOAbbreviation><\/Journal><ArticleTitle>Expression of an ASCL2 related stem cell signature and IGF2 in colorectal cancer liver metastases with 11p15.5 gain.<\/ArticleTitle><Pagination><MedlinePgn>1236-44<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1136\/gut.2009.195701<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND AND AIMS\" NlmCategory=\"OBJECTIVE\">Liver metastases are the leading cause of death in colorectal cancer. To gain better insight into the biology of metastasis and possibly identify new therapeutic targets we systematically investigated liver-metastasis-specific molecular aberrations.","authors":"Stange, DE., Engel, F., Longerich, T., Koo, BK., Koch, M., Delhomme, N., Aigner, M., Toedt, G., Schirmacher, P., Lichter, P., Weitz, J., Radlwimmer, B.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Gut","volume":"59","issue":"9","page":"1236-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10581237","title":"Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances.","abstract":"The probability that two sites on a linear DNA molecule will contact each other by looping depends on DNA flexibility. Although the flexibility of naked DNA in vitro is well characterized, looping in chromatin is poorly understood. By extending existing theory, we present a single equation that describes DNA looping over all distances. We also show that DNA looping in vitro can be measured accurately by FLP recombination between sites from 74 bp to 15 kb apart. In agreement with previous work, a persistence length of 50 nm was determined. FLP recombination of the same substrates in mammalian cells showed that chromatin increases the flexibility of DNA at short distances, giving an apparent persistence length of 27 nm.","authors":"Ringrose, L., Chabanis, S., Angrand, PO., Woodroofe, C., Stewart, AF.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"EMBO J","volume":"18","issue":"23","page":"6630-41","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2000-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24692358","title":"Is salamander limb regeneration really perfect? Anatomical and morphogenetic analysis of forelimb muscle regeneration in GFP-transgenic axolotls as a basis for regenerative, developmental, and evolutionary studies.","abstract":"The axolotl Ambystoma mexicanum is one of the most commonly used model organisms in developmental and regenerative studies because it can reconstitute what is believed to be a completely normal anatomical and functional forelimb\/hindlimb after amputation. However, to date it has not been confirmed whether each regenerated forelimb muscle is really a \"perfect\" copy of the original muscle. This study describes the regeneration of the arm, forearm, hand, and some pectoral muscles (e.g., coracoradialis) in transgenic axolotls that express green fluorescent protein (GFP) in muscle fibers. The observations found that: (1) there were muscle anomalies in 43% of the regenerated forelimbs; (2) however, on average in each regenerated forelimb there are anomalies in only 2.5% of the total number of muscles examined, and there were no significant differences observed in the specific insertion and origin of the other muscles analyzed; (3) one of the most notable and common anomalies (seen in 35% of the regenerated forelimbs) was the presence of a fleshy coracoradialis at the level of the arm; this is a particularly outstanding configuration because in axolotls and in urodeles in general this muscle only has a thin tendon at the level of the arm, and the additional fleshy belly in the regenerated arms is strikingly similar to the fleshy biceps brachii of amniotes, suggesting a remarkable parallel between a regeneration defect and a major phenotypic change that occurred during tetrapod limb evolution; (4) during forelimb muscle regeneration there was a clear proximo-distal and radio-ulnar morphogenetic gradient, as seen in normal development, but also a ventro-dorsal gradient in the order of regeneration, which was not previously described in the literature. These results have broader implications for regenerative, evolutionary, developmental and morphogenetic studies.","authors":"Diogo, R., Nacu, E., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Anat Rec (Hoboken)","volume":"297","issue":"6","page":"1076-89","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22711569","title":"Dramatic expansion and developmental expression diversification of the methuselah gene family during recent Drosophila evolution.","abstract":"Functional studies of the methuselah\/methuselah-like (mth\/mthl) gene family have focused on the founding member mth, but little is known regarding the developmental functions of this receptor or any of its paralogs. We undertook a comprehensive analysis of developmental expression and sequence divergence in the mth\/mthl gene family. Using in situ hybridization techniques, we detect expression of six genes (mthl1, 5, 9, 11, 13, and 14) in the embryo during gastrulation and development of the gut, heart, and lymph glands. Four receptors (mthl3, 4, 6, and 8) are expressed in the larval central nervous system, imaginal discs, or both, and two receptors (mthl10 and mth) are expressed in both embryos and larvae. Phylogenetic analysis of all mth\/mthl genes in five Drosophila species, mosquito and flour beetle structured the mth\/mthl family into several subclades. mthl1, 5, and 14 are present in most species, each forming a separate clade. A newly identified Drosophila mthl gene (CG31720; herein mthl15) formed another ancient clade. The remaining Drosophila receptors, including mth, are members of a large \"superclade\" that diversified relatively recently during dipteran evolution, in many cases within the melanogaster subgroup. Comparing the expression patterns of the mth\/mthl \"superclade\" paralogs to the embryonic expression of the singleton ortholog in Tribolium suggests both subfunctionalization and acquisition of novel functionalities. Taken together, our findings shed novel light on mth as a young member of an adaptively evolving developmental gene family.","authors":"Patel, MV., Hallal, DA., Jones, JW., Bronner, DN., Zein, R., Caravas, J., Husain, Z., Friedrich, M., Vanberkum, MF.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Exp Zool B Mol Dev Evol","volume":"318","issue":"5","page":"368-87","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22393260","title":"A critical role for the Wnt effector Tcf4 in adult intestinal homeostatic self-renewal.","abstract":"Throughout life, intestinal Lgr5+ stem cells give rise to proliferating transient amplifying cells in crypts, which subsequently differentiate into one of the five main cell types and migrate along the crypt-villus axis. These dynamic processes are coordinated by a relatively small number of evolutionarily conserved signaling pathways, which includes the Wnt signaling pathway. The DNA-binding proteins of the T-cell factor family, Tcf1\/Tcf7, Lef, Tcf3\/Tcf7l1, and Tcf4\/Tcf7l2, constitute the downstream effectors of the Wnt signaling pathway. While Tcf4 is the major member active during embryogenesis, the role of these Wnt effectors in the homeostasis of the adult mouse intestinal epithelium is unresolved. Using Tcf1-\/-, Tcf3(flox), and novel Tcf4(flox) mice, we demonstrate an essential role for Tcf4 during homeostasis of the adult mouse intestine.","authors":"van Es, JH., Haegebarth, A., Kujala, P., Itzkovitz, S., Koo, BK., Boj, SF., Korving, J., van den Born, M., van Oudenaarden, A., Robine, S., Clevers, H.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Mol Cell Biol","volume":"32","issue":"10","page":"1918-27","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10871280","title":"CYK-4: A Rho family gtpase activating protein (GAP) required for central spindle formation and cytokinesis.","abstract":"During cytokinesis of animal cells, the mitotic spindle plays at least two roles. Initially, the spindle positions the contractile ring. Subsequently, the central spindle, which is composed of microtubule bundles that form during anaphase, promotes a late step in cytokinesis. How the central spindle assembles and functions in cytokinesis is poorly understood. The cyk-4 gene has been identified by genetic analysis in Caenorhabditis elegans. Embryos from cyk-4(t1689ts) mutant hermaphrodites initiate, but fail to complete, cytokinesis. These embryos also fail to assemble the central spindle. We show that the cyk-4 gene encodes a GTPase activating protein (GAP) for Rho family GTPases. CYK-4 activates GTP hydrolysis by RhoA, Rac1, and Cdc42 in vitro. RNA-mediated interference of RhoA, Rac1, and Cdc42 indicates that only RhoA is essential for cytokinesis and, thus, RhoA is the likely target of CYK-4 GAP activity for cytokinesis. CYK-4 and a CYK-4:GFP fusion protein localize to the central spindle and persist at cell division remnants. CYK-4 localization is dependent on the kinesin-like protein ZEN-4\/CeMKLP1 and vice versa. These data suggest that CYK-4 and ZEN-4\/CeMKLP1 cooperate in central spindle assembly. Central spindle localization of CYK-4 could accelerate GTP hydrolysis by RhoA, thereby allowing contractile ring disassembly and completion of cytokinesis.","authors":"Jantsch-Plunger, V., G\u00f6nczy, P., Romano, A., Schnabel, H., Hamill, D., Schnabel, R., Hyman, AA., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Cell Biol","volume":"149","issue":"7","page":"1391-404","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2000-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22196214","title":"WNTing embryonic stem cells.","abstract":"Embryonic stem cells (ESCs) - undifferentiated cells originating from preimplantation stage embryos - have prolonged self-renewal capacity and are pluripotent. Activation of the canonical Wnt pathway is implicated in maintenance of and exit from the pluripotent state. Recent findings demonstrate that the essential mediator of canonical Wnt signaling, \u03b2-catenin, is dispensable for ESC maintenance; however, its activation inhibits differentiation through derepression of T cell factor 3 (Tcf3)-bound genes. Wnt agonists are useful in deriving ESCs from recalcitrant mouse strains and the rat and in nuclear reprogramming of somatic stem cells. We discuss recent advances in our understanding of the role of canonical Wnt signaling in the regulation of ESC self-renewal and how its manipulation can improve pluripotent ESC derivation and maintenance.","authors":"Wray, J., Hartmann, C.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Trends Cell Biol","volume":"22","issue":"3","page":"159-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27863220","title":"Germline Transgenic Methods for Tracking Cells and Testing Gene Function during Regeneration in the Axolotl.","abstract":null,"authors":"Khattak, S., Schuez, M., Richter, T., Knapp, D., Haigo, SL., Sandoval-Guzm\u00e1n, T., Hradlikova, K., Duemmler, A., Kerney, R., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Stem Cell Reports","volume":"2","issue":"2","page":"243","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28009285","title":"Anabolism-Associated Mitochondrial Stasis Driving Lymphocyte Differentiation over Self-Renewal.","abstract":"Regeneration requires related cells to diverge in fate. We show that activated lymphocytes yield sibling cells with unequal elimination of aged mitochondria. Disparate mitochondrial clearance impacts cell fate and reflects larger constellations of opposing metabolic states. Differentiation driven by an anabolic constellation of PI3K\/mTOR activation, aerobic glycolysis, inhibited autophagy, mitochondrial stasis, and ROS production is balanced with self-renewal maintained by a catabolic constellation of AMPK activation, mitochondrial elimination, oxidative metabolism, and maintenance of FoxO1 activity. Perturbations up and down the metabolic pathways shift the balance of nutritive constellations and cell fate owing to self-reinforcement and reciprocal inhibition between anabolism and catabolism. Cell fate and metabolic state are linked by transcriptional regulators, such as IRF4 and FoxO1, with dual roles in lineage and metabolic choice. Instructing some cells to utilize nutrients for anabolism and differentiation while other cells catabolically self-digest and self-renew may enable growth and repair in metazoa.","authors":"Adams, WC., Chen, YH., Kratchmarov, R., Yen, B., Nish, SA., Lin, WW., Rothman, NJ., Luchsinger, LL., Klein, U., Busslinger, M., Rathmell, JC., Snoeck, HW., Reiner, SL.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Rep","volume":"17","issue":"12","page":"3142-3152","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22671929","title":"Targeted therapy of multiple myeloma: the changing paradigm at the beginning of the new millennium.","abstract":"Multiple myeloma (MM) is a malignant hematological neoplasmand constitutes 10% of blood cancers. Recently, it has become evident that almost all cases of MM are preceded by gammopathy of undetermined significance (MGUS). MM is diagnosed by the presence of paraprotein in serum or urine, detected by serum electrophoresis and immunofixation, infiltration of malignant plasma cells in the bone marrow and related organ, or tissue damage. Cytogenetic status, International Staging System (ISS) and the quality of response to therapy are the most important prognostic factors. In the last decade the availability of new effective drugs, such as thalidomide, lenalidomide and bortezomib have provided a new therapeutic scenario expected to impact favorably on the outcome of MM patients. Today, for younger patients a triple-agent induction regimen incorporating novel agents followed by autologous stem cell transplantation (ASCT) is the best approach. In this setting ongoing clinical trials are evaluating the efficacy of consolidation and maintenance therapy based on the use of new drugs. For patients noteligible for ASCT the best initial regimens are combination therapy with melphalan and prednisone plus either thalidomide or bortezomibor the combination of lenalidomide and dexamethasone. Supportive therapy includes the use of erythropoietin and bisphosphonates according to the updated guidelines. In the future the identification of candidate therapeutic targets through gene expression profiling (GEP) and single-nucleotide polymorphism (SNP) analysis, as well as the availability of the targeted investigative agents will lead to a substantial progress in the development and implementation of personalized medicine in MM.","authors":"Morabito, F., Recchia, AG., Mazzone, C., Gentile, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Curr Cancer Drug Targets","volume":"12","issue":"7","page":"743-56","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-155","title":"Stem cell-derived organoid cultures and genome editing tools.","abstract":null,"authors":"Andersson-Rolf A, Koo BK","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell Gene Therapy Insights","volume":"1","issue":"2","page":"243-251","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24504478","title":"Optimized axolotl (Ambystoma mexicanum) husbandry, breeding, metamorphosis, transgenesis and tamoxifen-mediated recombination.","abstract":"The axolotl (Mexican salamander, Ambystoma mexicanum) has become a very useful model organism for studying limb and spinal cord regeneration because of its high regenerative capacity. Here we present a protocol for successfully mating and breeding axolotls in the laboratory throughout the year, for metamorphosing axolotls by a single i.p. injection and for axolotl transgenesis using I-SceI meganuclease and the mini Tol2 transposon system. Tol2-mediated transgenesis provides different features and advantages compared with I-SceI-mediated transgenesis, and it can result in more than 30% of animals expressing the transgene throughout their bodies so that they can be directly used for experimentation. By using Tol2-mediated transgenesis, experiments can be performed within weeks (e.g., 5-6 weeks for obtaining 2-3-cm-long larvae) without the need to establish germline transgenic lines (which take 12-18 months). In addition, we describe here tamoxifen-induced Cre-mediated recombination in transgenic axolotls.","authors":"Khattak, S., Murawala, P., Andreas, H., Kappert, V., Schuez, M., Sandoval-Guzm\u00e1n, T., Crawford, K., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Protoc","volume":"9","issue":"3","page":"529-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19237598","title":"Identification of cell cycle-arrested quiescent osteoclast precursors in vivo.","abstract":"Osteoclasts are multinucleated cells that resorb bone. Although osteoclasts originate from the monocyte\/macrophage lineage, osteoclast precursors are not well characterized in vivo. The relationship between proliferation and differentiation of osteoclast precursors is examined in this study using murine macrophage cultures treated with macrophage colony-stimulating factor (M-CSF) and receptor activator of NF-kappaB (RANK) ligand (RANKL). Cell cycle-arrested quiescent osteoclast precursors (QuOPs) were identified as the committed osteoclast precursors in vitro. In vivo experiments show that QuOPs survive for several weeks and differentiate into osteoclasts in response to M-CSF and RANKL. Administration of 5-fluorouracil to mice induces myelosuppression, but QuOPs survive and differentiate into osteoclasts in response to an active vitamin D(3) analogue given to those mice. Mononuclear cells expressing c-Fms and RANK but not Ki67 are detected along bone surfaces in the vicinity of osteoblasts in RANKL-deficient mice. These results suggest that QuOPs preexist at the site of osteoclastogenesis and that osteoblasts are important for maintenance of QuOPs.","authors":"Mizoguchi, T., Muto, A., Udagawa, N., Arai, A., Yamashita, T., Hosoya, A., Ninomiya, T., Nakamura, H., Yamamoto, Y., Kinugawa, S., Nakamura, M., Nakamichi, Y., Kobayashi, Y., Nagasawa, S., Oda, K., Tanaka, H., Tagaya, M., Penninger, JM., Ito, M., Takahashi, N.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Biol","volume":"184","issue":"4","page":"541-54","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22171067","title":"Air motion sensing hairs of arthropods detect high frequencies at near-maximal mechanical efficiency.","abstract":"Using measurements based on particle image velocimetry in combination with a novel compact theoretical framework to describe hair mechanics, we found that spider and cricket air motion sensing hairs work close to the physical limit of sensitivity and energy transmission in a broad range of relatively high frequencies. In this range, the hairs closely follow the motion of the incoming flow because a minimum of energy is dissipated by forces acting in their basal articulation. This frequency band is located beyond the frequency at which the angular displacement of the hair is maximum which is between about 40 and 600 Hz, depending on hair length (Barth et al. [1] Phil. Trans. R. Soc. Lond. B 340, 445-461 (doi:10.1098\/rstb.1993.0084)). Given that the magnitude of natural airborne signals is known to decrease with frequency, our results point towards the possible existence of spectral signatures in the higher frequency range that may be weak but of biological significance.","authors":"Bathellier, B., Steinmann, T., Barth, FG., Casas, J.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J R Soc Interface","volume":"9","issue":"71","page":"1131-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22142223","title":"Helios transcription factor expression depends on Gsx2 and Dlx1&amp;2 function in developing striatal matrix neurons.","abstract":"Development of the nervous system is finely regulated by consecutive expression of cell-specific transcription factors. Here we show that Helios, a member of the Ikaros transcription factor family, is expressed in ectodermal and neuroectodermal-derived tissues. During embryonic development, Helios is expressed by several brain structures including the lateral ganglionic eminence (LGE, the striatal anlage); the cingulated, insular and retrosplenial cortex; the hippocampus; and the accessory olfactory bulb. Moreover, Helios is also expressed by Purkinje neurons during postnatal cerebellar development. Within the LGE, Helios expression follows a dynamic spatio-temporal pattern starting at embryonic stages (E14.5), peaking at E18.5, and completely disappearing during postnatal development. Helios is expressed by a small population of nestin-positive neural progenitor cells located in the subventricular zone as well as by a larger population of immature neurons distributed throughout the mantle zone. In the later, Helios is preferentially expressed in the matrix compartment, where it colocalizes with Bcl11b and Foxp1, well-known markers of striatal projection neurons. In addition, we observed that Helios expression is not detected in Dlx1\/2 and Gsx2 null mutants, while its expression is maintained in Ascl1 mutants. These findings allow us to introduce a new transcription factor in the cascade of events that take part of striatal development postulating the existence of at least 4 different neural progenitors in the LGE. An Ascl1-independent but Gsx2- &amp; Dlx1\/2-dependent precursor will express Helios defining a new lineage for a subset of matrix striatal neurons.","authors":"Mart\u00edn-Ib\u00e1\u00f1ez, R., Crespo, E., Esgleas, M., Urban, N., Wang, B., Waclaw, R., Georgopoulos, K., Mart\u00ednez, S., Campbell, K., Vicario-Abej\u00f3n, C., Alberch, J., Chan, S., Kastner, P., Rubenstein, JL., Canals, JM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Stem Cells Dev","volume":"21","issue":"12","page":"2239-51","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-156","title":"Rapid, one-step generation of biallelic conditional gene knockouts.","abstract":null,"authors":"Andersson-Rolf A, Mustata RC, Merenda A, Perera S, Grego T, Kim J, Andrews K, Fink J, Skarnes WC, Koo BK.","publication_status":"preprint","journalpubyear":"2016","journaltitle":"BioRxiv","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/056549v1","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16061481","title":"The vitamin K-dependent carboxylase has been acquired by Leptospira pathogens and shows altered activity that suggests a role other than protein carboxylation.","abstract":"Leptospirosis is an emerging infectious disease whose pathology includes a hemorrhagic response, and sequencing of the Leptospira interrogans genome revealed an ortholog of the vitamin K-dependent (VKD) carboxylase as one of several hemostatic proteins present in the bacterium. Until now, the VKD carboxylase was known to be present only in the animal kingdom (i.e. metazoans that include mammals, fish, snails, and insects), and this restricted distribution and high sequence similarity between metazoan and Leptospira orthologs strongly suggests that Leptospira acquired the VKD carboxylase by horizontal gene transfer. In metazoans, the VKD carboxylase is bifunctional, acting as an epoxidase that oxygenates vitamin K to a strong base and a carboxylase that uses the base to carboxylate Glu residues in VKD proteins, rendering them active in hemostasis and other physiologies. In contrast, the Leptospira ortholog showed epoxidase but not detectable carboxylase activity and divergence in a region of identity in all known metazoan VKD carboxylases that is important to Glu interaction. Furthermore, although the mammalian carboxylase is regulated so that vitamin K epoxidation does not occur unless Glu substrate is present, the Leptospira VKD epoxidase showed unfettered epoxidation in the absence of Glu substrate. Finally, human VKD protein orthologs were not detected in the L. interrogans genome. The combined data, then, suggest that Leptospira exapted the metazoan VKD carboxylase for some use other than VKD protein carboxylation, such as using the strong vitamin K base to drive a new reaction or to promote oxidative damage or depleting vitamin K to indirectly inhibit host VKD protein carboxylation.","authors":"Rishavy, MA., Hallgren, KW., Yakubenko, AV., Zuerner, RL., Runge, KW., Berkner, KL.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Biol Chem","volume":"280","issue":"41","page":"34870-7","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2005-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26543203","title":"Deletions and de novo mutations of SOX11 are associated with a neurodevelopmental disorder with features of Coffin-Siris syndrome.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">26543203<\/PMID><DateCompleted><Year>2016<\/Year><Month>07<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>01<\/Month><Day>31<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1468-6244<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>53<\/Volume><Issue>3<\/Issue><PubDate><Year>2016<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>Journal of medical genetics<\/Title><ISOAbbreviation>J Med Genet<\/ISOAbbreviation><\/Journal><ArticleTitle>Deletions and de novo mutations of SOX11 are associated with a neurodevelopmental disorder with features of Coffin-Siris syndrome.<\/ArticleTitle><Pagination><MedlinePgn>152-62<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1136\/jmedgenet-2015-103393<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">SOX11 is a transcription factor proposed to play a role in brain development. The relevance of SOX11 to human developmental disorders was suggested by a recent report of SOX11 mutations in two patients with Coffin-Siris syndrome. Here we further investigate the role of SOX11 variants in neurodevelopmental disorders.","authors":"Hempel, A., Pagnamenta, AT., Blyth, M., Mansour, S., McConnell, V., Kou, I., Ikegawa, S., Tsurusaki, Y., Matsumoto, N., Lo-Castro, A., Plessis, G., Albrecht, B., Battaglia, A., Taylor, JC., Howard, MF., Keays, D., Sohal, AS., K\u00fchl, SJ., Kini, U., McNeill, A.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Med Genet","volume":"53","issue":"3","page":"152-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16024649","title":"Expression of a natural tumor antigen by thymic epithelial cells impairs the tumor-protective CD4+ T-cell repertoire.","abstract":"A variety of antigens that display a highly tissue-specific expression pattern have recently found to be also expressed in medullary thymic epithelial cells (mTEC). This unique feature of mTEC plays an important role in preventing hazardous autoimmune responses through thymic tolerization of T-cell subsets directed against autoantigens but could also limit the possibility of exploiting tumor-associated antigens for immune-mediated targeting of cancers. Our present study shows that expression of carcinoembryonic antigen (CEA) in thymic epithelial cells of CEA-transgenic mice results in tolerization of a major fraction of the CD4+ T-cell repertoire against this antigen, thereby markedly limiting the effect of CEA-specific immunization against CEA-overexpressing tumors. The expression of CEA in mTEC of CEA-transgenic mice is mirrored by its expression in human mTEC, arguing that promiscuous gene expression in these thymic stromal cells needs to be considered as a potential hurdle for immunotherapies of cancer that target tissue-specific autoantigens.","authors":"Bos, R., van Duikeren, S., van Hall, T., Kaaijk, P., Taubert, R., Kyewski, B., Klein, L., Melief, CJ., Offringa, R.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cancer Res","volume":"65","issue":"14","page":"6443-9","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2005-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16000382","title":"Mind bomb 1 is essential for generating functional Notch ligands to activate Notch.","abstract":"The Delta-Notch signaling pathway is an evolutionarily conserved intercellular signaling mechanism essential for cell fate specification. Mind bomb 1 (Mib1) has been identified as a ubiquitin ligase that promotes the endocytosis of Delta. We now report that mice lacking Mib1 die prior to embryonic day 11.5, with pan-Notch defects in somitogenesis, neurogenesis, vasculogenesis and cardiogenesis. The Mib1-\/- embryos exhibit reduced expression of Notch target genes Hes5, Hey1, Hey2 and Heyl, with the loss of N1icd generation. Interestingly, in the Mib1-\/- mutants, Dll1 accumulated in the plasma membrane, while it was localized in the cytoplasm near the nucleus in the wild types, indicating that Mib1 is essential for the endocytosis of Notch ligand. In accordance with the pan-Notch defects in Mib1-\/- embryos, Mib1 interacts with and regulates all of the Notch ligands, jagged 1 and jagged 2, as well as Dll1, Dll3 and Dll4. Our results show that Mib1 is an essential regulator, but not a potentiator, for generating functional Notch ligands to activate Notch signaling.","authors":"Koo, BK., Lim, HS., Song, R., Yoon, MJ., Yoon, KJ., Moon, JS., Kim, YW., Kwon, MC., Yoo, KW., Kong, MP., Lee, J., Chitnis, AB., Kim, CH., Kong, YY.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Development","volume":"132","issue":"15","page":"3459-70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-10-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11201744","title":"CD45 is a JAK phosphatase and negatively regulates cytokine receptor signalling.","abstract":"The regulation of tyrosine phosphorylation and associated signalling through antigen, growth-factor and cytokine receptors is mediated by the reciprocal activities of protein tyrosine kinases and protein tyrosine phosphatases (PTPases). The transmembrane PTPase CD45 is a key regulator of antigen receptor signalling in T and B cells. Src-family kinases have been identified as primary molecular targets for CD45 (ref. 4). However, CD45 is highly expressed in all haematopoietic lineages at all stages of development, indicating that CD45 could regulate other cell types and might act on additional substrates. Here we show that CD45 suppresses JAK (Janus kinase) kinases and negatively regulates cytokine receptor signalling. Targeted disruption of the cd45 gene leads to enhanced cytokine and interferon-receptor-mediated activation of JAKs and STAT (signal transducer and activators of transcription) proteins. In vitro, CD45 directly dephosphorylates and binds to JAKs. Functionally, CD45 negatively regulates interleukin-3-mediated cellular proliferation, erythropoietin-dependent haematopoieisis and antiviral responses in vitro and in vivo. Our data identify an unexpected and novel function for CD45 as a haematopoietic JAK phosphatase that negatively regulates cytokine receptor signalling.","authors":"Irie-Sasaki, J., Sasaki, T., Matsumoto, W., Opavsky, A., Cheng, M., Welstead, G., Griffiths, E., Krawczyk, C., Richardson, CD., Aitken, K., Iscove, N., Koretzky, G., Johnson, P., Liu, P., Rothstein, DM., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nature","volume":"409","issue":"6818","page":"349-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22623674","title":"Integration of H-2Z1, a somatosensory cortex-expressed transgene, interferes with the expression of the Satb1 and Tbc1d5 flanking genes and affects the differentiation of a subset of cortical interneurons.","abstract":"H-2Z1 is an enhancer trap transgenic mouse line in which the lacZ reporter delineates the somatosensory area of the cerebral cortex where it is expressed in a subset of layer IV neurons. In the search of somatosensory specific genes or regulatory sequences, we mapped the H-2Z1 transgene insertion site to chromosome 17, 100 and 460 kb away from Tbc1d5 and Satb1 flanking genes. We show here that insertion of the H-2Z1 transgene results in three distinct outcomes. First, a genetic background-sensitive expression of lacZ in several brain and body structures. While four genes in a 1 Mb region around the insertion are expressed in the barrel cortex, H-2Z1 expression resembles more that of its two direct neighbors. Moreover, H-2Z1 closely reports most of the body and brain expression sites of the Satb1 chromatin remodeling gene including tooth buds, thymic epithelium, pontine nuclei, fastigial cerebellar nuclei, and cerebral cortex. Second, the H-2Z1 transgene causes insertional mutagenesis of Tbc1d5 and Satb1, leading to a strong decrease in their expressions. Finally, insertion of H-2Z1 affects the differentiation of a subset of cortical GABAergic interneurons, a possible consequence of downregulation of Satb1 expression. Thus, the H-2Z1 \"somatosensory\" transgene is inserted in the regulatory landscape of two genes highly expressed in the developing somatosensory cortex and reports for a subdomain of their expression profiles. Together, our data suggest that regulation of H-2Z1 expression results from local and remote genetic interactions.","authors":"Narboux-N\u00eame, N., Go\u00efame, R., Matt\u00e9i, MG., Cohen-Tannoudji, M., Wassef, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Neurosci","volume":"32","issue":"21","page":"7287-300","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16007070","title":"Initiation of epigenetic reprogramming of the X chromosome in somatic nuclei transplanted to a mouse oocyte.","abstract":"The active and inactive X chromosomes have distinct epigenetic marks in somatic nuclei, which undergo reprogramming after transplantation into oocytes. We show that, despite the disappearance of Xist RNA coating in 30 min, the epigenetic memory of the inactive X persists with the precocious appearance of histone H3 trimethylation of lysine 27 (H3-3meK27), without the expected colocalization with Eed\/Ezh2. Subsequently, Xist re-appears on the original inactive X, and the silent Xist on the active X undergoes re-activation, resulting in unusual biallelic Xist RNA domains. Despite this abnormal Xist expression pattern, colocalization of H3-3meK27 and Eed is thereafter confined to a single Xist domain, which is presumably on the original inactive X. These epigenetic events differ markedly from the kinetics of preferential paternal X inactivation in normal embryos. All the epigenetic marks on the X are apparently erased in the epiblast, suggesting that the oocyte and epiblast may have distinct properties for stepwise programming of the genome.","authors":"Bao, S., Miyoshi, N., Okamoto, I., Jenuwein, T., Heard, E., Azim Surani, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"EMBO Rep","volume":"6","issue":"8","page":"748-54","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26693180","title":"Surviving at a distance: organ specific metastasis.","abstract":"The clinical manifestation of metastasis in a vital organ is the final stage of cancer progression and the main culprit of cancer related mortality. Once established, metastasis is devastating, yet only a small proportion of the cancer cells that leave a tumor succeed at infiltrating, surviving, and ultimately overtaking a distant organ. The bottlenecks that challenge cancer cells in newly invaded microenvironments are organ specific and consequently demand distinct mechanisms for metastatic colonization. Here we review the metastatic traits that allow cancer cells to colonize distinct organ sites.","authors":"Obenauf, AC., Massagu\u00e9, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Trends Cancer","volume":"1","issue":"1","page":"76-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10744629","title":"Mitochondrio-nuclear translocation of AIF in apoptosis and necrosis.","abstract":"Apoptosis inducing factor (AIF) is a novel apoptotic effector protein that induces chromatin condensation and large-scale ( approximately 50 kbp) DNA fragmentation when added to purified nuclei in vitro. Confocal and electron microscopy reveal that, in normal cells, AIF is strictly confined to mitochondria and thus colocalizes with heat shock protein 60 (hsp60). On induction of apoptosis by staurosporin, c-Myc, etoposide, or ceramide, AIF (but not hsp60) translocates to the nucleus. This suggests that only the outer mitochondrial membrane (which retains AIF in the intermembrane space) but not the inner membrane (which retains hsp60 in the matrix) becomes protein permeable. The mitochondrio-nuclear redistribution of AIF is prevented by a Bcl-2 protein specifically targeted to mitochondrial membranes. The pan-caspase inhibitor Z-VAD. fmk does not prevent the staurosporin-induced translocation of AIF, although it does inhibit oligonucleosomal DNA fragmentation and arrests chromatin condensation at an early stage. ATP depletion is sufficient to cause AIF translocation to the nucleus, and this phenomenon is accelerated by the apoptosis inducer staurosporin. However, in conditions in which both glycolytic and respiratory ATP generation is inhibited, cells fail to manifest any sign of chromatin condensation and advanced DNA fragmentation, thus manifesting a 'necrotic' phenotype. Both in the presence of Z-VAD. fmk and in conditions of ATP depletion, AIF translocation correlates with the appearance of large-scale DNA fragmentation. Altogether, these data are compatible with the hypothesis that AIF is a caspase-independent mitochondrial death effector responsible for partial chromatinolysis.","authors":"Daugas, E., Susin, SA., Zamzami, N., Ferri, KF., Irinopoulou, T., Larochette, N., Pr\u00e9vost, MC., Leber, B., Andrews, D., Penninger, J., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"FASEB J","volume":"14","issue":"5","page":"729-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22589274","title":"KRas induces a Src\/PEAK1\/ErbB2 kinase amplification loop that drives metastatic growth and therapy resistance in pancreatic cancer.","abstract":"Early biomarkers and effective therapeutic strategies are desperately needed to treat pancreatic ductal adenocarcinoma (PDAC), which has a dismal 5-year patient survival rate. Here, we report that the novel tyrosine kinase PEAK1 is upregulated in human malignancies, including human PDACs and pancreatic intraepithelial neoplasia (PanIN). Oncogenic KRas induced a PEAK1-dependent kinase amplification loop between Src, PEAK1, and ErbB2 to drive PDAC tumor growth and metastasis in vivo. Surprisingly, blockade of ErbB2 expression increased Src-dependent PEAK1 expression, PEAK1-dependent Src activation, and tumor growth in vivo, suggesting a mechanism for the observed resistance of patients with PDACs to therapeutic intervention. Importantly, PEAK1 inactivation sensitized PDAC cells to trastuzumab and gemcitabine therapy. Our findings, therefore, suggest that PEAK1 is a novel biomarker, critical signaling hub, and new therapeutic target in PDACs.","authors":"Kelber, JA., Reno, T., Kaushal, S., Metildi, C., Wright, T., Stoletov, K., Weems, JM., Park, FD., Mose, E., Wang, Y., Hoffman, RM., Lowy, AM., Bouvet, M., Klemke, RL.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cancer Res","volume":"72","issue":"10","page":"2554-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31969617","title":"A high sensitivity ZENK monoclonal antibody to map neuronal activity in Aves.","abstract":"The transcription factor ZENK is an immediate early gene that has been employed as a surrogate marker to map neuronal activity in the brain. It has been used in a wide variety of species, however, commercially available antibodies have limited immunoreactivity in birds. To address this issue we generated a new mouse monoclonal antibody, 7B7-A3, raised against ZENK from the rock pigeon (Columba livia). We show that 7B7-A3 labels clZENK in both immunoblots and histological stainings with high sensitivity and selectivity for its target. Using a sound stimulation paradigm we demonstrate that 7B7-A3 can detect activity-dependent ZENK expression at key stations of the central auditory pathway of the pigeon. Finally, we compare staining efficiency across three avian species and confirm that 7B7-A3 is compatible with immunohistochemical detection of ZENK in the rock pigeon, zebra finch, and domestic chicken. Taken together, 7B7-A3 represents a useful tool for the avian neuroscience community to map functional activity in the brain.","authors":"Nordmann, GC., Malkemper, EP., Landler, L., Ushakova, L., Nimpf, S., Heinen, R., Schuechner, S., Ogris, E., Keays, DA.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Rep","volume":"10","issue":"1","page":"915","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28101297","title":"CD36\/Sirtuin 1 Axis Impairment Contributes to Hepatic Steatosis in ACE2-Deficient Mice.","abstract":"<i>Background and Aims<\/i>. Angiotensin converting enzyme 2 (ACE2) is an important component of the renin-angiotensin system. Since angiotensin peptides have been shown to be involved in hepatic steatosis, we aimed to evaluate the hepatic lipid profile in ACE2-deficient (ACE2<sup>-\/y<\/sup>) mice. <i>Methods<\/i>. Male C57BL\/6 and ACE2<sup>-\/y<\/sup> mice were analyzed at the age of 3 and 6 months for alterations in the lipid profiles of plasma, faeces, and liver and for hepatic steatosis. <i>Results<\/i>. ACE2<sup>-\/y<\/sup> mice showed lower body weight and white adipose tissue at all ages investigated. Moreover, these mice had lower levels of cholesterol, triglycerides, and nonesterified fatty acids in plasma. Strikingly, ACE2<sup>-\/y<\/sup> mice showed high deposition of lipids in the liver. Expression of CD36, a protein involved in the uptake of triglycerides in liver, was increased in ACE2<sup>-\/y<\/sup> mice. Concurrently, these mice exhibited an increase in hepatic oxidative stress, evidenced by increased lipid peroxidation and expression of uncoupling protein 2, and downregulation of sirtuin 1. ACE2<sup>-\/y<\/sup> mice also showed impairments in glucose metabolism and insulin signaling in the liver. <i>Conclusions<\/i>. Deletion of ACE2 causes CD36\/sirtuin 1 axis impairment and thereby interferes with lipid homeostasis, leading to lipodystrophy and steatosis.","authors":"Nunes-Souza, V., Alenina, N., Qadri, F., Penninger, JM., Santos, RA., Bader, M., Rabelo, LA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Oxid Med Cell Longev","volume":"2016","issue":null,"page":"6487509","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22506286","title":"Organization and expression of the Australian sheep  blowfly (Lucilia cuprina) hsp23, hsp24, hsp70 and  hsp83 genes.","abstract":"In this study we report the isolation and characterization of a heat shock protein 70 (hsp70) gene, the hsp83 gene and two genes that encode small Hsps (Lchsp23 and Lchsp24) from the Australian sheep blowfly, Lucilia cuprina, a major agricultural pest. Phylogenetic analyses indicate that the LcHsp23 protein is the orthologue of Drosophila melanogaster Hsp23 and LcHsp24 is the orthologue of Sarcophaga crassipalpis Hsp23. Quantitative reverse-transcriptase PCR analysis showed that the basal level of Lchsp83 RNA is relatively high at all developmental stages and only moderately induced by heat shock. In contrast, Lchsp70 transcripts are present at low levels and strongly induced by heat shock at all stages. The basal levels of expression and degrees of heat induction of the Lchsp23 and Lchsp24 transcripts were more variable across the different developmental stages. Putative heat shock factor binding sites were identified in the Lchsp24, Lchsp70 and Lchsp83 gene promoters. The isolation of these hsp gene promoters will facilitate constitutive or conditional expression of a gene of interest in transgenic Lucilia.","authors":"Concha, C., Edman, RM., Belikoff, EJ., Schiemann, AH., Carey, B., Scott, MJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Insect Mol Biol","volume":"21","issue":"2","page":"169-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26714523","title":"An inducible retroviral expression system for tandem affinity purification mass-spectrometry-based proteomics identifies MLKL as an HSP90 client.","abstract":"on Status=\"Publisher\" Owner=\"NLM\">\n<PMID Version=\"1\">26714523<\/PMID>\n<DateCreated>\n<Year>2015<\/Year>\n<Month>12<\/Month>\n<Day>30<\/Day>\n<\/DateCreated>\n<DateRevised>\n<Year>2015<\/Year>\n<Month>12<\/Month>\n<Day>31<\/Day>\n<\/DateRevised>\n<Article PubModel=\"Print-Electronic\">\n<Journal>\n<ISSN IssnType=\"Electronic\">1535-9484<\/ISSN>\n<JournalIssue CitedMedium=\"Internet\">\n<PubDate>\n<Year>2015<\/Year>\n<Month>Dec<\/Month>\n<Day>29<\/Day>\n<\/PubDate>\n<\/JournalIssue>\n<Title>Molecular &amp; cellular proteomics : MCP<\/Title>\n<ISOAbbreviation>Mol. Cell Proteomics<\/ISOAbbreviation>\n<\/Journal>\n<ArticleTitle>An inducible retroviral expression system for tandem affinity purification mass-spectrometry-based proteomics identifies MLKL as an HSP90 client.<\/ArticleTitle>\n<Pagination>\n<MedlinePgn\/>\n<\/Pagination>\n<ELocationID EIdType=\"pii\">mcp.O115.055350<\/ELocationID>\n<Abstract>\n<AbstractText NlmCategory=\"UNASSIGNED\">Tandem affinity purification-mass spectrometry (TAP-MS) is a popular strategy for the identification of protein-protein interactions, characterization of protein complexes, and entire networks. Its employment in cellular settings best fitting the relevant physiology is limited by convenient expression vector systems. We developed an easy-to-handle, inducible, dually selectable retroviral expression vector allowing dose-and time dependent control of bait proteins bearing the efficient streptavidin-hemagglutinin (SH)-tag at their N- or C-termini. Concomitant expression of a reporter fluorophore allows to monitor bait-expressing cells by flow cytometry or microscopy, and enables high-throughput phenotypic assays. We used the system to successfully characterize the interactome of the neuroblastoma RAS viral oncogene homolog (NRAS) G12D mutant and exploited the advantage of reporter fluorophore expression by tracking cytokine-independent cell growth using flow cytometry. Moreover, we tested the feasibility of studying cytotoxicity-mediating proteins with the vector system on the cell death-inducing mixed lineage kinase domain-like protein (MLKL) S358D mutant. Interaction proteomics analysis of MLKL S358D identified heat shock protein 90 (HSP90) as a high-confidence interacting protein. Further phenotypic characterization established MLKL as a novel HSP90 client. In summary, this novel inducible-expression system enables SH-tag-based interaction studies in the cell line proficient for the respective phenotypic or signaling context and constitutes a valuable tool for experimental approaches requiring inducible or traceable protein expression.","authors":"Bigenzahn, JW., Fauster, A., Rebsamen, M., Kandasamy, RK., Scorzoni, S., Vladimer, GI., Mueller, AC., Gstaiger, M., Zuber, J., Bennett, KL., Superti-Furga, G.","publication_status":"aheadofprint","journalpubyear":"2015","journaltitle":"Mol Cell Proteomics","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30975723","title":"The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain <i>Cd4<\/i> silencing in cytotoxic T cells.","abstract":"The transcriptional repression of alternative lineage genes is critical for cell fate commitment. Mechanisms by which locus-specific gene silencing is initiated and heritably maintained during cell division are not clearly understood. To study the maintenance of silent gene states, we investigated how the <i>Cd4<\/i> gene is stably repressed in CD8<sup>+<\/sup> T cells. Through CRISPR and shRNA screening, we identified the histone chaperone CAF-1 as a critical component for <i>Cd4<\/i> repression. We found that the large subunit of CAF-1, Chaf1a, requires the N-terminal KER domain to associate with the histone deacetylases HDAC1\/2 and the histone demethylase LSD1, enzymes that also participate in <i>Cd4<\/i> silencing. When CAF-1 was lacking, <i>Cd4<\/i> derepression was markedly enhanced in the absence of the de novo DNA methyltransferase Dnmt3a but not the maintenance DNA methyltransferase Dnmt1. In contrast to Dnmt1, Dnmt3a deficiency did not significantly alter levels of DNA methylation at the <i>Cd4<\/i> locus. Instead, Dnmt3a deficiency sensitized CD8<sup>+<\/sup> T cells to <i>Cd4<\/i> derepression mediated by compromised functions of histone-modifying factors, including the enzymes associated with CAF-1. Thus, we propose that the heritable silencing of the <i>Cd4<\/i> gene in CD8<sup>+<\/sup> T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone-modifying enzymes.","authors":"Ng, C., Aichinger, M., Nguyen, T., Au, C., Najar, T., Wu, L., Mesa, KR., Liao, W., Quivy, JP., Hubert, B., Almouzni, G., Zuber, J., Littman, DR.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Genes Dev","volume":"33","issue":"11-12","page":"669-683","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15956281","title":"Altered body iron distribution and microcytosis in mice deficient in iron regulatory protein 2 (IRP2).","abstract":"Iron regulatory protein 2 (IRP2)-deficient mice have been reported to suffer from late-onset neurodegeneration by an unknown mechanism. We report that young adult Irp2-\/- mice display signs of iron mismanagement within the central iron recycling pathway in the mammalian body, the liver-bone marrow-spleen axis, with altered body iron distribution and compromised hematopoiesis. In comparison with wild-type littermates, Irp2-\/- mice are mildly microcytic with reduced serum hemoglobin levels and hematocrit. Serum iron and transferrin saturation are unchanged, and hence microcytosis is not due to an overt decrease in systemic iron availability. The liver and duodenum are iron loaded, while the spleen is iron deficient, associated with a reduced expression of the iron exporter ferroportin. A reduction in transferrin receptor 1 (TfR1) mRNA levels in the bone marrow of Irp2-\/- mice can plausibly explain the microcytosis by an intrinsic defect in erythropoiesis due to a failure to adequately protect TfR1 mRNA against degradation. This study links a classic regulator of cellular iron metabolism to systemic iron homeostasis and erythropoietic TfR1 expression. Furthermore, this work uncovers aspects of mammalian iron metabolism that can or cannot be compensated for by the expression of IRP1.","authors":"Galy, B., Ferring, D., Minana, B., Bell, O., Janser, HG., Muckenthaler, M., Sch\u00fcmann, K., Hentze, MW.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Blood","volume":"106","issue":"7","page":"2580-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22499122","title":"Identification of distinct gene expression profiles between esophageal squamous cell carcinoma and adjacent normal epithelial tissues.","abstract":"Esophageal squamous cell carcinoma (ESCC) is a predominant type of esophageal cancer, which is a malignant tumor originating from the esophageal mucosa or gland and is aggressive with poor prognosis.  Identification of new gene expression patterns would be helpful for providing new targets for the early detection and treatment of ESCC patients.  In the present study, we employed cDNA array technology to compare gene expression profiles between ESCC tissues and adjacent normal epithelial tissues from ESCC patients.  There was at least a 4-fold change in the expression levels of 72 genes that were significantly increased and 107 genes that were decreased in ESCC compared with normal esophageal epithelium.  Among them, genes known to be involved in ESCC were found, including matrix metalloproteinases, transcription factors SOX-4 and SOX-17, the Wingless-type MMTV integration site family member 2, and cell cycle regulators.  Moreover, we have newly identified the two genes that are down-regulated in ESCC: monoamine oxidase A, an enzyme that catalyzes monoamines oxidation and 15-hydroxyprostaglandin dehydrogenase [NAD+], a prostaglandin-synthesizing enzyme that physiologically antagonizes COX-2.  Likewise, we found the three genes that are up-regulated in ESCC: CD7, a cell surface glycoprotein member of the immunoglobulin superfamily, LIM-domain kinase 1, a small subfamily with an unique combination of two N-terminal LIM motifs and a C-terminal protein kinase domain, and TTK protein kinase, a previously unidentified member of the kinase family.  These newly identified genes may be involved in the progression of the tumor and\/or represent properties specific to ESCC.","authors":"Tao, Y., Chai, D., Ma, L., Zhang, T., Feng, Z., Cheng, Z., Wu, S., Qin, Y., Lai, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Tohoku J Exp Med","volume":"226","issue":"4","page":"301-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10652277","title":"Antiapoptotic activity of Stat5 required during terminal stages of myeloid differentiation.","abstract":"Stat5 is activated by multiple receptors of hematopoietic cytokines. To study its role during hematopoiesis, we have generated primary chicken myeloblasts expressing different dominant-negative (dn) alleles of Stat5. This caused a striking inability to generate mature cells, due to massive apoptosis during differentiation. Bcl-2 was able to rescue differentiating cells expressing dnStat5 from apoptosis, suggesting that during cytokine-dependent differentiation the main function of the protein is to ensure cell survival. Our findings with dnStat5-expressing chicken myeloblasts were confirmed with primary hematopoietic cells from Stat5a\/Stat5b-deficient mice. Bone marrow cells from these animals displayed a strong increase in apoptotic cell death during GM-CSF-dependent functional maturation in vitro. The antiapoptotic protein Bcl-x was induced by GM-CSF and IL-3 in a Stat5-dependent fashion. Ectopic expression of Bcl-x rescued Stat5-deficient bone marrow cells from apoptosis, indicating that Stat5 promotes the survival of myeloid progenitor cells through its ability to induce transcription of the bcl-x gene. Finally, the recruitment of myeloid cells to inflammatory sites was found strongly impeded in Stat5-deficient mice. Taken together, our findings suggest that Stat5 may promote cytokine-dependent survival and proliferation of differentiating myeloid progenitor cells in stress or pathological situations, such as inflammation.","authors":"Kieslinger, M., Woldman, I., Moriggl, R., Hofmann, J., Marine, JC., Ihle, JN., Beug, H., Decker, T.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Genes Dev","volume":"14","issue":"2","page":"232-44","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2000-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26627013","title":"The CDK9 Inhibitor Dinaciclib Exerts Potent Apoptotic and Antitumor Effects in Preclinical Models of MLL-Rearranged Acute Myeloid Leukemia.","abstract":"Translocations of the mixed lineage leukemia (MLL) gene occur in 60% to 80% of all infant acute leukemias and are markers of poor prognosis. MLL-AF9 and other MLL fusion proteins aberrantly recruit epigenetic regulatory proteins, including histone deacetylases (HDAC), histone methyltransferases, bromodomain-containing proteins, and transcription elongation factors to mediate chromatin remodeling and regulate tumorigenic gene expression programs. We conducted a small-molecule inhibitor screen to test the ability of candidate pharmacologic agents targeting epigenetic and transcriptional regulatory proteins to induce apoptosis in leukemic cells derived from genetically engineered mouse models of MLL-AF9-driven acute myeloid leukemia (AML). We found that the CDK inhibitor dinaciclib and HDAC inhibitor panobinostat were the most potent inducers of apoptosis in short-term in vitro assays. Treatment of MLL-rearranged leukemic cells with dinaciclib resulted in rapidly decreased expression of the prosurvival protein Mcl-1, and accordingly, overexpression of Mcl-1 protected AML cells from dinaciclib-induced apoptosis. Administration of dinaciclib to mice bearing MLL-AF9-driven human and mouse leukemias elicited potent antitumor responses and significantly prolonged survival. Collectively, these studies highlight a new therapeutic approach to potentially overcome the resistance of MLL-rearranged AML to conventional chemotherapies and prompt further clinical evaluation of CDK inhibitors in AML patients harboring MLL fusion proteins.","authors":"Baker, A., Gregory, GP., Verbrugge, I., Kats, L., Hilton, JJ., Vidacs, E., Lee, EM., Lock, RB., Zuber, J., Shortt, J., Johnstone, RW.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cancer Res","volume":"76","issue":"5","page":"1158-69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37028395","title":"It takes two to untangle: Combined stimulation of adult neurogenesis reverts AD symptoms.","abstract":"Alzheimer's disease (AD) is associated with reduced adult hippocampal neurogenesis and impaired hippocampal-dependent behaviors. Li et&#xa0;al.<sup>1<\/sup> report that stimulating adult neurogenesis combined with new-born neuron activation ameliorates behavioral symptoms and plaque deposition in AD mouse models. This supports boosting adult neurogenesis as a potential therapeutic approach for AD-related cognitive decline.","authors":"Gabarr\u00f3-Solanas, R., Urb\u00e1n, N.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Cell Stem Cell","volume":"30","issue":"4","page":"333-334","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22411984","title":"The blueprint of the type-3 injectisome.","abstract":"Type-3 secretion systems are sophisticated syringe-like nanomachines present in many animal and plant Gram-negative pathogens. They are capable of translocating an arsenal of specific bacterial toxins (effector proteins) from the prokaryotic cytoplasm across the three biological membranes directly into the eukaryotic cytosol, some of which modulate host cell mechanisms for the benefit of the pathogen. They populate a particular biological niche, which is maintained by specific, pathogen-dependent effectors. In contrast, the needle complex, which is the central component of this specialized protein delivery machine, is structurally well-conserved. It is a large supramolecular cylindrical structure composed of multiple copies of a relatively small subset of proteins, is embedded in the bacterial membranes and protrudes from the pathogen's surface with a needle filament. A central channel traverses the entire needle complex, and serves as a hollow conduit for proteins destined to travel this secretion pathway. In the past few years, there has been a tremendous increase in an understanding on both the structural and the mechanistic level. This review will thus focus on new insights of this remarkable molecular machine.","authors":"Kosarewicz, A., K\u00f6nigsmaier, L., Marlovits, TC.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"367","issue":"1592","page":"1140-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22136931","title":"Forward and reverse genetics through derivation of haploid mouse embryonic stem cells.","abstract":"All somatic mammalian cells carry two copies of chromosomes (diploidy), whereas organisms with a single copy of their genome, such as yeast, provide a basis for recessive genetics. Here we report the generation of haploid mouse ESC lines from parthenogenetic embryos. These cells carry 20 chromosomes, express stem cell markers, and develop into all germ layers in vitro and in vivo. We also developed a reversible mutagenesis protocol that allows saturated genetic recessive screens and results in homozygous alleles. This system allowed us to generate a knockout cell line for the microRNA processing enzyme Drosha. In a forward genetic screen, we identified Gpr107 as a molecule essential for killing by ricin, a toxin being used as a bioweapon. Our results open the possibility of combining the power of a haploid genome with pluripotency of embryonic stem cells to uncover fundamental biological processes in defined cell types at a genomic scale.","authors":"Elling, U., Taubenschmid, J., Wirnsberger, G., O'Malley, R., Demers, SP., Vanhaelen, Q., Shukalyuk, AI., Schmauss, G., Schramek, D., Schnuetgen, F., von Melchner, H., Ecker, JR., Stanford, WL., Zuber, J., Stark, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Cell Stem Cell","volume":"9","issue":"6","page":"563-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19056890","title":"The cohesin complex and its roles in chromosome biology.","abstract":"Cohesin is a chromosome-associated multisubunit protein complex that is highly conserved in eukaryotes and has close homologs in bacteria. Cohesin mediates cohesion between replicated sister chromatids and is therefore essential for chromosome segregation in dividing cells. Cohesin is also required for efficient repair of damaged DNA and has important functions in regulating gene expression in both proliferating and post-mitotic cells. Here we discuss how cohesin associates with DNA, how these interactions are controlled during the cell cycle; how binding of cohesin to DNA may mediate sister chromatid cohesion, DNA repair, and gene regulation; and how defects in these processes can lead to human disease.","authors":"Peters, JM., Tedeschi, A., Schmitz, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genes Dev","volume":"22","issue":"22","page":"3089-114","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26447190","title":"Functional-genetic dissection of HDAC dependencies in mouse lymphoid and myeloid malignancies.","abstract":"Histone deacetylase (HDAC) inhibitors (HDACis) have demonstrated activity in hematological and solid malignancies. Vorinostat, romidepsin, belinostat, and panobinostat are Food and Drug Administration-approved for hematological malignancies and inhibit class II and\/or class I HDACs, including HDAC1, 2, 3, and 6. We combined genetic and pharmacological approaches to investigate whether suppression of individual or multiple Hdacs phenocopied broad-acting HDACis in 3 genetically distinct leukemias and lymphomas. Individual Hdacs were depleted in murine acute myeloid leukemias (MLL-AF9;Nras(G12D); PML-RAR\u03b1 acute promyelocytic leukemia [APL] cells) and E\u00b5-Myc lymphoma in vitro and in vivo. Strikingly, Hdac3-depleted cells were selected against in competitive assays for all 3 tumor types. Decreased proliferation following Hdac3 knockdown was not prevented by BCL-2 overexpression, caspase inhibition, or knockout of Cdkn1a in E\u00b5-Myc lymphoma, and depletion of Hdac3 in vivo significantly reduced tumor burden. Interestingly, APL cells depleted of Hdac3 demonstrated a more differentiated phenotype. Consistent with these genetic studies, the HDAC3 inhibitor RGFP966 reduced proliferation of E\u00b5-Myc lymphoma and induced differentiation in APL. Genetic codepletion of Hdac1 with Hdac2 was pro-apoptotic in E\u00b5-Myc lymphoma in vitro and in vivo and was phenocopied by the HDAC1\/2-specific agent RGFP233. This study demonstrates the importance of HDAC3 for the proliferation of leukemia and lymphoma cells, suggesting that HDAC3-selective inhibitors could prove useful for the treatment of hematological malignancies. Moreover, our results demonstrate that codepletion of Hdac1 with Hdac2 mediates a robust pro-apoptotic response. Our integrated genetic and pharmacological approach provides important insights into the individual or combinations of HDACs that could be prioritized for targeting in a range of hematological malignancies.","authors":"Matthews, GM., Mehdipour, P., Cluse, LA., Falkenberg, KJ., Wang, E., Roth, M., Santoro, F., Vidacs, E., Stanley, K., House, CM., Rusche, JR., Vakoc, CR., Zuber, J., Minucci, S., Johnstone, RW.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Blood","volume":"126","issue":"21","page":"2392-403","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23505351","title":"Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.","abstract":"The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we performed deep RNA sequencing of the blastema over a time course in the axolotl, a species whose genome has not been sequenced. Using a novel comparative approach to analyzing RNA-seq data, we characterized the transcriptional dynamics of the regenerating axolotl limb with respect to the human gene set. This approach involved de novo assembly of axolotl transcripts, RNA-seq transcript quantification without a reference genome, and transformation of abundances from axolotl contigs to human genes. We found a prominent burst in oncogene expression during the first day and blastemal\/limb bud genes peaking at 7 to 14 days. In addition, we found that limb patterning genes, SALL genes, and genes involved in angiogenesis, wound healing, defense\/immunity, and bone development are enriched during blastema formation and development. Finally, we identified a category of genes with no prior literature support for limb regeneration that are candidates for further evaluation based on their expression pattern during the regenerative process.","authors":"Stewart, R., Rasc\u00f3n, CA., Tian, S., Nie, J., Barry, C., Chu, LF., Ardalani, H., Wagner, RJ., Probasco, MD., Bolin, JM., Leng, N., Sengupta, S., Volkmer, M., Habermann, B., Tanaka, EM., Thomson, JA., Dewey, CN.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"PLoS Comput Biol","volume":"9","issue":"3","page":"e1002936","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37024756","title":"Author Correction: PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing.","abstract":null,"authors":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Torma, F., Orthofer, M., Yarwood, R., Heinz, LX., Sedlyarov, V., Miranda, ND., Taylor, A., Grapentine, S., Al-Murshedi, F., Abot, A., Weidinger, A., Kutchukian, C., Sanchez, C., Cronin, SJF., Novatchkova, M., Kavirayani, A., Schuetz, T., Haubner, B., Haas, L., Hagelkruys, A., Jackowski, S., Kozlov, AV., Jacquemond, V., Knauf, C., Superti-Furga, G., Rullman, E., Gustafsson, T., McDermot, J., Lowe, M., Radak, Z., Chamberlain, JS., Bakovic, M., Banka, S., Penninger, JM.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Nat Metab","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7823956","title":"A deficiency of the small GTPase rab8 inhibits membrane traffic in developing neurons.","abstract":"One of the major activities of developing neurons is the transport of new membrane to the growing axon. Candidates for playing a key role in the regulation of this intense traffic are the small GTP-binding proteins of the rab family. We have used hippocampal neurons in culture and analyzed membrane traffic activity after suppressing the expression of the small GTP-binding protein rab8. Inhibition of protein expression was accomplished by using sequence-specific antisense oligonucleotides. While rab8 depletion resulted in the blockage of morphological maturation in 95% of the neurons, suppression of expression of another rab protein, rab3a, had no effect, and all neurons developed normal axons and dendrites. The impairment of neuronal maturation by rab8 antisense treatment was due to inhibition of membrane traffic. Thus, by using video-enhanced differential interference contrast microscopy, we observed in the rab8-depleted cells a dramatic reduction in the number of vesicles undergoing anterograde transport. Moreover, by incubating antisense-treated neurons with Bodipy-labeled ceramide, a fluorescent marker for newly formed exocytic vesicles, we observed fluorescence labeling restricted to the Golgi apparatus, whereas in control cells labeling was found also in the neurites. These results show the role of the small GTPase rab8 in membrane traffic during neuronal process outgrowth.","authors":"Huber, LA., Dupree, P., Dotti, CG.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Mol Cell Biol","volume":"15","issue":"2","page":"918-24","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1995-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32619470","title":"Condensin: The Little Motor Protein that Could.","abstract":"Kong et\u00a0al. (2020) present the low-resolution structure of the ATP\u0263S-bound human condensin I and II complexes and demonstrate that human condensins can extrude DNA loops in a symmetric and asymmetric fashion and compact nucleosome-bound DNA.","authors":"Goloborodko, A.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Mol Cell","volume":"79","issue":"1","page":"3-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15890652","title":"The 1.3 A crystal structure of the flavoprotein YqjM reveals a novel class of Old Yellow Enzymes.","abstract":"Here we report the crystal structure of YqjM, a homolog of Old Yellow Enzyme (OYE) that is involved in the oxidative stress response of Bacillus subtilis. In addition to the oxidized and reduced enzyme form, the structures of complexes with p-hydroxybenzaldehyde and p-nitrophenol, respectively, were solved. As for other OYE family members, YqjM folds into a (alpha\/beta)8-barrel and has one molecule of flavin mononucleotide bound non-covalently at the COOH termini of the beta-sheet. Most of the interactions that control the electronic properties of the flavin mononucleotide cofactor are conserved within the OYE family. However, in contrast to all members of the OYE family characterized to date, YqjM exhibits several unique structural features. For example, the enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers. Moreover, the protein displays a shared active site architecture where an arginine finger (Arg336) at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal Tyr28 instead of a COOH-terminal tyrosine in OYE and its homologs. The structural information led to a specific data base search from which a new class of OYE oxidoreductases was identified that exhibits a strict conservation of active site residues, which are critical for this subfamily, most notably Cys26, Tyr28, Lys109, and Arg336. Therefore, YqjM is the first representative of a new bacterial subfamily of OYE homologs.","authors":"Kitzing, K., Fitzpatrick, TB., Wilken, C., Sawa, J., Bourenkov, GP., Macheroux, P., Clausen, T.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Biol Chem","volume":"280","issue":"30","page":"27904-13","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2005-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22048776","title":"Fabrication of cell container arrays with overlaid surface topographies.","abstract":"This paper presents cell culture substrates in the form of microcontainer arrays with overlaid surface topographies, and a technology for their fabrication. The new fabrication technology is based on microscale thermoforming of thin polymer films whose surfaces are topographically prepatterned on a micro- or nanoscale. For microthermoforming, we apply a new process on the basis of temporary back moulding of polymer films and use the novel concept of a perforated-sheet-like mould. Thermal micro- or nanoimprinting is applied for prepatterning. The novel cell container arrays are fabricated from polylactic acid (PLA) films. The thin-walled microcontainer structures have the shape of a spherical calotte merging into a hexagonal shape at their upper circumferential edges. In the arrays, the cell containers are arranged densely packed in honeycomb fashion. The inner surfaces of the highly curved container walls are provided with various topographical micro- and nanopatterns. For a first validation of the microcontainer arrays as in vitro cell culture substrates, C2C12 mouse premyoblasts are cultured in containers with microgrooved surfaces and shown to align along the grooves in the three-dimensional film substrates. In future stem-cell-biological and tissue engineering applications, microcontainers fabricated using the proposed technology may act as geometrically defined artificial microenvironments or niches.","authors":"Truckenm\u00fcller, R., Giselbrecht, S., Escalante-Marun, M., Groenendijk, M., Papenburg, B., Rivron, N., Unadkat, H., Saile, V., Subramaniam, V., van den Berg, A., van Blitterswijk, C., Wessling, M., de Boer, J., Stamatialis, D.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Biomed Microdevices","volume":"14","issue":"1","page":"95-107","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26825123","title":"Muscle RANK is a key regulator of Ca2+ storage, SERCA activity, and function of fast-twitch skeletal muscles.","abstract":"Receptor-activator of nuclear factor-\u03baB (RANK), its ligand RANKL, and the soluble decoy receptor osteoprotegerin are the key regulators of osteoclast differentiation and bone remodeling. Here we show that RANK is also expressed in fully differentiated myotubes and skeletal muscle. Muscle RANK deletion has inotropic effects in denervated, but not in sham, extensor digitorum longus (EDL) muscles preventing the loss of maximum specific force while promoting muscle atrophy, fatigability, and increased proportion of fast-twitch fibers. In denervated EDL muscles, RANK deletion markedly increased stromal interaction molecule 1 content, a Ca(2+)sensor, and altered activity of the sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) modulating Ca(2+)storage. Muscle RANK deletion had no significant effects on the sham or denervated slow-twitch soleus muscles. These data identify a novel role for RANK as a key regulator of Ca(2+)storage and SERCA activity, ultimately affecting denervated skeletal muscle function.","authors":"Dufresne, SS., Dumont, NA., Boulanger-Piette, A., Fajardo, VA., Gamu, D., Kake-Guena, SA., David, RO., Bouchard, P., Lavergne, \u00c9., Penninger, JM., Pape, PC., Tupling, AR., Frenette, J.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Am J Physiol Cell Physiol","volume":"310","issue":"8","page":"C663-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15824097","title":"Mind bomb-2 is an E3 ligase for Notch ligand.","abstract":"The zebrafish gene, mind bomb (mib), encodes a protein that positively regulates of the Delta-mediated Notch signaling. It interacts with the intracellular domain of Delta to promote its ubiquitination and endocytosis. In our search for the mouse homologue of zebrafish mind bomb, we cloned two homologues in the mouse genome: a mouse orthologue (mouse mib1) and a paralogue, named mind bomb-2 (mib2), which is evolutionarily conserved from Drosophila to human. Both Mib1 and Mib2 have an E3 ubiquitin ligase activity in their C-terminal RING domain and interact with Xenopus Delta (XD) via their N-terminal region. Mib2 is also able to ligate ubiquitin to XD and shift the membrane localization of Delta to intracellular vesicles. Importantly, Mib2 rescues both the neuronal and vascular defects in the zebrafish mib(ta52b) mutants. In contrast to the functional similarities between Mib1 and Mib2, mib2 is highly expressed in adult tissues, but almost not at all in embryos, whereas mib1 is abundantly expressed in both embryos and adult tissues. These data suggest that Mib2 has functional similarities to Mib1, but might have distinct roles in Notch signaling as an E3 ubiquitin ligase.","authors":"Koo, BK., Yoon, KJ., Yoo, KW., Lim, HS., Song, R., So, JH., Kim, CH., Kong, YY.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Biol Chem","volume":"280","issue":"23","page":"22335-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15793568","title":"Spinophilin regulates Ca2+ signalling by binding the N-terminal domain of RGS2 and the third intracellular loop of G-protein-coupled receptors.","abstract":"Signalling by G proteins is controlled by the regulator of G-protein signalling (RGS) proteins that accelerate the GTPase activity of Galpha subunits and act in a G-protein-coupled receptor (GPCR)-specific manner. The conserved RGS domain accelerates the G subunit GTPase activity, whereas the variable amino-terminal domain participates in GPCR recognition. How receptor recognition is achieved is not known. Here, we show that the scaffold protein spinophilin (SPL), which binds the third intracellular loop (3iL) of several GPCRs, binds the N-terminal domain of RGS2. SPL also binds RGS1, RGS4, RGS16 and GAIP. When expressed in Xenopus laevis oocytes, SPL markedly increased inhibition of alpha-adrenergic receptor (alphaAR) Ca2+ signalling by RGS2. Notably, the constitutively active mutant alphaAR(A293E) (the mutation being in the 3iL) did not bind SPL and was relatively resistant to inhibition by RGS2. Use of betaAR-alphaAR chimaeras identified the 288REKKAA293 sequence as essential for the binding of SPL and inhibition of Ca2+ signalling by RGS2. Furthermore, alphaAR-evoked Ca2+ signalling is less sensitive to inhibition by SPL in rgs2-\/- cells and less sensitive to inhibition by RGS2 in spl-\/- cells. These findings provide a general mechanism by which RGS proteins recognize GPCRs to confer signalling specificity.","authors":"Wang, X., Zeng, W., Soyombo, AA., Tang, W., Ross, EM., Barnes, AP., Milgram, SL., Penninger, JM., Allen, PB., Greengard, P., Muallem, S.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Cell Biol","volume":"7","issue":"4","page":"405-11","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15779987","title":"Ultrathin coatings from isocyanate terminated star PEG prepolymers: patterning of proteins on the layers.","abstract":"This study presents the easy and fast patterning of low molecular weight molecules that act as binding partners for proteins on Star PEG coatings. These coatings are prepared from isocyanate terminated star shaped prepolymers and form a highly cross-linked network on the substrate in which the stars are connected via urea groups and free amino groups are present. Streptavidin has been patterned on these layers by microcontact printing (muCP) of an amino reactive biotin derivative and consecutive binding of streptavidin to the biotin. Patterns of Ni(2+)-nitriltriacetic acid (NTA) receptors have been prepared by printing amino functional NTA molecules in freshly prepared Star PEG layers that still contain amino reactive isocyanate groups. Complexation of the NTA groups with Ni(II) ions enabled the binding of His-tag enhanced green fluorescent protein (EGFP) in the desired pattern on the substrates. Since the unmodified Star PEG layers prevent unspecific protein adsorption, His-EGFP could selectively be bound to the sample by immersion into crude, nonpurified His-tag EGFP containing cell lysate.","authors":"Groll, J., Haubensak, W., Ameringer, T., Moeller, M.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Langmuir","volume":"21","issue":"7","page":"3076-83","pdf":null,"JrId":"22883","fulltextlink":null,"preprintlink":null,"articledate":"2006-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26824653","title":"Trim28 Haploinsufficiency Triggers Bi-stable Epigenetic Obesity.","abstract":"More than one-half billion people are obese, and despite progress in genetic research, much of the heritability of obesity remains enigmatic. Here, we identify a Trim28-dependent network capable of triggering obesity in a non-Mendelian, \"on\/off\" manner. Trim28(+\/D9) mutant mice exhibit a bi-modal body-weight distribution, with isogenic animals randomly emerging as either normal or obese and few intermediates. We find that the obese-\"on\" state is characterized by reduced expression of an imprinted gene network including Nnat, Peg3, Cdkn1c, and Plagl1 and that independent targeting of these alleles recapitulates the stochastic bi-stable disease phenotype. Adipose tissue transcriptome analyses in children indicate that humans too cluster into distinct sub-populations, stratifying according to Trim28 expression, transcriptome organization, and obesity-associated imprinted gene dysregulation. These data provide evidence of discrete polyphenism in mouse and man and thus carry important implications for complex trait genetics, evolution, and medicine.","authors":"Dalgaard, K., Landgraf, K., Heyne, S., Lempradl, A., Longinotto, J., Gossens, K., Ruf, M., Orthofer, M., Strogantsev, R., Selvaraj, M., Lu, TT., Casas, E., Teperino, R., Surani, MA., Zvetkova, I., Rimmington, D., Tung, YC., Lam, B., Larder, R., Yeo, GS., O'Rahilly, S., Vavouri, T., Whitelaw, E., Penninger, JM., Jenuwein, T., Cheung, CL., Ferguson-Smith, AC., Coll, AP., K\u00f6rner, A., Pospisilik, JA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"164","issue":"3","page":"353-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23293283","title":"Connective tissue cells, but not muscle cells, are involved in establishing the proximo-distal outcome of limb regeneration in the axolotl.","abstract":"During salamander limb regeneration, only the structures distal to the amputation plane are regenerated, a property known as the rule of distal transformation. Multiple cell types are involved in limb regeneration; therefore, determining which cell types participate in distal transformation is important for understanding how the proximo-distal outcome of regeneration is achieved. We show that connective tissue-derived blastema cells obey the rule of distal transformation. They also have nuclear MEIS, which can act as an upper arm identity regulator, only upon upper arm amputation. By contrast, myogenic cells do not obey the rule of distal transformation and display nuclear MEIS upon amputation at any proximo-distal level. These results indicate that connective tissue cells, but not myogenic cells, are involved in establishing the proximo-distal outcome of regeneration and are likely to guide muscle patterning. Moreover, we show that, similarly to limb development, muscle patterning in regeneration is influenced by \u03b2-catenin signalling.","authors":"Nacu, E., Glausch, M., Le, HQ., Damanik, FF., Schuez, M., Knapp, D., Khattak, S., Richter, T., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Development","volume":"140","issue":"3","page":"513-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15775980","title":"Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis.","abstract":"SU(VAR)3-9 like histone methyltransferases control heterochromatic domains in eukaryotes. In Arabidopsis, 10 SUVH genes encode SU(VAR)3-9 homologues where SUVH1, SUVH2 and SUVH4 (KRYPTONITE) represent distinct subgroups of SUVH genes. Loss of SUVH1 and SUVH4 causes weak reduction of heterochromatic histone H3K9 dimethylation, whereas in SUVH2 null plants mono- and dimethyl H3K9, mono- and dimethyl H3K27, and monomethyl H4K20, the histone methylation marks of Arabidopsis heterochromatin are significantly reduced. Like animal SU(VAR)3-9 proteins SUVH2 displays strong dosage-dependent effects. Loss of function suppresses, whereas overexpression enhances, gene silencing, causes ectopic heterochromatization and significant growth defects. Furthermore, modification of transgene silencing by SUVH2 is partially transmitted to the offspring plants. This epigenetic stability correlates with heritable changes in DNA methylation. Mutational dissection of SUVH2 indicates an implication of its N-terminus and YDG domain in directing DNA methylation to target sequences, a prerequisite for consecutive histone methylation. Gene silencing by SUVH2 depends on MET1 and DDM1, but not CMT3. In Arabidopsis, SUVH2 with its histone H3K9 and H4K20 methylation activity has a central role in heterochromatic gene silencing.","authors":"Naumann, K., Fischer, A., Hofmann, I., Krauss, V., Phalke, S., Irmler, K., Hause, G., Aurich, AC., Dorn, R., Jenuwein, T., Reuter, G.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"EMBO J","volume":"24","issue":"7","page":"1418-29","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15769890","title":"The role of endothelial PI3Kgamma activity in neutrophil trafficking.","abstract":"Phosphoinositide 3-kinase gamma (PI3Kgamma) in neutrophils plays a critical role in the directed migration of these cells into inflamed tissues. In this study, we demonstrate the importance of the endothelial component of PI3Kgamma activity relative to its leukocyte counterpart in supporting neutrophil interactions with the inflamed vessel wall. Despite the reconstitution of class-Ib PI3K function in neutrophils of p110gamma-\/- mice, we observed a 45% reduction in accumulation of these cells in an acute lung injury model. Mechanistically, this appears to result from a perturbation in selectin-mediated adhesion as manifested by a 70% reduction in wild-type (WT) neutrophil attachment to and 17-fold increase in rolling velocities on p110gamma-\/- microvessels in vivo in response to tumor necrosis factor alpha (TNFalpha). This alteration in adhesion was further augmented by a deficiency in p110delta, suggesting that the activity of both catalytic subunits is required for efficient capture of neutrophils by cytokine-stimulated endothelium. Interestingly, E-selectin-mediated adhesion in p110gamma-\/-) mice was impaired by more than 95%, but no defect in nuclear factor kappa B (NF-kappaB)-induced gene expression was observed. These findings suggest a previously unrecognized partnership between class-I PI3Ks expressed in leukocytes and endothelium, the combination of which is required for the efficient trafficking of immunocompetent cells to sites of inflammation.","authors":"Puri, KD., Doggett, TA., Huang, CY., Douangpanya, J., Hayflick, JS., Turner, M., Penninger, J., Diacovo, TG.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Blood","volume":"106","issue":"1","page":"150-7","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2005-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28219927","title":"Molecular role of the PAX5-ETV6 oncoprotein in promoting B-cell acute lymphoblastic leukemia.","abstract":"PAX5 is a tumor suppressor in B-ALL, while the role of PAX5 fusion proteins in B-ALL development is largely unknown. Here, we studied the function of PAX5-ETV6 and PAX5-FOXP1 in mice expressing these proteins from the <i>Pax5<\/i> locus. Both proteins arrested B-lymphopoiesis at the pro-B to pre-B-cell transition and, contrary to their proposed dominant-negative role, did not interfere with the expression of most regulated Pax5 target genes. Pax5-Etv6, but not Pax5-Foxp1, cooperated with loss of the Cdkna2a\/b tumor suppressors in promoting B-ALL development. Regulated Pax5-Etv6 target genes identified in these B-ALLs encode proteins implicated in pre-B-cell receptor (BCR) signaling and migration\/adhesion, which could contribute to the proliferation, survival, and tissue infiltration of leukemic B cells. Together with similar observations made in human PAX5-ETV6<sup>+<\/sup> B-ALLs, these data identified PAX5-ETV6 as a potent oncoprotein that drives B-cell leukemia development.","authors":"Smeenk, L., Fischer, M., Jurado, S., Jaritz, M., Azaryan, A., Werner, B., Roth, M., Zuber, J., Stanulla, M., den Boer, ML., Mullighan, CG., Strehl, S., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"EMBO J","volume":"36","issue":"6","page":"718-735","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23122288","title":"Stem cells in the land of the rising sun: ISSCR 2012.","abstract":"The 2012 annual meeting of the International Society for Stem Cell Research (ISSCR) marked the Tenth Anniversary of the ISSCR. Held in Japan, the meeting showcased recent discoveries and surveyed the remarkable progress that has been made in a decade of stem cell research.","authors":"Plath, K., Srivastava, D., Alvarez-Buylla, A., Tanaka, EM., Kriegstein, AR.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Stem Cell","volume":"11","issue":"5","page":"607-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24859753","title":"Fluorogenic probes for live-cell imaging of the cytoskeleton.","abstract":"We introduce far-red, fluorogenic probes that combine minimal cytotoxicity with excellent brightness and photostability for fluorescence imaging of actin and tubulin in living cells. Applied in stimulated emission depletion (STED) microscopy, they reveal the ninefold symmetry of the centrosome and the spatial organization of actin in the axon of cultured rat neurons with a resolution unprecedented for imaging cytoskeletal structures in living cells.","authors":"Lukinavi\u010dius, G., Reymond, L., D'Este, E., Masharina, A., G\u00f6ttfert, F., Ta, H., G\u00fcther, A., Fournier, M., Rizzo, S., Waldmann, H., Blaukopf, C., Sommer, C., Gerlich, DW., Arndt, HD., Hell, SW., Johnsson, K.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Methods","volume":"11","issue":"7","page":"731-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31230958","title":"Mitotic Chromosome Mechanics: How Cells Segregate Their Genome.","abstract":"During mitosis, replicated chromosomes segregate such that each daughter cell receives one copy of the genome. Faithful mechanical transport during mitosis requires that chromosomes undergo extensive structural changes as the cell cycle progresses, resulting in the formation of compact, cylindrical bodies. Such structural changes encompass a range of different activities, including longitudinal condensation of the chromosome axis, global chromatin compaction, resolution of sister chromatids, and individualisation of chromosomes into separate bodies. After mitosis, chromosomes undergo further reorganisation to rebuild interphase cell nuclei. Here we review the requirements for mitotic chromosomes to successfully transmit genetic information to daughter cells and the biophysical principles that underpin such requirements.","authors":"Batty, P., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Trends Cell Biol","volume":"29","issue":"9","page":"717-726","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28110180","title":"Combinatorial function of transcription factors and cofactors.","abstract":"Differential gene expression gives rise to the many cell types of complex organisms. Enhancers regulate transcription by binding transcription factors (TFs), which in turn recruit cofactors to activate RNA Polymerase II at core promoters. Transcriptional regulation is typically mediated by distinct combinations of TFs, enabling a relatively small number of TFs to generate a large diversity of cell types. However, how TFs achieve combinatorial enhancer control and how enhancers, enhancer-bound TFs, and the cofactors they recruit regulate RNA Polymerase II activity is not entirely clear. Here, we review how TF synergy is mediated at the level of DNA binding and after binding, the role of cofactors and the post-translational modifications they catalyze, and discuss different models of enhancer-core-promoter communication.","authors":"Reiter, F., Wienerroither, S., Stark, A.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Curr Opin Genet Dev","volume":"43","issue":null,"page":"73-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30710114","title":"Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute.","abstract":"Genome-wide screening using CRISPR coupled with nuclease Cas9 (CRISPR-Cas9) is a powerful technology for the systematic evaluation of gene function. Statistically principled analysis is needed for the accurate identification of gene hits and associated pathways. Here, we describe how to perform computational analysis of CRISPR screens using the MAGeCKFlute pipeline. MAGeCKFlute combines the MAGeCK and MAGeCK-VISPR algorithms and incorporates additional downstream analysis functionalities. MAGeCKFlute is distinguished from other currently available tools by its comprehensive pipeline, which contains a series of functions for analyzing CRISPR screen data. This protocol explains how to use MAGeCKFlute to perform quality control (QC), normalization, batch effect removal, copy-number bias correction, gene hit identification and downstream functional enrichment analysis for CRISPR screens. We also describe gene identification and data analysis in CRISPR screens involving drug treatment. Completing the entire MAGeCKFlute pipeline requires ~3 h on a desktop computer running Linux or Mac OS with R support.","authors":"Wang, B., Wang, M., Zhang, W., Xiao, T., Chen, CH., Wu, A., Wu, F., Traugh, N., Wang, X., Li, Z., Mei, S., Cui, Y., Shi, S., Lipp, JJ., Hinterndorfer, M., Zuber, J., Brown, M., Li, W., Liu, XS.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Protoc","volume":"14","issue":"3","page":"756-780","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26845587","title":"Paul Ehrlich (1854-1915) and His Contributions to the Foundation and Birth of Translational Medicine.","abstract":"Translational research and precision medicine are based on a profound knowledge of cellular and molecular mechanisms contributing to various physiologic processes and pathologic reactions in diverse organs. Whereas specific molecular interactions and mechanisms have been identified during the past 5 decades, the underlying principles were defined much earlier and originate from to the seminal observations made by outstanding researchers between 1850 and 1915. One of the most outstanding exponents of these scientists is Paul Ehrlich. His work resulted not only in the foundation and birth of modern hematology and immunology, but also led to the development of chemotherapy and specific targeted treatment concepts. In 2015, the Medical University of Vienna organized a memorial meeting, with the aim of honoring Paul Ehrlich's contributions to science, and to commemorate the 100th anniversary of his death. The authors of the current review served as faculty members and dedicate this paper to Paul Ehrlich and his remarkable contributions to medicine.","authors":"Valent, P., Groner, B., Schumacher, U., Superti-Furga, G., Busslinger, M., Kralovics, R., Zielinski, C., Penninger, JM., Kerjaschki, D., Stingl, G., Smolen, JS., Valenta, R., Lassmann, H., Kovar, H., J\u00e4ger, U., Kornek, G., M\u00fcller, M., S\u00f6rgel, F.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Innate Immun","volume":"8","issue":"2","page":"111-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23103585","title":"Muscle and connective tissue progenitor populations show distinct Twist1 and Twist3 expression profiles during axolotl limb regeneration.","abstract":"Limb regeneration involves re-establishing a limb development program from cells within adult tissues. Identifying molecular handles that provide insight into the relationship between cell differentiation status and cell lineage is an important step to study limb blastema cell formation. Here, using single cell PCR, focusing on newly isolated Twist1 sequences, we molecularly profile axolotl limb blastema cells using several progenitor cell markers. We link their molecular expression profile to their embryonic lineage via cell tracking experiments. We use in situ hybridization to determine the spatial localization and extent of overlap of different markers and cell types. Finally, we show by single cell PCR that the mature axolotl limb harbors a small but significant population of Twist1(+) cells.","authors":"Kragl, M., Roensch, K., N\u00fcsslein, I., Tazaki, A., Taniguchi, Y., Tarui, H., Hayashi, T., Agata, K., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Dev Biol","volume":"373","issue":"1","page":"196-204","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18677406","title":"Paraspeckle protein p54nrb links Sox9-mediated transcription with RNA processing during chondrogenesis in mice.","abstract":"The Sox9 transcription factor plays an essential role in promoting chondrogenesis and regulating expression of chondrocyte extracellular-matrix genes. To identify genes that interact with Sox9 in promoting chondrocyte differentiation, we screened a cDNA library generated from the murine chondrogenic ATDC5 cell line to identify activators of the collagen, type II, alpha 1 (Col2a1) promoter. Here we have shown that paraspeckle regulatory protein 54-kDa nuclear RNA-binding protein (p54nrb) is an essential link between Sox9-regulated transcription and maturation of Sox9-target gene mRNA. We found that p54nrb physically interacted with Sox9 and enhanced Sox9-dependent transcriptional activation of the Col2a1 promoter. In ATDC5 cells, p54nrb colocalized with Sox9 protein in nuclear paraspeckle bodies, and knockdown of p54(nrb) suppressed Sox9-dependent Col2a1 expression and promoter activity. We generated a p54nrb mutant construct lacking RNA recognition motifs, and overexpression of mutant p54nrb in ATDC5 cells markedly altered the appearance of paraspeckle bodies and inhibited the maturation of Col2a1 mRNA. The mutant p54nrb inhibited chondrocyte differentiation of mesenchymal cells and mouse metatarsal explants. Furthermore, transgenic mice expressing the mutant p54nrb in the chondrocyte lineage exhibited dwarfism associated with impairment of chondrogenesis. These data suggest that p54nrb plays an important role in the regulation of Sox9 function and the formation of paraspeckle bodies during chondrogenesis.","authors":"Hata, K., Nishimura, R., Muramatsu, S., Matsuda, A., Matsubara, T., Amano, K., Ikeda, F., Harley, VR., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Clin Invest","volume":"118","issue":"9","page":"3098-108","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24833723","title":"TUBB5 and its disease-associated mutations influence the terminal differentiation and dendritic spine densities of cerebral cortical neurons.","abstract":"The microtubule cytoskeleton is critical for the generation and maturation of neurons in the developing mammalian nervous system. We have previously shown that mutations in the \u03b2-tubulin gene TUBB5 cause microcephaly with structural brain abnormalities in humans. While it is known that TUBB5 is necessary for the proper generation and migration of neurons, little is understood of the role it plays in neuronal differentiation and connectivity. Here, we report that perturbations to TUBB5 disrupt the morphology of cortical neurons, their neuronal complexity, axonal outgrowth, as well as the density and shape of dendritic spines in the postnatal murine cortex. The features we describe are consistent with defects in synaptic signaling. Cellular-based assays have revealed that TUBB5 substitutions have the capacity to alter the dynamic properties and polymerization rates of the microtubule cytoskeleton. Together, our studies show that TUBB5 is essential for neuronal differentiation and dendritic spine formation in vivo, providing insight into the underlying cellular pathology associated with TUBB5 disease states.","authors":"Ngo, L., Haas, M., Qu, Z., Li, SS., Zenker, J., Teng, KS., Gunnersen, JM., Breuss, M., Habgood, M., Keays, DA., Heng, JI.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Hum Mol Genet","volume":"23","issue":"19","page":"5147-58","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28366588","title":"DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells.","abstract":"Blastocyst-derived embryonic stem cells (ESCs) and gonad-derived embryonic germ cells (EGCs) represent two classic types of pluripotent cell lines, yet their molecular equivalence remains incompletely understood. Here, we compare genome-wide methylation patterns between isogenic ESC and EGC lines to define epigenetic similarities and differences. Surprisingly, we find that sex rather than cell type drives methylation patterns in ESCs and EGCs. Cell fusion experiments further reveal that the ratio of X chromosomes to autosomes dictates methylation levels, with female hybrids being hypomethylated and male hybrids being hypermethylated. We show that the X-linked MAPK phosphatase DUSP9 is upregulated in female compared to male ESCs, and its heterozygous loss in female ESCs leads to male-like methylation levels. However, male and female blastocysts are similarly hypomethylated, indicating that sex-specific methylation differences arise in culture. Collectively, our data demonstrate the epigenetic similarity of sex-matched ESCs and EGCs and identify DUSP9 as a regulator of female-specific hypomethylation.","authors":"Choi, J., Clement, K., Huebner, AJ., Webster, J., Rose, CM., Brumbaugh, J., Walsh, RM., Lee, S., Savol, A., Etchegaray, JP., Gu, H., Boyle, P., Elling, U., Mostoslavsky, R., Sadreyev, R., Park, PJ., Gygi, SP., Meissner, A., Hochedlinger, K.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Stem Cell","volume":"20","issue":"5","page":"706-719.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27640184","title":"Efficient generation and reversion of chromosomal translocations using CRISPR\/Cas technology.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">27640184<\/PMID><DateCompleted><Year>2017<\/Year><Month>08<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>17<\/Volume><Issue>1<\/Issue><PubDate><Year>2016<\/Year><Month>09<\/Month><Day>17<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Efficient generation and reversion of chromosomal translocations using CRISPR\/Cas technology.<\/ArticleTitle><Pagination><MedlinePgn>739<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12864-016-3084-5<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Chromosomal translocations are a hallmark of cancer cells and give rise to fusion oncogenes. To gain insight into the mechanisms governing tumorigenesis, adequate model cell lines are required.","authors":"Lekomtsev, S., Aligianni, S., Lapao, A., B\u00fcrckst\u00fcmmer, T.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"BMC Genomics","volume":"17","issue":"1","page":"739","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15750601","title":"The molecular scaffold Gab2 is a crucial component of RANK signaling and osteoclastogenesis.","abstract":"Morphogenesis and remodeling of bone involve synthesis of bone matrix by osteoblasts and coordinate resorption of bone by osteoclasts. Defective bone remodeling caused by altered osteoclast activity underlies a multitude of osteopenic disorders. Receptor activator of NF-kappaB (RANK) and its ligand RANKL have been identified as essential factors involved in osteoclast development and bone remodeling, but their mechanism and interacting factors have not been fully characterized. Here we report that the molecular adapter Grb-2-associated binder-2 (Gab2) associates with RANK and mediates RANK-induced activation of NF-kappaB, Akt and Jnk. Inactivation of the gene encoding Gab2 in mice results in osteopetrosis and decreased bone resorption as a result of defective osteoclast differentiation. We also show that Gab2 has a crucial role in the differentiation of human progenitor cells into osteoclasts. We have thus identified a new, key regulatory scaffold molecule, Gab2, that controls select RANK signaling pathways and is essential for osteoclastogenesis and bone homeostasis.","authors":"Wada, T., Nakashima, T., Oliveira-dos-Santos, AJ., Gasser, J., Hara, H., Schett, G., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Med","volume":"11","issue":"4","page":"394-9","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"2005-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15758452","title":"Wnt-signaling and skeletogenesis.","abstract":"Members of the Wnt gene family, encoding secreted cystein-rich glycoproteins, have been isolated from a variety of organisms. They serve as important developmental signaling molecules and have been implicated to play crucial roles in such diverse processes as cancer, organogenesis and pattern formation. Experiments by Zakany and Duboule, and Rudnicki and Brown have suggested a role for Wnt molecules in negatively regulating chondrogenesis. However, neither of the two Wnt genes used in these studies is endogenously expressed in chondrogenic regions. We and others have found that in the chick limb at least four members of the Wnt gene family, Wnt-4, Wnt-5a, Wnt-5b, and Wnt-14, are expressed in defined regions of the developing chondrogenic elements. With the exception of Wnt-5b, which is expressed in perichondrial cells and prehypertrophic chondrocytes, the expression of the three other Wnt genes is restricted to the perichondrium surrounding the cartilage element. Viral misexpression studies in the chick suggested that Wnt-4 acts as a positive signal originating from the joint region and when misexpressed accelerates chondrocyte maturation, while Wnt-5a and Wnt-5b both negatively regulate chondrocyte maturation. We have further shown that they utilize different signaling pathways; while Wnt-4 signals through the canonical Wnt-pathway, Wnt-5a and Wnt-5b do not. Interestingly, the delay in chondrocyte maturation due to Wnt-5a misexpression is associated with an up regulation of Wnt-5b expression in the prehypertropic chondrocytes. Concomitantly, Wnt-5b misexpression also delays chondrocyte maturation. However, preliminary studies suggest that the two Wnt genes affect different steps in the maturation process. Wnt signaling, however, is not only regulating chondrogenesis but is also involved in the segmentation process of the appendicular skeleton. Localized misexpression of the fourth Wnt gene, Wnt-14, which is expressed early in the presumptive joint region, induces morphological and molecular changes indicative of an early joint interzone, suggesting that Wnt-14 plays a pivotal role in the induction of the joint interzone.","authors":"Hartmann, C.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Musculoskelet Neuronal Interact","volume":"2","issue":"3","page":"274-6","pdf":null,"JrId":"32168","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24870230","title":"Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors.","abstract":"RNA ligases have essential roles in many cellular processes in eukaryotes, archaea and bacteria, including in RNA repair and stress-induced splicing of messenger RNA. In archaea and eukaryotes, RNA ligases also have a role in transfer RNA splicing to generate functional tRNAs required for protein synthesis. We recently identified the human tRNA splicing ligase, a multimeric protein complex with RTCB (also known as HSPC117, C22orf28, FAAP and D10Wsu52e) as the essential subunit. The functions of the additional complex components ASW (also known as C2orf49), CGI-99 (also known as C14orf166), FAM98B and the DEAD-box helicase DDX1 in the context of RNA ligation have remained unclear. Taking advantage of clusters of eukaryotic orthologous groups, here we find that archease (ARCH; also known as ZBTB8OS), a protein of unknown function, is required for full activity of the human tRNA ligase complex and, in cooperation with DDX1, facilitates the formation of an RTCB-guanylate intermediate central to mammalian RNA ligation. Our findings define a role for DDX1 in the context of the human tRNA ligase complex and suggest that the widespread co-occurrence of archease and RtcB proteins implies evolutionary conservation of their functional interplay.","authors":"Popow, J., Jurkin, J., Schleiffer, A., Martinez, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nature","volume":"511","issue":"7507","page":"104-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23084810","title":"Regeneration and reprogramming.","abstract":"Recent reprogramming studies indicate that mammalian, somatic cells have the potential to achieve pluripotent states and undergo cell type switching. Such cellular traits are observed under natural conditions in animals that regenerate complex organs. A number of invertebrates display the amazing trait of whole body regeneration. Underlying this trait is the maintenance of pluripotent cells in somatic tissue, and molecular studies indicate the use of common players associated with pluripotency and germ cell properties between these invertebrates and mammalian pluripotent cells. In regenerative vertebrates, heart regeneration, lens regeneration, and retinal regeneration provide good examples of dedifferentiation and transdifferentiation. The molecular factors associated with these phenomena are discussed.","authors":"Knapp, D., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Curr Opin Genet Dev","volume":"22","issue":"5","page":"485-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24859752","title":"FlyMAD: rapid thermogenetic control of neuronal activity in freely walking Drosophila.","abstract":"Rapidly and selectively modulating the activity of defined neurons in unrestrained animals is a powerful approach in investigating the circuit mechanisms that shape behavior. In Drosophila melanogaster, temperature-sensitive silencers and activators are widely used to control the activities of genetically defined neuronal cell types. A limitation of these thermogenetic approaches, however, has been their poor temporal resolution. Here we introduce FlyMAD (the fly mind-altering device), which allows thermogenetic silencing or activation within seconds or even fractions of a second. Using computer vision, FlyMAD targets an infrared laser to freely walking flies. As a proof of principle, we demonstrated the rapid silencing and activation of neurons involved in locomotion, vision and courtship. The spatial resolution of the focused beam enabled preferential targeting of neurons in the brain or ventral nerve cord. Moreover, the high temporal resolution of FlyMAD allowed us to discover distinct timing relationships for two neuronal cell types previously linked to courtship song.","authors":"Bath, DE., Stowers, JR., H\u00f6rmann, D., Poehlmann, A., Dickson, BJ., Straw, AD.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Methods","volume":"11","issue":"7","page":"756-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27783951","title":"A Nuclear Role for miR-9 and Argonaute Proteins in Balancing Quiescent and Activated Neural Stem Cell States.","abstract":"Throughout life, adult neural stem cells (NSCs) produce new neurons and glia that contribute to crucial brain functions. Quiescence is an essential protective feature of adult NSCs; however, the establishment and maintenance of this state remain poorly understood. We demonstrate that in the adult zebrafish pallium, the brain-enriched miR-9 is expressed exclusively in a subset of quiescent NSCs, highlighting a heterogeneity within these cells, and is necessary to maintain NSC quiescence. Strikingly, miR-9, along with Argonaute proteins (Agos), is localized to the nucleus of quiescent NSCs, and manipulating their nuclear\/cytoplasmic ratio impacts quiescence. Mechanistically, miR-9 permits efficient Notch signaling to promote quiescence, and we identify the RISC protein TNRC6 as a mediator of miR-9\/Agos nuclear localization in\u00a0vivo. We propose a conserved non-canonical role for nuclear miR-9\/Agos in controlling the balance between NSC quiescence and activation, a key step in maintaining adult germinal pools.","authors":"Katz, S., Cussigh, D., Urb\u00e1n, N., Blomfield, I., Guillemot, F., Bally-Cuif, L., Coolen, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Rep","volume":"17","issue":"5","page":"1383-1398","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27737960","title":"SWI\/SNF regulates a transcriptional program that induces senescence to prevent liver cancer.","abstract":"Oncogene-induced senescence (OIS) is a potent tumor suppressor mechanism. To identify senescence regulators relevant to cancer, we screened an shRNA library targeting genes deleted in hepatocellular carcinoma (HCC). Here, we describe how knockdown of the SWI\/SNF component ARID1B prevents OIS and cooperates with RAS to induce liver tumors. ARID1B controls p16<sup>INK4a<\/sup> and p21<sup>CIP1a<\/sup> transcription but also regulates DNA damage, oxidative stress, and p53 induction, suggesting that SWI\/SNF uses additional mechanisms to regulate senescence. To systematically identify SWI\/SNF targets regulating senescence, we carried out a focused shRNA screen. We discovered several new senescence regulators, including ENTPD7, an enzyme that hydrolyses nucleotides. ENTPD7 affects oxidative stress, DNA damage, and senescence. Importantly, expression of ENTPD7 or inhibition of nucleotide synthesis in ARID1B-depleted cells results in re-establishment of senescence. Our results identify novel mechanisms by which epigenetic regulators can affect tumor progression and suggest that prosenescence therapies could be employed against SWI\/SNF-mutated cancers.","authors":"Tordella, L., Khan, S., Hohmeyer, A., Banito, A., Klotz, S., Raguz, S., Martin, N., Dhamarlingam, G., Carroll, T., Gonz\u00e1lez Meljem, JM., Deswal, S., Mart\u00ednez-Barbera, JP., Garc\u00eda-Escudero, R., Zuber, J., Zender, L., Gil, J.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Genes Dev","volume":"30","issue":"19","page":"2187-2198","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26890681","title":"A cryoinjury model in neonatal mice for cardiac translational and regeneration research.","abstract":"The introduction of injury models for neonatal mouse hearts has accelerated research on the mechanisms of cardiac regeneration in mammals. However, some existing models, such as apical resection and ligation of the left anterior descending artery, produce variable results, which may be due to technical difficulties associated with these methods. Here we present an alternative model for the study of cardiac regeneration in neonatal mice in which cryoinjury is used to induce heart injury. This model yields a reproducible injury size, does not induce known mechanisms of cardiac regeneration and leads to a sustained reduction of cardiac function. This protocol uses reusable cryoprobes that can be assembled in 5 min, with the entire procedure taking 15 min per pup. The subsequent heart collection and fixation takes 2 d to complete. Cryoinjury results in a myocardial scar, and the size of injury can be scaled by the use of different cryoprobes (0.5 and 1.5 mm). Cryoinjury models are medically relevant to diseases in human infants with heart disease. In summary, the myocardial cryoinjury model in neonatal mice described here is a useful tool for cardiac translational and regeneration research.","authors":"Polizzotti, BD., Ganapathy, B., Haubner, BJ., Penninger, JM., K\u00fchn, B.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Protoc","volume":"11","issue":"3","page":"542-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15750587","title":"Role of the RB1 family in stabilizing histone methylation at constitutive heterochromatin.","abstract":"Here, we show a role for the RB1 family proteins in directing full heterochromatin formation. Mouse embryonic fibroblasts that are triply deficient for RB1 (retinoblastoma 1), RBL1 (retinoblastoma-like 1) and RBL2 (retinoblastoma-like 2) - known as TKO cells - show a marked genomic instability, which is coincidental with decreased DNA methylation, increased acetylation of histone H3 and decreased tri-methylation of histone H4 at lysine 20 (H4K20). Chromatin immunoprecipitation showed that H4K20 tri-methylation was specifically decreased at pericentric and telomeric chromatin. These defects are independent of E2F family function. Indeed, we show a direct interaction between the RB1 proteins and the H4K20 tri-methylating enzymes Suv4-20h1 and Suv4-20h2, indicating that the RB1 family has a role in controlling H4K20 tri-methylation by these histone methyltransferases. These observations indicate that the RB1 family is involved in maintaining overall chromatin structure and, in particular, that of constitutive heterochromatin, linking tumour suppression and the epigenetic definition of chromatin.","authors":"Gonzalo, S., Garc\u00eda-Cao, M., Fraga, MF., Schotta, G., Peters, AH., Cotter, SE., Egu\u00eda, R., Dean, DC., Esteller, M., Jenuwein, T., Blasco, MA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Cell Biol","volume":"7","issue":"4","page":"420-8","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15728131","title":"Derivation of 2 categories of plasmacytoid dendritic cells in murine bone marrow.","abstract":"Plasmacytoid dendritic cells (pDCs) competent to make type I interferon were rigorously defined as a Ly-6C(+) and CD11c(Lo) subset of the B220(+)CD19(-) CD43(+)CD24(Lo) bone marrow (BM) Fraction A. Otherwise similar Ly6C(-) cells expressed the natural killer (NK) markers DX5 and NK1.1. pDCs represented a stable, discrete, and long-lived population. Stem cells and early lymphoid progenitors (ELPs), but not prolymphocytes, were effective precursors of pDCs, and their differentiation was blocked by ligation of Notch receptors. Furthermore, pDCs were present in the BM of RAG1(-\/-), CD127\/IL-7Ra(-\/-), and Pax5(-\/-) mice. pDCs in RAG1\/GFP knock-in mice could be subdivided, and immunoglobulin D(H)-J(H) rearrangements, as well as transcripts for the B-lineage-related genes Pax5, mb1\/CD79a, ebf, and Bcl11a, were identified only in the green fluorescent protein-positive (GFP(+)) pDC1 subset. All pDCs expressed terminal deoxynucleotidyl transferase (TdT), the ETS transcription factor Spi-B, the nuclear factor-kappaB transcription factor RelB, toll-like receptor 9 (TLR9), and interferon consensus sequence binding protein (ICSBP)\/interferon regulatory factor 8 (IRF-8) transcripts; lacked CD16 and granulocyte colony-stimulating factor receptor (G-CSFR); and were uniformly interleukin-7 receptor alpha (IL-7Ralpha(-)) AA4.1(Lo), CD27(-), Flk-2(Lo), c-Kit(-), DX-5(-), and CD11b(-), while CD4 and CD8alpha were variable. GFP(+) pDC1 subset was less potent than GFP(-) pDC2s in T allostimulation and production of tumor necrosis factor alpha (TNFalpha), interferon alpha (IFNalpha), and interleukin-6 (IL-6), while only pDC2s made IFNgamma and IL-12 p70. Thus, 2 functionally specialized subsets of pDCs arise in bone marrow from progenitors that diverge from B, T, and NK lineages at an early stage.","authors":"Pelayo, R., Hirose, J., Huang, J., Garrett, KP., Delogu, A., Busslinger, M., Kincade, PW.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Blood","volume":"105","issue":"11","page":"4407-15","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2005-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23018959","title":"Regenerative biology: Skin, heal thyself.","abstract":null,"authors":"Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nature","volume":"489","issue":"7417","page":"508-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24950427","title":"Genome wide functional genetics in haploid cells.","abstract":"Some organisms such as yeast or males of social insects are haploid, i.e. they carry a single set of chromosomes, while haploidy in mammals is exclusively restricted to mature germ cells. A single copy of the genome provides the basis for genetic analyses where any recessive mutation of essential genes will show a clear phenotype due to the absence of a second gene copy. Most prominently, haploidy in yeast has been utilized for recessive genetic screens that have markedly contributed to our understanding of development, basic physiology, and disease. Somatic mammalian cells carry two copies of chromosomes (diploidy) that obscure genetic analysis. Near haploid human leukemic cells however have been developed as a high throughput screening tool. Although deemed impossible, we and others have generated mammalian haploid embryonic stem cells from parthenogenetic mouse embryos. Haploid stem cells open the possibility of combining the power of a haploid genome with pluripotency of embryonic stem cells to uncover fundamental biological processes in defined cell types at a genomic scale. Haploid genetics has thus become a powerful alternative to RNAi or CRISPR based screens.","authors":"Elling, U., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"FEBS Lett","volume":"588","issue":"15","page":"2415-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10940312","title":"Protein kinase C alpha controls erythropoietin receptor signaling.","abstract":"Protein kinase C (PKC) is implied in the activation of multiple targets of erythropoietin (Epo) signaling, but its exact role in Epo receptor (EpoR) signal transduction and in the regulation of erythroid proliferation and differentiation remained elusive. We analyzed the effect of PKC inhibitors with distinct modes of action on EpoR signaling in primary human erythroblasts and in a recently established murine erythroid cell line. Active PKC appeared essential for Epo-induced phosphorylation of the Epo receptor itself, STAT5, Gab1, Erk1\/2, AKT, and other downstream targets. Under the same conditions, stem cell factor-induced signal transduction was not impaired. LY294002, a specific inhibitor of phosphoinositol 3-kinase, also suppressed Epo-induced signal transduction, which could be partially relieved by activators of PKC. PKC inhibitors or LY294002 did not affect membrane expression of the EpoR, the association of JAK2 with the EpoR, or the in vitro kinase activity of JAK2. The data suggest that PKC controls EpoR signaling instead of being a downstream effector. PKC and phosphoinositol 3-kinase may act in concert to regulate association of the EpoR complex such that it is responsive to ligand stimulation. Reduced PKC-activity inhibited Epo-dependent differentiation, although it did not effect Epo-dependent \"renewal divisions\" induced in the presence of Epo, stem cell factor, and dexamethasone.","authors":"von Lindern, M., Parren-van Amelsvoort, M., van Dijk, T., Deiner, E., van den Akker, E., van Emst-de Vries, S., Willems, P., Beug, H., L\u00f6wenberg, B.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Biol Chem","volume":"275","issue":"44","page":"34719-27","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2000-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27729457","title":"Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila.","abstract":"The posttranscriptional addition of nucleotides to the 3' end of RNA regulates the maturation, function, and stability of RNA species in all domains of life. Here, we show that in flies, 3' terminal RNA uridylation triggers the processive, 3'-to-5' exoribonucleolytic decay via the RNase II\/R enzyme CG16940, a homolog of the human Perlman syndrome exoribonuclease Dis3l2. Together with the TUTase Tailor, dmDis3l2 forms the cytoplasmic, terminal RNA uridylation-mediated processing (TRUMP) complex that functionally cooperates in the degradation of structured RNA RNA immunoprecipitation and high-throughput sequencing reveals a variety of TRUMP complex substrates, including abundant non-coding RNA, such as 5S rRNA, tRNA, snRNA, snoRNA, and the essential RNase MRP Based on genetic and biochemical evidence, we propose a key function of the TRUMP complex in the cytoplasmic quality control of RNA polymerase III transcripts. Together with high-throughput biochemical characterization of dmDis3l2 and bacterial RNase R, our results imply a conserved molecular function of RNase II\/R enzymes as \"readers\" of destabilizing posttranscriptional marks-uridylation in eukaryotes and adenylation in prokaryotes-that play important roles in RNA surveillance.","authors":"Reim\u00e3o-Pinto, MM., Manzenreither, RA., Burkard, TR., Sledz, P., Jinek, M., Mechtler, K., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"EMBO J","volume":"35","issue":"22","page":"2417-2434","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24413089","title":"Autophagy in non-small cell lung carcinogenesis: A positive regulator of antitumor immunosurveillance.","abstract":"In a mouse model of non-small cell lung carcinogenesis, we recently found that the inactivation of the essential autophagy gene Atg5 causes an acceleration of the early phases of oncogenesis. Thus, hyperplastic lesions and adenomas are more frequent at early stages after adenoviral delivery of Cre recombinase via inhalation, when Cre-in addition to activating the KRas(G12D) oncogene-inactivates both alleles of the Atg5 gene. The accelerated oncogenesis of autophagy-deficient tumors developing in KRas;Atg5(fl\/fl) mice (as compared with autophagy-competent KRas;Atg5(fl\/+) control tumors) correlates with an increased infiltration by FOXP3(+) regulatory T cells (Tregs). Depletion of such Tregs by means of specific monoclonal antibodies inhibits the accelerated oncogenesis of autophagy-deficient tumors down to the level observed in autophagy-competent controls. Subsequent analyses revealed that the combination of KRas activation and Atg5 inactivation favors the expression of ENTPD1\/CD39, an ecto-ATPase that initiates the conversion of extracellular ATP, which is immunostimulatory, into adenosine, which is immunosuppressive. Pharmacological inhibition of ENTPD1 or blockade of adenosinergic receptors reduces the infiltration of KRas;Atg5(fl\/fl) tumors by Tregs and reverses accelerated oncogenesis. Altogether these data favor a model according to which autophagy deficiency favors oncogenesis via changes in the tumor microenvironment that ultimately entail the Treg-mediated inhibition of anticancer immunosurveillance.","authors":"Rao, S., Yang, H., Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Autophagy","volume":"10","issue":"3","page":"529-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24583015","title":"Dependency of the spindle assembly checkpoint on Cdk1 renders the anaphase transition irreversible.","abstract":"Activation of anaphase-promoting complex\/cyclosome (APC\/C(Cdc20)) by Cdc20 is delayed by the spindle assembly checkpoint (SAC). When all kinetochores come under tension, the SAC is turned off and APC\/C(Cdc20) degrades cyclin B and securin, which activates separase [1]. The latter then cleaves cohesin holding sister chromatids together [2]. Because cohesin cleavage also destroys the tension responsible for turning off the SAC, cells must possess a mechanism to prevent SAC reactivation during anaphase, which could be conferred by a dependence of the SAC on Cdk1 [3-5]. To test this, we analyzed mouse oocytes and embryos expressing nondegradable cyclin B together with a Cdk1-resistant form of separase. After biorientation and SAC inactivation, APC\/C(Cdc20) activates separase but the resulting loss of (some) cohesion is accompanied by SAC reactivation and APC\/C(Cdc20) inhibition, which aborts the process of further securin degradation. Cyclin B is therefore the only APC\/C(Cdc20) substrate whose degradation at the onset of anaphase is necessary to prevent SAC reactivation. The mutual activation of tension sensitive SAC and Cdk1 creates a bistable system that ensures complete activation of separase and total downregulation of Cdk1 when all chromosomes have bioriented.","authors":"Rattani, A., Vinod, PK., Godwin, J., Tachibana-Konwalski, K., Wolna, M., Malumbres, M., Nov\u00e1k, B., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Biol","volume":"24","issue":"6","page":"630-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15719069","title":"Essential role of RSK2 in c-Fos-dependent osteosarcoma development.","abstract":"Inactivation of the growth factor-regulated S6 kinase RSK2 causes Coffin-Lowry syndrome in humans, an X-linked mental retardation condition associated with progressive skeletal abnormalities. Here we show that mice lacking RSK2 develop a progressive skeletal disease, osteopenia due to impaired osteoblast function and normal osteoclast differentiation. The phenotype is associated with decreased expression of Phex, an endopeptidase regulating bone mineralization. This defect is probably not mediated by RSK2-dependent phosphorylation of c-Fos on serine 362 in the C-terminus. However, in the absence of RSK2, c-Fos-dependent osteosarcoma formation is impaired. The lack of c-Fos phosphorylation leads to reduced c-Fos protein levels, which are thought to be responsible for decreased proliferation and increased apoptosis of transformed osteoblasts. Therefore, RSK2-dependent stabilization of c-Fos is essential for osteosarcoma formation in mice and may also be important for human osteosarcomas.","authors":"David, JP., Mehic, D., Bakiri, L., Schilling, AF., Mandic, V., Priemel, M., Idarraga, MH., Reschke, MO., Hoffmann, O., Amling, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Clin Invest","volume":"115","issue":"3","page":"664-72","pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":"2005-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15719364","title":"Rapid in vivo analysis of mutant forms of the LAT adaptor using Pax5-Lat double-deficient pro-B cells.","abstract":"Following injection into recombinase-activating gene-deficient (Rag1(-\/-)) mice, pro-B cells lacking the Pax5 transcription factor (Pax5(-\/-)) develop into most major hematopoietic lineages, with the notable exception of B cells. We assessed whether Pax5(-\/-) pro-B cells that were also rendered deficient for the linker for activation of T cells (LAT), an adaptor essential for T cell receptor signaling, can be used for the rapid in vivo analysis of mutant forms of LAT. We showed that Pax5(-\/-) Lat(-\/-) pro-B cell lines can be infected with recombinant retroviruses expressing a LAT cDNA and sorted for the expression of LAT. When injected into Rag1(-\/-) mice, they restore normal intrathymic T cell development and give rise to functional peripheral T cells. Considering that the handling of Pax5(-\/-) pro-B cell lines is easier than that of bone marrow hematopoietic precursors, we used them for the rapid functional analysis of a novel Lat allelic series. When compared to knock-in and transgenic approaches, a major advantage of our Pax5(-\/-) pro-B cell-based experimental approach consists in the production of mice bearing a given mutation within 2-3 months. Therefore, it constitutes a powerful first-line screen for mutations worth fastidious knock-in approaches.","authors":"Ardouin, L., Rolink, AG., Mura, AM., Gommeaux, J., Melchers, F., Busslinger, M., Malissen, M., Malissen, B.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Eur J Immunol","volume":"35","issue":"3","page":"977-86","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21970955","title":"Pax5: a master regulator of B cell development and leukemogenesis.","abstract":"The B cell lineage of the hematopoietic system is responsible for the generation of high-affinity antibodies, which provide humoral immunity for protection against foreign pathogens. B cell commitment and development depend on many transcription factors including Pax5. Here, we review the different functions of Pax5 in regulating various aspects of B lymphopoiesis. At B cell commitment, Pax5 restricts the developmental potential of lymphoid progenitors to the B cell pathway by repressing B-lineage-inappropriate genes, while it simultaneously promotes B cell development by activating B-lymphoid-specific genes. Pax5 thereby controls gene transcription by recruiting chromatin-remodeling, histone-modifying, and basal transcription factor complexes to its target genes. Moreover, Pax5 contributes to the diversity of the antibody repertoire by controlling V(H)-DJ(H) recombination by inducing contraction of the immunoglobulin heavy-chain locus in pro-B cells, which is likely mediated by PAIR elements in the 5' region of the V(H) gene cluster. Importantly, all mature B cell types depend on Pax5 for their differentiation and function. Pax5 thus controls the identity of B lymphocytes throughout B cell development. Consequently, conditional loss of Pax5 allows mature B cells from peripheral lymphoid organs to develop into functional T cells in the thymus via dedifferentiation to uncommitted progenitors in the bone marrow. Pax5 has also been implicated in human B cell malignancies because it can function as a haploinsufficient tumor suppressor or oncogenic translocation fusion protein in B cell precursor acute lymphoblastic leukemia.","authors":"Medvedovic, J., Ebert, A., Tagoh, H., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Adv Immunol","volume":"111","issue":null,"page":"179-206","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31350118","title":"Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis.","abstract":"Argonaute-bound microRNAs silence mRNA expression in a dynamic and regulated manner to control organismal development, physiology, and disease. We employed metabolic small RNA sequencing for a comprehensive view on intracellular microRNA kinetics in Drosophila. Based on absolute rate of biogenesis and decay, microRNAs rank among the fastest produced and longest-lived cellular transcripts, disposing up to 10<sup>5<\/sup> copies per cell at steady-state. Mature microRNAs are produced within minutes, revealing tight intracellular coupling of biogenesis that is selectively disrupted by pre-miRNA-uridylation. Control over Argonaute protein homeostasis generates a kinetic bottleneck that cooperates with non-coding RNA surveillance to ensure faithful microRNA loading. Finally, regulated small RNA decay enables the selective rapid turnover of Ago1-bound microRNAs, but not of Ago2-bound small interfering RNAs (siRNAs), reflecting key differences in the robustness of small RNA silencing pathways. Time-resolved small RNA sequencing opens new experimental avenues to deconvolute the timescales, molecular features, and regulation of small RNA silencing pathways in living cells.","authors":"Reichholf, B., Herzog, VA., Fasching, N., Manzenreither, RA., Sowemimo, I., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mol Cell","volume":"75","issue":"4","page":"756-768.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27374406","title":"Essential Role of the PfRh5\/PfRipr\/CyRPA Complex during Plasmodium falciparum Invasion of Erythrocytes.","abstract":"Plasmodium falciparum parasites in the merozoite stage invade human erythrocytes and cause malaria. Invasion requires multiple interactions between merozoite ligands and erythrocyte receptors. P.\u00a0falciparum reticulocyte binding homolog 5 (PfRh5) forms a complex with the PfRh5-interacting protein (PfRipr) and Cysteine-rich protective antigen (CyRPA) and binds erythrocytes via the host receptor basigin. However, the specific role that PfRipr and CyRPA play during invasion is unclear. Using P.\u00a0falciparum lines conditionally expressing PfRipr and CyRPA, we show that loss of PfRipr or CyRPA function blocks growth due to the inability of merozoites to invade erythrocytes. Super-resolution microscopy revealed that PfRipr, CyRPA, and PfRh5 colocalize at the junction between merozoites and erythrocytes during invasion. PfRipr, CyRPA, and PfRipr\/CyRPA\/PfRh5-basigin complex is required for triggering the Ca(2+) release and establishing the tight junction. Together, these results establish that the PfRh5\/PfRipr\/CyRPA complex is essential in the sequential molecular events leading to parasite invasion of human erythrocytes.","authors":"Volz, JC., Yap, A., Sisquella, X., Thompson, JK., Lim, NT., Whitehead, LW., Chen, L., Lampe, M., Tham, WH., Wilson, D., Nebl, T., Marapana, D., Triglia, T., Wong, W., Rogers, KL., Cowman, AF.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Host Microbe","volume":"20","issue":"1","page":"60-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26898469","title":"Chromosome Cohesion Established by Rec8-Cohesin in Fetal Oocytes Is Maintained without Detectable Turnover in Oocytes Arrested for Months in Mice.","abstract":"Sister chromatid cohesion mediated by the cohesin complex is essential for chromosome segregation in mitosis and meiosis [1]. Rec8-containing cohesin, bound to Smc3\/Smc1\u03b1 or Smc3\/Smc1\u03b2, maintains bivalent cohesion in mammalian meiosis [2-6]. In females, meiotic DNA replication and recombination occur in fetal oocytes. After birth, oocytes arrest at the prolonged dictyate stage until recruited to grow into mature oocytes that divide at ovulation. How cohesion is maintained in arrested oocytes remains a pivotal question relevant to maternal age-related aneuploidy. Hypothetically, cohesin turnover regenerates cohesion in oocytes. Evidence for post-replicative cohesion establishment mechanism exists, in yeast and invertebrates [7, 8]. In mouse fetal oocytes, cohesin loading factor Nipbl\/Scc2 localizes to chromosome axes during recombination [9, 10]. Alternatively, cohesion is maintained without turnover. Consistent with this, cohesion maintenance does not require Smc1\u03b2 transcription, but unlike Rec8, Smc1\u03b2 is not required for establishing bivalent cohesion [11, 12]. Rec8 maintains cohesion without turnover during weeks of oocyte growth [3]. Whether the same applies to months or decades of arrest is unknown. Here, we test whether Rec8 activated in arrested mouse oocytes builds cohesion revealed by TEV cleavage and live-cell imaging. Rec8 establishes cohesion when activated during DNA replication in fetal oocytes using tamoxifen-inducible Cre. In contrast, no new cohesion is detected when Rec8 is activated in arrested oocytes by tamoxifen despite cohesin synthesis. We conclude that cohesion established in fetal oocytes is maintained for months without detectable turnover in dictyate-arrested oocytes. This implies that women's fertility depends on the longevity of cohesin proteins that established cohesion in utero.","authors":"Burkhardt, S., Borsos, M., Szydlowska, A., Godwin, J., Williams, SA., Cohen, PE., Hirota, T., Saitou, M., Tachibana-Konwalski, K.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Curr Biol","volume":"26","issue":"5","page":"678-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21915788","title":"Programmed DNA elimination in Tetrahymena: a small RNA-mediated genome surveillance mechanism.","abstract":"RNA interference (RNAi) was initially discovered as a post-transcriptional gene silencing mechanism in which short RNAs are used to target complementary RNAs for degradation. During the past several years, it has been demonstrated that RNAi-related processes are also involved in transcriptional gene silencing by directing formation of heterochromatin. The dynamic DNA rearrangement during sexual reproduction of the ciliated protozoan Tetrahymena provides an extreme example of RNAi-directed heterochromatin formation. In this process, small RNAs of \u223c28-29 nt, which are processed by the Dicer-like protein Dcl1p and are associated with the Argonaute family protein Twi1p, induce heterochromatin formation at complementary genomic sequences by recruiting the histone H3 lysine 9\/27 methyltransferase Ezl1p and chromodomain proteins. Eventually these heterochromatinized regions are targeted for DNA elimination. In many eukaryotes, one of the major roles for RNAi-related mechanisms is silencing transposons, and DNA elimination in Tetrahymena is also believed to have evolved as a transposon defense by removing transposon-related sequences from the somatic genome. Because DNA elimination is achieved by the coordinated actions of noncoding RNA transcription, RNA processing, RNA transport, RNA-RNA and RNA-protein interactions, RNA degradation and RNA-directed chromatin modifications, DNA elimination in Tetrahymena is a useful model to study 'RNA infrastructure'.","authors":"Kataoka, K., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Adv Exp Med Biol","volume":"722","issue":null,"page":"156-73","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15712243","title":"Phosphoproteome and transcriptome analysis of the neuronal response to a CDK5 inhibitor.","abstract":"In Alzheimer's disease and amyotrophic lateral sclerosis deregulation of cyclin-dependent kinase 5 (CDK5) causes hyperphosphorylation of tau and neurofilament proteins, respectively, leading to neuronal cell death. We have demonstrated recently that pharmacological inhibition of CDK5 protects neurons under various stressful conditions (Weishaupt J. H., et al., Molec. Cell. Neurosci. 2003, 24, 489-502). To get an overview on the cellular mechanisms of action we analyzed global changes in protein phosphorylation in cultured cerebellar granule neurons by [(32)P]orthophosphate labeling after administration of a CDK5 inhibitor. Since CDK5 has recently been shown to phosphorylate and inactivate transcription factor MEF2, we included gene expression profiling using cDNA microarrays. By two-dimensional gel electrophoresis and matrix assisted laser desorption\/ionisation-time of flight (MALDI-TOF)-mass spectrometry we identified several phosphoproteins that were modulated by compound administration. Among them syndapin I which is involved in vesicle recycling, and dynein light intermediate chain 2 which represents a regulatory subunit of the dynein protein complex. These findings are consistent with the known physiological function of CDK5 in synaptic signaling and axonal transport. Moreover, we detected phosphoproteins acting in neuronal surival and\/or neurite outgrowth, such as cofilin and collapsin response mediator protein. Subsequent testing in cell cultures revealed that the CDK5 inhibitor blocked mitochondrial translocation of pro-apoptotic cofilin in cerebellar granule neurons and enhanced neurite outgrowth in dorsal root ganglia. Numerous genes exhibiting MEF2 consensus binding sequences were modulated by CDK5 inhibitor treatment. Among them some that may contribute to neurite elongation or neuronal survival, but also several genes functioning in synaptic transmission. Taken together, phosphoproteome and transcriptome analysis indicate that the compound promotes both neuronal survival and neurite outgrowth, but also may affect synaptic function in cultured neurons.","authors":"Gillardon, F., Steinlein, P., B\u00fcrger, E., Hildebrandt, T., Gerner, C.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Proteomics","volume":"5","issue":"5","page":"1299-307","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2005-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26494711","title":"Silencio\/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery.","abstract":"The repression of transposable elements in eukaryotes often involves their transcriptional silencing via targeted chromatin modifications. In animal gonads, nuclear Argonaute proteins of the PIWI clade complexed with small guide RNAs (piRNAs) serve as sequence specificity determinants in this process. How binding of nuclear PIWI-piRNA complexes to nascent transcripts orchestrates heterochromatin formation and transcriptional silencing is unknown. Here, we characterize CG9754\/Silencio as an essential piRNA pathway factor that is required for Piwi-mediated transcriptional silencing in Drosophila. Ectopic targeting of Silencio to RNA or DNA is sufficient to elicit silencing independently of Piwi and known piRNA pathway factors. Instead, Silencio requires the H3K9 methyltransferase Eggless\/SetDB1 for its silencing ability. In agreement with this, SetDB1, but not Su(var)3-9, is required for Piwi-mediated transcriptional silencing genome-wide. Due to its interaction with the target-engaged Piwi-piRNA complex, we suggest that Silencio acts as linker between the sequence specificity factor Piwi and the cellular heterochromatin machinery.","authors":"Sienski, G., Batki, J., Senti, KA., D\u00f6nertas, D., Tirian, L., Meixner, K., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Genes Dev","volume":"29","issue":"21","page":"2258-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21648017","title":"Gene expression profile of the regeneration epithelium during axolotl limb regeneration.","abstract":"Urodele amphibians are unique among adult vertebrates in their ability to regenerate missing limbs. The process of limb regeneration requires several key tissues including a regeneration-competent wound epidermis called the regeneration epithelium (RE). We used microarray analysis to profile gene expression of the RE in the axolotl, a Mexican salamander. A list of 125 genes and expressed sequence tags (ESTs) showed a \u22651.5-fold expression in the RE than in a wound epidermis covering a lateral cuff wound. A subset of the RE ESTs and genes were further characterized for expression level changes over the time-course of regeneration. This study provides the first large scale identification of specific gene expression in the RE.","authors":"Campbell, LJ., Su\u00e1rez-Castillo, EC., Ortiz-Zuazaga, H., Knapp, D., Tanaka, EM., Crews, CM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Dev Dyn","volume":"240","issue":"7","page":"1826-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28355183","title":"Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition.","abstract":"Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism. The maternal genome inherited from the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in the zygote. How these two epigenetically distinct genomes are spatially organized is poorly understood. Existing chromosome conformation capture-based methods are not applicable to oocytes and zygotes owing to a paucity of material. To study three-dimensional chromatin organization in rare cell types, we developed a single-nucleus Hi-C (high-resolution chromosome conformation capture) protocol that provides greater than tenfold more contacts per cell than the previous method. Here we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition in mice and is distinct in paternal and maternal nuclei within single-cell zygotes. Features of genomic organization including compartments, topologically associating domains (TADs) and loops are present in individual oocytes when averaged over the genome, but the presence of each feature at a locus varies between cells. At the sub-megabase level, we observed stochastic clusters of contacts that can occur across TAD boundaries but average into TADs. Notably, we found that TADs and loops, but not compartments, are present in zygotic maternal chromatin, suggesting that these are generated by different mechanisms. Our results demonstrate that the global chromatin organization of zygote nuclei is fundamentally different from that of other interphase cells. An understanding of this zygotic chromatin 'ground state' could potentially provide insights into reprogramming cells to a state of totipotency.","authors":"Flyamer, IM., Gassler, J., Imakaev, M., Brand\u00e3o, HB., Ulianov, SV., Abdennur, N., Razin, SV., Mirny, LA., Tachibana-Konwalski, K.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"544","issue":"7648","page":"110-114","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28104888","title":"Root diffusion barrier control by a vasculature-derived peptide binding to the SGN3 receptor.","abstract":"The root endodermis forms its extracellular diffusion barrier by developing ringlike impregnations called Casparian strips. A factor responsible for their establishment is the SCHENGEN3\/GASSHO1 (SGN3\/GSO1) receptor-like kinase. Its loss of function causes discontinuous Casparian strips. SGN3 also mediates endodermal overlignification of other Casparian strip mutants. Yet, without ligand, SGN3 function remained elusive. Here we report that schengen2 (sgn2) is defective in an enzyme sulfating peptide ligands. On the basis of this observation, we identified two stele-expressed peptides (CASPARIAN STRIP INTEGRITY FACTORS, CIF1\/2) that complement sgn2 at nanomolar concentrations and induce Casparian strip mislocalization as well as overlignification-all of which depend on SGN3. Direct peptide binding to recombinant SGN3 identifies these peptides as SGN3 ligands. We speculate that CIF1\/2-SGN3 is part of a barrier surveillance system, evolved to guarantee effective sealing of the supracellular Casparian strip network.","authors":"Doblas, VG., Smakowska-Luzan, E., Fujita, S., Alassimone, J., Barberon, M., Madalinski, M., Belkhadir, Y., Geldner, N.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Science","volume":"355","issue":"6322","page":"280-284","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24998533","title":"Dachsous-dependent asymmetric localization of spiny-legs determines planar cell polarity orientation in Drosophila.","abstract":"In Drosophila, planar cell polarity (PCP) molecules such as Dachsous (Ds) may function as global directional cues directing the asymmetrical localization of PCP core proteins such as Frizzled (Fz). However, the relationship between Ds asymmetry and Fz localization in the eye is opposite to that in the wing, thereby causing controversy regarding how these two systems are connected. Here, we show that this relationship is determined by the ratio of two Prickle (Pk) isoforms, Pk and Spiny-legs (Sple). Pk and Sple form different complexes with distinct subcellular localizations. When the amount of Sple is increased in the wing, Sple induces a reversal of PCP using the Ds-Ft system. A mathematical model demonstrates that Sple is the key regulator connecting Ds and the core proteins. Our model explains the previously noted discrepancies in terms of the differing relative amounts of Sple in the eye and wing.","authors":"Ayukawa, T., Akiyama, M., Mummery-Widmer, JL., Stoeger, T., Sasaki, J., Knoblich, JA., Senoo, H., Sasaki, T., Yamazaki, M.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell Rep","volume":"8","issue":"2","page":"610-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25189209","title":"A transcriptional mechanism integrating inputs from extracellular signals to activate hippocampal stem cells.","abstract":"The activity of adult stem cells is regulated by signals emanating from the surrounding tissue. Many niche signals have been identified, but it is unclear how they influence the choice of stem cells to remain quiescent or divide. Here we show that when stem cells of the adult hippocampus receive activating signals, they first induce the expression of the transcription factor Ascl1 and only subsequently exit quiescence. Moreover, lowering Ascl1 expression reduces the proliferation rate of hippocampal stem cells, and inactivating Ascl1 blocks quiescence exit completely, rendering them unresponsive to activating stimuli. Ascl1 promotes the proliferation of hippocampal stem cells by directly regulating the expression of cell-cycle regulatory genes. Ascl1 is similarly required for stem cell activation in the adult subventricular zone. Our results support a model whereby Ascl1 integrates inputs from both stimulatory and inhibitory signals and converts them into a transcriptional program activating adult neural stem cells.","authors":"Andersen, J., Urb\u00e1n, N., Achimastou, A., Ito, A., Simic, M., Ullom, K., Martynoga, B., Lebel, M., G\u00f6ritz, C., Fris\u00e9n, J., Nakafuku, M., Guillemot, F.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Neuron","volume":"83","issue":"5","page":"1085-97","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21880920","title":"Enhanced sucrose and cocaine self-administration and cue-induced drug seeking after loss of VGLUT2 in midbrain dopamine neurons in mice.","abstract":"The mesostriatal dopamine (DA) system contributes to several aspects of responses to rewarding substances and is implicated in conditions such as drug addiction and eating disorders. A subset of DA neurons has been shown to express the type 2 Vesicular glutamate transporter (Vglut2) and may therefore corelease glutamate. In the present study, we analyzed mice with a conditional deletion of Vglut2 in DA neurons (Vglut2(f\/f;DAT-Cre)) to address the functional significance of the glutamate-DA cophenotype for responses to cocaine and food reinforcement. Biochemical parameters of striatal DA function were also examined by using DA receptor autoradiography, immediate-early gene quantitative in situ hybridization after cocaine challenge, and DA-selective in vivo chronoamperometry. Mice in which Vglut2 expression had been abrogated in DA neurons displayed enhanced operant self-administration of both high-sucrose food and intravenous cocaine. Furthermore, cocaine seeking maintained by drug-paired cues was increased by 76%, showing that reward-dependent plasticity is perturbed in these mice. In addition, several lines of evidence suggest that adaptive changes occurred in both the ventral and dorsal striatum in the absence of VGLUT2: DA receptor binding was increased, and basal mRNA levels of the DA-induced early genes Nur77 and c-fos were elevated as after cocaine induction. Furthermore, in vivo challenge of the DA system by potassium-evoked depolarization revealed less DA release in both striatal areas. This study demonstrates that absence of VGLUT2 in DA neurons leads to perturbations of reward consumption as well as reward-associated memory, features of particular relevance for addictive-like behavior.","authors":"Alsi\u00f6, J., Nordenankar, K., Arvidsson, E., Birgner, C., Mahmoudi, S., Halbout, B., Smith, C., Fortin, GM., Olson, L., Descarries, L., Trudeau, L\u00c9., Kullander, K., L\u00e9vesque, D., Wall\u00e9n-Mackenzie, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Neurosci","volume":"31","issue":"35","page":"12593-603","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33384458","title":"The Organoid Cell Atlas.","abstract":null,"authors":"Bock, C., Boutros, M., Camp, JG., Clarke, L., Clevers, H., Knoblich, JA., Liberali, P., Regev, A., Rios, AC., Stegle, O., Stunnenberg, HG., Teichmann, SA., Treutlein, B., Vries, RGJ.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Biotechnol","volume":"39","issue":"1","page":"13-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22957800","title":"Anatomy of the pectoral and forelimb muscles of wildtype and green fluorescent protein-transgenic axolotls and comparison with other tetrapods including humans: a basis for regenerative, evolutionary and developmental studies.","abstract":"The axolotl Ambystoma mexicanum is one of the most used model organisms in evolutionary, developmental and regenerative studies, particularly because it can reconstitute a fully functional and complete forelimb\/hindlimb. Surprisingly, there is no publication that describes all the pectoral and forelimb muscles of this species or provides a comparative framework between these muscles and those of other model organisms and of modern humans. In the present paper we describe and illustrate all these muscles in A.\u00a0mexicanum and provide the first report about the myology of adults of a model organism that is based on analyses and dissections of both wildtype animals and transgenic animals that express green fluorescent protein (GFP) in muscle fibers. On the one hand, the inclusion of GFP-transgenic animals allows us to show the muscles as more commonly seen, and thus easier to understand, by current developmental and regenerative biologists. On the other hand, by including wildtype and GFP-transgenic animals and by visualizing these latter animals with and without a simultaneous transmission laser light, we were able to obtain a more complete and clearer understanding of the exact limit of the fleshy and tendinous parts of the muscles and their specific connections with the skeletal elements. This in turn allowed us to settle some controversies in previous anatomical and comparative studies. As most developmental, regenerative and evolutionary biologists are interested in comparing their observations of A.\u00a0mexicanum with observations in other model organisms, and ultimately in using this information to increase the understanding of human evolution and medicine, we also provide tables showing the homologies between the pectoral and forelimb muscles of axolotls, of model organisms such as mice, frogs and chicken, and of Homo sapiens. An example illustrating the outcomes of using our methodology and of our observations is that they revealed that, contrary to what is often stated in the literature, A.\u00a0mexicanum has a muscle coracoradialis that has both a well developed proximal fleshy belly and a distal long and thin tendon, supporting the idea that this muscle very likely corresponds to at least part of the amniote biceps brachii. Our observations also: (i) confirmed that the flexores digitorum minimi, interphalangeus digiti 3, pronator quadratus and palmaris profundus 1 are present as distinct muscles in A.\u00a0mexicanum, supporting the idea that the latter muscle does not correspond to the pronator accessorius of reptiles; (ii) confirmed that the so-called extensor antebrachii radialis is present as a distinct muscle in this species and, importantly, indicated that this muscle corresponds to the supinator of other tetrapods; (iii) showed that, contrary to some other urodeles, including some other Ambystoma species, there is no distinct muscle epitrochleoanconeus in A.\u00a0mexicanum and; (iv) showed that the ulnar and radial bundles of the abductor et extensor digiti 1 correspond to the abductor pollicis longus and extensor pollicis longus of other tetrapods, respectively.","authors":"Diogo, R., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Anat","volume":"221","issue":"6","page":"622-35","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27343549","title":"TNF-driven cell fate: till HACE do us part.","abstract":null,"authors":"Tortola, L., Nitsch, R., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Oncotarget","volume":"7","issue":"29","page":"44871-44872","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23964093","title":"Epigenomic enhancer annotation reveals a key role for NFIX in neural stem cell quiescence.","abstract":"The majority of neural stem cells (NSCs) in the adult brain are quiescent, and this fraction increases with aging. Although signaling pathways that promote NSC quiescence have been identified, the transcriptional mechanisms involved are mostly unknown, largely due to lack of a cell culture model. In this study, we first demonstrate that NSC cultures (NS cells) exposed to BMP4 acquire cellular and transcriptional characteristics of quiescent cells. We then use epigenomic profiling to identify enhancers associated with the quiescent NS cell state. Motif enrichment analysis of these enhancers predicts a major role for the nuclear factor one (NFI) family in the gene regulatory network controlling NS cell quiescence. Interestingly, we found that the family member NFIX is robustly induced when NS cells enter quiescence. Using genome-wide location analysis and overexpression and silencing experiments, we demonstrate that NFIX has a major role in the induction of quiescence in cultured NSCs. Transcript profiling of NS cells overexpressing or silenced for Nfix and the phenotypic analysis of the hippocampus of Nfix mutant mice suggest that NFIX controls the quiescent state by regulating the interactions of NSCs with their microenvironment.","authors":"Martynoga, B., Mateo, JL., Zhou, B., Andersen, J., Achimastou, A., Urb\u00e1n, N., van den Berg, D., Georgopoulou, D., Hadjur, S., Wittbrodt, J., Ettwiller, L., Piper, M., Gronostajski, RM., Guillemot, F.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Genes Dev","volume":"27","issue":"16","page":"1769-86","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26561583","title":"Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes.","abstract":"During meiosis, homologous chromosomes associate to form the synaptonemal complex (SC), a structure essential for fertility. Information about the epigenetic features of chromatin within this structure at the level of superresolution microscopy is largely lacking. We combined single-molecule localization microscopy (SMLM) with quantitative analytical methods to describe the epigenetic landscape of meiotic\u2002chromosomes at the pachytene stage in mouse oocytes. DNA is found to be nonrandomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin [trimethylation of histone H3 at lysine (Lys) 27 (H3K27me3)] are found at 500-nm intervals along the SC, whereas one of the ends of the SC displays a large and dense cluster of centromeric histone mark [trimethylation of histone H3 at Lys 9 (H3K9me3)]. Chromatin associated with active transcription [trimethylation of histone H3 at Lys 4 (H3K4me3)] is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 with an average spread larger than their periodicity. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher order genome organization is yet to be elucidated.","authors":"Prakash, K., Fournier, D., Redl, S., Best, G., Borsos, M., Tiwari, VK., Tachibana-Konwalski, K., Ketting, RF., Parekh, SH., Cremer, C., Birk, UJ.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Proc Natl Acad Sci U S A","volume":"112","issue":"47","page":"14635-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21828272","title":"An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance.","abstract":"Although human cancers have complex genotypes and are genomically unstable, they often remain dependent on the continued presence of single-driver mutations-a phenomenon dubbed \"oncogene addiction.\" Such dependencies have been demonstrated in mouse models, where conditional expression systems have revealed that oncogenes able to initiate cancer are often required for tumor maintenance and progression, thus validating the pathways they control as therapeutic targets. Here, we implement an integrative approach that combines genetically defined mouse models, transcriptional profiling, and a novel inducible RNAi platform to characterize cellular programs that underlie addiction to MLL-AF9-a fusion oncoprotein involved in aggressive forms of acute myeloid leukemia (AML). We show that MLL-AF9 contributes to leukemia maintenance by enforcing a Myb-coordinated program of aberrant self-renewal involving genes linked to leukemia stem cell potential and poor prognosis in human AML. Accordingly, partial and transient Myb suppression precisely phenocopies MLL-AF9 withdrawal and eradicates aggressive AML in vivo without preventing normal myelopoiesis, indicating that strategies to inhibit Myb-dependent aberrant self-renewal programs hold promise as effective and cancer-specific therapeutics. Together, our results identify Myb as a critical mediator of oncogene addiction in AML, delineate relevant Myb target genes that are amenable to pharmacologic inhibition, and establish a general approach for dissecting oncogene addiction in vivo.","authors":"Zuber, J., Rappaport, AR., Luo, W., Wang, E., Chen, C., Vaseva, AV., Shi, J., Weissmueller, S., Fellmann, C., Fellman, C., Taylor, MJ., Weissenboeck, M., Graeber, TG., Kogan, SC., Vakoc, CR., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Genes Dev","volume":"25","issue":"15","page":"1628-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21814026","title":"[Central regulation of body temperature by RANKL\/RANK pathway].","abstract":"Receptor-activator of NF-\u03baB ligand (RANKL) and its specific receptor RANK are key regulators of bone remodeling, lymph node formation, establishment of the thymic microenviroment, mammary gland development during pregnancy, bone metastasis in cancer and sex-hormone, progestin, -driven breast cancer. RANKL and RANK are also expressed in the central nervous systems (CNS) especially existed in the main region of thermoregulation. Central RANKL injection to the rodents induces fever via PGE(2)\/EP3R pathway. This pathway is related with inflammation related fever. On the other hand, female mice with RANK gene deletion in neuron and astrocytes show increased their basal body temperature at the dark phase, which suggests RANKL\/RANK system also regulates physiological thremoregulation in female. Not only in rodents but also in human, two children with a homozygous RANK mutation exhibit an abrogated fever response in pneumonia compare with the age-matched children with pneumonia. Thus, the central RANKL\/RANK pathway has an important role for thermoregulation.","authors":"Hanada, R., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Clin Calcium","volume":"21","issue":"8","page":"1201-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28041895","title":"Induction of Expansion and Folding in Human Cerebral Organoids.","abstract":"An expansion of the cerebral neocortex is thought to be the foundation for the unique intellectual abilities of humans. It has been suggested that an increase in the proliferative potential of neural progenitors (NPs) underlies the expansion of the cortex and its\u00a0convoluted appearance. Here we show that increasing NP proliferation induces expansion and folding in an in\u00a0vitro model of human corticogenesis. Deletion of PTEN stimulates proliferation and generates significantly larger and substantially folded cerebral organoids. This genetic modification allows sustained cell cycle re-entry, expansion of the progenitor population, and delayed neuronal differentiation, all key features of the developing human cortex. In contrast, Pten deletion in mouse organoids does not lead to folding. Finally, we utilized the expanded cerebral organoids to show that infection with Zika virus impairs cortical growth and folding. Our study provides new insights into the mechanisms regulating the structure and organization of the human cortex.","authors":"Li, Y., Muffat, J., Omer, A., Bosch, I., Lancaster, MA., Sur, M., Gehrke, L., Knoblich, JA., Jaenisch, R.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Stem Cell","volume":"20","issue":"3","page":"385-396.e3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15661906","title":"Differential control of CD28-regulated in vivo immunity by the E3 ligase Cbl-b.","abstract":"The E3 ubiquitin ligase Casitas B cell lymphoma-b (Cbl-b) plays a critical role in the development of autoimmunity and sets the threshold for T cell activation. In the absence of Cbl-b, T cells stimulated via the TCR respond similarly to those that have received a CD28-mediated costimulatory signal, suggesting that the absence of Cbl-b substitutes for CD28-mediated costimulation. In this study, we show that loss of Cbl-b restores Ig class switching and germinal center formation in Vav1 mutant mice in response to an in vivo viral challenge. Genetic inactivation of Cbl-b also rescues impaired antiviral IgG production in CD28-mutant mice. Moreover, loss of CD28 results in disorganization of follicular dendritic cell clusters, which is also rescued by the Cbl-b mutation. Intriguingly, despite restored antiviral in vivo immunity and follicular dendritic cell clusters, loss of Cbl-b did not rescue germinal center formation in CD28-deficient mice. Mechanistically, in vivo vesicular stomatitis virus-induced IL-4 and IFN-gamma production and up-regulation of the inducible costimulatory molecule ICOS were dependent on CD28, and could not be rescued by the loss of Cbl-b. These data provide genetic evidence that CD28-dependent in vivo immune responses and Ig class switching can be genetically uncoupled from germinal center formation and ICOS induction by Cbl-b-Vav1-regulated signaling pathways.","authors":"Krawczyk, CM., Jones, RG., Atfield, A., Bachmaier, K., Arya, S., Odermatt, B., Ohashi, PS., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Immunol","volume":"174","issue":"3","page":"1472-8","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22829665","title":"Reconstitution of the central and peripheral nervous system during salamander tail regeneration.","abstract":"We show that after tail amputation in Ambystoma mexicanum (Axolotl) the correct number and spacing of dorsal root ganglia are regenerated. By transplantation of spinal cord tissue and nonclonal neurospheres, we show that the central spinal cord represents a source of peripheral nervous system cells. Interestingly, melanophores migrate from preexisting precursors in the skin. Finally, we demonstrate that implantation of a clonally derived spinal cord neurosphere can result in reconstitution of all examined cell types in the regenerating central spinal cord, suggesting derivation of a cell with spinal cord stem cell properties.","authors":"McHedlishvili, L., Mazurov, V., Grassme, KS., Goehler, K., Robl, B., Tazaki, A., Roensch, K., Duemmler, A., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Proc Natl Acad Sci U S A","volume":"109","issue":"34","page":"E2258-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21778523","title":"Fast flexible modeling of RNA structure using internal coordinates.","abstract":"Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.","authors":"Flores, SC., Sherman, MA., Bruns, CM., Eastman, P., Altman, RB.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"IEEE\/ACM Trans Comput Biol Bioinform","volume":"8","issue":"5","page":"1247-57","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18570253","title":"Expression and regulation of HTRA1 during chick and early mouse development.","abstract":"HTRA1, a member of the high temperature requirement factor A family, is a secreted serine protease that can bind to and inactivate members of the transforming growth factor-beta (TGFbeta) family, modulate insulin-like growth factor signaling and stimulate long range fibroblast growth factor (FGF) signaling in Xenopus. In vertebrates, so far homologues from mouse, human, and Xenopus have been cloned and studied. Here we report the cloning of the chicken HTRA1 homologue from a screen for FGF8 inducible genes in chick facial mesenchyme. We characterize its expression pattern from gastrulation (Hamburger and Hamilton stage 4) to day 4 of development, and in forming inner organs and limbs. We show that chick HTRA1 has a dynamic expression pattern that differs significantly from the expression of its mouse homolog. We, furthermore, demonstrate that FGF signaling is necessary and sufficient for HTRA1 expression in chick facial and forelimb mesenchyme, but is not required for HTRA1 expression in HH11 embryos.","authors":"Ferrer-Vaquer, A., Maurey, P., Werzowa, J., Firnberg, N., Leibbrandt, A., Neub\u00fcser, A.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Dev Dyn","volume":"237","issue":"7","page":"1893-900","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25129145","title":"Jagunal homolog 1 is a critical regulator of neutrophil function in fungal host defense.","abstract":"Neutrophils are key innate immune effector cells that are essential to fighting bacterial and fungal pathogens. Here we report that mice carrying a hematopoietic lineage-specific deletion of Jagn1 (encoding Jagunal homolog 1) cannot mount an efficient neutrophil-dependent immune response to the human fungal pathogen Candida albicans. Global glycobiome analysis identified marked alterations in the glycosylation of proteins involved in cell adhesion and cytotoxicity in Jagn1-deficient neutrophils. Functional analysis confirmed marked defects in neutrophil migration in response to Candida albicans infection and impaired formation of cytotoxic granules, as well as defective myeloperoxidase release and killing of Candida albicans. Treatment with granulocyte\/macrophage colony-stimulating factor (GM-CSF) protected mutant mice from increased weight loss and accelerated mortality after Candida albicans challenge. Notably, GM-CSF also restored the defective fungicidal activity of bone marrow cells from humans with JAGN1 mutations. These data directly identify Jagn1 (JAGN1 in humans) as a new regulator of neutrophil function in microbial pathogenesis and uncover a potential treatment option for humans.","authors":"Wirnsberger, G., Zwolanek, F., Stadlmann, J., Tortola, L., Liu, SW., Perlot, T., J\u00e4rvinen, P., D\u00fcrnberger, G., Kozieradzki, I., Sarao, R., De Martino, A., Boztug, K., Mechtler, K., Kuchler, K., Klein, C., Elling, U., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Genet","volume":"46","issue":"9","page":"1028-33","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25135934","title":"A cooperative mechanism drives budding yeast kinetochore assembly downstream of CENP-A.","abstract":"Kinetochores are megadalton-sized protein complexes that mediate chromosome-microtubule interactions in eukaryotes. How kinetochore assembly is triggered specifically on centromeric chromatin is poorly understood. Here we use biochemical reconstitution experiments alongside genetic and structural analysis to delineate the contributions of centromere-associated proteins to kinetochore assembly in yeast. We show that the conserved kinetochore subunits Ame1(CENP-U) and Okp1(CENP-Q) form a DNA-binding complex that associates with the microtubule-binding KMN network via a short Mtw1 recruitment motif in the N terminus of Ame1. Point mutations in the Ame1 motif disrupt kinetochore function by preventing KMN assembly on chromatin. Ame1-Okp1 directly associates with the centromere protein C (CENP-C) homologue Mif2 to form a cooperative binding platform for outer kinetochore assembly. Our results indicate that the key assembly steps, CENP-A recognition and outer kinetochore recruitment, are executed through different yeast constitutive centromere-associated network subunits. This two-step mechanism may protect against inappropriate kinetochore assembly similar to rate-limiting nucleation steps used by cytoskeletal polymers.","authors":"Hornung, P., Troc, P., Malvezzi, F., Maier, M., Demianova, Z., Zimniak, T., Litos, G., Lampert, F., Schleiffer, A., Brunner, M., Mechtler, K., Herzog, F., Marlovits, TC., Westermann, S.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Cell Biol","volume":"206","issue":"4","page":"509-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-11-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28024147","title":"Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution.","abstract":"Gene expression is controlled by enhancers that activate transcription from the core promoters of their target genes. Although a key function of core promoters is to convert enhancer activities into gene transcription, whether and how strongly they activate transcription in response to enhancers has not been systematically assessed on a genome-wide level. Here we describe self-transcribing active core promoter sequencing (STAP-seq), a method to determine the responsiveness of genomic sequences to enhancers, and apply it to the Drosophila melanogaster genome. We cloned candidate fragments at the position of the core promoter (also called minimal promoter) in reporter plasmids with or without a strong enhancer, transfected the resulting library into cells, and quantified the transcripts that initiated from each candidate for each setup by deep sequencing. In the presence of a single strong enhancer, the enhancer responsiveness of different sequences differs by several orders of magnitude, and different levels of responsiveness are associated with genes of different functions. We also identify sequence features that predict enhancer responsiveness and discuss how different core promoters are employed for the regulation of gene expression.","authors":"Arnold, CD., Zabidi, MA., Pagani, M., Rath, M., Schernhuber, K., Kazmar, T., Stark, A.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Biotechnol","volume":"35","issue":"2","page":"136-144","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27707753","title":"MicroRNA-34\/449 controls mitotic spindle orientation during mammalian cortex development.","abstract":"Correct orientation of the mitotic spindle determines the plane of cellular cleavage and is crucial for organ development. In the developing cerebral cortex, spindle orientation defects result in severe neurodevelopmental disorders, but the precise mechanisms that control this important event are not fully understood. Here, we use a combination of high-content screening and mouse genetics to identify the miR-34\/449 family as key regulators of mitotic spindle orientation in the developing cerebral cortex. By screening through all cortically expressed miRNAs in HeLa cells, we show that several members of the miR-34\/449 family control mitotic duration and spindle rotation. Analysis of miR-34\/449 knockout (KO) mouse embryos demonstrates significant spindle misorientation phenotypes in cortical progenitors, resulting in an excess of radial glia cells at the expense of intermediate progenitors and a significant delay in neurogenesis. We identify the junction adhesion molecule-A (JAM-A) as a key target for miR-34\/449 in the developing cortex that might be responsible for those defects. Our data indicate that miRNA-dependent regulation of mitotic spindle orientation is crucial for cell fate specification during mammalian neurogenesis.","authors":"Fededa, JP., Esk, C., Mierzwa, B., Stanyte, R., Yuan, S., Zheng, H., Ebnet, K., Yan, W., Knoblich, JA., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"EMBO J","volume":"35","issue":"22","page":"2386-2398","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22575762","title":"A new approach to transcription factor screening for reprogramming of fibroblasts to cardiomyocyte-like cells.","abstract":"The simultaneous overexpression of several transcription factors has emerged as a successful strategy to convert fibroblasts into other cell types including pluripotent cells, neurons, and cardiomyocytes. The selection and screening of factors are critical, and have often involved testing a large pool of transcription factors, followed by successive removal of single factors. Here, to identify a cardiac transcription factor combination facilitating mouse fibroblast reprogramming into cardiomyocytes, we directly screened all triplet combinations of 10 candidate factors combined with a Q-PCR assay reporting induction of multiple cardiac-specific genes. Through this screening method the combination of Tbx5, Mef2c, and Myocd was identified to upregulate a broader spectrum of cardiac genes compared to the combination of Tbx5, Mef2c, and Gata4 that was recently shown to induce reprogramming of fibroblasts into cardiomyocytes. Cells cotransduced with Tbx5, Mef2c, Myocd expressed cardiac contractile proteins, had cardiac-like potassium and sodium currents and action potentials could be elicited. In summary the alternative screening approach that is presented here avoided the elimination of transcription factors whose potency is masked in complex transcription factor mixes. Furthermore, our results point to the importance of verifying multiple lineage specific genes when assessing reprogramming.","authors":"Protze, S., Khattak, S., Poulet, C., Lindemann, D., Tanaka, EM., Ravens, U.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Mol Cell Cardiol","volume":"53","issue":"3","page":"323-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21735360","title":"B lymphocyte lineage specification, commitment and epigenetic control of transcription by early B cell factor 1.","abstract":"Early B cell factor 1 (EBF1) is a transcription factor that is critical for both B lymphopoiesis and B cell function. EBF1 is a requisite component of the B lymphocyte transcriptional network and is essential for B lineage specification. Recent studies revealed roles for EBF1 in B cell commitment. EBF1 binds its target genes via a DNA-binding domain including a unique 'zinc knuckle', which mediates a novel mode of DNA recognition. Chromatin immunoprecipitation of EBF1 in pro-B cells defined hundreds of new, as well as previously identified, target genes. Notably, expression of the pre-B cell receptor (pre-BCR), BCR and PI3K\/Akt\/mTOR signaling pathways is controlled by EBF1. In this review, we highlight these current developments and explore how EBF1 functions as a tissue-specific regulator of chromatin structure at B cell-specific genes.","authors":"Hagman, J., Ram\u00edrez, J., Lukin, K.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Curr Top Microbiol Immunol","volume":"356","issue":"","page":"17-38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15643673","title":"Cell-cycle-dependent regulation of DNA replication and its relevance to cancer pathology.","abstract":"The highly orchestrated process of DNA replication ensures the accurate inheritance of genetic information from one cell generation to the next. The exact execution of DNA replication depends on a large number of proteins that are being studied extensively in the cell cycle field. Some of these proteins, such as the minichromosome maintenance proteins (MCMs), are essential for the process of DNA replication itself. Others such as geminin are specifically required to limit DNA replication to once per cell cycle. Together, these proteins protect the stability of the human genome in cycling cells. Their expression has been compared with routinely used proliferation markers, such as Ki-67 (MIB-1) and proliferating cell nuclear antigen (PCNA), which fulfil the requirements of molecular tumour markers to varying extents. However, it is with regard to the depth of our understanding of antigen biology that the MCM proteins and geminin qualify exceptionally well as novel cell-cycle biomarkers for routine use in clinical practice, particularly in cancer detection and estimation of prognosis. Expression microarray analysis has also independently identified MCMs and their interacting proteins as determinants of the inherent aggressiveness of a wide range of epithelial malignancies.","authors":"Tachibana, KE., Gonzalez, MA., Coleman, N.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Pathol","volume":"205","issue":"2","page":"123-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25217051","title":"Msh4 and Msh5 function in SC-independent chiasma formation during the streamlined meiosis of Tetrahymena.","abstract":"ZMM proteins have been defined in budding yeast as factors that are collectively involved in the formation of interfering crossovers (COs) and synaptonemal complexes (SCs), and they are a hallmark of the predominant meiotic recombination pathway of most organisms. In addition to this so-called class I CO pathway, a minority of crossovers are formed by a class II pathway, which involves the Mus81-Mms4 endonuclease complex. This is the only CO pathway in the SC-less meiosis of the fission yeast. ZMM proteins (including SC components) were always found to be co-occurring and hence have been regarded as functionally linked. Like the fission yeast, the protist Tetrahymena thermophila does not possess a SC, and its COs are dependent on Mus81-Mms4. Here we show that the ZMM proteins Msh4 and Msh5 are required for normal chiasma formation, and we propose that they have a pro-CO function outside a canonical class I pathway in Tetrahymena. Thus, the two-pathway model is not tenable as a general rule.","authors":"Shodhan, A., Lukaszewicz, A., Novatchkova, M., Loidl, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genetics","volume":"198","issue":"3","page":"983-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10453004","title":"Lipopolysaccharide induces in macrophages the synthesis of the suppressor of cytokine signaling 3 and suppresses signal transduction in response to the activating factor IFN-gamma.","abstract":"The goal of this study was to investigate how bacterial LPS affects macrophage responsiveness to the activating factor IFN-gamma. Pretreatment of macrophages with LPS for &lt;2 h increased the transcriptional response to IFN-gamma. In contrast, simultaneous stimulation with IFN-gamma and LPS, or pretreatment with LPS for &gt;4 h, suppressed Stat1 tyrosine 701 phosphorylation, dimerization, and transcriptional activity in response to IFN-gamma. Consistently, the induction of MHCII protein by IFN-gamma was antagonized by LPS pretreatment. Neutralizing Abs to IL-10 were without effect on LPS-mediated suppression of Stat1 activation. Decreased IFN-gamma signal transduction after LPS treatment corresponded to a direct induction of suppressor of cytokine signaling3 (SOCS3) mRNA and protein. Under the same conditions socs1, socs2, and cis genes were not transcribed. In transfection assays, SOCS3 was found to suppress the transcriptional response of macrophages to IFN-gamma. A causal link of decreased IFN-gamma signaling to SOCS3 induction was also suggested by the LPS-dependent reduction of IFN-gamma-mediated Janus kinase 1 (JAK1) activation. Further consistent with inhibitory activity of SOCS3, LPS also inhibited the JAK2-dependent activation of Stat5 by GM-CSF. Our results thus link the deactivating effect of chronic LPS exposure on macrophages with its ability to induce SOCS3.","authors":"Stoiber, D., Kovarik, P., Cohney, S., Johnston, JA., Steinlein, P., Decker, T.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Immunol","volume":"163","issue":"5","page":"2640-7","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"1999-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28002811","title":"Aberrant regulation of RANKL\/OPG in women at high risk of developing breast cancer.","abstract":"Breast cancer is the most common female cancer, affecting approximately one in eight women during their lifetime in North America and Europe. Receptor Activator of NF-kB Ligand (RANKL), its receptor RANK and the natural antagonist osteoprotegerin (OPG) are essential regulators of bone resorption. We have initially shown that RANKL\/RANK are essential for hormone-driven mammary epithelial proliferation in pregnancy and RANKL\/RANK have been implicated in mammary stem cell biology. Using genetic mouse-models, we and others identified the RANKL\/RANK system as a key regulator of sex hormone, BRCA1-mutation, and oncogene-driven breast cancer and we proposed that RANKL\/RANK might be involved in the initiation of breast tumors. We now report that in postmenopausal women without known genetic predisposition, high RANKL and progesterone serum levels stratify a subpopulation of women at high risk of developing breast cancer 12-24 months before diagnosis (5.33-fold risk, 95%CI 1.5-25.4; P=0.02). In women with established breast cancer, we demonstrate that RANKL\/OPG ratios change dependent on the presence of circulating tumor cells (CTCs). Finally, we show in a prospective human breast cancer cohort that alterations in RANKL\/OPG ratios are significantly associated with breast cancer manifestation. These data indicate that the RANKL\/RANK\/OPG system is deregulated in post-menopausal women at high risk for breast cancer and in women with circulating tumor cells. Thus, serum levels of RANKL\/OPG are potentially indicative of predisposition and progression of breast cancer in humans. Advancement of our findings towards clinical application awaits prior validation in independent patient cohorts.","authors":"Kiechl, S., Schramek, D., Widschwendter, M., Fourkala, EO., Zaikin, A., Jones, A., Jaeger, B., Rack, B., Janni, W., Scholz, C., Willeit, J., Weger, S., Mayr, A., Teschendorff, A., Rosenthal, A., Fraser, L., Philpott, S., Dubeau, L., Keshtgar, M., Roylance, R., Jacobs, IJ., Menon, U., Schett, G., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Oncotarget","volume":"8","issue":"3","page":"3811-3825","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27984718","title":"A Zygotic Checkpoint for Unrepaired Lesions.","abstract":"DNA demethylation, a process involving DNA repair, is critical for reprogramming of the paternal genome during the oocyte-to-zygote transition. A new study by Ladst\u00e4tter and Tachibana-Konwalski shows that a Chk1-mediated zygotic checkpoint monitors the cohesin-dependent repair of DNA lesions arising from DNA demethylation, which prevents zygotes carrying unrepaired lesions from entering mitosis.","authors":"Zou, L.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"167","issue":"7","page":"1676-1678","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"392504","title":"Control of phosphoenolpyruvate-dependent phosphotransferase-mediated sugar transport in Escherichia coli by energization of the cell membrane.","abstract":"The phosphoenolpyruvate-dependent phosphotransferase-mediated sugar transport in Escherichia coli is inhibited by the energized of the membrane. This was shown in intact cells as well as in membrane vesicles. Relaxation of the proton gradient by uncouplers stimulated the uptake of sugars via the phosphotransferase system in aerobically cultured cells. No such effect was seen in anaerobic cells, apparently because the cell membrane of these cells is poorly energized. Energization by respiration of D-lactate or ascorbate inhibited the phosphotransferase uptake system in membrane vesicles. This inhibition was reversed by the addition of cyanide. Oxamate, a specific inhibitor of lactate dehydrogenase, prevented the inhibitory effect of D-lactate. Membrane vesicles prepared from a cytochrome-less mutant were not energized by D-lactate oxidation and the phosphotransferase uptake system was not inhibited.","authors":"Reider, E., Wagner, EF., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Proc Natl Acad Sci U S A","volume":"76","issue":"11","page":"5529-33","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1980-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16943855","title":"Neuroprotection by GDNF-secreting stem cells in a Huntington's disease model: optical neuroimage tracking of brain-grafted cells.","abstract":"The use of stem cells for reconstructive or neuroprotective strategies can benefit from new advances in neuroimaging techniques to track grafted cells. In the present work, we analyze the potential of a neural stem cell (NSC) line, which stably expresses the glial cell line-derived neurotrophic factor (GDNF) and the firefly luciferase gene (GDNF\/Luc-NSC), for cell therapy in a Huntington's disease mouse model. Our results show that detection of light photons is an effective method to quantify the proliferation rate and to characterize the migration pathways of transplanted NSCs. Intravenous administration of luciferine, the luciferase substract, into the grafted animals allowed the detection of implanted cells in real time by an optical neuroimaging methodology, overpassing the limits of serial histological analyses. We observed that transplanted GDNF\/Luc-NSCs survive after grafting and expand more when transplanted in quinolinate-lesioned nude mouse striata than when transplanted in non-lesioned mice. We also demonstrate that GDNF\/Luc-NSCs prevent the degeneration of striatal neurons in the excitotoxic mouse model of Huntington's disease and reduce the amphetamine-induced rotational behavior in mice bearing unilateral lesions.","authors":"Pineda, JR., Rubio, N., Akerud, P., Urb\u00e1n, N., Badimon, L., Arenas, E., Alberch, J., Blanco, J., Canals, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Gene Ther","volume":"14","issue":"2","page":"118-28","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21715613","title":"Multiplicative dynamics underlie the emergence of the log-normal distribution of spine sizes in the neocortex in vivo.","abstract":"What fundamental properties of synaptic connectivity in the neocortex stem from the ongoing dynamics of synaptic changes? In this study, we seek to find the rules shaping the stationary distribution of synaptic efficacies in the cortex. To address this question, we combined chronic imaging of hundreds of spines in the auditory cortex of mice in vivo over weeks with modeling techniques to quantitatively study the dynamics of spines, the morphological correlates of excitatory synapses in the neocortex. We found that the stationary distribution of spine sizes of individual neurons can be exceptionally well described by a log-normal function. We furthermore show that spines exhibit substantial volatility in their sizes at timescales that range from days to months. Interestingly, the magnitude of changes in spine sizes is proportional to the size of the spine. Such multiplicative dynamics are in contrast with conventional models of synaptic plasticity, learning, and memory, which typically assume additive dynamics. Moreover, we show that the ongoing dynamics of spine sizes can be captured by a simple phenomenological model that operates at two timescales of days and months. This model converges to a log-normal distribution, bridging the gap between synaptic dynamics and the stationary distribution of synaptic efficacies.","authors":"Loewenstein, Y., Kuras, A., Rumpel, S.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Neurosci","volume":"31","issue":"26","page":"9481-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24896182","title":"Genome-scale functional characterization of Drosophila developmental enhancers in vivo.","abstract":"Transcriptional enhancers are crucial regulators of gene expression and animal development and the characterization of their genomic organization, spatiotemporal activities and sequence properties is a key goal in modern biology. Here we characterize the in vivo activity of 7,705 Drosophila melanogaster enhancer candidates covering 13.5% of the non-coding non-repetitive genome throughout embryogenesis. 3,557 (46%) candidates are active, suggesting a high density with 50,000 to 100,000 developmental enhancers genome-wide. The vast majority of enhancers display specific spatial patterns that are highly dynamic during development. Most appear to regulate their neighbouring genes, suggesting that the cis-regulatory genome is organized locally into domains, which are supported by chromosomal domains, insulator binding and genome evolution. However, 12 to 21 per cent of enhancers appear to skip non-expressed neighbours and regulate a more distal gene. Finally, we computationally identify cis-regulatory motifs that are predictive and required for enhancer activity, as we validate experimentally. This work provides global insights into the organization of an animal regulatory genome and the make-up of enhancer sequences and confirms and generalizes principles from previous studies. All enhancer patterns are annotated manually with a controlled vocabulary and all results are available through a web interface (http:\/\/enhancers.starklab.org), including the raw images of all microscopy slides for manual inspection at arbitrary zoom levels.","authors":"Kvon, EZ., Kazmar, T., Stampfel, G., Y\u00e1\u00f1ez-Cuna, JO., Pagani, M., Schernhuber, K., Dickson, BJ., Stark, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nature","volume":"512","issue":"7512","page":"91-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21068061","title":"Efficient regeneration by activation of neurogenesis in homeostatically quiescent regions of the adult vertebrate brain.","abstract":"In contrast to mammals, salamanders and teleost fishes can efficiently repair the adult brain. It has been hypothesised that constitutively active neurogenic niches are a prerequisite for extensive neuronal regeneration capacity. Here, we show that the highly regenerative salamander, the red spotted newt, displays an unexpectedly similar distribution of active germinal niches with mammals under normal physiological conditions. Proliferation zones in the adult newt brain are restricted to the forebrain, whereas all other regions are essentially quiescent. However, ablation of midbrain dopamine neurons in newts induced ependymoglia cells in the normally quiescent midbrain to proliferate and to undertake full dopamine neuron regeneration. Using oligonucleotide microarrays, we have catalogued a set of differentially expressed genes in these activated ependymoglia cells. This strategy identified hedgehog signalling as a key component of adult dopamine neuron regeneration. These data show that brain regeneration can occur by activation of neurogenesis in quiescent brain regions.","authors":"Berg, DA., Kirkham, M., Beljajeva, A., Knapp, D., Habermann, B., Ryge, J., Tanaka, EM., Simon, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Development","volume":"137","issue":"24","page":"4127-34","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15575971","title":"Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15575971<\/PMID><DateCompleted><Year>2005<\/Year><Month>10<\/Month><Day>19<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>5<\/Volume><Issue>12<\/Issue><PubDate><Year>2004<\/Year><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins.<\/ArticleTitle><Pagination><MedlinePgn>R97<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Can sequence segments coding for subcellular targeting or for posttranslational modifications occur in proteins that are not substrates in either of these processes? Although considerable effort has been invested in achieving low false-positive prediction rates, even accurate sequence-analysis tools for the recognition of these motifs generate a small but noticeable number of protein hits that lack the appropriate biological context but cannot be rationalized as false positives.","authors":"Neuberger, G., Kunze, M., Eisenhaber, F., Berger, J., Hartig, A., Brocard, C.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Genome Biol","volume":"5","issue":"12","page":"R97","pdf":null,"JrId":"21904","fulltextlink":null,"preprintlink":null,"articledate":"2005-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27702987","title":"Linear ubiquitination by LUBEL has a role in Drosophila heat stress response.","abstract":"The HOIP ubiquitin E3 ligase generates linear ubiquitin chains by forming a complex with HOIL-1L and SHARPIN in mammals. Here, we provide the first evidence of linear ubiquitination induced by a HOIP orthologue in Drosophila We identify Drosophila CG11321, which we named Linear Ubiquitin E3 ligase (LUBEL), and find that it catalyzes linear ubiquitination in vitro We detect endogenous linear ubiquitin chain-derived peptides by mass spectrometry in Drosophila Schneider 2 cells and adult flies. Furthermore, using CRISPR\/Cas9 technology, we establish linear ubiquitination-defective flies by mutating residues essential for the catalytic activity of LUBEL Linear ubiquitination signals accumulate upon heat shock in flies. Interestingly, flies with LUBEL mutations display reduced survival and climbing defects upon heat shock, which is also observed upon specific LUBEL depletion in muscle. Thus, LUBEL is involved in the heat response by controlling linear ubiquitination in flies.","authors":"Asaoka, T., Almagro, J., Ehrhardt, C., Tsai, I., Schleiffer, A., Deszcz, L., Junttila, S., Ringrose, L., Mechtler, K., Kavirayani, A., Gyenesei, A., Hofmann, K., Duchek, P., Rittinger, K., Ikeda, F.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"EMBO Rep","volume":"17","issue":"11","page":"1624-1640","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25125150","title":"NDST1 missense mutations in autosomal recessive intellectual disability.","abstract":"NDST1 was recently proposed as a candidate gene for autosomal recessive intellectual disability in two families. It encodes a bifunctional GlcNAc N-deacetylase\/N-sulfotransferase with important functions in heparan sulfate biosynthesis. In mice, Ndst1 is crucial for embryonic development and homozygous null mutations are perinatally lethal. We now report on two additional unrelated families with homozygous missense NDST1 mutations. All mutations described to date predict the substitution of conserved amino acids in the sulfotransferase domain, and mutation modeling predicts drastic alterations in the local protein conformation. Comparing the four families, we noticed significant overlap in the clinical features, including both demonstrated and apparent intellectual disability, muscular hypotonia, epilepsy, and postnatal growth deficiency. Furthermore, in Drosophila, knockdown of sulfateless, the NDST ortholog, impairs long-term memory, highlighting its function in cognition. Our data confirm NDST1 mutations as a cause of autosomal recessive intellectual disability with a distinctive phenotype, and support an important function of NDST1 in human development.","authors":"Reuter, MS., Musante, L., Hu, H., Diederich, S., Sticht, H., Ekici, AB., Uebe, S., Wienker, TF., Bartsch, O., Zechner, U., Oppitz, C., Keleman, K., Jamra, RA., Najmabadi, H., Schweiger, S., Reis, A., Kahrizi, K.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Am J Med Genet A","volume":"164A","issue":"11","page":"2753-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15546916","title":"LAP2alpha and BAF transiently localize to telomeres and specific regions on chromatin during nuclear assembly.","abstract":"Lamina-associated polypeptide (LAP) 2alpha is a LEM (lamina-associated polypeptide emerin MAN1) family protein associated with nucleoplasmic A-type lamins and chromatin. Using live cell imaging and fluorescence microscopy we demonstrate that LAP2alpha was mostly cytoplasmic in metaphase and associated with telomeres in anaphase. Telomeric LAP2alpha clusters grew in size, formed 'core' structures on chromatin adjacent to the spindle in telophase, and translocated to the nucleoplasm in G1 phase. A subfraction of lamin C and emerin followed LAP2alpha to the core region early on, whereas LAP2beta, lamin B receptor and lamin B initially bound to more peripheral regions of chromatin, before they spread to core structures with different kinetics. Furthermore, the DNA-crosslinking protein barrier-to-autointegration factor (BAF) bound to LAP2alpha in vitro and in mitotic extracts, and subfractions of BAF relocalized to core structures with LAP2alpha. We propose that LAP2alpha and a subfraction of BAF form defined complexes in chromatin core regions and may be involved in chromatin reorganization during early stages of nuclear assembly.","authors":"Dechat, T., Gajewski, A., Korbei, B., Gerlich, D., Daigle, N., Haraguchi, T., Furukawa, K., Ellenberg, J., Foisner, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Cell Sci","volume":"117","issue":"Pt 25","page":"6117-28","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25257309","title":"SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs.","abstract":"Although splicing is essential for the expression of most eukaryotic genes, inactivation of splicing factors causes specific defects in mitosis. The molecular cause of this defect is unknown. Here, we show that the spliceosome subunits SNW1 and PRPF8 are essential for sister chromatid cohesion in human cells. A transcriptome-wide analysis revealed that SNW1 or PRPF8 depletion affects the splicing of specific introns in a subset of pre-mRNAs, including pre-mRNAs encoding the cohesion protein sororin and the APC\/C subunit APC2. SNW1 depletion causes cohesion defects predominantly by reducing sororin levels, which causes destabilisation of cohesin on DNA. SNW1 depletion also reduces APC\/C activity and contributes to cohesion defects indirectly by delaying mitosis and causing \"cohesion fatigue\". Simultaneous expression of sororin and APC2 from intron-less cDNAs restores cohesion in SNW1-depleted cells. These results indicate that the spliceosome is required for mitosis because it enables expression of genes essential for cohesion. Our transcriptome-wide identification of retained introns in SNW1- and PRPF8-depleted cells may help to understand the aetiology of diseases associated with splicing defects, such as retinosa pigmentosum and cancer.","authors":"van der Lelij, P., Stocsits, RR., Ladurner, R., Petzold, G., Kreidl, E., Koch, B., Schmitz, J., Neumann, B., Ellenberg, J., Peters, JM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"EMBO J","volume":"33","issue":"22","page":"2643-58","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15549172","title":"Physiological roles of angiotensin-converting enzyme 2.","abstract":"Angiotensin-converting enzyme 2 (ACE2) is a recently discovered homologue of the key enzyme of the renin-angiotensin system, the angiotensin-converting enzyme. The ACE2 enzyme is mainly expressed in cardiac blood vessels and tubular epithelia of the kidneys. Together with ACE2's unique metallocarboxypeptidase activity, the restricted tissue distribution suggests a distinctive physiological function in blood pressure, blood flow and fluid regulation. The ace2 gene was mapped to quantitative trait loci affecting susceptibility to hypertension in rats. Furthermore, ACE2 appears to be a negative regulator of ACE in the heart. ACE2 messenger RNA and protein levels are substantially regulated in the kidney of diabetic and pregnant rats. The mechanism of ACE2 function and its physiologic significance are not yet fully understood; however, as ACE2 differs in its specificity and physiological role from ACE, this opens a new potential venue for drug discovery aimed at cardiovascular disease, hypertension and diabetic complications.","authors":"Danilczyk, U., Eriksson, U., Oudit, GY., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell Mol Life Sci","volume":"61","issue":"21","page":"2714-9","pdf":null,"JrId":"20436","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28135257","title":"One-step generation of conditional and reversible gene knockouts.","abstract":"Loss-of-function studies are key for investigating gene function, and CRISPR technology has made genome editing widely accessible in model organisms and cells. However, conditional gene inactivation in diploid cells is still difficult to achieve. Here, we present CRISPR-FLIP, a strategy that provides an efficient, rapid and scalable method for biallelic conditional gene knockouts in diploid or aneuploid cells, such as pluripotent stem cells, 3D organoids and cell lines, by co-delivery of CRISPR-Cas9 and a universal conditional intronic cassette.","authors":"Andersson-Rolf, A., Mustata, RC., Merenda, A., Kim, J., Perera, S., Grego, T., Andrews, K., Tremble, K., Silva, JC., Fink, J., Skarnes, WC., Koo, BK.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Methods","volume":"14","issue":"3","page":"287-289","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20303986","title":"A model for cyst lumen expansion and size regulation via fluid secretion.","abstract":"Many internal epithelial organs derive from cysts, which are tissues comprised of bent epithelial cell layers enclosing a lumen. Ion accumulation in the lumen drives water influx and consequently water accumulation and cyst expansion. Lumen-size recognition is important for the regulation of organ size. When lumen size and cyst size are not controlled, diseases can result; for instance, renal failure of the kidney. We develop a mechanistic mathematical model of lumen expansion in order to investigate the mechanisms for saturation of cyst growth. We include fluid accumulation in the lumen, osmotic and elastic pressure, ion transport and stretch-induced cell division. We find that the lumen volume increases in two phases: first, due to fluid accumulation stretching the cells, then in the second phase, the volume increase follows the increase in cell number until proliferation ceases as stretch forces relax. The model is quantitatively fitted to published data of in vitro cyst growth and predicts steady state lumen size as a function of the model parameters.","authors":"Gin, E., Tanaka, EM., Brusch, L.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Theor Biol","volume":"264","issue":"3","page":"1077-88","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21543620","title":"Active and passive antennal movements during visually guided steering in flying Drosophila.","abstract":"Insects use feedback from a variety of sensory modalities, including mechanoreceptors on their antennae, to stabilize the direction and speed of flight. Like all arthropod appendages, antennae not only supply sensory information but may also be actively positioned by control muscles. However, how flying insects move their antennae during active turns and how such movements might influence steering responses are currently unknown. Here we examined the antennal movements of flying Drosophila during visually induced turns in a tethered flight arena. In response to both rotational and translational patterns of visual motion, Drosophila actively moved their antennae in a direction opposite to that of the visual motion. We also observed two types of passive antennal movements: small tonic deflections of the antenna and rapid oscillations at wing beat frequency. These passive movements are likely the result of wing-induced airflow and increased in magnitude when the angular distance between the wing and the antenna decreased. In response to rotational visual motion, increases in passive antennal movements appear to trigger a reflex that reduces the stroke amplitude of the contralateral wing, thereby enhancing the visually induced turn. Although the active antennal movements significantly increased antennal oscillation by bringing the arista closer to the wings, it did not significantly affect the turning response in our head-fixed, tethered flies. These results are consistent with the hypothesis that flying Drosophila use mechanosensory feedback to detect changes in the wing induced airflow during visually induced turns and that this feedback plays a role in regulating the magnitude of steering responses.","authors":"Mamiya, A., Straw, AD., T\u00f3masson, E., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Neurosci","volume":"31","issue":"18","page":"6900-14","pdf":null,"JrId":"5035","fulltextlink":null,"preprintlink":null,"articledate":"2011-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20147243","title":"Axolotl (Ambystoma mexicanum) limb and tail amputation.","abstract":null,"authors":"Kragl, M., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cold Spring Harb Protoc","volume":"2009","issue":"8","page":"pdb.prot5267","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27916276","title":"A Surveillance Mechanism Ensures Repair of DNA Lesions during Zygotic Reprogramming.","abstract":"Sexual reproduction culminates in a totipotent zygote with the potential to produce a whole organism. Sperm chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications generate a totipotent embryo. Active DNA demethylation of the paternal genome has been proposed to involve base excision and DNA repair-based mechanisms. The nature and consequence of DNA lesions generated during reprogramming are not known. Using mouse genetics and chemical biology, we discovered that Tet3-dependent zygotic reprogramming generates paternal DNA lesions that are monitored by a surveillance mechanism. In\u00a0vivo structure-function rescue assays revealed that cohesin-dependent repair of paternal DNA lesions prevents activation of a Chk1-dependent checkpoint\u00a0that delays mitotic entry. Culturing conditions affect checkpoint stringency, which has implications for human in\u00a0vitro fertilization. We propose the zygotic checkpoint senses DNA lesions generated during paternal DNA demethylation and ensures reprogrammed loci are repaired before mitosis to prevent chromosome fragmentation, embryo loss, and infertility.","authors":"Ladst\u00e4tter, S., Tachibana-Konwalski, K.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"167","issue":"7","page":"1774-1787.e13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31560237","title":"Spectral recording of gene expression history by fluorescent timer protein.","abstract":"Monitoring spatio-temporal patterns of gene expression by fluorescent proteins requires longitudinal observation, which is often difficult to implement. Here, we fuse a fluorescent timer (FT) protein with an immediate early gene (IEG) promoter to track live gene expression in single cells. This results in a stimulus- and time-dependent spectral shift from blue to red for subsequent monitoring with fluorescence activated cell sorting (FACS) and live cell imaging. This spectral shift enables imputing the time point of activity <i>post-hoc<\/i> to dissociate early and late responders from a single snapshot in time. Thus, we provide a tool for tracking stimulus-driven IEG expression and demonstrate proof of concept exploiting promoter::FT fusions, adding new dimensions to experiments that require reconstructing spatio-temporal patterns of gene expression in cells, tissues or living organisms.","authors":"Tr\u00f6scher, AR., Werner, B., Kaouane, N., Haubensak, W.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Biotechniques","volume":"67","issue":"4","page":"154-164","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28044412","title":"Adult gastric stem cells and their niches.","abstract":"Adult gastric stem cells replenish the gastric epithelium throughout life. Recent studies have identified diverse populations of stem cells, progenitor cells, and even differentiated cells that can regain stem cell capacity, so highlighting an unexpected plasticity within the gastric epithelium, both in the corpus and antrum. Two niches seem to co-exist in the gastric unit: one in the isthmus region and the other at the base of the gland, although the precise features of the cell populations and the two niches are currently under debate. A variety of gastric organoid models have been established, providing new insights into niche factors required by the gastric stem cell populations. Here we review our current knowledge of gastric stem cell populations, their markers and interactions, important niche factors, and different gastric organoid systems. WIREs Dev Biol 2017, 6:e261. doi: 10.1002\/wdev.261 For further resources related to this article, please visit the WIREs website.","authors":"Bartfeld, S., Koo, BK.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Wiley Interdiscip Rev Dev Biol","volume":"6","issue":"2","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27909245","title":"Heterochromatin aggregation during DNA elimination in Tetrahymena is facilitated by a prion-like protein.","abstract":"Regulated aggregations of prion and prion-like proteins play physiological roles in various biological processes. However, their structural roles in the nucleus are poorly understood. Here, we show that the prion-like protein Jub6p is involved in the regulation of chromatin structure in the ciliated protozoan Tetrahymena thermophila Jub6p forms sodium dodecyl sulfate (SDS)-resistant aggregates when it is ectopically expressed in vegetative cells and binds to RNA in vitro Jub6p is a heterochromatin component and is important for the formation of heterochromatin bodies during the process of programmed DNA elimination. We suggest that RNA-protein aggregates formed by Jub6p are an essential architectural component for the assembly of heterochromatin bodies.","authors":"Kataoka, K., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"J Cell Sci","volume":"130","issue":"2","page":"480-489","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27653973","title":"Decoding sORF translation - from small proteins to gene regulation.","abstract":"Translation is best known as the fundamental mechanism by which the ribosome converts a sequence of nucleotides into a string of amino acids. Extensive research over many years has elucidated the key principles of translation, and the majority of translated regions were thought to be known. The recent discovery of wide-spread translation outside of annotated protein-coding open reading frames (ORFs) came therefore as a surprise, raising the intriguing possibility that these newly discovered translated regions might have unrecognized protein-coding or gene-regulatory functions. Here, we highlight recent findings that provide evidence that some of these newly discovered translated short ORFs (sORFs) encode functional, previously missed small proteins, while others have regulatory roles. Based on known examples we will also speculate about putative additional roles and the potentially much wider impact that these translated regions might have on cellular homeostasis and gene regulation.","authors":"Cabrera-Quio, LE., Herberg, S., Pauli, A.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"RNA Biol","volume":"13","issue":"11","page":"1051-1059","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31558570","title":"EvoChromo: towards a synthesis of chromatin biology and evolution.","abstract":"Over the past few years, interest in chromatin and its evolution has grown. To further advance these interests, we organized a workshop with the support of The Company of Biologists to debate the current state of knowledge regarding the origin and evolution of chromatin. This workshop led to prospective views on the development of a new field of research that we term 'EvoChromo'. In this short Spotlight article, we define the breadth and expected impact of this new area of scientific inquiry on our understanding of both chromatin and evolution.","authors":"Drinnenberg, IA., Berger, F., Els\u00e4sser, SJ., Andersen, PR., Ausi\u00f3, J., Bickmore, WA., Blackwell, AR., Erwin, DH., Gahan, JM., Gaut, BS., Harvey, ZH., Henikoff, S., Kao, JY., Kurdistani, SK., Lemos, B., Levine, MT., Luger, K., Malik, HS., Mart\u00edn-Dur\u00e1n, JM., Peichel, CL., Renfree, MB., Rutowicz, K., Sarkies, P., Schmitz, RJ., Technau, U., Thornton, JW., Warnecke, T., Wolfe, KH.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Development","volume":"146","issue":"19","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27983963","title":"Simultaneous paralogue knockout using a CRISPR-concatemer in mouse small intestinal organoids.","abstract":"Approaches based on genetic modification have been invaluable for investigating a wide array of biological processes, with gain- and loss-of-function approaches frequently used to investigate gene function. However, the presence of paralogues, and hence possible genetic compensation, for many genes necessitates the knockout (KO) of all paralogous genes in order to observe clear phenotypic change. CRISPR technology, the most recently described tool for gene editing, can generate KOs with unprecedented ease and speed and has been used in adult stem cell-derived organoids for single gene knockout, gene knock-in and gene correction. However, the simultaneous targeting of multiple genes in organoids by CRISPR technology has not previously been described. Here we describe a rapid, scalable and cost effective method for generating double knockouts in organoids. By concatemerizing multiple gRNA expression cassettes, we generated a 'gRNA concatemer vector'. Our method allows the rapid assembly of annealed synthetic DNA oligos into the final vector in a single step. This approach facilitates simultaneous delivery of multiple gRNAs to allow up to 4 gene KO in one step, or potentially to increase the efficiency of gene knockout by providing multiple gRNAs targeting one gene. As a proof of concept, we knocked out negative regulators of the Wnt pathway in small intestinal organoids, thereby removing their growth dependence on the exogenous Wnt enhancer, R-spondin1.","authors":"Andersson-Rolf, A., Merenda, A., Mustata, RC., Li, T., Dietmann, S., Koo, BK.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Dev Biol","volume":"420","issue":"2","page":"271-277","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15457214","title":"Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3.","abstract":"Both DNA methylation and post-translational histone modifications contribute to gene silencing, but the mechanistic relationship between these epigenetic marks is unclear. Mutations in two Arabidopsis genes, the KRYPTONITE (KYP) histone H3 lysine 9 (H3K9) methyltransferase and the CHROMOMETHYLASE3 (CMT3) DNA methyltransferase, cause a reduction of CNG DNA methylation, suggesting that H3K9 methylation controls CNG DNA methylation. Here we show that the chromodomain of CMT3 can directly interact with the N-terminal tail of histone H3, but only when it is simultaneously methylated at both the H3K9 and H3K27 positions. Furthermore, using chromatin immunoprecipitation analysis and immunohistolocalization experiments, we found that H3K27 methylation colocalizes with H3K9 methylation at CMT3-controlled loci. The H3K27 methylation present at heterochromatin was not affected by mutations in KYP or in several Arabidopsis PcG related genes including the Enhancer of Zeste homologs, suggesting that a novel pathway controls heterochromatic H3K27 methylation. Our results suggest a model in which H3K9 methylation by KYP, and H3K27 methylation by an unknown enzyme provide a combinatorial histone code for the recruitment of CMT3 to silent loci.","authors":"Lindroth, AM., Shultis, D., Jasencakova, Z., Fuchs, J., Johnson, L., Schubert, D., Patnaik, D., Pradhan, S., Goodrich, J., Schubert, I., Jenuwein, T., Khorasanizadeh, S., Jacobsen, SE.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"EMBO J","volume":"23","issue":"21","page":"4286-96","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20147241","title":"Axolotl (Ambystoma mexicanum) embryonic transplantation methods.","abstract":null,"authors":"Nacu, E., Knapp, D., Tanaka, EM., Epperlein, HH.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cold Spring Harb Protoc","volume":"2009","issue":"8","page":"pdb.prot5265","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10934015","title":"Functional equivalence of the transcription factors Pax2 and Pax5 in mouse development.","abstract":"Pax2 and Pax5 arose by gene duplication at the onset of vertebrate evolution and have since diverged in their developmental expression patterns. They are expressed in different organs of the mouse embryo except for their coexpression at the midbrain-hindbrain boundary (MHB), which functions as an organizing center to control midbrain and cerebellum development. During MHB development, Pax2 expression is initiated prior to Pax5 transcription, and Pax2(-\/-) embryos fail to generate the posterior midbrain and cerebellum, whereas Pax5(-\/-) mice exhibit only minor patterning defects in the same brain regions. To investigate whether these contrasting phenotypes are caused by differences in the temporal expression or biochemical activity of these two transcription factors, we have generated a knock-in (ki) mouse, which expresses a Pax5 minigene under the control of the Pax2 locus. Midbrain and cerebellum development was entirely rescued in Pax2(5ki\/5ki) embryos. Pax5 could furthermore completely substitute for the Pax2 function during morphogenesis of the inner ear and genital tracts, despite the fact that the Pax5 transcript of the Pax2(5ki )allele was expressed only at a fivefold lower level than the wild-type Pax2 mRNA. As a consequence, the Pax2(5ki )allele was able to rescue most but not all Pax2 mutant defects in the developing eye and kidney, both of which are known to be highly sensitive to Pax2 protein dosage. Together these data demonstrate that the transcription factors Pax2 and Pax5 have maintained equivalent biochemical functions since their divergence early in vertebrate evolution.","authors":"Bouchard, M., Pfeffer, P., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Development","volume":"127","issue":"17","page":"3703-13","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2000-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27983962","title":"Organoids: A new in vitro model system for biomedical science and disease modelling and promising source for cell-based transplantation.","abstract":null,"authors":"Koo, BK., Huch, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Dev Biol","volume":"420","issue":"2","page":"197-198","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27881737","title":"RANKL\/RANK: from bone loss to the prevention of breast cancer.","abstract":"RANK and RANKL, a receptor ligand pair belonging to the tumour necrosis factor family, are the critical regulators of osteoclast development and bone metabolism. Besides their essential function in bone, RANK and RANKL have also been identified as the key factors for the formation of a lactating mammary gland in pregnancy. Mechanistically, RANK and RANKL link the sex hormone progesterone with stem cell expansion and proliferation of mammary epithelial cells. Based on their normal physiology, RANKL\/RANK control the onset of hormone-induced breast cancer through the expansion of mammary progenitor cells. Recently, we and others were able to show that RANK and RANKL are also critical regulators of BRCA1-mutation-driven breast cancer. Currently, the preventive strategy for BRCA1-mutation carriers includes preventive mastectomy, associated with wide-ranging risks and psychosocial effects. The search for an alternative non-invasive prevention strategy is therefore of paramount importance. As our work strongly implicates RANK and RANKL as key molecules involved in the initiation of BRCA1-associated breast cancer, we propose that anti-RANKL therapy could be a feasible preventive strategy for women carrying BRCA1 mutations, and by extension to other women with high risk of breast cancer.","authors":"Sigl, V., Jones, LP., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Open Biol","volume":"6","issue":"11","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18423196","title":"Identification of oxidative stress and Toll-like receptor 4 signaling as a key pathway of acute lung injury.","abstract":"Multiple lung pathogens such as chemical agents, H5N1 avian flu, or SARS cause high lethality due to acute respiratory distress syndrome. Here we report that Toll-like receptor 4 (TLR4) mutant mice display natural resistance to acid-induced acute lung injury (ALI). We show that TLR4-TRIF-TRAF6 signaling is a key disease pathway that controls the severity of ALI. The oxidized phospholipid (OxPL) OxPAPC was identified to induce lung injury and cytokine production by lung macrophages via TLR4-TRIF. We observed OxPL production in the lungs of humans and animals infected with SARS, Anthrax, or H5N1. Pulmonary challenge with an inactivated H5N1 avian influenza virus rapidly induces ALI and OxPL formation in mice. Loss of TLR4 or TRIF expression protects mice from H5N1-induced ALI. Moreover, deletion of ncf1, which controls ROS production, improves the severity of H5N1-mediated ALI. Our data identify oxidative stress and innate immunity as key lung injury pathways that control the severity of ALI.","authors":"Imai, Y., Kuba, K., Neely, GG., Yaghubian-Malhami, R., Perkmann, T., van Loo, G., Ermolaeva, M., Veldhuizen, R., Leung, YH., Wang, H., Liu, H., Sun, Y., Pasparakis, M., Kopf, M., Mech, C., Bavari, S., Peiris, JS., Slutsky, AS., Akira, S., Hultqvist, M., Holmdahl, R., Nicholls, J., Jiang, C., Binder, CJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell","volume":"133","issue":"2","page":"235-49","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27875273","title":"SIRT2 regulates nuclear envelope reassembly through ANKLE2 deacetylation.","abstract":"Sirtuin 2 (SIRT2) is an NAD-dependent deacetylase known to regulate microtubule dynamics and cell cycle progression. SIRT2 has also been implicated in the pathology of cancer, neurodegenerative diseases and progeria. Here, we show that SIRT2 depletion or overexpression causes nuclear envelope reassembly defects. We link this phenotype to the recently identified regulator of nuclear envelope reassembly ANKLE2. ANKLE2 acetylation at K302 and phosphorylation at S662 are dynamically regulated throughout the cell cycle by SIRT2 and are essential for normal nuclear envelope reassembly. The function of SIRT2 therefore extends beyond the regulation of microtubules to include the regulation of nuclear envelope dynamics.","authors":"Kaufmann, T., Kukolj, E., Brachner, A., Beltzung, E., Bruno, M., Kostrhon, S., Opravil, S., Hudecz, O., Mechtler, K., Warren, G., Slade, D.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Cell Sci","volume":"129","issue":"24","page":"4607-4621","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15339652","title":"Dexras1 potentiates photic and suppresses nonphotic responses of the circadian clock.","abstract":"Circadian rhythms of physiology and behavior are generated by biological clocks that are synchronized to the cyclic environment by photic or nonphotic cues. The interactions and integration of various entrainment pathways to the clock are poorly understood. Here, we show that the Ras-like G protein Dexras1 is a critical modulator of the responsiveness of the master clock to photic and nonphotic inputs. Genetic deletion of Dexras1 reduces photic entrainment by eliminating a pertussis-sensitive circadian response to NMDA. Mechanistically, Dexras1 couples NMDA and light input to Gi\/o and ERK activation. In addition, the mutation greatly potentiates nonphotic responses to neuropeptide Y and unmasks a nonphotic response to arousal. Thus, Dexras1 modulates the responses of the master clock to photic and nonphotic stimuli in opposite directions. These results identify a signaling molecule that serves as a differential modulator of the gated photic and nonphotic input pathways to the circadian timekeeping system.","authors":"Cheng, HY., Obrietan, K., Cain, SW., Lee, BY., Agostino, PV., Joza, NA., Harrington, ME., Ralph, MR., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Neuron","volume":"43","issue":"5","page":"715-28","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10855492","title":"Destruction of the securin Pds1p occurs at the onset of anaphase during both meiotic divisions in yeast.","abstract":"Sister chromatid cohesion is established during DNA replication and depends on a multiprotein complex called cohesin. At the onset of anaphase the cohesive structures that hold sisters together must be destroyed to allow segregation of sisters. In the budding yeast Saccharomyces cerevisiae loss of sister chromatid cohesion depends on a separating protein (separin) called Esp1. At the metaphase to anaphase transition, separin is activated by proteolysis of its inhibitory subunit (securin) called Pds1. This process is mediated by the anaphase promoting complex and an accessory protein Cdc20. In meiosis a single round of DNA replication is followed by two successive rounds of segregation. Thus loss of cohesion is spun out over two divisions. By studying the mechanisms that initiate anaphase in meiotic division we show that the yeast securin Pds1p is present in meiotic nuclei and is destroyed at the onset of each meiotic division. We also show that securin destruction depends on Cdc20p which accumulates within nuclei around the time of Pds1p's disappearance.","authors":"Salah, SM., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Chromosoma","volume":"109","issue":"1-2","page":"27-34","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"2000-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27573765","title":"Clonal Evolution of Stem Cells in the Gastrointestinal Tract.","abstract":"The field of gastrointestinal epithelial stem cells is a rapidly developing area of adult stem cell research. The discovery of Lgr5(+) intestinal stem cells has enabled us to study many hidden aspects of the biology of gastrointestinal adult stem cells. Marked by Lgr5 and Troy, several novel endodermal stem cells have been identified in the gastrointestinal tract. A precise working model of stem cell propagation, dynamics, and plasticity has been revealed by a genetic labeling method, termed lineage tracing. This chapter introduces the reidentification of crypt base columnar cells as Lgr5(+) stem cells in the intestine. Subsequently, it will discuss dynamic clonal evolution and cellular plasticity in the intestinal stem cell zone, as well as in stem cell zones of stomach glands.","authors":"Fink, J., Koo, BK.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Adv Exp Med Biol","volume":"908","issue":null,"page":"11-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20147240","title":"Generation of transgenic axolotls (Ambystoma mexicanum).","abstract":null,"authors":"Khattak, S., Richter, T., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cold Spring Harb Protoc","volume":"2009","issue":"8","page":"pdb.prot5264","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10811620","title":"Transcriptional repression by Pax5 (BSAP) through interaction with corepressors of the Groucho family.","abstract":"Pax5 (BSAP) functions as both a transcriptional activator and repressor during midbrain patterning, B-cell development and lymphomagenesis. Here we demonstrate that Pax5 exerts its repression function by recruiting members of the Groucho corepressor family. In a yeast two-hybrid screen, the groucho-related gene product Grg4 was identified as a Pax5 partner protein. Both proteins interact cooperatively via two separate domains: the N-terminal Q and central SP regions of Grg4, and the octapeptide motif and C-terminal transactivation domain of Pax5. The phosphorylation state of Grg4 is altered in vivo upon Pax5 binding. Moreover, Grg4 efficiently represses the transcriptional activity of Pax5 in an octapeptide-dependent manner. Similar protein interactions resulting in transcriptional repression were also observed between distantly related members of both the Pax2\/5\/8 and Groucho protein families. In agreement with this evolutionary conservation, the octapeptide motif of Pax proteins functions as a Groucho-dependent repression domain in Drosophila embryos. These data indicate that Pax proteins can be converted from transcriptional activators to repressors through interaction with corepressors of the Groucho protein family.","authors":"Eberhard, D., Jim\u00e9nez, G., Heavey, B., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"EMBO J","volume":"19","issue":"10","page":"2292-303","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2000-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15322556","title":"The anaphase promoting complex\/cyclosome is recruited to centromeres by the spindle assembly checkpoint.","abstract":"The anaphase promoting complex\/cyclosome (APC\/C) is crucial to the control of cell division (for a review, see ref. 1). It is a multi-subunit ubiquitin ligase that, at defined points during mitosis, targets specific proteins for proteasomal degradation. The APC\/C is itself regulated by the spindle or kinetochore checkpoint, which has an important role in maintaining genomic stability by preventing sister chromatid separation until all chromosomes are correctly aligned on the mitotic spindle. The spindle checkpoint regulates the APC\/C by inactivating Cdc20, an important co-activator of the APC\/C. There is also evidence to indicate that the spindle checkpoint components and Cdc20 are spatially regulated by the mitotic apparatus, in particular they are recruited to improperly attached kinetochores. Here, we show that the APC\/C itself co-localizes with components of the spindle checkpoint to improperly attached kinetochores. Indeed, we provide evidence that the spindle checkpoint machinery is required to recruit the APC\/C to kinetochores. Our data indicate that the APC\/C could be regulated directly by the spindle checkpoint.","authors":"Acquaviva, C., Herzog, F., Kraft, C., Pines, J.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nat Cell Biol","volume":"6","issue":"9","page":"892-8","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27799150","title":"Rapid movement and transcriptional re-localization of human cohesin on DNA.","abstract":"The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring-shaped protein complexes that are thought to function by entrapping DNA It has been proposed that cohesin is recruited to specific genomic locations from distal loading sites by an unknown mechanism, which depends on transcription, and it has been speculated that cohesin movements along DNA could create three-dimensional genomic organization by loop extrusion. However, whether cohesin can translocate along DNA is unknown. Here, we used single-molecule imaging to show that cohesin can diffuse rapidly on DNA in a manner consistent with topological entrapment and can pass over some DNA-bound proteins and nucleosomes but is constrained in its movement by transcription and DNA-bound CCCTC-binding factor (CTCF). These results indicate that cohesin can be positioned in the genome by moving along DNA, that transcription can provide directionality to these movements, that CTCF functions as a boundary element for moving cohesin, and they are consistent with the hypothesis that cohesin spatially organizes the genome via loop extrusion.","authors":"Davidson, IF., Goetz, D., Zaczek, MP., Molodtsov, MI., Huis In 't Veld, PJ., Weissmann, F., Litos, G., Cisneros, DA., Ocampo-Hafalla, M., Ladurner, R., Uhlmann, F., Vaziri, A., Peters, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"EMBO J","volume":"35","issue":"24","page":"2671-2685","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15315937","title":"Hypoxic induction of Ctgf is directly mediated by Hif-1.","abstract":"CTGF plays a significant role in the development of renal fibrosis by mediating the fibrotic effects of transforming growth factor (TGF)-beta(1) and has been shown to be hypoxia inducible in human breast cancer cells. It has been suggested that hypoxia is an important underlying cause for the development of renal fibrosis through the modulation of profibrotic genes. One of the key mediators of the cell's response to lowered oxygen environments is hypoxia-inducible-factor-1 (HIF-1), a basic helix-loop-helix transcription factor, which enables cells to adapt to hypoxia by regulating the expression of genes involved in increasing oxygen availability (VEGF, erythropoietin) and enhancing glucose uptake and metabolism (Glut-1, PGK). In this paper, we have used primary tubular epithelial cell cultures from a tetracycline-inducible-Hif-1alpha knockout murine model to further elucidate the role of Hif-1 in the hypoxic-induction of Ctgf expression. We show that hypoxia response elements present upstream of Ctgf enable direct interaction of Hif-1 transcription factor with the Ctgf promoter, resulting in increased transcription of Ctgf mRNA. Cells deficient in Hif-1alpha were incapable of inducing Ctgf mRNA in response to hypoxia, suggesting an absolute requirement of Hif-1. Furthermore, the observed Hif-1-mediated hypoxic stimulation of Ctgf expression was found to occur independently of TGF-beta(1) signaling. Our findings have important implications for a number of fibrotic disorders in which hypoxia, CTGF, and TGF-beta(1) are involved, including renal, dermal, hepatic, and pulmonary fibrosis.","authors":"Higgins, DF., Biju, MP., Akai, Y., Wutz, A., Johnson, RS., Haase, VH.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Am J Physiol Renal Physiol","volume":"287","issue":"6","page":"F1223-32","pdf":null,"JrId":"21625","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20147239","title":"Axolotl (Ambystoma mexicanum) in vitro fertilization.","abstract":null,"authors":"Khattak, S., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cold Spring Harb Protoc","volume":"2009","issue":"8","page":"pdb.prot5263","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27013243","title":"Retrotransposon derepression leads to activation of the unfolded protein response and apoptosis in pro-B cells.","abstract":"The H3K9me3-specific histone methyltransferase Setdb1 impacts on transcriptional regulation by repressing both developmental genes and retrotransposons. How impaired retrotransposon silencing may lead to developmental phenotypes is currently unclear. Here, we show that loss of Setdb1 in pro-B cells completely abrogates B cell development. In pro-B cells, Setdb1 is dispensable for silencing of lineage-inappropriate developmental genes. Instead, we detect strong derepression of endogenous murine leukemia virus (MLV) copies. This activation coincides with an unusual change in chromatin structure, with only partial loss of H3K9me3 and unchanged DNA methylation, but strongly increased H3K4me3. Production of MLV proteins leads to activation of the unfolded protein response pathway and apoptosis. Thus, our data demonstrate that B cell development depends on the proper repression of retrotransposon sequences through Setdb1.","authors":"Pasquarella, A., Ebert, A., Pereira de Almeida, G., Hinterberger, M., Kazerani, M., Nuber, A., Ellwart, J., Klein, L., Busslinger, M., Schotta, G.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Development","volume":"143","issue":"10","page":"1788-99","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27560176","title":"Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation.","abstract":"Adult somatic tissues have proven difficult to expand in vitro, largely because of the complexity of recreating appropriate environmental signals in culture. We have overcome this problem recently and developed culture conditions for adult stem cells that allow the long-term expansion of adult primary tissues from small intestine, stomach, liver and pancreas into self-assembling 3D structures that we have termed 'organoids'. We provide a detailed protocol that describes how to grow adult mouse and human liver and pancreas organoids, from cell isolation and long-term expansion to genetic manipulation in vitro. Liver and pancreas cells grow in a gel-based extracellular matrix (ECM) and a defined medium. The cells can self-organize into organoids that self-renew in vitro while retaining their tissue-of-origin commitment, genetic stability and potential to differentiate into functional cells in vitro (hepatocytes) and in vivo (hepatocytes and endocrine cells). Genetic modification of these organoids opens up avenues for the manipulation of adult stem cells in vitro, which could facilitate the study of human biology and allow gene correction for regenerative medicine purposes. The complete protocol takes 1-4 weeks to generate self-renewing 3D organoids and to perform genetic manipulation experiments. Personnel with basic scientific training can conduct this protocol.","authors":"Broutier, L., Andersson-Rolf, A., Hindley, CJ., Boj, SF., Clevers, H., Koo, BK., Huch, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Protoc","volume":"11","issue":"9","page":"1724-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26634741","title":"Adult stem cell lineage tracing and deep tissue imaging.","abstract":"Lineage tracing is a widely used method for understanding cellular dynamics in multicellular organisms during processes such as development, adult tissue maintenance, injury repair and tumorigenesis. Advances in tracing or tracking methods, from light microscopy-based live cell tracking to fluorescent label-tracing with two-photon microscopy, together with emerging tissue clearing strategies and intravital imaging approaches have enabled scientists to decipher adult stem and progenitor cell properties in various tissues and in a wide variety of biological processes. Although technical advances have enabled time-controlled genetic labeling and simultaneous live imaging, a number of obstacles still need to be overcome. In this review, we aim to provide an in-depth description of the traditional use of lineage tracing as well as current strategies and upcoming new methods of labeling and imaging.","authors":"Fink, J., Andersson-Rolf, A., Koo, BK.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"BMB Rep","volume":"48","issue":"12","page":"655-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25429058","title":"Genetically corrected iPSCs as cell therapy for recessive dystrophic epidermolysis bullosa.","abstract":"Recessive dystrophic epidermolysis bullosa (RDEB) is caused by mutations in the gene encoding type VII collagen, resulting in fragile skin and mucous membranes that blister easily in response to mechanical stress. Induced pluripotent stem cells (iPSCs) carry the potential to fundamentally change cell-based therapies for human diseases, in particular for RDEB, for which no effective treatments are available. To provide proof of principle on the applicability of iPSCs for the treatment of RDEB, we developed iPSCs from type VII collagen (Col7a1) mutant mice that exhibited skin fragility and blistering resembling human RDEB. Genetically repaired iPSCs could be differentiated into functional fibroblasts that reexpressed and secreted type VII collagen. Corrected iPSC-derived fibroblasts did not form tumors in vivo and could be traced up to 16 weeks after intradermal injection. Moreover, iPSC-based cell therapy resulted in faithful and long-term restoration of type VII collagen deposition at the epidermal-dermal junction of Col7a1 mutant mice. Intradermal injection of genetically repaired iPSC-derived fibroblasts restored the mechanical resistance to skin blistering in mice with RDEB, suggesting that RDEB skin could be effectively and safely repaired using iPSC-based cell therapy.","authors":"Wenzel, D., Bayerl, J., Nystr\u00f6m, A., Bruckner-Tuderman, L., Meixner, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Sci Transl Med","volume":"6","issue":"264","page":"264ra165","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20147230","title":"Ambystoma mexicanum, the axolotl: a versatile amphibian model for regeneration, development, and evolution studies.","abstract":null,"authors":"Voss, SR., Epperlein, HH., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cold Spring Harb Protoc","volume":"2009","issue":"8","page":"pdb.emo128","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25158095","title":"The PHD finger of p300 influences its ability to acetylate histone and non-histone targets.","abstract":"In enzymes that regulate chromatin structure, the combinatorial occurrence of modules that alter and recognise histone modifications is a recurrent feature. In this study, we explored the functional relationship between the acetyltransferase domain and the adjacent bromodomain\/PHD finger (bromo\/PHD) region of the transcriptional coactivator p300. We found that the bromo\/PHD region of p300 can bind to the acetylated catalytic domain in vitro and augment the catalytic activity of the enzyme. Deletion of the PHD finger, but not the bromodomain, impaired the ability of the enzyme to acetylate histones in vivo, whilst it enhanced p300 self-acetylation. A point mutation in the p300 PHD finger that is related to the Rubinstein-Taybi syndrome resulted in increased self-acetylation but retained the ability to acetylate histones. Hence, the PHD finger appears to negatively regulate self-acetylation. Furthermore, our data suggest that the PHD finger has a role in the recruitment of p300 to chromatin.","authors":"Rack, JGM., Lutter, T., Kj\u00e6reng Bjerga, GE., Guder, C., Ehrhardt, C., V\u00e4rv, S., Ziegler, M., Aasland, R.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Mol Biol","volume":"426","issue":"24","page":"3960-3972","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15292238","title":"Role of regulator of G protein signaling 2 (RGS2) in Ca(2+) oscillations and adaptation of Ca(2+) signaling to reduce excitability of RGS2-\/- cells.","abstract":"Regulators of G protein signaling (RGS) proteins accelerate the GTPase activity of Galpha subunits to determine the duration of the stimulated state and control G protein-coupled receptor-mediated cell signaling. RGS2 is an RGS protein that shows preference toward Galpha(q). To better understand the role of RGS2 in Ca(2+) signaling and Ca(2+) oscillations, we characterized Ca(2+) signaling in cells derived from RGS2(-\/-) mice. Deletion of RGS2 modified the kinetic of inositol 1,4,5-trisphosphate (IP(3)) production without affecting the peak level of IP(3), but rather increased the steady-state level of IP(3) at all agonist concentrations. The increased steady-state level of IP(3) led to an increased frequency of [Ca(2+)](i) oscillations. The cells were adapted to deletion of RGS2 by reducing Ca(2+) signaling excitability. Reduced excitability was achieved by adaptation of all transporters to reduce Ca(2+) influx into the cytosol. Thus, IP(3) receptor 1 was down-regulated and IP(3) receptor 3 was up-regulated in RGS2(-\/-) cells to reduce the sensitivity for IP(3) to release Ca(2+) from the endoplasmic reticulum to the cytosol. Sarco\/endoplasmic reticulum Ca(2+) ATPase 2b was up-regulated to more rapidly remove Ca(2+) from the cytosol of RGS2(-\/-) cells. Agonist-stimulated Ca(2+) influx was reduced, and Ca(2+) efflux by plasma membrane Ca(2+) was up-regulated in RGS2(-\/-) cells. The result of these adaptive mechanisms was the reduced excitability of Ca(2+) signaling, as reflected by the markedly reduced response of RGS2(-\/-) cells to changes in the endoplasmic reticulum Ca(2+) load and to an increase in extracellular Ca(2+). These findings highlight the central role of RGS proteins in [Ca(2+)](i) oscillations and reveal a prominent plasticity and adaptability of the Ca(2+) signaling apparatus.","authors":"Wang, X., Huang, G., Luo, X., Penninger, JM., Muallem, S.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Biol Chem","volume":"279","issue":"40","page":"41642-9","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2004-11-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27043818","title":"Correction to \"Comprehensive Cross-Linking Mass Spectrometry Reveals Parallel Orientation and Flexible Conformations of Plant HOP2-MND1\".","abstract":null,"authors":"Rampler, E., Stranzl, T., Orban-Nemeth, Z., Hollenstein, DM., Hudecz, O., Schl\u00f6gelhofer, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Proteome Res","volume":"15","issue":"5","page":"1732","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26224885","title":"ACE2 Deficiency Worsens Epicardial Adipose Tissue Inflammation and Cardiac Dysfunction in Response to Diet-Induced Obesity.","abstract":"Obesity is increasing in prevalence and is strongly associated with metabolic and cardiovascular disorders. The renin-angiotensin system (RAS) has emerged as a key pathogenic mechanism for these disorders; angiotensin (Ang)-converting enzyme 2 (ACE2) negatively regulates RAS by metabolizing Ang II into Ang 1-7. We studied the role of ACE2 in obesity-mediated cardiac dysfunction. ACE2 null (ACE2KO) and wild-type (WT) mice were fed a high-fat diet (HFD) or a control diet and studied at 6 months of age. Loss of ACE2 resulted in decreased weight gain but increased glucose intolerance, epicardial adipose tissue (EAT) inflammation, and polarization of macrophages into a proinflammatory phenotype in response to HFD. Similarly, human EAT in patients with obesity and heart failure displayed a proinflammatory macrophage phenotype. Exacerbated EAT inflammation in ACE2KO-HFD mice was associated with decreased myocardial adiponectin, decreased phosphorylation of AMPK, increased cardiac steatosis and lipotoxicity, and myocardial insulin resistance, which worsened heart function. Ang 1-7 (24 \u00b5g\/kg\/h) administered to ACE2KO-HFD mice resulted in ameliorated EAT inflammation and reduced cardiac steatosis and lipotoxicity, resulting in normalization of heart failure. In conclusion, ACE2 plays a novel role in heart disease associated with obesity wherein ACE2 negatively regulates obesity-induced EAT inflammation and cardiac insulin resistance.","authors":"Patel, VB., Mori, J., McLean, BA., Basu, R., Das, SK., Ramprasath, T., Parajuli, N., Penninger, JM., Grant, MB., Lopaschuk, GD., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Diabetes","volume":"65","issue":"1","page":"85-95","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31932776","title":"MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells.","abstract":"The ultimate goal of biological super-resolution fluorescence microscopy is to provide three-dimensional resolution at the size scale of a fluorescent marker. Here we show that by localizing individual switchable fluorophores with a probing donut-shaped excitation beam, MINFLUX nanoscopy can provide resolutions in the range of 1 to 3\u2009nm for structures in fixed and living cells. This progress has been facilitated by approaching each fluorophore iteratively with the probing-donut minimum, making the resolution essentially uniform and isotropic over scalable fields of view. MINFLUX imaging of nuclear pore complexes of a mammalian cell shows that this true nanometer-scale resolution is obtained in three dimensions and in two color channels. Relying on fewer detected photons than standard camera-based localization, MINFLUX nanoscopy is poised to open a new chapter in the imaging of protein complexes and distributions in fixed and living cells.","authors":"Gwosch, KC., Pape, JK., Balzarotti, F., Hoess, P., Ellenberg, J., Ries, J., Hell, SW.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Methods","volume":"17","issue":"2","page":"217-224","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27165551","title":"You Are What You Eat: Linking Metabolic Asymmetry and Cell Fate Choice.","abstract":"To defend against pathogens, activated immune cells must rapidly produce diverse lymphocyte subtypes. In a recent report in Nature, Verbist et\u00a0al. (2016) describe how a regulatory loop acting between metabolic and transcriptional programs, centered around the asymmetric cell division machinery and the proto-oncogene c-Myc, establishes distinct T\u00a0cell fates.","authors":"Landskron, L., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Dev Cell","volume":"37","issue":"3","page":"206-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19763104","title":"Considering the evolution of regeneration in the central nervous system.","abstract":"For many years the mammalian CNS has been seen as an organ that is unable to regenerate. However, it was also long known that lower vertebrate species are capable of impressive regeneration of CNS structures. How did this situation arise through evolution? Increasing cellular and molecular understanding of regeneration in different animal species coupled with studies of adult neurogenesis in mammals is providing a basis for addressing this question. Here we compare CNS regeneration among vertebrates and speculate on how this ability may have emerged or been restricted.","authors":"Tanaka, EM., Ferretti, P.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Rev Neurosci","volume":"10","issue":"10","page":"713-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33002421","title":"Combinatorial Action of Temporally Segregated Transcription Factors.","abstract":"Combinatorial action of transcription factors (TFs) with partially overlapping expression is a widespread strategy to generate novel gene-expression patterns and, thus, cellular diversity. Known mechanisms underlying combinatorial activity require co-expression of TFs within the same cell. Here, we describe the mechanism by which two TFs that are never co-expressed generate a new, intersectional expression pattern in C.\u00a0elegans embryos: lineage-specific priming of a gene by a transiently expressed TF generates a unique intersection with a second TF acting on the same gene four cell divisions later; the second TF is expressed in multiple cells but only activates transcription in those where priming occurred. Early induction of active transcription is necessary and sufficient to establish a competent state, maintained by broadly expressed regulators in the absence of the initial trigger. We uncover additional cells diversified through this mechanism. Our findings define a mechanism for combinatorial TF activity with important implications for generation of cell-type diversity.","authors":"Charest, J., Daniele, T., Wang, J., Bykov, A., Mandlbauer, A., Asparuhova, M., R\u00f6hsner, J., Guti\u00e9rrez-P\u00e9rez, P., Cochella, L.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Dev Cell","volume":"55","issue":"4","page":"483-499.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15282614","title":"Cell cycle regulation of central spindle assembly.","abstract":"The bipolar mitotic spindle is responsible for segregating sister chromatids at anaphase. Microtubule motor proteins generate spindle bipolarity and enable the spindle to perform mechanical work. A major change in spindle architecture occurs at anaphase onset when central spindle assembly begins. This structure regulates the initiation of cytokinesis and is essential for its completion. Central spindle assembly requires the centralspindlin complex composed of the Caenorhabditis elegans ZEN-4 (mammalian orthologue MKLP1) kinesin-like protein and the Rho family GAP CYK-4 (MgcRacGAP). Here we describe a regulatory mechanism that controls the timing of central spindle assembly. The mitotic kinase Cdk1\/cyclin B phosphorylates the motor domain of ZEN-4 on a conserved site within a basic amino-terminal extension characteristic of the MKLP1 subfamily. Phosphorylation by Cdk1 diminishes the motor activity of ZEN-4 by reducing its affinity for microtubules. Preventing Cdk1 phosphorylation of ZEN-4\/MKLP1 causes enhanced metaphase spindle localization and defects in chromosome segregation. Thus, phosphoregulation of the motor domain of MKLP1 kinesin ensures that central spindle assembly occurs at the appropriate time in the cell cycle and maintains genomic stability.","authors":"Mishima, M., Pavicic, V., Gr\u00fcneberg, U., Nigg, EA., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nature","volume":"430","issue":"7002","page":"908-13","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26780092","title":"Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.","abstract":"The transcriptional state of a cell reflects a variety of biological factors, from cell-type-specific features to transient processes such as the cell cycle, all of which may be of interest. However, identifying such aspects from noisy single-cell RNA-seq data remains challenging. We developed pathway and gene set overdispersion analysis (PAGODA) to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.","authors":"Fan, J., Salathia, N., Liu, R., Kaeser, GE., Yung, YC., Herman, JL., Kaper, F., Fan, JB., Zhang, K., Chun, J., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Methods","volume":"13","issue":"3","page":"241-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-06","doi":"10.1038\/nmeth.3734","first_author":"Fan, J.","corresponding_authors":"Kharchenko, PV."},{"pmid":"26795246","title":"The Helix-Loop-Helix Protein ID2 Governs NK Cell Fate by Tuning Their Sensitivity to Interleukin-15.","abstract":"The inhibitor of DNA binding 2 (Id2) is essential for natural killer (NK) cell development with its canonical role being to antagonize E-protein function and alternate lineage fate. Here we have identified a key role for Id2 in regulating interleukin-15 (IL-15) receptor signaling and homeostasis of NK cells by repressing multiple E-protein target genes including Socs3. Id2 deletion in mature NK cells was incompatible with their homeostasis due to impaired IL-15 receptor signaling and metabolic function and this could be rescued by strong IL-15 receptor stimulation or genetic ablation of Socs3. During NK cell maturation, we observed an inverse correlation between E-protein target genes and Id2. These results shift the current paradigm on the role of ID2, indicating that it is required not only to antagonize E-proteins during NK cell commitment, but constantly required to titrate E-protein activity to regulate NK cell fitness and responsiveness to IL-15.","authors":"Delconte, RB., Shi, W., Sathe, P., Ushiki, T., Seillet, C., Minnich, M., Kolesnik, TB., Rankin, LC., Mielke, LA., Zhang, JG., Busslinger, M., Smyth, MJ., Hutchinson, DS., Nutt, SL., Nicholson, SE., Alexander, WS., Corcoran, LM., Vivier, E., Belz, GT., Carotta, S., Huntington, ND.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Immunity","volume":"44","issue":"1","page":"103-115","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15271649","title":"Phosphatidylinositol 3-kinase regulates Ca2+ signaling in pancreatic acinar cells through inhibition of sarco(endo)plasmic reticulum Ca2+-ATPase.","abstract":"Calcium is a key mediator of hormone-induced enzyme secretion in pancreatic acinar cells. At the same time, abnormal Ca(2+) responses are associated with pancreatitis. We have recently shown that inhibition of phosphatidylinositol 3-kinase (PI3-kinase) by LY-294002 and wortmannin, as well as genetic deletion of PI3-kinase-gamma, regulates Ca(2+) responses and the Ca(2+)-sensitive trypsinogen activation in pancreatic acinar cells. The present study sought to determine the mechanisms of PI3-kinase involvement in Ca(2+) responses induced in these cells by CCK and carbachol. The PI3-kinase inhibitors inhibited both Ca(2+) influx and mobilization from intracellular stores induced by stimulation of acini with physiological and pathological concentrations of CCK, as well as with carbachol. PI3-kinase inhibition facilitated the decay of cytosolic free Ca(2+) concentration ([Ca(2+)](i)) oscillations observed in individual acinar cells. The PI3-kinase inhibitors decreased neither CCK-induced inositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)] production nor Ins(1,4,5)P(3)-induced Ca(2+) mobilization, suggesting that the effect of PI3-kinase inhibition is not through Ins(1,4,5)P(3) or Ins(1,4,5)P(3) receptors. PI3-kinase inhibition did not affect Ca(2+) mobilization induced by thapsigargin, a specific inhibitor of sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA). Moreover, SERCA blockade with thapsigargin abolished the effects of pharmacological and genetic PI3-kinase inhibition on [Ca(2+)](i) signals, suggesting SERCA as a downstream target of PI3-kinase. Both pharmacological PI3-kinase inhibition and genetic deletion of PI3-kinase-gamma increased the amount of Ca(2+) in intracellular stores during CCK stimulation. Finally, addition of the PI3-kinase product phosphatidylinositol 3,4,5-trisphosphate to permeabilized acini significantly attenuated Ca(2+) reloading into the endoplasmic reticulum. The results indicate that PI3-kinase regulates Ca(2+) signaling in pancreatic acinar cells through its inhibitory effect on SERCA.","authors":"Fischer, L., Gukovskaya, AS., Young, SH., Gukovsky, I., Lugea, A., Buechler, P., Penninger, JM., Friess, H., Pandol, SJ.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Am J Physiol Gastrointest Liver Physiol","volume":"287","issue":"6","page":"G1200-12","pdf":null,"JrId":"21621","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15263099","title":"Crystal structure of the p14\/MP1 scaffolding complex: how a twin couple attaches mitogen-activated protein kinase signaling to late endosomes.","abstract":"Signaling pathways in eukaryotic cells are often controlled by the formation of specific signaling complexes, which are coordinated by scaffold and adaptor proteins. Elucidating their molecular architecture is essential to understand the spatial and temporal regulation of cellular signaling. p14 and MP1 form a tight (K(d) = 12.8 nM) endosomal adaptor\/scaffold complex, which regulates mitogen-activated protein kinase (MAPK) signaling. Here, we present the 1.9-A crystal structure of a biologically functional p14\/MP1 complex. The overall topology of the individual MP1 and p14 proteins is almost identical, having a central five-stranded beta-sheet sandwiched between a two-helix and a one-helix layer. Formation of the p14\/MP1 heterodimer proceeds by beta-sheet augmentation and yields a unique, almost symmetrical, complex with several potential protein-binding sites on its surface. Mutational analysis allowed identification of the p14 endosomal adaptor motif, which seems to orient the complex relative to the endosomal membrane. Two highly conserved and hydrophobic protein-binding sites are located on the opposite \"cytoplasmic\" face of the p14\/MP1 heterodimer and might therefore function as docking sites for the target proteins extracellular regulated kinase (ERK) 1 and MAPK\/ERK kinase 1. Furthermore, detailed sequence analyses revealed that MP1\/p14, together with profilins, define a protein superfamily of small subcellular adaptor proteins, named ProflAP. Taken together, the presented work provides insight into the spatial regulation of MAPK signaling, illustrating how p14 and MP1 collaborate as an endosomal adaptor\/scaffold complex.","authors":"Kurzbauer, R., Teis, D., de Araujo, ME., Maurer-Stroh, S., Eisenhaber, F., Bourenkov, GP., Bartunik, HD., Hekman, M., Rapp, UR., Huber, LA., Clausen, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Proc Natl Acad Sci U S A","volume":"101","issue":"30","page":"10984-9","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520245","title":"\u03b2-globin matrix attachment region improves stable genomic expression of the Sleeping Beauty transposon.","abstract":"The liver is an attractive target for gene therapy due to its extensive capability for protein production and the numerous diseases resulting from a loss of gene function it normally provides. The Sleeping Beauty Transposon (SB-Tn)(1) system is a non-viral vector capable of delivering and mediating therapeutic transgene(s) insertion into the host genome for long-term expression. A current challenge for this system is the low efficiency of integration of the transgene. In this study we use a human hepatoma cell line (HuH-7) and primary human blood outgrowth endothelial cells (BOECs) to test vectors containing DNA elements to enhance transposition without integrating themselves. We employed the human \u03b2-globin matrix attachment region (MAR) and the Simian virus 40 (SV40) nuclear translocation signal to increase the percent of HuH-7 cells persistently expressing a GFP::Zeo reporter construct by \u223c50% for each element; while combining both did not show an additive effect. Interestingly, both elements together displayed an additive effect on the number of insertion sites, and in BOECs the SV40 alone appeared to have an inhibitory effect on transposition. In long-term cultures the loss of plasmid DNA, transposase expression and mapping of insertion sites demonstrated bona fide transposition without episomal expression. These results show that addition of the \u03b2-globin MAR and potentially other elements to the backbone of SB-Tn system can enhance transposition and expression of therapeutic transgenes. These findings may have a significant influence on the use of SB transgene delivery to liver for the treatment of a wide variety of disorders.","authors":"Sjeklocha, L., Chen, Y., Daly, MC., Steer, CJ., Kren, BT.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Cell Biochem","volume":"112","issue":"9","page":"2361-2375","pdf":null,"JrId":"4590","fulltextlink":null,"preprintlink":null,"articledate":"2011-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26657283","title":"Polysialylation controls dendritic cell trafficking by regulating chemokine recognition.","abstract":"The addition of polysialic acid to N- and\/or O-linked glycans, referred to as polysialylation, is a rare posttranslational modification that is mainly known to control the developmental plasticity of the nervous system. Here we show that CCR7, the central chemokine receptor controlling immune cell trafficking to secondary lymphatic organs, carries polysialic acid. This modification is essential for the recognition of the CCR7 ligand CCL21. As a consequence, dendritic cell trafficking is abrogated in polysialyltransferase-deficient mice, manifesting as disturbed lymph node homeostasis and unresponsiveness to inflammatory stimuli. Structure-function analysis of chemokine-receptor interactions reveals that CCL21 adopts an autoinhibited conformation, which is released upon interaction with polysialic acid. Thus, we describe a glycosylation-mediated immune cell trafficking disorder and its mechanistic basis.","authors":"Kiermaier, E., Moussion, C., Veldkamp, CT., Gerardy-Schahn, R., de Vries, I., Williams, LG., Chaffee, GR., Phillips, AJ., Freiberger, F., Imre, R., Taleski, D., Payne, RJ., Braun, A., F\u00f6rster, R., Mechtler, K., M\u00fchlenhoff, M., Volkman, BF., Sixt, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Science","volume":"351","issue":"6269","page":"186-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15247270","title":"Translational control of putative protooncogene Nm23-M2 by cytokines via phosphoinositide 3-kinase signaling.","abstract":"The expansion and differentiation of hematopoietic progenitors is regulated by cytokine and growth factor signaling. To examine how signal transduction controls the gene expression program required for progenitor expansion, we screened ATLAS filters with polysome-associated mRNA derived from erythroid progenitors stimulated with erythropoietin and\/or stem cell factor. The putative proto-oncogene nucleoside diphosphate kinase B (ndpk-B or nm23-M2) was identified as an erythropoietin and stem cell factor target gene. Factor-induced expression of nm23-M2 was regulated specifically at the level of polysome association by a phosphoinositide 3-kinase-dependent mechanism. Identification of the transcription initiation site revealed that nm23-M2 mRNA starts with a terminal oligopyrimidine sequence, which is known to render mRNA translation dependent on mitogenic factors. Recently, the nm23-M2 locus was identified as a common leukemia retrovirus integration site, suggesting that it plays a role in leukemia development. The expression of Nm23 from a retroviral vector in the absence of its 5'-untranslated region caused constitutive polysome association of nm23-M2. Polysome-association and protein expression of endogenous nm23-M2 declined during differentiation of erythroid progenitors, suggesting a role for Nm23-M2 in progenitor expansion. Taken together, nm23-m2 exemplifies that cytokine-dependent control of translation initiation is an important mechanism of gene expression regulation.","authors":"Joosten, M., Bl\u00e1zquez-Domingo, M., Lindeboom, F., Boulm\u00e9, F., Van Hoven-Beijen, A., Habermann, B., L\u00f6wenberg, B., Beug, H., M\u00fcllner, EW., Delwel, R., Von Lindern, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Biol Chem","volume":"279","issue":"37","page":"38169-76","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31092928","title":"Transcriptional cofactors display specificity for distinct types of core promoters.","abstract":"Transcriptional cofactors (COFs) communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression<sup>1<\/sup>. Although some COFs have been shown to prefer certain promoter types<sup>2-5<\/sup> over others (for example, see\u00a0refs <sup>6,7<\/sup>), the extent to which different COFs display intrinsic specificities for distinct promoters is unclear. Here we use a high-throughput promoter-activity assay in Drosophila melanogaster S2 cells to screen 23 COFs for their ability to activate 72,000 candidate core promoters (CPs). We observe differential activation of CPs, indicating distinct regulatory preferences or 'compatibilities'<sup>8,9<\/sup> between COFs and specific types of CPs. These functionally distinct CP types are differentially enriched for known sequence elements<sup>2,4<\/sup>, such as the TATA box, downstream promoter element (DPE) or TCT motif, and display distinct chromatin properties at endogenous loci. Notably, the CP types differ in their relative abundance of H3K4me3 and H3K4me1 marks (see also refs <sup>10-12<\/sup>), suggesting that these histone modifications might distinguish trans-regulatory factors rather than promoter- versus enhancer-type cis-regulatory elements. We confirm the existence of distinct COF-CP compatibilities in two additional Drosophila cell lines and in human cells, for which we find COFs that prefer TATA-box or CpG-island promoters, respectively. Distinct compatibilities between COFs and promoters can explain how different enhancers specifically activate distinct sets of genes<sup>9<\/sup>, alternative promoters within the same genes, and distinct transcription start sites within the same promoter<sup>13<\/sup>. Thus, COF-promoter compatibilities may underlie distinct transcriptional programs in species as divergent as flies and humans.","authors":"Haberle, V., Arnold, CD., Pagani, M., Rath, M., Schernhuber, K., Stark, A.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nature","volume":"570","issue":"7759","page":"122-126","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32694680","title":"Author Correction: Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signalling.","abstract":"An amendment to this paper has been published and can be accessed via a link at the top of the paper.","authors":"Finger, F., Ottens, F., Springhorn, A., Drexel, T., Proksch, L., Metz, S., Cochella, L., Hoppe, T.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Metab","volume":"2","issue":"1","page":"126","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-00-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26903600","title":"Sororin actively maintains sister chromatid\u00a0cohesion.","abstract":"Cohesion between sister chromatids is established during DNA replication but needs to be maintained to enable proper chromosome-spindle attachments in mitosis or meiosis. Cohesion is mediated by cohesin, but also depends on cohesin acetylation and sororin. Sororin contributes to cohesion by stabilizing cohesin on DNA. Sororin achieves this by inhibiting WAPL, which otherwise releases cohesin from DNA and destroys cohesion. Here we describe mouse models which enable the controlled depletion of sororin by gene deletion or auxin-induced degradation. We show that sororin is essential for embryonic development, cohesion maintenance, and proper chromosome segregation. We further show that the acetyltransferases ESCO1 and ESCO2 are essential for stabilizing cohesin on chromatin, that their only function in this process is to acetylate cohesin's SMC3 subunit, and that DNA replication is also required for stable cohesin-chromatin interactions. Unexpectedly, we find that sororin interacts dynamically with the cohesin complexes it stabilizes. This implies that sororin recruitment to cohesin does not depend on the DNA replication machinery or process itself, but on a property that cohesin acquires during cohesion establishment.","authors":"Ladurner, R., Kreidl, E., Ivanov, MP., Ekker, H., Idarraga-Amado, MH., Busslinger, GA., Wutz, G., Cisneros, DA., Peters, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"EMBO J","volume":"35","issue":"6","page":"635-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26953350","title":"ARHGEF17 is an essential spindle assembly checkpoint factor that targets Mps1 to kinetochores.","abstract":"To prevent genome instability, mitotic exit is delayed until all chromosomes are properly attached to the mitotic spindle by the spindle assembly checkpoint (SAC). In this study, we characterized the function of ARHGEF17, identified in a genome-wide RNA interference screen for human mitosis genes. Through a series of quantitative imaging, biochemical, and biophysical experiments, we showed that ARHGEF17 is essential for SAC activity, because it is the major targeting factor that controls localization of the checkpoint kinase Mps1 to the kinetochore. This mitotic function is mediated by direct interaction of the central domain of ARHGEF17 with Mps1, which is autoregulated by the activity of Mps1 kinase, for which ARHGEF17 is a substrate. This mitosis-specific role is independent of ARHGEF17's RhoGEF activity in interphase. Our study thus assigns a new mitotic function to ARHGEF17 and reveals the molecular mechanism for a key step in SAC establishment.","authors":"Isokane, M., Walter, T., Mahen, R., Nijmeijer, B., H\u00e9rich\u00e9, JK., Miura, K., Maffini, S., Ivanov, MP., Kitajima, TS., Peters, JM., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Cell Biol","volume":"212","issue":"6","page":"647-59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30078556","title":"Self-Renewing Trophoblast Organoids Recapitulate the Developmental Program of the Early Human Placenta.","abstract":"Defective placentation is the underlying cause of various pregnancy complications, such as severe intrauterine growth restriction and preeclampsia. However, studies on human placental development are hampered by the lack of a self-renewing in\u00a0vitro model that would recapitulate formation of trophoblast progenitors and differentiated subtypes, syncytiotrophoblast (STB) and invasive extravillous trophoblast (EVT), in a 3D orientation. Hence, we established long-term expanding organoid cultures from purified first-trimester cytotrophoblasts (CTBs). Molecular analyses revealed that the CTB organoid cultures (CTB-ORGs) express markers of trophoblast stemness and proliferation and are highly similar to primary CTBs at the level of global gene expression. Whereas CTB-ORGs spontaneously generated STBs, withdrawal of factors for self-renewal induced trophoblast outgrowth, expressing the EVT progenitor marker NOTCH1, and provoked formation of adjacent, distally located HLA-G<sup>+<\/sup> EVTs. In summary, we established human CTB-ORGs that grow and differentiate under defined culture conditions, allowing future human placental disease modeling.","authors":"Haider, S., Meinhardt, G., Saleh, L., Kunihs, V., Gamperl, M., Kaindl, U., Ellinger, A., Burkard, TR., Fiala, C., Pollheimer, J., Mendjan, S., Latos, PA., Kn\u00f6fler, M.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Stem Cell Reports","volume":"11","issue":"2","page":"537-551","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520201","title":"Mitochondria-targeted ubiquinone (MitoQ) decreases ethanol-dependent micro and macro hepatosteatosis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520201<\/PMID><DateCompleted><Year>2011<\/Year><Month>09<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1527-3350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>54<\/Volume><Issue>1<\/Issue><PubDate><Year>2011<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>Hepatology (Baltimore, Md.)<\/Title><ISOAbbreviation>Hepatology<\/ISOAbbreviation><\/Journal><ArticleTitle>Mitochondria-targeted ubiquinone (MitoQ) decreases ethanol-dependent micro and macro hepatosteatosis.<\/ArticleTitle><Pagination><MedlinePgn>153-63<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/hep.24377<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Chronic alcohol-induced liver disease results in inflammation, steatosis, and increased oxidative and nitrosative damage to the mitochondrion. We hypothesized that targeting an antioxidant to the mitochondria would prevent oxidative damage and attenuate the steatosis associated with alcoholic liver disease. To test this we investigated the effects of mitochondria-targeted ubiquinone (MitoQ) (5 and 25 mg\/kg\/day for 4 weeks) in male Sprague-Dawley rats consuming ethanol using the Lieber-DeCarli diet with pair-fed controls. Hepatic steatosis, 3-nitrotyrosine (3-NT), 4-hydroxynonenal (4-HNE), hypoxia inducible factor \u03b1 (HIF1\u03b1), and the activity of the mitochondrial respiratory chain complexes were assessed. As reported previously, ethanol consumption resulted in hepatocyte ballooning, increased lipid accumulation in the form of micro and macrovesicular steatosis, and induction of cytochrome P450 2E1 (CYP2E1). MitoQ had a minor effect on the ethanol-dependent decrease in mitochondrial respiratory chain proteins and their activities; however, it did decrease hepatic steatosis in ethanol-consuming animals and prevented the ethanol-induced formation of 3-NT and 4-HNE. Interestingly, MitoQ completely blocked the increase in HIF1\u03b1 in all ethanol-fed groups, which has previously been demonstrated in cell culture models and shown to be essential in ethanol-dependent hepatosteatosis.","authors":"Chacko, BK., Srivastava, A., Johnson, MS., Benavides, GA., Chang, MJ., Ye, Y., Jhala, N., Murphy, MP., Kalyanaraman, B., Darley-Usmar, VM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Hepatology","volume":"54","issue":"1","page":"153-63","pdf":null,"JrId":"4093","fulltextlink":null,"preprintlink":null,"articledate":"2011-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520133","title":"Does the length of uvula affect the palatal implant outcome in the management of habitual snoring?","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520133<\/PMID><DateCompleted><Year>2011<\/Year><Month>06<\/Month><Day>28<\/Day><\/DateCompleted><DateRevised><Year>2011<\/Year><Month>04<\/Month><Day>26<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1531-4995<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>121<\/Volume><Issue>5<\/Issue><PubDate><Year>2011<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>The Laryngoscope<\/Title><ISOAbbreviation>Laryngoscope<\/ISOAbbreviation><\/Journal><ArticleTitle>Does the length of uvula affect the palatal implant outcome in the management of habitual snoring?<\/ArticleTitle><Pagination><MedlinePgn>1112-6<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/lary.21731<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\/HYPOTHESIS\" NlmCategory=\"OBJECTIVE\">To evaluate the impact of the uvular length on the efficacy of palatal implants in primary snoring.","authors":"Akpinar, ME., Yigit, O., Kocak, I., Altundag, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Laryngoscope","volume":"121","issue":"5","page":"1112-6","pdf":null,"JrId":"5476","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15175325","title":"Reciprocal roles of MSX2 in regulation of osteoblast and adipocyte differentiation.","abstract":"Mice deficient in the Msx2 gene manifest defects in skull ossification and a marked reduction in bone formation associated with decreases in osteoblast numbers, thus suggesting that Msx2 is involved in bone formation. However, the precise role of Msx2 during osteoblast differentiation is not fully understood. In the present study, we investigated the role of Msx2 in the regulation of osteoblast differentiation in the multipotent mesenchymal cell lines C3H10T1\/2 and C2C12 and in murine primary osteoblasts. Introduction of Msx2 induced alkaline phosphatase activity in C3H10T1\/2 and C2C12 cells and promoted the calcification of murine primary osteoblasts. This effect of Msx2 was also observed in mesenchymal cells isolated from Runx2-deficient mice. Interestingly the expression of Msx2 was induced by bone morphogenetic protein 2 treatment in Runx2-deficient mesenchymal cells. In contrast, Msx2 diminished peroxisome proliferator-activated receptor gamma (PPARgamma) expression and adipogenesis of the preadipocytic cell line 3T3-F442A. Moreover Msx2 inhibited the transcriptional activity of PPARgamma, CCAAT\/enhancer-binding protein beta (C\/EBPbeta), and C\/EBPdelta and blocked adipocyte differentiation of mesenchymal cells induced by overexpression of PPARgamma, C\/EBPalpha, C\/EBPbeta, or C\/EBPdelta. These data indicate that Msx2 promotes osteoblast differentiation independently of Runx2 and negatively regulates adipocyte differentiation through inhibition of PPARgamma and the C\/EBP family.","authors":"Ichida, F., Nishimura, R., Hata, K., Matsubara, T., Ikeda, F., Hisada, K., Yatani, H., Cao, X., Komori, T., Yamaguchi, A., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Biol Chem","volume":"279","issue":"32","page":"34015-22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27239039","title":"De Novo Mutations in DENR Disrupt Neuronal Development and Link Congenital Neurological Disorders to Faulty mRNA Translation Re-initiation.","abstract":"Disruptions to neuronal mRNA translation are hypothesized to underlie human neurodevelopmental syndromes. Notably, the mRNA translation re-initiation factor DENR is a regulator of eukaryotic translation and cell growth, but its mammalian functions are unknown. Here, we report that Denr influences the migration of murine cerebral cortical neurons in\u00a0vivo with its binding partner Mcts1, whereas perturbations to Denr impair the long-term positioning, dendritic arborization, and dendritic spine characteristics of postnatal projection neurons. We characterized de novo missense mutations in DENR (p.C37Y and p.P121L) detected in two unrelated human subjects diagnosed with brain developmental disorder to find that each variant impairs the function of DENR in mRNA translation re-initiation and disrupts the migration and terminal branching of cortical neurons in different ways. Thus, our findings link human brain disorders to impaired mRNA translation re-initiation through perturbations in DENR (OMIM: 604550) function in neurons.","authors":"Haas, MA., Ngo, L., Li, SS., Schleich, S., Qu, Z., Vanyai, HK., Cullen, HD., Cardona-Alberich, A., Gladwyn-Ng, IE., Pagnamenta, AT., Taylor, JC., Stewart, H., Kini, U., Duncan, KE., Teleman, AA., Keays, DA., Heng, JI.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Rep","volume":"15","issue":"10","page":"2251-2265","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27114510","title":"Mechanism of APC\/CCDC20 activation by mitotic phosphorylation.","abstract":"Chromosome segregation and mitotic exit are initiated by the 1.2-MDa ubiquitin ligase APC\/C (anaphase-promoting complex\/cyclosome) and its coactivator CDC20 (cell division cycle 20). To avoid chromosome missegregation, APC\/C(CDC20) activation is tightly controlled. CDC20 only associates with APC\/C in mitosis when APC\/C has become phosphorylated and is further inhibited by a mitotic checkpoint complex until all chromosomes are bioriented on the spindle. APC\/C contains 14 different types of subunits, most of which are phosphorylated in mitosis on multiple sites. However, it is unknown which of these phospho-sites enable APC\/C(CDC20) activation and by which mechanism. Here we have identified 68 evolutionarily conserved mitotic phospho-sites on human APC\/C bound to CDC20 and have used the biGBac technique to generate 47 APC\/C mutants in which either all 68 sites or subsets of them were replaced by nonphosphorylatable or phospho-mimicking residues. The characterization of these complexes in substrate ubiquitination and degradation assays indicates that phosphorylation of an N-terminal loop region in APC1 is sufficient for binding and activation of APC\/C by CDC20. Deletion of the N-terminal APC1 loop enables APC\/C(CDC20) activation in the absence of mitotic phosphorylation or phospho-mimicking mutations. These results indicate that binding of CDC20 to APC\/C is normally prevented by an autoinhibitory loop in APC1 and that its mitotic phosphorylation relieves this inhibition. The predicted location of the N-terminal APC1 loop implies that this loop controls interactions between the N-terminal domain of CDC20 and APC1 and APC8. These results reveal how APC\/C phosphorylation enables CDC20 to bind and activate the APC\/C in mitosis.","authors":"Qiao, R., Weissmann, F., Yamaguchi, M., Brown, NG., VanderLinden, R., Imre, R., Jarvis, MA., Brunner, MR., Davidson, IF., Litos, G., Haselbach, D., Mechtler, K., Stark, H., Schulman, BA., Peters, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Proc Natl Acad Sci U S A","volume":"113","issue":"19","page":"E2570-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15163312","title":"Heat shock protein 70 (Hsp70) subtype expression in neuroendocrine tissue and identification of a neuroendocrine tumour-specific Hsp70 truncation.","abstract":"In order to identify neuroendocrine tumour-specific protein expression, we generated monoclonal antibodies (mAbs) with a tumour-related reaction pattern using a human insulinoma as immunogen. One of the generated mAbs (mAb 1D4) exhibited striking immunoreactivity against various neuroendocrine tumours without staining pancreatic islets of Langerhans. Furthermore, mAb 1D4 immunostained a characteristic subtype of hypothalamic neurones. Using two-dimensional (2-D) gel electrophoresis, mAb 1D4 immunoblotting and mass spectrometry, heat shock protein 70 (Hsp70) isoforms were identified as the mAb 1D4-specific antigen. In hypothalamic tissue, the presence of two different Hsp70 isoforms (Hsp70-8 and Hsp70-1) was revealed by 2-D gel immunoblots and consecutive mass spectrometric peptide analysis. In contrast, insulinoma and other neuroendocrine tumours displayed solely Hsp70-8 expression. Moreover, the tumour-specific presence of an additional mAb 1D4 immunoreactive protein of 40 kDa was observed in eight out of eight tested neuroendocrine tumours. For this variant, exclusively, peptides derived from the C terminus excluding the 299 amino-terminal residues were detected. In cultured tumour-derived fibroblasts, expression of the truncated Hsp70-8 subtype was not present. In conclusion, we have demonstrated a neuroendocrine tumour-specific expression pattern of Hsp70 isoforms and identified an as yet unknown N-terminally truncated Hsp70-8 variant.","authors":"Zierhut, B., Mechtler, K., Gartner, W., Daneva, T., Base, W., Weissel, M., Niederle, B., Wagner, L.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Endocr Relat Cancer","volume":"11","issue":"2","page":"377-89","pdf":null,"JrId":"21439","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15170751","title":"Determining sequences and post-translational modifications of novel conotoxins in Conus victoriae using cDNA sequencing and mass spectrometry.","abstract":"A combination of cDNA cloning and detailed mass spectrometric analyses was employed to identify novel conotoxins from Conus victoriae. Eleven conotoxin sequences were determined using molecular methods: one belonging to the A superfamily (Vc1.1), six belonging to the O superfamily (Vc6.1-Vc6.6) and four members of the T superfamily (Vc5.1-Vc5.4). In order to verify the sequences and identify the post-translational modifications (excluding the disulfide connectivity) of three Conus victoriae conotoxins, vc1a, vc5a and vc6a, deduced from sequences Vc1.1, Vc5.1, and Vc6.1, respectively, liquid chromatography\/electrospray ionization ion trap mass spectrometry, matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry and nanospray ionization ion trap mass spectrometry with collisionally induced dissociation were performed on reduced and alkylated venom fractions. We report that vc1a, the native form of alpha-conotoxin Vc1.1 (an unmodified 16 amino acid residue peptide that has notable pain-relieving capabilities), includes a hydroxyproline and a gamma-carboxyglutamate residue. Conotoxin vc5a is a 10-residue peptide with two disulfide bonds and a hydroxyproline and vc6a is a 25 amino acid peptide with three disulfide bonds.","authors":"Jakubowski, JA., Keays, DA., Kelley, WP., Sandall, DW., Bingham, JP., Livett, BG., Gayler, KR., Sweedler, JV.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Mass Spectrom","volume":"39","issue":"5","page":"548-57","pdf":null,"JrId":"20380","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27411589","title":"Caloric Restriction Mimetics Enhance Anticancer Immunosurveillance.","abstract":"Caloric restriction mimetics (CRMs) mimic the biochemical effects of nutrient deprivation by reducing lysine acetylation of cellular proteins, thus triggering autophagy. Treatment with the CRM hydroxycitrate, an inhibitor of ATP citrate lyase, induced the depletion of regulatory T\u00a0cells (which dampen anticancer immunity) from autophagy-competent, but not autophagy-deficient, mutant KRAS-induced lung cancers in mice, thereby improving anticancer immunosurveillance and reducing tumor mass. Short-term fasting or treatment with several chemically unrelated autophagy-inducing CRMs, including hydroxycitrate and spermidine, improved the inhibition of tumor growth by chemotherapy in\u00a0vivo. This effect was only observed for autophagy-competent tumors, depended on the presence of T lymphocytes, and was accompanied by the depletion of regulatory T\u00a0cells from the tumor bed.","authors":"Pietrocola, F., Pol, J., Vacchelli, E., Rao, S., Enot, DP., Baracco, EE., Levesque, S., Castoldi, F., Jacquelot, N., Yamazaki, T., Senovilla, L., Marino, G., Aranda, F., Durand, S., Sica, V., Chery, A., Lachkar, S., Sigl, V., Bloy, N., Buque, A., Falzoni, S., Ryffel, B., Apetoh, L., Di Virgilio, F., Madeo, F., Maiuri, MC., Zitvogel, L., Levine, B., Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cancer Cell","volume":"30","issue":"1","page":"147-160","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31266943","title":"A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription.","abstract":"Cells maintain the balance between homeostasis and inflammation by adapting and integrating the activity of intracellular signaling cascades, including the JAK-STAT pathway. Our understanding of how a tailored switch from homeostasis to a strong receptor-dependent response is coordinated remains limited. Here, we use an integrated transcriptomic and proteomic approach to analyze transcription-factor binding, gene expression and in vivo proximity-dependent labelling of proteins in living cells under homeostatic and interferon (IFN)-induced conditions. We show that interferons (IFN) switch murine macrophages from resting-state to induced gene expression by alternating subunits of transcription factor ISGF3. Whereas preformed STAT2-IRF9 complexes control basal expression of IFN-induced genes (ISG), both type I IFN and IFN-\u03b3 cause promoter binding of a complete ISGF3 complex containing STAT1, STAT2 and IRF9. In contrast to the dogmatic view of ISGF3 formation in the cytoplasm, our results suggest a model wherein the assembly of the ISGF3 complex occurs on DNA.","authors":"Platanitis, E., Demiroz, D., Schneller, A., Fischer, K., Capelle, C., Hartl, M., Gossenreiter, T., M\u00fcller, M., Novatchkova, M., Decker, T.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"2921","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21349430","title":"The distal V(H) gene cluster of the Igh locus contains distinct regulatory elements with Pax5 transcription factor-dependent activity in pro-B cells.","abstract":"V(H)-DJ(H) recombination of the immunoglobulin heavy chain (Igh) locus is temporally and spatially controlled during early B cell development, and yet no regulatory elements other than the V(H) gene promoters have been identified throughout the entire V(H) gene cluster. Here, we discovered regulatory sequences that are interspersed in the distal V(H) gene region. These conserved repeat elements were characterized by the presence of Pax5 transcription factor-dependent active chromatin by binding of the regulators Pax5, E2A, CTCF, and Rad21, as well as by Pax5-dependent antisense transcription in pro-B cells. The Pax5-activated intergenic repeat (PAIR) elements were no longer bound by Pax5 in pre-B and B cells consistent with the loss of antisense transcription, whereas E2A and CTCF interacted with PAIR elements throughout early B cell development. The pro-B cell-specific and Pax5-dependent activity of the PAIR elements suggests that they are involved in the regulation of distal V(H)-DJ(H) recombination at the Igh locus.","authors":"Ebert, A., McManus, S., Tagoh, H., Medvedovic, J., Salvagiotto, G., Novatchkova, M., Tamir, I., Sommer, A., Jaritz, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Immunity","volume":"34","issue":"2","page":"175-87","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2011-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31296964","title":"Publisher Correction: Sequencing cell-type-specific transcriptomes with SLAM-ITseq.","abstract":"An amendment to this paper has been published and can be accessed via a link at the top of the paper.","authors":"Matsushima, W., Herzog, VA., Neumann, T., Gapp, K., Zuber, J., Ameres, SL., Miska, EA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Protoc","volume":"14","issue":"8","page":"2597","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27411010","title":"Sucralose Promotes Food Intake through NPY and a Neuronal Fasting Response.","abstract":"Non-nutritive sweeteners like sucralose are consumed by billions of people. While animal and human studies have demonstrated a link between synthetic sweetener consumption and metabolic dysregulation, the mechanisms responsible remain unknown. Here we use a diet supplemented with sucralose to investigate the long-term effects of sweet\/energy imbalance. In flies, chronic sweet\/energy imbalance promoted hyperactivity, insomnia, glucose intolerance, enhanced sweet taste perception, and a sustained increase in\u00a0food and calories consumed, effects that are reversed upon sucralose removal. Mechanistically, this response was mapped to the ancient insulin, catecholamine, and NPF\/NPY systems and the energy sensor AMPK, which together comprise a novel neuronal starvation response pathway. Interestingly, chronic sweet\/energy imbalance promoted increased food intake in mammals as well, and this also occurs through an NPY-dependent mechanism. Together, our data show that chronic consumption of a sweet\/energy imbalanced diet triggers a conserved neuronal fasting response and increases the motivation to eat.","authors":"Wang, QP., Lin, YQ., Zhang, L., Wilson, YA., Oyston, LJ., Cotterell, J., Qi, Y., Khuong, TM., Bakhshi, N., Planchenault, Y., Browman, DT., Lau, MT., Cole, TA., Wong, AC., Simpson, SJ., Cole, AR., Penninger, JM., Herzog, H., Neely, GG.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Metab","volume":"24","issue":"1","page":"75-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15137940","title":"Cdc14 phosphatase induces rDNA condensation and resolves cohesin-independent cohesion during budding yeast anaphase.","abstract":"At anaphase onset, the protease separase triggers chromosome segregation by cleaving the chromosomal cohesin complex. Here, we show that cohesin destruction in metaphase is sufficient for segregation of much of the budding yeast genome, but not of the long arm of chromosome XII that contains the rDNA repeats. rDNA in metaphase, unlike most other sequences, remains in an undercondensed and topologically entangled state. Separase, concomitantly with cleaving cohesin, activates the phosphatase Cdc14. We find that Cdc14 exerts two effects on rDNA, both mediated by the condensin complex. Lengthwise condensation of rDNA shortens the chromosome XII arm sufficiently for segregation. This condensation depends on the aurora B kinase complex. Independently of condensation, Cdc14 induces condensin-dependent resolution of cohesin-independent rDNA linkage. Cdc14-dependent sister chromatid resolution at the rDNA could introduce a temporal order to chromosome segregation.","authors":"Sullivan, M., Higuchi, T., Katis, VL., Uhlmann, F.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cell","volume":"117","issue":"4","page":"471-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27798612","title":"Fast volumetric calcium imaging across multiple cortical layers using sculpted light.","abstract":"Although whole-organism calcium imaging in small and semi-transparent animals has been demonstrated, capturing the functional dynamics of large-scale neuronal circuits in awake behaving mammals at high speed and resolution has remained one of the main frontiers in systems neuroscience. Here we present a method based on light sculpting that enables unbiased single- and dual-plane high-speed (up to 160 Hz) calcium imaging as well as in vivo volumetric calcium imaging of a mouse cortical column (0.5 mm \u00d7 0.5 mm \u00d7 0.5 mm) at single-cell resolution and fast volume rates (3-6 Hz). We achieved this by tailoring the point-spread function of our microscope to the structures of interest while maximizing the signal-to-noise ratio using a home-built fiber laser amplifier with pulses that are synchronized to the imaging voxel speed. This enabled in vivo recording of calcium dynamics of several thousand neurons across cortical layers and in the hippocampus of awake behaving mice.","authors":"Prevedel, R., Verhoef, AJ., Pern\u00eda-Andrade, AJ., Weisenburger, S., Huang, BS., N\u00f6bauer, T., Fern\u00e1ndez, A., Delcour, JE., Golshani, P., Baltuska, A., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Methods","volume":"13","issue":"12","page":"1021-1028","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27795562","title":"Loss-of-function genetic tools for animal models: cross-species and cross-platform differences.","abstract":"Our understanding of the genetic mechanisms that underlie biological processes has relied extensively on loss-of-function (LOF) analyses. LOF methods target DNA, RNA or protein to reduce or to ablate gene function. By analysing the phenotypes that are caused by these perturbations the wild-type function of genes can be elucidated. Although all LOF methods reduce gene activity, the choice of approach (for example, mutagenesis, CRISPR-based gene editing, RNA interference, morpholinos or pharmacological inhibition) can have a major effect on phenotypic outcomes. Interpretation of the LOF phenotype must take into account the biological process that is targeted by each method. The practicality and efficiency of LOF methods also vary considerably between model systems. We describe parameters for choosing the optimal combination of method and system, and for interpreting phenotypes within the constraints of each method.","authors":"Housden, BE., Muhar, M., Gemberling, M., Gersbach, CA., Stainier, DY., Seydoux, G., Mohr, SE., Zuber, J., Perrimon, N.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Rev Genet","volume":"18","issue":"1","page":"24-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26023187","title":"Porcupine inhibitor suppresses paracrine Wnt-driven growth of Rnf43;Znrf3-mutant neoplasia.","abstract":"Rnf43 (RING finger protein 43) and Znrf3 (zinc\/RING finger protein 3) (RZ) are two closely related transmembrane E3 ligases, encoded by Wnt target genes, that remove surface Wnt (wingless-int) receptors. The two genes are mutated in various human cancers. Such tumors are predicted to be hypersensitive to, yet still depend on, secreted Wnts. We previously showed that mutation of RZ in the intestine yields rapidly growing adenomas containing LGR5(+) (leucine-rich repeat-containing G-protein coupled receptor 5) stem cells and Wnt3-producing Paneth cells. We now show that removal of Paneth cells by Math1 mutation inhibits RZ(-\/-) tumor formation. Similarly, deletion of Wnt3 inhibits tumorigenesis. Treatment of mice carrying RZ(-\/-) intestinal neoplasia with a small molecule Wnt secretion inhibitor (porcupine inhibitor C59) strongly inhibited growth, whereas adjacent normal crypts remained intact. These results establish that paracrine Wnt secretion is an essential driver of RZ(-\/-) tumor growth and imply that a therapeutic window exists for the use of porcupine inhibitors for RZ-mutant cancers.","authors":"Koo, BK., van Es, JH., van den Born, M., Clevers, H.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Proc Natl Acad Sci U S A","volume":"112","issue":"24","page":"7548-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25720990","title":"The RANKL-RANK Story.","abstract":"Receptor activator of nuclear factor x03BA;B (RANK) and its ligand (RANKL) have originally been described for their key roles in bone metabolism and the immune system. Subsequently, it has been shown that the RANKL-RANK system is critical in the formation of mammary epithelia in lactating females and the thermoregulation of the central nervous system. RANKL and RANK are under the tight control of the female sex hormones estradiol and progesterone. A reduction of the circulating female sex hormones leading to an increase in RANKL-RANK signaling is the leading cause of osteoporosis in postmenopausal women. Denosumab, a human monoclonal anti-RANKL antibody, has been approved for the treatment of postmenopausal osteoporosis, where it is showing great promise. In addition, RANKL-RANK signaling also plays a critical role in other bone pathologies, bone metastasis or hormone-driven breast cancer. This review will highlight some of the functions of RANKL-RANK in bone turnover, the immune system and brain with a focus on the regulatory role of the female sex hormones.","authors":"Nagy, V., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Gerontology","volume":"61","issue":"6","page":"534-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19537854","title":"The temporomandibular joint in a rheumatoid arthritis patient after orthodontic treatment.","abstract":"A 32-year-old Japanese female patient consulted the authors' dental clinic with a 4.5-year history of rheumatoid arthritis (RA). She complained of pain during mouth opening and difficulty in eating due to masticatory dysfunction caused by an anterior open bite. Imaging showed severe erosion and flattening of both condyles. RA stabilized after pharmacological therapy and became inactive during the orthodontic therapy aimed at reconstructing an optimal occlusion capable of promoting functional repositioning of the mandible. At present, 4 years and 2 months postretention, the reconstructed occlusion remains stable, and both condyles continue to be remodeled. The distance from reference position to intercuspal position has gradually decreased throughout the 4-year posttreatment and postretention periods. Orthodontic therapy that comprehensively reconstructs occlusion and enhances the functioning of the mandible can induce remodeling of eroded condyles, even those with a history of rheumatoid arthritis.","authors":"Sasaguri, K., Ishizaki-Takeuchi, R., Kuramae, S., Tanaka, EM., Sakurai, T., Sato, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Angle Orthod","volume":"79","issue":"4","page":"804-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27694961","title":"Mutations in the HECT domain of NEDD4L lead to AKT-mTOR pathway deregulation and cause periventricular nodular heterotopia.","abstract":"Neurodevelopmental disorders with periventricular nodular heterotopia (PNH) are etiologically heterogeneous, and their genetic causes remain in many cases unknown. Here we show that missense mutations in NEDD4L mapping to the HECT domain of the encoded E3 ubiquitin ligase lead to PNH associated with toe syndactyly, cleft palate and neurodevelopmental delay. Cellular and expression data showed sensitivity of PNH-associated mutants to proteasome degradation. Moreover, an in utero electroporation approach showed that PNH-related mutants and excess wild-type NEDD4L affect neurogenesis, neuronal positioning and terminal translocation. Further investigations, including rapamycin-based experiments, found differential deregulation of pathways involved. Excess wild-type NEDD4L leads to disruption of Dab1 and mTORC1 pathways, while PNH-related mutations are associated with deregulation of mTORC1 and AKT activities. Altogether, these data provide insights into the critical role of NEDD4L in the regulation of mTOR pathways and their contributions in cortical development.","authors":"Broix, L., Jagline, H., Ivanova, E., Schmucker, S., Drouot, N., Clayton-Smith, J., Pagnamenta, AT., Metcalfe, KA., Isidor, B., Louvier, UW., Poduri, A., Taylor, JC., Tilly, P., Poirier, K., Saillour, Y., Lebrun, N., Stemmelen, T., Rudolf, G., Muraca, G., Saintpierre, B., Elmorjani, A., Mo\u00efse, M., Weirauch, NB., Guerrini, R., Boland, A., Olaso, R., Masson, C., Tripathy, R., Keays, D., Beldjord, C., Nguyen, L., Godin, J., Kini, U., Nischk\u00e9, P., Deleuze, JF., Bahi-Buisson, N., Sumara, I., Hinckelmann, MV., Chelly, J.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Genet","volume":"48","issue":"11","page":"1349-1358","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27688400","title":"Neuron type-specific miRNA represses two broadly expressed genes to modulate an avoidance behavior in C. elegans.","abstract":"Two broad gene classes are distinguished within multicellular organisms: cell type-specific genes, which confer particular cellular properties, and ubiquitous genes that support general cellular functions. However, certain so-called ubiquitous genes show functionally relevant cell type-specific repression. How such repression is achieved is poorly understood. MicroRNAs (miRNAs) are repressors, many of which are expressed with high cell type specificity. Here we show that mir-791, expressed exclusively in the CO<sub>2<\/sub>-sensing neurons in Caenorhabditis elegans, represses two otherwise broadly expressed genes. This repression is necessary for normal neuronal function and behavior of the animals toward CO<sub>2<\/sub> miRNA-mediated repression of broadly transcribed genes is a previously unappreciated strategy for cellular specialization.","authors":"Drexel, T., Mahofsky, K., Latham, R., Zimmer, M., Cochella, L.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Genes Dev","volume":"30","issue":"18","page":"2042-2047","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27665606","title":"A reproducible protocol for neonatal ischemic injury and cardiac regeneration in neonatal mice.","abstract":"Cardiac regeneration is one of the prime visions in cardiovascular research. The mouse neonatal apical resection and left anterior descending artery (LAD) ligation model introduced novel in vivo mammalian assays to study cardiac regeneration. However, recent reports and editorials discussed and critically questioned the value and technical reproducibility of the mouse neonatal myocardial infarction approach, making it paramount to develop and use a reproducible model system. We established a mouse neonatal myocardial infarction model by visually confirmed ligation of the LAD using microsurgery. TdT-mediated dUTP nick-end labeling (TUNEL) proved reproducible massive myocardial infarctions in a defined region of the apex and anterior wall of neonatal and 7-day-old mice. Whereas hearts ligated on postnatal day 7 displayed chronic injury, cardiac samples ligated immediately after birth always showed complete structural regeneration after long-term follow-up. Cardiac regeneration was observed in all mouse stains (C57BL\/6J, ICR, and mixed background C57BL\/6JxSv129) tested so far. We present a detailed in vivo protocol to study complex mechanisms of complete cardiac repair following ischemic cardiac damage. Neonatal LAD ligation surgery is feasible, and results in reproducible myocardial infarctions 24\u00a0h after ligation, and no structural myocardial defects are detectable following long-term follow-up. We encourage the cardiovascular community to use our protocol and teaching video to answer key scientific questions in the field of cardiac regeneration.","authors":"Haubner, BJ., Schuetz, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Basic Res Cardiol","volume":"111","issue":"6","page":"64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21294583","title":"In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening.","abstract":"Nicotinic acetylcholine receptors (nAChR) are pentameric ligand gated ion channels whose activity can be modulated by endogenous neurotransmitters as well as by synthetic ligands that bind the same or distinct sites from the natural ligand. The subtype of \u03b17 nAChR has been considered as a potenial therapeutic target for Alzheimer's disease, schizophrenia and other neurological and psychiatric disorders. Here we have developed a homology model of \u03b17 nAChR based on two high resolution crystal structures with Brookhaven Protein Data Bank (PDB) codes 2QC1 and 2WN9 for threading on one monomer and then for building a pentamer, respectively. A number of small molecule binding sites are identified using Pocket Finder (J. An, M. Tortov, and R. Abagyan, Molecular &amp; Cellular Proteomics, 4.6, 752-761 (2005)) of Internal Coordinate Mechanics (ICM). Remarkably, these computer-identified sites match perfectly with ordered solvent densities found in the high-resolution crystal structure of \u03b11 nAChR, suggesting that the surface cavities in the \u03b17 nAChR model are likely binding sites of small molecules. A high throughput virtual screening by flexible ligand docking of 5008 small molecule compounds was performed at three potential allosteric modulator (AM) binding sites of \u03b17 nAChR using Molsoft ICM software (R. Abagyan, M. Tortov and D. Kuznetsov, J Comput Chem 15, 488-506, (1994)). Some experimentally verified allosteric modulators of \u03b17 like CCMI comp-6, LY 7082101, 5-HI, TQS, PNU-120596, genistein, and NS-1738 ranked among top 100 compounds, while the rest of the compounds in the list could guide further search for new allosteric modulators.","authors":"Dey, R., Chen, L.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Biomol Struct Dyn","volume":"28","issue":"5","page":"695-715","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15073183","title":"Nuclear factor of activated T-cells (NFAT) rescues osteoclastogenesis in precursors lacking c-Fos.","abstract":"Osteoclasts are specialized macrophages that resorb bone. Mice lacking the AP-1 component c-Fos are osteopetrotic because of a lack of osteoclast differentiation and show an increased number of macrophages. The nature of the critical function of c-Fos in osteoclast differentiation is not known. Microarray analysis revealed that Nfatc1, another key regulator of osteoclastogenesis, was down-regulated in Fos(-\/-) osteoclast precursors. Chromatin immunoprecipitation assay showed that c-Fos bound to the Nfatc1 and Acp5 promoters in osteoclasts. In vitro promoter analyses identified nuclear factor of activated T-cells (NFAT)\/AP-1 sites in the osteoclast-specific Acp5 and Calcr promoters. Moreover, in Fos(-\/-) precursors gene transfer of an active form of NFAT restored transcription of osteoclast-specific genes in the presence of receptor activator of the NF-kappaB ligand (RANKL), rescuing bone resorption. In the absence of RANKL, however, Fos(-\/-) precursors were insensitive to NFAT-induced osteoclastogenesis unlike wild-type precursors. These data indicate that lack of Nfatc1 expression is the cause of the differentiation block in Fos(-\/-) osteoclast precursors and that transcriptional induction of Nfatc1 is a major function of c-Fos in osteoclast differentiation.","authors":"Matsuo, K., Galson, DL., Zhao, C., Peng, L., Laplace, C., Wang, KZ., Bachler, MA., Amano, H., Aburatani, H., Ishikawa, H., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Biol Chem","volume":"279","issue":"25","page":"26475-80","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27562506","title":"A code within a code: how codons influence mRNA stability.","abstract":null,"authors":"Martinez, J., Zagrovic, B.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"EMBO J","volume":"35","issue":"19","page":"2064-2065","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21245830","title":"Non-coding RNAs as regulators of embryogenesis.","abstract":"Non-coding RNAs (ncRNAs) are emerging as key regulators of embryogenesis. They control embryonic gene expression by several means, ranging from microRNA-induced degradation of mRNAs to long ncRNA-mediated modification of chromatin. Many aspects of embryogenesis seem to be controlled by ncRNAs, including the maternal-zygotic transition, the maintenance of pluripotency, the patterning of the body axes, the specification and differentiation of cell types and the morphogenesis of organs. Drawing from several animal model systems, we describe two emerging themes for ncRNA function: promoting developmental transitions and maintaining developmental states. These examples also highlight the roles of ncRNAs in ensuring a robust commitment to one of two possible cell fates.","authors":"Pauli, A., Rinn, JL., Schier, AF.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Rev Genet","volume":"12","issue":"2","page":"136-49","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27468760","title":"Frontline Science: Coincidental null mutation of Csf2r\u03b1 in a colony of PI3K\u03b3-\/- mice causes alveolar macrophage deficiency and fatal respiratory viral infection.","abstract":"PI3Ks have been identified as key signaling proteins involved in many basic biologic processes in health and disease. Transgenic animals have been essential tools to study the underlying molecular mechanisms in this context and therefore, have been widely used to elucidate the role of these factors in many different settings. More specifically, PI3K\u03b3, a subunit highly expressed in the hematopoietic system, has been implicated to play an important role in many inflammatory diseases as well as cancer. Here, we report identification of multiple, additional, previously unknown mutations in the genome of a widely used PI3K\u03b3-deficient (PI3K\u03b3<sup>-\/-<\/sup>) mouse colony. These include a STOP mutation in the GM-CSFR\u03b1 chain, leading to a complete and specific deficiency in GM-CSF signaling. PI3K\u03b3<sup>-\/-<\/sup> animals consequently lacked alveolar macrophages (AMs) and succumbed rapidly to influenza virus infection. Furthermore, PI3K\u03b3<sup>-\/-<\/sup> mice carried an additional mutation that affects mucin 2 (Muc2) transcripts. This protein is strongly involved in the regulation of colorectal cancer, and indeed, conflicting reports have indicated that PI3K\u03b3<sup>-\/-<\/sup> animals spontaneously develop colorectal tumors. Thus, we uncover previously unknown, confounding factors present in a strain of PI3K\u03b3<sup>-\/-<\/sup> mice, leading to additional deficiencies in important signaling pathways with potentially wide-ranging implications for the interpretation of previous studies. By separating the mutations, we established a unique Csf2ra<sup>-\/-<\/sup> mouse model that allows us to study the role of cell intrinsic GM-CSFR signaling in vivo without confounding variables introduced by defective IL-5R and IL-3R signaling in mice lacking the common \u03b2 chain (Csf2rb).","authors":"Schneider, C., Nobs, SP., Heer, AK., Hirsch, E., Penninger, J., Siggs, OM., Kopf, M.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"J Leukoc Biol","volume":"101","issue":"2","page":"367-376","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7806943","title":"Tolerance and self-reactivity in V gamma 1.1C gamma 4 transgenic mice.","abstract":"Immunological tolerance is the process of inhibiting or eliminating lymphocytes that recognize self-derived antigens. By removing potentially harmful self-reactive clones, this mechanism allows for the random generation of a diverse repertoire of T-cells capable of responding to foreign pathogens. Although all self-reactive T-cells should be removed from the repertoire, it is quite clear from many recent studies that a significant fraction of T-cells bearing gamma delta T-cell receptors (TCR) recognize self-derived antigens in normal healthy mice. The presence of self-reactive T-cells in healthy animals presents a paradox which may be explained by understanding the transient expression of the antigens (e.g., MHC class Ib, Heat Shock Proteins) that have been identified for gamma delta T-cells thus far. Data from experiments with V gamma 1.1C gamma 4 transgenic mice demonstrating the presence of self-reactive gamma delta T-cells and their influence on lymphoid development and immune surveillance will be examined in this review.","authors":"Ferrick, DA., Gemmell-Hori, L., Sydora, B., Mulvania, T., Penninger, JM., Kronenberg, M., Mak, TW.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Int Rev Immunol","volume":"11","issue":"4","page":"295-304","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1995-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27159579","title":"Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk.","abstract":"Bromodomain-containing proteins of the BET family recognize histone lysine acetylation and mediate transcriptional activation of target genes such as the MYC oncogene. Pharmacological inhibitors of BET domains promise therapeutic benefits in a variety of cancers. We performed a high-diversity chemical compound screen for agents capable of modulating BRD4-dependent heterochromatization of a generic reporter in human cells. In addition to known and new compounds targeting BRD4, we identified small molecules that mimic BRD4 inhibition without direct engagement. One such compound was a potent inhibitor of the second bromodomain of TAF1. Using this inhibitor, we discovered that TAF1 synergizes with BRD4 to control proliferation of cancer cells, making TAF1 an attractive epigenetic target in cancers driven by MYC.","authors":"Sdelci, S., Lardeau, CH., Tallant, C., Klepsch, F., Klaiber, B., Bennett, J., Rathert, P., Schuster, M., Penz, T., Fedorov, O., Superti-Furga, G., Bock, C., Zuber, J., Huber, KV., Knapp, S., M\u00fcller, S., Kubicek, S.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Chem Biol","volume":"12","issue":"7","page":"504-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22993660","title":"Cell-free derivatives from mesenchymal stem cells are effective in wound therapy.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22993660<\/PMID><DateCompleted><Year>2012<\/Year><Month>09<\/Month><Day>21<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>09<\/Month><Day>30<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1948-0210<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>4<\/Volume><Issue>5<\/Issue><PubDate><Year>2012<\/Year><Month>May<\/Month><Day>26<\/Day><\/PubDate><\/JournalIssue><Title>World journal of stem cells<\/Title><ISOAbbreviation>World J Stem Cells<\/ISOAbbreviation><\/Journal><ArticleTitle>Cell-free derivatives from mesenchymal stem cells are effective in wound therapy.<\/ArticleTitle><Pagination><MedlinePgn>35-43<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"AIM\" NlmCategory=\"OBJECTIVE\">To compare the efficacy of cell-free derivatives from Bone marrow derived human mesenchymal stem cells (hMSCs) in wound therapy.","authors":"Mishra, PJ., Mishra, PJ., Banerjee, D.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"World J Stem Cells","volume":"4","issue":"5","page":"35-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31554955","title":"Generation of blood vessel organoids from human pluripotent stem cells.","abstract":"Blood vessels are fundamental to animal life and have critical roles in many diseases, such as stroke, myocardial infarction and diabetes. The vasculature is formed by endothelial cells that line the vessel and are covered with mural cells, specifically pericytes in smaller vessels and vascular smooth muscle cells (vSMCs) in larger-diameter vessels. Both endothelial cells and mural cells are essential for proper blood vessel function and can be derived from human pluripotent stem cells (hPSCs). Here, we describe a protocol to generate self-organizing 3D human blood vessel organoids from hPSCs that exhibit morphological, functional and molecular features of human microvasculature. These organoids are differentiated via mesoderm induction of hPSC aggregates and subsequent differentiation into endothelial networks and pericytes in a 3D collagen I-Matrigel matrix. Blood vessels form within 2-3 weeks and can be further grown in scalable suspension culture. Importantly, in vitro-differentiated human blood vessel organoids transplanted into immunocompromised mice gain access to the mouse circulation and specify into functional arteries, arterioles and veins.","authors":"Wimmer, RA., Leopoldi, A., Aichinger, M., Kerjaschki, D., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Protoc","volume":"14","issue":"11","page":"3082-3100","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27241552","title":"RANKL\/RANK control Brca1 mutation- .","abstract":"Breast cancer is the most common female cancer, affecting approximately one in eight women during their life-time. Besides environmental triggers and hormones, inherited mutations in the breast cancer 1 (BRCA1) or BRCA2 genes markedly increase the risk for the development of breast cancer. Here, using two different mouse models, we show that genetic inactivation of the key osteoclast differentiation factor RANK in the mammary epithelium markedly delayed onset, reduced incidence, and attenuated progression of Brca1;p53 mutation-driven mammary cancer. Long-term pharmacological inhibition of the RANK ligand RANKL in mice abolished the occurrence of Brca1 mutation-driven pre-neoplastic lesions. Mechanistically, genetic inactivation of Rank or RANKL\/RANK blockade impaired proliferation and expansion of both murine Brca1;p53 mutant mammary stem cells and mammary progenitors from human BRCA1 mutation carriers. In addition, genome variations within the RANK locus were significantly associated with risk of developing breast cancer in women with BRCA1 mutations. Thus, RANKL\/RANK control progenitor cell expansion and tumorigenesis in inherited breast cancer. These results present a viable strategy for the possible prevention of breast cancer in BRCA1 mutant patients.","authors":"Sigl, V., Owusu-Boaitey, K., Joshi, PA., Kavirayani, A., Wirnsberger, G., Novatchkova, M., Kozieradzki, I., Schramek, D., Edokobi, N., Hersl, J., Sampson, A., Odai-Afotey, A., Lazaro, C., Gonzalez-Suarez, E., Pujana, MA., Cimba, F., Heyn, H., Vidal, E., Cruickshank, J., Berman, H., Sarao, R., Ticevic, M., Uribesalgo, I., Tortola, L., Rao, S., Tan, Y., Pfeiler, G., Lee, EY., Bago-Horvath, Z., Kenner, L., Popper, H., Singer, C., Khokha, R., Jones, LP., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Res","volume":"26","issue":"7","page":"761-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27160902","title":"The Tumor Suppressor Hace1 Is a Critical Regulator of TNFR1-Mediated Cell Fate.","abstract":"The HECT domain E3 ligase HACE1 has been identified as a tumor suppressor in multiple cancers. Here, we report that HACE1 is a central gatekeeper of TNFR1-induced cell fate. Genetic inactivation of\u00a0HACE1 inhibits TNF-stimulated NF-\u03baB activation and TNFR1-NF-\u03baB-dependent pathogen clearance in\u00a0vivo. Moreover, TNF-induced apoptosis was impaired in hace1 mutant cells and knockout mice in\u00a0vivo. Mechanistically, HACE1 is essential for the ubiquitylation of the adaptor protein TRAF2 and formation of the apoptotic caspase-8 effector complex. Intriguingly, loss of HACE1 does not impair TNFR1-mediated necroptotic cell fate via RIP1 and RIP3 kinases. Loss of HACE1 predisposes animals to colonic inflammation and carcinogenesis in\u00a0vivo, which is markedly alleviated by genetic inactivation of RIP3 kinase and TNFR1. Thus, HACE1 controls TNF-elicited cell fate decisions and exerts tumor suppressor and anti-inflammatory activities via a TNFR1-RIP3 kinase-necroptosis pathway.","authors":"Tortola, L., Nitsch, R., Bertrand, MJM., Kogler, M., Redouane, Y., Kozieradzki, I., Uribesalgo, I., Fennell, LM., Daugaard, M., Klug, H., Wirnsberger, G., Wimmer, R., Perlot, T., Sarao, R., Rao, S., Hanada, T., Takahashi, N., Kernbauer, E., Demir\u00f6z, D., Lang, M., Superti-Furga, G., Decker, T., Pichler, A., Ikeda, F., Kroemer, G., Vandenabeele, P., Sorensen, PH., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Rep","volume":"15","issue":"7","page":"1481-1492","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27064449","title":"LGR4 is a receptor for RANKL and negatively regulates osteoclast differentiation and bone resorption.","abstract":"Tumor necrosis factor (TNF) superfamily member 11 (TNFSF11, also known as RANKL) regulates multiple physiological or pathological functions, including osteoclast differentiation and osteoporosis. TNFRSF11A (also called RANK) is considered to be the sole receptor for RANKL. Herein we report that leucine-rich repeat-containing G-protein-coupled receptor 4 (LGR4, also called GPR48) is another receptor for RANKL. LGR4 competes with RANK to bind RANKL and suppresses canonical RANK signaling during osteoclast differentiation. RANKL binding to LGR4 activates the G\u03b1q and GSK3-\u03b2 signaling pathway, an action that suppresses the expression and activity of nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 1 (NFATC1) during osteoclastogenesis. Both whole-body (Lgr4(-\/-)) and monocyte conditional knockout mice of Lgr4 (Lgr4 CKO) exhibit osteoclast hyperactivation (including elevation of osteoclast number, surface area, and size) and increased bone erosion. The soluble LGR4 extracellular domain (ECD) binds RANKL and inhibits osteoclast differentiation in vivo. Moreover, LGR4-ECD therapeutically abrogated RANKL-induced bone loss in three mouse models of osteoporosis. Therefore, LGR4 acts as a second RANKL receptor that negatively regulates osteoclast differentiation and bone resorption.","authors":"Luo, J., Yang, Z., Ma, Y., Yue, Z., Lin, H., Qu, G., Huang, J., Dai, W., Li, C., Zheng, C., Xu, L., Chen, H., Wang, J., Li, D., Siwko, S., Penninger, JM., Ning, G., Xiao, J., Liu, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Med","volume":"22","issue":"5","page":"539-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27064256","title":"Genome-wide association study identifies five new susceptibility loci for primary angle closure glaucoma.","abstract":"Primary angle closure glaucoma (PACG) is a major cause of blindness worldwide. We conducted a genome-wide association study (GWAS) followed by replication in a combined total of 10,503 PACG cases and 29,567 controls drawn from 24 countries across Asia, Australia, Europe, North America, and South America. We observed significant evidence of disease association at five new genetic loci upon meta-analysis of all patient collections. These loci are at EPDR1 rs3816415 (odds ratio (OR) = 1.24, P = 5.94 \u00d7 10(-15)), CHAT rs1258267 (OR = 1.22, P = 2.85 \u00d7 10(-16)), GLIS3 rs736893 (OR = 1.18, P = 1.43 \u00d7 10(-14)), FERMT2 rs7494379 (OR = 1.14, P = 3.43 \u00d7 10(-11)), and DPM2-FAM102A rs3739821 (OR = 1.15, P = 8.32 \u00d7 10(-12)). We also confirmed significant association at three previously described loci (P &lt; 5 \u00d7 10(-8) for each sentinel SNP at PLEKHA7, COL11A1, and PCMTD1-ST18), providing new insights into the biology of PACG.","authors":"Khor, CC., Do, T., Jia, H., Nakano, M., George, R., Abu-Amero, K., Duvesh, R., Chen, LJ., Li, Z., Nongpiur, ME., Perera, SA., Qiao, C., Wong, HT., Sakai, H., Barbosa de Melo, M., Lee, MC., Chan, AS., Azhany, Y., Dao, TL., Ikeda, Y., Perez-Grossmann, RA., Zarnowski, T., Day, AC., Jonas, JB., Tam, PO., Tran, TA., Ayub, H., Akhtar, F., Micheal, S., Chew, PT., Aljasim, LA., Dada, T., Luu, TT., Awadalla, MS., Kitnarong, N., Wanichwecharungruang, B., Aung, YY., Mohamed-Noor, J., Vijayan, S., Sarangapani, S., Husain, R., Jap, A., Baskaran, M., Goh, D., Su, DH., Wang, H., Yong, VK., Yip, LW., Trinh, TB., Makornwattana, M., Nguyen, TT., Leuenberger, EU., Park, KH., Wiyogo, WA., Kumar, RS., Tello, C., Kurimoto, Y., Thapa, SS., Pathanapitoon, K., Salmon, JF., Sohn, YH., Fea, A., Ozaki, M., Lai, JS., Tantisevi, V., Khaing, CC., Mizoguchi, T., Nakano, S., Kim, CY., Tang, G., Fan, S., Wu, R., Meng, H., Nguyen, TT., Tran, TD., Ueno, M., Martinez, JM., Ramli, N., Aung, YM., Reyes, RD., Vernon, SA., Fang, SK., Xie, Z., Chen, XY., Foo, JN., Sim, KS., Wong, TT., Quek, DT., Venkatesh, R., Kavitha, S., Krishnadas, SR., Soumittra, N., Shantha, B., Lim, BA., Ogle, J., de Vasconcellos, JP., Costa, VP., Abe, RY., de Souza, BB., Sng, CC., Aquino, MC., Kosior-Jarecka, E., Fong, GB., Tamanaja, VC., Fujita, R., Jiang, Y., Waseem, N., Low, S., Pham, HN., Al-Shahwan, S., Craven, ER., Khan, MI., Dada, R., Mohanty, K., Faiq, MA., Hewitt, AW., Burdon, KP., Gan, EH., Prutthipongsit, A., Patthanathamrongkasem, T., Catacutan, MA., Felarca, IR., Liao, CS., Rusmayani, E., Istiantoro, VW., Consolandi, G., Pignata, G., Lavia, C., Rojanapongpun, P., Mangkornkanokpong, L., Chansangpetch, S., Chan, JC., Choy, BN., Shum, JW., Than, HM., Oo, KT., Han, AT., Yong, VH., Ng, XY., Goh, SR., Chong, YF., Hibberd, ML., Seielstad, M., Png, E., Dunstan, SJ., Chau, NV., Bei, J., Zeng, YX., Karkey, A., Basnyat, B., Pasutto, F., Paoli, D., Frezzotti, P., Wang, JJ., Mitchell, P., Fingert, JH., Allingham, RR., Hauser, MA., Lim, ST., Chew, SH., Ebstein, RP., Sakuntabhai, A., Park, KH., Ahn, J., Boland, G., Snippe, H., Stead, R., Quino, R., Zaw, SN., Lukasik, U., Shetty, R., Zahari, M., Bae, HW., Oo, NL., Kubota, T., Manassakorn, A., Ho, WL., Dallorto, L., Hwang, YH., Kiire, CA., Kuroda, M., Djamal, ZE., Peregrino, JI., Ghosh, A., Jeoung, JW., Hoan, TS., Srisamran, N., Sandragasu, T., Set, SH., Doan, VH., Bhattacharya, SS., Ho, CL., Tan, DT., Sihota, R., Loon, SC., Mori, K., Kinoshita, S., Hollander, AI., Qamar, R., Wang, YX., Teo, YY., Tai, ES., Hartleben-Matkin, C., Lozano-Giral, D., Saw, SM., Cheng, CY., Zenteno, JC., Pang, CP., Bui, HT., Hee, O., Craig, JE., Edward, DP., Yonahara, M., Neto, JM., Guevara-Fujita, ML., Xu, L., Ritch, R., Liza-Sharmini, AT., Wong, TY., Al-Obeidan, S., Do, NH., Sundaresan, P., Tham, CC., Foster, PJ., Vijaya, L., Tashiro, K., Vithana, EN., Wang, N., Aung, T.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Genet","volume":"48","issue":"5","page":"556-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20874763","title":"The vasopressin V1b receptor modulates plasma corticosterone responses to dehydration-induced stress.","abstract":"Vasopressin V1b receptor knockout (V1b\u207b\/\u207b) mice were used to investigate a putative role for the V1b receptor (V1bR) in fluid regulation and in the hypothalamic-neurohypophysial system (HNS) and hypothalamic-pituitary-adrenal (HPA) axis responses to osmotic stress induced by water deprivation (WD). Male wild-type and V1b\u207b\/\u207b mice were housed in metabolic cages to allow determination of water intake and urine volume and osmolality. When provided with food and water ad lib., spontaneous urine volume and urine osmolality did not differ between genotypes. Similarly, WD for 24 h caused comparable decreases in urine volume and increases in urine osmolality irrespective of genotype. WD resulted in an increase in plasma corticosterone concentration in wild-type animals; however, this WD-induced increase in plasma corticosterone was significantly attenuated in V1b\u207b\/\u207b mice. Comparable increases in neuronal activation, indicated by increased c-fos mRNA expression, and in vasopressin mRNA expression occurred in both the supraoptic nucleus and paraventricular nucleus (PVN) of wild-type and V1b\u207b\/\u207b mice following WD; however, the WD-induced decrease in corticotrophin-releasing hormone mRNA expression seen in the PVN of wild-type mice was not observed in the PVN of V1b\u207b\/\u207b mice. These data suggest that, although the vasopressin V1bR is not required for normal HNS function, it is necessary for a full HPA-axis response to the osmotic stress of WD.","authors":"Roberts, EM., Pope, GR., Newson, MJ., Lolait, SJ., O'Carroll, AM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Neuroendocrinol","volume":"23","issue":"1","page":"12-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-04-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15001709","title":"Isolation of antibiotic resistance mutations in the rRNA by using an in vitro selection system.","abstract":"Genetic, biochemical, and structural data support an essential role for the ribosomal RNA in all steps of the translation process. Although in vivo genetic selection techniques have been used to identify mutations in the rRNAs that result in various miscoding phenotypes and resistance to known ribosome-targeted antibiotics, these are limited because the resulting mutant ribosomes must be only marginally disabled if they are able to support growth of the cell. Furthermore, in vivo, it is not possible to control the environment in precise ways that might allow for the isolation of certain types of rRNA variants. To overcome these limitations, we have developed an in vitro selection system for the isolation of functionally competent ribosomal particles from populations containing variant rRNAs. Here, we describe this system and present an example of its application to the selection of antibiotic resistance mutations. From a pool of 4,096 23S rRNA variants, a double mutant (A2058U\/A2062G) was isolated after iteration of the selection process. This mutant was highly resistant to clindamycin in in vitro translation reactions and yet was not viable in Escherichia coli. These data establish that this system has the potential to identify mutations in the rRNA not readily accessed by comparable in vivo systems, thus allowing for more exhaustive ribosomal genetic screens.","authors":"Cochella, L., Green, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Proc Natl Acad Sci U S A","volume":"101","issue":"11","page":"3786-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14981248","title":"Transportin2 functions as importin and mediates nuclear import of HuR.","abstract":"The RanGTP-binding nuclear transport receptors transportin1 (TRN1) and transportin2 (TRN2) are highly similar in sequence but are reported to function in nuclear import and export, respectively. Here we show that TRN2 possesses properties of a nuclear import receptor. TRN1\/2 both interacted with a similar set of RNA-binding proteins in a RanGTP-sensitive manner. TRN2 bound RanGTP with high affinity, a feature of nuclear import receptors. As expected of an import complex, RanGTP also disrupted the interaction between TRN2 and HuR, an RNA-binding protein previously described as a TRN2 export substrate. The HuR nucleocytoplasmic shuttling signal, a sequence resembling the M9 nuclear import signal of hnRNP A1, was necessary and sufficient for TRN-mediated nuclear import of HuR in vitro. Finally, crosscompetition experiments demonstrated that HuR nucleocytoplasmic shuttling signal and M9 are imported along redundant pathways involving TRN1\/2, substantiating the function of TRN2 in nuclear import.","authors":"G\u00fcttinger, S., M\u00fchlh\u00e4usser, P., Koller-Eichhorn, R., Brennecke, J., Kutay, U.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Proc Natl Acad Sci U S A","volume":"101","issue":"9","page":"2918-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26968342","title":"An Essential Role for SHARPIN in the Regulation of Caspase 1 Activity in Sepsis.","abstract":"Sepsis is burdened by high mortality due to uncontrolled inflammatory response to pathogens. Increased caspase 1 activation causing maturation of IL1\u03b2\/18 remains a therapeutic challenge in sepsis. SHARPIN (shank-associated regulator of G-protein signaling homology domain-interacting protein), a component of the LUBAC (linear ubiquitin chain-assembly complex), regulates inflammation, with unknown effects on caspase 1 activation. Mice lacking Casp1, Casp11, or both in a Sharpin-deficient background were generated, exposed to lipopolysaccharide-induced endotoxemia, and injected with caspase 1 inhibitor. We monitored survival, Il1\u03b2\/18, and caspase 1\/11 levels in plasma and organs and deciphered mechanisms of SHARPIN-dependent caspase 1 inhibition. A correlation between LUBAC and active caspase 1 was found in blood mononuclear cells from septic patients. SHARPIN bound caspase 1 and disrupted p20\/p10 dimer formation, the last step of caspase 1 processing, thereby inhibiting enzyme activation and maturation of IL1\u03b2\/18 in a LUBAC-independent manner. In septic patients, LUBAC-independent decline in SHARPIN correlated with enhancement of active caspase 1 in circulating mononuclear cells. Septic Sharpin-deficient mice displayed enrichment in mature Il1\u03b2\/18 and active caspase 1, and shortened survival. Inhibition of caspase 1 reduced levels of Il1\u03b2\/18 and splenic cell death, and prolonged survival in septic Sharpin-deficient mice. Our findings identify SHARPIN as a potent in\u00a0vivo caspase 1 inhibitor and propose the caspase 1-SHARPIN interaction as a target in sepsis.","authors":"Nastase, MV., Zeng-Brouwers, J., Frey, H., Hsieh, LT., Poluzzi, C., Beckmann, J., Schroeder, N., Pfeilschifter, J., Lopez-Mosqueda, J., Mersmann, J., Ikeda, F., Iozzo, RV., Dikic, I., Schaefer, L.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Am J Pathol","volume":"186","issue":"5","page":"1206-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26779602","title":"Multifunctional role of the transcription factor Blimp-1 in coordinating plasma cell differentiation.","abstract":"The transcription factor Blimp-1 is necessary for the generation of plasma cells. Here we studied its functions in plasmablast differentiation by identifying regulated Blimp-1 target genes. Blimp-1 promoted the migration and adhesion of plasmablasts. It directly repressed genes encoding several transcription factors and Aicda (which encodes the cytidine deaminase AID) and thus silenced B cell-specific gene expression, antigen presentation and class-switch recombination in plasmablasts. It directly activated genes, which led to increased expression of the plasma cell regulator IRF4 and proteins involved in immunoglobulin secretion. Blimp-1 induced the transcription of immunoglobulin genes by controlling the 3' enhancers of the loci encoding the immunoglobulin heavy chain (Igh) and \u03ba-light chain (Igk) and, furthermore, regulated the post-transcriptional expression switch from the membrane-bound form of the immunoglobulin heavy chain to its secreted form by activating Ell2 (which encodes the transcription-elongation factor ELL2). Notably, Blimp-1 recruited chromatin-remodeling and histone-modifying complexes to regulate its target genes. Hence, many essential functions of plasma cells are under the control of Blimp-1.","authors":"Minnich, M., Tagoh, H., B\u00f6nelt, P., Axelsson, E., Fischer, M., Cebolla, B., Tarakhovsky, A., Nutt, SL., Jaritz, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Immunol","volume":"17","issue":"3","page":"331-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14961024","title":"Tension between two kinetochores suffices for their bi-orientation on the mitotic spindle.","abstract":"The movement of sister chromatids to opposite spindle poles during anaphase depends on the prior capture of sister kinetochores by microtubules with opposing orientations (amphitelic attachment or bi-orientation). In addition to proteins necessary for the kinetochore-microtubule attachment, bi-orientation requires the Ipl1 (Aurora B in animal cells) protein kinase and tethering of sister chromatids by cohesin. Syntelic attachments, in which sister kinetochores attach to microtubules with the same orientation, must be either 'avoided' or 'corrected'. Avoidance might be facilitated by the juxtaposition of sister kinetochores such that they face in opposite directions; kinetochore geometry is therefore deemed important. Error correction, by contrast, is thought to stem from the stabilization of kinetochore-spindle pole connections by tension in microtubules, kinetochores, or the surrounding chromatin arising from amphitelic but not syntelic attachment. The tension model predicts that any type of connection between two kinetochores suffices for efficient bi-orientation. Here we show that the two kinetochores of engineered, unreplicated dicentric chromosomes in Saccharomyces cerevisiae bi-orient efficiently, implying that sister kinetochore geometry is dispensable for bi-orientation. We also show that Ipl1 facilitates bi-orientation by promoting the turnover of kinetochore-spindle pole connections in a tension-dependent manner.","authors":"Dewar, H., Tanaka, K., Nasmyth, K., Tanaka, TU.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Nature","volume":"428","issue":"6978","page":"93-7","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26773150","title":"NK Cell-Specific Gata3 Ablation Identifies the Maturation Program Required for Bone Marrow Exit and Control of Proliferation.","abstract":"NK cells are innate lymphocytes capable of eliciting an innate immune response to pathogens. NK cells develop and become mature in the bone marrow (BM) before they migrate out to peripheral organs. Although the developmental program leading to mature NK cells has been studied in the context of several transcription factors, the stage-specific role of GATA3 in NK cell development has been incompletely understood. Using NKp46-Cre-Gata3(fl\/fl) mice in which Gata3 deficiency was induced as early as the immature stage of NK cell differentiation, we demonstrated that GATA3 is required for the NK cell maturation beyond the CD27 single-positive stage and is indispensable for the maintenance of liver-resident NK cells. The frequencies of NK cells from NKp46-Cre-Gata3(fl\/fl) mice were found higher in the BM but lower in peripheral organs compared with control littermates, indicating that GATA3 controls the maturation program required for BM egress. Despite the defect in maturation, upon murine CMV infection, NK cells from NKp46-Cre-Gata3(fl\/fl) mice expanded vigorously, achieving NK cell frequencies surpassing those in controls and therefore provided comparable protection. The heightened proliferation of NK cells from NKp46-Cre-Gata3(fl\/fl) mice was cell intrinsic and associated with enhanced upregulation of CD25 expression. Taken together, our results demonstrate that GATA3 is a critical regulator for NK cell terminal maturation and egress out of the BM and that immature NK cells present in the periphery of NKp46-Cre-Gata3(fl\/fl) mice can rapidly expand and provide a reservoir of NK cells capable of mounting an efficient cytotoxic response upon virus infection.","authors":"Ali, AK., Oh, JS., Vivier, E., Busslinger, M., Lee, SH.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Immunol","volume":"196","issue":"4","page":"1753-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26440891","title":"Mammary Stem Cell Self-Renewal Is Regulated by Slit2\/Robo1 Signaling through SNAI1 and mINSC.","abstract":"Tissue homeostasis requires somatic stem cell maintenance; however, mechanisms regulating this process during organogenesis are not well understood. Here, we identify asymmetrically renewing basal and luminal stem cells in the mammary end bud. We demonstrate that SLIT2\/ROBO1 signaling regulates the choice between self-renewing asymmetric cell divisions (ACDs) and expansive symmetric cell divisions (SCDs) by governing Inscuteable (mInsc), a key member of the spindle orientation machinery, through the transcription factor Snail (SNAI1). Loss of SLIT2\/ROBO1 signaling increases SNAI1 in the nucleus. Overexpression of SNAI1 increases mInsc expression, an effect that is inhibited by SLIT2 treatment. Increased mInsc does not change cell proliferation in the mammary gland (MG) but instead causes more basal cap cells to divide via SCD, at the expense of ACD, leading to more stem cells and larger outgrowths. Together, our studies provide insight into how the number of mammary stem cells is regulated by the extracellular cue SLIT2.","authors":"Ballard, MS., Zhu, A., Iwai, N., Stensrud, M., Mapps, A., Postiglione, MP., Knoblich, JA., Hinck, L.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell Rep","volume":"13","issue":"2","page":"290-301","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14757750","title":"Cleavage furrow positioning.","abstract":"To complete the cell cycle, the cleavage furrow draws the plasma membrane toward the cell center, pinching the cytoplasm into two lobes that are subsequently separated into two cells. The position of the cleavage furrow is induced by the mitotic spindle during early anaphase. Although the mechanism of cleavage furrow positioning is not understood at a molecular level, recent results suggest that it might be mediated by local relief from the inhibitory effects of microtubules.","authors":"Glotzer, M.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Cell Biol","volume":"164","issue":"3","page":"347-51","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2004-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20869537","title":"The actin cytoskeleton in whole mount preparations and sections.","abstract":"In non-muscle cells, the actin cytoskeleton plays a key role by providing a scaffold contributing to the definition of cell shape, force for driving cell motility, cytokinesis, endocytosis, and propulsion of pathogens, as well as tracks for intracellular transport. A thorough understanding of these processes requires insight into the spatial and temporal organisation of actin filaments into diverse higher-order structures, such as networks, parallel bundles, and contractile arrays. Transmission and scanning electron microscopy can be used to visualise the actin cytoskeleton, but due to the delicate nature of actin filaments, they are easily affected by standard preparation protocols, yielding variable degrees of ultrastructural preservation. In this chapter, we describe different conventional and cryo-approaches to visualise the actin cytoskeleton using transmission electron microscopy and discuss their specific advantages and drawbacks. In the first part, we present three different whole mount techniques, which allow visualisation of actin in the peripheral, thinly spread parts of cells grown in monolayers. In the second part, we describe specific issues concerning the visualisation of actin in thin sections. Techniques for three-dimensional visualisation of actin, protein localisation, and correlative light and electron microscopy are also included.","authors":"Resch, GP., Urban, E., Jacob, S.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Methods Cell Biol","volume":"96","issue":null,"page":"529-64","pdf":null,"JrId":"5785","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26293662","title":"Mutations in PIGY: expanding the phenotype of inherited glycosylphosphatidylinositol deficiencies.","abstract":"Glycosylphosphatidylinositol (GPI)-anchored proteins are ubiquitously expressed in the human body and are important for various functions at the cell surface. Mutations in many GPI biosynthesis genes have been described to date in patients with multi-system disease and together these constitute a subtype of congenital disorders of glycosylation. We used whole exome sequencing in two families to investigate the genetic basis of disease and used RNA and cellular studies to investigate the functional consequences of sequence variants in the PIGY gene. Two families with different phenotypes had homozygous recessive sequence variants in the GPI biosynthesis gene PIGY. Two sisters with c.137T&gt;C (p.Leu46Pro) PIGY variants had multi-system disease including dysmorphism, seizures, severe developmental delay, cataracts and early death. There were significantly reduced levels of GPI-anchored proteins (CD55 and CD59) on the surface of patient-derived skin fibroblasts (\u223c20-50% compared with controls). In a second, consanguineous family, two siblings had moderate development delay and microcephaly. A homozygous PIGY promoter variant (c.-540G&gt;A) was detected within a 7.7 Mb region of autozygosity. This variant was predicted to disrupt a SP1 consensus binding site and was shown to be associated with reduced gene expression. Mutations in PIGY can occur in coding and non-coding regions of the gene and cause variable phenotypes. This article contributes to understanding of the range of disease phenotypes and disease genes associated with deficiencies of the GPI-anchor biosynthesis pathway and also serves to highlight the potential importance of analysing variants detected in 5'-UTR regions despite their typically low coverage in exome data.","authors":"Ilkovski, B., Pagnamenta, AT., O'Grady, GL., Kinoshita, T., Howard, MF., Lek, M., Thomas, B., Turner, A., Christodoulou, J., Sillence, D., Knight, SJ., Popitsch, N., Keays, DA., Anzilotti, C., Goriely, A., Waddell, LB., Brilot, F., North, KN., Kanzawa, N., Macarthur, DG., Taylor, JC., Kini, U., Murakami, Y., Clarke, NF.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Hum Mol Genet","volume":"24","issue":"21","page":"6146-59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26105993","title":"The Expression of Tubb2b Undergoes a Developmental Transition in Murine Cortical Neurons.","abstract":"The development of the mammalian brain requires the generation, migration, and differentiation of neurons, cellular processes that are dependent on a dynamic microtubule cytoskeleton. Mutations in tubulin genes, which encode for the structural subunits of microtubules, cause detrimental neurological disorders known as the tubulinopathies. The disease spectra associated with different tubulin genes are overlapping but distinct, an observation believed to reflect functional specification of this multigene family. Perturbation of the \u03b2-tubulin TUBB2B is known to cause polymicrogyria, pachygyria, microcephaly, and axon guidance defects. Here we provide a detailed analysis of the expression pattern of its murine homolog Tubb2b. The generation and characterization of BAC-transgenic eGFP reporter mouse lines has revealed that it is highly expressed in progenitors and postmitotic neurons during cortical development. This contrasts with the 8-week-old cortex, in which Tubb2b expression is restricted to macroglia, and expression is almost completely absent in mature neurons. This developmental transition in neurons is mirrored in the adult hippocampus and the cerebellum but is not a universal feature of Tubb2b; its expression persists in a population of postmitotic neurons in the 8-week-old retina. We propose that the dynamic spatial and temporal expression of Tubb2b reflects specific functional requirements of the microtubule cytoskeleton.","authors":"Breuss, M., Morandell, J., Nimpf, S., Gstrein, T., Lauwers, M., Hochstoeger, T., Braun, A., Chan, K., S\u00e1nchez Guajardo, ER., Zhang, L., Suplata, M., Heinze, KG., Elsayad, K., Keays, DA.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Comp Neurol","volume":"523","issue":"15","page":"2161-86","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20845426","title":"Regulation of Tbx22 during facial and palatal development.","abstract":"Mutations in the gene encoding the T-box transcription factor TBX22 cause X-linked cleft palate and ankyloglossia in humans. Here we show that Tbx22 expression during facial and palatal development is regulated by FGF and BMP signaling. Our results demonstrate that FGF8 induces Tbx22 in the early face while BMP4 represses and thus restricts its expression. This regulation is conserved between chicken and mouse, although the Tbx22-expression patterns differ considerably between these two species. We suggest that these species-specific differences may result at least in part from differences in the spatiotemporal patterns of BMP activity, but we exclude a direct repression of Tbx22 by the BMP-inducible transcriptional repressor MSX1. Together these findings help to integrate Tbx22 into the molecular network of factors regulating facial development.","authors":"Fuchs, A., Inthal, A., Herrmann, D., Cheng, S., Nakatomi, M., Peters, H., Neub\u00fcser, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Dev Dyn","volume":"239","issue":"11","page":"2860-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14676216","title":"A novel interaction between kinesin and p120 modulates p120 localization and function.","abstract":"p120-catenin exists in a membrane-associated cadherin-bound pool, a cytosolic pool that affects Rho GTPases, and a nuclear pool that is thought to associate with the methylation-relevant transcriptional repressor Kaiso. We show here that cytoplasmic p120 can also associate both directly and indirectly with the microtubule network, and that p120 traffics along microtubules toward their plus ends. The direct binding required most of the armadillo repeats and was mutually exclusive for interaction with E-cadherin. Perturbing the p120-microtubule interaction with nocodazole or taxol markedly affected both the tubulin interaction and the balance between cytoplasmic and nuclear p120. The indirect binding occurred via a novel interaction between a segment of the p120 N-terminal domain and conventional kinesin heavy chains. Selective uncoupling of the p120-kinesin interaction by overexpression of the respective p120 and kinesin-binding fragments promoted nuclear p120 accumulation. In addition, expression of full-length kinesin reduced the nuclear accumulation of p120 and blocked the branching phenotype associated with p120 overexpression. Taken together, the data suggest that kinesin affects both the targeting and activity of p120 at several cellular locations.","authors":"Yanagisawa, M., Kaverina, IN., Wang, A., Fujita, Y., Reynolds, AB., Anastasiadis, PZ.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Biol Chem","volume":"279","issue":"10","page":"9512-21","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2004-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26055303","title":"Identification of bromodomain-containing protein-4 as a novel marker and epigenetic target in mast cell leukemia.","abstract":"Advanced systemic mastocytosis (SM) is a life-threatening neoplasm characterized by uncontrolled growth and accumulation of neoplastic mast cells (MCs) in various organs and a poor survival. So far, no curative treatment concept has been developed for these patients. We identified the epigenetic reader bromodomain-containing protein-4 (BRD4) as novel drug target in aggressive SM (ASM) and MC leukemia (MCL). As assessed by immunohistochemistry and PCR, neoplastic MCs expressed substantial amounts of BRD4 in ASM and MCL. The human MCL lines HMC-1 and ROSA also expressed BRD4, and their proliferation was blocked by a BRD4-specific short hairpin RNA. Correspondingly, the BRD4-targeting drug JQ1 induced dose-dependent growth inhibition and apoptosis in HMC-1 and ROSA cells, regardless of the presence or absence of KIT D816V. In addition, JQ1 suppressed the proliferation of primary neoplastic MCs obtained from patients with ASM or MCL (IC50: 100-500\u2009nm). In drug combination experiments, midostaurin (PKC412) and all-trans retinoic acid were found to cooperate with JQ1 in producing synergistic effects on survival in HMC-1 and ROSA cells. Taken together, we have identified BRD4 as a promising drug target in advanced SM. Whether JQ1 or other BET-bromodomain inhibitors are effective in vivo in patients with advanced SM remains to be elucidated.","authors":"Wedeh, G., Cerny-Reiterer, S., Eisenwort, G., Herrmann, H., Blatt, K., Hadzijusufovic, E., Sadovnik, I., M\u00fcllauer, L., Schwaab, J., Hoffmann, T., Bradner, JE., Radia, D., Sperr, WR., Hoermann, G., Reiter, A., Horny, HP., Zuber, J., Arock, M., Valent, P.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Leukemia","volume":"29","issue":"11","page":"2230-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25956709","title":"Direct and indirect targeting of MYC to treat acute myeloid leukemia.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">25956709<\/PMID><DateCompleted><Year>2015<\/Year><Month>10<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1432-0843<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>76<\/Volume><Issue>1<\/Issue><PubDate><Year>2015<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>Cancer chemotherapy and pharmacology<\/Title><ISOAbbreviation>Cancer Chemother Pharmacol<\/ISOAbbreviation><\/Journal><ArticleTitle>Direct and indirect targeting of MYC to treat acute myeloid leukemia.<\/ArticleTitle><Pagination><MedlinePgn>35-46<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s00280-015-2766-z<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE\" NlmCategory=\"OBJECTIVE\">Acute myeloid leukemia (AML) is the most common acute leukemia in adults and is often resistant to conventional therapies. The MYC oncogene is commonly overexpressed in AML but has remained an elusive target. We aimed to examine the consequences of targeting MYC both directly and indirectly in AML overexpressing MYC\/Myc due to trisomy 8\/15 (human\/mouse), FLT3-ITD mutation, or gene amplification.","authors":"Brondfield, S., Umesh, S., Corella, A., Zuber, J., Rappaport, AR., Gaillard, C., Lowe, SW., Goga, A., Kogan, SC.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cancer Chemother Pharmacol","volume":"76","issue":"1","page":"35-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17889796","title":"In vitro analysis of microRNA processing using recombinant Dicer and cytoplasmic extracts of HeLa cells.","abstract":"MicroRNAs (miRNAs) constitute a novel class of short, non-coding RNAs that play crucial roles as silencers of gene expression during biological processes such as development, growth control, cell death, and differentiation. To ensure correct function, the expression of miRNAs must be tightly regulated, a process that is believed to take place at the promoter level. Regulation of the miRNA processing cascade has only recently been shown to play an important role as well and we envision the discovery of additional factors affecting or modulating miRNA processing and ultimately miRNA expression. The biochemical analysis of such factors requires a robust assay to monitor miRNA processing. Here, we discuss protocols and techniques that were used to investigate how the expression of brain-specific miRNA miR-138 is controlled at the level of precursor-miRNA (pre-miRNA) processing.","authors":"Leuschner, PJ., Martinez, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Methods","volume":"43","issue":"2","page":"105-9","pdf":null,"JrId":"20385","fulltextlink":null,"preprintlink":null,"articledate":"2007-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25100204","title":"Development of siRNA payloads to target KRAS-mutant cancer.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">25100204<\/PMID><DateCompleted><Year>2016<\/Year><Month>05<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">2159-8290<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>4<\/Volume><Issue>10<\/Issue><PubDate><Year>2014<\/Year><Month>Oct<\/Month><\/PubDate><\/JournalIssue><Title>Cancer discovery<\/Title><ISOAbbreviation>Cancer Discov<\/ISOAbbreviation><\/Journal><ArticleTitle>Development of siRNA payloads to target KRAS-mutant cancer.<\/ArticleTitle><Pagination><MedlinePgn>1182-1197<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1158\/2159-8290.CD-13-0900<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">RNAi is a powerful tool for target identification and can lead to novel therapies for pharmacologically intractable targets such as KRAS. RNAi therapy must combine potent siRNA payloads with reliable in vivo delivery for efficient target inhibition. We used a functional \"Sensor\" assay to establish a library of potent siRNAs against RAS pathway genes and to show that they efficiently suppress their targets at low dose. This reduces off-target effects and enables combination gene knockdown. We administered Sensor siRNAs in vitro and in vivo and validated the delivery of KRAS siRNA alone and siRNA targeting the complete RAF effector node (A\/B\/CRAF) as promising strategies to treat KRAS-mutant colorectal cancer. We further demonstrate that improved therapeutic efficacy is achieved by formulating siRNA payloads that combine both single-gene siRNA and node-targeted siRNAs (KRAS + PIK3CA\/B). The customizable nature of Sensor siRNA payloads offers a universal platform for the combination target identification and development of RNAi therapeutics.","authors":"Yuan, TL., Fellmann, C., Lee, CS., Ritchie, CD., Thapar, V., Lee, LC., Hsu, DJ., Grace, D., Carver, JO., Zuber, J., Luo, J., McCormick, F., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cancer Discov","volume":"4","issue":"10","page":"1182-1197","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24825175","title":"Chasing Phosphoarginine Proteins: Development of a Selective Enrichment Method Using a Phosphatase Trap.","abstract":"Arginine phosphorylation is an emerging post-translational protein modification implicated in the bacterial stress response. Although early reports suggested that arginine phosphorylation also occurs in higher eukaryotes, its overall prevalence was never studied using modern mass spectrometry methods, owing to technical difficulties arising from the acid lability of phosphoarginine. As shown recently, the McsB and YwlE proteins from Bacillus subtilis function as a highly specific protein arginine kinase and phosphatase couple, shaping the phosphoarginine proteome. Using a B. subtilis \u0394ywlE strain as a source for arginine-phosphorylated proteins, we were able to adapt mass spectrometry (MS) protocols to the special chemical properties of the arginine modification. Despite this progress, the analysis of protein arginine phosphorylation in eukaryotes is still challenging, given the great abundance of serine\/threonine phosphorylations that would compete with phosphoarginine during the phosphopeptide enrichment procedure, as well as during data-dependent MS acquisition. We thus set out to establish a method for the selective enrichment of arginine-phosphorylated proteins as an initial step in the phosphoproteomic analysis. For this purpose, we developed a substrate-trapping mutant of the YwlE phosphatase that retains binding affinity toward arginine-phosphorylated proteins but cannot hydrolyze the captured substrates. By testing a number of active site substitutions, we identified a YwlE mutant (C9A) that stably binds to arginine-phosphorylated proteins. We further improved the substrate-trapping efficiency by impeding the oligomerization of the phosphatase mutant. The engineered YwlE trap efficiently captured arginine-phosphorylated proteins from complex B. subtilis \u0394ywlE cell extracts, thus facilitating identification of phosphoarginine sites in the large pool of cellular protein modifications. In conclusion, we present a novel tool for the selective enrichment and subsequent MS analysis of arginine phosphorylation, which is a largely overlooked protein modification that might be important for eukaryotic cell signaling.","authors":"Trentini, DB., Fuhrmann, J., Mechtler, K., Clausen, T.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mol Cell Proteomics","volume":"13","issue":"8","page":"1953-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14585831","title":"Stress induces mitochondria-mediated apoptosis independent of SAPK\/JNK activation in embryonic stem cells.","abstract":"SAPK\/JNK, which belongs to the family of mitogen-activated protein kinase (MAPK), is activated by many types of cellular stresses or extracellular signals and is involved in embryonic development, immune responses, and cell survival or apoptosis. However, the physiological roles of SAPK\/JNK in the signaling of stress-induced apoptosis are still controversial. To evaluate the precise function, SAPK\/JNK-inactivated mouse embryonic stem (ES) cells were generated by disrupting genes of the MAPK activators, SEK1 and MKK7. Although SAPK\/JNK activation by various stresses was completely abolished in sek1(-\/-) mkk7(-\/-) ES cells, apoptotic responses including DNA fragmentation and caspase 3 activation still occurred normally, which displays a sharp contrast to apaf1(-\/-) ES cells exhibiting profound defects in the mitochondria-dependent apoptosis. These normal apoptotic responses without SAPK\/JNK activation were also observed in fibroblasts derived from sek1(-\/-) mkk7(-\/-) ES cells. Instead, interleukin-1 beta (IL-1 beta)-induced IL-6 gene expression was greatly suppressed in sek1(-\/-) mkk7(-\/-) fibroblasts. These results clearly show that SAPK\/JNK activation is responsible for the inflammatory cytokine-induced gene expression but not essentially required for the mitochondria-dependent apoptosis at least in ES or fibroblast-like cells, which are prototypes of all cell lineages.","authors":"Nishitai, G., Shimizu, N., Negishi, T., Kishimoto, H., Nakagawa, K., Kitagawa, D., Watanabe, T., Momose, H., Ohata, S., Tanemura, S., Asaka, S., Kubota, J., Saito, R., Yoshida, H., Mak, TW., Wada, T., Penninger, JM., Azuma, N., Nishina, H., Katada, T.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Biol Chem","volume":"279","issue":"3","page":"1621-6","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24508173","title":"Neural circuit components of the Drosophila OFF motion vision pathway.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24508173<\/PMID><DateCompleted><Year>2014<\/Year><Month>09<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2014<\/Year><Month>02<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>24<\/Volume><Issue>4<\/Issue><PubDate><Year>2014<\/Year><Month>Feb<\/Month><Day>17<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Neural circuit components of the Drosophila OFF motion vision pathway.<\/ArticleTitle><Pagination><MedlinePgn>385-92<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2014.01.006<\/ELocationID><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0960-9822(14)00007-4<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Detecting the direction of visual motion is an\u00a0essential task of the early visual system. The Reichardt detector has been proven to be a faithful description of the underlying computation in insects. A series of recent studies addressed the neural implementation of the Reichardt detector in Drosophila revealing the overall layout in parallel ON and OFF channels, its input neurons from the lamina (L1\u2192ON, and L2\u2192OFF), and the respective output neurons to the lobula plate (ON\u2192T4, and OFF\u2192T5). While anatomical studies showed that T4 cells receive input from L1 via Mi1 and Tm3 cells, the neurons connecting L2 to T5 cells have not been identified so far. It is, however, known that L2 contacts, among others, two neurons, called Tm2 and L4, which show a pronounced directionality in their wiring.","authors":"Meier, M., Serbe, E., Maisak, MS., Haag, J., Dickson, BJ., Borst, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Biol","volume":"24","issue":"4","page":"385-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24332542","title":"cis-regulatory requirements for tissue-specific programs of the circadian clock.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24332542<\/PMID><DateCompleted><Year>2014<\/Year><Month>08<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>05<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>24<\/Volume><Issue>1<\/Issue><PubDate><Year>2014<\/Year><Month>Jan<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>cis-regulatory requirements for tissue-specific programs of the circadian clock.<\/ArticleTitle><Pagination><MedlinePgn>1-10<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0960-9822(13)01403-6<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2013.11.017<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Broadly expressed transcriptions factors (TFs) control tissue-specific programs of gene expression through interactions with local TF networks. A prime example is the circadian clock: although the conserved TFs CLOCK (CLK) and CYCLE (CYC) control a transcriptional circuit throughout animal bodies, rhythms in behavior and physiology are generated tissue specifically. Yet, how CLK and CYC determine tissue-specific clock programs has remained unclear.","authors":"Meireles-Filho, ACA., Bardet, AF., Y\u00e1\u00f1ez-Cuna, JO., Stampfel, G., Stark, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Biol","volume":"24","issue":"1","page":"1-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14560016","title":"Cbl-3-deficient mice exhibit normal epithelial development.","abstract":"Cbl family proteins are evolutionarily conserved ubiquitin ligases that negatively regulate signaling from tyrosine kinase-coupled receptors. The mammalian cbl family consists of c-Cbl, Cbl-b, and the recently cloned Cbl-3 (also known as Cbl-c). In this study, we describe the detailed expression pattern of murine Cbl-3 and report the generation and characterization of Cbl-3-deficient mice. Cbl-3 exhibits an expression pattern distinct from those of c-Cbl and Cbl-b, with high levels of Cbl-3 expression in epithelial cells of the gastrointestinal tract and epidermis, as well as the respiratory, urinary, and reproductive systems. Cbl-3 expression was not detected in nonepithelial cells, but within epithelial tissues, the levels of Cbl-3 expression varied from undetectable in the alveoli of the lungs to very strong in the cecum and colon. Despite this restricted expression pattern, Cbl-3-deficient mice were viable, healthy, and fertile and displayed no histological abnormalities up to 18 months of age. Proliferation of epithelial cells in the epidermises and gastrointestinal tracts was unaffected by the loss of Cbl-3. Moreover, Cbl-3 was not required for attenuation of epidermal growth factor-stimulated Erk activation in primary keratinocytes. Thus, Cbl-3 is dispensable for normal epithelial development and function.","authors":"Griffiths, EK., Sanchez, O., Mill, P., Krawczyk, C., Hojilla, CV., Rubin, E., Nau, MM., Khokha, R., Lipkowitz, S., Hui, CC., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Mol Cell Biol","volume":"23","issue":"21","page":"7708-18","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2003-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23980024","title":"Identification of transcription factor binding sites from ChIP-seq data at high resolution.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Curated\" Owner=\"NLM\"><PMID Version=\"1\">23980024<\/PMID><DateCompleted><Year>2014<\/Year><Month>03<\/Month><Day>31<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1367-4811<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>29<\/Volume><Issue>21<\/Issue><PubDate><Year>2013<\/Year><Month>Nov<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Identification of transcription factor binding sites from ChIP-seq data at high resolution.<\/ArticleTitle><Pagination><MedlinePgn>2705-13<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/bioinformatics\/btt470<\/ELocationID><Abstract><AbstractText Label=\"MOTIVATION\" NlmCategory=\"BACKGROUND\">Chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-seq) is widely used to study the in vivo binding sites of transcription factors (TFs) and their regulatory targets. Recent improvements to ChIP-seq, such as increased resolution, promise deeper insights into transcriptional regulation, yet require novel computational tools to fully leverage their advantages.","authors":"Bardet, AF., Steinmann, J., Bafna, S., Knoblich, JA., Zeitlinger, J., Stark, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Bioinformatics","volume":"29","issue":"21","page":"2705-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28642382","title":"A global brain state underlies <i>C. elegans<\/i> sleep behavior.","abstract":"How the brain effectively switches between and maintains global states, such as sleep and wakefulness, is not yet understood. We used brainwide functional imaging at single-cell resolution to show that during the developmental stage of lethargus, the <i>Caenorhabditis elegans<\/i> brain is predisposed to global quiescence, characterized by systemic down-regulation of neuronal activity. Only a few specific neurons are exempt from this effect. In the absence of external arousing cues, this quiescent brain state arises by the convergence of neuronal activities toward a fixed-point attractor embedded in an otherwise dynamic neural state space. We observed efficient spontaneous and sensory-evoked exits from quiescence. Our data support the hypothesis that during global states such as sleep, neuronal networks are drawn to a baseline mode and can be effectively reactivated by signaling from arousing circuits.","authors":"Nichols, ALA., Eichler, T., Latham, R., Zimmer, M.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Science","volume":"356","issue":"6344","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14561405","title":"The meiosis I-to-meiosis II transition in mouse oocytes requires separase activity.","abstract":"Faithful segregation of homologous chromosomes during the first meiotic division is essential for further embryo development. The question at issue is whether the same mechanisms ensuring correct separation of sister chromatids in mitosis are at work during the first meiotic division. In mitosis, sister chromatids are linked by a cohesin complex holding them together until their disjunction at anaphase. Their disjunction is mediated by Separase, which cleaves the cohesin. The activation of Separase requires prior degradation of its associated inhibitor, called securin. Securin is a target of the APC\/C (Anaphase Promoting Complex\/Cyclosome), a cell cycle-regulated ubiquitin ligase that ubiquitinates securin at the metaphase-to-anaphase transition and thereby targets it for degradation by the 26S proteasome. After securin degradation, Separase cleaves the cohesins and triggers chromatid separation, a prerequisite for anaphase. In yeast and worms, the segregation of homologous chromosomes in meiosis I depends on the APC\/C and Separase activity. Yet, it is unclear if Separase is required for the first meiotic division in vertebrates because APC\/C activity is thought to be dispensable in frog oocytes. We therefore investigated if Separase activity is required for correct chromosome segregation in meiosis I in mouse oocytes.","authors":"Terret, ME., Wassmann, K., Waizenegger, I., Maro, B., Peters, JM., Verlhac, MH.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"20","page":"1797-802","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3458176","title":"Self-inactivating retroviral vectors designed for transfer of whole genes into mammalian cells.","abstract":"A retrovirus-derived vector called self-inactivating (SIN) vector was designed for the transduction of whole genes into mammalian cells. SIN vectors contain a deletion of 299 base pairs in the 3' long terminal repeat (LTR), which includes sequences encoding the enhancer and promoter functions. When viruses derived from such vectors were used to infect NIH 3T3 cells, the deletion was transferred to the 5' LTR, resulting in the transcriptional inactivation of the provirus in the infected cell. Introduction of a hybrid gene (human metallothionein-promoted c-fos) into cells via a SIN vector was not associated with rearrangements and led to the formation of an authentic mRNA transcript, which in some cases was induced by cadmium. SIN vectors should be particularly useful in gene transfer experiments designed to study the regulated expression of genes in mammalian cells. Absence of enhancer and promoter sequences in both LTRs of the integrated provirus should also minimize the possibility of activating cellular oncogenes and may provide a safer alternative to be used in human gene therapy.","authors":"Yu, SF., von R\u00fcden, T., Kantoff, PW., Garber, C., Seiberg, M., R\u00fcther, U., Anderson, WF., Wagner, EF., Gilboa, E.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Proc Natl Acad Sci U S A","volume":"83","issue":"10","page":"3194-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1986-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14534245","title":"Impaired long-term memory and NR2A-type NMDA receptor-dependent synaptic plasticity in mice lacking c-Fos in the CNS.","abstract":"The immediate early gene c-fos is part of the activator protein-1 transcription factor and has been postulated to participate in the molecular mechanisms of learning and memory. To test this hypothesis in vivo, we generated mice with a nervous system-specific c-fos knock-out using the Cre-loxP system. Adult mice lacking c-Fos in the CNS (c-fosDeltaCNS) showed normal general and emotional behavior but were specifically impaired in hippocampus-dependent spatial and associative learning tasks. These learning deficits correlated with a reduction of long-term potentiation (LTP) in hippocampal CA3-CA1 synapses. The magnitude of LTP was restored by a repeated tetanization procedure, suggesting impaired LTP induction in c-fosDeltaCNS mice. This rescue was blocked by a selective inhibitor of NR2B-type NMDA receptors. This blockade was compensated in wild-type mice by NR2A-type NMDA receptor-activated signaling pathways, thus indicating that these pathways are compromised in c-fosDeltaCNS mice. In summary, our data suggest a role for c-Fos in hippocampus-dependent learning and memory as well as in NMDA receptor-dependent LTP formation.","authors":"Fleischmann, A., Hvalby, O., Jensen, V., Strekalova, T., Zacher, C., Layer, LE., Kvello, A., Reschke, M., Spanagel, R., Sprengel, R., Wagner, EF., Gass, P.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Neurosci","volume":"23","issue":"27","page":"9116-22","pdf":null,"JrId":"5035","fulltextlink":null,"preprintlink":null,"articledate":"2003-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3359993","title":"Characterization of the hormone-binding domain of the chicken c-erbA\/thyroid hormone receptor protein.","abstract":"To identify and characterize the hormone-binding domain of the thyroid hormone receptor, we analyzed the ligand-binding capacities of proteins representing chimeras between the normal receptor and P75gag-v-erbA, the retrovirus-encoded form deficient in binding ligand. Our results show that several mutations present in the carboxy-terminal half of P75gag-v-erbA co-operate in abolishing hormone binding, and that the ligand-binding domain resides in a position analogous to that of steroid receptors. Furthermore, a point mutation that is located between the putative DNA and ligand-binding domains of P75gag-v-erbA and that renders it biologically inactive fails to affect hormone binding by the c-erbA protein. These results suggest that the mutation changed the ability of P75gag-v-erbA to affect transcription since it also had no effect on DNA binding. Our data also suggest that hormone-independent activity of P75gag-v-erbA provided a selective advantage to the avian erythroblastosis virus during the original selection for a highly oncogenic strain of the virus.","authors":"Mu\u00f1oz, A., Zenke, M., Gehring, U., Sap, J., Beug, H., Vennstr\u00f6m, B.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"EMBO J","volume":"7","issue":"1","page":"155-9","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1988-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23284678","title":"Tumor development, growth characteristics and spectrum of genetic aberrations in the TH-MYCN mouse model of neuroblastoma.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23284678<\/PMID><DateCompleted><Year>2013<\/Year><Month>06<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>26<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><Issue>12<\/Issue><PubDate><Year>2012<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Tumor development, growth characteristics and spectrum of genetic aberrations in the TH-MYCN mouse model of neuroblastoma.<\/ArticleTitle><Pagination><MedlinePgn>e51297<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0051297<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The TH-MYCN transgenic neuroblastoma model, with targeted MYCN expression to the developing neural crest, has been used to study neuroblastoma development and evaluate novel targeted tumor therapies.","authors":"Rasmuson, A., Segerstr\u00f6m, L., Nethander, M., Finnman, J., Elfman, LH., Javanmardi, N., Nilsson, S., Johnsen, JI., Martinsson, T., Kogner, P.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"12","page":"e51297","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19362531","title":"Cohesin acetylation: from antiestablishment to establishment.","abstract":"In a recent issue of Molecular Cell, Rowland et al. (2009) report that acetylation of cohesin in S phase transiently counteracts an intrinsic \"antiestablishment\" activity and, thus, enables establishment of sister chromatid cohesion.","authors":"Peters, JM., Bhaskara, V.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Cell","volume":"34","issue":"1","page":"1-2","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20839297","title":"Atomic forces for geometry-dependent point multipole and gaussian multipole models.","abstract":"In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise because of (1) the transfer of torque between neighboring atoms and (2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In this study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives partial derivative D(m'm)(l)\/partial derivative Omega. The force equations can be applied to electrostatic models based on atomic point multipoles or gaussian multipole charge density. Hydrogen-bonded dimers are used to test the intermolecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential. The electrostatic energies and forces are compared with their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, whereas geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models.","authors":"Elking, DM., Perera, L., Duke, R., Darden, T., Pedersen, LG.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Comput Chem","volume":"31","issue":"15","page":"2702-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12950631","title":"Conserved and divergent functions of Drosophila atonal, amphibian, and mammalian Ath5 genes.","abstract":"Insect and vertebrate eyes differ in their formation, cellular composition, neural connectivity, and visual function. Despite this diversity, Drosophila atona and its vertebrate Ortholog in the eye, Ath5, each regulate determination of the first retinal neuron class-R8 photo-receptors and retinal ganglion cells (RGCs)-in their respective organisms. We have performed a cross-species functional comparison of these genes. In ato mutant Drosophila, ectopic Xenopus Ath5 (Xath5) rescues photoreceptor cell development comparably with atonaI. In contrast, mouse Ath5 (Math5) induces formation of very few ommatidia, and most of these lack R8 cells. In the developing frog eye, ectopic atonal, like Xath5, promotes the differentiation RGCs. Despite strong conservation of atonaI, Xath5, and Math5 structure and shared function, other factors must contribute to the species specificity of retinal neuron determination. These observations suggest that the atonaI family may occupy a position in a gene hierarchy where differences in gene regulation or function can be correlated with evolutionary diversity of eye development.","authors":"Sun, Y., Kanekar, SL., Vetter, ML., Gorski, S., Jan, YN., Glaser, T., Brown, NL.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Evol Dev","volume":"5","issue":"5","page":"532-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14525765","title":"Activated Fps\/Fes partially rescues the in vivo developmental potential of Flk1-deficient vascular progenitor cells.","abstract":"Relatively little is known about the modulators of the vascular endothelial growth factor A (VEGF-A)\/Flk1 signaling cascade. To functionally characterize this pathway, VEGF-A stimulation of endothelial cells was performed. VEGF-A-mediated Flk1 activation resulted in increased translocation of the endogenous Fps\/Fes cytoplasmic tyrosine kinase to the plasma membrane and increased tyrosine phosphorylation, suggesting a role for Fps\/Fes in VEGF-A\/Flk1 signaling events. Addition of a myristoylation consensus sequence to Fps\/Fes resulted in VEGF-A-independent membrane localization of Fps\/Fes in endothelial cells. Expression of the activated Fps\/Fes protein in Flk1-deficient embryonic stem (ES) cells rescued their contribution to the developing vascular endothelium in vivo by using ES cell-derived chimeras. Activated Fps\/Fes contributed to this rescue event by restoring the migratory potential to Flk1 null progenitors, which is required for movement of hemangioblasts from the primitive streak region into the yolk sac proper. Activated Fps\/Fes in the presence of Flk1 increased the number of hemangioblast colonies in vitro and increased the number of mesodermal progenitors in vivo. These results suggest that Fps\/Fes may act synergistically with Flk1 to modulate hemangioblast differentiation into the endothelium. We have also demonstrated that activated Fps\/Fes causes hemangioma formation in vivo, independently of Flk1, as a result of increasing vascular progenitor density.","authors":"Haigh, JJ., Ema, M., Haigh, K., Gertsenstein, M., Greer, P., Rossant, J., Nagy, A., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Blood","volume":"103","issue":"3","page":"912-20","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23082199","title":"Associations between pathogens in the upper respiratory tract of young children: interplay between viruses and bacteria.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23082199<\/PMID><DateCompleted><Year>2013<\/Year><Month>04<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><Issue>10<\/Issue><PubDate><Year>2012<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Associations between pathogens in the upper respiratory tract of young children: interplay between viruses and bacteria.<\/ArticleTitle><Pagination><MedlinePgn>e47711<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0047711<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">High rates of potentially pathogenic bacteria and respiratory viruses can be detected in the upper respiratory tract of healthy children. Investigating presence of and associations between these pathogens in healthy individuals is still a rather unexplored field of research, but may have implications for interpreting findings during disease.","authors":"van den Bergh, MR., Biesbroek, G., Rossen, JW., de Steenhuijsen Piters, WA., Bosch, AA., van Gils, EJ., Wang, X., Boonacker, CW., Veenhoven, RH., Bruin, JP., Bogaert, D., Sanders, EA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"10","page":"e47711","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23080021","title":"Contribution of mature hepatocytes to small hepatocyte-like progenitor cells in retrorsine-exposed rats with chimeric livers.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23080021<\/PMID><DateCompleted><Year>2013<\/Year><Month>04<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2013<\/Year><Month>11<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1527-3350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>57<\/Volume><Issue>3<\/Issue><PubDate><Year>2013<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>Hepatology (Baltimore, Md.)<\/Title><ISOAbbreviation>Hepatology<\/ISOAbbreviation><\/Journal><ArticleTitle>Contribution of mature hepatocytes to small hepatocyte-like progenitor cells in retrorsine-exposed rats with chimeric livers.<\/ArticleTitle><Pagination><MedlinePgn>1215-24<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/hep.26104<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">The potential lineage relationship between hepatic oval cells, small hepatocyte-like progenitor cells (SHPCs), and hepatocytes in liver regeneration is debated. To test whether mature hepatocytes can give rise to SHPCs, rats with dipeptidyl peptidase IV (DPPIV) chimeric livers, which harbored endogenous DPPIV-deficient hepatocytes and transplanted DPPIV-positive hepatocytes, were subjected to retrorsine treatment followed by partial hepatectomy (PH). DPPIV-positive hepatocytes comprised about half of the DPPIV chimeric liver mass. Tissues from DPPIV chimeric livers after retrorsine\/PH treatment showed large numbers of SHPC clusters. None of the SHPC clusters were stained positive for DPPIV in any analyzed samples. Furthermore, serial sections stained for gamma-glutamyl-transpeptidase (GGT, a marker of fetal hepatoblasts) and glucose-6-phosphatase (G6Pase, a marker of mature hepatocytes) showed inverse expression of the two enzymes and a staining pattern consistent with a lineage that begins with GGT(+)\/G6Pase(-) to GGT(-)\/G6Pase(+) within a single SHPC cluster. Using double immunofluorescence staining for markers specific for hepatic oval cells and hepatocytes in serial sections, oval cell proliferations with CK-19(+)\/laminin(+) and OV-6(+)\/C\/EBP-\u03b1(-) were shown to extend from periportal areas into the SPHC clusters, differentiating into hepatic lineage by progressive loss of CK-19\/laminin expression and appearance of C\/EBP-\u03b1 expression towards the cluster side. Cells in the epithelial cell adhesion molecule (EpCAM(+)) SHPC clusters showed membranous EpCAM(+)\/HNF-4\u03b1(+) (hepatocyte nuclear factor-4\u03b1) staining and were contiguous to the surrounding cytoplasmic EpCAM(+)\/HNF-4\u03b1(-) ductular oval cells. Extensive elimination of oval cell response by repeated administration of 4,4'-methylenedianiline (DAPM) to retrorsine-exposed rats impaired the emergence of SHPC clusters.","authors":"Chen, YH., Chang, MH., Chien, CS., Wu, SH., Yu, CH., Chen, HL.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Hepatology","volume":"57","issue":"3","page":"1215-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29955892","title":"How to create state-of-the-art genetic model systems: strategies for optimal CRISPR-mediated genome editing.","abstract":"Model systems with defined genetic modifications are powerful tools for basic research and translational disease modelling. Fortunately, generating state-of-the-art genetic model systems is becoming more accessible to non-geneticists due to advances in genome editing technologies. As a consequence, solely relying on (transient) overexpression of (mutant) effector proteins is no longer recommended since scientific standards increasingly demand genetic modification of endogenous loci. In this review, we provide up-to-date guidelines with respect to homology-directed repair (HDR)-mediated editing of mammalian model systems, aimed at assisting researchers in designing an efficient genome editing strategy.","authors":"Bollen, Y., Post, J., Koo, BK., Snippert, HJG.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nucleic Acids Res","volume":"46","issue":"13","page":"6435-6454","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20822488","title":"RNA-directed epigenetic regulation of DNA rearrangements.","abstract":"Ciliated protozoa undergo extensive DNA rearrangements, including DNA elimination, chromosome breakage and DNA unscrambling, when the germline micronucleus produces the new macronucleus during sexual reproduction. It has long been known that many of these events are epigenetically controlled by DNA sequences of the parental macronuclear genome. Recent studies in some model ciliates have revealed that these epigenetic regulations are mediated by non-coding RNAs. DNA elimination in Paramecium and Tetrahymena is regulated by small RNAs that are produced and operated by an RNAi (RNA interference)-related mechanism. It has been proposed that the small RNAs from the micronuclear genome can be used to identify eliminated DNAs by whole-genome comparison of the parental macronucleus and the micronucleus. In contrast, DNA unscrambling in Oxytricha is guided by long non-coding RNAs that are produced from the somatic parental macronuclear genome. These RNAs are proposed to act as templates for the direct unscrambling events that occur in the developing macronucleus. The possible evolutionary benefits of these RNA-directed epigenetic regulations of DNA rearrangement in ciliates are discussed in the present chapter.","authors":"Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Essays Biochem","volume":"48","issue":"1","page":"89-100","pdf":null,"JrId":"3591","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22936674","title":"CagA mediates epigenetic regulation to attenuate let-7 expression in Helicobacter pylori-related carcinogenesis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22936674<\/PMID><DateCompleted><Year>2013<\/Year><Month>12<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1468-3288<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>62<\/Volume><Issue>11<\/Issue><PubDate><Year>2013<\/Year><Month>Nov<\/Month><\/PubDate><\/JournalIssue><Title>Gut<\/Title><ISOAbbreviation>Gut<\/ISOAbbreviation><\/Journal><ArticleTitle>CagA mediates epigenetic regulation to attenuate let-7 expression in Helicobacter pylori-related carcinogenesis.<\/ArticleTitle><Pagination><MedlinePgn>1536-46<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1136\/gutjnl-2011-301625<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">MicroRNAs (miRNAs) act as tumour suppressor genes or oncogenes in the regulation of multiple carcinogenic processes. Aberrant miRNA expression is reported in Helicobacter pylori (H pylori)-related gastritis and gastric cancer. The cytotoxin-associated gene A (CagA) of H pylori has a pathophysiologically important role in gastric carcinogenesis. A study was undertaken to evaluate the effect of CagA on miRNA expression and its regulatory mechanism.","authors":"Hayashi, Y., Tsujii, M., Wang, J., Kondo, J., Akasaka, T., Jin, Y., Li, W., Nakamura, T., Nishida, T., Iijima, H., Tsuji, S., Kawano, S., Hayashi, N., Takehara, T.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Gut","volume":"62","issue":"11","page":"1536-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22646865","title":"New approaches for pediatric rhabdomyosarcoma drug discovery: targeting combinatorial signaling.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22646865<\/PMID><DateCompleted><Year>2012<\/Year><Month>10<\/Month><Day>02<\/Day><\/DateCompleted><DateRevised><Year>2014<\/Year><Month>07<\/Month><Day>31<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1746-045X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>6<\/Volume><Issue>10<\/Issue><PubDate><Year>2011<\/Year><Month>Oct<\/Month><\/PubDate><\/JournalIssue><Title>Expert opinion on drug discovery<\/Title><ISOAbbreviation>Expert Opin Drug Discov<\/ISOAbbreviation><\/Journal><ArticleTitle>New approaches for pediatric rhabdomyosarcoma drug discovery: targeting combinatorial signaling.<\/ArticleTitle><Pagination><MedlinePgn>1103-25<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1517\/17460441.2011.611498<\/ELocationID><Abstract><AbstractText Label=\"INTRODUCTION\" NlmCategory=\"BACKGROUND\">Rhabdomyosarcomas (RMS) are rare heterogeneous pediatric tumors that are treated by surgery, chemotherapy and irradiation. New therapeutic approaches are needed, especially in the advanced stages to target the pro-oncogenic signals. Exploring the molecular interactions of the regulatory signals and their roles in the developmental aspects of different subtypes of RMS is essential to identify potential targets and develop new therapeutic drugs.","authors":"Rengaswamy, V., Kontny, U., R\u00f6ssler, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Expert Opin Drug Discov","volume":"6","issue":"10","page":"1103-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3284746","title":"Characterization of a transcription factor involved in mother cell specific transcription of the yeast HO gene.","abstract":"The yeast HO gene, which encodes an endonuclease involved in initiating mating type interconversion, is expressed in mother cells but not in daughters. It has been demonstrated that the SWI5 gene, which is an activator of HO expression, plays a critical role in this differential mother\/daughter expression of HO. In this paper we describe the cloning and sequencing of the SWI5 gene. The predicted amino acid sequence derived from the cloned SWI5 gene shows homology with the repeated DNA-binding domains ('zinc fingers') of Xenopus transcription factor TFIIIA. A region of the HO promoter involved in the SWI5-dependent transcriptional activation of HO was identified by deletion analysis of the HO promoter in the chromosome, and by testing the ability of HO DNA fragments to activate transcription in the context of a heterologous promoter. The SWI5 gene product was overproduced in yeast from the GAL1-10 promoter, since the SWI5 protein is made at very low levels in wild-type strains, and protein extracts were used to demonstrate that the SWI5 protein binds in vitro to a segment of the HO promoter required for transcriptional activation in vivo.","authors":"Stillman, DJ., Bankier, AT., Seddon, A., Groenhout, EG., Nasmyth, KA.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"EMBO J","volume":"7","issue":"2","page":"485-94","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1988-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12907453","title":"JunB inhibits proliferation and transformation in B-lymphoid cells.","abstract":"The activator protein 1 (AP-1) member JunB has recently been implicated in leukemogenesis. Here we surveyed human lymphoma samples for expression of JunB and other AP-1 members (c-Jun, c-Fos, Fra1, JunD). JunB was strongly expressed in T-cell lymphomas, but non-Hodgkin B-cell lymphomas do not or only weakly express JunB. We therefore asked whether JunB acted as a negative regulator of B-cell development, proliferation, and transformation. We used transgenic mice that expressed JunB under the control of the ubiquitin C promoter; these displayed increased JunB levels in both B- and T-lymphoid cells. JunB transgenic cells of B-lymphoid, but not of T-lymphoid, origin responded poorly to mitogenic stimuli. Furthermore, JunB transgenic cells were found to be less susceptible to the transforming potential of the Abelson oncogene in vitro. In addition, overexpression of JunB partially protected transgenic mice against the oncogenic challenge in vivo. However, transformed B cells eventually escaped from the inhibitory effect of JunB: the proliferative response was similar in explanted tumor-derived cells from transgenic animals and those from wild-type controls. Our results identify JunB as a novel regulator of B-cell proliferation and transformation.","authors":"Szremska, AP., Kenner, L., Weisz, E., Ott, RG., Passegu\u00e9, E., Artwohl, M., Freissmuth, M., Stoxreiter, R., Theussl, HC., Parzer, SB., Moriggl, R., Wagner, EF., Sexl, V.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Blood","volume":"102","issue":"12","page":"4159-65","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12869505","title":"Cooperative signaling between cytokine receptors and the glucocorticoid receptor in the expansion of erythroid progenitors: molecular analysis by expression profiling.","abstract":"Erythroid progenitors undergo renewal (proliferation without apparent differentiation) in response to erythropoietin (Epo), stem cell factor (SCF), and glucocorticoids (dexamethasone) (Dex). SCF and Dex cooperate with Epo to promote proliferation and inhibit differentiation of erythroid progenitors, while Epo alone is required to protect erythroid cells from apoptosis during terminal red cell maturation. To examine the mechanism of the synergistic interactions of Epo, SCF, and Dex, we analyzed gene expression patterns using DNA chip-based large-scale comparative gene profiling using microarrays enriched in hematopoietic transcripts or containing randomly selected genes. Differentially regulated genes were validated by real-time reverse transcription-polymerase chain reaction (RT-PCR). The results reveal cooperative regulation of gene expression by glucocorticoids and Epo\/SCF on a number of genes, such as CIS, BTG1, VDUP1, CXCR4, GILZ, and RIKEN29300106B05. While Epo and SCF never showed opposite effects on gene expression, Dex either enhanced or attenuated the effect of Epo and\/or SCF. Several glucocorticoid receptor (GR)-target genes were regulated by Dex only in the presence of Epo and\/or SCF, suggesting that the GR functions in the context of a larger transactivation complex to regulate these genes. The data also suggest that modulation of cytokine-induced signals by the GR is an important mechanism in erythroid progenitor renewal.","authors":"Kolbus, A., Bl\u00e1zquez-Domingo, M., Carotta, S., Bakker, W., Luedemann, S., von Lindern, M., Steinlein, P., Beug, H.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Blood","volume":"102","issue":"9","page":"3136-46","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22637703","title":"Transcriptome analysis identifies TNF superfamily receptors as potential therapeutic targets in alcoholic hepatitis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22637703<\/PMID><DateCompleted><Year>2013<\/Year><Month>04<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1468-3288<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>62<\/Volume><Issue>3<\/Issue><PubDate><Year>2013<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>Gut<\/Title><ISOAbbreviation>Gut<\/ISOAbbreviation><\/Journal><ArticleTitle>Transcriptome analysis identifies TNF superfamily receptors as potential therapeutic targets in alcoholic hepatitis.<\/ArticleTitle><Pagination><MedlinePgn>452-60<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1136\/gutjnl-2011-301146<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">Alcoholic hepatitis (AH) is a severe clinical condition that needs novel therapies. The identification of targets for therapy is hampered by the lack of animal models of advanced AH. The authors performed a translational study through a transcriptome analysis in patients with AH to identify new molecular targets.","authors":"Aff\u00f2, S., Dominguez, M., Lozano, JJ., Sancho-Bru, P., Rodrigo-Torres, D., Morales-Ibanez, O., Moreno, M., Mill\u00e1n, C., Loaeza-del-Castillo, A., Altamirano, J., Garc\u00eda-Pag\u00e1n, JC., Arroyo, V., Gin\u00e8s, P., Caballer\u00eda, J., Schwabe, RF., Bataller, R.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Gut","volume":"62","issue":"3","page":"452-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3009024","title":"v-erbA cooperates with sarcoma oncogenes in leukemic cell transformation.","abstract":"The v-erbB, v-src, v-fps, v-sea, and v-Ha-ras oncogenes induce avian erythroid progenitor cells to self-renew in an erythropoietin-independent manner. These transformed erythroblasts retain both their capacity to differentiate into erythrocytes and their requirement for complex growth media. However, previous studies showed that erythroblasts transformed by v-erbB plus v-erbA (which by itself is not oncogenic) are blocked in differentiation and grow in standard media. Here we show that the introduction of v-erbA into erythroblasts transformed with v-src, v-fps, v-sea, or v-Ha-ras likewise induces a fully transformed phenotype. It also reduces the capacity of ts sea- and ts erbB-transformed erythroblasts to differentiate terminally in an erythropoietin-dependent manner after a temperature shift. Cooperativity involving v-erbA also occurs in vivo since chicks infected with a retroviral construct encoding v-erbA and v-src develop both acute erythroblastosis and sarcomas.","authors":"Kahn, P., Frykberg, L., Brady, C., Stanley, I., Beug, H., Vennstr\u00f6m, B., Graf, T.","publication_status":"ppublish","journalpubyear":"1986","journaltitle":"Cell","volume":"45","issue":"3","page":"349-56","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1986-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20620951","title":"Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases.","abstract":"The life span of a mammalian mRNA is determined, in part, by the binding of regulatory proteins and small RNA-guided complexes. The conserved endonuclease activity of Argonaute2 requires extensive complementarity between a small RNA and its target and is not used by animal microRNAs, which pair with their targets imperfectly. Here we investigate the endonucleolytic function of Ago2 and other nucleases by transcriptome-wide profiling of mRNA cleavage products retaining 5' phosphate groups in mouse embryonic stem cells (mESCs). We detect a prominent signature of Ago2-dependent cleavage events and validate several such targets. Unexpectedly, a broader class of Ago2-independent cleavage sites is also observed, indicating participation of additional nucleases in site-specific mRNA cleavage. Within this class, we identify a cohort of Drosha-dependent mRNA cleavage events that functionally regulate mRNA levels in mESCs, including one in the Dgcr8 mRNA. Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals.","authors":"Karginov, FV., Cheloufi, S., Chong, MM., Stark, A., Smith, AD., Hannon, GJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Mol Cell","volume":"38","issue":"6","page":"781-8","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20593419","title":"Mice lacking the orphan receptor ror1 have distinct skeletal abnormalities and are growth retarded.","abstract":"Ror1 is a member of the Ror-family receptor tyrosine kinases. Ror1 is broadly expressed in various tissues and organs during mouse embryonic development. However, so far little is known about its function. The closely related family member Ror2 was shown to play a crucial role in skeletogenesis and has been shown to act as a co-receptor for Wnt5a mediating non-canonical Wnt-signaling. Previously, it has been shown that during embryonic development Ror1 acts in part redundantly with Ror2 in the skeletal and cardiovascular systems. In this study, we report that loss of the orphan receptor Ror1 results in a variety of phenotypic defects within the skeletal and urogenital systems and that Ror1 mutant mice display a postnatal growth retardation phenotype.","authors":"Lyashenko, N., Weissenb\u00f6ck, M., Sharir, A., Erben, RG., Minami, Y., Hartmann, C.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Dev Dyn","volume":"239","issue":"8","page":"2266-77","pdf":null,"JrId":"1281","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37408019","title":"HiCognition: a visual exploration and hypothesis testing tool for 3D genomics.","abstract":"Genome browsers facilitate integrated analysis of multiple genomics datasets yet visualize only a few regions at a time and lack statistical functions for extracting meaningful information. We present HiCognition, a visual exploration and machine-learning tool based on a new genomic region set concept, enabling detection of patterns and associations between 3D chromosome conformation and collections of 1D genomics profiles of any type. By revealing how transcription and cohesion subunit isoforms contribute to chromosome conformation, we showcase how the flexible user interface and machine learning tools of HiCognition help to understand the relationship between the structure and function of the genome.","authors":"Langer, CCH., Mitter, M., Stocsits, RR., Gerlich, DW.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Genome Biol","volume":"24","issue":"1","page":"158","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22342966","title":"Disruption of Trp53 in livers of mice induces formation of carcinomas with bilineal differentiation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22342966<\/PMID><DateCompleted><Year>2012<\/Year><Month>06<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2012<\/Year><Month>04<\/Month><Day>24<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1528-0012<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>142<\/Volume><Issue>5<\/Issue><PubDate><Year>2012<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>Gastroenterology<\/Title><ISOAbbreviation>Gastroenterology<\/ISOAbbreviation><\/Journal><ArticleTitle>Disruption of Trp53 in livers of mice induces formation of carcinomas with bilineal differentiation.<\/ArticleTitle><Pagination><MedlinePgn>1229-1239.e3<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1053\/j.gastro.2012.02.009<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\" NlmCategory=\"OBJECTIVE\">p53 limits the self-renewal of stem cells from various tissues. Loss of p53, in combination with other oncogenic events, results in aberrant self-renewal and transformation of progenitor cells. It is not known whether loss of p53 is sufficient to induce tumor formation in liver.","authors":"Katz, SF., Lechel, A., Obenauf, AC., Begus-Nahrmann, Y., Kraus, JM., Hoffmann, EM., Duda, J., Eshraghi, P., Hartmann, D., Liss, B., Schirmacher, P., Kestler, HA., Speicher, MR., Rudolph, KL.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Gastroenterology","volume":"142","issue":"5","page":"1229-1239.e3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12818157","title":"Identifying the MAGUK protein Carma-1 as a central regulator of humoral immune responses and atopy by genome-wide mouse mutagenesis.","abstract":"In a genome-wide ENU mouse mutagenesis screen a recessive mouse mutation, unmodulated, was isolated with profound defects in humoral immune responses, selective deficits in B cell activation by antigen receptors and T cell costimulation by CD28, and gradual development of atopic dermatitis with hyper-IgE. Mutant B cells are specifically defective in forming connections between antigen receptors and two key signaling pathways for immunogenic responses, NF-kappaB and JNK, but signal normally to calcium, NFAT, and ERK. The mutation alters a conserved leucine in the coiled-coil domain of CARMA-1\/CARD11, a member of the MAGUK protein family implicated in organizing multimolecular signaling complexes. These results define Carma-1 as a key regulator of the plasticity in antigen receptor signaling that underpins opposing mechanisms of immunity and tolerance.","authors":"Jun, JE., Wilson, LE., Vinuesa, CG., Lesage, S., Blery, M., Miosge, LA., Cook, MC., Kucharska, EM., Hara, H., Penninger, JM., Domashenz, H., Hong, NA., Glynne, RJ., Nelms, KA., Goodnow, CC.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Immunity","volume":"18","issue":"6","page":"751-62","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12808045","title":"Calponin repeats regulate actin filament stability and formation of podosomes in smooth muscle cells.","abstract":"Phorbol ester induces actin cytoskeleton rearrangements in cultured vascular smooth muscle cells. Calponin and SM22 alpha are major components of differentiated smooth muscle and potential regulators of actin cytoskeleton interactions. Here we show that actin fibers decorated with h1 CaP remain stable, whereas SM22 alpha-decorated actin bundles undergo rapid reorganization into podosomes within 30 min of PDBu exposure. Ectopic expression of GFP alpha-actinin had no effect on the stability of the actin cytoskeleton and alpha-actinin was transported rapidly into PDBu-induced podosomes. Our results demonstrate the involvement of CaP and SM22 alpha in coordinating the balance between stabilization and dynamics of the actin cytoskeleton in mammalian smooth muscle. We provide evidence for the existence of two functionally distinct actin filament populations and introduce a molecular mechanism for the stabilization of the actin cytoskeleton by the unique actin-binding interface formed by calponin family-specific CLIK23 repeats.","authors":"Gimona, M., Kaverina, I., Resch, GP., Vignal, E., Burgstaller, G.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Mol Biol Cell","volume":"14","issue":"6","page":"2482-91","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17729270","title":"Crystal structure of the flavin reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8: Structural basis for the flavin affinity.","abstract":"The two-component enzyme, 4-hydroxyphenylacetate 3-monooxygenase, catalyzes the conversion of 4-hydroxyphenylacetate to 3,4-dihydroxyphenylacetate. In the overall reaction, the oxygenase component (HpaB) introduces a hydroxyl group into the benzene ring of 4-hydroxyphenylacetate using molecular oxygen and reduced flavin, while the reductase component (HpaC) provides free reduced flavins for HpaB. The crystal structures of HpaC from Thermus thermophilus HB8 in the ligand-free form, the FAD-containing form, and the ternary complex with FAD and NAD(+) were determined. In the ligand-free form, two large grooves are present at the dimer interface, and are occupied by water molecules. A structural analysis of HpaC containing FAD revealed that FAD has a low occupancy, indicating that it is not tightly bound to HpaC. This was further confirmed in flavin dissociation experiments, showing that FAD can be released from HpaC. The structure of the ternary complex revealed that FAD and NAD(+) are bound in the groove in the extended and folded conformation, respectively. The nicotinamide ring of NAD(+) is sandwiched between the adenine ring of NAD(+) and the isoalloxazine ring of FAD. The distance between N5 of the isoalloxazine ring and C4 of the nicotinamide ring is about 3.3 A, sufficient to permit hydride transfer. The structures of these three states are essentially identical, however, the side chains of several residues show small conformational changes, indicating an induced fit upon binding of NADH. Inactivity with respect to NADPH can be explained as instability of the binding of NADPH with the negatively charged 2'-phosphate group buried inside the complex, as well as a possible repulsive effect by the dipole of helix alpha1. A comparison of the binding mode of FAD with that in PheA2 from Bacillus thermoglucosidasius A7, which contains FAD as a prosthetic group, reveals remarkable conformational differences in a less conserved loop region (Gly83-Gly94) involved in the binding of the AMP moiety of FAD. These data suggest that variations in the affinities for FAD in the reductases of the two-component flavin-diffusible monooxygenase family may be attributed to difference in the interaction between the AMP moiety of FAD and the less conserved loop region which possibly shows structural divergence.","authors":"Kim, SH., Hisano, T., Iwasaki, W., Ebihara, A., Miki, K.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Proteins","volume":"70","issue":"3","page":"718-30","pdf":null,"JrId":"6646","fulltextlink":null,"preprintlink":null,"articledate":"2008-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21752895","title":"Variants in STAT5B associate with serum TC and LDL-C levels.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21752895<\/PMID><DateCompleted><Year>2011<\/Year><Month>11<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2017<\/Year><Month>09<\/Month><Day>22<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1945-7197<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>96<\/Volume><Issue>9<\/Issue><PubDate><Year>2011<\/Year><Month>Sep<\/Month><\/PubDate><\/JournalIssue><Title>The Journal of clinical endocrinology and metabolism<\/Title><ISOAbbreviation>J Clin Endocrinol Metab<\/ISOAbbreviation><\/Journal><ArticleTitle>Variants in STAT5B associate with serum TC and LDL-C levels.<\/ArticleTitle><Pagination><MedlinePgn>E1496-501<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1210\/jc.2011-0322<\/ELocationID><Abstract><AbstractText Label=\"CONTEXT\" NlmCategory=\"BACKGROUND\">Known genetic variants influencing serum lipid levels do not adequately account for the observed population variability of these phenotypes. The GH\/signal transducers and activators of transcription (STAT) signaling pathway is an evolutionary conserved system that exerts strong effects on metabolism, including that of lipids.","authors":"Kornfeld, JW., Isaacs, A., Vitart, V., Pospisilik, JA., Meitinger, T., Gyllensten, U., Wilson, JF., Rudan, I., Campbell, H., Penninger, JM., Sexl, V., Moriggl, R., van Duijn, C., Pramstaller, PP., Hicks, AA.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Clin Endocrinol Metab","volume":"96","issue":"9","page":"E1496-501","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21546487","title":"Phosphatidylinositol-3-kinase gamma plays a central role in blood-brain barrier dysfunction in acute experimental stroke.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21546487<\/PMID><DateCompleted><Year>2011<\/Year><Month>09<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4628<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>42<\/Volume><Issue>7<\/Issue><PubDate><Year>2011<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>Stroke<\/Title><ISOAbbreviation>Stroke<\/ISOAbbreviation><\/Journal><ArticleTitle>Phosphatidylinositol-3-kinase gamma plays a central role in blood-brain barrier dysfunction in acute experimental stroke.<\/ArticleTitle><Pagination><MedlinePgn>2033-44<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/STROKEAHA.110.601369<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND AND PURPOSE\" NlmCategory=\"OBJECTIVE\">Phosphoinositide 3-kinase (PI3K)-\u03b3 is linked to inflammation and oxidative stress. This study was conducted to investigate the role of the PI3K\u03b3 in the blood-brain barrier dysfunction and brain damage induced by focal cerebral ischemia\/reperfusion.","authors":"Jin, R., Song, Z., Yu, S., Piazza, A., Nanda, A., Penninger, JM., Granger, DN., Li, G.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Stroke","volume":"42","issue":"7","page":"2033-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11259394","title":"Dominant cell death induction by extramitochondrially targeted apoptosis-inducing factor.","abstract":"The complete AIF cDNA comprising the amino-terminal mitochondrial localization sequence (MLS) and the oxidoreductase domain has been fused in its carboxyl terminus to enhanced green fluorescent protein (GFP), thereby engineering an AIF-GFP fusion protein that is selectively targeted to the mitochondrial intermembrane space. Upon induction of apoptosis, the AIF-GFP protein translocates together with cytochrome c (Cyt-c) to the extramitochondrial compartment. Microinjection of recombinant AIF leads to the release of AIF-GFP and Cyt-c-GFP, indicating that ectopic AIF can favor permeabilization of the outer mitochondrial membrane. These mitochondrial effects of AIF are caspase independent, whereas the Cyt-c-microinjection induced translocation of AIF-GFP and Cyt-c-GFP is suppressed by the pan-caspase inhibitor Z-VAD.fmk. Upon prolonged culture, transfection-enforced overexpression of AIF results in spontaneous translocation of AIF-GFP from mitochondria, nuclear chromatin condensation, and cell death. These effects are caspase independent and do not rely on the oxidoreductase function of AIF. Spontaneous AIF-GFP translocation and subsequent nuclear apoptosis can be retarded by overexpression of a Bcl-2 protein selectively targeted to mitochondria, but not by a Bcl-2 protein targeted to the endoplasmic reticulum. Overexpression of a mutant AIF protein in which the MLS has been deleted (AIF Delta 1-100) results in the primary cytosolic accumulation of AIF. AIF Delta 1-100-induced cell death is suppressed by neither Z-VAD.fmk or by Bcl-2. Thus, extramitochondrially targeted AIF is a dominant cell death inducer.","authors":"Loeffler, M., Daugas, E., Susin, SA., Zamzami, N., Metivier, D., Nieminen, AL., Brothers, G., Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"FASEB J","volume":"15","issue":"3","page":"758-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12734400","title":"IRSp53 is colocalised with WAVE2 at the tips of protruding lamellipodia and filopodia independently of Mena.","abstract":"The insulin receptor tyrosine kinase substrate p53 (IRSp53) links Rac and WAVE2 and has been implicated in lamellipodia protrusion. Recently, however, IRSp53 has been reported to bind to both Cdc42 and Mena to induce filopodia. To shed independent light on IRSp53 function we determined the localisations and dynamics of IRSp53 and WAVE2 in B16 melanoma cells. In cells spread well on a laminin substrate, IRSp53 was localised by antibody labelling at the tips of both lamellipodia and filopodia. The same localisation was observed in living cells with IRSp53 tagged with enhanced green florescence protein (EGFP-IRSp53), but only during protrusion. From the transfection of deletion mutants the N-terminal region of IRSp53, which binds active Rac, was shown to be responsible for its localisation. Although IRSp53 has been reported to regulate filopodia formation with Mena, EGFP-IRSp53 showed the same localisation in MVD7 Ena\/VASP (vasodilator stimulated phosphoprotein) family deficient cells. WAVE2 tagged with DsRed1 colocalised with EGFP-IRSp53 at the tips of protruding lamellipodia and filopodia and, in double-transfected cells, the IRSp53 signal in filopodia decreased before that of WAVE2 during retraction. These results suggest an alternative modulatory role for IRSp53 in the extension of both filopodia and lamellipodia, through WAVE2.","authors":"Nakagawa, H., Miki, H., Nozumi, M., Takenawa, T., Miyamoto, S., Wehland, J., Small, JV.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Cell Sci","volume":"116","issue":"Pt 12","page":"2577-83","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2004-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12737807","title":"Division of the nucleolus and its release of CDC14 during anaphase of meiosis I depends on separase, SPO12, and SLK19.","abstract":"Disjunction of maternal and paternal centromeres during meiosis I requires crossing over between homologous chromatids, which creates chiasmata that hold homologs together. It also depends on a mechanism ensuring that maternal and paternal sister kinetochore pairs attach to oppositely oriented microtubules. Proteolytic cleavage of cohesin's Rec8 subunit by separase destroys cohesion between sister chromatid arms at anaphase I and thereby resolves chiasmata. The Spo12 and Slk19 proteins have been implicated in regulating meiosis I kinetochore orientation and\/or in preventing cleavage of Rec8 at centromeres. We show here that the role of these proteins is instead to promote nucleolar segregation, including release of the Cdc14 phosphatase required for Cdk1 inactivation and disassembly of the anaphase I spindle. Separase is also required but surprisingly not its protease activity. It has two mechanistically different roles during meiosis I. Loss of the protease-independent function alone results in a second meiotic division occurring on anaphase I spindles in spo12delta and slk19delta mutants.","authors":"Buonomo, SB., Rabitsch, KP., Fuchs, J., Gruber, S., Sullivan, M., Uhlmann, F., Petronczki, M., T\u00f3th, A., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Dev Cell","volume":"4","issue":"5","page":"727-39","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21288478","title":"Flt3-ITD alters chemotherapy response in vitro and in vivo in a p53-dependent manner.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21288478<\/PMID><DateCompleted><Year>2011<\/Year><Month>06<\/Month><Day>06<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>12<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1873-2399<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>39<\/Volume><Issue>4<\/Issue><PubDate><Year>2011<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>Experimental hematology<\/Title><ISOAbbreviation>Exp Hematol<\/ISOAbbreviation><\/Journal><ArticleTitle>Flt3-ITD alters chemotherapy response in vitro and in vivo in a p53-dependent manner.<\/ArticleTitle><Pagination><MedlinePgn>473-485.e4<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.exphem.2011.01.009<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">The FLT3 internal tandem duplication (Flt3-ITD) confers a worse prognosis for patients with acute myeloid leukemia (AML); however, the mechanisms involved are unknown. As AML is treated with cytarabine (Ara-C) and an anthracycline, we sought to determine the effects of the Flt3-ITD on response to these agents.","authors":"Pardee, TS., Zuber, J., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Exp Hematol","volume":"39","issue":"4","page":"473-485.e4","pdf":null,"JrId":"3651","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37524970","title":"A fine balancing act: how epitranscriptome regulates dosage compensation in mammals.","abstract":null,"authors":"Jachowicz, JW.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Nat Struct Mol Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520475","title":"Adnexal masses difficult to classify as benign or malignant using subjective assessment of gray-scale and Doppler ultrasound findings: logistic regression models do not help.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520475<\/PMID><DateCompleted><Year>2011<\/Year><Month>12<\/Month><Day>21<\/Day><\/DateCompleted><DateRevised><Year>2016<\/Year><Month>11<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1469-0705<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>38<\/Volume><Issue>4<\/Issue><PubDate><Year>2011<\/Year><Month>Oct<\/Month><\/PubDate><\/JournalIssue><Title>Ultrasound in obstetrics &amp; gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology<\/Title><ISOAbbreviation>Ultrasound Obstet Gynecol<\/ISOAbbreviation><\/Journal><ArticleTitle>Adnexal masses difficult to classify as benign or malignant using subjective assessment of gray-scale and Doppler ultrasound findings: logistic regression models do not help.<\/ArticleTitle><Pagination><MedlinePgn>456-65<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/uog.9030<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">To develop a logistic regression model that can discriminate between benign and malignant adnexal masses perceived to be difficult to classify by subjective evaluation of gray-scale and Doppler ultrasound findings (subjective assessment) and to compare its diagnostic performance with that of subjective assessment, serum CA 125 and the risk of malignancy index (RMI).","authors":"Valentin, L., Ameye, L., Savelli, L., Fruscio, R., Leone, FP., Czekierdowski, A., Lissoni, AA., Fischerova, D., Guerriero, S., Van Holsbeke, C., Van Huffel, S., Timmerman, D.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Ultrasound Obstet Gynecol","volume":"38","issue":"4","page":"456-65","pdf":null,"JrId":"8585","fulltextlink":null,"preprintlink":null,"articledate":"2011-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520314","title":"The CUSUM test applied in prospective nuchal translucency quality review.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520314<\/PMID><DateCompleted><Year>2011<\/Year><Month>06<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2011<\/Year><Month>04<\/Month><Day>26<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1469-0705<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>37<\/Volume><Issue>5<\/Issue><PubDate><Year>2011<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>Ultrasound in obstetrics &amp; gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology<\/Title><ISOAbbreviation>Ultrasound Obstet Gynecol<\/ISOAbbreviation><\/Journal><ArticleTitle>The CUSUM test applied in prospective nuchal translucency quality review.<\/ArticleTitle><Pagination><MedlinePgn>582-7<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/uog.8860<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\" NlmCategory=\"OBJECTIVE\">To design a cumulative sum (CUSUM) test for prospective nuchal translucency (NT) measurement quality review that is as stringent as the retrospective quality review methods based on distribution parameters currently in use.","authors":"Sabri\u00e0, J., Barcel\u00f3-Vidal, C., Arigita, M., Jimenez, JM., Puerto, B., Borrell, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Ultrasound Obstet Gynecol","volume":"37","issue":"5","page":"582-7","pdf":null,"JrId":"8585","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520265","title":"Medicinal leeches and the microsurgeon: a four-year study, clinical series and risk benefit review.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520265<\/PMID><DateCompleted><Year>2011<\/Year><Month>09<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2011<\/Year><Month>05<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1098-2752<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>31<\/Volume><Issue>4<\/Issue><PubDate><Year>2011<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>Microsurgery<\/Title><ISOAbbreviation>Microsurgery<\/ISOAbbreviation><\/Journal><ArticleTitle>Medicinal leeches and the microsurgeon: a four-year study, clinical series and risk benefit review.<\/ArticleTitle><Pagination><MedlinePgn>281-7<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/micr.20860<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">There are case reports and small series in the literature relating to the use of medicinal leeches by plastic surgeons; however, larger series from individual units are rare. The aim of this article is to present a comprehensive 4-year case series of the use of medicinal leeches, discuss the current evidence regarding indications, risks, and benefits and highlight the recent updates regarding leech speciation.","authors":"Whitaker, IS., Josty, IC., Hawkins, S., Azzopardi, E., Naderi, N., Graf, J., Damaris, L., Lineaweaver, WC., Kon, M.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Microsurgery","volume":"31","issue":"4","page":"281-7","pdf":null,"JrId":"5739","fulltextlink":null,"preprintlink":null,"articledate":"2011-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520231","title":"Plasma epidermal growth factor levels predict cognitive decline in Parkinson disease.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520231<\/PMID><DateCompleted><Year>2011<\/Year><Month>06<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1531-8249<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>69<\/Volume><Issue>4<\/Issue><PubDate><Year>2011<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>Annals of neurology<\/Title><ISOAbbreviation>Ann Neurol<\/ISOAbbreviation><\/Journal><ArticleTitle>Plasma epidermal growth factor levels predict cognitive decline in Parkinson disease.<\/ArticleTitle><Pagination><MedlinePgn>655-63<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/ana.22271<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">Most people with Parkinson disease (PD) eventually develop cognitive impairment (CI). However, neither the timing of onset nor the severity of cognitive symptoms can be accurately predicted. We sought plasma-based biomarkers for CI in PD.","authors":"Chen-Plotkin, AS., Hu, WT., Siderowf, A., Weintraub, D., Goldmann Gross, R., Hurtig, HI., Xie, SX., Arnold, SE., Grossman, M., Clark, CM., Shaw, LM., McCluskey, L., Elman, L., Van Deerlin, VM., Lee, VM., Soares, H., Trojanowski, JQ.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Ann Neurol","volume":"69","issue":"4","page":"655-63","pdf":null,"JrId":"656","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520132","title":"Transantral balloon dilation plus posterior ethmoidectomy.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520132<\/PMID><DateCompleted><Year>2011<\/Year><Month>06<\/Month><Day>28<\/Day><\/DateCompleted><DateRevised><Year>2012<\/Year><Month>11<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1531-4995<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>121<\/Volume><Issue>5<\/Issue><PubDate><Year>2011<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>The Laryngoscope<\/Title><ISOAbbreviation>Laryngoscope<\/ISOAbbreviation><\/Journal><ArticleTitle>Transantral balloon dilation plus posterior ethmoidectomy.<\/ArticleTitle><Pagination><MedlinePgn>1108-11<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/lary.21720<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\/HYPOTHESIS\" NlmCategory=\"OBJECTIVE\">Transantral endoscopic balloon dilatation (TABD) was recently introduced for the management of limited mild maxillary and ethmoid disease. An expanded approach by inserting surgical tools into the antrum via a second port, directed toward the maxillary ostium, ethmoid infundibulum, and posterior ethmoids will allow for the treatment of moderate disease as well.","authors":"Kizhner, V., Setzen, M., Krespi, YP.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Laryngoscope","volume":"121","issue":"5","page":"1108-11","pdf":null,"JrId":"5476","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11208135","title":"Both calmodulin and the unconventional myosin Myr4 regulate membrane trafficking along the recycling pathway of MDCK cells.","abstract":"In epithelial cells, endocytosed transferrin and its receptor, which cycle basolaterally, have been shown to transit through recycling endosomes which can also be accessed by markers internalized from the apical surface. In this work, we have used an in vitro assay to follow transfer of an endocytosed marker from apical or basolateral early endosomes to recycling endosomes labeled with transferrin. We show that calmodulin (CaM) function is necessary for transfer and identified myr4, a member of the unconventional myosin superfamily known to use CaM as a light chain, as a possible target protein for CaM. Since myr4 is believed to act as an actin-based mechanoenzyme, we tested the role of polymerized actin in the assay. Our data show that conditions which either prevent actin polymerization or induce the breakdown of existing filaments strongly inhibit interactions between recycling endosomes and either set of early endosomes. Altogether, our data indicate that trafficking at early steps of the endocytic pathway in Madin-Darby Canine Kidney cells depends on the actin-based mechanoenzyme myr4, its light chain CaM, and polymerized actin.","authors":"Huber, LA., Fialka, I., Paiha, K., Hunziker, W., Sacks, DB., B\u00e4hler, M., Way, M., Gagescu, R., Gruenberg, J.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Traffic","volume":"1","issue":"6","page":"494-503","pdf":null,"JrId":"21894","fulltextlink":null,"preprintlink":null,"articledate":"2001-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31133746","title":"MTHFD1 interaction with BRD4 links folate metabolism to transcriptional regulation.","abstract":"The histone acetyl reader bromodomain-containing protein 4 (BRD4) is an important regulator of chromatin structure and transcription, yet factors modulating its activity have remained elusive. Here we describe two complementary screens for genetic and physical interactors of BRD4, which converge on the folate pathway enzyme MTHFD1 (methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1). We show that a fraction of MTHFD1 resides in the nucleus, where it is recruited to distinct genomic loci by direct interaction with BRD4. Inhibition of either BRD4 or MTHFD1 results in similar changes in nuclear metabolite composition and gene expression; pharmacological inhibitors of the two pathways synergize to impair cancer cell viability in vitro and in vivo. Our finding that MTHFD1 and other metabolic enzymes are chromatin associated suggests a direct role for nuclear metabolism in the control of gene expression.","authors":"Sdelci, S., Rendeiro, AF., Rathert, P., You, W., Lin, JG., Ringler, A., Hofst\u00e4tter, G., Moll, HP., G\u00fcrtl, B., Farlik, M., Schick, S., Klepsch, F., Oldach, M., Buphamalai, P., Schischlik, F., M\u00e1jek, P., Parapatics, K., Schmidl, C., Schuster, M., Penz, T., Buckley, DL., Hudecz, O., Imre, R., Wang, SY., Maric, HM., Kralovics, R., Bennett, KL., M\u00fcller, AC., Mechtler, K., Menche, J., Bradner, JE., Winter, GE., Klavins, K., Casanova, E., Bock, C., Zuber, J., Kubicek, S.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Genet","volume":"51","issue":"6","page":"990-998","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21285291","title":"Enhanced susceptibility to biomechanical stress in ACE2 null mice is prevented by loss of the p47(phox) NADPH oxidase subunit.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21285291<\/PMID><DateCompleted><Year>2011<\/Year><Month>10<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1755-3245<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>91<\/Volume><Issue>1<\/Issue><PubDate><Year>2011<\/Year><Month>Jul<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Cardiovascular research<\/Title><ISOAbbreviation>Cardiovasc Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Enhanced susceptibility to biomechanical stress in ACE2 null mice is prevented by loss of the p47(phox) NADPH oxidase subunit.<\/ArticleTitle><Pagination><MedlinePgn>151-61<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/cvr\/cvr036<\/ELocationID><Abstract><AbstractText Label=\"AIMS\" NlmCategory=\"OBJECTIVE\">Angiotensin-converting enzyme 2 (ACE2) is an important negative regulator of the renin-angiotensin system. Loss of ACE2 enhances the susceptibility to heart disease but the mechanism remains elusive. We hypothesized that ACE2 deficiency activates the NADPH oxidase system in pressure overload-induced heart failure.","authors":"Bodiga, S., Zhong, JC., Wang, W., Basu, R., Lo, J., Liu, GC., Guo, D., Holland, SM., Scholey, JW., Penninger, JM., Kassiri, Z., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Cardiovasc Res","volume":"91","issue":"1","page":"151-61","pdf":null,"JrId":"2812","fulltextlink":null,"preprintlink":null,"articledate":"2011-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21083380","title":"Mutations in GNA11 in uveal melanoma.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21083380<\/PMID><DateCompleted><Year>2010<\/Year><Month>12<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>02<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1533-4406<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>363<\/Volume><Issue>23<\/Issue><PubDate><Year>2010<\/Year><Month>Dec<\/Month><Day>02<\/Day><\/PubDate><\/JournalIssue><Title>The New England journal of medicine<\/Title><ISOAbbreviation>N Engl J Med<\/ISOAbbreviation><\/Journal><ArticleTitle>Mutations in GNA11 in uveal melanoma.<\/ArticleTitle><Pagination><MedlinePgn>2191-9<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1056\/NEJMoa1000584<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Uveal melanoma is the most common intraocular cancer. There are no effective therapies for metastatic disease. Mutations in GNAQ, the gene encoding an alpha subunit of heterotrimeric G proteins, are found in 40% of uveal melanomas.","authors":"Van Raamsdonk, CD., Griewank, KG., Crosby, MB., Garrido, MC., Vemula, S., Wiesner, T., Obenauf, AC., Wackernagel, W., Green, G., Bouvier, N., Sozen, MM., Baimukanova, G., Roy, R., Heguy, A., Dolgalev, I., Khanin, R., Busam, K., Speicher, MR., O'Brien, J., Bastian, BC.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"N Engl J Med","volume":"363","issue":"23","page":"2191-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20933422","title":"A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20933422<\/PMID><DateCompleted><Year>2011<\/Year><Month>02<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>10<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>20<\/Volume><Issue>20<\/Issue><PubDate><Year>2010<\/Year><Month>Oct<\/Month><Day>26<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands.<\/ArticleTitle><Pagination><MedlinePgn>1787-98<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2010.09.006<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Developmental abnormalities observed in Cornelia de Lange syndrome have been genetically linked to mutations in the cohesin machinery. These and other recent experimental findings have led to the suggestion that cohesin, in addition to its canonical function of mediating sister chromatid cohesion, might also be involved in regulating gene expression.","authors":"Pauli, A., van Bemmel, JG., Oliveira, RA., Itoh, T., Shirahige, K., van Steensel, B., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Curr Biol","volume":"20","issue":"20","page":"1787-98","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12719437","title":"Interaction of activator of G-protein signaling 3 (AGS3) with LKB1, a serine\/threonine kinase involved in cell polarity and cell cycle progression: phosphorylation of the G-protein regulatory (GPR) motif as a regulatory mechanism for the interaction of GPR motifs with Gi alpha.","abstract":"Activator of G-protein signaling 3 (AGS3) has a modular domain structure consisting of seven tetratricopeptide repeats (TPRs) and four G-protein regulatory (GPR) motifs. Each GPR motif binds to the alpha subunit of Gi\/Go (Gialpha &gt; Goalpha) stabilizing the GDP-bound conformation of Galpha and apparently competing with Gbetagamma for GalphaGDP binding. As an initial approach to identify regulatory mechanisms for AGS3-G-protein interactions, a yeast two-hybrid screen was initiated using the TPR and linker region of AGS3 as bait. This screen identified the serine\/threonine kinase LKB1, which is involved in the regulation of cell cycle progression and polarity. Protein interaction assays in mammalian systems using transfected cells or brain lysate indicated the regulated formation of a protein complex consisting of LKB1, AGS3, and G-proteins. The interaction between AGS3 and LKB1 was also observed with orthologous proteins in Drosophila where both proteins are involved in cell polarity. LKB1 immunoprecipitates from COS7 cells transfected with LKB1 phosphorylated the GPR domains of AGS3 and the related protein LGN but not the AGS3-TPR domain. GPR domain phosphorylation was completely blocked by a consensus GPR motif peptide, and placement of a phosphate moiety within a consensus GPR motif reduced the ability of the peptide to interact with G-proteins. These data suggest that phosphorylation of GPR domains may be a general mechanism regulating the interaction of GPR-containing proteins with G-proteins. Such a mechanism may be of particular note in regard to localized signal processing in the plasma membrane involving G-protein subunits and\/or intracellular functions regulated by heterotrimeric G-proteins that occur independently of a typical G-protein-coupled receptor.","authors":"Blumer, JB., Bernard, ML., Peterson, YK., Nezu, J., Chung, P., Dunican, DJ., Knoblich, JA., Lanier, SM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Biol Chem","volume":"278","issue":"26","page":"23217-20","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20581279","title":"Object preference by walking fruit flies, Drosophila melanogaster, is mediated by vision and graviperception.","abstract":"Walking fruit flies, Drosophila melanogaster, use visual information to orient towards salient objects in their environment, presumably as a search strategy for finding food, shelter or other resources. Less is known, however, about the role of vision or other sensory modalities such as mechanoreception in the evaluation of objects once they have been reached. To study the role of vision and mechanoreception in exploration behavior, we developed a large arena in which we could track individual fruit flies as they walked through either simple or more topologically complex landscapes. When exploring a simple, flat environment lacking three-dimensional objects, flies used visual cues from the distant background to stabilize their walking trajectories. When exploring an arena containing an array of cones, differing in geometry, flies actively oriented towards, climbed onto, and explored the objects, spending most of their time on the tallest, steepest object. A fly's behavioral response to the geometry of an object depended upon the intrinsic properties of each object and not a relative assessment to other nearby objects. Furthermore, the preference was not due to a greater attraction towards tall, steep objects, but rather a change in locomotor behavior once a fly reached and explored the surface. Specifically, flies are much more likely to stop walking for long periods when they are perched on tall, steep objects. Both the vision system and the antennal chordotonal organs (Johnston's organs) provide sufficient information about the geometry of an object to elicit the observed change in locomotor behavior. Only when both these sensory systems were impaired did flies not show the behavioral preference for the tall, steep objects.","authors":"Robie, AA., Straw, AD., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Exp Biol","volume":"213","issue":"Pt 14","page":"2494-506","pdf":null,"JrId":"4720","fulltextlink":null,"preprintlink":null,"articledate":"2010-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20847309","title":"Loss of PI3K\u03b3 enhances cAMP-dependent MMP remodeling of the myocardial N-cadherin adhesion complexes and extracellular matrix in response to early biomechanical stress.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20847309<\/PMID><DateCompleted><Year>2010<\/Year><Month>12<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2014<\/Year><Month>11<\/Month><Day>20<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4571<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>107<\/Volume><Issue>10<\/Issue><PubDate><Year>2010<\/Year><Month>Nov<\/Month><Day>12<\/Day><\/PubDate><\/JournalIssue><Title>Circulation research<\/Title><ISOAbbreviation>Circ Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Loss of PI3K\u03b3 enhances cAMP-dependent MMP remodeling of the myocardial N-cadherin adhesion complexes and extracellular matrix in response to early biomechanical stress.<\/ArticleTitle><Pagination><MedlinePgn>1275-89<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/CIRCRESAHA.110.229054<\/ELocationID><Abstract><AbstractText Label=\"RATIONALE\" NlmCategory=\"BACKGROUND\">Mechanotransduction and the response to biomechanical stress is a fundamental response in heart disease. Loss of phosphoinositide 3-kinase (PI3K)\u03b3, the isoform linked to G protein-coupled receptor signaling, results in increased myocardial contractility, but the response to pressure overload is controversial.","authors":"Guo, D., Kassiri, Z., Basu, R., Chow, FL., Kandalam, V., Damilano, F., Liang, W., Izumo, S., Hirsch, E., Penninger, JM., Backx, PH., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Circ Res","volume":"107","issue":"10","page":"1275-89","pdf":null,"JrId":"2974","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20481592","title":"Peptide orientation affects selectivity in ion-exchange chromatography.","abstract":"Here we demonstrate that separation of proteolytic peptides, having the same net charge and one basic residue, is affected by their specific orientation toward the stationary phase in ion-exchange chromatography. In electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) with an anion-exchange material, the C-terminus of the peptides is, on average, oriented toward the stationary phase. In cation exchange, the average peptide orientation is the opposite. Data with synthetic peptides, serving as orientation probes, indicate that in tryptic\/Lys-C peptides the C-terminal carboxyl group appears to be in a zwitterionic bond with the side chain of the C-terminal Lys\/Arg residue. In effect, the side chain is then less basic than the N-terminus, accounting for the specific orientation of tryptic and Lys-C peptides. Analyses of larger sets of peptides, generated from lysates by either Lys-N, Lys-C, or trypsin, reveal that specific peptide orientation affects the ability of charged side chains, such as phosphate residues, to influence retention. Phosphorylated residues that are remote in the sequence from the binding site affect retention less than those that are closer. When a peptide contains multiple charged sites, then orientation is observed to be less rigid and retention tends to be governed by the peptide's net charge rather than its sequence. These general observations could be of value in confirming a peptide's identification and, in particular, phosphosite assignments in proteomics analyses. More generally, orientation accounts for the ability of chromatography to separate peptides of the same composition but different sequence.","authors":"Alpert, AJ., Petritis, K., Kangas, L., Smith, RD., Mechtler, K., Mitulovi\u0107, G., Mohammed, S., Heck, AJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Anal Chem","volume":"82","issue":"12","page":"5253-9","pdf":null,"JrId":"519","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12702202","title":"Protein prenyltransferases.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">12702202<\/PMID><DateCompleted><Year>2003<\/Year><Month>05<\/Month><Day>02<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>07<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>4<\/Volume><Issue>4<\/Issue><PubDate><Year>2003<\/Year><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Protein prenyltransferases.<\/ArticleTitle><Pagination><MedlinePgn>212<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"SUMMARY\" NlmCategory=\"CONCLUSIONS\">Three different protein prenyltransferases (farnesyltransferase and geranylgeranyltransferases I and II) catalyze the attachment of prenyl lipid anchors 15 or 20 carbons long to the carboxyl termini of a variety of eukaryotic proteins. Farnesyltransferase and geranylgeranyltransferase I both recognize a 'Ca1a2X' motif on their protein substrates; geranylgeranyltransferase II recognizes a different, non-CaaX motif. Each enzyme has two subunits. The genes encoding CaaX protein prenyltransferases are considerably longer than those encoding non-CaaX subunits, as a result of longer introns. Alternative splice forms are predicted to occur, but the extent to which each splice form is translated and the functions of the different resulting isoforms remain to be established. Farnesyltransferase-inhibitor drugs have been developed as anti-cancer agents and may also be able to treat several other diseases. The effects of these inhibitors are complicated, however, by the overlapping substrate specificities of geranylgeranyltransferase I and farnesyltransferase.","authors":"Maurer-Stroh, S., Washietl, S., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Genome Biol","volume":"4","issue":"4","page":"212","pdf":null,"JrId":"21904","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19875753","title":"Pathological and molecular characteristics distinguishing contralateral metastatic from new primary breast cancer.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19875753<\/PMID><DateCompleted><Year>2010<\/Year><Month>09<\/Month><Day>27<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>08<\/Month><Day>14<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1569-8041<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>21<\/Volume><Issue>6<\/Issue><PubDate><Year>2010<\/Year><Month>Jun<\/Month><\/PubDate><\/JournalIssue><Title>Annals of oncology : official journal of the European Society for Medical Oncology<\/Title><ISOAbbreviation>Ann Oncol<\/ISOAbbreviation><\/Journal><ArticleTitle>Pathological and molecular characteristics distinguishing contralateral metastatic from new primary breast cancer.<\/ArticleTitle><Pagination><MedlinePgn>1237-1242<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0923-7534(19)39285-3<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/annonc\/mdp470<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Breast cancer patients have a cumulative lifetime risk of 2%-15% of developing a contralateral metastatic or ex novo primary cancer. From prognostic and therapeutic viewpoints, it is important to differentiate metastatic from second primary. To distinguish these entities, we investigated whether the pattern of X chromosome inactivation could determine whether the two tumors derived from different progenitor cells.","authors":"Banelli, B., Casciano, I., Di Vinci, A., Gatteschi, B., Levaggi, A., Carli, F., Bighin, C., Salvi, S., Allemanni, G., Ghiorzo, P., Pronzato, P., Venturini, M., Romani, M., Del Mastro, L.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Ann Oncol","volume":"21","issue":"6","page":"1237-1242","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19568234","title":"Type I collagen inhibits differentiation and promotes a stem cell-like phenotype in human colorectal carcinoma cells.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19568234<\/PMID><DateCompleted><Year>2009<\/Year><Month>07<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1532-1827<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>101<\/Volume><Issue>2<\/Issue><PubDate><Year>2009<\/Year><Month>Jul<\/Month><Day>21<\/Day><\/PubDate><\/JournalIssue><Title>British journal of cancer<\/Title><ISOAbbreviation>Br J Cancer<\/ISOAbbreviation><\/Journal><ArticleTitle>Type I collagen inhibits differentiation and promotes a stem cell-like phenotype in human colorectal carcinoma cells.<\/ArticleTitle><Pagination><MedlinePgn>320-6<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1038\/sj.bjc.6605143<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Human colorectal cancer is caused by mutations and is thought to be maintained by a population of cancer stem cells. Further phenotypic changes occurring at the invasive edge suggest that colon cancer cells are also regulated by their microenvironment. Type I collagen, a promoter of the malignant phenotype in pancreatic carcinoma cells, is highly expressed at the invasive front of human colorectal cancer.","authors":"Kirkland, SC.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Br J Cancer","volume":"101","issue":"2","page":"320-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19453650","title":"SARS-coronavirus modulation of myocardial ACE2 expression and inflammation in patients with SARS.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19453650<\/PMID><DateCompleted><Year>2010<\/Year><Month>02<\/Month><Day>22<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1365-2362<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>39<\/Volume><Issue>7<\/Issue><PubDate><Year>2009<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>European journal of clinical investigation<\/Title><ISOAbbreviation>Eur J Clin Invest<\/ISOAbbreviation><\/Journal><ArticleTitle>SARS-coronavirus modulation of myocardial ACE2 expression and inflammation in patients with SARS.<\/ArticleTitle><Pagination><MedlinePgn>618-25<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/j.1365-2362.2009.02153.x<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Angiotensin converting enzyme 2 (ACE2), a monocarboxylase that degrades angiotensin II to angiotensin 1-7, is also the functional receptor for severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and is highly expressed in the lungs and heart. Patients with SARS also suffered from cardiac disease including arrhythmias, sudden cardiac death, and systolic and diastolic dysfunction.","authors":"Oudit, GY., Kassiri, Z., Jiang, C., Liu, PP., Poutanen, SM., Penninger, JM., Butany, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Eur J Clin Invest","volume":"39","issue":"7","page":"618-25","pdf":null,"JrId":"3611","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17453015","title":"Drosophila olfactory memory: single genes to complex neural circuits.","abstract":"A central goal of neuroscience is to understand how neural circuits encode memory and guide behaviour. Studying simple, genetically tractable organisms, such as Drosophila melanogaster, can illuminate principles of neural circuit organization and function. Early genetic dissection of D. melanogaster olfactory memory focused on individual genes and molecules. These molecular tags subsequently revealed key neural circuits for memory. Recent advances in genetic technology have allowed us to manipulate and observe activity in these circuits, and even individual neurons, in live animals. The studies have transformed D. melanogaster from a useful organism for gene discovery to an ideal model to understand neural circuit function in memory.","authors":"Keene, AC., Waddell, S.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nat Rev Neurosci","volume":"8","issue":"5","page":"341-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19762681","title":"Myeloid differentiation factor-88\/interleukin-1 signaling controls cardiac fibrosis and heart failure progression in inflammatory dilated cardiomyopathy.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19762681<\/PMID><DateCompleted><Year>2009<\/Year><Month>11<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2013<\/Year><Month>11<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4571<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>105<\/Volume><Issue>9<\/Issue><PubDate><Year>2009<\/Year><Month>Oct<\/Month><Day>23<\/Day><\/PubDate><\/JournalIssue><Title>Circulation research<\/Title><ISOAbbreviation>Circ Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Myeloid differentiation factor-88\/interleukin-1 signaling controls cardiac fibrosis and heart failure progression in inflammatory dilated cardiomyopathy.<\/ArticleTitle><Pagination><MedlinePgn>912-20<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/CIRCRESAHA.109.199802<\/ELocationID><Abstract><AbstractText Label=\"RATIONALE\" NlmCategory=\"BACKGROUND\">The myeloid differentiation factor (MyD)88\/interleukin (IL)-1 axis activates self-antigen-presenting cells and promotes autoreactive CD4(+) T-cell expansion in experimental autoimmune myocarditis, a mouse model of inflammatory heart disease.","authors":"Blyszczuk, P., Kania, G., Dieterle, T., Marty, RR., Valaperti, A., Berthonneche, C., Pedrazzini, T., Berger, CT., Dirnhofer, S., Matter, CM., Penninger, JM., L\u00fcscher, TF., Eriksson, U.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Circ Res","volume":"105","issue":"9","page":"912-20","pdf":null,"JrId":"2974","fulltextlink":null,"preprintlink":null,"articledate":"2009-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20430749","title":"Cortical domain correction repositions the polarity boundary to match the cytokinesis furrow in C. elegans embryos.","abstract":"In asymmetrically dividing cells, a failure to coordinate cell polarity with the site of cell division can lead to cell fate transformations and tumorigenesis. Cell polarity in C. elegans embryos is defined by PAR proteins, which occupy reciprocal halves of the cell cortex. During asymmetric division, the boundary between the anterior and posterior PAR domains precisely matches the site of cell division, ensuring exclusive segregation of cell fate. The PAR domains determine the site of cell division by positioning the mitotic spindle, suggesting one means by which cell polarity and cell division might be coordinated. Here, we report that cell polarity and cell division are coordinated through an additional mechanism: the site of cell division repositions the PAR-2 boundary. Galpha-mediated microtubule-cortex interactions appear to direct cortical flows of PAR-2 and myosin toward the site of cell division, which acts as a PAR-2 and myosin sink. Embryos with defects in PAR-2 boundary correction undergo mis-segregation of cortical polarity and cytoplasmic determinants, suggesting that PAR domain correction might help prevent cell fate transformation.","authors":"Schenk, C., Bringmann, H., Hyman, AA., Cowan, CR.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Development","volume":"137","issue":"10","page":"1743-53","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2010-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19276263","title":"Apo2L\/TRAIL inhibits tumor growth and bone destruction in a murine model of multiple myeloma.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19276263<\/PMID><DateCompleted><Year>2009<\/Year><Month>04<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Print\">1078-0432<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>15<\/Volume><Issue>6<\/Issue><PubDate><Year>2009<\/Year><Month>Mar<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Clinical cancer research : an official journal of the American Association for Cancer Research<\/Title><ISOAbbreviation>Clin Cancer Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Apo2L\/TRAIL inhibits tumor growth and bone destruction in a murine model of multiple myeloma.<\/ArticleTitle><Pagination><MedlinePgn>1998-2009<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1158\/1078-0432.CCR-08-2444<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE\" NlmCategory=\"OBJECTIVE\">Multiple myeloma is an incurable disease, for which the development of new therapeutic approaches is required. Here, we report on the efficacy of recombinant soluble Apo2L\/tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) to inhibit tumor progression and bone destruction in a xenogeneic model of human multiple myeloma.","authors":"Labrinidis, A., Diamond, P., Martin, S., Hay, S., Liapis, V., Zinonos, I., Sims, NA., Atkins, GJ., Vincent, C., Ponomarev, V., Findlay, DM., Zannettino, AC., Evdokiou, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Clin Cancer Res","volume":"15","issue":"6","page":"1998-2009","pdf":null,"JrId":"8794","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19269943","title":"Predictive diagnosis of the cancer prone Li-Fraumeni syndrome by accident: new challenges through whole genome array testing.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19269943<\/PMID><DateCompleted><Year>2009<\/Year><Month>09<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1468-6244<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>46<\/Volume><Issue>5<\/Issue><PubDate><Year>2009<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>Journal of medical genetics<\/Title><ISOAbbreviation>J Med Genet<\/ISOAbbreviation><\/Journal><ArticleTitle>Predictive diagnosis of the cancer prone Li-Fraumeni syndrome by accident: new challenges through whole genome array testing.<\/ArticleTitle><Pagination><MedlinePgn>341-4<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1136\/jmg.2008.064972<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Li-Fraumeni syndrome greatly increases the risk of developing several types of cancer and is usually caused by TP53 germline mutations. Predictive testing of at-risk family members is only offered after a complex genetic counselling process. Recently the clinical implementation of array comparative genomic hybridisation (CGH) has revolutionised the diagnosis of patients with syndromic or non-syndromic mental retardation and has evolved to a routinely performed high resolution whole genome scan.","authors":"Schwarzbraun, T., Obenauf, AC., Langmann, A., Gruber-Sedlmayr, U., Wagner, K., Speicher, MR., Kroisel, PM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Med Genet","volume":"46","issue":"5","page":"341-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20227040","title":"Tumor stroma-derived TGF-beta limits myc-driven lymphomagenesis via Suv39h1-dependent senescence.","abstract":"Activated RAS\/BRAF oncogenes induce cellular senescence as a tumor-suppressive barrier in early cancer development, at least in part, via an oncogene-evoked DNA damage response (DDR). In contrast, Myc activation-although producing a DDR as well-is known to primarily elicit an apoptotic countermeasure. Using the Emu-myc transgenic mouse lymphoma model, we show here in vivo that apoptotic lymphoma cells activate macrophages to secrete transforming growth factor beta (TGF-beta) as a critical non-cell-autonomous inducer of cellular senescence. Accordingly, neutralization of TGF-beta action, like genetic inactivation of the senescence-related histone methyltransferase Suv39h1, significantly accelerates Myc-driven tumor development via cancellation of cellular senescence. These findings, recapitulated in human aggressive B cell lymphomas, demonstrate that tumor-prompted stroma-derived signals may limit tumorigenesis by feedback senescence induction.","authors":"Reimann, M., Lee, S., Loddenkemper, C., D\u00f6rr, JR., Tabor, V., Aichele, P., Stein, H., D\u00f6rken, B., Jenuwein, T., Schmitt, CA.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cancer Cell","volume":"17","issue":"3","page":"262-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19229324","title":"C\/EBPbeta Promotes transition from proliferation to hypertrophic differentiation of chondrocytes through transactivation of p57.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19229324<\/PMID><DateCompleted><Year>2009<\/Year><Month>04<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>4<\/Volume><Issue>2<\/Issue><PubDate><Year>2009<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>C\/EBPbeta Promotes transition from proliferation to hypertrophic differentiation of chondrocytes through transactivation of p57.<\/ArticleTitle><Pagination><MedlinePgn>e4543<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0004543<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Although transition from proliferation to hypertrophic differentiation of chondrocytes is a crucial step for endochondral ossification in physiological skeletal growth and pathological disorders like osteoarthritis, the underlying mechanism remains an enigma. This study investigated the role of the transcription factor CCAAT\/enhancer-binding protein beta (C\/EBPbeta) in chondrocytes during endochondral ossification.","authors":"Hirata, M., Kugimiya, F., Fukai, A., Ohba, S., Kawamura, N., Ogasawara, T., Kawasaki, Y., Saito, T., Yano, F., Ikeda, T., Nakamura, K., Chung, UI., Kawaguchi, H.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS One","volume":"4","issue":"2","page":"e4543","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18983611","title":"Stromal cells promote bone invasion by suppressing bone formation in ameloblastoma.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18983611<\/PMID><DateCompleted><Year>2009<\/Year><Month>01<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2008<\/Year><Month>11<\/Month><Day>05<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1365-2559<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>53<\/Volume><Issue>4<\/Issue><PubDate><Year>2008<\/Year><Month>Oct<\/Month><\/PubDate><\/JournalIssue><Title>Histopathology<\/Title><ISOAbbreviation>Histopathology<\/ISOAbbreviation><\/Journal><ArticleTitle>Stromal cells promote bone invasion by suppressing bone formation in ameloblastoma.<\/ArticleTitle><Pagination><MedlinePgn>458-67<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/j.1365-2559.2008.03127.x<\/ELocationID><Abstract><AbstractText Label=\"AIMS\" NlmCategory=\"OBJECTIVE\">To study the stromal variation and role of stromal-tumour cell interaction in impaired bone formation as well as enhanced bone resorption in ameloblastoma.","authors":"Sathi, GS., Nagatsuka, H., Tamamura, R., Fujii, M., Gunduz, M., Inoue, M., Rivera, RS., Nagai, N.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Histopathology","volume":"53","issue":"4","page":"458-67","pdf":null,"JrId":"4076","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18978943","title":"Osteoclasts are active in bone forming metastases of prostate cancer patients.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18978943<\/PMID><DateCompleted><Year>2009<\/Year><Month>02<\/Month><Day>03<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>3<\/Volume><Issue>11<\/Issue><PubDate><Year>2008<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Osteoclasts are active in bone forming metastases of prostate cancer patients.<\/ArticleTitle><Pagination><MedlinePgn>e3627<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0003627<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Bone forming metastases are a common and disabling consequence of prostate cancer (CaP). The potential role of osteoclast activity in CaP bone metastases is not completely explained. In this study, we investigated ex vivo whether the osteolytic activity is present and how it is ruled in CaP patients with bone forming metastases.","authors":"Roato, I., D'Amelio, P., Gorassini, E., Grimaldi, A., Bonello, L., Fiori, C., Delsedime, L., Tizzani, A., De Libero, A., Isaia, G., Ferracini, R.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"PLoS One","volume":"3","issue":"11","page":"e3627","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17499227","title":"Angiotensin II-mediated oxidative stress and inflammation mediate the age-dependent cardiomyopathy in ACE2 null mice.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">17499227<\/PMID><DateCompleted><Year>2007<\/Year><Month>08<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Print\">0008-6363<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>75<\/Volume><Issue>1<\/Issue><PubDate><Year>2007<\/Year><Month>Jul<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Cardiovascular research<\/Title><ISOAbbreviation>Cardiovasc Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Angiotensin II-mediated oxidative stress and inflammation mediate the age-dependent cardiomyopathy in ACE2 null mice.<\/ArticleTitle><Pagination><MedlinePgn>29-39<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"OBJECTIVES\" NlmCategory=\"OBJECTIVE\">The peptidase action of angiotensin converting enzyme 2 (ACE2) allows it to function as a negative regulator of the renin-angiotensin system. Current pharmacotherapies for human heart failure, such as ACE inhibitors and angiotensin and aldosterone receptor blockers, increase the activity of ACE2 in the heart. In this study, we investigate the mechanism for the age-dependent cardiomyopathy in ACE2 null mice.","authors":"Oudit, GY., Kassiri, Z., Patel, MP., Chappell, M., Butany, J., Backx, PH., Tsushima, RG., Scholey, JW., Khokha, R., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cardiovasc Res","volume":"75","issue":"1","page":"29-39","pdf":null,"JrId":"2812","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12682231","title":"IL-1 receptor-associated kinase 4 is essential for IL-18-mediated NK and Th1 cell responses.","abstract":"IL-18 is an important cytokine for both innate and adaptive immunity. NK T cells and Th1 cells depend on IL-18 for their divergent functions. The IL-18R, IL-1R, and mammalian Toll-like receptors (TLRs) share homologous intracellular domains known as the TLR\/IL-1R\/plant R domain. Previously, we reported that IL-1R-associated kinase (IRAK)-4 plays a critical role in IL-1R and TLR signaling cascades and is essential for the innate immune response. Because TLR\/IL-1R\/plant R-containing receptors mediate signal transduction in a similar fashion, we investigated the role of IRAK-4 in IL-18R signaling. In this study, we show that IL-18-induced responses such as NK cell activity, Th1 IFN-gamma production, and Th1 cell proliferation are severely impaired in IRAK-4-deficient mice. IRAK-4(-\/-) Th1 cells also do not exhibit NF-kappaB activation or IkappaB degradation in response to IL-18. Moreover, AP-1 activation which is triggered by c-Jun N-terminal kinase activation is also completely inhibited in IRAK-4(-\/-) Th1 cells. These results suggest that IRAK-4 is an essential component of the IL-18 signaling cascade.","authors":"Suzuki, N., Chen, NJ., Millar, DG., Suzuki, S., Horacek, T., Hara, H., Bouchard, D., Nakanishi, K., Penninger, JM., Ohashi, PS., Yeh, WC.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Immunol","volume":"170","issue":"8","page":"4031-5","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12655644","title":"Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins.","abstract":"GPI lipid anchoring is an important post-translational modification of eukaryote proteins in the endoplasmic reticulum. In total, 19 genes have been directly implicated in the anchor synthesis and the substrate protein modification pathway. Here, the molecular functions of the respective proteins and their evolution are analyzed in the context of reported literature data and sequence analysis studies for the complete pathway (http:\/\/mendel.imp.univie.ac.at\/SEQUENCES\/gpi-biosynthesis\/) and questions for future experimental investigation are discussed. Studies of two of these proteins have provided new mechanistic insights. The cytosolic part of PIG-A\/GPI3 has a two-domain alpha\/beta\/alpha-layered structure; it is suggested that its C-terminal subsegment binds UDP-GlcNAc whereas the N-terminal domain interacts with the phosphatidylinositol moiety. The lumenal part of PIG-T\/GPI16 apparently consists of a beta-propeller with a central hole that regulates the access of substrate protein C termini to the active site of the cysteine protease PIG-K\/GPI8 (gating mechanism) as well as of a polypeptide hook that embraces PIG-K\/GPI8. This structural proposal would explain the paradoxical properties of the GPI lipid anchor signal motif and of PIG-K\/GPI8 orthologs without membrane insertion regions in some species.","authors":"Eisenhaber, B., Maurer-Stroh, S., Novatchkova, M., Schneider, G., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Bioessays","volume":"25","issue":"4","page":"367-85","pdf":null,"JrId":"1014","fulltextlink":null,"preprintlink":null,"articledate":"2003-07-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12691672","title":"The role of ACE2 in cardiovascular physiology.","abstract":"The renin-angiotensin system (RAS) is critically involved in cardiovascular and renal function and in disease conditions, and has been shown to be a far more complex system than initially thought. A recently discovered homologue of angiotensin-converting enzyme (ACE)--ACE2--appears to negatively regulate the RAS. ACE2 cleaves Ang I and Ang II into the inactive Ang 1-9 and Ang 1-7, respectively. ACE2 is highly expressed in kidney and heart and is especially confined to the endothelium. With quantitative trait locus (QTL) mapping, ACE2 was defined as a QTL on the X chromosome in rat models of hypertension. In these animal models, kidney ACE2 messenger RNA and protein expression were markedly reduced, making ACE2 a candidate gene for this QTL. Targeted disruption of ACE2 in mice failed to elicit hypertension, but resulted in severe impairment in myocardial contractility with increased angiotensin II levels. Genetic ablation of ACE in the ACE2 null mice rescued the cardiac phenotype. These genetic data show that ACE2 is an essential regulator of heart function in vivo. Basal renal morphology and function were not altered by the inactivation of ACE2. The novel role of ACE2 in hydrolyzing several other peptides-such as the apelin peptides, opioids, and kinin metabolites-raises the possibility that peptide systems other than angiotensin and its derivatives also may have an important role in regulating cardiovascular and renal function.","authors":"Oudit, GY., Crackower, MA., Backx, PH., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Trends Cardiovasc Med","volume":"13","issue":"3","page":"93-101","pdf":null,"JrId":"21207","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20162728","title":"Disruption of the growth hormone--signal transducer and activator of transcription 5--insulinlike growth factor 1 axis severely aggravates liver fibrosis in a mouse model of cholestasis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20162728<\/PMID><DateCompleted><Year>2010<\/Year><Month>04<\/Month><Day>21<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>12<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1527-3350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>51<\/Volume><Issue>4<\/Issue><PubDate><Year>2010<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>Hepatology (Baltimore, Md.)<\/Title><ISOAbbreviation>Hepatology<\/ISOAbbreviation><\/Journal><ArticleTitle>Disruption of the growth hormone--signal transducer and activator of transcription 5--insulinlike growth factor 1 axis severely aggravates liver fibrosis in a mouse model of cholestasis.<\/ArticleTitle><Pagination><MedlinePgn>1319-26<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/hep.23469<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Growth hormone (GH) resistance and low serum levels of insulinlike growth factor 1 (IGF-1) are common features in human liver fibrosis and cirrhosis. Signal transducer and activator of transcription 5 (STAT5) controls several vital functions in the liver, including GH-mediated transcription of IGF-1. To investigate the role of STAT5 in liver fibrogenesis, we specifically deleted the Stat5a\/b locus both in hepatocytes and cholangiocytes in the multidrug resistance gene 2 knockout (Mdr2(-\/-)) mouse model of cholestasis. Double knockout mice develop an early and severe liver fibrosis phenotype, accompanied by perturbed expression of key regulators of bile acid homeostasis. Deletion of Stat5 resulted in GH resistance, and IGF-1 levels in serum were undetectable. We could observe reduced expression of important hepatoprotective genes, such as epidermal growth factor receptor (Egfr), hepatocyte nuclear factor 6 (Hnf6), prolactin receptor (Prlr), and leukemia inhibitory factor receptor (Lifr) as well as increased numbers of apoptotic hepatocytes.","authors":"Blaas, L., Kornfeld, JW., Schramek, D., Musteanu, M., Zollner, G., Gumhold, J., van Zijl, F., Schneller, D., Esterbauer, H., Egger, G., Mair, M., Kenner, L., Mikulits, W., Eferl, R., Moriggl, R., Penninger, J., Trauner, M., Casanova, E.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Hepatology","volume":"51","issue":"4","page":"1319-26","pdf":null,"JrId":"4093","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16401773","title":"MyD88 signaling controls autoimmune myocarditis induction.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">16401773<\/PMID><DateCompleted><Year>2006<\/Year><Month>03<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2013<\/Year><Month>11<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4539<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>113<\/Volume><Issue>2<\/Issue><PubDate><Year>2006<\/Year><Month>Jan<\/Month><Day>17<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>MyD88 signaling controls autoimmune myocarditis induction.<\/ArticleTitle><Pagination><MedlinePgn>258-65<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Experimental autoimmune myocarditis (EAM) is a CD4+ T-cell-mediated mouse model of postviral cardiomyopathy. Activation of interleukin-1 type 1 and Toll-like receptors that share the common downstream adaptor molecule MyD88 is required for disease induction. The specific role of MyD88 in myocarditis, however, is not known.","authors":"Marty, RR., Dirnhofer, S., Mauermann, N., Schweikert, S., Akira, S., Hunziker, L., Penninger, JM., Eriksson, U.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Circulation","volume":"113","issue":"2","page":"258-65","pdf":null,"JrId":"2979","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17381338","title":"Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors.","abstract":"The mRNA is bound and poised in the decoding center of the small subunit of the ribosome where the genetic code is translated by the tRNAs, which recognize sense codons, and by the release factors, which recognize stop-codons. Structural and biochemical studies have identified key universally conserved nucleotides, G530, A1492, and A1493, that are important for selection of cognate tRNA species during elongation. Here, we present evidence that these same universally conserved nucleotides are also important for interactions with the release factors, but must assume a very different structure during stopcodon recognition. These data provide mechanistic insight into how the decoding center of the ribosome has evolved to recognize distinct substrates with high fidelity, which in turn regulates the downstream chemical events of peptidyl transfer and peptide release.","authors":"Youngman, EM., Cochella, L., Brunelle, JL., He, S., Green, R.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"71","issue":null,"page":"545-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20064463","title":"A reconfigured pattern of MLL occupancy within mitotic chromatin promotes rapid transcriptional reactivation following mitotic exit.","abstract":"Mixed lineage leukemia (MLL) and its metazoan Trithorax orthologs have been linked with the epigenetic maintenance of transcriptional activity. To identify mechanisms by which MLL perpetuates active transcription in dividing cells, we investigated its role during M phase of the cell cycle. Unlike other chromatin-modifying enzymes examined, we found that MLL associates with gene promoters packaged within condensed mitotic chromosomes. Genome-wide location analysis identified a globally rearranged pattern of MLL occupancy during mitosis in a manner favoring genes that were highly transcribed during interphase. Knockdown experiments revealed that MLL retention at gene promoters during mitosis accelerates transcription reactivation following mitotic exit. MLL tethers Menin, RbBP5, and ASH2L to its occupied sites during mitosis, but is dispensable for preserving histone H3K4 methylation. These findings implicate mitotic bookmarking as a component of Trithorax-based gene regulation, which may facilitate inheritance of active gene expression states during cell division.","authors":"Blobel, GA., Kadauke, S., Wang, E., Lau, AW., Zuber, J., Chou, MM., Vakoc, CR.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Cell","volume":"36","issue":"6","page":"970-83","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10192389","title":"Independent regulation of the two Pax5 alleles during B-cell development.","abstract":"The developmental control genes of the Pax family are frequently associated with mouse mutants and human disease syndromes. The function of these transcription factors is sensitive to gene dosage, as mutation of one allele or a modest increase in gene number results in phenotypic abnormalities. Pax5 has an important role in B-cell and midbrain development. By following the expression of individual Pax5 alleles at the single-cell level, we demonstrate here that Pax5 is subject to allele-specific regulation during B-lymphopoiesis. Pax5 is predominantly transcribed from only one allele in early progenitors and mature B cells, whereas it switches to a biallelic transcription mode in immature B cells. The allele-specific regulation of Pax5 is stochastic, reversible, independent of parental origin and correlates with synchronous replication, in contrast with imprinted and other monoallelically expressed genes. As a consequence, B-lymphoid tissues are mosaics with respect to the transcribed Pax5 allele, and thus mutation of one allele in heterozygous mice results in deletion of the cell population expressing the mutant allele due to loss of Pax5 function at the single-cell level. Similar allele-specific regulation may be a common mechanism causing the haploinsufficiency and frequent association of other Pax genes with human disease.","authors":"Nutt, SL., Vambrie, S., Steinlein, P., Kozmik, Z., Rolink, A., Weith, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nat Genet","volume":"21","issue":"4","page":"390-5","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15125796","title":"Arthritis induces lymphocytic bone marrow inflammation and endosteal bone formation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15125796<\/PMID><DateCompleted><Year>2005<\/Year><Month>02<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2006<\/Year><Month>11<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Print\">0884-0431<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>19<\/Volume><Issue>6<\/Issue><PubDate><Year>2004<\/Year><Month>Jun<\/Month><\/PubDate><\/JournalIssue><Title>Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research<\/Title><ISOAbbreviation>J Bone Miner Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Arthritis induces lymphocytic bone marrow inflammation and endosteal bone formation.<\/ArticleTitle><Pagination><MedlinePgn>990-8<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"UNLABELLED\">Arthritis can destroy the cortical bone barrier and expose bone marrow to synovial tissue. This study examines bone marrow changes in arthritis and its effects on cortical bone remodeling. Bone marrow next to arthritic lesions exhibits B-lymphocyte-rich infiltrates, which express BMPs and stimulate endosteal bone formation. Thus, bone marrow actively participates in the arthritic process.","authors":"G\u00f6rtz, B., Hayer, S., Redlich, K., Zwerina, J., Tohidast-Akrad, M., Tuerk, B., Hartmann, C., Kollias, G., Steiner, G., Smolen, JS., Schett, G.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Bone Miner Res","volume":"19","issue":"6","page":"990-8","pdf":null,"JrId":"104","fulltextlink":null,"preprintlink":null,"articledate":"2005-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20044804","title":"Mitogen-inducible gene-6 is a negative regulator of epidermal growth factor receptor signaling in hepatocytes and human hepatocellular carcinoma.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20044804<\/PMID><DateCompleted><Year>2010<\/Year><Month>04<\/Month><Day>21<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>18<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1527-3350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>51<\/Volume><Issue>4<\/Issue><PubDate><Year>2010<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>Hepatology (Baltimore, Md.)<\/Title><ISOAbbreviation>Hepatology<\/ISOAbbreviation><\/Journal><ArticleTitle>Mitogen-inducible gene-6 is a negative regulator of epidermal growth factor receptor signaling in hepatocytes and human hepatocellular carcinoma.<\/ArticleTitle><Pagination><MedlinePgn>1383-90<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/hep.23428<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">The mitogen-inducible gene-6 (mig-6) is a multi-adaptor protein implicated in the regulation of the HER family of receptor tyrosine kinases. We have reported recently that mig-6 is a negative regulator of epidermal growth factor receptor (EGFR)-dependent skin morphogenesis and tumor formation in vivo. In the liver, ablation of mig-6 leads to an increase in EGFR protein levels, suggesting that mig-6 is a negative regulator of EGFR function. In line with this observation, primary hepatocytes isolated from mig-6 knockout and wild-type control mice display sustained mitogenic signaling in response to EGF. In order to explore the role of mig-6 in the liver in vivo, we analyzed liver regeneration in mig-6 knockout and wild-type control mice. Interestingly, mig-6 knockout mice display enhanced hepatocyte proliferation in the initial phases after partial hepatectomy. This phenotype correlates with activation of endogenous EGFR signaling, predominantly through the protein kinase B pathway. In addition, mig-6 is an endogenous inhibitor of EGFR signaling and EGF-induced tumor cell migration in human liver cancer cell lines. Moreover, mig-6 is down-regulated in human hepatocellular carcinoma and this correlates with increased EGFR expression.","authors":"Reschke, M., Ferby, I., Stepniak, E., Seitzer, N., Horst, D., Wagner, EF., Ullrich, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Hepatology","volume":"51","issue":"4","page":"1383-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20042793","title":"Platelet-derived growth factors for GMP-compliant propagation of mesenchymal stromal cells.","abstract":"Stem cell-based therapies are a promising prospect for regenerative medicine. Particularly, human multipotent mesenchymal stromal cells (MSCs) are currently in focus regarding their regenerative and immune modulating capacities. An increasing number of clinical trials investigating MSC efficiency and safety are ongoing. Ex vivo propagation of human MSCs is considered to be a prerequisite for MSC therapy. The to date standard use of fetal bovine serum in cell culture bears risks including xenoimmunization and transmission of pathogens. Alternatively, human platelet-derived growth factors have been efficiently implemented into routine MSC expansion protocols. In compliance with good manufacturing practice we established an effective time- and resource-saving procedure for MSC propagation in an animal serum-free system. Bone marrow was seeded without manipulation directly in pooled human platelet lysate (pHPL) and L-glutamine supplemented minimum essential medium without antibiotics. Clinical scale expanded MSCs were harvested already after primary culture. MSC quality, identity, purity and function were assessed according to a defined panel of release criteria and comparative genomic hybridization was used to determine genomic stability. Because various potential risks of MSCs have recently been reported, further research is required to prove efficiency and long-term safety of human MSCs for cell therapy.","authors":"Schallmoser, K., Rohde, E., Bartmann, C., Obenauf, AC., Reinisch, A., Strunk, D.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Biomed Mater Eng","volume":"19","issue":"4-5","page":"271-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19950118","title":"Ikaros-1 couples cell cycle arrest of late striatal precursors with neurogenesis of enkephalinergic neurons.","abstract":"During central nervous system development, several transcription factors regulate the differentiation of progenitor cells to postmitotic neurons. Here we describe a novel role for Ikaros-1 in the generation of late-born striatal neurons. Our results show that Ikaros-1 is expressed in the boundary of the striatal germinal zone (GZ)\/mantle zone (MZ), where it induces cell cycle arrest of neural progenitors by up-regulation of the cyclin-dependent kinase inhibitor (CDKi) p21(Cip1\/Waf1). This effect is coupled with the neuronal differentiation of late precursors, which in turn is critical for the second wave of striatal neurogenesis that gives rise to matrix neurons. Consistently, Ikaros(-\/-) mice had fewer striatal projecting neurons and, in particular, enkephalin (ENK)-positive neurons. In addition, overexpression of Ikaros-1 in primary striatal cultures increases the number of calbindin- and ENK-positive neurons. Our results also show that Ikaros-1 acts downstream of the Dlx family of transcription factors, insofar as its expression is lost in Dlx1\/2 double knockout mice. However, we demonstrate that Ikaros-1 and Ebf-1 independently regulate the final determination of the two populations of striatal projection neurons of the matrix compartment, ENK- and substance P-positive neurons. In conclusion, our findings identify Ikaros-1 as a modulator of cell cycle exit of neural progenitors that gives rise to the neurogenesis of ENK-positive striatal neurons.","authors":"Mart\u00edn-Ib\u00e1\u00f1ez, R., Crespo, E., Urb\u00e1n, N., Sergent-Tanguy, S., Herranz, C., Jaumot, M., Valiente, M., Long, JE., Pineda, JR., Andreu, C., Rubenstein, JL., Mar\u00edn, O., Georgopoulos, K., Mengod, G., Fari\u00f1as, I., Bachs, O., Alberch, J., Canals, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Comp Neurol","volume":"518","issue":"3","page":"329-51","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10076805","title":"Recombinant soluble low-density lipoprotein receptor fragment inhibits common cold infection.","abstract":"A fragment of the human low-density lipoprotein receptor encompassing the seven ligand-binding repeats fused to a C-terminal oligo-His tag was expressed in Sf9 insect cells. The melittin signal sequence encoded in the baculovirus vector led to secretion of the protein into the cell supernatant in a soluble form. The receptor fragment bound its natural ligand beta-migrating very-low-density lipoprotein and human rhinovirus serotype 2 in non-reducing ligand blots. Infection of all minor group human rhinovirus serotypes investigated was inhibited by the presence of the receptor fragment during viral challenge of HeLa cells. Infection is inhibited by aggregation of the virions.","authors":"Marlovits, TC., Zechmeister, T., Schwihla, H., Ronacher, B., Blaas, D.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Mol Recognit","volume":"11","issue":"1-6","page":"49-51","pdf":null,"JrId":"1617","fulltextlink":null,"preprintlink":null,"articledate":"1999-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12842007","title":"Shortstop recruits EB1\/APC1 and promotes microtubule assembly at the muscle-tendon junction.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">12842007<\/PMID><DateCompleted><Year>2004<\/Year><Month>02<\/Month><Day>19<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>13<\/Volume><Issue>13<\/Issue><PubDate><Year>2003<\/Year><Month>Jul<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Shortstop recruits EB1\/APC1 and promotes microtubule assembly at the muscle-tendon junction.<\/ArticleTitle><Pagination><MedlinePgn>1086-95<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Shot (previously named Kakapo), is a Drosophila Plakin family member containing both Actin binding and microtubule binding domains. In Drosophila, it is required for a wide range of processes, including axon extension, dendrite formation, axonal terminal arborization at the neuromuscular junction, tendon cell development, and adhesion of wing epithelium.","authors":"Subramanian, A., Prokop, A., Yamamoto, M., Sugimura, K., Uemura, T., Betschinger, J., Knoblich, JA., Volk, T.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"13","page":"1086-95","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9786992","title":"Silent synapses in the developing rat visual cortex: evidence for postsynaptic expression of synaptic plasticity.","abstract":"In the developing visual cortex activity-dependent refinement of synaptic connectivity is thought to involve synaptic plasticity processes analogous to long-term potentiation (LTP). The recently described conversion of so-called silent synapses to functional ones might underlie some forms of LTP. Using whole-cell recording and minimal stimulation procedures in immature pyramidal neurons, we demonstrate here the existence of functionally silent synapses, i.e., glutamatergic synapses that show only NMDA receptor-mediated transmission, in the neonatal rat visual cortex. The incidence of silent synapses strongly decreased during early postnatal development. After pairing presynaptic stimulation with postsynaptic depolarization, silent synapses were converted to functional ones in an LTP-like manner, as indicated by the long-lasting induction of AMPA receptor-mediated synaptic transmission. This conversion was dependent on the activation of NMDA receptors during the pairing protocol. The selective activation of NMDA receptors at silent synapses could be explained presynaptically by assuming a lower glutamate concentration compared with functional ones. However, we found no differences in glutamate concentration-dependent properties of NMDA receptor-mediated PSCs, suggesting that synaptic glutamate concentration is similar in silent and functional synapses. Our results thus support a postsynaptic mechanism underlying silent synapses, i.e., that they do not contain functional AMPA receptors. Synaptic plasticity at silent synapses might be expressed postsynaptically by modification of nonfunctional AMPA receptors or rapid membrane insertion of AMPA receptors. This conversion of silent synapses to functional ones might play a major role in activity-dependent synaptic refinement during development of the visual cortex.","authors":"Rumpel, S., Hatt, H., Gottmann, K.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Neurosci","volume":"18","issue":"21","page":"8863-74","pdf":null,"JrId":"5035","fulltextlink":null,"preprintlink":null,"articledate":"1998-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10037605","title":"Chlamydia infections and heart disease linked through antigenic mimicry.","abstract":"Chlamydia infections are epidemiologically linked to human heart disease. A peptide from the murine heart muscle-specific alpha myosin heavy chain that has sequence homology to the 60-kilodalton cysteine-rich outer membrane proteins of Chlamydia pneumoniae, C. psittaci, and C. trachomatis was shown to induce autoimmune inflammatory heart disease in mice. Injection of the homologous Chlamydia peptides into mice also induced perivascular inflammation, fibrotic changes, and blood vessel occlusion in the heart, as well as triggering T and B cell reactivity to the homologous endogenous heart muscle-specific peptide. Chlamydia DNA functioned as an adjuvant in the triggering of peptide-induced inflammatory heart disease. Infection with C. trachomatis led to the production of autoantibodies to heart muscle-specific epitopes. Thus, Chlamydia-mediated heart disease is induced by antigenic mimicry of a heart muscle-specific protein.","authors":"Bachmaier, K., Neu, N., de la Maza, LM., Pal, S., Hessel, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Science","volume":"283","issue":"5406","page":"1335-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19308697","title":"Assays for mitotic chromosome condensation in live yeast and mammalian cells.","abstract":"The dynamic reorganization of chromatin into rigid and compact mitotic chromosomes is of fundamental importance for faithful chromosome segregation. Owing to the difficulty of investigating this process under physiological conditions, the exact morphological transitions and the molecular machinery driving chromosome condensation remain poorly defined. Here, we review how imaging-based methods can be used to quantitate chromosome condensation in vivo, focusing on yeast and animal tissue culture cells as widely used model systems. We discuss approaches how to address structural dynamics of condensing chromosomes and chromosome segments, as well as to probe for mechanical properties of mitotic chromosomes. Application of such methods to systematic perturbation studies will provide a means to reveal the molecular networks underlying the regulation of mitotic chromosome condensation.","authors":"Neurohr, G., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Chromosome Res","volume":"17","issue":"2","page":"145-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12194817","title":"Regulation of human separase by securin binding and autocleavage.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">12194817<\/PMID><DateCompleted><Year>2003<\/Year><Month>03<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>12<\/Volume><Issue>16<\/Issue><PubDate><Year>2002<\/Year><Month>Aug<\/Month><Day>20<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Regulation of human separase by securin binding and autocleavage.<\/ArticleTitle><Pagination><MedlinePgn>1368-78<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Sister chromatid separation is initiated by separase, a protease that cleaves cohesin and thereby dissolves sister chromatid cohesion. Separase is activated by the degradation of its inhibitor securin and by the removal of inhibitory phosphates. In human cells, separase activation also coincides with the cleavage of separase, but it is not known if this reaction activates separase, which protease cleaves separase, and how separase cleavage is regulated.","authors":"Waizenegger, I., Gim\u00e9nez-Abi\u00e1n, JF., Wernic, D., Peters, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"16","page":"1368-78","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2003-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12105167","title":"Expression of CYR61, an angiogenic immediate early gene, in arteriosclerosis and its regulation by angiotensin II.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">12105167<\/PMID><DateCompleted><Year>2002<\/Year><Month>07<\/Month><Day>19<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>30<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1524-4539<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>106<\/Volume><Issue>2<\/Issue><PubDate><Year>2002<\/Year><Month>Jul<\/Month><Day>09<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>Expression of CYR61, an angiogenic immediate early gene, in arteriosclerosis and its regulation by angiotensin II.<\/ArticleTitle><Pagination><MedlinePgn>254-60<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The renin-angiotensin system is thought to be involved in development and progression of arteriosclerosis, thereby contributing to adverse cardiovascular events. To elucidate the role of angiotensin II (Ang II) at a cellular level, we analyzed the Ang II-induced gene expression profile.","authors":"Hilfiker, A., Hilfiker-Kleiner, D., Fuchs, M., Kaminski, K., Lichtenberg, A., Rothk\u00f6tter, HJ., Schieffer, B., Drexler, H.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Circulation","volume":"106","issue":"2","page":"254-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19940926","title":"Central control of fever and female body temperature by RANKL\/RANK.","abstract":"Receptor-activator of NF-kappaB ligand (TNFSF11, also known as RANKL, OPGL, TRANCE and ODF) and its tumour necrosis factor (TNF)-family receptor RANK are essential regulators of bone remodelling, lymph node organogenesis and formation of a lactating mammary gland. RANKL and RANK are also expressed in the central nervous system. However, the functional relevance of RANKL\/RANK in the brain was entirely unknown. Here we report that RANKL and RANK have an essential role in the brain. In both mice and rats, central RANKL injections trigger severe fever. Using tissue-specific Nestin-Cre and GFAP-Cre rank(floxed) deleter mice, the function of RANK in the fever response was genetically mapped to astrocytes. Importantly, Nestin-Cre and GFAP-Cre rank(floxed) deleter mice are resistant to lipopolysaccharide-induced fever as well as fever in response to the key inflammatory cytokines IL-1beta and TNFalpha. Mechanistically, RANKL activates brain regions involved in thermoregulation and induces fever via the COX2-PGE(2)\/EP3R pathway. Moreover, female Nestin-Cre and GFAP-Cre rank(floxed) mice exhibit increased basal body temperatures, suggesting that RANKL and RANK control thermoregulation during normal female physiology. We also show that two children with RANK mutations exhibit impaired fever during pneumonia. These data identify an entirely novel and unexpected function for the key osteoclast differentiation factors RANKL\/RANK in female thermoregulation and the central fever response in inflammation.","authors":"Hanada, R., Leibbrandt, A., Hanada, T., Kitaoka, S., Furuyashiki, T., Fujihara, H., Trichereau, J., Paolino, M., Qadri, F., Plehm, R., Klaere, S., Komnenovic, V., Mimata, H., Yoshimatsu, H., Takahashi, N., von Haeseler, A., Bader, M., Kilic, SS., Ueta, Y., Pifl, C., Narumiya, S., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nature","volume":"462","issue":"7272","page":"505-9","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11165488","title":"Expression of members of the Fgf family and their receptors during midfacial development.","abstract":"Members of the FGF family play diverse roles in patterning, cell proliferation and differentiation during embryogenesis. To begin to address their function during craniofacial development we have analyzed the expression of 18 members of the Fgf family (Fgf1-15, -17, -18 and -20) and the four members of the FGF-receptor family in the prospective midfacial region between E9.5 and E11.5 by whole-mount in situ hybridization. We show that at E9.5, Fgf3, -8, -9, -10 and -17 are broadly expressed in midfacial ectoderm. Concomitant with the outgrowth of the nasal processes at E10.5, expression of Fgf3, -8, -9, -10, -15, -17 and -18 was detected in spatially restricted regions of ectoderm at the edge of the nasal pit and at the oral edge of the medial nasal process. Expression of Fgf8, Fgf9, Fgf10 and Fgf17 was still observed in these domains at E11.5. In contrast to the restricted expression patterns of the ligands, FgfR1 and FgfR2 were broadly expressed in facial mesenchyme and ectoderm, respectively, indicating a wide competence of midfacial tissue to respond to FGF signaling.","authors":"Bachler, M., Neub\u00fcser, A.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Mech Dev","volume":"100","issue":"2","page":"313-6","pdf":null,"JrId":"1825","fulltextlink":null,"preprintlink":null,"articledate":"2001-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19924867","title":"Stoichiometry determination of the MP1-p14 complex using a novel and cost-efficient method to produce an equimolar mixture of standard peptides.","abstract":"Determination of protein complex stoichiometry can be achieved by absolute quantification of the interacting constituents based on isotope dilution mass spectrometry. Current available platforms for the generation of standard peptides are cost-intensive and deliver variable results concerning the equimolarity of the standard peptides. Here we describe a novel and cost-efficient method to generate an equimolar mixture of standard peptides, which we call the equimolarity through equalizer peptide (EtEP) strategy. The rationale of the strategy allows equalization of internal standard peptides and absolute quantification of any protein of interest via a single peptide, from which the exact amount was determined by amino acid analysis. This and the use of the mTRAQ reagent significantly decrease the costs of absolute quantification and stoichiometry determination. We used the EtEP strategy to determine the MP1-p14 complex stoichiometry of two different concentrations, one simulating a condition following tandem affinity purification. Absolute quantification of MP1-p14 was performed on two different mass spectrometers, and the 1:1 stoichiometry was confirmed with high accuracy and precision. On the basis of the quantification of MP1-p14, we demonstrate the importance to assess completeness of protein digestion and discuss the use of peptides containing labile amino acids and the choice of instrumentation.","authors":"Holzmann, J., Pichler, P., Madalinski, M., Kurzbauer, R., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Anal Chem","volume":"81","issue":"24","page":"10254-61","pdf":null,"JrId":"519","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17167088","title":"The molecular gatekeeper Dexras1 sculpts the photic responsiveness of the mammalian circadian clock.","abstract":"The mammalian master clock, located in the suprachiasmatic nucleus (SCN), is exquisitely sensitive to photic timing cues, but the key molecular events that sculpt both the phasing and magnitude of responsiveness are not understood. Here, we show that the Ras-like G-protein Dexras1 is a critical factor in these processes. Dexras1-deficient mice (dexras1-\/-) exhibit a restructured nighttime phase response curve and a loss of gating to photic resetting during the day. Dexras1 affects the photic sensitivity by repressing or activating time-of-day-specific signaling pathways that regulate extracellular signal-regulated kinase (ERK)\/mitogen-activated protein kinase (MAPK). During the late night, Dexras1 limits the capacity of pituitary adenylate cyclase (PAC) activating peptide (PACAP)\/PAC1 to affect ERK\/MAPK, and in the early night, light-induced phase delays, which are mediated predominantly by NMDA receptors, are reduced as reported previously. Daytime photic phase advances are mediated by a novel signaling pathway that does not affect the SCN core but rather stimulates ERK\/MAPK in the SCN shell and triggers downregulation of clock protein expression.","authors":"Cheng, HY., Dziema, H., Papp, J., Mathur, DP., Koletar, M., Ralph, MR., Penninger, JM., Obrietan, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Neurosci","volume":"26","issue":"50","page":"12984-95","pdf":null,"JrId":"5035","fulltextlink":null,"preprintlink":null,"articledate":"2007-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9311990","title":"Kr\u00fcppel target gene knockout participates in the proper innervation of a specific set of Drosophila larval muscles.","abstract":"Kr\u00fcppel (Kr) encodes a zinc finger-type transcription factor expressed in spatially and temporally restricted patterns during Drosophila embryogenesis. Molecular targets and the mechanism of Kr action have been studied extensively during the early segmentation process, but only little is known about Kr requirement during later development. We report the identification of a target gene of Kr, termed knockout (ko), isolated by virtue of Kr\u00fcppel in vitro binding sites. Loss and gain of function experiments show that Kr activity maintains ko expression in a subset of muscles. ko encodes a novel protein expressed in several embryonic tissues including Kr-expressing muscles. Movements of embryos deficient for ko activity are uncoordinated. Their muscle pattern is normal, but the patterns of neuromuscular innervation are specifically disarranged. The results suggest that the Kr target gene ko is required for proper innervation of specific muscles by RP motoneurons.","authors":"Hartmann, C., Landgraf, M., Bate, M., J\u00e4ckle, H.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"EMBO J","volume":"16","issue":"17","page":"5299-309","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1997-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10199887","title":"Generation of humanized mice susceptible to peptide-induced inflammatory heart disease.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">10199887<\/PMID><DateCompleted><Year>1999<\/Year><Month>05<\/Month><Day>06<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>23<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1524-4539<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>99<\/Volume><Issue>14<\/Issue><PubDate><Year>1999<\/Year><Month>Apr<\/Month><Day>13<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>Generation of humanized mice susceptible to peptide-induced inflammatory heart disease.<\/ArticleTitle><Pagination><MedlinePgn>1885-91<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Dilated cardiomyopathy (DCM) is a major cause of sudden cardiac death. In certain mouse major histocompatibility complex (MHC) backgrounds, myocarditis and inflammatory cardiomyopathy can be triggered by immunization with heart muscle-specific proteins. Similarly, chronic heart disease in humans has been linked to certain HLA alleles, such as HLA-DQ6. However, there is no experimental evidence showing that human MHC class II molecules and peptides derived from human proteins are involved in the pathogenesis of myocarditis and DCM.","authors":"Bachmaier, K., Neu, N., Yeung, RS., Mak, TW., Liu, P., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Circulation","volume":"99","issue":"14","page":"1885-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32858748","title":"Mitophagy is induced by short ubiquitin chains on mitochondria.","abstract":"Mitophagy has a critical role in maintaining cellular homeostasis by removing damaged mitochondria. In this issue, Yamano et al. (2020. J. Cell Biol. https:\/\/doi.org\/10.1083\/jcb.201912144) uncover that a novel complex of the autophagy adaptor optineurin and the membrane protein ATG9A specifically regulate ubiquitin-induced mitophagy.","authors":"Ikeda, F.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Cell Biol","volume":"219","issue":"9","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16978391","title":"Formation and nuclear export of preribosomes are functionally linked to the small-ubiquitin-related modifier pathway.","abstract":"Ribosomal precursor particles are initially assembled in the nucleolus prior to their transfer to the nucleoplasm and export to the cytoplasm. In a screen to identify thermosensitive (ts) mutants defective in the export of pre-60S ribosomal subunit, we isolated the rix16-1 mutant. In this strain, nucleolar accumulation of the Rpl25-eGFP reporter was complemented by UBA2 (a subunit of the E1 sumoylation enzyme). Mutations in UBC9 (E2 enzyme), ULP1 [small-ubiquitin-related modifier (SUMO) isopeptidase] and SMT3 (SUMO-1) caused 60S export defects. A directed analysis of the SUMO proteome revealed that many ribosome biogenesis factors are sumoylated. Importantly, preribosomal particles along both the 60S and the 40S synthesis pathways were decorated with SUMO, showing its direct involvement. Consistent with this, early 60S assembly factors were genetically linked to SUMO conjugation. Notably, the SUMO deconjugating enzyme Ulp1, which localizes to the nuclear pore complex (NPC), was functionally linked to the 60S export factor Mtr2. Together our data suggest that sumoylation of preribosomal particles in the nucleus and subsequent desumoylation at the NPC is necessary for efficient ribosome biogenesis and export in eukaryotes.","authors":"Panse, VG., Kressler, D., Pauli, A., Petfalski, E., Gn\u00e4dig, M., Tollervey, D., Hurt, E.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Traffic","volume":"7","issue":"10","page":"1311-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32698000","title":"Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers.","abstract":"It is currently assumed that 3D chromosomal organization plays a central role in transcriptional control. However, depletion of cohesin and CTCF affects the steady-state levels of only a minority of transcripts. Here, we use high-resolution Capture Hi-C to interrogate the dynamics of chromosomal contacts of all annotated human gene promoters upon degradation of cohesin and CTCF. We show that a majority of promoter-anchored contacts are lost in these conditions, but many contacts with distinct properties are maintained, and some new ones are gained. The rewiring of contacts between promoters and active enhancers upon cohesin degradation associates with rapid changes in target gene transcription as detected by SLAM sequencing (SLAM-seq). These results provide a mechanistic explanation for the limited, but consistent, effects of cohesin and CTCF depletion on steady-state transcription and suggest the existence of both cohesin-dependent and -independent mechanisms of enhancer-promoter pairing.","authors":"Thiecke, MJ., Wutz, G., Muhar, M., Tang, W., Bevan, S., Malysheva, V., Stocsits, R., Neumann, T., Zuber, J., Fraser, P., Schoenfelder, S., Peters, JM., Spivakov, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Rep","volume":"32","issue":"3","page":"107929","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19851091","title":"Recombinant angiotensin-converting enzyme 2 improves pulmonary blood flow and oxygenation in lipopolysaccharide-induced lung injury in piglets.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19851091<\/PMID><DateCompleted><Year>2010<\/Year><Month>02<\/Month><Day>22<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1530-0293<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>38<\/Volume><Issue>2<\/Issue><PubDate><Year>2010<\/Year><Month>Feb<\/Month><\/PubDate><\/JournalIssue><Title>Critical care medicine<\/Title><ISOAbbreviation>Crit Care Med<\/ISOAbbreviation><\/Journal><ArticleTitle>Recombinant angiotensin-converting enzyme 2 improves pulmonary blood flow and oxygenation in lipopolysaccharide-induced lung injury in piglets.<\/ArticleTitle><Pagination><MedlinePgn>596-601<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1097\/CCM.0b013e3181c03009<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">To study angiotensin-converting enzyme 2 in a piglet model with acute respiratory distress syndrome and to evaluate the therapeutic potential of this substance in a preclinical setting, as this model allows the assessment of the same parameters required for monitoring the disease in human intensive care medicine. The acute respiratory distress syndrome is the most severe form of acute lung injury with a high mortality rate. As yet, there is no specific therapy for improving the clinical outcome. Recently, angiotensin-converting enzyme 2, which inactivates angiotensin II, has been shown to ameliorate acute lung injury in mice.","authors":"Treml, B., Neu, N., Kleinsasser, A., Gritsch, C., Finsterwalder, T., Geiger, R., Schuster, M., Janzek, E., Loibner, H., Penninger, J., Loeckinger, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Crit Care Med","volume":"38","issue":"2","page":"596-601","pdf":null,"JrId":"3206","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7603032","title":"Activation of HIV transcription by human foamy virus in transgenic mice.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">7603032<\/PMID><DateCompleted><Year>1995<\/Year><Month>08<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2008<\/Year><Month>11<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0023-6837<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>73<\/Volume><Issue>1<\/Issue><PubDate><Year>1995<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>Laboratory investigation; a journal of technical methods and pathology<\/Title><ISOAbbreviation>Lab Invest<\/ISOAbbreviation><\/Journal><ArticleTitle>Activation of HIV transcription by human foamy virus in transgenic mice.<\/ArticleTitle><Pagination><MedlinePgn>103-10<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Although infection by HIV-1 is the primary cause of AIDS, cofactorial agents of an infectious nature may be involved in the pathogenesis of the disease. The present work addresses the cofactorial potential of human foamy virus (HFV) in AIDS. It has been suggested that HFV seroprevalence reaches 5% in East Africa, and HFV seroprevalence in East African patients suffering from AIDS and AIDS-related complex may be as high as 20%. Although the pathogenic potential of HFV in humans has not yet been investigated in detail, HFV transgenic mice develop an encephalopathy reminiscent of some of the features of HIV-associated brain diseases.","authors":"Marino, S., Kretschmer, C., Brandner, S., Cavard, C., Zider, A., Briand, P., Isenmann, S., Wagner, EF., Aguzzi, A.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Lab Invest","volume":"73","issue":"1","page":"103-10","pdf":null,"JrId":"5462","fulltextlink":null,"preprintlink":null,"articledate":"1995-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20530212","title":"Tubulin polyglutamylation stimulates spastin-mediated microtubule severing.","abstract":"Posttranslational glutamylation of tubulin is present on selected subsets of microtubules in cells. Although the modification is expected to contribute to the spatial and temporal organization of the cytoskeleton, hardly anything is known about its functional relevance. Here we demonstrate that glutamylation, and in particular the generation of long glutamate side chains, promotes the severing of microtubules. In human cells, the generation of long side chains induces spastin-dependent microtubule disassembly and, consistently, only microtubules modified by long glutamate side chains are efficiently severed by spastin in vitro. Our study reveals a novel control mechanism for microtubule mass and stability, which is of fundamental importance to cellular physiology and might have implications for diseases related to microtubule severing.","authors":"Lacroix, B., van Dijk, J., Gold, ND., Guizetti, J., Aldrian-Herrada, G., Rogowski, K., Gerlich, DW., Janke, C.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Cell Biol","volume":"189","issue":"6","page":"945-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"154","title":"Influence of hematocrit, blood gas tensions, and pH on pressure-flow relations in the isolated canine lung.","abstract":"An isolated perfused canine lung preparation in which determinants of vascular caliber could be individually controlled was developed. The relation of pulmonary arterial (Pa), venous (PV), and alveolar (PA) pressures was such that Pa greater than PA greater than PV throughout the whole lung. The addition of isoprenaline to the perfusate abolished vascular reactivity. Once stability was reached, vascular cross-sectional area remained acceptably constant for 2.25 hours as judged by normalized conductance. The influence of perfusate hematocrit, blood gas tensions, and pH on pressure-flow relations was then studied in 15 isolated canine lungs. The hematocrit-vascular conductance relation was derived at constant perfusion pressure. Conductance varied linearly with hematocrit over a range of 16.5 to 89.5%. Mean pulmonary arterial blood gas tensions were: PO2 = 121 mm Hg, PCO2 = 28 mm Hg, and pH = 7.46. Acute respiratory acidosis (PO2 = 30 mm Hg, PCO2 = 81 mm Hg, pH = 7.17) and lactic acidosis and hypoxemia (PO2 = 32 mm Hg, PCO2 = 21 mm Hg, pH = 6.96) did not significantly alter this relation. Transformation of the conductance-hematocrit data indicated that hematocrit was the most important determinant of relative apparent viscosity of the blood. Both acute respiratory and lactic acidosis failed to significantly increase relative viscosity within the range of hematocrit usually found in secondary polycythemia.","authors":"Bucens, D., Pain, MC.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Circ Res","volume":"37","issue":"5","page":"588-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19800577","title":"Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model.","abstract":"Short hairpin RNAs (shRNAs) capable of stably suppressing gene function by RNA interference (RNAi) can mimic tumor-suppressor-gene loss in mice. By selecting for shRNAs capable of accelerating lymphomagenesis in a well-characterized mouse lymphoma model, we identified over ten candidate tumor suppressors, including Sfrp1, Numb, Mek1, and Angiopoietin 2. Several components of the DNA damage response machinery were also identified, including Rad17, which acts as a haploinsufficient tumor suppressor that responds to oncogenic stress and whose loss is associated with poor prognosis in human patients. Our results emphasize the utility of in vivo RNAi screens, identify and validate a diverse set of tumor suppressors, and have therapeutic implications.","authors":"Bric, A., Miething, C., Bialucha, CU., Scuoppo, C., Zender, L., Krasnitz, A., Xuan, Z., Zuber, J., Wigler, M., Hicks, J., McCombie, RW., Hemann, MT., Hannon, GJ., Powers, S., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cancer Cell","volume":"16","issue":"4","page":"324-35","pdf":null,"JrId":"29778","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12654243","title":"Global chromosome positions are transmitted through mitosis in mammalian cells.","abstract":"We investigated positioning of chromosomes during the cell cycle in live mammalian cells with a combined experimental and computational approach. By non-invasive labeling of chromosome subsets and tracking by 4D imaging, we could show that no global rearrangements occurred in interphase. Using the same assay, we also observed a striking order of chromosomes throughout mitosis. By contrast, our computer simulation based on stochastic movements of individual chromosomes predicted randomization of chromosome order in mitosis. In vivo, a quantitative assay for single chromosome positioning during mitosis revealed strong similarities between daughter and mother cells. These results demonstrate that global chromosome positions are heritable through the cell cycle in mammalian cells. Based on tracking of labeled chromosomes and centromeres during chromosome segregation and experimental perturbations of chromosomal order, we propose that chromosome specific timing of sister chromatid separation transmits chromosomal positions from one cell generation to the next.","authors":"Gerlich, D., Beaudouin, J., Kalbfuss, B., Daigle, N., Eils, R., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Cell","volume":"112","issue":"6","page":"751-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19754359","title":"Crosstalk between epidermal growth factor receptor- and insulin-like growth factor-1 receptor signaling: implications for cancer therapy.","abstract":"Both the epidermal growth factor receptor (EGFR) and the insulin-like growth factor-1 receptor (IGF-1R) can contribute to tumor development and -progression through their effects on cell proliferation, inhibition of apoptosis, angiogenesis, anchorage-independent growth and tumor-associated inflammation. EGFR-targeting monoclonal antibodies and small molecule tyrosine kinase inhibitors are currently in clinical use for the treatment of several types of cancer. However, primary and acquired resistance to these agents often occurs and thereby limits the clinical efficacy of mono-specific targeted therapy. Results from both in vitro and in vivo studies indicate that cross-talk between EGFR and IGF-1R can lead to acquired resistance against EGFR-targeted drugs. This review describes the interface between the EGFR and IGF-1R signaling networks and the implications of the extensive cross-talk between these two receptor systems for cancer therapy. EGFR and IGF-1R interact on multiple levels, either through a direct association between the two receptors, by mediating the availability of each others ligands, or indirectly, via common interaction partners such as G protein coupled receptors (GPCR) or downstream signaling molecules. This multi-layered cross-talk and its involvement in the induction of resistance to targeted therapies provide a clear rationale for dual targeting of EGFR and IGF-1R. We discuss several (potential) strategies to simultaneously inhibit EGFR and IGF-1R signaling as promising novel therapeutic approaches.","authors":"van der Veeken, J., Oliveira, S., Schiffelers, RM., Storm, G., van Bergen En Henegouwen, PM., Roovers, RC.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Curr Cancer Drug Targets","volume":"9","issue":"6","page":"748-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9190818","title":"Comparative characterization of SecA from the alpha-subclass purple bacterium Rhodobacter capsulatus and Escherichia coli reveals differences in membrane and precursor specificity.","abstract":"We have cloned the secA gene of the alpha-subclass purple bacterium Rhodobacter capsulatus, a close relative to the mitochondrial ancestor, and purified the protein after expression in Escherichia coli. R. capsulatus SecA contains 904 amino acids with 53% identity to E. coli and 54% identity to Caulobacter crescentus SecA. In contrast to the nearly equal partitioning of E. coli SecA between the cytosol and plasma membrane, R. capsulatus SecA is recovered predominantly from the membrane fraction. A SecA-deficient, cell-free synthesis-translocation system prepared from R. capsulatus is used to demonstrate translocation activity of the purified R. capsulatus SecA. This translocation activity is then compared to that of the E. coli counterpart by using various precursor proteins and inside-out membrane vesicles prepared from both bacteria. We find a preference of the R. capsulatus SecA for the homologous membrane vesicles whereas E. coli SecA is active with either type of membrane. Furthermore, the two SecA proteins clearly select between distinct precursor proteins. In addition, we show here for the first time that a bacterial c-type cytochrome utilizes the canonical, Sec-dependent export pathway.","authors":"Helde, R., Wiesler, B., Wachter, E., Neub\u00fcser, A., Hoffschulte, HK., Hengelage, T., Schimz, KL., Stuart, RA., M\u00fcller, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Bacteriol","volume":"179","issue":"12","page":"4003-12","pdf":null,"JrId":"4540","fulltextlink":null,"preprintlink":null,"articledate":"1997-07-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31004710","title":"MICAL2 is expressed in cancer associated neo-angiogenic capillary endothelia and it is required for endothelial cell viability, motility and VEGF response.","abstract":"The capacity of inducing angiogenesis is a recognized hallmark of cancer cells. The cancer microenvironment, characterized by hypoxia and inflammatory signals, promotes proliferation, migration and activation of quiescent endothelial cells (EC) from surrounding vascular network. Current anti-angiogenic drugs present side effects, temporary efficacy, and issues of primary resistance, thereby calling for the identification of new therapeutic targets. MICALs are a unique family of redox enzymes that destabilize F-actin in cytoskeletal dynamics. MICAL2 mediates Semaphorin3A-NRP2 response to VEGFR1 in rat ECs. MICAL2 also enters the p130Cas interactome in response to VEGF in HUVEC. Previously, we showed that MICAL2 is overexpressed in metastatic cancer. A small-molecule inhibitor of MICAL2 exists (CCG-1423). Here we report that 1) MICAL2 is expressed in neo-angiogenic ECs in human solid tumors (kidney and breast carcinoma, glioblastoma and cardiac myxoma, n\u202f=\u202f67, were analyzed with immunohistochemistry) and in animal models of ischemia\/inflammation neo-angiogenesis, but not in normal capillary bed; 2) MICAL2 protein pharmacological inhibition (CCG-1423) or gene KD reduce EC viability and functional performance; 3) MICAL2 KD disables ECs response to VEGF in vitro. Whole-genome gene expression profiling reveals MICAL2 involvement in angiogenesis and vascular development pathways. Based on these results, we propose that MICAL2 expression in ECs participates to inflammation-induced neo-angiogenesis and that MICAL2 inhibition should be tested in cancer- and noncancer-associated neo-angiogenesis, where chronic inflammation represents a relevant pathophysiological mechanism.","authors":"Barravecchia, I., Mariotti, S., Pucci, A., Scebba, F., De Cesari, C., Bicciato, S., Tagliafico, E., Tenedini, E., Vindigni, C., Cecchini, M., Berti, G., Vitiello, M., Poliseno, L., Mazzanti, CM., Angeloni, D.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Biochim Biophys Acta Mol Basis Dis","volume":"1865","issue":"9","page":"2111-2124","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19745491","title":"Fight for chromallocyte.","abstract":"This paper reports on the most important recent technological event and its significance to the human race: chromallocyte designed by Robert Freitas--a nanorobot that would be capable of replacing chromosomes on a cell by cell basis throughout the body in vivo. The significance of chromallocyte comes from its ability to painlessly reverse the effects of genetic disease and other accumulated damage to our genes thus preventing aging. It could reduce suffering, save lives and enhance human potential. By analogy to the successful effort to put man on the moon, we should aim at chromallocyte landing on the liver by 2039 which would commemorate 70th anniversary of man landing on the Moon. The same strategic planning principle could be applied. We should have a dream with a deadline of 2039.","authors":"Bushko, RG.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Stud Health Technol Inform","volume":"149","issue":"","page":"322-31","pdf":null,"JrId":"21248","fulltextlink":null,"preprintlink":null,"articledate":"2010-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19731623","title":"RANKL\/RANK as key factors for osteoclast development and bone loss in arthropathies.","abstract":"Osteoporosis or rheumatoid arthritis are bone diseases affecting hundreds of millions of people worldwide and thus pose a tremendous burden to health care. Ground-breaking discoveries made in basic science over the last decade shed light on the molecular mechanisms of bone metabolism and bone turnover. Thereby, it became possible over the past years to devise new and promising strategies for treating such diseases. In particular, three molecules, the receptor activator of NF-kappaB (RANK), its ligand RANKL and the decoy receptor of RANKL, osteoprotegerin (OPG), have been a major focus of scientists and pharmaceutical companies alike, since experiments using mice in which these genes have been inactivated unanimously established their pivotal role as central regulators ofosteoclast function. RANK(L) signaling not only activates a variety of downstream signaling pathways required for osteoclast development, but crosstalk with other signaling pathways also fine-tunes bone homeostasis both in normal physiology and disease. Consequently, novel drugs specifically targeting RANK-RANKL and their signaling pathways in osteoclasts are expected to revolutionize the treatment ofvarious bone diseases, such as cancer metastases, osteoporosis, or arthropathies.","authors":"Leibbrandt, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Adv Exp Med Biol","volume":"649","issue":null,"page":"100-13","pdf":null,"JrId":"280","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28202522","title":"Histone Acetyltransferase Activity of MOF Is Required for <i>MLL-AF9<\/i> Leukemogenesis.","abstract":"Chromatin-based mechanisms offer therapeutic targets in acute myeloid leukemia (AML) that are of great current interest. In this study, we conducted an RNAi-based screen to identify druggable chromatin regulator-based targets in leukemias marked by oncogenic rearrangements of the <i>MLL<\/i> gene. In this manner, we discovered the H4K16 histone acetyltransferase (HAT) MOF to be important for leukemia cell growth. Conditional deletion of <i>Mof<\/i> in a mouse model of <i>MLL-AF9<\/i>-driven leukemogenesis reduced tumor burden and prolonged host survival. RNA sequencing showed an expected downregulation of genes within DNA damage repair pathways that are controlled by MOF, as correlated with a significant increase in yH2AX nuclear foci in <i>Mof<\/i>-deficient <i>MLL-AF9<\/i> tumor cells. In parallel, <i>Mof<\/i> loss also impaired global H4K16 acetylation in the tumor cell genome. Rescue experiments with catalytically inactive mutants of MOF showed that its enzymatic activity was required to maintain cancer pathogenicity. In support of the role of MOF in sustaining H4K16 acetylation, a small-molecule inhibitor of the HAT component MYST blocked the growth of both murine and human <i>MLL-AF9<\/i> leukemia cell lines. Furthermore, <i>Mof<\/i> inactivation suppressed leukemia development in an <i>NUP98-HOXA9<\/i>-driven AML model. Taken together, our results establish that the HAT activity of MOF is required to sustain <i>MLL-AF9<\/i> leukemia and may be important for multiple AML subtypes. Blocking this activity is sufficient to stimulate DNA damage, offering a rationale to pursue MOF inhibitors as a targeted approach to treat <i>MLL<\/i>-rearranged leukemias. <i>Cancer Res; 77(7); 1753-62. \u00a92017 AACR<\/i>.","authors":"Valerio, DG., Xu, H., Chen, CW., Hoshii, T., Eisold, ME., Delaney, C., Cusan, M., Deshpande, AJ., Huang, CH., Lujambio, A., Zheng, YG., Zuber, J., Pandita, TK., Lowe, SW., Armstrong, SA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cancer Res","volume":"77","issue":"7","page":"1753-1762","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31858691","title":"Why (and how) we should publish negative data.","abstract":"Negative data and refutations are a crucial element of the scientific process. But it needs solid arguments to convince editors and reviewers to publish negative results.","authors":"Nimpf, S., Keays, DA.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"EMBO Rep","volume":"21","issue":"1","page":"e49775","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28596378","title":"Molecular definitions of autophagy and related processes.","abstract":"Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about the use of appropriate terms to indicate specific types of autophagy and some components of the autophagy machinery, which may have detrimental effects on the expansion of the field. Driven by the overt recognition of such a potential obstacle, a panel of leading experts in the field attempts here to define several autophagy-related terms based on specific biochemical features. The ultimate objective of this collaborative exchange is to formulate recommendations that facilitate the dissemination of knowledge within and outside the field of autophagy research.","authors":"Galluzzi, L., Baehrecke, EH., Ballabio, A., Boya, P., Bravo-San Pedro, JM., Cecconi, F., Choi, AM., Chu, CT., Codogno, P., Colombo, MI., Cuervo, AM., Debnath, J., Deretic, V., Dikic, I., Eskelinen, EL., Fimia, GM., Fulda, S., Gewirtz, DA., Green, DR., Hansen, M., Harper, JW., J\u00e4\u00e4ttel\u00e4, M., Johansen, T., Juhasz, G., Kimmelman, AC., Kraft, C., Ktistakis, NT., Kumar, S., Levine, B., Lopez-Otin, C., Madeo, F., Martens, S., Martinez, J., Melendez, A., Mizushima, N., M\u00fcnz, C., Murphy, LO., Penninger, JM., Piacentini, M., Reggiori, F., Rubinsztein, DC., Ryan, KM., Santambrogio, L., Scorrano, L., Simon, AK., Simon, HU., Simonsen, A., Tavernarakis, N., Tooze, SA., Yoshimori, T., Yuan, J., Yue, Z., Zhong, Q., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"EMBO J","volume":"36","issue":"13","page":"1811-1836","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31284834","title":"Monitoring Cell-Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31284834<\/PMID><DateCompleted><Year>2020<\/Year><Month>05<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>05<\/Month><Day>18<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4571<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>125<\/Volume><Issue>4<\/Issue><PubDate><Year>2019<\/Year><Month>08<\/Month><Day>02<\/Day><\/PubDate><\/JournalIssue><Title>Circulation research<\/Title><ISOAbbreviation>Circ Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Monitoring Cell-Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress.<\/ArticleTitle><Pagination><MedlinePgn>431-448<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/CIRCRESAHA.119.314817<\/ELocationID><Abstract><AbstractText Label=\"RATIONALE\">Gene expression profiles have been mainly determined by analysis of transcript abundance. However, these analyses cannot capture posttranscriptional gene expression control at the level of translation, which is a key step in the regulation of gene expression, as evidenced by the fact that transcript levels often poorly correlate with protein levels. Furthermore, genome-wide transcript profiling of distinct cell types is challenging due to the fact that lysates from tissues always represent a mixture of cells.","authors":"Doroudgar, S., Hofmann, C., Boileau, E., Malone, B., Riechert, E., Gorska, AA., Jakobi, T., Sandmann, C., J\u00fcrgensen, L., Kmietczyk, V., Malovrh, E., Burghaus, J., Rettel, M., Stein, F., Younesi, F., Friedrich, UA., Mauz, V., Backs, J., Kramer, G., Katus, HA., Dieterich, C., V\u00f6lkers, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Circ Res","volume":"125","issue":"4","page":"431-448","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28424523","title":"Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl.","abstract":"Mammalian genomes are spatially organized by CCCTC-binding factor (CTCF) and cohesin into chromatin loops and topologically associated domains, which have important roles in gene regulation and recombination. By binding to specific sequences, CTCF defines contact points for cohesin-mediated long-range chromosomal cis-interactions. Cohesin is also present at these sites, but has been proposed to be loaded onto DNA elsewhere and to extrude chromatin loops until it encounters CTCF bound to DNA. How cohesin is recruited to CTCF sites, according to this or other models, is unknown. Here we show that the distribution of cohesin in the mouse genome depends on transcription, CTCF and the cohesin release factor Wings apart-like (Wapl). In CTCF-depleted fibroblasts, cohesin cannot be properly recruited to CTCF sites but instead accumulates at transcription start sites of active genes, where the cohesin-loading complex is located. In the absence of both CTCF and Wapl, cohesin accumulates in up to 70 kilobase-long regions at 3'-ends of active genes, in particular if these converge on each other. Changing gene expression modulates the position of these 'cohesin islands'. These findings indicate that transcription can relocate mammalian cohesin over long distances on DNA, as previously reported for yeast cohesin, that this translocation contributes to positioning cohesin at CTCF sites, and that active genes can be freed from cohesin either by transcription-mediated translocation or by Wapl-mediated release.","authors":"Busslinger, GA., Stocsits, RR., van der Lelij, P., Axelsson, E., Tedeschi, A., Galjart, N., Peters, JM.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"544","issue":"7651","page":"503-507","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30292241","title":"Correction to: The role of fibrinolysis inhibition in engineered vascular networks derived from endothelial cells and adipose-derived stem cells.","abstract":"The original article [1] contains numerous value errors in the graphs in Fig.\u00a02b regarding the markers describing the values for total tubule length and mean tubule length without aprotinin at 2.5\u00a0mg\/ml concentration of fibrinogen. The corrected version of this figure can be viewed ahead.","authors":"M\u00fchleder, S., Pill, K., Schaupper, M., Labuda, K., Priglinger, E., Hofbauer, P., Charwat, V., Marx, U., Redl, H., Holnthoner, W.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Stem Cell Res Ther","volume":"9","issue":"1","page":"261","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12538633","title":"Global transcription profiling of estrogen activity: estrogen receptor alpha regulates gene expression in the kidney.","abstract":"Estrogen receptors (ERs) are expressed in numerous organs, although only a few organs are considered classical targets for estrogens. We have completed a systematic survey of estrogen regulation of approximately 10,000 genes in 13 tissues from wild-type and ERbetaKO mice treated sc with vehicle or 17beta-estradiol (E2) for 6 wk. The uterus and pituitary had the greatest number of genes regulated by E2, whereas the kidney had the third largest number of regulated genes. In situ hybridizations localized E2 regulation in the kidney to the juxtamedullary region of the cortex in both the mouse and rat. The ED(50) for gene inductions in the kidney was 3 micro g\/kg.d, comparable with the 2.4 micro g\/kg.d ED(50) for c-fos induction in the uterus. E2 regulations in the kidney were intact in ERbetaKO mice, and the ERalpha-selective agonist propylpyrazole triol acted similarly to E2, together suggesting an ERalpha-mediated mechanism. Several genes were induced within 2 h of E2 treatment, suggesting a direct activity of ERalpha within the kidney. Finally, the combination of the activation function (AF)1-selective agonist tamoxifen plus ERalphaKO(CH) mice expressing an AF1-deleted version of ERalpha allowed delineation of genes with differing requirements for AF1 or AF2 activity in the kidney.","authors":"Jelinsky, SA., Harris, HA., Brown, EL., Flanagan, K., Zhang, X., Tunkey, C., Lai, K., Lane, MV., Simcoe, DK., Evans, MJ.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Endocrinology","volume":"144","issue":"2","page":"701-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28803330","title":"BIME2, a novel gene required for interhomolog meiotic recombination in the protist model organism Tetrahymena.","abstract":"Meiotic recombination is initiated by DNA double-strand breaks (DSBs). Most DSBs are converted into nonreciprocal exchanges (gene conversions) or crossovers (COs) between sister chromatids. Only a minority of DSBs are processed toward interhomolog COs, the precursors of the chiasmata that connect homologous chromosomes. Dmc1, the meiosis-specific paralog of the universal recombination protein Rad51, is required for interhomolog COs; in its absence, univalents are primarily formed. Here, we report a ciliate-specific novel meiotic gene, BIME2, which also promotes interhomolog crossing over. In the bime2\u0394 mutant, DSBs are formed and repaired normally, but bivalent formation is strongly reduced. Bime2 protein forms foci on chromatin during meiotic prophase, and chromatin localization of Bime2 and Dmc1 is largely interdependent. Bime2 distantly resembles budding yeast Rdh54\/Tid1 and the vertebrate Rad54B helicases and may have similar functions in promoting or stabilizing Dmc1 nucleoprotein filaments.","authors":"Shodhan, A., Novatchkova, M., Loidl, J.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Chromosome Res","volume":"25","issue":"3-4","page":"291-298","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12566416","title":"Activation of dendritic cells through the interleukin 1 receptor 1 is critical for the induction of autoimmune myocarditis.","abstract":"Dilated cardiomyopathy, resulting from myocarditis, is the most common cause of heart failure in young patients. We here show that interleukin (IL)-1 receptor type 1-deficient (IL-1R1(-\/-)) mice are protected from development of autoimmune myocarditis after immunization with alpha-myosin-peptide(614-629). CD4(+) T cells from immunized IL-1R1(-\/-) mice proliferated poorly and failed to transfer disease after injection into naive severe combined immunodeficiency (SCID) mice. In vitro stimulation experiments suggested that the function of IL-1R1(-\/-)CD4(+) T cells was not intrinsically defect, but their activation by dendritic cells was impaired in IL-1R1(-\/-) mice. Accordingly, production of tumor necrosis factor (TNF)-alpha, IL-1, IL-6, and IL-12p70 was reduced in dendritic cells lacking the IL-1 receptor type 1. In fact, injection of immature, antigen-loaded IL-1R1(+\/+) but not IL-1R1(-\/-) dendritic cells into IL-1R1(-\/-) mice fully restored disease susceptibility by rendering IL-1R1(-\/-) CD4(+) T cells pathogenic. Thus, IL-1R1 triggering is required for efficient activation of dendritic cells, which is in turn a prerequisite for induction of autoreactive CD4(+) T cells and autoimmunity.","authors":"Eriksson, U., Kurrer, MO., Sonderegger, I., Iezzi, G., Tafuri, A., Hunziker, L., Suzuki, S., Bachmaier, K., Bingisser, RM., Penninger, JM., Kopf, M.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Exp Med","volume":"197","issue":"3","page":"323-31","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2003-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28733833","title":"Neuroanatomy of pain-deficiency and cross-modal activation in calcium channel subunit (CACN) \u03b12\u03b43 knockout mice.","abstract":"The phenotype of calcium channel subunit (CACN) \u03b12\u03b43 knockout (KO) mice includes sensory cross-activation and deficient pain perception. Sensory cross-activation defines the activation of a sensory cortical region by input from another modality due to reorganization in the brain such as after sensory loss. To obtain mechanistic insight into both phenomena, we employed a comprehensive battery of neuroanatomical techniques. While CACN\u03b12\u03b43 was ubiquitously expressed in wild-type mice, it was absent in \u03b12\u03b43 KO animals. Immunostaining of \u03b11A, \u03b11B, and \u03b11E revealed upregulation of N-type and R-type, but not P\/Q-type Ca<sub>v<\/sub>2 channels in cortical neurons of CACN\u03b12\u03b43 KO mice. Compared to wild-type mice, axonal processes in somatosensory cortex were enhanced, and dendritic processes reduced, in CACN\u03b12\u03b43 KO mice. Immunohistochemical and MRI analyses, investigating morphology, thalamocortical and intra-\/intercortical trajectories, revealed a disparity between projection and commissural fibers with reduction of the number of spatial specificity of thalamocortical projections. L1cam staining revealed wide-ranging projections of thalamocortical fibers reaching both somatosensory\/motor and visual cortical areas. Activation (c-fos<sup>+<\/sup>) of excitatory and inhibitory neurons suggested that deficient pain perception in \u03b12\u03b43 KO mice is unlikely to result from cortical disinhibition. Collectively, our data demonstrate that knock out of CACN \u03b12\u03b43 results in some structural abnormalities whose functional implications converge to dedifferentiation of sensory activation.","authors":"Landmann, J., Richter, F., Oros-Peusquens, AM., Shah, NJ., Classen, J., Neely, GG., Richter, A., Penninger, JM., Bechmann, I.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Brain Struct Funct","volume":"223","issue":"1","page":"111-130","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28536151","title":"Is magnetogenetics the new optogenetics?","abstract":null,"authors":"Nimpf, S., Keays, DA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"EMBO J","volume":"36","issue":"12","page":"1643-1646","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12479813","title":"Induction and activation of the transcription factor NFATc1 (NFAT2) integrate RANKL signaling in terminal differentiation of osteoclasts.","abstract":"Signaling by RANKL is essential for terminal differentiation of monocytes\/macrophages into osteoclasts. The TRAF6 and c-Fos signaling pathways both play important roles downstream of RANKL. We show here that RANKL selectively induces NFATc1 expression via these two pathways. RANKL also evokes Ca(2+) oscillations that lead to calcineurin-mediated activation of NFATc1, and therefore triggers a sustained NFATc1-dependent transcriptional program during osteoclast differentiation. We also show that NFATc1-deficient embryonic stem cells fail to differentiate into osteoclasts in response to RANKL stimulation, and that ectopic expression of NFATc1 causes precursor cells to undergo efficient differentiation without RANKL signaling. Thus, NFATc1 may represent a master switch for regulating terminal differentiation of osteoclasts, functioning downstream of RANKL.","authors":"Takayanagi, H., Kim, S., Koga, T., Nishina, H., Isshiki, M., Yoshida, H., Saiura, A., Isobe, M., Yokochi, T., Inoue, J., Wagner, EF., Mak, TW., Kodama, T., Taniguchi, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Dev Cell","volume":"3","issue":"6","page":"889-901","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2003-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28473526","title":"Modeling Renal Cell Carcinoma in Mice: <i>Bap1<\/i> and <i>Pbrm1<\/i> Inactivation Drive Tumor Grade.","abstract":"Clear cell renal cell carcinoma (ccRCC) is characterized by <i>BAP1<\/i> and <i>PBRM1<\/i> mutations, which are associated with tumors of different grade and prognosis. However, whether <i>BAP1<\/i> and <i>PBRM1<\/i> loss causes ccRCC and determines tumor grade is unclear. We conditionally targeted <i>Bap1<\/i> and <i>Pbrm1<\/i> (with <i>Vhl<\/i>) in the mouse using several Cre drivers. <i>Sglt2<\/i> and <i>Villin<\/i> proximal convoluted tubule drivers failed to cause tumorigenesis, challenging the conventional notion of ccRCC origins. In contrast, targeting with PAX8, a transcription factor frequently overexpressed in ccRCC, led to ccRCC of different grades. <i>Bap1<\/i>-deficient tumors were of high grade and showed greater mTORC1 activation than <i>Pbrm1<\/i>-deficient tumors, which exhibited longer latency. Disrupting one allele of the mTORC1 negative regulator, <i>Tsc1<\/i>, in <i>Pbrm1<\/i>-deficient kidneys triggered higher grade ccRCC. This study establishes <i>Bap1<\/i> and <i>Pbrm1<\/i> as lineage-specific drivers of ccRCC and histologic grade, implicates mTORC1 as a tumor grade rheostat, and suggests that ccRCCs arise from Bowman capsule cells.<b>Significance:<\/b> Determinants of tumor grade and aggressiveness across cancer types are poorly understood. Using ccRCC as a model, we show that <i>Bap1<\/i> and <i>Pbrm1<\/i> loss drives tumor grade. Furthermore, we show that the conversion from low grade to high grade can be promoted by activation of mTORC1. <i>Cancer Discov; 7(8); 900-17. \u00a92017 AACR.<\/i><i>See related commentary by Leung and Kim, p. 802<\/i><i>This article is highlighted in the In This Issue feature, p. 783<\/i>.","authors":"Gu, YF., Cohn, S., Christie, A., McKenzie, T., Wolff, N., Do, QN., Madhuranthakam, AJ., Pedrosa, I., Wang, T., Dey, A., Busslinger, M., Xie, XJ., Hammer, RE., McKay, RM., Kapur, P., Brugarolas, J.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cancer Discov","volume":"7","issue":"8","page":"900-917","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28841419","title":"DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.","abstract":"Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a\u00a0key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF's association with inner nuclear membrane proteins but instead relies on BAF's ability to\u00a0bridge distant DNA sites. Live-cell imaging and in\u00a0vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce\u00a0a densely cross-bridged chromatin layer that is\u00a0mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function.","authors":"Samwer, M., Schneider, MWG., Hoefler, R., Schmalhorst, PS., Jude, JG., Zuber, J., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell","volume":"170","issue":"5","page":"956-972.e23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28436956","title":"Identification of subepithelial mesenchymal cells that induce IgA and diversify gut microbiota.","abstract":"Immunoglobulin A (IgA) maintains a symbiotic equilibrium with intestinal microbes. IgA induction in the gut-associated lymphoid tissues (GALTs) is dependent on microbial sampling and cellular interaction in the subepithelial dome (SED). However it is unclear how IgA induction is predominantly initiated in the SED. Here we show that previously unrecognized mesenchymal cells in the SED of GALTs regulate bacteria-specific IgA production and diversify the gut microbiota. Mesenchymal cells expressing the cytokine RANKL directly interact with the gut epithelium to control CCL20 expression and microfold (M) cell differentiation. The deletion of mesenchymal RANKL impairs M cell-dependent antigen sampling and B cell-dendritic cell interaction in the SED, which results in a reduction in IgA production and a decrease in microbial diversity. Thus, the subepithelial mesenchymal cells that serve as M cell inducers have a fundamental role in the maintenance of intestinal immune homeostasis.","authors":"Nagashima, K., Sawa, S., Nitta, T., Tsutsumi, M., Okamura, T., Penninger, JM., Nakashima, T., Takayanagi, H.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Immunol","volume":"18","issue":"6","page":"675-682","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12471259","title":"Ectoderm to mesoderm lineage switching during axolotl tail regeneration.","abstract":"Foreign environments may induce adult stem cells to switch lineages and populate multiple tissue types, but whether this mechanism is used for tissue repair remains uncertain. Urodele amphibians can regenerate fully functional, multitissue structures including the limb and tail. To determine whether lineage switching is an integral feature of this regeneration, we followed individual spinal cord cells live during tail regeneration in the axolotl. Spinal cord cells frequently migrate into surrounding tissue to form regenerating muscle and cartilage. Thus, in axolotls, cells switch lineage during a real example of regeneration.","authors":"Echeverri, K., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Science","volume":"298","issue":"5600","page":"1993-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12446835","title":"The membrane protein FeoB contains an intramolecular G protein essential for Fe(II) uptake in bacteria.","abstract":"G proteins are critical for the regulation of membrane protein function and signal transduction. Nevertheless, coupling between G proteins and membrane proteins with multiple membrane-spanning domains has so far been observed only in higher organisms. Here we show that the polytopic membrane protein FeoB, which is essential for Fe(II) uptake in bacteria, contains a guanine-nucleotide-specific nucleotide binding site. We identify the G4-motif, NXXD, responsible for guanine nucleotide specificity, and show that GTP hydrolysis occurs very slowly. In contrast to typical G proteins, the association and dissociation of GDP were found to be faster than for GTP, suggesting that in the absence of additional factors, FeoB's G protein domain may exist mostly in the GTP-bound form. Furthermore, the binding of GTP is required for efficient Fe(II) uptake through the FeoB-dependent system. Notably, even in bacteria, this covalent linkage between a G protein and a polytopic membrane protein appears, to our knowledge, to be unique. These findings raise the intriguing question whether FeoB represents a primordial archetype of G protein-regulated membrane proteins.","authors":"Marlovits, TC., Haase, W., Herrmann, C., Aller, SG., Unger, VM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Proc Natl Acad Sci U S A","volume":"99","issue":"25","page":"16243-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2003-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19703390","title":"Breast cancer stem cells: eradication by differentiation therapy?","abstract":"During metastasis, migrating breast cancer stem cells undergo a loss of polarity leading to an epithelial-to-mesenchymal transition (EMT). Gupta et al. (2009) use this attribute of cancer stem cells to develop a high-throughput screen, which successfully identifies small molecules that specifically inhibit cancer stem cell proliferation through the induction of differentiation.","authors":"Beug, H.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"138","issue":"4","page":"623-5","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31545418","title":"Link between spermine oxidase and apoptosis antagonizing transcription factor: A new pathway in neuroblastoma.","abstract":"Neuroblastoma (NB) is a heterogeneous extra\u2011cranial childhood type of cancer, responsible for approximately\u00a015% of all paediatric cancer\u2011related deaths. Although several critical genetic aberrations have been related to NB, only a few established molecular markers have been associated with prognosis [V\u2011myc avian myelocytomatosis viral oncogene\u00a0(MYCN) locus amplification, deletions of part of chromosome\u00a01p, 11q23 and gain of 17q]. Regrettably, direct evidence of NB\u2011related tumour suppressors or oncogenes has not been currently identified at these chromosomal regions. MYCN locus amplification is present in approximately 20\u201130% of cases and is associated with a poor clinical outcome, representing the most important genetic prognostic marker. The functional guidelines for the prognosis of NB identify high\u2011risk patients (&lt;40% survival probabilities), but fail to identify patients at low and intermediate stages of the disease, which remains an issue to be resolved in NB. It has been shown that in NB cell lines and in a total\u2011spermine oxidase\u00a0(SMOX) transgenic mouse model, SMOX overexpression induces cellular stress via reactive oxygen species\u00a0(ROS) imbalance. In this study, we demonstrated that the high expression level of the cytoprotective gene, apoptosis-antagonizing transcription factor\u00a0(AATF), was driven by SMOX gene overexpression in both NB cells and Total\u2011SMOX mice. The anti\u2011apoptotic effect of AATF was supported by analysing the inhibition of the expression of the pro\u2011apoptotic genes, BAX, BAK and PUMA, which were decreased, in both the in\u00a0vitro and in\u00a0vivo SMOX overexpressing model systems investigated. On the whole, this study supports the hypothesis that the SMOX gene can be considered as a novel anti\u2011apoptotic marker in NB.","authors":"Fratini, E., Cervelli, M., Mariottini, P., Kanamori, Y., Amendola, R., Agostinelli, E.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Int J Oncol","volume":"55","issue":"5","page":"1149-1156","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12426318","title":"A central role for the JNK pathway in mediating the antagonistic activity of pro-inflammatory cytokines against transforming growth factor-beta-driven SMAD3\/4-specific gene expression.","abstract":"We have focused our attention on the molecular events underlying the antagonistic activities of pro-inflammatory cytokines against transforming growth factor-beta (TGF-beta)\/SMAD signaling. Using jnk1\/2-knockout (jnk(-\/-)) and I kappa B kinase-gamma\/nemo(-\/-) fibroblasts, we have determined the specific roles played by the JNK\/AP-1 and NF-kappa B\/Rel pathways in this phenomenon. We demonstrate that, in a cellular context devoid of JNK activity (i.e. jnk(-\/-) fibroblasts), interleukin-1 and tumor necrosis factor-alpha (TNF-alpha) did not inhibit the formation of SMAD-DNA complexes and the resulting SMAD-driven transcription in response to TGF-beta. On the other hand, lack of NF-kappa B activity in nemo(-\/-) fibroblasts did not affect the antagonistic effect of pro-inflammatory cytokines against TGF-beta. In the latter cell type, overexpression of antisense c-jun mRNA or of a dominant-negative form of MKK4 blocked the inhibitory activity of TNF-alpha, similar to what was observed in normal human dermal fibroblasts. Among JNK substrates, c-Jun and JunB (but not activating transcription factor-2) antagonized TGF-beta\/SMAD signaling in a JNK-dependent manner. Overexpression of JNK1 in jnk(-\/-) fibroblasts restored the ability of cytokines and Jun proteins to interfere with SMAD signaling. In junAA mouse embryo fibroblasts, in which c-Jun can no longer be phosphorylated by JNK, JunB substituted for c-Jun in mediating the cytokine effect against SMAD-driven transcription in a JNK-dependent manner. These results suggest a critical role for JNK-mediated c-Jun and JunB phosphorylation in transmitting the inhibitory effect of pro-inflammatory cytokines against TGF-beta-induced SMAD signaling. In addition, we demonstrate that such a JNK-dependent regulatory mechanism underlies the antagonistic activity of TNF-alpha against TGF-beta-induced up-regulation of type I and III collagens in fibroblasts.","authors":"Verrecchia, F., Tacheau, C., Wagner, EF., Mauviel, A.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Biol Chem","volume":"278","issue":"3","page":"1585-93","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2003-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19455604","title":"Increased RANKL expression is related to tumour migration and metastasis of renal cell carcinomas.","abstract":"Receptor activator of NF-kappaB ligand (RANKL) and its receptor, receptor activator of NF-kappaB (RANK), play a key role in osteoclastogenesis, and osteoprotegerin (OPG) acts as a decoy receptor for RANKL. We investigated the role of the RANKL-RANK-OPG system in renal cell carcinomas (RCCs), which frequently metastasize to bones. Real-time quantitative PCR revealed that RANKL mRNA expression was higher in clear cell RCCs than in papillary and chromophobe RCCs. Similarly, RANKL protein expression level in clear cell RCCs was higher than that in papillary and chromophobe RCCs, showing positive correlations with the primary tumour stage and distant metastasis. There was no significant association between the expression level of RANK, OPG and histological subtypes of RCC. RANKL and RANK expression was observed in metastatic RCCs in the bone and other organs, suggesting that they play a role in metastasis to the bone and other organs. Recombinant RANKL protein stimulated migration of a clear cell RCC cell line, Caki-1, in vitro, and this enhanced migration was inhibited by the administration of recombinant OPG protein. Furthermore, multivariate Cox analysis revealed that elevated RANKL and RANK expression with low-OPG expression was a significant and independent predictor of recurrence, bone metastasis and a poor prognosis. These data suggest that the RANKL-RANK-OPG system is involved not only in the bone metastasis of RCCs but also in metastasis to other organs through the stimulation of cancer cell migration.","authors":"Mikami, S., Katsube, K., Oya, M., Ishida, M., Kosaka, T., Mizuno, R., Mochizuki, S., Ikeda, T., Mukai, M., Okada, Y.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Pathol","volume":"218","issue":"4","page":"530-9","pdf":null,"JrId":"5121","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28691904","title":"Synthetic lethality between the cohesin subunits <i>STAG1<\/i> and <i>STAG2<\/i> in diverse cancer contexts.","abstract":"Recent genome analyses have identified recurrent mutations in the cohesin complex in a wide range of human cancers. Here we demonstrate that the most frequently mutated subunit of the cohesin complex, <i>STAG2<\/i>, displays a strong synthetic lethal interaction with its paralog <i>STAG1<\/i>. Mechanistically, STAG1 loss abrogates sister chromatid cohesion in <i>STAG2<\/i> mutated but not in wild-type cells leading to mitotic catastrophe, defective cell division and apoptosis. STAG1 inactivation inhibits the proliferation of STAG2 mutated but not wild-type bladder cancer and Ewing sarcoma cell lines. Restoration of STAG2 expression in a mutated bladder cancer model alleviates the dependency on STAG1. Thus, STAG1 and STAG2 support sister chromatid cohesion to redundantly ensure cell survival. STAG1 represents a vulnerability of cancer cells carrying mutations in the major emerging tumor suppressor <i>STAG2<\/i> across different cancer contexts. Exploiting synthetic lethal interactions to target recurrent cohesin mutations in cancer, e.g. by inhibiting STAG1, holds the promise for the development of selective therapeutics.","authors":"van der Lelij, P., Lieb, S., Jude, J., Wutz, G., Santos, CP., Falkenberg, K., Schlattl, A., Ban, J., Schwentner, R., Hoffmann, T., Kovar, H., Real, FX., Waldman, T., Pearson, MA., Kraut, N., Peters, JM., Zuber, J., Petronczki, M.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Elife","volume":"6","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12391321","title":"Tissue-specific RNA interference in postimplantation mouse embryos with endoribonuclease-prepared short interfering RNA.","abstract":"RNA interference (RNAi) using double-stranded RNA has been used for the systematic analysis of gene function in invertebrate organisms. Here we have explored the use of short interfering RNA (siRNA) to knock down gene expression during the development of mammalian postimplantation embryos. The developing CNS system of embryonic day 10 mouse embryos was used as a model tissue. siRNA prepared by endoribonuclease digestion (esiRNA) was injected into the lumen of the neural tube at specific regions and delivered into neuroepithelial cells by directed electroporation. Injected and electroporated embryos were grown for 1 day in whole-embryo culture and the effects of RNAi were examined. esiRNA directed against beta-galactosidase (beta-gal), coelectroporated into neuroepithelial cells together with reporter plasmids expressing GFP and beta-gal, abolished expression of beta-gal but not GFP, showing the specificity of the esiRNA-mediated RNAi. To demonstrate RNAi of endogenous gene expression, we used heterozygous embryos of a knock-in mouse line expressing GFP from the Tis21 locus, a gene turned on in neuroepithelial cells that switch from proliferation to neurogenesis. GFP-directed esiRNA electroporated into neuroepithelial cells of such embryos blocked the GFP expression normally occurring on the onset of neurogenesis. Taken together, our data indicate that esiRNA delivered in a tissue-specific manner by topical injection followed by directed electroporation can efficiently silence endogenous gene expression in mammalian postimplantation embryos.","authors":"Calegari, F., Haubensak, W., Yang, D., Huttner, WB., Buchholz, F.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Proc Natl Acad Sci U S A","volume":"99","issue":"22","page":"14236-40","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2002-12-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31753851","title":"DNA loop extrusion by human cohesin.","abstract":"Eukaryotic genomes are folded into loops and topologically associating domains, which contribute to chromatin structure, gene regulation, and gene recombination. These structures depend on cohesin, a ring-shaped DNA-entrapping adenosine triphosphatase (ATPase) complex that has been proposed to form loops by extrusion. Such an activity has been observed for condensin, which forms loops in mitosis, but not for cohesin. Using biochemical reconstitution, we found that single human cohesin complexes form DNA loops symmetrically at rates up to 2.1 kilo-base pairs per second. Loop formation and maintenance depend on cohesin's ATPase activity and on NIPBL-MAU2, but not on topological entrapment of DNA by cohesin. During loop formation, cohesin and NIPBL-MAU2 reside at the base of loops, which indicates that they generate loops by extrusion. Our results show that cohesin and NIPBL-MAU2 form an active holoenzyme that interacts with DNA either pseudo-topologically or non-topologically to extrude genomic interphase DNA into loops.","authors":"Davidson, IF., Bauer, B., Goetz, D., Tang, W., Wutz, G., Peters, JM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Science","volume":"366","issue":"6471","page":"1338-1345","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28283481","title":"Inhibition of Pol I transcription treats murine and human AML by targeting the leukemia-initiating cell population.","abstract":"Despite the development of novel drugs, the prospects for many patients with acute myeloid leukemia (AML) remain dismal. This study reveals that the selective inhibitor of RNA polymerase I (Pol I) transcription, CX-5461, effectively treats aggressive AML, including mixed-lineage leukemia-driven AML, and outperforms standard chemotherapies. In addition to the previously characterized mechanism of action of CX-5461 (ie, the induction of p53-dependent apoptotic cell death), the inhibition of Pol I transcription also demonstrates potent efficacy in p53null AML in vivo. This significant survival advantage in both p53WT and p53null leukemic mice treated with CX-5461 is associated with activation of the checkpoint kinases 1\/2, an aberrant G2\/M cell-cycle progression and induction of myeloid differentiation of the leukemic blasts. The ability to target the leukemic-initiating cell population is thought to be essential for lasting therapeutic benefit. Most strikingly, the acute inhibition of Pol I transcription reduces both the leukemic granulocyte-macrophage progenitor and leukemia-initiating cell (LIC) populations, and suppresses their clonogenic capacity. This suggests that dysregulated Pol I transcription is essential for the maintenance of their leukemia-initiating potential. Together, these findings demonstrate the therapeutic utility of this new class of inhibitors to treat highly aggressive AML by targeting LICs.","authors":"Hein, N., Cameron, DP., Hannan, KM., Nguyen, NN., Fong, CY., Sornkom, J., Wall, M., Pavy, M., Cullinane, C., Diesch, J., Devlin, JR., George, AJ., Sanij, E., Quin, J., Poortinga, G., Verbrugge, I., Baker, A., Drygin, D., Harrison, SJ., Rozario, JD., Powell, JA., Pitson, SM., Zuber, J., Johnstone, RW., Dawson, MA., Guthridge, MA., Wei, A., McArthur, GA., Pearson, RB., Hannan, RD.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Blood","volume":"129","issue":"21","page":"2882-2895","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16626291","title":"Chromatin-remodelling factors and the maintenance of transcriptional states through DNA replication.","abstract":"At the replication fork, nucleosomes, transcription factors and RNA polymerases are stripped off the DNA, the DNA double strands are unzipped and DNA methylation marks may be erased. Therefore DNA replication is both a 'curse' and 'bliss' for the epigenome, as it disrupts its stability by causing chromatin perturbations, yet it offers an opportunity to initiate changes in chromatin architecture and gene expression patterns, especially during development. Thus the DNA replication site is a critical point for regulation. It has become apparent that there is a close functional relationship between those factors that regulate transcriptional competence and the DNA replication programme. In this review we discuss novel insights into how chromatin-remodelling factors at replication sites are involved in both the maintenance and regulation of transcriptional states.","authors":"Aligianni, S., Varga-Weisz, P.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Biochem Soc Symp","volume":null,"issue":"73","page":"97-108","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28847004","title":"A heterochromatin-dependent transcription machinery drives piRNA expression.","abstract":"Nuclear small RNA pathways safeguard genome integrity by establishing transcription-repressing heterochromatin at transposable elements. This inevitably also targets the transposon-rich source loci of the small RNAs themselves. How small RNA source loci are efficiently transcribed while transposon promoters are potently silenced is not understood. Here we show that, in Drosophila, transcription of PIWI-interacting RNA (piRNA) clusters-small RNA source loci in animal gonads-is enforced through RNA polymerase II pre-initiation complex formation within repressive heterochromatin. This is accomplished through Moonshiner, a paralogue of a basal transcription factor IIA (TFIIA) subunit, which is recruited to piRNA clusters via the heterochromatin protein-1 variant Rhino. Moonshiner triggers transcription initiation within piRNA clusters by recruiting the TATA-box binding protein (TBP)-related factor TRF2, an animal TFIID core variant. Thus, transcription of heterochromatic small RNA source loci relies on direct recruitment of the core transcriptional machinery to DNA via histone marks rather than sequence motifs, a concept that we argue is a recurring theme in evolution.","authors":"Andersen, PR., Tirian, L., Vunjak, M., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"549","issue":"7670","page":"54-59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28385664","title":"Proceedings of the EuBIC Winter School 2017.","abstract":"The 2017 EuBIC Winter School was held from January 10th to January 13th 2017 in Semmering, Austria. This meeting gathered international researchers in the fields of bioinformatics and proteomics to discuss current challenges in data analysis and biological interpretation. This article outlines the scientific program and exchanges that took place on this occasion and presents the current challenges of this ever-growing field.","authors":"Willems, S., Bouyssi\u00e9, D., David, M., Locard-Paulet, M., Mechtler, K., Schw\u00e4mmle, V., Uszkoreit, J., Vaudel, M., Dorfer, V.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"J Proteomics","volume":"161","issue":null,"page":"78-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12376107","title":"SEK1\/MKK4-mediated SAPK\/JNK signaling participates in embryonic hepatoblast proliferation via a pathway different from NF-kappaB-induced anti-apoptosis.","abstract":"Mice lacking the stress-signaling kinase SEK1 die from embryonic day 10.5 (E10.5) to E12.5. Although a defect in liver formation is accompanied with the embryonic lethality of sek1(-\/-) mice, the mechanism of the liver defect has remained unknown. In the present study, we first produced a monoclonal antibody specifically recognizing murine hepatoblasts for the analysis of liver development and further investigated genetic interaction ofsek1 with tumor necrosis factor-alpha receptor 1 gene (tnfr1) and protooncogene c-jun, which are also responsible for liver formation and cell apoptosis. The defective liver formation in sek1(-\/-) embryos was not protected by additionaltnfr1 mutation, which rescues the embryonic lethality of mice lacking NF-kappaB signaling components. There was a progressive increase in the hepatoblast cell numbers of wild-type embryos from E10.5 to E12.5. Instead, impaired hepatoblast proliferation was observed in sek1(-\/-) livers from E10.5, though fetal liver-specific gene expression was normal. The impaired phenotype in sek1(-\/-) livers was more severe than in c-jun(-\/-) embryos, and sek1(-\/-) c-jun(-\/-) embryos died more rapidly before E8.5. The hepatoblast proliferation required no hematopoiesis, since liver development was not impaired in AML1(-\/-) mice that lack hematopoietic functions. Stimulation of stress-activated protein kinase\/c-Jun N-terminal kinase by hepatocyte growth factor was attenuated in sek1(-\/-) livers. Thus, SEK1 appears to play a crucial role in hepatoblast proliferation and survival in a manner apparently different from NF-kappaB or c-Jun.","authors":"Watanabe, T., Nakagawa, K., Ohata, S., Kitagawa, D., Nishitai, G., Seo, J., Tanemura, S., Shimizu, N., Kishimoto, H., Wada, T., Aoki, J., Arai, H., Iwatsubo, T., Mochita, M., Watanabe, T., Satake, M., Ito, Y., Matsuyama, T., Mak, TW., Penninger, JM., Nishina, H., Katada, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Dev Biol","volume":"250","issue":"2","page":"332-47","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2002-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11780141","title":"Chromosomal silencing and localization are mediated by different domains of Xist RNA.","abstract":"The gene Xist initiates the chromosomal silencing process of X inactivation in mammals. Its product, a noncoding RNA, is expressed from and specifically associates with the inactive X chromosome in female cells. Here we use an inducible Xist expression system in mouse embryonic stem cells that recapitulates long-range chromosomal silencing to elucidate which Xist RNA sequences are necessary for chromosomal association and silencing. We show that chromosomal association and spreading of Xist RNA can be functionally separated from silencing by specific mutations. Silencing requires a conserved repeat sequence located at the 5' end of Xist. Deletion of this element results in Xist RNA that still associates with chromatin and spreads over the chromosome but does not effect transcriptional repression. Association of Xist RNA with chromatin is mediated by functionally redundant sequences that act cooperatively and are dispersed throughout the remainder of Xist but show little or no homology.","authors":"Wutz, A., Rasmussen, TP., Jaenisch, R.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nat Genet","volume":"30","issue":"2","page":"167-74","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28854362","title":"Loss of Apela Peptide in Mice Causes Low Penetrance Embryonic Lethality and Defects in Early Mesodermal Derivatives.","abstract":"Apela (also known as Elabela, Ende, and Toddler) is a small signaling peptide that activates the G-protein-coupled receptor Aplnr to stimulate cell migration during zebrafish gastrulation. Here, using CRISPR\/Cas9 to generate a null, reporter-expressing allele, we study the role of Apela in the developing mouse embryo. We found that loss of Apela results in low-penetrance cardiovascular defects that manifest after the onset of circulation. Three-dimensional micro-computed tomography revealed a higher penetrance of vascular remodeling defects, from which some mutants recover, and identified extraembryonic anomalies as the earliest morphological distinction in Apela mutant embryos. Transcriptomics at late gastrulation identified aberrant upregulation of erythroid and myeloid markers in mutant embryos prior to the appearance of physical malformations. Double-mutant analyses showed that loss of Apela signaling impacts early Aplnr-expressing mesodermal populations independently of the alternative ligand Apelin, leading to lethal cardiac defects in some Apela null embryos.","authors":"Freyer, L., Hsu, CW., Nowotschin, S., Pauli, A., Ishida, J., Kuba, K., Fukamizu, A., Schier, AF., Hoodless, PA., Dickinson, ME., Hadjantonakis, AK.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Rep","volume":"20","issue":"9","page":"2116-2130","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31368600","title":"Endosome and Golgi-associated degradation (EGAD) of membrane proteins regulates sphingolipid metabolism.","abstract":"Cellular homeostasis requires the ubiquitin-dependent degradation of membrane proteins. This was assumed to be mediated exclusively either by endoplasmic reticulum-associated degradation (ERAD) or by endosomal sorting complexes required for transport (ESCRT)-dependent lysosomal degradation. We identified in Saccharomyces cerevisiae an additional pathway that selectively extracts membrane proteins at Golgi and endosomes for degradation by cytosolic proteasomes. One endogenous substrate of this endosome and Golgi-associated degradation pathway (EGAD) is the ER-resident membrane protein Orm2, a negative regulator of sphingolipid biosynthesis. Orm2 degradation is initiated by phosphorylation, which triggers its ER export. Once on Golgi and endosomes, Orm2 is poly-ubiquitinated by the membrane-embedded \"Defective in SREBP cleavage\" (Dsc) ubiquitin ligase complex. Cdc48\/VCP then extracts ubiquitinated Orm2 from membranes, which is tightly coupled to the proteasomal degradation of Orm2. Thereby, EGAD prevents the accumulation of Orm2 at the ER and in post-ER compartments and promotes the controlled de-repression of sphingolipid biosynthesis. Thus, the selective degradation of membrane proteins by EGAD contributes to proteostasis and lipid homeostasis in eukaryotic cells.","authors":"Schmidt, O., Weyer, Y., Baumann, V., Widerin, MA., Eising, S., Angelova, M., Schleiffer, A., Kremser, L., Lindner, H., Peter, M., Fr\u00f6hlich, F., Teis, D.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"EMBO J","volume":"38","issue":"15","page":"e101433","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28394884","title":"Long-term, hormone-responsive organoid cultures of human endometrium in a chemically defined medium.","abstract":"In humans, the endometrium, the uterine mucosal lining, undergoes dynamic changes throughout the menstrual cycle and pregnancy. Despite the importance of the endometrium as the site of implantation and nutritional support for the conceptus, there are no long-term culture systems that recapitulate endometrial function in\u00a0vitro. We adapted conditions used to establish human adult stem-cell-derived organoid cultures to generate three-dimensional cultures of normal and decidualized human endometrium. These organoids expand long-term, are genetically stable and differentiate following treatment with reproductive hormones. Single cells from both endometrium and decidua can generate a fully functional organoid. Transcript analysis confirmed great similarity between organoids and the primary tissue of origin. On exposure to pregnancy signals, endometrial organoids develop characteristics of early pregnancy. We also derived organoids from malignant endometrium, and so provide a foundation to study common diseases, such as endometriosis and endometrial cancer, as well as the physiology of early\u00a0gestation.","authors":"Turco, MY., Gardner, L., Hughes, J., Cindrova-Davies, T., Gomez, MJ., Farrell, L., Hollinshead, M., Marsh, SGE., Brosens, JJ., Critchley, HO., Simons, BD., Hemberger, M., Koo, BK., Moffett, A., Burton, GJ.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Cell Biol","volume":"19","issue":"5","page":"568-577","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19406801","title":"Providencia sneebia sp. nov. and Providencia burhodogranariea sp. nov., isolated from wild Drosophila melanogaster.","abstract":"Multiple isolates of the genus Providencia were obtained from the haemolymph of wild-caught Drosophila melanogaster fruit flies. Sixteen isolates were distinguished from the six previously described species based on 16S rRNA gene sequences. These isolates belonged to two distinct groups, which we propose each comprise previously undescribed species. Two isolates, designated A(T) and B(T), were characterized by DNA sequences of the fusA, lepA, leuS, gyrB and ileS housekeeping genes, whole-genome DNA-DNA hybridizations with their nearest relatives and utilization of substrates for metabolism. The closest phylogenetic relatives of strain A(T) are strain B(T) (86.9 % identity for the housekeeping genes) and Providencia stuartii DSM 4539(T) (86.0 % identity). The closest phylogenetic relatives of strain B(T) are strain A(T) (86.9 % identity) and P. stuartii DSM 4539(T) (86.6 % identity). The type strains of described species in this genus shared between 84.1 and 90.1 % identity for these sequences. DNA-DNA hybridization between the strain pairs A(T)-B(T), A(T)-P. stuartii DSM 4539(T) and B(T)-P. stuartii DSM 4539(T) all resulted in less than 25 % relatedness. In addition, patterns of utilization of amygdalin, arbutin, aesculin, salicin, d-sorbitol, trehalose, inositol, d-adonitol and d-galactose distinguish strains A(T) and B(T) from other members of this genus. Strains A(T) and B(T) therefore represent novel species, for which the names Providencia sneebia sp. nov. (type strain A(T) =DSM 19967(T) =ATCC BAA-1589(T)) and Providencia burhodogranariea sp. nov. (type strain B(T) =DSM 19968(T) =ATCC BAA-1590(T)) are proposed.","authors":"Juneja, P., Lazzaro, BP.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Int J Syst Evol Microbiol","volume":"59","issue":"Pt 5","page":"1108-11","pdf":null,"JrId":"21505","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28781166","title":"Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation.","abstract":"Little is known about the spliceosome's structure before its extensive remodeling into a catalytically active complex. Here, we report a 3D cryo-EM structure of a pre-catalytic human spliceosomal B complex. The U2 snRNP-containing head domain is connected to the B complex main body via three main bridges. U4\/U6.U5 tri-snRNP proteins, which are located in the main body, undergo significant rearrangements during tri-snRNP integration into the B\u00a0complex. These include formation of a partially closed Prp8 conformation that creates, together with Dim1, a 5' splice site (ss) binding pocket, displacement of Sad1, and rearrangement of Brr2 such that it contacts its U4\/U6 substrate and is poised for the subsequent spliceosome activation step. The molecular organization of several B-specific proteins suggests that they are involved in negatively regulating Brr2, positioning the U6\/5'ss helix, and stabilizing the B complex structure. Our results indicate significant differences between the early activation phase of human and yeast spliceosomes.","authors":"Bertram, K., Agafonov, DE., Dybkov, O., Haselbach, D., Leelaram, MN., Will, CL., Urlaub, H., Kastner, B., L\u00fchrmann, R., Stark, H.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell","volume":"170","issue":"4","page":"701-713.e11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23850451","title":"Structural determinants and mechanism of mammalian CRM1 allostery.","abstract":"Proteins carrying nuclear export signals cooperatively assemble with the export factor CRM1 and the effector protein RanGTP. In lower eukaryotes, this cooperativity is coupled to CRM1 conformational changes; however, it is unknown if mammalian CRM1 maintains its compact conformation or shows similar structural flexibility. Here, combinations of small-angle X-ray solution scattering and electron microscopy experiments with molecular dynamics simulations reveal pronounced conformational flexibility in mammalian CRM1 and demonstrate that RanGTP binding induces association of its N- and C-terminal regions to form a toroid structure. The CRM1 toroid is stabilized mainly by local interactions between the terminal regions, rather than by global strain. The CRM1 acidic loop is key in transmitting the effect of this RanGTP-induced global conformational change to the NES-binding cleft by shifting its population to the open state, which displays enhanced cargo affinity. Cooperative CRM1 export complex assembly thus constitutes a highly dynamic process, encompassing an intricate interplay of global and local structural changes.","authors":"D\u00f6lker, N., Blanchet, CE., Vo\u00df, B., Haselbach, D., Kappel, C., Monecke, T., Svergun, DI., Stark, H., Ficner, R., Zachariae, U., Grubm\u00fcller, H., Dickmanns, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Structure","volume":"21","issue":"8","page":"1350-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28875993","title":"Cell organization by liquid phase separation.","abstract":null,"authors":"Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Rev Mol Cell Biol","volume":"18","issue":"10","page":"593","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12244116","title":"Requirement of phosphatidylinositol 3-kinase activation and calcium influx for leukotriene B4-induced enzyme release.","abstract":"Leukotriene B(4) (LTB(4)) is a potent lipid mediator involved in host defense and inflammatory responses. It causes chemotaxis, generation of reactive oxygen species, and degranulation. However, only little is known of the molecular mechanisms by which LTB(4) induces these biological activities. To analyze the intracellular signaling pathways to mediate lysosomal enzyme release through the cloned LTB(4) receptor (BLT1), we transfected BLT1 to rat basophilic leukemia cells (RBL-2H3). LTB(4) dose-dependently released beta-hexosaminidase, and the release was mostly inhibited when the cells were pretreated with pertussis toxin, indicating that the degranulation is mediated by G(i) proteins. LTB(4) activated phosphatidylinositol 3-kinase (PI3-K) through G(i), and inhibition of PI3-K by wortmannin or LY290042 inhibited degranulation. Granulocytes from PI3-Kgamma-deficient mice showed reduced LTB(4)-induced degranulation, suggesting that this isozyme of PI3-K is involved in the degranulation. LTB(4) also caused calcium release from intracellular stores and calcium influx from the outside milieu through G(i), but only the calcium influx is critical for the lysosomal enzyme release. Calcium influx and PI3-K activation are both downstream events of G(i), since they were inhibited by pertussis toxin. These two events are in essence independent each other, because calcium depletion did not affect PI3-K, and inhibition of PI3-K did not attenuate calcium influx significantly. Thus, our results have clearly shown that LTB(4) binds BLT1 and activates G(i)-like protein, and both PI3-Kgamma activation and a sustained calcium elevation by calcium influx are necessary for enzyme release in these cells.","authors":"Ito, N., Yokomizo, T., Sasaki, T., Kurosu, H., Penninger, J., Kanaho, Y., Katada, T., Hanaoka, K., Shimizu, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Biol Chem","volume":"277","issue":"47","page":"44898-904","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2003-01-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31363232","title":"Publisher Correction: The metabolite BH4 controls T cell proliferation in autoimmunity and cancer.","abstract":"An Amendment to this paper has been published and can be accessed via a link at the top of the paper.","authors":"Cronin, SJF., Seehus, C., Weidinger, A., Talbot, S., Reissig, S., Seifert, M., Pierson, Y., McNeill, E., Longhi, MS., Turnes, BL., Kreslavsky, T., Kogler, M., Hoffmann, D., Ticevic, M., da Luz Scheffer, D., Tortola, L., Cikes, D., Jais, A., Rangachari, M., Rao, S., Paolino, M., Novatchkova, M., Aichinger, M., Barrett, L., Latremoliere, A., Wirnsberger, G., Lametschwandtner, G., Busslinger, M., Zicha, S., Latini, A., Robson, SC., Waisman, A., Andrews, N., Costigan, M., Channon, KM., Weiss, G., Kozlov, AV., Tebbe, M., Johnsson, K., Woolf, CJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nature","volume":"572","issue":"7769","page":"E18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21792453","title":"A DNAzyme based label-free detection system for miniaturized assays.","abstract":"Sensitive detection assays are a prerequisite for the analysis of small amounts of samples derived from biological material. There is a great demand for highly sensitive and robust detection techniques to analyze biomolecules. The combination of catalytic active DNA (DNAzyme) with a peroxidase activity with rolling circle amplification (RCA) is a promising alternative to common detection systems. The rolling circle amplification leads to a product with tandemly linked copies of DNAzymes. The continuous signal generation of the amplified DNAzymes results in an increased sensitivity. The combination of two amplification reactions, namely RCA and DNAzymes, results in increased signal intensity by a factor of 10(6). With this approach the labeling of samples can be avoided. The advantage of the introduced assay is the usage of nucleic acids as biosensors for the detection of biomolecules. Coupling of the analyte molecule to the detection molecules allows the direct detection of the analyte molecule. The described label-free hotpot assay has a broad potential field of applications. The hotpot assay can be adapted to detect and analyze RNA, DNA and proteins down to femtomolar concentrations in a miniaturized platform with a total reaction solution of 50 nl. The applicability of the assay for diagnostics and research will be shown with a focus on high throughput systems using a nano-well platform.","authors":"K\u00f6ster, DM., Haselbach, D., Lehrach, H., Seitz, H.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mol Biosyst","volume":"7","issue":"10","page":"2882-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28934594","title":"Noncoding RNAs in Polycomb and Trithorax Regulation: A Quantitative Perspective.","abstract":"The question of how noncoding RNAs are involved in Polycomb group (PcG) and Trithorax group (TrxG) regulation has been on an extraordinary journey over the last three decades. Favored models have risen and fallen, and healthy debates have swept back and forth. The field has recently reached a critical mass of compelling data that throws light on several previously unresolved issues. The time is ripe for a fruitful combination of these findings with two other long-running avenues of research, namely the biochemical properties of the PcG\/TrxG system and the application of theoretical mathematical models toward an understanding of the system's regulatory properties. I propose that integrating our current knowledge of noncoding RNA into a quantitative biochemical and theoretical framework for PcG and TrxG regulation has the potential to reconcile several apparently conflicting models and identifies fascinating questions for future research.","authors":"Ringrose, L.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Annu Rev Genet","volume":"51","issue":null,"page":"385-411","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19386260","title":"SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells.","abstract":"The noncoding Xist RNA triggers silencing of one of the two female X chromosomes during X inactivation in mammals. Gene silencing by Xist is restricted to a special developmental context in early embryos and specific hematopoietic precursors. Here, we show that Xist can initiate silencing in a lymphoma model. We identify the special AT-rich binding protein SATB1 as an essential silencing factor. Loss of SATB1 in tumor cells abrogates the silencing function of Xist. In lymphocytes Xist localizes along SATB1-organized chromatin and SATB1 and Xist influence each other's pattern of localization. SATB1 and its homolog SATB2 are expressed during the initiation window for X inactivation in ES cells. Importantly, viral expression of SATB1 or SATB2 enables gene silencing by Xist in embryonic fibroblasts, which normally do not provide an initiation context. Thus, our data establish SATB1 as a crucial silencing factor contributing to the initiation of X inactivation.","authors":"Agrelo, R., Souabni, A., Novatchkova, M., Haslinger, C., Leeb, M., Komnenovic, V., Kishimoto, H., Gresh, L., Kohwi-Shigematsu, T., Kenner, L., Wutz, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Dev Cell","volume":"16","issue":"4","page":"507-16","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19339691","title":"Mouse models of human AML accurately predict chemotherapy response.","abstract":"The genetic heterogeneity of cancer influences the trajectory of tumor progression and may underlie clinical variation in therapy response. To model such heterogeneity, we produced genetically and pathologically accurate mouse models of common forms of human acute myeloid leukemia (AML) and developed methods to mimic standard induction chemotherapy and efficiently monitor therapy response. We see that murine AMLs harboring two common human AML genotypes show remarkably diverse responses to conventional therapy that mirror clinical experience. Specifically, murine leukemias expressing the AML1\/ETO fusion oncoprotein, associated with a favorable prognosis in patients, show a dramatic response to induction chemotherapy owing to robust activation of the p53 tumor suppressor network. Conversely, murine leukemias expressing MLL fusion proteins, associated with a dismal prognosis in patients, are drug-resistant due to an attenuated p53 response. Our studies highlight the importance of genetic information in guiding the treatment of human AML, functionally establish the p53 network as a central determinant of chemotherapy response in AML, and demonstrate that genetically engineered mouse models of human cancer can accurately predict therapy response in patients.","authors":"Zuber, J., Radtke, I., Pardee, TS., Zhao, Z., Rappaport, AR., Luo, W., McCurrach, ME., Yang, MM., Dolan, ME., Kogan, SC., Downing, JR., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genes Dev","volume":"23","issue":"7","page":"877-89","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16839882","title":"Resolution of chiasmata in oocytes requires separase-mediated proteolysis.","abstract":"In yeast, resolution of chiasmata in meiosis I requires proteolytic cleavage along chromosome arms of cohesin's Rec8 subunit by separase. Since activation of separase by the anaphase-promoting complex (APC\/C) is supposedly not required for meiosis I in Xenopus oocytes, it has been suggested that animal cells might resolve chiasmata by a separase-independent mechanism related to the so-called \"prophase pathway\" that removes cohesin from chromosome arms during mitosis. By expressing Cre recombinase from a zona pellucida promoter, we have deleted a floxed allele of separase specifically in mouse oocytes. This prevents removal of Rec8 from chromosome arms and resolution of chiasmata. It also hinders extrusion of the first polar body (PBE) and causes female sterility. mRNA encoding wild-type but not catalytically inactive separase restores chiasma resolution. Both types of mRNA restore PBE. Proteolytic activity of separase is therefore essential for Rec8's removal from chromosome arms and for chiasma resolution but not for PBE.","authors":"Kudo, NR., Wassmann, K., Anger, M., Schuh, M., Wirth, KG., Xu, H., Helmhart, W., Kudo, H., McKay, M., Maro, B., Ellenberg, J., de Boer, P., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell","volume":"126","issue":"1","page":"135-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12151083","title":"Core-binding factor alpha 1 (Cbfa1) induces osteoblastic differentiation of C2C12 cells without interactions with Smad1 and Smad5.","abstract":"Core-binding factor alpha(1) (Cbfa1) is an essential transcription factor for osteoblastic differentiation and osteogenesis. Bone morphogenetic protein (BMP) is also a powerful inducer of differentiation of pluripotent mesenchymal cells to osteoblast lineage and bone formation. Recent studies suggest that Cbfa1 plays a critical role during BMP-induced osteoblastic differentiation through association with cytoplasmic BMP signaling molecules, Smads. However, other studies have suggested that Cbfa1 may exhibit its osteogenic function without interaction with Smads. Therefore, it remains unclear whether association with Smad is essential for Cbfa1 function. In this study we examine the effects of Cbfa1 on osteoblastic differentiation in the presence or absence of interactions with Smad1 or Smad5 using C2C12 undifferentiated mesenchymal cells. Cbfa1 expression was induced upon stimulation with BMP-2 in C2C12 cells. Introduction of Cbfa1 into C2C12 cells induced osteoblastic differentiation and promoted transactivation of osteocalcin gene promoter without forming the complex with Smad1 or Smad5. Furthermore, in C2C12 cells in which the association of Cbfa1 with Smad1\/Smad5 was prevented by the overexpression of the natural antagonist, Smad6, Cbfa1 still induced osteoblastic differentiation and transactivated osteocalcin gene promoter, regardless of BMP-2 stimulation. These results suggest that the interactions with Smad1 or Smad5 are not essential for Cbfa1 to demonstrate its osteogenic actions. However, interactions with Smad1\/Smad5 enhance these osteogenic actions of Cbfa1. Of note, BMP-2-induced or Smad-induced osteoblastic differentiation was inhibited by dominant-negative Cbfa1, suggesting that the function of Cbfa1 is critical for BMP-2-induced osteoblastic differentiation. Our results suggest that Cbfa1 is essential and also sufficient to induce osteoblastic differentiation in undifferentiated mesenchymal cells, and establishment of an association with Smad1\/Smad5 enhances the osteogenic actions of Cbfa1. On the other hand, Cbfa1 expression requires the activation of Smad1\/Smad5 by BMP-2.","authors":"Nishimura, R., Hata, K., Harris, SE., Ikeda, F., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Bone","volume":"31","issue":"2","page":"303-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2003-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28100637","title":"A Zip3-like protein plays a role in crossover formation in the SC-less meiosis of the protist <i>Tetrahymena<\/i>.","abstract":"When programmed meiotic DNA double-strand breaks (DSBs) undergo recombinational repair, genetic crossovers (COs) may be formed. A certain level of this is required for the faithful segregation of chromosomes, but the majority of DSBs are processed toward a safer alternative, namely noncrossovers (NCOs), via nonreciprocal DNA exchange. At the crossroads between these two DSB fates is the Msh4-Msh5 (MutS\u03b3) complex, which stabilizes CO-destined recombination intermediates and members of the Zip3\/RNF212 family of RING finger proteins, which in turn stabilize MutS\u03b3. These proteins function in the context of the synaptonemal complex (SC) and mainly act on SC-dependent COs. Here we show that in the SC-less ciliate <i>Tetrahymena<\/i>, Zhp3 (a protein distantly related to Zip3\/RNF212), together with MutS\u03b3, is responsible for the majority of COs. This activity of Zhp3 suggests an evolutionarily conserved SC-independent strategy for balancing CO:NCO ratios. Moreover, we report a novel meiosis-specific protein, Sa15, as an interacting partner of Zhp3. Sa15 forms linear structures in meiotic prophase nuclei to which Zhp3 localizes. Sa15 is required for a wild-type level of CO formation. Its linear organization suggests the existence of an underlying chromosomal axis that serves as a scaffold for Zhp3 and other recombination proteins.","authors":"Shodhan, A., Kataoka, K., Mochizuki, K., Novatchkova, M., Loidl, J.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Mol Biol Cell","volume":"28","issue":"6","page":"825-833","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19329746","title":"Visual control of flight speed in Drosophila melanogaster.","abstract":"Flight control in insects depends on self-induced image motion (optic flow), which the visual system must process to generate appropriate corrective steering maneuvers. Classic experiments in tethered insects applied rigorous system identification techniques for the analysis of turning reactions in the presence of rotating pattern stimuli delivered in open-loop. However, the functional relevance of these measurements for visual free-flight control remains equivocal due to the largely unknown effects of the highly constrained experimental conditions. To perform a systems analysis of the visual flight speed response under free-flight conditions, we implemented a 'one-parameter open-loop' paradigm using 'TrackFly' in a wind tunnel equipped with real-time tracking and virtual reality display technology. Upwind flying flies were stimulated with sine gratings of varying temporal and spatial frequencies, and the resulting speed responses were measured from the resulting flight speed reactions. To control flight speed, the visual system of the fruit fly extracts linear pattern velocity robustly over a broad range of spatio-temporal frequencies. The speed signal is used for a proportional control of flight speed within locomotor limits. The extraction of pattern velocity over a broad spatio-temporal frequency range may require more sophisticated motion processing mechanisms than those identified in flies so far. In Drosophila, the neuromotor pathways underlying flight speed control may be suitably explored by applying advanced genetic techniques, for which our data can serve as a baseline. Finally, the high-level control principles identified in the fly can be meaningfully transferred into a robotic context, such as for the robust and efficient control of autonomous flying micro air vehicles.","authors":"Fry, SN., Rohrseitz, N., Straw, AD., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Exp Biol","volume":"212","issue":"Pt 8","page":"1120-30","pdf":null,"JrId":"4720","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12121614","title":"Apoptosis protection by the Epo target Bcl-X(L) allows factor-independent differentiation of primary erythroblasts.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">12121614<\/PMID><DateCompleted><Year>2003<\/Year><Month>02<\/Month><Day>04<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>12<\/Volume><Issue>13<\/Issue><PubDate><Year>2002<\/Year><Month>Jul<\/Month><Day>09<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Apoptosis protection by the Epo target Bcl-X(L) allows factor-independent differentiation of primary erythroblasts.<\/ArticleTitle><Pagination><MedlinePgn>1076-85<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Erythropoietin (Epo) is required for correct execution of the erythroid differentiation program. Erythropoiesis requires Bcl-X(L), a major late target of Epo-receptor signaling. Mice lacking Bcl-X(L) die around embryonic age E12.5, forming normal erythroid progenitors but lacking functional red cells. Recently, serum-free culture conditions for expansion of murine red cell progenitors were developed, yielding cells capable of in vivo-like terminal differentiation into enucleated erythrocytes, in response to Epo\/insulin. Here we address whether Epo function during terminal maturation involves a cytokine-independent \"default program,\" requiring only apoptosis inhibition through Epo-dependent upregulation of Bcl-X(L).","authors":"Dolznig, H., Habermann, B., Stangl, K., Deiner, EM., Moriggl, R., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"13","page":"1076-85","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2003-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12113170","title":"Tumour suppressor gene p53 mutation in a case of haemangiosarcoma of a dog.","abstract":"Haemangiosarcomas of dogs were analysed by molecular genetic techniques. Regions of the tumour suppressor gene p53, including the well-known tumour hot spots (codons 175, 245, 248, 249, 273 and 282) were screened. A 24 bp deletion was detected in exon 5 of the gene.","authors":"Mayr, B., Zwetkoff, S., Schaffner, G., Reifinger, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Acta Vet Hung","volume":"50","issue":"2","page":"157-60","pdf":null,"JrId":"221","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28980625","title":"Autophagy suppresses Ras-driven epithelial tumourigenesis by limiting the accumulation of reactive oxygen species.","abstract":"This corrects the article DOI: 10.1038\/onc.2017.175.","authors":"Manent, J., Banerjee, S., de Matos Simoes, R., Zoranovic, T., Mitsiades, C., Penninger, JM., Simpson, KJ., Humbert, PO., Richardson, HE.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Oncogene","volume":"36","issue":"40","page":"5658-5660","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28954863","title":"A deep learning and novelty detection framework for rapid phenotyping in high-content screening.","abstract":"Supervised machine learning is a powerful and widely used method for analyzing high-content screening data. Despite its accuracy, efficiency, and versatility, supervised machine learning has drawbacks, most notably its dependence on a priori knowledge of expected phenotypes and time-consuming classifier training. We provide a solution to these limitations with <i>CellCognition Explorer<\/i>, a generic novelty detection and deep learning framework. Application to several large-scale screening data sets on nuclear and mitotic cell morphologies demonstrates that <i>CellCognition Explorer<\/i> enables discovery of rare phenotypes without user training, which has broad implications for improved assay development in high-content screening.","authors":"Sommer, C., Hoefler, R., Samwer, M., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Mol Biol Cell","volume":"28","issue":"23","page":"3428-3436","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12098702","title":"Reversion of B cell commitment upon loss of Pax5 expression.","abstract":"The transcription factor Pax5 is essential for initiating B cell lineage commitment, but its role in maintaining commitment is unknown. Using conditional Pax5 inactivation in committed pro-B cells, we demonstrate that Pax5 is required not only to initiate its B lymphoid transcription program, but also to maintain it in early B cell development. As a consequence of Pax5 inactivation, previously committed pro-B cells regained the capacity to differentiate into macrophages in vitro and to reconstitute T cell development in vivo in RAG2-\/- mice. Hence, Pax5 expression is continuously required to maintain B cell lineage commitment, because its loss converts committed pro-B cells into hematopoietic progenitors with multilineage potential.","authors":"Mikkola, I., Heavey, B., Horcher, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Science","volume":"297","issue":"5578","page":"110-3","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28246208","title":"Creating to understand - developmental biology meets engineering in Paris.","abstract":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called 'Engineering the embryo'. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the <i>in vitro<\/i> manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations.","authors":"Kicheva, A., Rivron, NC.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Development","volume":"144","issue":"5","page":"733-736","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28867286","title":"Load Adaptation of Lamellipodial Actin Networks.","abstract":"Actin filaments polymerizing against membranes power endocytosis, vesicular traffic, and cell motility. In\u00a0vitro reconstitution studies suggest that the structure and the dynamics of actin networks respond to\u00a0mechanical forces. We demonstrate that lamellipodial actin of migrating cells responds to mechanical load when membrane tension is modulated. In\u00a0a\u00a0steady state, migrating cell filaments assume the canonical dendritic geometry, defined by\u00a0Arp2\/3-generated 70\u00b0 branch points. Increased tension triggers a dense network with a broadened range of\u00a0angles, whereas decreased tension causes a shift to a sparse configuration dominated by filaments growing perpendicularly to the plasma membrane. We show that these responses emerge from the geometry of branched actin: when load per filament decreases, elongation speed increases and perpendicular filaments gradually outcompete others because they polymerize the shortest distance to the membrane, where they are protected from capping. This network-intrinsic geometrical adaptation mechanism tunes protrusive force in response to mechanical load.","authors":"Mueller, J., Szep, G., Nemethova, M., de Vries, I., Lieber, AD., Winkler, C., Kruse, K., Small, JV., Schmeiser, C., Keren, K., Hauschild, R., Sixt, M.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell","volume":"171","issue":"1","page":"188-200.e16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32125455","title":"Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target.","abstract":null,"authors":"Zhang, H., Penninger, JM., Li, Y., Zhong, N., Slutsky, AS.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Intensive Care Med","volume":"46","issue":"4","page":"586-590","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37595564","title":"An ethical framework for human embryology with embryo models.","abstract":"A human embryo's legal definition and its entitlement to protection vary greatly worldwide. Recently, human&#xa0;pluripotent stem cells have been used to form in&#xa0;vitro models of early embryos that have challenged&#xa0;legal definitions and raised questions regarding their usage. In this light, we propose a refined legal definition of an embryo, suggest \"tipping points\" for when human embryo models could eventually be afforded similar protection to that of embryos, and then revisit basic ethical principles that might help&#xa0;to draft a roadmap for the gradual, justified usage of embryo models in a manner that aims to maximize benefits to society.","authors":"Rivron, NC., Martinez Arias, A., Pera, MF., Moris, N., M'hamdi, HI.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Cell","volume":"186","issue":"17","page":"3548-3557","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19323996","title":"Neurons detect increases and decreases in oxygen levels using distinct guanylate cyclases.","abstract":"Homeostatic sensory systems detect small deviations in temperature, water balance, pH, and energy needs to regulate adaptive behavior and physiology. In C. elegans, a homeostatic preference for intermediate oxygen (O2) levels requires cGMP signaling through soluble guanylate cyclases (sGCs), proteins that bind gases through an associated heme group. Here we use behavioral analysis, functional imaging, and genetics to show that reciprocal changes in O2 levels are encoded by sensory neurons that express alternative sets of sGCs. URX sensory neurons are activated by increases in O2 levels, and require the sGCs gcy-35 and gcy-36. BAG sensory neurons are activated by decreases in O2 levels, and require the sGCs gcy-31 and gcy-33. The sGCs are instructive O2 sensors, as forced expression of URX sGC genes causes BAG neurons to detect O2 increases. Both sGC expression and cell-intrinsic dynamics contribute to the differential roles of URX and BAG in O2-dependent behaviors.","authors":"Zimmer, M., Gray, JM., Pokala, N., Chang, AJ., Karow, DS., Marletta, MA., Hudson, ML., Morton, DB., Chronis, N., Bargmann, CI.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Neuron","volume":"61","issue":"6","page":"865-79","pdf":null,"JrId":"1600","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27234889","title":"Systematic evaluation of methyl ester bioisosteres in the context of developing alkenyldiarylmethanes (ADAMs) as non-nucleoside reverse transcriptase inhibitors (NNRTIs) for anti-HIV-1 chemotherapy.","abstract":"The alkenyldiarylmethanes (ADAMs) are a class of non-nucleoside reverse transcriptase inhibitors (NNRTIs) targeting HIV-1. Four chemically and metabolically stabilized ADAMs incorporating N-methoxyimidoyl halide replacements of the methyl esters of the lead compound were previously reported. In this study, twenty-five new ADAMs were synthesized in order to investigate the biological consequences of installing nine different methyl ester bioisosteres at three different locations. Attempts to define a universal rank order of methyl ester bioisosteres and discover the 'best' one in terms of inhibitory activity versus HIV-1 reverse transcriptase (RT) led to the realization that the potencies are critically dependent on the surrounding structure at each location, and therefore the definition of universal rank order is impossible. This investigation produced several new non-nucleoside reverse transcriptase inhibitors in which all three of the three methyl esters of the lead compound were replaced by methyl ester bioisosteres, resulting in compounds that are more potent as HIV-1 RT inhibitors and antiviral agents than the lead compound itself and are expected to also be more metabolically stable than the lead compound.","authors":"Hoshi, A., Sakamoto, T., Takayama, J., Xuan, M., Okazaki, M., Hartman, TL., Buckheit, RW., Pannecouque, C., Cushman, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Bioorg Med Chem","volume":"24","issue":"13","page":"3006-3022","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29961260","title":"Manipulating Cohesin Levels in Live Mouse Oocytes.","abstract":"The cohesin complex is essential for chromosome segregation in mitosis and meiosis. Cohesin is a tripartite protein complex that holds sister chromatids together from DNA replication until anaphase. In mammals, meiotic DNA replication occurs in oogonia of embryos and chromosome segregation occurs in oocytes of sexually mature females. Sister chromatid cohesion establishment and chromosome segregation are thus separated by months in the mouse and decades in the human. The meiotic cohesin complex that maintains sister chromatid cohesion must therefore hold replicated sisters together for a long time in oocytes. Remarkably, this is achieved by establishing cohesion exclusively in prenatal oocytes. Meiotic cohesion in females is\u00a0maintained without detectable turnover and cohesin\u00a0is therefore thought to be a long-lived protein complex. Nevertheless, the lifespan of cohesin molecules is limited as chromosomal cohesin levels\u00a0decline with maternal age. The age-related loss of cohesin and weakened cohesion correlate with an age-related increase in chromosome missegregation of meiosis I oocytes that results in aneuploid eggs. Therefore, loss of chromosomal cohesin has been proposed to be a leading cause of the maternal age effect. To better understand cohesin deterioration in oocytes, it is crucial to gain insights into mammalian cohesion establishment and maintenance mechanisms by manipulating cohesin in live oocytes.This chapter describes techniques that address the manipulation of meiotic cohesin levels in mouse oocytes. First, we describe how cohesin can be efficiently removed from meiotic chromosomes by injecting mRNA encoding TEV protease in live oocytes expressing cohesin with engineered TEV recognition sites, followed by imaging. Secondly, we describe how cohesin expression can be induced during different stages of oocyte development using genetically modified mouse strains. In particular, we describe how to determine the deletion timing of germline-specific Cre recombinases using \u03b2-galactosidase staining of fetal ovaries. Lastly, we provide guidance on how to quantify cohesin levels on metaphase I chromosome spreads.","authors":"Szyd\u0142owska, A., Ladst\u00e4tter, S., Tachibana, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Methods Mol Biol","volume":"1818","issue":null,"page":"113-128","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29925635","title":"Afatinib restrains K-RAS-driven lung tumorigenesis.","abstract":"On the basis of clinical trials using first-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), it became a doctrine that V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (<i>K-RAS<\/i>) mutations drive resistance to EGFR inhibition in non-small cell lung cancer (NSCLC). Conversely, we provide evidence that EGFR signaling is engaged in K-RAS-driven lung tumorigenesis in humans and in mice. Specifically, genetic mouse models revealed that deletion of <i>Egfr<\/i> quenches mutant K-RAS activity and transiently reduces tumor growth. However, EGFR inhibition initiates a rapid resistance mechanism involving non-EGFR ERBB family members. This tumor escape mechanism clarifies the disappointing outcome of first-generation TKIs and suggests high therapeutic potential of pan-ERBB inhibitors. On the basis of various experimental models including genetically engineered mouse models, patient-derived and cell line-derived xenografts, and in vitro experiments, we demonstrate that the U.S. Food and Drug Administration-approved pan-ERBB inhibitor afatinib effectively impairs K-RAS-driven lung tumorigenesis. Our data support reconsidering the use of pan-ERBB inhibition in clinical trials to treat <i>K-RAS<\/i>-mutated NSCLC.","authors":"Moll, HP., Pranz, K., Musteanu, M., Grabner, B., Hruschka, N., Mohrherr, J., Aigner, P., Stiedl, P., Brcic, L., Laszlo, V., Schramek, D., Moriggl, R., Eferl, R., Moldvay, J., Dezso, K., Lopez-Casas, PP., Stoiber, D., Hidalgo, M., Penninger, J., Sibilia, M., Gy\u0151rffy, B., Barbacid, M., Dome, B., Popper, H., Casanova, E.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Sci Transl Med","volume":"10","issue":"446","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26775648","title":"3D high throughput screening and profiling of embryoid bodies in thermoformed microwell plates.","abstract":"3D organoids using stem cells to study development and disease are now widespread. These models are powerful to mimic in vivo situations but are currently associated with high variability and low throughput. For biomedical research, platforms are thus necessary to increase reproducibility and allow high-throughput screens (HTS). Here, we introduce a microwell platform, integrated in standard culture plates, for functional HTS. Using micro-thermoforming, we form round-bottom microwell arrays from optically clear cyclic olefin polymer films, and assemble them with bottom-less 96-well plates. We show that embryonic stem cells aggregate faster and more reproducibly (centricity, circularity) as compared to a state-of-the-art microwell array. We then run a screen of a chemical library to direct differentiation into primitive endoderm (PrE) and, using on-chip high content imaging (HCI), we identify molecules, including regulators of the cAMP pathway, regulating tissue size, morphology and PrE gene activity. We propose that this platform will benefit to the systematic study of organogenesis in vitro.","authors":"Vrij, EJ., Espinoza, S., Heilig, M., Kolew, A., Schneider, M., van Blitterswijk, CA., Truckenm\u00fcller, RK., Rivron, NC.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Lab Chip","volume":"16","issue":"4","page":"734-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16713563","title":"Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II.","abstract":"Over the past years, a large number of histone posttranslational modifications have been described, some of which function to attain a repressed chromatin structure, while others facilitate activation by allowing access of regulators to DNA. Histone H2B monoubiquitination is a mark associated with transcriptional activity. Using a highly reconstituted chromatin-transcription system incorporating the inducible RARbeta2 promoter, we find that the establishment of H2B monoubiquitination by RNF20\/40 and UbcH6 is dependent on the transcription elongation regulator complex PAF, the histone chaperone FACT, and transcription. H2B monoubiquitination facilitates FACT function, thereby stimulating transcript elongation and the generation of longer transcripts. These in vitro analyses and corroborating in vivo experiments demonstrate that elongation by RNA polymerase II through the nucleosomal barrier is minimally dependent upon (1) FACT and (2) the recruitment of PAF and the H2B monoubiquitination machinery.","authors":"Pavri, R., Zhu, B., Li, G., Trojer, P., Mandal, S., Shilatifard, A., Reinberg, D.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell","volume":"125","issue":"4","page":"703-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29305318","title":"Behavioral phenotyping of calcium channel (CACN) subunit \u03b12\u03b43 knockout mice: Consequences of sensory cross-modal activation.","abstract":"Sensory cross-activation is still ill-defined and research concerning the consequences of sensory mergence on normal brain function is very limited. Human studies describe behavioral benefits of people with synesthesia- a peculiar form of perception possibly due to cross-modal activation- regarding sensory and memory abilities. Here, we studied behavioral alterations in calcium channel (CACN) subunit \u03b12\u03b43 knockout (KO) mice exhibiting pain-induced cortical cross-modal activation. Knockout mice exhibited an increased response upon touch of a pinna and impaired audition, while elementary olfaction, vision, somatosensation and motor function were not altered. In contrast to synesthetic humans for whom enhanced memory function had been described, \u03b12\u03b43 KO mice might have developed defects for object-based memory. However, in a task requiring use of multiple modalities, mutant mice revealed an enhanced performance compared to wild-type controls. Furthermore, several tests revealed evidence for increased anxiety-like behavior of \u03b12\u03b43 KO animals. In summary, deficits in single sensory abilities and a potential gain in processing simultaneous sensory information in \u03b12\u03b43 KO mice might represent behavioral correlates of sensory cross-activation. Further, our data suggest a role of CACN\u03b12\u03b43 within the functionality of the sensory system, but not the motor system and general health.","authors":"Landmann, J., Richter, F., Classen, J., Richter, A., Penninger, JM., Bechmann, I.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Behav Brain Res","volume":"364","issue":null,"page":"393-402","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12089509","title":"Origin of regulatory T cells with known specificity for antigen.","abstract":"T cell receptor agonists can induce the differentiation of regulatory T (T(R)) cells. We report here that the immunoglobulin kappa-controlled expression of an agonist in different cell types correlated with the phenotype of the generated T(R) cells. We found that aberrant expression on thymic stroma yielded predominantly CD4(+)CD25(+) T(R) cells, which--under physiological conditions--may be induced by ectopically expressed organ-specific antigens and thus prevent organ-specific autoimmunity. Expression of the agonist antigen by nonactivated hematopoietic cells produced mostly CD4(+)CD25(-) T(R) cells. This subset can be derived from mature monospecific T cells without \"tutoring\" by other T cells and can be generated in the absence of a functioning thymus. Suppression of CD4(+) T cell proliferative responses by both CD25(+) and CD25(-) subsets was interleukin 10 (IL-10) independent and was overcome by IL-2. These data suggest that distinct pathways can be exploited to interfere with unwanted immune responses.","authors":"Apostolou, I., Sarukhan, A., Klein, L., von Boehmer, H.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nat Immunol","volume":"3","issue":"8","page":"756-63","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19309095","title":"Beyond photobleaching, laser illumination unbinds fluorescent proteins.","abstract":"Confocal and two-photon fluorescence microscopy techniques using genetically encoded fluorescent probes are widely used in cell biology. Beyond the common problems of photobleaching and phototoxicity, we present evidence that photounbinding also has the potential to compromise such methods, especially in quantitative studies. We show that laser intensities within excitation regimes typical for imaging approaches such as as fluorescence recovery after photobleaching (FRAP), photolysis, or fluorescence correlation spectroscopy (FCS) experiments can cause the dissociation of antibodies from their ligands. Indeed, both one- and two-photon excitation of a fluorescent anti-GFP antibody caused its dissociation from immobilized GFP in vitro. Importantly, with two-photon excitation, the laser intensity threshold for photobleaching was the same as for photounbinding. By contrast, with single-photon excitation, we found a range of laser intensities where photobleaching can be separated from photounbinding. This photounbinding effect was visualized and measured by rebinding a second fluorescent anti-GFP (Green Fluorescent Protein) antibody, indicating that the GFP remained functional for reassociation following the photoinduced dissociation. Finally, we show that this unbinding effect occurs only when at least one binding partner carries a fluorescent label. Our results show that this photounbinding effect can readily remain masked or be misinterpreted as photobleaching, which can compromise the quantitative interpretation of binding studies made using fluorescence microscopy.","authors":"Heinze, KG., Costantino, S., De Koninck, P., Wiseman, PW.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Phys Chem B","volume":"113","issue":"15","page":"5225-33","pdf":null,"JrId":"30073","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12070128","title":"Human securin proteolysis is controlled by the spindle checkpoint and reveals when the APC\/C switches from activation by Cdc20 to Cdh1.","abstract":"Progress through mitosis is controlled by the sequential destruction of key regulators including the mitotic cyclins and securin, an inhibitor of anaphase whose destruction is required for sister chromatid separation. Here we have used live cell imaging to determine the exact time when human securin is degraded in mitosis. We show that the timing of securin destruction is set by the spindle checkpoint; securin destruction begins at metaphase once the checkpoint is satisfied. Furthermore, reimposing the checkpoint rapidly inactivates securin destruction. Thus, securin and cyclin B1 destruction have very similar properties. Moreover, we find that both cyclin B1 and securin have to be degraded before sister chromatids can separate. A mutant form of securin that lacks its destruction box (D-box) is still degraded in mitosis, but now this is in anaphase. This destruction requires a KEN box in the NH2 terminus of securin and may indicate the time in mitosis when ubiquitination switches from APCCdc20 to APCCdh1. Lastly, a D-box mutant of securin that cannot be degraded in metaphase inhibits sister chromatid separation, generating a cut phenotype where one cell can inherit both copies of the genome. Thus, defects in securin destruction alter chromosome segregation and may be relevant to the development of aneuploidy in cancer.","authors":"Hagting, A., Den Elzen, N., Vodermaier, HC., Waizenegger, IC., Peters, JM., Pines, J.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Cell Biol","volume":"157","issue":"7","page":"1125-37","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2002-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30006452","title":"A high-throughput method to identify trans-activation domains within transcription factor sequences.","abstract":"Even though transcription factors (TFs) are central players of gene regulation and have been extensively studied, their regulatory <i>trans<\/i>-activation domains (tADs) often remain unknown and a systematic functional characterization of tADs is lacking. Here, we present a novel high-throughput approach <i>tAD-seq<\/i> to functionally test thousands of candidate tADs from different TFs in parallel. The tADs we identify by pooled screening validate in individual luciferase assays, whereas neutral regions do not. Interestingly, the tADs are found at arbitrary positions within the TF sequences and can contain amino acid (e.g., glutamine) repeat regions or overlap structured domains, including helix-loop-helix domains that are typically annotated as DNA-binding. We also identified tADs in the non-native reading frames, confirming that random sequences can function as tADs, albeit weakly. The identification of tADs as short protein sequences sufficient for transcription activation will enable the systematic study of TF function, which-particularly for TFs of different transcription activating functionalities-is still poorly understood.","authors":"Arnold, CD., Nem\u010dko, F., Woodfin, AR., Wienerroither, S., Vlasova, A., Schleiffer, A., Pagani, M., Rath, M., Stark, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"EMBO J","volume":"37","issue":"16","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12075344","title":"Angiotensin-converting enzyme 2 is an essential regulator of heart function.","abstract":"Cardiovascular diseases are predicted to be the most common cause of death worldwide by 2020. Here we show that angiotensin-converting enzyme 2 (ace2) maps to a defined quantitative trait locus (QTL) on the X chromosome in three different rat models of hypertension. In all hypertensive rat strains, ACE2 messenger RNA and protein expression were markedly reduced, suggesting that ace2 is a candidate gene for this QTL. Targeted disruption of ACE2 in mice results in a severe cardiac contractility defect, increased angiotensin II levels, and upregulation of hypoxia-induced genes in the heart. Genetic ablation of ACE on an ACE2 mutant background completely rescues the cardiac phenotype. But disruption of ACER, a Drosophila ACE2 homologue, results in a severe defect of heart morphogenesis. These genetic data for ACE2 show that it is an essential regulator of heart function in vivo.","authors":"Crackower, MA., Sarao, R., Oudit, GY., Yagil, C., Kozieradzki, I., Scanga, SE., Oliveira-dos-Santos, AJ., da Costa, J., Zhang, L., Pei, Y., Scholey, J., Ferrario, CM., Manoukian, AS., Chappell, MC., Backx, PH., Yagil, Y., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nature","volume":"417","issue":"6891","page":"822-8","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29622725","title":"SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis.","abstract":"Defining direct targets of transcription factors and regulatory pathways is key to understanding their roles in physiology and disease. We combined SLAM-seq [thiol(SH)-linked alkylation for the metabolic sequencing of RNA], a method for direct quantification of newly synthesized messenger RNAs (mRNAs), with pharmacological and chemical-genetic perturbation in order to define regulatory functions of two transcriptional hubs in cancer, BRD4 and MYC, and to interrogate direct responses to BET bromodomain inhibitors (BETis). We found that BRD4 acts as general coactivator of RNA polymerase II-dependent transcription, which is broadly repressed upon high-dose BETi treatment. At doses triggering selective effects in leukemia, BETis deregulate a small set of hypersensitive targets including MYC. In contrast to BRD4, MYC primarily acts as a selective transcriptional activator controlling metabolic processes such as ribosome biogenesis and de novo purine synthesis. Our study establishes a simple and scalable strategy to identify direct transcriptional targets of any gene or pathway.","authors":"Muhar, M., Ebert, A., Neumann, T., Umkehrer, C., Jude, J., Wieshofer, C., Rescheneder, P., Lipp, JJ., Herzog, VA., Reichholf, B., Cisneros, DA., Hoffmann, T., Schlapansky, MF., Bhat, P., von Haeseler, A., K\u00f6cher, T., Obenauf, AC., Popow, J., Ameres, SL., Zuber, J.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Science","volume":"360","issue":"6390","page":"800-805","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30057273","title":"Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm.","abstract":"The biogenesis of the RNA payload of mature sperm\u00a0is of great interest, because RNAs delivered to the zygote at fertilization can affect early development. Here, we tested the hypothesis that small RNAs are trafficked to mammalian sperm during the process of post-testicular maturation in the epididymis. By characterizing small RNA dynamics during germ cell maturation in mice, we confirm and extend prior observations that sperm undergo a dramatic switch in the RNA payload from piRNAs to tRNA fragments (tRFs) upon exiting the testis and entering the epididymis. Small RNA delivery to sperm could be recapitulated in\u00a0vitro by incubating testicular spermatozoa with caput epididymosomes. Finally, tissue-specific metabolic labeling of RNAs in intact mice definitively shows that mature sperm carry RNAs that were originally synthesized in the epididymal epithelium. These data demonstrate that soma-germline RNA transfer occurs in male mammals, most likely via vesicular transport from the epididymis to maturing sperm.","authors":"Sharma, U., Sun, F., Conine, CC., Reichholf, B., Kukreja, S., Herzog, VA., Ameres, SL., Rando, OJ.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Dev Cell","volume":"46","issue":"4","page":"481-494.e6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22388744","title":"Sonic Hedgehog-activated engineered blood vessels enhance bone tissue formation.","abstract":"Large bone defects naturally regenerate via a highly vascularized tissue which progressively remodels into cartilage and bone. Current approaches in bone tissue engineering are restricted by delayed vascularization and fail to recapitulate this stepwise differentiation toward bone tissue. Here, we use the morphogen Sonic Hedgehog (Shh) to induce the in vitro organization of an endothelial capillary network in an artificial tissue. We show that endogenous Hedgehog activity regulates angiogenic genes and the formation of vascular lumens. Exogenous Shh further induces the in vitro development of the vasculature (vascular lumen formation, size, distribution). Upon implantation, the in vitro development of the vasculature improves the in vivo perfusion of the artificial tissue and is necessary to contribute to, and enhance, the formation of de novo mature bone tissue. Similar to the regenerating callus, the artificial tissue undergoes intramembranous and endochondral ossification and forms a trabecular-like bone organ including bone-marrow-like cavities. These findings open the door for new strategies to treat large bone defects by closely mimicking natural endochondral bone repair.","authors":"Rivron, NC., Raiss, CC., Liu, J., Nandakumar, A., Sticht, C., Gretz, N., Truckenm\u00fcller, R., Rouwkema, J., van Blitterswijk, CA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Proc Natl Acad Sci U S A","volume":"109","issue":"12","page":"4413-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41330383","title":"Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants.","abstract":"Selective autophagy is a fundamental protein quality control pathway that safeguards proteostasis by degrading damaged or surplus cellular components, particularly under stress. This process is orchestrated by selective autophagy receptors (SARs) that recruit specific cargo for degradation. Although significant strides have been made in understanding the molecular framework of selective autophagy, the diversity of SAR repertoires across species remains largely unexplored. Through a comparative interactome analysis across five model organisms, we identified a suite of conserved and lineage-specific SAR candidates. Among these, we validated coupling of ubiquitin to endoplasmic reticulum degradation- and protein rich in the amino acids E, L, K, and S-domain-containing SAR (CESAR) as a conserved SAR critical for proteostasis under heat stress. CESAR specifically facilitates the degradation of ubiquitinated protein aggregates and is indispensable for heat stress tolerance. Altogether, our study establishes a robust pipeline and a rich resource for SAR discovery. It also positions CESAR as a pivotal regulator of proteostasis, with broad implications for improving stress resilience in plants.","authors":"S\u00e1nchez de Medina Hern\u00e1ndez, V., Nava-Garc\u00eda, MM., Bianchi, A., Clavel, M., Papareddy, RK., Benchalel, L., Andreev, VI., Mathur, V., Mohseni, A., Garc\u00eda-Le\u00f3n, M., Gao, P., de la Concepci\u00f3n, JC., Picchianti, L., Grujic, N., Kobylinska, R., Abdrakhmanov, A., Duverg\u00e9, H., Anand, G., Leibrock, N., Ma, J., Raffeiner, M., Crawford, TS., Argir\u00f2, L., Matuszkiewicz, M., Wun, CL., Kanne, JV., Meinhart, A., Roitinger, E., B\u00e4urle, I., Kang, BH., Petersen, M., \u00dcst\u00fcn, S., Kulathu, Y., Clausen, T., Ramundo, S., Dagdas, Y.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Dev Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-02","doi":"10.1016\/j.devcel.2025.11.001","first_author":"S&#xe1;nchez de Medina Hern&#xe1;ndez, V.","corresponding_authors":"S&#xe1;nchez de Medina Hern&#xe1;ndez, V., Dagdas, Y."},{"pmid":"30038282","title":"Epigenetic regulation of brain region-specific microglia clearance activity.","abstract":"The rapid elimination of dying neurons and nonfunctional synapses in the brain is carried out by microglia, the resident myeloid cells of the brain. Here we show that microglia clearance activity in the adult brain is regionally regulated and depends on the rate of neuronal attrition. Cerebellar, but not striatal or cortical, microglia exhibited high levels of basal clearance activity, which correlated with an elevated degree of cerebellar neuronal attrition. Exposing forebrain microglia to apoptotic cells activated gene-expression programs supporting clearance activity. We provide evidence that the polycomb repressive complex 2 (PRC2) epigenetically restricts the expression of genes that support clearance activity in striatal and cortical microglia. Loss of PRC2 leads to aberrant activation of a microglia clearance phenotype, which triggers changes in neuronal morphology and behavior. Our data highlight a key role of epigenetic mechanisms in preventing microglia-induced neuronal alterations that are frequently associated with neurodegenerative and psychiatric diseases.","authors":"Ayata, P., Badimon, A., Strasburger, HJ., Duff, MK., Montgomery, SE., Loh, YE., Ebert, A., Pimenova, AA., Ramirez, BR., Chan, AT., Sullivan, JM., Purushothaman, I., Scarpa, JR., Goate, AM., Busslinger, M., Shen, L., Losic, B., Schaefer, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Neurosci","volume":"21","issue":"8","page":"1049-1060","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30089685","title":"Lidocaine is a nocebo treatment for trigeminally mediated magnetic orientation in birds.","abstract":"Even though previously described iron-containing structures in the upper beak of pigeons were almost certainly macrophages, not magnetosensitive neurons, behavioural and neurobiological evidence still supports the involvement of the ophthalmic branch of the trigeminal nerve (V1) in magnetoreception. In previous behavioural studies, inactivation of putative V1-associated magnetoreceptors involved either application of the surface anaesthetic lidocaine to the upper beak or sectioning of V1. Here, we compared the effects of lidocaine treatment, V1 ablations and sham ablations on magnetic field-driven neuronal activation in V1-recipient brain regions in European robins. V1 sectioning led to significantly fewer Egr-1-expressing neurons in the trigeminal brainstem than in the sham-ablated birds, whereas lidocaine treatment had no effect on neuronal activation. Furthermore, Prussian blue staining showed that nearly all iron-containing cells in the subepidermal layer of the upper beak are nucleated and are thus not part of the trigeminal nerve, and iron-containing cells appeared in highly variable numbers at inconsistent locations between individual robins and showed no systematic colocalization with a neuronal marker. Our data suggest that lidocaine treatment has been a nocebo to the birds and a placebo for the experimenters. Currently, the nature and location of any V1-associated magnetosensor remains elusive.","authors":"Engels, S., Treiber, CD., Salzer, MC., Michalik, A., Ushakova, L., Keays, DA., Mouritsen, H., Heyers, D.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"J R Soc Interface","volume":"15","issue":"145","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28825703","title":"Virtual reality for freely moving animals.","abstract":"Standard animal behavior paradigms incompletely mimic nature and thus limit our understanding of behavior and brain function. Virtual reality (VR) can help, but it poses challenges. Typical VR systems require movement restrictions but disrupt sensorimotor experience, causing neuronal and behavioral alterations. We report the development of FreemoVR, a VR system for freely moving animals. We validate immersive VR for mice, flies, and zebrafish. FreemoVR allows instant, disruption-free environmental reconfigurations and interactions between real organisms and computer-controlled agents. Using the FreemoVR platform, we established a height-aversion assay in mice and studied visuomotor effects in Drosophila and zebrafish. Furthermore, by photorealistically mimicking zebrafish we discovered that effective social influence depends on a prospective leader balancing its internally preferred directional choice with social interaction. FreemoVR technology facilitates detailed investigations into neural function and behavior through the precise manipulation of sensorimotor feedback loops in unrestrained animals.","authors":"Stowers, JR., Hofbauer, M., Bastien, R., Griessner, J., Higgins, P., Farooqui, S., Fischer, RM., Nowikovsky, K., Haubensak, W., Couzin, ID., Tessmar-Raible, K., Straw, AD.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Methods","volume":"14","issue":"10","page":"995-1002","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29804673","title":"Analysis of chromosomes from mouse oocytes and mammalian cultured cells by light microscopy.","abstract":"As carriers of the genetic material, chromosomes are of prime interest in the life sciences. Although all aspects of chromosome biology should ideally be studied in living cells, the isolation of chromosomes can greatly facilitate their analysis. This can be achieved by lysing mitotic or meiotic cells under conditions where their content, including their chromosomes, is spread out on the surface of microscopy glass slides. Here we describe three such chromosome spreading techniques, which have been instrumental in analyzing chromosomes from either mouse oocytes or mammalian cultured cells in mitosis. For both chromosomes from oocytes and mitotic cells, we describe immunofluorescence protocols that enable the visualization of proteins with specific antibodies. For mitotic chromosomes, we also provide a classic protocol for Giemsa staining. This protocol cannot be used to localize proteins but is useful to determine structural features of chromosomes, such as sister chromatid cohesion and chromosome condensation. The question of how chromosome nondisjunction during the meiotic division causes aneuploidy is of great interest in oocyte chromosome research. Because we have found that ploidy in mouse oocytes can be determined more reliably in fixed cells than in spread chromosomes, we also describe a protocol for the in situ fixation and immunofluorescence analysis of chromosomes in mouse oocytes.","authors":"Silva, MCC., Wutz, G., Tachibana, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Methods Cell Biol","volume":"144","issue":null,"page":"287-305","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19592088","title":"Tissue assembly and organization: developmental mechanisms in microfabricated tissues.","abstract":"In vitro-generated tissues hold significant promise in modern biology since they can potentially mimic physiological and pathological tissues. However, these are currently structurally and functionally of limited complexity and necessitate self-organization and recapitulation of tissue development mechanisms in vitro. Tools derived from nano- and microfabrications along with bottom-up strategies are emerging to allow the fabrication of primitive tissues structures that can remodel overtime. Subsequently, clues are accumulating to show that, beyond genetic material, both intrinsic tissue architectures and microenvironmental cues can lead to morphogenesis related mechanisms in vitro. The question arises, however, as how we may design and assemble structures prone to adequate tissue remodeling, predict and manipulate those developmental mechanisms in vitro? Systems integrating architectural, physical and molecular cues will allow more systematic investigation of basic principles of tissue morphogenesis, differentiation or maintenance and will feedback to reproduce the dynamic of tissue development in vitro and form more complex tissues.","authors":"Rivron, NC., Rouwkema, J., Truckenm\u00fcller, R., Karperien, M., De Boer, J., Van Blitterswijk, CA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Biomaterials","volume":"30","issue":"28","page":"4851-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-10-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29995849","title":"Prespliceosome structure provides insights into spliceosome assembly and regulation.","abstract":"The spliceosome catalyses the excision of introns from pre-mRNA in two steps, branching and exon ligation, and is assembled from five small nuclear ribonucleoprotein particles (snRNPs; U1, U2, U4, U5, U6) and numerous non-snRNP factors<sup>1<\/sup>. For branching, the intron 5' splice site and the branch point sequence are selected and brought\u00a0by the U1 and U2 snRNPs into the prespliceosome<sup>1<\/sup>, which is a focal point for regulation by alternative splicing factors<sup>2<\/sup>. The U4\/U6.U5 tri-snRNP subsequently joins the prespliceosome to form the complete pre-catalytic spliceosome. Recent studies have revealed the structural basis of the branching and exon-ligation reactions<sup>3<\/sup>, however, the structural basis of the early events in spliceosome assembly remains poorly understood<sup>4<\/sup>. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae prespliceosome at near-atomic resolution. The structure reveals an induced stabilization of the 5' splice site in the U1 snRNP, and provides structural insights into the functions of the human alternative splicing factors LUC7-like (yeast Luc7) and TIA-1 (yeast Nam8), both of\u00a0which have been linked to human disease<sup>5,6<\/sup>. In the prespliceosome, the U1 snRNP associates with the U2 snRNP through a stable contact with the U2 3' domain and a transient yeast-specific contact with the U2 SF3b-containing 5' region, leaving its tri-snRNP-binding interface fully exposed. The results suggest mechanisms for 5' splice site transfer to the U6 ACAGAGA region within the assembled spliceosome and for its subsequent conversion to the activation-competent B-complex spliceosome<sup>7,8<\/sup>. Taken together, the data provide a working model to investigate the early steps of spliceosome assembly.","authors":"Plaschka, C., Lin, PC., Charenton, C., Nagai, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"559","issue":"7714","page":"419-422","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19308321","title":"Evolutionary and functional epitopes of the Sp\u00e4tzle protein: new insights into activation of the Toll receptor.","abstract":"Sp\u00e4tzle, a dimeric ligand, binds to the Drosophila Toll receptor and activates the signal pathway functioning in both embryonic patterning and innate immunity. Here, we used the evolutionary trace approach based on phylogenetic information to predict the evolutionary epitope of Sp\u00e4tzle and found that it mainly clusters in several adjacent loops of Sp\u00e4tzle far from the cystine-knot structural domain. We designed six mutants of Sp\u00e4tzle based on the evolutionary epitope and transfected them into a stable cell line expressing the luciferase reporter gene under the control of the drosomycin promoter. Luciferase assays showed that these mutants cannot significantly activate the drosomycin promoter, suggesting the involvement of these sites in binding of Sp\u00e4tzle to the Toll receptor. These data highlight the importance of the Trp-loop of the mushroom-shaped Sp\u00e4tzle dimer in Toll receptor activation and demonstrate that evolution-guided site-specific mutagenesis represents a useful and promising strategy for understanding the ligand-receptor interaction.","authors":"Wang, Y., Zhu, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell Mol Life Sci","volume":"66","issue":"9","page":"1595-602","pdf":null,"JrId":"20436","fulltextlink":null,"preprintlink":null,"articledate":"2009-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29795340","title":"Author Correction: The axolotl genome and the evolution of key tissue formation regulators.","abstract":"In the originally published version of this Article, the sequenced axolotl strain (the homozygous white mutant) was denoted as 'D\/D' rather than 'd\/d' in Fig. 1a and the accompanying legend, the main text and the Methods section. The original Article has been corrected online.","authors":"Nowoshilow, S., Schloissnig, S., Fei, JF., Dahl, A., Pang, AWC., Pippel, M., Winkler, S., Hastie, AR., Young, G., Roscito, JG., Falcon, F., Knapp, D., Powell, S., Cruz, A., Cao, H., Habermann, B., Hiller, M., Tanaka, EM., Myers, EW.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"559","issue":"7712","page":"E2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29786093","title":"Author Correction: High-speed volumetric imaging of neuronal activity in freely moving rodents.","abstract":"In the version of this Brief Communication originally published online, ref. 21 included details for a conference paper (Pegard, N. C. et al. Paper presented at Novel Techniques in Microscopy: Optics in the Life Sciences, Vancouver, BC, Canada, 12-15 April 2015). The correct reference is the following: P\u00e9gard, N. C. et al. Optica 3, 517-524 (2016). This error has been corrected in the print, HTML and PDF versions of the paper.","authors":"Skocek, O., N\u00f6bauer, T., Weilguny, L., Traub, FM., Xia, CN., Molodtsov, MI., Grama, A., Yamagata, M., Aharoni, D., Cox, DD., Golshani, P., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Methods","volume":"15","issue":"6","page":"469","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19303852","title":"Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation.","abstract":"Activation of nuclear factor-kappaB (NF-kappaB), a key mediator of inducible transcription in immunity, requires binding of NF-kappaB essential modulator (NEMO) to ubiquitinated substrates. Here, we report that the UBAN (ubiquitin binding in ABIN and NEMO) motif of NEMO selectively binds linear (head-to-tail) ubiquitin chains. Crystal structures of the UBAN motif revealed a parallel coiled-coil dimer that formed a heterotetrameric complex with two linear diubiquitin molecules. The UBAN dimer contacted all four ubiquitin moieties, and the integrity of each binding site was required for efficient NF-kappaB activation. Binding occurred via a surface on the proximal ubiquitin moiety and the canonical Ile44 surface on the distal one, thereby providing specificity for linear chain recognition. Residues of NEMO involved in binding linear ubiquitin chains are required for NF-kappaB activation by TNF-alpha and other agonists, providing an explanation for the detrimental effect of NEMO mutations in patients suffering from X-linked ectodermal dysplasia and immunodeficiency.","authors":"Rahighi, S., Ikeda, F., Kawasaki, M., Akutsu, M., Suzuki, N., Kato, R., Kensche, T., Uejima, T., Bloor, S., Komander, D., Randow, F., Wakatsuki, S., Dikic, I.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Cell","volume":"136","issue":"6","page":"1098-109","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29950668","title":"Dorsal tegmental dopamine neurons gate associative learning of fear.","abstract":"Functional neuroanatomy of Pavlovian fear has identified neuronal circuits and synapses associating conditioned stimuli with aversive events. Hebbian plasticity within these networks requires additional reinforcement to store particularly salient experiences into long-term memory. Here we have identified a circuit that reciprocally connects the ventral periaqueductal gray and dorsal raphe region with the central amygdala and that gates fear learning. We found that ventral periaqueductal gray and dorsal raphe dopaminergic (vPdRD) neurons encode a positive prediction error in response to unpredicted shocks and may reshape intra-amygdala connectivity via a dopamine-dependent form of long-term potentiation. Negative feedback from the central amygdala to vPdRD neurons might limit reinforcement to events that have not been predicted. These findings add a new module to the midbrain dopaminergic circuit architecture underlying associative reinforcement learning and identify vPdRD neurons as a critical component of Pavlovian fear conditioning. We propose that dysregulation of vPdRD neuronal activity may contribute to fear-related psychiatric disorders.","authors":"Groessl, F., Munsch, T., Meis, S., Griessner, J., Kaczanowska, J., Pliota, P., Kargl, D., Badurek, S., Kraitsy, K., Rassoulpour, A., Zuber, J., Lessmann, V., Haubensak, W.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Neurosci","volume":"21","issue":"7","page":"952-962","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24836921","title":"Bayesian approach to single-cell differential expression analysis.","abstract":"Single-cell data provide a means to dissect the composition of complex tissues and specialized cellular environments. However, the analysis of such measurements is complicated by high levels of technical noise and intrinsic biological variability. We describe a probabilistic model of expression-magnitude distortions typical of single-cell RNA-sequencing measurements, which enables detection of differential expression signatures and identification of subpopulations of cells in a way that is more tolerant of noise.","authors":"Kharchenko, PV., Silberstein, L., Scadden, DT.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Methods","volume":"11","issue":"7","page":"740-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-02","doi":"10.1038\/nmeth.2967","first_author":"Kharchenko, PV.","corresponding_authors":"Scadden, DT."},{"pmid":"19299724","title":"IL-7 Dependence in human B lymphopoiesis increases during progression of ontogeny from cord blood to bone marrow.","abstract":"IL-7 is critical for B cell production in adult mice; however, its role in human B lymphopoiesis is controversial. One challenge was the inability to differentiate human cord blood (CB) or adult bone marrow (BM) hematopoietic stem cells (HSCs) without murine stroma. Here, we examine the role of IL-7 in human B cell development using a novel, human-only model based on coculturing human HSCs on primary human BM stroma. In this model, IL-7 increases human B cell production by &gt;60-fold from both CB and adult BM HSCs. IL-7-induced increases are dose-dependent and specific to CD19(+) cells. STAT5 phosphorylation and expression of the Ki-67 proliferation Ag indicate that IL-7 acts directly on CD19(+) cells to increase proliferation at the CD34(+) and CD34(-) pro-B cell stages. Without IL-7, HSCs in CB, but not BM, give rise to a small but consistent population of CD19(lo) B lineage cells that express EBF (early B cell factor) and PAX-5 and respond to subsequent IL-7 stimulation. Flt3 ligand, but not thymic stromal-derived lymhopoietin (TSLP), was required for the IL-7-independent production of human B lineage cells. As compared with CB, adult BM shows a reduction of in vitro generative capacity that is progressively more profound in developmentally sequential populations, resulting in an approximately 50-fold reduction in IL-7-dependent B lineage generative capacity. These data provide evidence that IL-7 is essential for human B cell production from adult BM and that IL-7-induced expansion of the pro-B compartment is increasingly critical for human B cell production during the progression of ontogeny.","authors":"Parrish, YK., Baez, I., Milford, TA., Benitez, A., Galloway, N., Rogerio, JW., Sahakian, E., Kagoda, M., Huang, G., Hao, QL., Sevilla, Y., Barsky, LW., Zielinska, E., Price, MA., Wall, NR., Dovat, S., Payne, KJ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Immunol","volume":"182","issue":"7","page":"4255-66","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29899063","title":"CDK6 Antagonizes p53-Induced Responses during Tumorigenesis.","abstract":"Tumor formation is a multistep process during which cells acquire genetic and epigenetic changes until they reach a fully transformed state. We show that CDK6 contributes to tumor formation by regulating transcriptional responses in a stage-specific manner. In early stages, the CDK6 kinase induces a complex transcriptional program to block p53 in hematopoietic cells. Cells lacking CDK6 kinase function are required to mutate <i>TP53<\/i> (encoding p53) to achieve a fully transformed immortalized state. CDK6 binds to the promoters of genes including the p53 antagonists <i>Prmt5, Ppm1d<\/i>, and <i>Mdm4<\/i> The findings are relevant to human patients: Tumors with low levels of CDK6 have mutations in <i>TP53<\/i> significantly more often than expected.<b>Significance:<\/b> CDK6 acts at the interface of p53 and RB by driving cell-cycle progression and antagonizing stress responses. While sensitizing cells to p53-induced cell death, specific inhibition of CDK6 kinase activity may provoke the outgrowth of p53-mutant clones from premalignant cells. <i>Cancer Discov; 8(7); 884-97. \u00a92018 AACR.<\/i><i>This article is highlighted in the In This Issue feature, p. 781<\/i>.","authors":"Bellutti, F., Tigan, AS., Nebenfuehr, S., Dolezal, M., Zojer, M., Grausenburger, R., Hartenberger, S., Kollmann, S., Doma, E., Prchal-Murphy, M., Uras, IZ., H\u00f6llein, A., Neuberg, DS., Ebert, BL., Ringler, A., Mueller, AC., Loizou, JI., Hinds, PW., Vogl, C., Heller, G., Kubicek, S., Zuber, J., Malumbres, M., Farlik, M., Villunger, A., Kollmann, K., Sexl, V.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cancer Discov","volume":"8","issue":"7","page":"884-897","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19260055","title":"Raldh3 gene expression pattern in the developing chicken inner ear.","abstract":"Retinoic acid (RA), an active metabolite of vitamin A, is a diffusible molecule that regulates the expression of several families of genes, playing a key role in specification processes during chordate development. With the aim of defining its possible role in the developing chick inner ear, we obtained in this work a detailed spatiotemporal distribution of the enzymes involved in its synthesis, the retinaldehyde dehydrogenases (RALH1-4). Our results showed that, in contrast to the mouse inner ear, Raldh3 expression was the only Raldh gene detected in the developing chick inner ear, where it appears as early as stage 18. During inner ear morphogenesis, Raldh3 expression was predominantly observed in the endolymphatic system. The Raldh3 expression pattern delimited totally or partially the Bmp4-positive presumptive territories of vestibular sensory epithelia by stage 24 and the basilar papilla at stage 34, suggesting a possible involvement of RA in their specification. In addition, several vestibular sensory areas showed some Raldh3-expressing cells close to the Raldh3-positive domain. These results suggest that the RA signaling pathway may play a role in the initial patterning of the otic epithelium and cell differentiation therein, providing local positional information. Having in mind this Raldh3 expression pattern, we discuss the regulatory interactions among the RA, bone morphogenetic protein, and fibroblast growth factor signaling pathways in the specification of otic sensory elements. Our investigation may underpin further experimental studies aimed at understanding the possible role of signaling pathways in patterning of the developing chick inner ear.","authors":"S\u00e1nchez-Guardado, LO., Ferran, JL., Mijares, J., Puelles, L., Rodr\u00edguez-Gallardo, L., Hidalgo-S\u00e1nchez, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Comp Neurol","volume":"514","issue":"1","page":"49-65","pdf":null,"JrId":"4668","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32591072","title":"Species-specific mechanisms during fertilization.","abstract":"The perpetuation and preservation of distinct species rely on mechanisms that ensure that only interactions between gametes of the same species can give rise to viable and fertile offspring. Species-specificity can act at various stages, ranging from physical\/behavioral pre-copulatory mechanisms, to pre-zygotic incompatibility during fertilization, to post-zygotic hybrid incompatibility. Herein, we focus on our current knowledge of the molecular mechanisms responsible for species-specificity during fertilization. While still poorly understood, decades of research have led to the discovery of molecules implicated in species-specific gamete interactions, starting from initial sperm-egg attraction to the binding of sperm and egg. While many of these molecules have been described as species-specific in their mode of action, relatively few have been demonstrated as such with definitive evidence. Thus, we also raise remaining questions that need to be addressed in order to characterize gamete interaction molecules as species-specific.","authors":"Gert, KR., Pauli, A.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Curr Top Dev Biol","volume":"140","issue":null,"page":"121-144","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16481437","title":"Functional dissection of Reelin signaling by site-directed disruption of Disabled-1 adaptor binding to apolipoprotein E receptor 2: distinct roles in development and synaptic plasticity.","abstract":"The Reelin signaling pathway controls neuronal positioning in human and mouse brain during development as well as modulation of long-term potentiation (LTP) and behavior in the adult. Reelin signals by binding to two transmembrane receptors, apolipoprotein E receptor 2 (Apoer2) and very-low-density lipoprotein receptor. After Reelin binds to the receptors, Disabled-1 (Dab1), an intracellular adaptor protein that binds to the cytoplasmic tails of the receptors, becomes phosphorylated on tyrosine residues, initiating a signaling cascade that includes activation of Src-family kinases and Akt. Here, we have created a line of mutant mice (Apoer2 EIG) in which the Apoer2 NFDNPVY motif has been altered to EIGNPVY to disrupt the Apoer2-Dab1 interaction to further study Reelin signaling in development and adult brain. Using primary neuronal cultures stimulated with recombinant Reelin, we find that normal Reelin signaling requires the wild-type NFDNPVY sequence and likely the interaction of Apoer2 with Dab1. Furthermore, examination of hippocampal, cortical, and cerebellar layering reveals that the NFDNPVY sequence of Apoer2 is indispensable for normal neuronal positioning during development of the brain. Adult Apoer2 EIG mice display severe abnormalities in LTP and behavior that are distinct from those observed for mice lacking Apoer2. In Apoer2 EIG slices, LTP degraded to baseline within 30 min, and this was prevented in the presence of Reelin. Together, these findings emphasize the complexity of Reelin signaling in the adult brain, which likely requires multiple adaptor protein interactions with the intracellular domain of Apoer2.","authors":"Beffert, U., Durudas, A., Weeber, EJ., Stolt, PC., Giehl, KM., Sweatt, JD., Hammer, RE., Herz, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Neurosci","volume":"26","issue":"7","page":"2041-52","pdf":null,"JrId":"5035","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30127433","title":"Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation.","abstract":"Cohesin is important for 3D genome organization. Nevertheless, even the complete removal of cohesin has surprisingly little impact on steady-state gene transcription and enhancer activity. Here we show that cohesin is required for the core transcriptional response of primary macrophages to microbial signals, and for inducible enhancer activity that underpins inflammatory gene expression. Consistent with a role for inflammatory signals in promoting myeloid differentiation of hematopoietic stem and progenitor cells (HPSCs), cohesin mutations in HSPCs led to reduced inflammatory gene expression and increased resistance to differentiation-inducing inflammatory stimuli. These findings uncover an unexpected dependence of inducible gene expression on cohesin, link cohesin with myeloid differentiation, and may help explain the prevalence of cohesin mutations in human acute myeloid leukemia.","authors":"Cuartero, S., Weiss, FD., Dharmalingam, G., Guo, Y., Ing-Simmons, E., Masella, S., Robles-Rebollo, I., Xiao, X., Wang, YF., Barozzi, I., Djeghloul, D., Amano, MT., Niskanen, H., Petretto, E., Dowell, RD., Tachibana, K., Kaikkonen, MU., Nasmyth, KA., Lenhard, B., Natoli, G., Fisher, AG., Merkenschlager, M.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Immunol","volume":"19","issue":"9","page":"932-941","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30195063","title":"Roles of ubiquitin in autophagy and cell death.","abstract":"The balance between cell survival and cell death is often lost in human pathologies such as inflammation and cancer. Autophagy plays a critical role in cell survival: essential nutrients are generated by autophagy-dependent degradation and recycling of cellular garbage. On the other hand, cell death is induced by different programs, such as apoptosis, pyroptosis, and necroptosis. Emerging evidence is revealing how cell survival and cell death pathways are coordinated to determine cell fate. For instance, posttranslational modification of proteins with ubiquitin regulates many steps of autophagy and cell death pathways. In this review article, we will discuss how the ubiquitin system influences cell death and autophagy.","authors":"G\u00f3mez-D\u00edaz, C., Ikeda, F.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Semin Cell Dev Biol","volume":"93","issue":null,"page":"125-135","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18585808","title":"Vascularization in tissue engineering.","abstract":"Tissue engineering has been an active field of research for several decades now. However, the amount of clinical applications in the field of tissue engineering is still limited. One of the current limitations of tissue engineering is its inability to provide sufficient blood supply in the initial phase after implantation. Insufficient vascularization can lead to improper cell integration or cell death in tissue-engineered constructs. This review will discuss the advantages and limitations of recent strategies aimed at enhancing the vascularization of tissue-engineered constructs. We will illustrate that combining the efforts of different research lines might be necessary to obtain optimal results in the field.","authors":"Rouwkema, J., Rivron, NC., van Blitterswijk, CA.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Trends Biotechnol","volume":"26","issue":"8","page":"434-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-10-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29804679","title":"Single-nucleus Hi-C of mammalian oocytes and zygotes.","abstract":"The 3D folding of the genome is linked to essential nuclear processes including gene expression, DNA repair, and replication. Chromatin conformation capture assays such as Hi-C are providing unprecedented insights into higher-order chromatin structure. Bulk Hi-C of millions of cells enables detection of average chromatin features at high resolution but is challenging to apply to rare cell types. This chapter describes our recently developed single-nucleus Hi-C (snHi-C) approach for detection of chromatin contacts in single nuclei of murine oocytes and one-cell embryos (zygotes). The step-by-step protocol includes isolation of these cells, extraction of nuclei, fixation, restriction digestion, ligation, and whole genome amplification. Contacts obtained by snHi-C allow detection of chromatin features including loops, topologically associating domains, and compartments when averaged over the genome. The combination of snHi-C with other single-cell techniques in these and other rare cell types will likely provide a comprehensive picture of how chromatin architecture shapes cell identity.","authors":"Gassler, J., Flyamer, IM., Tachibana, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Methods Cell Biol","volume":"144","issue":null,"page":"389-407","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30196416","title":"Generation of FLIP and FLIP-FlpE Targeting Vectors for Biallelic Conditional and Reversible Gene Knockouts in Mouse and Human Cells.","abstract":"Rapid generation of conditional knockout models in a diploid system is challenging. Recently, CRISPR-FLIP strategy has been introduced, which facilitates the generation of biallelic conditional or reversible gene knockouts in various mammalian cell lines including mouse and human pluripotent stem cells by codelivery of the CRISPR\/Cas9 system and a universal intronic cassette-FLIP and FLIP-FlpE. Here, I describe the design and cloning method of FLIP and FLIP-FlpE targeting vectors for conditional and reversible gene knockouts. This method is applicable to mouse embryonic stem cells, human induced pluripotent stem cells, and adult stem cell-derived organoids.","authors":"Koo, BK.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Methods Mol Biol","volume":"1842","issue":null,"page":"255-264","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29679094","title":"Depletion of angiotensin-converting enzyme 2 reduces brain serotonin and impairs the running-induced neurogenic response.","abstract":"Physical exercise induces cell proliferation in the adult hippocampus in rodents. Serotonin (5-HT) and angiotensin (Ang) II are important mediators of the pro-mitotic effect of physical activity. Here, we examine precursor cells in the adult brain of mice lacking angiotensin-converting enzyme (ACE) 2, and explore the effect of an acute running stimulus on neurogenesis. ACE2 metabolizes Ang II to Ang-(1-7) and is essential for the intestinal uptake of tryptophan (Trp), the 5-HT precursor. In ACE2-deficient mice, we observed a decrease in brain 5-HT levels and no increase in the number of BrdU-positive cells following exercise. Targeting the Ang II\/AT1 axis by blocking the receptor, or experimentally increasing Trp\/5-HT levels in the brain of ACE2-deficient mice, did not rescue the running-induced effect. Furthermore, mice lacking the Ang-(1-7) receptor, Mas, presented a normal neurogenic response to exercise. Our results identify ACE2 as a novel factor required for exercise-dependent modulation of adult neurogenesis and essential for 5-HT metabolism.","authors":"Klempin, F., Mosienko, V., Matthes, S., Villela, DC., Todiras, M., Penninger, JM., Bader, M., Santos, RAS., Alenina, N.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell Mol Life Sci","volume":"75","issue":"19","page":"3625-3634","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11905810","title":"Knockout mice: a paradigm shift in modern immunology.","abstract":"In the past decade, advances in genetic engineering and mouse knockout technology have transformed our understanding of the immune system. In particular, new perspectives on T-cell development, co-stimulation and activation have emerged from the study of single and multiple gene-knockout animals, as well as from conditional knockout and 'knock-in' mutants. Analysis of these animals has clarified important intracellular signalling pathways and has shed light on the regulatory mechanisms that govern normal immune responses and autoimmunity.","authors":"Mak, TW., Penninger, JM., Ohashi, PS.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Rev Immunol","volume":"1","issue":"1","page":"11-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30254343","title":"A core problem in nuclear assembly.","abstract":null,"authors":"Samwer, M., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"561","issue":"7724","page":"467-468","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19240133","title":"Coherent but overlapping expression of microRNAs and their targets during vertebrate development.","abstract":"MicroRNAs (miRNAs) are small noncoding RNAs that direct post-transcriptional repression of protein-coding genes. In vertebrates, each highly conserved miRNA typically regulates hundreds of target mRNAs. However, the precise relationship between expression of the miRNAs and that of their targets has remained unclear, in part because of the scarcity of quantitative expression data at cellular resolution. Here we report quantitative analyses of mRNA levels in miRNA-expressing cells of the zebrafish embryo, capturing entire miRNA expression domains, purified to cellular resolution using fluorescent-activated cell sorting (FACS). Focus was on regulation by miR-206 and miR-133 in the developing somites and miR-124 in the developing central nervous system. Comparison of wild-type embryos and those lacking miRNAs revealed predicted targets that responded to the miRNAs and distinguished miRNA-mediated mRNA destabilization from other regulatory effects. For all three miRNAs examined, expression of the miRNAs and that of their predicted targets usually overlapped. A few targets were expressed at higher levels in miRNA-expressing cells than in the rest of the embryo, demonstrating that miRNA-mediated repression can act in opposition to other regulatory processes. However, for most targets expression was lower in miRNA-expressing cells than in the rest of the embryo, indicating that miRNAs usually operate in concert with the other regulatory machinery of the cell.","authors":"Shkumatava, A., Stark, A., Sive, H., Bartel, DP.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genes Dev","volume":"23","issue":"4","page":"466-81","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29735715","title":"ZNRF3 functions in mammalian sex determination by inhibiting canonical WNT signaling.","abstract":"Mammalian sex determination is controlled by the antagonistic interactions of two genetic pathways: The SRY-SOX9-FGF9 network promotes testis determination partly by opposing proovarian pathways, while RSPO1\/WNT-\u03b2-catenin\/FOXL2 signals control ovary development by inhibiting SRY-SOX9-FGF9. The molecular basis of this mutual antagonism is unclear. Here we show that ZNRF3, a WNT signaling antagonist and direct target of RSPO1-mediated inhibition, is required for sex determination in mice. XY mice lacking ZNRF3 exhibit complete or partial gonadal sex reversal, or related defects. These abnormalities are associated with ectopic WNT\/\u03b2-catenin activity and reduced <i>Sox9<\/i> expression during fetal sex determination. Using exome sequencing of individuals with 46,XY disorders of sex development, we identified three human <i>ZNRF3<\/i> variants in very rare cases of XY female presentation. We tested two missense variants and show that these disrupt ZNRF3 activity in both human cell lines and zebrafish embryo assays. Our data identify a testis-determining function for ZNRF3 and indicate a mechanism of direct molecular interaction between two mutually antagonistic organogenetic pathways.","authors":"Harris, A., Siggers, P., Corrochano, S., Warr, N., Sagar, D., Grimes, DT., Suzuki, M., Burdine, RD., Cong, F., Koo, BK., Clevers, H., St\u00e9vant, I., Nef, S., Wells, S., Brauner, R., Ben Rhouma, B., Belguith, N., Eozenou, C., Bignon-Topalovic, J., Bashamboo, A., McElreavey, K., Greenfield, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Proc Natl Acad Sci U S A","volume":"115","issue":"21","page":"5474-5479","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29671387","title":"Positioning Europe for the EPITRANSCRIPTOMICS challenge.","abstract":"The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20\u00a0years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the ~150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.","authors":"Jantsch, MF., Quattrone, A., O'Connell, M., Helm, M., Frye, M., Macias-Gonzales, M., Ohman, M., Ameres, S., Willems, L., Fuks, F., Oulas, A., Vanacova, S., Nielsen, H., Bousquet-Antonelli, C., Motorin, Y., Roignant, JY., Balatsos, N., Dinnyes, A., Baranov, P., Kelly, V., Lamm, A., Rechavi, G., Pelizzola, M., Liepins, J., Holodnuka Kholodnyuk, I., Zammit, V., Ayers, D., Drablos, F., Dahl, JA., Bujnicki, J., Jeronimo, C., Almeida, R., Neagu, M., Costache, M., Bankovic, J., Banovic, B., Kyselovic, J., Valor, LM., Selbert, S., Pir, P., Demircan, T., Cowling, V., Sch\u00e4fer, M., Rossmanith, W., Lafontaine, D., David, A., Carre, C., Lyko, F., Schaffrath, R., Schwartz, S., Verdel, A., Klungland, A., Purta, E., Timotijevic, G., Cardona, F., Davalos, A., Ballana, E., O Carroll, D., Ule, J., Fray, R.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"RNA Biol","volume":"15","issue":"6","page":"829-831","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-11-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16361109","title":"Structural analysis of the ZEN-4\/CeMKLP1 motor domain and its interaction with microtubules.","abstract":"The centralspindlin complex is required for the assembly and maintenance of the central spindle during late anaphase and the completion of cytokinesis. It is composed of two copies each of the kinesin-like protein ZEN-4, a Caenorhabditis elegans MKLP-1 (Kinesin-6 family), and the RhoGAP CYK-4. By using cryo-electron microscopy and helical 3D reconstruction, we are investigating the structural features of the interactions between monomeric and dimeric motor domain constructs of ZEN-4 and microtubules. We have calculated helically averaged 3D maps of microtubules decorated with ZEN-4 motor domain in the presence of AMP-PNP, ADP, ADP-AlF(4)(-), and nucleotide-free conditions. We used statistical difference mapping to compare these maps among each other and to related maps obtained from microtubules decorated with a well-characterized Kinesin-1 motor domain from Neurospora crassa. Thereby, we found distinct structural features in microtubule-ZEN-4 complexes that may directly relate to the functional properties of ZEN-4 and centralspindlin. Furthermore, we investigated the location, structure, and function of a highly conserved extension of approximately 50 residues unique to the Kinesin-6 subfamily, located in the motor core loop6\/beta4 region.","authors":"Hizlan, D., Mishima, M., Tittmann, P., Gross, H., Glotzer, M., Hoenger, A.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Struct Biol","volume":"153","issue":"1","page":"73-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30389916","title":"Parvalbumin<sup>+<\/sup> interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus.","abstract":"Parvalbumin-positive (PV<sup>+<\/sup>) GABAergic interneurons in hippocampal microcircuits are thought to play a key role in several higher network functions, such as feedforward and feedback inhibition, network oscillations, and pattern separation. Fast lateral inhibition mediated by GABAergic interneurons may implement a winner-takes-all mechanism in the hippocampal input layer. However, it is not clear whether the functional connectivity rules of granule cells (GCs) and interneurons in the dentate gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings from up to seven GCs and up to four PV<sup>+<\/sup> interneurons in the dentate gyrus, we find that connectivity is structured in space, synapse-specific, and enriched in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV<sup>+<\/sup> interneuron) is\u2009~\u200910-times more abundant than recurrent inhibition (in which a GC inhibits itself). Thus, unique connectivity rules may enable the dentate gyrus to perform specific higher-order computations.","authors":"Espinoza, C., Guzman, SJ., Zhang, X., Jonas, P.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Nat Commun","volume":"9","issue":"1","page":"4605","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2476680","title":"Adult follow-up of the acquired aphasia-epilepsy syndrome in childhood. Report of 7 cases.","abstract":"The authors report at adult age 7 patients (6 men, one woman) with the syndrome of \"acquired aphasia-epilepsy\", 6 of which had been previously studied as children. The results of the language, neuropsychological and socio-educational evaluation detailed many years after the onset of the aphasia are the subject of this report. One man has recovered completely, one has a normal oral language but is severely dyslexic, one has recovered normal comprehension but has severe expressive language problems. Four have absent language comprehension and lack of expressive speech, and only one of them has learned and is using sign language with some efficiency. None has developed functional written language. Attempts to offer a substitutive language to children with prolonged inability to understand and use oral language appears important but is fraught with problems. Although there are no conclusive data about the role of the continuous paroxysmal EEG discharges and the effect of their suppression with drug treatment on the prognosis of the aphasia, the definite fluctuations of the aphasia in some cases, the isolated recent case reports of definitive improvement with drug treatment justify further trials in this potentially severe and chronic condition.","authors":"Deonna, T., Peter, C., Ziegler, AL.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Neuropediatrics","volume":"20","issue":"3","page":"132-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1989-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11850619","title":"Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component.","abstract":"Post-translational modification of histone tails is thought to modulate higher-order chromatin structure. Combinations of modifications including acetylation, phosphorylation and methylation have been proposed to provide marks recognized by specific proteins. This is exemplified, in both mammalian cells and fission yeast, by transcriptionally silent constitutive pericentric heterochromatin. Such heterochromatin contains histones that are generally hypoacetylated and methylated by Suv39h methyltransferases at lysine 9 of histone H3 (H3-K9). Each of these modification states has been implicated in the maintenance of HP1 protein-binding at pericentric heterochromatin, in transcriptional silencing and in centromere function. In particular, H3-K9 methylation is thought to provide a marking system for the establishment and maintenance of stably repressed regions and heterochromatin subdomains. To address the question of how these two types of modifications, as well as other unidentified parameters, function to maintain pericentric heterochromatin, we used a combination of histone deacetylase inhibitors, RNAse treatments and an antibody raised against methylated branched H3-K9 peptides. Our results show that both H3-K9 acetylation and methylation can occur on independent sets of H3 molecules in pericentric heterochromatin. In addition, we identify an RNA- and histone modification-dependent structure that brings methylated H3-K9 tails together in a specific configuration required for the accumulation of HP1 proteins in these domains.","authors":"Maison, C., Bailly, D., Peters, AH., Quivy, JP., Roche, D., Taddei, A., Lachner, M., Jenuwein, T., Almouzni, G.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nat Genet","volume":"30","issue":"3","page":"329-34","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2002-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30542177","title":"Debate ethics of embryo models from stem cells.","abstract":null,"authors":"Rivron, N., Pera, M., Rossant, J., Martinez Arias, A., Zernicka-Goetz, M., Fu, J., van den Brink, S., Bredenoord, A., Dondorp, W., de Wert, G., Hyun, I., Munsie, M., Isasi, R.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"564","issue":"7735","page":"183-185","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19235923","title":"Induction of myeloid-derived suppressor cells by tumor exosomes.","abstract":"Myeloid-derived suppressor cells (MDSCs) promote tumor progression. The mechanisms of MDSC development during tumor growth remain unknown. Tumor exosomes (T-exosomes) have been implicated to play a role in immune regulation, however the role of exosomes in the induction of MDSCs is unclear. Our previous work demonstrated that exosomes isolated from tumor cells are taken up by bone marrow myeloid cells. Here, we extend those findings showing that exosomes isolated from T-exosomes switch the differentiation pathway of these myeloid cells to the MDSC pathway (CD11b(+)Gr-1(+)). The resulting cells exhibit MDSC phenotypic and functional characteristics including promotion of tumor growth. Furthermore, we demonstrated that in vivo MDSC mediated promotion of tumor progression is dependent on T-exosome prostaglandin E2 (PGE2) and TGF-beta molecules. T-exosomes can induce the accumulation of MDSCs expressing Cox2, IL-6, VEGF, and arginase-1. Antibodies against exosomal PGE2 and TGF-beta block the activity of these exosomes on MDSC induction and therefore attenuate MDSC-mediated tumor-promoting ability. Exosomal PGE2 and TGF-beta are enriched in T-exosomes when compared with exosomes isolated from the supernatants of cultured tumor cells (C-exosomes). The tumor microenvironment has an effect on the potency of T-exosome mediated induction of MDSCs by regulating the sorting and the amount of exosomal PGE2 and TGF-beta available. Together, these findings lend themselves to developing specific targetable therapeutic strategies to reduce or eliminate MDSC-induced immunosuppression and hence enhance host antitumor immunotherapy efficacy.","authors":"Xiang, X., Poliakov, A., Liu, C., Liu, Y., Deng, ZB., Wang, J., Cheng, Z., Shah, SV., Wang, GJ., Zhang, L., Grizzle, WE., Mobley, J., Zhang, HG.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Int J Cancer","volume":"124","issue":"11","page":"2621-33","pdf":null,"JrId":"4284","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30472189","title":"Nucleosome Turnover Regulates Histone Methylation Patterns over the Genome.","abstract":"Recent studies have indicated that nucleosome turnover is rapid, occurring several times per cell cycle. To access the effect of nucleosome turnover on the\u00a0epigenetic landscape, we investigated H3K79 methylation, which is produced by a single methyltransferase (Dot1l) with no known demethylase. Using chemical-induced proximity (CIP), we find that the valency of H3K79 methylation (mono-, di-, and tri-) is determined by nucleosome turnover rates. Furthermore, propagation of this mark is predicted by nucleosome turnover simulations over the genome and accounts for the asymmetric distribution of H3K79me toward the transcriptional unit. More broadly, a meta-analysis of other conserved histone modifications demonstrates that nucleosome turnover models predict both valency and chromosomal propagation of methylation marks. Based on data from worms, flies, and mice, we propose that the turnover of modified nucleosomes is a general means of propagation of epigenetic marks and a determinant of methylation valence.","authors":"Chory, EJ., Calarco, JP., Hathaway, NA., Bell, O., Neel, DS., Crabtree, GR.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mol Cell","volume":"73","issue":"1","page":"61-72.e3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2458954","title":"Expression of c-src and c-abl in embryonal carcinoma cells and adult mouse tissues.","abstract":"We have studied the expression of c-src and c-abl proto-oncogenes in early mouse development using embryonal carcinoma (EC) cells as a model system, and compared this to the expression pattern in adult tissues. In all three EC lines tested (F9, PC13, and P19), c-src and c-abl mRNA can be detected. When F9 and PC13 are induced to differentiate they form endodermal cells characteristic of the early embryo, and we found no change in c-src or c-abl expression. In contrast, P19 cells showed increased levels of both mRNAs both mRNAs when induced to differentiate along the neural pathway by retinoic acid, whereas differentiation along the muscle pathway by dimethyl sulfoxide resulted in decreased levels of c-abl expression. These results are consistent with the idea that c-src and c-abl have important functions in the differentiation of the cell types of the later embryo, but not in those of the early embryo.","authors":"Boulter, CA., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Exp Cell Res","volume":"179","issue":"1","page":"214-21","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1988-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30999204","title":"Identification and expression of microRNAs in european eels Anguilla anguilla from two natural sites with different pollution levels.","abstract":"MicroRNAs (miRNAs) are a class of small non-coding RNA that control multiple biological processes through negative post-transcriptional regulation of gene expression. Recently a role of miRNAs in the response of aquatic organisms to environmental toxicants emerged. Toxicant-induced changes in miRNA expression might then represent novel biomarkers to evaluate the health status of these organisms. In this study, we aimed to identify the miRNA repertoire in the liver of the European eel Anguilla anguilla and to compare their differential expression between a polluted site located in the Gironde Estuary and a pristine site in Arcachon Bay (France). A total of 299 mature miRNAs were identified. In polluted water, 19 miRNAs were up-regulated and 22 were down-regulated. We predicted that these differentially expressed miRNAs could target 490 genes that were involved in ribosome biogenesis, response to hormones, response to chemical and chromatin modification. Moreover, we observed only few examples (29) of negative correlation between the expression levels of miRNAs and their targets suggesting that, in the system studied, miRNAs might not only regulate gene expression directly by degrading mRNA but also by inhibiting protein translation or by regulating other epigenetic processes. This study is the first example of in situ investigation of the role of miRNAs in the response of a fish species to water quality. Our findings provide new insights into the involvement of epigenetic mechanisms in the response of animals chronically exposed to pollution and pave the way for the utilization of miRNAs in aquatic ecotoxicology.","authors":"Bertucci, A., Pierron, F., Ye, T., Gonzalez, P., Couture, P., Baudrimont, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Environ Pollut","volume":"250","issue":"","page":"274-283","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30909163","title":"Gene expression profiling of ovary identified eggshell proteins regulated by 20-hydroxyecdysone in Bactrocera dorsalis.","abstract":"The oriental fruit fly, Bactrocera dorsalis, is one of the most destructive pests worldwide. The frequent use of chemical insecticides has led B. dorsalis to develop resistance to many insecticides in recent decades. New high-throughput-sequenced transcriptomes, as well as genomes, have revealed a large number of reference genes for functional target identification. Here, we performed digital gene expression profiling of ovary and testis of B. dorsalis adults. Various genes were identified to be highly expressed in B. dorsalis ovary. The genes encoding components of eggshell, vitelline membrane proteins (Vmps) and chorion-related proteins, were identified to be tissue-specifically expressed in ovary. Five cytochrome P450 genes were also identified to be highly expressed in ovary. Three of them were ecdysone synthesis pathway genes indicating the ovary as a potential synthesis site of female. The up-regulated expression of Vmps by exogenous 20-hydroxyecdysone implied the hormonal regulation of eggshell formation during ovarian development. Many other genes with potential functions in ovarian development were also identified, including vitellogenin receptor, insulin receptor, NASP protein, and odorant binding protein. These findings should promote our understanding of the regulation of vitellogenesis and eggshell formation and enable exploration of potentially novel pest control targets.","authors":"Wei, D., Zhang, YX., Liu, YW., Li, WJ., Chen, ZX., Smagghe, G., Wang, JJ.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Comp Biochem Physiol Part D Genomics Proteomics","volume":"30","issue":"","page":"206-216","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11756443","title":"Structure and function of threonine synthase from yeast.","abstract":"Threonine synthase catalyzes the final step of threonine biosynthesis, the pyridoxal 5'-phosphate (PLP)-dependent conversion of O-phosphohomoserine into threonine and inorganic phosphate. Threonine is an essential nutrient for mammals, and its biosynthetic machinery is restricted to bacteria, plants, and fungi; therefore, threonine synthase represents an interesting pharmaceutical target. The crystal structure of threonine synthase from Saccharomyces cerevisiae has been solved at 2.7 A resolution using multiwavelength anomalous diffraction. The structure reveals a monomer as active unit, which is subdivided into three distinct domains: a small N-terminal domain, a PLP-binding domain that covalently anchors the cofactor and a so-called large domain, which contains the main of the protein body. All three domains show the typical open alpha\/beta architecture. The cofactor is bound at the interface of all three domains, buried deeply within a wide canyon that penetrates the whole molecule. Based on structural alignments with related enzymes, an enzyme-substrate complex was modeled into the active site of yeast threonine synthase, which revealed essentials for substrate binding and catalysis. Furthermore, the comparison with related enzymes of the beta-family of PLP-dependent enzymes indicated structural determinants of the oligomeric state and thus rationalized for the first time how a PLP enzyme acts in monomeric form.","authors":"Garrido-Franco, M., Ehlert, S., Messerschmidt, A., Marinkovic', S., Huber, R., Laber, B., Bourenkov, GP., Clausen, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Biol Chem","volume":"277","issue":"14","page":"12396-405","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30910826","title":"Transient localization of the Arp2\/3 complex initiates neuronal dendrite branching <i>in vivo<\/i>.","abstract":"The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved <i>in vivo<\/i> through a dynamic process of <i>de novo<\/i> branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through <i>in vivo<\/i> time-lapse imaging of the subcellular localization of actin during the process of branching of <i>Drosophila<\/i> larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2\/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2\/3 component marks the site of branchlet initiation <i>in vivo<\/i> These data position the activation of Arp2\/3 as an early hub for the initiation of branchlet formation.","authors":"St\u00fcrner, T., Tatarnikova, A., Mueller, J., Schaffran, B., Cuntz, H., Zhang, Y., Nemethova, M., Bogdan, S., Small, V., Tavosanis, G.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Development","volume":"146","issue":"7","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9219698","title":"Mating type switching in yeast controlled by asymmetric localization of ASH1 mRNA.","abstract":"Cell divisions that produce progeny differing in their patterns of gene expression are key to the development of multicellular organisms. In the budding yeast Saccharomyces cerevisiae, mother cells but not daughter cells can switch mating type because they selectively express the HO endonuclease gene. This asymmetry is due to the preferential accumulation of an unstable transcriptional repressor protein, Ash1p, in daughter cell nuclei. Here it is shown that ASH1 messenger RNA (mRNA) preferentially accumulates in daughter cells by a process that is dependent on actin and myosin. A cis-acting element in the 3'-untranslated region of ASH1 mRNA is sufficient to localize a chimeric RNA to daughter cells. These results suggest that localization of mRNA may have been an early property of the eukaryotic lineage.","authors":"Long, RM., Singer, RH., Meng, X., Gonzalez, I., Nasmyth, K., Jansen, RP.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Science","volume":"277","issue":"5324","page":"383-7","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30825599","title":"Revealing shared differential co-expression profiles in rice infected by virus from reoviridae and sequiviridae group.","abstract":"Differential co-expression is a cutting-edge approach to analyze gene expression data and identify both shared and divergent expression patterns. The availability of high-throughput gene expression datasets and efficient computational approaches have unfolded the opportunity to a systems level understanding of functional genomics of different stresses with respect to plants. We performed the meta-analysis of the available microarray data for reoviridae and sequiviridae infection in rice with the aim to identify the shared gene co-expression profile. The microarray data were downloaded from ArrayExpress and analyzed through a modified Weighted Gene Co-expression Network Analysis (WGCNA) protocol. WGCNA clustered the genes based on the expression intensities across the samples followed by identification of modules, eigengenes, principal components, topology overlap, module membership and module preservation. The module preservation analysis identified 4 modules; salmon (638 genes), midnightblue (584 genes), lightcyan (686 genes) and red (562 genes), which are highly preserved in both the cases. The networks in case of reoviridae infection showed neatly packed clusters whereas, in sequiviridae, the clusters were loosely connected which is due to the differences in the correlation values. We also identified 83 common transcription factors targeting the hub genes from all the identified modules. This study provides a coherent view of the comparative aspect of the expression of common genes involved in different virus infections which may aid in the identification of novel targets and development of new intervention strategy against the virus.","authors":"Sahu, J., Panda, D., Baruah, G., Patar, L., Sen, P., Borah, BK., Modi, MK.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Gene","volume":"698","issue":"","page":"82-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2452106","title":"Developmental regulation of micro-injected histone genes in sea urchin embryos.","abstract":"The developmental behavior of cloned histone genes of Psammechinus miliaris was studied by injection into eggs of two related sea urchin species followed by fertilization. All five early histone genes were faithfully expressed in early blastula embryos as shown by SP6 RNA mapping. A 5-10 times lower expression rate was estimated for the injected early H2A gene from its competition strength with the endogenous gene. Transcripts of this early H2A gene accumulated during the cleavage stages and decayed in late embryos in parallel with the endogenous early H2A mRNA. However, an introduced late H2B gene was incorrectly regulated, since its mRNA level did not increase from the blastula to the gastrula stage. The sperm H2B-1 gene, normally inactive in development, was 80 times less well expressed than the early H2A gene in transformed blastulae. A fusion gene with the early H2A promoter linked to the structural sperm H2B gene was, however, efficiently transcribed suggesting that all essential information for an early expression pattern is contained within the 5' region of the early H2A gene.","authors":"Vitelli, L., Kemler, I., Lauber, B., Birnstiel, ML., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"Dev Biol","volume":"127","issue":"1","page":"54-63","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"1988-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19229881","title":"In vitro regulation of proliferation and differentiation within a postnatal growth plate of the cranial base by parathyroid hormone-related peptide (PTHrP).","abstract":"Parathyroid hormone-related peptide (PTHrP) is known to be an important regulator of chondrocyte differentiation in embryonic growth plates, but little is known of its role in postnatal growth plates. The present study explores the role of PTHrP in regulating postnatal chondrocyte differentiation using a novel in vitro organ culture model based on the ethmoidal growth plate of the cranial base taken from the postnatal day 10 mouse. In vitro the ethmoidal growth plate continued to mineralize and the chondrocytes progressed to hypertrophy, as observed in vivo, but the proliferative zone was not maintained. Treatment with PTHrP inhibited mineralization and reduced alkaline phosphatase (ALP) activity in the hypertrophic zone in the ethmoidal growth plates grown ex vivo, and also increased the proliferation of non-hypertrophic chondrocytes. In addition, exogenous PTHrP reduced the expression of genes associated with terminal differentiation: type X collagen, Runx2, and ALP, as well as the PTH\/PTHrP receptor (PPR). Activation of the protein kinase A pathway using 8-Br-cAMP mimicked some of these pro-proliferative\/anti-differentiative effects of PTHrP. PTHrP and PPR were found to be expressed within the ethmoidal growth plate using semi-quantitative PCR, and in other cranial growth plates such as the spheno-occipital and pre-sphenoidal synchondroses. These results provide the first functional evidence that PTHrP regulates proliferation and differentiation within the postnatal, cranial growth plate. J. Cell. Physiol. 219: 688-697, 2009. (c) 2009 Wiley-Liss, Inc.","authors":"Wealthall, RJ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Physiol","volume":"219","issue":"3","page":"688-97","pdf":null,"JrId":"4586","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32270030","title":"Parallel PRC2\/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells.","abstract":"The transcriptional repressors Polycomb repressive complex 1 (PRC1) and PRC2 are required to maintain cell fate during embryonic development. PRC1 and PRC2 catalyze distinct histone modifications, establishing repressive chromatin at shared targets. How PRC1, which consists of canonical PRC1 (cPRC1) and variant PRC1 (vPRC1) complexes, and PRC2 cooperate to silence genes and support mouse embryonic stem cell (mESC) self-renewal is unclear. Using combinatorial genetic perturbations, we show that independent pathways of cPRC1 and vPRC1 are responsible for maintenance of H2A monoubiquitylation and silencing of shared target genes. Individual loss of PRC2-dependent cPRC1 or PRC2-independent vPRC1 disrupts only one pathway and does not impair mESC self-renewal capacity. However, loss of both pathways leads to mESC differentiation and activation of a subset of lineage-specific genes co-occupied by relatively high levels of PRC1\/PRC2. Thus, parallel pathways explain the differential requirements for PRC1 and PRC2 and provide robust silencing of lineage-specific genes.","authors":"Zepeda-Martinez, JA., Pribitzer, C., Wang, J., Bsteh, D., Golumbeanu, S., Zhao, Q., Burkard, TR., Reichholf, B., Rhie, SK., Jude, J., Moussa, HF., Zuber, J., Bell, O.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Adv","volume":"6","issue":"14","page":"eaax5692","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28008086","title":"Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes.","abstract":"We introduce MINFLUX, a concept for localizing photon emitters in space. By probing the emitter with a local intensity minimum of excitation light, MINFLUX minimizes the fluorescence photons needed for high localization precision. In our experiments, 22 times fewer fluorescence photons are required as compared to popular centroid localization. In superresolution microscopy, MINFLUX attained ~1-nm precision, resolving molecules only 6 nanometers apart. MINFLUX tracking of single fluorescent proteins increased the temporal resolution and the number of localizations per trace by a factor of 100, as demonstrated with diffusing 30<i>S<\/i> ribosomal subunits in living <i>Escherichia coli<\/i> As conceptual limits have not been reached, we expect this localization modality to break new ground for observing the dynamics, distribution, and structure of macromolecules in living cells and beyond.","authors":"Balzarotti, F., Eilers, Y., Gwosch, KC., Gynn\u00e5, AH., Westphal, V., Stefani, FD., Elf, J., Hell, SW.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Science","volume":"355","issue":"6325","page":"606-612","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37715641","title":"Improving single cell proteomics experiments: how can we best utilize latest-generation data acquisition and MS instrument architecture?","abstract":null,"authors":"Matzinger, M., Mechtler, K.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Expert Rev Proteomics","volume":null,"issue":null,"page":"1-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30679653","title":"A role for miR-132 in learned safety.","abstract":"Learned safety is a fear inhibitory mechanism, which regulates fear responses, promotes episodes of safety and generates positive affective states. Despite its potential as experimental model for several psychiatric illnesses, including post-traumatic stress disorder and depression, the molecular mechanisms of learned safety remain poorly understood, We here investigated the molecular mediators of learned safety, focusing on the characterization of miRNA expression in the basolateral amygdala (BLA). Comparing levels of 22 miRNAs in learned safety and learned fear trained mice, six safety-related miRNAs, including three members of the miR-132\/-212 family, were identified. A gain-of-function approach based upon in-vivo transfection of a specific miRNA mimic, and miR-132\/212 knock-out mice as loss-of-function tool were used in order to determine the relevance of miR-132 for learned safety at the behavioral and the neuronal functional levels. Using a designated bioinformatic approach, PTEN and GAT1 were identified as potential novel miR-132 target genes and further experimentally validated. We here firstly provide evidence for a regulation of amygdala miRNA expression in learned safety and propose miR-132 as signature molecule to be considered in future preclinical and translational approaches testing the transdiagnostic relevance of learned safety as intermediate phenotype in fear and stress-related disorders.","authors":"Ronovsky, M., Zambon, A., Cicvaric, A., Boehm, V., Hoesel, B., Moser, BA., Yang, J., Schmid, JA., Haubensak, WE., Monje, FJ., Pollak, DD.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Sci Rep","volume":"9","issue":"1","page":"528","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31378680","title":"Protein Kinase C\u03b9 and Wnt\/\u03b2-Catenin Signaling: Alternative Pathways to Kras\/Trp53-Driven Lung Adenocarcinoma.","abstract":"We report that mouse LSL-Kras<sup>G12D<\/sup>;Trp53<sup>fl\/fl<\/sup> (KP)-mediated lung adenocarcinoma (LADC) tumorigenesis can proceed through both PKC\u03b9-dependent and PKC\u03b9-independent pathways. The predominant pathway involves PKC\u03b9-dependent transformation of bronchoalveolar stem cells (BASCs). However, KP mice harboring conditional knock out Prkci alleles (KPI mice) develop LADC tumors through PKC\u03b9-independent transformation of Axin2<sup>+<\/sup> alveolar type 2 (AT2) stem cells. Transformed growth of KPI, but not KP, tumors is blocked by Wnt pathway inhibition in\u00a0vitro and in\u00a0vivo. Furthermore, a KPI-derived genomic signature predicts sensitivity of human LADC cells to Wnt inhibition, and identifies a distinct subset of primary LADC tumors exhibiting a KPI-like genotype. Thus, LADC can develop through both PKC\u03b9-dependent and PKC\u03b9-independent pathways, resulting in tumors exhibiting distinct oncogenic signaling and pharmacologic vulnerabilities.","authors":"Yin, N., Liu, Y., Khoor, A., Wang, X., Thompson, EA., Leitges, M., Justilien, V., Weems, C., Murray, NR., Fields, AP.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cancer Cell","volume":"36","issue":"2","page":"156-167.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31189595","title":"Apelin protects against abdominal aortic aneurysm and the therapeutic role of neutral endopeptidase resistant apelin analogs.","abstract":"Abdominal aortic aneurysm (AAA) remains the second most frequent vascular disease with high mortality but has no approved medical therapy. We investigated the direct role of apelin (APLN) in AAA and identified a unique approach to enhance APLN action as a therapeutic intervention for this disease. Loss of APLN potentiated angiotensin II (Ang II)-induced AAA formation, aortic rupture, and reduced survival. Formation of AAA was driven by increased smooth muscle cell (SMC) apoptosis and oxidative stress in <i>Apln<\/i> <sup>-\/y<\/sup> aorta and in APLN-deficient cultured murine and human aortic SMCs. Ang II-induced myogenic response and hypertension were greater in <i>Apln<\/i> <sup>-\/y<\/sup> mice, however, an equivalent hypertension induced by phenylephrine, an \u03b1-adrenergic agonist, did not cause AAA or rupture in <i>Apln<\/i> <sup>-\/y<\/sup> mice. We further identified Ang converting enzyme 2 (ACE2), the major negative regulator of the renin-Ang system (RAS), as an important target of APLN action in the vasculature. Using a combination of genetic, pharmacological, and modeling approaches, we identified neutral endopeptidase (NEP) that is up-regulated in human AAA tissue as a major enzyme that metabolizes and inactivates APLN-17 peptide. We designed and synthesized a potent APLN-17 analog, APLN-NMeLeu9-A2, that is resistant to NEP cleavage. This stable APLN analog ameliorated Ang II-mediated adverse aortic remodeling and AAA formation in an established model of AAA, high-fat diet (HFD) in <i>Ldlr<\/i> <sup>-\/-<\/sup> mice. Our findings define a critical role of APLN in AAA formation through induction of ACE2 and protection of vascular SMCs, whereas stable APLN analogs provide an effective therapy for vascular diseases.","authors":"Wang, W., Shen, M., Fischer, C., Basu, R., Hazra, S., Couvineau, P., Paul, M., Wang, F., Toth, S., Mix, DS., Poglitsch, M., Gerard, NP., Bouvier, M., Vederas, JC., Penninger, JM., Kassiri, Z., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Proc Natl Acad Sci U S A","volume":"116","issue":"26","page":"13006-13015","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11717312","title":"Hormone-sensitive lipase deficiency in mice causes diglyceride accumulation in adipose tissue, muscle, and testis.","abstract":"Hormone-sensitive lipase (HSL) is expressed predominantly in white and brown adipose tissue where it is believed to play a crucial role in the lipolysis of stored triglycerides (TG), thereby providing the body with energy substrate in the form of free fatty acids (FFA). From in vitro assays, HSL is known to hydrolyze TG, diglycerides (DG), cholesteryl esters, and retinyl esters. In the current study we have generated HSL knock-out mice and demonstrate three lines of evidence that HSL is instrumental in the catabolism of DG in vivo. First, HSL deficiency in mice causes the accumulation of DG in white adipose tissue, brown adipose tissue, skeletal muscle, cardiac muscle, and testis. Second, when tissue extracts were used in an in vitro lipase assay, a reduced FFA release and the accumulation of DG was observed in HSL knock-out mice which did not occur when tissue extracts from control mice were used. Third, in vitro lipolysis experiments with HSL-deficient fat pads demonstrated that the isoproterenol-stimulated release of FFA was decreased and DG accumulated intracellularly resulting in the essential absence of the isoproterenol-stimulated glycerol formation typically observed in control fat pads. Additionally, the absence of HSL in white adipose tissue caused a shift of the fatty acid composition of the TG moiety toward increased long chain fatty acids implying a substrate specificity of the enzyme in vivo. From these in vivo results we conclude that HSL is the rate-limiting enzyme for the cellular catabolism of DG in adipose tissue and muscle.","authors":"Haemmerle, G., Zimmermann, R., Hayn, M., Theussl, C., Waeg, G., Wagner, E., Sattler, W., Magin, TM., Wagner, EF., Zechner, R.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Biol Chem","volume":"277","issue":"7","page":"4806-15","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34009726","title":"Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users.","abstract":"Proteomics research infrastructures and core facilities within the Core for Life alliance advocate for community policies for quality control to ensure high standards in proteomics services.","authors":"Chiva, C., Mendes Maia, T., Panse, C., Stejskal, K., Douch\u00e9, T., Matondo, M., Loew, D., Helm, D., Rettel, M., Mechtler, K., Impens, F., Nanni, P., Shevchenko, A., Sabid\u00f3, E.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"EMBO Rep","volume":"22","issue":"6","page":"e52626","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22702840","title":"Plasmonics meets far-field optical nanoscopy.","abstract":"Plasmonics and near-field optical nanoscopy both deal with expanding optics into the subwavelength regime. However, these two fields have so far followed parallel paths of development and only recently have researchers started to explore combinations of their concepts with potential synergy. In this Perspective, we provide an up-to-date summary of the successful combinations reported and give insight into some new possibilities.","authors":"Balzarotti, F., Stefani, FD.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"ACS Nano","volume":"6","issue":"6","page":"4580-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16360688","title":"Control of Shugoshin function during fission-yeast meiosis.","abstract":"Meiosis consists of a single round of DNA replication followed by two consecutive nuclear divisions. During the first division (MI), sister kinetochores must orient toward the same pole to favor reductional segregation. Correct chromosome segregation during the second division (MII) requires the retention of centromeric cohesion until anaphase II. The spindle checkpoint protein Bub1 is essential for both processes in fission yeast . When bub1 is deleted, the Shugoshin protein Sgo1 is not recruited to centromeres, cohesin Rec8 does not persist at centromeres, and sister-chromatid cohesion is lost by the end of MI. Deletion of bub1 also affects kinetochore orientation because sister centromeres can move to opposite spindle poles in approximately 30% of MI divisions. We show here that these two functions are separable within the Bub1 protein. The N terminus of Bub1 is necessary and sufficient for Sgo1 targeting to centromeres and the protection of cohesion, whereas the C-terminal kinase domain acts together with Sgo2, the second fission-yeast Shugoshin protein, to promote sister-kinetochore co-orientation during MI. Additional analyses suggest that the protection of centromeric cohesion does not operate when sister kinetochores attach to opposite spindle poles during MI. Sgo1-mediated protection of centromere cohesion might therefore be regulated by the mode of kinetochore attachment.","authors":"Vaur, S., Cubizolles, F., Plane, G., Genier, S., Rabitsch, PK., Gregan, J., Nasmyth, K., Vanoosthuyse, V., Hardwick, KG., Javerzat, JP.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"24","page":"2263-70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30351950","title":"apQuant: Accurate Label-Free Quantification by Quality Filtering.","abstract":"Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results. We employ Percolator to assess the quality of quantified peptides. This allows to extract accurate and reliable quantitative results based on false discovery rate. Benchmarking our approach on previously published public data shows that it considerably outperforms currently available algorithms. apQuant is available free of charge as a node for Proteome Discoverer.","authors":"Doblmann, J., Dusberger, F., Imre, R., Hudecz, O., Stanek, F., Mechtler, K., D\u00fcrnberger, G.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Proteome Res","volume":"18","issue":"1","page":"535-541","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30122475","title":"Neutralizing Gatad2a-Chd4-Mbd3\/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency.","abstract":"Mbd3, a member of nucleosome remodeling and deacetylase (NuRD) co-repressor complex, was previously identified as an inhibitor for deterministic induced pluripotent stem cell (iPSC) reprogramming, where up to 100% of donor cells successfully complete the process. NuRD can assume multiple mutually exclusive conformations, and it remains unclear whether this deterministic phenotype can be attributed to a specific Mbd3\/NuRD subcomplex. Moreover, since complete ablation of Mbd3 blocks somatic cell proliferation, we aimed to explore functionally relevant alternative ways to neutralize Mbd3-dependent NuRD activity. We identify Gatad2a, a NuRD-specific subunit, whose complete deletion specifically disrupts Mbd3\/NuRD repressive activity on the pluripotency circuitry during iPSC differentiation and reprogramming without ablating somatic cell proliferation. Inhibition of Gatad2a facilitates deterministic murine iPSC reprogramming within 8\u00a0days. We validate a distinct molecular axis, Gatad2a-Chd4-Mbd3, within Mbd3\/NuRD as being critical for blocking reestablishment of naive pluripotency and further highlight signaling-dependent and post-translational modifications of Mbd3\/NuRD that influence its interactions and assembly.","authors":"Mor, N., Rais, Y., Sheban, D., Peles, S., Aguilera-Castrejon, A., Zviran, A., Elinger, D., Viukov, S., Geula, S., Krupalnik, V., Zerbib, M., Chomsky, E., Lasman, L., Shani, T., Bayerl, J., Gafni, O., Hanna, S., Buenrostro, JD., Hagai, T., Masika, H., Vainorius, G., Bergman, Y., Greenleaf, WJ., Esteban, MA., Elling, U., Levin, Y., Massarwa, R., Merbl, Y., Novershtern, N., Hanna, JH.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell Stem Cell","volume":"23","issue":"3","page":"412-425.e10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19143022","title":"EGFR ligand switch in late stage prostate cancer contributes to changes in cell signaling and bone remodeling.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19143022<\/PMID><DateCompleted><Year>2009<\/Year><Month>03<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>12<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1097-0045<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>69<\/Volume><Issue>5<\/Issue><PubDate><Year>2009<\/Year><Month>Apr<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>The Prostate<\/Title><ISOAbbreviation>Prostate<\/ISOAbbreviation><\/Journal><ArticleTitle>EGFR ligand switch in late stage prostate cancer contributes to changes in cell signaling and bone remodeling.<\/ArticleTitle><Pagination><MedlinePgn>528-37<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/pros.20903<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Bone metastasis occurs frequently in advanced prostate cancer (PCa) patients; however, it is not known why this happens. The epidermal growth factor receptor (EGFR) ligand EGF is available to early stage PCa; whereas, TGF-alpha is available when PCa metastasizes. Since the microenvironment of metastases has been shown to play a role in the survival of the tumor, we examined whether the ligands had effects on cell survival and proliferation in early and late PCa.","authors":"DeHaan, AM., Wolters, NM., Keller, ET., Ignatoski, KM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Prostate","volume":"69","issue":"5","page":"528-37","pdf":null,"JrId":"6523","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30232269","title":"Leukotriene B4 promotes neovascularization and macrophage recruitment in murine wet-type AMD models.","abstract":"Age-related macular degeneration (AMD), a progressive chronic disease of the central retina, is associated with aging and is a leading cause of blindness worldwide. Here, we demonstrate that leukotriene B4 (LTB4) receptor 1 (BLT1) promotes laser-induced choroidal neovascularization (CNV) in a mouse model for wet-type AMD. CNV was significantly less in BLT1-deficient (BLT1-KO) mice compared with BLT1-WT controls. Expression of several proangiogenic and profibrotic factors was lower in BLT1-KO eyes than in BLT1-WT eyes. LTB4 production in the eyes was substantially increased in the early phase after laser injury. BLT1 was highly expressed in M2 macrophages in vitro and in vivo, and ocular BLT1+ M2 macrophages were increased in the aged eyes after laser injury. Furthermore, M2 macrophages were rapidly attracted by LTB4 and subsequently produced VEGF-A- through BLT1-mediated signaling. Consequently, intravitreal injection of M2 macrophages augmented CNV formation, which was attenuated by BLT1 deficiency. Thus, laser-induced injury to the retina triggered LTB4 production and attracted M2 macrophages via BLT1, leading to development of CNV. A selective BLT1 antagonist (CP105696) and 3 LTB4 inhibitors (zileuton, MK-886, and bestatin) reduced CNV in a dose-dependent manner. CP105696 also inhibited the accumulation of BLT1+ M2 macrophages in the laser-injured eyes of aged mice. Together, these results indicate that the LTB4-BLT1 axis is a potentially novel therapeutic target for CNV of wet-type AMD.","authors":"Sasaki, F., Koga, T., Ohba, M., Saeki, K., Okuno, T., Ishikawa, K., Nakama, T., Nakao, S., Yoshida, S., Ishibashi, T., Ahmadieh, H., Kanavi, MR., Hafezi-Moghadam, A., Penninger, JM., Sonoda, KH., Yokomizo, T.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"JCI Insight","volume":"3","issue":"18","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31000436","title":"Mouse ANKRD31 Regulates Spatiotemporal Patterning of Meiotic Recombination Initiation and Ensures Recombination between X and Y Sex Chromosomes.","abstract":"Orderly segregation of chromosomes during meiosis requires that crossovers form between homologous chromosomes by recombination. Programmed DNA double-strand breaks (DSBs) initiate meiotic recombination. We identify ANKRD31 as a key component of complexes of DSB-promoting proteins that assemble on meiotic chromosome axes. Genome-wide, ANKRD31 deficiency causes delayed recombination initiation. In addition, loss of ANKRD31 alters DSB distribution because of reduced selectivity for sites that normally attract DSBs. Strikingly, ANKRD31 deficiency also abolishes uniquely high rates of recombination that normally characterize pseudoautosomal regions (PARs) of X and Y chromosomes. Consequently, sex chromosomes do not form crossovers, leading to chromosome segregation failure in ANKRD31-deficient spermatocytes. These defects co-occur with a genome-wide delay in assembling DSB-promoting proteins on autosome axes and loss\u00a0of a specialized PAR-axis domain that is highly enriched for DSB-promoting proteins in wild type. Thus, we propose a model for spatiotemporal patterning of recombination by ANKRD31-dependent control of axis-associated DSB-promoting proteins.","authors":"Papanikos, F., Cl\u00e9ment, JAJ., Testa, E., Ravindranathan, R., Grey, C., Dereli, I., Bondarieva, A., Valerio-Cabrera, S., Stanzione, M., Schleiffer, A., Jansa, P., Lustyk, D., Fei, JF., Adams, IR., Forejt, J., Barchi, M., de Massy, B., Toth, A.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mol Cell","volume":"74","issue":"5","page":"1069-1085.e11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19085839","title":"Receptor activator of nuclear factor-kappa B ligand (RANKL) stimulates bone-associated tumors through functional RANK expressed on bone-associated cancer cells?","abstract":"Primary and secondary bone tumors clearly deteriorate quality of life and the activity of daily living of patients. These undesirable diseases become a major social and economic burden. As both primary and secondary bone tumors develop in the unique bone tissue, it is therefore necessary to understand bone cell biology in tumor bone environment. Recent findings of the Receptor Activator of Nuclear Factor-kappaB ligand (RANKL)\/RANK\/osteoprotegerin (OPG) molecular triad, the key regulators of bone remodeling, opened new era of bone research. Although RANK is an essential receptor for osteoclast formation, activation and survival, functional RANK expression has been recently identified on several bone-associated tumor cells. When RANK is expressed on secondary bone tumor cells, it is implicated in tumor cell migration, whereas this is not the case for primary bone tumors. In any case, RANK is not involved in RANK-positive cell proliferation or death. In two models of bone metastases secondary to melanoma or prostate carcinoma, in vivo neutralization of RANKL by OPG resulted in complete protection from paralysis, due to metastases of vertebral body, and a marked reduction in tumor burden in bones, but not in other organs. OPG also decreased tumor formation and tumor burden in a mouse model of primary bone tumor, osteosarcoma. In all these models, tumor cells express RANK. These data revealed that local differentiation factors, such as RANKL, play an important role in cell migration in a metastatic tissue-specific manner. These findings substantiate the novel direct role of RANKL\/RANK in bone-associated tumors, and its capability of representing new therapeutic targets.","authors":"Mori, K., Ando, K., Heymann, D., R\u00e9dini, F.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Histol Histopathol","volume":"24","issue":"2","page":"235-42","pdf":null,"JrId":"2079","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27126030","title":"Comment on \"Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics\".","abstract":"Li et al (Research Articles, 28 August 2015, aab3500) purport to present solutions to long-standing challenges in live-cell microscopy, reporting relatively fast acquisition times in conjunction with improved image resolution. We question the methods' reliability to visualize specimen features at sub-100-nanometer scales, because the mandatory mathematical processing of the recorded data leads to artifacts that are either difficult or impossible to disentangle from real features. We are also concerned about the chosen approach of subjectively comparing images from different super-resolution methods, as opposed to using quantitative measures.","authors":"Sahl, SJ., Balzarotti, F., Keller-Findeisen, J., Leutenegger, M., Westphal, V., Egner, A., Lavoie-Cardinal, F., Chmyrov, A., Grotjohann, T., Jakobs, S.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Science","volume":"352","issue":"6285","page":"527","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19076348","title":"RANK\/RANKL: regulators of immune responses and bone physiology.","abstract":"Bone-related diseases, such as osteoporosis and rheumatoid arthritis, affect hundreds of millions of people worldwide and pose a tremendous burden to health care. By deepening our understanding of the molecular mechanisms of bone metabolism and bone turnover, it became possible over the past years to devise new and promising strategies for treating such diseases. In particular, three tumor necrosis factor (TNF) family molecules, the receptor activator of NF-kappaB (RANK), its ligand RANKL, and the decoy receptor of RANKL, osteoprotegerin (OPG), have attracted the attention of scientists and pharmaceutical companies alike. Genetic experiments revolving around these molecules established their pivotal role as central regulators of osteoclast development and osteoclast function. RANK-RANKL signaling not only activates a variety of downstream signaling pathways required for osteoclast development, but crosstalk with other signaling pathways also fine-tunes bone homeostasis both in normal physiology and disease. In addition, RANKL and RANK have essential roles in lymph node formation, establishment of the thymic microenvironment, and development of a lactating mammary gland during pregnancy. Consequently, novel drugs specifically targeting RANK, RANKL, and their signaling pathways in osteoclasts are expected to revolutionize the treatment of various ailments associated with bone loss, such as arthritis, periodontal disease, cancer metastases, and osteoporosis.","authors":"Leibbrandt, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Ann N Y Acad Sci","volume":"1143","issue":null,"page":"123-50","pdf":null,"JrId":"611","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25423166","title":"Dual channel RESOLFT nanoscopy by using fluorescent state kinetics.","abstract":"We show that RESOLFT fluorescence nanoscopy, a low light level scanning superresolution technique employing reversibly switchable fluorescent proteins (rsFPs), is capable of dual-channel live-cell imaging that is virtually free of chromatic errors and temporal offsets. This is accomplished using rsEGFP and Dronpa, two rsFPs having similar spectra but different kinetics of switching and fluorescence emission. Our approach is demonstrated by imaging protein distributions and dynamics in living neurons and neuronal tissues.","authors":"Testa, I., D'Este, E., Urban, NT., Balzarotti, F., Hell, SW.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nano Lett","volume":"15","issue":"1","page":"103-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31591571","title":"Ikaros prevents autoimmunity by controlling anergy and Toll-like receptor signaling in B cells.","abstract":"The establishment of a diverse B cell antigen receptor (BCR) repertoire by V(D)J recombination also generates autoreactive B cells. Anergy is one tolerance mechanism; it renders autoreactive B cells insensitive to stimulation by self-antigen, whereas Toll-like receptor (TLR) signaling can reactivate anergic B cells. Here, we describe a critical role of the transcription factor Ikaros in controlling BCR anergy and TLR signaling. Mice with specific deletion of Ikaros in mature B cells developed systemic autoimmunity. Ikaros regulated many anergy-associated genes, including Zfp318, which is implicated in the attenuation of BCR responsiveness by promoting immunoglobulin D expression in anergic B cells. TLR signaling was hyperactive in Ikaros-deficient B cells, which failed to upregulate feedback inhibitors of the MyD88-nuclear factor \u03baB signaling pathway. Systemic inflammation was lost on expression of a non-self-reactive BCR or loss of MyD88 in Ikaros-deficient B cells. Thus, Ikaros acts as a guardian preventing autoimmunity by promoting BCR anergy and restraining TLR signaling.","authors":"Schwickert, TA., Tagoh, H., Schindler, K., Fischer, M., Jaritz, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Immunol","volume":"20","issue":"11","page":"1517-1529","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16313345","title":"Fos\/AP-1 proteins in bone and the immune system.","abstract":"The skeleton and the immune system share a variety of different cytokines and transcription factors, thereby mutually influencing each other. These interactions are not confined to the bone marrow cavity where bone cells and hematopoietic cells exist in proximity but also occur at locations that are target sites for inflammatory bone diseases. The newly established research area termed 'osteoimmunology' attempts to unravel these skeletal\/immunological relationships. Studies towards a molecular understanding of inflammatory bone diseases from an immunological as well as a bone-centered perspective have been very successful and led to the identification of several signaling pathways that are causally involved in inflammatory bone loss. Induction of receptor activator of nuclear factor (NF)-kappaB ligand (RANKL) signals by activated T cells and subsequent activation of the key transcription factors Fos\/activator protein-1 (AP-1), NF-kappaB, and NF for activation of T cells c1 (NFATc1) are in the center of the signaling networks leading to osteoclast-mediated bone loss. Conversely, nature has employed the interferon system to antagonize excessive osteoclast differentiation, although this counteracting activity appears to be overruled under pathological conditions. Here, we focus on Fos\/AP-1 functions in osteoimmunology, because this osteoclastogenic transcription factor plays a central role in inflammatory bone loss by regulating genes like NFATc1 as well as the interferon system. We also attempt to put potential therapeutic strategies for inflammatory bone diseases in perspective.","authors":"Wagner, EF., Eferl, R.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Immunol Rev","volume":"208","issue":null,"page":"126-40","pdf":null,"JrId":"4161","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7607212","title":"Selective inhibition of p70 S6 kinase activation by phosphatidylinositol 3-kinase inhibitors.","abstract":"Treatment of fibroblasts with wortmannin or demethoxyviridin, two potent inhibitors of phosphatidylinositol 3-kinase, prevents the activation of ribosomal protein S6 kinase, which is induced by a variety of external stimuli. Concentrations giving 50% inhibition of 45 nM (wortmannin) and 400 nM (demethoxyviridin) were obtained when epidermal growth factor was used as an S6 kinase activator; with platelet-derived growth factor, the concentrations giving 50% inhibition were about three-times higher. Western-blot analysis and immunocomplex kinase assays showed that wortmannin and demethoxyviridin specifically block the phosphorylation and activation of p70 S6 kinase without affecting the M(r) 90,000 ribosomal S6 kinase (p90rsk) or mitogen-activated protein kinases. Consistent with the irreversible nature of the inhibition of phosphatidylinositol 3-kinase by these compounds, treatment of cells with wortmannin, followed by washing out of the inhibitor, still led to inhibition of p70 S6 kinase activation. Several S6 kinase agonists not previously known to activate phosphatidylinositol 3-kinase (A23187, bombesin and phorbol 12-myristate 13-acetate) were found to increase the production of phosphatidylinositol 3,4,5-trisphosphate in a wortmannin-sensitive manner. These results support a model in which phosphatidylinositol 3-kinase acts upstream of p70 S6 kinase in a mitogenic signalling pathway; the existence of a phosphatidylinositol 3-kinase-independent pathway is also evident.","authors":"Petritsch, C., Woscholski, R., Edelmann, HM., Parker, PJ., Ballou, LM.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Eur J Biochem","volume":"230","issue":"2","page":"431-8","pdf":null,"JrId":"3607","fulltextlink":null,"preprintlink":null,"articledate":"1995-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31636255","title":"Molecular features of the UNC-45 chaperone critical for binding and folding muscle myosin.","abstract":"Myosin is a motor protein that is essential for a variety of processes ranging from intracellular transport to muscle contraction. Folding and assembly of myosin relies on a specific chaperone, UNC-45. To address its substrate-targeting mechanism, we reconstitute the interplay between Caenorhabditis elegans UNC-45 and muscle myosin MHC-B in insect cells. In addition to providing a cellular chaperone assay, the established system enabled us to produce large amounts of functional muscle myosin, as evidenced by a biochemical and structural characterization, and to directly monitor substrate binding to UNC-45. Data from in vitro and cellular chaperone assays, together with crystal structures of binding-deficient UNC-45 mutants, highlight the importance of utilizing a flexible myosin-binding domain. This so-called UCS domain can adopt discrete conformations to efficiently bind and fold substrate. Moreover, our data uncover the molecular basis of temperature-sensitive UNC-45 mutations underlying one of the most prominent motility defects in C. elegans.","authors":"Hellerschmied, D., Lehner, A., Franicevic, N., Arnese, R., Johnson, C., Vogel, A., Meinhart, A., Kurzbauer, R., Deszcz, L., Gazda, L., Geeves, M., Clausen, T.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"4781","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16243032","title":"Quantitative analysis of protein dynamics during asymmetric cell division.","abstract":"In dividing Drosophila sensory organ precursor (SOP) cells, the fate determinant Numb and its associated adaptor protein Pon localize asymmetrically and segregate into the anterior daughter cell, where Numb influences cell fate by repressing Notch signaling. Asymmetric localization of both proteins requires the protein kinase aPKC and its substrate Lethal (2) giant larvae (Lgl). Because both Numb and Pon localization require actin and myosin, lateral transport along the cell cortex has been proposed as a possible mechanism for their asymmetric distribution. Here, we use quantitative live analysis of GFP-Pon and Numb-GFP fluorescence and fluorescence recovery after photobleaching (FRAP) to characterize the dynamics of Numb and Pon localization during SOP division. We demonstrate that Numb and Pon rapidly exchange between a cytoplasmic pool and the cell cortex and that preferential recruitment from the cytoplasm is responsible for their asymmetric distribution during mitosis. Expression of a constitutively active form of aPKC impairs membrane recruitment of GFP-Pon. This defect can be rescued by coexpression of nonphosphorylatable Lgl, indicating that Lgl is the main target of aPKC. We propose that a high-affinity binding site is asymmetrically distributed by aPKC and Lgl and is responsible for asymmetric localization of cell-fate determinants during mitosis.","authors":"Mayer, B., Emery, G., Berdnik, D., Wirtz-Peitz, F., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"20","page":"1847-54","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-06-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11535596","title":"Calcium-regulated DNA binding and oligomerization of the neuronal calcium-sensing protein, calsenilin\/DREAM\/KChIP3.","abstract":"Calsenilin\/DREAM\/KChIP3, a member of the recoverin branch of the EF-hand superfamily, interacts with presenilins, serves as a calcium-regulated transcriptional repressor, and interacts with A-type potassium channels. Here we report physicochemical characterization of calcium binding, oligomerization, and DNA binding of human calsenilin\/DREAM\/KChIP3. Equilibrium Ca(2+) binding measurements indicate that the protein binds 3 Ca(2+) with a dissociation constant of 14 microM and a Hill coefficient of 0.7. Dynamic light scattering and size exclusion chromatography show that the Ca(2+)-bound protein exists as a dimer at protein concentrations lower than 150 microM and forms a tetramer at concentrations above 200 microM. The Ca(2+)-free protein is a tetramer in the concentration range 20-450 microM. Isothermal titration calorimetry and dynamic light scattering indicate that the Ca(2+)-free protein tetramer binds endothermically (DeltaH = +25 kcal\/mol) to four molecules of DNA derived from the downstream regulatory element (DRE) of either the prodynorphin or c-fos genes. One DRE molecule binds tightly to the protein with a dissociation constant (K(d)) of 75 nM, and the other three bind more weakly (K(d) = 640 nM). No significant DNA binding was observed for the Ca(2+)-bound protein. The N-terminal protein fragment (residues 1-70) binds nonspecifically to DRE in a Ca(2+)-independent manner, whereas a C-terminal fragment containing the four EF-hands (residues 65-256) binds DRE (K(d) = 200 nM) in a Ca(2+)-regulated and sequence-specific fashion. The C-terminal fragment is a tetramer in the Ca(2+)-free state and dissociates into dimers at saturating Ca(2+) levels.","authors":"Osawa, M., Tong, KI., Lilliehook, C., Wasco, W., Buxbaum, JD., Cheng, HY., Penninger, JM., Ikura, M., Ames, JB.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Biol Chem","volume":"276","issue":"44","page":"41005-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31585074","title":"Imaging the Emergence of Behavior.","abstract":"In this issue of Cell, Wan et\u00a0al. (2019) track comprehensively the development of individual neurons, along with their activity, during zebrafish spinal cord development. They find that mostly motor neurons are the founders of initially small neuronal-activity ensembles, coalescing into larger populations establishing the first motor patterns.","authors":"Uzel, K., Zimmer, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell","volume":"179","issue":"2","page":"285-286","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31160788","title":"Derivation and maintenance of mouse haploid embryonic stem cells.","abstract":"Ploidy represents the number of chromosome sets in a cell. Although gametes have a haploid genome (n), most mammalian cells have diploid genomes (2n). The diploid status of most cells correlates with the number of probable alleles for each autosomal gene and makes it difficult to target these genes via mutagenesis techniques. Here, we describe a 7-week protocol for the derivation of mouse haploid embryonic stem cells (hESCs) from female gametes that also outlines how to maintain the cells once derived. We detail additional procedures that can be used with cell lines obtained from the mouse Haplobank, a biobank of &gt;100,000 individual mouse hESC lines with targeted mutations in 16,970 genes. hESCs can spontaneously diploidize and can be maintained in both haploid and diploid states. Mouse hESCs are genomically and karyotypically stable, are innately immortal and isogenic, and can be derived in an array of differentiated cell types; they are thus highly amenable to genetic screens and to defining molecular connectivity pathways.","authors":"Elling, U., Woods, M., Forment, JV., Fu, B., Yang, F., Ng, BL., Vicente, JR., Adams, DJ., Doe, B., Jackson, SP., Penninger, JM., Balmus, G.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Protoc","volume":"14","issue":"7","page":"1991-2014","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19021528","title":"Target site effects in the RNA interference and microRNA pathways.","abstract":"In RNAi (RNA interference), siRNAs (small interfering RNAs) are loaded into the RISC (RNA-induced silencing complex), which then mediates endonucleolytic cleavage of complementary target RNAs. Although RNAi has become one of the most powerful tools in molecular biology to assess gene function, there remains a great number of ineffective siRNAs. It is already known that the assembly and activation of RISC is a crucial determinant of RNAi activity, but downstream effects such as target accessibility have not been analysed extensively. Therefore we assessed the effect of target site accessibility and found that it significantly improves the potency of siRNAs. Similarly, miRNAs (microRNAs) act by repressing protein synthesis through imperfect base-pairing to the 3'-UTR (untranslated region) of target mRNAs. We found that predicted target sites reside in regions of high accessibility and tested whether this criterion could be used in the search of functional miRNA targets. In addition, we performed reporter gene assays to test whether accessibility correlates with measured mRNA suppression levels. The results of our initial study suggest that secondary structures might add a so far underrepresented layer of complexity in the recognition of RNA targets by miRNAs.","authors":"Obernosterer, G., Tafer, H., Martinez, J.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Biochem Soc Trans","volume":"36","issue":"Pt 6","page":"1216-9","pdf":null,"JrId":"3328","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31784531","title":"CRISPR-Switch regulates sgRNA activity by Cre recombination for sequential editing of two loci.","abstract":"CRISPR-Cas9 is an efficient and versatile tool for genome engineering in many species. However, inducible CRISPR-Cas9 editing systems that regulate Cas9 activity or sgRNA expression often suffer from significant limitations, including reduced editing capacity, off-target effects, or leaky expression. Here, we develop a precisely controlled sgRNA expression cassette that can be combined with widely-used Cre systems, termed CRISPR-Switch (SgRNA With Induction\/Termination by Cre Homologous recombination). Switch-ON facilitates controlled, rapid induction of sgRNA activity. In turn, Switch-OFF-mediated termination of editing improves generation of heterozygous genotypes and can limit off-target effects. Furthermore, we design sequential CRISPR-Switch-based editing of two loci in a strictly programmable manner and determined the order of mutagenic events that leads to development of glioblastoma in mice. Thus, CRISPR-Switch substantially increases the versatility of gene editing through precise and rapid switching ON or OFF sgRNA activity, as well as switching OVER to secondary sgRNAs.","authors":"Chylinski, K., Hubmann, M., Hanna, RE., Yanchus, C., Michlits, G., Uijttewaal, ECH., Doench, J., Schramek, D., Elling, U.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"5454","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16169489","title":"Novel genes required for meiotic chromosome segregation are identified by a high-throughput knockout screen in fission yeast.","abstract":"Two rounds of chromosome segregation after only a single round of DNA replication enable the production of haploid gametes from diploid precursors during meiosis. To identify genes involved in meiotic chromosome segregation, we developed an efficient strategy to knock out genes in the fission yeast on a large scale. We used this technique to delete 180 functionally uncharacterized genes whose expression is upregulated during meiosis. Deletion of two genes, sgo1 and mde2, caused massive chromosome missegregation. sgo1 is required for retention of centromeric sister-chromatid cohesion after anaphase I. We show here that mde2 is required for formation of the double-strand breaks necessary for meiotic recombination.","authors":"Gregan, J., Rabitsch, PK., Sakem, B., Csutak, O., Latypov, V., Lehmann, E., Kohli, J., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"18","page":"1663-9","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31243395","title":"Sequencing cell-type-specific transcriptomes with SLAM-ITseq.","abstract":"Analysis of cell-type-specific transcriptomes is vital for understanding the biology of tissues and organs in the context of multicellular organisms. In this Protocol Extension, we combine a previously developed cell-type-specific metabolic RNA labeling method (thiouracil (TU) tagging) and a pipeline to detect the labeled transcripts by a novel RNA sequencing (RNA-seq) method, SLAMseq (thiol (SH)-linked alkylation for the metabolic sequencing of RNA). By injecting a uracil analog, 4-thiouracil, into transgenic mice that express cell-type-specific uracil phosphoribosyltransferase (UPRT), an enzyme required for 4-thiouracil incorporation into newly synthesized RNA, only cells expressing UPRT synthesize thiol-containing RNA. Total RNA isolated from a tissue of interest is then sequenced with SLAMseq, which introduces thymine to cytosine (T&gt;C) conversions at the sites of the incorporated 4-thiouracil. The resulting sequencing reads are then mapped with the T&gt;C-aware alignment software, SLAM-DUNK, which allows mapping of reads containing T&gt;C mismatches. The number of T&gt;C conversions per transcript is further analyzed to identify which transcripts are synthesized in the UPRT-expressing cells. Thus, our method, SLAM-ITseq (SLAMseq in tissue), enables cell-specific transcriptomics without laborious FACS-based cell sorting or biochemical isolation of the labeled transcripts used in TU tagging. In the murine tissues we assessed previously, this method identified ~5,000 genes that are expressed in a cell type of interest from the total RNA pool from the tissue. Any laboratory with access to a high-throughput sequencer and high-power computing can adapt this protocol with ease, and the entire pipeline can be completed in &lt;5 d.","authors":"Matsushima, W., Herzog, VA., Neumann, T., Gapp, K., Zuber, J., Ameres, SL., Miska, EA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Protoc","volume":"14","issue":"8","page":"2261-2278","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19013827","title":"Transcript versus transcription?","abstract":"Numerous sense-antisense gene pairs have been discovered in various organisms. Antisense genes play important roles in establishing parentally imprinted gene expression patterns in mammals. Typically, protein-coding sense genes are reciprocally regulated by their non-coding antisense partners. One example for antisense regulation is the Xist (X-inactive specific transcript) and Tsix gene pair, which is pivotal in X-inactivation. Xist works as a functional RNA molecule that recruits repressive chromatin factors towards one of the female Xs for inactivation. Antisense Tsix transcription negatively regulates Xist and protects one X-chromosome in cis from inactivation by Xist. Albeit, the precise molecular mechanism is still obscure it has been shown that Tsix transcription regulates the chromatin structure by altering histone tail modifications and DNA methylation at the Xist promoter. In addition, Xist and Tsix RNA form an RNA duplexes in vivo and are processed to small RNAs, which have a potential regulatory function. Here we review the latest findings and based on ample experimental data consider models for antisense-mediated gene regulation in X-inactivation.","authors":"Shibata, S., Wutz, A.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Epigenetics","volume":"3","issue":"5","page":"246-9","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18986213","title":"Network hubs buffer environmental variation in Saccharomyces cerevisiae.","abstract":"Regulatory and developmental systems produce phenotypes that are robust to environmental and genetic variation. A gene product that normally contributes to this robustness is termed a phenotypic capacitor. When a phenotypic capacitor fails, for example when challenged by a harsh environment or mutation, the system becomes less robust and thus produces greater phenotypic variation. A functional phenotypic capacitor provides a mechanism by which hidden polymorphism can accumulate, whereas its failure provides a mechanism by which evolutionary change might be promoted. The primary example to date of a phenotypic capacitor is Hsp90, a molecular chaperone that targets a large set of signal transduction proteins. In both Drosophila and Arabidopsis, compromised Hsp90 function results in pleiotropic phenotypic effects dependent on the underlying genotype. For some traits, Hsp90 also appears to buffer stochastic variation, yet the relationship between environmental and genetic buffering remains an important unresolved question. We previously used simulations of knockout mutations in transcriptional networks to predict that many gene products would act as phenotypic capacitors. To test this prediction, we use high-throughput morphological phenotyping of individual yeast cells from single-gene deletion strains to identify gene products that buffer environmental variation in Saccharomyces cerevisiae. We find more than 300 gene products that, when absent, increase morphological variation. Overrepresented among these capacitors are gene products that control chromosome organization and DNA integrity, RNA elongation, protein modification, cell cycle, and response to stimuli such as stress. Capacitors have a high number of synthetic-lethal interactions but knockouts of these genes do not tend to cause severe decreases in growth rate. Each capacitor can be classified based on whether or not it is encoded by a gene with a paralog in the genome. Capacitors with a duplicate are highly connected in the protein-protein interaction network and show considerable divergence in expression from their paralogs. In contrast, capacitors encoded by singleton genes are part of highly interconnected protein clusters whose other members also tend to affect phenotypic variability or fitness. These results suggest that buffering and release of variation is a widespread phenomenon that is caused by incomplete functional redundancy at multiple levels in the genetic architecture.","authors":"Levy, SF., Siegal, ML.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"PLoS Biol","volume":"6","issue":"11","page":"e264","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2009-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16139208","title":"Molecular, anatomical, and functional organization of the Drosophila olfactory system.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">16139208<\/PMID><DateCompleted><Year>2006<\/Year><Month>03<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2006<\/Year><Month>11<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>15<\/Volume><Issue>17<\/Issue><PubDate><Year>2005<\/Year><Month>Sep<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Molecular, anatomical, and functional organization of the Drosophila olfactory system.<\/ArticleTitle><Pagination><MedlinePgn>1535-47<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Olfactory receptor neurons (ORNs) convey chemical information into the brain, producing internal representations of odors detected in the periphery. A comprehensive understanding of the molecular and neural mechanisms of odor detection and processing requires complete maps of odorant receptor (Or) expression and ORN connectivity, preferably at single-cell resolution.","authors":"Couto, A., Alenius, M., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"17","page":"1535-47","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31871840","title":"A novel approach to immunoapheresis of C3a\/C3 and proteomic identification of associates.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31871840<\/PMID><DateRevised><Year>2020<\/Year><Month>10<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Print\">2167-8359<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>7<\/Volume><PubDate><Year>2019<\/Year><\/PubDate><\/JournalIssue><Title>PeerJ<\/Title><ISOAbbreviation>PeerJ<\/ISOAbbreviation><\/Journal><ArticleTitle>A novel approach to immunoapheresis of C3a\/C3 and proteomic identification of associates.<\/ArticleTitle><Pagination><MedlinePgn>e8218<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.7717\/peerj.8218<\/ELocationID><Abstract><AbstractText Label=\"Background\" NlmCategory=\"UNASSIGNED\">Complement factor C3 represents the central component of the complement cascade and its activation split product C3a plays an important role in inflammation and disease. Many human disorders are linked to dysregulation of the complement system and alteration in interaction molecules. Therefore, various therapeutic approaches to act on the complement system have been initiated.","authors":"Winnicki, W., Pichler, P., Mechtler, K., Imre, R., Steinmacher, I., Seng\u00f6lge, G., Knafl, D., Beilhack, G., Wagner, L.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PeerJ","volume":"7","issue":null,"page":"e8218","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31735675","title":"A Putative Mechanism for Magnetoreception by Electromagnetic Induction in the Pigeon Inner Ear.","abstract":"A diverse array of vertebrate species employs the Earth's magnetic field to assist navigation. Despite compelling behavioral evidence that a magnetic sense exists, the location of the primary sensory cells and the underlying molecular mechanisms remain unknown [1]. To date, most research has focused on a light-dependent radical-pair-based concept and a system that is proposed to rely on biogenic magnetite (Fe<sub>3<\/sub>O<sub>4<\/sub>) [2, 3]. Here, we explore an overlooked hypothesis that predicts that animals detect magnetic fields by electromagnetic induction within the semicircular canals of the inner ear [4]. Employing an assay that relies on the neuronal activity marker C-FOS, we confirm that magnetic exposure results in activation of the caudal vestibular nuclei in pigeons that is independent of light [5]. We show experimentally and by physical calculations that magnetic stimulation can induce electric fields in the pigeon semicircular canals that are within the physiological range of known electroreceptive systems. Drawing on this finding, we report the presence of a splice isoform of a voltage-gated calcium channel (Ca<sub>V<\/sub>1.3) in the pigeon inner ear that has been shown to mediate electroreception in skates and sharks [6]. We propose that pigeons detect magnetic fields by electromagnetic induction within the semicircular canals that is dependent on the presence of apically located voltage-gated cation channels in a population of electrosensory hair cells.","authors":"Nimpf, S., Nordmann, GC., Kagerbauer, D., Malkemper, EP., Landler, L., Papadaki-Anastasopoulou, A., Ushakova, L., Wenninger-Weinzierl, A., Novatchkova, M., Vincent, P., Lendl, T., Colombini, M., Mason, MJ., Keays, DA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Curr Biol","volume":"29","issue":"23","page":"4052-4059.e4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31824960","title":"The Role of Iron Regulation in Immunometabolism and Immune-Related Disease.","abstract":"Immunometabolism explores how the intracellular metabolic pathways in immune cells can regulate their function under different micro-environmental and (patho-)-physiological conditions (Pearce, 2010; Buck et al., 2015; O'Neill and Pearce, 2016). In the last decade great advances have been made in studying and manipulating metabolic programs in immune cells. Immunometabolism has primarily focused on glycolysis, the TCA cycle and oxidative phosphorylation (OXPHOS) as well as free fatty acid synthesis and oxidation. These pathways are important for providing the energy needs of cell growth, membrane rigidity, cytokine production and proliferation. In this review, we will however, highlight the specific role of iron metabolism at the cellular and organismal level, as well as how the bioavailability of this metal orchestrates complex metabolic programs in immune cell homeostasis and inflammation. We will also discuss how dysregulation of iron metabolism contributes to alterations in the immune system and how these novel insights into iron regulation can be targeted to metabolically manipulate immune cell function under pathophysiological conditions, providing new therapeutic opportunities for autoimmunity and cancer.","authors":"Cronin, SJF., Woolf, CJ., Weiss, G., Penninger, JM.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Front Mol Biosci","volume":"6","issue":null,"page":"116","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31290979","title":"Estrogen Signaling Drives Ciliogenesis in Human Endometrial Organoids.","abstract":"The human endometrium is the inner lining of the uterus consisting of stromal and epithelial (secretory and ciliated) cells. It undergoes a hormonally regulated monthly cycle of growth, differentiation, and desquamation. However, how these cyclic changes control the balance between secretory and ciliated cells remains unclear. Here, we established endometrial organoids to investigate the estrogen (E2)-driven control of cell fate decisions in human endometrial epithelium. We demonstrate that they preserve the structure, expression patterns, secretory properties, and E2 responsiveness of their tissue of origin. Next, we show that the induction of ciliated cells is orchestrated by the coordinated action of E2 and NOTCH signaling. Although E2 is the primary driver, inhibition of NOTCH signaling provides a permissive environment. However, inhibition of NOTCH alone is not sufficient to trigger ciliogenesis. Overall, we provide insights into endometrial biology and propose endometrial organoids as a robust and powerful model for studying ciliogenesis in vitro.","authors":"Haider, S., Gamperl, M., Burkard, TR., Kunihs, V., Kaindl, U., Junttila, S., Fiala, C., Schmidt, K., Mendjan, S., Kn\u00f6fler, M., Latos, PA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Endocrinology","volume":"160","issue":"10","page":"2282-2297","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18972529","title":"Enhanced detection and identification of multiply phosphorylated peptides using TiO2 enrichment in combination with MALDI TOF\/TOF MS.","abstract":"The analysis of PTMs such as phosphorylation has become an important field in MS because they can directly indicate protein states and interactions. Whereas the characterization of singly and doubly phosphorylated peptides has almost become routine, identifying phosphorylation events at multiple residues within a small region of a protein is still problematic. The identification of multiple modifications can be further hampered by low sequence information due to multiple neutral losses from phosphorylated side chains. Here we present a strategy for the analysis of complex phosphopeptides that combines peptide enrichment by titanium dioxide, separation by RP separation on monolithic columns and MS using high energy HE-CAD in a MALDI TOF\/TOF analyser. Using synthetic phosphopeptides our approach is compared to multistage activation (MSA) MS\/MS and the recently described electron transfer dissociation (ETD) method using an ESI-LTQ mass spectrometer.","authors":"Schmidt, A., Csaszar, E., Ammerer, G., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Proteomics","volume":"8","issue":"21","page":"4577-92","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31585123","title":"Mouse Models of Human Gastric Cancer Subtypes With Stomach-Specific CreERT2-Mediated Pathway Alterations.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31585123<\/PMID><DateCompleted><Year>2019<\/Year><Month>12<\/Month><Day>31<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>03<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1528-0012<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>157<\/Volume><Issue>6<\/Issue><PubDate><Year>2019<\/Year><Month>12<\/Month><\/PubDate><\/JournalIssue><Title>Gastroenterology<\/Title><ISOAbbreviation>Gastroenterology<\/ISOAbbreviation><\/Journal><ArticleTitle>Mouse Models of Human Gastric Cancer Subtypes With Stomach-Specific CreERT2-Mediated Pathway Alterations.<\/ArticleTitle><Pagination><MedlinePgn>1599-1614.e2<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0016-5085(19)41368-1<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1053\/j.gastro.2019.09.026<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\">Patterns of genetic alterations characterize different molecular subtypes of human gastric cancer. We aimed to establish mouse models of these subtypes.","authors":"Seidlitz, T., Chen, YT., Uhlemann, H., Sch\u00f6lch, S., Kochall, S., Merker, SR., Klimova, A., Hennig, A., Schweitzer, C., Pape, K., Baretton, GB., Welsch, T., Aust, DE., Weitz, J., Koo, BK., Stange, DE.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Gastroenterology","volume":"157","issue":"6","page":"1599-1614.e2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31849950","title":"Allies or Enemies-The Multifaceted Role of Myeloid Cells in the Tumor Microenvironment.","abstract":"For decades, cancer was considered a disease driven by genetic mutations in tumor cells, therefore afflicting a single cell type. This simplified view was slowly replaced by the understanding that interactions between malignant cells and neighboring stromal and immune cells-the tumor microenvironment (TME)-profoundly shape cancer progression. This understanding paved the way for an entirely new form of therapy that targets the immune cell compartment, which has revolutionized the treatment of cancer. In particular, agents activating T lymphocytes have become a key focus of these therapies, as they can induce durable responses in several cancer types. However, T cell targeting agents only benefit a fraction of patients. Thus, it is crucial to identify the roles of other immune cell types in the TME and understand how they influence T cell function and\/or whether they present valuable therapeutic targets themselves. In this review, we focus on the myeloid compartment of the TME, a heterogeneous mix of cell types with diverse effector functions. We describe how distinct myeloid cell types can act as enemies of cancer cells by inducing or enhancing an existing immune response, while others act as strong allies, supporting tumor cells in their malignant growth and establishing an immune evasive TME. Specifically, we focus on the role of myeloid cells in the response and resistance to immunotherapy, and how modulating their numbers and\/or state could provide alternative therapeutic entry-points.","authors":"Haas, L., Obenauf, AC.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Front Immunol","volume":"10","issue":null,"page":"2746","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11470404","title":"A screen for genes required for meiosis and spore formation based on whole-genome expression.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11470404<\/PMID><DateCompleted><Year>2001<\/Year><Month>09<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>11<\/Volume><Issue>13<\/Issue><PubDate><Year>2001<\/Year><Month>Jul<\/Month><Day>10<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>A screen for genes required for meiosis and spore formation based on whole-genome expression.<\/ArticleTitle><Pagination><MedlinePgn>1001-9<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Meiosis is the process by which gametes are generated with half the ploidy of somatic cells. This reduction is achieved by three major differences in chromosome behavior during meiosis as compared to mitosis: the production of chiasmata by recombination, the protection of centromere-proximal sister chromatid cohesion, and the monoorientation of sister kinetochores during meiosis I. Mistakes in any of these processes lead to chromosome missegregation.","authors":"Rabitsch, KP., T\u00f3th, A., G\u00e1lov\u00e1, M., Schleiffer, A., Schaffner, G., Aigner, E., Rupp, C., Penkner, AM., Moreno-Borchart, AC., Primig, M., Esposito, RE., Klein, F., Knop, M., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Curr Biol","volume":"11","issue":"13","page":"1001-9","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7584087","title":"Lipopolysaccharide is a frequent contaminant of plasmid DNA preparations and can be toxic to primary human cells in the presence of adenovirus.","abstract":"Endotoxin (lipopolysaccharide, LPS) is commonly found as a contaminant in plasmid DNA preparations. We demonstrate here that the quantities of LPS typically contaminating DNA preparations can generate a toxicity to primary cells (primary human skin fibroblasts, primary human melanoma cells) in the presence of entry-competent adenovirus particles. Toxicity can be observed with as little as 100 ng\/ml free LPS or 100 pg\/ml LPS when the LPS is assembled into polylysine\/adenovirus complexes. Simple and effective methods of removing the contaminating LPS using either a polymyxin B resin or Triton X-114 extraction are described. Treatment of DNA samples to remove LPS eliminates the toxicity to primary cells.","authors":"Cotten, M., Baker, A., Saltik, M., Wagner, E., Buschle, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Gene Ther","volume":"1","issue":"4","page":"239-46","pdf":null,"JrId":"8603","fulltextlink":null,"preprintlink":null,"articledate":"1995-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11418587","title":"Impaired synergistic activation of stress-activated protein kinase SAPK\/JNK in mouse embryonic stem cells lacking SEK1\/MKK4: different contribution of SEK2\/MKK7 isoforms to the synergistic activation.","abstract":"Stress-activated protein kinase\/c-Jun NH(2)-terminal kinase (SAPK\/JNK), which is a member of the mitogen-activated protein kinase (MAPK) family, plays an important role in a stress-induced signaling cascade. SAPK\/JNK activation requires the phosphorylation of Thr and Tyr residues in its Thr-Pro-Tyr motif, and SEK1 (MKK4) and MKK7 (SEK2) have been identified as the upstream MAPK kinases. Here we examined the activation and phosphorylation sites of SAPK\/JNK and differentiated the contribution of SEK1 and MKK7alpha1, -gamma1, and -gamma2 isoforms to the MAPK activation. In SEK1-deficient mouse embryonic stem cells, stress-induced SAPK\/JNK activation was markedly impaired, and this defect was accompanied with a decreased level of the Tyr phosphorylation. Analysis in HeLa cells co-transfected with the two MAPK kinases revealed that the Thr and Tyr of SAPK\/JNK were independently phosphorylated in response to heat shock by MKK7gamma1 and SEK1, respectively. However, MKK7alpha1 failed to phosphorylate the Thr of SAPK\/JNK unless its Tyr residue was phosphorylated by SEK1. In contrast, MKK7gamma2 had the ability to phosphorylate both Thr and Tyr residues. In all cases, the dual phosphorylation of the Thr and Tyr residues was essentially required for the full activation of SAPK\/JNK. These data provide the first evidence that synergistic activation of SAPK\/JNK requires both phosphorylation at the Thr and Tyr residues in living cells and that the preference for the Thr and Tyr phosphorylation was different among the members of MAPK kinases.","authors":"Wada, T., Nakagawa, K., Watanabe, T., Nishitai, G., Seo, J., Kishimoto, H., Kitagawa, D., Sasaki, T., Penninger, JM., Nishina, H., Katada, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Biol Chem","volume":"276","issue":"33","page":"30892-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32222741","title":"Ptaquiloside from bracken (Pteridium spp.) promotes oral carcinogenesis initiated by HPV16 in transgenic mice.","abstract":"Bracken (Pteridium spp.) is a common weed that is consumed as food especially in Asia, and is suspected of promoting carcinogenesis induced by papillomaviruses in the digestive and urinary systems. This is particularly worrying because the incidence of head-and-neck cancers associated with the human papillomavirus (HPV) is rapidly increasing, and HPV co-carcinogens urgently need to be identified. This study tested the hypothesis that two bracken compounds, ptaquiloside and rutin, are able to promote head-and-neck and bladder carcinogenesis in HPV16-transgenic mice. Expression of HPV16 E6 and E7 in oral and bladder tissues was confirmed using quantitative real-time PCR. Mice were exposed orally to ptaquiloside (0.5 mg per animal per week for 10 weeks from 20 weeks-old) or rutin (413 mg kg-1 day-1 for 24 weeks from 6 weeks-old), sacrificed at 30 weeks-old and studied histologically. HPV16 E6 and E7 expression was higher in oral mucosa compared with the bladder (p 0.001). Importantly, ptaquiloside, but not rutin, increased the incidence of oral squamous cell carcinomas (p = 1.2 \u00d7 10-8) in HPV16-transgenic mice. Also, cancers of unexposed transgenic mice were restricted to the tongue base, while ptaquiloside-exposed mice showed multifocal lesions throughout the oral cavity. Wild-type controls showed no oral lesions. No bladder lesions were observed in any treated or untreated group. These results indicate that ptaquiloside from bracken is able to promote oral carcinogenesis initiated by HPV16. Rutin did not show any carcinogenic effects in this model. The absence of bladder lesions may reflect an insufficient incubation period or factors related to the specific viral oncogenes present in this model.","authors":"Gil da Costa, RM., Neto, T., Est\u00eav\u00e3o, D., Moutinho, M., F\u00e9lix, A., Medeiros, R., Lopes, C., Bastos, MMSM., Oliveira, PA.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Food Funct","volume":"11","issue":"4","page":"3298-3305","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32029896","title":"BCAT2-mediated BCAA catabolism is critical for development of pancreatic ductal adenocarcinoma.","abstract":"Branched-chain amino acid (BCAA) metabolism is potentially linked with development of pancreatic ductal adenocarcinoma (PDAC)<sup>1-4<\/sup>. BCAA transaminase 2 (BCAT2) was essential for the collateral lethality conferred by deletion of malic enzymes in PDAC and the BCAA-BCAT metabolic pathway contributed to non-small-cell lung carcinomas (NSCLCs) other than PDAC<sup>3,4<\/sup>. However, the underlying mechanism remains undefined. Here we reveal that BCAT2 is elevated in mouse models and in human PDAC. Furthermore, pancreatic tissue-specific knockout of Bcat2 impedes progression of pancreatic intraepithelial neoplasia (PanIN) in LSL-Kras<sup>G12D\/+<\/sup>; Pdx1-Cre (KC) mice. Functionally, BCAT2 enhances BCAA uptake to sustain BCAA catabolism and mitochondrial respiration. Notably, BCAA enhances growth of pancreatic ductal organoids from KC mice in a dose-dependent manner, whereas addition of branched-chain \u03b1-keto acid (BCKA) and nucleobases rescues growth of KC organoids that is suppressed by BCAT2 inhibitor. Moreover, KRAS stabilizes BCAT2, which is mediated by spleen tyrosine kinase (SYK) and E3 ligase tripartite-motif-containing protein 21 (TRIM21). In addition, BCAT2 inhibitor ameliorates PanIN formation in KC mice. Of note, a lower-BCAA diet also impedes PDAC development in mouse models of PDAC. Thus, BCAT2-mediated BCAA catabolism is critical for development of PDAC harbouring KRAS mutations. Targeting BCAT2 or lowering dietary BCAA may have translational significance.","authors":"Li, JT., Yin, M., Wang, D., Wang, J., Lei, MZ., Zhang, Y., Liu, Y., Zhang, L., Zou, SW., Hu, LP., Zhang, ZG., Wang, YP., Wen, WY., Lu, HJ., Chen, ZJ., Su, D., Lei, QY.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Cell Biol","volume":"22","issue":"2","page":"167-174","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31899800","title":"E\u03bc and 3'RR transcriptional enhancers of the IgH locus cooperate to promote c-myc-induced mature B-cell lymphomas.","abstract":"Numerous B-cell lymphomas feature translocations linking oncogenes to different locations in the immunoglobulin heavy chain (IgH) locus. During Burkitt lymphoma (BL), IgH breakpoints for c-myc translocation stand either close to JH segments or within switch regions. Transcription, accessibility, and remodeling of the IgH locus are under the control of the 2 potent cis-acting enhancer elements: E\u03bc and the 3' regulatory region (3'RR). To ensure their respective contributions to oncogene deregulation in the context of the endogenous IgH locus, we studied transgenic mice harboring a knock-in of c-myc in various positions of the IgH locus (3' to JH segments, 5' to C\u03bc with E\u03bc deletion and C\u03b1). The observed spectrum of tumors, kinetics of emergence, and transcriptome analysis provide strong evidence that both E\u03bc and 3'RR deregulate c-myc and cooperate together to promote B-cell lymphomagenesis. Transgenics mimicking endemic BL (with c-myc placed 3' to JH segments) exhibited the highest rate of B-cell lymphoma emergence, the highest Ki67 index of proliferation, and the highest transcriptomic similarities to human BL. The 3'RR enhancer alone deregulated c-myc and initiated the development of BL-like lymphomas, suggesting that its targeting would be of therapeutic interest to reduce c-myc oncogenicity in vivo.","authors":"Ghazzaui, N., Issaoui, H., Ferrad, M., Carrion, C., Cook-Moreau, J., Denizot, Y., Boyer, F.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Blood Adv","volume":"4","issue":"1","page":"28-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16137758","title":"Asymmetric Rab 11 endosomes regulate delta recycling and specify cell fate in the Drosophila nervous system.","abstract":"Drosophila sensory organ precursor (SOP) cells are a well-studied model system for asymmetric cell division. During SOP division, the determinants Numb and Neuralized segregate into the pIIb daughter cell and establish a distinct cell fate by regulating Notch\/Delta signaling. Here, we describe a Numb- and Neuralized-independent mechanism that acts redundantly in cell-fate specification. We show that trafficking of the Notch ligand Delta is different in the two daughter cells. In pIIb, Delta passes through the recycling endosome which is marked by Rab 11. In pIIa, however, the recycling endosome does not form because the centrosome fails to recruit Nuclear fallout, a Rab 11 binding partner that is essential for recycling endosome formation. Using a mammalian cell culture system, we demonstrate that recycling endosomes are essential for Delta activity. Our results suggest that cells can regulate signaling pathways and influence their developmental fate by inhibiting the formation of individual endocytic compartments.","authors":"Emery, G., Hutterer, A., Berdnik, D., Mayer, B., Wirtz-Peitz, F., Gaitan, MG., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Cell","volume":"122","issue":"5","page":"763-73","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2005-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31994197","title":"HPV16 is sufficient to induce squamous cell carcinoma specifically in the tongue base in transgenic mice.","abstract":"Head and neck squamous cell carcinomas (HNSCCs) associated with human papillomavirus (HPV) occur specifically in the tonsils and the tongue base, but the reasons for this specificity remain unknown. We studied the distribution of oral and pharyngeal lesions in HPV16-transgenic mice where the expression of all the HPV16 early genes is targeted to keratinising squamous epithelia by the cytokeratin 14 (Krt14) gene promoter. At 30 weeks of age, 100% of mice developed low- and high-grade intraepithelial dysplasia at multiple sites. Twenty per cent of animals developed invasive cancers that remarkably were restricted to the tongue base, in association with the circumvallate papilla. The lesions maintained expression of CK14 (KRT14) and the HPV16 E6 and E7 oncogenes, and displayed deregulated cell proliferation and up-regulation of p16<sup>INK4A<\/sup> . Malignant lesions were poorly differentiated and destroyed the tongue musculature. We hypothesised that the tongue base area might contain a transformation zone similar to those observed in the cervix and anus, explaining why HPV-positive cancers target that area specifically. Immunohistochemistry for two transformation zone markers, CK7 (KRT7) and p63 (TP63), revealed a squamocolumnar junction in the terminal duct of von Ebner's gland, composed of CK7<sup>+<\/sup> luminal cells and p63<sup>+<\/sup> basal cells. Dysplastic and invasive lesions retained diffuse p63 expression but only scattered positivity for CK7. Site-specific HPV-induced carcinogenesis in the tongue base may be explained by the presence of a transformation zone in the circumvallate papilla. This mouse model reproduces key morphological and molecular features of HPV-positive HNSCC, providing a unique in vivo tool for basic and translational research. \u00a9 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.","authors":"Mestre, VF., Medeiros-Fonseca, B., Est\u00eav\u00e3o, D., Casaca, F., Silva, S., F\u00e9lix, A., Silva, F., Cola\u00e7o, B., Seixas, F., Bastos, MM., Lopes, C., Medeiros, R., Oliveira, PA., Gil da Costa, RM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Pathol","volume":"251","issue":"1","page":"4-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-169","title":"DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations","abstract":null,"authors":"Peycheva,M., Neumann, T., Malzl, D., Nazarova, M., Schoeberl, U., and Pavri, R. ","publication_status":"preprint","journalpubyear":"2021","journaltitle":"bioRxiv ","volume":"2021.05.29.446276","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.05.29.446276v1","preprintlink":null,"articledate":"2021-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25647662","title":"The interaction between epigenetics, nutrition and the development of cancer.","abstract":"Unlike the genome, the epigenome can be modified and hence some epigenetic risk markers have the potential to be reversed. Such modifications take place by means of drugs, diet or environmental exposures. It is widely accepted that epigenetic modifications take place during early embryonic and primordial cell development, but it is also important that we gain an understanding of the potential for such changes later in life. These \"later life\" epigenetic modifications in response to dietary intervention are the focus of this paper. The epigenetic modifications investigated include DNA methylation, histone modifications and the influence of microRNAs. The epigenotype could be used not only to predict susceptibility to certain cancers but also to assess the effectiveness of dietary modifications to reduce such risk. The influence of diet or dietary components on epigenetic modifications and the impact on cancer initiation or progression has been assessed herein.","authors":"Bishop, KS., Ferguson, LR.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Nutrients","volume":"7","issue":"2","page":"922-47","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31612958","title":"An improved platform for functional assessment of large protein libraries in mammalian cells.","abstract":"Multiplex genetic assays can simultaneously test thousands of genetic variants for a property of interest. However, limitations of existing multiplex assay methods in cultured mammalian cells hinder the breadth, speed and scale of these experiments. Here, we describe a series of improvements that greatly enhance the capabilities of a Bxb1 recombinase-based landing pad system for conducting different types of multiplex genetic assays in various mammalian cell lines. We incorporate the landing pad into a lentiviral vector, easing the process of generating new landing pad cell lines. We also develop several new landing pad versions, including one where the Bxb1 recombinase is expressed from the landing pad itself, improving recombination efficiency more than 2-fold and permitting rapid prototyping of transgenic constructs. Other versions incorporate positive and negative selection markers that enable drug-based enrichment of recombinant cells, enabling the use of larger libraries and reducing costs. A version with dual convergent promoters allows enrichment of recombinant cells independent of transgene expression, permitting the assessment of libraries of transgenes that perturb cell growth and survival. Lastly, we demonstrate these improvements by assessing the effects of a combinatorial library of oncogenes and tumor suppressors on cell growth. Collectively, these advancements make multiplex genetic assays in diverse cultured cell lines easier, cheaper and more effective, facilitating future studies probing how proteins impact cell function, using transgenic variant libraries tested individually or in combination.","authors":"Matreyek, KA., Stephany, JJ., Chiasson, MA., Hasle, N., Fowler, DM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nucleic Acids Res","volume":"48","issue":"1","page":"e1","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18959483","title":"Evolutionary plasticity of polycomb\/trithorax response elements in Drosophila species.","abstract":"cis-Regulatory DNA elements contain multiple binding sites for activators and repressors of transcription. Among these elements are enhancers, which establish gene expression states, and Polycomb\/Trithorax response elements (PREs), which take over from enhancers and maintain transcription states of several hundred developmentally important genes. PREs are essential to the correct identities of both stem cells and differentiated cells. Evolutionary differences in cis-regulatory elements are a rich source of phenotypic diversity, and functional binding sites within regulatory elements turn over rapidly in evolution. However, more radical evolutionary changes that go beyond motif turnover have been difficult to assess. We used a combination of genome-wide bioinformatic prediction and experimental validation at specific loci, to evaluate PRE evolution across four Drosophila species. Our results show that PRE evolution is extraordinarily dynamic. First, we show that the numbers of PREs differ dramatically between species. Second, we demonstrate that functional binding sites within PREs at conserved positions turn over rapidly in evolution, as has been observed for enhancer elements. Finally, although it is theoretically possible that new elements can arise out of nonfunctional sequence, evidence that they do so is lacking. We show here that functional PREs are found at nonorthologous sites in conserved gene loci. By demonstrating that PRE evolution is not limited to the adaptation of preexisting elements, these findings document a novel dimension of cis-regulatory evolution.","authors":"Hauenschild, A., Ringrose, L., Altmutter, C., Paro, R., Rehmsmeier, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"PLoS Biol","volume":"6","issue":"10","page":"e261","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31633304","title":"Targeting YAP to overcome acquired resistance to ALK inhibitors in ALK-rearranged lung cancer.","abstract":"Clinical benefit of ALK tyrosine kinase inhibitors (ALK-TKIs) in ALK-rearranged lung cancer has been limited by the inevitable development of acquired resistance, and bypass-molecular resistance mechanisms remain poorly understood. We investigated a novel therapeutic target through screening FDA-approved drugs in ALK-TKI-resistant models. Cerivastatin, the rate-limiting enzyme inhibitor of the mevalonate pathway, showed anti-cancer activity against ALK-TKI resistance in\u00a0vitro\/in\u00a0vivo, accompanied by cytoplasmic retention and subsequent inactivation of transcriptional co-regulator YAP. The marked induction of YAP-targeted oncogenes (EGFR, AXL, CYR61, and TGF\u03b2R2) in resistant cells was abolished by cerivastatin. YAP silencing suppressed tumor growth in resistant cells, patient-derived xenografts, and EML4-ALK transgenic mice, whereas YAP overexpression decreased the responsiveness of parental cells to ALK inhibitor. In matched patient samples before\/after ALK inhibitor treatment, nuclear accumulation of YAP was mainly detected in post-treatment samples. High expression of YAP in pretreatment samples was correlated with poor response to ALK-TKIs. Our findings highlight a crucial role of YAP in ALK-TKI resistance and provide a rationale for targeting YAP as a potential treatment option for ALK-rearranged patients with acquired resistance to ALK inhibitors.","authors":"Yun, MR., Choi, HM., Lee, YW., Joo, HS., Park, CW., Choi, JW., Kim, DH., Kang, HN., Pyo, KH., Shin, EJ., Shim, HS., Soo, RA., Yang, JC., Lee, SS., Chang, H., Kim, MH., Hong, MH., Kim, HR., Cho, BC.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"EMBO Mol Med","volume":"11","issue":"12","page":"e10581","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18799150","title":"The cytokine RANKL produced by positively selected thymocytes fosters medullary thymic epithelial cells that express autoimmune regulator.","abstract":"The thymic medulla provides a microenvironment where medullary thymic epithelial cells (mTECs) express autoimmune regulator and diverse tissue-restricted genes, contributing to launching self-tolerance. Positive selection is essential for thymic medulla formation via a previously unknown mechanism. Here we show that the cytokine RANK ligand (RANKL) was produced by positively selected thymocytes and regulated the cellularity of mTEC by interacting with RANK and osteoprotegerin. Forced expression of RANKL restored thymic medulla in mice lacking positive selection, whereas RANKL perturbation impaired medulla formation. These results indicate that RANKL produced by positively selected thymocytes is responsible for fostering thymic medulla formation, thereby establishing central tolerance.","authors":"Hikosaka, Y., Nitta, T., Ohigashi, I., Yano, K., Ishimaru, N., Hayashi, Y., Matsumoto, M., Matsuo, K., Penninger, JM., Takayanagi, H., Yokota, Y., Yamada, H., Yoshikai, Y., Inoue, J., Akiyama, T., Takahama, Y.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Immunity","volume":"29","issue":"3","page":"438-50","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2008-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34048695","title":"ISSCR guidelines for the transfer of human pluripotent stem cells and their direct derivatives into animal hosts.","abstract":"The newly revised 2021 ISSCR Guidelines for Stem Cell Research and Clinical Translation includes scientific and ethical guidance for the transfer of human pluripotent stem cells and their direct derivatives into animal models. In this white paper, the ISSCR subcommittee that drafted these guidelines for research involving the use of nonhuman embryos and postnatal animals explains and summarizes their recommendations.","authors":"Hyun, I., Clayton, EW., Cong, Y., Fujita, M., Goldman, SA., Hill, LR., Monserrat, N., Nakauchi, H., Pedersen, RA., Rooke, HM., Takahashi, J., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Stem Cell Reports","volume":"16","issue":"6","page":"1409-1415","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31534167","title":"Non-hematopoietic STAT6 induces epithelial tight junction dysfunction and promotes intestinal inflammation and tumorigenesis.","abstract":"Enhanced gut permeability due to dysregulated epithelial tight junction is often associated with inflammatory bowel diseases (IBD), which have a greater risk for developing colorectal cancer. STAT6 activation was detected in inflamed colonic epithelium of active IBD patients, suggesting a role of epithelial STAT6 in colitis development. Here, we demonstrated that non-hematopoietic STAT6, but not hematopoietic STAT6, triggered DSS-induced colitis and subsequent tumorigenesis. This could be due to the enhancing-effect of STAT6 on gut permeability and microbiota translocation via interruption of epithelial tight junction integrity. Mechanistically, long-myosin light-chain kinase (MLCK1) was identified as a target of STAT6, leading to epithelial tight junction dysfunction and microbiota-driven colitis. Furthermore, neutralization of IL-13, which was primarily derived from type 2 innate lymphoid cells (ILC2) in a microbiota-dependent way, inhibited epithelial STAT6 activation and improved gut permeability and DSS-induced colitis. Importantly, pharmacological inhibition of STAT6 reduces murine intestinal tumor formation, and tumoral p-STAT6 levels positively correlated to the clinical stage and poor prognosis of human colorectal cancer. Thus, our study reveals a direct role of STAT6 in the disruption of epithelial tight junction integrity and colitis development, and suggests STAT6 as a potential therapeutic and prophylactic target for IBD and colitis-associated cancer.","authors":"Lin, Y., Li, B., Yang, X., Liu, T., Shi, T., Deng, B., Zhang, Y., Jia, L., Jiang, Z., He, R.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mucosal Immunol","volume":"12","issue":"6","page":"1304-1315","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11309624","title":"Degradation of a cohesin subunit by the N-end rule pathway is essential for chromosome stability.","abstract":"Cohesion between sister chromatids is established during DNA replication and depends on a protein complex called cohesin. At the metaphase-anaphase transition in the yeast Saccharomyces cerevisiae, the ESP1-encoded protease separin cleaves SCC1, a subunit of cohesin with a relative molecular mass of 63,000 (Mr 63K). The resulting 33K carboxy-terminal fragment of SCC1 bears an amino-terminal arginine-a destabilizing residue in the N-end rule. Here we show that the SCC1 fragment is short-lived (t1\/2 approximately 2 min), being degraded by the ubiquitin\/proteasome-dependent N-end rule pathway. Overexpression of a long-lived derivative of the SCC1 fragment is lethal. In ubr1Delta cells, which lack the N-end rule pathway, we found a highly increased frequency of chromosome loss. The bulk of increased chromosome loss in ubr1Delta cells is caused by metabolic stabilization of the ESP1-produced SCC1 fragment. This fragment is the first physiological substrate of the N-end rule pathway that is targeted through its N-terminal residue. A number of yeast proteins bear putative cleavage sites for the ESP1 separin, suggesting other physiological substrates and functions of the N-end rule pathway.","authors":"Rao, H., Uhlmann, F., Nasmyth, K., Varshavsky, A.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nature","volume":"410","issue":"6831","page":"955-9","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11157052","title":"c-Jun NH2-terminal kinase (JNK)1 and JNK2 have similar and stage-dependent roles in regulating T cell apoptosis and proliferation.","abstract":"Apoptotic and mitogenic stimuli activate c-Jun NH2-terminal kinases (JNKs) in T cells. Although T cells express both JNK1 and JNK2 isozymes, the absence of JNK2 alone can result in resistance to anti-CD3-induced thymocyte apoptosis and defective mature T cell proliferation. Similar defects in thymocyte apoptosis and mature T cell proliferation, the latter due to reduced interleukin 2 production, are also caused by JNK1 deficiency. Importantly, T cell function was compromised in Jnk1(+\/-)Jnk2(+\/-) double heterozygous mice, indicating that JNK1 and JNK2 play similar roles in regulating T cell function. The reduced JNK dose results in defective c-Jun NH2-terminal phosphorylation in thymocytes but not in peripheral T cells, in which nuclear factors of activated T cells (NK-ATs)-DNA binding activity is affected. Thus, JNK1 and JNK2 control similar functions during T cell maturation through differential targeting of distinct substrates.","authors":"Sabapathy, K., Kallunki, T., David, JP., Graef, I., Karin, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Exp Med","volume":"193","issue":"3","page":"317-28","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2001-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31923184","title":"Autophagy gene haploinsufficiency drives chromosome instability, increases migration, and promotes early ovarian tumors.","abstract":"Autophagy, particularly with BECN1, has paradoxically been highlighted as tumor promoting in Ras-driven cancers, but potentially tumor suppressing in breast and ovarian cancers. However, studying the specific role of BECN1 at the genetic level is complicated due to its genomic proximity to BRCA1 on both human (chromosome 17) and murine (chromosome 11) genomes. In human breast and ovarian cancers, the monoallelic deletion of these genes is often co-occurring. To investigate the potential tumor suppressor roles of two of the most commonly deleted autophagy genes in ovarian cancer, BECN1 and MAP1LC3B were knocked-down in atypical (BECN1+\/+ and MAP1LC3B+\/+) ovarian cancer cells. Ultra-performance liquid chromatography mass-spectrometry metabolomics revealed reduced levels of acetyl-CoA which corresponded with elevated levels of glycerophospholipids and sphingolipids. Migration rates of ovarian cancer cells were increased upon autophagy gene knockdown. Genomic instability was increased, resulting in copy-number alteration patterns which mimicked high grade serous ovarian cancer. We further investigated the causal role of Becn1 haploinsufficiency for oncogenesis in a MISIIR SV40 large T antigen driven spontaneous ovarian cancer mouse model. Tumors were evident earlier among the Becn1+\/- mice, and this correlated with an increase in copy-number alterations per chromosome in the Becn1+\/- tumors. The results support monoallelic loss of BECN1 as permissive for tumor initiation and potentiating for genomic instability in ovarian cancer.","authors":"Delaney, JR., Patel, CB., Bapat, J., Jones, CM., Ramos-Zapatero, M., Ortell, KK., Tanios, R., Haghighiabyaneh, M., Axelrod, J., DeStefano, JW., Tancioni, I., Schlaepfer, DD., Harismendy, O., La Spada, AR., Stupack, DG.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"PLoS Genet","volume":"16","issue":"1","page":"e1008558","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30599077","title":"Amyloid-\u03b2 pathology enhances pathological fibrillary tau seeding induced by Alzheimer PHF in vivo.","abstract":"Neuropathological analysis in Alzheimer's disease (AD) and experimental evidence in transgenic models overexpressing frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17) mutant tau suggest that amyloid-\u03b2 pathology enhances the development of tau pathology. In this work, we analyzed this interaction independently of the overexpression of an FTDP-17 mutant tau, by analyzing tau pathology in wild-type (WT), 5xFAD, APP<sup>-\/-<\/sup> and tau<sup>-\/-<\/sup> mice after stereotaxic injection in the somatosensory cortex of short-length native human AD-PHF. Gallyas and phosphotau-positive tau inclusions developed in WT, 5xFAD, and APP<sup>-\/-<\/sup> but not in tau<sup>-\/-<\/sup> mice. Ultrastructural analysis demonstrated their intracellular localization and that they were composed of straight filaments. These seeded tau inclusions were composed only of endogenous murine tau exhibiting a tau antigenic profile similar to tau aggregates in AD. Insoluble tau level was higher and ipsilateral anteroposterior and contralateral cortical spreading of tau inclusions was more important in AD-PHF-injected 5xFAD mice than in WT mice. The formation of large plaque-associated dystrophic neurites positive for oligomeric and phosphotau was observed in 5xFAD mice injected with AD-PHF but never in control-injected or in non-injected 5xFAD mice. An increased level of the p25 activator of CDK5 kinase was found in AD-PHF-injected 5xFAD mice. These data demonstrate in vivo that the presence of A\u03b2 pathology enhances experimentally induced tau seeding of endogenous, wild-type tau expressed at physiological level, and demonstrate the fibrillar nature of heterotopically seeded endogenous tau. These observations further support the hypothesis that A\u03b2 enhances tau pathology development in AD through increased pathological tau spreading.","authors":"Vergara, C., Houben, S., Suain, V., Yilmaz, Z., De Decker, R., Vanden Dries, V., Boom, A., Mansour, S., Leroy, K., Ando, K., Brion, JP.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Acta Neuropathol","volume":"137","issue":"3","page":"397-412","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32122998","title":"Mapping the Chromosomal Insertion Site of the GFP Transgene of UBC-GFP Mice to the MHC Locus.","abstract":"GFP is frequently used as a marker for tracking donor cells adoptively transplanted into recipient animals. The human ubiquitin C promoter (UBC)-driven-GFP transgenic mouse is a commonly used source of donor cells for this purpose. This mouse was initially generated in the C57BL\/6 inbred strain and has been backcrossed into the BALB\/cBy strain for over 11 generations. Both the C57BL\/6 inbred and BALB\/cBy congenic UBC-GFP lines are commercially available and have been widely distributed. These UBC-GFP lines can be a convenient resource for tracking donor cells in both syngenic MHC-matched and in allogenic MHC-mismatched studies as C57BL\/6 (H-2<sup>b<\/sup>) and BALB\/cBy (H-2<sup>d<\/sup>) have disparate MHC haplotypes. In this report, we surprisingly discover that the UBC-GFP BALB\/cBy congenic mice still retain the H-2<sup>b<\/sup> MHC haplotype of their original C57BL\/6 founder, suggesting that the UBC-GFP transgene integration site is closely linked to the MHC locus on chromosome 17. Using linear amplification-mediated PCR, we successfully map the UBC-GFP transgene to the MHC locus. This study highlights the importance and urgency of mapping the transgene integration site of transgenic mouse strains used in biomedical research. Furthermore, this study raises the possibility of alternative interpretations of previous studies using congenic UBC-GFP mice and focuses attention on the necessity for rigor and reproducibility in scientific research.","authors":"Liu, S., Lockhart, JR., Fontenard, S., Berlett, M., Ryan, TM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Immunol","volume":"204","issue":"7","page":"1982-1987","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16077977","title":"Preferential inhibition of bone metastases by 5'-deoxy-5-fluorouridine and capecitabine in the 4T1\/luc mouse breast cancer model.","abstract":"5'-deoxy-5-fluorouridine (5'-DFUR) and capecitabine are oral anti-cancer agents, which are enzymatically converted to 5-fluorouracil (5-FU) by thymidine phosphorylase in humans and uridine phosphorylase in mice. Since the activity of these phosphorylases is higher in cancerous tissue than in normal tissue, systemic administration of 5'-DFUR and capecitabine achieves high intratumoral 5-FU levels and low adverse effects on non-tumoral tissue. Accordingly, 5'-DFUR and capecitabine are widely used for the treatment of cancer patients. In the present study, we examined the effects of 5'-DFUR and capecitabine on bone metastases, one of the most common complications of breast cancer, using an animal model in which inoculation of 4T1\/luc mouse breast cancer cells into the mammary fat pads of female BALB\/c mice developed spontaneous metastases in distant organs including bone, lung and liver. Mice received 4T1\/luc cell inoculation in the mammary fat pad at day 0 and oral 5'-DFUR (31, 62, 123 or 246 mg\/kg) or capecitabine (90, 180 or 359 mg\/kg) daily from day 7 to day 21. Both 5'-DFUR and capecitabine significantly inhibited orthotopic tumor formation and distant metastases to bone, lung and liver in a dose-dependent manner. Of note, the lowest dose of 5'-DFUR (31 mg\/kg) and capecitabine (90 mg\/kg), which failed to inhibit orthotopic tumor development and the lung and liver metastases, significantly reduced the bone metastases. In conclusion, our results suggest that oral 5'-DFUR and capecitabine are effective for the treatment of primary and secondary breast tumors. Most notably, they also suggest that these agents are preferentially beneficial for bone metastases.","authors":"Hiraga, T., Hata, K., Ikeda, F., Kitagaki, J., Fujimoto-Ouchi, K., Tanaka, Y., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Oncol Rep","volume":"14","issue":"3","page":"695-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11278689","title":"NADH oxidase activity of mitochondrial apoptosis-inducing factor.","abstract":"Apoptosis-inducing factor (AIF) is a mitochondrial flavoprotein, which translocates to the nucleus during apoptosis and causes chromatin condensation and large scale DNA fragmentation. Here we report the biochemical characterization of AIF's redox activity. Natural AIF purified from mitochondria and recombinant AIF purified from bacteria (AIFDelta1-120) exhibit NADH oxidase activity, whereas superoxide anion (O(2)(-)) is formed. AIFDelta1-120 is a monomer of 57 kDa containing 1 mol of noncovalently bound FAD\/mol of protein. ApoAIFDelta1-120, which lacks FAD, has no NADH oxidase activity. However, native AIFDelta1-120, apoAIFDelta1-120, and the reconstituted (FAD-containing) holoAIFDelta1-120 protein exhibit a similar apoptosis-inducing potential when microinjected into the cytoplasm of intact cells. Inhibition of the redox function, by external addition of superoxide dismutase or covalent derivatization of FAD with diphenyleneiodonium, failed to affect the apoptogenic function of AIFDelta1-120 assessed on purified nuclei in a cell-free system. Conversely, blockade of the apoptogenic function of AIFDelta1-120 with the thiol reagent para- chloromercuriphenylsulfonic acid did not affect its NADH oxidase activity. Altogether, these data indicate that AIF has a marked oxidoreductase activity which can be dissociated from its apoptosis-inducing function.","authors":"Miramar, MD., Costantini, P., Ravagnan, L., Saraiva, LM., Haouzi, D., Brothers, G., Penninger, JM., Peleato, ML., Kroemer, G., Susin, SA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Biol Chem","volume":"276","issue":"19","page":"16391-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31594448","title":"Landscape of RNA editing reveals new insights into the dynamic gene regulation of spermatogenesis.","abstract":"Spermatogenesis is an important physiological process associated with male infertility. As a kind of post-transcriptional regulation, RNA editings (REs) change the genetic information at the mRNA level. But whether there are REs and what's the role of REs during the process are still unclear. In this study, we integrated published RNA-Seq datasets and established a landscape of RNA REs during the development of mouse spermatogenesis. Totally, 7530 editing sites occurred in 2012 genes among all types of male germ cells were found, these sites enrich on some regions of chromosomes, including chromosome 17 and both ends of chromosome Y. We also found about half of the REs in CDSs can cause amino acids changes. Some non-synonymous REs which exist in specific genes may play important roles in spermatogenesis. Finally, we verified a non-synonymous A-to-I RNA editing site in <i>Cog3<\/i> and a stoploss editing in <i>Tssk6<\/i> during spermatogenesis. In short, we systematically analyzed the dynamic landscape of RNA editing at different stages of spermatogenesis.","authors":"Wang, X., Wu, X., Zhu, Z., Li, H., Li, T., Li, Q., Zhang, P., Li, L., Che, D., Xiao, X., Liu, T., Hua, J., Liao, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell Cycle","volume":"18","issue":"23","page":"3351-3364","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31544793","title":"Genetic analysis of the mandible morphology in DDD.Cg-<i>A<\/i><i><sup>y<\/sup><\/i>\/Sgn and C57BL\/6J inbred mice.","abstract":"Quantitative trait loci (QTL) mapping analysis was performed for the mandible morphology in DDD.Cg-<i>A<\/i><i><sup>y<\/sup><\/i>\/Sgn and C57BL\/6J inbred mice. The size and shape of the mandible was analysed by landmark-based geometric morphometrics as the centroid size and principal components (PCs), respectively. The <i>A<\/i><i><sup>y<\/sup><\/i> allele at the <i>agouti<\/i> locus significantly reduced the mandible size in DDD\/Sgn background, and substantially altered the mandible shape in both strain backgrounds. Single-QTL scans, by including the <i>agouti<\/i> locus genotype (<i>A<\/i><i><sup>y<\/sup><\/i> or non-<i>A<\/i><i><sup>y<\/sup><\/i>) as an additive covariate, identified three significant QTL for the centroid size on chromosomes 5, 6 and 17, along with four suggestive QTL on chromosomes 2, 12, 18 and 19. These QTLs explained 46.85% of the centroid size variation in F<sub>2<\/sub> mice. When the F<sub>2<\/sub><i>A<\/i><i><sup>y<\/sup><\/i> and F<sub>2<\/sub> non-<i>A<\/i><i><sup>y<\/sup><\/i> mice were analysed separately, additional significant QTL were identified on chromosomes 12 and 15 in F<sub>2<\/sub> non-<i>A<\/i><i><sup>y<\/sup><\/i> mice. Single-QTL scans also identified 15 significant QTL for the PC1, PC2 and PC3. When the <i>agouti<\/i> locus genotype was included as an interactive covariate, nine significant QTLs were identified. Unexpectedly, these agouti-interacting QTLs were identified for relatively minor PCs, for which no significant single-QTL were identified. Therefore, it was suggested that the alteration of the mandible shape in <i>A<\/i><i><sup>y<\/sup><\/i> mice was the consequence of interactions between the <i>A<\/i><i><sup>y<\/sup><\/i> allele and genes that themselves have relatively small phenotypic effect. Although further <i>in vivo<\/i> studies are required, we postulated <i>Pkd1<\/i> as a possible candidate gene underlying QTL for the centroid size on chromosome 17.","authors":"Suto, JI.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Genet","volume":"98","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18755003","title":"Unravelling the structure of the lamellipodium.","abstract":"Summary Pushing at the cell front is the business of lamellipodia and understanding how lamellipodia function requires knowledge of their structural organization. Analysis of extracted, critical-point-dried cells by electron microscopy has led to a current dogma that the lamellipodium pushes as a branched array of actin filaments, with a branching angle of 70 degrees , defined by the Arp2\/3 complex. Comparison of different preparative methods indicates that the critical-point-drying-replica technique introduces distortions into actin networks, such that crossing filaments may appear branched. After negative staining and from preliminary studies by cryo-electron tomography, no clear evidence could be found for actin filament branching in lamellipodia. From recent observations of a sub-class of actin speckles in lamellipodia that exhibit a dynamic behaviour similar to speckles in the lamella region behind, it has been proposed that the lamellipodium surfs on top of the lamella. Negative stain electron microscopy and cryo-electron microscopy of fixed cells, which reveal the entire complement of filaments in lamellipodia show, however, that there is no separate, second array of filaments beneath the lamellipodium network. From present data, we conclude that the lamellipodium is a distinct protrusive entity composed of a network of primarily unbranched actin filaments. Cryo-electron tomography of snap-frozen intact cells will be required to finally clarify the three-dimensional arrangement of actin filaments in lamellipodia in vivo.","authors":"Small, JV., Auinger, S., Nemethova, M., Koestler, S., Goldie, KN., Hoenger, A., Resch, GP.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Microsc","volume":"231","issue":"3","page":"479-85","pdf":null,"JrId":"4961","fulltextlink":null,"preprintlink":null,"articledate":"2008-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31102955","title":"Confirmation of Ath26 locus on chromosome 17 and identification of Cyp4f13 as an atherosclerosis modifying gene.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31102955<\/PMID><DateCompleted><Year>2020<\/Year><Month>07<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>07<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-1484<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>286<\/Volume><PubDate><Year>2019<\/Year><Month>07<\/Month><\/PubDate><\/JournalIssue><Title>Atherosclerosis<\/Title><ISOAbbreviation>Atherosclerosis<\/ISOAbbreviation><\/Journal><ArticleTitle>Confirmation of Ath26 locus on chromosome 17 and identification of Cyp4f13 as an atherosclerosis modifying gene.<\/ArticleTitle><Pagination><MedlinePgn>71-78<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0021-9150(19)30412-5<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.atherosclerosis.2019.05.007<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND AND AIMS\">We previously demonstrated that Apoe<sup>-\/-<\/sup> mice on DBA\/2 vs. AKR genetic background have &gt;10-fold larger atherosclerotic lesions. Prior quantitative trait locus mapping via strain intercrossing identified a region on chromosome 17, Ath26, as the strongest atherosclerosis-modifying locus. We aimed to confirm Ath26, identify candidate genes, and validate the candidate gene effects on atherosclerosis.","authors":"Han, J., Robinet, P., Ritchey, B., Andro, H., Smith, JD.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Atherosclerosis","volume":"286","issue":"","page":"71-78","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30853403","title":"Mutation in NADPH oxidase 3 (NOX3) impairs SHH signaling and increases cerebellar neural stem\/progenitor cell proliferation.","abstract":"Abnormalities in cerebellar structure and function may cause ataxia, a neurological dysfunction of motor coordination. In the course of the present study, we characterized a mutant mouse lineage with an ataxia-like phenotype. We localized the mutation on chromosome 17 and mapped it to position 1534 of the Nox3 gene, resulting in p.Asn64Tyr change. The primary defect observed in Nox3<sup>eqlb<\/sup> mice was increased proliferation of cerebellar granule cell precursors (GCPs). cDNA microarray comparing Nox3<sup>eqlb<\/sup> and BALB\/c neonatal cerebellum revealed changes in the expression of genes involved in the control of cell proliferation. Nox3<sup>eqlb<\/sup> GCPs and NSC produce higher amounts of reactive oxygen species (ROS) and upregulate the expression of SHH target genes, such as Gli1-3 and Ccnd1 (CyclinD1). We hypothesize that this new mutation is responsible for an increase in proliferation via stimulation of the SHH pathway. We suggest this mutant mouse lineage as a new model to investigate the role of ROS in neuronal precursor cell proliferation.","authors":"Mazzonetto, PC., Ariza, CB., Ocanha, SG., de Souza, TA., Ko, GM., Menck, CFM., Massironi, SMG., Porcionatto, MA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Biochim Biophys Acta Mol Basis Dis","volume":"1865","issue":"6","page":"1502-1515","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1840125","title":"Biology of murine gamma delta T cells.","abstract":"Murine lymphocytes express either a T-cell receptor alpha beta or a gamma delta heterodimer. The function of alpha beta cells are well characterized, while gamma delta cells remain an enigmatic population. In the mouse, gamma delta cells appear in significant proportions in the epithelia of various nonlymphoid tissues such as the skin, intestine, tongue, lung, and reproductive organs. While gamma delta T-cell subsets with distinct antigen receptor repertoires are associated with certain organs, diversified populations of gamma delta cells showing heterogeneous TCR phenotypes, as a result of junctional region diversification and usage of different V chains, can be found in the lymphoid organs and in the intestinal epithelia. Recent evidence has shown that gamma delta cells might recognize heat shock proteins, possibly in association with classical and nonpolymorphic MHC molecules. Together with their tissue distribution, gamma delta cells may represent the first line of defense of the immune system. gamma delta Cells are the first T cells to colonize the thymus. Intriguingly, there is more evidence to support the hypothesis that they might also affect the development of alpha beta cells and other hematopoietic stem cells.","authors":"Cheng, SH., Penninger, JM., Ferrick, DA., Molina, TJ., Wallace, VA., Mak, TW.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Crit Rev Immunol","volume":"11","issue":"3-4","page":"145-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1992-07-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18708581","title":"Study of an RNA helicase implicates small RNA-noncoding RNA interactions in programmed DNA elimination in Tetrahymena.","abstract":"Tetrahymena eliminates micronuclear-limited sequences from the developing macronucleus during sexual reproduction. Homology between the sequences to be eliminated and approximately 28-nucleotide small RNAs (scnRNAs) associated with an Argonaute family protein Twi1p likely underlies this elimination process. However, the mechanism by which Twi1p-scnRNA complexes identify micronuclear-limited sequences is not well understood. We show that a Twi1p-associated putative RNA helicase Ema1p is required for the interaction between Twi1p and chromatin. This requirement explains the phenotypes of EMA1 KO strains, including loss of selective down-regulation of scnRNAs homologous to macronuclear-destined sequences, loss of H3K9 and K27 methylation in the developing new macronucleus, and failure to eliminate DNA. We further demonstrate that Twi1p interacts with noncoding transcripts derived from parental and developing macronuclei and this interaction is greatly reduced in the absence of Ema1p. We propose that Ema1p functions in DNA elimination by stimulating base-pairing interactions between scnRNAs and noncoding transcripts in both parental and developing new macronuclei.","authors":"Aronica, L., Bednenko, J., Noto, T., DeSouza, LV., Siu, KW., Loidl, J., Pearlman, RE., Gorovsky, MA., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genes Dev","volume":"22","issue":"16","page":"2228-41","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30553886","title":"Differential accumulation of Tau phosphorylated at residues Thr231, Ser262 and Thr205 in hippocampal interneurons and its modulation by Tau mutations (VLW) and amyloid-\u03b2 peptide.","abstract":"Alzheimer's disease (AD) is characterized by the accumulation of amyloid-\u03b2 peptide (A\u03b2) and hyperphosphorylated Tau protein (P-Tau). Our recent data showed a differential accumulation of Tau protein phosphorylated at residue Thr231 (pThr231) in distinct hippocampal neurons in VLW mice-a model that overexpresses mutated human Tau. Here we demonstrate that, in VLW mice, the accumulation of human P-Tau in pyramidal cells induces the phosphorylation of murine Tau at residue Thr231 in hippocampal interneurons. In addition, we show that pSer262 and pThr205 Tau are present specifically in the soma of some hippocampal interneurons in control mice. Analysis of J20 mice-a model that accumulates A\u03b2-and of VLW animals showed that the density of hippocampal interneurons accumulating pThr205 Tau is lower in VLW mice than in controls. In contrast, the density of interneurons accumulating pThr205 Tau in J20 mice was increased compared to controls in hippocampal regions with a higher A\u03b2 plaque load, thereby suggesting that pThr205 Tau is induced by A\u03b2. No significant differences were found between the density of hippocampal interneurons positive for pSer262 Tau in VLW or J20 mice compared to control animals. We also show that pSer262 and pThr205 Tau are present in the soma of some hippocampal interneurons containing Parvalbumin, Calbindin or Calretinin in control, VLW, and J20 mice. Moreover, our results reveal that some interneurons in human hippocampi of cases of AD and control cases accumulate pSer262 and pThr205 Tau. Taken together, these data point to a specific role of pSer262 and pThr205 Tau in the soma of hippocampal interneurons in control and pathological conditions.","authors":"D\u00e1vila-Bouziguet, E., Targa-Fabra, G., \u00c1vila, J., Soriano, E., Pascual, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Neurobiol Dis","volume":"125","issue":"","page":"232-244","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11192622","title":"Lesion-induced changes in NMDA receptor subunit mRNA expression in rat visual cortex.","abstract":"Focal lesions in the visual cortex are well known to induce pronounced perilesional reorganization of the neuronal circuitry. Since NMDA receptors crucially control synaptic plasticity and reorganization, we studied lesion-induced changes in their subunit expression and biophysical properties. Between 8 and 10 days after focal thermolesioning, pyramidal neurones in the near surround of the lesion were studied in acute brain slices. We found a significant decrease in the ratio of NR2A and NR2B subunit mRNA as compared to neurones from sham operated animals. Interestingly, no significant differences in the properties of NMDA receptor-mediated postsynaptic currents (NMDA PSCs) were observed between lesioned and sham operated animals. Thus, the observed perilesional changes in the NR2A\/NR2B mRNA ratio appear to be subthreshold to result in significant changes in the functional properties of NMDA receptors.","authors":"Rumpel, S., Hoffmann, H., Hatt, H., Gottmann, K., Mittmann, T., Eysel, UT.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Neuroreport","volume":"11","issue":"18","page":"4021-5","pdf":null,"JrId":"1199","fulltextlink":null,"preprintlink":null,"articledate":"2001-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26493646","title":"Functional and genetic deconstruction of the cellular origin in liver cancer.","abstract":"During the past decade, research on primary liver cancers has particularly highlighted the uncommon plasticity of differentiated parenchymal liver cells (that is, hepatocytes and cholangiocytes (also known as biliary epithelial cells)), the role of liver progenitor cells in malignant transformation, the importance of the tumour microenvironment and the molecular complexity of liver tumours. Whereas other reviews have focused on the landscape of genetic alterations that promote development and progression of primary liver cancers and the role of the tumour microenvironment, the crucial importance of the cellular origin of liver cancer has been much less explored. Therefore, in this Review, we emphasize the importance and complexity of the cellular origin in tumour initiation and progression, and attempt to integrate this aspect with recent discoveries in tumour genomics and the contribution of the disrupted hepatic microenvironment to liver carcinogenesis.","authors":"Marquardt, JU., Andersen, JB., Thorgeirsson, SS.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Rev Cancer","volume":"15","issue":"11","page":"653-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31100412","title":"The ATP-binding cassette transporter ABCF1 is a hepatic oncofetal protein that promotes chemoresistance, EMT and cancer stemness in hepatocellular carcinoma.","abstract":"ATP-binding cassette (ABC) transporters mediate multidrug resistance and cancer stem cell properties in various model systems. Yet, their biological significance in cancers, especially in hepatocellular carcinoma (HCC), remains unclear. In this study, we investigated the function of ABCF1 in HCC and explored its potential as a therapeutic target. ABCF1 was highly expressed in fetal mouse livers but not in normal adult livers. ABCF1 expression was upregulated in HCCs. These results demonstrate that ABCF1 functions as a hepatic oncofetal protein. We further demonstrated elevated ABCF1 expression in HCC cells upon acquiring chemoresistance. Suppression of ABCF1 by siRNA sensitized both parental cells and chemoresistant cells to chemotherapeutic agents. Reversely, ABCF1 overexpression promoted chemoresistance and drug efflux. In addition, overexpression of ABCF1 enhanced migration, spheroid and colony formation and epithelial-mesenchymal transition (EMT) induction. RNA sequencing analysis revealed EMT inducers HIF1\u03b1\/IL8 and Sox4 as potential mediators for the oncogenic effect of ABCF1 in HCC progression. Together, this study illustrates that ABCF1 is a novel potential therapeutic target for HCC treatment.","authors":"Fung, SW., Cheung, PF., Yip, CW., Ng, LW., Cheung, TT., Chong, CC., Lee, C., Lai, PB., Chan, AW., Tsao, GS., Wong, CH., Chan, SL., Lo, KW., Cheung, ST.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cancer Lett","volume":"457","issue":"","page":"98-109","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18676810","title":"A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse.","abstract":"H4K20 methylation is a broad chromatin modification that has been linked with diverse epigenetic functions. Several enzymes target H4K20 methylation, consistent with distinct mono-, di-, and trimethylation states controlling different biological outputs. To analyze the roles of H4K20 methylation states, we generated conditional null alleles for the two Suv4-20h histone methyltransferase (HMTase) genes in the mouse. Suv4-20h-double-null (dn) mice are perinatally lethal and have lost nearly all H4K20me3 and H4K20me2 states. The genome-wide transition to an H4K20me1 state results in increased sensitivity to damaging stress, since Suv4-20h-dn chromatin is less efficient for DNA double-strand break (DSB) repair and prone to chromosomal aberrations. Notably, Suv4-20h-dn B cells are defective in immunoglobulin class-switch recombination, and Suv4-20h-dn deficiency impairs the stem cell pool of lymphoid progenitors. Thus, conversion to an H4K20me1 state results in compromised chromatin that is insufficient to protect genome integrity and to process a DNA-rearranging differentiation program in the mouse.","authors":"Schotta, G., Sengupta, R., Kubicek, S., Malin, S., Kauer, M., Call\u00e9n, E., Celeste, A., Pagani, M., Opravil, S., De La Rosa-Velazquez, IA., Espejo, A., Bedford, MT., Nussenzweig, A., Busslinger, M., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genes Dev","volume":"22","issue":"15","page":"2048-61","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25448606","title":"Role of miRNAs in endometrial cancer.","abstract":"Endometrial cancer (EC) is the most common gynecologic malignancy. MicroRNAs (miRNAs) were recently associated with carcinogenesis and progression of EC. In this review, we discuss recent advances and the emerging role of miRNAs in EC and their clinical implications, with special emphasis on the differences between deregulated miRNAs in type I and type II EC, as well as the impact of this dysregulation on EC initiation and progression.","authors":"Li, S., Zhang, J., Wan, X.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Histol Histopathol","volume":"30","issue":"5","page":"539-48","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26454884","title":"Regulation of Aquaporin 3 Expression by the AhR Pathway Is Critical to Cell Migration.","abstract":"The regulation of cell migration is a key factor for the dissemination of metastatic cells during tumor progression. Aquaporins are membrane channels which allow transmembrane fluxes of water and glycerol in cells in a variety of mammalian tissues. Here, we show that AQP3, which has been incriminated in cancer progression, is regulated by the AhR, or dioxin receptor. AhR is a transcription factor which is triggered in response to environmental pollutants and it has been shown to regulate several cellular processes including cell migration and plasticity. In vivo, upon exposure to the aryl hydrocarbon receptor (AhR) ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the expression of AQP3 is increased significantly in several murine tissues including the liver. In vitro, treatment of human HepG2 cells with TCDD also increased the expression of AQP3 mRNA and protein. These effects resulted from the activation of AhR as shown by RNA interference, chromatin immunoprecipitation and the use of several AhR ligands. Immunofluorescence and real-time analysis of cell migration (XCelligence) demonstrated that knockdown of AQP3 mRNA using small interfering RNA impairs the remodeling of cell shape and the triggering of cell migration that is induced by TCDD. Our work reveals, for the first time, a link between exposure to pollutant and the induction of an aquaporin which has been suspected to play a role during metastasis.","authors":"Bui, LC., Tomkiewicz, C., Pierre, S., Chevallier, A., Barouki, R., Coumoul, X.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Toxicol Sci","volume":"149","issue":"1","page":"158-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32039017","title":"ErbB2 Targeted Epigenetic Modulation: Anti-tumor Efficacy of the ADC Trastuzumab-HDACi ST8176AA1.","abstract":"Targeted therapy using monoclonal antibodies conjugated to toxins is gaining space in the treatment of cancer. Here, we report the anti-tumor effect of a new antibody drug conjugate (ADC) delivering a HDAC inhibitor to ErbB2+ solid tumors. Trastuzumab was partially reduced with tris [2-carboxyethyl] phosphine (TCEP) and conjugated to ST7464AA1, the active form of the prodrug HDAC inhibitor ST7612AA1, through a maleimide-thiol linker to obtain the Antibody Drug Conjugate (ADC) ST8176AA1. The average drug\/antibody ratio (DAR) was 4.5 as measured by hydrophobic interaction chromatography (HIC). Binding of ST8176AA1 to ErbB2 receptor and internalization in tumor cells were investigated by enzyme-linked immunosorbent assay (ELISA), surface plasmon resonance (SPR), cytofluorimetry, and High Content Screening (HCS) Imaging. The biological activity of the ADC was evaluated <i>in vitro<\/i> and <i>in vivo<\/i> by measuring cell proliferation\/cell cycle, apoptosis\/DNA damage, tubulin, and histone acetylation and modulation of Epithelial\/Mesenchymal Transition (EMT) markers. Receptor binding and internalization of ST8176AA1 were confirmed to be similar to trastuzumab. Higher anti-tumor activity of ST8176AA1 compared to trastuzumab was observed <i>in vitro<\/i> in tumor cell lines. Such higher activity correlated with increased acetylation of histones and alfa-tubulin as a consequence of HDAC inhibitor-mediated epigenetic modulation that also induced increased expression of ErbB2 and estrogen receptor in triple negative breast cancer cells. Consistently with <i>in vitro<\/i> data, ST8176AA1 exhibited higher tumor growth inhibition than trastuzumab in xenograft models of ovary and colon carcinoma and in two patient-derived xenograft (PDX) models of pancreatic carcinoma. Immunohistochemistry analysis of tumor masses showed lower expression of the proliferation marker Ki67 and higher expression of cleaved caspase-3 in mice treated with the ADC compared to those treated with trastuzumab and results correlated with increased acetylation of both histones and tubulin. Collectively, present data indicate that ADC ST8176AA1 can target epigenetic modulation to ErbB2+ tumors. Interestingly, the amount of HDACi estimated to be delivered at the ST8176AA1 effective dose would correspond to ~1\/1,000 of ST7612AA1 effective dose. Therefore, ST8176AA1 is an attractive new therapeutic candidate because it exhibits increased anti-tumor potency compared to trastuzumab by exerting epigenetic modulation at a much safer dose compared to standard HDACi-based therapeutic protocols.","authors":"Milazzo, FM., Vesci, L., Anastasi, AM., Chiapparino, C., Rosi, A., Giannini, G., Taddei, M., Cini, E., Faltoni, V., Petricci, E., Battistuzzi, G., Salvini, L., Carollo, V., De Santis, R.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Front Oncol","volume":"9","issue":"","page":"1534","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31583260","title":"DKK2 Impairs Tumor Immunity Infiltration and Correlates with Poor Prognosis in Pancreatic Ductal Adenocarcinoma.","abstract":"Pancreatic ductal adenocarcinoma (PDAC) remains one of the most devastating cancer types despite the improvement of modern medicine. In our present study, we found that dickkopf-related protein 2 (DKK2) shares a higher expression in PDAC compared with adjacent pancreas tissue in tissue microarray. In addition, an elevated expression of DKK2 predicts poorer prognosis of patients and positively correlated with poor tumor differentiation. Multivariate Cox regression analysis was also performed and confirmed that the expression of DKK2 is an independent prognostic factor in PDAC. A high expression of DKK2 correlates with cell migration and epithelial mesenchymal transition based on gene set enrichment analysis (GSEA) while knockdown of DKK2 in PDAC cells resulted in impaired cellular migration. Furthermore, GSEA predicts negative correlation between tumor immunity invasion and DKK2 expression. We then confirmed these results and demonstrated that a higher expression of DKK2 imparts the recruitment of CD8<sup>+<\/sup> T cells. Our work suggested that DKK2 imparts tumor immune evasion and is associated with poor prognosis in pancreatic ductal adenocarcinoma.","authors":"Yang, J., Jiang, Y., He, R., Liu, W., Yang, M., Tao, L., Fu, X., Shen, Y., Li, J., Liu, D., Huo, Y., Zhang, J., Hua, R., Zhang, Z., Sun, Y.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"J Immunol Res","volume":"2019","issue":"","page":"8656282","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11157055","title":"Protective role of Raf-1 in Salmonella-induced macrophage apoptosis.","abstract":"Invasive Salmonella induces macrophage apoptosis via the activation of caspase-1 by the bacterial protein SipB. Here we show that infection of macrophages with Salmonella causes the activation and degradation of Raf-1, an important intermediate in macrophage proliferation and activation. Raf-1 degradation is SipB- and caspase-1-dependent, and is prevented by proteasome inhibitors. To study the functional significance of Raf-1 in this process, the c-raf-1 gene was inactivated by Cre-loxP-mediated recombination in vivo. Macrophages lacking c-raf-1 are hypersensitive towards pathogen-induced apoptosis. Surprisingly, activation of the antiapoptotic mitogen-activated protein kinase kinase (MEK)\/extracellular signal-regulated kinase (ERK) and nuclear factor kappaB pathways is normal in Raf-1-deficient macrophages, and mitochondrial fragility is not increased. Instead, pathogen-mediated activation of caspase-1 is enhanced selectively, implying that Raf-1 antagonizes stimulus-induced caspase-1 activation and apoptosis.","authors":"Jesenberger, V., Procyk, KJ., R\u00fcth, J., Schreiber, M., Theussl, HC., Wagner, EF., Baccarini, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Exp Med","volume":"193","issue":"3","page":"353-64","pdf":null,"JrId":"4724","fulltextlink":null,"preprintlink":null,"articledate":"2001-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31610265","title":"KAT2A succinyltransferase activity-mediated 14-3-3\u03b6 upregulation promotes \u03b2-catenin stabilization-dependent glycolysis and proliferation of pancreatic carcinoma cells.","abstract":"Frequently occurring histone lysine succinylation is a newly identified histone modification that can be regulated by KAT2A histone succinyltransferase, which is also a histone acetyltransferase. KAT2A histone succinyltransferase activity is important for tumorigenesis; however, the mechanism underlying this tumor-promoting effect remains elusive. Here we demonstrate that KAT2A is highly expressed in human pancreatic ductal adenocarcinoma (PDAC) specimens and positively correlated with advanced stages of PDAC and short patients' survival. In addition, KAT2A expression in PDAC specimens is correlated with 14-3-3\u03b6 expression, and KAT2A regulates H3K79 succinylation in the promoter region of YWHAZ (encoding for 14-3-3\u03b6) to promote YWHAZ mRNA and 14-3-3\u03b6 expression, thereby preventing \u03b2-catenin degradation. Expression of succinyltransferase activity-defective KAT2A Y645A reduces H3K79 succinylation and 14-3-3\u03b6 expression, leading to decreased \u03b2-catenin stability and subsequently decreased expression of cyclin D1, c-Myc, GLUT1, and LDHA. KAT2A-mediated 14-3-3\u03b6 and \u03b2-catenin expression promotes glycolysis, cell proliferation, and migration and invasion of PDAC cells with epithelial-to-mesenchymal transition. These findings reveal a novel and instrumental role of KAT2A-mediated histone succinylation in regulation of gene expression and \u03b2-catenin stability to promote tumor cell proliferation and invasion.","authors":"Tong, Y., Guo, D., Yan, D., Ma, C., Shao, F., Wang, Y., Luo, S., Lin, L., Tao, J., Jiang, Y., Lu, Z., Xing, D.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cancer Lett","volume":"469","issue":"","page":"1-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18617038","title":"Correlated light and electron microscopy of the cytoskeleton.","abstract":"The cytoskeleton of cultured cells can be most easily visualized in the electron microscope by simultaneous extraction and fixation with Triton-glutaraldehyde mixtures, followed by negative staining. Actin filaments are better preserved by stabilization with phalloidin, either during or after the primary fixation step. A technique is described for the combination of this procedure with live cell microscopy. Optimal conditions for light microscopy are achieved by culturing cells on coverslips coated with formvar film. For cell relocation a gold finder grid pattern is embossed on the film by evaporation through a tailor-made mask. After video microscopy and fixation, the film is floated from the coverslip and an electron microscope grid added to the film with the central hole of the grid over the region of interest. Accurate positioning is achieved under a dissecting microscope, using forceps mounted in a micromanipulator. Examples are shown of the changes in organization of actin filaments in the lamellipodia of migrating melanoma cells resulting from changes in protrusion rate. The technique is applicable to alternative processing procedures after fixation, including cryoelectron tomography.","authors":"Auinger, S., Small, JV.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Methods Cell Biol","volume":"88","issue":null,"page":"257-72","pdf":null,"JrId":"5785","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1825680","title":"Expression of human CSF-1 receptor induces CSF-1-dependent proliferation in murine myeloid but not in T-lymphoid cells.","abstract":"The receptor for human macrophage colony stimulating factor (CSF-1R) was introduced into hematopoietic cell lines of myeloid and T-lymphoid origin, both of which normally do not express the CSF-1R. Infection of an interleukin-3 (IL-3)-dependent mouse myeloid cell line (FDC-P1) with a high titer retroviral vector expressing the human c-fms c-DNA, enabled CSF-1-dependent proliferation in short-term liquid culture assays as well as in clonal culture systems. CSF-1-dependent cell lines could be established after sorting for CSF-1R positive cells. In contrast to FDC-P1 cells, expression of the CSF-1R in CTLL cells, an IL-2-dependent mouse cytotoxic T-cell line, and in T-cell growth factor III\/P40-dependent helper T-cells, ST2\/K9.4a2, did not lead to CSF-1-dependent proliferation. These observations lead to the conclusion that ectopically expressed CSF-1R may function on certain myeloid cells where it is normally not expressed, suggesting the presence of signal transduction pathways which can be utilized by that foreign receptor. In contrast, it appears that T-lymphoid cells lack such a signalling mechanism, indicating that quite different modes of transducing mitogenic signals from the cell membrane to the nucleus must have developed during myeloid and T-lymphoid differentiation.","authors":"von R\u00fcden, T., Mouchiroud, G., Bourette, RP., Ouazana, R., Blanchet, JP., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Leukemia","volume":"5","issue":"1","page":"3-7","pdf":null,"JrId":"5536","fulltextlink":null,"preprintlink":null,"articledate":"1991-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34048692","title":"ISSCR Guidelines for Stem Cell Research and Clinical Translation: The 2021 update.","abstract":"The International Society for Stem Cell Research has updated its Guidelines for Stem Cell Research and Clinical Translation in order to address advances in stem cell science and other relevant fields, together with the associated ethical, social, and policy issues that have arisen since the last update in 2016. While growing to encompass the evolving science, clinical applications of stem cells, and the increasingly complex implications of stem cell research for society, the basic principles underlying the Guidelines remain unchanged, and they will continue to serve as the standard for the field and as a resource for scientists, regulators, funders, physicians, and members of the public, including patients. A summary of the key updates and issues is presented here.","authors":"Lovell-Badge, R., Anthony, E., Barker, RA., Bubela, T., Brivanlou, AH., Carpenter, M., Charo, RA., Clark, A., Clayton, E., Cong, Y., Daley, GQ., Fu, J., Fujita, M., Greenfield, A., Goldman, SA., Hill, L., Hyun, I., Isasi, R., Kahn, J., Kato, K., Kim, JS., Kimmelman, J., Knoblich, JA., Mathews, D., Montserrat, N., Mosher, J., Munsie, M., Nakauchi, H., Naldini, L., Naughton, G., Niakan, K., Ogbogu, U., Pedersen, R., Rivron, N., Rooke, H., Rossant, J., Round, J., Saitou, M., Sipp, D., Steffann, J., Sugarman, J., Surani, A., Takahashi, J., Tang, F., Turner, L., Zettler, PJ., Zhai, X.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Stem Cell Reports","volume":"16","issue":"6","page":"1398-1408","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31091208","title":"Inhibition of LONP1 Suppresses Pancreatic Cancer Progression Via c-Jun N-Terminal Kinase Pathway-Meditated Epithelial-Mesenchymal Transition.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31091208<\/PMID><DateCompleted><Year>2020<\/Year><Month>02<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>02<\/Month><Day>20<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1536-4828<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>48<\/Volume><Issue>5<\/Issue><PubDate><MedlineDate>2019 May\/Jun<\/MedlineDate><\/PubDate><\/JournalIssue><Title>Pancreas<\/Title><ISOAbbreviation>Pancreas<\/ISOAbbreviation><\/Journal><ArticleTitle>Inhibition of LONP1 Suppresses Pancreatic Cancer Progression Via c-Jun N-Terminal Kinase Pathway-Meditated Epithelial-Mesenchymal Transition.<\/ArticleTitle><Pagination><MedlinePgn>629-635<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1097\/MPA.0000000000001321<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\">The aim of this study was to investigate the role of LONP1 in the progression of pancreatic cancer.","authors":"Liu, C., Wang, H., Li, H., Chen, X., Wu, X., Lu, B., Zhang, W., Zhou, Y., Xiao, GG., Gao, G.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Pancreas","volume":"48","issue":"5","page":"629-635","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15952736","title":"Afamin is a novel human vitamin E-binding glycoprotein characterization and in vitro expression.","abstract":"Hydrophobic vitamins are transported in human plasma and extravascular fluids by carrier proteins. No specific protein has been described so far for vitamin E, which plays a crucial role in protecting against oxidative damage and disease. We report here the purification of a 75-kDa glycoprotein with vitamin E-binding properties by stepwise chromatography of lipoprotein-depleted human plasma and monitoring of vitamin E (alpha-tocopherol)-binding activity. Partial sequencing identified this protein as afamin, a previously described member of the albumin gene family with four or five potential N-glycosylation sites. Glycosylation analysis indicated that &gt;90% of the glycans were sialylated biantennary complex structures. The vitamin E-binding properties were confirmed using recombinantly expressed afamin. Qualitative and quantitative analysis of plasma and extravascular fluids revealed an abundant presence of this protein not only in plasma (59.8+\/-13.3 microg\/mL) but also in extravascular fluids such as follicular (34.4+\/-12.7 microg\/mL) and cerebrospinal (0.28+\/-0.16 microg\/mL) fluids, suggesting potential roles for afamin in fertility and neuroprotection. Afamin is partly (13%) bound to plasma lipoproteins. Afamin and vitamin E concentrations significantly correlate in follicular and cerebrospinal fluids but not in plasma. The vitamin E association of afamin in follicular fluid was directly demonstrated by gel filtration chromatography and immunoprecipitation which complements the in vitro findings for purified native and recombinant afamin.","authors":"Jerkovic, L., Voegele, AF., Chwatal, S., Kronenberg, F., Radcliffe, CM., Wormald, MR., Lobentanz, EM., Ezeh, B., Eller, P., Dejori, N., Dieplinger, B., Lottspeich, F., Sattler, W., Uhr, M., Mechtler, K., Dwek, RA., Rudd, PM., Baier, G., Dieplinger, H.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"J Proteome Res","volume":"4","issue":"3","page":"889-99","pdf":null,"JrId":"30137","fulltextlink":null,"preprintlink":null,"articledate":"2005-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30841420","title":"ProNGF siRNA inhibits cell proliferation and invasion of pancreatic cancer cells and promotes anoikis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30841420<\/PMID><DateCompleted><Year>2019<\/Year><Month>06<\/Month><Day>21<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1950-6007<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>111<\/Volume><PubDate><Year>2019<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie<\/Title><ISOAbbreviation>Biomed Pharmacother<\/ISOAbbreviation><\/Journal><ArticleTitle>ProNGF siRNA inhibits cell proliferation and invasion of pancreatic cancer cells and promotes anoikis.<\/ArticleTitle><Pagination><MedlinePgn>1066-1073<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0753-3322(18)35135-7<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.biopha.2019.01.002<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Precursor of nerve growth factor (proNGF) was previously considered biologically inactive; however, it has recently been identified as having important roles in the pathology of cancer development.","authors":"Xu, J., Song, J., Yang, X., Guo, J., Wang, T., Zhuo, W.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Biomed Pharmacother","volume":"111","issue":"","page":"1066-1073","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30705403","title":"PRRX1 isoforms cooperate with FOXM1 to regulate the DNA damage response in pancreatic cancer cells.","abstract":"PRRX1 is a homeodomain transcriptional factor, which has two isoforms, PRXX1A and PRRX1B. The PRRX1 isoforms have been demonstrated to be important in pancreatic cancer, especially in the regulation of epithelial-to-mesenchymal transition (EMT) in Pancreatic Ductal Adenocarcinoma (PDAC) and of mesenchymal-to-epithelial transition (MET) in liver metastasis. In order to determine the functional underpinnings of PRRX1 and its isoforms, we have unraveled a new interplay between PRRX1 and the FOXM1 transcriptional factors. Our detailed biochemical analysis reveals the direct physical interaction between PRRX1 and FOXM1 proteins that requires the PRRX1A\/B 200-222\/217 amino acid (aa) region and the FOXM1 Forkhead domain. Additionally, we demonstrate the cooperation between PRRX1 and FOXM1 in the regulation of FOXM1-dependent transcriptional activity. Moreover, we establish FOXM1 as a critical downstream target of PRRX1 in pancreatic cancer cells. We demonstrate a novel role for PRRX1 in the regulation of genes involved in DNA repair pathways. Indeed, we show that expression of PRRX1 isoforms may limit the induction of DNA damage in pancreatic cancer cells. Finally, we demonstrate that targeting FOXM1 with the small molecule inhibitor FDI6 suppress pancreatic cancer cell proliferation and induces their apoptotic cell death. FDI6 sensitizes pancreatic cancer cells to Etoposide and Gemcitabine induced apoptosis. Our data provide new insights into PRRX1's involvement in regulating DNA damage and provide evidence of a possible PRRX1-FOXM1 axis that is critical for PDAC cells.","authors":"Marchand, B., Pitarresi, JR., Reichert, M., Suzuki, K., Laczk\u00f3, D., Rustgi, AK.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Oncogene","volume":"38","issue":"22","page":"4325-4339","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11084048","title":"Molecular cloning and characterization of endosialin, a C-type lectin-like cell surface receptor of tumor endothelium.","abstract":"Endosialin, the antigen identified with monoclonal antibody FB5, is a highly restricted 165-kDa cell surface glycoprotein expressed by tumor blood vessel endothelium in a broad range of human cancers but not detected in blood vessels or other cell types in many normal tissues. Functional analysis of endosialin has been hampered by a lack of information about its molecular structure. In this study, we describe the purification and partial amino acid sequencing of endosialin, leading to the cloning of a full-length cDNA with an open reading frame of 2274 base pairs. The endosialin cDNA encodes a type I membrane protein of 757 amino acids with a predicted molecular mass of 80.9 kDa. The sequence matches with an expressed sequence tag of unknown function in public data bases, named TEM1, which was independently linked to tumor endothelium by serial analysis of gene expression profiling. Bioinformatic evaluation classifies endosialin as a C-type lectin-like protein, composed of a signal leader peptide, five globular extracellular domains (including a C-type lectin domain, one domain with similarity to the Sushi\/ccp\/scr pattern, and three EGF repeats), followed by a mucin-like region, a transmembrane segment, and a short cytoplasmic tail. Carbohydrate analysis shows that the endosialin core protein carries abundantly sialylated, O-linked oligosaccharides and is sensitive to O-sialoglycoprotein endopeptidase, placing it in the group of sialomucin-like molecules. The N-terminal 360 amino acids of endosialin show homology to thrombomodulin, a receptor involved in regulating blood coagulation, and to complement receptor C1qRp. This structural kinship may indicate a function for endosialin as a tumor endothelial receptor for as yet unknown ligands, a notion now amenable to molecular investigation.","authors":"Christian, S., Ahorn, H., Koehler, A., Eisenhaber, F., Rodi, HP., Garin-Chesa, P., Park, JE., Rettig, WJ., Lenter, MC.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Biol Chem","volume":"276","issue":"10","page":"7408-14","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18626995","title":"Stochastic dynamics of the nerve growth cone and its microtubules during neurite outgrowth.","abstract":"The controlled extension of neurites is essential not only for nervous system development, but also for effective nerve regeneration after injury. This process is critically dependent on microtubule assembly since axons fail to elongate in the presence of drugs which disrupt normal assembly dynamics. For this reason, neurite outgrowth is potentially controllable by manipulation of the assembly state of the intracellular array of microtubules. Therefore, understanding how microtubule assembly dynamics and neurite outgrowth are coupled, in the absence of drugs, can lend valuable insight into the control and guidance of the outgrowth process. In the present study we characterized the stochastic dynamics of neurite outgrowth and its corresponding microtubule array, which advances concomitantly with the advance of the nerve growth cone, the highly motile structure at the terminus of the growing neurite, using reported fluorescent microscopic image sequences (Tanaka and Kirschner, 1991, J. Cell Biol. 115:345-363). Although previously modeled as an uncorrelated random walk, the stochastic advance of the growth cone was found to be anticorrelated over a time scale of approximately 4 min, meaning that growth cone advances tended to be followed by growth cone retractions approximately 4 min later. The observed anticorrelation most likely reflects the periodic stops and starts of neurite outgrowth that have been reported anecdotally. A strikingly similar pattern of anticorrelation was also identified in the advance of the growth cone's microtubule array. Cross-correlation analysis showed that growth cone dynamics tended to precede microtubule dynamics on a time scale of approximately 0-2 min, while microtubules tended to precede growth cone dynamics on a approximately 0-20-s time scale, indicating a close temporal coupling between microtubule and growth cone dynamics. Finally, the scaling of the mean-squared displacements with time for both the growth cone and microtubules suggested a fractional Brownian motion model which accounts for the observed anticorrelation of growth cone and microtubule advance. (c) 1996 John Wiley &amp; Sons, Inc.","authors":"Odde, DJ., Tanaka, EM., Hawkins, SS., Buettner, HM.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Biotechnol Bioeng","volume":"50","issue":"4","page":"452-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30683911","title":"Quasimesenchymal phenotype predicts systemic metastasis in pancreatic ductal adenocarcinoma.","abstract":"Metastasis following surgical resection is a leading cause of mortality in pancreatic ductal adenocarcinoma. Epithelial-mesenchymal transition is thought to play an important role in metastasis, although its clinical relevance in metastasis remains uncertain. We evaluated a panel of RNA in-situ hybridization probes for epithelial-mesenchymal transition-related genes expressed in circulating tumor cells. We assessed the predictive value of this panel for metastasis in pancreatic ductal adenocarcinoma and, to determine if the phenotype is generalizable between cancers, in colonic adenocarcinoma. One hundred fifty-eight pancreatic ductal adenocarcinomas and 205 colonic adenocarcinomas were classified as epithelial or quasimesenchymal phenotype using dual colorimetric RNA-in-situ hybridization. SMAD4 expression on pancreatic ductal adenocarcinomas was assessed by immunohistochemistry. Pancreatic ductal adenocarcinomas with quasimesenchymal phenotype had a significantly shorter disease-specific survival (P\u2009=\u20090.031) and metastasis-free survival (P\u2009=\u20090.0001) than those with an epithelial phenotype. Pancreatic ductal adenocarcinomas with SMAD4 loss also had lower disease-specific survival (P\u2009=\u20090.041) and metastasis-free survival (P\u2009=\u20090.001) than those with intact SMAD4. However, the quasimesenchymal phenotype proved a more robust predictor of metastases-area under the curve for quasimesenchymal\u2009=\u20090.8; SMAD4\u2009=\u20090.6. The quasimesenchymal phenotype also predicted metastasis-free survival (P\u2009=\u20090.004) in colonic adenocarcinoma. Epithelial-mesenchymal transition defined two phenotypes with distinct metastatic capabilities-epithelial phenotype tumors with predominantly organ-confined disease and quasimesenchymal phenotype with high risk of metastatic disease in two epithelial malignancies. Collectively, this work validates the relevance of epithelial-mesenchymal transition in human gastrointestinal tumors.","authors":"Mahadevan, KK., Arora, KS., Amzallag, A., Williams, E., Kulkarni, AS., Fernandez-Del Castillo, C., Lillemoe, KD., Bardeesy, N., Hong, TS., Ferrone, CR., Ting, DT., Deshpande, V.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mod Pathol","volume":"32","issue":"6","page":"844-854","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30628651","title":"MicroRNA-200b and -301 are associated with gemcitabine response as biomarkers in pancreatic carcinoma cells.","abstract":"Chemotherapy resistance (congenital or acquired) is one of the principal challenges for the treatment of pancreatic carcinoma. Recent evidence has demonstrated that epithelial to mesenchymal transition\u00a0(EMT) is associated with chemoresistance in pancreatic carcinoma cells. However, the molecular mechanism underlying the development of chemoresistance remains unknown, and limited therapeutic options are available. Therefore, to anticipate individual chemosensitivity or acquired chemoresistance for patients with pancreatic carcinoma, predictive biomarkers are urgently required. Extensive evidence suggests that microRNAs (miRNAs) serve a crucial role in regulating EMT. The aim of this study was to examine the potential role of miRNA (miR)\u2011200b and miR\u2011301 in predicting the chemo\u2011responses to treatment for pancreatic carcinoma. The present results demonstrate that miR\u2011200b expression predicted chemo\u2011sensitivity and may have potential as a biomarker. In six different pancreatic carcinoma cell lines (Capan\u20111, Capan\u20112, Panc\u20111, MIAPaCa\u20112, BxPC\u20113 and PL45 cells), the expression of miR\u2011200b correlated positively with chemosensitivity. Moreover, the enhanced expression of miR\u2011200b increased chemosensitivity and induced mesenchymal to epithelial transition. Conversely, miR\u2011301 modulated gemcitabine resistance and induced EMT through the downregulation of cadherin\u00a01 expression. In addition, gemcitabine\u2011resistant cells (Capan\u20112 and Panc\u20111) exhibited upregulated miR\u2011301 expression and downregulated gemcitabine\u2011induced apoptosis. In summary, these two miRNAs may serve roles as biomarkers in pancreatic carcinoma, miR\u2011200b expression may predict chemosensitivity, and elevated miR\u2011301 expression may have potential applications in the prediction of acquired gemcitabine resistance.","authors":"Funamizu, N., Lacy, CR., Kamada, M., Yanaga, K., Manome, Y.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Int J Oncol","volume":"54","issue":"3","page":"991-1000","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30559202","title":"TP53INP1 deficiency maintains murine B lymphopoiesis in aged bone marrow through redox-controlled IL-7R\/STAT5 signaling.","abstract":"Bone marrow (BM) produces all blood and immune cells deriving from hematopoietic stem cells (HSCs). The decrease of immune cell production during aging is one of the features of immunosenescence. The impact of redox dysregulation in BM aging is still poorly understood. Here we use TP53INP1-deficient (KO) mice endowed with chronic oxidative stress to assess the influence of aging-associated redox alterations in BM homeostasis. We show that TP53INP1 deletion has no impact on aging-related accumulation of HSCs. In contrast, the aging-related contraction of the lymphoid compartment is mitigated in TP53INP1 KO mice. B cells that accumulate in old KO BM are differentiating cells that can mature into functional B cells. Importantly, this phenotype results from B cell-intrinsic events associated with defective redox control. Finally, we show that oxidative stress in aged TP53INP1-deficient mice maintains STAT5 expression and activation in early B cells, driving high <i>Pax5<\/i> expression, which provides a molecular mechanism for maintenance of B cell development upon aging.","authors":"Zidi, B., Vincent-Fabert, C., Pouyet, L., Seillier, M., Vandevelde, A., N'guessan, P., Poplineau, M., Guittard, G., Mancini, SJC., Duprez, E., Carrier, A.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Proc Natl Acad Sci U S A","volume":"116","issue":"1","page":"211-216","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26301565","title":"Histone reader BRWD1 targets and restricts recombination to the Igk locus.","abstract":"B lymphopoiesis requires that immunoglobulin genes be accessible to RAG1-RAG2 recombinase. However, the RAG proteins bind widely to open chromatin, which suggests that additional mechanisms must restrict RAG-mediated DNA cleavage. Here we show that developmental downregulation of interleukin 7 (IL-7)-receptor signaling in small pre-B cells induced expression of the bromodomain-family member BRWD1, which was recruited to a specific epigenetic landscape at Igk dictated by pre-B cell receptor (pre-BCR)-dependent Erk activation. BRWD1 enhanced RAG recruitment, increased gene accessibility and positioned nucleosomes 5' to each J\u03ba recombination signal sequence. BRWD1 thus targets recombination to Igk and places recombination within the context of signaling cascades that control B cell development. Our findings represent a paradigm in which, at any particular antigen-receptor locus, specialized mechanisms enforce lineage- and stage-specific recombination.","authors":"Mandal, M., Hamel, KM., Maienschein-Cline, M., Tanaka, A., Teng, G., Tuteja, JH., Bunker, JJ., Bahroos, N., Eppig, JJ., Schatz, DG., Clark, MR.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Immunol","volume":"16","issue":"10","page":"1094-103","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18572100","title":"Differential transcriptional modulation of biological processes in adipocyte triglyceride lipase and hormone-sensitive lipase-deficient mice.","abstract":"Adipocyte triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL) are intracellular lipases that mobilize triglycerides, the main energy source in mammals. Deletion of genes encoding ATGL (Pnpla2) or HSL (Lipe) in mice results in striking phenotypic differences, suggesting distinct roles for these lipases. The goal of the present study was to identify the biological processes that are modulated in the metabolic tissues of ATGL- and HSL-deficient mice. DNA microarrays were employed to provide full genome coverage concerning the types of genes that are differentially expressed in wild-type and mutant mice. For both mouse models, transcript signatures were identified in white adipose tissue, brown adipose tissue (BAT), skeletal muscle (SM), cardiac muscle (CM), and liver. Genetic ablation of ATGL and HSL alters the transcript levels of a large number of genes in metabolic tissues. The genes affected in the two models are, however, largely different ones. Indeed, only one biological process was modulated in the same way in both mouse models, namely the down-regulation of fatty acid metabolism in BAT. The most pronounced modulation of biological processes was observed in ATGL-\/- CM, in which a concerted down-regulation of transcripts associated with oxidative pathways was observed. In HSL-\/- mice, in contrast, the most marked changes were seen in SM, namely, alterations in transcript levels reflecting a change of energy source from lipid to carbohydrate. The transcript signatures also provided novel insights into the metabolic derangements that are characteristic of ATGL-\/- mice. Our findings suggest that ATGL and HSL differentially modulate biological processes in metabolic tissues. We hypothesize that the intermediary metabolites of the lipolytic pathways are signaling molecules and activators of a wide range of biochemical and cellular processes in mammals.","authors":"Pinent, M., Hackl, H., Burkard, TR., Prokesch, A., Papak, C., Scheideler, M., H\u00e4mmerle, G., Zechner, R., Trajanoski, Z., Strauss, JG.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genomics","volume":"92","issue":"1","page":"26-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24850218","title":"Genetic and epigenetic control of early lymphocyte development.","abstract":"T, B, and NK lymphocytes are generated from pluripotent hematopoietic stem cells through a successive series of lineage restriction processes. Many regulatory components, such as transcription factors, cytokines\/cytokine receptors, and signal transduction molecules orchestrate cell fate specification and determination. In particular, transcription factors play a key role in regulating lineage-associated gene programs. Recent findings suggest the involvement of epigenetic factors in the maintenance of cell fate. Here, we review the early developmental events during lymphocyte lineage determination, focusing on the transcriptional networks and epigenetic regulation. Finally, we also discuss the developmental relationship between acquired and innate lymphoid cells.","authors":"Ikawa, T.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Top Microbiol Immunol","volume":"381","issue":"","page":"1-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25975824","title":"Epigenetic dynamics during CD4(+) T cells lineage commitment.","abstract":"T cell lymphopoiesis is a complex, stepwise process in which the transcriptional program of the progenitor cells is progressively adapted in order to generate mature phenotypes. This transcriptional program in differentiated cells is also very flexible, allowing the silencing or activation of critical genes in response to extrinsic or intrinsic stimuli, or, in the case of progenitors, to developmental signals. Thus, progenitor and mature cells must maintain a balance between stability, to preserve their phenotypic identity, and plasticity, to respond and adapt to stimuli. A long-standing question is, therefore, how the transcriptional program is regulated to allow both controlled differentiation and a flexible response. Here we review the contribution of epigenetic mechanisms to transcriptional control during CD4(+) T cell differentiation and the ways in which these mechanisms interact with key transcription factors to ensure proper maturation and maintenance of cell identity. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.","authors":"Rodriguez, RM., Lopez-Larrea, C., Suarez-Alvarez, B.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Int J Biochem Cell Biol","volume":"67","issue":"","page":"75-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19151746","title":"Epigenetic control of T-helper-cell differentiation.","abstract":"Naive CD4(+) T cells give rise to T-helper-cell subsets with functions that are tailored to their respective roles in host defence. The specification of T-helper-cell subsets is controlled by networks of lineage-specifying transcription factors, which bind to regulatory elements in genes that encode cytokines and other transcription factors. The nuclear context in which these transcription factors act is affected by epigenetic processes, which allow programmes of gene expression to be inherited by progeny cells that at the same time retain the potential for change in response to altered environmental signals. In this Review, we describe these epigenetic processes and discuss how they collaborate to govern the fate and function of T helper cells.","authors":"Wilson, CB., Rowell, E., Sekimata, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Rev Immunol","volume":"9","issue":"2","page":"91-105","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-04-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24868087","title":"The Cebpa +37-kb enhancer directs transgene expression to myeloid progenitors and to long-term hematopoietic stem cells.","abstract":"C\/EBP\u03b1 is expressed preferentially in myeloid compared with lymphoid or erythroid cells and directs myeloid lineage specification. C\/EBP\u03b1 is also expressed at lower levels in HSCs and in several nonhematopoietic tissues. The Cebpa gene has a conserved, 450-bp segment at +37 kb that harbors enhancer-specific epigenetic marks and is activate in a myeloid cell line. Herein, we characterize transgenic C57BL\/6 mice, in which the Cebpa enhancer and 845-bp promoter regulate a hCD4 reporter. FACS analysis, in vitro colony assays, and in vivo competitive and secondary transplantation revealed that myeloid but not MEPs or lymphoid progenitors and also functional LT-HSCs are found almost exclusively in the Cebpa-hCD4(+) compared with hCD4(-) marrow population. hCD4(+) CMP yielded predominantly myeloid, whereas hCD4(-) CMP generated mainly Meg\/E colonies. Providing insight into control of CMP maturation, Cebpa and Pu.1 RNAs were preferentially expressed in hCD4(+) CMP, Scl, Gata2, Gata1, Klf1, Ets1, and Fli1 predominated in hCD4(-) CMP, and Runx1, Myb, HoxA9, and Erg levels were similar in both. Cebpa-hCD4 transgene expression was lacking in multiple nonhematopoietic tissues. In summary, the +37-kb Cebpa enhancer and promoter are sufficient for marrow myeloid progenitor and LT-HSC-specific expression.","authors":"Guo, H., Ma, O., Friedman, AD.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Leukoc Biol","volume":"96","issue":"3","page":"419-26","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18554062","title":"A guide to accurate measurement of diffusion using fluorescence correlation techniques with blinking quantum dot nanoparticle labels.","abstract":"Fluctuation-based fluorescence correlation techniques are widely used to study dynamics of fluorophore labeled biomolecules in cells. Semiconductor quantum dots (QDs) have been developed as bright and photostable fluorescent probes for various biological applications. However, the fluorescence intermittency of QDs, commonly referred to as \"blinking\", is believed to complicate quantitative correlation spectroscopy measurements of transport properties, as it is an additional source of fluctuations that contribute on a wide range of time scales. The QD blinking fluctuations obey power-law distributions so there is no single characteristic fluctuation time for this phenomenon. Consequently, it is highly challenging to separate fluorescence blinking fluctuations from those due to transport dynamics. Here, we quantify the bias introduced by QD blinking in transport measurements made using fluctuation methods. Using computer simulated image time series of diffusing point emitters with set \"on\" and \"off\" time emission characteristics, we show that blinking results in a systematic overestimation of the diffusion coefficients measured with correlation analysis when a simple diffusion model is used to fit the time correlation decays. The relative error depends on the inherent blinking power-law statistics, the sampling rate relative to the characteristic diffusion time and blinking times, and the total number of images in the time series. This systematic error can be significant; moreover, it can often go unnoticed in common transport model fits of experimental data. We propose an alternative fitting model that incorporates blinking and improves the accuracy of the recovered diffusion coefficients. We also show how to completely eliminate the bias by applying k-space image correlation spectroscopy, which completely separates the diffusion and blinking dynamics, and allows the simultaneous recovery of accurate diffusion coefficients and QD blinking probability distribution function exponents.","authors":"Bachir, AI., Kolin, DL., Heinze, KG., Hebert, B., Wiseman, PW.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Chem Phys","volume":"128","issue":"22","page":"225105","pdf":null,"JrId":"4599","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15737577","title":"Epigenetic control of B cell differentiation.","abstract":"Gene expression, differentiation and the specialized function of various cell types are controlled epigenetically by post-translational histone modifications. These modifications establish a \"histone code\" that is recognized by various regulatory proteins, thereby creating a stable pattern of gene expression. The focus of this review is to discuss how the chromatin modifications regulate immunoglobulin gene rearrangement and B cell differentiation.","authors":"Su, IH., Tarakhovsky, A.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Semin Immunol","volume":"17","issue":"2","page":"167-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19114986","title":"Epigenetic control of FOXP3 expression: the key to a stable regulatory T-cell lineage?","abstract":"Regulatory T (T(Reg)) cells constitute a unique T-cell lineage that has a crucial role in immunological tolerance. Several years ago, forkhead box P3 (FOXP3) was identified as the transcription factor that was responsible for determining the development and function of these cells. However, the underlying mechanisms that are involved in the regulation of the FOXP3 gene remain unclear and therefore preclude accurate identification and manipulation of T(Reg) cells. In this Progress article, we summarize recent advances in understanding how FOXP3 expression is controlled and highlight evidence suggesting that epigenetic regulation of the FOXP3 locus contributes to its role as a lineage-specification factor.","authors":"Huehn, J., Polansky, JK., Hamann, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Rev Immunol","volume":"9","issue":"2","page":"83-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-04-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22997486","title":"Epigenetic regulation of B lymphocyte differentiation, transdifferentiation, and reprogramming.","abstract":"B cell development is a multistep process that is tightly regulated at the transcriptional level. In recent years, investigators have shed light on the transcription factor networks involved in all the differentiation steps comprising B lymphopoiesis. The interplay between transcription factors and the epigenetic machinery involved in establishing the correct genomic landscape characteristic of each cellular state is beginning to be dissected. The participation of \"epigenetic regulator-transcription factor\" complexes is also crucial for directing cells during reprogramming into pluripotency or lineage conversion. In this context, greater knowledge of epigenetic regulation during B cell development, transdifferentiation, and reprogramming will enable us to understand better how epigenetics can control cell lineage commitment and identity. Herein, we review the current knowledge about the epigenetic events that contribute to B cell development and reprogramming.","authors":"Barneda-Zahonero, B., Roman-Gonzalez, L., Collazo, O., Mahmoudi, T., Parra, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Comp Funct Genomics","volume":"2012","issue":"","page":"564381","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"125","title":"Endoscopic papillotomy and removal of gall stones.","abstract":"Endoscopic papillotomy was attempted in 59 patients with extrahepatic obstruction of the biliary duct system and was actually performed in 50 patients. A special high-frequency diathermy knife was introduced via a duodenoscope into the terminal common bile duct and the roof of the papilla was incised. In 33 out of 39 patients with choledocholithiasis the stones passed into the duodenum spontaneously or were removed endoscopically. Papillary stenosis without ductal stones was successfully treated with this method in eight out of 11 patients. One perforation of the duodenocholedochal junction occurred and was repaired surgically. Endoscopic papillotomy and stone extraction is a relatively safe and effective method of treating extrahepatic jaundice.","authors":"Classen, M., Safrany, L.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Br Med J","volume":"4","issue":"5993","page":"371-4","pdf":null,"JrId":"1912","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16027038","title":"Early B-cell factor 'pioneers' the way for B-cell development.","abstract":"Early B-cell factor (EBF) is a DNA-binding protein required for B-cell lymphopoiesis. The lack of EBF results in an early developmental blockade, including the lack of functional B cells and Igs. Recent studies have elucidated a central role for EBF in the specification of B-lineage cells. EBF directs progenitor cells to undergo B lymphopoiesis and activates transcription of B cell-specific genes in the absence of upstream regulators. How EBF mediates these effects has yet to be thoroughly explored, however, it initiates epigenetic modifications necessary for gene activation and the function of other transcriptional regulators, including Pax5. Together, these observations suggest a molecular basis for the role of EBF in the hierarchical network of factors that control B lymphopoiesis.","authors":"Hagman, J., Lukin, K.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Trends Immunol","volume":"26","issue":"9","page":"455-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15723116","title":"Principles of microRNA-target recognition.","abstract":"MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression in plants and animals. Although their biological importance has become clear, how they recognize and regulate target genes remains less well understood. Here, we systematically evaluate the minimal requirements for functional miRNA-target duplexes in vivo and distinguish classes of target sites with different functional properties. Target sites can be grouped into two broad categories. 5' dominant sites have sufficient complementarity to the miRNA 5' end to function with little or no support from pairing to the miRNA 3' end. Indeed, sites with 3' pairing below the random noise level are functional given a strong 5' end. In contrast, 3' compensatory sites have insufficient 5' pairing and require strong 3' pairing for function. We present examples and genome-wide statistical support to show that both classes of sites are used in biologically relevant genes. We provide evidence that an average miRNA has approximately 100 target sites, indicating that miRNAs regulate a large fraction of protein-coding genes and that miRNA 3' ends are key determinants of target specificity within miRNA families.","authors":"Brennecke, J., Stark, A., Russell, RB., Cohen, SM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"PLoS Biol","volume":"3","issue":"3","page":"e85","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10944349","title":"Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme.","abstract":"The enzyme PdxJ catalyzes the condensation of 1-deoxy-D-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). The protein from Escherichia coli has been crystallized in several forms under different conditions. The best diffracting crystals were obtained by a combination of the hanging-drop vapour-diffusion and microseeding techniques. Using an in-house image plate, the PdxJ crystals diffracted under cryo-conditions to 2.6 A resolution. The space group has been determined as C222(1), with unit-cell parameters a = 132.5, b = 154. 4, c = 131.4 A, corresponding to four monomers per asymmetric unit. In the search for heavy-atom derivatives, a mercury derivative has been interpreted. The 12 mercury sites located are related by 222 symmetry and, in combination with self-rotation search analyses and gel-filtration experiments, indicate the quaternary assembly of PdxJ into octamers with 422 symmetry.","authors":"Garrido Franco, M., Huber, R., Schmidt, FS., Laber, B., Clausen, T.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Acta Crystallogr D Biol Crystallogr","volume":"56","issue":"Pt 8","page":"1045-8","pdf":null,"JrId":"20879","fulltextlink":null,"preprintlink":null,"articledate":"2000-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18473763","title":"The role of genetics in inflammatory bowel disease.","abstract":"The volume of research undertaken on the genetic susceptibility of inflammatory bowel disease (IBD) has been tremendous. Genome-wide linkage studies pointed towards more than 10 chromosomal regions and fine-mapping of these regions led to the identification of a number of genes, including CARD15 (NOD2), DLG5, OCTN1 and 2, TLR4 and CARD4 (NOD1). With the recent completion of the human genome project, whole genome association studies (WGAS) have now become possible and have identified additional genes (IL23R, IRGM, PTGER4, ATG16L1) for Crohn's disease and ulcerative colitis, that have subsequently been replicated. At present, the CARD15 gene is still the most understood susceptibility gene, explaining around 20% of the genetic predisposition to Crohn's disease. Prediction of disease phenotype and response to the main therapies has for many years been a dream for physicians treating IBD patients. Only now, we start to accumulate some evidence proving that genetic factors indeed influence both the clinical course of IBD patients and their likelihood of responding to certain therapies. In the coming years, we expect an exponential increase in the efforts devoted to research in this area. The optimal prediction of both disease behaviour and response to therapy might result from complex combinations of clinical, biochemical, serological and genetic factors.","authors":"Henckaerts, L., Figueroa, C., Vermeire, S., Sans, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Drug Targets","volume":"9","issue":"5","page":"361-8","pdf":null,"JrId":"22465","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32362320","title":"Omics and the molecular exercise physiology.","abstract":"Exercise is a well-known non-pharmacologic agent used to prevent and treat a wide range of pathologic conditions such as metabolic and cardiovascular disease. In this sense, the classic field of exercise physiology has determined the main theoretical and practical bases of physiologic adaptations in response to exercise. However, the last decades were marked by significant advances in analytical laboratory techniques, where the field of biochemistry, genetics and molecular biology promoted exercise science to enter a new era. Regardless of its application, whether in the field of disease prevention or performance, the association of molecular biology with exercise physiology has been fundamental for unveiling knowledge of the molecular mechanisms related to the adaptation to exercise. This chapter will address the natural evolution of exercise physiology toward genetics and molecular biology, emphasizing the collection of integrated analytical approaches that composes the OMICS and their contribution to the field of molecular exercise physiology.","authors":"Gomes, C., Almeida, JA., Franco, OL., Petriz, B.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Adv Clin Chem","volume":"96","issue":"","page":"55-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15713650","title":"A CCAAT\/enhancer binding protein beta isoform, liver-enriched inhibitory protein, regulates commitment of osteoblasts and adipocytes.","abstract":"Although both osteoblasts and adipocytes have a common origin, i.e., mesenchymal cells, the molecular mechanisms that define the direction of two different lineages are presently unknown. In this study, we investigated the role of a transcription factor, CCAAT\/enhancer binding protein beta (C\/EBPbeta), and its isoform in the regulation of balance between osteoblast and adipocyte differentiation. We found that C\/EBPbeta, which is induced along with osteoblast differentiation, promotes the differentiation of mesenchymal cells into an osteoblast lineage in cooperation with Runx2, an essential transcription factor for osteogenesis. Surprisingly, an isoform of C\/EBPbeta, liver-enriched inhibitory protein (LIP), which lacks the transcriptional activation domain, stimulates transcriptional activity and the osteogenic action of Runx2, although LIP inhibits adipogenesis in a dominant-negative fashion. Furthermore, LIP physically associates with Runx2 and binds to the C\/EBP binding element present in the osteocalcin gene promoter. These data indicate that LIP functions as a coactivator for Runx2 and preferentially promotes the osteoblast differentiation of mesenchymal cells. Thus, identification of a novel role of the C\/EBPbeta isoform provides insight into the molecular basis of the regulation of osteoblast and adipocyte commitment.","authors":"Hata, K., Nishimura, R., Ueda, M., Ikeda, F., Matsubara, T., Ichida, F., Hisada, K., Nokubi, T., Yamaguchi, A., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Mol Cell Biol","volume":"25","issue":"5","page":"1971-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37340143","title":"Author Correction: SCON-a Short Conditional intrON for conditional knockout with one-step zygote injection.","abstract":null,"authors":"Wu, SS., Lee, H., Sz\u00e9p-Bakonyi, R., Colozza, G., Boese, A., Gert, KR., Hallay, N., Lee, JH., Kim, J., Zhu, Y., Linssen, MM., Pilat-Carotta, S., Hohenstein, P., Theussl, HC., Pauli, A., Koo, BK.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Exp Mol Med","volume":"55","issue":"6","page":"1278-1280","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10880431","title":"Crystal structure of cystalysin from Treponema denticola: a pyridoxal 5'-phosphate-dependent protein acting as a haemolytic enzyme.","abstract":"Cystalysin is a C(beta)-S(gamma) lyase from the oral pathogen Treponema denticola catabolyzing L-cysteine to produce pyruvate, ammonia and H(2)S. With its ability to induce cell lysis, cystalysin represents a new class of pyridoxal 5'-phosphate (PLP)-dependent virulence factors. The crystal structure of cystalysin was solved at 1.9 A resolution and revealed a folding and quaternary arrangement similar to aminotransferases. Based on the active site architecture, a detailed catalytic mechanism is proposed for the catabolism of S-containing amino acid substrates yielding H(2)S and cysteine persulfide. Since no homologies were observed with known haemolysins the cytotoxicity of cystalysin is attributed to this chemical reaction. Analysis of the cystalysin-L-aminoethoxyvinylglycine (AVG) complex revealed a 'dead end' ketimine PLP derivative, resulting in a total loss of enzyme activity. Cystalysin represents an essential factor of adult periodontitis, therefore the structure of the cystalysin-AVG complex may provide the chemical basis for rational drug design.","authors":"Krupka, HI., Huber, R., Holt, SC., Clausen, T.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"EMBO J","volume":"19","issue":"13","page":"3168-78","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2000-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7561091","title":"Alloreactive gamma delta thymocytes utilize distinct costimulatory signals from peripheral T cells.","abstract":"Interactions between CD28\/CTLA-4 on T cells and CD80 (B7.1) and CD86 (B7.2) counter receptors provide crucial costimulatory signals for TCR-alpha beta+ lymphocytes. To test the role of CD28 in thymic development and activation of TCR-gamma delta+ T cells, we introduced the alloreactive V gamma 2V alpha 11.3 TCR into CD28-deficient mice (CD28-\/-). We show that positive and negative selection of gamma delta Tg thymocytes proceeded normally in the absence of CD28. Although mature Tg gamma delta+ thymocytes required a second costimulatory signal for proliferation, gamma delta+ thymocytes from CD28-\/- and CD28+\/- littermates responded equally well to the alloantigen Tlab. Alloreactivity of CD28-\/- and CD28+\/- Tg gamma delta+ thymocytes could not be blocked with mAbs against CD80 and CD86 ligands. Thus gamma delta thymocytes utilize a costimulatory system during development and alloresponses that is independent of CD28\/CD80 and CD28\/CD86 interactions. By contrast to V gamma 2V alpha 11.3+ thymocytes, alloreactivity of V gamma 2V alpha 11.3+ lymph node T cells depended on CD28 costimulation and was severely impaired in CD28-\/- mice. These data provide functional evidence that maturation and selection of gamma delta cells is independent of CD28. These results also indicate that distinct costimulatory pathways are operational in mature thymocytes and peripheral T cells.","authors":"Penninger, JM., Timms, E., Shahinian, A., Jezo-Bremond, A., Nishina, H., Ionescu, J., Hedrick, SM., Mak, TW.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Immunol","volume":"155","issue":"8","page":"3847-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1995-11-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11156426","title":"Fibroblast growth factors are required for efficient tumor angiogenesis.","abstract":"Although the function of vascular endothelial growth factor in the induction of tumor angiogenesis is well understood, the role of a second group of angiogenic factors, the fibroblast growth factors (FGFs), remains elusive. We used a recombinant adenovirus expressing soluble FGF receptor (AdsFGFR) to interfere with FGF function in tumor angiogenesis. AdsFGFR repressed endothelial cell proliferation in vitro and inhibited tumor angiogenesis in an ex vivo bioassay, in which endothelial cells were cocultured with angiogenic tumor biopsies in a collagen gel. Moreover, AdsFGFR repressed tumor angiogenesis and hence tumor growth in vivo in allograft transplantation experiments. Whereas adenoviral expression of a soluble form of VEGF receptor 1 (AdsFlt) predominantly affected the initiation of tumor angiogenesis, soluble FGF receptor (sFGFR) appeared to impair the maintenance of tumor angiogenesis. The combination of sFGFR and soluble Flt exhibited a synergistic effect in the repression of tumor growth. Finally, i.v. injection of AdsFGFR resulted in a dramatic repression of tumor growth in a transgenic mouse model of pancreatic beta cell carcinogenesis. Similar to control infections with AdsFlt, tumor-associated vessel density was decreased, indicating that the expression of sFGFR impaired tumor angiogenesis. These data indicate that FGFs play a critical role in tumor angiogenesis.","authors":"Compagni, A., Wilgenbus, P., Impagnatiello, MA., Cotten, M., Christofori, G.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Cancer Res","volume":"60","issue":"24","page":"7163-9","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"2001-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10839747","title":"Review of microbial infections and the immune response to cardiac antigens.","abstract":"Heart disease is the most prevalent cause of morbidity and mortality in rich countries. Multiple pathogens are epidemiologically linked to human heart disease, and autoinflammatory responses to heart-specific epitopes revealed to the host's immune system (e.g., due to the cytopathic effects of cardiotropic viruses) or attacked by autoaggresive lymphocytes activated by mimicking peptides present in bacteria may be causative in the pathogenesis of chronic inflammatory cardiomyopathy. The experimental system of murine chronic autoimmune myocarditis has been used to analyze aspects of the host immune response. This review presents insights gained by use of this murine model system into molecular mechanisms governing activation of autoaggressive lymphocytes, target organ susceptibility, and cardiopathogenic epitope mapping and discusses mimicking endogenous epitopes found in pathogens.","authors":"Penninger, JM., Bachmaier, K.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Infect Dis","volume":"181 Suppl 3","issue":null,"page":"S498-504","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2000-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15694314","title":"Phosphorylation-induced autoinhibition regulates the cytoskeletal protein Lethal (2) giant larvae.","abstract":"During asymmetric cell division, cell fate determinants localize asymmetrically and segregate into one of the two daughter cells. In Drosophila neuroblasts, the asymmetric localization of cell fate determinants to the basal cell cortex requires aPKC. aPKC localizes to the apical cell cortex and phosphorylates the cytoskeletal protein Lethal (2) giant larvae (Lgl). Upon phosphorylation, Lgl dissociates from the cytoskeleton and becomes inactive. Here, we show that phosphorylation regulates Lgl by allowing an autoinhibitory interaction of the N terminus with the C terminus of the protein. We demonstrate that interaction with the cytoskeleton is mediated by a C-terminal domain while the N terminus is not required. Instead, the N terminus can bind to the C terminus and can compete for binding to the cytoskeleton. Interaction between the N- and C-terminal domains requires phosphorylation of Lgl by aPKC. Our results suggest that unphosphorylated, active Lgl exists in an open conformation that interacts with the cytoskeleton while phosphorylation changes the protein to an autoinhibited state.","authors":"Betschinger, J., Eisenhaber, F., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Biol","volume":"15","issue":"3","page":"276-82","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2005-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37430131","title":"How embryos sort themselves out.","abstract":null,"authors":"Pinheiro, D.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Rev Mol Cell Biol","volume":"24","issue":"12","page":"856","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41128661","title":"A Plastic EMP1+ to LGR5+ Cell State Conversion as a Bypass to KRASG12D Pharmacologic Inhibition in Metastatic Colorectal Cancer.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">41128661<\/PMID><DateCompleted><Year>2026<\/Year><Month>02<\/Month><Day>06<\/Day><\/DateCompleted><DateRevised><Year>2026<\/Year><Month>02<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">2159-8290<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>16<\/Volume><Issue>2<\/Issue><PubDate><Year>2026<\/Year><Month>Feb<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>Cancer discovery<\/Title><ISOAbbreviation>Cancer Discov<\/ISOAbbreviation><\/Journal><ArticleTitle>A Plastic EMP1+ to LGR5+ Cell State Conversion as a Bypass to KRASG12D Pharmacologic Inhibition in Metastatic Colorectal Cancer.<\/ArticleTitle><Pagination><StartPage>320<\/StartPage><EndPage>344<\/EndPage><MedlinePgn>320-344<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1158\/2159-8290.CD-25-0679<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Inhibitors of the oncogene KRAS hold promise for treating metastatic colorectal cancer (mCRC). In this study, we show that a selective, covalent small-molecule inhibitor of the active (ON) conformation of RAS-G12D, RMC-9945, exerts durable disease control in preclinical colorectal cancer models of early liver metastasis, but its therapeutic activity was diminished in the advanced metastatic disease. RMC-9945-treated metastases underwent a transition from a poor prognosis-associated Emp1+ transcriptional state to a WNT-driven Lgr5+ stem cell-like state that withstands the absence of RAS-G12D activity. This cell state change occurred within hours of RAS(ON) inhibitor treatment through a shift in transcription factor usage that involved limited chromatin remodeling. Forced conversion of metastatic cells to the Lgr5+ state through RAS-G12D inhibition, followed by genetic ablation of this population, reduced metastatic burden and prolonged survival in a mouse mCRC model. Overall, these preclinical findings demonstrate a central role for oncogenic KRAS in governing cellular plasticity in mCRC.","authors":"Centonze, A., Roura, AJ., Novillo-Font, M., Giordano, C., Hernando-Momblona, X., Llanses, M., Prats, P., Sevillano, M., Cabot, D., Novell, M., Pabst, G., Andersch, F., Ca\u00f1ellas-Socias, A., Zhang, C., Giakoumakis, NN., Sparks, H., Dunsby, C., Colombelli, J., Fern\u00e1ndez-Barral, A., Sancho, E., Stephan-Otto Attolini, C., Mu\u00f1oz, A., Barbachano, A., Palmer, HG., Mart\u00ednez-Quintanilla, J., Zuber, J., Blaj, C., Quintana, E., Cortina, C., Marti-Renom, MA., Batlle, E.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Cancer Discov","volume":"16","issue":"2","page":"320-344","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-02-06","doi":"10.1158\/2159-8290.CD-25-0679","first_author":"Centonze, A.","corresponding_authors":null},{"pmid":"32200413","title":"Influence of estradiol treatment on bone marrow cell differentiation in collagenase-induced arthritis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">32200413<\/PMID><DateCompleted><Year>2020<\/Year><Month>12<\/Month><Day>01<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1420-908X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>69<\/Volume><Issue>5<\/Issue><PubDate><Year>2020<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>Inflammation research : official journal of the European Histamine Research Society ... [et al.]<\/Title><ISOAbbreviation>Inflamm Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Influence of estradiol treatment on bone marrow cell differentiation in collagenase-induced arthritis.<\/ArticleTitle><Pagination><MedlinePgn>533-543<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s00011-020-01338-w<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE AND DESIGN\" NlmCategory=\"OBJECTIVE\">Estrogen is one of the important regulators of the balance between bone formation and bone resorption that can modulate the levels and activity of certain growth factors and cytokines. In this study, we investigated the effect of 17\u03b2-estradiol (ED) on bone marrow (BM) cell differentiation in vivo and ex vivo in a mouse model of collagenase-induced osteoarthritis (CIOA).","authors":"Ganova, P., Zhivkova, R., Kolarov, A., Ivanovska, N.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Inflamm Res","volume":"69","issue":"5","page":"533-543","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15678420","title":"Molecular machines for protein degradation.","abstract":"One of the most precisely regulated processes in living cells is intracellular protein degradation. The main component of the degradation machinery is the 20S proteasome present in both eukaryotes and prokaryotes. In addition, there exist other proteasome-related protein-degradation machineries, like HslVU in eubacteria. Peptides generated by proteasomes and related systems can be used by the cell, for example, for antigen presentation. However, most of the peptides must be degraded to single amino acids, which are further used in cell metabolism and for the synthesis of new proteins. Tricorn protease and its interacting factors are working downstream of the proteasome and process the peptides into amino acids. Here, we summarise the current state of knowledge about protein-degradation systems, focusing in particular on the proteasome, HslVU, Tricorn protease and its interacting factors and DegP. The structural information about these protein complexes opens new possibilities for identifying, characterising and elucidating the mode of action of natural and synthetic inhibitors, which affects their function. Some of these compounds may find therapeutic applications in contemporary medicine.","authors":"Groll, M., Bochtler, M., Brandstetter, H., Clausen, T., Huber, R.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Chembiochem","volume":"6","issue":"2","page":"222-56","pdf":null,"JrId":"26872","fulltextlink":null,"preprintlink":null,"articledate":"2005-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"104","title":"[Level of nicotinamide coenzymes in the liver and myocardium of rats poisoned with dichlorethane].","abstract":"Experiments were conducted on male rats. A study was made of the content of nicotinamide coenzymes in the liver and myocardium 24 hours after the administration of 0.5 ml of dichloroethane into the stomach. In parallel with disturbance of the morphological structure of the liver and of the myocardium, increase in the activity of alanine and aspargic aminotranspherases in the blood serum, dichloroethane reduced the content of nicotinamide coenzymes and deranged the ratio of their oxidized and reduced forms in these organs.","authors":"Natsiuk, MV., Chekman, IS.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biull Eksp Biol Med","volume":"79","issue":"4","page":"58-60","pdf":null,"JrId":"1214","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10715213","title":"Crystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly.","abstract":"NifS-like proteins are ubiquitous, homodimeric, proteins which belong to the alpha-family of pyridoxal-5'-phoshate dependent enzymes. They are proposed to donate elementary sulphur, generated from cysteine, via a cysteinepersulphide intermediate during iron sulphur cluster biosynthesis, an important albeit not well understood process. Here, we report on the crystal structure of a NifS-like protein from the hyperthermophilic bacterium Thermotoga maritima (tmNifS) at 2.0 A resolution. The tmNifS is structured into two domains, the larger bearing the pyridoxal-5'-phosphate-binding active site, the smaller hosting the active site cysteine in the middle of a highly flexible loop, 12 amino acid residues in length. Once charged with sulphur the loop could possibly deliver S(0) directly to regions far remote from the protein. Based on the three-dimensional structures of the native as well as the substrate complexed form and on spectrophotometric results, a mechanism of sulphur activation is proposed. The His99, which stacks on top of the pyridoxal-5'-phosphate co-factor, is assigned a crucial role during the catalytic cycle by acting as an acid-base catalyst and is believed to have a pK(a) value depending on the co-factor redox state.","authors":"Kaiser, JT., Clausen, T., Bourenkow, GP., Bartunik, HD., Steinbacher, S., Huber, R.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Mol Biol","volume":"297","issue":"2","page":"451-64","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2000-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31985756","title":"Essential cell-extrinsic requirement for PDIA6 in lymphoid and myeloid development.","abstract":"In a forward genetic screen of N-ethyl-N-nitrosourea (ENU)-induced mutant mice for aberrant immune function, we identified mice with a syndromic disorder marked by growth retardation, diabetes, premature death, and severe lymphoid and myeloid hypoplasia together with diminished T cell-independent (TI) antibody responses. The causative mutation was in Pdia6, an essential gene encoding protein disulfide isomerase A6 (PDIA6), an oxidoreductase that functions in nascent protein folding in the endoplasmic reticulum. The immune deficiency caused by the Pdia6 mutation was, with the exception of a residual T cell developmental defect, completely rescued in irradiated wild-type recipients of PDIA6-deficient bone marrow cells, both in the absence or presence of competition. The viable hypomorphic allele uncovered in these studies reveals an essential role for PDIA6 in hematopoiesis, but one extrinsic to cells of the hematopoietic lineage. We show evidence that this role is in the proper folding of Wnt3a, BAFF, IL-7, and perhaps other factors produced by the extra-hematopoietic compartment that contribute to the development and lineage commitment of hematopoietic cells.","authors":"Choi, JH., Zhong, X., Zhang, Z., Su, L., McAlpine, W., Misawa, T., Liao, TC., Zhan, X., Russell, J., Ludwig, S., Li, X., Tang, M., Anderton, P., Moresco, EMY., Beutler, B.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Exp Med","volume":"217","issue":"4","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31649139","title":"Self-organization of <i>parS<\/i> centromeres by the ParB CTP hydrolase.","abstract":"ParABS systems facilitate chromosome segregation and plasmid partitioning in bacteria and archaea. ParB protein binds centromeric <i>parS<\/i> DNA sequences and spreads to flanking DNA. We show that ParB is an enzyme that hydrolyzes cytidine triphosphate (CTP) to cytidine diphosphate (CDP). <i>parS<\/i> DNA stimulates cooperative CTP binding by ParB and CTP hydrolysis. A nucleotide cocrystal structure elucidates the catalytic center of the dimerization-dependent ParB CTPase. Single-molecule imaging and biochemical assays recapitulate features of ParB spreading from <i>parS<\/i> in the presence but not absence of CTP. These findings suggest that centromeres assemble by self-loading of ParB DNA sliding clamps at <i>parS<\/i> ParB CTPase is not related to known nucleotide hydrolases and might be a promising target for developing new classes of antibiotics.","authors":"Soh, YM., Davidson, IF., Zamuner, S., Basquin, J., Bock, FP., Taschner, M., Veening, JW., De Los Rios, P., Peters, JM., Gruber, S.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Science","volume":"366","issue":"6469","page":"1129-1133","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32157750","title":"Oestrogen-activated autophagy has a negative effect on the anti-osteoclastogenic function of oestrogen.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">32157750<\/PMID><DateCompleted><Year>2020<\/Year><Month>04<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>04<\/Month><Day>24<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1365-2184<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>53<\/Volume><Issue>4<\/Issue><PubDate><Year>2020<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>Cell proliferation<\/Title><ISOAbbreviation>Cell Prolif<\/ISOAbbreviation><\/Journal><ArticleTitle>Oestrogen-activated autophagy has a negative effect on the anti-osteoclastogenic function of oestrogen.<\/ArticleTitle><Pagination><MedlinePgn>e12789<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/cpr.12789<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\" NlmCategory=\"OBJECTIVE\">Oestrogen is known to inhibit osteoclastogenesis, and numerous studies have identified it as an autophagic activator. To date, the role of oestrogen in the autophagy of osteoclast precursors (OCPs) during osteoclastogenesis remains unclear. This study aimed to determine the effect of autophagy regulated by the biologically active form of oestrogen (17\u03b2-estradiol) on osteoclastogenesis.","authors":"Cheng, L., Zhu, Y., Ke, D., Xie, D.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Prolif","volume":"53","issue":"4","page":"e12789","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18464734","title":"Genome analysis of the platypus reveals unique signatures of evolution.","abstract":"We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.","authors":"Warren, WC., Hillier, LW., Marshall Graves, JA., Birney, E., Ponting, CP., Gr\u00fctzner, F., Belov, K., Miller, W., Clarke, L., Chinwalla, AT., Yang, SP., Heger, A., Locke, DP., Miethke, P., Waters, PD., Veyrunes, F., Fulton, L., Fulton, B., Graves, T., Wallis, J., Puente, XS., L\u00f3pez-Ot\u00edn, C., Ord\u00f3\u00f1ez, GR., Eichler, EE., Chen, L., Cheng, Z., Deakin, JE., Alsop, A., Thompson, K., Kirby, P., Papenfuss, AT., Wakefield, MJ., Olender, T., Lancet, D., Huttley, GA., Smit, AF., Pask, A., Temple-Smith, P., Batzer, MA., Walker, JA., Konkel, MK., Harris, RS., Whittington, CM., Wong, ES., Gemmell, NJ., Buschiazzo, E., Vargas Jentzsch, IM., Merkel, A., Schmitz, J., Zemann, A., Churakov, G., Kriegs, JO., Brosius, J., Murchison, EP., Sachidanandam, R., Smith, C., Hannon, GJ., Tsend-Ayush, E., McMillan, D., Attenborough, R., Rens, W., Ferguson-Smith, M., Lef\u00e8vre, CM., Sharp, JA., Nicholas, KR., Ray, DA., Kube, M., Reinhardt, R., Pringle, TH., Taylor, J., Jones, RC., Nixon, B., Dacheux, JL., Niwa, H., Sekita, Y., Huang, X., Stark, A., Kheradpour, P., Kellis, M., Flicek, P., Chen, Y., Webber, C., Hardison, R., Nelson, J., Hallsworth-Pepin, K., Delehaunty, K., Markovic, C., Minx, P., Feng, Y., Kremitzki, C., Mitreva, M., Glasscock, J., Wylie, T., Wohldmann, P., Thiru, P., Nhan, MN., Pohl, CS., Smith, SM., Hou, S., Nefedov, M., de Jong, PJ., Renfree, MB., Mardis, ER., Wilson, RK.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nature","volume":"453","issue":"7192","page":"175-83","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18394895","title":"Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila.","abstract":"During oogenesis, female animals load their eggs with messenger RNAs (mRNAs) that will be translated to produce new proteins in the developing embryo. Some of these maternally provided mRNAs are stable and continue to contribute to development long after the onset of transcription of the embryonic (zygotic) genome. However, a subset of maternal mRNAs are degraded during the transition from purely maternal to mixed maternal-zygotic gene expression. In Drosophila, two independent RNA degradation pathways are used to promote turnover of maternal transcripts during the maternal-to-zygotic transition [1]. The first is driven by maternally encoded factors, including SMAUG [2], whereas the second is activated about 2 hr after fertilization, coinciding with the onset of zygotic transcription. Here, we report that a cluster of zygotically expressed microRNAs (miRNAs) targets maternal mRNAs for turnover, as part of the zygotic degradation pathway. miRNAs are small noncoding RNAs that silence gene expression by repressing translation of their target mRNAs and by promoting mRNA turnover. Intriguingly, use of miRNAs to promote mRNA turnover during the maternal-to-zygotic transition appears to be a conserved phenomenon because a comparable role was reported for miR-430 in zebrafish [3]. The finding that unrelated miRNAs regulate the maternal to zygotic transition in different animals suggests convergent evolution.","authors":"Bushati, N., Stark, A., Brennecke, J., Cohen, SM.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Biol","volume":"18","issue":"7","page":"501-6","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31922317","title":"The role and potential mechanism of p75NTR in mineralization via in vivo p75NTR knockout mice and in vitro ectomesenchymal stem cells.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31922317<\/PMID><DateCompleted><Year>2020<\/Year><Month>03<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1365-2184<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>53<\/Volume><Issue>2<\/Issue><PubDate><Year>2020<\/Year><Month>Feb<\/Month><\/PubDate><\/JournalIssue><Title>Cell proliferation<\/Title><ISOAbbreviation>Cell Prolif<\/ISOAbbreviation><\/Journal><ArticleTitle>The role and potential mechanism of p75NTR in mineralization via in vivo p75NTR knockout mice and in vitro ectomesenchymal stem cells.<\/ArticleTitle><Pagination><MedlinePgn>e12758<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/cpr.12758<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">The aim of this study is to investigate the role and potential mechanism of p75NTR in mineralization in vivo using p75NTR-knockout mice and in vitro using ectomesenchymal stem cells (EMSCs).","authors":"Zhao, M., Wang, Y., Li, G., Li, J., Yang, K., Liu, C., Wen, X., Song, J.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Prolif","volume":"53","issue":"2","page":"e12758","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31889368","title":"IGFBP7 acts as a negative regulator of RANKL-induced osteoclastogenesis and oestrogen deficiency-induced bone loss.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31889368<\/PMID><DateCompleted><Year>2020<\/Year><Month>03<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1365-2184<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>53<\/Volume><Issue>2<\/Issue><PubDate><Year>2020<\/Year><Month>Feb<\/Month><\/PubDate><\/JournalIssue><Title>Cell proliferation<\/Title><ISOAbbreviation>Cell Prolif<\/ISOAbbreviation><\/Journal><ArticleTitle>IGFBP7 acts as a negative regulator of RANKL-induced osteoclastogenesis and oestrogen deficiency-induced bone loss.<\/ArticleTitle><Pagination><MedlinePgn>e12752<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/cpr.12752<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\" NlmCategory=\"OBJECTIVE\">Insulin-like growth factor-binding protein 7 (IGFBP7) is a low-affinity insulin growth factor (IGF) binder that may play an important role in bone metabolism. We previously reported that IGFBP7 enhanced osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs) via the Wnt\/\u03b2-catenin signalling pathway. In this study, we tried to reveal its function in osteoclast differentiation and osteoporosis.","authors":"Ye, C., Hou, W., Chen, M., Lu, J., Chen, E., Tang, L., Hang, K., Ding, Q., Li, Y., Zhang, W., He, R.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Prolif","volume":"53","issue":"2","page":"e12752","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37943927","title":"How do molecular motors fold the genome?","abstract":"A potential mechanism of DNA loop extrusion by molecular motors is discussed.","authors":"Dekker, C., Haering, CH., Peters, JM., Rowland, BD.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Science","volume":"382","issue":"6671","page":"646-648","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31826586","title":"[Potential mechanism of transcription factor peroxisome proliferator-activated receptor-gamma coactivator-1 beta on promoting osteoclastogenesis].","abstract":"<b>Objective:<\/b> To investigate the role of transcription factor peroxisome proliferator-activated receptor-gamma coactivator-1 beta (PGC-1\u03b2) on osteoclastogenesis and related regulatory mechanism in the mouse monocyte-macrophage cell line (RAW264.7). <b>Methods:<\/b> PGC-1\u03b2 expression and location in RAW264.7 cells was detected by immunofluorescence, flow cytometry and western blot analysis with nuclear protein extraction. RAW264.7 cells were transfected with lentivirus for gene silencing or over-expression of PGC-1\u03b2 and cultured with macrophage colony-stimulating factor and receptor activator for nuclear factor-\u03baB ligand. Cell viability was detected by cell counting kit-8. Cell apoptosis and cell cycle were detected by flow cytometry. Mature osteoclasts and their bone resorption activity were determined by tartrate-resistant acid phosphatase (TRAP) expression and toluidine blue staining. Western blot analysis was performed for detecting dendritic cell-specific transmembrane protein (DC-STAMP), cathepsin K, TRAP and matrix metalloproteinase (MMP)-9 expression, as well as cytoplasmic NF-\u03baB-inducing kinase (NIK) and nuclear RelB. <b>Results:<\/b> PGC-1\u03b2 expression was observed in the nuclei of RAW264.7 cells. Down-regulation or overexpression of PGC-1\u03b2 in RAW264.7 cells did not affect cell viability, apoptosis or cell cycle. Down-regulation of PGC-1\u03b2 decreased the count of mature osteoclasts (49\u00b121 cells vs. 147\u00b142 cells, <i>P=<\/i>0.004) and the pit area of bone resorption lacunae (42.11\u03bcm(2)\u00b111.30 \u03bcm(2) vs. 204.80\u03bcm(2)\u00b131.09 \u03bcm(2), <i>P&lt;<\/i>0.001), as well as the expression of cathepsin K, TRAP and MMP-9, but not DC-STAMP. Overexpression of PGC-1\u03b2 promoted osteoclast differentiation and bone resorption activity, as well as the expression of cathepsin K, TRAP and MMP-9. Down-regulation of PGC-1\u03b2 suppressed the protein expression of cytoplasmic NIK and nuclear RelB in RAW264.7 cells. <b>Conclusion:<\/b> PGC-1\u03b2 can promote the differentiation of RAW264.7 into osteoclasts and improve the bone resorption ability of the cells via activation of NIK\/RelB pathway, which might be a promising therapeutic target for osteoporosis.","authors":"Wang, JW., Ma, JD., Jing, J., Wei, XN., Li, QH., Liang, JJ., Zheng, DH., Dai, L.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Zhonghua Yi Xue Za Zhi","volume":"99","issue":"46","page":"3638-3644","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18393943","title":"Specific effects of KChIP3\/calsenilin\/DREAM, but not KChIPs 1, 2 and 4, on calcium signalling and regulated secretion in PC12 cells.","abstract":"The KChIPs (K+ channel-interacting proteins) are members of the NCS (neuronal calcium sensor) protein family of Ca2+-binding proteins. It is unclear to what extent the KChIPs have distinct functions although they all interact with Kv4 K+ channels. KChIP3 has also been shown to repress transcription of specific genes via binding to DRE (downstream regulatory element) motifs and all KChIPs may share this function. In the present study, we have compared the function of isoforms of the four KChIPs. KChIPs 1-4 were found to stimulate the traffic of Kv4.2 channels to the plasma membrane. KChIP3 expression in PC12 cells resulted in an increase in exocytosis evoked by activation of purinergic receptors. In contrast, KChIPs 1, 2 and 4, although expressed to the same extent, had no effect on secretion. In addition, KChIP3 but not KChIPs 1, 2 and 4 modified the ATP-induced Ca2+ signal resulting in a delay in recovery after the peak Ca2+ elevation and also specifically resulted in down-regulation of the Na+\/Ca2+ exchanger NCX3, which could explain the effects on the Ca2+ signal and secretion. Regulation of NCX3 by KChIP3 has been shown to occur via its DREAM (DRE antagonist modulator) function [Gomez-Villafuertes, Torres, Barrio, Savignac, Gabellini, Rizzato, Pintado, Gutierrez-Adan, Mellstrom, Carafoli and Naranjo (2005) J. Neurosci. 25, 10822-10830] suggesting that this activity might depend on the cellular context of expression of the various KChIPs. These results reveal a new role for KChIP3 in the regulation of Ca2+-regulated secretion and also suggest that the functions of each of the KChIPs may be more specialized than previously appreciated.","authors":"Venn, N., Haynes, LP., Burgoyne, RD.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Biochem J","volume":"413","issue":"1","page":"71-80","pdf":null,"JrId":"1011","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15671661","title":"Plasticity and reprogramming of differentiated cells in amphibian regeneration: partial purification of a serum factor that triggers cell cycle re-entry in differentiated muscle cells.","abstract":"The reversal of cellular differentiation to form proliferating progenitor cells is a critical aspect of regenerative ability in the urodele amphibians. This process has been studied using skeletal muscle during limb or tail regeneration, or dorsal iris epithelium during lens regeneration. An unknown activity in serum triggers cell cycle re-entry from the differentiated state. Here we describe the biochemical properties and fractionation of this serum factor. The factor is a glycoprotein that associates with large molecular weight complexes. The purification and molecular identification of the serum factor represents an important avenue in understanding regenerative ability and dedifferentiation capacity on a molecular basis.","authors":"Straube, WL., Brockes, JP., Drechsel, DN., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Cloning Stem Cells","volume":"6","issue":"4","page":"333-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7553850","title":"The formation of Golgi stacks from vesiculated Golgi membranes requires two distinct fusion events.","abstract":"We have reconstituted the fusion and assembly of vesiculated Golgi membranes (VGMs) into functionally active stacks of cisternae. A kinetic analysis of this assembly process revealed that highly dispersed VGMs of 60-90 nm diameter first fuse to form larger vesicles of 200-300 nm diameter that are clustered together. These vesicles then fuse to form tubular elements and short cisternae, which finally assemble into stacks of cisternae. We now provide evidence that the sequential stack formation from VGMs reflects two distinct fusion processes: the first event is N-ethyl-maleimide (NEM)-sensitive factor (NSF) dependent, and the second fusion event requires an NSF-like NEM-sensitive ATPase called p97. Interestingly, while the earliest steps in stack formation share some similarities with events catalyzing fusion of transport vesicles to its target membrane, neither GTP gamma S nor Rab-GDI, inhibitors of vesicular protein traffic, inhibit stack formation.","authors":"Acharya, U., Jacobs, R., Peters, JM., Watson, N., Farquhar, MG., Malhotra, V.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell","volume":"82","issue":"6","page":"895-904","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1995-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18381497","title":"Developmentally informed research on the effectiveness of clinical trials: a primer for assessing how developmental issues may influence treatment responses among adolescents with alcohol use problems.","abstract":"The goal of this article is to familiarize readers with the adolescent developmental issues and processes most likely to affect responses to treatment for alcohol use problems. Although the need for research that blends developmental science and treatment outcome research is widely acknowledged, scant information exists about developmentally informed approaches to treatment research with alcohol-abusing teens. Exactly how developmental issues may influence treatment responses among adolescents with alcohol use problems remains an open question. In the hope of moving developmentally informed research forward, this article reports findings from a literature review regarding the degree to which developmental issues and processes have been considered in adolescent alcohol treatment research. Moreover, promising concepts and methods from applied developmental science are discussed, as are various developmental processes and transitions that may influence adolescent risk behavior. Finally, guidance is provided regarding how applied developmental science conceptualizations and methods may be incorporated successfully into randomized, clinical trials with adolescents with alcohol use problems.","authors":"Wagner, EF.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Pediatrics","volume":"121 Suppl 4","issue":null,"page":"S337-47","pdf":null,"JrId":"6405","fulltextlink":null,"preprintlink":null,"articledate":"2008-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"40920972","title":"Protective Role of Apelin in a Mouse Model of Post-Intensive Care Syndrome.","abstract":"Post-intensive care syndrome (PICS) is a serious condition involving physical weakness, depression, and cognitive impairment that develop during or after an ICU stay, often resulting in long-term declines in quality of life. Patients with acute respiratory distress syndrome and severe coronavirus disease (COVID-19) are at particularly high risk, yet the molecular mechanisms underlying PICS remain poorly understood. Here, we identify impaired Apelin-APJ signaling as a potential contributor to PICS pathogenesis through the disruption of interorgan homeostasis. Using a mouse model combining acute lung injury and hindlimb immobilization, we observed PICS-like features, including muscle atrophy, lung inflammation, and neurobehavioral abnormalities such as anxiety-like behavior and special working memory. Single-cell RNA sequencing in brain revealed upregulation of gene programs associated with Alzheimer's disease, depression, and neuroinflammation, particularly in endothelial cells and microglia. Concurrently, Apelin-APJ signaling was downregulated in skeletal muscle. These changes were exacerbated in Apelin-deficient mice and attenuated by muscle-specific Apelin overexpression, which also reduced systemic IL-6 and restored circulating Apelin levels. In survivors of ARDS who had severe COVID-19, ICU-acquired weakness was associated with reduced plasma Apelin and elevated IL-6 levels. Transcriptomic profiling of peripheral blood mononuclear cells from patients with ICU-acquired weakness showed gene expression signatures linked to depression and neurodegeneration, mirroring murine findings. These data suggest that impaired Apelin-APJ signaling may play a role in PICS pathophysiology. Although skeletal muscle appears to contribute to systemic Apelin levels, further studies are needed to clarify tissue-specific roles. Modulating this pathway could offer a therapeutic strategy to mitigate long-term outcomes in ICU survivors.","authors":"Imai, Y., Kinugasa, Y., Nukiwa, R., Covarrubias, MAL., Thwin, KK., Yonezaki, K., Shimizu, T., Yamasaki, S., Shintani, Y., Hashimoto, H., Suzuki, Y., Fujino, Y., Kubodera, K., Kotani, T., Furuyashiki, T., Penninger, J., Slutsky, AS.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Am J Respir Cell Mol Biol","volume":"74","issue":"2","page":"241-256","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-02-25","doi":"10.1165\/rcmb.2025-0028OC","first_author":"Imai, Y.","corresponding_authors":"Slutsky, AS."},{"pmid":"31703162","title":"Htra1 is a Novel Transcriptional Target of RUNX2 That Promotes Osteogenic Differentiation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31703162<\/PMID><DateCompleted><Year>2019<\/Year><Month>11<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1421-9778<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>53<\/Volume><Issue>5<\/Issue><PubDate><Year>2019<\/Year><\/PubDate><\/JournalIssue><Title>Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology<\/Title><ISOAbbreviation>Cell Physiol Biochem<\/ISOAbbreviation><\/Journal><ArticleTitle>Htra1 is a Novel Transcriptional Target of RUNX2 That Promotes Osteogenic Differentiation.<\/ArticleTitle><Pagination><MedlinePgn>832-850<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.33594\/000000176<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\/AIMS\" NlmCategory=\"OBJECTIVE\">Runt-related transcription factor 2 (Runx2) is a master regulator of osteogenic differentiation, but most of the direct downstream targets of RUNX2 during osteogenesis are unknown. Likewise, High-temperature requirement factor A1 (HTRA1) is a serine protease expressed in bone, yet the role of Htra1 during osteoblast differentiation remains elusive. We investigated the role of Htra1 in osteogenic differentiation and the transcriptional regulation of Htra1 by RUNX2 in primary mouse mesenchymal progenitor cells.","authors":"Iyyanar, PPR., Thangaraj, MP., Eames, BF., Nazarali, AJ.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell Physiol Biochem","volume":"53","issue":"5","page":"832-850","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29414528","title":"Control of B-1a cell development by instructive BCR signaling.","abstract":"B-1a cells remain one of the most enigmatic lymphocyte subsets. In this review, we discuss recent advances in our understanding of the development of these cells and their regulation by the transcription factors Bhlhe41 and Arid3a as well as by the RNA-binding protein Lin28b. A large body of literature supports an instructive role of BCR signaling in B-1a cell development and lineage commitment, which is initiated only after signaling from an autoreactive BCR. While both fetal and adult hematopoiesis can generate B-1a cells, the contribution of adult hematopoiesis to the B-1a cell compartment is low under physiological conditions. We discuss several models that can reconcile the instructive role of BCR signaling with this fetal bias in B-1a cell development.","authors":"Kreslavsky, T., Wong, JB., Fischer, M., Skok, JA., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Curr Opin Immunol","volume":"51","issue":null,"page":"24-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31733158","title":"DKK1 and TNF-alpha influence osteogenic differentiation of adBMP9-infected-rDFCs.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Curated\" Owner=\"NLM\"><PMID Version=\"1\">31733158<\/PMID><DateCompleted><Year>2020<\/Year><Month>03<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>03<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1601-0825<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>26<\/Volume><Issue>2<\/Issue><PubDate><Year>2020<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>Oral diseases<\/Title><ISOAbbreviation>Oral Dis<\/ISOAbbreviation><\/Journal><ArticleTitle>DKK1 and TNF-alpha influence osteogenic differentiation of adBMP9-infected-rDFCs.<\/ArticleTitle><Pagination><MedlinePgn>360-369<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/odi.13235<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVES\" NlmCategory=\"OBJECTIVE\">Rat dental follicle cells (rDFCs) function as precursor cells of periodontal tissues. Bone morphogenetic protein (BMP9) plays an important role in proliferation and differentiation. Tumour necrosis factor-alpha (TNF-alpha) is an important contributor to bone resorption. Wnt canonical pathway can be inhibited by Dickkopf 1 (DKK1). The aim of the study was to enhance the osteogenesis of BMP9 treated rDFCs in an inflammatory environment and elucidate the mechanism.","authors":"Li, X., Chen, D., Jing, X., Li, C.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Oral Dis","volume":"26","issue":"2","page":"360-369","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15619371","title":"Genotyping of Toxoplasma gondii strains isolated from dogs with neurological signs.","abstract":"From 111 dogs with neurological signs admitted in this research in a 22-month period, brain samples of 34 animals were inoculated in mice in order to isolate Toxoplasma gondii. From these 34 dogs, 9 strains of T. gondii were isolated and the genetic characterization performed by restriction analysis (RFLP) of the SAG-2 gene. RFLP analysis showed that four of them were classified as Type I, and five as Type III. The present report is the first description of genotyping of T. gondii isolated from brain samples of naturally infected dogs, in Brazil.","authors":"da Silva, AV., Pezerico, SB., de Lima, VY., d'Arc Moretti, L., Pinheiro, JP., Tanaka, EM., Ribeiro, MG., Langoni, H.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Vet Parasitol","volume":"127","issue":"1","page":"23-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31589963","title":"Drug-induced modifications and modulations of microRNAs and long non-coding RNAs for future therapy against Glioblastoma Multiforme.","abstract":"Non-coding RNAs are known to participate in cancer initiation, progression, and metastasis by regulating the status of chromatin epigenetics and gene expression. Although these non-coding RNAs do not possess defined protein-coding potential, they are involved in the expression and stability of messenger RNA (mRNA). The length of microRNAs (miRs) ranges between 20 and 22 nt, whereas, long non-coding RNAs (lncRNAs) length ranges between 200 nt to 1\u202fKb. In the case of circular RNAs (circRNAs), the size varies depending upon the length of the exon from where they were derived. Epigenetic regulations of miR and lncRNA genes will influence the gene expression by modulating histone acetylation and methylation patterns. Especially, lncRNAs will act as a scaffold for various epigenetic proteins, such as EZH2 and LSD1, and influence the chromatin epigenetic state at various genomic loci involved at silencing. Thus investigations on the expression of lncRNAs and designing drugs to modulate the expression of these genes will have a profound impact on future therapeutics against cancers such as Glioblastoma Multiforme (GBM) and also against various other diseases. With the recent advancements in genome-wide transcriptomic studies, scientists are focused on the non-coding RNAs and their regulations on various cellular processes involved in GBM and on other types of cancer as well as trying to understand possible epigenetic modulations that help in generating promising therapeutics for the future generations. In this review, the involvement of epigenetic proteins, enzymes that change chromatin architecture and epigenetic landscape and new roles of lncRNAs that are involved in GBM progression are elaborately discussed.","authors":"Janaki Ramaiah, M., Divyapriya, K., Kartik Kumar, S., Rajesh, YBRD.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Gene","volume":"723","issue":"","page":"144126","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41803172","title":"Non-canonical muscle stem cells and other lessons from regenerative vertebrates.","abstract":"In this perspective, we explore the developmental mechanisms of muscle stem cells in multiple non-mammalian vertebrate species, and we compare these phenomena to those in mammals. Particularly, we discuss two recently described populations of noncanonical muscle progenitors in regenerative vertebrates: one in zebrafish and one in axolotl. We discuss the capabilities of these two populations during muscle development and regeneration, including the implications for muscle repair in mammals.","authors":"Jamwal, VS., Masselink, W., Crawford, K., Murawala, P.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"NPJ Regen Med","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-03-10","doi":"10.1038\/s41536-026-00468-9","first_author":"Jamwal, VS.","corresponding_authors":"Murawala, P."},{"pmid":"30734835","title":"Exosomes: from carcinogenesis and metastasis to diagnosis and treatment of gastric cancer.","abstract":"Exosomes represent an important group of extracellular vesicles with a defined size between 40 and 150\u00a0nm and cup-shaped construction which have a pivotal role in elimination of intracellular debris and intercellular signaling networks. A line of evidence revealed the impact of different types of exosomes in initiation, progression, and metastasis of gastric cancer (GC). These bioactive vesicles mediate tumor and stromal communication network through modulation of cell signaling for carcinogenesis and pre-metastatic niche formation in distant organs. Exosomes contain various cargos including DNAs (mitochondrial and genomic), proteins, transposable elements, and RNAs (coding and noncoding) with different compositions related to functional status of origin cells. In this review, we summarize the main roles of key exosomal cargos in induction of exosome-mediated signaling in cancer cells. Body fluids are employed frequently as the source of exosomes released by tumor cells with a potential role in early diagnosis of GC and chemoresistance. These vesicles as non-toxic and non-immunogenic carriers are also found to be applied for novel drug delivery systems.","authors":"Kahroba, H., Hejazi, MS., Samadi, N.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell Mol Life Sci","volume":"76","issue":"9","page":"1747-1758","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18328704","title":"Impaired synaptic plasticity and motor learning in mice with a point mutation implicated in human speech deficits.","abstract":"The most well-described example of an inherited speech and language disorder is that observed in the multigenerational KE family, caused by a heterozygous missense mutation in the FOXP2 gene. Affected individuals are characterized by deficits in the learning and production of complex orofacial motor sequences underlying fluent speech and display impaired linguistic processing for both spoken and written language. The FOXP2 transcription factor is highly similar in many vertebrate species, with conserved expression in neural circuits related to sensorimotor integration and motor learning. In this study, we generated mice carrying an identical point mutation to that of the KE family, yielding the equivalent arginine-to-histidine substitution in the Foxp2 DNA-binding domain. Homozygous R552H mice show severe reductions in cerebellar growth and postnatal weight gain but are able to produce complex innate ultrasonic vocalizations. Heterozygous R552H mice are overtly normal in brain structure and development. Crucially, although their baseline motor abilities appear to be identical to wild-type littermates, R552H heterozygotes display significant deficits in species-typical motor-skill learning, accompanied by abnormal synaptic plasticity in striatal and cerebellar neural circuits.","authors":"Groszer, M., Keays, DA., Deacon, RM., de Bono, JP., Prasad-Mulcare, S., Gaub, S., Baum, MG., French, CA., Nicod, J., Coventry, JA., Enard, W., Fray, M., Brown, SD., Nolan, PM., P\u00e4\u00e4bo, S., Channon, KM., Costa, RM., Eilers, J., Ehret, G., Rawlins, JN., Fisher, SE.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Curr Biol","volume":"18","issue":"5","page":"354-62","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"95","title":"[Luminescence study of the effect of temperature on the conformational state of fibrinogen].","abstract":"Results are presented of measuring fibrinogen fluorescence parameters in temperature range of 20-80 degrees C at different pH of the solution. It was found that the temperature increase from 20 to 40 degrees C for solutions with pH of 4,5-9,3 were not accompanied by the conformational changes of fibrinogen macromolecules. In the temperature range of 40-50 degrees C for neutral solutions conformational reconstruction of fibrinogen of undenatured character took place. Temperature increase above 50-55 degrees C brings about significant structural changes of fibrinogen molecule which are of denaturation nature.","authors":"Konev, SV., Katibnikov, MA., Bandarin, VA., Niamaa, D., Barkovski\u012d, EV.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biofizika","volume":"20","issue":"4","page":"586-90","pdf":null,"JrId":"1060","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10435633","title":"Formation of transformed endothelial cells in the absence of VEGFR-2\/Flk-1 by Polyoma middle T oncogene.","abstract":"The middle T antigen of murine Polyomavirus (PymT) rapidly transforms endothelial cells leading to vascular malformations reminiscent of endothelial tumors or hemangiomas. Flk-1, a receptor tyrosine kinase which is activated upon binding of its ligand VEGF, is predominantly expressed in endothelial cells and essential for the formation of blood vessels since absence of Flk-1 prevents the development of mature endothelial cells in mice and in ES-cell differentiation experiments. To investigate the role of Flk-1 in PymT-induced vascular tumor formation, we studied the expression of Flk-1 and VEGF in PymT-transformed endothelial cells (Endothelioma cells, END. cells). The receptor and its ligand were both expressed in END. cells suggesting that a VEGF\/Flk-1 autocrine loop might be causally involved in the formation of vascular tumors. To test this hypothesis, ES cells lacking Flk-1 were generated and the transforming potential of PymT was analysed after in vitro differentiation. Flk-1(-\/-) END. cell lines were established which are morphologically identical to flk-1(+\/+) END. cells and which express several markers characteristic for endothelial cells. This result suggests that PymT functionally replaces the requirement of Flk-1 in expansion and\/or survival of endothelial progenitor cells. Therefore, flk-1(-\/-) END. cells provide a powerful tool to dissect the downstream signaling pathways of Flk-1.","authors":"M\u00fchlner, U., M\u00f6hle-Steinlein, U., Wizigmann-Voos, S., Christofori, G., Risau, W., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Oncogene","volume":"18","issue":"29","page":"4200-10","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30280185","title":"Suppressing cell growth and inducing apoptosis by inhibiting miR\u201123a\u20115p in human bladder cancer.","abstract":"MicroRNAs (miRNAs) are a class of non\u2011coding RNAs, which are important in the initiation and progression of cancer. miRNA\u201123a\u20115p (miR\u201123a\u20115p) is a novel miRNA, which promotes cell growth and survival in several types of cancer. The aim of the present study was to investigate the expression and functional significance of miR\u201123a\u20115p in bladder cancer. Microchip assays have shown that miR\u201123a\u20115p is significantly upregulated in human bladder cancer. In the present study, it was found that miR\u201123a\u20115p was upregulated in bladder cancer tissues, compared with paired normal urothelial tissues by reverse transcription\u2011quantitative polymerase chain reaction. The impact of miR\u201123a\u20115p on cell proliferation, cell migration and apoptosis was determined by a 3\u2011(4,5\u2011dimethylthi\u2011azol\u20112\u2011yl)\u20112,5\u2011diphenyltetrazolium bromide assay, wound scratch assay and flow cytometry. The inhibition of cell proliferation and induction of apoptosis were also observed in miR\u201123a\u20115p inhibitor\u2011transfected T24 and SW780 human bladder cancer cells. These data suggested that miR\u201123a\u20115p has an oncogenic role and may be a therapeutic target for bladder cancer.","authors":"Li, Y., Quan, J., Pan, X., Zhou, J., He, A., Lai, Y., Zhou, G.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Mol Med Rep","volume":"18","issue":"6","page":"5256-5260","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41820618","title":"Serum coating enables feeder-free culture of naive human pluripotent stem cells preserving developmental potential.","abstract":"Naive human pluripotent stem cells (hPSCs) represent a pre-implantation epiblast state able to efficiently differentiate into embryonic and extraembryonic pre-implantation lineages and to self-organise in vitro into blastocyst-like structures called blastoids. Naive hPSC maintenance routinely relies on co-culture with mouse embryonic fibroblast (MEFs) as feeder cells, a method prone to variability and analytical confounders. Here, we describe a feeder-free culture system based on serum coating that supports long-term maintenance of naive hPSCs. Across five laboratories, 30 serum batches were evaluated for the expansion of eight naive hPSCs lines for up to 25 passages. Mass spectrometry analysis identified fibronectin and collagens as extracellular matrix proteins consistently present in serum coating. Cells cultured on serum coating displayed growth kinetics, clonogenic capacity, mutation rates, and global gene expression profiles comparable to MEF-based cultures. Importantly, serum-cultured naive hPSCs efficiently underwent germ layer specification, retained trophectoderm competence, and generated blastoids with efficiency similar to MEF-based cultures. Collectively, serum coating provides a scalable, cost-effective, and robust alternative to feeder-based systems, preserving genomic stability and developmental potential while eliminating MEF-associated disadvantages and variability. This platform facilitates large-scale applications of naive hPSCs and enables more reproducible mechanistic studies.","authors":"Rossignoli, G., Oberhuemer, M., Brun, IS., Zorzan, I., Osnato, A., Wenzel, A., van Genderen, E., Drusin, A., Panebianco, G., Magri, N., Becker, M., Solis, MA., Colantuono, C., van Knippenberg, SSFA., Pham, TXA., Khodeer, S., Grumati, P., Cacchiarelli, D., Martini, P., Rivron, N., Pasque, V., \u017bylicz, JJ., Leeb, M., Martello, G.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"EMBO J","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-03-13","doi":"10.1038\/s44318-026-00714-2","first_author":"Rossignoli, G.","corresponding_authors":"Martello, G."},{"pmid":"29589094","title":"Impact of dietary compounds on cancer-related gut microbiota and microRNA.","abstract":"Cancer is one of the most common causes of death worldwide. Extensive research has been conducted on cancer; regardless, the link between cancer and diet remains undetermined. Recent studies have emphasized the importance of miRNAs in cancer-associated pathways from the perspective of dietary modulation. We highlighted the recent data on dietary modulation of gut microbiota and miRNAs related to cancer on the basis of recently published results. The targets of miRNAs are oncogenes or tumor suppressors that mediate the progression and initiation of carcinogenesis. Different miRNAs display complex expression profiles in response to dietary manipulation. Various dietary components, such as fatty acids, resveratrol, isothiocyanate, and curcumin, have been effectively used in cancer prevention and treatment. This potency is attributed to the capability of these components to alter miRNA expression, thereby modulating the vital pathways involved in metastasis, invasion, apoptosis, tumor growth, and cell proliferation.","authors":"Riaz Rajoka, MS., Jin, M., Haobin, Z., Li, Q., Shao, D., Huang, Q., Shi, J.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Appl Microbiol Biotechnol","volume":"102","issue":"10","page":"4291-4303","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"94","title":"[Relation between fluorescence and circular dichroism of the complex of the fluorescence probe 4-dimethylaminochalcone with serum albumin].","abstract":"The fluorescence probe(4-dimethylaminochalcone; DMH) was noncovalently linked to human serum albumin (HSA). The variation of pH was due to serum albumin structural changes, which was determined in terms of DMH and HSA fluorescence and CD spectra. Considerable changes of fluorescence and CD spectra were observed at pH 8 and 10, where there is ionization of two more recently titrated tyrosin residues. It is assumed that these two tyrosine residues are in binding region and quench the fluorescence of DMH between pH 4 to 8. Quenching disappears if these residues are ionized (pH greater than 8) or if the protein undergoes the N -F transition (pH less than 4).","authors":"Dobretsov, GE., Kharitonenkov, IG., Mishiev, VE., Vladimirov, IuA.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biofizika","volume":"20","issue":"4","page":"581-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28748501","title":"A step-by-step microRNA guide to cancer development and metastasis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">28748501<\/PMID><DateCompleted><Year>2018<\/Year><Month>04<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>03<\/Month><Day>06<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">2211-3436<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>40<\/Volume><Issue>4<\/Issue><PubDate><Year>2017<\/Year><Month>Aug<\/Month><\/PubDate><\/JournalIssue><Title>Cellular oncology (Dordrecht)<\/Title><ISOAbbreviation>Cell Oncol (Dordr)<\/ISOAbbreviation><\/Journal><ArticleTitle>A step-by-step microRNA guide to cancer development and metastasis.<\/ArticleTitle><Pagination><MedlinePgn>303-339<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s13402-017-0341-9<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Cancer is one of the leading causes of mortality. The neoplastic transformation of normal cells to cancer cells is caused by a progressive accumulation of genetic and epigenetic alterations in oncogenes, tumor suppressor genes and epigenetic regulators, providing cells with new properties, collectively known as the hallmarks of cancer. During the process of neoplastic transformation cells progressively acquire novel characteristics such as unlimited growth potential, increased motility and the ability to migrate and invade adjacent tissues, the ability to spread from the tumor of origin to distant sites, and increased resistance to various types of stresses, mostly attributed to the activation of genetic stress-response programs. Accumulating evidence indicates a crucial role of microRNAs (miRNAs or miRs) in the initiation and progression of cancer, acting either as oncogenes (oncomirs) or as tumor suppressors via several molecular mechanisms. MiRNAs comprise a class of small ~22\u00a0bp long noncoding RNAs that play a key role in the regulation of gene expression at the post-transcriptional level, acting as negative regulators of mRNA translation and\/or stability. MiRNAs are involved in the regulation of a variety of biological processes including cell cycle progression, DNA damage responses and apoptosis, epithelial-to-mesenchymal cell transitions, cell motility and stemness through complex and interactive transcription factor-miRNA regulatory networks.","authors":"Markopoulos, GS., Roupakia, E., Tokamani, M., Chavdoula, E., Hatziapostolou, M., Polytarchou, C., Marcu, KB., Papavassiliou, AG., Sandaltzopoulos, R., Kolettas, E.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Oncol (Dordr)","volume":"40","issue":"4","page":"303-339","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27997852","title":"The roles of oncogenic miRNAs and their therapeutic importance in breast cancer.","abstract":"Since the discovery of tumour suppressive miRNA in 2002, the dysregulation of miRNAs was implicated in many cancers, exhibiting both tumour suppressive and oncogenic roles. Dysregulation of miRNAs was found to be involved in the initiation of oncogenesis, as well as the progression, invasion and metastasis of cancers. While normal miRNA inhibitory functions help regulate gene expression in the cell, oncogenic miRNA, when dysregulated can lead to suppression of critical pathways that control apoptosis, cell cycle progression, growth and proliferation. This suppression allows for the upregulation of pro-oncogenic factors that drive cell survival, growth and proliferation. Due to emerging discoveries, oncogenic miRNAs are proving to be a critical component in cancers, such as breast cancer, and may provide novel avenues for cancer treatment. In this article, we discuss the roles of the most studied oncogenic miRNAs in breast cancer including clusters and families involved as well as the less studied and recently discovered oncogenic miRNAs. These miRNAs provide valuable information into the complexity of regulatory elements affected by their overexpression and the overall impact in the progression of breast cancer. Also, identifying miRNAs causing or leading to resistance or sensitivity to current anti-cancer drugs prior to treatment may lead to an improvement in treatment selection and overall patient response. This review summarizes known and recently discovered miRNAs in literature found to have oncogenic roles in breast cancer initiation and the progression, invasion and metastasis of the disease.","authors":"O'Bryan, S., Dong, S., Mathis, JM., Alahari, SK.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Eur J Cancer","volume":"72","issue":"","page":"1-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10421575","title":"Depletion of syntaxins in the early Caenorhabditis elegans embryo reveals a role for membrane fusion events in cytokinesis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">10421575<\/PMID><DateCompleted><Year>1999<\/Year><Month>11<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>9<\/Volume><Issue>14<\/Issue><PubDate><Year>1999<\/Year><Month>Jul<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Depletion of syntaxins in the early Caenorhabditis elegans embryo reveals a role for membrane fusion events in cytokinesis.<\/ArticleTitle><Pagination><MedlinePgn>738-45<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">During cytokinesis, the plasma membrane of the parent cell is resolved into the two plasma membranes of the daughter cells. Membrane fusion events mediated by the machinery that participates in intracellular vesicle trafficking might contribute to this process. Two classes of molecules that are required for membrane fusion are the t-SNAREs and the v-SNAREs. The t-SNAREs (syntaxins) comprise a multi-gene family that has been suggested to mediate, at least in part, selective membrane fusion events in the cell.","authors":"Jantsch-Plunger, V., Glotzer, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Curr Biol","volume":"9","issue":"14","page":"738-45","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1999-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31748204","title":"Dynamics of activating and repressive histone modifications in <i>Drosophila<\/i> neural stem cell lineages and brain tumors.","abstract":"During central nervous system development, spatiotemporal gene expression programs mediate specific lineage decisions to generate neuronal and glial cell types from neural stem cells (NSCs). However, little is known about the epigenetic landscape underlying these highly complex developmental events. Here, we perform ChIP-seq on distinct subtypes of <i>Drosophila<\/i> FACS-purified NSCs and their differentiated progeny to dissect the epigenetic changes accompanying the major lineage decisions <i>in vivo<\/i> By analyzing active and repressive histone modifications, we show that stem cell identity genes are silenced during differentiation by loss of their activating marks and not via repressive histone modifications. Our analysis also uncovers a new set of genes specifically required for altering lineage patterns in type II neuroblasts (NBs), one of the two main <i>Drosophila<\/i> NSC identities. Finally, we demonstrate that this subtype specification in NBs, unlike NSC differentiation, requires Polycomb-group-mediated repression.","authors":"Abdusselamoglu, MD., Landskron, L., Bowman, SK., Eroglu, E., Burkard, T., Kingston, RE., Knoblich, JA.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Development","volume":"146","issue":"23","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15568982","title":"Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins.","abstract":"During the development of multicellular organisms, cells become different from one another by changing their genetic program in response to transient stimuli. Long after the stimulus is gone, \"cellular memory\" mechanisms enable cells to remember their chosen fate over many cell divisions. The Polycomb and Trithorax groups of proteins, respectively, work to maintain repressed or active transcription states of developmentally important genes through many rounds of cell division. Here we review current ideas on the protein and DNA components of this transcriptional memory system and how they interact dynamically with each other to orchestrate cellular memory for several hundred genes.","authors":"Ringrose, L., Paro, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Annu Rev Genet","volume":"38","issue":"","page":"413-43","pdf":null,"JrId":"668","fulltextlink":null,"preprintlink":null,"articledate":"2005-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27371785","title":"Blueberry inhibits invasion and angiogenesis in 7,12-dimethylbenz[a]anthracene (DMBA)-induced oral squamous cell carcinogenesis in hamsters via suppression of TGF-\u03b2 and NF-\u03baB signaling pathways.","abstract":"Aberrant activation of oncogenic signaling pathways plays a pivotal role in tumor initiation and progression. The purpose of the present study was to investigate the chemopreventive and therapeutic efficacy of blueberry in the hamster buccal pouch (HBP) carcinogenesis model based on its ability to target TGF-\u03b2, PI3K\/Akt, MAPK and NF-\u03baB signaling and its impact on invasion and angiogenesis. Squamous cell carcinomas were induced in the HBP by 7,12-dimethylbenz[a]anthracene (DMBA). The effect of blueberry on the oncogenic signaling pathways and downstream events was analyzed by quantitative real-time PCR and immunoblotting. Experiments with the ECV304 cell line were performed to explore the mechanism by which blueberry regulates angiogenesis. Blueberry supplementation inhibited the development and progression of HBP carcinomas by abrogating TGF-\u03b2 and PI3K\/Akt pathways. Although blueberry failed to influence MAPK, it suppressed NF-\u03baB activation by preventing nuclear translocation of NF-\u03baB p65. Blueberry also modulated the expression of the oncomiR miR-21 and the tumor suppressor let-7. Collectively, these changes induced a shift to an anti-invasive and anti-angiogenic phenotype as evidenced by downregulating matrix metalloproteinases and vascular endothelial growth factor. Blueberry also inhibited angiogenesis in ECV304 cells by suppressing migration and tube formation. The results of the present study suggest that targeting oncogenic signaling pathways that influence acquisition of cancer hallmarks is an effective strategy for chemointervention. Identification of modulatory effects on phosphorylation, intracellular localization of oncogenic transcription factors and microRNAs unraveled by the present study as key mechanisms of action of blueberry is critical from a therapeutic perspective.","authors":"Baba, AB., Kowshik, J., Krishnaraj, J., Sophia, J., Dixit, M., Nagini, S.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Nutr Biochem","volume":"35","issue":"","page":"37-47","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15550674","title":"Fat mobilization in adipose tissue is promoted by adipose triglyceride lipase.","abstract":"Mobilization of fatty acids from triglyceride stores in adipose tissue requires lipolytic enzymes. Dysfunctional lipolysis affects energy homeostasis and may contribute to the pathogenesis of obesity and insulin resistance. Until now, hormone-sensitive lipase (HSL) was the only enzyme known to hydrolyze triglycerides in mammalian adipose tissue. Here, we report that a second enzyme, adipose triglyceride lipase (ATGL), catalyzes the initial step in triglyceride hydrolysis. It is interesting that ATGL contains a \"patatin domain\" common to plant acyl-hydrolases. ATGL is highly expressed in adipose tissue of mice and humans. It exhibits high substrate specificity for triacylglycerol and is associated with lipid droplets. Inhibition of ATGL markedly decreases total adipose acyl-hydrolase activity. Thus, ATGL and HSL coordinately catabolize stored triglycerides in adipose tissue of mammals.","authors":"Zimmermann, R., Strauss, JG., Haemmerle, G., Schoiswohl, G., Birner-Gruenberger, R., Riederer, M., Lass, A., Neuberger, G., Eisenhaber, F., Hermetter, A., Zechner, R.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Science","volume":"306","issue":"5700","page":"1383-6","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2004-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10395816","title":"Finishing the cell cycle.","abstract":"The eukaryotic cell division cycle consists of two characteristic states: G1, when replication origins of chromosomes are in a pre-replicative state, and S\/G2\/M, when they are in a post-replicative state (Nasmyth, 1995). Using straightforward biochemical kinetics, we show that these two states can be created by antagonistic interactions between cyclin-dependent kinases (Cdk) and their foes: the cyclin-degradation machinery (APC) and a stoichiometric inhibitor (CKI). Irreversible transitions between these two self-maintaining steady states drive progress through the cell cycle: at \"Start\" a cell leaves the G1 state and commences chromosome replication, and at \"Finish\" the cell separates the products of replication to the incipient daughter cells and re-enters G1. We propose that a protein-phosphatase, by up-regulating the APC and by stabilizing the CKI, plays an essential role at Finish. The phosphatase acts in parallel pathways; hence, cells can leave mitosis in the absence of cyclin degradation or in the absence of the CKI.","authors":"Nov\u00e1k, B., T\u00f3th, A., Csik\u00e1sz-Nagy, A., Gy\u00f6rffy, B., Tyson, JJ., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Theor Biol","volume":"199","issue":"2","page":"223-33","pdf":null,"JrId":"5295","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25866219","title":"miR-29b inhibits the progression of esophageal squamous cell carcinoma by targeting MMP-2.","abstract":"Accumulating evidence has shown that microRNAs (miRNAs) are aberrantly expressed in human esophageal cancer and crucial to tumorigenesis. Herein, we identified the role of miR-29b in esophageal squamous cell carcinoma (ESCC) development in vitro and in vivo. MiR-29b expression was investigated in thirty cases of ESCC samples as well as four ESCC cell lines by real-time PCR. Transwell assays were conducted to explore the effects of miR-29b on the invasion of human ESCC cell lines. The impact of overexpression of miR-29b on putative target MMP-2 were subsequently confirmed via Western blot. Our results indicated that MiR-29b expression was frequently down-regulated in ESCC specimens and cell lines compared with adjacent normal tissues (p&lt;0.05). Overexpression of miR-29b suppressed (p&lt;0.05) ESCC cell invasion, as well as the growth of xenograft tumors in mice. Overexpression of miR-29b significantly decreased (p&lt;0.05) the protein level of MMP-2, which has previously been identified as a\u00a0direct target of miR-29b. Thus, our study demonstrated that overexpression of miR-29b inhibits tumor growth in part by targeting MMP-2. Our findings revealed that miR-29b may act as a\u00a0tumor suppressor in ESCC, whose dysregulation may be involved in the initiation and development of human ESCC.","authors":"Qi, Y., Li, X., Zhao, S.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Neoplasma","volume":"62","issue":"3","page":"384-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"--","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10362336","title":"Variations of p53 in cultured fibroblasts of patients with lung cancer who have a presumed genetic predisposition.","abstract":"The authors studied cultured skin fibroblasts of 64 patients with lung cancer for constitutive mutations of the p53 tumor suppressor gene by using polymerase chain reaction and single-strand conformation polymorphism covering the entire coding region. The patients were considered to be genetically predisposed because lung cancer had developed in 25 of them before age 46 and because 42 of them had at least one first-degree relative with lung cancer. One mutation was detected at position 235 coding for serine instead of asparagine in the conserved DNA binding domain. The Pro\/Pro genotype at codon 72 of p53, considered to harbor an increased risk for lung cancer, could not be detected with increased frequency in this study's patients. From these data, the authors conclude that constitutive variations of the p53 gene do not represent a major genetic determinant for lung cancer.","authors":"Auer, H., Warncke, K., Nowak, D., Koops, F., Jaeger, U., Kurzbauer, R., Ruediger, HW.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Am J Clin Oncol","volume":"22","issue":"3","page":"278-82","pdf":null,"JrId":"413","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29264953","title":"The Agrobacterium F-Box Protein Effector VirF Destabilizes the Arabidopsis GLABROUS1 Enhancer\/Binding Protein-Like Transcription Factor VFP4, a Transcriptional Activator of Defense Response Genes.","abstract":"Agrobacterium-mediated genetic transformation not only represents a technology of choice to genetically manipulate plants, but it also serves as a model system to study mechanisms employed by invading pathogens to counter the myriad defenses mounted against them by the host cell. Here, we uncover a new layer of plant defenses that is targeted by A. tumefaciens to facilitate infection. We show that the Agrobacterium F-box effector VirF, which is exported into the host cell, recognizes an Arabidopsis transcription factor VFP4 and targets it for proteasomal degradation. We hypothesize that VFP4 resists Agrobacterium infection and that the bacterium utilizes its VirF effector to degrade VFP4 and thereby mitigate the VFP4-based defense. Indeed, loss-of-function mutations in VFP4 resulted in differential expression of numerous biotic stress-response genes, suggesting that one of the functions of VFP4 is to control a spectrum of plant defenses, including those against Agrobacterium tumefaciens. We identified one such gene, ATL31, known to mediate resistance to bacterial pathogens. ATL31 was transcriptionally repressed in VFP4 loss-of-function plants and activated in VFP4 gain-of-function plants. Gain-of-function lines of VFP4 and ATL31 exhibited recalcitrance to Agrobacterium tumorigenicity, suggesting that A. tumefaciens may utilize the host ubiquitin\/proteasome system to destabilize transcriptional regulators of the host disease response machinery.","authors":"Garc\u00eda-Cano, E., Hak, H., Magori, S., Lazarowitz, SG., Citovsky, V.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Mol Plant Microbe Interact","volume":"31","issue":"5","page":"576-586","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34093135","title":"Editorial: Regeneration and Brain Repair.","abstract":null,"authors":"Rylander Ottosson, D., Grade, S., Heuer, A.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Front Cell Neurosci","volume":"15","issue":null,"page":"687992","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29059433","title":"An ERBB1-3 Neutralizing Antibody Mixture With High Activity Against Drug-Resistant HER2+ Breast Cancers With ERBB Ligand Overexpression.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">29059433<\/PMID><DateCompleted><Year>2017<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>02<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1460-2105<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>109<\/Volume><Issue>11<\/Issue><PubDate><Year>2017<\/Year><Month>11<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Journal of the National Cancer Institute<\/Title><ISOAbbreviation>J Natl Cancer Inst<\/ISOAbbreviation><\/Journal><ArticleTitle>An ERBB1-3 Neutralizing Antibody Mixture With High Activity Against Drug-Resistant HER2+ Breast Cancers With ERBB Ligand Overexpression.<\/ArticleTitle><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/jnci\/djx065<\/ELocationID><Abstract><AbstractText Label=\"Background\">Plasticity of the ERBB receptor network has been suggested to cause acquired resistance to anti-human epidermal growth factor receptor 2 (HER2) therapies. Thus, we studied whether a novel approach using an ERBB1-3-neutralizing antibody mixture can block these compensatory mechanisms of resistance.","authors":"Schwarz, LJ., Hutchinson, KE., Rexer, BN., Estrada, MV., Gonzalez Ericsson, PI., Sanders, ME., Dugger, TC., Formisano, L., Guerrero-Zotano, A., Red-Brewer, M., Young, CD., Lantto, J., Pedersen, MW., Kragh, M., Horak, ID., Arteaga, CL.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"J Natl Cancer Inst","volume":"109","issue":"11","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10590077","title":"Impaired ferritin mRNA translation in primary erythroid progenitors: shift to iron-dependent regulation by the v-ErbA oncoprotein.","abstract":"In immortalized cells of the erythroid lineage, the iron-regulatory protein (IRP) has been suggested to coregulate biosynthesis of the iron storage protein ferritin and the erythroid delta-aminolevulinate synthase (eALAS), a key enzyme in heme production. Under iron scarcity, IRP binds to an iron-responsive element (IRE) located in ferritin and eALAS mRNA leaders, causing a block of translation. In contrast, IRP-IRE interaction is reduced under high iron conditions, allowing efficient translation. We show here that primary chicken erythroblasts (ebls) proliferating or differentiating in culture use a drastically different regulation of iron metabolism. Independently of iron administration, ferritin H (ferH) chain mRNA translation was massively decreased, whereas eALAS transcripts remained constitutively associated with polyribosomes, indicating efficient translation. Variations in iron supply had minor but significant effects on eALAS mRNA polysome recruitment but failed to modulate IRP-affinity to the ferH-IRE in vitro. However, leukemic ebls transformed by the v-ErbA\/v-ErbB-expressing avian erythroblastosis virus showed an iron-dependent reduction of IRP mRNA-binding activity, resulting in mobilization of ferH mRNA into polysomes. Hence, we analyzed a panel of ebls overexpressing v-ErbA and\/or v-ErbB oncoproteins as well as the respective normal cellular homologues (c-ErbA\/TRalpha, c-ErbB\/EGFR). It turned out that v-ErbA, a mutated class II nuclear hormone receptor that arrests erythroid differentiation, caused the change in ferH mRNA translation. Accordingly, inhibition of v-ErbA function in these leukemic ebls led to a switch from iron-responsive to iron-independent ferH expression.","authors":"Mikulits, W., Schranzhofer, M., Bauer, A., Dolznig, H., Lobmayr, L., Infante, AA., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Blood","volume":"94","issue":"12","page":"4321-32","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2000-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34079126","title":"Tracing oncogene-driven remodelling of the intestinal stem cell niche.","abstract":"Interactions between tumour cells and the surrounding microenvironment contribute to tumour progression, metastasis and recurrence<sup>1-3<\/sup>. Although mosaic analyses in Drosophila have advanced our understanding of such interactions<sup>4,5<\/sup>, it has been difficult to engineer parallel approaches in vertebrates. Here we present an oncogene-associated, multicolour reporter mouse model-the Red2Onco system-that allows differential tracing of mutant and wild-type cells in the same tissue. By applying this system to the small intestine, we show that oncogene-expressing mutant crypts alter the cellular organization of neighbouring wild-type crypts, thereby driving accelerated clonal drift. Crypts that express oncogenic KRAS or PI3K secrete BMP ligands that suppress local stem cell activity, while changes in PDGFR<sup>lo<\/sup>CD81<sup>+<\/sup> stromal cells induced by crypts with oncogenic PI3K alter the WNT signalling environment. Together, these results show how oncogene-driven paracrine remodelling creates a niche environment that is detrimental to the maintenance of wild-type tissue, promoting field transformation dominated by oncogenic clones.","authors":"Yum, MK., Han, S., Fink, J., Wu, SS., Dabrowska, C., Trendafilova, T., Mustata, R., Chatzeli, L., Azzarelli, R., Pshenichnaya, I., Lee, E., England, F., Kim, JK., Stange, DE., Philpott, A., Lee, JH., Koo, BK., Simons, BD.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature","volume":"594","issue":"7863","page":"442-447","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18251700","title":"JNK\/c-Jun signaling mediates an anti-apoptotic effect of RANKL in osteoclasts.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18251700<\/PMID><DateCompleted><Year>2008<\/Year><Month>08<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1523-4681<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>23<\/Volume><Issue>6<\/Issue><PubDate><Year>2008<\/Year><Month>Jun<\/Month><\/PubDate><\/JournalIssue><Title>Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research<\/Title><ISOAbbreviation>J Bone Miner Res<\/ISOAbbreviation><\/Journal><ArticleTitle>JNK\/c-Jun signaling mediates an anti-apoptotic effect of RANKL in osteoclasts.<\/ArticleTitle><Pagination><MedlinePgn>907-14<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1359\/jbmr.080211<\/ELocationID><Abstract><AbstractText Label=\"INTRODUCTION\" NlmCategory=\"BACKGROUND\">RANKL is known to be important not only for differentiation and activation of osteoclasts but also for their survival. Experimentally, apoptosis of osteoclasts is rapidly induced by the deprivation of RANKL. RANKL activates Elk-related tyrosine kinase (ERK), p38, c-Jun N-terminal kinase (JNK), and NF-kappaB pathways through TRAF6 in osteoclasts and the precursor cells. It has been shown that ERK is critical for regulation of osteoclast survival. However, an involvement of other RANKL signaling pathways such as JNK signaling in survival of osteoclasts has not been fully understood yet.","authors":"Ikeda, F., Matsubara, T., Tsurukai, T., Hata, K., Nishimura, R., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Bone Miner Res","volume":"23","issue":"6","page":"907-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31145866","title":"Pathway-Based High-Throughput Chemical Screen Identifies Compounds That Decouple Heterochromatin Transformations.","abstract":"Heterochromatin protein 1 (HP1) facilitates the formation of repressive heterochromatin domains by recruiting histone lysine methyltransferase enzymes to chromatin, resulting in increased levels of histone H3K9me3. To identify chemical inhibitors of the HP1-heterochromatin gene repression pathway, we combined a cell-based assay that utilized chemical-mediated recruitment of HP1 to an endogenous active gene with high-throughput flow cytometry. Here we characterized small molecule inhibitors that block HP1-mediated heterochromatin formation. Our lead compounds demonstrated dose-dependent inhibition of HP1-stimulated gene repression and were validated in an orthogonal cell-based system. One lead inhibitor was improved by a change in stereochemistry, resulting in compound 2, which was further used to decouple the inverse relationship between H3K9 and H3K4 methylation states. We identified molecular components that bound compound 2, either directly or indirectly, by chemical affinity purification with a biotin-tagged derivative, followed by quantitative proteomic techniques. In summary, our pathway-based chemical screening approach resulted in the discovery of new inhibitors of HP1-mediated heterochromatin formation while identifying exciting new molecular interactions in the pathway to explore in the future. This modular platform can be expanded to test a wide range of chromatin modification pathways yielding inhibitors that are cell permeable and function in a physiologically relevant setting.","authors":"MacDonald, IA., Butler, KV., Herring, LE., Clinkscales, SE., Yelagandula, R., Stecher, K., Bell, O., Graves, LM., Jin, J., Hathaway, NA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"SLAS Discov","volume":"24","issue":"8","page":"802-816","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30859831","title":"Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.","abstract":"Label-free quantification has become a common-practice in many mass spectrometry-based proteomics experiments. In recent years, we and others have shown that spectral clustering can considerably improve the analysis of (primarily large-scale) proteomics data sets. Here we show that spectral clustering can be used to infer additional peptide-spectrum matches and improve the quality of label-free quantitative proteomics data in data sets also containing only tens of MS runs. We analyzed four well-known public benchmark data sets that represent different experimental settings using spectral counting and peak intensity based label-free quantification. In both approaches, the additionally inferred peptide-spectrum matches through our spectra-cluster algorithm improved the detectability of low abundant proteins while increasing the accuracy of the derived quantitative data, without increasing the data sets' noise. Additionally, we developed a Proteome Discoverer node for our spectra-cluster algorithm which allows anyone to rebuild our proposed pipeline using the free version of Proteome Discoverer.","authors":"Griss, J., Stanek, F., Hudecz, O., D\u00fcrnberger, G., Perez-Riverol, Y., Vizca\u00edno, JA., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Proteome Res","volume":"18","issue":"4","page":"1477-1485","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32332999","title":"A safe and reusable imaging chamber compatible with organic solvents.","abstract":"High refractive index organic solvents are commonly used as an imaging medium in tissue clearing approaches. While effective, such solvents provide serious concerns for the safety of users and the equipment, especially in a central microscopy unit. To overcome these concerns, we have developed a large and reusable imaging chamber compatible with the universal mounting frame AK (PeCon GmbH). This chamber is easy to assemble and significantly improves the working environment in a central microscopy unit, where hazardous chemicals could negatively affect equipment and people. To encourage the uptake of these chambers, the design is made publicly available for download.","authors":"Colombini, M., Pasierbek, P., Masselink, W.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Microscopy (Oxf)","volume":"69","issue":"5","page":"321-323","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27099310","title":"SUMO Ligase Protein Inhibitor of Activated STAT1 (PIAS1) Is a Constituent Promyelocytic Leukemia Nuclear Body Protein That Contributes to the Intrinsic Antiviral Immune Response to Herpes Simplex Virus 1.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">27099310<\/PMID><DateCompleted><Year>2017<\/Year><Month>05<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic-Print\"><Journal><ISSN IssnType=\"Electronic\">1098-5514<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>90<\/Volume><Issue>13<\/Issue><PubDate><Year>2016<\/Year><Month>07<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Journal of virology<\/Title><ISOAbbreviation>J Virol<\/ISOAbbreviation><\/Journal><ArticleTitle>SUMO Ligase Protein Inhibitor of Activated STAT1 (PIAS1) Is a Constituent Promyelocytic Leukemia Nuclear Body Protein That Contributes to the Intrinsic Antiviral Immune Response to Herpes Simplex Virus 1.<\/ArticleTitle><Pagination><MedlinePgn>5939-5952<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1128\/JVI.00426-16<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Aspects of intrinsic antiviral immunity are mediated by promyelocytic leukemia nuclear body (PML-NB) constituent proteins. During herpesvirus infection, these antiviral proteins are independently recruited to nuclear domains that contain infecting viral genomes to cooperatively promote viral genome silencing. Central to the execution of this particular antiviral response is the small ubiquitin-like modifier (SUMO) signaling pathway. However, the participating SUMOylation enzymes are not fully characterized. We identify the SUMO ligase protein inhibitor of activated STAT1 (PIAS1) as a constituent PML-NB protein. We show that PIAS1 localizes at PML-NBs in a SUMO interaction motif (SIM)-dependent manner that requires SUMOylated or SUMOylation-competent PML. Following infection with herpes simplex virus 1 (HSV-1), PIAS1 is recruited to nuclear sites associated with viral genome entry in a SIM-dependent manner, consistent with the SIM-dependent recruitment mechanisms of other well-characterized PML-NB proteins. In contrast to that of Daxx and Sp100, however, the recruitment of PIAS1 is enhanced by PML. PIAS1 promotes the stable accumulation of SUMO1 at nuclear sites associated with HSV-1 genome entry, whereas the accumulation of other evaluated PML-NB proteins occurs independently of PIAS1. We show that PIAS1 cooperatively contributes to HSV-1 restriction through mechanisms that are additive to those of PML and cooperative with those of PIAS4. The antiviral mechanisms of PIAS1 are counteracted by ICP0, the HSV-1 SUMO-targeted ubiquitin ligase, which disrupts the recruitment of PIAS1 to nuclear domains that contain infecting HSV-1 genomes through mechanisms that do not directly result in PIAS1 degradation.","authors":"Brown, JR., Conn, KL., Wasson, P., Charman, M., Tong, L., Grant, K., McFarlane, S., Boutell, C.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"J Virol","volume":"90","issue":"13","page":"5939-5952","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18240141","title":"JunD suppresses bone formation and contributes to low bone mass induced by estrogen depletion.","abstract":"JunD is an activator protein-1 (AP-1) component though its function in skeletal system is still not fully understood. To elucidate the role of JunD in the regulation of bone metabolism, we analyzed JunD-deficient mice. JunD deficiency significantly increased bone mass and trabecular number. This bone mass enhancement was due to JunD deficiency-induced increase in bone formation activities in vivo. Such augmentation of bone formation was associated with simultaneous increase in bone resorption while the former was dominant over the latter as accumulation of bone mass occurred in JunD-deficient mice. In a pathological condition relevant to postmenopausal osteoporosis, ovariectomy reduced bone mass in wild type (WT) mice as known before. Interestingly, JunD deficiency suppressed ovariectomy-induced increase in bone resorption and kept high bone mass. In addition, JunD deficiency also enhanced new bone formation after bone marrow ablation. Examination of molecular bases for these observations revealed that JunD deficiency enhanced expression levels of c-jun, fra-1, and fra-2 in bone in conjunction with elevated expression levels of runx2, type I collagen, and osteocalcin. Thus, JunD is involved in estrogen depletion-induced osteopenia via its action to suppress bone formation and to enhance bone resorption.","authors":"Kawamata, A., Izu, Y., Yokoyama, H., Amagasa, T., Wagner, EF., Nakashima, K., Ezura, Y., Hayata, T., Noda, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"J Cell Biochem","volume":"103","issue":"4","page":"1037-45","pdf":null,"JrId":"4590","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32724856","title":"Native Mass Spectrometry Can Effectively Predict PROTAC Efficacy.","abstract":"Protein degraders, also known as proteolysis targeting chimeras (PROTACs), are bifunctional small molecules that promote cellular degradation of a protein of interest (POI). PROTACs act as molecular mediators, bringing an E3 ligase and a POI into proximity, thus promoting ubiquitination and degradation of the targeted POI. Despite their great promise as next-generation pharmaceutical drugs, the development of new PROTACs is challenged by the complexity of the system, which involves binary and ternary interactions between components. Here, we demonstrate the strength of native mass spectrometry (nMS), a label-free technique, to provide novel insight into PROTAC-mediated protein interactions. We show that nMS can monitor the formation of ternary E3-PROTAC-POI complexes and detect various intermediate species in a single experiment. A unique benefit of the method is its ability to reveal preferentially formed E3-PROTAC-POI combinations in competition experiments with multiple substrate proteins, thereby positioning it as an ideal high-throughput screening strategy during the development of new PROTACs.","authors":"Beveridge, R., Kessler, D., Rumpel, K., Ettmayer, P., Meinhart, A., Clausen, T.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"ACS Cent Sci","volume":"6","issue":"7","page":"1223-1230","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18172160","title":"A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands.","abstract":"MicroRNAs (miRNAs) are approximately 22-nucleotide RNAs that are processed from characteristic precursor hairpins and pair to sites in messages of protein-coding genes to direct post-transcriptional repression. Here, we report that the miRNA iab-4 locus in the Drosophila Hox cluster is transcribed convergently from both DNA strands, giving rise to two distinct functional miRNAs. Both sense and antisense miRNA products target neighboring Hox genes via highly conserved sites, leading to homeotic transformations when ectopically expressed. We also report sense\/antisense miRNAs in mouse and find antisense transcripts close to many miRNAs in both flies and mammals, suggesting that additional sense\/antisense pairs exist.","authors":"Stark, A., Bushati, N., Jan, CH., Kheradpour, P., Hodges, E., Brennecke, J., Bartel, DP., Cohen, SM., Kellis, M.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genes Dev","volume":"22","issue":"1","page":"8-13","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2008-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26947079","title":"CARMA3 Is a Host Factor Regulating the Balance of Inflammatory and Antiviral Responses against Viral Infection.","abstract":"Host response to RNA virus infection is sensed by RNA sensors such as RIG-I, which induces MAVS-mediated NF-\u03baB and IRF3 activation to promote inflammatory and antiviral responses, respectively. Here, we have found that CARMA3, a scaffold protein previously shown to mediate NF-\u03baB activation induced by GPCR and EGFR, positively regulates MAVS-induced NF-\u03baB activation. However, our data suggest that CARMA3 sequesters MAVS from forming high-molecular-weight aggregates, thereby suppressing TBK1\/IRF3 activation. Interestingly, following NF-\u03baB activation upon virus infection, CARMA3 is targeted for proteasome-dependent degradation, which releases MAVS to activate IRF3. When challenged with vesicular stomatitis virus or influenza A virus, CARMA3-deficient mice showed reduced disease symptoms compared to those of wild-type mice as a result of less inflammation and a stronger ability to clear infected virus. Altogether, our results reveal the role of CARMA3 in regulating the balance of host antiviral and pro-inflammatory responses against RNA virus infection.","authors":"Jiang, C., Zhou, Z., Quan, Y., Zhang, S., Wang, T., Zhao, X., Morrison, C., Heise, MT., He, W., Miller, MS., Lin, X.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Rep","volume":"14","issue":"10","page":"2389-401","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33292096","title":"Unsupervised learning of control signals and their encodings in <i>Caenorhabditis elegans<\/i> whole-brain recordings.","abstract":"A major goal of computational neuroscience is to understand the relationship between synapse-level structure and network-level functionality. <i>Caenorhabditis elegans<\/i> is a model organism to probe this relationship due to the historic availability of the synaptic structure (connectome) and recent advances in whole brain calcium imaging techniques. Recent work has applied the concept of network controllability to neuronal networks, discovering some neurons that are able to drive the network to a certain state. However, previous work uses a linear model of the network dynamics, and it is unclear if the real neuronal network conforms to this assumption. Here, we propose a method to build a global, low-dimensional model of the dynamics, whereby an underlying global linear dynamical system is actuated by temporally sparse control signals. A key novelty of this method is discovering candidate control signals that the network uses to control itself. We analyse these control signals in two ways, showing they are interpretable and biologically plausible. First, these control signals are associated with transitions between behaviours, which were previously annotated via expert-generated features. Second, these signals can be predicted both from neurons previously implicated in behavioural transitions but also additional neurons previously unassociated with these behaviours. The proposed mathematical framework is generic and can be generalized to other neurosensory systems, potentially revealing transitions and their encodings in a completely unsupervised way.","authors":"Fieseler, C., Zimmer, M., Kutz, JN.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J R Soc Interface","volume":"17","issue":"173","page":"20200459","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26730808","title":"A FRET-Based Assay for the Identification and Characterization of Cereblon Ligands.","abstract":"Cereblon serves as an ubiquitin ligase substrate receptor that can be tuned toward different target proteins by various cereblon-binding agents. This offers one of the most promising avenues for targeted protein degradation in cancer therapy, but cereblon binding can also mediate teratogenic effects. We present an effective assay that is suited for high-throughput screening of compound libraries for off-target cereblon interactions but also can guide lead optimization and rational design of novel cereblon effector molecules.","authors":"Boichenko, I., Deiss, S., B\u00e4r, K., Hartmann, MD., Hernandez Alvarez, B.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Med Chem","volume":"59","issue":"2","page":"770-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33569855","title":"Post-translational Wnt receptor regulation: Is the fog slowly clearing?: The molecular mechanism of RNF43\/ZNRF3 ubiquitin ligases is not yet fully elucidated and still controversial.","abstract":"Wnt signaling plays pivotal roles during our entire lives, from conception to death, through the regulation of morphogenesis in developing embryos and the maintenance of tissue homeostasis in adults. The regulation of Wnt signaling occurs on several levels: at the receptor level on the plasma membrane, at the \u03b2-catenin protein level in the cytoplasm, and through transcriptional regulation in the nucleus. Several recent studies have focused on the mechanisms of Wnt receptor regulation, following the discovery that the Wnt receptor frizzled (Fzd) is a target of the ubiquitin ligases, RNF43 and ZNRF3. RNF43 and ZNRF3 are homologous genes that are mutated in several cancers. The details underlying their mechanism of action continue to unfold, while at the same time raising many new questions. In this review, we discuss advances and controversies in our understanding of Wnt receptor regulation.","authors":"Tsukiyama, T., Koo, BK., Hatakeyama, S.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Bioessays","volume":"43","issue":"4","page":"e2000297","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17994088","title":"Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.","abstract":"Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.","authors":"Stark, A., Lin, MF., Kheradpour, P., Pedersen, JS., Parts, L., Carlson, JW., Crosby, MA., Rasmussen, MD., Roy, S., Deoras, AN., Ruby, JG., Brennecke, J., Hodges, E., Hinrichs, AS., Caspi, A., Paten, B., Park, SW., Han, MV., Maeder, ML., Polansky, BJ., Robson, BE., Aerts, S., van Helden, J., Hassan, B., Gilbert, DG., Eastman, DA., Rice, M., Weir, M., Hahn, MW., Park, Y., Dewey, CN., Pachter, L., Kent, WJ., Haussler, D., Lai, EC., Bartel, DP., Hannon, GJ., Kaufman, TC., Eisen, MB., Clark, AG., Smith, D., Celniker, SE., Gelbart, WM., Kellis, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"450","issue":"7167","page":"219-32","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2008-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17994087","title":"Evolution of genes and genomes on the Drosophila phylogeny.","abstract":"Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.","authors":"Clark, AG., Eisen, MB., Smith, DR., Bergman, CM., Oliver, B., Markow, TA., Kaufman, TC., Kellis, M., Gelbart, W., Iyer, VN., Pollard, DA., Sackton, TB., Larracuente, AM., Singh, ND., Abad, JP., Abt, DN., Adryan, B., Aguade, M., Akashi, H., Anderson, WW., Aquadro, CF., Ardell, DH., Arguello, R., Artieri, CG., Barbash, DA., Barker, D., Barsanti, P., Batterham, P., Batzoglou, S., Begun, D., Bhutkar, A., Blanco, E., Bosak, SA., Bradley, RK., Brand, AD., Brent, MR., Brooks, AN., Brown, RH., Butlin, RK., Caggese, C., Calvi, BR., Bernardo de Carvalho, A., Caspi, A., Castrezana, S., Celniker, SE., Chang, JL., Chapple, C., Chatterji, S., Chinwalla, A., Civetta, A., Clifton, SW., Comeron, JM., Costello, JC., Coyne, JA., Daub, J., David, RG., Delcher, AL., Delehaunty, K., Do, CB., Ebling, H., Edwards, K., Eickbush, T., Evans, JD., Filipski, A., Findeiss, S., Freyhult, E., Fulton, L., Fulton, R., Garcia, AC., Gardiner, A., Garfield, DA., Garvin, BE., Gibson, G., Gilbert, D., Gnerre, S., Godfrey, J., Good, R., Gotea, V., Gravely, B., Greenberg, AJ., Griffiths-Jones, S., Gross, S., Guigo, R., Gustafson, EA., Haerty, W., Hahn, MW., Halligan, DL., Halpern, AL., Halter, GM., Han, MV., Heger, A., Hillier, L., Hinrichs, AS., Holmes, I., Hoskins, RA., Hubisz, MJ., Hultmark, D., Huntley, MA., Jaffe, DB., Jagadeeshan, S., Jeck, WR., Johnson, J., Jones, CD., Jordan, WC., Karpen, GH., Kataoka, E., Keightley, PD., Kheradpour, P., Kirkness, EF., Koerich, LB., Kristiansen, K., Kudrna, D., Kulathinal, RJ., Kumar, S., Kwok, R., Lander, E., Langley, CH., Lapoint, R., Lazzaro, BP., Lee, SJ., Levesque, L., Li, R., Lin, CF., Lin, MF., Lindblad-Toh, K., Llopart, A., Long, M., Low, L., Lozovsky, E., Lu, J., Luo, M., Machado, CA., Makalowski, W., Marzo, M., Matsuda, M., Matzkin, L., McAllister, B., McBride, CS., McKernan, B., McKernan, K., Mendez-Lago, M., Minx, P., Mollenhauer, MU., Montooth, K., Mount, SM., Mu, X., Myers, E., Negre, B., Newfeld, S., Nielsen, R., Noor, MA., O'Grady, P., Pachter, L., Papaceit, M., Parisi, MJ., Parisi, M., Parts, L., Pedersen, JS., Pesole, G., Phillippy, AM., Ponting, CP., Pop, M., Porcelli, D., Powell, JR., Prohaska, S., Pruitt, K., Puig, M., Quesneville, H., Ram, KR., Rand, D., Rasmussen, MD., Reed, LK., Reenan, R., Reily, A., Remington, KA., Rieger, TT., Ritchie, MG., Robin, C., Rogers, YH., Rohde, C., Rozas, J., Rubenfield, MJ., Ruiz, A., Russo, S., Salzberg, SL., Sanchez-Gracia, A., Saranga, DJ., Sato, H., Schaeffer, SW., Schatz, MC., Schlenke, T., Schwartz, R., Segarra, C., Singh, RS., Sirot, L., Sirota, M., Sisneros, NB., Smith, CD., Smith, TF., Spieth, J., Stage, DE., Stark, A., Stephan, W., Strausberg, RL., Strempel, S., Sturgill, D., Sutton, G., Sutton, GG., Tao, W., Teichmann, S., Tobari, YN., Tomimura, Y., Tsolas, JM., Valente, VL., Venter, E., Venter, JC., Vicario, S., Vieira, FG., Vilella, AJ., Villasante, A., Walenz, B., Wang, J., Wasserman, M., Watts, T., Wilson, D., Wilson, RK., Wing, RA., Wolfner, MF., Wong, A., Wong, GK., Wu, CI., Wu, G., Yamamoto, D., Yang, HP., Yang, SP., Yorke, JA., Yoshida, K., Zdobnov, E., Zhang, P., Zhang, Y., Zimin, AV., Baldwin, J., Abdouelleil, A., Abdulkadir, J., Abebe, A., Abera, B., Abreu, J., Acer, SC., Aftuck, L., Alexander, A., An, P., Anderson, E., Anderson, S., Arachi, H., Azer, M., Bachantsang, P., Barry, A., Bayul, T., Berlin, A., Bessette, D., Bloom, T., Blye, J., Boguslavskiy, L., Bonnet, C., Boukhgalter, B., Bourzgui, I., Brown, A., Cahill, P., Channer, S., Cheshatsang, Y., Chuda, L., Citroen, M., Collymore, A., Cooke, P., Costello, M., D'Aco, K., Daza, R., De Haan, G., DeGray, S., DeMaso, C., Dhargay, N., Dooley, K., Dooley, E., Doricent, M., Dorje, P., Dorjee, K., Dupes, A., Elong, R., Falk, J., Farina, A., Faro, S., Ferguson, D., Fisher, S., Foley, CD., Franke, A., Friedrich, D., Gadbois, L., Gearin, G., Gearin, CR., Giannoukos, G., Goode, T., Graham, J., Grandbois, E., Grewal, S., Gyaltsen, K., Hafez, N., Hagos, B., Hall, J., Henson, C., Hollinger, A., Honan, T., Huard, MD., Hughes, L., Hurhula, B., Husby, ME., Kamat, A., Kanga, B., Kashin, S., Khazanovich, D., Kisner, P., Lance, K., Lara, M., Lee, W., Lennon, N., Letendre, F., LeVine, R., Lipovsky, A., Liu, X., Liu, J., Liu, S., Lokyitsang, T., Lokyitsang, Y., Lubonja, R., Lui, A., MacDonald, P., Magnisalis, V., Maru, K., Matthews, C., McCusker, W., McDonough, S., Mehta, T., Meldrim, J., Meneus, L., Mihai, O., Mihalev, A., Mihova, T., Mittelman, R., Mlenga, V., Montmayeur, A., Mulrain, L., Navidi, A., Naylor, J., Negash, T., Nguyen, T., Nguyen, N., Nicol, R., Norbu, C., Norbu, N., Novod, N., O'Neill, B., Osman, S., Markiewicz, E., Oyono, OL., Patti, C., Phunkhang, P., Pierre, F., Priest, M., Raghuraman, S., Rege, F., Reyes, R., Rise, C., Rogov, P., Ross, K., Ryan, E., Settipalli, S., Shea, T., Sherpa, N., Shi, L., Shih, D., Sparrow, T., Spaulding, J., Stalker, J., Stange-Thomann, N., Stavropoulos, S., Stone, C., Strader, C., Tesfaye, S., Thomson, T., Thoulutsang, Y., Thoulutsang, D., Topham, K., Topping, I., Tsamla, T., Vassiliev, H., Vo, A., Wangchuk, T., Wangdi, T., Weiand, M., Wilkinson, J., Wilson, A., Yadav, S., Young, G., Yu, Q., Zembek, L., Zhong, D., Zimmer, A., Zwirko, Z., Jaffe, DB., Alvarez, P., Brockman, W., Butler, J., Chin, C., Gnerre, S., Grabherr, M., Kleber, M., Mauceli, E., MacCallum, I.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"450","issue":"7167","page":"203-18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33930333","title":"The oxidoreductase PYROXD1 uses NAD(P)<sup>+<\/sup> as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response.","abstract":"The tRNA ligase complex (tRNA-LC) splices precursor tRNAs (pre-tRNA), and Xbp1-mRNA during the unfolded protein response (UPR). In aerobic conditions, a cysteine residue bound to two metal ions in its ancient, catalytic subunit RTCB could make the tRNA-LC susceptible to oxidative inactivation. Here, we confirm this hypothesis and reveal a co-evolutionary association between the tRNA-LC and PYROXD1, a conserved and essential oxidoreductase. We reveal that PYROXD1 preserves the activity of the mammalian tRNA-LC in pre-tRNA splicing and UPR. PYROXD1 binds the tRNA-LC in the presence of NAD(P)H and converts RTCB-bound NAD(P)H into NAD(P)<sup>+<\/sup>, a typical oxidative co-enzyme. However, NAD(P)<sup>+<\/sup> here acts as an antioxidant and protects the tRNA-LC from oxidative inactivation, which is dependent on copper ions. Genetic variants of PYROXD1 that cause human myopathies only partially support tRNA-LC activity. Thus, we establish the tRNA-LC as an oxidation-sensitive metalloenzyme, safeguarded by the flavoprotein PYROXD1 through an unexpected redox mechanism.","authors":"Asanovi\u0107, I., Strandback, E., Kroupova, A., Pasajlic, D., Meinhart, A., Tsung-Pin, P., Djokovic, N., Anrather, D., Schuetz, T., Suskiewicz, MJ., Sillamaa, S., K\u00f6cher, T., Beveridge, R., Nikolic, K., Schleiffer, A., Jinek, M., Hartl, M., Clausen, T., Penninger, J., Macheroux, P., Weitzer, S., Martinez, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Mol Cell","volume":"81","issue":"12","page":"2520-2532.e16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31329099","title":"The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop.","abstract":"Neural progenitors undergo temporal patterning to generate diverse neurons in a chronological order. This process is well-studied in the developing <i>Drosophila<\/i> brain and conserved in mammals. During larval stages, intermediate neural progenitors (INPs) serially express Dichaete (D), grainyhead (Grh) and eyeless (Ey\/Pax6), but how the transitions are regulated is not precisely understood. Here, we developed a method to isolate transcriptomes of INPs in their distinct temporal states to identify a complete set of temporal patterning factors. Our analysis identifies odd-paired (opa), as a key regulator of temporal patterning. Temporal patterning is initiated when the SWI\/SNF complex component Osa induces D and its repressor Opa at the same time but with distinct kinetics. Then, high Opa levels repress D to allow Grh transcription and progress to the next temporal state. We propose that Osa and its target genes opa and D form an incoherent feedforward loop (FFL) and a new mechanism allowing the successive expression of temporal identities.","authors":"Abdusselamoglu, MD., Eroglu, E., Burkard, TR., Knoblich, JA.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Elife","volume":"8","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33574069","title":"Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex.","abstract":"Nuclear Argonaute proteins, guided by their bound small RNAs to nascent target transcripts, mediate cotranscriptional silencing of transposons and repetitive genomic loci through heterochromatin formation. The molecular mechanisms involved in this process are incompletely understood. Here, we show that the SFiNX complex, a silencing mediator downstream from nuclear Piwi-piRNA complexes in <i>Drosophila<\/i>, facilitates cotranscriptional silencing as a homodimer. The dynein light chain protein Cut up\/LC8 mediates SFiNX dimerization, and its function can be bypassed by a heterologous dimerization domain, arguing for a constitutive SFiNX dimer. Dimeric, but not monomeric SFiNX, is capable of forming molecular condensates in a nucleic acid-stimulated manner. Mutations that prevent SFiNX dimerization result in loss of condensate formation in vitro and the inability of Piwi to initiate heterochromatin formation and silence transposons in vivo. We propose that multivalent SFiNX-nucleic acid interactions are critical for heterochromatin establishment at piRNA target loci in a cotranscriptional manner.","authors":"Schnabl, J., Wang, J., Hohmann, U., Gehre, M., Batki, J., Andreev, VI., Purkhauser, K., Fasching, N., Duchek, P., Novatchkova, M., Mechtler, K., Plaschka, C., Patel, DJ., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Genes Dev","volume":"35","issue":"5-6","page":"392-409","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15457338","title":"A gene-driven ENU-based approach to generating an allelic series in any gene.","abstract":"N-ethyl-N-nitrosourea (ENU) introduces mutations throughout the mouse genome at relatively high efficiency. Successful high-throughput phenotype screens have been reported and alternative screens using sequence-based approaches have been proposed. For the purpose of generating an allelic series in selected genes by a sequence-based approach, we have constructed an archive of over 4000 DNA samples from individual F1 ENU-mutagenized mice paralleled by frozen sperm samples. Together with our previously reported archive, the total size now exceeds 6000 individuals. A gene-based screen of 27.4 Mbp of DNA, carried out using denaturing high-performance liquid chromatography (DHPLC), found a mutation rate of 1 in 1.01 Mbp of which 1 in 1.82 Mbp were potentially functional. Screening of whole or selected regions of genes on subsets of the archive has allowed us to identify 15 new alleles from 9 genes out of 15 tested. This is a powerful adjunct to conventional mutagenesis strategies and has the advantage of generating a variety of alleles with potentially different phenotypic outcomes that facilitate the investigation of gene function. It is now available to academic collaborators as a community resource.","authors":"Quwailid, MM., Hugill, A., Dear, N., Vizor, L., Wells, S., Horner, E., Fuller, S., Weedon, J., McMath, H., Woodman, P., Edwards, D., Campbell, D., Rodger, S., Carey, J., Roberts, A., Glenister, P., Lalanne, Z., Parkinson, N., Coghill, EL., McKeone, R., Cox, S., Willan, J., Greenfield, A., Keays, D., Brady, S., Spurr, N., Gray, I., Hunter, J., Brown, SD., Cox, RD.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Mamm Genome","volume":"15","issue":"8","page":"585-91","pdf":null,"JrId":"2084","fulltextlink":null,"preprintlink":null,"articledate":"2005-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21173845","title":"New genetic resources for mammalian developmental biologists.","abstract":"The utilization of homologous recombination in embryonic stem cells as a means to generate mice carrying pre-determined modifications of genomic sequences has revolutionized the study of developmental biology. Recognizing the potential efficiencies that can be obtained by high-throughput production at centralized technology centers, a number of large-scale efforts for generating mice with targeted mutations have been funded. These programs are reaching fruition, and a variety of libraries of embryonic stem cells with defined mutations are now available.","authors":"Beier, DR.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"F1000 Biol Rep","volume":"2","issue":"","page":"72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31358947","title":"The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31358947<\/PMID><DateCompleted><Year>2020<\/Year><Month>06<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>02<\/Month><Day>12<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1530-0366<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>22<\/Volume><Issue>1<\/Issue><PubDate><Year>2020<\/Year><Month>01<\/Month><\/PubDate><\/JournalIssue><Title>Genetics in medicine : official journal of the American College of Medical Genetics<\/Title><ISOAbbreviation>Genet Med<\/ISOAbbreviation><\/Journal><ArticleTitle>The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom.<\/ArticleTitle><Pagination><MedlinePgn>85-94<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1038\/s41436-019-0618-7<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE\">The translation of genome sequencing into routine health care has been slow, partly because of concerns about affordability. The aspirational cost of sequencing a genome is $1000, but there is little evidence to support this estimate. We estimate the cost of using genome sequencing in routine clinical care in patients with cancer or rare diseases.","authors":"Schwarze, K., Buchanan, J., Fermont, JM., Dreau, H., Tilley, MW., Taylor, JM., Antoniou, P., Knight, SJL., Camps, C., Pentony, MM., Kvikstad, EM., Harris, S., Popitsch, N., Pagnamenta, AT., Schuh, A., Taylor, JC., Wordsworth, S.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Genet Med","volume":"22","issue":"1","page":"85-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15383284","title":"Structure and stability of cohesin's Smc1-kleisin interaction.","abstract":"A multisubunit complex called cohesin forms a huge ring structure that mediates sister chromatid cohesion, possibly by entrapping sister DNAs following replication. Cohesin's kleisin subunit Scc1 completes the ring, connecting the ABC-like ATPase heads of a V-shaped Smc1\/3 heterodimer. Proteolytic cleavage of Scc1 by separase triggers sister chromatid disjunction, presumably by breaking the Scc1 bridge. One half of the SMC-kleisin bridge is revealed here by a crystal structure of Smc1's ATPase complexed with Scc1's C-terminal domain. The latter forms a winged helix that binds a pair of beta strands in Smc1's ATPase head. Mutation of conserved residues within the contact interface destroys Scc1's interaction with Smc1\/3 heterodimers and eliminates cohesin function. Interaction of Scc1's N terminus with Smc3 depends on prior C terminus connection with Smc1. There is little or no turnover of Smc1-Scc1 interactions within cohesin complexes in vivo because expression of noncleavable Scc1 after DNA replication does not hinder anaphase.","authors":"Haering, CH., Schoffnegger, D., Nishino, T., Helmhart, W., Nasmyth, K., L\u00f6we, J.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Mol Cell","volume":"15","issue":"6","page":"951-64","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2004-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30951975","title":"Functional-genetic approaches to understanding drug response and resistance.","abstract":"Drug development remains a slow and expensive process, while the effective use of established therapeutics is widely hampered by our limited understanding of response and resistance mechanisms. Functional-genetic tools such as CRISPR\/Cas9, advanced RNAi methods, and targeted protein degradation, together with other emerging technologies such as time-resolved and single-cell transcriptomics, fundamentally change the way we can search for candidate therapeutic targets and evaluate them before drug development. In addition, for already available therapeutics these tools open vast opportunities for probing response mechanisms and predictive biomarkers, and thereby guide the development of personalized therapies. Here, we review promising applications and remaining limitations of recently established functional-genetic tools for high-throughput screening and the in-depth analysis of candidate targets and established drugs.","authors":"Hinterndorfer, M., Zuber, J.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Curr Opin Genet Dev","volume":"54","issue":null,"page":"41-47","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33992161","title":"Concepts and functions of small RNA pathways in C. elegans.","abstract":"A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or \"non-self\" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.","authors":"Ketting, RF., Cochella, L.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Curr Top Dev Biol","volume":"144","issue":null,"page":"45-89","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17978569","title":"Skeletal development--Wnts are in control.","abstract":"Approximately 200 individual skeletal elements, which differ in shape and size, are the building blocks of the vertebrate skeleton. Various features of the individual skeletal elements, such as their location, shape, growth and differentiation rate, are being determined during embryonic development. A few skeletal elements, such as the lateral halves of the clavicle and parts of the skull are formed by a process called intramembranous ossification, whereby mesenchymal cells differentiate directly into osteoblasts, while the majority of skeletal elements are formed via endochondral ossification. The latter process starts with the formation of a cartilaginous template, which eventually is being replaced by bone. This requires co-regulation of differentiation of the cell-types specific for cartilage and bone, chondrocytes and osteoblasts, respectively. In recent years it has been demonstrated that Wnt family members and their respective intracellular pathways, such as non-canonical and the canonical Wnt\/beta-catenin pathway, play important and diverse roles during different steps of vertebrate skeletal development. Based on the recent discoveries modulation of the canonical Wnt-signaling pathway could be an interesting approach to direct stem cells into certain skeletal lineages.","authors":"Hartmann, C.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Cells","volume":"24","issue":"2","page":"177-84","pdf":null,"JrId":"8634","fulltextlink":null,"preprintlink":null,"articledate":"2007-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33106586","title":"Metabolic regulation by PPAR\u03b3 is required for IL-33-mediated activation of ILC2s in lung and adipose tissue.","abstract":"Type 2 innate lymphoid cells (ILC2s) play a critical role early in the response to infection by helminths and in the development of allergic reactions. ILC2s are also involved in the physiologic regulation of adipose tissue and its metabolic response to cold shock. We find that the metabolic sensor peroxisome proliferator-activated receptor gamma (PPAR\u03b3) is highly expressed in ILC2s of the lung and adipose tissue and increases responsiveness to IL-33. In turn, activation of ILC2 by IL-33 leads to increased expression of PPAR\u03b3, a prerequisite for proliferation and expression of the effector cytokines IL-5 and IL-13. In contrast, pharmacological inhibition of PPAR\u03b3 leads to decreased expression of CD36 and fatty acid uptake, a necessary source of energy for ILC2s and of potential ligands for PPAR\u03b3. As a consequence, treatment of mice with a PPAR\u03b3 antagonist reduces\u00a0the severity of an ILC2-dependent acute airway inflammation. Together, our results demonstrate the critical role of the metabolic sensor PPAR\u03b3 for the functions of ILC2s.","authors":"Fali, T., Aychek, T., Ferhat, M., Jouzeau, JY., Busslinger, M., Moulin, D., Eberl, G.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Mucosal Immunol","volume":"14","issue":"3","page":"585-593","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33558315","title":"Stem cell quiescence: the challenging path to activation.","abstract":"Quiescence is a cellular state in which a cell remains out of the cell cycle but retains the capacity to divide. The unique ability of adult stem cells to maintain quiescence is crucial for life-long tissue homeostasis and regenerative capacity. Quiescence has long been viewed as an inactive state but recent studies have shown that it is in fact an actively regulated process and that adult stem cells are highly reactive to extrinsic stimuli. This has fuelled hopes of boosting the reactivation potential of adult stem cells to improve tissue function during ageing. In this Review, we provide a perspective of the quiescent state and discuss how quiescent adult stem cells transition into the cell cycle. We also discuss current challenges in the field, highlighting recent technical advances that could help overcome some of these challenges.","authors":"Urb\u00e1n, N., Cheung, TH.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Development","volume":"148","issue":"3","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32514112","title":"Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles.","abstract":"CRISPR-Cas9 screens have emerged as a transformative approach to systematically probe gene functions. The quality and success of these screens depends on the frequencies of loss-of-function alleles, particularly in negative-selection screens widely applied for probing essential genes. Using optimized screening workflows, we performed essentialome screens in cancer cell lines and embryonic stem cells and achieved dropout efficiencies that could not be explained by common frameshift frequencies. We find that these superior effect sizes are mainly determined by the impact of in-frame mutations on protein function, which can be predicted based on amino acid composition and conservation. We integrate protein features into a 'Bioscore' and fuse it with improved predictors of single-guide RNA activity and indel formation to establish a score that captures all relevant processes in CRISPR-Cas9 mutagenesis. This Vienna Bioactivity CRISPR score (www.vbc-score.org) outperforms previous prediction tools and enables the selection of sgRNAs that effectively produce loss-of-function alleles.","authors":"Michlits, G., Jude, J., Hinterndorfer, M., de Almeida, M., Vainorius, G., Hubmann, M., Neumann, T., Schleiffer, A., Burkard, TR., Fellner, M., Gijsbertsen, M., Traunbauer, A., Zuber, J., Elling, U.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Methods","volume":"17","issue":"7","page":"708-716","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9876179","title":"Defective liver formation and liver cell apoptosis in mice lacking the stress signaling kinase SEK1\/MKK4.","abstract":"The stress signaling kinase SEK1\/MKK4 is a direct activator of stress-activated protein kinases (SAPKs; also called Jun-N-terminal kinases, JNKs) in response to a variety of cellular stresses, such as changes in osmolarity, metabolic poisons, DNA damage, heat shock or inflammatory cytokines. We have disrupted the sek1 gene in mice using homologous recombination. Sek1(-\/- )embryos display severe anemia and die between embryonic day 10.5 (E10.5) and E12.5. Haematopoiesis from yolk sac precursors and vasculogenesis are normal in sek1(-\/- )embryos. However, hepatogenesis and liver formation were severely impaired in the mutant embryos and E11.5 and E12.5 sek1(-\/- )embryos had greatly reduced numbers of parenchymal hepatocytes. Whereas formation of the primordial liver from the visceral endoderm appeared normal, sek1(-\/-) liver cells underwent massive apoptosis. These results provide the first genetic link between stress-responsive kinases and organogenesis in mammals and indicate that SEK1 provides a crucial and specific survival signal for hepatocytes.","authors":"Nishina, H., Vaz, C., Billia, P., Nghiem, M., Sasaki, T., De la Pompa, JL., Furlonger, K., Paige, C., Hui, C., Fischer, KD., Kishimoto, H., Iwatsubo, T., Katada, T., Woodgett, JR., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Development","volume":"126","issue":"3","page":"505-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9063494","title":"Cellular and molecular mechanisms of murine autoimmune myocarditis.","abstract":"Dilated cardiomyopathy is a prevalent cause of progressive heart disease and sudden death, and most patients with cardiomyopathy have a history of viral myocarditis. Coxsackie B3 (CB3) picornaviruses can be detected in as many as 50% of these patients and CB3 infections have been epidemiologically linked to chronic heart disease. Several clinical and experimental studies suggest that chronic stages of disease are mediated by an autoimmune response against heart muscle myosin. Human heart disease can be mimicked in mice using cardiac myosin as autoantigen. Murine cardiac myosin-induced myocarditis is an organ-specific autoimmune disease and mediated by CD4+ T cells that recognize a myosin-specific peptide in association with MHC class II molecules. Here, the recent discovery of autoimmune epitopes derived from the alpha isoform of cardiac myosin, the functional roles of surface receptor and signal transduction molecules, and the molecular mechanisms of target organ susceptibility will be discussed.","authors":"Penninger, JM., Pummerer, C., Liu, P., Neu, N., Bachmaier, K.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"APMIS","volume":"105","issue":"1","page":"1-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34142657","title":"The linear ubiquitin chain assembly complex (LUBAC) generates heterotypic ubiquitin chains.","abstract":"The linear ubiquitin chain assembly complex (LUBAC) is the only known ubiquitin ligase for linear\/Met1-linked ubiquitin chain formation. One of the LUBAC components, heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1L), was recently shown to catalyse oxyester bond formation between ubiquitin and some substrates. However, oxyester bond formation in the context of LUBAC has not been directly observed. Here, we present the first 3D reconstruction of human LUBAC obtained by electron microscopy and report its generation of heterotypic ubiquitin chains containing linear linkages with oxyester-linked branches. We found that this event depends on HOIL-1L catalytic activity. By cross-linking mass spectrometry showing proximity between the catalytic RING-in-between-RING (RBR) domains, a coordinated ubiquitin relay mechanism between the HOIL-1-interacting protein (HOIP) and HOIL-1L ligases is suggested. In mouse embryonic fibroblasts, these heterotypic chains were induced by TNF, which is reduced in cells expressing an HOIL-1L catalytic inactive mutant. In conclusion, we demonstrate that LUBAC assembles heterotypic ubiquitin chains by the concerted action of HOIP and HOIL-1L.","authors":"Rodriguez Carvajal, A., Grishkovskaya, I., Gomez Diaz, C., Vogel, A., Sonn-Segev, A., Kushwah, MS., Schodl, K., Deszcz, L., Orban-Nemeth, Z., Sakamoto, S., Mechtler, K., Kukura, P., Clausen, T., Haselbach, D., Ikeda, F.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Elife","volume":"10","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.05.27.117952v2","articledate":"2021-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28654728","title":"Finding Similar Nucleotide Sequences Using Network BLAST Searches.","abstract":"The Basic Local Alignment Search Tool (BLAST) is the first tool in the annotation of nucleotide or amino acid sequences. BLAST is a flagship of bioinformatics due to its performance and user-friendliness. Beginners and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNAs, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn. Understanding results is assisted by taxonomy reports, genomic views, and multiple alignments. We interpret expected frequency thresholds, biological significance, and statistical significance. Weak hits provide no evidence, but indicate hints for further analyses. We find genes that may code for homologous proteins by translated BLAST. We reduce false positives by filtering out low-complexity regions. Parsed BLAST results can be integrated into analysis pipelines. Links in the output connect to Entrez and PubMed, as well as structural, sequence, interaction, and expression databases. This facilitates integration with a wide spectrum of biological knowledge. \u00a9 2017 by John Wiley &amp; Sons, Inc.","authors":"Ladunga, I.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Curr Protoc Bioinformatics","volume":"58","issue":"","page":"3.3.1-3.3.25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17974953","title":"Discovery of endothelial to mesenchymal transition as a source for carcinoma-associated fibroblasts.","abstract":"Activated fibroblasts are associated with many different tumors. Myofibroblasts, activated fibroblasts, and perivascular mesenchymal cells such as pericytes play a role in cancer progression. Many studies suggest that myofibroblasts facilitate tumor growth and cancer progression. The source for myofibroblasts and other activated fibroblasts within the tumors is still debated. Although de novo activation of quiescent fibroblasts into alpha-smooth muscle actin (alpha SMA)-positive myofibroblasts is one likely source, epithelial to mesenchymal transition and bone marrow recruitment are also evolving as possible mechanisms for the emergence of a heterogeneous population of carcinoma-associated fibroblasts. Here, we show that transforming growth factor-beta1 could induce proliferating endothelial cells to undergo a phenotypic conversion into fibroblast-like cells. Such endothelial to mesenchymal transition (EndMT) is associated with the emergence of mesenchymal marker fibroblast-specific protein-1 (FSP1) and down-regulation of CD31\/PECAM. Additionally, we show EndMT in tumors using the B16F10 melanoma model and the Rip-Tag2 spontaneous pancreatic carcinoma model. Crossing Tie2-Cre mice with R26Rosa-lox-Stop-lox-LacZ mice allows for irreversible tagging of endothelial cells. We provide unequivocal evidence for EndMT at the invasive front of the tumors in these transgenic mice. Collectively, our results show that EndMT is a unique mechanism for the accumulation of carcinoma-associated fibroblasts and suggest that antiangiogenic treatment of tumors may have a direct effect in decreasing activated fibroblasts that likely facilitate cancer progression.","authors":"Zeisberg, EM., Potenta, S., Xie, L., Zeisberg, M., Kalluri, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cancer Res","volume":"67","issue":"21","page":"10123-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9841924","title":"Vav regulates peptide-specific apoptosis in thymocytes.","abstract":"The protooncogene Vav functions as a GDP\/GTP exchange factor (GEF) for Rho-like small GTPases involved in cytoskeletal reorganization and cytokine production in T cells. Gene-targeted mice lacking Vav have a severe defect in positive and negative selection of T cell antigen receptor transgenic thymocytes in vivo, and vav-\/- thymocytes are completely resistant to peptide-specific and anti-CD3\/anti-CD28-mediated apoptosis. Vav acts upstream of mitochondrial pore opening and caspase activation. Biochemically, Vav regulates peptide-specific Ca2+ mobilization and actin polymerization. Peptide-specific cell death was blocked both by cytochalasin D inhibition of actin polymerization and by inhibition of protein kinase C (PKC). Activation of PKC with phorbol ester restored peptide-specific apoptosis in vav-\/- thymocytes. Vav was found to bind constitutively to PKC-theta in thymocytes. Our results indicate that peptide-triggered thymocyte apoptosis is mediated via Vav activation, changes in the actin cytoskeleton, and subsequent activation of a PKC isoform.","authors":"Kong, YY., Fischer, KD., Bachmann, MF., Mariathasan, S., Kozieradzki, I., Nghiem, MP., Bouchard, D., Bernstein, A., Ohashi, PS., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Exp Med","volume":"188","issue":"11","page":"2099-111","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-01-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21966401","title":"Determining signalling nodes for apoptosis by a genetic high-throughput screen.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21966401<\/PMID><DateCompleted><Year>2012<\/Year><Month>06<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>10<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>6<\/Volume><Issue>9<\/Issue><PubDate><Year>2011<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Determining signalling nodes for apoptosis by a genetic high-throughput screen.<\/ArticleTitle><Pagination><MedlinePgn>e25023<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0025023<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">With the ever-increasing information emerging from the various sequencing and gene annotation projects, there is an urgent need to elucidate the cellular functions of the newly discovered genes. The genetically regulated cell suicide of apoptosis is especially suitable for such endeavours as it is governed by a vast number of factors.","authors":"Lin, B., Huntley, D., Abuali, G., Langley, SR., Sindelar, G., Petretto, E., Butcher, S., Grimm, S.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"PLoS One","volume":"6","issue":"9","page":"e25023","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9822576","title":"TGFbeta signaling is necessary for carcinoma cell invasiveness and metastasis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9822576<\/PMID><DateCompleted><Year>1998<\/Year><Month>12<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>03<\/Month><Day>19<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>8<\/Volume><Issue>23<\/Issue><PubDate><Year>1998<\/Year><Month>Nov<\/Month><Day>19<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>TGFbeta signaling is necessary for carcinoma cell invasiveness and metastasis.<\/ArticleTitle><Pagination><MedlinePgn>1243-52<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Invasive growth of epithelial tumor cells, a major cause of death from cancer in humans, involves loss of epithelial polarity and dedifferentiation. Transforming growth factor beta (TGFbeta) is regarded as a major tumor suppressor during early tumor development because it inhibits cell-cycle progression and tumor growth. Many dedifferentiated, late-stage tumors are resistant to growth inhibition by TGFbeta, however, and even secrete TGFbeta. In line with this, TGFbeta is involved in angiogenesis, wound healing and epithelial-mesenchymal transition (EMT) during development. Ha-Ras-transformed mammary epithelial cells (EpRas) undergo TGFbeta-induced EMT maintained via a TGFbeta autocrine loop. Thus, we have analyzed whether signal transduction by the TGFbeta receptor (TGFbetaR) is required for local tumor cell invasion and metastasis.","authors":"Oft, M., Heider, KH., Beug, H.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Curr Biol","volume":"8","issue":"23","page":"1243-52","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1998-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34108481","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine.","abstract":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2'-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.","authors":"Prattes, M., Grishkovskaya, I., Hodirnau, VV., R\u00f6ssler, I., Klein, I., Hetzmannseder, C., Zisser, G., Gruber, CC., Gruber, K., Haselbach, D., Bergler, H.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"3483","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9843488","title":"Crystal structure of Escherichia coli cystathionine gamma-synthase at 1.5 A resolution.","abstract":"The transsulfuration enzyme cystathionine gamma-synthase (CGS) catalyses the pyridoxal 5'-phosphate (PLP)-dependent gamma-replacement of O-succinyl-L-homoserine and L-cysteine, yielding L-cystathionine. The crystal structure of the Escherichia coli enzyme has been solved by molecular replacement with the known structure of cystathionine beta-lyase (CBL), and refined at 1.5 A resolution to a crystallographic R-factor of 20.0%. The enzyme crystallizes as an alpha4 tetramer with the subunits related by non-crystallographic 222 symmetry. The spatial fold of the subunits, with three functionally distinct domains and their quaternary arrangement, is similar to that of CBL. Previously proposed reaction mechanisms for CGS can be checked against the structural model, allowing interpretation of the catalytic and substrate-binding functions of individual active site residues. Enzyme-substrate models pinpoint specific residues responsible for the substrate specificity, in agreement with structural comparisons with CBL. Both steric and electrostatic designs of the active site seem to achieve proper substrate selection and productive orientation. Amino acid sequence and structural alignments of CGS and CBL suggest that differences in the substrate-binding characteristics are responsible for the different reaction chemistries. Because CGS catalyses the only known PLP-dependent replacement reaction at Cgamma of certain amino acids, the results will help in our understanding of the chemical versatility of PLP.","authors":"Clausen, T., Huber, R., Prade, L., Wahl, MC., Messerschmidt, A.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"EMBO J","volume":"17","issue":"23","page":"6827-38","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1999-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17875687","title":"Membrane-bound heparin-binding epidermal growth factor like growth factor regulates E-cadherin expression in pancreatic carcinoma cells.","abstract":"Heparin-binding epidermal growth factor-like growth factor (HB-EGF) is a member of the EGF growth factor family. Initially synthesized as a membrane-bound precursor (pro-HB-EGF), it is cleaved at the juxtamembrane domain to release the soluble form of HB-EGF (s-HB-EGF) by sheddases, including matrix metalloproteinases (MMP) and a disintegrin and metalloproteinases. This is a process referred to as ectodomain shedding and is implicated in the process of all ligands of the EGF receptor (EGFR) family. The tumorigenic potential of s-HB-EGF has been studied extensively; however, the role of pro-HB-EGF in tumor progression is unknown, despite the fact that a considerable amount of pro-HB-EGF remains on the cell membrane. Our data here clearly indicated the distinct role of pro-HB-EGF in the regulation of E-cadherin expression and the epithelial-mesenchymal transition. We showed here that the expression of pro-HB-EGF was associated with the differentiation status in pancreatic tumors and cell lines. Expression of noncleaved pro-HB-EGF in pancreatic cells resulted in the up-regulation of E-cadherin through suppression of ZEB1, which is a transcriptional repressor of E-cadherin. Inhibition of HB-EGF shedding using a MMP inhibitor, GM6001, also dramatically augmented the E-cadherin expression while suppressing the EGFR activation. Moreover, up-regulation of E-cadherin by pro-HB-EGF not only resulted in cellular morphologic change but also decreased cell motility and enhanced apoptotic sensitivity in response to gemcitabine-erlotinib treatment. Collectively, our data defined a distinct role of pro-HB-EGF in the regulation of E-cadherin, suggesting that inhibition of shedding may be a novel approach to suppress pancreatic metastasis and sensitize cells to cancer therapy.","authors":"Wang, F., Sloss, C., Zhang, X., Lee, SW., Cusack, JC.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cancer Res","volume":"67","issue":"18","page":"8486-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22024092","title":"Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22024092<\/PMID><DateCompleted><Year>2012<\/Year><Month>01<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1745-6150<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>6<\/Volume><PubDate><Year>2011<\/Year><Month>Oct<\/Month><Day>25<\/Day><\/PubDate><\/JournalIssue><Title>Biology direct<\/Title><ISOAbbreviation>Biol Direct<\/ISOAbbreviation><\/Journal><ArticleTitle>Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins.<\/ArticleTitle><Pagination><MedlinePgn>57<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1745-6150-6-57<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Sequence homology considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-spanning stretches composed of non-polar residues. Simple, quantitative criteria are desirable for identifying transmembrane helices (TMs) that must be included into or should be excluded from start sequence segments in similarity searches aimed at finding distant homologues.","authors":"Wong, WC., Maurer-Stroh, S., Eisenhaber, F.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Biol Direct","volume":"6","issue":"","page":"57","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17805299","title":"p53 is regulated by the lysine demethylase LSD1.","abstract":"p53, the tumour suppressor and transcriptional activator, is regulated by numerous post-translational modifications, including lysine methylation. Histone lysine methylation has recently been shown to be reversible; however, it is not known whether non-histone proteins are substrates for demethylation. Here we show that, in human cells, the histone lysine-specific demethylase LSD1 (refs 3, 4) interacts with p53 to repress p53-mediated transcriptional activation and to inhibit the role of p53 in promoting apoptosis. We find that, in vitro, LSD1 removes both monomethylation (K370me1) and dimethylation (K370me2) at K370, a previously identified Smyd2-dependent monomethylation site. However, in vivo, LSD1 shows a strong preference to reverse K370me2, which is performed by a distinct, but unknown, methyltransferase. Our results indicate that K370me2 has a different role in regulating p53 from that of K370me1: K370me1 represses p53 function, whereas K370me2 promotes association with the coactivator 53BP1 (p53-binding protein 1) through tandem Tudor domains in 53BP1. Further, LSD1 represses p53 function through the inhibition of interaction of p53 with 53BP1. These observations show that p53 is dynamically regulated by lysine methylation and demethylation and that the methylation status at a single lysine residue confers distinct regulatory output. Lysine methylation therefore provides similar regulatory complexity for non-histone proteins and for histones.","authors":"Huang, J., Sengupta, R., Espejo, AB., Lee, MG., Dorsey, JA., Richter, M., Opravil, S., Shiekhattar, R., Bedford, MT., Jenuwein, T., Berger, SL.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"449","issue":"7158","page":"105-8","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2007-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17643378","title":"A physical assay for sister chromatid cohesion in vitro.","abstract":"Cohesion between sister chromatids depends on a multiprotein complex called cohesin that has been proposed to hold sister DNAs together by trapping them inside a large tripartite ring. Sister chromatid cohesion has hitherto only been detected by using cytological methods in living cells. We show here that cohesion between the sister DNAs of circular minichromosomes established in vivo can be detected in vitro by velocity gradient sedimentation and agarose-gel electrophoresis. This ex vivo cohesion does not depend on intercatenation of sister DNAs but is destroyed by cleavage of cohesin's Scc1 subunit or minichromosome linearization. These data represent the best evidence so far that the cohesin ring physically holds sister DNAs together and are consistent with the notion that it does so by using a topological principle involving the trapping DNAs inside its ring.","authors":"Ivanov, D., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Cell","volume":"27","issue":"2","page":"300-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33187978","title":"JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality.","abstract":"Using AI, we identified baricitinib as having antiviral and anticytokine efficacy. We now show a 71% (95% CI 0.15 to 0.58) mortality benefit in 83 patients with moderate-severe SARS-CoV-2 pneumonia with few drug-induced adverse events, including a large elderly cohort (median age, 81 years). An additional 48 cases with mild-moderate pneumonia recovered uneventfully. Using organotypic 3D cultures of primary human liver cells, we demonstrate that interferon-\u03b12 increases ACE2 expression and SARS-CoV-2 infectivity in parenchymal cells by greater than fivefold. RNA-seq reveals gene response signatures associated with platelet activation, fully inhibited by baricitinib. Using viral load quantifications and superresolution microscopy, we found that baricitinib exerts activity rapidly through the inhibition of host proteins (numb-associated kinases), uniquely among antivirals. This reveals mechanistic actions of a Janus kinase-1\/2 inhibitor targeting viral entry, replication, and the cytokine storm and is associated with beneficial outcomes including in severely ill elderly patients, data that incentivize further randomized controlled trials.","authors":"Stebbing, J., S\u00e1nchez Nievas, G., Falcone, M., Youhanna, S., Richardson, P., Ottaviani, S., Shen, JX., Sommerauer, C., Tiseo, G., Ghiadoni, L., Virdis, A., Monzani, F., Rizos, LR., Forfori, F., Avenda\u00f1o C\u00e9spedes, A., De Marco, S., Carrozzi, L., Lena, F., S\u00e1nchez-Jurado, PM., Lacerenza, LG., Cesira, N., Caldevilla Bernardo, D., Perrella, A., Niccoli, L., M\u00e9ndez, LS., Matarrese, D., Goletti, D., Tan, YJ., Monteil, V., Dranitsaris, G., Cantini, F., Farcomeni, A., Dutta, S., Burley, SK., Zhang, H., Pistello, M., Li, W., Romero, MM., Andr\u00e9s Pretel, F., Sim\u00f3n-Talero, RS., Garc\u00eda-Molina, R., Kutter, C., Felce, JH., Nizami, ZF., Miklosi, AG., Penninger, JM., Menichetti, F., Mirazimi, A., Abizanda, P., Lauschke, VM.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Sci Adv","volume":"7","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34183122","title":"Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets.","abstract":"Alternative cleavage and polyadenylation generates mRNA 3' isoforms in a cell type-specific manner. Due to finite available RNA sequencing data of organisms with vast cell type complexity, currently available gene annotation resources are incomplete, which poses significant challenges to the comprehensive interpretation and quantification of transcriptomes. In this chapter, we introduce 3'GAmES, a stand-alone computational pipeline for the identification and quantification of novel mRNA 3'end isoforms from 3'mRNA sequencing data. 3'GAmES expands available repositories and improves comprehensive gene-tag counting by cost-effective 3' mRNA sequencing, faithfully mirroring whole-transcriptome RNAseq measurements. By employing R and bash shell scripts (assembled in a Singularity container) 3'GAmES systematically augments cell type-specific 3' ends of RNA polymerase II transcripts and increases the sensitivity of quantitative gene expression profiling by 3' mRNA sequencing. Public access: https:\/\/github.com\/AmeresLab\/3-GAmES.git.","authors":"Bhat, P., Burkard, TR., Herzog, VA., Pauli, A., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Methods Enzymol","volume":"655","issue":null,"page":"205-223","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17626874","title":"Molecular biology. How and when the genome sticks together.","abstract":null,"authors":"Watrin, E., Peters, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Science","volume":"317","issue":"5835","page":"209-10","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33036834","title":"The future of Cochrane Neonatal.","abstract":"Cochrane Neonatal was first established in 1993, as one of the original review groups of the Cochrane Collaboration. In fact, the origins of Cochrane Neonatal precede the establishment of the collaboration. In the 1980's, the National Perinatal Epidemiology Unit at Oxford, led by Dr. Iain Chalmers, established the \"Oxford Database of Perinatal Trials\" (ODPT), a register of virtually all randomized controlled trials in perinatal medicine to provide a resource for reviews of the safety and efficacy of interventions used in perinatal care and to foster cooperative and coordinated research efforts in the perinatal field [1]. An effort that was clearly ahead of its time, ODPT comprised four main elements: a register of published reports of trials; a register of unpublished trials; a register of ongoing and planned trials; and data derived from pooled overviews (meta-analyses) of trials. This core effort grew into the creation of the seminal books, \"Effective Care in Pregnancy and Childbirth\" as well as \"Effective Care of the Newborn Infant\" [2,3]. As these efforts in perinatal medicine grew, Iain Chalmers thought well beyond perinatal medicine into the creation of a worldwide collaboration that became Cochrane [4]. The mission of the Cochrane Collaboration is to promote evidence-informed health decision-making by producing high-quality, relevant, accessible systematic reviews and other synthesized research evidence (www.cochrane.org). Cochrane Neonatal has continued to be one of the most productive review groups, publishing between 25 tpo to 40 new or updated systematic reviews each year. The impact factor has been steadily increasing over four years and now rivals most of the elite journals in pediatric medicine. Cochrane Neonatal has been a worldwide effort. Currently, there are 404 reviews involving 1206 authors from 52 countries. What has Cochrane done for babies? Reviews from Cochrane Neonatal have informed guidelines and recommendations worldwide. From January 2018 through June 2020, 77 international guidelines cited 221 Cochrane Neonatal reviews. These recommendations have included recommendations of the use of postnatal steroids, inhaled nitric oxide, feeding guidelines for preterm infants and other core aspects of neonatal practice. In addition, Cochrane Reviews has been the impetus for important research, including the large-scale trial of prophylactic indomethacin therapy, a variety of trials of postnatal steroids, trials of emollient ointment and probiotic trials [6]. While justifiably proud of these accomplishments, one needs to examine the future contribution of Cochrane Neonatal to the neonatal community. The future of Cochrane Neonatal is inexorably linked to the future of neonatal research. Obviously, there is no synthesis of trials data if, as a community, we fail to provide the core substrate for that research. As we look at the current trials' environment, fewer randomized controlled trial related to neonates are being published in recent years. A simple search of PubMed, limiting the search to \"neonates\" and \"randomized controlled trials\" shows that in the year 2000, 321 randomized controlled trials were published. These peaked five years ago, in 2015, with close to 900 trials being published. However, in 2018, only 791 studies are identified. Does this decrease represent a meaningful change in the neonatal research environment? Quite possibly. There are shifting missions of clinical neonatology at academic medical institutions, at least in the United States, with a focus on business aspects as well as other important competing clinical activities. Quality improvement has taken over as one of the major activities at both private and academic neonatal practices. Clearly, this is a needed improvement. All units at levels need to be dedicated to improving the outcomes of the sick and fragile population we care for. However, this need not be at the expense of formal clinical trials. It is understandable that this approach would be taken. Newer interventions frequently relate to complex systems of care and not the simple single interventions. Even trials that might traditionally have been done as randomized controlled trials, such as the introduction of a new mode of ventilation, are in reality complex challenges to the ability of institutions to create systems to adapt to these new technologies. Cost of doing trials has always been a barrier. The challenging regulatory and ethical environment contributes to these problems as well [7]. Despite these barriers, how does the research agenda of the neonatal community move forward in the 21st Century? We need to reassess how we create and disseminate our research findings. Innovative trial designs will allow us to address complex issues that we may not have tackled with conventional trials. Adaptive designs may allow us to look at potentially life-saving therapies in a way that feel more efficient and more ethical [8]. Clarifying issues such as the use of inhaled nitric oxide in preterm infants would be greatly served if we even knew whether or not there are hypoxemic preterm infant who would benefit from this therapy [9]. Current trials do not suggest so, yet current practice tells us that a significant number of these babies will receive inhaled nitric oxide [10-13]. Adaptive design, such as those done with trials of extracorporeal membrane oxygenation (ECMO), would allow us to quickly assess whether, in fact, these therapies are life-saving and allow us to consider whether or not further trials are needed [14,15]. Our understanding that many interventions involve entire systems approaches does not relegate us only to doing quality improvement work. Cluster designs may allow us to test more complex interventions that have usually been under the purview of quality improvement [16-18]. Cluster trials are well suited for such investigations and can be done with the least interruption to ongoing care. Ultimately, quality improvement is the application of the best evidence available (evidence-based medicine is \"what to do\" and evidence-based practice is \"how to do\"). [19,20]. Nascent efforts, such as the statement on \"embedding necessary research into culture and health\" (the ENRICH statement) call for the conduct of large, efficient pragmatic trials to evaluate neonatal outcomes, as in part called for in the ALPHA Collaboration [21,22]. This statement envisions an international system to identify important research questions by consulting regularly with all stakeholders, including patients, public health professionals, researchers, providers, policy makers, regulators, funders of industry. The ENRICH statement envisions a pathway to enable individuals, educational institutions, hospitals and health-care facilities to confirm their status as research-friendly by integrating an understanding of trials, other research and critical thinking and to teaching learning and culture, as well as an engagement with funders, professional organizations and regulatory bodies and other stake holders to raise awareness of the value of efficient international research to reduce barriers to large international pragmatic trials and other collaborative studies. In the future, if trials are to be done on this scale or trials are prospectively designed to be analyzed together, core outcome measures must be identified and standardized. That clinical trials supply estimates of outcomes that are relevant to patients and their families is critical. In addition, current neonatal research evaluates many different outcomes using multiple measures. A given measure can have multiple widely used definitions. Bronchopulmonary dysplasia (or chronic lung disease just to add to the confusion) quickly comes to mind [23,24]. The use of multiple definitions when attempting to measure the same outcome prevents synthesis of trial results and meta-analysis and hinders efforts to refine our estimates of effects. Towards that end, Webbe and colleagues have set out to develop a core outcome set for neonatal research [25]. Key stakeholders in the neonatal community reviewed multiple outcomes reported in neonatal trials and qualitative studies. Based on consensus, key outcome measures were identified, including survival, sepsis, necrotizing enterocolitis, brain injury on imaging, retinopathy or prematurity, gross motor ability, general cognitive ability, quality of life, adverse events, visual impairment or blindness, hearing impairment or deafness, chronic lung disease\/bronchopulmonary dysplasia. Trials registration has to be a continued focus of the neonatal community. Trials registration allows for systematic reviewers to understand whether or not reporting bias has occurred [26]. It also allows for transparent incorporation of these core outcome measures. Ultimately, trials registration should include public reporting of all of these core outcomes and, in the future, access to data on an individual level such that more sophisticated individual patient data meta-analysis could occur. Lastly, there is no reason to see clinical trials and quality improvement as separate or exclusive activities. In fact, in the first NICQ Collaborative, conducted by Vermont Oxford Network, participation in a trial of postnatal steroids was considered part of the quality improvement best practices as opposed to simply choosing an as-of-yet unproven approach to use of this potent drug [27]. What role will Cochrane Neonatal play as we move forward in the 21st Century? As the neonatal community moves forward with its' research agenda, Cochrane Neonatal must not only follow but also lead with innovative approaches to synthesizing research findings. Cochrane Neonatal must continue to work closely with guideline developers. The relationship between systematic review production and guideline development is clearly outlined in reports from the Institute of Medicine [28,29]. Both are essential to guideline development; the systematic review group culling the evidence for the benefits and harms of a given intervention and the guideline group addressing the contextual issues of cost, feasibility, implementation and the values and preferences of individuals and societies. Most national and international guidelines groups now routinely use systematic reviews as the evidence basis for their guidelines and recommendations. Examples of the partnership between Cochrane Neonatal and international guideline development can be seen in our support of the World Health Organization (WHO) guidelines on the use of vitamin A or the soon to be published recommendations from the International Liaison Committee on Resuscitation (ILCOR) on cord management in preterm and term infants [30]. In the future, we need to collaborate early in the guideline development process so that the reviews are fit for purpose and meet the needs of the guideline developers and the end users. Towards this end, all Cochrane Neonatal reviews now contain GRADE assessments of the key clinical findings reported in the systematic review [31]. Addition of these assessments addresses the critical issue of our confidence in the findings. We are most confident in evidence provided by randomized controlled trials but this assessment can be can be downgraded if the studies that reported on the outcome in question had a high risk of bias, indirectness, inconsistency of results, or imprecision, or where there is evidence of reporting bias. Information provided by GRADE assessments is seen as critical in the process of moving from the evidence to formal recommendations [32]. We need to explore complex reviews, such as network (NMA) or multiple treatment comparison (MCT) meta-analyses, to address issues not formally addressed in clinical trials [33]. In conditions where there are multiple effective interventions, it is rare for all possible interventions to have been tested against each other [34]. A solution could be provided by network meta-analysis, which allows for comparing all treatments with each other, even if randomized controlled trials are not available for some treatment comparisons [34]. Network meta-analysis uses both direct (head-to-head) randomized clinical trial (RCT) evidence as well as indirect evidence from RCTs to compare the relative effectiveness of all included interventions [35]. However, Mills and colleagues note that the methodological quality of MTCs may be difficult for clinicians to interpret because the number of interventions evaluated may be large and the methodological approaches may be complex [35]. Cochrane Neonatal must take a role in both the creation of such analyses and the education of the neonatal community regarding the pitfalls of such an approach. The availability of individual patient data will make more sophisticated analyses more available to the community. Although the current crop of individual patient data meta-analyses (including the reviews of elective high frequency ventilation, inhaled nitric oxide and oxygen targets) have not differed substantially from the findings of the trials level reviews (suggesting that, in fact, sick neonates are more alike that unalike), there still will be a large role for individual patient data meta-analysis, at least to end the unfound conclusions that these therapies are effective in various subgroups (be it issues of sex, disease severity, or clinical setting) [36-39]. Future trials should take a lesson from the NeOProM Collaborative [37,39]. Given the difficulty in generating significant sample size and creating funding in any single environment, trials with similar protocols should be conducted in a variety of healthcare settings with an eye towards both study level and individual patient level meta-analysis at the conclusion of those trials, allowing for broader contribution to the trials data, more rapid accrual of sample size, and more precise results. We need to educate the neonatal community regarding the use and abuse of diagnostic tests. Diagnostic tests are a critical component of healthcare but also contribute greatly to the cost of medical care worldwide. These costs include the cost of the tests themselves and the costs of misdiagnosis and treatment of individuals who will not benefit from those treatments. Clinicians may have a limited understanding of diagnostic test accuracy, the ability of a diagnostic test to distinguish between patients with and without the disease or target condition [41,42]. Efforts such as Choosing Wisely have tried to identify these deficiencies [40]. As Cochrane has increased the general literacy of both the medical and general population regarding the interpretation of the results of interventions on various diseases, so should Cochrane move forward and improve the understanding of diagnostic testing. We need to become more efficient at creating and maintaining our reviews. The time spent to produce systematic reviews is far too great. In average, it takes between 2\u00bd to 6\u00bd\u00a0years to produce a systematic review, requiring intense time input for highly trained and expensive experts. Innovations in the ways in which we produce systematic reviews can make the review process more efficient by outsourcing some of the tasks or crowdsourcing to machine learning. We need to let the crowd and machine learning innovations help us sort the massive amounts of information needed to conduct systematic reviews. It can also allow for \"live\" updating of critical reviews where the research landscape is quickly changing [43]. Lastly, Cochrane Neonatal must focus more on users of the reviews and not necessarily authors of the reviews. Current Cochrane programming speaks of Cochrane training with an eye towards developing the skills of individuals who will conduct systematic reviews. While this is clearly needed and laudable, the fact of the matter is that most of the community will be \"users\" of the reviews. Individuals who need to understand how to use and interpret the findings of systematic reviews. These review users include clinicians, guideline developers, policy makers and families. Incorporation of GRADE guidelines has been a huge step in adding transparency to the level of uncertainty we have in our findings. From a family's perspective, we need to overcome the environment of mistrust or misunderstanding of scientific evidence and how we convey what we know, and our uncertainty about what we know, to parents and families.","authors":"Soll, RF., Ovelman, C., McGuire, W.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Early Hum Dev","volume":"150","issue":null,"page":"105191","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33922891","title":"AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data.","abstract":"(1) Background: A simplistic understanding of the central dogma falls short in correlating the number of genes in the genome to the number of proteins in the proteome. Post-transcriptional alternative splicing contributes to the complexity of the proteome and is critical in understanding gene expression. mRNA-sequencing (RNA-seq) has been widely used to study the transcriptome and provides opportunity to detect alternative splicing events among different biological conditions. Despite the popularity of studying transcriptome variants with RNA-seq, few efficient and user-friendly bioinformatics tools have been developed for the genome-wide detection and visualization of alternative splicing events. (2) Results: We propose AS-Quant, (<i>A<\/i>lternative <i>S<\/i>plicing <i>Quant<\/i>itation), a robust program to identify alternative splicing events from RNA-seq data. We then extended AS-Quant to visualize the splicing events with short-read coverage plots along with complete gene annotation. The tool works in three major steps: (i) calculate the read coverage of the potential spliced exons and the corresponding gene; (ii) categorize the events into five different categories according to the annotation, and assess the significance of the events between two biological conditions; (iii) generate the short reads coverage plot for user specified splicing events. Our extensive experiments on simulated and real datasets demonstrate that AS-Quant outperforms the other three widely used baselines, SUPPA2, rMATS, and diffSplice for detecting alternative splicing events. Moreover, the significant alternative splicing events identified by AS-Quant between two biological contexts were validated by RT-PCR experiment. (3) Availability: AS-Quant is implemented in Python 3.0. Source code and a comprehensive user's manual are freely available online.","authors":"Fahmi, NA., Nassereddeen, H., Chang, J., Park, M., Yeh, H., Sun, J., Fan, D., Yong, J., Zhang, W.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Int J Mol Sci","volume":"22","issue":"9","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33805528","title":"Cellular Control of Protein Turnover via the Modification of the Amino Terminus.","abstract":"The first amino acid of a protein has an important influence on its metabolic stability. A number of ubiquitin ligases contain binding domains for different amino-terminal residues of their substrates, also known as N-degrons, thereby mediating turnover. This review summarizes, in an exemplary way, both older and more recent findings that unveil how destabilizing amino termini are generated. In most cases, a step of proteolytic cleavage is involved. Among the over 500 proteases encoded in the genome of higher eukaryotes, only a few are known to contribute to the generation of N-degrons. It can, therefore, be expected that many processing paths remain to be discovered.","authors":"Winter, N., Novatchkova, M., Bachmair, A.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Int J Mol Sci","volume":"22","issue":"7","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33838105","title":"Organoid modeling of Zika and herpes simplex virus 1 infections reveals virus-specific responses leading to microcephaly.","abstract":"Viral infection in early pregnancy is a major cause of microcephaly. However, how distinct viruses impair human brain development remains poorly understood. Here we use human brain organoids to study the mechanisms underlying microcephaly caused by Zika virus (ZIKV) and herpes simplex virus (HSV-1). We find that both viruses efficiently replicate in brain organoids and attenuate their growth by causing cell death. However, transcriptional profiling reveals that ZIKV and HSV-1 elicit distinct cellular responses and that HSV-1 uniquely impairs neuroepithelial identity. Furthermore, we demonstrate that, although both viruses fail to potently induce the type I interferon system, the organoid defects caused by their infection can be rescued by distinct type I interferons. These phenotypes are not seen in 2D cultures, highlighting the superiority of brain organoids in modeling viral infections. These results uncover virus-specific mechanisms and complex cellular immune defenses associated with virus-induced microcephaly.","authors":"Krenn, V., Bosone, C., Burkard, TR., Spanier, J., Kalinke, U., Calistri, A., Salata, C., Rilo Christoff, R., Pestana Garcez, P., Mirazimi, A., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell Stem Cell","volume":"28","issue":"8","page":"1362-1379.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34121307","title":"A critical relationship between bone and fat: the role of bone marrow adipose-derived RANKL in bone metabolism.","abstract":"Recent studies have unveiled unique functions of the bone marrow adipose tissue (BMAT), which represent over 10% of the total adipose tissue mass in healthy adults. Increasing evidence is emerging as to how BMAT deposition and osteoporosis are linked under normal and pathophysiological conditions, which is opening up novel treatment avenues. However, the means by which bone marrow adipocytes (BMAs) regulate bone remodeling and their involvement in osteoporosis remained unknown. A study in this issue of EMBO Reports (Hu et al, 2021) and a study in Journal of Clinical Investigation (Yu et al, 2021) reports independently that BMA-derived RANKL regulates osteoclastogenesis and bone remodeling, indicating that excessive RANKL generated by BMAs is an underlying cause for osteoporosis.","authors":"Onji, M., Werschler, N., Penninger, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"EMBO Rep","volume":"22","issue":"7","page":"e52986","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33767413","title":"Genome folding through loop extrusion by SMC complexes.","abstract":"Genomic DNA is folded into loops and topologically associating domains (TADs), which serve important structural and regulatory roles. It has been proposed that these genomic structures are formed by a loop extrusion process, which is mediated by structural maintenance of chromosomes (SMC) protein complexes. Recent single-molecule studies have shown that the SMC complexes condensin and cohesin are indeed able to extrude DNA into loops. In this Review, we discuss how the loop extrusion hypothesis can explain key features of genome architecture; cellular functions of loop extrusion, such as separation of replicated DNA molecules, facilitation of enhancer-promoter interactions and immunoglobulin gene recombination; and what is known about the mechanism of loop extrusion and its regulation, for example, by chromatin boundaries that depend on the DNA binding protein CTCF. We also discuss how the loop extrusion hypothesis has led to a paradigm shift in our understanding of both genome architecture and the functions of SMC complexes.","authors":"Davidson, IF., Peters, JM.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Rev Mol Cell Biol","volume":"22","issue":"7","page":"445-464","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34004152","title":"Fibroblast dedifferentiation as a determinant of successful regeneration.","abstract":"Limb regeneration, while observed lifelong in salamanders, is restricted in post-metamorphic Xenopus laevis frogs. Whether this loss is due to systemic factors or an intrinsic incapability of cells to form competent stem cells has been unclear. Here, we use genetic fate mapping to establish that connective tissue (CT) cells form the post-metamorphic frog blastema, as in the case of axolotls. Using heterochronic transplantation into the limb bud and single-cell transcriptomic profiling, we show that axolotl CT cells dedifferentiate and integrate to form lineages, including cartilage. In contrast, frog blastema CT cells do not fully re-express the limb bud progenitor program, even when transplanted into the limb bud. Correspondingly, transplanted cells contribute to extraskeletal CT, but not to the developing cartilage. Furthermore, using single-cell RNA-seq analysis we find that embryonic and adult frog cartilage differentiation programs are molecularly distinct. This work defines intrinsic restrictions in CT dedifferentiation as a limitation in adult regeneration.","authors":"Lin, TY., Gerber, T., Taniguchi-Sugiura, Y., Murawala, P., Hermann, S., Grosser, L., Shibata, E., Treutlein, B., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Dev Cell","volume":"56","issue":"10","page":"1541-1551.e6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15240665","title":"Expression of the B7.1 costimulatory molecule on pancreatic beta cells abrogates the requirement for CD4 T cells in the development of type 1 diabetes.","abstract":"Although HLA-DQ8 has been implicated as a key determinant of genetic susceptibility to human type 1 diabetes, spontaneous diabetes has been observed in HLA-DQ8 transgenic mice that lack expression of murine MHC class II molecules (mII(-\/-)) only when the potent costimulatory molecule, B7.1, is transgenically expressed on pancreatic beta cells. To study the contribution of HLA-DQ8 to the development of diabetes in this model, we crossed RIP-B7.1mII(-\/-) mice with a set of transgenic mouse lines that differed in their HLA-DQ8 expression patterns on APC subpopulations, in particular dendritic cells and cortical thymic epithelial cells. Surprisingly, we found that even in the absence of HLA-DQ8 and CD4 T cells, a substantial fraction of the RIP-B7.1mII(-\/-) mice developed diabetes. This disease process was remarkable for not only showing insulitis, but also inflammatory destruction of the exocrine pancreas with diffusely up-regulated expression of MHC class I and ICAM-1 molecules. Expression of HLA-DQ8 markedly increased the kinetics and frequency of diabetes, with the most severe disease in the lines with the highest levels of HLA-DQ8 on cortical thymic epithelial cells and the largest numbers of CD4 T cells. However, the adoptive transfer of diabetes was not HLA-DQ8-dependent and disease could be rapidly induced with purified CD8 T cells alone. Expression of B7.1 in the target tissue can thus dramatically alter the cellular and molecular requirements for the development of autoimmunity.","authors":"Havari, E., Lennon-Dumenil, AM., Klein, L., Neely, D., Taylor, JA., McInerney, MF., Wucherpfennig, KW., Lipes, MA.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"J Immunol","volume":"173","issue":"2","page":"787-96","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2004-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33824176","title":"Self-organized cell migration across scales - from single cell movement to tissue formation.","abstract":"Self-organization is a key feature of many biological and developmental processes, including cell migration. Although cell migration has traditionally been viewed as a biological response to extrinsic signals, advances within the past two decades have highlighted the importance of intrinsic self-organizing properties to direct cell migration on multiple scales. In this Review, we will explore self-organizing mechanisms that lay the foundation for both single and collective cell migration. Based on <i>in vitro<\/i> and <i>in vivo<\/i> examples, we will discuss theoretical concepts that underlie the persistent migration of single cells in the absence of directional guidance cues, and the formation of an autonomous cell collective that drives coordinated migration. Finally, we highlight the general implications of self-organizing principles guiding cell migration for biological and medical research.","authors":"Stock, J., Pauli, A.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Development","volume":"148","issue":"7","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32393902","title":"Ubiquitin chain-elongating enzyme UBE2S activates the RING E3 ligase APC\/C for substrate priming.","abstract":"The interplay between E2 and E3 enzymes regulates the polyubiquitination of substrates in eukaryotes. Among the several RING-domain E3 ligases in humans, many utilize two distinct E2s for polyubiquitination. For example, the cell cycle regulatory E3, human anaphase-promoting complex\/cyclosome (APC\/C), relies on UBE2C to prime substrates with ubiquitin (Ub) and on UBE2S to extend polyubiquitin chains. However, the potential coordination between these steps in ubiquitin chain formation remains undefined. While numerous studies have unveiled how RING E3s stimulate individual E2s for Ub transfer, here we change perspective to describe a case where the chain-elongating E2 UBE2S feeds back and directly stimulates the E3 APC\/C to promote substrate priming and subsequent multiubiquitination by UBE2C. Our work reveals an unexpected model for the mechanisms of RING E3-dependent ubiquitination and for the diverse and complex interrelationship between components of the ubiquitination cascade.","authors":"Martinez-Chacin, RC., Bodrug, T., Bolhuis, DL., Kedziora, KM., Bonacci, T., Ordureau, A., Gibbs, ME., Weissmann, F., Qiao, R., Grant, GD., Cook, JG., Peters, JM., Wade Harper, J., Emanuele, MJ., Brown, NG.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Struct Mol Biol","volume":"27","issue":"6","page":"550-560","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33823204","title":"Targeting autophagy in ischemic stroke: From molecular mechanisms to clinical therapeutics.","abstract":"Stroke constitutes the second leading cause of death and a major cause of disability worldwide. Stroke is normally classified as either ischemic or hemorrhagic stroke (HS) although 87% of cases belong to ischemic nature. Approximately 700,000 individuals suffer an ischemic stroke (IS) in the US each year. Recent evidence has denoted a rather pivotal role for defective macroautophagy\/autophagy in the pathogenesis of IS. Cellular response to stroke includes autophagy as an adaptive mechanism that alleviates cellular stresses by removing long-lived or damaged organelles, protein aggregates, and surplus cellular components via the autophagosome-lysosomal degradation process. In this context, autophagy functions as an essential cellular process to maintain cellular homeostasis and organismal survival. However, unchecked or excessive induction of autophagy has been perceived to be detrimental and its contribution to neuronal cell death remains largely unknown. In this review, we will summarize the role of autophagy in IS, and discuss potential strategies, particularly, employment of natural compounds for IS treatment through manipulation of autophagy.","authors":"Ajoolabady, A., Wang, S., Kroemer, G., Penninger, JM., Uversky, VN., Pratico, D., Henninger, N., Reiter, RJ., Bruno, A., Joshipura, K., Aslkhodapasandhokmabad, H., Klionsky, DJ., Ren, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Pharmacol Ther","volume":"225","issue":null,"page":"107848","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32065581","title":"ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin<sup>STAG1<\/sup> from WAPL.","abstract":"Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes <i>via<\/i> extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL. Although WAPL limits cohesin's chromatin residence time to minutes, it has been reported that some loops exist for hours. How these loops can persist is unknown. We show that during G1-phase, mammalian cells contain acetylated cohesin<sup>STAG1<\/sup> which binds chromatin for hours, whereas cohesin<sup>STAG2<\/sup> binds chromatin for minutes. Our results indicate that CTCF and the acetyltransferase ESCO1 protect a subset of cohesin<sup>STAG1<\/sup> complexes from WAPL, thereby enable formation of long and presumably long-lived loops, and that ESCO1, like CTCF, contributes to boundary formation in chromatin looping. Our data are consistent with a model of nested loop extrusion, in which acetylated cohesin<sup>STAG1<\/sup> forms stable loops between CTCF sites, demarcating the boundaries of more transient cohesin<sup>STAG2<\/sup> extrusion activity.","authors":"Wutz, G., Ladurner, R., St Hilaire, BG., Stocsits, RR., Nagasaka, K., Pignard, B., Sanborn, A., Tang, W., V\u00e1rnai, C., Ivanov, MP., Schoenfelder, S., van der Lelij, P., Huang, X., D\u00fcrnberger, G., Roitinger, E., Mechtler, K., Davidson, IF., Fraser, P., Lieberman-Aiden, E., Peters, JM.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Elife","volume":"9","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9653645","title":"Molecular cloning and expression analysis of five novel genes in chromosome 1p36.","abstract":"The human chromosome 1p36 region displays frequent nonrandom chromosomal deletions and translocations in a number of human malignancies; these are thought to inactivate tumor suppressor genes. To identify these putative tumor suppressors we employed exon trapping, cDNA selection, and zoo blot analysis to clone five new genes located in 1p36. Two of these represent novel genes and were designated C1orf1 and xylan 1,4-beta-xylosidase 1 (XBX1). Two further genes represented new members of known gene families: PTPRZ2 was a tyrosine phosphatase and FRAP2 represented a FKBP12-rapamycin-associated protein. The fifth gene identified, ENO1L1, was significantly homologous to c-myc promoter binding protein, MBP-1, and to enolase 1 (ENO1). It colocalized with alpha enolase (ENO1) on a single P1 clone. ENO1L1 differed from both ENO1 and MBP-1 in the organization of its 5' untranslated sequences. Second, MBP-1 contained two single-base insertions not present in either ENO1 or ENO1L1 sequences, which led to a shift in the MBP-1 reading frame. Expression analysis revealed two brain-specific transcripts of 7.9 and 6.5 kb for PTPRZ2. In contrast, C1orf1, FRAP2, ENO1L1, and XBX1 appeared to be expressed ubiquitously in the tissues tested, with transcript sizes of 4.5, 8.7, 1.75, and 4.5 kb, respectively. Using fluorescence in situ hybridization, we mapped the five novel genes relative to chromosome 1p36 breakpoints present in three established tumor cell lines and one nontumor cell line. The karyotypic abnormalities in these cell lines were exploited as chromosomal landmarks; we could thus show that the telomere to centromere gene order was PTPRZ2-(MBP-1\/ENO1\/ENO1L1)-(C1orf1\/XBX1)-+ ++FRAP2. The localization of these genes to a chromosomal region that is prone to deletions in human cancers makes them potential candidate tumor suppressors.","authors":"Onyango, P., Lubyova, B., Gardellin, P., Kurzbauer, R., Weith, A.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Genomics","volume":"50","issue":"2","page":"187-98","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"1998-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32147529","title":"The search for translational pain outcomes to refine analgesic development: Where did we come from and where are we going?","abstract":"Pain measures traditionally used in rodents record mere reflexes evoked by sensory stimuli; the results thus may not fully reflect the human pain phenotype. Alterations in physical and emotional functioning, pain-depressed behaviors and facial pain expressions were recently proposed as additional pain outcomes to provide a more accurate measure of clinical pain in rodents, and hence to potentially enhance analgesic drug development. We aimed to review how preclinical pain assessment has evolved since the development of the tail flick test in 1941, with a particular focus on a critical analysis of some nonstandard pain outcomes, and a consideration of how sex differences may affect the performance of these pain surrogates. We tracked original research articles in Medline for the following periods: 1973-1977, 1983-1987, 1993-1997, 2003-2007, and 2014-2018. We identified 606 research articles about alternative surrogate pain measures, 473 of which were published between 2014 and 2018. This indicates that preclinical pain assessment is moving toward the use of these measures, which may soon become standard procedures in preclinical pain laboratories.","authors":"Gonz\u00e1lez-Cano, R., Montilla-Garc\u00eda, \u00c1., Ruiz-Cantero, MC., Bravo-Caparr\u00f3s, I., Tejada, M\u00c1., Nieto, FR., Cobos, EJ.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Neurosci Biobehav Rev","volume":"113","issue":null,"page":"238-261","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17600970","title":"Reporter gene insertions reveal a strictly B lymphoid-specific expression pattern of Pax5 in support of its B cell identity function.","abstract":"The transcription factor Pax5 is essential for B cell commitment and development. Although the detail Pax5 expression pattern within the hemopoietic system is still largely unknown, we previously reported that Pax5 is monoallelically transcribed in pro-B and mature B cells. In this study, we have investigated the expression of Pax5 at single-cell resolution by inserting a GFP or human Cd2 indicator gene under the translational control of an internal ribosomal entry sequence into the 3' untranslated region of Pax5. These insertions were noninvasive, as B cell development was normal in Pax5(ihCd2\/ihCd2) and Pax5(ihGFP\/iGFP) mice. Transheterozygous Pax5(ihCd2\/iGFP) mice coexpressed GPF and human CD2 at similar levels from pro-B to mature B cells, thus demonstrating biallelic expression of Pax5 at all stages of B cell development. No reporter gene expression could be detected in plasma cells and non-B cells of hemopoietic system. Moreover, the vast majority of common lymphoid progenitors and pre-pro-B in the bone marrow of Pax5(ihGFP\/iGFP) mice did not yet express GFP, indicating that Pax5 expression is fully switched on only during the transition form uncommitted pre-pro-B cells to committed pro-B cells. Hence, the transcriptional initiation and B cell-specific expression of Pax5 is entirely consistent with its B cell lineage commitment function.","authors":"Fuxa, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Immunol","volume":"178","issue":"12","page":"8222-8","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2007-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31805502","title":"AMPK leads to phosphorylation of the transcription factor Nrf2, tuning transactivation of selected target genes.","abstract":"The transcription factor Nrf2 (nuclear factor (erythroid-derived 2)-like 2) and the kinase AMPK (AMP-activated protein kinase) participate in the cellular adaptive response to redox or energy stress. Despite accumulating evidence for positive cooperativity between both proteins, information about direct post-translational modification of Nrf2 by AMPK in living cells is scarce. Here, MS-based analysis of immunoprecipitated Nrf2 revealed serine 374, 408 and 433 in human Nrf2 to be hyperphosphorylated as a function of activated AMPK. A direct phosphate-transfer by AMPK to those sites was indicated by in vitro kinase assays with recombinant proteins as well as interaction of AMPK and Nrf2 in cells, evident by co-immunoprecipitation. Mutation of serine 374, 408 and 433 to alanine did not markedly affect half-life, nuclear accumulation or induction of reporter gene expression upon Nrf2 activation with sulforaphane. However, some selected endogenous Nrf2 target genes responded with decreased induction when the identified phosphosites were mutated, whereas others remained unaffected. Notably, the genes susceptible to the mutation of the phosphorylation sites in Nrf2 consistently showed reduced induction in AMPK\u03b11 -\/-cells. Overall, our data reveal AMPK-triggered phosphorylation of Nrf2 at three serine residues, apparently determining the extent of transactivation of selected target genes.","authors":"Matzinger, M., Fischhuber, K., P\u00f6l\u00f6ske, D., Mechtler, K., Heiss, EH.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Redox Biol","volume":"29","issue":null,"page":"101393","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31757807","title":"PDS5 proteins are required for proper cohesin dynamics and participate in replication fork protection.","abstract":"Cohesin is a chromatin-bound complex that mediates sister chromatid cohesion and facilitates long-range interactions through DNA looping. How the transcription and replication machineries deal with the presence of cohesin on chromatin remains unclear. The dynamic association of cohesin with chromatin depends on WAPL cohesin release factor (WAPL) and on PDS5 cohesin-associated factor (PDS5), which exists in two versions in vertebrate cells, PDS5A and PDS5B. Using genetic deletion in mouse embryo fibroblasts and a combination of CRISPR-mediated gene editing and RNAi-mediated gene silencing in human cells, here we analyzed the consequences of PDS5 depletion for DNA replication. We found that either PDS5A or PDS5B is sufficient for proper cohesin dynamics and that their simultaneous removal increases cohesin's residence time on chromatin and slows down DNA replication. A similar phenotype was observed in WAPL-depleted cells. Cohesin down-regulation restored normal replication fork rates in PDS5-deficient cells, suggesting that chromatin-bound cohesin hinders the advance of the replisome. We further show that PDS5 proteins are required to recruit WRN helicase-interacting protein 1 (WRNIP1), RAD51 recombinase (RAD51), and BRCA2 DNA repair associated (BRCA2) to stalled forks and that in their absence, nascent DNA strands at unprotected forks are degraded by MRE11 homolog double-strand break repair nuclease (MRE11). These findings indicate that PDS5 proteins participate in replication fork protection and also provide insights into how cohesin and its regulators contribute to the response to replication stress, a common feature of cancer cells.","authors":"Morales, C., Ruiz-Torres, M., Rodr\u00edguez-Acebes, S., Lafarga, V., Rodr\u00edguez-Corsino, M., Meg\u00edas, D., Cisneros, DA., Peters, JM., M\u00e9ndez, J., Losada, A.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Biol Chem","volume":"295","issue":"1","page":"146-157","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17587808","title":"Beta-catenin\/LEF-1 signalling in breast cancer--central players activated by a plethora of inputs.","abstract":"Although the role of Wnt signalling in breast cancer is far from being fully understood, in the last years its importance has been reported frequently. Besides stimulation by canonical Wnt signalling, the downstream effectors beta-catenin and the transcriptional modulators of the T-cell factor\/lymphoid enhancer-binding factor (TCF\/LEF) family can also be activated by other inputs including the TGF-beta pathway. Wnt and TGF-beta signalling are both major signal transduction pathways, which provide important cues during development and tumor progression. However, particularly TGF-beta has a complicated influence on oncogenesis, which ranges from suppressive to promoting activity. Signalling pathways activated in parallel with TGF-beta might determine the oncogenic influence, and therefore place signals cooperating with TGF-beta into the limelight. During early development Wnt and TGF-beta signalling collaborate extensively. Here we provide an overview of the known interactions of Wnt with TGF-beta signalling in development and metastasis, particularly in breast cancer. We want to focus on the Wnt-activated transcription factor complex beta-catenin\/LEF-1, its upstream activators, its downstream targets and consequences on the cellular level in response to beta-catenin\/LEF-1 activation.","authors":"Gebeshuber, CA., Sladecek, S., Grunert, S.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cells Tissues Organs","volume":"185","issue":"1-3","page":"51-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17543864","title":"Asymmetric CLASP-dependent nucleation of noncentrosomal microtubules at the trans-Golgi network.","abstract":"Proper organization of microtubule arrays is essential for intracellular trafficking and cell motility. It is generally assumed that most if not all microtubules in vertebrate somatic cells are formed by the centrosome. Here we demonstrate that a large number of microtubules in untreated human cells originate from the Golgi apparatus in a centrosome-independent manner. Both centrosomal and Golgi-emanating microtubules need gamma-tubulin for nucleation. Additionally, formation of microtubules at the Golgi requires CLASPs, microtubule-binding proteins that selectively coat noncentrosomal microtubule seeds. We show that CLASPs are recruited to the trans-Golgi network (TGN) at the Golgi periphery by the TGN protein GCC185. In sharp contrast to radial centrosomal arrays, microtubules nucleated at the peripheral Golgi compartment are preferentially oriented toward the leading edge in motile cells. We propose that Golgi-emanating microtubules contribute to the asymmetric microtubule networks in polarized cells and support diverse processes including post-Golgi transport to the cell front.","authors":"Efimov, A., Kharitonov, A., Efimova, N., Loncarek, J., Miller, PM., Andreyeva, N., Gleeson, P., Galjart, N., Maia, AR., McLeod, IX., Yates, JR., Maiato, H., Khodjakov, A., Akhmanova, A., Kaverina, I.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Dev Cell","volume":"12","issue":"6","page":"917-30","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32160519","title":"MERTK-Dependent Ensheathment of Photoreceptor Outer Segments by Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium.","abstract":"Maintenance of a healthy photoreceptor-retinal pigment epithelium (RPE) interface is essential for vision. At the center of this interface, apical membrane protrusions stemming from the RPE ensheath photoreceptor outer segments (POS), and are possibly involved in the recycling of POS through phagocytosis. The molecules that regulate POS ensheathment and its relationship to phagocytosis remain to be deciphered. By means of ultrastructural analysis, we revealed that Mer receptor tyrosine kinase (MERTK) ligands, GAS6 and PROS1, rather than \u03b1V\u03b25 integrin receptor ligands, triggered POS ensheathment by human embryonic stem cell (hESC)-derived RPE. Furthermore, we found that ensheathment is required for POS fragmentation before internalization. Consistently, POS ensheathment, fragmentation, and internalization were abolished in MERTK mutant RPE, and rescue of MERTK expression in retinitis pigmentosa (RP38) patient RPE counteracted these defects. Our results suggest that loss of ensheathment due to MERTK dysfunction might contribute to vision impairment in RP38 patients.","authors":"Almedawar, S., Vafia, K., Schreiter, S., Neumann, K., Khattak, S., Kurth, T., Ader, M., Karl, MO., Tsang, SH., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Stem Cell Reports","volume":"14","issue":"3","page":"374-389","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33750771","title":"Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation.","abstract":"Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800\u00c5-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.","authors":"Miletic, S., Fahrenkamp, D., Goessweiner-Mohr, N., Wald, J., Pantel, M., Vesper, O., Kotov, V., Marlovits, TC.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"1546","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9637488","title":"Cooperation between CD44 and LFA-1\/CD11a adhesion receptors in lymphokine-activated killer cell cytotoxicity.","abstract":"IL-2-activated NK cells exhibit cytotoxic activity against a wide variety of tumor cells in a non-MHC-restricted fashion and in the absence of prior sensitization. The molecular mechanisms that regulate the cytotoxicity and attachment of activated killer cells to tumor target cells are not known. We provide genetic evidence in CD44(-\/-) and LFA-1(-\/-) mice that the cell adhesion receptors LFA-1 and CD44 regulate the cytotoxic activity of IL-2-activated NK cells against a variety of different tumor cells. This defect in cytotoxicity was significantly enhanced in mice that carried a double mutation of both CD44 and LFA-1. In vitro differentiation, TNF-alpha and IFN-gamma production, and expression of the cytolytic effector molecules perforin and Fas-L were comparable among IL-2-activated NK cells from LFA-1(-\/-), CD44(-\/-), CD44(-\/-)LFA-1(-\/-), and control mice. However, CD44(-\/-), LFA-1(-\/-), and CD44(-\/-)LFA-1(-\/-) IL-2-activated NK cells showed impaired binding and conjugate formation with target cells. We also show that hyaluronic acid is the principal ligand on tumor cells for CD44-mediated cytotoxicity of IL-2-activated NK cells. These results provide the first genetic evidence of the role of adhesion receptors in IL-2-activated NK killing. These data also indicate that distinct adhesion receptors cooperate to mediate binding between effector and target cells required for the initiation of \"natural\" cytotoxicity.","authors":"Matsumoto, G., Nghiem, MP., Nozaki, N., Schmits, R., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Immunol","volume":"160","issue":"12","page":"5781-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33731935","title":"Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.","abstract":null,"authors":"Rajewsky, N., Almouzni, G., Gorski, SA., Aerts, S., Amit, I., Bertero, MG., Bock, C., Bredenoord, AL., Cavalli, G., Chiocca, S., Clevers, H., De Strooper, B., Eggert, A., Ellenberg, J., Fern\u00e1ndez, XM., Figlerowicz, M., Gasser, SM., Hubner, N., Kjems, J., Knoblich, JA., Krabbe, G., Lichter, P., Linnarsson, S., Marine, JC., Marioni, JC., Marti-Renom, MA., Netea, MG., Nickel, D., Nollmann, M., Novak, HR., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, JL., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, FJ., Torres-Padilla, ME., Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M., Voet, T.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature","volume":"592","issue":"7852","page":"E8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37552050","title":"Precision RNAi using synthetic shRNAmir target sites.","abstract":"Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient and inducible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.","authors":"Hoffmann, T., H\u00f6rmann, A., Corcokovic, M., Zmajkovic, J., Hinterndorfer, M., Salkanovic, J., Spreitzer, F., K\u00f6ferle, A., Gitschtaler, K., Popa, A., Oberndorfer, S., Andersch, F., Schaefer, M., Fellner, M., Budano, N., Ruppert, JG., Chetta, P., Wurm, M., Zuber, J., Neum\u00fcller, RA.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Elife","volume":"12","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17495927","title":"The human RNA kinase hClp1 is active on 3' transfer RNA exons and short interfering RNAs.","abstract":"RNA interference allows the analysis of gene function by introducing synthetic, short interfering RNAs (siRNAs) into cells. In contrast to siRNA and microRNA duplexes generated endogenously by the RNaseIII endonuclease Dicer, synthetic siRNAs display a 5' OH group. However, to become incorporated into the RNA-induced silencing complex (RISC) and mediate target RNA cleavage, the guide strand of an siRNA needs to display a phosphate group at the 5' end. The identity of the responsible kinase has so far remained elusive. Monitoring siRNA phosphorylation, we applied a chromatographic approach that resulted in the identification of the protein hClp1 (human Clp1), a known component of both transfer RNA splicing and messenger RNA 3'-end formation machineries. Here we report that the kinase hClp1 phosphorylates and licenses synthetic siRNAs to become assembled into RISC for subsequent target RNA cleavage. More importantly, we reveal the physiological role of hClp1 as the RNA kinase that phosphorylates the 5' end of the 3' exon during human tRNA splicing, allowing the subsequent ligation of both exon halves by an unknown tRNA ligase. The investigation of this novel enzymatic activity of hClp1 in the context of mRNA 3'-end formation, where no RNA phosphorylation event has hitherto been predicted, remains a challenge for the future.","authors":"Weitzer, S., Martinez, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"447","issue":"7141","page":"222-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31786012","title":"Nested Neuronal Dynamics Orchestrate a Behavioral Hierarchy across Timescales.","abstract":"Classical and modern ethological studies suggest that animal behavior is organized hierarchically across timescales, such that longer-timescale behaviors are composed of specific shorter-timescale actions. Despite progress relating neuronal dynamics to single-timescale behavior, it remains unclear how different timescale dynamics interact to give rise to such higher-order behavioral organization. Here, we show, in the nematode Caenorhabditis elegans, that a behavioral hierarchy spanning three timescales is implemented by nested neuronal dynamics. At the uppermost hierarchical level, slow neuronal population dynamics spanning brain and motor periphery control two faster motor neuron oscillations, toggling them between different activity states and functional roles. At lower hierarchical levels, these faster oscillations are further nested in a manner that enables flexible behavioral control in an otherwise rigid hierarchical framework. Our findings establish nested neuronal activity patterns as a repeated dynamical motif of the C.\u00a0elegans nervous system, which together implement a controllable hierarchical organization of behavior.","authors":"Kaplan, HS., Salazar Thula, O., Khoss, N., Zimmer, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Neuron","volume":"105","issue":"3","page":"562-576.e9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17488623","title":"Polo-like kinase 1 triggers the initiation of cytokinesis in human cells by promoting recruitment of the RhoGEF Ect2 to the central spindle.","abstract":"Cytokinesis of animal cells requires ingression of the actomyosin-based contractile ring between segregated sister genomes. Localization of the RhoGEF Ect2 to the central spindle at anaphase promotes local activation of the RhoA GTPase, which induces assembly and ingression of the contractile ring. Here we have used BI 2536, an inhibitor of the mitotic kinase Plk1, to analyze the functions of this enzyme during late mitosis in human cells. We show that Plk1 acts after Cdk1 inactivation and independently from Aurora B to promote RhoA accumulation at the equator, contractile ring formation, and cleavage furrow ingression. Inhibition of Plk1 abolishes the interaction of Ect2 with its activator and midzone anchor, HsCyk-4, thereby preventing localization of Ect2 to the central spindle. We propose that late mitotic Plk1 activity promotes recruitment of Ect2 to the central spindle, triggering the initiation of cytokinesis and contributing to cleavage plane specification in human cells.","authors":"Petronczki, M., Glotzer, M., Kraut, N., Peters, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Dev Cell","volume":"12","issue":"5","page":"713-25","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2007-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33823549","title":"A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation.","abstract":"The lysine specific demethylase 1 (LSD1) plays a pivotal role in cellular differentiation by regulating the expression of key developmental genes in concert with different coregulatory proteins. This process is impaired in different cancer types and incompletely understood. To comprehensively identify functional coregulators of LSD1, we established a novel tractable fluorescent reporter system to monitor LSD1 activity in living cells. Combining this reporter system with a state-of-the-art multiplexed RNAi screen, we identify the DEAD-box helicase 19A (DDX19A) as a novel coregulator and demonstrate that suppression of Ddx19a results in an increase of R-loops and reduced LSD1-mediated gene silencing. We further show that DDX19A binds to tri-methylated lysine 27 of histone 3 (H3K27me3) and it regulates gene expression through the removal of transcription promoting R-loops. Our results uncover a novel transcriptional regulatory cascade where the downregulation of genes is dependent on the LSD1 mediated demethylation of histone H3 lysine 4 (H3K4). This allows the polycomb repressive complex 2 (PRC2) to methylate H3K27, which serves as a binding site for DDX19A. Finally, the binding of DDX19A leads to the efficient removal of R-loops at active promoters, which further de-represses LSD1 and PRC2, establishing a positive feedback loop leading to a robust repression of the target gene.","authors":"Pinter, S., Knodel, F., Choudalakis, M., Schnee, P., Kroll, C., Fuchs, M., Broehm, A., Weirich, S., Roth, M., Eisler, SA., Zuber, J., Jeltsch, A., Rathert, P.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nucleic Acids Res","volume":"49","issue":"8","page":"4350-4370","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33723339","title":"Author Correction: Cytoskeletal disorganization underlies PABPN1-mediated myogenic disability.","abstract":null,"authors":"Olie, CS., van der Wal, E., Cikes, D., Maton, L., de Greef, JC., Lin, IH., Chen, YF., Kareem, E., Penninger, JM., Kessler, BM., Raz, V.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Sci Rep","volume":"11","issue":"1","page":"6429","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17460772","title":"Signal transducer and activator of transcription 3 activation promotes invasive growth of colon carcinomas through matrix metalloproteinase induction.","abstract":"Signal transducer and activator of transcription 3 (STAT3) is aberrantly activated in colorectal carcinomas (CRCs). Here, we define the relationship between STAT3 function and the malignant properties of colon carcinoma cells. Elevated activation of STAT3 enhances invasive growth of the CRC cell lines. To address mechanisms through which STAT3 influences invasiveness, the protease mRNA expression pattern of CRC biopsies was analyzed and correlated with the STAT3 activity status. These studies revealed a striking coincidence of STAT3 activation and strong expression of matrix metalloproteinases MMP-1, -3, -7, and -9. Immunohistological examination of CRC tumor specimens showed a clear colocalization of MMP-1 and activated STAT3. Experimentally induced STAT3 activity in CRC cell lines enhanced both the level of MMP-1 mRNA and secreted MMP-1 enzymatic activity. A direct connection of STAT3 activity and transcription from the MMP-1 promoter was shown by reporter gene experiments. Moreover, high-affinity binding of STAT3 to STAT recognition elements in both the MMP-1 and MMP-3 promoter was demonstrated. Xenograft tumors arising from implantation of CRC cells into nude mice showed simultaneous appearance and colocalization of p-Y-STAT3 and MMP-1 expression. Our results link aberrant activity of STAT3 in CRC to malignant tumor progression through upregulated expression of MMPs.","authors":"Tsareva, SA., Moriggl, R., Corvinus, FM., Wiederanders, B., Sch\u00fctz, A., Kovacic, B., Friedrich, K.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Neoplasia","volume":"9","issue":"4","page":"279-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9527487","title":"Preparative two-dimensional gel electrophoresis of membrane proteins.","abstract":"Electrophoretic techniques, and especially two-dimensional gel electrophoresis (2-DE), have provided an indispensable set of tools for the separation of complex protein mixtures as well as for the identification of protein-protein interactions. Nevertheless, after its introduction more than twenty years ago and even with recent technical developments, the separation of integral and peripheral membrane proteins, in amounts sufficient for microsequencing, is still a difficult task. Lipids present in the membrane as well as the low solubility of hydrophobic membrane proteins result in protein aggregation both on the sample application point and on isoelectric focusing. As a consequence many proteins do not enter the first or second dimension of 2-DE. Here we describe the modification of a protocol using a combination of 3-[(3-cholamidopropyl)-dimethylammonio]-1-propane sulfonate (CHAPS), chaotropic agents (thiourea, urea), Tris base and reducing agents (1,4-dithioerythritol) to improve solubilization of integral and peripheral membrane proteins. Preparative amounts of membrane proteins (up to 2 mg) were loaded during reswelling of dry immobilized pH gradients and the resulting Coomassie staining patterns were largely superimposable with silver-stained gels obtained from identical samples (4 microg). This indicates that the recovery of proteins from the sample is not significantly compromised by the scale-up procedure. A direct application of this method for the characterization and identification of membrane proteins from cellular organelles is described in another paper in this issue (I. Fialka et al., Electrophoresis 1997, 18, 2582-2590).","authors":"Pasquali, C., Fialka, I., Huber, LA.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Electrophoresis","volume":"18","issue":"14","page":"2573-81","pdf":null,"JrId":"3579","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17430201","title":"Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure?","abstract":"Given the huge number of sequences of otherwise uncharacterized protein sequences, computer-aided prediction of posttranslational modifications (PTMs) and translocation signals from amino acid sequence becomes a necessity. We have contributed to this multi-faceted, worldwide effort with the development of predictors for GPI lipid anchor sites, for N-terminal N-myristoylation sites, for farnesyl and geranylgeranyl anchor attachment as well as for the PTS1 peroxisomal signal. Although the substrate protein sequence signals for various PTMs or translocation systems vary dramatically, we found that their principal architecture is similar for all the cases studied. Typically, a small stretch of the amino acid residues is buried in the catalytic cleft of the protein-modifying enzyme (or the binding site of the transporter). This piece most intensely interacts with the enzyme and its sequence variability is most restricted. This stretch is surrounded by linker segments that connect the part bound by the enzyme with the rest of the substrate protein. These residues are, as a trend, small with a flexible backbone and polar. Due to the mechanistic requirements of binding to the enzyme, we suggest that most PTM sites are necessarily embedded into intrinsically disordered regions (except for cases of autocatalytic PTMs, PTMs executed in the unfolded state or non-enzymatic PTMs) and this issue requires consideration in structural studies of proteins with complex architecture. Surprisingly, some proteins carry sequence signals for posttranslational modification or translocation that remain hidden in the normal biological context but can become fully functional in certain conditions.","authors":"Eisenhaber, B., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Curr Protein Pept Sci","volume":"8","issue":"2","page":"197-203","pdf":null,"JrId":"29991","fulltextlink":null,"preprintlink":null,"articledate":"2007-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17392786","title":"A single class of olfactory neurons mediates behavioural responses to a Drosophila sex pheromone.","abstract":"Insects, like many other animals, use sex pheromones to coordinate their reproductive behaviours. Volatile pheromones are detected by odorant receptors expressed in olfactory receptor neurons (ORNs). Whereas fruit odours typically activate multiple ORN classes, pheromones are thought to act through single dedicated classes of ORN. This model predicts that activation of such an ORN class should be sufficient to trigger the appropriate behavioural response. Here we show that the Drosophila melanogaster male-specific pheromone 11-cis-vaccenyl acetate (cVA) acts through the receptor Or67d to regulate both male and female mating behaviour. Mutant males that lack Or67d inappropriately court other males, whereas mutant females are less receptive to courting males. These data suggest that cVA has opposite effects in the two sexes: inhibiting mating behaviour in males but promoting mating behaviour in females. Replacing Or67d with moth pheromone receptors renders these ORNs sensitive to the corresponding moth pheromones. In such flies, moth pheromones elicit behavioural responses that mimic the normal response to cVA. Thus, activation of a single ORN class is both necessary and sufficient to mediate behavioural responses to the Drosophila sex pheromone cVA.","authors":"Kurtovic, A., Widmer, A., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Nature","volume":"446","issue":"7135","page":"542-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33759252","title":"MS Amanda 2.0: Advancements in the standalone implementation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">33759252<\/PMID><DateCompleted><Year>2021<\/Year><Month>11<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>11<\/Month><Day>29<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1097-0231<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>35<\/Volume><Issue>11<\/Issue><PubDate><Year>2021<\/Year><Month>Jun<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Rapid communications in mass spectrometry : RCM<\/Title><ISOAbbreviation>Rapid Commun Mass Spectrom<\/ISOAbbreviation><\/Journal><ArticleTitle>MS Amanda 2.0: Advancements in the standalone implementation.<\/ArticleTitle><Pagination><MedlinePgn>e9088<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/rcm.9088<\/ELocationID><Abstract><AbstractText Label=\"RATIONALE\" NlmCategory=\"BACKGROUND\">Database search engines are the preferred method to identify peptides in mass spectrometry data. However, valuable software is in this context not only defined by a powerful algorithm to separate correct from false identifications, but also by constant maintenance and continuous improvements.","authors":"Dorfer, V., Strobl, M., Winkler, S., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Rapid Commun Mass Spectrom","volume":"35","issue":"11","page":"e9088","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26510014","title":"Genetic and epigenetic variation in the lineage specification of regulatory T cells.","abstract":"Regulatory T (Treg) cells, which suppress autoimmunity and other inflammatory states, are characterized by a distinct set of genetic elements controlling their gene expression. However, the extent of genetic and associated epigenetic variation in the Treg cell lineage and its possible relation to disease states in humans remain unknown. We explored evolutionary conservation of regulatory elements and natural human inter-individual epigenetic variation in Treg cells to identify the core transcriptional control program of lineage specification. Analysis of single nucleotide polymorphisms in core lineage-specific enhancers revealed disease associations, which were further corroborated by high-resolution genotyping to fine map causal polymorphisms in lineage-specific enhancers. Our findings suggest that a small set of regulatory elements specify the Treg lineage and that genetic variation in Treg cell-specific enhancers may alter Treg cell function contributing to polygenic disease.","authors":"Arvey, A., van der Veeken, J., Plitas, G., Rich, SS., Concannon, P., Rudensky, AY.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Elife","volume":"4","issue":null,"page":"e07571","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10459018","title":"Analysis of CD44-containing lipid rafts: Recruitment of annexin II and stabilization by the actin cytoskeleton.","abstract":"CD44, the major cell surface receptor for hyaluronic acid (HA), was shown to localize to detergent-resistant cholesterol-rich microdomains, called lipid rafts, in fibroblasts and blood cells. Here, we have investigated the molecular environment of CD44 within the plane of the basolateral membrane of polarized mammary epithelial cells. We show that CD44 partitions into lipid rafts that contain annexin II at their cytoplasmic face. Both CD44 and annexin II were released from these lipid rafts by sequestration of plasma membrane cholesterol. Partition of annexin II and CD44 to the same type of lipid rafts was demonstrated by cross-linking experiments in living cells. First, when CD44 was clustered at the cell surface by anti-CD44 antibodies, annexin II was recruited into the cytoplasmic leaflet of CD44 clusters. Second, the formation of intracellular, submembranous annexin II-p11 aggregates caused by expression of a trans-dominant mutant of annexin II resulted in coclustering of CD44. Moreover, a frequent redirection of actin bundles to these clusters was observed. These basolateral CD44\/annexin II-lipid raft complexes were stabilized by addition of GTPgammaS or phalloidin in a semipermeabilized and cholesterol-depleted cell system. The low lateral mobility of CD44 in the plasma membrane, as assessed with fluorescent recovery after photobleaching (FRAP), was dependent on the presence of plasma membrane cholesterol and an intact actin cytoskeleton. Disruption of the actin cytoskeleton dramatically increased the fraction of CD44 which could be recovered from the light detergent-insoluble membrane fraction. Taken together, our data indicate that in mammary epithelial cells the vast majority of CD44 interacts with annexin II in lipid rafts in a cholesterol-dependent manner. These CD44-containing lipid microdomains interact with the underlying actin cytoskeleton.","authors":"Oliferenko, S., Paiha, K., Harder, T., Gerke, V., Schw\u00e4rzler, C., Schwarz, H., Beug, H., G\u00fcnthert, U., Huber, LA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Cell Biol","volume":"146","issue":"4","page":"843-54","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1999-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17348039","title":"Interplay of leukemia inhibitory factor and retinoic acid on neural differentiation of mouse embryonic stem cells.","abstract":"Embryonic stem (ES) cells have great potential for cell replacement in neurodegenerative disorders. Implantation of these cells into the brain, however, requires their prior differentiation. We examined the interplay between leukemia inhibitory factor (LIF) and retinoic acid (RA) on neural differentiation of mouse ES (mES) cells. Mouse embryonic stem cells were allowed to form cell aggregates, the so-called embryoid bodies (EBs), in the absence or presence of LIF. In the absence of LIF, mES cells downregulated the expression of the undifferentiated mES cell marker Oct-3\/4, and increased mRNA levels of two neural precursor markers, Sox-1 and Nestin, as well as the neuronal marker beta-tubulin III. This neuronal differentiation was enhanced by treating EBs with RA. Moreover, RA irreversibly increased the number of postmitotic neurons in culture, as shown by the reduction of proliferating mES cells and the increase in beta-tubulin III-positive cells 6 days after RA removal, which in turn affected mES cell viability. The addition of LIF during EBs formation, however, blocked completely this neuronal differentiation. Our findings also showed that pre-differentiation of mES cells in vitro avoided the teratocarcinoma formation observed when proliferating mES cells were grafted into the brain. In addition, mES cells pre-differentiated with RA in culture showed a reduction in proliferation and the presence of neural phenotypes after grafting. In conclusion, the present results indicate that RA enhances neuronal differentiation of mES cells in the absence of LIF, although it compromises cell viability and transplantation.","authors":"Mart\u00edn-Ib\u00e1\u00f1ez, R., Urb\u00e1n, N., Sergent-Tanguy, S., Pineda, JR., Garrido-Clua, N., Alberch, J., Canals, JM.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Neurosci Res","volume":"85","issue":"12","page":"2686-701","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9469814","title":"Mass spectrometric analysis of the anaphase-promoting complex from yeast: identification of a subunit related to cullins.","abstract":"Entry into anaphase and exit from mitosis depend on a ubiquitin-protein ligase complex called the anaphase-promoting complex (APC) or cyclosome. At least 12 different subunits were detected in the purified particle from budding yeast, including the previously identified proteins Apc1p, Cdc16p, Cdc23p, Cdc26p, and Cdc27p. Five additional subunits purified in low nanogram amounts were identified by tandem mass spectrometric sequencing. Apc2p, Apc5p, and the RING-finger protein Apc11p are conserved from yeast to humans. Apc2p is similar to the cullin Cdc53p, which is a subunit of the ubiquitin-protein ligase complex SCFCdc4 required for the initiation of DNA replication.","authors":"Zachariae, W., Shevchenko, A., Andrews, PD., Ciosk, R., Galova, M., Stark, MJ., Mann, M., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Science","volume":"279","issue":"5354","page":"1216-9","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34160864","title":"Gaze mechanisms enabling the detection of faint stars in the night sky.","abstract":"For millennia, people have used \"averted vision\" to improve their detection of faint celestial objects, a technique first documented around 325 BCE. Yet, no studies have assessed gaze location during averted vision to determine what pattern best facilitates perception. Here, we characterized averted vision while recording eye-positions of dark-adapted human participants, for the first time. We simulated stars of apparent magnitudes 3.3 and 3.5, matching their brightness to Megrez (the dimmest star in the Big Dipper) and Tau Ceti. Participants indicated whether each star was visible from a series of fixation locations, providing a comprehensive map of detection performance in all directions. Contrary to prior predictions, maximum detection was first achieved at ~8\u00b0 from the star, much closer to the fovea than expected from rod-cone distributions alone. These findings challenge the assumption of optimal detection at the rod density peak and provide the first systematic assessment of an age-old facet of human vision.","authors":"Alexander, RG., Mintz, RJ., Custodio, PJ., Macknik, SL., Vaziri, A., Venkatakrishnan, A., Gindina, S., Martinez-Conde, S.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Eur J Neurosci","volume":"54","issue":"4","page":"5357-5367","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33810967","title":"Editorial: From chromatin to dynamic loops and liquid-like phases: New views on the cell nucleus.","abstract":null,"authors":"Skok, J., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Curr Opin Cell Biol","volume":"70","issue":null,"page":"iii-v","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33336514","title":"Toward whole tissue imaging of axolotl regeneration.","abstract":"The axolotl is a highly regenerative organism and has been studied in laboratories for over 150\u2009years. Despite a long-standing fascination with regeneration in general and axolotl specifically, we are still scratching the surface trying to visualize and understand the complex cellular behavior that underlies axolotl regeneration. In this review, we will discuss the progress that has been made in visualizing these processes focusing on four major aspects: cell labeling approaches, the removal of pigmentation, reductionist approaches to perform live cell imaging, and finally recent developments applying tissue clearing strategies to visualize the processes that underly regeneration. We also provide several suggestions that the community could consider exploring, notably the generation of novel alleles that further reduce pigmentation as well as improvements in tissue clearing strategies.","authors":"Masselink, W., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Dev Dyn","volume":"250","issue":"6","page":"800-806","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41865189","title":"Low-resolution FAIMS for increased peptide coverage in low-load and single-cell proteomics.","abstract":"Field Asymmetric Ion Mobility Spectrometry (FAIMS) is an indispensable tool in single-cell and low-input proteomics. Here, we show that tuning FAIMS resolution via electrode temperature modulation improves sensitivity. We demonstrate that lowering FAIMS resolution broadens the compensation voltage window, thereby increasing ion transmission. This significantly improves ion counts, quantitative precision and peptide identifications by 25-34%. These results were mirrored when analyzing single cell samples.","authors":"Hoch, DG., Belford, M., Heil, LR., Mechtler, K., Matzinger, M.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Sci Rep","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-03-22","doi":"10.1038\/s41598-026-45228-3","first_author":"Hoch, DG.","corresponding_authors":"Matzinger, M."},{"pmid":"32180900","title":"Inducible knock-out of BCL6 in lymphoma cells results in tumor stasis.","abstract":"Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphomas worldwide and is characterized by a high diversity of genetic and molecular alterations. Chromosomal translocations and mutations leading to deregulated expression of the transcriptional repressor BCL6 occur in a significant fraction of DLBCL patients. An oncogenic role of BCL6 in the initiation of DLBCL has been shown as the constitutive expression of BCL6 in mice recapitulates the pathogenesis of human DLBCL. However, the role of BCL6 in tumor maintenance remains poorly investigated due to the absence of suitable genetic models and limitations of pharmacological inhibitors. Here, we have utilized tetracycline-inducible CRISPR\/Cas9 mutagenesis to study the consequences of BCL6 deletion in established DLBCL models in culture and <i>in vivo<\/i>. We show that BCL6 knock-out in SU-DHL-4 cells <i>in vitro<\/i> results in an anti-proliferative response 4-7 days after Cas9 induction that was characterized by cell cycle (G1) arrest. Conditional BCL6 deletion in established DLBCL tumors <i>in vivo<\/i> induced a significant tumor growth inhibition with initial tumor stasis followed by slow tumor growth kinetics. Our findings support a role of BCL6 in the maintenance of lymphoma growth and showcase the utility of inducible CRISPR\/Cas9 systems for probing oncogene addiction.","authors":"Schlager, S., Salomon, C., Olt, S., Albrecht, C., Ebert, A., Bergner, O., Wachter, J., Trapani, F., Gerlach, D., Voss, T., Traunbauer, A., Jude, J., Hinterndorfer, M., Minnich, M., Schweifer, N., Blake, SM., Zinzalla, V., Drobits, B., McConnell, DB., Kraut, N., Pearson, M., Zuber, J., Koegl, M.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Oncotarget","volume":"11","issue":"9","page":"875-890","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34301885","title":"Arrest of WNT\/\u03b2-catenin signaling enables the transition from pluripotent to differentiated germ cells in mouse ovaries.","abstract":"Germ cells form the basis for sexual reproduction by producing gametes. In ovaries, primordial germ cells exit the cell cycle and the pluripotency-associated state, differentiate into oogonia, and initiate meiosis. Despite the importance of germ cell differentiation for sexual reproduction, signaling pathways regulating their fate remain largely unknown. Here, we show in mouse embryonic ovaries that germ cell-intrinsic \u03b2-catenin activity maintains pluripotency and that its repression is essential to allow differentiation and meiosis entry in a timely manner. Accordingly, in \u03b2-catenin loss-of-function and gain-of-function mouse models, the germ cells precociously enter meiosis or remain in the pluripotent state, respectively. We further show that interaction of \u03b2-catenin and the pluripotent-associated factor POU5F1 in the nucleus is associated with germ cell pluripotency. The exit of this complex from the nucleus correlates with germ cell differentiation, a process promoted by the up-regulation of <i>Znrf3<\/i>, a negative regulator of WNT\/\u03b2-catenin signaling. Together, these data identify the molecular basis of the transition from primordial germ cells to oogonia and demonstrate that \u03b2-catenin is a central gatekeeper in ovarian differentiation and gametogenesis.","authors":"Le Rolle, M., Massa, F., Siggers, P., Turchi, L., Loubat, A., Koo, BK., Clevers, H., Greenfield, A., Schedl, A., Chaboissier, MC., Chassot, AA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Proc Natl Acad Sci U S A","volume":"118","issue":"30","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33822486","title":"The FBXW7-NOTCH interactome: A ubiquitin proteasomal system-induced crosstalk modulating oncogenic transformation in human tissues.","abstract":"on Status=\"Publisher\" Owner=\"NLM\"><PMID Version=\"1\">33822486<\/PMID><DateRevised><Year>2021<\/Year><Month>06<\/Month><Day>16<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">2573-8348<\/ISSN><JournalIssue CitedMedium=\"Internet\"><PubDate><Year>2021<\/Year><Month>Apr<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>Cancer reports (Hoboken, N.J.)<\/Title><ISOAbbreviation>Cancer Rep (Hoboken)<\/ISOAbbreviation><\/Journal><ArticleTitle>The FBXW7-NOTCH interactome: A ubiquitin proteasomal system-induced crosstalk modulating oncogenic transformation in human tissues.<\/ArticleTitle><Pagination><MedlinePgn>e1369<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/cnr2.1369<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Ubiquitin ligases or E3 ligases are well programmed to regulate molecular interactions that operate at a post-translational level. Skp, Cullin, F-box containing complex (or SCF complex) is a multidomain E3 ligase known to mediate the degradation of a wide range of proteins through the proteasomal pathway. The three-dimensional domain architecture of SCF family proteins suggests that it operates through a novel and adaptable \"super-enzymatic\" process that might respond to targeted therapeutic modalities in cancer.","authors":"Kar, R., Jha, SK., Ojha, S., Sharma, A., Dholpuria, S., Raju, VSR., Prasher, P., Chellappan, DK., Gupta, G., Kumar Singh, S., Paudel, KR., Hansbro, PM., Kumar Singh, S., Ruokolainen, J., Kesari, KK., Dua, K., Jha, NK.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Cancer Rep (Hoboken)","volume":"","issue":"","page":"e1369","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32653859","title":"Water-filtered Infrared A and visible light (wIRA\/VIS) treatment reduces Chlamydia caviae-induced ocular inflammation and infectious load in a Guinea pig model of inclusion conjunctivitis.","abstract":"Trachoma is a devastating neglected tropical disease caused by Chlamydia trachomatis and the leading global cause of infectious blindness. Although antibiotic treatment against trachoma is efficient (SAFE strategy), additional affordable therapeutic strategies are of high interest. Water-filtered infrared A and visible light (wIRA\/VIS) irradiation has proven to reduce chlamydial infectivity in vitro and ex vivo. The aim of this study was to evaluate whether wIRA\/VIS can reduce chlamydial infection load and\/or ocular pathology in vivo, in a guinea pig model of inclusion conjunctivitis. Guinea pigs were infected with 1\u00a0\u00d7\u00a010<sup>6<\/sup> inclusion-forming units\/eye of Chlamydia caviae via the ocular conjunctiva on day 0. In infected animals, wIRA\/VIS irradiation (2100\u00a0W\/m<sup>2<\/sup>) was applied on day 2 (single treatment) and on days 2 and 4 (double treatment) post-infection (pi). wIRA\/VIS reduced the clinical pathology score on days 7 and 14 pi and the conjunctival chlamydial load on days 2, 4, 7, and 14 pi in comparison with C. caviae-infected, not irradiated, controls. Furthermore, numbers of chlamydial inclusions were decreased in wIRA\/VIS treated C. caviae-infected guinea pigs on day 21 pi compared to C. caviae-infected, non-irradiated, controls. Double treatment with wIRA\/VIS (days 2 and 4 pi) was more efficient than a single treatment on day 2 pi. wIRA\/VIS treatment did neither induce macroscopic nor histologic changes in ocular tissues. Our results indicate that wIRA\/VIS shows promising efficacy to reduce chlamydial infectivity in vivo without causing irradiation related pathologies in the follow-up period. wIRA\/VIS irradiation is a promising approach to reduce trachoma transmission and pathology of ocular chlamydial infection.","authors":"Inic-Kanada, A., Stojanovic, M., Miljkovic, R., Stein, E., Filipovic, A., Frohns, A., Z\u00f6ller, N., Kuratli, J., Barisani-Asenbauer, T., Borel, N.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Photochem Photobiol B","volume":"209","issue":null,"page":"111953","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-160","title":"Cardioids reveal self-organizing principles of human cardiogenesis","abstract":null,"authors":"Pablo Hofbauer, Stefan Jahnel, Nora Papai, Magdalena Giesshammer, Mirjam Penc, Katherina Tavernini, Nastasja Grdseloff, Christy Meledeth, Alison Deyett, Clara Schmidt, Claudia Ctortecka, \u0160ejla \u0160alic, Maria Novatchkova, Sasha Mendjan","publication_status":"preprint","journalpubyear":"2020","journaltitle":"BioRxiv","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.07.06.189431v1","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37985870","title":"Changing the public perception of human embryology.","abstract":null,"authors":"Rivron, NC., Martinez-Arias, A., Sermon, K., Mummery, C., Sch\u00f6ler, HR., Wells, J., Nichols, J., Hadjantonakis, AK., Lancaster, MA., Morris, N., Fu, J., Sturmey, RG., Niakan, K., Rossant, J., Kato, K.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Nat Cell Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17312149","title":"Reporter gene insertions reveal a strictly B lymphoid-specific expression pattern of Pax5 in support of its B cell identity function.","abstract":"The transcription factor Pax5 is essential for B cell commitment and development. Although the detailed Pax5 expression pattern within the hemopoietic system is still largely unknown, we previously reported that Pax5 is monoallelically transcribed in pro-B and mature B cells. In this study, we have investigated the expression of Pax5 at single-cell resolution by inserting a GFP or human cd2 indicator gene under the translational control of an internal ribosomal entry site element into the 3' untranslated region of Pax5. These insertions were noninvasive, as B cell development was normal in Pax5(ihCd2\/ihCd2) and Pax5(iGFP\/iGFP) mice. Transheterozygous Pax5(ihCd2\/iGFP) mice coexpressed GFP and human CD2 at similar levels from pro-B to mature B cells, thus demonstrating biallelic expression of Pax5 at all stages of B cell development. No reporter gene expression could be detected in plasma cells and non-B cells of the hemopoietic system. Moreover, the vast majority of common lymphoid progenitors and pre-pro-B cells in the bone marrow Pax5(iGFP\/iGFP) mice did not yet express GFP, indicating that Pax5 expression is fully switched on only during the transition from uncommitted pre-pro-B cells to committed pro-B cells. Hence, the transcriptional initiation and B cell-specific expression of Pax5 is entirely consistent with its B cell lineage commitment function.","authors":"Fuxa, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Immunol","volume":"178","issue":"5","page":"3031-7","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33782721","title":"Organoids: ready for the revolution?","abstract":null,"authors":"Koo, BK., Bartfeld, S., Alev, C.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Mol Med (Berl)","volume":"99","issue":"4","page":"441-442","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9425348","title":"Mechanisms of asymmetric cell division during animal development.","abstract":"Recent years have seen the discovery of machineries for asymmetric cell division in a number of different organisms. The Inscuteable protein is a central component of such a machinery in Drosophila. Within dividing Drosophila neural precursor cells, Inscuteable directs both the orientation of the mitotic spindle and the asymmetric segregation of the proteins Numb, Prospero and Miranda into one of the two daughter cells. Numb can act by repressing signalling via the transmembrane receptor Notch, whereas Miranda localizes the transcription factor Prospero which initiates daughter cell specific gene expression. The identification of Numb homologs in other species has suggested that this machinery might be conserved from Drosophila to vertebrates.","authors":"Knoblich, JA.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Curr Opin Cell Biol","volume":"9","issue":"6","page":"833-41","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"1998-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9425346","title":"The mechanism and control of cytokinesis.","abstract":"Cytokinesis is under active investigation in each of the dominant experimental model systems. During 1996 and 1997, several developments necessitated the reassessment of the prevailing model for cytokinesis. In addition, the inventory of proteins required for cytokinesis has grown considerably. However, a molecular understanding of cytokinesis still remains elusive.","authors":"Glotzer, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Curr Opin Cell Biol","volume":"9","issue":"6","page":"815-23","pdf":null,"JrId":"1628","fulltextlink":null,"preprintlink":null,"articledate":"1998-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31254094","title":"Evidence for bidirectional and trans-synaptic parasympathetic and sympathetic propagation of alpha-synuclein in rats.","abstract":"The conversion of endogenous alpha-synuclein (asyn) to pathological asyn-enriched aggregates is a hallmark of Parkinson's disease (PD). These inclusions can be detected in the central and enteric nervous system (ENS). Moreover, gastrointestinal symptoms can appear up to 20\u00a0years before the diagnosis of PD. The dual-hit hypothesis posits that pathological asyn aggregation starts in the ENS, and retrogradely spreads to the brain. In this study, we tested this hypothesis by directly injecting preformed asyn fibrils into the duodenum wall of wild-type rats and transgenic rats with excess levels of human asyn. We provide a meticulous characterization of the bacterial artificial chromosome (BAC) transgenic rat model with respect to initial propagation of pathological asyn along the parasympathetic and sympathetic pathways to the brainstem, by performing immunohistochemistry at early time points post-injection. Induced pathology was observed in all key structures along the sympathetic and parasympathetic pathways (ENS, autonomic ganglia, intermediolateral nucleus of the spinal cord (IML), heart, dorsal motor nucleus of the vagus, and locus coeruleus (LC)) and persisted for at least 4\u00a0months post-injection. In contrast, asyn propagation was not detected in wild-type rats, nor in vehicle-injected BAC rats. The presence of pathology in the IML, LC, and heart indicate trans-synaptic spread of the pathology. Additionally, the observed asyn inclusions in the stomach and heart may indicate secondary anterograde propagation after initial retrograde spreading. In summary, trans-synaptic propagation of asyn in the BAC rat model is fully compatible with the \"body-first hypothesis\" of PD etiopathogenesis. To our knowledge, this is the first animal model evidence of asyn propagation to the heart, and the first indication of bidirectional asyn propagation via the vagus nerve, i.e., duodenum-to-brainstem-to-stomach. The BAC rat model could be very valuable for detailed mechanistic studies of the dual-hit hypothesis, and for studies of disease modifying therapies targeting early pathology in the gastrointestinal tract.","authors":"Van Den Berge, N., Ferreira, N., Gram, H., Mikkelsen, TW., Alstrup, AKO., Casadei, N., Tsung-Pin, P., Riess, O., Nyengaard, JR., Tamg\u00fcney, G., Jensen, PH., Borghammer, P.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Acta Neuropathol","volume":"138","issue":"4","page":"535-550","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-159","title":"Cerebral organoid model reveals excessive proliferation of human caudal late interneuron progenitors in Tuberous Sclerosis Complex","abstract":null,"authors":"Oliver L. Eichm\u00fcller, Nina S. Corsini, \u00c1bel V\u00e9rtesy, Theresa Scholl, Victoria-Elisabeth Gruber, Angela M. Peer, Julia Chu, Maria Novatchkova, Mercedes F. Paredes, Martha Feucht, J\u00fcrgen A. Knoblich","publication_status":"preprint","journalpubyear":"2020","journaltitle":"BioRxiv","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.02.27.967802v1","preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32691695","title":"Dysregulation in Akt\/mTOR\/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.","abstract":"How severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections engage cellular host pathways and innate immunity in infected cells remains largely elusive. We performed an integrative proteo-transcriptomics analysis in SARS-CoV-2 infected Huh7 cells to map the cellular response to the invading virus over time. We identified four pathways, ErbB, HIF-1, mTOR and TNF signaling, among others that were markedly modulated during the course of the SARS-CoV-2 infection <i>in vitro<\/i>. Western blot validation of the downstream effector molecules of these pathways revealed a dose-dependent activation of Akt, mTOR, S6K1 and 4E-BP1 at 24 hours post infection (hpi). However, we found a significant inhibition of HIF-1\u03b1 through 24hpi and 48hpi of the infection, suggesting a crosstalk between the SARS-CoV-2 and the Akt\/mTOR\/HIF-1 signaling pathways. Inhibition of the mTOR signaling pathway using Akt inhibitor MK-2206 showed a significant reduction in virus production. Further investigations are required to better understand the molecular sequelae in order to guide potential therapy in the management of severe coronavirus disease 2019 (COVID-19) patients.","authors":"Appelberg, S., Gupta, S., Svensson Akusj\u00e4rvi, S., Ambikan, AT., Mikaeloff, F., Saccon, E., V\u00e9gv\u00e1ri, \u00c1., Benfeitas, R., Sperk, M., St\u00e5hlberg, M., Krishnan, S., Singh, K., Penninger, JM., Mirazimi, A., Neogi, U.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Emerg Microbes Infect","volume":"9","issue":"1","page":"1748-1760","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34326327","title":"How will our understanding of human development evolve over the next 10 years.","abstract":null,"authors":"Brivanlou, AH., Rivron, N., Gleicher, N.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"4614","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17289593","title":"Reversal of H3K9me2 by a small-molecule inhibitor for the G9a histone methyltransferase.","abstract":"Histone lysine methylation has important roles in the organization of chromatin domains and the regulation of gene expression. To analyze its function and modulate its activity, we screened for specific inhibitors against histone lysine methyltransferases (HMTases) using recombinant G9a as the target enzyme. From a chemical library comprising 125,000 preselected compounds, seven hits were identified. Of those, one inhibitor, BIX-01294 (diazepin-quinazolin-amine derivative), does not compete with the cofactor S-adenosyl-methionine, and selectively impairs the G9a HMTase and the generation of H3K9me2 in vitro. In cellular assays, transient incubation of several cell lines with BIX-01294 lowers bulk H3K9me2 levels that are restored upon removal of the inhibitor. Importantly, chromatin immunoprecipitation at several G9a target genes demonstrates reversible reduction of promoter-proximal H3K9me2 in inhibitor-treated mouse ES cells and fibroblasts. Our data identify a biologically active HMTase inhibitor that allows for the transient modulation of H3K9me2 marks in mammalian chromatin.","authors":"Kubicek, S., O'Sullivan, RJ., August, EM., Hickey, ER., Zhang, Q., Teodoro, ML., Rea, S., Mechtler, K., Kowalski, JA., Homon, CA., Kelly, TA., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Mol Cell","volume":"25","issue":"3","page":"473-81","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2007-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33176163","title":"The Transcription Factor Foxp3 Shapes Regulatory T Cell Identity by Tuning the Activity of trans-Acting Intermediaries.","abstract":"Regulatory T (Treg) cell identity is defined by the lineage-specifying transcription factor (TF) Foxp3. Here we examined mechanisms of Foxp3 function by leveraging naturally occurring genetic variation in wild-derived inbred mice, which enables the identification of DNA sequence motifs driving epigenetic features. Chromatin accessibility, TF binding, and gene expression patterns in resting and activated subsets of Treg cells, conventional CD4 T\u00a0cells, and cells expressing a Foxp3 reporter null allele revealed that the majority of Foxp3-dependent changes occurred at sites not bound by Foxp3. Chromatin accessibility of these indirect Foxp3 targets depended on the presence of DNA binding motifs for other TFs, including TCF1. Foxp3 expression correlated with decreased TCF1 and reduced accessibility of TCF1-bound chromatin regions. Deleting one copy of the Tcf7 gene recapitulated Foxp3-dependent negative regulation of chromatin accessibility. Thus, Foxp3 defines Treg cell identity in a largely indirect manner by fine-tuning the activity of other major chromatin remodeling TFs such as TCF1.","authors":"van der Veeken, J., Glasner, A., Zhong, Y., Hu, W., Wang, ZM., Bou-Puerto, R., Charbonnier, LM., Chatila, TA., Leslie, CS., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Immunity","volume":"53","issue":"5","page":"971-984.e5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33827918","title":"The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci.","abstract":"Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with genome expansion is unclear, and how acute changes in gene regulation, as during axolotl limb regeneration, occur in the context of a vast genome has remained a riddle. Here, we describe the chromosome-scale assembly of the giant, 32 Gb axolotl genome. Hi-C contact data revealed the scaling properties of interphase and mitotic chromosome organization. Analysis of the assembly yielded understanding of the evolution of large, syntenic multigene clusters, including the Major Histocompatibility Complex (MHC) and the functional regulatory landscape of the Fibroblast Growth Factor 8 (<i>Axfgf8<\/i>) region. The axolotl serves as a primary model for studying successful regeneration.","authors":"Schloissnig, S., Kawaguchi, A., Nowoshilow, S., Falcon, F., Otsuki, L., Tardivo, P., Timoshevskaya, N., Keinath, MC., Smith, JJ., Voss, SR., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Proc Natl Acad Sci U S A","volume":"118","issue":"15","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17276334","title":"Ran and Rac in mouse eggs: cortical polarity and spindle positioning.","abstract":"Polar body formation in eggs proceeds through two extreme asymmetric divisions, requiring precise coordination between spindle position and the polarized acto-myosin cortex. Two new studies appearing in this issue of Developmental Cell implicate the small GTPases Ran and Rac in cortical polarity of the mouse egg.","authors":"Cowan, C.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Dev Cell","volume":"12","issue":"2","page":"174-6","pdf":null,"JrId":"22411","fulltextlink":null,"preprintlink":null,"articledate":"2007-03-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17218254","title":"Mutations in alpha-tubulin cause abnormal neuronal migration in mice and lissencephaly in humans.","abstract":"The development of the mammalian brain is dependent on extensive neuronal migration. Mutations in mice and humans that affect neuronal migration result in abnormal lamination of brain structures with associated behavioral deficits. Here, we report the identification of a hyperactive N-ethyl-N-nitrosourea (ENU)-induced mouse mutant with abnormalities in the laminar architecture of the hippocampus and cortex, accompanied by impaired neuronal migration. We show that the causative mutation lies in the guanosine triphosphate (GTP) binding pocket of alpha-1 tubulin (Tuba1) and affects tubulin heterodimer formation. Phenotypic similarity with existing mouse models of lissencephaly led us to screen a cohort of patients with developmental brain anomalies. We identified two patients with de novo mutations in TUBA3, the human homolog of Tuba1. This study demonstrates the utility of ENU mutagenesis in the mouse as a means to discover the basis of human neurodevelopmental disorders.","authors":"Keays, DA., Tian, G., Poirier, K., Huang, GJ., Siebold, C., Cleak, J., Oliver, PL., Fray, M., Harvey, RJ., Moln\u00e1r, Z., Pi\u00f1on, MC., Dear, N., Valdar, W., Brown, SD., Davies, KE., Rawlins, JN., Cowan, NJ., Nolan, P., Chelly, J., Flint, J.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Cell","volume":"128","issue":"1","page":"45-57","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31837995","title":"Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos.","abstract":"In mammals, chromatin organization undergoes drastic reorganization during oocyte development. However, the dynamics of three-dimensional chromatin structure in this process is poorly characterized. Using low-input Hi-C (genome-wide chromatin conformation capture), we found that a unique chromatin organization gradually appears during mouse oocyte growth. Oocytes at late stages show self-interacting, cohesin-independent compartmental domains marked by H3K27me3, therefore termed Polycomb-associating domains (PADs). PADs and inter-PAD (iPAD) regions form compartment-like structures with strong inter-domain interactions among nearby PADs. PADs disassemble upon meiotic resumption from diplotene arrest but briefly reappear on the maternal genome after fertilization. Upon maternal depletion of Eed, PADs are largely intact in oocytes, but their\u00a0reestablishment after fertilization is compromised. By contrast, depletion of Polycomb repressive complex 1 (PRC1) proteins attenuates PADs in oocytes, which is associated with substantial gene de-repression in PADs. These data reveal a critical role of Polycomb in regulating chromatin architecture during mammalian oocyte growth and early development.","authors":"Du, Z., Zheng, H., Kawamura, YK., Zhang, K., Gassler, J., Powell, S., Xu, Q., Lin, Z., Xu, K., Zhou, Q., Ozonov, EA., V\u00e9ron, N., Huang, B., Li, L., Yu, G., Liu, L., Au Yeung, WK., Wang, P., Chang, L., Wang, Q., He, A., Sun, Y., Na, J., Sun, Q., Sasaki, H., Tachibana, K., Peters, AHFM., Xie, W.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Mol Cell","volume":"77","issue":"4","page":"825-839.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17215307","title":"Mammalian Polycomb Scmh1 mediates exclusion of Polycomb complexes from the XY body in the pachytene spermatocytes.","abstract":"The product of the Scmh1 gene, a mammalian homolog of Drosophila Sex comb on midleg, is a constituent of the mammalian Polycomb repressive complexes 1 (Prc1). We have identified Scmh1 as an indispensable component of the Prc1. During progression through pachytene, Scmh1 was shown to be excluded from the XY body at late pachytene, together with other Prc1 components such as Phc1, Phc2, Rnf110 (Pcgf2), Bmi1 and Cbx2. We have identified the role of Scmh1 in mediating the survival of late pachytene spermatocytes. Apoptotic elimination of Scmh1(-\/-) spermatocytes is accompanied by the preceding failure of several specific chromatin modifications at the XY body, whereas synapsis of homologous autosomes is not affected. It is therefore suggested that Scmh1 is involved in regulating the sequential changes in chromatin modifications at the XY chromatin domain of the pachytene spermatocytes. Restoration of defects in Scmh1(-\/-) spermatocytes by Phc2 mutation indicates that Scmh1 exerts its molecular functions via its interaction with Prc1. Therefore, for the first time, we are able to indicate a functional involvement of Prc1 during the meiotic prophase of male germ cells and a regulatory role of Scmh1 for Prc1, which involves sex chromosomes.","authors":"Takada, Y., Isono, K., Shinga, J., Turner, JM., Kitamura, H., Ohara, O., Watanabe, G., Singh, PB., Kamijo, T., Jenuwein, T., Burgoyne, PS., Koseki, H.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Development","volume":"134","issue":"3","page":"579-90","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2007-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33318189","title":"FXR mediates T cell-intrinsic responses to reduced feeding during infection.","abstract":"Reduced nutrient intake is a widely conserved manifestation of sickness behavior with poorly characterized effects on adaptive immune responses. During infectious challenges, naive T cells encountering their cognate antigen become activated and differentiate into highly proliferative effector T cells. Despite their evident metabolic shift upon activation, it remains unclear how effector T cells respond to changes in nutrient availability in vivo. Here, we show that spontaneous or imposed feeding reduction during infection decreases the numbers of splenic lymphocytes. Effector T cells showed cell-intrinsic responses dependent on the nuclear receptor Farnesoid X Receptor (FXR). Deletion of FXR in T cells prevented starvation-induced loss of lymphocytes and increased effector T cell fitness in nutrient-limiting conditions, but imparted greater weight loss to the host. FXR deficiency increased the contribution of glutamine and fatty acids toward respiration and enhanced cell survival under low-glucose conditions. Provision of glucose during anorexia of infection rescued effector T cells, suggesting that this sugar is a limiting nutrient for activated lymphocytes and that alternative fuel usage may affect cell survival in starved animals. Altogether, we identified a mechanism by which the host scales immune responses according to food intake, featuring FXR as a T cell-intrinsic sensor.","authors":"Campbell, C., Marchildon, F., Michaels, AJ., Takemoto, N., van der Veeken, J., Schizas, M., Pritykin, Y., Leslie, CS., Intlekofer, AM., Cohen, P., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Proc Natl Acad Sci U S A","volume":"117","issue":"52","page":"33446-33454","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17185323","title":"Polycomb\/Trithorax response elements and epigenetic memory of cell identity.","abstract":"Polycomb\/Trithorax group response elements (PRE\/TREs) are fascinating chromosomal pieces. Just a few hundred base pairs long, these elements can remember and maintain the active or silent transcriptional state of their associated genes for many cell generations, long after the initial determining activators and repressors have disappeared. Recently, substantial progress has been made towards understanding the nuts and bolts of PRE\/TRE function at the molecular level and in experimentally mapping PRE\/TRE sites across whole genomes. Here we examine the insights, controversies and new questions that have been generated by this recent flood of data.","authors":"Ringrose, L., Paro, R.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Development","volume":"134","issue":"2","page":"223-32","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2007-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33579756","title":"A new society for regenerative biologists.","abstract":null,"authors":"Poss, KD., Tanaka, EM.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Development","volume":"148","issue":"3","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9365268","title":"A rapid, quantitative and inexpensive method for detecting apoptosis by flow cytometry in transiently transfected cells.","abstract":"We describe a rapid and quantitative flow cytometric method for determining the apoptotic or anti-apoptotic potential of a gene in various cell types. A plasmid carrying green fluorescent protein (GFP) is co-transfected with an expression vector encoding the gene of interest. Subsequently cells are stained with propidium iodide and, utilising flow cytometry, transfected, GFP-expressing single cells are detected and apoptotic cells in this population are identified by their DNA content of &lt;2 N. The method detects apoptosis as reliably as established methods using in situ nick-end labelling but is faster, easier and less expensive.","authors":"Lamm, GM., Steinlein, P., Cotten, M., Christofori, G.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Nucleic Acids Res","volume":"25","issue":"23","page":"4855-7","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1998-01-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32851187","title":"The biophysical, molecular, and anatomical landscape of pigeon CRY4: A candidate light-based quantal magnetosensor.","abstract":"The biophysical and molecular mechanisms that enable animals to detect magnetic fields are unknown. It has been proposed that birds have a light-dependent magnetic compass that relies on the formation of radical pairs within cryptochrome molecules. Using spectroscopic methods, we show that pigeon cryptochrome clCRY4 is photoreduced efficiently and forms long-lived spin-correlated radical pairs via a tetrad of tryptophan residues. We report that clCRY4 is broadly and stably expressed within the retina but enriched at synapses in the outer plexiform layer in a repetitive manner. A proteomic survey for retinal-specific clCRY4 interactors identified molecules that are involved in receptor signaling, including glutamate receptor-interacting protein 2, which colocalizes with clCRY4. Our data support a model whereby clCRY4 acts as an ultraviolet-blue photoreceptor and\/or a light-dependent magnetosensor by modulating glutamatergic synapses between horizontal cells and cones.","authors":"Hochstoeger, T., Al Said, T., Maestre, D., Walter, F., Vilceanu, A., Pedron, M., Cushion, TD., Snider, W., Nimpf, S., Nordmann, GC., Landler, L., Edelman, N., Kruppa, L., D\u00fcrnberger, G., Mechtler, K., Schuechner, S., Ogris, E., Malkemper, EP., Weber, S., Schleicher, E., Keays, DA.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Adv","volume":"6","issue":"33","page":"eabb9110","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9157597","title":"Plasminogen-dependent and -independent proteolytic activity of murine endothelioma cells with targeted inactivation of fibrinolytic genes.","abstract":"Plasminogen-dependent and -independent proteolytic activity of marine endothelioma (End) cells that were derived from mice with targeted inactivation of the tissue-type plasminogen activator (t-PA-\/-), urokinase-type plasminogen activator (u-PA-\/-) or plasminogen activator inhibitor-1 (PAI-1-\/-) genes was studied with the use of fibrin and extracellular matrix degradation assays. In a buffer milieu, the activation rate of plasminogen (final concentration 0.25 microM) with wild-type and t-PA-\/- End cells (3 x 10(4) to 4 x 10(6) cells\/ml) was comparable, but it was about 4-fold reduced with u-PA-\/- End cells and 3-fold enhanced with PAI-1-\/- End cells. Plasminogen activation was markedly reduced by addition of amiloride or of anti-murine u-PA antibodies but not by addition of anti-murine t-PA antibodies, and it was not stimulated by addition of fibrin. Lysis of 125I-fibrin labeled matrix in the presence of plasminogen was comparable with wild-type, t-PA-\/- and PAI-1-\/- End cells (50% lysis in 3 h with 0.7 to 1.5 x 10(6) cells\/ml), but was significantly reduced with u-PA-\/- End cells (50% lysis in 20 h with 0.87 x 10(6) cells\/ml). Lysis of 3H-proline labeled extracellular matrix in the presence of plasminogen with wild-type, t-PA-\/- and PAI-1-\/- End cells (20% lysis in 48 h with 3 to 5 x 10(6) cells\/ml) was comparable, but it was virtually abolished with u-PA-\/- End cells. In the absence of plasminogen, lysis of both the fibrin and the extracellular matrix by all four cell types was drastically reduced and was virtually abolished by addition of phenylmethylsulfonylfluoride or 1,10 phenanthroline. These data indicate that the proteolytic activity of the transformed murine endothelioma cells, measured in plasminogen activation or matrix degradation assays, is essentially u-PA-related and largely plasminogen-dependent.","authors":"Lijnen, HR., Wagner, EF., Collen, D.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Thromb Haemost","volume":"77","issue":"2","page":"362-7","pdf":null,"JrId":"7724","fulltextlink":null,"preprintlink":null,"articledate":"1997-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33891860","title":"A unified atlas of CD8 T\u00a0cell dysfunctional states in cancer and infection.","abstract":"CD8 T\u00a0cells play an essential role in defense against viral and bacterial infections and in tumor immunity. Deciphering T\u00a0cell loss of functionality is complicated by the conspicuous heterogeneity of CD8 T\u00a0cell states described across experimental and clinical settings. By carrying out a unified analysis of over 300 assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) experiments from 12 studies of CD8 T\u00a0cells in cancer and infection, we defined a shared differentiation trajectory toward dysfunction and its underlying transcriptional drivers and revealed a universal early bifurcation of functional and dysfunctional T\u00a0cell states across models. Experimental dissection of acute and chronic viral infection using single-cell ATAC (scATAC)-seq and allele-specific single-cell RNA (scRNA)-seq identified state-specific drivers and captured the emergence of similar TCF1<sup>+<\/sup> progenitor-like populations at an early branch point, at which functional and dysfunctional T\u00a0cells diverge. Our atlas of CD8 T\u00a0cell states will facilitate mechanistic studies of T\u00a0cell immunity and translational efforts.","authors":"Pritykin, Y., van der Veeken, J., Pine, AR., Zhong, Y., Sahin, M., Mazutis, L., Pe'er, D., Rudensky, AY., Leslie, CS.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Mol Cell","volume":"81","issue":"11","page":"2477-2493.e10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17182555","title":"Osteoprotegerin reduces the serum level of receptor activator of NF-kappaB ligand derived from osteoblasts.","abstract":"Osteoprotegerin (OPG) is a decoy receptor for receptor activator of NF-kappaB ligand (RANKL). We previously reported that OPG deficiency elevated the circulating level of RANKL in mice. Using OPG(-\/-) mice, we investigated whether OPG is involved in the shedding of RANKL by cells expressing RANKL. Osteoblasts and activated T cells in culture released a large amount of RANKL in the absence of OPG. OPG or a soluble form of receptor activator of NF-kappaB (the receptor of RANKL) suppressed the release of RANKL from those cells. OPG- and T cell-double-deficient mice showed an elevated serum RANKL level equivalent to that of OPG(-\/-) mice, indicating that circulating RANKL is mainly derived from bone. The serum level of RANKL in OPG(-\/-) mice was increased by ovariectomy or administration of 1alpha,25-dihydroxyvitamin D(3). Expression of RANKL mRNA in bone, but not thymus or spleen, was increased in wild-type and OPG(-\/-) mice by 1alpha,25-dihydroxyvitamin D(3). These results suggest that OPG suppresses the shedding of RANKL from osteoblasts and that the serum RANKL in OPG(-\/-) mice exactly reflects the state of bone resorption.","authors":"Nakamichi, Y., Udagawa, N., Kobayashi, Y., Nakamura, M., Yamamoto, Y., Yamashita, T., Mizoguchi, T., Sato, M., Mogi, M., Penninger, JM., Takahashi, N.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"J Immunol","volume":"178","issue":"1","page":"192-200","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2007-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32930709","title":"A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans.","abstract":"Jagunal homolog 1 (JAGN1) has been identified as a critical regulator of neutrophil biology in mutant mice and rare-disease patients carrying JAGN1 mutations. Here, we report that Jagn1 deficiency results in alterations in the endoplasmic reticulum (ER) of antibody-producing cells as well as decreased antibody production and secretion. Consequently, mice lacking Jagn1 in B cells exhibit reduced serum immunoglobulin (Ig) levels at steady state and fail to mount an efficient humoral immune response upon immunization with specific antigens or when challenged with viral infections. We also demonstrate that Jagn1 deficiency in B cells results in aberrant IgG N-glycosylation leading to enhanced Fc receptor binding. Jagn1 deficiency in particular affects fucosylation of IgG subtypes in mice as well as rare-disease patients with loss-of-function mutations in JAGN1. Moreover, we show that ER stress affects antibody glycosylation. Our data uncover a novel and key role for JAGN1 and ER stress in antibody glycosylation and humoral immunity in mice and humans.","authors":"Hagelkruys, A., Wirnsberger, G., Stadlmann, J., W\u00f6hner, M., Horrer, M., Vilagos, B., Jonsson, G., Kogler, M., Tortola, L., Novatchkova, M., B\u00f6nelt, P., Hoffmann, D., Koglgruber, R., Steffen, U., Schett, G., Busslinger, M., Bergthaler, A., Klein, C., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Exp Med","volume":"218","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-00-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32908163","title":"Deficiency of the SMOC2 matricellular protein impairs bone healing and produces age-dependent bone loss.","abstract":"Secreted extracellular matrix components which regulate craniofacial development could be reactivated and play roles in adult wound healing. We report a patient with a loss-of-function of the secreted matricellular protein SMOC2 (SPARC related modular calcium binding 2) presenting severe oligodontia, microdontia, tooth root deficiencies, alveolar bone hypoplasia, and a range of skeletal malformations. Turning to a mouse model, Smoc2-GFP reporter expression indicates SMOC2 dynamically marks a range of dental and bone progenitors. While germline Smoc2 homozygous mutants are viable, tooth number anomalies, reduced tooth size, altered enamel prism patterning, and spontaneous age-induced periodontal bone and root loss are observed in this mouse model. Whole-genome RNA-sequencing analysis of embryonic day (E) 14.5 cap stage molars revealed reductions in early expressed enamel matrix components (Odontogenic ameloblast-associated protein) and dentin dysplasia targets (Dentin matrix acidic phosphoprotein 1). We tested if like other matricellular proteins SMOC2 was required for regenerative repair. We found that the Smoc2-GFP reporter was reactivated in adjacent periodontal tissues 4\u00a0days after tooth avulsion injury. Following maxillary tooth injury, Smoc2<sup>-\/-<\/sup> mutants had increased osteoclast activity and bone resorption surrounding the extracted molar. Interestingly, a 10-day treatment with the cyclooxygenase 2 (COX2) inhibitor ibuprofen (30\u00a0mg\/kg body weight) blocked tooth injury-induced bone loss in Smoc2<sup>-\/-<\/sup> mutants, reducing matrix metalloprotease (Mmp)9. Collectively, our results indicate that endogenous SMOC2 blocks injury-induced jaw bone osteonecrosis and offsets age-induced periodontal decay.","authors":"Morkmued, S., Clauss, F., Schuhbaur, B., Fraulob, V., Mathieu, E., Hemmerl\u00e9, J., Clevers, H., Koo, BK., Doll\u00e9, P., Bloch-Zupan, A., Niederreither, K.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Rep","volume":"10","issue":"1","page":"14817","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32916131","title":"Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis.","abstract":"Metabolic reprogramming is a key feature of many cancers, but how and when it contributes to tumorigenesis remains unclear. Here we demonstrate that metabolic reprogramming induced by mitochondrial fusion can be rate-limiting for immortalization of tumor-initiating cells (TICs) and trigger their irreversible dedication to tumorigenesis. Using single-cell transcriptomics, we find that Drosophila brain tumors contain a rapidly dividing stem cell population defined by upregulation of oxidative phosphorylation (OxPhos). We combine targeted metabolomics and in\u00a0vivo genetic screening to demonstrate that OxPhos is required for tumor cell immortalization but dispensable in neural stem cells (NSCs) giving rise to tumors. Employing an in\u00a0vivo NADH\/NAD<sup>+<\/sup> sensor, we show that NSCs precisely increase OxPhos during immortalization. Blocking OxPhos or mitochondrial fusion stalls TICs in quiescence and prevents tumorigenesis through impaired NAD<sup>+<\/sup> regeneration. Our work establishes a unique connection between cellular metabolism and immortalization of tumor-initiating cells.","authors":"Bonnay, F., Veloso, A., Steinmann, V., K\u00f6cher, T., Abdusselamoglu, MD., Bajaj, S., Rivelles, E., Landskron, L., Esterbauer, H., Zinzen, RP., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell","volume":"182","issue":"6","page":"1490-1507.e19","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31422906","title":"Discovery and Characterization of a Cellular Potent Positive Allosteric Modulator of the Polycomb Repressive Complex 1 Chromodomain, CBX7.","abstract":"Polycomb-directed repression of gene expression is frequently misregulated in human diseases. A quantitative and target-specific cellular assay was utilized to discover the first potent positive allosteric modulator (PAM) peptidomimetic, UNC4976, of nucleic acid binding by CBX7, a chromodomain methyl-lysine reader of Polycomb repressive complex 1. The PAM activity of UNC4976 resulted in enhanced efficacy across three orthogonal cellular assays by simultaneously antagonizing H3K27me3-specific recruitment of CBX7 to target genes while increasing non-specific binding to DNA and RNA. PAM activity thereby reequilibrates PRC1 away from H3K27me3 target regions. Together, our discovery and characterization of UNC4976 not only revealed the most cellularly potent PRC1-specific chemical probe to date, but also uncovers a potential mechanism of Polycomb regulation with implications for non-histone lysine methylated interaction partners.","authors":"Lamb, KN., Bsteh, D., Dishman, SN., Moussa, HF., Fan, H., Stuckey, JI., Norris, JL., Cholensky, SH., Li, D., Wang, J., Sagum, C., Stanton, BZ., Bedford, MT., Pearce, KH., Kenakin, TP., Kireev, DB., Wang, GG., James, LI., Bell, O., Frye, SV.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell Chem Biol","volume":"26","issue":"10","page":"1365-1379.e22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17050849","title":"A \"bright zone\" in male hoverfly (Eristalis tenax) eyes and associated faster motion detection and increased contrast sensitivity.","abstract":"Eyes of the hoverfly Eristalis tenax are sexually dimorphic such that males have a fronto-dorsal region of large facets. In contrast to other large flies in which large facets are associated with a decreased interommatidial angle to form a dorsal \"acute zone\" of increased spatial resolution, we show that a dorsal region of large facets in males appears to form a \"bright zone\" of increased light capture without substantially increased spatial resolution. Theoretically, more light allows for increased performance in tasks such as motion detection. To determine the effect of the bright zone on motion detection, local properties of wide field motion detecting neurons were investigated using localized sinusoidal gratings. The pattern of local preferred directions of one class of these cells, the HS cells, in Eristalis is similar to that reported for the blowfly Calliphora. The bright zone seems to contribute to local contrast sensitivity; high contrast sensitivity exists in portions of the receptive field served by large diameter facet lenses of males and is not observed in females. Finally, temporal frequency tuning is also significantly faster in this frontal portion of the world, particularly in males, where it overcompensates for the higher spatial-frequency tuning and shifts the predicted local velocity optimum to higher speeds. These results indicate that increased retinal illuminance due to the bright zone of males is used to enhance contrast sensitivity and speed motion detector responses. Additionally, local neural properties vary across the visual world in a way not expected if HS cells serve purely as matched filters to measure yaw-induced visual motion.","authors":"Straw, AD., Warrant, EJ., O'Carroll, DC.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Exp Biol","volume":"209","issue":"Pt 21","page":"4339-54","pdf":null,"JrId":"4720","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-162","title":"Head-to-head comparison of direct-input RT-PCR and RT-LAMP against RT-qPCR on extracted RNA for rapid SARS-CoV-2 diagnostics. ","abstract":null,"authors":"Kellner MJ, Matl M, Ross JJ, Schnabl J, Handler D, Heinen R, Schaeffer J, Hufnagl P, Indra A, Dekens MPS, Fritsche-Polanz R, F\u00f6dinger M, Zuber J, Vienna Covid-19 Detection Initiative (VCDI), Allerberger F, Pauli A, Brennecke J","publication_status":"preprint","journalpubyear":"2021","journaltitle":"medRxiv","volume":"2021.01.19.21250079","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.medrxiv.org\/content\/10.1101\/2021.01.19.21250079v1","preprintlink":null,"articledate":"2021-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32968280","title":"Conformation of sister chromatids in the replicated human genome.","abstract":"The three-dimensional organization of the genome supports regulated gene expression, recombination, DNA repair, and chromosome segregation during mitosis. Chromosome conformation capture (Hi-C)<sup>1,2<\/sup> analysis has revealed a complex genomic landscape of internal chromosomal structures in vertebrate cells<sup>3-7<\/sup>, but the identical sequence of sister chromatids has made it difficult to determine how they topologically interact in replicated chromosomes. Here we describe sister-chromatid-sensitive Hi-C (scsHi-C), which is based on labelling of nascent DNA with 4-thio-thymidine and nucleoside conversion chemistry. Genome-wide conformation maps of human chromosomes reveal that sister-chromatid pairs interact most frequently at the boundaries of topologically associating domains (TADs). Continuous loading of a dynamic cohesin pool separates sister-chromatid pairs inside TADs and is required to focus sister-chromatid contacts at TAD boundaries. We identified a subset of TADs that are overall highly paired and are characterized by facultative heterochromatin and insulated topological domains that form separately within individual sister chromatids. The rich pattern of sister-chromatid topologies and our scsHi-C technology will make it possible to investigate how physical interactions between identical DNA molecules contribute to DNA repair, gene expression, chromosome segregation, and potentially other biological processes.","authors":"Mitter, M., Gasser, C., Takacs, Z., Langer, CCH., Tang, W., Jessberger, G., Beales, CT., Neuner, E., Ameres, SL., Peters, JM., Goloborodko, A., Micura, R., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nature","volume":"586","issue":"7827","page":"139-144","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32965059","title":"RNF43 truncations trap CK1 to drive niche-independent self-renewal in cancer.","abstract":"Wnt\/\u03b2-catenin signaling is a primary pathway for stem cell maintenance during tissue renewal and a frequent target for mutations in cancer. Impaired Wnt receptor endocytosis due to loss of the ubiquitin ligase RNF43 gives rise to Wnt-hypersensitive tumors that are susceptible to anti-Wnt-based therapy. Contrary to this paradigm, we identify a class of RNF43 truncating cancer mutations that induce \u03b2-catenin-mediated transcription, despite exhibiting retained Wnt receptor downregulation. These mutations interfere with a ubiquitin-independent suppressor role of the RNF43 cytosolic tail that involves Casein kinase 1 (CK1) binding and phosphorylation. Mechanistically, truncated RNF43 variants trap CK1 at the plasma membrane, thereby preventing \u03b2-catenin turnover and propelling ligand-independent target gene transcription. Gene editing of human colon stem cells shows that RNF43 truncations cooperate with p53 loss to drive a niche-independent program for self-renewal and proliferation. Moreover, these RNF43 variants confer decreased sensitivity to anti-Wnt-based therapy. Our data demonstrate the relevance of studying patient-derived mutations for understanding disease mechanisms and improved applications of precision medicine.","authors":"Spit, M., Fenderico, N., Jordens, I., Radaszkiewicz, T., Lindeboom, RG., Bugter, JM., Cristobal, A., Ootes, L., van Osch, M., Janssen, E., Boonekamp, KE., Hanakova, K., Potesil, D., Zdrahal, Z., Boj, SF., Medema, JP., Bryja, V., Koo, BK., Vermeulen, M., Maurice, MM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"EMBO J","volume":"39","issue":"18","page":"e103932","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16990132","title":"Monopolar attachment of sister kinetochores at meiosis I requires casein kinase 1.","abstract":"In meiosis, a single round of DNA replication is followed by two consecutive rounds of chromosome segregation, called meiosis I and II. Disjunction of maternal from paternal centromeres during meiosis I depends on the attachment of sister kinetochores to microtubules emanating from the same pole. In budding yeast, monopolar attachment requires recruitment to kinetochores of the monopolin complex. How monopolin promotes monopolar attachment was unclear, as its subunits are poorly conserved and lack similarities to proteins with known functions. We show here that the monopolin subunit Mam1 binds tightly to Hrr25, a highly conserved casein kinase 1 delta\/epsilon (CK1delta\/epsilon), and recruits it to meiosis I centromeres. Hrr25 kinase activity and Mam1 binding are both essential for monopolar attachment. Since CK1delta\/epsilon activity is important for accurate chromosome segregation during meiosis I also in fission yeast, phosphorylation of kinetochore proteins by CK1delta\/epsilon might be an evolutionary conserved process required for monopolar attachment.","authors":"Petronczki, M., Matos, J., Mori, S., Gregan, J., Bogdanova, A., Schwickart, M., Mechtler, K., Shirahige, K., Zachariae, W., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Cell","volume":"126","issue":"6","page":"1049-64","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2006-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23599463","title":"Comment on \"Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters\".","abstract":"Conrad et al. (Reports, 10 August 2012, p. 742) reported a doubling of RNA polymerase II (Pol II) occupancy at X-linked promoters to support 5' recruitment as the key mechanism for dosage compensation in Drosophila. However, they employed an erroneous data-processing step, overestimating Pol II differences. Reanalysis of the data fails to support the authors' model for dosage compensation.","authors":"Ferrari, F., Jung, YL., Kharchenko, PV., Plachetka, A., Alekseyenko, AA., Kuroda, MI., Park, PJ.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Science","volume":"340","issue":"6130","page":"273","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-30","doi":"10.1126\/science.1231815","first_author":"Ferrari, F.","corresponding_authors":"Park, PJ."},{"pmid":"9327748","title":"Podoplanin, novel 43-kd membrane protein of glomerular epithelial cells, is down-regulated in puromycin nephrosis.","abstract":"Puromycin aminonucleoside nephrosis (PAN), a rat model of human minimal change nephropathy, is characterized by extensive flattening of glomerular epithelial cell (podocyte) foot processes and by severe proteinuria. For comparison of expression of glomerular membrane proteins of normal and PAN rats, a membrane protein fraction of isolated rat glomeruli was prepared and monoclonal antibodies were raised against it. An IgG-secreting clone designated LF3 was selected that specifically immunolabeled podocytes of normal but not of PAN rats. The antigen of LF3 IgG was identified as a 43-kd glycoprotein. Molecular cloning of its cDNA was performed in a delta gt11 expression library prepared from mRNA of isolated rat glomeruli. The predicted amino acid sequence indicated a 166-amino-acid integral membrane protein with a single membrane-spanning domain, two potential phosphorylation sites in its short cytoplasmic tail, and six potential O-glycosylation sites in the large ectodomain. High amino acid sequence identities were found to membrane glycoproteins of rat lung and bone and mouse thymus epithelial cells as well as to a phorbol-ester-induced protein in a mouse osteoblast cell line and to a canine influenza C virus receptor. In PAN, expression of this 43-kd protein was selectively reduced to &lt; 30%, as determined by quantitative immunogold electron microscopy, immunoblotting, and Northern blotting. These data provide evidence that transcription of the 43-kd transmembrane podocyte glycoprotein is specifically down-regulated in PAN. To indicate that this protein could be associated with transformation of arborized foot processes to flat feet (Latin, pes planus) we have called it podoplanin.","authors":"Breiteneder-Geleff, S., Matsui, K., Soleiman, A., Meraner, P., Poczewski, H., Kalt, R., Schaffner, G., Kerjaschki, D.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Am J Pathol","volume":"151","issue":"4","page":"1141-52","pdf":null,"JrId":"449","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16943447","title":"Comparative analysis and \"expression space\" coverage of the production of prokaryotic membrane proteins for structural genomics.","abstract":"Membrane proteins comprise up to one-third of prokaryotic and eukaryotic genomes, but only a very small number of membrane protein structures are known. Membrane proteins are challenging targets for structural biology, primarily due to the difficulty in producing and purifying milligram quantities of these proteins. We are evaluating different methods to produce and purify large numbers of prokaryotic membrane proteins for subsequent structural and functional analysis. Here, we present the comparative expression data for 37 target proteins, all of them secondary transporters, from the mesophilic organism Salmonella typhimurium and the two hyperthermophilic organisms Aquifex aeolicus and Pyrococcus furiosus in three different Escherichia coli expression vectors. In addition, we study the use of Lactococcus lactis as a host for integral membrane protein expression. Overall, 78% of the targets were successfully produced under at least one set of conditions. Analysis of these results allows us to assess the role of different variables in increasing \"expression space\" coverage for our set of targets. This analysis implies that to maximize the number of nonhomologous targets that are expressed, orthologous targets should be chosen and tested in two vectors with different types of promoters, using C-terminal tags. In addition, E. coli is shown to be a robust host for the expression of prokaryotic transporters, and is superior to L. lactis. These results therefore suggest appropriate strategies for high-throughput heterologous overproduction of membrane proteins.","authors":"Surade, S., Klein, M., Stolt-Bergner, PC., Muenke, C., Roy, A., Michel, H.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Protein Sci","volume":"15","issue":"9","page":"2178-89","pdf":null,"JrId":"2312","fulltextlink":null,"preprintlink":null,"articledate":"2006-11-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31612716","title":"Improved Sensitivity in Low-Input Proteomics Using Micropillar Array-Based Chromatography.","abstract":"Capitalizing on the massive increase in sample concentrations which are produced by extremely low elution volumes, nanoliquid chromatography-electrospray ionization-tandem mass spectrometry (nano-LC-ESI-MS\/MS) is currently one of the most sensitive analytical technologies for the comprehensive characterization of complex protein samples. However, despite tremendous technological improvements made in the production and the packing of monodisperse spherical particles for nanoflow high-pressure liquid chromatography (HPLC), current state-of-the-art systems still suffer from limits in operation at the maximum potential of the technology. With the recent introduction of the \u03bcPAC system, which provides perfectly ordered micropillar array based chromatographic support materials, completely new chromatographic concepts for optimization toward the needs of ultrasensitive proteomics become available. Here we report on a series of benchmarking experiments comparing the performance of a commercially available 50 cm micropillar array column to a widely used nanoflow HPLC column for the proteomics analysis of 10 ng of tryptic HeLa cell digest. Comparative analysis of LC-MS\/MS-data corroborated that micropillar array cartridges provide outstanding chromatographic performance, excellent retention time stability, and increased sensitivity in the analysis of low-input proteomics samples and thus repeatedly yielded almost twice as many unique peptide and unique protein group identifications when compared to conventional nanoflow HPLC columns.","authors":"Stadlmann, J., Hudecz, O., Kr\u0161\u0161\u00e1kov\u00e1, G., Ctortecka, C., Van Raemdonck, G., Op De Beeck, J., Desmet, G., Penninger, JM., Jacobs, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Anal Chem","volume":"91","issue":"22","page":"14203-14207","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31027997","title":"Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8\u00a0T Cells.","abstract":"Stable changes in chromatin states and gene expression in cells of the immune system form the basis for memory of infections and other challenges. Here, we used naturally occurring cis-regulatory variation in wild-derived inbred mouse strains to explore the mechanisms underlying long-lasting versus transient gene regulation in CD8 T\u00a0cells responding to acute viral infection. Stably responsive DNA elements were characterized by dramatic and congruent chromatin remodeling events affecting multiple neighboring sites and required distinct transcription factor (TF) binding motifs for their accessibility. Specifically, we found that cooperative recruitment of T-box and Runx family transcription factors to shared targets mediated stable chromatin remodeling upon T\u00a0cell activation. Our observations provide insights into the molecular mechanisms driving virus-specific CD8 T\u00a0cell responses and suggest a general mechanism for the formation of transcriptional and epigenetic memory applicable to other immune and non-immune cells.","authors":"van der Veeken, J., Zhong, Y., Sharma, R., Mazutis, L., Dao, P., Pe'er, D., Leslie, CS., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Immunity","volume":"50","issue":"5","page":"1202-1217.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41875051","title":"Human stem cell-based embryo models: innovation, ethics, and policy.","abstract":"The aim of this White Paper is to establish a foundational framework for research, technological development, and regulation in the emerging field of stem cell-based embryo models (SCBEMs). These models, generated from Pluripotent Stem Cells, are designed to recapitulate essential events in early stages of human development. They have the potential to illuminate the early stages of embryo development and implantation and hold promise as an avenue to address global health challenges, including infertility and pregnancy loss, congenital, neonatal and adult conditions, and the need for organ transplants. While SCBEMs are not a substitute for human embryos, their tractability for large-scale analysis and their abilities to model the earliest stages of embryonic development suggest that they will have a significant impact on reproductive biology and regenerative medicine. But SCBEMs do not just raise novel scientific questions; they pose ethical and legal questions that need to be addressed. The paper stems from a meeting of a core group of researchers that met at the Institut Pasteur in Paris in November 2024 and represents the views of an extended group that has worked to elaborate the documents as a consensus for the field. Here, we provide a framework to guide research in this new field. We do this by summarizing the state of the science, assessing current SCBEM research in relation to its primary future applications and addressing the need for continued ethical and regulatory oversight associated with this new field.","authors":"Arias, AM., Rivron, N., Tajbakhsh, S., Johnston, J., Alev, C., Bally-Cuif, L., B\u00f6ke, E., Cavazza, T., Cave, E., Cyranoski, D., David, L., Esteban, MA., Fu, J., Geijsen, N., de Graeff, N., Hanna, JH., Hopwood, N., Inamdar, MS., Lanner, F., Leeners, B., Liu, Z., Jean Leon, M., Minchiotti, G., Moris, N., Munsie, M., Niakan, KK., Pourquie, O., Pasque, V., Pera, M., Peng, Y., Petropoulos, S., Ramanathan, S., Rossant, J., Rugg-Gunn, P., Saitou, M., Sermon, K., Silva, J., Theunissen, T., Turco, M., Wallingford, J., Wang, H., Warmflash, A., Wu, J., Yu, L.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Hum Reprod","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-03-24","doi":"10.1093\/humrep\/deag035","first_author":"Arias, AM.","corresponding_authors":"Yu, L."},{"pmid":"16912279","title":"c-Jun\/AP-1 controls liver regeneration by repressing p53\/p21 and p38 MAPK activity.","abstract":"The AP-1 transcription factor c-Jun is a key regulator of hepatocyte proliferation. Mice lacking c-Jun in the liver (c-jun (Deltali*)) display impaired liver regeneration after partial hepatectomy (PH). This phenotype correlates with increased protein levels of the cdk-inhibitor p21 in the liver. We performed PH experiments in several double-knockout mouse models to genetically identify the signaling events regulated by c-Jun. Inactivation of p53 in c-jun (Deltali*) mice abrogated both hepatocyte cell cycle block and increased p21 protein expression. Consistently, liver regeneration was rescued in c-jun (Deltali*) p21 (-\/-) double-mutant mice. This indicated that c-Jun controls hepatocyte proliferation by a p53\/p21-dependent mechanism. Analyses of p21 mRNA and protein expression in livers of c-jun (Deltali*) mice after PH revealed that the accumulation of p21 protein is due to a post-transcriptional\/post-translational mechanism. We have investigated several candidate pathways implicated in the regulation of p21 expression, and observed increased activity of the stress kinase p38 in regenerating livers of c-jun (Deltali*) mice. Importantly, conditional deletion of p38alpha in livers of c-jun (Deltali*) mice fully restored hepatocyte proliferation and attenuated increased p21 protein levels after PH. These data demonstrate that c-Jun\/AP-1 regulates liver regeneration through a novel molecular pathway that involves p53, p21, and the stress kinase p38alpha.","authors":"Stepniak, E., Ricci, R., Eferl, R., Sumara, G., Sumara, I., Rath, M., Hui, L., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Genes Dev","volume":"20","issue":"16","page":"2306-14","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27499023","title":"Memory of Inflammation in Regulatory T Cells.","abstract":"Eukaryotic cells can \"remember\" transient encounters with a wide range of stimuli, inducing lasting states of altered responsiveness. Regulatory T (Treg) cells are a specialized lineage of suppressive CD4 T\u00a0cells that act as critical negative regulators of inflammation in various biological contexts. Treg cells exposed to inflammatory conditions acquire strongly enhanced suppressive function. Using inducible genetic tracing, we analyzed the long-term stability of activation-induced transcriptional, epigenomic, and functional changes in Treg cells. We found that the inflammation-experienced Treg cell population reversed many activation-induced changes and lost its enhanced suppressive function over time. The \"memory-less\" potentiation of Treg suppressor function may help avoid a state of generalized immunosuppression that could otherwise result from repeated activation.","authors":"van der Veeken, J., Gonzalez, AJ., Cho, H., Arvey, A., Hemmers, S., Leslie, CS., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"166","issue":"4","page":"977-990","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9294610","title":"Structure and chromosomal assignment of the mouse fra-1 gene, and its exclusion as a candidate gene for oc (osteosclerosis).","abstract":"We have determined the genomic structure of the mouse fra-1 gene, which consists of four exons and three introns at positions also found in the other members of the fos gene family. Fra-1 is expressed rather highly in the brain and testes of adult mice, and at low levels in most other tissues. Absence of c-Fos leads to significantly reduced serum stimulation of fra-1 expression in gene targeted mouse fibroblasts, demonstrating that mitogen induction of fra-1 is partially mediated by c-Fos\/AP-1. A polymorphic (CA)n microsatellite marker was found in intron 2 of fra-1 and used to map the gene to the centromeric region of mouse chromosome 19. Since fra-1 maps to the same genomic region as oc (osteosclerosis), an autosomal recessive disorder leading to the bone remodelling disease osteopetrosis, we tested it as a candidate gene for oc. The segregation of fra-1 in two different crosses of mice carrying oc and an allelism test between oc and a targeted disruption of fra-1 demonstrate that fra-1 and oc are two distinct genes rather than oc being a mutant allele of fra-1.","authors":"Schreiber, M., Poirier, C., Franchi, A., Kurzbauer, R., Guenet, JL., Carle, GF., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Oncogene","volume":"15","issue":"10","page":"1171-8","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26605529","title":"A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance.","abstract":"T-cell receptor (TCR) signalling has a key role in determining T-cell fate. Precursor cells expressing TCRs within a certain low-affinity range for complexes of self-peptide and major histocompatibility complex (MHC) undergo positive selection and differentiate into naive T cells expressing a highly diverse self-MHC-restricted TCR repertoire. In contrast, precursors displaying TCRs with a high affinity for 'self' are either eliminated through TCR-agonist-induced apoptosis (negative selection) or restrained by regulatory T (Treg) cells, whose differentiation and function are controlled by the X-chromosome-encoded transcription factor Foxp3 (reviewed in ref. 2). Foxp3 is expressed in a fraction of self-reactive T cells that escape negative selection in response to agonist-driven TCR signals combined with interleukin 2 (IL-2) receptor signalling. In addition to Treg cells, TCR-agonist-driven selection results in the generation of several other specialized T-cell lineages such as natural killer T cells and innate mucosal-associated invariant T cells. Although the latter exhibit a restricted TCR repertoire, Treg cells display a highly diverse collection of TCRs. Here we explore in mice whether a specialized mechanism enables agonist-driven selection of Treg cells with a diverse TCR repertoire, and the importance this holds for self-tolerance. We show that the intronic Foxp3 enhancer conserved noncoding sequence 3 (CNS3) acts as an epigenetic switch that confers a poised state to the Foxp3 promoter in precursor cells to make Treg cell lineage commitment responsive to a broad range of TCR stimuli, particularly to suboptimal ones. CNS3-dependent expansion of the TCR repertoire enables Treg cells to control self-reactive T cells effectively, especially when thymic negative selection is genetically impaired. Our findings highlight the complementary roles of these two main mechanisms of self-tolerance.","authors":"Feng, Y., van der Veeken, J., Shugay, M., Putintseva, EV., Osmanbeyoglu, HU., Dikiy, S., Hoyos, BE., Moltedo, B., Hemmers, S., Treuting, P., Leslie, CS., Chudakov, DM., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nature","volume":"528","issue":"7580","page":"132-136","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14706509","title":"Molecular aspects of epithelial cell plasticity: implications for local tumor invasion and metastasis.","abstract":"Carcinomas arising from epithelial cells represent the most prevalent malignancies in humans, and metastasis is the major cause for the death of carcinoma patients. The breakdown of epithelial cell homeostasis leading to aggressive cancer progression has been correlated with the loss of epithelial characteristics and the acquisition of a migratory phenotype. This phenomenon, referred to as epithelial to mesenchymal transition (EMT), is considered as a crucial event in late stage tumorigenesis. Here we summarize the multitude of EMT models derived from different tissues, and review the diversity of molecular mechanisms contributing to the plasticity of epithelial cells. In particular, the synergism between activation of Ras, provided by the aberrant stimulation of receptor tyrosine kinases, and transforming growth factor (TGF)-beta signaling plays a pivotal role in inducing EMT of various epithelial cell types. Cytokines such as TGF-beta and extracellular matrix molecules are thought to fundamentally contribute to the microenvironmental interaction between stromal and malignant cells, and provide the basis for a broad repertoire of epithelial differentiation. Investigations of EMT tumor models, which represent in vitro correlates to local invasion and metastasis in vivo, facilitate the identification of diagnostic markers for a more accurate and faithful clinical and pathological assessment of epithelial tumors. In addition, the analysis of molecular mechanisms involved in EMT might yield novel therapeutic targets for the specific treatment of aggressive carcinomas.","authors":"Gotzmann, J., Mikula, M., Eger, A., Schulte-Hermann, R., Foisner, R., Beug, H., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Mutat Res","volume":"566","issue":"1","page":"9-20","pdf":null,"JrId":"5976","fulltextlink":null,"preprintlink":null,"articledate":"2004-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33098150","title":"MKK7 deficiency in mature neurons impairs parental behavior in mice.","abstract":"c-Jun N-terminal kinases (JNKs) are constitutively activated in mammalian brains and are indispensable for their development and neural functions. MKK7 is an upstream activator of all JNKs. However, whether the common JNK signaling pathway regulates the brain's control of social behavior remains unclear. Here, we show that female mice in which Mkk7 is deleted specifically in mature neurons (Mkk7<sup>flox\/flox<\/sup> Syn-Cre mice) give birth to a normal number of pups but fail to raise them due to a defect in pup retrieval. To explore the mechanism underlying this abnormality, we performed comprehensive behavioral tests. Mkk7<sup>flox\/flox<\/sup> Syn-Cre mice showed normal locomotor functions and cognitive ability but exhibited depression-like behavior. cDNA microarray analysis of mutant brain revealed an altered gene expression pattern. Quantitative RT-PCR analysis demonstrated that mRNA expression levels of genes related to neural signaling pathways and a calcium channel were significantly different from controls. In addition, loss of neural MKK7 had unexpected regulatory effects on gene expression patterns in oligodendrocytes. These findings indicate that MKK7 has an important role in regulating the gene expression patterns responsible for promoting normal social behavior and staving off depression.","authors":"Shin, T., Hiraoka, Y., Yamasaki, T., Marth, JD., Penninger, JM., Kanai-Azuma, M., Tanaka, K., Kofuji, S., Nishina, H.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Genes Cells","volume":"26","issue":"1","page":"5-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9288745","title":"Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs.","abstract":"In eukaryotic cells, firing of DNA replication origins normally does not recur until after M phase. This characteristic is thought to be due to the properties of \"initiation\" proteins like Orc, Cdc6, and Mcms. Using formaldehyde cross-linking, we show that Cdc6p and Mcm7p associate specifically with replication origins during G1 but not during G2 in S. cerevisiae. Mcm7p's association with origins depends on Cdc6p. Ectopic expression of Cdc6p enables it to associate with origins during G2, but this fails to recruit Mcm7p. Our data suggest that the loading of Mcm proteins onto origins is regulated by two mechanisms: first, by Cdc6p occupancy, and second, by S- and M-CDKs, whose activity during S, G2, and M phases prevents Mcm loading.","authors":"Tanaka, T., Knapp, D., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Cell","volume":"90","issue":"4","page":"649-60","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1997-10-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34375000","title":"Identification of lectin receptors for conserved SARS-CoV-2 glycosylation sites.","abstract":"New SARS-CoV-2 variants are continuously emerging with critical implications for therapies or vaccinations. The 22 N-glycan sites of Spike remain highly conserved among SARS-CoV-2 variants, opening an avenue for robust therapeutic intervention. Here we used a comprehensive library of mammalian carbohydrate-binding proteins (lectins) to probe critical sugar residues on the full-length trimeric Spike and the receptor binding domain (RBD) of SARS-CoV-2. Two lectins, Clec4g and CD209c, were identified to strongly bind to Spike. Clec4g and CD209c binding to Spike was dissected and visualized in real time and at single molecule resolution using atomic force microscopy. 3D modelling showed that both lectins can bind to a glycan within the RBD-ACE2 interface and thus interferes with Spike binding to cell surfaces. Importantly, Clec4g and CD209c significantly reduced SARS-CoV-2 infections. These data report the first extensive map and 3D structural modelling of lectin-Spike interactions and uncovers candidate receptors involved in Spike binding and SARS-CoV-2 infections. The capacity of CLEC4G and mCD209c lectins to block SARS-CoV-2 viral entry holds promise for pan-variant therapeutic interventions.","authors":"Hoffmann, D., Mereiter, S., Jin Oh, Y., Monteil, V., Elder, E., Zhu, R., Canena, D., Hain, L., Laurent, E., Gr\u00fcnwald-Gruber, C., Klausberger, M., Jonsson, G., Kellner, MJ., Novatchkova, M., Ticevic, M., Chabloz, A., Wirnsberger, G., Hagelkruys, A., Altmann, F., Mach, L., Stadlmann, J., Oostenbrink, C., Mirazimi, A., Hinterdorfer, P., Penninger, JM.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"EMBO J","volume":null,"issue":null,"page":"e108375","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33623882","title":"Precision Medicine in Hematology 2021: Definitions, Tools, Perspectives, and Open Questions.","abstract":"During the past few years, our understanding of molecular mechanisms and cellular interactions relevant to malignant blood cell disorders has improved substantially. New insights include a detailed knowledge about disease-initiating exogenous factors, endogenous (genetic, somatic, epigenetic) elicitors or facilitators of disease evolution, and drug actions and interactions that underlie efficacy and adverse event profiles in defined cohorts of patients. As a result, precision medicine and personalized medicine are rapidly growing new disciplines that support the clinician in making the correct diagnosis, in predicting outcomes, and in optimally selecting patients for interventional therapies. In addition, precision medicine tools are greatly facilitating the development of new drugs, therapeutic approaches, and new multiparametric prognostic scoring models. However, although the emerging roles of precision medicine and personalized medicine in hematology and oncology are clearly visible, several questions remain. For example, it remains unknown how precision medicine tools can be implemented in healthcare systems and whether all possible approaches are also affordable. In addition, there is a need to define terminologies and to relate these to specific and context-related tools and strategies in basic and applied science. To discuss these issues, a working conference was organized in September 2019. The outcomes of this conference are summarized herein and include a proposal for definitions, terminologies, and applications of precision and personalized medicine concepts and tools in hematologic neoplasms. We also provide proposals aimed at reducing costs, thereby making these applications affordable in daily practice.","authors":"Valent, P., Orfao, A., Kubicek, S., Staber, P., Haferlach, T., Deininger, M., Kollmann, K., Lion, T., Virgolini, I., Winter, G., Hantschel, O., Kenner, L., Zuber, J., Grebien, F., Moriggl, R., Hoermann, G., Hermine, O., Andreeff, M., Bock, C., Mughal, T., Constantinescu, SN., Kralovics, R., Sexl, V., Skoda, R., Superti-Furga, G., J\u00e4ger, U.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Hemasphere","volume":"5","issue":"3","page":"e536","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33833428","title":"The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W.","abstract":"Mobile transposable elements (TEs) not only participate in genome evolution but also threaten genome integrity. In healthy cells, TEs that encode all of the components that are necessary for their mobility are specifically silenced, yet the precise mechanism remains unknown. Here, we characterize the mechanism used by a conserved class of chromatin remodelers that prevent TE mobility. In the Arabidopsis chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), we identify two conserved binding domains for the histone variant H2A.W, which marks plant heterochromatin. DDM1 is necessary and sufficient for the deposition of H2A.W onto potentially mobile TEs, yet does not act on TE fragments or host protein-coding genes. DDM1-mediated H2A.W deposition changes the properties of chromatin, resulting in the silencing of TEs and, therefore, prevents their mobility. This distinct mechanism provides insights into the interplay between TEs and their host in the contexts of evolution and disease, and potentiates innovative strategies for targeted gene silencing.","authors":"Osakabe, A., Jamge, B., Axelsson, E., Montgomery, SA., Akimcheva, S., Kuehn, AL., Pisupati, R., Lorkovi\u0107, ZJ., Yelagandula, R., Kakutani, T., Berger, F.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Cell Biol","volume":"23","issue":"4","page":"391-400","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16903854","title":"Postnatal development of the murine cerebellar cortex: formation and early dispersal of basket, stellate and Golgi neurons.","abstract":"The cerebellar cortex consists of a small set of neuronal cell types interconnected in a highly stereotyped way. While the development of cerebellar cortical projection neurons, i.e. Purkinje cells, and that of granule cells has been elucidated in considerable detail, that of cerebellar cortical inhibitory interneurons is still rather fragmentarily understood. Here, we use mice expressing green fluorescent protein (GFP) from the Pax2 locus to analyse the ontogenesis of these cells. Numbers of Pax2-positive inhibitory interneuronal precursors increase following a classical sigmoidal growth curve to yield a total of some 905.000 +\/- 77.000 cells. Maximal cell increase occurs at about postnatal day (P)5.4, and some 75% of all inhibitory interneurons are generated prior to P7. Conjoint analysis of the developmental accruement of Pax2-GFP-positive cells and their cell cycle distribution reveals that, at least at P0 and P3, the numerical increase of these cells results primarily from proliferation of a Pax2-negative precursor population and suggests that Pax2 expression begins at or around the final mitosis. Following their terminal mitosis, inhibitory cerebellar cortical interneurons go through a protracted quiescent phase in which they maintain expression of the cell cycle marker Ki-67. During this phase, they translocate into the nascent molecular layer, where they stall next to premigratory granule cell precursors without penetrating this population of cells. These observations provide a quantitative description of cerebellar cortical inhibitory interneuron genesis and early differentiation, and define Pax2 as a marker expressed in basket and stellate cells, from around their final mitosis to their incipient histogenetic integration.","authors":"Weisheit, G., Gliem, M., Endl, E., Pfeffer, PL., Busslinger, M., Schilling, K.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Eur J Neurosci","volume":"24","issue":"2","page":"466-78","pdf":null,"JrId":"2607","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10430025","title":"Monoallelic expression of Pax5: a paradigm for the haploinsufficiency of mammalian Pax genes?","abstract":"It is generally assumed that most mammalian genes are transcribed from both alleles. Hence, the diploid state of the genome offers the advantage that a loss-of-function mutation in one allele can be compensated for by the remaining wild-type allele of the same gene. Indeed, the vast majority of human disease syndromes and engineered mutations in the mouse genome are recessive, indicating that recessiveness is the 'default' state. However, a minority of genes are semi-dominant, as heterozygous loss-of-function mutation in these genes leads to phenotypic abnormalities. This condition, known as haploinsufficiency, has been described for five of the nine mammalian Pax genes, which are associated with mouse developmental mutants and human disease syndromes. Recently we have reported that the Pax5 gene is subject to allele-specific regulation during B cell development. Pax5 is predominantly transcribed from only one of its two alleles in early B-lymphoid progenitors and mature B cells, while it transiently switches to a biallelic mode of transcription in pre-B and immature B cells. As a consequence, B-lymphoid tissues are mosaic with regard to the transcribed allele, and heterozygous mutation of Pax5 therefore results in deletion of B lymphocytes expressing only the mutant allele. The allele-specific regulation of Pax5 raises the intriguing possibility that monoallelic expression may also be the mechanism causing the haploinsufficiency of other Pax genes. In this review, we discuss different models accounting for the haploinsufficiency of mammalian Pax genes, provide further evidence in support of the allele-specific regulation of Pax5 and discuss the implication of these findings in the context of the recent literature describing the stochastic and monoallelic activation of other hematopoietic genes.","authors":"Nutt, SL., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Biol Chem","volume":"380","issue":"6","page":"601-11","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9264411","title":"Mechanism of transformation by v-ErbA: substitution for steroid hormone receptor function in self renewal induction.","abstract":"V-ErbA, a mutated thyroid hormone receptor (TR) alpha cooperates with tyrosine kinase oncoproteins to induce fatal erythroleukemia in chicks. In vitro, v-ErbA employs a similar cooperation to induce sustained proliferation and arrest differentiation of committed erythroid progenitors. V-ErbA has been proposed to function as a dominant-negative c-ErbA\/TR alpha, since it lacks an AF-2 transactivation domain and cannot be activated by hormone but retains the capacity to bind corepressors. However, v-ErbA fails to heterodimerize with the coreceptor RXR, exhibits an altered DNA binding specificity and fails to suppress the action of coexpressed TR alpha\/c-ErbA in erythroblasts. In this paper, we identify a novel mechanism by which v-ErbA contributes to leukemogenesis. Recently, the glucocorticoid receptor (GR) was identified as a key regulator of proliferation and differentiation in normal erythroid progenitors. For this, the GR required to cooperate with endogenous receptor tyrosine kinases (c-Kit) and with the estrogen receptor (ER). Here, we demonstrate that v-ErbA can substitute for the ligand-activated GR and ER, inducing proliferation and arresting differentiation in the presence of specific GR and ER antagonists. Like the GR, v-ErbA required to cooperate with c-Kit for both proliferation induction and differentiation arrest, being devoid of biological activity in the absence of an active c-Kit. In self-renewing erythroblasts, v-ErbA not only repressed known v-ErbA target genes but also maintained high expression of c-myb. These biological activities of v-ErbA depended on distinct mutations in the DNA-binding domain. Additionally, v-ErbA acted as a partial, weak repressor of c-ErbA\/TR alpha function in normal erythroblasts. It could be converted into a truly dominant-negative receptor by restoring its ability to heterodimerize with RXR.","authors":"Bauer, A., Ulrich, E., Andersson, M., Beug, H., von Lindern, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Oncogene","volume":"15","issue":"6","page":"701-15","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1997-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25672759","title":"miR-182 is largely dispensable for adaptive immunity: lack of correlation between expression and function.","abstract":"MicroRNA (miR)-mediated regulation of protein abundance is a pervasive mechanism of directing cellular processes. The well-studied and abundant miR-182 has previously been implicated in many aspects of T cell function, DNA repair, and cancer. In this study, we show that miR-182 is the most highly induced miR in B cells undergoing class-switch recombination. To elucidate the requirement of miR-182 in lymphocyte function, we extensively characterized mice with a targeted deletion of Mir182. We show that despite its dramatic induction, loss of miR-182 has minimal impact on B cell development, the ability of B cells to undergo class-switch recombination ex vivo and to undergo Ag-driven affinity maturation in vivo. Furthermore, in striking contrast to knockdown studies that demonstrated the requirement of miR-182 in T cell function, miR-182-deficient mice display no defect in T cell development and activation. Finally, we show that T cell-dependent immune response to experimental Listeria monocytogenes infection is intact in miR-182-deficient mice. We conclude that, contrary to previous studies, miR-182 does not play a significant role in all measured aspects of mouse adaptive immunity. This striking absence of a phenotype highlights the lack of correlation between expression pattern and functional requirement, underscores the limitations of using knockdown approaches to assess miR requirements, and suggests that miR networks may compensate for the chronic loss of specific miRs.","authors":"Pucella, JN., Yen, WF., Kim, MV., van der Veeken, J., Luo, CT., Socci, ND., Naito, Y., Li, MO., Iwai, N., Chaudhuri, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Immunol","volume":"194","issue":"6","page":"2635-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9232781","title":"Canine tumour suppressor gene p53--mutation in a case of adenoma of circumanal glands.","abstract":"Highly conserved regions of the tumour suppressor gene p53, including the typical human tumour hot spots (codons 175, 245, 248, 249, 273 and 282), were investigated in various canine neoplasms. A mutation CGG--&gt;TGG (arginine--&gt;tryptophan) was detected in codon 249 in an adenoma of the circumanal gland.","authors":"Mayr, B., Schaffner, W., Botto, I., Reifinger, M., Loupal, G.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Vet Res Commun","volume":"21","issue":"5","page":"369-73","pdf":null,"JrId":"7996","fulltextlink":null,"preprintlink":null,"articledate":"1997-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9155022","title":"The heat shock protein 83 (Hsp83) is required for Raf-mediated signalling in Drosophila.","abstract":"The heat shock protein Hsp90 has been shown to associate with various cellular signalling proteins such as steroid hormone receptors, src-like kinases and the serine\/threonine kinase Raf. While the interaction between steroid hormone receptors and Hsp90 appears to be essential for ligand binding and activation of the receptors, the role of Hsp90 in Raf activation is less clear. We have identified mutations in the hsp83 gene, the Drosophila homologue of hsp90, in a search for dominant mutations that attenuate signalling from Raf in the developing eye. The mutations result in single amino acid substitutions in the Hsp83 protein and cause a dominant-negative effect on the function of the wild-type protein. We show that both wild-type and mutant forms of Hsp83 bind to the activated Drosophila Raf but the mutant Hsp83 protein causes a reduction in the kinase activity of Raf. Our results indicate that Hsp83 is essential for Raf function in vivo.","authors":"van der Straten, A., Rommel, C., Dickson, B., Hafen, E.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"EMBO J","volume":"16","issue":"8","page":"1961-9","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25126783","title":"Control of the inheritance of regulatory T cell identity by a cis element in the Foxp3 locus.","abstract":"In multicellular organisms, specialized functions are delegated to distinct cell types whose identity and functional integrity are maintained upon challenge. However, little is known about the mechanisms enabling lineage inheritance and their biological implications. Regulatory T (Treg) cells, which express the transcription factor Foxp3, suppress fatal autoimmunity throughout the lifespan of animals. Here, we show that a dedicated Foxp3 intronic element CNS2 maintains Treg cell lineage identity by acting as a sensor of the essential Treg cell growth factor IL-2 and its downstream target STAT5. CNS2 sustains Foxp3 expression during division of mature Treg cells when IL-2 is limiting and counteracts proinflammatory cytokine signaling that leads to the loss of Foxp3. CNS2-mediated stable inheritance of Foxp3 expression is critical for adequate suppression of diverse types of chronic inflammation by Treg cells and prevents their differentiation into inflammatory effector cells. The described mechanism may represent a general principle of the inheritance of differentiated cell states.","authors":"Feng, Y., Arvey, A., Chinen, T., van der Veeken, J., Gasteiger, G., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell","volume":"158","issue":"4","page":"749-763","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16890534","title":"Live-cell imaging reveals a stable cohesin-chromatin interaction after but not before DNA replication.","abstract":"Cohesin is a multisubunit protein complex that links sister chromatids from replication until segregation. The lack of obvious cohesin-targeting-specific sequences on DNA, as well as cohesin's molecular arrangement as a large ring, has led to the working hypothesis that cohesin acts as a direct topological linker. To preserve the identity of sister chromatids, such a linkage would need to stably persist throughout the entire S and G2 phases of the cell cycle. Unexpectedly, cohesin binds chromatin already in telophase, and a large fraction dissociates from chromosomes during prophase in a phosphorylation-dependent manner, whereas initiation of anaphase requires proteolytic cleavage of only a small fraction of cohesin. These observations raised the question of how and when cohesin interacts with chromatin during the cell cycle. Here, we report a cell-cycle dependence in the stability of cohesin binding to chromatin. Using photobleaching and quantitative live-cell imaging, we identified several cohesin pools with different chromatin binding stabilities. Although all chromatin bound cohesin dissociated after a mean residence time of less than 25 min before replication, about one-third of cohesin was bound much more stably after S phase and persisted until metaphase, consistent with long-lived links mediating cohesion between sister chromatids.","authors":"Gerlich, D., Koch, B., Dupeux, F., Peters, JM., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr Biol","volume":"16","issue":"15","page":"1571-8","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33852321","title":"MS Annika: A New Cross-Linking Search Engine.","abstract":"Cross-linking mass spectrometry (XL-MS) has become a powerful technique that enables insights into protein structures and protein interactions. The development of cleavable cross-linkers has further promoted XL-MS through search space reduction, thereby allowing for proteome-wide studies. These new analysis possibilities foster the development of new cross-linkers, which not every search engine can deal with out of the box. In addition, some search engines for XL-MS data also struggle with the validation of identified cross-linked peptides, that is, false discovery rate (FDR) estimation, as FDR calculation is hampered by the fact that not only one but two peptides in a single spectrum have to be correct. We here present our new search engine, MS Annika, which can identify cross-linked peptides in MS2 spectra from a wide variety of cleavable cross-linkers. We show that MS Annika provides realistic estimates of FDRs without the need of arbitrary score cutoffs, being able to provide on average 44% more identifications at a similar or better true FDR than comparable tools. In addition, MS Annika can be used on proteome-wide studies due to fast, parallelized processing and provides a way to visualize the identified cross-links in protein 3D structures.","authors":"Pirklbauer, GJ., Stieger, CE., Matzinger, M., Winkler, S., Mechtler, K., Dorfer, V.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Proteome Res","volume":"20","issue":"5","page":"2560-2569","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24733379","title":"Transcriptional control of regulatory T-cell differentiation.","abstract":"Regulatory T (Treg) cells are essential for maintaining peripheral tolerance and for limiting excessive inflammatory responses under various conditions. The lineage-specific transcription factor Foxp3 has a critical role in Treg-cell biology. Foxp3 forms large protein complexes and cooperates with environmentally induced transcription factors to shape the Treg-cell transcriptional program. Here, we discuss mechanisms of gene regulation that underlie Treg-cell differentiation and function with an emphasis on studies from our laboratory.","authors":"van der Veeken, J., Arvey, A., Rudensky, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"78","issue":null,"page":"215-22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34252074","title":"Caenorhabditis elegans RMI2 functional homolog-2 (RMIF-2) and RMI1 (RMH-1) have both overlapping and distinct meiotic functions within the BTR complex.","abstract":"Homologous recombination is a high-fidelity repair pathway for DNA double-strand breaks employed during both mitotic and meiotic cell divisions. Such repair can lead to genetic exchange, originating from crossover (CO) generation. In mitosis, COs are suppressed to prevent sister chromatid exchange. Here, the BTR complex, consisting of the Bloom helicase (HIM-6 in worms), topoisomerase 3 (TOP-3), and the RMI1 (RMH-1 and RMH-2) and RMI2 scaffolding proteins, is essential for dismantling joint DNA molecules to form non-crossovers (NCOs) via decatenation. In contrast, in meiosis COs are essential for accurate chromosome segregation and the BTR complex plays distinct roles in CO and NCO generation at different steps in meiotic recombination. RMI2 stabilizes the RMI1 scaffolding protein, and lack of RMI2 in mitosis leads to elevated sister chromatid exchange, as observed upon RMI1 knockdown. However, much less is known about the involvement of RMI2 in meiotic recombination. So far, RMI2 homologs have been found in vertebrates and plants, but not in lower organisms such as Drosophila, yeast, or worms. We report the identification of the Caenorhabditis elegans functional homolog of RMI2, which we named RMIF-2. The protein shows a dynamic localization pattern to recombination foci during meiotic prophase I and concentration into recombination foci is mutually dependent on other BTR complex proteins. Comparative analysis of the rmif-2 and rmh-1 phenotypes revealed numerous commonalities, including in regulating CO formation and directing COs toward chromosome arms. Surprisingly, the prevalence of heterologous recombination was several fold lower in the rmif-2 mutant, suggesting that RMIF-2 may be dispensable or less strictly required for some BTR complex-mediated activities during meiosis.","authors":"Velkova, M., Silva, N., Dello Stritto, MR., Schleiffer, A., Barraud, P., Hartl, M., Jantsch, V.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"PLoS Genet","volume":"17","issue":"7","page":"e1009663","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-166","title":"E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP","abstract":null,"authors":"Ahel J, Fletcher A, Grabarczyk DB, Roitinger E, Deszcz L, Lehner A, Virdee S, Clausen T. ","publication_status":"preprint","journalpubyear":"2021","journaltitle":"bioRxiv","volume":"2021.05.10.443411","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.05.10.443411v1","preprintlink":null,"articledate":"2021-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33847896","title":"Terminal \u03b12,6-sialylation of epidermal growth factor receptor modulates antibody therapy response of colorectal cancer cells.","abstract":"on Status=\"In-Process\" Owner=\"NLM\"><PMID Version=\"1\">33847896<\/PMID><DateRevised><Year>2021<\/Year><Month>08<\/Month><Day>05<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">2211-3436<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>44<\/Volume><Issue>4<\/Issue><PubDate><Year>2021<\/Year><Month>Aug<\/Month><\/PubDate><\/JournalIssue><Title>Cellular oncology (Dordrecht)<\/Title><ISOAbbreviation>Cell Oncol (Dordr)<\/ISOAbbreviation><\/Journal><ArticleTitle>Terminal \u03b12,6-sialylation of epidermal growth factor receptor modulates antibody therapy response of colorectal cancer cells.<\/ArticleTitle><Pagination><MedlinePgn>835-850<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s13402-021-00606-z<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The epidermal growth factor receptor (EGFR) is a key protein involved in cancer development. Monoclonal antibodies targeting EGFR are approved for the treatment of metastatic colorectal cancer (CRC). Despite the beneficial clinical effects observed in subgroups of patients, the acquisition of resistance to treatment remains a major concern. Protein N-glycosylation of cellular receptors is known to regulate physiological processes leading to activation of downstream signaling pathways. In the present study, the role of EGFR-specific terminal \u237a2,6-sialylation was analyzed in modulation of the malignant phenotype of CRC cells and their resistance to monoclonal antibody Cetuximab-based therapy.","authors":"Rodrigues, JG., Duarte, HO., Gomes, C., Balma\u00f1a, M., Martins, \u00c1M., Hensbergen, PJ., de Ru, AH., Lima, J., Albergaria, A., van Veelen, PA., Wuhrer, M., Gomes, J., Reis, CA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell Oncol (Dordr)","volume":"44","issue":"4","page":"835-850","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33215740","title":"Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling.","abstract":"HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), is a critical regulator of inflammation. However, how HOIP itself is regulated to control inflammatory responses is unclear. Here, we discover that site-specific ubiquitination of K784 within human HOIP promotes tumor necrosis factor (TNF)-induced inflammatory signaling. A HOIP K784R mutant is catalytically active but shows reduced induction of an NF-\u03baB reporter relative to wild-type HOIP. HOIP K784 is evolutionarily conserved, equivalent to HOIP K778 in mice. We generated Hoip<sup>K778R\/K778R<\/sup> knock-in mice, which show no overt developmental phenotypes; however, in response to TNF, Hoip<sup>K778R\/K778R<\/sup> mouse embryonic fibroblasts display mildly suppressed NF-\u03baB activation and increased apoptotic markers. On the other hand, HOIP K778R enhances the TNF-induced formation of TNFR complex II and an interaction between TNFR complex II and LUBAC. Loss of the LUBAC component SHARPIN leads to embryonic lethality in Hoip<sup>K778R\/K778R<\/sup> mice, which is rescued by knockout of TNFR1. We propose that site-specific ubiquitination of HOIP regulates a LUBAC-dependent switch between survival and apoptosis in TNF signaling.","authors":"Fennell, LM., Gomez Diaz, C., Deszcz, L., Kavirayani, A., Hoffmann, D., Yanagitani, K., Schleiffer, A., Mechtler, K., Hagelkruys, A., Penninger, J., Ikeda, F.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"EMBO J","volume":"39","issue":"24","page":"e103303","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33852883","title":"Unraveling the Developmental Roadmap toward Human Brown AdiposeTissue.","abstract":null,"authors":"Carobbio, S., Guenantin, AC., Bahri, M., Rodriguez-Fdez, S., Honig, F., Kamzolas, I., Samuelson, I., Long, K., Awad, S., Lukovic, D., Erceg, S., Bassett, A., Mendjan, S., Vallier, L., Rosen, BS., Chiarugi, D., Vidal-Puig, A.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Stem Cell Reports","volume":"16","issue":"4","page":"1010","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24728351","title":"Inflammation-induced repression of chromatin bound by the transcription factor Foxp3 in regulatory T cells.","abstract":"The transcription factor Foxp3 is indispensable for the ability of regulatory T cells (Treg cells) to suppress fatal inflammation. Here we characterized the role of Foxp3 in chromatin remodeling and the regulation of gene expression in actively suppressive Treg cells in an inflammatory setting. Although genome-wide occupancy of regulatory elements in DNA by Foxp3 was similar in resting Treg cells and those activated in vivo, Foxp3-bound enhancer elements in the DNA were poised for repression only in activated Treg cells. Following activation, Foxp3-bound sites showed diminished accessibility of chromatin and selective deposition of histone H3 trimethylated at Lys27 (H3K27me3), which was associated with recruitment of the histone methyltransferase Ezh2 and downregulation of the expression of nearby genes. Thus, Foxp3 poises its targets for repression by facilitating the formation of repressive chromatin in Treg cells upon their activation in response to inflammatory cues.","authors":"Arvey, A., van der Veeken, J., Samstein, RM., Feng, Y., Stamatoyannopoulos, JA., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Immunol","volume":"15","issue":"6","page":"580-587","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34155263","title":"A genome-wide CRISPR\/Cas9 screen to identify phagocytosis modulators in monocytic THP-1 cells.","abstract":"Phagocytosis of microbial pathogens, dying or dead cells, and cell debris is essential to maintain tissue homeostasis. Impairment of these processes is associated with autoimmunity, developmental defects and toxic protein accumulation. However, the underlying molecular mechanisms of phagocytosis remain incompletely understood. Here, we performed a genome-wide CRISPR knockout screen to systematically identify regulators involved in phagocytosis of Staphylococcus (S.) aureus by human monocytic THP-1 cells. The screen identified 75 hits including known regulators of phagocytosis, e.g. members of the actin cytoskeleton regulation Arp2\/3 and WAVE complexes, as well as genes previously not associated with phagocytosis. These novel genes are involved in translational control (EIF5A and DHPS) and the UDP glycosylation pathway (SLC35A2, SLC35A3, UGCG and UXS1) and were further validated by single gene knockout experiments. Whereas the knockout of EIF5A and DHPS impaired phagocytosis, knocking out SLC35A2, SLC35A3, UGCG and UXS1 resulted in increased phagocytosis. In addition to S. aureus phagocytosis, the above described genes also modulate phagocytosis of Escherichia coli and yeast-derived zymosan A. In summary, we identified both known and unknown genetic regulators of phagocytosis, the latter providing a valuable resource for future studies dissecting the underlying molecular and cellular mechanisms and their role in human disease.","authors":"Lindner, B., Martin, E., Steininger, M., Bundalo, A., Lenter, M., Zuber, J., Schuler, M.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Sci Rep","volume":"11","issue":"1","page":"12973","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34127787","title":"Central amygdala circuitry modulates nociceptive processing through differential hierarchical interaction with affective network dynamics.","abstract":"The central amygdala (CE) emerges as a critical node for affective processing. However, how CE local circuitry interacts with brain wide affective states is yet uncharted. Using basic nociception as proxy, we find that gene expression suggests diverging roles of the two major CE neuronal populations, protein kinase C \u03b4-expressing (PKC\u03b4<sup>+<\/sup>) and somatostatin-expressing (SST<sup>+<\/sup>) cells. Optogenetic (o)fMRI demonstrates that PKC\u03b4<sup>+<\/sup>\/SST<sup>+<\/sup> circuits engage specific separable functional subnetworks to modulate global brain dynamics by a differential bottom-up vs. top-down hierarchical mesoscale mechanism. This diverging modulation impacts on nocifensive behavior and may underly CE control of affective processing.","authors":"Wank, I., Pliota, P., Badurek, S., Kraitsy, K., Kaczanowska, J., Griessner, J., Kreitz, S., Hess, A., Haubensak, W.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Commun Biol","volume":"4","issue":"1","page":"732","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31463991","title":"The H3 histone chaperone NASP<sup>SIM3<\/sup> escorts CenH3 in Arabidopsis.","abstract":"Centromeres define the chromosomal position where kinetochores form to link the chromosome to microtubules during mitosis and meiosis. Centromere identity is determined by incorporation of a specific histone H3 variant termed CenH3. As for other histones, escort and deposition of CenH3 must be ensured by histone chaperones, which handle the non-nucleosomal CenH3 pool and replenish CenH3 chromatin in dividing cells. Here, we show that the Arabidopsis orthologue of the mammalian NUCLEAR AUTOANTIGENIC SPERM PROTEIN (NASP) and Schizosaccharomyces pombe histone chaperone Sim3 is a soluble nuclear protein that binds the histone variant CenH3 and affects its abundance at the centromeres. NASP<sup>SIM3<\/sup> is co-expressed with Arabidopsis CenH3 in dividing cells and binds directly to both the N-terminal tail and the histone fold domain of non-nucleosomal CenH3. Reduced NASP<sup>SIM3<\/sup> expression negatively affects CenH3 deposition, identifying NASP<sup>SIM3<\/sup> as a CenH3 histone chaperone.","authors":"Le Goff, S., Ke\u00e7eli, BN., Je\u0159\u00e1bkov\u00e1, H., Heckmann, S., Rutten, T., Cotterell, S., Schubert, V., Roitinger, E., Mechtler, K., Franklin, FCH., Tatout, C., Houben, A., Geelen, D., Probst, AV., Lermontova, I.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Plant J","volume":"101","issue":"1","page":"71-86","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33938624","title":"Ub and Dub of RNF43\/ZNRF3 in the WNT signalling pathway.","abstract":"The E3 ubiquitin ligases RING finger protein 43 (RNF43) and zinc and RING finger 3 (ZNRF3) have received great attention for their critical role in regulating WNT signalling during adult stem cell homeostasis. By promoting the turnover of WNT receptors, Frizzled and LRP5\/6, RNF43 and ZNRF3 ensure that proper levels of WNT activity are maintained in stem cells. The molecular mechanism of RNF43\/ZNRF3 activity is beginning to emerge from several recent studies, yet little is known about the regulation of RNF43\/ZNRF3 at the post-translational level. A study in this issue of EMBO Reports identifies the deubiquitinating enzyme USP42 as a key regulator of WNT signalling, which acts by antagonizing the ubiquitin-dependent clearance of RNF43\/ZNRF3 induced by R-spondins (Giebel et al, 2021).","authors":"Colozza, G., Koo, BK.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"EMBO Rep","volume":"22","issue":"5","page":"e52970","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34035246","title":"Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq.","abstract":"The COVID-19 pandemic has demonstrated the need for massively-parallel, cost-effective tests monitoring viral spread. Here we present SARSeq, saliva analysis by RNA sequencing, a method to detect SARS-CoV-2 and other respiratory viruses on tens of thousands of samples in parallel. SARSeq relies on next generation sequencing of multiple amplicons generated in a multiplexed RT-PCR reaction. Two-dimensional, unique dual indexing, using four indices per sample, enables unambiguous and scalable assignment of reads to individual samples. We calibrate SARSeq on SARS-CoV-2 synthetic RNA, virions, and hundreds of human samples of various types. Robustness and sensitivity were virtually identical to quantitative RT-PCR. Double-blinded benchmarking to gold standard quantitative-RT-PCR performed by human diagnostics laboratories confirms this high sensitivity. SARSeq can be used to detect Influenza A and B viruses and human rhinovirus in parallel, and can be expanded for detection of other pathogens. Thus, SARSeq is ideally suited for differential diagnostic of infections during a pandemic.","authors":"Yelagandula, R., Bykov, A., Vogt, A., Heinen, R., \u00d6zkan, E., Strobl, MM., Baar, JC., Uzunova, K., Hajdusits, B., Kordic, D., Suljic, E., Kurtovic-Kozaric, A., Izetbegovic, S., Schaeffer, J., Hufnagl, P., Zoufaly, A., Seitz, T., F\u00f6dinger, M., Allerberger, F., Stark, A., Cochella, L., Elling, U.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"3132","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29396393","title":"UFD-2 is an adaptor-assisted E3 ligase targeting unfolded proteins.","abstract":"Muscle development requires the coordinated activities of specific protein folding and degradation factors. UFD-2, a U-box ubiquitin ligase, has been reported to play a central role in this orchestra regulating the myosin chaperone UNC-45. Here, we apply an integrative in vitro and in vivo approach to delineate the substrate-targeting mechanism of UFD-2 and elucidate its distinct mechanistic features as an E3\/E4 enzyme. Using Caenorhabditis elegans as model system, we demonstrate that UFD-2 is not regulating the protein levels of UNC-45 in muscle cells, but rather shows the characteristic properties of a bona fide E3 ligase involved in protein quality control. Our data demonstrate that UFD-2 preferentially targets unfolded protein segments. Moreover, the UNC-45 chaperone can serve as an adaptor protein of UFD-2 to poly-ubiquitinate unfolded myosin, pointing to a possible role of the UFD-2\/UNC-45 pair in maintaining proteostasis in muscle cells.","authors":"Hellerschmied, D., Roessler, M., Lehner, A., Gazda, L., Stejskal, K., Imre, R., Mechtler, K., Dammermann, A., Clausen, T.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Nat Commun","volume":"9","issue":"1","page":"484","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24226773","title":"Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation.","abstract":"Intestinal microbes provide multicellular hosts with nutrients and confer resistance to infection. The delicate balance between pro- and anti-inflammatory mechanisms, essential for gut immune homeostasis, is affected by the composition of the commensal microbial community. Regulatory T cells (Treg cells) expressing transcription factor Foxp3 have a key role in limiting inflammatory responses in the intestine. Although specific members of the commensal microbial community have been found to potentiate the generation of anti-inflammatory Treg or pro-inflammatory T helper 17 (TH17) cells, the molecular cues driving this process remain elusive. Considering the vital metabolic function afforded by commensal microorganisms, we reasoned that their metabolic by-products are sensed by cells of the immune system and affect the balance between pro- and anti-inflammatory cells. We tested this hypothesis by exploring the effect of microbial metabolites on the generation of anti-inflammatory Treg cells. We found that in mice a short-chain fatty acid (SCFA), butyrate, produced by commensal microorganisms during starch fermentation, facilitated extrathymic generation of Treg cells. A boost in Treg-cell numbers after provision of butyrate was due to potentiation of extrathymic differentiation of Treg cells, as the observed phenomenon was dependent on intronic enhancer CNS1 (conserved non-coding sequence 1), essential for extrathymic but dispensable for thymic Treg-cell differentiation. In addition to butyrate, de novo Treg-cell generation in the periphery was potentiated by propionate, another SCFA of microbial origin capable of histone deacetylase (HDAC) inhibition, but not acetate, which lacks this HDAC-inhibitory activity. Our results suggest that bacterial metabolites mediate communication between the commensal microbiota and the immune system, affecting the balance between pro- and anti-inflammatory mechanisms.","authors":"Arpaia, N., Campbell, C., Fan, X., Dikiy, S., van der Veeken, J., deRoos, P., Liu, H., Cross, JR., Pfeffer, K., Coffer, PJ., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nature","volume":"504","issue":"7480","page":"451-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16821134","title":"Histone modification and the control of heterochromatic gene silencing in Drosophila.","abstract":"Covalent modifications of histones index structurally and functionally distinct chromatin domains in eukaryotic nuclei. Drosophila with its polytene chromosomes and developed genetics allows detailed cytological as well as functional analysis of epigenetic histone modifications involved in the control of gene expression pattern during development. All H3K9 mono- and dimethylation together with all H3K27 methylation states and H4K20 trimethylation are predominant marks of pericentric heterochromatin. In euchromatin, bands and interbands are differentially indexed. H3K4 and H3K36 methylation together with H3S10 phosphorylation are predominant marks of interband regions whereas in bands different H3K27 and H4K20 methylation states are combined with acetylation of H3K9 and H3K14. Genetic dissection of heterochromatic gene silencing in position-effect variegation (PEV) by Su(var) and E(var) mutations allowed identification and functional analysis of key factors controlling the formation of heterochromatin. SU(VAR)3-9 association with heterochromatic sequences followed by H3K9 methylation initiates the establishment of repressive SU(VAR)3-9\/HP1\/SU(VAR)3-7 protein complexes. Differential enzymatic activities of novel point mutants demonstrate that the silencing potential of SU(VAR)3-9 is mainly determined by the kinetic properties of the HMTase reaction. In Su(var)3-9ptn a significantly enhanced enzymatic activity results in H3K9 hypermethylation, enhanced gene silencing and extensive chromatin compaction. Mutations in factors controlling active histone modification marks revealed the dynamic balance between euchromatin and heterochromatin. Further analysis and definition of Su(var) and E(var) genes in Drosophila will increase our understanding of the molecular hierarchy of processes controlling higher-order structures in chromatin.","authors":"Ebert, A., Lein, S., Schotta, G., Reuter, G.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Chromosome Res","volume":"14","issue":"4","page":"377-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32143824","title":"Tyrosine pre-transfer RNA fragments are linked to p53-dependent neuronal cell death via PKM2.","abstract":"Fragments of transfer RNA (tRNA), derived either from pre-tRNA or mature tRNA, have been discovered to play an essential role in the pathogenesis of various disorders such as neurodegenerative disease. CLP1 is an RNA kinase involved in tRNA biogenesis, and mutations in its encoding gene are responsible for pontocerebellar hypoplasia type-10. Mutation of the CLP1 gene results in the accumulation of tRNA fragments of several different kinds. These tRNA fragments are expected to be associated with the disease pathogenesis. However, it is still unclear which of the tRNA fragments arising from the CLP1 gene mutation has the greatest impact on the onset of neuronal disease. We found that 5' tRNA fragments derived from tyrosine pre-tRNA (5' Tyr-tRF) caused p53-dependent neuronal cell death predominantly more than other types of tRNA fragment. We also showed that 5' Tyr-tRF bound directly to pyruvate kinase M2 (PKM2). Injection of zebrafish embryos with PKM2 mRNA ameliorated the neuronal defects induced in zebrafish embryos by 5' Tyr-tRF. Our findings partially uncovered a mechanistic link between 5' Tyr-tRF and neuronal cell death that is regulated by PKM2.","authors":"Inoue, M., Hada, K., Shiraishi, H., Yatsuka, H., Fujinami, H., Morisaki, I., Nishida, Y., Matsubara, E., Ishitani, T., Hanada, R., Matsumoto, M., Penninger, JM., Ihara, K., Hanada, T.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Biochem Biophys Res Commun","volume":"525","issue":"3","page":"726-732","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33179852","title":"Human soluble ACE2 improves the effect of remdesivir in SARS-CoV-2 infection.","abstract":"There is a critical need for safe and effective drugs for COVID-19. Only remdesivir has received authorization for COVID-19 and has been shown to improve outcomes but not decrease mortality. However, the dose of remdesivir is limited by hepatic and kidney toxicity. ACE2 is the critical cell surface receptor for SARS-CoV-2. Here, we investigated additive effect of combination therapy using remdesivir with recombinant soluble ACE2 (high\/low dose) on Vero E6 and kidney organoids, targeting two different modalities of SARS-CoV-2 life cycle: cell entry via its receptor ACE2 and intracellular viral RNA replication. This combination treatment markedly improved their therapeutic windows against SARS-CoV-2 in both models. By using single amino-acid resolution screening in haploid ES cells, we report a singular critical pathway required for remdesivir toxicity, namely, Adenylate Kinase 2. The data provided here demonstrate that combining two therapeutic modalities with different targets, common strategy in HIV treatment, exhibit strong additive effects at sub-toxic concentrations. Our data lay the groundwork for the study of combinatorial regimens in future COVID-19 clinical trials.","authors":"Monteil, V., Dyczynski, M., Lauschke, VM., Kwon, H., Wirnsberger, G., Youhanna, S., Zhang, H., Slutsky, AS., Hurtado Del Pozo, C., Horn, M., Montserrat, N., Penninger, JM., Mirazimi, A.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"EMBO Mol Med","volume":"13","issue":"1","page":"e13426","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34019794","title":"Cardioids reveal self-organizing principles of human cardiogenesis.","abstract":"Organoids capable of forming tissue-like structures have transformed our ability to model human development and disease. With the notable exception of the human heart, lineage-specific self-organizing organoids have been reported for all major organs. Here, we established self-organizing cardioids from human pluripotent stem cells that intrinsically specify, pattern, and morph into chamber-like structures containing a cavity. Cardioid complexity can be controlled by signaling that instructs the separation of cardiomyocyte and endothelial layers and by directing epicardial spreading, inward migration, and differentiation. We find that cavity morphogenesis is governed by a mesodermal WNT-BMP signaling axis and requires its target HAND1, a transcription factor linked to developmental heart chamber defects. Upon cryoinjury, cardioids initiated a cell-type-dependent accumulation of extracellular matrix, an early hallmark of both regeneration and heart disease. Thus, human cardioids represent a powerful platform to mechanistically dissect self-organization, congenital heart defects and serve as a foundation for future translational research.","authors":"Hofbauer, P., Jahnel, SM., Papai, N., Giesshammer, M., Deyett, A., Schmidt, C., Penc, M., Tavernini, K., Grdseloff, N., Meledeth, C., Ginistrelli, LC., Ctortecka, C., \u0160alic, \u0160., Novatchkova, M., Mendjan, S.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell","volume":"184","issue":"12","page":"3299-3317.e22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22227023","title":"Tumor-targeted Nanobullets: Anti-EGFR nanobody-liposomes loaded with anti-IGF-1R kinase inhibitor for cancer treatment.","abstract":"The epidermal growth factor receptor (EGFR) is a validated target for anti-cancer therapy and several EGFR inhibitors are used in the clinic. Over the years, an increasing number of studies have reported on the crosstalk between EGFR and other receptors that can contribute to accelerated cancer development or even acquisition of resistance to anti-EGFR therapies. Combined targeting of EGFR and insulin-like growth factor 1 receptor (IGF-1R) is a rational strategy to potentiate anti-cancer treatment and possibly retard resistance development. In the present study, we have pursued this by encapsulating the kinase inhibitor AG538 in anti-EGFR nanobody-liposomes. The thus developed dual-active nanobody-liposomes associated with EGFR-(over)expressing cells in an EGFR-specific manner and blocked both EGFR and IGF-1R activation, due to the presence of the EGFR-blocking nanobody EGa1 and the anti-IGF-1R kinase inhibitor AG538 respectively. AG538-loaded nanobody-liposomes induced a strong inhibition of tumor cell proliferation even upon short-term exposure followed by a drug-free wash-out period. Therefore, AG538-loaded nanobody-liposomes are a promising anti-cancer formulation due to efficient intracellular delivery of AG538 in combination with antagonistic and downregulating properties of the EGa1 nanobody-liposomes.","authors":"van der Meel, R., Oliveira, S., Altintas, I., Haselberg, R., van der Veeken, J., Roovers, RC., van Bergen en Henegouwen, PM., Storm, G., Hennink, WE., Schiffelers, RM., Kok, RJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Control Release","volume":"159","issue":"2","page":"281-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16857008","title":"The epigenetic magic of histone lysine methylation.","abstract":"Epigenetic mechanisms control eukaryotic development beyond DNA-stored information. There are several pathways, including histone tail modifications, histone variant incorporation, nucleosome remodelling, DNA methylation and noncoding RNAs that together all contribute to the dynamic 'make-up' of chromatin under distinct developmental options. The histone tail modifications are most variable and over 50 marks have by now been mapped. While the majority of these modifications are transient, histone lysine methylation and, in particular, a histone lysine tri-methyl state has been regarded as a more robust signal, consistent with proposed roles to impart long-term epigenetic memory. Based on the paradigm of SET-domain histone lysine methyltransferases (HMTases) and chromo-domain adaptor proteins, and in conjunction with the Sir Hans Krebs Medal 2005, I describe here my personal view on the discovery of the first HMTase in 2000, and the subsequent advances on the biology of histone lysine methylation. This discovery has changed my scientific career and significantly contributed to a better understanding of epigenetic control, with important implications for heterochromatin formation, X inactivation, Polycomb group silencing and novel insights into stem cell research, nuclear reprogramming and cancer.","authors":"Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"FEBS J","volume":"273","issue":"14","page":"3121-35","pdf":null,"JrId":"32231","fulltextlink":null,"preprintlink":null,"articledate":"2006-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20362020","title":"Downregulation of EGFR by a novel multivalent nanobody-liposome platform.","abstract":"The epidermal growth factor receptor (EGFR) is a recognized target for tumor therapy and monoclonal antibodies (mAbs, e.g. cetuximab) have been developed to inhibit receptor activation. Besides blocking ligand (e.g. EGF) binding to the receptor, reports have shown that mAbs promote slow receptor internalization and degradation in lysosomes, i.e. downregulation. The efficacy of receptor downregulation was recently shown to depend on the size of receptor clusters formed at the cell surface. In this study, a multivalent platform is presented, consisting of nanobodies recognizing the ectodomain of EGFR (EGa1) coupled to PEG-liposomes, and the in vitro and in vivo effects of this system on EGFR internalization and downregulation were investigated. Nanobodies are the smallest functional antigen-binding immunoglobulin fragments and the EGa1 nanobody has been described as an EGFR-antagonist. EGa1-liposomes (EGa1-L) induced a more than 90% removal of EGFR from the cell surface, as a result of receptor internalization. Furthermore, this massive sequestration of EGFR mediated by EGa1-L lead to receptor degradation, while no degradation was detected with the monovalent nanobody. The downregulatory capacity here reported was found to be independent of the epitope on EGFR recognized by the grafted nanobody, and exclusive to the nanobody-liposomes, as anti-EGFR single chain variable fragments (scFv) coupled to liposomes were unable to induce this effect. Importantly, EGa1-L induced a significant inhibition of tumor cell proliferation, in vitro, an effect likely mediated by the combination of receptor downregulation and receptor antagonism. Also in vivo, EGFR downregulation was observed in tumors of mice intravenously injected with EGa1-L, indicating that this multivalent platform blocks ligand binding to the receptor and simultaneously induces the downregulation of EGFR.","authors":"Oliveira, S., Schiffelers, RM., van der Veeken, J., van der Meel, R., Vongpromek, R., van Bergen En Henegouwen, PM., Storm, G., Roovers, RC.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Control Release","volume":"145","issue":"2","page":"165-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34006412","title":"Ferritinophagy and ferroptosis in the management of metabolic diseases.","abstract":"Ferroptosis is a form of regulated cell death modality associated with disturbed iron-homeostasis and unrestricted lipid peroxidation. Ample evidence has depicted an essential role for ferroptosis as either the cause or consequence for human diseases, denoting the likely therapeutic promises for targeting ferroptosis in the preservation of human health. Ferritinophagy, a selective form of autophagy, contributes to the initiation of ferroptosis through degradation of ferritin, which triggers labile iron overload (IO), lipid peroxidation, membrane damage, and cell death. In this review, we will delineate the role of ferritinophagy in ferroptosis, and its underlying regulatory mechanisms, to unveil the therapeutic value of ferritinophagy as a target in the combat of ferroptosis to manage metabolic diseases.","authors":"Ajoolabady, A., Aslkhodapasandhokmabad, H., Libby, P., Tuomilehto, J., Lip, GYH., Penninger, JM., Richardson, DR., Tang, D., Zhou, H., Wang, S., Klionsky, DJ., Kroemer, G., Ren, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Trends Endocrinol Metab","volume":"32","issue":"7","page":"444-462","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28724941","title":"Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data.","abstract":"Normalization of high-throughput small RNA sequencing (sRNA-Seq) data is required to compare sRNA levels across different samples. Commonly used relative normalization approaches can cause erroneous conclusions due to fluctuating small RNA populations between tissues. We developed a set of sRNA spike-in oligonucleotides (sRNA spike-ins) that enable absolute normalization of sRNA-Seq data across independent experiments, as well as the genome-wide estimation of sRNA:mRNA stoichiometries when used together with mRNA spike-in oligonucleotides.","authors":"Lutzmayer, S., Enugutti, B., Nodine, MD.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Sci Rep","volume":"7","issue":"1","page":"5913","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33247447","title":"Ustilago maydis effector Jsi1 interacts with Topless corepressor, hijacking plant jasmonate\/ethylene signaling.","abstract":"Ustilago maydis is the causal agent of maize smut disease. During the colonization process, the fungus secretes effector proteins that suppress immune responses and redirect the host metabolism in favor of the pathogen. As effectors play a critical role during plant colonization, their identification and functional characterization are essential to understanding biotrophy and disease. Using biochemical, molecular, and transcriptomic techniques, we performed a functional characterization of the U.\u00a0maydis effector Jasmonate\/Ethylene signaling inducer\u00a01 (Jsi1). Jsi1 interacts with several members of the plant corepressor family Topless\/Topless related (TPL\/TPR). Jsi1 expression in Zea mays and Arabidopsis thaliana leads to transcriptional induction of the ethylene response factor (ERF) branch of the jasmonate\/ethylene (JA\/ET) signaling pathway. In A.\u00a0thaliana, activation of the ERF branch leads to biotrophic susceptibility. Jsi1 likely activates the ERF branch via an EAR (ET-responsive element binding-factor-associated amphiphilic repression) motif, which resembles EAR motifs from plant ERF transcription factors, that interacts with TPL\/TPR proteins. EAR-motif-containing effector candidates were identified from different fungal species, including Magnaporthe oryzae, Sporisorium scitamineum, and Sporisorium reilianum. Interaction between plant TPL proteins and these effector candidates from biotrophic and hemibiotrophic fungi indicates the convergent evolution of effectors modulating the TPL\/TPR corepressor hub.","authors":"Darino, M., Chia, KS., Marques, J., Aleksza, D., Soto-Jim\u00e9nez, LM., Saado, I., Uhse, S., Borg, M., Betz, R., Bindics, J., Zienkiewicz, K., Feussner, I., Petit-Houdenot, Y., Djamei, A.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"New Phytol","volume":"229","issue":"6","page":"3393-3407","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33581058","title":"Coordinated changes in cellular behavior ensure the lifelong maintenance of the hippocampal stem cell population.","abstract":"Neural stem cell numbers fall rapidly in the hippocampus of juvenile mice but stabilize during adulthood, ensuring lifelong hippocampal neurogenesis. We show that this stabilization of stem cell numbers in young adults is the result of coordinated changes in stem cell behavior. Although proliferating neural stem cells in juveniles differentiate rapidly, they increasingly return to a resting state of shallow quiescence and progress through additional self-renewing divisions in adulthood. Single-cell transcriptomics, modeling, and label retention analyses indicate that resting cells have a higher activation rate and greater contribution to neurogenesis than dormant cells, which have not left quiescence. These changes in stem cell behavior result from a progressive reduction in expression of the pro-activation protein ASCL1 because of increased post-translational degradation. These cellular mechanisms help reconcile current contradictory models of hippocampal neural stem cell (NSC) dynamics and may contribute to the different rates of decline of hippocampal neurogenesis in mammalian species, including humans.","authors":"Harris, L., Rigo, P., Stiehl, T., Gaber, ZB., Austin, SHL., Masdeu, MDM., Edwards, A., Urb\u00e1n, N., Marciniak-Czochra, A., Guillemot, F.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell Stem Cell","volume":"28","issue":"5","page":"863-876.e6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27761245","title":"Activation of an exonic splice-donor site in exon 30 of <i>CDK5RAP2<\/i> in a patient with severe microcephaly and pigmentary abnormalities.","abstract":"This report constitutes the first report of a cryptic exonic splice-donor site in <i>CDK5RAP2<\/i>, highlights the importance of evaluating novel splice mutations, and suggests that the phenotypic range associated with <i>CDK5RAP2<\/i> mutations may include skin pigmentary abnormalities.","authors":"Pagnamenta, AT., Howard, MF., Knight, SJ., Keays, DA., Quaghebeur, G., Taylor, JC., Kini, U.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Clin Case Rep","volume":"4","issue":"10","page":"952-956","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14579333","title":"Predictions without templates: new folds, secondary structure, and contacts in CASP5.","abstract":"We present the assessment of CASP5 predictions in the new fold category. For coordinate predictions, we considered five targets with new folds and eight lying on the fold recognition borderline. We performed detailed visual and numerical comparisons between predicted and experimental structures to assess prediction accuracy. The two procedures largely agreed, but the visual inspection identified instances where metrics, such as GDT_TS, ranked what we considered incorrect predictions highly. We found the quality of the best predictions to be very good: for nearly every target at least one group predicted a structure close to the correct one. However, selection of the best of five models is still problematic. The group of David Baker once again proved to be best overall, with many individual highlights. However, high quality and consistency were also seen from others, suggesting that the community is moving toward general procedures to predict accurate structures for proteins showing no resemblance to anything seen before. Predictions for secondary structure showed at best limited progress since CASP4. The number of targets is probably too small to spot differences in performance between methods, suggesting that such predictions might be better evaluated with schemes involving more proteins. For contact predictions, accuracies are still low, although there were several instances of accurate and useful contacts predicted de novo, and new approaches hint at future progress.","authors":"Aloy, P., Stark, A., Hadley, C., Russell, RB.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Proteins","volume":"53 Suppl 6","issue":null,"page":"436-56","pdf":null,"JrId":"6646","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33979599","title":"SnapShot: Embryo models.","abstract":null,"authors":"Rivron, N., Fu, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Stem Cell Reports","volume":"16","issue":"5","page":"1142-1142.e1","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34054841","title":"Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies.","abstract":"Proper lymphopoiesis and immune responses depend on the spatiotemporal control of multiple processes, including gene expression, DNA recombination and cell fate decisions. High-order 3D chromatin organization is increasingly appreciated as an important regulator of these processes and dysregulation of genomic architecture has been linked to various immune disorders, including lymphoid malignancies. In this review, we present the general principles of the 3D chromatin topology and its dynamic reorganization during various steps of B and T lymphocyte development and activation. We also discuss functional interconnections between architectural, epigenetic and transcriptional changes and introduce major key players of genomic organization in B\/T lymphocytes. Finally, we present how alterations in architectural factors and\/or 3D genome organization are linked to dysregulation of the lymphopoietic transcriptional program and ultimately to hematological malignancies.","authors":"Scourzic, L., Salataj, E., Apostolou, E.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Front Immunol","volume":"12","issue":"","page":"669881","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33986293","title":"Antigen-driven EGR2 expression is required for exhausted CD8<sup>+<\/sup> T cell stability and maintenance.","abstract":"Chronic stimulation of CD8<sup>+<\/sup> T cells triggers exhaustion, a distinct differentiation state with diminished effector function. Exhausted cells exist in multiple differentiation states, from stem-like progenitors that are the key mediators of the response to checkpoint blockade, through to terminally exhausted cells. Due to its clinical relevance, there is substantial interest in defining the pathways that control differentiation and maintenance of these subsets. Here, we show that chronic antigen induces the anergy-associated transcription factor EGR2 selectively within progenitor exhausted cells in both chronic LCMV and tumours. EGR2 enables terminal exhaustion and stabilizes the exhausted transcriptional state by both direct EGR2-dependent control of key exhaustion-associated genes, and indirect maintenance of the exhausted epigenetic state. We show that EGR2 is a regulator of exhaustion that epigenetically and transcriptionally maintains the differentiation competency of progenitor exhausted cells.","authors":"Wagle, MV., Vervoort, SJ., Kelly, MJ., Van Der Byl, W., Peters, TJ., Martin, BP., Martelotto, LG., N\u00fcssing, S., Ramsbottom, KM., Torpy, JR., Knight, D., Reading, S., Thia, K., Miosge, LA., Howard, DR., Gloury, R., Gabriel, SS., Utzschneider, DT., Oliaro, J., Powell, JD., Luciani, F., Trapani, JA., Johnstone, RW., Kallies, A., Goodnow, CC., Parish, IA.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"2782","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14555986","title":"The proto-oncoprotein c-Fos negatively regulates hepatocellular tumorigenesis.","abstract":"Hepatocytes adopt an invasive and metastatic phenotype caused by the cooperation of transforming growth factor (TGF)-beta and oncogenic Ha-Ras. In the initial phase of this process, c-Fos is rapidly induced by TGF-beta, but then decreases to undetectable levels. Here, we investigated the functional implications of c-Fos activation and its contribution to hepatocellular tumorigenesis. By employing conditional c-Fos expression, we observed that continuous activation of c-Fos and consequently AP-1 activity leads to depolarization of differentiated murine epithelial hepatocytes. Most remarkably, this change in morphology was associated with inhibition of proliferation and induction of cell death. Coexpression of antiapoptotic Bcl-XL or scavenging of reactive oxygen species was sufficient to prevent the c-Fos-mediated phenotype. In contrast, the cooperation of c-Fos with oncogenic Ha-Ras or a Ras mutant selectively activating the MAPK pathway even enhanced c-Fos-induced effects. Showing the negative role in hepatocellular tumorigenesis, c-Fos repressed oncogenic Ras-driven anchorage-independent growth in vitro and strongly suppressed tumour formation in vivo. Taken together, we demonstrate that c-Fos modulates plasticity of epithelial hepatocytes and acts tumour suppressive in neoplastic hepatocytes by stimulating cell cycle inhibition and cell death.","authors":"Mikula, M., Gotzmann, J., Fischer, AN., Wolschek, MF., Thallinger, C., Schulte-Hermann, R., Beug, H., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Oncogene","volume":"22","issue":"43","page":"6725-38","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2003-11-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33979590","title":"It takes a village to form embryo models.","abstract":null,"authors":"Rivron, N., Fu, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Stem Cell Reports","volume":"16","issue":"5","page":"1011-1013","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32839611","title":"Fibroblasts as a source of self-antigens for central immune tolerance.","abstract":"Fibroblasts are one of the most common but also neglected types of stromal cells, the heterogeneity of which underlies the specific function of tissue microenvironments in development and regeneration. In the thymus, autoreactive T cells are thought to be negatively selected by reference to the self-antigens expressed in medullary epithelial cells, but the contribution of other stromal cells to tolerance induction has been poorly examined. In the present study, we report a PDGFR<sup>+<\/sup> gp38<sup>+<\/sup> DPP4<sup>-<\/sup> thymic fibroblast subset that is required for T cell tolerance induction. The deletion of the lymphotoxin \u03b2-receptor in thymic fibroblasts caused an autoimmune phenotype with decreased expression of tissue-restricted and fibroblast-specific antigens, offering insight into the long-sought target of lymphotoxin signaling in the context of the regulation of autoimmunity. Thus, thymic medullary fibroblasts play an essential role in the establishment of central tolerance by producing a diverse array of self-antigens.","authors":"Nitta, T., Tsutsumi, M., Nitta, S., Muro, R., Suzuki, EC., Nakano, K., Tomofuji, Y., Sawa, S., Okamura, T., Penninger, JM., Takayanagi, H.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Immunol","volume":"21","issue":"10","page":"1172-1180","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14517394","title":"Novel forms of acidic fibroblast growth factor-1 are constitutively exported by beta tumor cell lines independent from conventional secretion and apoptosis.","abstract":"Acidic and basic fibroblast growth factors (FGF-1 and FGF-2) are strong mitogens for many tumor cell types and potent inducers of angiogenesis in vitro and in vivo. It is notable that these proteins lack classical signal sequences for secretion; the mechanism by which they are released from cells remains obscure. We demonstrate here that FGF-1 is constitutively exported by tumor cell lines derived from highly angiogenic beta cell tumors of transgenic mice. Remarkably, FGF-1 is sequestered as a latent form in the conditioned medium, as assessed by a lack of mitogenic activity and heparin affinity. High salt treatment of conditioned medium unveils the sequestered FGF-1 as novel high molecular weight forms with reduced heparin affinity and a molecular mass of approximately 30-40kDa; we refer to these as exported forms of FGF-1 (XP-FGF-1). Reducing and denaturing agents convert XP-FGF-1 into the 18kDa monomeric form of FGF-1, indicating it represents tight aggregates of FGF-1. XP-FGF-1 is found in cell lysate as well as conditioned medium, suggesting that they represent export intermediates. Brefeldin A, an inhibitor of conventional secretion, does not interfere with FGF-1 export. Moreover, cell lysis or apoptosis are not involved in this export pathway. Therefore, these data demonstrate that FGF-1 is constitutively exported by beta tumor cell lines via a novel secretory pathway so as to facilitate tumor growth and angiogenesis.","authors":"Christofori, G., Luef, S.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Angiogenesis","volume":"1","issue":"1","page":"55-70","pdf":null,"JrId":"22063","fulltextlink":null,"preprintlink":null,"articledate":"1997-00-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16818776","title":"The histone methyltransferase Suv39h1 increases class switch recombination specifically to IgA.","abstract":"Ab class (isotype) switching allows the humoral immune system to adaptively respond to different infectious organisms. Isotype switching occurs by intrachromosomal DNA recombination between switch (S) region sequences associated with C(H) region genes. Although isotype-specific transcription of unrearranged (germline) C(H) genes is required for switching, recent results suggest that isotype specificity is also determined by the sequences of downstream (acceptor) S regions. In the current study, we identify the histone methyltransferase Suv39h1 as a novel Salpha-specific factor that specifically increases IgA switching (Smu-Salpha recombination) in a transiently transfected plasmid S substrate, and demonstrate that this effect requires the histone methyltransferase activity of Suv39h1. Additionally, B cells from Suv39h1-deficient mice have an isotype-specific reduction in IgA switching with no effect on the level of germline Ialpha-Calpha transcripts. Taken together, our results suggest that Suv39h1 activity inhibits the activity of a sequence-specific DNA-binding protein that represses switch recombination to IgA.","authors":"Bradley, SP., Kaminski, DA., Peters, AH., Jenuwein, T., Stavnezer, J.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"J Immunol","volume":"177","issue":"2","page":"1179-88","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2006-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9178902","title":"ICE-proteases mediate HTLV-I Tax-induced apoptotic T-cell death.","abstract":"The Tax protein of Human T-cell leukemia virus type 1 (HTLV-1) is important for the T-cell immortalizing properties of this virus in vitro and is considered to be responsible for the early stages of leukemogenesis in infected hosts. Tax can upregulate expression of TNF-alpha and TNF-beta, as well as potentiate apoptosis in activated T-cells and in serum starved murine fibroblasts. To examine the role of CD95 (APO-1\/Fas) and ICE-proteases in Tax-mediated active T-cell death, Jurkat T cells expressing (APO(S)) or lacking (APO(R)) cell surface expression of CD95 (APO-1\/Fas) were genetically modified to express hormone-inducible HTLV-1 Tax constructs. Hormone-inducible action of Tax alone was sufficient to promote programmed cell death in CD95-expressing Jurkat T-cell clones. In contrast, clones lacking CD95 surface expression were resistant to the antiproliferative action of Tax. Both APO(S) and APO(R) clones exhibited Tax-dependent upregulation of CD95 ligand and TNF-alpha. Blocking experiments suggested that while the apoptotic action of Tax critically required ICE-protease function it was largely independent of cell surface interaction of CD95 ligand or TNF-alpha with their corresponding receptors. These observations strongly implicate ICE-proteases in Tax-induced T-cell death, and suggest a possible involvement of CD95 in this process.","authors":"Chlichlia, K., Busslinger, M., Peter, ME., Walczak, H., Krammer, PH., Schirrmacher, V., Khazaie, K.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Oncogene","volume":"14","issue":"19","page":"2265-72","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33288951","title":"Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution.","abstract":"Osteoclasts are the exclusive bone-resorbing cells, playing a central role in bone metabolism, as well as the bone damage that occurs under pathological conditions<sup>1,2<\/sup>. In postnatal life, haematopoietic stem-cell-derived precursors give rise to osteoclasts in response to stimulation with macrophage colony-stimulating factor and receptor activator of nuclear factor-\u03baB ligand, both of which are produced by osteoclastogenesis-supporting cells such as osteoblasts and osteocytes<sup>1-3<\/sup>. However, the precise mechanisms underlying cell fate specification during osteoclast differentiation remain unclear. Here, we report the transcriptional profiling of 7,228 murine cells undergoing in vitro osteoclastogenesis, describing the stepwise events that take place during the osteoclast fate decision process. Based on our single-cell transcriptomic dataset, we find that osteoclast precursor cells transiently express CD11c, and deletion of receptor activator of nuclear factor-\u03baB specifically in CD11c-expressing cells inhibited osteoclast formation in vivo and in vitro. Furthermore, we identify Cbp\/p300-interacting transactivator with Glu\/Asp-rich carboxy-terminal domain 2 (Cited2) as the molecular switch triggering terminal differentiation of osteoclasts, and deletion of Cited2 in osteoclast precursors in vivo resulted in a failure to commit to osteoclast fate. Together, the results of this study provide a detailed molecular road map of the osteoclast differentiation process, refining and expanding our understanding of the molecular mechanisms underlying osteoclastogenesis.","authors":"Tsukasaki, M., Huynh, NC., Okamoto, K., Muro, R., Terashima, A., Kurikawa, Y., Komatsu, N., Pluemsakunthai, W., Nitta, T., Abe, T., Kiyonari, H., Okamura, T., Sakai, M., Matsukawa, T., Matsumoto, M., Kobayashi, Y., Penninger, JM., Takayanagi, H.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Metab","volume":"2","issue":"12","page":"1382-1390","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33976212","title":"The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation.","abstract":"In flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of the linker histone H1, and specific epigenetic modifications, such as high levels of DNA methylation at both CG and non-CG sites. How H2A.W regulates heterochromatin organization and interacts with other heterochromatic features is unclear. Here, we create a h2a.w null mutant via CRISPR-Cas9, h2a.w-2, to analyze the in vivo function of H2A.W. We find that H2A.W antagonizes deposition of H1 at heterochromatin and that non-CG methylation and accessibility are moderately decreased in h2a.w-2 heterochromatin. Compared to H1 loss alone, combined loss of H1 and H2A.W greatly increases accessibility and facilitates non-CG DNA methylation in heterochromatin, suggesting co-regulation of heterochromatic features by H2A.W and H1. Our results suggest that H2A.W helps maintain optimal heterochromatin accessibility and DNA methylation by promoting chromatin compaction together with H1, while also inhibiting excessive H1 incorporation.","authors":"Bourguet, P., Picard, CL., Yelagandula, R., P\u00e9lissier, T., Lorkovi\u0107, ZJ., Feng, S., Pouch-P\u00e9lissier, MN., Schm\u00fccker, A., Jacobsen, SE., Berger, F., Mathieu, O.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"2683","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32847850","title":"Functional and Structural Insights into a Vif\/PPP2R5 Complex Elucidated Using Patient HIV-1 Isolates and Computational Modeling.","abstract":"Human immunodeficiency virus type 1 (HIV-1) Vif recruits a cellular ubiquitin ligase complex to degrade antiviral APOBEC3 enzymes (APOBEC3C-H) and PP2A phosphatase regulators (PPP2R5A to PPP2R5E). While APOBEC3 antagonism is the canonical function of HIV-1 Vif, this viral accessory protein is also known to trigger G<sub>2<\/sub>\/M cell cycle arrest. Vif initiates G<sub>2<\/sub>\/M arrest by degrading multiple PPP2R5 family members, an activity prevalent among diverse HIV-1 and simian immunodeficiency virus (SIV) isolates. Here, computational protein-protein docking was used to delineate a Vif\/CBF-\u03b2\/PPP2R5 complex in which Vif is predicted to bind the same PPP2R5 surface as physiologic phosphatase targets. This model was tested using targeted mutagenesis of amino acid residues within or adjacent to the putative interface to show loss or retention, respectively, of Vif-induced PPP2R5 degradation activity. Additionally, expression of a peptide that mimics cellular targets of PPP2R5s robustly inhibited Vif-mediated degradation of PPP2R5A but not APOBEC3G. Moreover, live-cell imaging studies examining Vif-mediated degradation of PPP2R5A and APOBEC3G within the same cell revealed that PPP2R5A degradation kinetics are comparable to those of APOBEC3G with a half-life of roughly 6\u2009h postinfection, demonstrating that Vif can concurrently mediate the degradation of distinct cellular substrates. Finally, experiments with a panel of patient-derived Vif isolates indicated that PPP2R5A degradation activity is common in patient-derived isolates. Taken together, these results support a model in which PPP2R5 degradation and global changes in the cellular phosphoproteome are likely to be advantageous for viral pathogenesis.<b>IMPORTANCE<\/b> A critical function of HIV-1 Vif is to counteract the family of APOBEC3 innate immune proteins. It is also widely accepted that Vif induces G<sub>2<\/sub>\/M cell cycle arrest in several different cell types. Recently, it has been shown that Vif degrades multiple PPP2R5 phosphoregulators to induce the G<sub>2<\/sub>\/M arrest phenotype. Here, computational approaches are used to test a structural model of the Vif\/PPP2R5 complex. In addition, imaging studies are used to show that Vif degrades these PPP2R5 substrates in roughly the same time frame as APOBEC3 degradation and that this activity is prevalent in patient-derived Vif isolates. These studies are important by further defining PPP2R5 proteins as a bona fide substrate of HIV-1 Vif.","authors":"Salamango, DJ., McCann, JL., Demir, \u00d6., Becker, JT., Wang, J., Lingappa, JR., Temiz, NA., Brown, WL., Amaro, RE., Harris, RS.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"J Virol","volume":"94","issue":"21","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16791829","title":"Phosphoproteomics strategies for the functional analysis of signal transduction.","abstract":"Protein phosphorylation is a key regulatory mechanism of cellular signalling processes. The analysis of phosphorylated proteins and the characterisation of phosphorylation sites under different biological conditions are some of the most challenging tasks in current proteomics research. Reduction of the sample complexity is one major step for the analysis of low-abundance kinase substrates, which can be achieved by various subcellular fractionation techniques. One strategy is the enrichment of phosphorylated proteins or peptides by immunoprecipitation or chromatography, e.g. immobilised metal affinity chromatography, prior to analysis. 2-DE gels are powerful tools for the analysis of phosphoproteins when combined with new multiplexing techniques like DIGE, phosphospecific stains, autoradiography or immunoblotting. In addition, several gel-free methods combining chromatography with highly sensitive MS have been successfully applied for the analysis of complex phosphoproteomes. Recently developed approaches like KESTREL or 'chemical genetics' and also protein microarrays offer new possibilities for the identification of specific kinase targets. This review summarises various strategies for the analyses of phosphoproteins with a special focus on the identification of novel kinase substrates.","authors":"Morandell, S., Stasyk, T., Grosstessner-Hain, K., Roitinger, E., Mechtler, K., Bonn, GK., Huber, LA.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Proteomics","volume":"6","issue":"14","page":"4047-56","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2006-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33461212","title":"Giant lungfish genome elucidates the conquest of land by vertebrates.","abstract":"Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, 'conquered' the land and ultimately gave rise to all land vertebrates, including humans<sup>1-3<\/sup>. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14\u00d7 larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17\u00a0fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods<sup>4,5<\/sup>, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.","authors":"Meyer, A., Schloissnig, S., Franchini, P., Du, K., Woltering, JM., Irisarri, I., Wong, WY., Nowoshilow, S., Kneitz, S., Kawaguchi, A., Fabrizius, A., Xiong, P., Dechaud, C., Spaink, HP., Volff, JN., Simakov, O., Burmester, T., Tanaka, EM., Schartl, M.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature","volume":"590","issue":"7845","page":"284-289","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12882526","title":"Mechanisms in epithelial plasticity and metastasis: insights from 3D cultures and expression profiling.","abstract":"Most human tumors are of epithelial origin (carcinomas) and metastases from such tumors lead to &gt;80% of all cancer deaths. In contrast to aberrant control of proliferation, cell cycle, apoptosis, angiogenesis, and lifespan, mechanisms involved in local invasion and metastasis are still insufficiently understood. We will review a set of (often conflicting) in vitro\/in vivo data that suggest the existence of several types of epithelial cell plasticity changes towards a fibroblastoid, invasive phenotype, which increasingly emerge as crucial events during metastasis. New cellular models were identified, which form organotypic structures under near-physiological 3D-culture conditions in vitro as well as tumors\/metastases in vivo. In these models, key proteins and signaling pathways were identified (e.g., TGFbeta, ERK\/MAPK, PI3K, and PDGF), which specify distinct types of epithelial plasticity correlated with steps in cancer progression and metastasis. The existence of several distinct epithelial plasticity phenotypes is also strongly suggested by expression profiling of polysome-bound mRNA, yielding a better representation of the proteome than conventional expression profiling.","authors":"Jechlinger, M., Gr\u00fcnert, S., Beug, H.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Mammary Gland Biol Neoplasia","volume":"7","issue":"4","page":"415-32","pdf":null,"JrId":"21181","fulltextlink":null,"preprintlink":null,"articledate":"2003-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33426508","title":"Purified Bighead protein efficiently promotes head development in the South African clawed frog, <i>Xenopus laevis<\/i>.","abstract":"Vertebrate embryonic development is regulated by a few families of extracellular signaling molecules. <i>Xenopus laevis<\/i> embryos offer an excellent system to study the cell-cell communication signals that govern embryonic patterning. In the frog embryos, Wnt\/\u03b2-catenin plays a pivotal role in regulating embryonic axis development, and modulation of the Wnt pathway is required for proper antero-posterior patterning. Recently, a novel secreted, organizer-specific Wnt inhibitor, Bighead, was identified that acts by downregulating Lrp6 plasma membrane levels. Here, I describe a method to purify biologically active Bighead protein and confirm that Bighead promotes <i>Xenopus<\/i> head development<i>.<\/i>","authors":"Colozza, G.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"MicroPubl Biol","volume":"2021","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22120048","title":"Evidence for dosage compensation between the X chromosome and autosomes in mammals.","abstract":null,"authors":"Kharchenko, PV., Xi, R., Park, PJ.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Genet","volume":"43","issue":"12","page":"1167-9; author reply 1171-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-20","doi":"10.1038\/ng.991","first_author":"Kharchenko, PV.","corresponding_authors":"Park, PJ."},{"pmid":"31127039","title":"Histone deacetylase 4 promotes type I interferon signaling, restricts DNA viruses, and is degraded via vaccinia virus protein C6.","abstract":"Interferons (IFNs) represent an important host defense against viruses. Type I IFNs induce JAK-STAT signaling and expression of IFN-stimulated genes (ISGs), which mediate antiviral activity. Histone deacetylases (HDACs) perform multiple functions in regulating gene expression and some class I HDACs and the class IV HDAC, HDAC11, influence type I IFN signaling. Here, HDAC4, a class II HDAC, is shown to promote type I IFN signaling and coprecipitate with STAT2. Pharmacological inhibition of class II HDAC activity, or knockout of HDAC4 from HEK-293T and HeLa cells, caused a defective response to IFN-\u03b1. This defect in HDAC4<sup>-\/-<\/sup> cells was rescued by reintroduction of HDAC4 or catalytically inactive HDAC4, but not HDAC1 or HDAC5. ChIP analysis showed HDAC4 was recruited to ISG promoters following IFN stimulation and was needed for binding of STAT2 to these promoters. The biological importance of HDAC4 as a virus restriction factor was illustrated by the observations that (<i>i<\/i>) the replication and spread of vaccinia virus (VACV) and herpes simplex virus type 1 (HSV-1) were enhanced in HDAC4<sup>-\/-<\/sup> cells and inhibited by overexpression of HDAC4; and (<i>ii<\/i>) HDAC4 is targeted for proteasomal degradation during VACV infection by VACV protein C6, a multifunctional IFN antagonist that coprecipitates with HDAC4 and is necessary and sufficient for HDAC4 degradation.","authors":"Lu, Y., Stuart, JH., Talbot-Cooper, C., Agrawal-Singh, S., Huntly, B., Smid, AI., Snowden, JS., Dupont, L., Smith, GL.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Proc Natl Acad Sci U S A","volume":"116","issue":"24","page":"11997-12006","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16723697","title":"Loss of angiotensin-converting enzyme-2 leads to the late development of angiotensin II-dependent glomerulosclerosis.","abstract":"Angiotensin-converting enzyme-2 (ACE2), a membrane-bound carboxymonopeptidase highly expressed in the kidney, functions as a negative regulator of the renin-angiotensin system. Here we report early accumulation of fibrillar collagen in the glomerular mesangium of male ACE2 mutant (ACE2-\/y) mice followed by development of glomerulosclerosis by 12 months of age whereas female ACE2 mutant (ACE2-\/-) mice were relatively protected. Progressive kidney injury was associated with increased deposition of collagen I, collagen III and fibronectin in the glomeruli and increased urinary albumin excretion compared to age-matched control mice. These structural and functional changes in the glomeruli of male ACE2 mutant mice were prevented by treatment with the angiotensin II type-1 receptor antagonist irbesartan. Loss of ACE2 was associated with a marked increase in renal lipid peroxidation product formation and activation of mitogen-activated protein kinase and extracellular signal-regulated kinases 1 and 2 in glomeruli, events that are also prevented by angiotensin II type-1 receptor blockade. We conclude that deletion of the ACE2 gene leads to the development of angiotensin II-dependent glomerular injury in male mice. These findings have important implications for our understanding of ACE2, the renin-angiotensin system, and gender in renal injury, with ACE2 likely to be an important therapeutic target in kidney disease.","authors":"Oudit, GY., Herzenberg, AM., Kassiri, Z., Wong, D., Reich, H., Khokha, R., Crackower, MA., Backx, PH., Penninger, JM., Scholey, JW.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Am J Pathol","volume":"168","issue":"6","page":"1808-20","pdf":null,"JrId":"449","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30420784","title":"Centrosomal protein TRIM43 restricts herpesvirus infection by regulating nuclear lamina integrity.","abstract":"Tripartite motif (TRIM) proteins mediate antiviral host defences by either directly targeting viral components or modulating innate immune responses. Here we identify a mechanism of antiviral restriction in which a TRIM E3 ligase controls viral replication by regulating the structure of host cell centrosomes and thereby nuclear lamina integrity. Through RNAi screening we identified several TRIM proteins, including TRIM43, that control the reactivation of Kaposi's sarcoma-associated herpesvirus. TRIM43 was distinguished by its ability to restrict a broad range of herpesviruses and its profound upregulation during herpesvirus infection as part of a germline-specific transcriptional program mediated by the transcription factor DUX4. TRIM43 ubiquitinates the centrosomal protein pericentrin, thereby targeting it for proteasomal degradation, which subsequently leads to alterations of the nuclear lamina that repress active viral chromatin states. Our study identifies a role of the TRIM43-pericentrin-lamin axis in intrinsic immunity, which may be targeted for therapeutic intervention against herpesviral infections.","authors":"Full, F., van Gent, M., Sparrer, KMJ., Chiang, C., Zurenski, MA., Scherer, M., Brockmeyer, NH., Heinzerling, L., St\u00fcrzl, M., Korn, K., Stamminger, T., Ensser, A., Gack, MU.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Microbiol","volume":"4","issue":"1","page":"164-176","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9139696","title":"Cloning and functional characterization of the ornithokinin receptor. Recognition of the major kinin receptor antagonist, HOE140, as a full agonist.","abstract":"Kinins are proinflammatory peptides that dilate vessels, increase vascular permeability, contract smooth muscles, and provoke pain. The known mammalian kinin receptors are classified as two subtypes, i.e. the B1 receptor triggered by [des-Arg9]bradykinin and inhibited by [des-Arg9,Leu8]bradykinin, and the B2 receptor stimulated by bradykinin and antagonized by HOE140. Here we report the cloning of a non-mammalian kinin receptor gene amplified from genomic chicken DNA. The protein predicted from the open reading frame shows 31 and 49% sequence identity to the human B1 and B2 receptors, respectively, suggesting that it represents a G protein-coupled receptor of the kinin receptor family. The recombinantly expressed chicken receptor had IC50 values of 4.7 nM for the authentic ligand, ornithokinin ([Thr6,Leu8]bradykinin), 3.8 nM for HOE140, and &gt;\/=10 microM for bradykinin, [des-Arg9]bradykinin, and [des-Arg9,Leu8]bradykinin. Ornithokinin and HOE140 at nanomolar concentrations stimulated intracellular inositol phosphate accumulation and induced a significant transient rise in intracelluar free Ca2+, whereas bradykinin was ineffective even at 100 nM. Hence the principal B2 receptor antagonist HOE140 is a potent agonist of the chicken kinin receptor. This unique pharmacological profile classifies the ornithokinin receptor as a novel subtype among kinin receptors and will facilitate further molecular studies on ligand binding and receptor activation.","authors":"Schroeder, C., Beug, H., M\u00fcller-Esterl, W.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Biol Chem","volume":"272","issue":"19","page":"12475-81","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33422934","title":"How DNA loop extrusion mediated by cohesin enables V(D)J recombination.","abstract":"'Structural maintenance of chromosomes' (SMC) complexes are required for the folding of genomic DNA into loops. Theoretical considerations and single-molecule experiments performed with the SMC complexes cohesin and condensin indicate that DNA folding occurs via loop extrusion. Recent work indicates that this process is essential for the assembly of antigen receptor genes by V(D)J recombination in developing B and T cells of the vertebrate immune system. Here, I review how recent studies of the mouse immunoglobulin heavy chain locus Igh have provided evidence for this hypothesis\u00a0and how the formation of chromatin loops by cohesin and regulation of this process by CTCF and Wapl might ensure that all variable gene segments in this locus (V<sub>H<\/sub> segments) participate in recombination with a re-arranged DJ<sub>H<\/sub> segment, to ensure generation of a maximally diverse repertoire of B-cell receptors and antibodies.","authors":"Peters, JM.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Curr Opin Cell Biol","volume":"70","issue":null,"page":"75-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12867029","title":"Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">12867029<\/PMID><DateCompleted><Year>2004<\/Year><Month>01<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>13<\/Volume><Issue>14<\/Issue><PubDate><Year>2003<\/Year><Month>Jul<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin.<\/ArticleTitle><Pagination><MedlinePgn>1192-200<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Histone H3 lysine 9 (H3-K9) methylation and DNA methylation are characteristic hallmarks of mammalian heterochromatin. H3-K9 methylation was recently shown to be a prerequisite for DNA methylation in Neurospora crassa and Arabidopsis thaliana. Currently, it is unknown whether a similar dependence exists in mammalian organisms.","authors":"Lehnertz, B., Ueda, Y., Derijck, AA., Braunschweig, U., Perez-Burgos, L., Kubicek, S., Chen, T., Li, E., Jenuwein, T., Peters, AH.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"14","page":"1192-200","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33600438","title":"Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition.","abstract":"Post-transcriptional regulation of gene expression is crucial during the oocyte-to-embryo transition, a highly dynamic process characterized by the absence of nuclear transcription. Thus, changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified, it remains unclear which machineries contribute to remodeling the maternal transcriptome. Here, we focused on the degradation factor Ski7 in zebrafish. Homozygous ski7 mutant fish had higher proportions of both poor quality eggs and eggs that were unable to develop beyond the one-cell stage. Consistent with the idea that Ski7 participates in remodeling the maternal RNA content, transcriptome profiling identified hundreds of misregulated mRNAs in the absence of Ski7. Furthermore, upregulated genes were generally lowly expressed in wild type, suggesting that Ski7 maintains low transcript levels for this subset of genes. Finally, GO enrichment and proteomic analyses of misregulated factors implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Our results provide first insights into the physiological role of vertebrate Ski7 as a post-transcriptional regulator during the oocyte-to-embryo transition.","authors":"Cabrera-Quio, LE., Schleiffer, A., Mechtler, K., Pauli, A.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"PLoS Genet","volume":"17","issue":"2","page":"e1009390","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33562253","title":"Heme Biosynthesis mRNA Expression Signature: Towards a Novel Prognostic Biomarker in Patients with Diffusely Infiltrating Gliomas.","abstract":"Diffusely infiltrating gliomas are characterized by a variable clinical course, and thus novel prognostic biomarkers are needed. The heme biosynthesis cycle constitutes a fundamental metabolic pathway and might play a crucial role in glioma biology. The aim of this study was thus to investigate the role of the heme biosynthesis mRNA expression signature on prognosis in a large glioma patient cohort. Glioma patients with available sequencing data on heme biosynthesis expression were retrieved from The Cancer Genome Atlas (TCGA). In each patient, the heme biosynthesis mRNA expression signature was calculated and categorized into low, medium, and high expression subgroups. Differences in progression-free and overall survival between these subgroups were investigated including a multivariate analysis correcting for WHO grade, tumor subtype, and patient age and sex. In a total of 693 patients, progression-free and overall survival showed a strictly monotonical decrease with increasing mRNA expression signature subgroups. In detail, median overall survival was 134.2 months in the low, 79.9 months in the intermediate, and 16.5 months in the high mRNA expression signature subgroups, respectively. The impact of mRNA expression signature on progression-free and overall survival was independent of the other analyzed prognostic factors. Our data indicate that the heme biosynthesis mRNA expression signature might serve as an additional novel prognostic marker in patients with diffusely infiltrating gliomas to optimize postoperative management.","authors":"Mischkulnig, M., Kiesel, B., L\u00f6tsch, D., Roetzer, T., Borkovec, M., Wadiura, LI., Roessler, K., Hervey-Jumper, S., Penninger, JM., Berger, MS., Widhalm, G., Erhart, F.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Cancers (Basel)","volume":"13","issue":"4","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33453168","title":"Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters.","abstract":"The MYC oncoprotein globally affects the function of RNA polymerase II (RNAPII). The ability of MYC to promote transcription elongation depends on its ubiquitylation. Here, we show that MYC and PAF1c (polymerase II-associated factor 1 complex) interact directly and mutually enhance each other's association with active promoters. PAF1c is rapidly transferred from MYC onto RNAPII. This transfer is driven by the HUWE1 ubiquitin ligase and is required for MYC-dependent transcription elongation. MYC and HUWE1 promote histone H2B ubiquitylation, which alters chromatin structure both for transcription elongation and double-strand break repair. Consistently, MYC suppresses double-strand break accumulation in active genes in a strictly PAF1c-dependent manner. Depletion of PAF1c causes transcription-dependent accumulation of double-strand breaks, despite widespread repair-associated DNA synthesis. Our data show that the transfer of PAF1c from MYC onto RNAPII efficiently couples transcription elongation with double-strand break repair to maintain the genomic integrity of MYC-driven tumor cells.","authors":"Endres, T., Solvie, D., Heidelberger, JB., Andrioletti, V., Baluapuri, A., Ade, CP., Muhar, M., Eilers, U., Vos, SM., Cramer, P., Zuber, J., Beli, P., Popov, N., Wolf, E., Gallant, P., Eilers, M.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Mol Cell","volume":"81","issue":"4","page":"830-844.e13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33452254","title":"Sequencing of the Arabidopsis NOR2 reveals its distinct organization and tissue-specific rRNA ribosomal variants.","abstract":"Despite vast differences between organisms, some characteristics of their genomes are conserved, such as the nucleolus organizing region (NOR). The NOR is constituted of multiple, highly repetitive rDNA genes, encoding the catalytic ribosomal core RNAs which are transcribed from 45S rDNA units. Their precise sequence information and organization remain uncharacterized. Here, using a combination of long- and short-read sequencing technologies we assemble contigs of the Arabidopsis NOR2 rDNA domain. We identify several expressed rRNA gene variants which are integrated into translating ribosomes in a tissue-specific manner. These findings support the concept of tissue specific ribosome subpopulations that differ in their rRNA composition and provide insights into the higher order organization of NOR2.","authors":"Sims, J., Sestini, G., Elgert, C., von Haeseler, A., Schl\u00f6gelhofer, P.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"387","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41971526","title":null,"abstract":null,"authors":"","publication_status":null,"journalpubyear":null,"journaltitle":null,"volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33385708","title":"Insights into gene regulation: From regulatory genomic elements to DNA-protein and protein-protein interactions.","abstract":"Transcription is orchestrated by non-coding regulatory elements embedded in chromatin, which exist within the larger context of chromosome topology. Here, we review recent insights into the functions of non-coding regulatory elements and their protein interactors during transcription control. A picture emerges in which the topological environment constraints enhancer-promoter interactions and specific enhancer-bound proteins with distinct promoter-compatibilities refine target promoter choice. Such compatibilities are encoded within the sequences of enhancers and promoters and realized by diverse transcription factors and cofactors with distinct biochemical activities. An emerging property of transcription factors and cofactors is the formation of nuclear microenvironments or membraneless compartments that can have properties of phase-separated liquids. These environments are able to selectively enrich certain proteins and small molecules over others. Further investigation into the interaction of transcriptional regulators with themselves and regulatory DNA elements will help reveal the complexities of gene regulation within the context of the nucleus.","authors":"Serebreni, L., Stark, A.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Curr Opin Cell Biol","volume":"70","issue":null,"page":"58-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33362792","title":"All About the RNA: Interferon-Stimulated Genes That Interfere With Viral RNA Processes.","abstract":"Interferon (IFN) signaling induces the expression of a wide array of genes, collectively referred to as IFN-stimulated genes (ISGs) that generally function to inhibit viral replication. RNA viruses are frequently targeted by ISGs through recognition of viral replicative intermediates and molecular features associated with viral genomes, or the lack of molecular features associated with host mRNAs. The ISGs reviewed here primarily inhibit viral replication in an RNA-centric manner, working to sense, degrade, or repress expression of viral RNA. This review focuses on dissecting how these ISGs exhibit multiple antiviral mechanisms, often through use of varied co-factors, highlighting the complexity of the type I IFN response. Specifically, these ISGs can mediate antiviral effects through viral RNA degradation, viral translation inhibition, or both. While the OAS\/RNase L pathway globally degrades RNA and arrests translation, ISG20 and ZAP employ targeted RNA degradation and translation inhibition to block viral replication. Meanwhile, SHFL targets translation by inhibiting -1 ribosomal frameshifting, which is required by many RNA viruses. Finally, a number of E3 ligases inhibit viral transcription, an attractive antiviral target during the lifecycle of negative-sense RNA viruses which must transcribe their genome prior to translation. Through this review, we aim to provide an updated perspective on how these ISGs work together to form a complex network of antiviral arsenals targeting viral RNA processes.","authors":"Yang, E., Li, MMH.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Front Immunol","volume":"11","issue":"","page":"605024","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33303745","title":"Inhibition of RANK signaling in breast cancer induces an anti-tumor immune response orchestrated by CD8+ T cells.","abstract":"Most breast cancers exhibit low immune infiltration and are unresponsive to immunotherapy. We hypothesized that inhibition of the\u00a0receptor activator of nuclear factor-\u03baB\u00a0(RANK) signaling pathway may enhance immune activation. Here we report that loss of RANK signaling in mouse tumor cells increases leukocytes, lymphocytes, and CD8<sup>+<\/sup> T cells, and reduces macrophage and neutrophil infiltration. CD8<sup>+<\/sup> T cells mediate the attenuated tumor phenotype observed upon RANK loss, whereas neutrophils, supported by RANK-expressing tumor cells, induce immunosuppression. RANKL inhibition increases the anti-tumor effect of immunotherapies in breast cancer through a tumor cell mediated effect. Comparably, pre-operative single-agent denosumab in premenopausal early-stage breast cancer patients from the Phase-II D-BEYOND clinical trial (NCT01864798) is well tolerated, inhibits RANK pathway and increases tumor infiltrating lymphocytes and CD8<sup>+<\/sup> T cells. Higher RANK signaling activation in tumors and serum RANKL levels at baseline predict these immune-modulatory effects. No changes in tumor cell proliferation (primary endpoint) or other secondary endpoints are observed. Overall, our preclinical and clinical findings reveal that tumor cells exploit RANK pathway as a mechanism to evade immune surveillance and support the use of RANK pathway inhibitors to prime luminal breast cancer for immunotherapy.","authors":"G\u00f3mez-Aleza, C., Nguyen, B., Yoldi, G., Ciscar, M., Barranco, A., Hern\u00e1ndez-Jim\u00e9nez, E., Maetens, M., Salgado, R., Zafeiroglou, M., Pellegrini, P., Venet, D., Garaud, S., Trinidad, EM., Ben\u00edtez, S., Vuylsteke, P., Polastro, L., Wildiers, H., Simon, P., Lindeman, G., Larsimont, D., Van den Eynden, G., Velghe, C., Roth\u00e9, F., Willard-Gallo, K., Michiels, S., Mu\u00f1oz, P., Walzer, T., Planelles, L., Penninger, J., Azim, HA., Loi, S., Piccart, M., Sotiriou, C., Gonz\u00e1lez-Su\u00e1rez, E.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"6335","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33299006","title":"Wnt-inducible Lrp6-APEX2 interacting proteins identify ESCRT machinery and Trk-fused gene as components of the Wnt signaling pathway.","abstract":"The canonical Wnt pathway serves as a hub connecting diverse cellular processes, including \u03b2-catenin signaling, differentiation, growth, protein stability, macropinocytosis, and nutrient acquisition in lysosomes. We have proposed that sequestration of \u03b2-catenin destruction complex components in multivesicular bodies (MVBs) is required for sustained canonical Wnt signaling. In this study, we investigated the events that follow activation of the canonical Wnt receptor Lrp6 using an APEX2-mediated proximity labeling approach. The Wnt co-receptor Lrp6 was fused to APEX2 and used to biotinylate targets that are recruited near the receptor during Wnt signaling at different time periods. Lrp6 proximity targets were identified by mass spectrometry, and revealed that many endosomal proteins interacted with Lrp6 within 5\u00a0min of Wnt3a treatment. Interestingly, we found that Trk-fused gene (TFG), previously known to regulate the cell secretory pathway and to be rearranged in thyroid and lung cancers, was strongly enriched in the proximity of Lrp6. TFG depletion with siRNA, or knock-out with CRISPR\/Cas9, significantly reduced Wnt\/\u03b2-catenin signaling in cell culture. In vivo, studies in the Xenopus system showed that TFG is required for endogenous Wnt-dependent embryonic patterning. The results suggest that the multivesicular endosomal machinery and the novel player TFG have important roles in Wnt signaling.","authors":"Colozza, G., Jami-Alahmadi, Y., Dsouza, A., Tejeda-Mu\u00f1oz, N., Albrecht, LV., Sosa, EA., Wohlschlegel, JA., De Robertis, EM.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Rep","volume":"10","issue":"1","page":"21555","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33216712","title":"The amygdala instructs insular feedback for affective learning.","abstract":"Affective responses depend on assigning value to environmental predictors of threat or reward. Neuroanatomically, this affective value is encoded at both cortical and subcortical levels. However, the purpose of this distributed representation across functional hierarchies remains unclear. Using fMRI in mice, we mapped a discrete cortico-limbic loop between insular cortex (IC), central amygdala (CE), and nucleus basalis of Meynert (NBM), which decomposes the affective value of a conditioned stimulus (CS) into its salience and valence components. In IC, learning integrated unconditioned stimulus (US)-evoked bodily states into CS valence. In turn, CS salience in the CE recruited these CS representations bottom-up via the cholinergic NBM. This way, the CE incorporated interoceptive feedback from IC to improve discrimination of CS valence. Consequently, opto-\/chemogenetic uncoupling of hierarchical information flow disrupted affective learning and conditioned responding. Dysfunctional interactions in the IC\u2194CE\/NBM network may underlie intolerance to uncertainty, observed in autism and related psychiatric conditions.","authors":"Kargl, D., Kaczanowska, J., Ulonska, S., Groessl, F., Piszczek, L., Lazovic, J., Buehler, K., Haubensak, W.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Elife","volume":"9","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41919951","title":null,"abstract":null,"authors":"","publication_status":null,"journalpubyear":null,"journaltitle":null,"volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33223522","title":"Gastric organoids-an in vitro model system for the study of gastric development and road to personalized medicine.","abstract":"Gastric cancer ranks as the fifth most common human malignancy and the third leading cause of cancer related deaths. Depending on tumor stage, endoscopic or surgical resection supported by perioperative chemotherapy is the only curative option for patients. Due to late clinical manifestation and missing reliable biomarkers, early detection is challenging and overall survival remains poor. Organoids are cell aggregates cultured in three-dimensions that grow with similar characteristics as their tissue-of-origin. Due to their self-renewal and proliferative capacity, organoids can be maintained long term in culture and expanded in many cases in an unlimited fashion. Patient-derived organoid (PDO) libraries function as living biobanks, allowing the in depth analysis of tissue specific function, development and disease. The recent successful establishment of gastric cancer PDOs opens up new perspectives for multiple translational clinical applications. Here, we review different adult stem cell derived gastric organoid model systems and focus on their establishment, phenotypic and genotypic characterizations as well as their use in predicting therapy response.","authors":"Seidlitz, T., Koo, BK., Stange, DE.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell Death Differ","volume":"28","issue":"1","page":"68-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33199607","title":"Structure-function analysis of microRNA 3'-end trimming by Nibbler.","abstract":"Nibbler (Nbr) is a 3'-to-5' exoribonuclease whose catalytic 3'-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr's N-terminal domain (NTD) and exonucleolytic domain (EXO) in miRNA 3'-end trimming. We have solved the crystal structures of the NTD core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of <i>Aedes aegypti<\/i> Nbr adopts a HEAT-like repeat scaffold with basic patches constituting an RNA-binding surface exhibiting a preference for binding double-strand RNA (dsRNA) over single-strand RNA (ssRNA). Structure-guided functional assays in <i>Drosophila<\/i> S2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, which depends on basic surface patches. Gain-of-function experiments revealed a potential role of the NTD in recruiting Nbr to Argonaute-bound small RNA substrates. The EXO domain of <i>A. aegypti<\/i> and <i>Drosophila melanogaster<\/i> Nbr adopt a mixed \u03b1\/\u03b2-scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr's EXO domain exhibits Mn<sup>2+<\/sup>-dependent ssRNA-specific 3'-to-5' exoribonuclease activity. Modeling of a 3' terminal Uridine into the catalytic pocket of Nbr EXO indicates that 2'-<i>O<\/i>-methylation of the 3'-U would result in a steric clash with a tryptophan side chain, suggesting that 2'-<i>O<\/i>-methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease EXO domain.","authors":"Xie, W., Sowemimo, I., Hayashi, R., Wang, J., Burkard, TR., Brennecke, J., Ameres, SL., Patel, DJ.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Proc Natl Acad Sci U S A","volume":"117","issue":"48","page":"30370-30379","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33191911","title":"Structure of the human core transcription-export complex reveals a hub for multivalent interactions.","abstract":"The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56\/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and licenses mRNA for nuclear export by loading the export factor NXF1-NXT1. How TREX integrates these marks and achieves high selectivity for mature mRNA is poorly understood. Here, we report the cryo-electron microscopy structure of the human THO-UAP56\/DDX39B complex at 3.3 \u00c5 resolution. The seven-subunit THO-UAP56\/DDX39B complex multimerizes into a 28-subunit tetrameric assembly, suggesting that selective recognition of mature mRNA is facilitated by the simultaneous sensing of multiple, spatially distant mRNA regions and maturation marks. Two UAP56\/DDX39B RNA helicases are juxtaposed at each end of the tetramer, which would allow one bivalent ALYREF protein to bridge adjacent helicases and regulate the TREX-mRNA interaction. Our structural and biochemical results suggest a conserved model for TREX complex function that depends on multivalent interactions between proteins and mRNA.","authors":"P\u00fchringer, T., Hohmann, U., Fin, L., Pacheco-Fiallos, B., Schellhaas, U., Brennecke, J., Plaschka, C.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Elife","volume":"9","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33168544","title":"Neuronal circuits and the magnetic sense: central questions.","abstract":"Magnetoreception is the ability to sense the Earth's magnetic field, which is used for orientation and navigation. Behavioural experiments have shown that it is employed by many species across all vertebrate classes; however, our understanding of how magnetic information is processed and integrated within the central nervous system is limited. In this Commentary, we review the progress in birds and rodents, highlighting the role of the vestibular and trigeminal systems as well as that of the hippocampus. We reflect on the strengths and weaknesses of the methodologies currently at our disposal, the utility of emerging technologies and identify questions that we feel are critical for the advancement of the field. We expect that magnetic circuits are likely to share anatomical motifs with other senses, which culminates in the formation of spatial maps in telencephalic areas of the brain. Specifically, we predict the existence of spatial cells that encode defined components of the Earth's magnetic field.","authors":"Malkemper, EP., Nimpf, S., Nordmann, GC., Keays, DA.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"J Exp Biol","volume":"223","issue":"Pt 21","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33151691","title":"Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction Networks <i>in Vivo<\/i>.","abstract":"Cross-linking mass spectrometry (XL-MS) has matured into a potent tool to identify protein-protein interactions or to uncover protein structures in living cells, tissues, or organelles. The unique ability to investigate the interplay of proteins within their native environment delivers valuable complementary information to other advanced structural biology techniques. This Review gives a comprehensive overview of the current possible applications as well as the remaining limitations of the technique, focusing on cross-linking in highly complex biological systems like cells, organelles, or tissues. Thanks to the commercial availability of most reagents and advances in user-friendly data analysis, validation, and visualization tools, studies using XL-MS can, in theory, now also be utilized by nonexpert laboratories.","authors":"Matzinger, M., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Proteome Res","volume":"20","issue":"1","page":"78-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21315506","title":"Inhibition of topoisomerase II\u03b1: novel function of wedelolactone.","abstract":"The naturally occurring coumestan wedelolactone has been previously shown to reduce growth of various cancer cells. So far, the growth-suppressing effect of wedelolactone has been attributed to the inhibition of the NF\u03baB transcription factor and\/or androgen receptors. We found that wedelolactone suppressed growth and induced apoptosis of androgen receptor-negative MDA-MB-231 breast cancer cells at concentrations that did not inhibit the NF\u03baB activity. The cells responded to wedelolactone by the S and G2\/M phase cell cycle arrest and induction of the DNA damage signaling. Wedelolactone interacted with dsDNA and inhibited the activity of DNA topoisomerase II\u03b1. We conclude that wedelolactone can act as growth suppressor independently of NF\u03baB and androgen receptors.","authors":"Benes, P., Knopfova, L., Trcka, F., Nemajerova, A., Pinheiro, D., Soucek, K., Fojta, M., Smarda, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Cancer Lett","volume":"303","issue":"1","page":"29-38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-05-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33137126","title":"A proteomic survey of microtubule-associated proteins in a R402H TUBA1A mutant mouse.","abstract":"Microtubules play a critical role in multiple aspects of neurodevelopment, including the generation, migration and differentiation of neurons. A recurrent mutation (R402H) in the \u03b1-tubulin gene TUBA1A is known to cause lissencephaly with cerebellar and striatal phenotypes. Previous work has shown that this mutation does not perturb the chaperone-mediated folding of tubulin heterodimers, which are able to assemble and incorporate into the microtubule lattice. To explore the molecular mechanisms that cause the disease state we generated a new conditional mouse line that recapitulates the R402H variant. We show that heterozygous mutants present with laminar phenotypes in the cortex and hippocampus, as well as a reduction in striatal size and cerebellar abnormalities. We demonstrate that homozygous expression of the R402H allele causes neuronal death and exacerbates a cell intrinsic defect in cortical neuronal migration. Microtubule sedimentation assays coupled with quantitative mass spectrometry demonstrated that the binding and\/or levels of multiple microtubule associated proteins (MAPs) are perturbed by the R402H mutation including VAPB, REEP1, EZRIN, PRNP and DYNC1l1\/2. Consistent with these data we show that the R402H mutation impairs dynein-mediated transport which is associated with a decoupling of the nucleus to the microtubule organising center. Our data support a model whereby the R402H variant is able to fold and incorporate into microtubules, but acts as a gain of function by perturbing the binding of MAPs.","authors":"Leca, I., Phillips, AW., Hofer, I., Landler, L., Ushakova, L., Cushion, TD., D\u00fcrnberger, G., Stejskal, K., Mechtler, K., Keays, DA.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"PLoS Genet","volume":"16","issue":"11","page":"e1009104","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33085675","title":"Correction: The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes.","abstract":"[This corrects the article DOI: 10.1371\/journal.pgen.1008268.].","authors":"Andergassen, D., Muckenhuber, M., Bammer, PC., Kulinski, TM., Theussl, HC., Shimizu, T., Penninger, JM., Pauler, FM., Hudson, QJ.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"PLoS Genet","volume":"16","issue":"10","page":"e1009151","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33077830","title":"Cytoskeletal disorganization underlies PABPN1-mediated myogenic disability.","abstract":"Muscle wasting and atrophy are regulated by multiple molecular processes, including mRNA processing. Reduced levels of the polyadenylation binding protein nucleus 1 (PABPN1), a multifactorial regulator of mRNA processing, cause muscle atrophy. A proteomic study in muscles with reduced PABPN1 levels suggested dysregulation of sarcomeric and cytoskeletal proteins. Here we investigated the hypothesis that reduced PABPN1 levels lead to an aberrant organization of the cytoskeleton. MURC, a plasma membrane-associated protein, was found to be more abundant in muscles with reduced PABPN1 levels, and it was found to be expressed at regions showing regeneration. A polarized cytoskeletal organization is typical for muscle cells, but muscle cells with reduced PABPN1 levels (named as shPAB) were characterized by a disorganized cytoskeleton that lacked polarization. Moreover, cell mechanical features and myogenic differentiation were significantly reduced in shPAB cells. Importantly, restoring cytoskeletal stability, by actin overexpression, was beneficial for myogenesis, expression of sarcomeric proteins and proper localization of MURC in shPAB cell cultures and in shPAB muscle bundle. We suggest that poor cytoskeletal mechanical features are caused by altered expression levels of cytoskeletal proteins and contribute to muscle wasting and atrophy.","authors":"Olie, CS., van der Wal, E., Cikes, D., Maton, L., de Greef, JC., Lin, IH., Chen, YF., Kareem, E., Penninger, JM., Kessler, BM., Raz, V.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Rep","volume":"10","issue":"1","page":"17621","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33026191","title":"LSD1 inhibition induces differentiation and cell death in Merkel cell carcinoma.","abstract":"Merkel cell carcinoma (MCC) is a highly aggressive, neuroendocrine skin cancer that lacks actionable mutations, which could be utilized for targeted therapies. Epigenetic regulators governing cell identity may represent unexplored therapeutic entry points. Here, we targeted epigenetic regulators in a pharmacological screen and discovered that the lysine-specific histone demethylase 1A (LSD1\/KDM1A) is required for MCC growth in\u00a0vitro and in\u00a0vivo. We show that LSD1 inhibition in MCC disrupts the LSD1-CoREST complex leading to displacement and degradation of HMG20B (BRAF35), a poorly characterized complex member that is essential for MCC proliferation. Inhibition of LSD1 causes derepression of transcriptional master regulators of the neuronal lineage, activates a gene expression signature resembling normal Merkel cells, and induces cell cycle arrest and cell death. Our study unveils the importance of LSD1 for maintaining cellular plasticity and proliferation in MCC. There is also growing evidence that cancer cells exploit cellular plasticity and dedifferentiation programs to evade destruction by the immune system. The combination of LSD1 inhibitors with checkpoint inhibitors may thus represent a promising treatment strategy for MCC patients.","authors":"Leiendecker, L., Jung, PS., Krecioch, I., Neumann, T., Schleiffer, A., Mechtler, K., Wiesner, T., Obenauf, AC.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"EMBO Mol Med","volume":"12","issue":"11","page":"e12525","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32997393","title":"Targeting foam cell formation in inflammatory brain diseases by the histone modifier MS-275.","abstract":"on Status=\"In-Process\" Owner=\"NLM\"><PMID Version=\"1\">32997393<\/PMID><DateRevised><Year>2021<\/Year><Month>04<\/Month><Day>29<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">2328-9503<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><Issue>11<\/Issue><PubDate><Year>2020<\/Year><Month>11<\/Month><\/PubDate><\/JournalIssue><Title>Annals of clinical and translational neurology<\/Title><ISOAbbreviation>Ann Clin Transl Neurol<\/ISOAbbreviation><\/Journal><ArticleTitle>Targeting foam cell formation in inflammatory brain diseases by the histone modifier MS-275.<\/ArticleTitle><Pagination><MedlinePgn>2161-2177<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/acn3.51200<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\">To assess class I-histone deacetylase (HDAC) inhibition on formation of lipid-accumulating, disease-promoting phagocytes upon myelin load in vitro, relevant for neuroinflammatory disorders like multiple sclerosis (MS) and cerebral X-linked adrenoleukodystrophy (X-ALD).","authors":"Zierfuss, B., Weinhofer, I., Buda, A., Popitsch, N., Hess, L., Moos, V., Hametner, S., Kemp, S., K\u00f6hler, W., Forss-Petter, S., Seiser, C., Berger, J.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Ann Clin Transl Neurol","volume":"7","issue":"11","page":"2161-2177","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30482618","title":"Posing the APC\/C E3 Ubiquitin Ligase to Orchestrate Cell Division.","abstract":"The anaphase promoting complex\/cyclosome (APC\/C) E3 ligase controls mitosis and nonmitotic pathways through interactions with proteins that coordinate ubiquitylation. Since the discovery that the catalytic subunits of APC\/C are conformationally dynamic cullin and RING proteins, many unexpected and intricate regulatory mechanisms have emerged. Here, we review structural knowledge of this regulation, focusing on: (i) coactivators, E2 ubiquitin (Ub)-conjugating enzymes, and inhibitors engage or influence multiple sites on APC\/C including the cullin-RING catalytic core; and (ii) the outcomes of these interactions rely on mobility of coactivators and cullin-RING domains, which permits distinct conformations specifying different functions. Thus, APC\/C is not simply an interaction hub, but is instead a dynamic, multifunctional molecular machine whose structure is remodeled by binding partners to achieve temporal ubiquitylation regulating cell division.","authors":"Watson, ER., Brown, NG., Peters, JM., Stark, H., Schulman, BA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Trends Cell Biol","volume":"29","issue":"2","page":"117-134","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32997739","title":"Severe Coronavirus Disease 2019 (COVID-19) is Associated With Elevated Serum Immunoglobulin (Ig) A and Antiphospholipid IgA Antibodies.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Automated\" Owner=\"NLM\"><PMID Version=\"1\">32997739<\/PMID><DateCompleted><Year>2021<\/Year><Month>11<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>11<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1537-6591<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>73<\/Volume><Issue>9<\/Issue><PubDate><Year>2021<\/Year><Month>11<\/Month><Day>02<\/Day><\/PubDate><\/JournalIssue><Title>Clinical infectious diseases : an official publication of the Infectious Diseases Society of America<\/Title><ISOAbbreviation>Clin Infect Dis<\/ISOAbbreviation><\/Journal><ArticleTitle>Severe Coronavirus Disease 2019 (COVID-19) is Associated With Elevated Serum Immunoglobulin (Ig) A and Antiphospholipid IgA Antibodies.<\/ArticleTitle><Pagination><MedlinePgn>e2869-e2874<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/cid\/ciaa1496<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Severe coronavirus disease 2019 (COVID-19) frequently entails complications that bear similarities to autoimmune diseases. To date, there are little data on possible immunoglobulin (Ig) A-mediated autoimmune responses. Here, we aim to determine whether COVID-19 is associated with a vigorous total IgA response and whether IgA antibodies are associated with complications of severe illness. Since thrombotic events are frequent in severe COVID-19 and resemble hypercoagulation of antiphospholipid syndrome, our approach focused on antiphospholipid antibodies (aPL).","authors":"Hasan Ali, O., Bomze, D., Risch, L., Brugger, SD., Paprotny, M., Weber, M., Thiel, S., Kern, L., Albrich, WC., Kohler, P., Kahlert, CR., Vernazza, P., B\u00fchler, PK., Sch\u00fcpbach, RA., G\u00f3mez-Mejia, A., Popa, AM., Bergthaler, A., Penninger, JM., Flatz, L.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Clin Infect Dis","volume":"73","issue":"9","page":"e2869-e2874","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32971570","title":"Dual deficiency of angiotensin-converting enzyme-2 and Mas receptor enhances angiotensin II-induced hypertension and hypertensive nephropathy.","abstract":"Angiotensin-converting enzyme-2 (ACE2) and Mas receptor are the major components of the ACE2\/Ang 1-7\/Mas axis and have been shown to play a protective role in hypertension and hypertensive nephropathy individually. However, the effects of dual deficiency of ACE2 and Mas (ACE2\/Mas) on Ang II-induced hypertensive nephropathy remain unexplored, which was investigated in this study in a mouse model of hypertension induced in either ACE2 knockout (KO) or Mas KO mice and in double ACE2\/Mas KO mice by subcutaneously chronic infusion of Ang II. Compared with wild-type (WT) animals, mice lacking either ACE2 or Mas significantly increased blood pressure over 7-28\u00a0days following a chronic Ang II infusion (P\u00a0&lt;\u00a0.001), which was further exacerbated in double ACE2\/Mas KO mice (P\u00a0&lt;\u00a0.001). Furthermore, compared to a single ACE2 or Mas KO mice, mice lacking ACE2\/Mas developed more severe renal injury including higher levels of serum creatinine and a further reduction in creatinine clearance, and progressive renal inflammation and fibrosis. Mechanistically, worsen hypertensive nephropathy in double ACE2\/Mas KO mice was associated with markedly enhanced AT1-ERK1\/2-Smad3 and NF-\u03baB signalling, thereby promoting renal fibrosis and renal inflammation in the hypertensive kidney. In conclusion, ACE2 and Mas play an additive protective role in Ang II-induced hypertension and hypertensive nephropathy. Thus, restoring the ACE2\/Ang1-7\/Mas axis may represent a novel therapy for hypertension and hypertensive nephropathy.","authors":"Ni, J., Yang, F., Huang, XR., Meng, J., Chen, J., Bader, M., Penninger, JM., Fung, E., Yu, XQ., Lan, HY.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Cell Mol Med","volume":"24","issue":"22","page":"13093-13103","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32963223","title":"A theoretical model of Polycomb\/Trithorax action unites stable epigenetic memory and dynamic regulation.","abstract":"Polycomb and Trithorax group proteins maintain stable epigenetic memory of gene expression states for some genes, but many targets show highly dynamic regulation. Here we combine experiment and theory to examine the mechanistic basis of these different modes of regulation. We present a mathematical model comprising a Polycomb\/Trithorax response element (PRE\/TRE) coupled to a promoter and including Drosophila developmental timing. The model accurately recapitulates published studies of PRE\/TRE mediated epigenetic memory of both silencing and activation. With minimal parameter changes, the same model can also recapitulate experimental data for a different PRE\/TRE that allows dynamic regulation of its target gene. The model predicts that both cell cycle length and PRE\/TRE identity are critical for determining whether the system gives stable memory or dynamic regulation. Our work provides a simple unifying framework for a rich repertoire of PRE\/TRE functions, and thus provides insights into\u00a0 genome-wide Polycomb\/Trithorax regulation.","authors":"Reinig, J., Ruge, F., Howard, M., Ringrose, L.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"4782","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32934222","title":"A phospho-switch controls RNF43-mediated degradation of Wnt receptors to suppress tumorigenesis.","abstract":"Frequent mutation of the tumour suppressor RNF43 is observed in many cancers, particularly colon malignancies. RNF43, an E3 ubiquitin ligase, negatively regulates Wnt signalling by inducing degradation of the Wnt receptor Frizzled. In this study, we discover that RNF43 activity requires phosphorylation at a triplet of conserved serines. This phospho-regulation of RNF43 is required for zebrafish development and growth of mouse intestinal organoids. Cancer-associated mutations that abrogate RNF43 phosphorylation cooperate with active Ras to promote tumorigenesis by abolishing the inhibitory function of RNF43 in Wnt signalling while maintaining its inhibitory function in p53 signalling. Our data suggest that RNF43 mutations cooperate with KRAS mutations to promote multi-step tumorigenesis via the Wnt-Ras-p53 axis in human colon cancers. Lastly, phosphomimetic substitutions of the serine trio restored the tumour suppressive activity of extracellular oncogenic mutants. Therefore, harnessing phospho-regulation of RNF43 might be a potential therapeutic strategy for tumours with RNF43 mutations.","authors":"Tsukiyama, T., Zou, J., Kim, J., Ogamino, S., Shino, Y., Masuda, T., Merenda, A., Matsumoto, M., Fujioka, Y., Hirose, T., Terai, S., Takahashi, H., Ishitani, T., Nakayama, KI., Ohba, Y., Koo, BK., Hatakeyama, S.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"4586","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24525182","title":"Making the most of the midbody remnant: specification of the dorsal-ventral axis.","abstract":"In this issue of Developmental Cell, Singh and Pohl (2014) report that myosin II cortical flow and the midbody remnant participate in the specification of the C.\u00a0elegans embryo dorsal-ventral axis.","authors":"Pinheiro, D., Bella\u00efche, Y.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Dev Cell","volume":"28","issue":"3","page":"219-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21131980","title":"An assessment of histone-modification antibody quality.","abstract":"We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http:\/\/compbio.med.harvard.edu\/antibodies\/).","authors":"Egelhofer, TA., Minoda, A., Klugman, S., Lee, K., Kolasinska-Zwierz, P., Alekseyenko, AA., Cheung, MS., Day, DS., Gadel, S., Gorchakov, AA., Gu, T., Kharchenko, PV., Kuan, S., Latorre, I., Linder-Basso, D., Luu, Y., Ngo, Q., Perry, M., Rechtsteiner, A., Riddle, NC., Schwartz, YB., Shanower, GA., Vielle, A., Ahringer, J., Elgin, SC., Kuroda, MI., Pirrotta, V., Ren, B., Strome, S., Park, PJ., Karpen, GH., Hawkins, RD., Lieb, JD.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Struct Mol Biol","volume":"18","issue":"1","page":"91-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-02-11","doi":"10.1038\/nsmb.1972","first_author":"Egelhofer, TA.","corresponding_authors":"Lieb, JD."},{"pmid":"32886546","title":"Toxin-Antidote Elements Across the Tree of Life.","abstract":"In life's constant battle for survival, it takes one to kill but two to conquer. Toxin-antitoxin or toxin-antidote (TA) elements are genetic dyads that cheat the laws of inheritance to guarantee their transmission to the next generation. This seemingly simple genetic arrangement-a toxin linked to its antidote-is capable of quickly spreading and persisting in natural populations. TA elements were first discovered in bacterial plasmids in the 1980s and have recently been characterized in fungi, plants, and animals, where they underlie genetic incompatibilities and sterility in crosses between wild isolates. In this review, we provide a unified view of TA elements in both prokaryotic and eukaryotic organisms and highlight their similarities and differences at the evolutionary, genetic, and molecular levels. Finally, we propose several scenarios that could explain the paradox of the evolutionary origin of TA elements and argue that these elements may be key evolutionary players and that the full scope of their roles is only beginning to be uncovered.","authors":"Burga, A., Ben-David, E., Kruglyak, L.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Annu Rev Genet","volume":"54","issue":null,"page":"387-415","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32882949","title":"The E3 Ubiquitin-Protein Ligase Cullin 3 Regulates HIV-1 Transcription.","abstract":"The infectious life cycle of the human immunodeficiency virus type 1 (HIV-1) is characterized by an ongoing battle between a compendium of cellular proteins that either promote or oppose viral replication. On the one hand, HIV-1 utilizes dependency factors to support and sustain infection and complete the viral life cycle. On the other hand, both inducible and constitutively expressed host factors mediate efficient and functionally diverse antiviral processes that counteract an infection. To shed light into the complex interplay between HIV-1 and cellular proteins, we previously performed a targeted siRNA screen to identify and characterize novel regulators of viral replication and identified Cullin 3 (Cul3) as a previously undescribed factor that negatively regulates HIV-1 replication. Cul3 is a component of E3-ubiquitin ligase complexes that target substrates for ubiquitin-dependent proteasomal degradation. In the present study, we show that Cul3 is expressed in HIV-1 target cells, such as CD4+ T cells, monocytes, and macrophages and depletion of Cul3 using siRNA or CRISPR\/Cas9 increases HIV-1 infection in immortalized cells and primary CD4+ T cells. Conversely, overexpression of Cul3 reduces HIV-1 infection in single replication cycle assays. Importantly, the antiviral effect of Cul3 was mapped to the transcriptional stage of the viral life cycle, an effect which is independent of its role in regulating the G1\/S cell cycle transition. Using isogenic viruses that only differ in their promotor region, we find that the NF-\u03baB\/NFAT transcription factor binding sites in the LTR are essential for Cul3-dependent regulation of viral gene expression. Although Cul3 effectively suppresses viral gene expression, HIV-1 does not appear to antagonize the antiviral function of Cul3 by targeting it for degradation. Taken together, these results indicate that Cul3 is a negative regulator of HIV-1 transcription which governs productive viral replication in infected cells.","authors":"Langer, S., Yin, X., Diaz, A., Portillo, AJ., Gordon, DE., Rogers, UH., Marlett, JM., Krogan, NJ., Young, JAT., Pache, L., Chanda, SK.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Cells","volume":"9","issue":"9","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32879492","title":"Chromosome clustering by Ki-67 excludes cytoplasm during nuclear assembly.","abstract":"Gene expression in eukaryotes requires the effective separation of nuclear transcription and RNA processing from cytosolic translation<sup>1<\/sup>. This separation is achieved by the nuclear envelope, which controls the exchange of macromolecules through nuclear pores<sup>2<\/sup>. During mitosis, however, the nuclear envelope in animal and plant cells disassembles, allowing cytoplasmic and nuclear components to intermix<sup>3<\/sup>. When the nuclear envelope is reformed, cytoplasmic components are removed from the nucleus by receptor-mediated transport through nuclear pores<sup>2<\/sup>. These pores have a size limit of 39\u00a0nanometres<sup>4-7<\/sup>, which raises the question of how larger cytoplasmic molecules are cleared from the nucleus. Here we show in HeLa cells that large cytoplasmic components are displaced before nuclear envelope assembly by the movement of chromosomes to a dense cluster. This clustering occurs when chromosomes approach the poles of anaphase spindles, and is mediated by a microtubule-independent mechanism that involves the surfactant-like protein Ki-67. Ki-67 forms repulsive molecular brushes during the early stages of mitosis<sup>8<\/sup>, but during mitotic exit the brushes collapse and Ki-67 promotes chromosome clustering. We show that the exclusion of mature ribosomes from the nucleus after mitosis depends on Ki-67-regulated chromosome clustering. Thus, our study reveals that chromosome mechanics help to re-establish the compartmentalization of eukaryotic cells after open mitosis.","authors":"Cuylen-Haering, S., Petrovic, M., Hernandez-Armendariz, A., Schneider, MWG., Samwer, M., Blaukopf, C., Holt, LJ., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nature","volume":"587","issue":"7833","page":"285-290","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32851973","title":"A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress.","abstract":"Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the endoplasmic reticulum (ER). Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism. However, the degree to which ER-phagy is employed by other branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The C53\/UFL1\/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that bridges selective autophagy with ribosome-associated quality control in the ER.","authors":"Stephani, M., Picchianti, L., Gajic, A., Beveridge, R., Skarwan, E., Sanchez de Medina Hernandez, V., Mohseni, A., Clavel, M., Zeng, Y., Naumann, C., Matuszkiewicz, M., Turco, E., Loefke, C., Li, B., D\u00fcrnberger, G., Schutzbier, M., Chen, HT., Abdrakhmanov, A., Savova, A., Chia, KS., Djamei, A., Schaffner, I., Abel, S., Jiang, L., Mechtler, K., Ikeda, F., Martens, S., Clausen, T., Dagdas, Y.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Elife","volume":"9","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32850690","title":"Human Microphysiological Models of Intestinal Tissue and Gut Microbiome.","abstract":"The gastrointestinal (GI) tract is a complex system responsible for nutrient absorption, digestion, secretion, and elimination of waste products that also hosts immune surveillance, the intestinal microbiome, and interfaces with the nervous system. Traditional <i>in vitro<\/i> systems cannot harness the architectural and functional complexity of the GI tract. Recent advances in organoid engineering, microfluidic organs-on-a-chip technology, and microfabrication allows us to create better <i>in vitro<\/i> models of human organs\/tissues. These micro-physiological systems could integrate the numerous cell types involved in GI development and physiology, including intestinal epithelium, endothelium (vascular), nerve cells, immune cells, and their interplay\/cooperativity with the microbiome. In this review, we report recent progress in developing micro-physiological models of the GI systems. We also discuss how these models could be used to study normal intestinal physiology such as nutrient absorption, digestion, and secretion as well as GI infection, inflammation, cancer, and metabolism.","authors":"Steinway, SN., Saleh, J., Koo, BK., Delacour, D., Kim, DH.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Front Bioeng Biotechnol","volume":"8","issue":null,"page":"725","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32792620","title":"Sclerostin expression in trabecular bone is downregulated by osteoclasts.","abstract":"Bone tissues have trabecular bone with a high bone turnover and cortical bone with a low turnover. The mechanisms by which the turnover rate of these bone tissues is determined remain unclear. Osteocytes secrete sclerostin, a Wnt\/\u03b2-catenin signaling antagonist, and inhibit bone formation. We found that sclerostin expression in cortical bone is more marked than in trabecular bone in Sost reporter mice. Leukemia inhibitory factor (LIF) secreted from osteoclasts reportedly suppressed sclerostin expression and promoted bone formation. Here, we report that osteoclasts downregulate sclerostin expression in trabecular bone and promote bone turnover. Treatment of C57BL\/6 mice with an anti-RANKL antibody eliminated the number of osteoclasts and LIF-positive cells in trabecular bone. The number of sclerostin-positive cells was increased in trabecular bone, while the number of \u03b2-catenin-positive cells and bone formation were decreased in trabecular bone. Besides, Tnfsf11 heterozygous (Rankl<sup>+\/-<\/sup>) mice exhibited a decreased number of LIF-positive cells and increased number of sclerostin-positive cells in trabecular bone. Rankl<sup>+\/-<\/sup> mice exhibited a decreased number of \u03b2-catenin-positive cells and reduced bone formation in trabecular bone. Furthermore, in cultured osteoclasts, RANKL stimulation increased Lif mRNA expression, suggesting that RANKL signal increased LIF expression. In conclusion, osteoclasts downregulate sclerostin expression and promote trabecular bone turnover.","authors":"Koide, M., Yamashita, T., Murakami, K., Uehara, S., Nakamura, K., Nakamura, M., Matsushita, M., Ara, T., Yasuda, H., Penninger, JM., Takahashi, N., Udagawa, N., Kobayashi, Y.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Rep","volume":"10","issue":"1","page":"13751","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32750316","title":"Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration.","abstract":"Tissue regeneration is a multi-step process mediated by diverse cellular hierarchies and states that are also implicated in tissue dysfunction and pathogenesis. Here we leveraged single-cell RNA sequencing in combination with in\u00a0vivo lineage tracing and organoid models to finely map the trajectories of alveolar-lineage cells during injury repair and lung regeneration. We identified a distinct AT2-lineage population, damage-associated transient progenitors (DATPs), that arises during alveolar regeneration. We found that interstitial macrophage-derived IL-1\u03b2 primes a subset of AT2 cells expressing Il1r1 for conversion into DATPs via a HIF1\u03b1-mediated glycolysis pathway, which is required for mature AT1 cell differentiation. Importantly, chronic inflammation mediated by IL-1\u03b2 prevents AT1 differentiation, leading to aberrant accumulation of DATPs and impaired alveolar regeneration. Together, this stepwise mapping to cell fate transitions shows how an inflammatory niche controls alveolar regeneration by controlling stem cell fate and behavior.","authors":"Choi, J., Park, JE., Tsagkogeorga, G., Yanagita, M., Koo, BK., Han, N., Lee, JH.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Stem Cell","volume":"27","issue":"3","page":"366-382.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32719478","title":"Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters.","abstract":"We developed a functional lineage tracing tool termed CaTCH (CRISPRa tracing of clones in heterogeneous cell populations). CaTCH combines precise clonal tracing of millions of cells with the ability to retrospectively isolate founding clones alive before and during selection, allowing functional experiments. Using CaTCH, we captured rare clones representing as little as 0.001% of a population and investigated the emergence of resistance to targeted melanoma therapy in vivo.","authors":"Umkehrer, C., Holstein, F., Formenti, L., Jude, J., Froussios, K., Neumann, T., Cronin, SM., Haas, L., Lipp, JJ., Burkard, TR., Fellner, M., Wiesner, T., Zuber, J., Obenauf, AC.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Biotechnol","volume":"39","issue":"2","page":"174-178","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32636524","title":"Human organoids: model systems for human biology and medicine.","abstract":"The historical reliance of biological research on the use of animal models has sometimes made it challenging to address questions that are specific to the understanding of human biology and disease. But with the advent of human organoids - which are stem cell-derived 3D culture systems - it is now possible to re-create the architecture and physiology of human organs in remarkable detail. Human organoids provide unique opportunities for the study of human disease and complement animal models. Human organoids have been used to study infectious diseases, genetic disorders and cancers through the genetic engineering of human stem cells, as well as directly when organoids are generated from patient biopsy samples. This Review discusses the applications, advantages and disadvantages of human organoids as models of development and disease and outlines the challenges that have to be overcome for organoids to be able to substantially reduce the need for animal experiments.","authors":"Kim, J., Koo, BK., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Rev Mol Cell Biol","volume":"21","issue":"10","page":"571-584","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32620833","title":"Salmonella-based platform for efficient delivery of functional binding proteins to the cytosol.","abstract":"Protein-based affinity reagents (like antibodies or alternative binding scaffolds) offer wide-ranging applications for basic research and therapeutic approaches. However, whereas small chemical molecules efficiently reach intracellular targets, the delivery of macromolecules into the cytosol of cells remains a major challenge; thus cytosolic applications of protein-based reagents are rather limited. Some pathogenic bacteria have evolved a conserved type III secretion system (T3SS) which allows the delivery of effector proteins into eukaryotic cells. Here, we enhance the T3SS of an avirulent strain of Salmonella typhimurium to reproducibly deliver multiple classes of recombinant proteins into eukaryotic cells. The efficacy of the system is probed with both DARPins and monobodies to functionally inhibit the paradigmatic and largely undruggable RAS signaling pathway. Thus, we develop a bacterial secretion system for potent cytosolic delivery of therapeutic macromolecules.","authors":"Chabloz, A., Schaefer, JV., Kozieradzki, I., Cronin, SJF., Strebinger, D., Macaluso, F., Wald, J., Rabbitts, TH., Pl\u00fcckthun, A., Marlovits, TC., Penninger, JM.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Commun Biol","volume":"3","issue":"1","page":"342","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32363639","title":"Epigenetic regulation of insulin action and secretion - role in the pathogenesis of type 2 diabetes.","abstract":"The prevalence of type 2 diabetes (T2D) is rapidly increasing worldwide. Obesity, physical inactivity and ageing increase the risk of T2D. Epigenetic modifications can change due to environmental exposures and may thereby predispose to disease. This review aims at summarizing recent advances in epigenetics related to T2D, with a special focus on impaired insulin action and secretion in humans. There will be an emphasis on analyses in human tissues; both from T2D case-control cohorts and intervention studies. Current data support an important role for epigenetics in the pathogenesis of T2D. Numerous studies have found differential DNA methylation and gene expression in skeletal muscle, adipose tissue, the liver and pancreatic islets from subjects with T2D compared with nondiabetic controls. For example, PDX1 has increased DNA methylation and decreased expression in pancreatic islets from patients with T2D compared with nondiabetic controls. Nongenetic risk factors for T2D such as ageing, unhealthy diets and physical activity do also impact the epigenome in human tissues. Interestingly, physical activity altered DNA methylation of candidate genes for T2D such as THADA in muscle and FTO, KCNQ1 and TCF7L2 in adipose tissue. There is also a strong interaction between genetic and epigenetic factors that together seem to affect T2D. mQTL studies in human adipose tissue and pancreatic islets showed that SNPs associated with DNA methylation levels in numerous sites. Several of these SNPs are also associated with T2D. Recent data also support that DNA methylation of some sites in blood may be developed into biomarkers that predict T2D since methylation of, for example TXNIP, ABCG1 and SREBF1 associated with future T2D. Future studies should use this information for development of new therapies and biomarkers and thereby improve prediction, prevention and treatment of T2D and its complications.","authors":"Ling, C.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Intern Med","volume":"288","issue":"2","page":"158-167","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32612138","title":"Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe.","abstract":"To unravel vulnerabilities of KRAS-mutant CRC cells, a shRNA-based screen specifically inhibiting MAPK pathway components and targets was performed in CaCo2 cells harboring conditional oncogenic KRAS<sup>G12V<\/sup>. The custom-designed shRNA library comprised 121 selected genes, which were previously identified to be strongly regulated in response to MEK inhibition. The screen showed that CaCo2 cells expressing KRAS<sup>G12V<\/sup> were sensitive to the suppression of the DNA replication licensing factor minichromosome maintenance complex component 7 (MCM7), whereas KRAS<sup>wt<\/sup> CaCo2 cells were largely resistant to MCM7 suppression. Similar results were obtained in an isogenic DLD-1 cell culture model. Knockdown of MCM7 in a KRAS-mutant background led to replication stress as indicated by increased nuclear RPA focalization. Further investigation showed a significant increase in mitotic cells after simultaneous MCM7 knockdown and KRAS<sup>G12V<\/sup> expression. The increased percentage of mitotic cells coincided with strongly increased DNA damage in mitosis. Taken together, the accumulation of DNA damage in mitotic cells is due to replication stress that remained unresolved, which results in mitotic catastrophe and cell death. In summary, the data show a vulnerability of KRAS-mutant cells towards suppression of MCM7 and suggest that inhibiting DNA replication licensing might be a viable strategy to target KRAS-mutant cancers.","authors":"Gastl, B., Klotz-Noack, K., Klinger, B., Ispasanie, S., Salib, KHF., Zuber, J., Mamlouk, S., Bublitz, N., Bl\u00fcthgen, N., Horst, D., Morkel, M., Sch\u00e4fer, R., Sers, C.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Cell Death Dis","volume":"11","issue":"7","page":"499","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32606137","title":"Leukemia Cell of Origin Influences Apoptotic Priming and Sensitivity to LSD1 Inhibition.","abstract":"The cell of origin of oncogenic transformation is a determinant of therapeutic sensitivity, but the mechanisms governing cell-of-origin-driven differences in therapeutic response have not been delineated. Leukemias initiating in hematopoietic stem cells (HSC) are less sensitive to chemotherapy and highly express the transcription factor <i>MECOM<\/i> (EVI1) compared with leukemias derived from myeloid progenitors. Here, we compared leukemias initiated in either HSCs or myeloid progenitors to reveal a novel function for EVI1 in modulating p53 protein abundance and activity. HSC-derived leukemias exhibit decreased apoptotic priming, attenuated p53 transcriptional output, and resistance to lysine-specific demethylase 1 (LSD1) inhibitors in addition to classical genotoxic stresses. p53 loss of function in <i>Evi1<\/i> <sup>lo<\/sup> progenitor-derived leukemias induces resistance to LSD1 inhibition, and EVI1<sup>hi<\/sup> leukemias are sensitized to LSD1 inhibition by venetoclax. Our findings demonstrate a role for <i>EVI1<\/i> in p53 wild-type cancers in reducing p53 function and provide a strategy to circumvent drug resistance in chemoresistant <i>EVI1<\/i> <sup>hi<\/sup> acute myeloid leukemia. SIGNIFICANCE: We demonstrate that the cell of origin of leukemia initiation influences p53 activity and dictates therapeutic sensitivity to pharmacologic LSD1 inhibitors via the transcription factor EVI1. We show that drug resistance could be overcome in HSC-derived leukemias by combining LSD1 inhibition with venetoclax.<i>See related commentary by Gu et al., p. 1445<\/i>.<i>This article is highlighted in the In This Issue feature, p. 1426<\/i>.","authors":"Cai, SF., Chu, SH., Goldberg, AD., Parvin, S., Koche, RP., Glass, JL., Stein, EM., Tallman, MS., Sen, F., Famulare, CA., Cusan, M., Huang, CH., Chen, CW., Zou, L., Cordner, KB., DelGaudio, NL., Durani, V., Kini, M., Rex, M., Tian, HS., Zuber, J., Baslan, T., Lowe, SW., Rienhoff, HY., Letai, A., Levine, RL., Armstrong, SA.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cancer Discov","volume":"10","issue":"10","page":"1500-1513","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32587319","title":"Author Correction: iLoF: An intelligent Lab on Fiber Approach for Human Cancer Single-Cell Type Identification.","abstract":"An amendment to this paper has been published and can be accessed via a link at the top of the paper.","authors":"Paiva, JS., Jorge, PAS., Ribeiro, RSR., Balma\u00f1a, M., Campos, D., Mereiter, S., Jin, C., Karlsson, NG., Sampaio, P., Reis, CA., Cunha, JPS.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Rep","volume":"10","issue":"1","page":"10775","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32583531","title":"A Joint Action in Times of Pandemic: The German BioImaging Recommendations for Operating Imaging Core Facilities During the SARS-Cov-2 Emergency.","abstract":"Operating shared resource laboratories (SRLs) in times of pandemic is a challenge for research institutions. In a multiuser, high-turnover working space, the transmission of infectious agents is difficult to control. To address this challenge, imaging core facility managers being members of German BioImaging discussed how shared microscopes could be operated with minimal risk of spreading SARS-CoV-2 between users and staff. Here, we describe the resulting guidelines and explain their rationale, with a focus on separating users in space and time, protective face masks, and keeping surfaces virus-free. These recommendations may prove useful for other types of SRLs. \u00a9 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.","authors":"Dietzel, S., Ferrando-May, E., Fried, H., Kukat, C., Naumann, A., Nitschke, R., Pasierbek, P., Peychl, J., Rasse, TM., Schroth-Diez, B., St\u00f6ckl, MT., Terjung, S., Thuenauer, R., Tulok, S., Weidtkamp-Peters, S.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cytometry A","volume":"97","issue":"9","page":"882-886","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32573437","title":"Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism.","abstract":"RNF213 is the major susceptibility factor for Moyamoya disease, a progressive cerebrovascular disorder that often leads to brain stroke in adults and children. Characterization of disease-associated mutations has been complicated by the enormous size of RNF213. Here, we present the cryo-EM structure of mouse RNF213. The structure reveals the intricate fold of the 584 kDa protein, comprising an N-terminal stalk, a dynein-like core with six ATPase units, and a multidomain E3 module. Collaboration with UbcH7, a cysteine-reactive E2, points to an unexplored ubiquitin-transfer mechanism that proceeds in a RING-independent manner. Moreover, we show that pathologic MMD mutations cluster in the composite E3 domain, likely interfering with substrate ubiquitination. In conclusion, the structure of RNF213 uncovers a distinct type of an E3 enzyme, highlighting the growing mechanistic diversity in ubiquitination cascades. Our results also provide the molecular framework for investigating the emerging role of RNF213 in lipid metabolism, hypoxia, and angiogenesis.","authors":"Ahel, J., Lehner, A., Vogel, A., Schleiffer, A., Meinhart, A., Haselbach, D., Clausen, T.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Elife","volume":"9","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32358509","title":"PBRM1 loss defines a nonimmunogenic tumor phenotype associated with checkpoint inhibitor resistance in renal carcinoma.","abstract":"A non-immunogenic tumor microenvironment (TME) is a significant barrier to immune checkpoint blockade (ICB) response. The impact of Polybromo-1 (PBRM1) on TME and response to ICB in renal cell carcinoma (RCC) remains to be resolved. Here we show that PBRM1\/Pbrm1 deficiency reduces the binding of brahma-related gene 1 (BRG1) to the IFN\u03b3 receptor 2 (Ifngr2) promoter, decreasing\u00a0STAT1 phosphorylation and the subsequent expression of IFN\u03b3 target genes. An analysis of 3 independent patient cohorts and of murine pre-clinical models reveals that PBRM1 loss is associated with a less immunogenic TME and upregulated angiogenesis. Pbrm1 deficient Renca subcutaneous tumors in mice are more resistance to ICB, and a retrospective analysis of the IMmotion150 RCC study also suggests that PBRM1 mutation reduces benefit from ICB. Our study sheds light on the influence of PBRM1 mutations on IFN\u03b3-STAT1 signaling and TME, and can inform additional preclinical and clinical studies in RCC.","authors":"Liu, XD., Kong, W., Peterson, CB., McGrail, DJ., Hoang, A., Zhang, X., Lam, T., Pilie, PG., Zhu, H., Beckermann, KE., Haake, SM., Isgandrova, S., Martinez-Moczygemba, M., Sahni, N., Tannir, NM., Lin, SY., Rathmell, WK., Jonasch, E.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"2135","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32567732","title":"MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation.","abstract":"Mitochondrial function is critically dependent on the folding of the mitochondrial inner membrane into cristae; indeed, numerous human diseases are associated with aberrant crista morphologies. With the MICOS complex, OPA1 and the F<sub>1<\/sub> F<sub>o<\/sub> -ATP synthase, key players of cristae biogenesis have been identified, yet their interplay is poorly understood. Harnessing super-resolution light and 3D electron microscopy, we dissect the roles of these proteins in the formation of cristae in human mitochondria. We individually disrupted the genes of all seven MICOS subunits in human cells and re-expressed Mic10 or Mic60 in the respective knockout cell line. We demonstrate that assembly of the MICOS complex triggers remodeling of pre-existing unstructured cristae and de novo formation of crista junctions (CJs) on existing cristae. We show that the Mic60-subcomplex is sufficient for CJ formation, whereas the Mic10-subcomplex controls lamellar cristae biogenesis. OPA1 stabilizes tubular CJs and, along with the F<sub>1<\/sub> F<sub>o<\/sub> -ATP synthase, fine-tunes the positioning of the MICOS complex and CJs. We propose a new model of cristae formation, involving the coordinated remodeling of an unstructured crista precursor into multiple lamellar cristae.","authors":"Stephan, T., Br\u00fcser, C., Deckers, M., Steyer, AM., Balzarotti, F., Barbot, M., Behr, TS., Heim, G., H\u00fcbner, W., Ilgen, P., Lange, F., Pacheu-Grau, D., Pape, JK., Stoldt, S., Huser, T., Hell, SW., M\u00f6bius, W., Rehling, P., Riedel, D., Jakobs, S.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"EMBO J","volume":"39","issue":"14","page":"e104105","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32555348","title":"Proline-rich protein PRR19 functions with cyclin-like CNTD1 to promote meiotic crossing over in mouse.","abstract":"Orderly chromosome segregation is enabled by crossovers between homologous chromosomes in the first meiotic division. Crossovers arise from recombination-mediated repair of programmed DNA double-strand breaks (DSBs). Multiple DSBs initiate recombination, and most are repaired without crossover formation, although one or more generate crossovers on each chromosome. Although the underlying mechanisms are ill-defined, the differentiation and maturation of crossover-specific recombination intermediates requires the cyclin-like CNTD1. Here, we identify PRR19 as a partner of CNTD1. We find that, like CNTD1, PRR19 is required for timely DSB repair and the formation of crossover-specific recombination complexes. PRR19 and CNTD1 co-localise at crossover sites, physically interact, and are interdependent for accumulation, indicating a PRR19-CNTD1 partnership in crossing over. Further, we show that CNTD1 interacts with a cyclin-dependent kinase, CDK2, which also accumulates in crossover-specific recombination complexes. Thus, the PRR19-CNTD1 complex may enable crossover differentiation by regulating CDK2.","authors":"Bondarieva, A., Raveendran, K., Telychko, V., Rao, HBDP., Ravindranathan, R., Zorzompokou, C., Finsterbusch, F., Dereli, I., Papanikos, F., Tr\u00e4nkner, D., Schleiffer, A., Fei, JF., Klimova, A., Ito, M., Kulkarni, DS., Roeder, I., Hunter, N., T\u00f3th, A.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"3101","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32540400","title":"Introducing www.axolotl-omics.org - an integrated -omics data portal for the axolotl research community.","abstract":"Genomic resources are indispensable for biological investigations in model organisms. In recent years, a number of genomic resources including a full genome assembly, extensive transcriptomic data, as well as genome editing has been developed for the axolotl, a classical model organism for developmental, neurobiological and regeneration studies, making the axolotl a highly versatile system. Here we describe the Axolotl-omics website that allows rapid ortholog searches, and access to genome and transcriptomic resources.","authors":"Nowoshilow, S., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Exp Cell Res","volume":"394","issue":"1","page":"112143","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12842010","title":"Epigenetic marking correlates with developmental potential in cloned bovine preimplantation embryos.","abstract":"During differentiation, somatic nuclei acquire highly specialized DNA and chromatin modifications, which are thought to result in cellular memory of the differentiated state. Upon somatic nuclear transfer into oocytes, the donor nucleus may have to undergo reprogramming of these epigenetic marks in order to achieve totipotency. This may involve changes in epigenetic features similar to those that occur in normal embryos during early development. However, there is accumulating evidence that epigenetic reprogramming is severely deficient in cloned embryos. Several reports reveal inefficient demethylation and inappropriate reestablishment of DNA methylation in quantitative and qualitative patterns on somatic nuclear transfer. Here we examine histone H3 lysine 9 (H3-K9) methylation and acetylation in normal embryos and in those created by somatic nuclear transfer. We find that H3-K9 methylation is reprogrammed in parallel with DNA methylation in normal embryos. However, the majority of cloned embryos exhibit H3-K9 hypermethylation associated with DNA hypermethylation, suggesting a genome-wide failure of reprogramming. Strikingly, the precise epigenotype in cloned embryos depends on the donor cell type, and the proportion of embryos with normal epigenotypes correlates closely with the proportion developing to the blastocyst stage. These results suggest a mechanistic link between DNA and histone methylation in the mammalian embryo and reveal an association between epigenetic marks and developmental potential of cloned embryos.","authors":"Santos, F., Zakhartchenko, V., Stojkovic, M., Peters, A., Jenuwein, T., Wolf, E., Reik, W., Dean, W.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Curr Biol","volume":"13","issue":"13","page":"1116-21","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2004-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32369597","title":"The EMT modulator SNAI1 contributes to AML pathogenesis via its interaction with LSD1.","abstract":"Modulators of epithelial-to-mesenchymal transition (EMT) have recently emerged as novel players in the field of leukemia biology. The mechanisms by which EMT modulators contribute to leukemia pathogenesis, however, remain to be elucidated. Here we show that overexpression of SNAI1, a key modulator of EMT, is a pathologically relevant event in human acute myeloid leukemia (AML) that contributes to impaired differentiation, enhanced self-renewal, and proliferation of immature myeloid cells. We demonstrate that ectopic expression of Snai1 in hematopoietic cells predisposes mice to AML development. This effect is mediated by interaction with the histone demethylase KDM1A\/LSD1. Our data shed new light on the role of SNAI1 in leukemia development and identify a novel mechanism of LSD1 corruption in cancer. This is particularly pertinent given the current interest surrounding the use of LSD1 inhibitors in the treatment of multiple different malignancies, including AML.","authors":"Carmichael, CL., Wang, J., Nguyen, T., Kolawole, O., Benyoucef, A., De Mazi\u00e8re, C., Milne, AR., Samuel, S., Gillinder, K., Hediyeh-Zadeh, S., Vo, ANQ., Huang, Y., Knezevic, K., McInnes, WRL., Shields, BJ., Mitchell, H., Ritchie, ME., Lammens, T., Lintermans, B., Van Vlierberghe, P., Wong, NC., Haigh, K., Thoms, JAI., Toulmin, E., Curtis, DJ., Oxley, EP., Dickins, RA., Beck, D., Perkins, A., McCormack, MP., Davis, MJ., Berx, G., Zuber, J., Pimanda, JE., Kile, BT., Goossens, S., Haigh, JJ.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Blood","volume":"136","issue":"8","page":"957-973","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32467316","title":"STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers.","abstract":"The cohesin subunit <i>STAG2<\/i> has emerged as a recurrently inactivated tumor suppressor in human cancers. Using candidate approaches, recent studies have revealed a synthetic lethal interaction between <i>STAG2<\/i> and its paralog <i>STAG1<\/i> To systematically probe genetic vulnerabilities in the absence of STAG2, we have performed genome-wide CRISPR screens in isogenic cell lines and identified STAG1 as the most prominent and selective dependency of STAG2-deficient cells. Using an inducible degron system, we show that chemical genetic degradation of STAG1 protein results in the loss of sister chromatid cohesion and rapid cell death in STAG2-deficient cells, while sparing <i>STAG2<\/i>-wild-type cells. Biochemical assays and X-ray crystallography identify STAG1 regions that interact with the RAD21 subunit of the cohesin complex. STAG1 mutations that abrogate this interaction selectively compromise the viability of <i>STAG2<\/i>-deficient cells. Our work highlights the degradation of STAG1 and inhibition of its interaction with RAD21 as promising therapeutic strategies. These findings lay the groundwork for the development of STAG1-directed small molecules to exploit synthetic lethality in <i>STAG2<\/i>-mutated tumors.","authors":"van der Lelij, P., Newman, JA., Lieb, S., Jude, J., Katis, V., Hoffmann, T., Hinterndorfer, M., Bader, G., Kraut, N., Pearson, MA., Peters, JM., Zuber, J., Gileadi, O., Petronczki, M.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Life Sci Alliance","volume":"3","issue":"7","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32442405","title":"Identification of ALK in Thinness.","abstract":"There is considerable inter-individual variability in susceptibility to weight gain despite an equally obesogenic environment in large parts of the world. Whereas many studies have focused on identifying the genetic susceptibility to obesity, we performed a GWAS on metabolically healthy thin individuals (lowest 6<sup>th<\/sup> percentile of the population-wide BMI spectrum) in a uniquely phenotyped Estonian cohort. We discovered anaplastic lymphoma kinase (ALK) as a candidate thinness gene. In Drosophila, RNAi mediated knockdown of Alk led to decreased triglyceride levels. In mice, genetic deletion of Alk resulted in thin animals with marked resistance to diet- and leptin-mutation-induced obesity. Mechanistically, we found that ALK expression in hypothalamic neurons controls energy expenditure via sympathetic control of adipose tissue lipolysis. Our genetic and mechanistic experiments identify ALK as a thinness gene, which is involved in the resistance to weight gain.","authors":"Orthofer, M., Valsesia, A., M\u00e4gi, R., Wang, QP., Kaczanowska, J., Kozieradzki, I., Leopoldi, A., Cikes, D., Zopf, LM., Tretiakov, EO., Demetz, E., Hilbe, R., Boehm, A., Ticevic, M., N\u00f5ukas, M., Jais, A., Spirk, K., Clark, T., Amann, S., Lepamets, M., Neumayr, C., Arnold, C., Dou, Z., Kuhn, V., Novatchkova, M., Cronin, SJF., Tietge, UJF., M\u00fcller, S., Pospisilik, JA., Nagy, V., Hui, CC., Lazovic, J., Esterbauer, H., Hagelkruys, A., Tancevski, I., Kiefer, FW., Harkany, T., Haubensak, W., Neely, GG., Metspalu, A., Hager, J., Gheldof, N., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell","volume":"181","issue":"6","page":"1246-1262.e22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32366477","title":"HACE1 Prevents Lung Carcinogenesis via Inhibition of RAC-Family GTPases.","abstract":"HACE1 is an E3 ubiquitin ligase with important roles in tumor biology and tissue homeostasis. Loss or mutation of <i>HACE1<\/i> has been associated with the occurrence of a variety of neoplasms, but the underlying mechanisms have not been defined yet. Here, we report that <i>HACE1<\/i> is frequently mutated in human lung cancer. In mice, loss of <i>Hace1<\/i> led to enhanced progression of <i>KRas<sup>G12D<\/sup><\/i> -driven lung tumors. Additional ablation of the oncogenic GTPase <i>Rac1<\/i> partially reduced progression of <i>Hace1<sup>-\/-<\/sup><\/i> lung tumors. RAC2, a novel ubiquitylation target of HACE1, could compensate for the absence of its homolog RAC1 in <i>Hace1<\/i>-deficient, but not in HACE1-sufficient tumors. Accordingly, ablation of both <i>Rac1<\/i> and <i>Rac2<\/i> fully averted the increased progression of <i>KRas<sup>G12D<\/sup><\/i> -driven lung tumors in <i>Hace1<sup>-\/-<\/sup><\/i> mice. In patients with lung cancer, increased expression of <i>HACE1<\/i> correlated with reduced levels of <i>RAC1<\/i> and <i>RAC2<\/i> and prolonged survival, whereas elevated expression of <i>RAC1<\/i> and <i>RAC2<\/i> was associated with poor prognosis. This work defines HACE1 as a crucial regulator of the oncogenic activity of RAC-family GTPases in lung cancer development. SIGNIFICANCE: These findings reveal that mutation of the tumor suppressor HACE1 disrupts its role as a regulator of the oncogenic activity of RAC-family GTPases in human and murine lung cancer. GRAPHICAL ABSTRACT: http:\/\/cancerres.aacrjournals.org\/content\/canres\/80\/14\/3009\/F1.large.jpg.","authors":"Kogler, M., Tortola, L., Negri, GL., Leopoldi, A., El-Naggar, AM., Mereiter, S., Gomez-Diaz, C., Nitsch, R., Tortora, D., Kavirayani, AM., Gapp, BV., Rao, S., Uribesalgo, I., Hoffmann, D., Cikes, D., Novatchkova, M., Williams, DA., Trent, JM., Ikeda, F., Daugaard, M., Hagelkruys, A., Sorensen, PH., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cancer Res","volume":"80","issue":"14","page":"3009-3022","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32365404","title":"TDP43 proteinopathy is associated with aberrant DNA methylation in human amyotrophic lateral sclerosis.","abstract":"on Status=\"In-Process\" Owner=\"NLM\"><PMID Version=\"1\">32365404<\/PMID><DateRevised><Year>2021<\/Year><Month>03<\/Month><Day>17<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1365-2990<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>47<\/Volume><Issue>1<\/Issue><PubDate><Year>2021<\/Year><Month>02<\/Month><\/PubDate><\/JournalIssue><Title>Neuropathology and applied neurobiology<\/Title><ISOAbbreviation>Neuropathol Appl Neurobiol<\/ISOAbbreviation><\/Journal><ArticleTitle>TDP43 proteinopathy is associated with aberrant DNA methylation in human amyotrophic lateral sclerosis.<\/ArticleTitle><Pagination><MedlinePgn>61-72<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/nan.12625<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by motor neurone (MN) degeneration and death. ALS can be sporadic (sALS) or familial, with a number of associated gene mutations, including C9orf72 (C9ALS). DNA methylation is an epigenetic mechanism whereby a methyl group is attached to a cytosine (5mC), resulting in gene expression repression. 5mC can be further oxidized to 5-hydroxymethylcytosine (5hmC). DNA methylation has been studied in other neurodegenerative diseases, but little work has been conducted in ALS.","authors":"Appleby-Mallinder, C., Schaber, E., Kirby, J., Shaw, PJ., Cooper-Knock, J., Heath, PR., Highley, JR.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Neuropathol Appl Neurobiol","volume":"47","issue":"1","page":"61-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32365348","title":"Loss of Snord116 impacts lateral hypothalamus, sleep, and food-related behaviors.","abstract":"Imprinted genes are highly expressed in the hypothalamus; however, whether specific imprinted genes affect hypothalamic neuromodulators and their functions is unknown. It has been suggested that Prader-Willi syndrome (PWS), a neurodevelopmental disorder caused by lack of paternal expression at chromosome 15q11-q13, is characterized by hypothalamic insufficiency. Here, we investigate the role of the paternally expressed Snord116 gene within the context of sleep and metabolic abnormalities of PWS, and we report a significant role of this imprinted gene in the function and organization of the 2 main neuromodulatory systems of the lateral hypothalamus (LH) - namely, the orexin (OX) and melanin concentrating hormone (MCH) - systems. We observed that the dynamics between neuronal discharge in the LH and the sleep-wake states of mice with paternal deletion of Snord116 (PWScrm+\/p-) are compromised. This abnormal state-dependent neuronal activity is paralleled by a significant reduction in OX neurons in the LH of mutant mice. Therefore, we propose that an imbalance between OX- and MCH-expressing neurons in the LH of mutant mice reflects a series of deficits manifested in the PWS, such as dysregulation of rapid eye movement (REM) sleep, food intake, and temperature control.","authors":"Pace, M., Falappa, M., Freschi, A., Balzani, E., Berteotti, C., Lo Martire, V., Kaveh, F., Hovig, E., Zoccoli, G., Amici, R., Cerri, M., Urbanucci, A., Tucci, V.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"JCI Insight","volume":"5","issue":"12","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32363359","title":"ZBTB20-mediated titanium particle-induced peri-implant osteolysis by promoting macrophage inflammatory responses.","abstract":"Aseptic loosening (AL) caused by wear particles released from implant surfaces is one of the main causes for the failure of artificial joints, which is initiated by macrophage inflammatory responses. Emerging evidence suggests that the member of a broad-complex, tramtrack, bric-a-brac\/poxvirus and zinc finger (BTB\/POZ) family as well as zinc finger and BTB domain-containing protein 20 (ZBTB20) can inhibit I\u03baB\u03b1 gene transcription, promote NF-\u03baB activation, and initiate innate immune responses. The molecular mechanism(s) by which ZBTB20 contributes to titanium particle (TiP)-induced macrophage inflammatory responses and osteolysis has not been fully elucidated. Here, we showed that ZBTB20 increased either in the AL group's synovial membranes or in TiP-stimulated bone-marrow-derived macrophages (BMDMs) as compared to that in the control groups. Moreover, the knockdown of ZBTB20 led to the inhibition of proinflammatory factors induced by TiPs in BMDMs, such as tumor necrosis factor-\u03b1 (TNF-\u03b1), interleukin-6 (IL-6), and interferon-\u03b2 (IFN-\u03b2). Here, we also reported that the knockdown of ZBTB20 suppressed TiP-induced NF-\u03baB activation and M1 polarization as well as stabilized the trans Golgi network (TGN) in BMDMs. The dual-luciferase reporter assay identified the binding between the I\u03baB\u03b1 promoter and ZBTB20, and I\u03baB\u03b1 knockdown could rescue the antiinflammatory effects induced by the ZBTB20 knockdown in BMDMs. Finally, we found that sh-ZBTB20 lentivirus injection could reduce TiP-induced osteolysis in mouse calvaria, inhibiting TiP-induced proinflammatory factors and loss of bone volume\/total volume (BV\/TV) as well as bone mineral density (BMD). These results suggest that ZBTB20 positively regulated NF-\u03baB activation and M1 polarization as well as the production of TGN-derived tubular carriers in BMDMs, playing a positive role in macrophage activation and mouse cranial osteolysis induced by TiPs. It may be a potential therapeutic target for the prevention of aseptic loosening of prostheses.","authors":"Qiu, J., Peng, P., Xin, M., Wen, Z., Chen, Z., Lin, S., Kuang, M., Fu, Y., Fang, G., Li, S., Li, C., Mao, J., Qin, L., Ding, Y.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Biomater Sci","volume":"8","issue":"11","page":"3147-3163","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32363192","title":"Histone Deacetylase 11 Contributes to Renal Fibrosis by Repressing KLF15 Transcription.","abstract":"Renal fibrosis represents a key pathophysiological process in patients with chronic kidney diseases (CKD) and is typically associated with a poor prognosis. Renal tubular epithelial cells (RTECs), in response to a host of pro-fibrogenic stimuli, can <i>trans-<\/i>differentiate into myofibroblast-like cells and produce extracellular matrix proteins to promote renal fibrosis. In the present study we investigated the role of histone deacetylase 11 (HDAC11) in this process and the underlying mechanism. We report that expression levels of HDAC11 were up-regulated in the kidneys in several different animal models of renal fibrosis. HDAC11 was also up-regulated by treatment of Angiotensin II (Ang II) in cultured RTECs. Consistently, pharmaceutical inhibition with a small-molecule inhibitor of HDAC11 (quisinostat) attenuated unilateral ureteral obstruction (UUO) induced renal fibrosis in mice. Similarly, HDAC11 inhibition by quisinostat or HDAC11 depletion by siRNA blocked Ang II induced pro-fibrogenic response in cultured RTECs. Mechanistically, HDAC11 interacted with activator protein 2 (AP-2\u03b1) to repress the transcription of Kruppel-like factor 15 (KLF15). In accordance, KLF15 knockdown antagonized the effect of HDAC11 inhibition or depletion and enabled Ang II to promote fibrogenesis in RTECs. Therefore, we data unveil a novel AP-2\u03b1-HDAC11-KLF15 axis that contributes to renal fibrosis.","authors":"Mao, L., Liu, L., Zhang, T., Qin, H., Wu, X., Xu, Y.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Front Cell Dev Biol","volume":"8","issue":"","page":"235","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32363032","title":"Health impact of the Anthropocene: the complex relationship between gut microbiota, epigenetics, and human health, using obesity as an example.","abstract":"The growing prevalence of obesity worldwide poses a public health challenge in the current geological epoch, the Anthropocene. Global changes caused by urbanisation, loss of biodiversity, industrialisation, and land-use are happening alongside microbiota dysbiosis and increasing obesity prevalence. How alterations of the gut microbiota are associated with obesity and the epigenetic mechanism mediating this and other health outcome associations are in the process of being unveiled. Epigenetics is emerging as a key mechanism mediating the interaction between human body and the environment in producing disease. Evidence suggests that the gut microbiota plays a role in obesity as it contributes to different mechanisms, such as metabolism, body weight and composition, inflammatory responses, insulin signalling, and energy extraction from food. Consistently, obese people tend to have a different epigenetic profile compared to non-obese. However, evidence is usually scattered and there is a growing need for a structured framework to conceptualise this complexity and to help shaping complex solutions. In this paper, we propose a framework to analyse the observed associations between the alterations of microbiota and health outcomes and the role of epigenetic mechanisms underlying them using obesity as an example, in the current context of global changes within the Anthropocene.","authors":"Torp Austvoll, C., Gallo, V., Montag, D.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Glob Health Epidemiol Genom","volume":"5","issue":"","page":"e2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32362568","title":"Tumor specific methylome in Chinese high-grade serous ovarian cancer characterized by gene expression profile and tumor genotype.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">32362568<\/PMID><DateCompleted><Year>2021<\/Year><Month>02<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>02<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1095-6859<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>158<\/Volume><Issue>1<\/Issue><PubDate><Year>2020<\/Year><Month>07<\/Month><\/PubDate><\/JournalIssue><Title>Gynecologic oncology<\/Title><ISOAbbreviation>Gynecol Oncol<\/ISOAbbreviation><\/Journal><ArticleTitle>Tumor specific methylome in Chinese high-grade serous ovarian cancer characterized by gene expression profile and tumor genotype.<\/ArticleTitle><Pagination><MedlinePgn>178-187<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0090-8258(20)30988-4<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.ygyno.2020.04.688<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\">Extensive genetic and limited epigenetics have been characterized by the Cancer Genome Atlas (TCGA) among Western High-grade serous ovarian cancer (HGSOC). The present study aimed to characterize Chinese HGSOC at genome scale.","authors":"Song, F., Li, L., Zhang, B., Zhao, Y., Zheng, H., Yang, M., Li, X., Tian, J., Huang, C., Liu, L., Wang, Q., Zhang, W., Chen, K.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Gynecol Oncol","volume":"158","issue":"1","page":"178-187","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32251373","title":"Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction.","abstract":"Active enhancers are frequently transcribed, yet the regulatory role of enhancer transcription remains debated. Here, we depleted the RNA polymerase II pausing and elongation factor Spt5 in activated mouse B cells and found that approximately 50% of enhancer-gene pairs showed co-regulated transcription, consistent with a potential functional requirement for enhancer transcription. In particular, Spt5 depletion led to loss of super-enhancer-promoter physical interaction and gene expression at the immunoglobulin heavy-chain locus (Igh), abrogating antibody class switch recombination. This defect correlated strictly with loss of enhancer transcription but did not affect acetylation of histone H3 at lysine 27, chromatin accessibility and occupancy of Mediator and cohesin at the enhancer. Strikingly, CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restored Igh gene expression. Our work suggests that Spt5-mediated enhancer transcription underlies the physical and functional interaction between a subset of active enhancers and their target promoters.","authors":"Fitz, J., Neumann, T., Steininger, M., Wiedemann, EM., Garcia, AC., Athanasiadis, A., Schoeberl, UE., Pavri, R.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Genet","volume":"52","issue":"5","page":"505-515","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32362324","title":"Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis.","abstract":"Tissue-resident and recruited macrophages contribute to both host defense and pathology. Multiple macrophage phenotypes are represented in diseased tissues, but we lack deep understanding of mechanisms controlling diversification. Here, we investigate origins and epigenetic trajectories of hepatic macrophages during diet-induced non-alcoholic steatohepatitis (NASH). The NASH diet induced significant changes in Kupffer cell enhancers and gene expression, resulting in partial loss of Kupffer cell identity, induction of Trem2 and Cd9 expression, and cell death. Kupffer cell loss was compensated by gain of adjacent monocyte-derived macrophages that exhibited convergent epigenomes, transcriptomes, and functions. NASH-induced changes in Kupffer cell enhancers were driven by AP-1 and EGR that reprogrammed LXR functions required for Kupffer cell identity and survival to instead drive a scar-associated macrophage phenotype. These findings reveal mechanisms by which disease-associated environmental signals instruct resident and recruited macrophages to acquire distinct gene expression programs and corresponding functions.","authors":"Seidman, JS., Troutman, TD., Sakai, M., Gola, A., Spann, NJ., Bennett, H., Bruni, CM., Ouyang, Z., Li, RZ., Sun, X., Vu, BT., Pasillas, MP., Ego, KM., Gosselin, D., Link, VM., Chong, LW., Evans, RM., Thompson, BM., McDonald, JG., Hosseini, M., Witztum, JL., Germain, RN., Glass, CK.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Immunity","volume":"52","issue":"6","page":"1057-1074.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32361531","title":"Precision medicine in distinct heart failure phenotypes: Focus on clinical epigenetics.","abstract":"Heart failure (HF) management is challenging due to high clinical heterogeneity of this disease which makes patients responding differently to evidence-based standard therapy established by the current reductionist approach. Better understanding of the genetic and epigenetic interactions may clarify molecular signatures underlying maladaptive responses in HF, including metabolic shift, myocardial injury, fibrosis, and mitochondrial dysfunction. DNA methylation, histone modifications and micro-RNA (miRNAs) may be major epigenetic players in the pathogenesis of HF. DNA hypermethylation of the kruppel-like factor 15 (KLF15) gene plays a key role in switching the failing heart from oxidative to glycolytic metabolism. Moreover, hypomethylation at H3K9 promoter level of atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) genes also leads to reactivation of fetal genes in man. The role of miRNAs has been investigated in HF patients undergoing heart transplantation, for whom miR-10a, miR-155, miR-31, and miR-92 may be putative useful prognostic biomarkers. Recently, higher RNA methylation levels have been observed in ischemic human hearts, opening the era of \"epitranscriptome\" in the pathogenesis of HF. Currently, hydralazine, statins, apabetalone, and omega-3 polyunsatured fatty acids (PUFA) are being tested in clinical trials to provide epigenetic-driven therapeutic interventions. Moreover, network-oriented analysis could advance current medical practice by focusing on protein-protein interactions (PPIs) perturbing the \"cardiac\" interactome. In this review, we provide an epigenetic map of maladaptive responses in HF patients. Furthermore, we propose the \"EPi-transgeneratIonal network mOdeling for STratificatiOn of heaRt Morbidity\" (EPIKO-STORM), a clinical research strategy offering novel opportunities to stratify the natural history of HF.","authors":"Napoli, C., Benincasa, G., Donatelli, F., Ambrosio, G.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Am Heart J","volume":"224","issue":"","page":"113-128","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32361419","title":"Pulmonary surfactant phosphatidylcholines induce immunological adaptation of alveolar macrophages.","abstract":"Pulmonary surfactant plays an important role in lung surface tension, defense against invading pathogens, and immune response. Furthermore, alveolar macrophages (AM) that comprise the front line of immune defense against inhaled microorganisms are covered by a layer of pulmonary fluid. Phosphatidylcholines (PCs), including unsaturated lipids such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), are the most prevalent phospholipids in pulmonary surfactant. POPC reacts with ozone to produce 1-palmitoyl-2-(9-oxo-nonanoyl)-sn-glycero-3-phosphocholine (PONPC), a soluble mediator that initiates an inflammatory reaction in the lungs. However, the modulatory effects of POPC and PONPC on biology and activity of AM remain inconclusive. The exposure of AM (cell line AMJ2-C11) to POPC and PONPC was not directly related to the production of inflammatory mediators. However, AM, pre-incubated with POPC or PONPC, showed enhanced response after lipopolysaccharide (LPS) stimulation, and increased the production of nitric oxide and cytokines. This phenomenon was also observed for classical-polarized macrophages (M1). This increment on the production of inflammatory mediators was not associated with macrophage polarization, but with up-regulation of Tlr4 and Myd88 gene expression, which was in accordance with the adaptation of immune cells. This observation was confirmed by the histone acetylation epigenetic pathway. In contrast to the priming effect of POPC on AM activity, a harmful immune response, induced on incubation with PONPC, improved prostaglandin E<sub>2<\/sub> (PGE<sub>2<\/sub>) formation, resulting in diminished bacterial phagocytosis. Additionally, PONPC induced production of CXCL1\/KC, which potentially mediates neutrophil recruitment and enhances tissue inflammation. These results disclosed another dynamic mechanism by which pulmonary surfactant lipids (natural or oxidized) primed macrophage activity, thus affecting lung host defense.","authors":"da Costa Loureiro, L., da Costa Loureiro, L., Gabriel-Junior, EA., Zambuzi, FA., Fontanari, C., Sales-Campos, H., Frantz, FG., Faccioli, LH., Sorgi, CA.","publication_status":"aheadofprint","journalpubyear":"2020","journaltitle":"Mol Immunol","volume":"122","issue":"","page":"163-172","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32361261","title":"Individual species and cumulative mixture relationships of 24-hour urine metal concentrations with DNA methylation age variables in older men.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Automated\" Owner=\"NLM\"><PMID Version=\"1\">32361261<\/PMID><DateCompleted><Year>2020<\/Year><Month>11<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>07<\/Month><Day>02<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1096-0953<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>186<\/Volume><PubDate><Year>2020<\/Year><Month>07<\/Month><\/PubDate><\/JournalIssue><Title>Environmental research<\/Title><ISOAbbreviation>Environ Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Individual species and cumulative mixture relationships of 24-hour urine metal concentrations with DNA methylation age variables in older men.<\/ArticleTitle><Pagination><MedlinePgn>109573<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0013-9351(20)30466-7<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.envres.2020.109573<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Globally, toxic metal exposures are a well-recognized risk factor for many adverse health outcomes. DNA methylation-based measures of biological aging are predictive of disease, but have poorly understood relationships with metal exposures.","authors":"Nwanaji-Enwerem, JC., Colicino, E., Specht, AJ., Gao, X., Wang, C., Vokonas, P., Weisskopf, MG., Boyer, EW., Baccarelli, AA., Schwartz, J.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Environ Res","volume":"186","issue":"","page":"109573","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32360641","title":"The selected epigenetic effects of aminomethylphosphonic acid, a primary metabolite of glyphosate on human peripheral blood mononuclear cells (in vitro).","abstract":"Aminomethylphosphonic acid (AMPA) is a primary metabolite of glyphosate and amino-polyphosphonate. We have determined the effect of AMPA on selected epigenetic parameters and major cell cycle drivers in human peripheral blood mononuclear cells (PBMCs). The cells were incubated with AMPA at 0.5, 10 and 250\u202f\u03bcM for 24\u202fh. The performed analysis included: global DNA methylation by colorimetric measurement of 5-methylcytosine in DNA, methylation in the promoter regions of selected tumor suppressor genes (P16, P21, TP53) and proto-oncogenes (BCL2, CCND1) as well as the expression profile of the indicated genes by Real-Time PCR assays. The obtained results have revealed significant reduction of global DNA methylation level in PBMCs exposed to AMPA. Investigated xenobiotic changed methylation pattern of the P21 and TP53 suppressor gene promoters, but in case of other analyzed genes: P16, BCL2 and CCND1 no statistically significant changes have been noted. Gene profiling have shown that AMPA only changed the expression of CCND1. Summing up, our results have revealed a small potential disturbance in methylation processes and the absence of changes in expression of tested tumor suppressor genes (P16, P21, TP53) and protooncogenes (BCL2) in human PBMCs exposed to AMPA.","authors":"Wo\u017aniak, E., Reszka, E., Jab\u0142o\u0144ska, E., Mokra, K., Balcerczyk, A., Huras, B., Zakrzewski, J., Bukowska, B.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Toxicol In Vitro","volume":"66","issue":"","page":"104878","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30475900","title":"The RNA helicase DDX3X is an essential mediator of innate antimicrobial immunity.","abstract":"DExD\/H box RNA helicases, such as the RIG-I-like receptors (RLR), are important components of the innate immune system. Here we demonstrate a pivotal and sex-specific role for the heterosomal isoforms of the DEAD box RNA helicase DDX3 in the immune system. Mice lacking DDX3X during hematopoiesis showed an altered leukocyte composition in bone marrow and spleen and a striking inability to combat infection with Listeria monocytogenes. Alterations in innate immune responses resulted from decreased effector cell availability and function as well as a sex-dependent impairment of cytokine synthesis. Thus, our data provide further in vivo evidence for an essential contribution of a non-RLR DExD\/H RNA helicase to innate immunity and suggest it may contribute to sex-related differences in resistance to microbes and resilience to inflammatory disease.","authors":"Szappanos, D., Tschismarov, R., Perlot, T., Westermayer, S., Fischer, K., Platanitis, E., Kallinger, F., Novatchkova, M., Lassnig, C., M\u00fcller, M., Sexl, V., Bennett, KL., Foong-Sobis, M., Penninger, JM., Decker, T.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"PLoS Pathog","volume":"14","issue":"11","page":"e1007397","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32339205","title":"Hyd ubiquitinates the NF-\u03baB co-factor Akirin to operate an effective immune response in Drosophila.","abstract":"The Immune Deficiency (IMD) pathway in Drosophila melanogaster is activated upon microbial challenge with Gram-negative bacteria to trigger the innate immune response. In order to decipher this nuclear factor \u03baB (NF-\u03baB) signaling pathway, we undertook an in vitro RNAi screen targeting E3 ubiquitin ligases specifically and identified the HECT-type E3 ubiquitin ligase Hyperplastic discs (Hyd) as a new actor in the IMD pathway. Hyd mediated Lys63 (K63)-linked polyubiquitination of the NF-\u03baB cofactor Akirin was required for efficient binding of Akirin to the NF-\u03baB transcription factor Relish. We showed that this Hyd-dependent interaction was required for the transcription of immunity-related genes that are activated by both Relish and Akirin but was dispensable for the transcription of genes that depend solely on Relish. Therefore Hyd is key in NF-\u03baB transcriptional selectivity downstream of the IMD pathway. Drosophila depleted of Akirin or Hyd failed to express the full set of genes encoding immune-induced anti-microbial peptides and succumbed to immune challenges. We showed further that UBR5, the mammalian homolog of Hyd, was also required downstream of the NF-\u03baB pathway for the activation of Interleukin 6 (IL6) transcription by LPS or IL-1\u03b2 in cultured human cells. Our findings link the action of an E3 ubiquitin ligase to the activation of immune effector genes, deepening our understanding of the involvement of ubiquitination in inflammation and identifying a potential target for the control of inflammatory diseases.","authors":"Cammarata-Mouchtouris, A., Nguyen, XH., Acker, A., Bonnay, F., Goto, A., Orian, A., Fauvarque, MO., Boutros, M., Reichhart, JM., Matt, N.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"PLoS Pathog","volume":"16","issue":"4","page":"e1008458","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32295833","title":"Dysregulation of Exosome Cargo by Mutant Tau Expressed in Human-induced Pluripotent Stem Cell (iPSC) Neurons Revealed by Proteomics Analyses.","abstract":"Accumulation and propagation of hyperphosphorylated Tau (p-Tau) is a common neuropathological hallmark associated with neurodegeneration of Alzheimer's disease (AD), frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17), and related tauopathies. Extracellular vesicles, specifically exosomes, have recently been demonstrated to participate in mediating Tau propagation in brain. Exosomes produced by human induced pluripotent stem cell (iPSC)-derived neurons expressing mutant Tau (mTau), containing the P301L and V337M Tau mutations of FTDP-17, possess the ability to propagate p-Tau pathology after injection into mouse brain. To gain an understanding of the mTau exosome cargo involved in Tau pathogenesis, these pathogenic exosomes were analyzed by proteomics and bioinformatics. The data showed that mTau expression dysregulates the exosome proteome to result in 1) proteins uniquely present only in mTau, and not control exosomes, 2) the absence of proteins in mTau exosomes, uniquely present in control exosomes, and 3) shared proteins which were significantly upregulated or downregulated in mTau compared with control exosomes. Notably, mTau exosomes (not control exosomes) contain ANP32A (also known as I1PP2A), an endogenous inhibitor of the PP2A phosphatase which regulates the phosphorylation state of p-Tau. Several of the mTau exosome-specific proteins have been shown to participate in AD mechanisms involving lysosomes, inflammation, secretases, and related processes. Furthermore, the mTau exosomes lacked a substantial portion of proteins present in control exosomes involved in pathways of localization, vesicle transport, and protein binding functions. The shared proteins present in both mTau and control exosomes represented exosome functions of vesicle-mediated transport, exocytosis, and secretion processes. These data illustrate mTau as a dynamic regulator of the biogenesis of exosomes to result in acquisition, deletion, and up- or downregulation of protein cargo to result in pathogenic mTau exosomes capable of <i>in vivo<\/i> propagation of p-Tau neuropathology in mouse brain.","authors":"Podvin, S., Jones, A., Liu, Q., Aulston, B., Ransom, L., Ames, J., Shen, G., Lietz, CB., Jiang, Z., O'Donoghue, AJ., Winston, C., Ikezu, T., Rissman, RA., Yuan, S., Hook, V.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Mol Cell Proteomics","volume":"19","issue":"6","page":"1017-1034","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32292421","title":"Pathological Aspects of Neuronal Hyperploidization in Alzheimer's Disease Evidenced by Computer Simulation.","abstract":"When subjected to stress, terminally differentiated neurons are susceptible to reactivate the cell cycle and become hyperploid. This process is well documented in Alzheimer's disease (AD), where it may participate in the etiology of the disease. However, despite its potential importance, the effects of neuronal hyperploidy (NH) on brain function and its relationship with AD remains obscure. An important step forward in our understanding of the pathological effect of NH has been the development of transgenic mice with neuronal expression of oncogenes as model systems of AD. The analysis of these mice has demonstrated that forced cell cycle reentry in neurons results in most hallmarks of AD, including neurofibrillary tangles, A\u03b2 peptide deposits, gliosis, cognitive loss, and neuronal death. Nevertheless, in contrast to the pathological situation, where a relatively small proportion of neurons become hyperploid, neuronal cell cycle reentry in these mice is generalized. We have recently developed an <i>in vitro<\/i> system in which cell cycle is induced in a reduced proportion of differentiated neurons, mimicking the <i>in vivo<\/i> situation. This manipulation reveals that NH correlates with synaptic dysfunction and morphological changes in the affected neurons, and that membrane depolarization facilitates the survival of hyperploid neurons. This suggests that the integration of synaptically silent, hyperploid neurons in electrically active neural networks allows their survival while perturbing the normal functioning of the network itself, a hypothesis that we have tested <i>in silico<\/i>. In this perspective, we will discuss on these aspects trying to convince the reader that NH represents a relevant process in AD.","authors":"Barrio-Alonso, E., Fontana, B., Valero, M., Frade, JM.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Front Genet","volume":"11","issue":"","page":"287","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32286308","title":"Quantifying the heterogeneity of macromolecular machines by mass photometry.","abstract":"Sample purity is central to in vitro studies of protein function and regulation, and to the efficiency and success of structural studies using techniques such as x-ray crystallography and cryo-electron microscopy (cryo-EM). Here, we show that mass photometry (MP) can accurately characterize the heterogeneity of a sample using minimal material with high resolution within a matter of minutes. To benchmark our approach, we use negative stain electron microscopy (nsEM), a popular method for EM sample screening. We include typical workflows developed for structure determination that involve multi-step purification of a multi-subunit ubiquitin ligase and chemical cross-linking steps. When assessing the integrity and stability of large molecular complexes such as the proteasome, we detect and quantify assemblies invisible to nsEM. Our results illustrate the unique advantages of MP over current methods for rapid sample characterization, prioritization and workflow optimization.","authors":"Sonn-Segev, A., Belacic, K., Bodrug, T., Young, G., VanderLinden, RT., Schulman, BA., Schimpf, J., Friedrich, T., Dip, PV., Schwartz, TU., Bauer, B., Peters, JM., Struwe, WB., Benesch, JLP., Brown, NG., Haselbach, D., Kukura, P.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"1772","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24380642","title":"A multicellular view of cytokinesis in epithelial tissue.","abstract":"The study of cytokinesis in single-cell systems provided a wealth of knowledge on the molecular and biophysical mechanisms controlling daughter cell separation. In this review, we outline recent advances in the understanding of cytokinesis in epithelial tissues. These findings provide evidence for how the cytokinetic machinery adapts to a multicellular context and how the cytokinetic machinery is itself exploited by the tissue for the preservation of tissue function and architecture during proliferation. We propose that cytokinesis in epithelia should be viewed as a multicellular process, whereby the biochemical and mechanical interactions between the dividing cell and its neighbors are essential for successful daughter cell separation while defining epithelial tissue organization and preserving tissue integrity.","authors":"Herszterg, S., Pinheiro, D., Bella\u00efche, Y.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Trends Cell Biol","volume":"24","issue":"5","page":"285-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32250121","title":"Fast and Highly Efficient Affinity Enrichment of Azide-A-DSBSO Cross-Linked Peptides.","abstract":"Cross-linking mass spectrometry is an increasingly used, powerful technique to study protein-protein interactions or to provide structural information. Due to substochiometric reaction efficiencies, cross-linked peptides are usually low abundance. This results in challenging data evaluation and the need for an effective enrichment. Here we describe an improved, easy to implement, one-step method to enrich azide-tagged, acid-cleavable disuccinimidyl bis-sulfoxide (DSBSO) cross-linked peptides using dibenzocyclooctyne (DBCO) coupled Sepharose beads. We probed this method using recombinant Cas9 and <i>E.\u00a0coli<\/i> ribosome. For Cas9, the number of detectable cross-links was increased from \u223c100 before enrichment to 580 cross-links after enrichment. To mimic a cellular lysate, <i>E.\u00a0coli<\/i> ribosome was spiked into a tryptic HEK background at a ratio of 1:2-1:100. The number of detectable unique cross-links was maintained high at \u223c100. The estimated enrichment efficiency was improved by a factor of 4-5 (based on XL numbers) compared to enrichment via biotin and streptavidin. We were still able to detect cross-links from 0.25 \u03bcg cross-linked <i>E.\u00a0coli<\/i> ribosomes in a background of 100 \u03bcg tryptic HEK peptides, indicating a high enrichment sensitivity. In contrast to conventional enrichment techniques, like SEC, the time needed for preparation and MS measurement is significantly reduced. This robust, fast, and selective enrichment method for azide-tagged linkers will contribute to mapping protein-protein interactions, investigating protein architectures in more depth, and helping to understand complex biological processes.","authors":"Matzinger, M., Kandioller, W., Doppler, P., Heiss, EH., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Proteome Res","volume":"19","issue":"5","page":"2071-2079","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32211389","title":"Reduced Prenatal Pulmonary Lymphatic Function Is Observed in <i>Clp1<\/i> <sup><i>K\/K<\/i><\/sup> Embryos With Impaired Motor Functions Including Fetal Breathing Movements in Preparation of the Developing Lung for Inflation at Birth.","abstract":"Embryonic lungs must be inflated immediately after birth to establish respiration. In addition to pulmonary surfactant, recently, we have revealed lymphatic function as a previously unknown regulator of prenatal lung compliance that prepares the embryonic lung for inflation at birth. It is well-documented that the late gestation embryo performs episodic breathing-like movements called as fetal breathing movements (FBMs), but the physiological importance of these events is not clear. Here we aimed to study the physiological role of FBMs in preparation for air inflation at birth. <i>Clp1<\/i> <sup><i>K\/K<\/i><\/sup> late gestation embryos develop a progressive loss of spinal motor neurons associated with axonal degeneration and denervation of neuromuscular junctions serving as an ideal genetic model to test the possible role of FBMs. We demonstrated that <i>Clp1<\/i> <sup><i>K\/K<\/i><\/sup> newborns show impaired motor function resulting in fatal respiratory failure after birth. Next, we showed that the alveolar septa are thicker, and the alveolar area is reduced in <i>Clp1<\/i> <sup><i>K\/K<\/i><\/sup> late gestation embryos, while the expression of molecular markers of lung development are not affected. Importantly, pulmonary lymphatic vessels are dilated and the prenatal pulmonary lymphatic function is reduced in <i>Clp1<\/i> <sup><i>K\/K<\/i><\/sup> late gestation embryos. Our results have revealed that <i>Clp1<\/i> <sup><i>K\/K<\/i><\/sup> mice show impaired motor functions including FBMs, and late gestation <i>Clp1<\/i> <sup><i>K\/K<\/i><\/sup> embryos display reduced prenatal lymphatic function and impaired lung expansion represented as thickened alveolar septa and reduced alveolar area in preparation of the developing lung for inflation at birth. These findings suggest a possible mechanism that FBMs, similarly to breathing movements after birth, stimulate prenatal lymphatic function in pulmonary collecting lymphatics lacking smooth muscle coverage to prepare the developing lung for inflation and gas exchange at birth. Moreover, these results raise the possibility that stimulating FBMs during late gestation might be an effective way to reduce the risk of the development of neonatal respiratory failure.","authors":"Szot\u00e1k-Ajtay, K., Sz\u00f5ke, D., Kov\u00e1cs, G., Andr\u00e9ka, J., Brenner, GB., Giricz, Z., Penninger, J., Kahn, ML., Jakus, Z.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Front Bioeng Biotechnol","volume":"8","issue":null,"page":"136","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32210188","title":"A Wnt-BMP4 Signaling Axis Induces MSX and NOTCH Proteins and Promotes Growth Suppression and Differentiation in Neuroblastoma.","abstract":"The Wnt and bone morphogenetic protein (BMP) signaling pathways are known to be crucial in the development of neural crest lineages, including the sympathetic nervous system. Surprisingly, their role in paediatric neuroblastoma, the prototypic tumor arising from this lineage, remains relatively uncharacterised. We previously demonstrated that Wnt\/b-catenin signaling can have cell-type-specific effects on neuroblastoma phenotypes, including growth inhibition and differentiation, and that BMP4 mRNA and protein were induced by Wnt3a\/Rspo2. In this study, we characterised the phenotypic effects of BMP4 on neuroblastoma cells, demonstrating convergent induction of MSX homeobox transcription factors by Wnt and BMP4 signaling and BMP4-induced growth suppression and differentiation. An immunohistochemical analysis of BMP4 expression in primary neuroblastomas confirms a striking absence of BMP4 in poorly differentiated tumors, in contrast to a high expression in ganglion cells. These results are consistent with a tumor suppressive role for BMP4 in neuroblastoma. RNA sequencing following BMP4 treatment revealed induction of Notch signaling, verified by increases of Notch3 and Hes1 proteins. Together, our data demonstrate, for the first time, Wnt-BMP-Notch signaling crosstalk associated with growth suppression of neuroblastoma.","authors":"Szemes, M., Melegh, Z., Bellamy, J., Greenhough, A., Kollareddy, M., Catchpoole, D., Malik, K.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Cells","volume":"9","issue":"3","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32203874","title":"Brain-wide representations of ongoing behavior: a universal principle?","abstract":"Recent neuronal activity recordings of unprecedented breadth and depth in worms, flies, and mice have uncovered a surprising common feature: brain-wide behavior-related signals. These signals pervade, and even dominate, neuronal populations thought to function primarily in sensory processing. Such convergent findings across organisms suggest that brain-wide representations of behavior might be a universal neuroscientific principle. What purpose(s) do these representations serve? Here we review these findings along with suggested functions, including sensory prediction, context-dependent sensory processing, and, perhaps most speculatively, distributed motor command generation. It appears that a large proportion of the brain's energy and coding capacity is used to represent ongoing behavior; understanding the function of these representations should therefore be a major goal in neuroscience research.","authors":"Kaplan, HS., Zimmer, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Curr Opin Neurobiol","volume":"64","issue":null,"page":"60-69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32198488","title":"RANKL and OPG and their influence on breast volume changes during pregnancy in healthy women.","abstract":"Breast cancer risk is reduced by number of pregnancies and breastfeeding duration, however studies of breast changes during or after pregnancy are rare. Breast volume changes - although not linked to breast cancer risk - might be an interesting phenotype in this context for correlative studies, as changes of breast volume vary between pregnant women. Serum receptor activator of nuclear factor kappa B ligand (RANKL) and its antagonist osteoprotegerin (OPG) were measured prospectively before gestational week 12, and three-dimensional breast volume assessments were performed. A linear regression model including breast volume at the start of pregnancy, RANKL, OPG, and other factors was used to predict breast volume at term. The mean breast volume was 413\u2009mL at gestational week 12, increasing by a mean of 99\u2009mL up to gestational week 40. In addition to body mass index and breast volume at the beginning of pregnancy, RANKL and OPG appeared to influence breast volume with a mean increase by 32\u2009mL (P\u2009=\u20090.04) and a mean reduction by 27\u2009mL (P\u2009=\u20090.04), respectively. Linking the RANKL\/RANK\/OPG pathway with breast volume changes supports further studies aiming at analysing breast changes during pregnancy with regard to breast cancer risk.","authors":"Wunderle, M., Ruebner, M., H\u00e4berle, L., Schwenke, E., Hack, CC., Bayer, CM., Koch, MC., Schwitulla, J., Schulz-Wendtland, R., Kozieradzki, I., Lux, MP., Beckmann, MW., Jud, SM., Penninger, JM., Schneider, MO., Fasching, PA.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Rep","volume":"10","issue":"1","page":"5171","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32184238","title":"Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK\/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses.","abstract":"Human noroviruses (HuNoV) are a leading cause of viral gastroenteritis worldwide and a significant cause of morbidity and mortality in all age groups. The recent finding that HuNoV can be propagated in B cells and mucosa-derived intestinal epithelial organoids (IEOs) has transformed our ability to dissect the life cycle of noroviruses. Using transcriptome sequencing (RNA-Seq) of HuNoV-infected intestinal epithelial cells (IECs), we have found that replication of HuNoV in IECs results in interferon (IFN)-induced transcriptional responses and that HuNoV replication in IECs is sensitive to IFN. This contrasts with previous studies that suggested that the innate immune response may play no role in the restriction of HuNoV replication in immortalized cells. We demonstrated that inhibition of Janus kinase 1 (JAK1)\/JAK2 enhanced HuNoV replication in IECs. Surprisingly, targeted inhibition of cellular RNA polymerase II-mediated transcription was not detrimental to HuNoV replication but instead enhanced replication to a greater degree than blocking of JAK signaling directly. Furthermore, we demonstrated for the first time that IECs generated from genetically modified intestinal organoids, engineered to be deficient in the interferon response, were more permissive to HuNoV infection. Taking the results together, our work revealed that IFN-induced transcriptional responses restrict HuNoV replication in IECs and demonstrated that inhibition of these responses mediated by modifications of the culture conditions can greatly enhance the robustness of the norovirus culture system.<b>IMPORTANCE<\/b> Noroviruses are a major cause of gastroenteritis worldwide, and yet the challenges associated with their growth in culture have greatly hampered the development of therapeutic approaches and have limited our understanding of the cellular pathways that control infection. Here, we show that human intestinal epithelial cells, which represent the first point of entry of human noroviruses into the host, limit virus replication by induction of innate responses. Furthermore, we show that modulating the ability of intestinal epithelial cells to induce transcriptional responses to HuNoV infection can significantly enhance human norovirus replication in culture. Collectively, our findings provide new insights into the biological pathways that control norovirus infection but also identify mechanisms that enhance the robustness of norovirus culture.","authors":"Hosmillo, M., Chaudhry, Y., Nayak, K., Sorgeloos, F., Koo, BK., Merenda, A., Lillestol, R., Drumright, L., Zilbauer, M., Goodfellow, I.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"mBio","volume":"11","issue":"2","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32147820","title":"Novel role for CRK adaptor proteins as essential components of SRC\/FAK signaling for epithelial-mesenchymal transition and colorectal cancer aggressiveness.","abstract":"Epithelial-mesenchymal transition (EMT) is a cell plasticity process required for metastasis and chemoresistance of carcinoma cells. We report a crucial role of the signal adaptor proteins CRK and CRKL in promoting EMT and tumor aggressiveness, as well as resistance against chemotherapy in colorectal and pancreatic carcinoma. Genetic loss of either CRKL or CRK partially counteracted EMT in three independent cancer cell lines. Strikingly, complete loss of the CRK family shifted cells strongly toward the epithelial phenotype. Cells exhibited greatly increased E-cadherin and grew as large, densely packed clusters, completely lacked invasiveness and the ability to undergo EMT induced by cytokines or genetic activation of SRC. Furthermore, CRK family-deficiency significantly reduced cell survival, proliferation and chemoresistance, as well as ERK1\/2 phosphorylation and c-MYC protein levels. In accordance, MYC-target gene expression was identified as novel hallmark process positively regulated by CRK family proteins. Mechanistically, CRK proteins were identified as pivotal amplifiers of SRC\/FAK signaling at focal adhesions, mediated through a novel positive feedback loop depending on RAP1. Expression of the CRK family and the EMT regulator ZEB1 was significantly correlated in samples from colorectal cancer patients, especially in invasive regions. Further, high expression of CRK family genes was significantly associated with reduced survival in locally advanced colorectal cancer, as well as in pan-cancer datasets from the TCGA project. Thus, CRK family adaptor proteins are promising therapeutic targets to counteract EMT, chemoresistance, metastasis formation and minimal residual disease. As proof of concept, CRK family-mediated oncogenic signaling was successfully inhibited by a peptide-based inhibitor.","authors":"Franke, FC., Slusarenko, BO., Engleitner, T., Johannes, W., Laschinger, M., Rad, R., Nitsche, U., Janssen, KP.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Int J Cancer","volume":"147","issue":"6","page":"1715-1731","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32103002","title":"B38-CAP is a bacteria-derived ACE2-like enzyme that suppresses hypertension and cardiac dysfunction.","abstract":"Angiotensin-converting enzyme 2 (ACE2) is critically involved in cardiovascular physiology and pathology, and is currently clinically evaluated to treat acute lung failure. Here we show that the B38-CAP, a carboxypeptidase derived from Paenibacillus sp. B38, is an ACE2-like enzyme to decrease angiotensin II levels in mice. In protein 3D structure analysis, B38-CAP homolog shares structural similarity to mammalian ACE2 with low sequence identity. In vitro, recombinant B38-CAP protein catalyzed the conversion of angiotensin II to angiotensin 1-7, as well as other known ACE2 target peptides. Treatment with B38-CAP suppressed angiotensin II-induced hypertension, cardiac hypertrophy, and fibrosis in mice. Moreover, B38-CAP inhibited pressure overload-induced pathological hypertrophy, myocardial fibrosis, and cardiac dysfunction in mice. Our data identify the bacterial B38-CAP as an ACE2-like carboxypeptidase, indicating that evolution has shaped a bacterial carboxypeptidase to a human ACE2-like enzyme. Bacterial engineering could be utilized to design improved protein drugs for hypertension and heart failure.","authors":"Minato, T., Nirasawa, S., Sato, T., Yamaguchi, T., Hoshizaki, M., Inagaki, T., Nakahara, K., Yoshihashi, T., Ozawa, R., Yokota, S., Natsui, M., Koyota, S., Yoshiya, T., Yoshizawa-Kumagaye, K., Motoyama, S., Gotoh, T., Nakaoka, Y., Penninger, JM., Watanabe, H., Imai, Y., Takahashi, S., Kuba, K.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"1058","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32081911","title":"iLoF: An intelligent Lab on Fiber Approach for Human Cancer Single-Cell Type Identification.","abstract":"With the advent of personalized medicine, there is a movement to develop \"smaller\" and \"smarter\" microdevices that are able to distinguish similar cancer subtypes. Tumor cells display major differences when compared to their natural counterparts, due to alterations in fundamental cellular processes such as glycosylation. Glycans are involved in tumor cell biology and they have been considered to be suitable cancer biomarkers. Thus, more selective cancer screening assays can be developed through the detection of specific altered glycans on the surface of circulating cancer cells. Currently, this is only possible through time-consuming assays. In this work, we propose the \"intelligent\" Lab on Fiber (iLoF) device, that has a high-resolution, and which is a fast and portable method for tumor single-cell type identification and isolation. We apply an Artificial Intelligence approach to the back-scattered signal arising from a trapped cell by a micro-lensed optical fiber. As a proof of concept, we show that iLoF is able to discriminate two human cancer cell models sharing the same genetic background but displaying a different surface glycosylation profile with an accuracy above 90% and a speed rate of 2.3 seconds. We envision the incorporation of the iLoF in an easy-to-operate microchip for cancer identification, which would allow further biological characterization of the captured circulating live cells.","authors":"Paiva, JS., Jorge, PAS., Ribeiro, RSR., Balma\u00f1a, M., Campos, D., Mereiter, S., Jin, C., Karlsson, NG., Sampaio, P., Reis, CA., Cunha, JPS.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Rep","volume":"10","issue":"1","page":"3171","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30209039","title":"Tales from the crypt: intestinal niche signals in tissue renewal, plasticity and cancer.","abstract":"Rapidly renewing tissues such as the intestinal epithelium critically depend on the activity of small-sized stem cell populations that continuously generate new progeny to replace lost and damaged cells. The complex and tightly regulated process of intestinal homeostasis is governed by a variety of signalling pathways that balance cell proliferation and differentiation. Accumulating evidence suggests that stem cell control and daughter cell fate determination is largely dictated by the microenvironment. Here, we review recent developments in the understanding of intestinal stem cell dynamics, focusing on the roles, mechanisms and interconnectivity of prime signalling pathways that regulate stem cell behaviour in intestinal homeostasis. Furthermore, we discuss how mutational activation of these signalling pathways endows colorectal cancer cells with niche-independent growth advantages during carcinogenesis.","authors":"Spit, M., Koo, BK., Maurice, MM.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Open Biol","volume":"8","issue":"9","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32081435","title":"CLP1 acts as the main RNA kinase in mice.","abstract":"CLP1 plays an essential role in the protein complex involved in mRNA 3'-end formation and polyadenylation as well as in the tRNA splicing endonuclease (TSEN) complex involved in the splicing of precursor tRNAs. NOL9 localizes in the nucleolus of cells and plays an essential role in ribosomal RNA maturation. Both CLP1 and NOL9 are RNA kinases that phosphorylate the 5' end of RNAs. From the evidence that phosphorylation of the 5' end of a siRNA is essential for its efficient RNA cleavage, it was expected that CLP1 and NOL9 would be corresponding molecules. However, there had been no direct evidence that this is the case. In this study, murine NOL9 showed no apparent RNA kinase activity in cells or even in an RNA kinase assay using recombinant murine NOL9 protein. Although siRNA efficiency was decreased in CLP1 kinase-dead (Clp1<sup>K\/K<\/sup>) cells, it was not influenced by NOL9 overexpression. These findings indicate that in mouse cells it is CLP1 that mainly acts to phosphorylate the 5' end of RNAs in the siRNA pathway, with no apparent involvement of NOL9.","authors":"Fujinami, H., Shiraishi, H., Hada, K., Inoue, M., Morisaki, I., Higa, R., Shin, T., Kobayashi, T., Hanada, R., Penninger, JM., Mimata, H., Hanada, T.","publication_status":"aheadofprint","journalpubyear":"2020","journaltitle":"Biochem Biophys Res Commun","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32079226","title":"Role of Signal Transduction Pathways and Transcription Factors in Cartilage and Joint Diseases.","abstract":"<b>:<\/b> Osteoarthritis and rheumatoid arthritis are common cartilage and joint diseases that globally affect more than 200 million and 20 million people, respectively. Several transcription factors have been implicated in the onset and progression of osteoarthritis, including Runx2, C\/EBP\u03b2, HIF2\u03b1, Sox4, and Sox11. Interleukin-1 \u03b2 (IL-1\u03b2) leads to osteoarthritis through NF-\u0138B, I\u03baB\u03b6, and the Zn<sup>2+<\/sup>-ZIP8-MTF1 axis. IL-1, IL-6, and tumor necrosis factor \u03b1 (TNF\u03b1) play a major pathological role in rheumatoid arthritis through NF-\u0138B and JAK\/STAT pathways. Indeed, inhibitory reagents for IL-1, IL-6, and TNF\u03b1 provide clinical benefits for rheumatoid arthritis patients. Several growth factors, such as bone morphogenetic protein (BMP), fibroblast growth factor (FGF), parathyroid hormone-related protein (PTHrP), and Indian hedgehog, play roles in regulating chondrocyte proliferation and differentiation. Disruption and excess of these signaling pathways cause genetic disorders in cartilage and skeletal tissues. Fibrodysplasia ossificans progressive, an autosomal genetic disorder characterized by ectopic ossification, is induced by mutant ACVR1. Mechanistic target of rapamycin kinase (mTOR) inhibitors can prevent ectopic ossification induced by ACVR1 mutations. C-type natriuretic peptide is currently the most promising therapy for achondroplasia and related autosomal genetic diseases that manifest severe dwarfism. In these ways, investigation of cartilage and chondrocyte diseases at molecular and cellular levels has enlightened the development of effective therapies. Thus, identification of signaling pathways and transcription factors implicated in these diseases is important.","authors":"Nishimura, R., Hata, K., Takahata, Y., Murakami, T., Nakamura, E., Ohkawa, M., Ruengsinpinya, L.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Int J Mol Sci","volume":"21","issue":"4","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32029734","title":"A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes.","abstract":"Crosslinking-mass spectrometry (XL-MS) serves to identify interaction sites between proteins. Numerous search engines for crosslink identification exist, but lack of ground truth samples containing known crosslinks has precluded their systematic validation. Here we report on XL-MS data arising from measuring synthetic peptide libraries that provide the unique benefit of knowing which identified crosslinks are true and which are false. The data are analysed with the most frequently used search engines and the results filtered to an estimated false discovery rate of 5%. We find that the actual false crosslink identification rates range from 2.4 to 32%, depending on the analysis strategy employed. Furthermore, the use of MS-cleavable crosslinkers does not reduce the false discovery rate compared to non-cleavable crosslinkers. We anticipate that the datasets acquired during this research will further drive optimisation and development of XL-MS search engines, thereby advancing our understanding of vital biological interactions.","authors":"Beveridge, R., Stadlmann, J., Penninger, JM., Mechtler, K.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"742","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32019898","title":"The <i>parkin-coregulated gene<\/i> product PACRG promotes TNF signaling by stabilizing LUBAC.","abstract":"The <i>Parkin-coregulated gene<\/i> (<i>PACRG<\/i>), which encodes a protein of unknown function, shares a bidirectional promoter with <i>Parkin<\/i> (<i>PRKN<\/i>), which encodes an E3 ubiquitin ligase. Because PRKN is important in mitochondrial quality control and protection against stress, we tested whether PACRG also affected these pathways in various cultured human cell lines and in mouse embryonic fibroblasts. PACRG did not play a role in mitophagy but did play a role in tumor necrosis factor (TNF) signaling. Similarly to Parkin, PACRG promoted nuclear factor \u03baB (NF-\u03baB) activation in response to TNF. TNF-induced nuclear translocation of the NF-\u03baB subunit p65 and NF-\u03baB-dependent transcription were decreased in PACRG-deficient cells. Defective canonical NF-\u03baB activation in the absence of PACRG was accompanied by a decrease in linear ubiquitylation mediated by the linear ubiquitin chain assembly complex (LUBAC), which is composed of the two E3 ubiquitin ligases HOIP and HOIL-1L and the adaptor protein SHARPIN. Upon TNF stimulation, PACRG was recruited to the activated TNF receptor complex and interacted with LUBAC components. PACRG functionally replaced SHARPIN in this context. In SHARPIN-deficient cells, PACRG prevented LUBAC destabilization, restored HOIP-dependent linear ubiquitylation, and protected cells from TNF-induced apoptosis. This function of PACRG in positively regulating TNF signaling may help to explain the association of <i>PACRG<\/i> and <i>PRKN<\/i> polymorphisms with an increased susceptibility to intracellular pathogens.","authors":"Meschede, J., \u0160adi\u0107, M., Furthmann, N., Miedema, T., Sehr, DA., M\u00fcller-Rischart, AK., Bader, V., Berlemann, LA., Pilsl, A., Schlierf, A., Barkovits, K., Kachholz, B., Rittinger, K., Ikeda, F., Marcus, K., Schaefer, L., Tatzelt, J., Winklhofer, KF.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Sci Signal","volume":"13","issue":"617","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16700061","title":"Evolution of the mammary gland from the innate immune system?","abstract":"The mammary gland is a skin gland unique to the class Mammalia. Despite a growing molecular and histological understanding of the development and physiology of the mammary gland, its functional and morphological origins have remained speculative. Numerous theories on the origin of the mammary gland and lactation exist. The purpose of the mammary gland is to provide the newborn with copious amounts of milk, a unique body fluid that has a dual role of nutrition and immunological protection. Interestingly, antimicrobial enzymes, such as xanthine oxidoreductase or lysozyme, are directly involved in the evolution of the nutritional aspect of milk. We outline that xanthine oxidoreductase evolved a dual role in the mammary gland and hence provide new evidence supporting the hypothesis that the nutritional function of the milk evolved subsequent to its protective function. Therefore, we postulate that the mammary gland evolved from the innate immune system. In addition, we suggest that lactation partly evolved as an inflammatory response to tissue damage and infection, and discuss the observation that the two signaling pathways, NF-kB and Jak\/Stat, play central roles in inflammation as well as in lactation.","authors":"Vorbach, C., Capecchi, MR., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Bioessays","volume":"28","issue":"6","page":"606-16","pdf":null,"JrId":"1014","fulltextlink":null,"preprintlink":null,"articledate":"2006-11-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32001673","title":"Overexpression of apoptosis inducing factor aggravates hypoxic-ischemic brain injury in neonatal mice.","abstract":"Apoptosis inducing factor (AIF) has been shown to be a major contributor to neuron loss in the immature brain after hypoxia-ischemia (HI). Indeed, mice bearing a hypomorphic mutation causing reduced AIF expression are protected against neonatal HI. To further investigate the possible molecular mechanisms of this neuroprotection, we generated an AIF knock-in mouse by introduction of a latent transgene coding for flagged AIF protein into the Rosa26 locus, followed by its conditional activation by a ubiquitously expressed Cre recombinase. Such AIF transgenic mice overexpress the pro-apoptotic splice variant of AIF (AIF1) at both the mRNA (5.9 times higher) and protein level (2.4 times higher), but not the brain-specific AIF splice-isoform (AIF2). Excessive AIF did not have any apparent effects on the phenotype or physiological functions of the mice. However, brain injury (both gray and white matter) after neonatal HI was exacerbated in mice overexpressing AIF, coupled to enhanced translocation of mitochondrial AIF to the nucleus as well as enhanced caspase-3 activation in some brain regions, as indicated by immunohistochemistry. Altogether, these findings corroborate earlier studies demonstrating that AIF plays a causal role in neonatal HI brain injury.","authors":"Li, T., Li, K., Zhang, S., Wang, Y., Xu, Y., Cronin, SJF., Sun, Y., Zhang, Y., Xie, C., Rodriguez, J., Zhou, K., Hagberg, H., Mallard, C., Wang, X., Penninger, JM., Kroemer, G., Blomgren, K., Zhu, C.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Cell Death Dis","volume":"11","issue":"1","page":"77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-11-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31956281","title":"Interaction between growing oocytes and granulosa cells in vitro.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31956281<\/PMID><DateRevised><Year>2020<\/Year><Month>09<\/Month><Day>30<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Print\">1445-5781<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>19<\/Volume><Issue>1<\/Issue><PubDate><Year>2020<\/Year><Month>Jan<\/Month><\/PubDate><\/JournalIssue><Title>Reproductive medicine and biology<\/Title><ISOAbbreviation>Reprod Med Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Interaction between growing oocytes and granulosa cells in vitro.<\/ArticleTitle><Pagination><MedlinePgn>13-23<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/rmb2.12292<\/ELocationID><Abstract><AbstractText Label=\"Background\" NlmCategory=\"UNASSIGNED\">Oocyte growth is accompanied by follicular development in mammalian ovaries. Since the discovery of two oocyte-derived factors, growth differentiation factor 9 (GDF9), and bone morphogenetic protein 15 (BMP15), knowledge of the bidirectional communication between oocytes and granulosa cells for ovarian function and fertility has been accumulated. In addition, the growth culture system of oocytes has been improved, further promoting the studies on the communication between oocytes and granulosa cells in vitro.","authors":"Alam, MH., Miyano, T.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Reprod Med Biol","volume":"19","issue":"1","page":"13-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31918667","title":"MicroRNA-19b-3p promotes cell proliferation and osteogenic differentiation of BMSCs by interacting with lncRNA H19.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31918667<\/PMID><DateCompleted><Year>2020<\/Year><Month>03<\/Month><Day>03<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>03<\/Month><Day>03<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>21<\/Volume><Issue>1<\/Issue><PubDate><Year>2020<\/Year><Month>01<\/Month><Day>09<\/Day><\/PubDate><\/JournalIssue><Title>BMC medical genetics<\/Title><ISOAbbreviation>BMC Med Genet<\/ISOAbbreviation><\/Journal><ArticleTitle>MicroRNA-19b-3p promotes cell proliferation and osteogenic differentiation of BMSCs by interacting with lncRNA H19.<\/ArticleTitle><Pagination><MedlinePgn>11<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12881-020-0948-y<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">To investigated the role of miR-19b-3p in regulating bone marrow mesenchymal stem cell (BMSC) proliferation and osteoblast differentiation.","authors":"Xiaoling, G., Shuaibin, L., Kailu, L.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"BMC Med Genet","volume":"21","issue":"1","page":"11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31861691","title":"Are Leukaemic Stem Cells Restricted to a Single Cell Lineage?","abstract":"Cancer-stem-cell theory states that most, if not all, cancers arise from a stem\/uncommitted cell. This theory revolutionised our view to reflect that cancer consists of a hierarchy of cells that mimic normal cell development. Elegant studies of twins who both developed acute lymphoblastic leukaemia in childhood revealed that at least two genomic insults are required for cancer to develop. These 'hits' do not appear to confer a growth advantage to cancer cells, nor do cancer cells appear to be better equipped to survive than normal cells. Cancer cells created by investigators by introducing specific genomic insults generally belong to one cell lineage. For example, transgenic mice in which the LIM-only 2 (<i>LMO<\/i><i>2<\/i>,associated with human acute T-lymphoblastic leukaemia) and <i>BCR<\/i><i>-<\/i><i>ABL<\/i><sup>p210<\/sup> (associated with human chronic myeloid leukaemia) oncogenes were active solely within the haematopoietic stem-cell compartment developed T-lymphocyte and neutrophil lineage-restricted leukaemia, respectively. This recapitulated the human form of these diseases. This 'hardwiring' of lineage affiliation, either throughout leukaemic stem cell development or at a particular stage, is different to the behaviour of normal haematopoietic stem cells. While normal cells directly commit to a developmental pathway, they also remain versatile and can develop into a terminally differentiated cell that is not part of the initial lineage. Many cancer stem cells do not have this versatility, and this is an essential difference between normal and cancer stem cells. In this report, we review findings that support this notion.","authors":"Brown, G., S\u00e1nchez, L., S\u00e1nchez-Garc\u00eda, I.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Int J Mol Sci","volume":"21","issue":"1","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31854489","title":"Osteogenesis and bone remodeling: A focus on growth factors and bioactive peptides.","abstract":"Bone is one of the most frequently transplanted tissues. The bone structure and its physiological function and stem cells biology were known to be closely related to each other for many years. Bone is considered a home to the well-known systems of postnatal mesenchymal stem cells (MSCs). These bone resident MSCs provide a range of growth factors (GF) and cytokines to support cell growth following injury. These GFs include a group of proteins and peptides produced by different cells which are regulators of important cell functions such as division, migration, and differentiation. GF signaling controls the formation and development of the MSCs condensation and plays a critical role in regulating osteogenesis, chondrogenesis, and bone\/mineral homeostasis. Thus, a combination of both MSCs and GFs receives high expectations in regenerative medicine, particularly in bone repair applications. It is known that the delivery of exogenous GFs to the non-union bone fracture site remarkably improves healing results. Here we present updated information on bone tissue engineering with a specific focus on GF characteristics and their application in cellular functions and tissue healing. Moreover, the interrelation of GFs with the damaged bone microenvironment and their mechanistic functions are discussed.","authors":"Toosi, S., Behravan, J.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Biofactors","volume":"46","issue":"3","page":"326-340","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31822659","title":"All-trans retinoic acid enhances, and a pan-RAR antagonist counteracts, the stem cell promoting activity of EVI1 in acute myeloid leukemia.","abstract":"Ecotropic virus integration site 1 (EVI1), whose overexpression characterizes a particularly aggressive subtype of acute myeloid leukemia (AML), enhanced anti-leukemic activities of all-trans retinoic acid (atRA) in cell lines and patient samples. However, the drivers of leukemia formation, therapy resistance, and relapse are leukemic stem cells (LSCs), whose properties were hardly reflected in these experimental setups. The present study was designed to address the effects of, and interactions between, EVI1 and retinoids in AML LSCs. We report that Evi1 reduced the maturation of leukemic cells and promoted the abundance, quiescence, and activity of LSCs in an MLL-AF9-driven mouse model of AML. atRA further augmented these effects in an Evi1 dependent manner. EVI1 also strongly enhanced atRA regulated gene transcription in LSC enriched cells. One of their jointly regulated targets, Notch4, was an important mediator of their effects on leukemic stemness. In vitro exposure of leukemic cells to a pan-RAR antagonist caused effects opposite to those of atRA. In vivo antagonist treatment delayed leukemogenesis and reduced LSC abundance, quiescence, and activity in Evi1<sup>high<\/sup> AML. Key results were confirmed in human myeloid cell lines retaining some stem cell characteristics as well as in primary human AML samples. In summary, our study is the first to report the importance of EVI1 for key properties of AML LSCs. Furthermore, it shows that atRA enhances, and a pan-RAR antagonist counteracts, the effects of EVI1 on AML stemness, thus raising the possibility of using RAR antagonists in the therapy of EVI1<sup>high<\/sup> AML.","authors":"Nguyen, CH., Bauer, K., Hackl, H., Schlerka, A., Koller, E., Hladik, A., Stoiber, D., Zuber, J., Staber, PB., Hoelbl-Kovacic, A., Purton, LE., Grebien, F., Wieser, R.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Cell Death Dis","volume":"10","issue":"12","page":"944","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31817880","title":"Proteome Alterations in Equine Osteochondrotic Chondrocytes.","abstract":"Osteochondrosis is a failure of the endochondral ossification that affects developing joints in humans and several animal species. It is a localized idiopathic joint disorder characterized by focal chondronecrosis and growing cartilage retention, which can lead to the formation of fissures, subchondral bone cysts, or intra-articular fragments. Osteochondrosis is a complex multifactorial disease associated with extracellular matrix alterations and failure in chondrocyte differentiation, mainly due to genetic, biochemical, and nutritional factors, as well as traumas. This study describes the main proteomic alterations occurring in chondrocytes isolated from osteochondrotic cartilage fragments. A comparative analysis performed on equine osteochondrotic and healthy chondrocytes showed 26 protein species as differentially represented. In particular, quantitative changes in the extracellular matrix, cytoskeletal and chaperone proteins, and in cell adhesion and signaling molecules were observed in osteochondrotic cells, compared to healthy controls. Functional group analysis annotated most of these proteins in \"growth plate and cartilage development\", while others were included in \"glycolysis and gluconeogenesis\", \"positive regulation of protein import\", \"cell-cell adhesion mediator activity\", and \"mitochondrion nucleoid\". These results may help to clarify some chondrocyte functional alterations that may play a significant role in determining the onset and progression of equine osteochondrosis and, being related, of human juvenile osteochondrosis.","authors":"Chiaradia, E., Pepe, M., Orvietani, PL., Renzone, G., Magini, A., Sforna, M., Emiliani, C., Di Meo, A., Scaloni, A.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Int J Mol Sci","volume":"20","issue":"24","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31817503","title":"Specification of BMP Signaling.","abstract":"Bone Morphogenetic Proteins (BMPs) together with the Growth and Differentiation Factors (GDFs) form the largest subgroup of the Transforming Growth Factor (TGF)\u03b2 family and represent secreted growth factors, which play an essential role in many aspects of cell communication in higher organisms. As morphogens they exert crucial functions during embryonal development, but are also involved in tissue homeostasis and regeneration in the adult organism. Their involvement in maintenance and repair processes of various tissues and organs made these growth factors highly interesting targets for novel pharmaceutical applications in regenerative medicine. A hallmark of the TGF\u03b2 protein family is that all of the more than 30 growth factors identified to date signal by binding and hetero-oligomerization of a very limited set of transmembrane serine-threonine kinase receptors, which can be classified into two subgroups termed type I and type II. Only seven type I and five type II receptors exist for all 30plus TGF\u03b2 members suggesting a pronounced ligand-receptor promiscuity. Indeed, many TGF\u03b2 ligands can bind the same type I or type II receptor and a particular receptor of either subtype can usually interact with and bind various TGF\u03b2 ligands. The possible consequence of this ligand-receptor promiscuity is further aggravated by the finding that canonical TGF\u03b2 signaling of all family members seemingly results in the activation of just two distinct signaling pathways, that is either SMAD2\/3 or SMAD1\/5\/8 activation. While this would implicate that different ligands can assemble seemingly identical receptor complexes that activate just either one of two distinct pathways, in vitro and in vivo analyses show that the different TGF\u03b2 members exert quite distinct biological functions with high specificity. This discrepancy indicates that our current view of TGF\u03b2 signaling initiation just by hetero-oligomerization of two receptor subtypes and transduction via two main pathways in an on-off switch manner is too simplified. Hence, the signals generated by the various TGF\u03b2 members are either quantitatively interpreted using the subtle differences in their receptor-binding properties leading to ligand-specific modulation of the downstream signaling cascade or additional components participating in the signaling activation complex allow diversification of the encoded signal in a ligand-dependent manner at all cellular levels. In this review we focus on signal specification of TGF\u03b2 members, particularly of BMPs and GDFs addressing the role of binding affinities, specificities, and kinetics of individual ligand-receptor interactions for the assembly of specific receptor complexes with potentially distinct signaling properties.","authors":"Nickel, J., Mueller, TD.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Cells","volume":"8","issue":"12","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31815961","title":"Disrupting MLV integrase:BET protein interaction biases integration into quiescent chromatin and delays but does not eliminate tumor activation in a MYC\/Runx2 mouse model.","abstract":"Murine leukemia virus (MLV) integrase (IN) lacking the C-terminal tail peptide (TP) loses its interaction with the host bromodomain and extraterminal (BET) proteins and displays decreased integration at promoter\/enhancers and transcriptional start sites\/CpG islands. MLV lacking the IN TP via an altered open reading frame was used to infect tumorigenesis mouse model (MYC\/Runx2) animals to observe integration patterns and phenotypic effects, but viral passage resulted in the restoration of the IN TP through small deletions. Mice subsequently infected with an MLV IN lacking the TP coding sequence (TP-) showed an improved median survival by 15 days compared to wild type (WT) MLV infection. Recombination with polytropic endogenous retrovirus (ERV), Pmv20, was identified in seven mice displaying both fast and slow tumorigenesis, highlighting the strong selection within the mouse to maintain the full-length IN protein. Mapping the genomic locations of MLV in tumors from an infected mouse with no observed recombination with ERVs, TP-16, showed fewer integrations at TSS and CpG islands, compared to integrations observed in WT tumors. However, this mouse succumbed to the tumor in relatively rapid fashion (34 days). Analysis of the top copy number integrants in the TP-16 tumor revealed their proximity to known MLV common insertion site genes while maintaining the MLV IN TP- genotype. Furthermore, integration mapping in K562 cells revealed an insertion preference of MLV IN TP- within chromatin profile states associated with weakly transcribed heterochromatin with fewer integrations at histone marks associated with BET proteins (H3K4me1\/2\/3, and H3K27Ac). While MLV IN TP- showed a decreased overall rate of tumorigenesis compared to WT virus in the MYC\/Runx2 model, MLV integration still occurred at regions associated with oncogenic driver genes independently from the influence of BET proteins, either stochastically or through trans-complementation by functional endogenous Gag-Pol protein.","authors":"Loyola, L., Achuthan, V., Gilroy, K., Borland, G., Kilbey, A., Mackay, N., Bell, M., Hay, J., Aiyer, S., Fingerman, D., Villanueva, RA., Cameron, E., Kozak, CA., Engelman, AN., Neil, J., Roth, MJ.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PLoS Pathog","volume":"15","issue":"12","page":"e1008154","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36272095","title":"Now that We Got There, What Next?","abstract":"As seen in the protocols in this book, the opportunities to pursue work at the cellular and molecular work in salamanders have considerably broadened over the last years. The availability of genomic information and genome editing, and the possibility to image tissues live and other methods enhance the spectrum of biological questions accessible to all researchers. Here I provide a personal perspective on what I consider exciting future questions open for investigation.","authors":"Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Methods Mol Biol","volume":"2562","issue":null,"page":"471-479","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-25","doi":"10.1007\/978-1-0716-2659-7_31","first_author":null,"corresponding_authors":null},{"pmid":"31798753","title":"The role of PPAR\u03b3 in childhood obesity-induced fractures.","abstract":"Globally, obesity is on the rise with ~\u200930% of the world's population now obese, and childhood obesity is following similar trends. Childhood obesity has been associated with numerous chronic conditions, including musculoskeletal disorders. This review highlights the effects of childhood adiposity on bone density by way of analyzing clinical studies and further describing two severe skeletal conditions, slipped capital femoral epiphysis and Blount's disease. The latter half of this review discusses bone remodeling and cell types that mediate bone growth and strength, including key growth factors and transcription factors that help orchestrate this complex pathology. In particular, the transcriptional factor peroxisome proliferator-activated receptor gamma (PPAR\u03b3) is examined as it is a master regulator of adipocyte differentiation in mesenchymal stem cells (MSCs) that can also influence osteoblast populations. Obese individuals are known to have higher levels of PPAR\u03b3 expression which contributes to their increased adipocyte numbers and decreased bone density. Modulating PPAR*gamma* signaling can have significant effects on adipogenesis, thereby directing MSCs down the osteoblastogenesis pathway and in turn increasing bone mineral density. Lastly, we explore the potential of PPAR\u03b3 as a druggable target to decrease adiposity, increase bone density, and be a treatment for children with obesity-induced bone fractures.","authors":"McCann, MR., Ratneswaran, A.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Genes Nutr","volume":"14","issue":"","page":"31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31792216","title":"A cancer rainbow mouse for visualizing the functional genomics of oncogenic clonal expansion.","abstract":"Field cancerization is a premalignant process marked by clones of oncogenic mutations spreading through the epithelium. The timescales of intestinal field cancerization can be variable and the mechanisms driving the rapid spread of oncogenic clones are unknown. Here we use a Cancer rainbow (Crainbow) modelling system for fluorescently barcoding somatic mutations and directly visualizing the clonal expansion and spread of oncogenes. Crainbow shows that mutations of \u00df-catenin (Ctnnb1) within the intestinal stem cell results in widespread expansion of oncogenes during perinatal development but not in adults. In contrast, mutations that extrinsically disrupt the stem cell microenvironment can spread in adult intestine without delay. We observe the rapid spread of premalignant clones in Crainbow mice expressing oncogenic Rspondin-3 (RSPO3), which occurs by increasing crypt fission and inhibiting crypt fixation. Crainbow modelling provides insight into how somatic mutations rapidly spread and a plausible mechanism for predetermining the intratumor heterogeneity found in colon cancers.","authors":"Boone, PG., Rochelle, LK., Ginzel, JD., Lubkov, V., Roberts, WL., Nicholls, PJ., Bock, C., Flowers, ML., von Furstenberg, RJ., Stripp, BR., Agarwal, P., Borowsky, AD., Cardiff, RD., Barak, LS., Caron, MG., Lyerly, HK., Snyder, JC.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"5490","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31781601","title":"Identification of mRNAs Related to Tibial Cartilage Development of Yorkshire Piglets.","abstract":"Cartilage dysplasia is one of the important reasons for the weakness of pig limbs and hooves. Porcine rickets with weak limbs and hooves bring huge economic losses to the pig industry. However, research on the development of pig cartilage is lacking. This study investigated the key genes and molecular mechanisms involved in cartilage development via an RNA-seq technique. Samples of proximal tibia cartilage were collected from three normal piglets with 1 day, 14 days, and 28 days of age, respectively, and then these samples were divided into two comparison groups (1-day vs. 14-day group, 14-day vs. 28-day group). Through the transcriptome analysis, 108 differentially expressed genes (DEGs), such as <i>FORL2<\/i>, were obtained from 1-day vs. 14-day comparison group, and 3602 DEGs were obtained from 14-day vs. 28-day comparison group, including <i>SOX9<\/i>, <i>BMP6<\/i>, and <i>MMP13<\/i>. The gene ontology (GO) functional and KEGG pathway enrichment revealed that many functions of DEGs were related to bone development. The pathways of DEGs from Day 1 vs. Day 14 were mainly enriched in mineral absorption, but the DEGs of Day 14 vs. Day 28 were enriched in osteoclast differentiation. Then, the expression patterns of six candidate genes were verified via qPCR. In conclusion, candidate genes affecting cartilage development in Yorkshire pigs were obtained by transcriptome analysis, and the clues showed that Day 14 to Day 28 is a more active and extensive period in cartilage developments, which played a key role in revealing the molecular mechanism of pig cartilage development basis, also compensating for vacancies in cartilage research.","authors":"Feng, S., Du, X., Wang, C., Ye, D., Ma, G., Zhao, S., Wang, H., Liu, X.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Biomed Res Int","volume":"2019","issue":"","page":"2365416","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31757091","title":"Recent Insights into Long Bone Development: Central Role of Hedgehog Signaling Pathway in Regulating Growth Plate.","abstract":"The longitudinal growth of long bone, regulated by an epiphyseal cartilaginous component known as the \"growth plate\", is generated by epiphyseal chondrocytes. The growth plate provides a continuous supply of chondrocytes for endochondral ossification, a sequential bone replacement of cartilaginous tissue, and any failure in this process causes a wide range of skeletal disorders. Therefore, the cellular and molecular characteristics of the growth plate are of interest to many researchers. Hedgehog (Hh), well known as a mitogen and morphogen during development, is one of the best known regulatory signals in the developmental regulation of the growth plate. Numerous animal studies have revealed that signaling through the Hh pathway plays multiple roles in regulating the proliferation, differentiation, and maintenance of growth plate chondrocytes throughout the skeletal growth period. Furthermore, over the past few years, a growing body of evidence has emerged demonstrating that a limited number of growth plate chondrocytes transdifferentiate directly into the full osteogenic and multiple mesenchymal lineages during postnatal bone development and reside in the bone marrow until late adulthood. Current studies with the genetic fate mapping approach have shown that the commitment of growth plate chondrocytes into the skeletal lineage occurs under the influence of epiphyseal chondrocyte-derived Hh signals during endochondral bone formation. Here, we discuss the valuable observations on the role of the Hh signaling pathway in the growth plate based on mouse genetic studies, with some emphasis on recent advances.","authors":"Haraguchi, R., Kitazawa, R., Kohara, Y., Ikedo, A., Imai, Y., Kitazawa, S.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Int J Mol Sci","volume":"20","issue":"23","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31213597","title":"Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk.","abstract":"Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels of recombinant lines. We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. We use ceX-QTL to map a drug resistance locus with high resolution. We also map differences in gene expression in live worms and discovered that mutations in the co-chaperone sti-1 upregulate the transcription of HSP-90. Lastly, we use ceX-QTL to map loci that influence fitness genome-wide confirming previously reported causal variants and uncovering new fitness loci. ceX-QTL is fast, powerful and cost-effective, and will accelerate the study of complex traits in animals.","authors":"Burga, A., Ben-David, E., Lemus Vergara, T., Boocock, J., Kruglyak, L.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"2680","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31628323","title":"A kinase-independent role for CDK8 in BCR-ABL1<sup>+<\/sup> leukemia.","abstract":"Cyclin-dependent kinases (CDKs) are frequently deregulated in cancer and represent promising drug targets. We provide evidence that CDK8 has a key role in B-ALL. Loss of CDK8 in leukemia mouse models significantly enhances disease latency and prevents disease maintenance. Loss of CDK8 is associated with pronounced transcriptional changes, whereas inhibiting CDK8 kinase activity has minimal effects. Gene set enrichment analysis suggests that the mTOR signaling pathway is deregulated in CDK8-deficient cells and, accordingly, these cells are highly sensitive to mTOR inhibitors. Analysis of large cohorts of human ALL and AML patients reveals a significant correlation between the level of CDK8 and of mTOR pathway members. We have synthesized a small molecule YKL-06-101 that combines mTOR inhibition and degradation of CDK8, and induces cell death in human leukemic cells. We propose that simultaneous CDK8 degradation and mTOR inhibition might represent a potential therapeutic strategy for the treatment of ALL patients.","authors":"Menzl, I., Zhang, T., Berger-Becvar, A., Grausenburger, R., Heller, G., Prchal-Murphy, M., Edlinger, L., Knab, VM., Uras, IZ., Grundschober, E., Bauer, K., Roth, M., Skucha, A., Liu, Y., Hatcher, JM., Liang, Y., Kwiatkowski, NP., Fux, D., Hoelbl-Kovacic, A., Kubicek, S., Melo, JV., Valent, P., Weichhart, T., Grebien, F., Zuber, J., Gray, NS., Sexl, V.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"4741","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31601814","title":"BRG1 attenuates colonic inflammation and tumorigenesis through autophagy-dependent oxidative stress sequestration.","abstract":"Autophagy is a central component of integrated stress responses that influences many inflammatory diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC). While the core machinery is known, the molecular basis of the epigenetic regulation of autophagy and its role in colon inflammation remain largely undefined. Here, we report that BRG1, an ATPase subunit of the SWI\/SNF chromatin remodeling complex, is required for the homeostatic maintenance of intestinal epithelial cells (IECs) to prevent the inflammation and tumorigenesis. BRG1 emerges as a key regulator that directly governs the transcription of Atg16l1, Ambra1, Atg7 and Wipi2, which are important for autophagosome biogenesis. Defective autophagy in BRG1-deficient IECs results in excess reactive oxygen species (ROS), which leads to the defects in barrier integrity. Together, our results establish that BRG1 may represent an autophagy checkpoint that is pathogenetically linked to colitis and is therefore likely a potential therapeutic target for disease intervention.","authors":"Liu, M., Sun, T., Li, N., Peng, J., Fu, D., Li, W., Li, L., Gao, WQ.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"4614","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31601172","title":"Heart disease in a mutant mouse model of spontaneous eosinophilic myocarditis maps to three loci.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31601172<\/PMID><DateCompleted><Year>2020<\/Year><Month>02<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>02<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>20<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>Oct<\/Month><Day>11<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Heart disease in a mutant mouse model of spontaneous eosinophilic myocarditis maps to three loci.<\/ArticleTitle><Pagination><MedlinePgn>727<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12864-019-6108-0<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Heart disease (HD) is the major cause of morbidity and mortality in patients with hypereosinophilic diseases. Due to a lack of adequate animal models, our understanding of the pathophysiology of eosinophil-mediated diseases with heart complications is limited. We have discovered a mouse mutant, now maintained on an A\/J inbred background, that spontaneously develops hypereosinophilia in multiple organs. Cellular infiltration into the heart causes an eosinophilic myocarditis, with affected mice of the mutant line (i.e., A\/J<sup>HD<\/sup>) demonstrating extensive myocardial damage and remodeling that leads to HD and premature death, usually by 15-weeks old.","authors":"Zimmermann, N., Gibbons, WJ., Homan, SM., Prows, DR.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"BMC Genomics","volume":"20","issue":"1","page":"727","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31592189","title":"Structural analysis of urinary light chains and proteomic analysis of hyaline tubular casts in light chain associated kidney disorders.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31592189<\/PMID><DateRevised><Year>2020<\/Year><Month>09<\/Month><Day>30<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Print\">2167-8359<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>7<\/Volume><PubDate><Year>2019<\/Year><\/PubDate><\/JournalIssue><Title>PeerJ<\/Title><ISOAbbreviation>PeerJ<\/ISOAbbreviation><\/Journal><ArticleTitle>Structural analysis of urinary light chains and proteomic analysis of hyaline tubular casts in light chain associated kidney disorders.<\/ArticleTitle><Pagination><MedlinePgn>e7819<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.7717\/peerj.7819<\/ELocationID><Abstract><AbstractText Label=\"Background\" NlmCategory=\"UNASSIGNED\">Monoclonal overproduction of kappa and\/or lambda light chains might result in renal light chain deposition disease. Light chain associated cast nephropathy and renal AL-amyloidosis represent two further pathologies going along with monoclonal gammopathy of renal significance and multiple myeloma. While cast nephropathy often manifests with acute kidney injury, AL-amyloidosis is rather accompanied with chronic kidney disease.","authors":"Reiter, T., Knafl, D., Agis, H., Mechtler, K., Wagner, L., Winnicki, W.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PeerJ","volume":"7","issue":null,"page":"e7819","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31582763","title":"Highly structured homolog pairing reflects functional organization of the Drosophila genome.","abstract":"Trans-homolog interactions have been studied extensively in Drosophila, where homologs are paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with varying precision genome-wide, in addition to establishing trans-homolog domains and compartments. We also elucidate the structure of pairing with unprecedented detail, observing significant variation across the genome and revealing at least two forms of pairing: tight pairing, spanning contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional implication genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing, including the disruption of some interaction peaks.","authors":"AlHaj Abed, J., Erceg, J., Goloborodko, A., Nguyen, SC., McCole, RB., Saylor, W., Fudenberg, G., Lajoie, BR., Dekker, J., Mirny, LA., Wu, CT.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"4485","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31582744","title":"The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.","abstract":"Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.","authors":"Erceg, J., AlHaj Abed, J., Goloborodko, A., Lajoie, BR., Fudenberg, G., Abdennur, N., Imakaev, M., McCole, RB., Nguyen, SC., Saylor, W., Joyce, EF., Senaratne, TN., Hannan, MA., Nir, G., Dekker, J., Mirny, LA., Wu, CT.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"4486","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31560728","title":"Regulatory interaction between the ZPBP2-ORMDL3\/Zpbp2-Ormdl3 region and the circadian clock.","abstract":"Genome-wide association study (GWAS) loci for several immunity-mediated diseases (early onset asthma, inflammatory bowel disease (IBD), primary biliary cholangitis, and rheumatoid arthritis) map to chromosomal region 17q12-q21. The predominant view is that association between 17q12-q21 alleles and increased risk of developing asthma or IBD is due to regulatory variants. ORM sphingolipid biosynthesis regulator (ORMDL3) residing in this region is the most promising gene candidate for explaining association with disease. However, the relationship between 17q12-q21 alleles and disease is complex suggesting contributions from other factors, such as trans-acting genetic and environmental modifiers or circadian rhythms. Circadian rhythms regulate expression levels of thousands of genes and their dysregulation is implicated in the etiology of several common chronic inflammatory diseases. However, their role in the regulation of the 17q12-q21 genes has not been investigated. Moreover, the core clock gene nuclear receptor subfamily 1, group D, member 1 (NR1D1) resides about 200 kb distal to the GWAS region. We hypothesized that circadian rhythms influenced gene expression levels in 17q12-q21 region and conversely, regulatory elements in this region influenced transcription of the core clock gene NR1D1 in cis. To test these hypotheses, we examined the diurnal expression profiles of zona pellucida binding protein 2 (ZPBP2\/Zpbp2), gasdermin B (GSDMB), and ORMDL3\/Ormdl3 in human and mouse tissues and analyzed the impact of genetic variation in the ZPBP2\/Zpbp2 region on NR1D1\/Nr1d1 expression. We found that Ormdl3 and Zpbp2 were controlled by the circadian clock in a tissue-specific fashion. We also report that deletion of the Zpbp2 region altered the expression profile of Nr1d1 in lungs and ileum in a time-dependent manner. In liver, the deletion was associated with enhanced expression of Ormdl3. We provide the first evidence that disease-associated genes Zpbp2 and Ormdl3 are regulated by circadian rhythms and the Zpbp2 region influences expression of the core clock gene Nr1d1.","authors":"Chang, ML., Moussette, S., Gamero-Estevez, E., G\u00e1lvez, JH., Chiwara, V., Gupta, IR., Ryan, AK., Naumova, AK.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PLoS One","volume":"14","issue":"9","page":"e0223212","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31552825","title":"Id4 promotes the elimination of the pro-activation factor Ascl1 to maintain quiescence of adult hippocampal stem cells.","abstract":"Quiescence is essential for the long-term maintenance of adult stem cells but how stem cells maintain quiescence is poorly understood. Here, we show that neural stem cells (NSCs) in the adult mouse hippocampus actively transcribe the pro-activation factor Ascl1 regardless of their activated or quiescent states. We found that the inhibitor of DNA binding protein Id4 is enriched in quiescent NSCs and that elimination of Id4 results in abnormal accumulation of Ascl1 protein and premature stem cell activation. Accordingly, Id4 and other Id proteins promote elimination of Ascl1 protein in NSC cultures. Id4 sequesters Ascl1 heterodimerization partner E47, promoting Ascl1 protein degradation and stem cell quiescence. Our results highlight the importance of non-transcriptional mechanisms for the maintenance of NSC quiescence and reveal a role for Id4 as a quiescence-inducing factor, in contrast with its role of promoting the proliferation of embryonic neural progenitors.","authors":"Blomfield, IM., Rocamonde, B., Masdeu, MDM., Mulugeta, E., Vaga, S., van den Berg, DL., Huillard, E., Guillemot, F., Urb\u00e1n, N.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Elife","volume":"8","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31530634","title":"Transgenic Analyses in Drosophila Reveal That mCORL1 Is Functionally Distinct from mCORL2 and dCORL.","abstract":"Uncovering how new members of multigene families acquire new functions is an important topic in evolutionary and developmental genetics. CORL proteins (SKOR in mice, Fussel in humans and fussel in Flybase) are a family of CNS specific proteins related to mammalian Sno\/Ski oncogenes. Drosophila CORL (dCORL) participates in TGF-\u03b2 and insulin signaling during development and in adult homeostasis but roles for the two mouse CORL proteins (mCORL) are essentially unknown. A series of studies were conducted to test the hypothesis based on previous results that mCORL1 is more similar to dCORL than mCORL2. Neither an updated alignment nor ectopic expression in adult wings were able to distinguish mCORL1 or mCORL2 from dCORL. Transgene experiments employing a dCORL endogenous function in mushroom body neurons showed that mCORL1 is distinct from mCORL2 and dCORL. mCORL1 and mCORL2 are also distinct in biochemical assays of Smad-binding and BMP signaling. Taken together, the data suggests testable new hypotheses for mCORL2 function in mammalian TGF-\u03b2 and insulin signaling based on known roles for dCORL. Overall, the study reiterates the value of transgenic methods in Drosophila to provide new information on multigene family evolution and the function of family members in other species.","authors":"Stinchfield, MJ., Miyazawa, K., Newfeld, SJ.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"G3 (Bethesda)","volume":"9","issue":"11","page":"3781-3789","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31526477","title":"Evolution of neuronal anatomy and circuitry in two highly divergent nematode species.","abstract":"The nematodes <i>C. elegans<\/i> and <i>P. pacificus<\/i> populate diverse habitats and display distinct patterns of behavior. To understand how their nervous systems have diverged, we undertook a detailed examination of the neuroanatomy of the chemosensory system of <i>P. pacificus<\/i>. Using independent features such as cell body position, axon projections and lipophilic dye uptake, we have assigned homologies between the amphid neurons, their first-layer interneurons, and several internal receptor neurons of <i>P. pacificus<\/i> and <i>C. elegans.<\/i> We found that neuronal number and soma position are highly conserved. However, the morphological elaborations of several amphid cilia are different between them, most notably in the absence of 'winged' cilia morphology in <i>P. pacificus<\/i>. We established a synaptic wiring diagram of amphid sensory neurons and amphid interneurons in <i>P. pacificus<\/i> and found striking patterns of conservation and divergence in connectivity relative to <i>C. elegans<\/i>, but very little changes in relative neighborhood of neuronal processes. These findings demonstrate the existence of several constraints in patterning the nervous system and suggest that major substrates for evolutionary novelty lie in the alterations of dendritic structures and synaptic connectivity.","authors":"Hong, RL., Riebesell, M., Bumbarger, DJ., Cook, SJ., Carstensen, HR., Sarpolaki, T., Cochella, L., Castrejon, J., Moreno, E., Sieriebriennikov, B., Hobert, O., Sommer, RJ.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Elife","volume":"8","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31488102","title":"Oncogenic Akt-FOXO3 loop favors tumor-promoting modes and enhances oxidative damage-associated hepatocellular carcinogenesis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31488102<\/PMID><DateCompleted><Year>2020<\/Year><Month>02<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>02<\/Month><Day>26<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2407<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>19<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>Sep<\/Month><Day>05<\/Day><\/PubDate><\/JournalIssue><Title>BMC cancer<\/Title><ISOAbbreviation>BMC Cancer<\/ISOAbbreviation><\/Journal><ArticleTitle>Oncogenic Akt-FOXO3 loop favors tumor-promoting modes and enhances oxidative damage-associated hepatocellular carcinogenesis.<\/ArticleTitle><Pagination><MedlinePgn>887<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12885-019-6110-6<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Hepatocellular carcinoma (HCC) is the most prevalent primary liver cancer, accounting for 80-90% of cases. Mutations are commonly found in the signaling regulating the PI3K\/Akt pathway, leading to oncogenic cell proliferation and survival. Key transcription factors that are negatively regulated downstream of PI3K\/Akt are members of the forkhead box O family (FOXO). FOXOs were initially considered as tumor suppressors by inducing cell cycle arrest and apoptosis. However, there is increasing evidence showing that FOXOs, especially FOXO3, can support tumorigenesis.","authors":"Lu, M., Hartmann, D., Braren, R., Gupta, A., Wang, B., Wang, Y., Mogler, C., Cheng, Z., Wirth, T., Friess, H., Kleeff, J., H\u00fcser, N., Sunami, Y.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"BMC Cancer","volume":"19","issue":"1","page":"887","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31483844","title":"B7-1 drives TGF-\u03b2 stimulated pancreatic carcinoma cell migration and expression of EMT target genes.","abstract":"B7-1 proteins are routinely expressed on the surface of antigen presenting cells (APC) and within the innate immune system. They function to establish a biologically optimal and dynamic balance between immune activation and inhibition or self-tolerance. Interactions between B7-1 and its receptors, which include CD28, CTLA4 and PD-L1, contribute to both stimulatory as well as inhibitory or homeostatic regulation. In the current study, we investigated whether the tumor-promoting actions of transforming growth factor beta (TGF-\u03b2) disrupted this equilibrium in pancreatic cancer to promote malignant progression and an enhanced means to evade immune detection. The data show that B7-1 is (i) upregulated following treatment of pancreatic carcinoma cells with TGF-\u03b2; (ii) induced by TGF-\u03b2 via both Smad2\/3-dependent and independent pathways; (iii) required for pancreatic tumor cell in vitro migration\/invasion; and (iv) necessary for TGF-\u03b2 regulated epithelial-mesenchymal transition (EMT) through induction of Snail family members. Results from the proposed studies provide valuable insights into mechanisms whereby TGF-\u03b2 regulates both the innate immune response and intrinsic properties of pancreatic tumor growth.","authors":"Kang, JH., Jung, MY., Leof, EB.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PLoS One","volume":"14","issue":"9","page":"e0222083","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31480221","title":"Wnt\/\u03b2-Catenin Signaling: The Culprit in Pancreatic Carcinogenesis and Therapeutic Resistance.","abstract":"Pancreatic ductal adenocarcinoma (PDAC) is responsible for 7.3% of all cancer deaths. Even though there is a steady increase in patient survival for most cancers over the decades, the patient survival rate for pancreatic cancer remains low with current therapeutic strategies. The Wnt\/\u03b2-catenin pathway controls the maintenance of somatic stem cells in many tissues and organs and is implicated in pancreatic carcinogenesis by regulating cell cycle progression, apoptosis, epithelial-mesenchymal transition (EMT), angiogenesis, stemness, tumor immune microenvironment, etc. Further, dysregulated Wnt has been shown to cause drug resistance in pancreatic cancer. Although different Wnt antagonists are effective in pancreatic patients, limitations remain that must be overcome to increase the survival benefits associated with this emerging therapy. In this review, we have summarized the role of Wnt signaling in pancreatic cancer and suggested future directions to enhance the survival of pancreatic cancer patients.","authors":"Ram Makena, M., Gatla, H., Verlekar, D., Sukhavasi, S., K Pandey, M., C Pramanik, K.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Int J Mol Sci","volume":"20","issue":"17","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31467278","title":"Maximizing binary interactome mapping with a minimal number of assays.","abstract":"Complementary assays are required to comprehensively map complex biological entities such as genomes, proteomes and interactome networks. However, how various assays can be optimally combined to approach completeness while maintaining high precision often remains unclear. Here, we propose a framework for binary protein-protein interaction (PPI) mapping based on optimally combining assays and\/or assay versions to maximize detection of true positive interactions, while avoiding detection of random protein pairs. We have engineered a novel NanoLuc two-hybrid (N2H) system that integrates 12 different versions, differing by protein expression systems and tagging configurations. The resulting union of N2H versions recovers as many PPIs as 10 distinct assays combined. Thus, to further improve PPI mapping, developing alternative versions of existing assays might be as productive as designing completely new assays. Our findings should be applicable to systematic mapping of other biological landscapes.","authors":"Choi, SG., Olivet, J., Cassonnet, P., Vidalain, PO., Luck, K., Lambourne, L., Spirohn, K., Lemmens, I., Dos Santos, M., Demeret, C., Jones, L., Rangarajan, S., Bian, W., Coutant, EP., Janin, YL., van der Werf, S., Trepte, P., Wanker, EE., De Las Rivas, J., Tavernier, J., Twizere, JC., Hao, T., Hill, DE., Vidal, M., Calderwood, MA., Jacob, Y.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"3907","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31446798","title":"Differentially Expressed Proteins in Primary Endothelial Cells Derived From Patients With Acute Myocardial Infarction.","abstract":"Endothelial dysfunction is one of the primary factors in the onset and progression of atherothrombosis resulting in acute myocardial infarction (AMI). However, the pathological and cellular mechanisms of endothelial dysfunction in AMI have not been systematically studied. Protein expression profiling in combination with a protein network analysis was used by the mass spectrometry-based label-free quantification approach. This identified and quantified 2246 proteins, of which 335 were differentially regulated in coronary arterial endothelial cells from patients with AMI compared with controls. The differentially regulated protein profiles reveal the alteration of (1) metabolism of RNA, (2) platelet activation, signaling, and aggregation, (3) neutrophil degranulation, (4) metabolism of amino acids and derivatives, (5) cellular responses to stress, and (6) response to elevated platelet cytosolic Ca<sup>2+<\/sup> pathways. Increased production of oxidants and decreased production of antioxidant biomarkers as well as downregulation of proteins with antioxidant properties suggests a role for oxidative stress in mediating endothelial dysfunction during AMI. In conclusion, this is the first quantitative proteomics study to evaluate the cellular mechanisms of endothelial dysfunction in patients with AMI. A better understanding of the endothelial proteome and pathophysiology of AMI may lead to the identification of new drug targets.","authors":"Nukala, SB., Regazzoni, L., Aldini, G., Zodda, E., Tura-Ceide, O., Mills, NL., Cascante, M., Carini, M., D'Amato, A.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Hypertension","volume":"74","issue":"4","page":"947-956","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31434318","title":"RAC1B Suppresses TGF-\u03b2-Dependent Chemokinesis and Growth Inhibition through an Autoregulatory Feed-Forward Loop Involving PAR2 and ALK5.","abstract":"The small GTPase RAC1B functions as a powerful inhibitor of transforming growth factor (TGF)-\u03b21-induced epithelial-mesenchymal transition, cell motility, and growth arrest in pancreatic epithelial cells. Previous work has shown that RAC1B downregulates the TGF-\u03b2 type I receptor ALK5, but the molecular details of this process have remained unclear. Here, we hypothesized that RAC1B-mediated suppression of activin receptor-like kinase 5 (ALK5) involves proteinase-activated receptor 2 (PAR2), a G protein-coupled receptor encoded by <i>F2RL1<\/i> that is crucial for sustaining ALK5 expression. We found in pancreatic carcinoma Panc1 cells that PAR2 is upregulated by TGF-\u03b21 in an ALK5-dependent manner and that siRNA-mediated knockdown of RAC1B increased both basal and TGF-\u03b21-induced expression of PAR2. Further, the simultaneous knockdown of PAR2 and RAC1B rescued Panc1 cells from a RAC1B knockdown-induced increase in ALK5 abundance and the ALK5-mediated increase in TGF-\u03b21-induced migratory activity. Conversely, Panc1 cells with stable ectopic expression of RAC1B displayed reduced ALK5 expression, an impaired upregulation of PAR2, and a reduced migratory responsiveness to TGF-\u03b21 stimulation. However, these effects could be reversed by ectopic overexpression of PAR2. Moreover, the knockdown of PAR2 alone in Panc1 cells and HaCaT keratinocytes phenocopied RAC1B's ability to suppress ALK5 abundance and TGF-\u03b21-induced chemokinesis and growth inhibition. Lastly, we found that the RAC1B knockdown-induced increase in TGF-\u03b21-induced PAR2 mRNA expression was sensitive to pharmacological inhibition of MEK-ERK signaling. Our data show that in pancreatic and skin epithelial cells, downregulation of ALK5 activity by RAC1B is secondary to suppression of <i>F2RL1<\/i>\/PAR2 expression. Since <i>F2RL1<\/i> itself is a TGF-\u03b2 target gene and its upregulation by TGF-\u03b21 is mediated by ALK5 and MEK-ERK signaling, we suggest the existence of a feed-forward signaling loop involving ALK5 and PAR2 that is efficiently suppressed by RAC1B to restrict TGF-\u03b2-driven cell motility and growth inhibition.","authors":"Otterbein, H., Mihara, K., Hollenberg, MD., Lehnert, H., Witte, D., Ungefroren, H.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Cancers (Basel)","volume":"11","issue":"8","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31422913","title":"Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells.","abstract":"The gastric corpus epithelium is the thickest part of the gastrointestinal tract and is rapidly turned over. Several markers have been proposed for gastric corpus stem cells in both isthmus and base regions. However, the identity of isthmus stem cells (IsthSCs) and the interaction between distinct stem cell populations is still under debate. Here, based on unbiased genetic labeling and biophysical modeling, we show that corpus glands are compartmentalized into two independent zones, with slow-cycling stem cells maintaining the base and actively cycling stem cells maintaining the pit-isthmus-neck region through a\u00a0process of \"punctuated\" neutral drift dynamics. Independent lineage tracing based on Stmn1 and Ki67 expression confirmed that rapidly cycling IsthSCs maintain the pit-isthmus-neck region. Finally, single-cell RNA sequencing (RNA-seq) analysis is used to define the molecular identity and lineage relationship of a single, cycling, IsthSC population. These observations define the identity and functional behavior of IsthSCs.","authors":"Han, S., Fink, J., J\u00f6rg, DJ., Lee, E., Yum, MK., Chatzeli, L., Merker, SR., Josserand, M., Trendafilova, T., Andersson-Rolf, A., Dabrowska, C., Kim, H., Naumann, R., Lee, JH., Sasaki, N., Mort, RL., Basak, O., Clevers, H., Stange, DE., Philpott, A., Kim, JK., Simons, BD., Koo, BK.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell Stem Cell","volume":"25","issue":"3","page":"342-356.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31406378","title":"Cryptic activation of an Irf8 enhancer governs cDC1 fate specification.","abstract":"Induction of the transcription factor Irf8 in the common dendritic cell progenitor (CDP) is required for classical type 1 dendritic cell (cDC1) fate specification, but the mechanisms controlling this induction are unclear. In the present study Irf8 enhancers were identified via chromatin profiling of dendritic cells and CRISPR\/Cas9 genome editing was used to assess their roles in Irf8 regulation. An enhancer 32\u2009kilobases (kb) downstream of the Irf8 transcriptional start site (+32-kb Irf8) that was active in mature cDC1s was required for the development of this lineage, but not for its specification. Instead, a +41-kb Irf8 enhancer, previously thought to be active only in plasmacytoid dendritic cells, was found to also be transiently accessible in cDC1 progenitors, and deleting this enhancer prevented the induction of Irf8 in CDPs and abolished cDC1 specification. Thus, cryptic activation of the +41-kb Irf8 enhancer in dendritic cell progenitors is responsible for cDC1 fate specification.","authors":"Durai, V., Bagadia, P., Granja, JM., Satpathy, AT., Kulkarni, DH., Davidson, JT., Wu, R., Patel, SJ., Iwata, A., Liu, TT., Huang, X., Brise\u00f1o, CG., Grajales-Reyes, GE., W\u00f6hner, M., Tagoh, H., Kee, BL., Newberry, RD., Busslinger, M., Chang, HY., Murphy, TL., Murphy, KM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Immunol","volume":"20","issue":"9","page":"1161-1173","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31382494","title":"Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma.","abstract":"Expression of DNA repair genes was studied in uveal melanoma (UM) in order to identify genes that may play a role in metastases formation. We searched for genes that are differentially expressed between tumors with a favorable and unfavorable prognosis. Gene-expression profiling was performed on 64 primary UM from the Leiden University Medical Center (LUMC), Leiden, The Netherlands. The expression of 121 genes encoding proteins involved in DNA repair pathways was analyzed: a total of 44 genes differed between disomy 3 and monosomy 3 tumors. Results were validated in a cohort from Genoa and Paris and the The Cancer Genome Atlas (TCGA) cohort. Expression of the <i>PRKDC<\/i>, <i>WDR48<\/i>, <i>XPC<\/i>, and <i>BAP1<\/i> genes was significantly associated with clinical outcome after validation. <i>PRKDC<\/i> was highly expressed in metastasizing UM (<i>p<\/i> &lt; 0.001), whereas <i>WDR48<\/i>, <i>XPC<\/i>, and <i>BAP1<\/i> were lowly expressed (<i>p<\/i> &lt; 0.001, <i>p<\/i> = 0.006, <i>p<\/i> = 0.003, respectively). Low expression of <i>WDR48<\/i> and <i>XPC<\/i> was related to a large tumor diameter (<i>p<\/i> = 0.01 and <i>p<\/i> = 0.004, respectively), and a mixed\/epithelioid cell type (<i>p<\/i> = 0.007 and <i>p<\/i> = 0.03, respectively). We conclude that the expression of <i>WDR48<\/i>, <i>XPC<\/i>, and <i>BAP1<\/i> is significantly lower in UM with an unfavorable prognosis, while these tumors have a significantly higher expression of <i>PRKDC<\/i>. Pharmacological inhibition of DNA-PKcs resulted in decreased survival of UM cells. <i>PRKDC<\/i> may be involved in proliferation, invasion and metastasis of UM cells. Unraveling the role of DNA repair genes may enhance our understanding of UM biology and result in the identification of new therapeutic targets.","authors":"Dogrus\u00f6z, M., Ruschel Trasel, A., Cao, J., \u04aaolak, S., van Pelt, SI., Kroes, WGM., Teunisse, AFAS., Alsafadi, S., van Duinen, SG., Luyten, GPM., van der Velden, PA., Amaro, A., Pfeffer, U., Jochemsen, AG., Jager, MJ.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Cancers (Basel)","volume":"11","issue":"8","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31366361","title":"Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31366361<\/PMID><DateCompleted><Year>2020<\/Year><Month>01<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>03<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1465-542X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>21<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>07<\/Month><Day>31<\/Day><\/PubDate><\/JournalIssue><Title>Breast cancer research : BCR<\/Title><ISOAbbreviation>Breast Cancer Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers.<\/ArticleTitle><Pagination><MedlinePgn>85<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13058-019-1170-8<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Claudin-low breast cancer is a molecular subtype associated with poor prognosis and without targeted treatment options. The claudin-low subtype is defined by certain biological characteristics, some of which may be clinically actionable, such as high immunogenicity. In mice, the medroxyprogesterone acetate (MPA) and 7,12-dimethylbenzanthracene (DMBA)-induced mammary tumor model yields a heterogeneous set of tumors, a subset of which display claudin-low features. Neither the genomic characteristics of MPA\/DMBA-induced claudin-low tumors nor those of human claudin-low breast tumors have been thoroughly explored.","authors":"Fougner, C., Bergholtz, H., Kuiper, R., Norum, JH., S\u00f8rlie, T.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Breast Cancer Res","volume":"21","issue":"1","page":"85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31350812","title":"Sepiapterin Reductase Inhibition Leading to Selective Reduction of Inflammatory Joint Pain in Mice and Increased Urinary Sepiapterin Levels in Humans and Mice.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31350812<\/PMID><DateCompleted><Year>2020<\/Year><Month>03<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">2326-5205<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>72<\/Volume><Issue>1<\/Issue><PubDate><Year>2020<\/Year><Month>01<\/Month><\/PubDate><\/JournalIssue><Title>Arthritis &amp; rheumatology (Hoboken, N.J.)<\/Title><ISOAbbreviation>Arthritis Rheumatol<\/ISOAbbreviation><\/Journal><ArticleTitle>Sepiapterin Reductase Inhibition Leading to Selective Reduction of Inflammatory Joint Pain in Mice and Increased Urinary Sepiapterin Levels in Humans and Mice.<\/ArticleTitle><Pagination><MedlinePgn>57-66<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/art.41060<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\">To evaluate the antiinflammatory and analgesic effects of sepiapterin reductase (SPR) inhibition in a mouse model of inflammatory joint disease, and to determine whether urinary sepiapterin levels, as measured in mice and healthy human volunteers, could be useful as a noninvasive, translational biomarker of SPR inhibition\/target engagement.","authors":"Fujita, M., Scheffer, DDL., Turnes, BL., Cronin, SJF., Latr\u00e9moli\u00e8re, A., Costigan, M., Woolf, CJ., Latini, A., Andrews, NA.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Arthritis Rheumatol","volume":"72","issue":"1","page":"57-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31350353","title":"Protein engineering of a ubiquitin-variant inhibitor of APC\/C identifies a cryptic K48 ubiquitin chain binding site.","abstract":"Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub's C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at \"exosites.\" However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2-MDa E3 ligase anaphase-promoting complex\/cyclosome (APC\/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC\/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC\/C activity, have implications for the coordination of K48-linked Ub chain binding by APC\/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.","authors":"Watson, ER., Grace, CRR., Zhang, W., Miller, DJ., Davidson, IF., Prabu, JR., Yu, S., Bolhuis, DL., Kulko, ET., Vollrath, R., Haselbach, D., Stark, H., Peters, JM., Brown, NG., Sidhu, SS., Schulman, BA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Proc Natl Acad Sci U S A","volume":"116","issue":"35","page":"17280-17289","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31329595","title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes.","abstract":"Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.","authors":"Andergassen, D., Muckenhuber, M., Bammer, PC., Kulinski, TM., Theussl, HC., Shimizu, T., Penninger, JM., Pauler, FM., Hudson, QJ.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PLoS Genet","volume":"15","issue":"7","page":"e1008268","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31329577","title":"N-terminal \u03b2-strand underpins biochemical specialization of an ATG8 isoform.","abstract":"Autophagy-related protein 8 (ATG8) is a highly conserved ubiquitin-like protein that modulates autophagy pathways by binding autophagic membranes and a number of proteins, including cargo receptors and core autophagy components. Throughout plant evolution, ATG8 has expanded from a single protein in algae to multiple isoforms in higher plants. However, the degree to which ATG8 isoforms have functionally specialized to bind distinct proteins remains unclear. Here, we describe a comprehensive protein-protein interaction resource, obtained using in planta immunoprecipitation (IP) followed by mass spectrometry (MS), to define the potato ATG8 interactome. We discovered that ATG8 isoforms bind distinct sets of plant proteins with varying degrees of overlap. This prompted us to define the biochemical basis of ATG8 specialization by comparing two potato ATG8 isoforms using both in vivo protein interaction assays and in vitro quantitative binding affinity analyses. These experiments revealed that the N-terminal \u03b2-strand-and, in particular, a single amino acid polymorphism-underpins binding specificity to the substrate PexRD54 by shaping the hydrophobic pocket that accommodates this protein's ATG8-interacting motif (AIM). Additional proteomics experiments indicated that the N-terminal \u03b2-strand shapes the broader ATG8 interactor profiles, defining interaction specificity with about 80 plant proteins. Our findings are consistent with the view that ATG8 isoforms comprise a layer of specificity in the regulation of selective autophagy pathways in plants.","authors":"Zess, EK., Jensen, C., Cruz-Mireles, N., De la Concepcion, JC., Sklenar, J., Stephani, M., Imre, R., Roitinger, E., Hughes, R., Belhaj, K., Mechtler, K., Menke, FLH., Bozkurt, T., Banfield, MJ., Kamoun, S., Maqbool, A., Dagdas, YF.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PLoS Biol","volume":"17","issue":"7","page":"e3000373","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31321300","title":"HACE1 deficiency leads to structural and functional neurodevelopmental defects.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31321300<\/PMID><DateRevised><Year>2020<\/Year><Month>10<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Print\">2376-7839<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>5<\/Volume><Issue>3<\/Issue><PubDate><Year>2019<\/Year><Month>Jun<\/Month><\/PubDate><\/JournalIssue><Title>Neurology. Genetics<\/Title><ISOAbbreviation>Neurol Genet<\/ISOAbbreviation><\/Journal><ArticleTitle>HACE1 deficiency leads to structural and functional neurodevelopmental defects.<\/ArticleTitle><Pagination><MedlinePgn>e330<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1212\/NXG.0000000000000330<\/ELocationID><Abstract><AbstractText Label=\"Objective\" NlmCategory=\"UNASSIGNED\">We aim to characterize the causality and molecular and functional underpinnings of <i>HACE1<\/i> deficiency in a mouse model of a recessive neurodevelopmental syndrome called spastic paraplegia and psychomotor retardation with or without seizures (SPPRS).","authors":"Nagy, V., Hollstein, R., Pai, TP., Herde, MK., Buphamalai, P., Moeseneder, P., Lenartowicz, E., Kavirayani, A., Korenke, GC., Kozieradzki, I., Nitsch, R., Cicvaric, A., Monje Quiroga, FJ., Deardorff, MA., Bedoukian, EC., Li, Y., Yigit, G., Menche, J., Per\u00e7in, EF., Wollnik, B., Henneberger, C., Kaiser, FJ., Penninger, JM.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Neurol Genet","volume":"5","issue":"3","page":"e330","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-219","title":"The SPARK complex forms the molecular basis of vertebrate fertilization","abstract":null,"authors":"Deneke, VE., Suwita, JP., Wang, H., Tonai, S., Lu, Y., Panser, K., Schleiffer, A., Hollis, JA., Novatchkova, M., D\u00fcrnberger, G., Stejskal, K., Krssakova, G., Blaha, A., Andresan, AAR., Mirus, M., Marvanova, H., Chang, HY., Noda, T., Burga, A., Roitinger, E., Ikawa, M., Pauli, A. ","publication_status":"preprint","journalpubyear":"2026","journaltitle":"bioRxiv ","volume":"10.64898\/2026.05.13.724128","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.05.13.724128v1","preprintlink":null,"articledate":"2026-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31320644","title":"Live cell imaging reveals 3'-UTR dependent mRNA sorting to synapses.","abstract":"mRNA transport restricts translation to specific subcellular locations, which is the basis for many cellular functions. However, the precise process of mRNA sorting to synapses in neurons remains elusive. Here we use Rgs4 mRNA to investigate 3'-UTR-dependent transport by MS2 live-cell imaging. The majority of observed RNA granules display 3'-UTR independent bidirectional transport in dendrites. Importantly, the Rgs4 3'-UTR causes an anterograde transport bias, which requires the Staufen2 protein. Moreover, the 3'-UTR mediates dynamic, sustained mRNA recruitment to synapses. Visualization at high temporal resolution enables us to show mRNA patrolling dendrites, allowing transient interaction with multiple synapses, in agreement with the sushi-belt model. Modulation of neuronal activity by either chemical silencing or local glutamate uncaging regulates both the 3'-UTR-dependent transport bias and synaptic recruitment. This dynamic and reversible mRNA recruitment to active synapses would allow translation and synaptic remodeling in a spatially and temporally adaptive manner.","authors":"Bauer, KE., Segura, I., Gaspar, I., Scheuss, V., Illig, C., Ammer, G., Hutten, S., Basyuk, E., Fern\u00e1ndez-Moya, SM., Ehses, J., Bertrand, E., Kiebler, MA.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"3178","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31297036","title":"Identification of potential key genes and pathways predicting pathogenesis and prognosis for triple-negative breast cancer.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31297036<\/PMID><DateRevised><Year>2020<\/Year><Month>09<\/Month><Day>30<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Print\">1475-2867<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>19<\/Volume><PubDate><Year>2019<\/Year><\/PubDate><\/JournalIssue><Title>Cancer cell international<\/Title><ISOAbbreviation>Cancer Cell Int<\/ISOAbbreviation><\/Journal><ArticleTitle>Identification of potential key genes and pathways predicting pathogenesis and prognosis for triple-negative breast cancer.<\/ArticleTitle><Pagination><MedlinePgn>172<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12935-019-0884-0<\/ELocationID><Abstract><AbstractText Label=\"Background\" NlmCategory=\"UNASSIGNED\">Triple negative breast cancer (TNBC) is a specific subtype of breast cancer with a poor prognosis due to its aggressive biological behaviour and lack of therapeutic targets. We aimed to explore some novel genes and pathways related to TNBC prognosis through bioinformatics methods as well as potential initiation and progression mechanisms.","authors":"Lv, X., He, M., Zhao, Y., Zhang, L., Zhu, W., Jiang, L., Yan, Y., Fan, Y., Zhao, H., Zhou, S., Ma, H., Sun, Y., Li, X., Xu, H., Wei, M.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Cancer Cell Int","volume":"19","issue":"","page":"172","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31294654","title":"New insights into the roles of the <i>FOXO3<\/i> and <i>P27Kip1<\/i> genes in signaling pathways.","abstract":"<b>Background:<\/b> The forkhead box O3 (FOXO3) and p27Kip1 are two important genes in breast cancer progression. In the present study we analyzed the effect of simultaneous FOXO3 silencing and p27Kip1 activation on breast cancer cell survival and the potential targets of these changes in cancer molecular pathways. <b>Materials and methods:<\/b> The present study involved the cloning of <i>FOXO3a<\/i> shRNA and <i>p27Kip1<\/i> genes under the control of the bidirectional survivin promoter to down- and up-regulate <i>FOXO3<\/i> and <i>p27Kip1<\/i> genes, respectively. After transfection of the recombinant expression vector into the breast cancer cell line, the inhibition of cell growth was assessed by MTS and flow cytometry assays. Following the extraction of total mRNA and protein, the expression of target genes was evaluated by qPCR and Western blotting in both treated and untreated cell lines. Then, the downstream protein responses were examined by 2\u2009D electrophoresis. The differentially expressed proteins were also identified by mass spectrometry. <b>Results:<\/b> Rates of cell proliferation were significantly inhibited in the transfected cell line 72\u2009h post-transfection. Proteomic profiling of the cell line resulted in the identification of seven novel protein markers in breast cancer responsive to these changes in expression of <i>FOXO3<\/i> and <i>p27Kip1<\/i>. The changes in expression of these markers suggested that certain signaling pathways contribute to the development of breast cancer. <b>Conclusion:<\/b> Simultaneous silencing of <i>FOXO3<\/i> and activation of <i>p27Kip1<\/i> in MDA-MB-231 cells caused alterations in the expression level of several genes involved in apoptosis, cell proliferation, cell cycle control, tissue invasion, drug resistance, and metastasis. It seems that the identified genes might serve as useful biomarkers for breast cancer.","authors":"Mayahi, S., Golalipour, M., Yamchi, A., Jhingan, GD., Shahbazi, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Ups J Med Sci","volume":"124","issue":"3","page":"149-157","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31284422","title":"c-Met and PD-L1 on Circulating Exosomes as Diagnostic and Prognostic Markers for Pancreatic Cancer.","abstract":"Exosomes are membrane vesicles which offer potential as blood derived biomarkers for malign tumors in clinical practice. Pancreatic cancer is counted among cancer diseases with the highest mortality. The present work seeks to assess whether pancreatic carcinomas release exosomes which express c-Met (proto-oncogene mesenchymal-epithelial transition factor) and PD-L1 (programmed cell death 1 ligand 1), and whether the detection of such expression in serum has diagnostic or prognostic meaning for the affected patients. Exosome isolation was performed on culture media of one benign pancreatic cell line and ten pancreatic carcinoma cell lines as well as on serum samples from 55 patients with pancreatic ductal adenocarcinoma (PDAC), 26 patients with chronic pancreatitis and 10 patients with benign serous cyst adenoma of the pancreas. Exosomes were bound to latex beads and stained with antibodies against c-Met or PD-L1. Analysis of fluorescence intensity was performed by flow cytometry. In terms of c-Met, the mean fluorescence intensity of PDAC-patients was significantly higher than the fluorescence intensity of the comparative patients with benign disease (<i>p<\/i> &lt; 0.001). A diagnostic test based on c-Met resulted in a sensitivity of 70%, a specificity of 85% and a diagnostic odds ratio of 13:2. The specificity of the test can be further improved by combining it with the established tumor marker carbohydrate antigen 19-9 (CA 19-9). In addition, c-Met-positive patients showed a significantly shorter postoperative survival time (9.5 vs. 21.7 months, <i>p<\/i> &lt; 0.001). In terms of PD-L1, no significant difference between fluorescence intensity of PDAC-patients and comparative patients was detectable. However, PD-L1-positive PDAC-patients also showed a significantly shorter postoperative survival time (7.8 vs. 17.2 months, <i>p<\/i> = 0.043). Thus, both markers can be considered as negative prognostic factors.","authors":"Lux, A., Kahlert, C., Gr\u00fctzmann, R., Pilarsky, C.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Int J Mol Sci","volume":"20","issue":"13","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31278347","title":"Search for novel STAT3-dependent genes reveals SERPINA3 as a new STAT3 target that regulates invasion of human melanoma cells.","abstract":"Transcription factor signal transducer and activator of transcription 3 (STAT3) is constitutively activated in many cancers and promotes uncontrolled tumor growth and progression through multiple mechanisms. Compelling evidence shows tissue and cell-specific sets of STAT3 targets. Transcriptional targets of STAT3 in melanoma cells are largely unknown. Malignant melanoma is a deadly disease with highly aggressive and drug-resistant behavior. Less than 10% of patients with advanced melanomas reach the 5-year survival, partly due to the aggressive character of the tumor and ineffectiveness of current therapeutics for treating metastatic melanoma. STAT3 is constitutively activated in melanoma cells and plays important roles in its growth and angiogenesis in tumor xenograft studies. Moreover, highly metastatic melanoma cells have higher levels of active STAT3 than poorly metastatic ones. To identify genes that are driven by STAT3 in human melanoma cells, we performed JAK\/STAT signaling specific and global gene expression profiling of human melanoma cells with silenced STAT3 expression. For selected genes, we performed computational identification of putative STAT3-binding sites and validated direct interactions STAT3 with defined promoters by using chromatin immunoprecipitation followed by qPCR. We found that STAT3 knockdown does not affect human melanoma cell viability, proliferation, or response to chemotherapeutics. We show that STAT3 regulates a discrete set of genes in melanoma cells, including SERPINA3, a novel STAT3 target gene, which is functionally involved in regulation of melanoma migration and invasion. Knockdown of STAT3 impaired cell migration and invasion, in part via regulation of its transcriptional target SERPINA3. Our results present novel targets and functions of STAT3 in melanoma cells.","authors":"Kulesza, DW., Ramji, K., Maleszewska, M., Mieczkowski, J., Dabrowski, M., Chouaib, S., Kaminska, B.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Lab Invest","volume":"99","issue":"11","page":"1607-1621","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-220","title":"Hyaluronan Underlies the Emergence of Form, Fate, and Function in Human Cardioids","abstract":null,"authors":"Jahnel SM, Dimitriadi A, Kodnar J, Gerakopoulos V, Khurana Y, Mayrhauser M, Ilmer T, Aguech MA, Hall AR, Ishihara K, Mendjan S. ","publication_status":"preprint","journalpubyear":"2026","journaltitle":"bioRixv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.01.26.700345v2","articledate":"2026-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23478349","title":null,"abstract":null,"authors":"","publication_status":null,"journalpubyear":null,"journaltitle":null,"volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31278164","title":"The <i>Prrx1<\/i> limb enhancer marks an adult subpopulation of injury-responsive dermal fibroblasts.","abstract":"The heterogeneous properties of dermal cell populations have been posited to contribute toward fibrotic, imperfect wound healing in mammals. Here we characterize an adult population of dermal fibroblasts that maintain an active <i>Prrx1<\/i> enhancer which originally marked mesenchymal limb progenitors. In contrast to their abundance in limb development, postnatal <i>Prrx1<\/i> enhancer-positive cells (Prrx1<sup>enh+<\/sup>) make up a small subset of adult dermal cells (\u223c0.2%) and reside mainly within dermal perivascular and hair follicle niches. Lineage tracing of adult Prrx1<sup>enh+<\/sup> cells shows that they remain in their niches and in small numbers over a long period of time. Upon injury however, Prrx1<sup>enh+<\/sup> cells readily migrate into the wound bed and amplify, on average, 16-fold beyond their uninjured numbers. Additionally, following wounding dermal Prrx1<sup>enh+<\/sup> cells are found out of their dermal niches and contribute to subcutaneous tissue. Postnatal Prrx1<sup>enh+<\/sup> cells are uniquely injury-responsive despite being a meager minority in the adult skin.","authors":"Currie, JD., Grosser, L., Murawala, P., Schuez, M., Michel, M., Tanaka, EM., Sandoval-Guzm\u00e1n, T.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Biol Open","volume":"8","issue":"7","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31263413","title":"Sigma-1 Receptor Inhibition Reduces Neuropathic Pain Induced by Partial Sciatic Nerve Transection in Mice by Opioid-Dependent and -Independent Mechanisms.","abstract":"Sigma-1 (\u03c3<sub>1<\/sub>) receptor antagonists are promising tools for neuropathic pain treatment, but it is unknown whether \u03c3<sub>1<\/sub> receptor inhibition ameliorates the neuropathic signs induced by nerve transection, in which the pathophysiological mechanisms and response to drug treatment differ from other neuropathic pain models. In addition, \u03c3<sub>1<\/sub> antagonism ameliorates inflammatory pain through modulation of the endogenous opioid system, but it is unknown whether this occurs during neuropathic pain. We investigated the effect of \u03c3<sub>1<\/sub> inhibition on the painful hypersensitivity associated with the spared nerve injury (SNI) model in mice. Wild-type (WT) mice developed prominent cold (acetone test), mechanical (von Frey test), and heat hypersensitivity (Hargreaves test) after SNI. \u03c3<sub>1<\/sub> receptor knockout (\u1001\u03c3<sub>1<\/sub>-KO) mice did not develop cold allodynia and showed significantly less mechanical allodynia, although they developed heat hyperalgesia after SNI. The systemic acute administration of the selective \u03c3<sub>1<\/sub> receptor antagonist S1RA attenuated all three types of SNI-induced hypersensitivity in WT mice. These ameliorative effects of S1RA were reversed by the administration of the \u03c3<sub>1<\/sub> agonist PRE-084, and were absent in \u03c3<sub>1<\/sub>-KO mice, indicating the selectivity of S1RA-induced effects. The opioid antagonist naloxone and its peripherally restricted analog naloxone methiodide prevented S1RA-induced effects in mechanical and heat hypersensitivity, but not in cold allodynia, indicating that opioid-dependent and -independent mechanisms are involved in the effects of this \u03c3<sub>1<\/sub> antagonist. The repeated administration of S1RA twice a day during 10 days reduced SNI-induced cold, mechanical, and heat hypersensitivity without inducing analgesic tolerance during treatment. These effects were observed up to 12 h after the last administration, when S1RA was undetectable in plasma or brain, indicating long-lasting pharmacodynamic effects. These data suggest that \u03c3<sub>1<\/sub> antagonism may have therapeutic value for the treatment of neuropathic pain induced by the transection of peripheral nerves.","authors":"Bravo-Caparr\u00f3s, I., Perazzoli, G., Yeste, S., Cikes, D., Baeyens, JM., Cobos, EJ., Nieto, FR.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Front Pharmacol","volume":"10","issue":null,"page":"613","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31260457","title":"A polymorphic helix of a Salmonella needle protein relays signals defining distinct steps in type III secretion.","abstract":"Type III protein-secretion machines are essential for the interactions of many pathogenic or symbiotic bacterial species with their respective eukaryotic hosts. The core component of these machines is the injectisome, a multiprotein complex that mediates the selection of substrates, their passage through the bacterial envelope, and ultimately their delivery into eukaryotic target cells. The injectisome is composed of a large cytoplasmic complex or sorting platform, a multiring base embedded in the bacterial envelope, and a needle-like filament that protrudes several nanometers from the bacterial surface and is capped at its distal end by the tip complex. A characteristic feature of these machines is that their activity is stimulated by contact with target host cells. The sensing of target cells, thought to be mediated by the distal tip of the needle filament, generates an activating signal that must be transduced to the secretion machine by the needle filament. Here, through a multidisciplinary approach, including solid-state NMR (SSNMR) and cryo electron microscopy (cryo-EM) analyses, we have identified critical residues of the needle filament protein of a Salmonella Typhimurium type III secretion system that are involved in the regulation of the activity of the secretion machine. We found that mutations in the needle filament protein result in various specific phenotypes associated with different steps in the type III secretion process. More specifically, these studies reveal an important role for a polymorphic helix of the needle filament protein and the residues that line the lumen of its central channel in the control of type III secretion.","authors":"Guo, EZ., Desrosiers, DC., Zalesak, J., Tolchard, J., Berbon, M., Habenstein, B., Marlovits, T., Loquet, A., Gal\u00e1n, JE.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PLoS Biol","volume":"17","issue":"7","page":"e3000351","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12749729","title":"Utilizing functional genomics to identify new pain treatments : the example of nociceptin.","abstract":"Nociceptin\/orphanin FQ (noc\/oFQ) is the first novel bioactive substance to have been discovered by the implementation of a functional genomics\/reverse pharmacology approach. The neuropeptide was indeed identified in brain extracts as the natural ligand of a previously cloned orphan G protein-coupled receptor, the opioid receptor-like 1 (ORL1) receptor. Since its discovery in 1995, noc\/oFQ has been the subject of intensive study to establish its role in normal brain function and its possible involvement in neurophysiopathology. Although the neuropeptide, an inhibitor of neuronal activity, has been found to have a wide spectrum of pharmacological effects in vivo, none has been as intensively investigated as its action on nociception and nociceptive processing. There is now substantial evidence that noc\/oFQ has a modulatory role in nociception. However, dependent on the dose and site of injection, and possibly the animal's genetic background and even psychological status, the peptide has been variously reported to cause allodynia, hyperalgesia, analgesia, and even pain, in rodents. Overall, noc\/oFQ tends to facilitate pain when administered supraspinally, and to inhibit it when administered spinally. These opposing effects beg the obvious, yet still unanswered, question as to what would be the net effect on nociception of an ORL1 receptor ligand, agonist or antagonist, able to target supraspinal and spinal sites simultaneously. Owing to the research effort of several drug companies, such ligands, i.e. nonpeptidic, brain-penetrating agonists and antagonists, have recently been produced whose systematic screening in animal models of acute and inflammatory pain may help validate the ORL1 receptor as the target for novel, non-opioid analgesics.","authors":"Meunier, JC.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Am J Pharmacogenomics","volume":"3","issue":"2","page":"117-30","pdf":null,"JrId":"29769","fulltextlink":null,"preprintlink":null,"articledate":"2003-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31235369","title":"Shaping Striated Muscles with Ubiquitin Proteasome System in Health and Disease.","abstract":"For long-lived contractile cells, such as striated muscle cells, maintaining proteome integrity is a challenging task. These cells require hundreds of components that must be properly synthesized, folded, and incorporated into the basic contractile unit, the sarcomere. Muscle protein quality control in cells is mainly guaranteed by the ubiquitin-proteasome system (UPS), the lysosome-autophagy system, and various molecular chaperones. Recent studies establish the concept of dedicated UPS in the regulation of sarcomere assembly during development and in adult life to maintain the intricate and interwoven organization of protein complexes in muscle. Failure of sarcomere protein quality control often represents the basis of severe myopathies and cardiomyopathies in human, further highlighting its importance in producing and maintaining the contractile machinery of muscle cells in shape.","authors":"Hnia, K., Clausen, T., Moog-Lutz, C.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Trends Mol Med","volume":"25","issue":"9","page":"760-774","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31204999","title":"Absolute quantification of cohesin, CTCF and their regulators in human cells.","abstract":"The organisation of mammalian genomes into loops and topologically associating domains (TADs) contributes to chromatin structure, gene expression and recombination. TADs and many loops are formed by cohesin and positioned by CTCF. In proliferating cells, cohesin also mediates sister chromatid cohesion, which is essential for chromosome segregation. Current models of chromatin folding and cohesion are based on assumptions of how many cohesin and CTCF molecules organise the genome. Here we have measured absolute copy numbers and dynamics of cohesin, CTCF, NIPBL, WAPL and sororin by mass spectrometry, fluorescence-correlation spectroscopy and fluorescence recovery after photobleaching in HeLa cells. In G1-phase, there are ~250,000 nuclear cohesin complexes, of which ~ 160,000 are chromatin-bound. Comparison with chromatin immunoprecipitation-sequencing data implies that some genomic cohesin and CTCF enrichment sites are unoccupied in single cells at any one time. We discuss the implications of these findings for how cohesin can contribute to genome organisation and cohesion.","authors":"Holzmann, J., Politi, AZ., Nagasaka, K., Hantsche-Grininger, M., Walther, N., Koch, B., Fuchs, J., D\u00fcrnberger, G., Tang, W., Ladurner, R., Stocsits, RR., Busslinger, GA., Nov\u00e1k, B., Mechtler, K., Davidson, IF., Ellenberg, J., Peters, JM.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Elife","volume":"8","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31168069","title":"The genomic basis of mood instability: identification of 46 loci in 363,705 UK Biobank participants, genetic correlation with psychiatric disorders, and association with gene expression and function.","abstract":"Genome-wide association studies (GWAS) of psychiatric phenotypes have tended to focus on categorical diagnoses, but to understand the biology of mental illness it may be more useful to study traits which cut across traditional boundaries. Here, we report the results of a GWAS of mood instability as a trait in a large population cohort (UK Biobank, n\u2009=\u2009363,705). We also assess the clinical and biological relevance of the findings, including whether genetic associations show enrichment for nervous system pathways. Forty six unique loci associated with mood instability were identified with a SNP heritability estimate of 9%. Linkage Disequilibrium Score Regression (LDSR) analyses identified genetic correlations with Major Depressive Disorder (MDD), Bipolar Disorder (BD), Schizophrenia, anxiety, and Post Traumatic Stress Disorder (PTSD). Gene-level and gene set analyses identified 244 significant genes and 6 enriched gene sets. Tissue expression analysis of the SNP-level data found enrichment in multiple brain regions, and eQTL analyses highlighted an inversion on chromosome 17 plus two brain-specific eQTLs. In addition, we used a Phenotype Linkage Network (PLN) analysis and community analysis to assess for enrichment of nervous system gene sets using mouse orthologue databases. The PLN analysis found enrichment in nervous system PLNs for a community containing serotonin and melatonin receptors. In summary, this work has identified novel loci, tissues and gene sets contributing to mood instability. These findings may be relevant for the identification of novel trans-diagnostic drug targets and could help to inform future stratified medicine innovations in mental health.","authors":"Ward, J., Tunbridge, EM., Sandor, C., Lyall, LM., Ferguson, A., Strawbridge, RJ., Lyall, DM., Cullen, B., Graham, N., Johnston, KJA., Webber, C., Escott-Price, V., O'Donovan, M., Pell, JP., Bailey, MES., Harrison, PJ., Smith, DJ.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Mol Psychiatry","volume":"25","issue":"11","page":"3091-3099","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31109287","title":"Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Curated\" Owner=\"NLM\"><PMID Version=\"1\">31109287<\/PMID><DateCompleted><Year>2019<\/Year><Month>07<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2105<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>20<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>May<\/Month><Day>20<\/Day><\/PubDate><\/JournalIssue><Title>BMC bioinformatics<\/Title><ISOAbbreviation>BMC Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.<\/ArticleTitle><Pagination><MedlinePgn>258<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12859-019-2849-7<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and interpretation of such events in high-throughput sequencing datasets demands specialized bioinformatics approaches.","authors":"Neumann, T., Herzog, VA., Muhar, M., von Haeseler, A., Zuber, J., Ameres, SL., Rescheneder, P.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"BMC Bioinformatics","volume":"20","issue":"1","page":"258","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31108998","title":"RAC1B Suppresses TGF-\u03b21-Dependent Cell Migration in Pancreatic Carcinoma Cells through Inhibition of the TGF-\u03b2 Type I Receptor ALK5.","abstract":"The small GTPase Ras-related C3 botulinum toxin substrate 1B (RAC1B) has been shown previously by RNA interference-mediated knockdown (KD) to function as a powerful inhibitor of transforming growth factor (TGF)-\u03b21-induced cell migration and epithelial-mesenchymal transition in epithelial cells, but the underlying mechanism has remained enigmatic. Using pancreatic carcinoma cells, we show that both KD and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)\/Cas9-mediated knockout (KO) of RAC1B increased the expression of the TGF-\u03b2 type I receptor ALK5 (activin receptor-like kinase 5), but this effect was more pronounced in CRISPR-KO cells. Of note, in KO, but not KD cells, ALK5 upregulation was associated with resensitization of <i>TGFBR1<\/i> to induction by TGF-\u03b21 stimulation. RAC1B KO also increased TGF-\u03b21-induced C-terminal SMAD3 phosphorylation, SMAD3 transcriptional activity, growth inhibition, and cell migration. The KD of ALK5 expression by RNA interference or inactivation of the ALK5 kinase activity by dominant-negative interference or ATP-competitive inhibition rescued the cells from the RAC1B KD\/KO-mediated increase in TGF-\u03b21-induced cell migration, whereas the ectopic expression of kinase-active ALK5 mimicked this RAC1B KD\/KO effect. We conclude that RAC1B downregulates the abundance of ALK5 and SMAD3 signaling, thereby attenuating TGF-\u03b2\/SMAD3-driven cellular responses, such as growth inhibition and cell motility.","authors":"Ungefroren, H., Otterbein, H., Fiedler, C., Mihara, K., Hollenberg, MD., Gieseler, F., Lehnert, H., Witte, D.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Cancers (Basel)","volume":"11","issue":"5","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31077346","title":"O-glycan truncation enhances cancer-related functions of CD44 in gastric cancer.","abstract":"CD44 isoforms are often upregulated in gastric cancer and have been associated with increased metastatic potential and poor survival. To evaluate the functional impact of O-glycan truncation on CD44 we have analysed glyco-engineered cancer cell models displaying shortened O-glycans. Here, we demonstrate that induction of aberrant O-glycan termination through various molecular mechanisms affects CD44 molecular features. We show that CD44 is a major carrier of truncated O-glycans and that this truncation is accompanied by an increased hyaluronan binding capacity and affects extracellular shedding. In addition, short O-glycans promoted the colocalization of CD44v6 with the receptor tyrosine kinase RON and concomitantly increased activation. Our in\u00a0vitro findings were validated in gastric cancer clinical samples.","authors":"Mereiter, S., Martins, \u00c1M., Gomes, C., Balma\u00f1a, M., Macedo, JA., Polom, K., Roviello, F., Magalh\u00e3es, A., Reis, CA.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"FEBS Lett","volume":"593","issue":"13","page":"1675-1689","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31045356","title":"First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.","abstract":"The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.","authors":"Iacobucci, C., Piotrowski, C., Aebersold, R., Amaral, BC., Andrews, P., Bernfur, K., Borchers, C., Brodie, NI., Bruce, JE., Cao, Y., Chaignepain, S., Chavez, JD., Claverol, S., Cox, J., Davis, T., Degliesposti, G., Dong, MQ., Edinger, N., Emanuelsson, C., Gay, M., G\u00f6tze, M., Gomes-Neto, F., Gozzo, FC., Gutierrez, C., Haupt, C., Heck, AJR., Herzog, F., Huang, L., Hoopmann, MR., Kalisman, N., Klykov, O., Kuka\u010dka, Z., Liu, F., MacCoss, MJ., Mechtler, K., Mesika, R., Moritz, RL., Nagaraj, N., Nesati, V., Neves-Ferreira, AGC., Ninnis, R., Nov\u00e1k, P., O'Reilly, FJ., Pelzing, M., Petrotchenko, E., Piersimoni, L., Plasencia, M., Pukala, T., Rand, KD., Rappsilber, J., Reichmann, D., Sailer, C., Sarnowski, CP., Scheltema, RA., Schmidt, C., Schriemer, DC., Shi, Y., Skehel, JM., Slavin, M., Sobott, F., Solis-Mezarino, V., Stephanowitz, H., Stengel, F., Stieger, CE., Trabjerg, E., Trnka, M., Vilaseca, M., Viner, R., Xiang, Y., Yilmaz, S., Zelter, A., Ziemianowicz, D., Leitner, A., Sinz, A.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Anal Chem","volume":"91","issue":"11","page":"6953-6961","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31036804","title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing.","abstract":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","authors":"Moussa, HF., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., Michetti, L., Wang, J., Zepeda-Martinez, JA., Elling, U., Stuckey, JI., James, LI., Frye, SV., Bell, O.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"1931","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31010981","title":"Effects of quantitative trait loci determining testicular weight in DDD\/Sgn inbred mice are strongly influenced by circulating testosterone levels.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31010981<\/PMID><DateRevised><Year>2020<\/Year><Month>09<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Print\">1011-2367<\/ISSN><JournalIssue CitedMedium=\"Print\"><PubDate><Year>2019<\/Year><Month>Mar<\/Month><Day>07<\/Day><\/PubDate><\/JournalIssue><Title>Asian-Australasian journal of animal sciences<\/Title><ISOAbbreviation>Asian-Australas J Anim Sci<\/ISOAbbreviation><\/Journal><ArticleTitle>Effects of quantitative trait loci determining testicular weight in DDD\/Sgn inbred mice are strongly influenced by circulating testosterone levels.<\/ArticleTitle><Pagination><MedlinePgn>1826-1835<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.5713\/ajas.18.0783<\/ELocationID><Abstract><AbstractText Label=\"Objective\" NlmCategory=\"UNASSIGNED\">Testicular growth and development are strongly influenced by androgen. Although both testis weight and plasma testosterone level are inherited traits, the interrelationship between them is not fully established. Males of DDD\/Sgn (DDD) mice are known to have extremely heavy testes and very high plasma testosterone level among inbred mouse strains. We dissected the genetic basis of testis weight and analyzed the potential influence of plasma testosterone level in DDD mice.","authors":"Suto, JI., Kojima, M.","publication_status":"aheadofprint","journalpubyear":"2019","journaltitle":"Asian-Australas J Anim Sci","volume":"","issue":"","page":"1826-1835","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30993080","title":"A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30993080<\/PMID><DateRevised><Year>2020<\/Year><Month>09<\/Month><Day>29<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Print\">1790-045X<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>26<\/Volume><PubDate><Year>2019<\/Year><Month>Dec<\/Month><\/PubDate><\/JournalIssue><Title>Journal of biological research (Thessalonike, Greece)<\/Title><ISOAbbreviation>J Biol Res (Thessalon)<\/ISOAbbreviation><\/Journal><ArticleTitle>A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia.<\/ArticleTitle><Pagination><MedlinePgn>2<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s40709-019-0094-x<\/ELocationID><Abstract><AbstractText Label=\"Background\" NlmCategory=\"UNASSIGNED\">Alopecia or hair loss is a complex polygenetic and psychologically devastating disease affecting millions of men and women globally. Since the gene annotation and environmental knowledge is limited for alopecia, a systematic analysis for the identification of candidate biomarkers is required that could provide potential therapeutic targets for hair loss therapy.","authors":"Muhammad, SA., Fatima, N., Paracha, RZ., Ali, A., Chen, JY.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"J Biol Res (Thessalon)","volume":"26","issue":"","page":"2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30971701","title":"Staufen2-mediated RNA recognition and localization requires combinatorial action of multiple domains.","abstract":"Throughout metazoans, Staufen (Stau) proteins are core factors of mRNA localization particles. They consist of three to four double-stranded RNA binding domains (dsRBDs) and a C-terminal dsRBD-like domain. Mouse Staufen2 (mStau2)-like Drosophila Stau (dmStau) contains four dsRBDs. Existing data suggest that only dsRBDs 3-4 are necessary and sufficient for mRNA binding. Here, we show that dsRBDs 1 and 2 of mStau2 bind RNA with similar affinities and kinetics as dsRBDs 3 and 4. While RNA binding by these tandem domains is transient, all four dsRBDs recognize their target RNAs with high stability. Rescue experiments in Drosophila oocytes demonstrate that mStau2 partially rescues dmStau-dependent mRNA localization. In contrast, a rescue with mStau2 bearing RNA-binding mutations in dsRBD1-2 fails, confirming the physiological relevance of our findings. In summary, our data show that the dsRBDs 1-2 play essential roles in the mRNA recognition and function of Stau-family proteins of different species.","authors":"Heber, S., G\u00e1sp\u00e1r, I., Tants, JN., G\u00fcnther, J., Moya, SMF., Janowski, R., Ephrussi, A., Sattler, M., Niessing, D.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"1659","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30886860","title":"Identification of Candidate Genes and MicroRNAs for Acute Myocardial Infarction by Weighted Gene Coexpression Network Analysis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30886860<\/PMID><DateCompleted><Year>2019<\/Year><Month>07<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>02<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Electronic\">2314-6141<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>2019<\/Volume><PubDate><Year>2019<\/Year><\/PubDate><\/JournalIssue><Title>BioMed research international<\/Title><ISOAbbreviation>Biomed Res Int<\/ISOAbbreviation><\/Journal><ArticleTitle>Identification of Candidate Genes and MicroRNAs for Acute Myocardial Infarction by Weighted Gene Coexpression Network Analysis.<\/ArticleTitle><Pagination><MedlinePgn>5742608<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1155\/2019\/5742608<\/ELocationID><Abstract><AbstractText Label=\"Background\" NlmCategory=\"UNASSIGNED\">Identification of potential molecular targets of acute myocardial infarction is crucial to our comprehensive understanding of the disease mechanism. However, studies of gene coexpression analysis via jointing multiple microarray data of acute myocardial infarction still remain restricted.","authors":"Li, Y., He, XN., Li, C., Gong, L., Liu, M.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Biomed Res Int","volume":"2019","issue":"","page":"5742608","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-221","title":"Dissecting human fetal cardiac repair using cardioids","abstract":null,"authors":"Lavinia Ceci Ginistrelli, Tobias Ilmer, Lena Plank, Maria Novatchkova, Abhijeet Krishna, Enik\u0151 L\u00e1z\u00e1r, Rapha\u00ebl Mauron, Stefan H. Geyer, Lokesh Pimpale, Valeria V. Orlova, Katie McDole, Wolfgang J. Weninger, Sasha Mendjan","publication_status":"preprint","journalpubyear":"2026","journaltitle":"bioRixv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.30.735236v1","articledate":"2026-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30871075","title":"ATG-18 and EPG-6 are Both Required for Autophagy but Differentially Contribute to Lifespan Control in <i>Caenorhabditis elegans<\/i>.","abstract":"During macroautophagy, the human WIPI (WD-repeat protein interacting with phosphoinositides) proteins (WIPI1\u207b4) function as phosphatidylinositol 3-phosphate effectors at the nascent autophagosome. Likewise, the two WIPI homologues in <i>Caenorhabditis elegans<\/i>, ATG-18 and EPG-6, play important roles in autophagy, whereby ATG-18 is considered to act upstream of EPG-6 at the onset of autophagy. Due to its essential role in autophagy, ATG-18 was found to be also essential for lifespan extension in <i>Caenorhabditis elegans<\/i>; however, this has not yet been addressed with regard to EPG-6. Here, we wished to address this point and generated mutant strains that expressed the autophagy marker GFP::LGG-1 (GFP-LC3 in mammals) and harbored functional deletions of either <i>atg-18<\/i> (<i>atg18(gk378)<\/i>), <i>epg-6<\/i> (<i>epg-6(bp242)<\/i>) or both (<i>atg-18(gk378);epg-6(bp242)<\/i>). Using quantitative fluorescence microscopy, Western blotting, and lifespan assessments, we provide evidence that in the absence of either ATG-18 or EPG-6 autophagy was impaired, and while <i>atg-18<\/i> mutant animals showed a short-lived phenotype, lifespan was significantly increased in <i>epg-6<\/i> mutant animals. We speculate that the long-lived phenotype of <i>epg-6<\/i> mutant animals points towards an autophagy-independent function of EPG-6 in lifespan control that warrants further mechanistic investigations in future studies.","authors":"Takacs, Z., Sporbeck, K., Stoeckle, J., Prado Carvajal, MJ., Grimmel, M., Proikas-Cezanne, T.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Cells","volume":"8","issue":"3","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30819644","title":"Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination.","abstract":"The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in\u00a0vitro. We demonstrate that PCF11-mediated termination is essential for vertebrate development. A range of genomic analyses, including mNET-seq, 3' mRNA-seq, chromatin RNA-seq, and ChIP-seq, reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome-wide. PCF11 binds preferentially between closely spaced genes, where it prevents transcriptional interference and consequent gene downregulation. Notably, PCF11 is sub-stoichiometric to the CPA complex. Low levels of PCF11 are\u00a0maintained by an auto-regulatory mechanism involving premature termination of its own transcript and are important for normal development. Both in human cell culture and during zebrafish development, PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination.","authors":"Kamieniarz-Gdula, K., Gdula, MR., Panser, K., Nojima, T., Monks, J., Wi\u015bniewski, JR., Riepsaame, J., Brockdorff, N., Pauli, A., Proudfoot, NJ.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mol Cell","volume":"74","issue":"1","page":"158-172.e9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30817801","title":"Two isoforms of the RAC-specific guanine nucleotide exchange factor TIAM2 act oppositely on transmission ratio distortion by the mouse t-haplotype.","abstract":"Transmission ratio distortion (TRD) by the mouse t-haplotype, a variant region on chromosome 17, is a well-studied model of non-Mendelian inheritance. It is characterized by the high transmission ratio (up to 99%) of the t-haplotype from t\/+ males to their offspring. TRD is achieved by the exquisite ability of the responder (Tcr) to trigger non-Mendelian inheritance of homologous chromosomes. Several distorters (Tcd1-Tcd4), which act cumulatively, together promote the high transmission ratio of Tcr and the t-haplotype. Molecularly, TRD is brought about by deregulation of Rho signaling pathways via the distorter products, which impair sperm motility, and the t-sperm specific rescue of sperm motility by the responder. The t-sperm thus can reach the egg cells faster than +-sperm and fertilize them. Previously we have shown that the responder function is accomplished by a dominant negative form of sperm motility kinase (SMOKTCR), while the distorter functions are accomplished by the Rho G protein regulators TAGAP, FGD2 and NME3 proposed to function in two oppositely acting pathways. Here we identify the RAC1-specific guanine nucleotide exchange factor TIAM2 as modifier of t-haplotype TRD. Tiam2 is expressed in two isoforms, the full-length (Tiam2l) and a short transcript (Tiam2s). Tiam2s expression from the t-allele is strongly increased compared to the wild-type allele. By transgenic approaches we show that Tiam2s enhances t-haplotype transmission, while Tiam2l has the opposite effect. Our data show that a single modifier locus can encode different gene products exerting opposite effects on a trait. They also suggest that the expression ratio of the isoforms determines if the outcome is an enhancing or a suppressive effect on the trait.","authors":"Charron, Y., Willert, J., Lipkowitz, B., Kusecek, B., Herrmann, BG., Bauer, H.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PLoS Genet","volume":"15","issue":"2","page":"e1007964","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30808328","title":"HIF-1 transcription activity: HIF1A driven response in normoxia and in hypoxia.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30808328<\/PMID><DateCompleted><Year>2019<\/Year><Month>08<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>03<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>20<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>02<\/Month><Day>26<\/Day><\/PubDate><\/JournalIssue><Title>BMC medical genetics<\/Title><ISOAbbreviation>BMC Med Genet<\/ISOAbbreviation><\/Journal><ArticleTitle>HIF-1 transcription activity: HIF1A driven response in normoxia and in hypoxia.<\/ArticleTitle><Pagination><MedlinePgn>37<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12881-019-0767-1<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">HIF1A (Hypoxia-Inducible-Factor 1A) expression in solid tumors is relevant to establish resistance to therapeutic approaches. The use of compounds direct against hypoxia signaling and HIF1A does not show clinical efficiency because of changeable oxygen concentrations in solid tumor areas. The identification of HIF1A targets expressed in both normoxia and hypoxia and of HIF1A\/hypoxia signatures might meliorate the prognostic stratification and therapeutic successes in patients with high-risk solid tumors.","authors":"Cimmino, F., Avitabile, M., Lasorsa, VA., Montella, A., Pezone, L., Cantalupo, S., Visconte, F., Corrias, MV., Iolascon, A., Capasso, M.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"BMC Med Genet","volume":"20","issue":"1","page":"37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30787993","title":"MicroRNA-365 suppressed cell proliferation and migration via targeting PAX6 in glioblastoma.","abstract":"MicroRNAs (miRNAs) act an important role in the progression of tumor. In this study, we showed that the serum expression of miR-365 was downregulated in the glioblastoma compared with in the healthy controls. We also demonstrated that miR-365 expression was downregulated in glioblastoma tissues compared with the adjacent normal tissues. Overexpression of miR-365 suppressed the glioblastoma cell proliferation and migration. Moreover, ectopic expression of miR-365 promoted the expression of Ecadherin while inhibited the expression of N-cadherin and Vimentin in U87 cell. Furthermore, we identified PAX6 as a direct target gene of miR-365 in U87 cell. Overexpression of miR-365 suppressed glioblastoma cell proliferation and migration and epithelial-to-mesenchymal transition through inhibiting PAX6 expression. These results suggested that miR-365 played a tumor suppressor in glioblastoma.","authors":"Yuan, F., Liu, J., Pang, H., Tian, Y., Yuan, K., Li, Y., Wang, J., Bian, S., Zheng, Y., Dong, D., Li, Y., Li, M., Jiang, C., Hu, S., Li, Q.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Am J Transl Res","volume":"11","issue":"1","page":"361-369","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30765413","title":"Structural Basis of Nuclear pre-mRNA Splicing: Lessons from Yeast.","abstract":"Noncoding introns are removed from nuclear precursor messenger RNA (pre-mRNA) in a two-step phosphoryl transfer reaction by the spliceosome, a dynamic multimegadalton enzyme. Cryo-electron microscopy (cryo-EM) structures of the <i>Saccharomyces cerevisiae<\/i> spliceosome were recently determined in eight key states. Combined with the wealth of available genetic and biochemical data, these structures have revealed new insights into the mechanisms of spliceosome assembly, activation, catalysis, and disassembly. The structures show how a single RNA catalytic center forms during activation and accomplishes both steps of the splicing reaction. The structures reveal how spliceosomal helicases remodel the spliceosome for active site formation, substrate docking, reaction product undocking, and spliceosome disassembly and how they facilitate splice site proofreading. Although human spliceosomes contain additional proteins, their cryo-EM structures suggest that the underlying mechanism is conserved across all eukaryotes. In this review, we summarize the current structural understanding of pre-mRNA splicing.","authors":"Plaschka, C., Newman, AJ., Nagai, K.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Cold Spring Harb Perspect Biol","volume":"11","issue":"5","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30741923","title":"Hectd3 promotes pathogenic Th17 lineage through Stat3 activation and Malt1 signaling in neuroinflammation.","abstract":"Polyubiquitination promotes proteasomal degradation, or signaling and localization, of targeted proteins. Here we show that the E3 ubiquitin ligase Hectd3 is necessary for pathogenic Th17 cell generation in experimental autoimmune encephalomyelitis (EAE), a mouse model for human multiple sclerosis. Hectd3-deficient mice have lower EAE severity, reduced Th17 program and inefficient Th17 cell differentiation. However, Stat3, but not ROR\u03b3t, has decreased polyubiquitination, as well as diminished tyrosine-705 activating phosphorylation. Additionally, non-degradative polyubiquitination of Malt1, critical for NF-\u03baB activation and Th17 cell function, is reduced. Mechanistically, Hectd3 promotes K27-linked and K29-linked polyubiquitin chains on Malt1, and K27-linked polyubiquitin chains on Stat3. Moreover, Stat3 K180 and Malt1 K648 are targeted by Hectd3 for non-degradative polyubiquitination to mediate robust generation of ROR\u03b3t<sup>+<\/sup>IL-17A<sup>hi<\/sup> effector CD4<sup>+<\/sup> T cells. Thus, our studies delineate a mechanism connecting signaling related polyubiquitination of Malt1 and Stat3, leading to NF-kB activation and ROR\u03b3t expression, to pathogenic Th17 cell function in EAE.","authors":"Cho, JJ., Xu, Z., Parthasarathy, U., Drashansky, TT., Helm, EY., Zuniga, AN., Lorentsen, KJ., Mansouri, S., Cho, JY., Edelmann, MJ., Duong, DM., Gehring, T., Seeholzer, T., Krappmann, D., Uddin, MN., Califano, D., Wang, RL., Jin, L., Li, H., Lv, D., Zhou, D., Zhou, L., Avram, D.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Nat Commun","volume":"10","issue":"1","page":"701","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30714151","title":"LncRNA TUSC7 suppresses pancreatic carcinoma progression by modulating miR-371a-5p expression.","abstract":"Pancreatic carcinoma is one of the most common and lethal human malignancies worldwide. Long noncoding RNAs (lncRNAs) are a well-known type of nonprotein-coding transcripts implicated in cancer development and progression. Increasing evidence has indicated that lncRNA tumor suppressor candidate 7 (TUSC7) is a novel cancer suppressor gene in various cancers. Nevertheless, the function of TUSC7 in pancreatic carcinoma is urgent to be clarified. We found that TUSC7 was notably decreased in tissues and cell lines of pancreatic carcinoma. Moreover, the low expression of TUSC7 was correlated with advanced clinical grades and poorer overall survival. Our findings revealed that TUSC7 repressed cell proliferation, migration, invasion, epithelial-mesenchymal transition, and stemness whereas facilitated cell apoptosis of pancreatic carcinoma cells. Further investigations demonstrated that miR-371a-5p directly bound with TUSC7 and negatively regulated by TUSC7. MiR-371a-5p rescued the inhibitory effects of TUSC7 on the development of pancreatic carcinoma. We conclude that lncRNA TUSC7 suppresses pancreatic carcinoma progression by modulating miR-371a-5p expression, indicating an innovative therapeutic strategy for pancreatic carcinoma.","authors":"Yue, L., Guo, J.","publication_status":"aheadofprint","journalpubyear":"2019","journaltitle":"J Cell Physiol","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30709655","title":"HDAC1 and HDAC2 Regulate Intermediate Progenitor Positioning to Safeguard Neocortical Development.","abstract":"Neural progenitors with distinct potential to generate progeny are associated with a spatially distinct microenvironment. Neocortical intermediate progenitors (IPs) in the subventricular zone (SVZ) of the developing brain generate neurons for all cortical layers and are essential for cortical expansion. Here, we show that spatial control of IP positioning is essential for neocortical development. We demonstrate that HDAC1 and HDAC2 regulate the spatial positioning of IPs to form the SVZ. Developmental\u00a0stage-specific depletion of both HDAC1 and HDAC2 in radial glial progenitors results in mispositioning of IPs at the ventricular surface, where they divide and differentiate into neurons, thereby leading to the cortical malformation. We further identified the\u00a0proneural gene Neurogenin2 as a key target of\u00a0HDAC1 and HDAC2 for regulating IP positioning. Our results demonstrate the importance of the spatial positioning of neural progenitors in cortical development and reveal a mechanism underlying the establishment of the SVZ microenvironment.","authors":"Tang, T., Zhang, Y., Wang, Y., Cai, Z., Lu, Z., Li, L., Huang, R., Hagelkruys, A., Matthias, P., Zhang, H., Seiser, C., Xie, Y.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Neuron","volume":"101","issue":"6","page":"1117-1133.e5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30709367","title":"MiR-1287-5p inhibits triple negative breast cancer growth by interaction with phosphoinositide 3-kinase CB, thereby sensitizing cells for PI3Kinase inhibitors.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30709367<\/PMID><DateCompleted><Year>2019<\/Year><Month>07<\/Month><Day>22<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>03<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1465-542X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>21<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>02<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Breast cancer research : BCR<\/Title><ISOAbbreviation>Breast Cancer Res<\/ISOAbbreviation><\/Journal><ArticleTitle>MiR-1287-5p inhibits triple negative breast cancer growth by interaction with phosphoinositide 3-kinase CB, thereby sensitizing cells for PI3Kinase inhibitors.<\/ArticleTitle><Pagination><MedlinePgn>20<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13058-019-1104-5<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Non-coding RNAs and especially microRNAs have been discovered to act as master regulators of cancer initiation and progression. The aim of our study was to discover and characterize the function of yet functionally uncharacterized microRNAs in human breast carcinogenesis.","authors":"Schwarzenbacher, D., Klec, C., Pasculli, B., Cerk, S., Rinner, B., Karbiener, M., Ivan, C., Barbano, R., Ling, H., Wulf-Goldenberg, A., Stanzer, S., Rinnerthaler, G., Stoeger, H., Bauernhofer, T., Haybaeck, J., Hoefler, G., Jahn, SW., Parrella, P., Calin, GA., Pichler, M.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Breast Cancer Res","volume":"21","issue":"1","page":"20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30704043","title":"Modeling Host-Virus Interactions in Viral Infectious Diseases Using Stem-Cell-Derived Systems and CRISPR\/Cas9 Technology.","abstract":"Pathologies induced by viral infections have undergone extensive study, with traditional model systems such as two-dimensional (2D) cell cultures and in vivo mouse models contributing greatly to our understanding of host-virus interactions. However, the technical limitations inherent in these systems have constrained efforts to more fully understand such interactions, leading to a search for alternative in vitro systems that accurately recreate in vivo physiology in order to advance the study of viral pathogenesis. Over the last decade, there have been significant technological advances that have allowed researchers to more accurately model the host environment when modeling viral pathogenesis in vitro, including induced pluripotent stem cells (iPSCs), adult stem-cell-derived organoid culture systems and CRISPR\/Cas9-mediated genome editing. Such technological breakthroughs have ushered in a new era in the field of viral pathogenesis, where previously challenging questions have begun to be tackled. These include genome-wide analysis of host-virus crosstalk, identification of host factors critical for viral pathogenesis, and the study of viral pathogens that previously lacked a suitable platform, e.g., noroviruses, rotaviruses, enteroviruses, adenoviruses, and Zika virus. In this review, we will discuss recent advances in the study of viral pathogenesis and host-virus crosstalk arising from the use of iPSC, organoid, and CRISPR\/Cas9 technologies.","authors":"Kim, J., Koo, BK., Yoon, KJ.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Viruses","volume":"11","issue":"2","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30696701","title":"Arginine to Glutamine Variant in Olfactomedin Like 3 (<i>OLFML3<\/i>) Is a Candidate for Severe Goniodysgenesis and Glaucoma in the Border Collie Dog Breed.","abstract":"Goniodysgenesis is a developmental abnormality of the anterior chamber of the eye. It is generally considered to be congenital in dogs (<i>Canis lupus familiaris<\/i>), and has been associated with glaucoma and blindness. Goniodysgenesis and early-onset glaucoma initially emerged in Border Collies in Australia in the late 1990s and have subsequently been found in this breed in Europe and the USA. The objective of the present study was to determine the genetic basis of goniodysgenesis in Border Collies. Clinical diagnosis was based on results of examinations by veterinary ophthalmologists of affected and unaffected dogs from eleven different countries. Genotyping using the Illumina high density canine single nucleotide variant genotyping chip was used to identify a candidate genetic region. There was a highly significant peak of association over chromosome 17, with a <i>p<\/i>-value of 2 \u00d7 10<sup>-13<\/sup> Expression profiles and evolutionary conservation of candidate genes were assessed using public databases. Whole genome sequences of three dogs with glaucoma, three severely affected by goniodysgenesis and three unaffected dogs identified a missense variant in the olfactomedin like 3 (<i>OLFML3<\/i>) gene in all six affected animals. This was homozygous for the risk allele in all nine cases with glaucoma and 12 of 14 other severely affected animals. Of 67 reportedly unaffected animals, only one was homozygous for this variant (offspring of parents both with goniodysgenesis who were also homozygous for the variant). Analysis of pedigree information was consistent with an autosomal recessive mode of inheritance for severe goniodysgenesis (potentially leading to glaucoma) in this breed. The identification of a candidate genetic region and putative causative variant will aid breeders to reduce the frequency of goniodysgenesis and the risk of glaucoma in the Border Collie population.","authors":"Pugh, CA., Farrell, LL., Carlisle, AJ., Bush, SJ., Ewing, A., Trejo-Reveles, V., Matika, O., de Kloet, A., Walsh, C., Bishop, SC., Prendergast, JGD., Rainger, J., Schoenebeck, JJ., Summers, KM.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"G3 (Bethesda)","volume":"9","issue":"3","page":"943-954","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30691517","title":"Knockdown of FOXO3a induces epithelial-mesenchymal transition and promotes metastasis of pancreatic ductal adenocarcinoma by activation of the \u03b2-catenin\/TCF4 pathway through SPRY2.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30691517<\/PMID><DateCompleted><Year>2019<\/Year><Month>05<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>08<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1756-9966<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>38<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>Jan<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>Journal of experimental &amp; clinical cancer research : CR<\/Title><ISOAbbreviation>J Exp Clin Cancer Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Knockdown of FOXO3a induces epithelial-mesenchymal transition and promotes metastasis of pancreatic ductal adenocarcinoma by activation of the \u03b2-catenin\/TCF4 pathway through SPRY2.<\/ArticleTitle><Pagination><MedlinePgn>38<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13046-019-1046-x<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Early invasion and metastasis are responsible for the dismal prognosis of pancreatic ductal adenocarcinoma (PDAC), and epithelial-to-mesenchymal transition (EMT) is recognized as a crucial biological progress in driving tumor invasion and metastasis. The transcription factor FOXO3a is inactivated in various types of solid cancers and the loss of FOXO3a is associated with EMT and tumor metastasis. In this study, we sought to explore whether SPRY2, a regulator of receptor tyrosine kinase (RTK) signaling, is involved in FOXO3a-mediated EMT and metastasis in PDAC.","authors":"Li, J., Yang, R., Dong, Y., Chen, M., Wang, Y., Wang, G.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"J Exp Clin Cancer Res","volume":"38","issue":"1","page":"38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30691477","title":"JNK signalling mediates aspects of maternal immune activation: importance of maternal genotype in relation to schizophrenia risk.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30691477<\/PMID><DateCompleted><Year>2019<\/Year><Month>05<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1742-2094<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>16<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>Jan<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>Journal of neuroinflammation<\/Title><ISOAbbreviation>J Neuroinflammation<\/ISOAbbreviation><\/Journal><ArticleTitle>JNK signalling mediates aspects of maternal immune activation: importance of maternal genotype in relation to schizophrenia risk.<\/ArticleTitle><Pagination><MedlinePgn>18<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12974-019-1408-5<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Important insight into the mechanisms through which gene-environmental interactions cause schizophrenia can be achieved through preclinical studies combining prenatal immune stimuli with disease-related genetic risk modifications. Accumulating evidence associates JNK signalling molecules, including MKK7\/MAP2K7, with genetic risk. We tested the hypothesis that Map2k7 gene haploinsufficiency in mice would alter the prenatal immune response to the viral mimetic polyriboinosinic-polyribocytidylic acid (polyI:C), specifically investigating the impact of maternal versus foetal genetic variants.","authors":"Openshaw, RL., Kwon, J., McColl, A., Penninger, JM., Cavanagh, J., Pratt, JA., Morris, BJ.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"J Neuroinflammation","volume":"16","issue":"1","page":"18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20584328","title":"Estimating enrichment of repetitive elements from high-throughput sequence data.","abstract":"We describe computational methods for analysis of repetitive elements from short-read sequencing data, and apply them to study histone modifications associated with the repetitive elements in human and mouse cells. Our results demonstrate that while accurate enrichment estimates can be obtained for individual repeat types and small sets of repeat instances, there are distinct combinatorial patterns of chromatin marks associated with major annotated repeat families, including H3K27me3\/H3K9me3 differences among the endogenous retroviral element classes.","authors":"Day, DS., Luquette, LJ., Park, PJ., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Genome Biol","volume":"11","issue":"6","page":"R69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-11-03","doi":"10.1186\/gb-2010-11-6-r69","first_author":"Day, DS.","corresponding_authors":"Kharchenko, PV."},{"pmid":"30665888","title":"Broad applicability of a streamlined ethyl cinnamate-based clearing procedure.","abstract":"Turbidity and opaqueness are inherent properties of tissues that limit the capacity to acquire microscopic images through large tissues. Creating a uniform refractive index, known as tissue clearing, overcomes most of these issues. These methods have enabled researchers to image large and complex 3D structures with unprecedented depth and resolution. However, tissue clearing has been adopted to a limited extent due to a combination of cost, time, complexity of existing methods and potential negative impact on fluorescence signal. Here, we describe 2Eci (2nd generation ethyl cinnamate-based clearing), which can be used to clear a wide range of tissues in several species, including human organoids, <i>Drosophila melanogaster<\/i>, zebrafish, axolotl and <i>Xenopus laevis<\/i>, in as little as 1-5\u2005days, while preserving a broad range of fluorescent proteins, including GFP, mCherry, Brainbow and Alexa-conjugated fluorophores. Ethyl cinnamate is non-toxic and can easily be used in multi-user microscope facilities. This method opens up tissue clearing to a much broader group of researchers due to its ease of use, the non-toxic nature of ethyl cinnamate and broad applicability.","authors":"Masselink, W., Reumann, D., Murawala, P., Pasierbek, P., Taniguchi, Y., Bonnay, F., Meixner, K., Knoblich, JA., Tanaka, EM.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Development","volume":"146","issue":"3","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30662653","title":"AMPK-related kinase 5 (ARK5) enhances gemcitabine resistance in pancreatic carcinoma by inducing epithelial-mesenchymal transition.","abstract":"AMPK-related kinase 5 (ARK5) is a member of the human AMP-activated protein kinase (AMPK) family, which is associated with increased tumor survival and drug resistance in many cancers. However, the function of ARK5 in pancreatic carcinoma (PC) is unclear. Our study investigated the role of ARK5 in the chemo-resistance of PC and its underlying mechanism. PC cell lines that displayed high expression levels of ARK5 had low sensitivity to gemcitabine (GEM). Suppression of ARK5 increased sensitivity to GEM in PC cell lines. Western blotting and immunofluorescence showed that suppression of ARK5 upregulated expression of E-cadherin and downregulated vimentin expression. Suppression of ARK5 also inhibited the epithelial-mesenchymal transition (EMT) efficiency associated with GEM in PC cell lines and upregulation of ARK5 expression enhanced GEM resistance in PC cell lines by inducing Twist-mediated EMT. In addition, we found that suppression of ARK5 increased GEM sensitivity in PC cell lines under hypoxic conditions. ARK5 increases GEM resistance in PC cell lines via EMT, and suppression of ARK5 increases sensitivity to GEM under both normoxic and hypoxic conditions.","authors":"Wang, X., Song, Z., Chen, F., Yang, X., Wu, B., Xie, S., Zheng, X., Cai, Y., Chen, W., Zhong, Z.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Am J Transl Res","volume":"10","issue":"12","page":"4095-4106","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30628890","title":"The novel lncRNA <i>lnc-NR2F1<\/i> is pro-neurogenic and mutated in human neurodevelopmental disorders.","abstract":"Long noncoding RNAs (lncRNAs) have been shown to act as important cell biological regulators including cell fate decisions but are often ignored in human genetics. Combining differential lncRNA expression during neuronal lineage induction with copy number variation morbidity maps of a cohort of children with autism spectrum disorder\/intellectual disability versus healthy controls revealed focal genomic mutations affecting several lncRNA candidate loci. Here we find that a t(5:12) chromosomal translocation in a family manifesting neurodevelopmental symptoms disrupts specifically <i>lnc-NR2F1<\/i>. We further show that <i>lnc-NR2F1<\/i> is an evolutionarily conserved lncRNA functionally enhances induced neuronal cell maturation and directly occupies and regulates transcription of neuronal genes including autism-associated genes. Thus, integrating human genetics and functional testing in neuronal lineage induction is a promising approach for discovering candidate lncRNAs involved in neurodevelopmental diseases.","authors":"Ang, CE., Ma, Q., Wapinski, OL., Fan, S., Flynn, RA., Lee, QY., Coe, B., Onoguchi, M., Olmos, VH., Do, BT., Dukes-Rimsky, L., Xu, J., Tanabe, K., Wang, L., Elling, U., Penninger, JM., Zhao, Y., Qu, K., Eichler, EE., Srivastava, A., Wernig, M., Chang, HY.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Elife","volume":"8","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30600647","title":"A Comparative Perspective on Brain Regeneration in Amphibians and Teleost Fish.","abstract":"Regeneration of lost cells in the central nervous system, especially the brain, is present to varying degrees in different species. In mammals, neuronal cell death often leads to glial cell hypertrophy, restricted proliferation, and formation of a gliotic scar, which prevents neuronal regeneration. Conversely, amphibians such as frogs and salamanders and teleost fish possess the astonishing capacity to regenerate lost cells in several regions of their brains. While frogs lose their regenerative abilities after metamorphosis, teleost fish and salamanders are known to possess regenerative competence even throughout adulthood. In the last decades, substantial progress has been made in our understanding of the cellular and molecular mechanisms of brain regeneration in amphibians and fish. But how similar are the means of brain regeneration in these different species? In this review, we provide an overview of common and distinct aspects of brain regeneration in frog, salamander, and teleost fish species: from the origin of regenerated cells to the functional recovery of behaviors.","authors":"Lust, K., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Dev Neurobiol","volume":"79","issue":"5","page":"424-436","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30504824","title":"Central amygdala circuit dynamics underlying the benzodiazepine anxiolytic effect.","abstract":"Benzodiazepines (BZDs) have been a standard treatment for anxiety disorders for decades, but the neuronal circuit interactions mediating their anxiolytic effect remain largely unknown. Here, we find that systemic BZDs modulate central amygdala (CEA) microcircuit activity to gate amygdala output. Combining connectome data with immediate early gene (IEG) activation maps, we identified the CEA as a primary site for diazepam (DZP) anxiolytic action. Deep brain calcium imaging revealed that brain-wide DZP interactions shifted neuronal activity in CEA microcircuits. Chemogenetic silencing showed that PKC\u03b4<sup>+<\/sup>\/SST<sup>-<\/sup> neurons in the lateral CEA (CEAl) are necessary and sufficient to induce the DZP anxiolytic effect. We propose that BZDs block the relay of aversive signals through the CEA, in part by local binding to CEAl SST<sup>+<\/sup>\/PKC\u03b4<sup>-<\/sup> neurons and reshaping intra-CEA circuit dynamics. This work delineates a strategy to identify biomedically relevant circuit interactions of clinical drugs and highlights the critical role for CEA circuitry in the pathophysiology of anxiety.","authors":"Griessner, J., Pasieka, M., B\u00f6hm, V., Gr\u00f6ssl, F., Kaczanowska, J., Pliota, P., Kargl, D., Werner, B., Kaouane, N., Strobelt, S., Kreitz, S., Hess, A., Haubensak, W.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Mol Psychiatry","volume":"26","issue":"2","page":"534-544","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30455472","title":"Pulmonary phagocyte-derived NPY controls the pathology of severe influenza virus infection.","abstract":"Crosstalk between the autonomic nervous system and the immune system by means of the sympathetic and parasympathetic pathways is a critical process in host defence. Activation of the sympathetic nervous system results in the release of catecholamines as well as neuropeptide Y (NPY). Here, we investigated whether phagocytes are capable of the de novo production of NPY, as has been described for catecholamines. We show that the synthesis of NPY and its Y1 receptor (Y1R) is increased in phagocytes in lungs following severe influenza virus infection. The genetic deletion of Npy or Y1r specifically in phagocytes greatly improves the pathology of severe influenza virus infection, which is characterized by excessive virus replication and pulmonary inflammation. Mechanistically, it is the induction of suppressor of cytokine signalling 3 (SOCS3) via NPY-Y1R activation that is responsible for impaired antiviral response and promoting pro-inflammatory cytokine production, thereby enhancing the pathology of influenza virus infection. Thus, direct regulation of the NPY-Y1R-SOCS3 pathway on phagocytes may act as a fine-tuner of an innate immune response to virus infection, which could be a therapeutic target for lethal influenza virus infection.","authors":"Fujiwara, S., Hoshizaki, M., Ichida, Y., Lex, D., Kuroda, E., Ishii, KJ., Magi, S., Okada, M., Takao, H., Gandou, M., Imai, H., Hara, R., Herzog, H., Yoshimura, A., Okamura, H., Penninger, JM., Slutsky, AS., Uhlig, S., Kuba, K., Imai, Y.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Microbiol","volume":"4","issue":"2","page":"258-268","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30413718","title":"Targeting 17q23 amplicon to overcome the resistance to anti-HER2 therapy in HER2+ breast cancer.","abstract":"Chromosome 17q23 amplification occurs in ~11% of human breast cancers. Enriched in HER2+\u00a0breast cancers, the 17q23 amplification is significantly correlated with poor clinical outcomes. In addition to the previously identified oncogene WIP1, we uncover an oncogenic microRNA gene, MIR21, in a majority of the WIP1-containing 17q23 amplicons. The 17q23 amplification results in aberrant expression of WIP1 and miR-21, which not only promotes breast tumorigenesis, but also leads to resistance to anti-HER2 therapies. Inhibiting WIP1 and miR-21 selectively inhibits the proliferation, survival and tumorigenic potential of the HER2+\u00a0breast cancer cells harboring 17q23 amplification. To overcome the resistance of trastuzumab-based therapies in vivo, we develop pH-sensitive nanoparticles for specific co-delivery of the WIP1 and miR-21 inhibitors into HER2+\u00a0breast tumors, leading to a profound reduction of tumor growth. These results demonstrate the great potential of the combined treatment of WIP1 and miR-21 inhibitors for the trastuzumab-resistant HER2+\u00a0breast cancers.","authors":"Liu, Y., Xu, J., Choi, HH., Han, C., Fang, Y., Li, Y., Van der Jeught, K., Xu, H., Zhang, L., Frieden, M., Wang, L., Eyvani, H., Sun, Y., Zhao, G., Zhang, Y., Liu, S., Wan, J., Huang, C., Ji, G., Lu, X., He, X., Zhang, X.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Nat Commun","volume":"9","issue":"1","page":"4718","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30325918","title":"A genome-wide Drosophila epithelial tumorigenesis screen identifies Tetraspanin 29Fb as an evolutionarily conserved suppressor of Ras-driven cancer.","abstract":"Oncogenic mutations in the small GTPase Ras contribute to ~30% of human cancers. However, Ras mutations alone are insufficient for tumorigenesis, therefore it is paramount to identify cooperating cancer-relevant signaling pathways. We devised an in vivo near genome-wide, functional screen in Drosophila and discovered multiple novel, evolutionarily-conserved pathways controlling Ras-driven epithelial tumorigenesis. Human gene orthologs of the fly hits were significantly downregulated in thousands of primary tumors, revealing novel prognostic markers for human epithelial tumors. Of the top 100 candidate tumor suppressor genes, 80 were validated in secondary Drosophila assays, identifying many known cancer genes and multiple novel candidate genes that cooperate with Ras-driven tumorigenesis. Low expression of the confirmed hits significantly correlated with the KRASG12 mutation status and poor prognosis in pancreatic cancer. Among the novel top 80 candidate cancer genes, we mechanistically characterized the function of the top hit, the Tetraspanin family member Tsp29Fb, revealing that Tsp29Fb regulates EGFR signaling, epithelial architecture and restrains tumor growth and invasion. Our functional Drosophila screen uncovers multiple novel and evolutionarily conserved epithelial cancer genes, and experimentally confirmed Tsp29Fb as a key regulator of EGFR\/Ras induced epithelial tumor growth and invasion.","authors":"Zoranovic, T., Manent, J., Willoughby, L., Matos de Simoes, R., La Marca, JE., Golenkina, S., Cuiping, X., Gruber, S., Angjeli, B., Kanitz, EE., Cronin, SJF., Neely, GG., Wernitznig, A., Humbert, PO., Simpson, KJ., Mitsiades, CS., Richardson, HE., Penninger, JM.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"PLoS Genet","volume":"14","issue":"10","page":"e1007688","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30312291","title":"Genome amplification and cellular senescence are hallmarks of human placenta development.","abstract":"Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) \u03b2-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM.","authors":"Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., Lendl, T., Aumayr, K., Mairhofer, M., Zhu, X., Sch\u00fctz, B., Hannibal, RL., Lindau, R., Weil, B., Ernerudh, J., Neesen, J., Egger, G., Mikula, M., R\u00f6hrl, C., Urban, AE., Baker, J., Kn\u00f6fler, M., Pollheimer, J.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"PLoS Genet","volume":"14","issue":"10","page":"e1007698","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30135560","title":"Author Correction: Genetically engineered cerebral organoids model brain tumor formation.","abstract":"In the originally published paper, the \"before\" image for the afatinib condition in Fig. 6c was incorrect. Instead of an image displaying a GBM-3 neoplastic organoid before afatinib treatment, this panel showed an image from the GBM-2 control (DMSO) group before treatment. This error has now been corrected in the HTML and PDF versions of the article; the \"before, afatinib\" panel in Fig. 6c now shows a representative image from the indicated experiment. The color of all error bars in Fig. 6 has also been changed to black, for consistency. All statistical analysis and all conclusions presented in the article are unaffected by this error. Nevertheless, we apologize for the mistake.","authors":"Bian, S., Repic, M., Guo, Z., Kavirayani, A., Burkard, T., Bagley, JA., Krauditsch, C., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Methods","volume":"15","issue":"9","page":"748","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-08-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30201836","title":"Sensorimotor integration in <i>Caenorhabditis elegans<\/i>: a reappraisal towards dynamic and distributed computations.","abstract":"The nematode <i>Caenorhabditis elegans<\/i> is a tractable model system to study locomotion, sensory navigation and decision-making. In its natural habitat, it is thought to navigate complex multisensory environments in order to find food and mating partners, while avoiding threats like predators or toxic environments. While research in past decades has shed much light on the functions and mechanisms of selected sensory neurons, we are just at the brink of understanding how sensory information is integrated by interneuron circuits for action selection in the worm. Recent technological advances have enabled whole-brain Ca<sup>2+<\/sup> imaging and Ca<sup>2+<\/sup> imaging of neuronal activity in freely moving worms. A common principle emerging across multiple studies is that most interneuron activities are tightly coupled to the worm's instantaneous behaviour; notably, these observations encompass neurons receiving direct sensory neuron inputs. The new findings suggest that in the <i>C. elegans<\/i> brain, sensory and motor representations are integrated already at the uppermost sensory processing layers. Moreover, these results challenge a perhaps more intuitive view of sequential feed-forward sensory pathways that converge onto premotor interneurons and motor neurons. We propose that sensorimotor integration occurs rather in a distributed dynamical fashion. In this perspective article, we will explore this view, discuss the challenges and implications of these discoveries on the interpretation and design of neural activity experiments, and discuss possible functions. Furthermore, we will discuss the broader context of similar findings in fruit flies and rodents, which suggest generalizable principles that can be learnt from this amenable nematode model organism.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling <i>C. elegans<\/i> at cellular resolution'.","authors":"Kaplan, HS., Nichols, ALA., Zimmer, M.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"373","issue":"1758","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30082827","title":"Cbl-b deficiency provides protection against UVB-induced skin damage by modulating inflammatory gene signature.","abstract":"Exposure of skin to ultraviolet (UV) radiation induces DNA damage, inflammation, and immune suppression that ultimately lead to skin cancer. However, some of the pathways that regulate these events are poorly understood. We exposed mice to UVB to study its early effects in the absence of Cbl-b, a known suppressor of antitumor immune response in the skin. Cbl-b<sup>-\/-<\/sup> mice were protected from UV-induced cell damage as shown by the lower number of cyclobutane pyrimidine dimers and sunburn cells in exposed skin compared to wild-type mice. Microarray data revealed that deficiency of Cbl-b resulted in differential expression of genes involved in apoptosis evasion, tumor suppression and cell survival in UV-exposed skin. After UVB, Cbl-b<sup>-\/-<\/sup> mice upregulated gene expression pattern associated with regulation of epidermal cell proliferation linked to Wnt signaling mediators and enzymes that relate to cell removal and tissue remodeling like MMP12. Additionally, the skin of Cbl-b<sup>-\/-<\/sup> mice was protected from chronic inflammatory responses and epidermal hyperplasia in a 4-weeks UVB treatment protocol. Overall, our results suggest a novel role for Cbl-b in regulating inflammation and physiologic clearance of damaged cells in response to UVB by modulating inflammatory gene signature.","authors":"Singh, TP., Vieyra-Garcia, PA., Wagner, K., Penninger, J., Wolf, P.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Cell Death Dis","volume":"9","issue":"8","page":"835","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12729754","title":"Induction of short interspersed nuclear repeat-containing transcripts in epithelial cells upon infection with a chicken adenovirus.","abstract":"Chicken embryo lethal orphan adenovirus (CELO) is used as a vector for expression of exogenous genes in mammalian cells. Here, we analyzed transcriptional alterations in mouse epithelial host cells following infection with CELO using cDNA microarray analysis. Sequence data characterization revealed that a major portion of CELO-induced genes contained short interspersed nuclear elements of the B2 subclass (B2 SINEs). In fact, we could identify SINEs and other repetitive sequences as contributing significantly to the cDNAs used for microarray construction. Moreover, we found that the CELO protein Gam1 was able to mediate transcriptional activation of these B2 SINE-containing RNAs. We hypothesize that upregulation of B2-SINE-containing RNAs could be a novel contribution of Gam1 to CELO host cell infection.","authors":"Wick, N., Luedemann, S., Vietor, I., Cotten, M., Wildpaner, M., Schneider, G., Eisenhaber, F., Huber, LA.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"J Mol Biol","volume":"328","issue":"4","page":"779-90","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2003-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30018080","title":"CD44 is a RAS\/STAT5-regulated invasion receptor that triggers disease expansion in advanced mastocytosis.","abstract":"The Hermes receptor CD44 is a multifunctional adhesion molecule that plays an essential role in the homing and invasion of neoplastic stem cells in various myeloid malignancies. Although mast cells (MCs) reportedly express CD44, little is known about the regulation and function of this receptor in neoplastic cells in systemic mastocytosis (SM). We found that clonal CD34<sup>+<\/sup>\/CD38<sup>-<\/sup> stem cells, CD34<sup>+<\/sup>\/CD38<sup>+<\/sup> progenitor cells, and CD117<sup>++<\/sup>\/CD34<sup>-<\/sup> MCs invariably express CD44 in patients with indolent SM (ISM), SM with an associated hematologic neoplasm, aggressive SM, and MC leukemia (MCL). In addition, all human MCL-like cell lines examined (HMC-1, ROSA, and MCPV-1) displayed cytoplasmic and cell-surface CD44. We also found that expression of CD44 in neoplastic MCs depends on RAS-MEK and STAT5 signaling and increases with the aggressiveness of SM. Correspondingly, higher levels of soluble CD44 were measured in the sera of patients with advanced SM compared with ISM or cutaneous mastocytosis and were found to correlate with overall and progression-free survival. To investigate the functional role of CD44, a xenotransplantation model was employed using severe combined immunodeficient (SCID) mice, HMC-1.2 cells, and a short hairpin RNA (shRNA) against CD44. In this model, the shRNA-mediated knockdown of CD44 resulted in reduced MC expansion and tumor formation and prolonged survival in SCID mice compared with HMC-1.2 cells transduced with control shRNA. Together, our data show that CD44 is a RAS-MEK\/STAT5-driven MC invasion receptor that correlates with the aggressiveness of SM. Whether CD44 can serve as therapeutic target in advanced SM remains to be determined in forthcoming studies.","authors":"Mueller, N., Wicklein, D., Eisenwort, G., Jawhar, M., Berger, D., Stefanzl, G., Greiner, G., Boehm, A., Kornauth, C., Muellauer, L., Sehner, S., Hoermann, G., Sperr, WR., Staber, PB., Jaeger, U., Zuber, J., Arock, M., Schumacher, U., Reiter, A., Valent, P.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Blood","volume":"132","issue":"18","page":"1936-1950","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30009791","title":"TCEA1 regulates the proliferative potential of mouse myeloid cells.","abstract":"Leukemia is a malignance with complex pathogenesis and poor prognosis. Discovery of noval regulators amenable to leukemia could be of value to gain insight into the pathogenesis, diagnosis and prognosis of leukemia. Here, we conducted a large-scale shRNA library screening for functional regulators in the development of myeloid cells in primary cells. We identified eighteen candidate regulators in the primary screening. Those genes cover a wide range of cellular functions, including gene expression regulation, intracellular signaling transduction, nucleotide excision repair, cell cycle control and transcription regulation. In both primary screening and validation, shRNAs targeting Tcea1, encoding the transcription elongation factor A (SII) 1, exhibited the greatest influence on the proliferative potential of cells. Knocking down the expression of Tcea1 in the 32Dcl3 myeloid cell line led to enhanced proliferation of myeloid cells and blockage of myeloid differentiation induced by G-CSF. In addition, silence of Tcea1 inhibited apoptosis of myeloid cells. Thus, Tcea1 was identified as a gene which can influence the proliferative potential, survival and differentiation of myeloid cells. These findings have implications for how transcriptional elongation influences myeloid cell development and leukemic transformation.","authors":"Yang, T., Cui, H., Wen, M., Zuber, J., Kogan, SC., Wei, G.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Exp Cell Res","volume":"370","issue":"2","page":"551-560","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29997629","title":"Cleavage of Toll-Like Receptor 9 Ectodomain Is Required for <i>In Vivo<\/i> Responses to Single Strand DNA.","abstract":"Mouse toll-like receptor 9 (TLR9) is an endosomal sensor for single-stranded DNA. TLR9 is transported from the endoplasmic reticulum to endolysosomes by a multiple transmembrane protein Unc93 homolog B1, and proteolytically cleaved at its ectodomain. The structure of TLR9 and its biochemical analyses have shown that the proteolytic cleavage of TLR9 ectodomain enables TLR9-dimerization and TLR9 activation. However, the requirement of TLR9 cleavage <i>in vivo<\/i> has not been studied. We here show that the 13 amino acids deletion at the cleavage site made TLR9 resistant to proteolytic cleavage. The deletion mutation in the <i>Tlr9<\/i> gene impaired TLR9-dependent cytokine production in conventional dendritic cells from the mutant mice. Not only <i>in vitro, in vivo<\/i> production of inflammatory cytokines (TNF-\u03b1 and IL-12p40), chemokine (CCR5\/RANTES), and type I interferon (IFN-\u03b1) induced by administration of TLR9 ligand was also impaired. These results demonstrate that the TLR9 cleavage is required for TLR9 responses <i>in vivo<\/i>.","authors":"Fukui, R., Yamamoto, C., Matsumoto, F., Onji, M., Shibata, T., Murakami, Y., Kanno, A., Hayashi, T., Tanimura, N., Yoshida, N., Miyake, K.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Front Immunol","volume":"9","issue":null,"page":"1491","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29997242","title":"Ectopic otoconial formation in the lagena of the pigeon inner ear.","abstract":"The vertebrate inner ear contains vestibular receptors with dense crystals of calcium carbonate, the otoconia. The production and maintenance of otoconia is a delicate process, the perturbation of which can lead to severe vestibular dysfunction in humans. The details of these processes are not well understood. Here, we report the discovery of a new otoconial mass in the lagena of adult pigeons that was present in more than 70% of birds. Based on histological, tomographic and elemental analyses, we conclude that the structure likely represents an ectopically-formed otoconial assembly. Given its frequent natural occurrence, we suggest that the pigeon lagena is a valuable model system for investigating misregulated otoconial formation.This article has an associated First Person interview with the first author of the paper.","authors":"Malkemper, EP., Mason, MJ., Kagerbauer, D., Nimpf, S., Keays, DA.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Biol Open","volume":"7","issue":"8","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29973716","title":"Publisher Correction: An extracellular network of Arabidopsis leucine-rich repeat receptor kinases.","abstract":"In this Letter, an incorrect version of the Supplementary Information file was inadvertently used, which contained several errors. The details of references 59-65 were missing from the end of the Supplementary Discussion section on page 4. In addition, the section 'Text 3. Y2H on ICD interactions' incorrectly referred to 'Extended Data Fig. 4d' instead of 'Extended Data Fig. 3d' on page 3. Finally, the section 'Text 4. Interaction network analysis' incorrectly referred to 'Fig. 1b and Extended Data Fig. 6' instead of 'Fig. 2b and Extended Data Fig. 7' on page 3. These errors have all been corrected in the Supplementary Information.","authors":"Smakowska-Luzan, E., Mott, GA., Parys, K., Stegmann, M., Howton, TC., Layeghifard, M., Neuhold, J., Lehner, A., Kong, J., Gr\u00fcnwald, K., Weinberger, N., Satbhai, SB., Mayer, D., Busch, W., Madalinski, M., Stolt-Bergner, P., Provart, NJ., Mukhtar, MS., Zipfel, C., Desveaux, D., Guttman, DS., Belkhadir, Y.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"561","issue":"7722","page":"E8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29945865","title":"SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting.","abstract":"Cell type-specific transcriptome analysis is an essential tool for understanding biological processes in which diverse types of cells are involved. Although cell isolation methods such as fluorescence-activated cell sorting (FACS) in combination with transcriptome analysis have widely been used so far, their time-consuming and harsh procedures limit their applications. Here, we report a novel <i>in vivo<\/i> metabolic RNA sequencing method, SLAM-ITseq, which metabolically labels RNA with 4-thiouracil in a specific cell type <i>in vivo<\/i> followed by detection through an RNA-seq-based method that specifically distinguishes the thiolated uridine by base conversion. This method has successfully identified the cell type-specific transcriptome in three different tissues: endothelial cells in brain, epithelial cells in intestine and adipocytes in white adipose tissue. As this method does not require isolation of cells or RNA prior to the transcriptomic analysis, SLAM-ITseq provides an easy yet accurate snapshot of the transcriptional state <i>in vivo<\/i>.","authors":"Matsushima, W., Herzog, VA., Neumann, T., Gapp, K., Zuber, J., Ameres, SL., Miska, EA.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Development","volume":"145","issue":"13","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29904149","title":"Stress peptides sensitize fear circuitry to promote passive coping.","abstract":"Survival relies on optimizing behavioral responses through experience. Animals often react to acute stress by switching to passive behavioral responses when coping with environmental challenge. Despite recent advances in dissecting mammalian circuitry for Pavlovian fear, the neuronal basis underlying this form of non-Pavlovian anxiety-related behavioral plasticity remains poorly understood. Here, we report that aversive experience recruits the posterior paraventricular thalamus (PVT) and corticotropin-releasing hormone (CRH) and sensitizes a Pavlovian fear circuit to promote passive responding. Site-specific lesions and optogenetic manipulations reveal that PVT-to-central amygdala (CE) projections activate anxiogenic neuronal populations in the CE that release local CRH in response to acute stress. CRH potentiates basolateral (BLA)-CE connectivity and antagonizes inhibitory gating of CE output, a mechanism linked to Pavlovian fear, to facilitate the switch from active to passive behavior. Thus, PVT-amygdala fear circuitry uses inhibitory gating in the CE as a shared dynamic motif, but relies on different cellular mechanisms (postsynaptic long-term potentiation vs. presynaptic facilitation), to multiplex active\/passive response bias in Pavlovian and non-Pavlovian behavioral plasticity. These results establish a framework promoting stress-induced passive responding, which might contribute to passive emotional coping seen in human fear- and anxiety-related disorders.","authors":"Pliota, P., B\u00f6hm, V., Gr\u00f6ssl, F., Griessner, J., Valenti, O., Kraitsy, K., Kaczanowska, J., Pasieka, M., Lendl, T., Deussing, JM., Haubensak, W.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Mol Psychiatry","volume":"25","issue":"2","page":"428-441","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29215332","title":"Nodal patterning without Lefty inhibitory feedback is functional but fragile.","abstract":"Developmental signaling pathways often activate their own inhibitors. Such inhibitory feedback has been suggested to restrict the spatial and temporal extent of signaling or mitigate signaling fluctuations, but these models are difficult to rigorously test. Here, we determine whether the ability of the mesendoderm inducer Nodal to activate its inhibitor Lefty is required for development. We find that zebrafish <i>lefty<\/i> mutants exhibit excess Nodal signaling and increased specification of mesendoderm, resulting in embryonic lethality. Strikingly, development can be fully restored without feedback: Lethal patterning defects in <i>lefty<\/i> mutants can be rescued by ectopic expression of <i>lefty<\/i> far from its normal expression domain or by spatially and temporally uniform exposure to a Nodal inhibitor drug. While drug-treated mutants are less tolerant of mild perturbations to Nodal signaling levels than wild type embryos, they can develop into healthy adults. These results indicate that patterning without inhibitory feedback is functional but fragile.","authors":"Rogers, KW., Lord, ND., Gagnon, JA., Pauli, A., Zimmerman, S., Aksel, DC., Reyon, D., Tsai, SQ., Joung, JK., Schier, AF.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Elife","volume":"6","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29898918","title":"Mutations that prevent methylation of cohesin render sensitivity to DNA damage in <i>S. pombe<\/i>.","abstract":"The canonical role of cohesin is to mediate sister chromatid cohesion. In addition, cohesin plays important roles in processes such as DNA repair and regulation of gene expression. Mounting evidence suggests that various post-translational modifications, including phosphorylation, acetylation and sumoylation regulate cohesin functions. Our mass spectrometry analysis of cohesin purified from <i>Schizosaccharomyces pombe<\/i> cells revealed that the cohesin subunit Psm1 is methylated on two evolutionarily conserved lysine residues, K536 and K1200. We found that mutations that prevent methylation of Psm1 K536 and K1200 render sensitivity to DNA-damaging agents and show positive genetic interactions with mutations in genes encoding the Mus81-Eme1 endonuclease. Yeast two-hybrid and co-immunoprecipitation assays showed that there were interactions between subunits of the cohesin and Mus81-Eme1 complexes. We conclude that cohesin is methylated and that mutations that prevent methylation of Psm1 K536 and K1200 show synthetic phenotypes with mutants defective in the homologous recombination DNA repair pathway.","authors":"Sanyal, S., Molnarova, L., Richterova, J., Huraiova, B., Benko, Z., Polakova, S., Cipakova, I., Sevcovicova, A., Gaplovska-Kysela, K., Mechtler, K., Cipak, L., Gregan, J.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"J Cell Sci","volume":"131","issue":"13","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29942004","title":"Author Correction: Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data.","abstract":"In the version of this article initially published online, the authors used incorrectly defined restraints for specifying the distance between residues when using the HADDOCK portal. Following the publication of a Correspondence by the developers of the HADDOCK portal (Nat. Protoc. https:\/\/dx.doi.org\/10.1038\/s41596-018-0017-6, 2018) and a Reply by the authors of the Protocol (Nat. Protoc. https:\/\/dx.doi.org\/10.1038\/s41596-018-0018-5, 2018), the syntax in step 21 has been corrected. In addition, the input files (available as Supplementary Data 5-7) have been replaced.","authors":"Orb\u00e1n-N\u00e9meth, Z., Beveridge, R., Hollenstein, DM., Rampler, E., Stranzl, T., Hudecz, O., Doblmann, J., Schl\u00f6gelhofer, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Protoc","volume":"13","issue":"7","page":"1724","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29875394","title":"Publisher Correction: Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans.","abstract":"In the supplementary information PDF originally posted, there were discrepancies from the integrated supplementary information that appeared in the HTML; the former has been corrected as follows. In the legend to Supplementary Fig. 2c, \"major organs of the mouse\" has been changed to \"major organs of the adult mouse.\" In the legend to Supplementary Fig. 6d,h, \"At E14.5 Mbe\/Mbe mutants have a smaller percentage of Brdu positive cells in bin 3\" has been changed to \"At E14.5 Mbe\/Mbe mutants have a higher percentage of Brdu positive cells in bin 3.\"","authors":"Gstrein, T., Edwards, A., P\u0159istoupilov\u00e1, A., Leca, I., Breuss, M., Pilat-Carotta, S., Hansen, AH., Tripathy, R., Traunbauer, AK., Hochstoeger, T., Rosoklija, G., Repic, M., Landler, L., Str\u00e1neck\u00fd, V., D\u00fcrnberger, G., Keane, TM., Zuber, J., Adams, DJ., Flint, J., Honzik, T., Gut, M., Beltran, S., Mechtler, K., Sherr, E., Kmoch, S., Gut, I., Keays, DA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Neurosci","volume":"21","issue":"8","page":"1139","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29777171","title":"MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity.","abstract":"MLL-fusions represent a large group of leukemia drivers, whose diversity originates from the vast molecular heterogeneity of C-terminal fusion partners of MLL. While studies of selected MLL-fusions have revealed critical molecular pathways, unifying mechanisms across all MLL-fusions remain poorly understood. We present the first comprehensive survey of protein-protein interactions of seven distantly related MLL-fusion proteins. Functional investigation of 128 conserved MLL-fusion-interactors identifies a specific role for the lysine methyltransferase SETD2 in MLL-leukemia. SETD2 loss causes growth arrest and differentiation of AML cells, and leads to increased DNA damage. In addition to its role in H3K36 tri-methylation, SETD2 is required to maintain high H3K79 di-methylation and MLL-AF9-binding to critical target genes, such as Hoxa9. SETD2 loss synergizes with pharmacologic inhibition of the H3K79 methyltransferase DOT1L to induce DNA damage, growth arrest, differentiation, and apoptosis. These results uncover a dependency for SETD2 during MLL-leukemogenesis, revealing a novel actionable vulnerability in this disease.","authors":"Skucha, A., Ebner, J., Schm\u00f6llerl, J., Roth, M., Eder, T., C\u00e9sar-Razquin, A., Stukalov, A., Vittori, S., Muhar, M., Lu, B., Aichinger, M., Jude, J., M\u00fcller, AC., Gy\u0151rffy, B., Vakoc, CR., Valent, P., Bennett, KL., Zuber, J., Superti-Furga, G., Grebien, F.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Nat Commun","volume":"9","issue":"1","page":"1983","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29736000","title":"High-speed volumetric imaging of neuronal activity in freely moving rodents.","abstract":"Thus far, optical recording of neuronal activity in freely behaving animals has been limited to a thin axial range. We present a head-mounted miniaturized light-field microscope (MiniLFM) capable of capturing neuronal network activity within a volume of 700\u2009\u00d7\u2009600\u2009\u00d7\u2009360 \u00b5m<sup>3<\/sup> at 16\u2009Hz in the hippocampus of freely moving mice. We demonstrate that neurons separated by as little as ~15\u2009\u00b5m and at depths up to 360\u2009\u00b5m can be discriminated.","authors":"Skocek, O., N\u00f6bauer, T., Weilguny, L., Mart\u00ednez Traub, F., Xia, CN., Molodtsov, MI., Grama, A., Yamagata, M., Aharoni, D., Cox, DD., Golshani, P., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Methods","volume":"15","issue":"6","page":"429-432","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29709208","title":"A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity.","abstract":"The mammalian brain is a densely interconnected network that consists of millions to billions of neurons. Decoding how information is represented and processed by this neural circuitry requires the ability to capture and manipulate the dynamics of large populations at high speed and high resolution over a large area of the brain. Although the use of optical approaches by the neuroscience community has rapidly increased over the past two decades, most microscopy approaches are unable to record the activity of all neurons comprising a functional network across the mammalian brain at relevant temporal and spatial resolutions. In this review, we survey the recent development in optical technologies for Ca<sup>2+<\/sup> imaging in this regard and provide an overview of the strengths and limitations of each modality and its potential for scalability. We provide guidance from the perspective of a biological user driven by the typical biological applications and sample conditions. We also discuss the potential for future advances and synergies that could be obtained through hybrid approaches or other modalities.","authors":"Weisenburger, S., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Annu Rev Neurosci","volume":"41","issue":null,"page":"431-452","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29699580","title":"Genetic deletion of muscle RANK or selective inhibition of RANKL is not as effective as full-length OPG-fc in mitigating muscular dystrophy.","abstract":"Although there is a strong association between osteoporosis and skeletal muscle atrophy\/dysfunction, the functional relevance of a particular biological pathway that regulates synchronously bone and skeletal muscle physiopathology is still elusive. Receptor-activator of nuclear factor \u03baB (RANK), its ligand RANKL and the soluble decoy receptor osteoprotegerin (OPG) are the key regulators of osteoclast differentiation and bone remodelling. We thus hypothesized that RANK\/RANKL\/OPG, which is a key pathway for bone regulation, is involved in Duchenne muscular dystrophy (DMD) physiopathology. Our results show that muscle-specific RANK deletion (mdx-RANK <sup>mko<\/sup> ) in dystrophin deficient mdx mice improves significantly specific force [54% gain in force] of EDL muscles with no protective effect against eccentric contraction-induced muscle dysfunction. In contrast, full-length OPG-Fc injections restore the force of dystrophic EDL muscles [162% gain in force], protect against eccentric contraction-induced muscle dysfunction ex vivo and significantly improve functional performance on downhill treadmill and post-exercise physical activity. Since OPG serves a soluble receptor for RANKL and as a decoy receptor for TRAIL, mdx mice were injected with anti-RANKL and anti-TRAIL antibodies to decipher the dual function of OPG. Injections of anti-RANKL and\/or anti-TRAIL increase significantly the force of dystrophic EDL muscle [45% and 17% gains in force, respectively]. In agreement, truncated OPG-Fc that contains only RANKL domains produces similar gains, in terms of force production, than anti-RANKL treatments. To corroborate that full-length OPG-Fc also acts independently of RANK\/RANKL pathway, dystrophin\/RANK double-deficient mice were treated with full-length OPG-Fc for 10\u00a0days. Dystrophic EDL muscles exhibited a significant gain in force relative to untreated dystrophin\/RANK double-deficient mice, indicating that the effect of full-length OPG-Fc is in part independent of the RANKL\/RANK interaction. The sarco\/endoplasmic reticulum Ca<sup>2+<\/sup> ATPase (SERCA) activity is significantly depressed in dysfunctional and dystrophic muscles and full-length OPG-Fc treatment increased SERCA activity and SERCA-2a expression. These findings demonstrate the superiority of full-length OPG-Fc treatment relative to truncated OPG-Fc, anti-RANKL, anti-TRAIL or muscle RANK deletion in improving dystrophic muscle function, integrity and protection against eccentric contractions. In conclusion, full-length OPG-Fc represents an efficient alternative in the development of new treatments for muscular dystrophy in which a single therapeutic approach may be foreseeable to maintain both bone and skeletal muscle functions.","authors":"Dufresne, SS., Boulanger-Piette, A., Boss\u00e9, S., Argaw, A., Hamoudi, D., Marcadet, L., Gamu, D., Fajardo, VA., Yagita, H., Penninger, JM., Russell Tupling, A., Frenette, J.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Acta Neuropathol Commun","volume":"6","issue":"1","page":"31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29651983","title":"Comment on \"Magnetosensitive neurons mediate geomagnetic orientation in <i>Caenorhabditis elegans\"<\/i>.","abstract":"A diverse array of species on the planet employ the Earth's magnetic field as a navigational aid. As the majority of these animals are migratory, their utility to interrogate the molecular and cellular basis of the magnetic sense is limited. Vidal-Gadea and colleagues recently argued that the worm <i>Caenorhabditis elegans<\/i> possesses a magnetic sense that guides their vertical movement in soil. In making this claim, they relied on three different behavioral assays that involved magnetic stimuli. Here, we set out to replicate their results employing blinded protocols and double wrapped coils that control for heat generation. We find no evidence supporting the existence of a magnetic sense in <i>C. elegans<\/i>. We further show that the Vidal-Gadea hypothesis is problematic as the adoption of a correction angle and a fixed trajectory relative to the Earth's magnetic inclination does not necessarily result in vertical movement.","authors":"Landler, L., Nimpf, S., Hochstoeger, T., Nordmann, GC., Papadaki-Anastasopoulou, A., Keays, DA.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Elife","volume":"7","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29593293","title":"Beclin1 restricts RNA virus infection in plants through suppression and degradation of the viral polymerase.","abstract":"Autophagy emerges as an essential immunity defense against intracellular pathogens. Here we report that turnip mosaic virus (TuMV) infection activates autophagy in plants and that Beclin1 (ATG6), a core component of autophagy, inhibits virus replication. Beclin1 interacts with NIb, the RNA-dependent RNA polymerase (RdRp) of TuMV, via the highly conserved GDD motif and the interaction complex is targeted for autophagic degradation likely through the adaptor protein ATG8a. Beclin1-mediated NIb degradation is inhibited by autophagy inhibitors. Deficiency of Beclin1 or ATG8a enhances NIb accumulation and promotes viral infection and vice versa. These data suggest that Beclin1 may be a selective autophagy receptor. Overexpression of a Beclin1 truncation mutant that binds to NIb but lacks the ability to mediate NIb degradation also inhibits virus replication. The Beclin1-RdRp interaction further extends to several RNA viruses. Thus Beclin1 restricts viral infection through suppression and also likely autophagic degradation of the viral RdRp.","authors":"Li, F., Zhang, C., Li, Y., Wu, G., Hou, X., Zhou, X., Wang, A.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Nat Commun","volume":"9","issue":"1","page":"1268","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29580384","title":"The asymmetrically segregating lncRNA cherub is required for transforming stem cells into malignant cells.","abstract":"Tumor cells display features that are not found in healthy cells. How they become immortal and how their specific features can be exploited to combat tumorigenesis are key questions in tumor biology. Here we describe the long non-coding RNA cherub that is critically required for the development of brain tumors in <i>Drosophila<\/i> but is dispensable for normal development. In mitotic <i>Drosophila<\/i> neural stem cells, cherub localizes to the cell periphery and segregates into the differentiating daughter cell. During tumorigenesis, de-differentiation of cherub-high cells leads to the formation of tumorigenic stem cells that accumulate abnormally high cherub levels. We show that cherub establishes a molecular link between the RNA-binding proteins Staufen and Syncrip. As Syncrip is part of the molecular machinery specifying temporal identity in neural stem cells, we propose that tumor cells proliferate indefinitely, because cherub accumulation no longer allows them to complete their temporal neurogenesis program.","authors":"Landskron, L., Steinmann, V., Bonnay, F., Burkard, TR., Steinmann, J., Reichardt, I., Harzer, H., Laurenson, AS., Reichert, H., Knoblich, JA.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Elife","volume":"7","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29568378","title":"Human tripartite motif protein 52 is required for cell context-dependent proliferation.","abstract":"Tripartite motif (TRIM) proteins have been shown to play important roles in cancer development and progression by modulating cell proliferation or resistance from cell death during non-homeostatic stress conditions found in tumor micro-environments. In this study, we set out to investigate the importance for cellular fitness of the virtually uncharacterized family member TRIM52. The human <i>TRIM52<\/i> gene has arisen recently in evolution, making it unlikely that TRIM52 is required for basic cellular functions in normal cells. However, a recent genome-wide ablation screening study has suggested that TRIM52 may be essential for optimal proliferation or survival in certain genetic cancer backgrounds. Identifying genes which fit this concept of genetic context-dependent fitness in cancer cells is of interest as they are promising targets for tumor-specific therapy. We report here that <i>TRIM52<\/i> ablation significantly diminished the proliferation of specific glioblastoma cell lines in cell culture and mouse xenografts by compromising their cell cycle progression in a p53-dependent manner. Together, our findings point to a non-redundant TRIM52 function that is required for optimal proliferation.","authors":"Benke, S., Agerer, B., Haas, L., St\u00f6ger, M., Lercher, A., Gabler, L., Kiss, I., Scinicariello, S., Berger, W., Bergthaler, A., Obenauf, AC., Versteeg, GA.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Oncotarget","volume":"9","issue":"17","page":"13565-13581","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29535828","title":"Morphological alterations of cultured human colorectal matched tumour and healthy organoids.","abstract":"Organoids have extensive applications in many fields ranging from modelling human development and disease, personalised medicine, drug screening, etc. Moreover, in the last few years, several studies have evaluated the capacity of organoids as transplantation sources for therapeutic approaches and regenerative medicine. Nevertheless, depending on the origin of the cells and anatomical complications, an organoid transplant may make tissue regeneration difficult. However, some essential aspects of organoids including the morphological alterations and the growth pattern of the matched tumour and their healthy derived organoids have received less attention. Therefore, the current work focused on culturing matched healthy and tumour organoids from the same patient with colorectal cancer (CRC) and assessed their timed growth and structural differences on a daily basis. The healthy organoids underwent proliferation and branching morphogenesis, while the tumour organoids did not follow the same pattern, and the majority of them developed cystic structures instead. However, the number and size of tumour organoids were different from one patient to another. The differential morphological changes of the healthy versus human colonic tumour organoids likely linked to distinct molecular and cellular events during each day. Thus, while their specific structural features provide valuable <i>in vitro<\/i> models to study various aspects of human intestinal\/colon tissue homeostasis and CRC which avoid or replace the use of animals in research, this model may also hold a great promise for the transplantation and regenerative medicine applications.","authors":"Kashfi, SMH., Almozyan, S., Jinks, N., Koo, BK., Nateri, AS.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Oncotarget","volume":"9","issue":"12","page":"10572-10584","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29519939","title":"Improved Genome Assembly and Annotation for the Rock Pigeon (<i>Columba livia<\/i>).","abstract":"The domestic rock pigeon (<i>Columba livia<\/i>) is among the most widely distributed and phenotypically diverse avian species. <i>C. livia<\/i> is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the <i>C. livia<\/i> genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general.","authors":"Holt, C., Campbell, M., Keays, DA., Edelman, N., Kapusta, A., Maclary, E., T Domyan, E., Suh, A., Warren, WC., Yandell, M., Gilbert, MTP., Shapiro, MD.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"G3 (Bethesda)","volume":"8","issue":"5","page":"1391-1398","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29515774","title":"Unbiased compound-protein interface mapping and prediction of chemoresistance loci through forward genetics in haploid stem cells.","abstract":"Forward genetic screens in haploid mammalian cells have recently emerged as powerful tools for the discovery and investigation of recessive traits. Use of the haploid system provides unique genetic tractability and resolution. Upon positive selection, these screens typically employ analysis of loss-of-function (LOF) alleles and are thus limited to non-essential genes. Many relevant compounds, including anti-cancer therapeutics, however, target essential genes, precluding positive selection of LOF alleles. Here, we asked whether the use of random and saturating chemical mutagenesis might enable screens that identify essential biological targets of toxic compounds. We compare and contrast chemical mutagenesis with insertional mutagenesis. Selecting mutagenized cells with thapsigargin, an inhibitor of the essential Ca<sup>2+<\/sup> pump SERCA2, insertional mutagenesis retrieved cell clones overexpressing SERCA2. With chemical mutagenesis, we identify six single amino acid substitutions in the known SERCA2-thapsigargin binding interface that confer drug resistance. In a second screen, we used the anti-cancer drug MG132\/bortezomib (Velcade), which inhibits proteasome activity. Using chemical mutagenesis, we found 7 point mutations in the essential subunit Psmb5 that map to the bortezomib binding surface. Importantly, 4 of these had previously been identified in human tumors with acquired bortezomib resistance. Insertional mutagenesis did not identify Psmb5 in this screen, demonstrating the unique ability of chemical mutagenesis to identify relevant point mutations in essential genes. Thus, chemical mutagenesis in haploid embryonic stem cells can define the interaction of toxic small molecules with essential proteins at amino acid resolution, fully mapping small molecule-protein binding interfaces.","authors":"Horn, M., Kroef, V., Allmeroth, K., Schuller, N., Miethe, S., Peifer, M., Penninger, JM., Elling, U., Denzel, MS.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Oncotarget","volume":"9","issue":"11","page":"9838-9851","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29494253","title":"Cryo-EM Studies of Pre-mRNA Splicing: From Sample Preparation to Model Visualization.","abstract":"The removal of noncoding introns from pre-messenger RNA (pre-mRNA) is an essential step in eukaryotic gene expression and is catalyzed by a dynamic multi-megadalton ribonucleoprotein complex called the spliceosome. The spliceosome assembles on pre-mRNA substrates by the stepwise addition of small nuclear ribonucleoprotein particles and numerous protein factors. Extensive remodeling is required to form the RNA-based active site and to mediate the pre-mRNA branching and ligation reactions. In the past two years, cryo-electron microscopy (cryo-EM) structures of spliceosomes captured in different assembly and catalytic states have greatly advanced our understanding of its mechanism. This was made possible by long-standing efforts in the purification of spliceosome intermediates as well as recent developments in cryo-EM imaging and computational methodology. The resulting high-resolution densities allow for de novo model building in core regions of the complexes. In peripheral and less ordered regions, the combination of cross-linking, bioinformatics, biochemical, and genetic data is essential for accurate modeling. Here, we summarize these achievements and highlight the critical steps in obtaining near-atomic resolution structures of the spliceosome.","authors":"Wilkinson, ME., Lin, PC., Plaschka, C., Nagai, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Annu Rev Biophys","volume":"47","issue":null,"page":"175-199","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29438013","title":"The CCR4-NOT deadenylase complex controls Atg7-dependent cell death and heart function.","abstract":"Shortening and removal of the polyadenylate [poly(A)] tail of mRNA, a process called deadenylation, is a key step in mRNA decay that is mediated through the CCR4-NOT (carbon catabolite repression 4-negative on TATA-less) complex. In our investigation of the regulation of mRNA deadenylation in the heart, we found that this complex was required to prevent cell death. Conditional deletion of the CCR4-NOT complex components Cnot1 or Cnot3 resulted in the formation of autophagic vacuoles and cardiomyocyte death, leading to lethal heart failure accompanied by long QT intervals. Cnot3 bound to and shortened the poly(A) tail of the mRNA encoding the key autophagy regulator Atg7. In <i>Cnot3<\/i>-depleted hearts, <i>Atg7<\/i> expression was posttranscriptionally increased. Genetic ablation of <i>Atg7<\/i>, but not <i>Atg5<\/i>, increased survival and partially restored cardiac function of <i>Cnot1<\/i> or <i>Cnot3<\/i> knockout mice. We further showed that in <i>Cnot3<\/i>-depleted hearts, Atg7 interacted with p53 and modulated p53 activity to induce the expression of genes encoding cell death-promoting factors in cardiomyocytes, indicating that defects in deadenylation in the heart aberrantly activated Atg7 and p53 to promote cell death. Thus, mRNA deadenylation mediated by the CCR4-NOT complex is crucial to prevent Atg7-induced cell death and heart failure, suggesting a role for mRNA deadenylation in targeting autophagy genes to maintain normal cardiac homeostasis.","authors":"Yamaguchi, T., Suzuki, T., Sato, T., Takahashi, A., Watanabe, H., Kadowaki, A., Natsui, M., Inagaki, H., Arakawa, S., Nakaoka, S., Koizumi, Y., Seki, S., Adachi, S., Fukao, A., Fujiwara, T., Natsume, T., Kimura, A., Komatsu, M., Shimizu, S., Ito, H., Suzuki, Y., Penninger, JM., Yamamoto, T., Imai, Y., Kuba, K.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Sci Signal","volume":"11","issue":"516","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29433579","title":"The role of fibrinolysis inhibition in engineered vascular networks derived from endothelial cells and adipose-derived stem cells.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">29433579<\/PMID><DateCompleted><Year>2018<\/Year><Month>12<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>12<\/Month><Day>26<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1757-6512<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><Issue>1<\/Issue><PubDate><Year>2018<\/Year><Month>02<\/Month><Day>12<\/Day><\/PubDate><\/JournalIssue><Title>Stem cell research &amp; therapy<\/Title><ISOAbbreviation>Stem Cell Res Ther<\/ISOAbbreviation><\/Journal><ArticleTitle>The role of fibrinolysis inhibition in engineered vascular networks derived from endothelial cells and adipose-derived stem cells.<\/ArticleTitle><Pagination><MedlinePgn>35<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13287-017-0764-2<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Co-cultures of endothelial cells with mesenchymal stem cells currently represent one of the most promising approaches in providing oxygen and nutrient supply for microvascular tissue engineering. Still, to translate this model into clinics several in vitro parameters including growth medium and scaffold degradation need to be fine-tuned.","authors":"M\u00fchleder, S., Pill, K., Schaupper, M., Labuda, K., Priglinger, E., Hofbauer, P., Charwat, V., Marx, U., Redl, H., Holnthoner, W.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Stem Cell Res Ther","volume":"9","issue":"1","page":"35","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29426817","title":"The IAP family member BRUCE regulates autophagosome-lysosome fusion.","abstract":"Autophagy has an important role in cellular homeostasis by degrading and recycling cytotoxic components. Ubiquitination is known to target cargoes for autophagy; however, key components of this pathway remain elusive. Here we performed an RNAi screen to uncover ubiquitin modifiers that are required for starvation-induced macroautophagy in mammalian cells. Our screen uncovered BRUCE\/Apollon\/Birc6, an IAP protein, as a new autophagy regulator. Depletion of BRUCE leads to defective fusion of autophagosomes and lysosomes. Mechanistically, BRUCE selectively interacts with two ATG8 members GABARAP and GABARAPL1, as well as with Syntaxin 17, which are all critical regulators of autophagosome-lysosome fusion. In addition, BRUCE colocalizes with LAMP2. Interestingly, a non-catalytic N-terminal BRUCE fragment that is sufficient to bind GABARAP\/GABARAPL1 and Syntaxin 17, and to colocalize with LAMP2, rescues autolysosome formation in Bruce <sup>-\/-<\/sup> cells. Thus, BRUCE promotes autolysosome formation independently of its ubiquitin-conjugating activity and is a regulator of both macroautophagy and apoptosis.","authors":"Ebner, P., Poetsch, I., Deszcz, L., Hoffmann, T., Zuber, J., Ikeda, F.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Nat Commun","volume":"9","issue":"1","page":"599","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-03-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29383137","title":"Polycomb protein RING1A limits hematopoietic differentiation in myelodysplastic syndromes.","abstract":"Genetic lesions affecting epigenetic regulators are frequent in myelodysplastic syndromes (MDS). Polycomb proteins are key epigenetic regulators of differentiation and stemness that act as two multimeric complexes termed polycomb repressive complexes 1 and 2, PRC1 and PRC2, respectively. While components and regulators of PRC2 such as ASXL1 and EZH2 are frequently mutated in MDS and AML, little is known about the role of PRC1. To analyze the role of PRC1, we have taken a functional approach testing PRC1 components in loss- and gain-of-function experiments that we found overexpressed in advanced MDS patients or dynamically expressed during normal hematopoiesis. This approach allowed us to identify the enzymatically active component RING1A as the key PRC1 component in hematopoietic stem cells and MDS. Specifically, we found that RING1A is expressed in CD34<sup>+<\/sup> bone marrow progenitor cells and further overexpressed in high-risk MDS patients. Knockdown of RING1A in an MDS-derived AML cell line facilitated spontaneous and retinoic acid-induced differentiation. Similarly, inactivation of RING1A in primary CD34<sup>+<\/sup> cells augmented erythroid differentiation. Treatment with a small compound RING1 inhibitor reduced the colony forming capacity of CD34<sup>+<\/sup> cells from MDS patients and healthy controls. In MDS patients higher RING1A expression associated with an increased number of dysplastic lineages and blasts. Our data suggests that RING1A is deregulated in MDS and plays a role in the erythroid development defect.","authors":"Palau, A., Garz, AK., Diesch, J., Zwick, A., Malinverni, R., Valero, V., Lappin, K., Casquero, R., Lennartsson, A., Zuber, J., Navarro, T., Mills, KI., G\u00f6tze, KS., Buschbeck, M.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Oncotarget","volume":"8","issue":"70","page":"115002-115017","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16682347","title":"Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">16682347<\/PMID><DateCompleted><Year>2006<\/Year><Month>07<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>27<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>16<\/Volume><Issue>9<\/Issue><PubDate><Year>2006<\/Year><Month>May<\/Month><Day>09<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression.<\/ArticleTitle><Pagination><MedlinePgn>863-74<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Sister-chromatid cohesion depends on the cohesin complex whose association with chromatin is mediated by Scc2 and Scc4 in budding yeast. Both cohesin and Scc2 have been conserved from yeast to humans, but no Scc4 orthologs have been identified. Mutation of Scc2 orthologs causes defects in cohesion, transcription, and development, resulting in Cornelia de Lange syndrome in humans.","authors":"Watrin, E., Schleiffer, A., Tanaka, K., Eisenhaber, F., Nasmyth, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Curr Biol","volume":"16","issue":"9","page":"863-74","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2006-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29140244","title":"Subcellular analysis of pigeon hair cells implicates vesicular trafficking in cuticulosome formation and maintenance.","abstract":"Hair cells are specialized sensors located in the inner ear that enable the transduction of sound, motion, and gravity into neuronal impulses. In birds some hair cells contain an iron-rich organelle, the cuticulosome, that has been implicated in the magnetic sense. Here, we exploit histological, transcriptomic, and tomographic methods to investigate the development of cuticulosomes, as well as the molecular and subcellular architecture of cuticulosome positive hair cells. We show that this organelle forms rapidly after hatching in a process that involves vesicle fusion and nucleation of ferritin nanoparticles. We further report that transcripts involved in endocytosis, extracellular exosomes, and metal ion binding are differentially expressed in cuticulosome positive hair cells. These data suggest that the cuticulosome and the associated molecular machinery regulate the concentration of iron within the labyrinth of the inner ear, which might indirectly tune a magnetic sensor that relies on electromagnetic induction.","authors":"Nimpf, S., Malkemper, EP., Lauwers, M., Ushakova, L., Nordmann, G., Wenninger-Weinzierl, A., Burkard, TR., Jacob, S., Heuser, T., Resch, GP., Keays, DA.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Elife","volume":"6","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29302363","title":"Neuronal replacement therapy: previous achievements and challenges ahead.","abstract":"Lifelong neurogenesis and incorporation of newborn neurons into mature neuronal circuits operates in specialized niches of the mammalian brain and serves as role model for neuronal replacement strategies. However, to which extent can the remaining brain parenchyma, which never incorporates new neurons during the adulthood, be as plastic and readily accommodate neurons in networks that suffered neuronal loss due to injury or neurological disease? Which microenvironment is permissive for neuronal replacement and synaptic integration and which cells perform best? Can lost function be restored and how adequate is the participation in the pre-existing circuitry? Could aberrant connections cause malfunction especially in networks dominated by excitatory neurons, such as the cerebral cortex? These questions show how important connectivity and circuitry aspects are for regenerative medicine, which is the focus of this review. We will discuss the impressive advances in neuronal replacement strategies and success from exogenous as well as endogenous cell sources. Both have seen key novel technologies, like the groundbreaking discovery of induced pluripotent stem cells and direct neuronal reprogramming, offering alternatives to the transplantation of fetal neurons, and both herald great expectations. For these to become reality, neuronal circuitry analysis is key now. As our understanding of neuronal circuits increases, neuronal replacement therapy should fulfill those prerequisites in network structure and function, in brain-wide input and output. Now is the time to incorporate neural circuitry research into regenerative medicine if we ever want to truly repair brain injury.","authors":"Grade, S., G\u00f6tz, M.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"NPJ Regen Med","volume":"2","issue":null,"page":"29","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29286390","title":"A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations.","abstract":"Birth defects that involve the cerebral cortex - also known as malformations of cortical development (MCD) - are important causes of intellectual disability and account for 20-40% of drug-resistant epilepsy in childhood. High-resolution brain imaging has facilitated in vivo identification of a large group of MCD phenotypes. Despite the advances in brain imaging, genomic analysis and generation of animal models, a straightforward workflow to systematically prioritize candidate genes and to test functional effects of putative mutations is missing. To overcome this problem, an experimental strategy enabling the identification of novel causative genes for MCD was developed and validated. This strategy is based on identifying candidate genomic regions or genes via array-CGH or whole-exome sequencing and characterizing the effects of their inactivation or of overexpression of specific mutations in developing rodent brains via in utero electroporation. This approach led to the identification of the C6orf70 gene, encoding for a putative vesicular protein, to the pathogenesis of periventricular nodular heterotopia, a MCD caused by defective neuronal migration.","authors":"Conti, V., Carabalona, A., Pallesi-Pocachard, E., Leventer, RJ., Schaller, F., Parrini, E., Deparis, AA., Watrin, F., Buhler, E., Novara, F., Lise, S., Pagnamenta, AT., Kini, U., Taylor, JC., Zuffardi, O., Represa, A., Keays, DA., Guerrini, R., Falace, A., Cardoso, C.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"J Vis Exp","volume":null,"issue":"130","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29262611","title":"PARP inhibition causes premature loss of cohesion in cancer cells.","abstract":"Poly(ADP-ribose) polymerases (PARPs) regulate various aspects of cellular function including mitotic progression. Although PARP inhibitors have been undergoing various clinical trials and the PARP1\/2 inhibitor olaparib was approved as monotherapy for BRCA-mutated ovarian cancer, their mode of action in killing tumour cells is not fully understood. We investigated the effect of PARP inhibition on mitosis in cancerous (cervical, ovary, breast and osteosarcoma) and non-cancerous cells by live-cell imaging. The clinically relevant inhibitor olaparib induced strong perturbations in mitosis, including problems with chromosome alignment at the metaphase plate, anaphase delay, and premature loss of cohesion (cohesion fatigue) after a prolonged metaphase arrest, resulting in sister chromatid scattering. PARP1 and PARP2 depletion suppressed the phenotype while PARP2 overexpression enhanced it, suggesting that olaparib-bound PARP1 and PARP2 rather than the lack of catalytic activity causes this phenotype. Olaparib-induced mitotic chromatid scattering was observed in various cancer cell lines with increased protein levels of PARP1 and PARP2, but not in non-cancer or cancer cell lines that expressed lower levels of PARP1 or PARP2. Interestingly, the sister chromatid scattering phenotype occurred only when olaparib was added during the S-phase preceding mitosis, suggesting that PARP1 and PARP2 entrapment at replication forks impairs sister chromatid cohesion. Clinically relevant DNA-damaging agents that impair replication progression such as topoisomerase inhibitors and cisplatin were also found to induce sister chromatid scattering and metaphase plate alignment problems, suggesting that these mitotic phenotypes are a common outcome of replication perturbation.","authors":"Kukolj, E., Kaufmann, T., Dick, AE., Zeillinger, R., Gerlich, DW., Slade, D.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Oncotarget","volume":"8","issue":"61","page":"103931-103951","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29217591","title":"Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.","abstract":"Mammalian genomes are spatially organized into compartments, topologically associating domains (TADs), and loops to facilitate gene regulation and other chromosomal functions. How compartments, TADs, and loops are generated is unknown. It has been proposed that cohesin forms TADs and loops by extruding chromatin loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here, we show that cohesin suppresses compartments but is required for TADs and loops, that CTCF defines their boundaries, and that the cohesin unloading factor WAPL and its PDS5 binding partners control the length of loops. In the absence of WAPL and PDS5 proteins, cohesin forms extended loops, presumably by passing CTCF sites, accumulates in axial chromosomal positions (vermicelli), and condenses chromosomes. Unexpectedly, PDS5 proteins are also required for boundary function. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.","authors":"Wutz, G., V\u00e1rnai, C., Nagasaka, K., Cisneros, DA., Stocsits, RR., Tang, W., Schoenfelder, S., Jessberger, G., Muhar, M., Hossain, MJ., Walther, N., Koch, B., Kueblbeck, M., Ellenberg, J., Zuber, J., Fraser, P., Peters, JM.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"EMBO J","volume":"36","issue":"24","page":"3573-3599","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29137349","title":"Tumor <i>Trp53<\/i> status and genotype affect the bone marrow microenvironment in acute myeloid leukemia.","abstract":"The genetic heterogeneity of acute myeloid leukemia (AML) and the variable responses of individual patients to therapy suggest that different AML genotypes may influence the bone marrow (BM) microenvironment in different ways. We performed gene expression profiling of bone marrow mesenchymal stromal cells (BM-MSC) isolated from normal C57BL\/6 mice or mice inoculated with syngeneic murine leukemia cells carrying different human AML genotypes, developed in mice with <i>Trp53<\/i> wild-type or nullgenetic backgrounds. We identified a set of genes whose expression in BM-MSC was modulated by all four AML genotypes tested. In addition, there were sets of differentially-expressed genes in AML-exposed BM-MSC that were unique to the particular AML genotype or <i>Trp53<\/i> status. Our findings support the hypothesis that leukemia cells alter the transcriptome of surrounding BM stromal cells, in both common and genotype-specific ways. These changes are likely to be advantageous to AML cells, affecting disease progression and response to chemotherapy, and suggest opportunities for stroma-targeting therapy, including those based on AML genotype.","authors":"Jacamo, R., Davis, RE., Ling, X., Sonnylal, S., Wang, Z., Ma, W., Zhang, M., Ruvolo, P., Ruvolo, V., Wang, RY., McQueen, T., Lowe, S., Zuber, J., Kornblau, SM., Konopleva, M., Andreeff, M.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Oncotarget","volume":"8","issue":"48","page":"83354-83369","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29131160","title":"Human primary liver cancer-derived organoid cultures for disease modeling and drug screening.","abstract":"Human liver cancer research currently lacks in vitro models that can faithfully recapitulate the pathophysiology of the original tumor. We recently described a novel, near-physiological organoid culture system, wherein primary human healthy liver cells form long-term expanding organoids that retain liver tissue function and genetic stability. Here we extend this culture system to the propagation of primary liver cancer (PLC) organoids from three of the most common PLC subtypes: hepatocellular carcinoma (HCC), cholangiocarcinoma (CC) and combined HCC\/CC (CHC) tumors. PLC-derived organoid cultures preserve the histological architecture, gene expression and genomic landscape of the original tumor, allowing for discrimination between different tumor tissues and subtypes, even after long-term expansion in culture in the same medium conditions. Xenograft studies demonstrate that the tumorogenic potential, histological features and metastatic properties of PLC-derived organoids are preserved in vivo. PLC-derived organoids are amenable for biomarker identification and drug-screening testing and led to the identification of the ERK inhibitor SCH772984 as a potential therapeutic agent for primary liver cancer. We thus demonstrate the wide-ranging biomedical utilities of PLC-derived organoid models in furthering the understanding of liver cancer biology and in developing personalized-medicine approaches for the disease.","authors":"Broutier, L., Mastrogiovanni, G., Verstegen, MM., Francies, HE., Gavarr\u00f3, LM., Bradshaw, CR., Allen, GE., Arnes-Benito, R., Sidorova, O., Gaspersz, MP., Georgakopoulos, N., Koo, BK., Dietmann, S., Davies, SE., Praseedom, RK., Lieshout, R., IJzermans, JNM., Wigmore, SJ., Saeb-Parsy, K., Garnett, MJ., van der Laan, LJ., Huch, M.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Med","volume":"23","issue":"12","page":"1424-1435","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29118048","title":"RANK rewires energy homeostasis in lung cancer cells and drives primary lung cancer.","abstract":"Lung cancer is the leading cause of cancer deaths. Besides smoking, epidemiological studies have linked female sex hormones to lung cancer in women; however, the underlying mechanisms remain unclear. Here we report that the receptor activator of nuclear factor-kB (RANK), the key regulator of osteoclastogenesis, is frequently expressed in primary lung tumors, an active RANK pathway correlates with decreased survival, and pharmacologic RANK inhibition reduces tumor growth in patient-derived lung cancer xenografts. Clonal genetic inactivation of <i>KRas<\/i><sup><i>G12D<\/i><\/sup> in mouse lung epithelial cells markedly impairs the progression of <i>KRas<\/i><sup><i>G12D<\/i><\/sup> -driven lung cancer, resulting in a significant survival advantage. Mechanistically, RANK rewires energy homeostasis in human and murine lung cancer cells and promotes expansion of lung cancer stem-like cells, which is blocked by inhibiting mitochondrial respiration. Our data also indicate survival differences in <i>KRas<\/i><sup><i>G12D<\/i><\/sup> -driven lung cancer between male and female mice, and we show that female sex hormones can promote lung cancer progression via the RANK pathway. These data uncover a direct role for RANK in lung cancer and may explain why female sex hormones accelerate lung cancer development. Inhibition of RANK using the approved drug denosumab may be a therapeutic drug candidate for primary lung cancer.","authors":"Rao, S., Sigl, V., Wimmer, RA., Novatchkova, M., Jais, A., Wagner, G., Handschuh, S., Uribesalgo, I., Hagelkruys, A., Kozieradzki, I., Tortola, L., Nitsch, R., Cronin, SJ., Orthofer, M., Branstetter, D., Canon, J., Rossi, J., D'Arcangelo, M., Botling, J., Micke, P., Fleur, L., Edlund, K., Bergqvist, M., Ekman, S., Lendl, T., Popper, H., Takayanagi, H., Kenner, L., Hirsch, FR., Dougall, W., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Genes Dev","volume":"31","issue":"20","page":"2099-2112","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29117894","title":"Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling.","abstract":"Toddler\/Apela\/Elabela is a conserved secreted peptide that regulates mesendoderm development during zebrafish gastrulation. Two non-exclusive models have been proposed to explain Toddler function. The 'specification model' postulates that Toddler signaling enhances Nodal signaling to properly specify endoderm, whereas the 'migration model' posits that Toddler signaling regulates mesendodermal cell migration downstream of Nodal signaling. Here, we test key predictions of both models. We find that in <i>toddler<\/i> mutants Nodal signaling is initially normal and increasing endoderm specification does not rescue mesendodermal cell migration. Mesodermal cell migration defects in <i>toddler<\/i> mutants result from a decrease in animal pole-directed migration and are independent of endoderm. Conversely, endodermal cell migration defects are dependent on a Cxcr4a-regulated tether of the endoderm to mesoderm. These results suggest that Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling and indirectly affects endodermal cell migration via Cxcr4a-signaling.","authors":"Norris, ML., Pauli, A., Gagnon, JA., Lord, ND., Rogers, KW., Mosimann, C., Zon, LI., Schier, AF.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Elife","volume":"6","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28369070","title":"Probing the canonicity of the Wnt\/Wingless signaling pathway.","abstract":"The hallmark of canonical Wnt signaling is the transcriptional induction of Wnt target genes by the beta-catenin\/TCF complex. Several studies have proposed alternative interaction partners for beta-catenin or TCF, but the relevance of potential bifurcations in the distal Wnt pathway remains unclear. Here we study on a genome-wide scale the requirement for Armadillo (Arm, Drosophila beta-catenin) and Pangolin (Pan, Drosophila TCF) in the Wnt\/Wingless(Wg)-induced transcriptional response of Drosophila Kc cells. Using somatic genetics, we demonstrate that both Arm and Pan are absolutely required for mediating activation and repression of target genes. Furthermore, by means of STARR-sequencing we identified Wnt\/Wg-responsive enhancer elements and found that all responsive enhancers depend on Pan. Together, our results confirm the dogma of canonical Wnt\/Wg signaling and argue against the existence of distal pathway branches in this system.","authors":"Franz, A., Shlyueva, D., Brunner, E., Stark, A., Basler, K.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"PLoS Genet","volume":"13","issue":"4","page":"e1006700","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29110645","title":"Long intergenic non-protein-coding RNA 1567 (LINC01567) acts as a \"sponge\" against microRNA-93 in regulating the proliferation and tumorigenesis of human colon cancer stem cells.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">29110645<\/PMID><DateCompleted><Year>2018<\/Year><Month>07<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2407<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>17<\/Volume><Issue>1<\/Issue><PubDate><Year>2017<\/Year><Month>Nov<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>BMC cancer<\/Title><ISOAbbreviation>BMC Cancer<\/ISOAbbreviation><\/Journal><ArticleTitle>Long intergenic non-protein-coding RNA 1567 (LINC01567) acts as a \"sponge\" against microRNA-93 in regulating the proliferation and tumorigenesis of human colon cancer stem cells.<\/ArticleTitle><Pagination><MedlinePgn>716<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12885-017-3731-5<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Cancer stem cells (CSCs) are considered to be the major factor in tumor initiation, progression, metastasis, recurrence and chemoresistance. Maintaining the stemness and promoting differentiation of these cells involve various factors. Recently, long non-coding RNAs (lncRNAs) have been identified as new regulatory factors in human cancer cells. However, the function of lncRNAs in colon CSCs is still unknown.","authors":"Yu, X., Mi, L., Dong, J., Zou, J.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"BMC Cancer","volume":"17","issue":"1","page":"716","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29106370","title":"Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments.","abstract":"The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.","authors":"Spira, F., Cuylen-Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., Oldenbourg, R., Sixt, M., Gerlich, DW.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Elife","volume":"6","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29087939","title":"Efficient gene knockin in axolotl and its use to test the role of satellite cells in limb regeneration.","abstract":"Salamanders exhibit extensive regenerative capacities and serve as a unique model in regeneration research. However, due to the lack of targeted gene knockin approaches, it has been difficult to label and manipulate some of the cell populations that are crucial for understanding the mechanisms underlying regeneration. Here we have established highly efficient gene knockin approaches in the axolotl (<i>Ambystoma mexicanum<\/i>) based on the CRISPR\/Cas9 technology. Using a homology-independent method, we successfully inserted both the <i>Cherry<\/i> reporter gene and a larger membrane-tagged <i>Cherry-ER<\/i><sup><i>T2<\/i><\/sup><i>-Cre-ER<\/i><sup><i>T2<\/i><\/sup> (\u223c5-kb) cassette into axolotl <i>Sox2<\/i> and <i>Pax7<\/i> genomic loci. Depending on the size of the DNA fragments for integration, 5-15% of the F0 transgenic axolotl are positive for the transgene. Using these techniques, we have labeled and traced the PAX7-positive satellite cells as a major source contributing to myogenesis during axolotl limb regeneration. Our work brings a key genetic tool to molecular and cellular studies of axolotl regeneration.","authors":"Fei, JF., Schuez, M., Knapp, D., Taniguchi, Y., Drechsel, DN., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Proc Natl Acad Sci U S A","volume":"114","issue":"47","page":"12501-12506","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28806168","title":"Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression.","abstract":"To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the <i>Igf2r<\/i> cluster extending over 10 Mb in placenta.","authors":"Andergassen, D., Dotter, CP., Wenzel, D., Sigl, V., Bammer, PC., Muckenhuber, M., Mayer, D., Kulinski, TM., Theussl, HC., Penninger, JM., Bock, C., Barlow, DP., Pauler, FM., Hudson, QJ.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Elife","volume":"6","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28779160","title":"Age-dependent motor dysfunction due to neuron-specific disruption of stress-activated protein kinase MKK7.","abstract":"c-Jun N-terminal kinase (JNK) is a member of the mitogen-activated protein kinase family and controls various physiological processes including apoptosis. A specific upstream activator of JNKs is the mitogen-activated protein kinase kinase 7 (MKK7). It has been reported that MKK7-JNK signaling plays an important regulatory role in neural development, however, post-developmental functions in the nervous system have not been elucidated. In this study, we generated neuron-specific Mkk7 knockout mice (MKK7 cKO), which impaired constitutive activation of JNK in the nervous system. MKK7 cKO mice displayed impaired circadian behavioral rhythms and decreased locomotor activity. MKK7 cKO mice at 8 months showed motor dysfunctions such as weakness of hind-limb and gait abnormality in an age-dependent manner. Axonal degeneration in the spinal cord and muscle atrophy were also observed, along with accumulation of the axonal transport proteins JNK-interacting protein 1 and amyloid beta precursor protein in the brains and spinal cords of MKK7 cKO mice. Thus, the MKK7-JNK signaling pathway plays important roles in regulating circadian rhythms and neuronal maintenance in the adult nervous system.","authors":"Yamasaki, T., Deki-Arima, N., Kaneko, A., Miyamura, N., Iwatsuki, M., Matsuoka, M., Fujimori-Tonou, N., Okamoto-Uchida, Y., Hirayama, J., Marth, JD., Yamanashi, Y., Kawasaki, H., Yamanaka, K., Penninger, JM., Shibata, S., Nishina, H.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Sci Rep","volume":"7","issue":"1","page":"7348","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28745625","title":"A Protocol for Multiple Gene Knockout in Mouse Small Intestinal Organoids Using a CRISPR-concatemer.","abstract":"CRISPR\/Cas9 technology has greatly improved the feasibility and speed of loss-of-function studies that are essential in understanding gene function. In higher eukaryotes, paralogous genes can mask a potential phenotype by compensating the loss of a gene, thus limiting the information that can be obtained from genetic studies relying on single gene knockouts. We have developed a novel, rapid cloning method for guide RNA (gRNA) concatemers in order to create multi-gene knockouts following a single round of transfection in mouse small intestinal organoids. Our strategy allows for the concatemerization of up to four individual gRNAs into a single vector by performing a single Golden Gate shuffling reaction with annealed gRNA oligos and a pre-designed retroviral vector. This allows either the simultaneous knockout of up to four different genes, or increased knockout efficiency following the targeting of one gene by multiple gRNAs. In this protocol, we show in detail how to efficiently clone multiple gRNAs into the retroviral CRISPR-concatemer vector and how to achieve highly efficient electroporation in intestinal organoids. As an example, we show that simultaneous knockout of two pairs of genes encoding negative regulators of the Wnt signaling pathway (Axin1\/2 and Rnf43\/Znrf3) renders intestinal organoids resistant to the withdrawal of key growth factors.","authors":"Merenda, A., Andersson-Rolf, A., Mustata, RC., Li, T., Kim, H., Koo, BK.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"J Vis Exp","volume":null,"issue":"125","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28716934","title":"Sigma-1 receptors control immune-driven peripheral opioid analgesia during inflammation in mice.","abstract":"Sigma-1 antagonism potentiates the antinociceptive effects of opioid drugs, so sigma-1 receptors constitute a biological brake to opioid drug-induced analgesia. The pathophysiological role of this process is unknown. We aimed to investigate whether sigma-1 antagonism reduces inflammatory pain through the disinhibition of the endogenous opioidergic system in mice. The selective sigma-1 antagonists BD-1063 and S1RA abolished mechanical and thermal hyperalgesia in mice with carrageenan-induced acute (3 h) inflammation. Sigma-1-mediated antihyperalgesia was reversed by the opioid antagonists naloxone and naloxone methiodide (a peripherally restricted naloxone analog) and by local administration at the inflamed site of monoclonal antibody 3-E7, which recognizes the pan-opioid sequence Tyr-Gly-Gly-Phe at the <i>N<\/i> terminus of most endogenous opioid peptides (EOPs). Neutrophils expressed pro-opiomelanocortin, the precursor of \u03b2-endorphin (a known EOP), and constituted the majority of the acute immune infiltrate. \u03b2-endorphin levels increased in the inflamed paw, and this increase and the antihyperalgesic effects of sigma-1 antagonism were abolished by reducing the neutrophil load with in vivo administration of an anti-Ly6G antibody. The opioid-dependent sigma-1 antihyperalgesic effects were preserved 5 d after carrageenan administration, where macrophages\/monocytes were found to express pro-opiomelanocortin and to now constitute the majority of the immune infiltrate. These results suggest that immune cells harboring EOPs are needed for the antihyperalgesic effects of sigma-1 antagonism during inflammation. In conclusion, sigma-1 receptors curtail immune-driven peripheral opioid analgesia, and sigma-1 antagonism produces local opioid analgesia by enhancing the action of EOPs of immune origin, maximizing the analgesic potential of immune cells that naturally accumulate in painful inflamed areas.","authors":"Tejada, MA., Montilla-Garc\u00eda, A., Cronin, SJ., Cikes, D., S\u00e1nchez-Fern\u00e1ndez, C., Gonz\u00e1lez-Cano, R., Ruiz-Cantero, MC., Penninger, JM., Vela, JM., Baeyens, JM., Cobos, EJ.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Proc Natl Acad Sci U S A","volume":"114","issue":"31","page":"8396-8401","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28662661","title":"Non-model model organisms.","abstract":"Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.","authors":"Russell, JJ., Theriot, JA., Sood, P., Marshall, WF., Landweber, LF., Fritz-Laylin, L., Polka, JK., Oliferenko, S., Gerbich, T., Gladfelter, A., Umen, J., Bezanilla, M., Lancaster, MA., He, S., Gibson, MC., Goldstein, B., Tanaka, EM., Hu, CK., Brunet, A.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"BMC Biol","volume":"15","issue":"1","page":"55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28574479","title":"R Loops in the Regulation of Antibody Gene Diversification.","abstract":"For nearly three decades, R loops have been closely linked with class switch recombination (CSR), the process that generates antibody isotypes and that occurs via a complex cascade initiated by transcription-coupled mutagenesis in switch recombination sequences. R loops form during transcription of switch recombination sequences in vitro and in vivo, and there is solid evidence that R loops are required for efficient class switching. The classical model of R loops posits that they boost mutation rates by generating stable and long tracts of single-stranded DNA that serve as the substrate for activation induced deaminase (AID), the enzyme that initiates the CSR reaction cascade by co-transcriptionally mutating ssDNA in switch recombination sequences. Though logical and compelling, this model has not been supported by in vivo evidence. Indeed, several reports suggest that R loops may not be involved in recruiting AID activity to switch regions, meaning that R loops probably serve other unanticipated roles in CSR. Here, I review the key findings in this field to date and propose hypotheses that could help towards elucidating the precise function of R loops in CSR.","authors":"Pavri, R.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Genes (Basel)","volume":"8","issue":"6","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28545475","title":"Urinary neprilysin in the critically ill patient.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">28545475<\/PMID><DateCompleted><Year>2018<\/Year><Month>03<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2369<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>18<\/Volume><Issue>1<\/Issue><PubDate><Year>2017<\/Year><Month>May<\/Month><Day>25<\/Day><\/PubDate><\/JournalIssue><Title>BMC nephrology<\/Title><ISOAbbreviation>BMC Nephrol<\/ISOAbbreviation><\/Journal><ArticleTitle>Urinary neprilysin in the critically ill patient.<\/ArticleTitle><Pagination><MedlinePgn>172<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12882-017-0587-5<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Critically ill patients in intensive care face hazardous conditions. Among these, acute kidney injury (AKI) is frequently seen as a result of sepsis. Early diagnosis of kidney injury is of the utmost importance in the guidance of interventions or avoidance of treatment-induced kidney injury. On these grounds, we searched for markers that could indicate proximal tubular cell injury.","authors":"Pajenda, S., Mechtler, K., Wagner, L.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"BMC Nephrol","volume":"18","issue":"1","page":"172","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24315439","title":"Functional repair of CFTR by CRISPR\/Cas9 in intestinal stem cell organoids of cystic fibrosis patients.","abstract":"Single murine and human intestinal stem cells can be expanded in culture over long time periods as genetically and phenotypically stable epithelial organoids. Increased cAMP levels induce rapid swelling of such organoids by opening the cystic fibrosis transmembrane conductor receptor (CFTR). This response is lost in organoids derived from cystic fibrosis (CF) patients. Here we use the CRISPR\/Cas9 genome editing system to correct the CFTR locus by homologous recombination in cultured intestinal stem cells of CF patients. The corrected allele is expressed and fully functional as measured in clonally expanded organoids. This study provides proof of concept for gene correction by homologous recombination in primary adult stem cells derived from patients with a single-gene hereditary defect.","authors":"Schwank, G., Koo, BK., Sasselli, V., Dekkers, JF., Heo, I., Demircan, T., Sasaki, N., Boymans, S., Cuppen, E., van der Ent, CK., Nieuwenhuis, EE., Beekman, JM., Clevers, H.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Stem Cell","volume":"13","issue":"6","page":"653-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28541292","title":"Long-range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs.","abstract":"The proteasome holoenzyme is the major non-lysosomal protease; its proteolytic activity is essential for cellular homeostasis. Thus, it is an attractive target for the development of chemotherapeutics. While the structural basis of core particle (CP) inhibitors is largely understood, their structural impact on the proteasome holoenzyme remains entirely elusive. Here, we determined the structure of the 26S proteasome with and without the inhibitor Oprozomib. Drug binding modifies the energy landscape of conformational motion in the proteasome regulatory particle (RP). Structurally, the energy barrier created by Oprozomib triggers a long-range allosteric regulation, resulting in the stabilization of a non-productive state. Thereby, the chemical drug-binding signal is converted, propagated and amplified into structural changes over a distance of more than 150\u2009\u00c5 from the proteolytic site to the ubiquitin receptor Rpn10. The direct visualization of changes in conformational dynamics upon drug binding allows new ways to screen and develop future allosteric proteasome inhibitors.","authors":"Haselbach, D., Schrader, J., Lambrecht, F., Henneberg, F., Chari, A., Stark, H.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Nat Commun","volume":"8","issue":null,"page":"15578","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28485369","title":"Control of type III protein secretion using a minimal genetic system.","abstract":"Gram-negative bacteria secrete proteins using a type III secretion system (T3SS), which functions as a needle-like molecular machine. The many proteins involved in T3SS construction are tightly regulated due to its role in pathogenesis and motility. Here, starting with the 35\u2009kb Salmonella pathogenicity island 1 (SPI-1), we eliminated internal regulation and simplified the genetics by removing or recoding genes, scrambling gene order and replacing all non-coding DNA with synthetic genetic parts. This process results in a 16\u2009kb cluster that shares no sequence identity, regulation or organizational principles with SPI-1. Building this simplified system led to the discovery of essential roles for an internal start site (SpaO) and small RNA (InvR). Further, it can be controlled using synthetic regulatory circuits, including under SPI-1 repressing conditions. This work reveals an incredible post-transcriptional robustness in T3SS assembly and aids its control as a tool in biotechnology.","authors":"Song, M., Sukovich, DJ., Ciccarelli, L., Mayr, J., Fernandez-Rodriguez, J., Mirsky, EA., Tucker, AC., Gordon, DB., Marlovits, TC., Voigt, CA.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Nat Commun","volume":"8","issue":null,"page":"14737","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-11-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28482867","title":"Afadin controls cell polarization and mitotic spindle orientation in developing cortical radial glia.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">28482867<\/PMID><DateCompleted><Year>2018<\/Year><Month>03<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1749-8104<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>12<\/Volume><Issue>1<\/Issue><PubDate><Year>2017<\/Year><Month>May<\/Month><Day>08<\/Day><\/PubDate><\/JournalIssue><Title>Neural development<\/Title><ISOAbbreviation>Neural Dev<\/ISOAbbreviation><\/Journal><ArticleTitle>Afadin controls cell polarization and mitotic spindle orientation in developing cortical radial glia.<\/ArticleTitle><Pagination><MedlinePgn>7<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13064-017-0085-2<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">In developing tissues, cell polarity and tissue architecture play essential roles in the regulation of proliferation and differentiation. During cerebral cortical development, adherens junctions link highly polarized radial glial cells in a neurogenic niche that controls their behavior. How adherens junctions regulate radial glial cell polarity and\/or differentiation in mammalian cortical development is poorly understood.","authors":"Rakotomamonjy, J., Brunner, M., J\u00fcschke, C., Zang, K., Huang, EJ., Reichardt, LF., Chenn, A.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Neural Dev","volume":"12","issue":"1","page":"7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28414273","title":"Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage.","abstract":"Cartilaginous structures are at the core of embryo growth and shaping before the bone forms. Here we report a novel principle of vertebrate cartilage growth that is based on introducing transversally-oriented clones into pre-existing cartilage. This mechanism of growth uncouples the lateral expansion of curved cartilaginous sheets from the control of cartilage thickness, a process which might be the evolutionary mechanism underlying adaptations of facial shape. In rod-shaped cartilage structures (Meckel, ribs and skeletal elements in developing limbs), the transverse integration of clonal columns determines the well-defined diameter and resulting rod-like morphology. We were able to alter cartilage shape by experimentally manipulating clonal geometries. Using in silico modeling, we discovered that anisotropic proliferation might explain cartilage bending and groove formation at the macro-scale.","authors":"Kaucka, M., Zikmund, T., Tesarova, M., Gyllborg, D., Hellander, A., Jaros, J., Kaiser, J., Petersen, J., Szarowska, B., Newton, PT., Dyachuk, V., Li, L., Qian, H., Johansson, AS., Mishina, Y., Currie, JD., Tanaka, EM., Erickson, A., Dudley, A., Brismar, H., Southam, P., Coen, E., Chen, M., Weinstein, LS., Hampl, A., Arenas, E., Chagin, AS., Fried, K., Adameyko, I.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Elife","volume":"6","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28394313","title":"Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis.","abstract":"Mycobacteria are characterized by their impermeable outer membrane, which is rich in mycolic acids<sup>1<\/sup>. To transport substrates across this complex cell envelope, mycobacteria rely on type VII (also known as ESX) secretion systems<sup>2<\/sup>. In Mycobacterium tuberculosis, these ESX systems are essential for growth and full virulence and therefore represent an attractive target for anti-tuberculosis drugs<sup>3<\/sup>. However, the molecular details underlying type VII secretion are largely unknown, due to a lack of structural information. Here, we report the molecular architecture of the ESX-5 membrane complex from Mycobacterium xenopi determined at 13\u2005\u00c5 resolution by electron microscopy. The four core proteins of the ESX-5 complex (EccB<sub>5<\/sub>, EccC<sub>5<\/sub>, EccD<sub>5<\/sub> and EccE<sub>5<\/sub>) assemble with equimolar stoichiometry into an oligomeric assembly that displays six-fold symmetry. This membrane-associated complex seems to be embedded exclusively in the inner membrane, which indicates that additional components are required to translocate substrates across the mycobacterial outer membrane. Furthermore, the extended cytosolic domains of the EccC ATPase, which interact with secretion effectors, are highly flexible, suggesting an as yet unseen mode of substrate interaction. Comparison of our results with known structures of other bacterial secretion systems demonstrates that the architecture of type VII secretion system is fundamentally different, suggesting an alternative secretion mechanism.","authors":"Beckham, KS., Ciccarelli, L., Bunduc, CM., Mertens, HD., Ummels, R., Lugmayr, W., Mayr, J., Rettel, M., Savitski, MM., Svergun, DI., Bitter, W., Wilmanns, M., Marlovits, TC., Parret, AH., Houben, EN.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Nat Microbiol","volume":"2","issue":null,"page":"17047","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-222","title":"An ATP-gated molecular switch orchestrates human mRNA export","abstract":null,"authors":"Hohmann, U., Graf, M., Tiri\u00e1n, L., Pacheco-Fiallos, B., Schellhaas, U., Fin, L., Handler, D., Phillips, AW., Riabov-Bassat, D., Faraway, R., P\u00fchringer, T., Szalay, MF., Roitinger, E., Brennecke, J., Plaschka, C.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nature","volume":"649","issue":"8098","page":"1042-1050","pdf":null,"JrId":null,"fulltextlink":"https:\/\/pubmed.ncbi.nlm.nih.gov\/41198879\/","preprintlink":null,"articledate":"2025-11-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28347630","title":"Tubulins and brain development - The origins of functional specification.","abstract":"The development of the vertebrate central nervous system is reliant on a complex cascade of biological processes that include mitotic division, relocation of migrating neurons, and the extension of dendritic and axonal processes. Each of these cellular events requires the diverse functional repertoire of the microtubule cytoskeleton for the generation of forces, assembly of macromolecular complexes and transport of molecules and organelles. The tubulins are a multi-gene family that encode for the constituents of microtubules, and have been implicated in a spectrum of neurological disorders. Evidence is building that different tubulins tune the functional properties of the microtubule cytoskeleton dependent on the cell type, developmental profile and subcellular localisation. Here we review of the origins of the functional specification of the tubulin gene family in the developing brain at a transcriptional, translational, and post-transcriptional level. We remind the reader that tubulins are not just loading controls for your average Western blot.","authors":"Breuss, MW., Leca, I., Gstrein, T., Hansen, AH., Keays, DA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Mol Cell Neurosci","volume":"84","issue":null,"page":"58-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28012276","title":"Molecular basis of outer kinetochore assembly on CENP-T.","abstract":"Stable kinetochore-microtubule attachment is essential for cell division. It requires recruitment of outer kinetochore microtubule binders by centromere proteins C and T (CENP-C and CENP-T). To study the molecular requirements of kinetochore formation, we reconstituted the binding of the MIS12 and NDC80 outer kinetochore subcomplexes to CENP-C and CENP-T. Whereas CENP-C recruits a single MIS12:NDC80 complex, we show here that CENP-T binds one MIS12:NDC80 and two NDC80 complexes upon phosphorylation by the mitotic CDK1:Cyclin B complex at three distinct CENP-T sites. Visualization of reconstituted complexes by electron microscopy supports this model. Binding of CENP-C and CENP-T to MIS12 is competitive, and therefore CENP-C and CENP-T act in parallel to recruit two MIS12 and up to four NDC80 complexes. Our observations provide a molecular explanation for the stoichiometry of kinetochore components and its cell cycle regulation, and highlight how outer kinetochore modules bridge distances of well over 100 nm.","authors":"Huis In 't Veld, PJ., Jeganathan, S., Petrovic, A., Singh, P., John, J., Krenn, V., Weissmann, F., Bange, T., Musacchio, A.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Elife","volume":"5","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27977800","title":"Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus.","abstract":"Bacterial type III protein secretion systems inject effector proteins into eukaryotic host cells in order to promote survival and colonization of Gram-negative pathogens and symbionts. Secretion across the bacterial cell envelope and injection into host cells is facilitated by a so-called injectisome. Its small hydrophobic export apparatus components SpaP and SpaR were shown to nucleate assembly of the needle complex and to form the central \"cup\" substructure of a Salmonella Typhimurium secretion system. However, the in vivo placement of these components in the needle complex and their function during the secretion process remained poorly defined. Here we present evidence that a SpaP pentamer forms a 15 \u00c5 wide pore and provide a detailed map of SpaP interactions with the export apparatus components SpaQ, SpaR, and SpaS. We further refine the current view of export apparatus assembly, consolidate transmembrane topology models for SpaP and SpaR, and present intimate interactions of the periplasmic domains of SpaP and SpaR with the inner rod protein PrgJ, indicating how export apparatus and needle filament are connected to create a continuous conduit for substrate translocation.","authors":"Dietsche, T., Tesfazgi Mebrhatu, M., Brunner, MJ., Abrusci, P., Yan, J., Franz-Wachtel, M., Sch\u00e4rfe, C., Zilkenat, S., Grin, I., Gal\u00e1n, JE., Kohlbacher, O., Lea, S., Macek, B., Marlovits, TC., Robinson, CV., Wagner, S.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"PLoS Pathog","volume":"12","issue":"12","page":"e1006071","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27976684","title":"Profiling DNA damage response following mitotic perturbations.","abstract":"Genome integrity relies on precise coordination between DNA replication and chromosome segregation. Whereas replication stress attracted much attention, the consequences of mitotic perturbations for genome integrity are less understood. Here, we knockdown 47 validated mitotic regulators to show that a broad spectrum of mitotic errors correlates with increased DNA breakage in daughter cells. Unexpectedly, we find that only a subset of these correlations are functionally linked. We identify the genuine mitosis-born DNA damage events and sub-classify them according to penetrance of the observed phenotypes. To demonstrate the potential of this resource, we show that DNA breakage after cytokinesis failure is preceded by replication stress, which mounts during consecutive cell cycles and coincides with decreased proliferation. Together, our results provide a resource to gauge the magnitude and dynamics of DNA breakage associated with mitotic aberrations and suggest that replication stress might limit propagation of cells with abnormal karyotypes.","authors":"S Pedersen, R., Karemore, G., Gudjonsson, T., Rask, MB., Neumann, B., H\u00e9rich\u00e9, JK., Pepperkok, R., Ellenberg, J., Gerlich, DW., Lukas, J., Lukas, C.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Nat Commun","volume":"7","issue":null,"page":"13887","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27901467","title":"Structural basis for the disaggregase activity and regulation of Hsp104.","abstract":"The Hsp104 disaggregase is a two-ring ATPase machine that rescues various forms of non-native proteins including the highly resistant amyloid fibers. The structural-mechanistic underpinnings of how the recovery of toxic protein aggregates is promoted and how this potent unfolding activity is prevented from doing collateral damage to cellular proteins are not well understood. Here, we present structural and biochemical data revealing the organization of Hsp104 from <i>Chaetomium thermophilum<\/i> at 3.7 \u00c5 resolution. We show that the coiled-coil domains encircling the disaggregase constitute a 'restraint mask' that sterically controls the mobility and thus the unfolding activity of the ATPase modules. In addition, we identify a mechanical linkage that coordinates the activity of the two ATPase rings and accounts for the high unfolding potential of Hsp104. Based on these findings, we propose a general model for how Hsp104 and related chaperones operate and are kept under control until recruited to appropriate substrates.","authors":"Heuck, A., Schitter-Sollner, S., Suskiewicz, MJ., Kurzbauer, R., Kley, J., Schleiffer, A., Rombaut, P., Herzog, F., Clausen, T.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Elife","volume":"5","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23536629","title":"Id2-mediated inhibition of E2A represses memory CD8+ T cell differentiation.","abstract":"The transcription factor inhibitor of DNA binding (Id)2 modulates T cell fate decisions, but the molecular mechanism underpinning this regulation is unclear. In this study we show that loss of Id2 cripples effector differentiation and instead programs CD8(+) T cells to adopt a memory fate with increased Eomesodermin and Tcf7 expression. We demonstrate that Id2 restrains CD8(+) T cell memory differentiation by inhibiting E2A-mediated direct activation of Tcf7 and that Id2 expression level mirrors T cell memory recall capacity. As a result of the defective effector differentiation, Id2-deficient CD8(+) T cells fail to induce sufficient Tbx21 expression to generate short-lived effector CD8(+) T cells. Our findings reveal that the Id2\/E2A axis orchestrates T cell differentiation through the induction or repression of downstream transcription factors essential for effector and memory T cell differentiation.","authors":"Masson, F., Minnich, M., Olshansky, M., Bilic, I., Mount, AM., Kallies, A., Speed, TP., Busslinger, M., Nutt, SL., Belz, GT.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Immunol","volume":"190","issue":"9","page":"4585-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27892853","title":"Structure of the germline genome of <i>Tetrahymena thermophila<\/i> and relationship to the massively rearranged somatic genome.","abstract":"The germline genome of the binucleated ciliate <i>Tetrahymena thermophila<\/i> undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline\/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped <i>Tetrahymena<\/i> chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare <i>Tetrahymena<\/i>'s germline\/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.","authors":"Hamilton, EP., Kapusta, A., Huvos, PE., Bidwell, SL., Zafar, N., Tang, H., Hadjithomas, M., Krishnakumar, V., Badger, JH., Caler, EV., Russ, C., Zeng, Q., Fan, L., Levin, JZ., Shea, T., Young, SK., Hegarty, R., Daza, R., Gujja, S., Wortman, JR., Birren, BW., Nusbaum, C., Thomas, J., Carey, CM., Pritham, EJ., Feschotte, C., Noto, T., Mochizuki, K., Papazyan, R., Taverna, SD., Dear, PH., Cassidy-Hanley, DM., Xiong, J., Miao, W., Orias, E., Coyne, RS.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Elife","volume":"5","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27885987","title":"Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls.","abstract":"Axolotls are unique in their ability to regenerate the spinal cord. However, the mechanisms that underlie this phenomenon remain poorly understood. Previously, we showed that regenerating stem cells in the axolotl spinal cord revert to a molecular state resembling embryonic neuroepithelial cells and functionally acquire rapid proliferative divisions (Rodrigo Albors et al., 2015). Here, we refine the analysis of cell proliferation in space and time and identify a high-proliferation zone in the regenerating spinal cord that shifts posteriorly over time. By tracking sparsely-labeled cells, we also quantify cell influx into the regenerate. Taking a mathematical modeling approach, we integrate these quantitative datasets of cell proliferation, neural stem cell activation and cell influx, to predict regenerative tissue outgrowth. Our model shows that while cell influx and neural stem cell activation play a minor role, the acceleration of the cell cycle is the major driver of regenerative spinal cord outgrowth in axolotls.","authors":"Rost, F., Rodrigo Albors, A., Mazurov, V., Brusch, L., Deutsch, A., Tanaka, EM., Chara, O.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Elife","volume":"5","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27883036","title":"The mevalonate pathway regulates primitive streak formation via protein farnesylation.","abstract":"The primitive streak in peri-implantation embryos forms the mesoderm and endoderm and controls cell differentiation. The metabolic cues regulating primitive streak formation remain largely unknown. Here we utilised a mouse embryonic stem (ES) cell differentiation system and a library of well-characterised drugs to identify these metabolic factors. We found that statins, which inhibit the mevalonate metabolic pathway, suppressed primitive streak formation in vitro and in vivo. Using metabolomics and pharmacologic approaches we identified the downstream signalling pathway of mevalonate and revealed that primitive streak formation requires protein farnesylation but not cholesterol synthesis. A tagging-via-substrate approach revealed that nuclear lamin B1 and small G proteins were farnesylated in embryoid bodies and important for primitive streak gene expression. In conclusion, protein farnesylation driven by the mevalonate pathway is a metabolic cue essential for primitive streak formation.","authors":"Okamoto-Uchida, Y., Yu, R., Miyamura, N., Arima, N., Ishigami-Yuasa, M., Kagechika, H., Yoshida, S., Hosoya, T., Nawa, M., Kasama, T., Asaoka, Y., Alois, RW., Elling, U., Penninger, JM., Nishina, S., Azuma, N., Nishina, H.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Sci Rep","volume":"6","issue":null,"page":"37697","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27791065","title":"RNA-binding profiles of <i>Drosophila<\/i> CPEB proteins Orb and Orb2.","abstract":"Localized protein translation is critical in many biological contexts, particularly in highly polarized cells, such as neurons, to regulate gene expression in a spatiotemporal manner. The cytoplasmic polyadenylation element-binding (CPEB) family of RNA-binding proteins has emerged as a key regulator of mRNA transport and local translation required for early embryonic development, synaptic plasticity, and long-term memory (LTM). <i>Drosophila<\/i> Orb and Orb2 are single members of the CPEB1 and CPEB2 subfamilies of the CPEB proteins, respectively. At present, the identity of the mRNA targets they regulate is not fully known, and the binding specificity of the CPEB2 subfamily is a matter of debate. Using transcriptome-wide UV cross-linking and immunoprecipitation, we define the mRNA-binding sites and targets of <i>Drosophila<\/i> CPEBs. Both Orb and Orb2 bind linear cytoplasmic polyadenylation element-like sequences in the 3' UTRs of largely overlapping target mRNAs, with Orb2 potentially having a broader specificity. Both proteins use their RNA-recognition motifs but not the Zinc-finger region for RNA binding. A subset of Orb2 targets is translationally regulated in cultured S2 cells and fly head extracts. Moreover, pan-neuronal RNAi knockdown of these targets suggests that a number of these targets are involved in LTM. Our results provide a comprehensive list of mRNA targets of the two CPEB proteins in <i>Drosophila<\/i>, thus providing insights into local protein synthesis involved in various biological processes, including LTM.","authors":"Stepien, BK., Oppitz, C., Gerlach, D., Dag, U., Novatchkova, M., Kr\u00fcttner, S., Stark, A., Keleman, K.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Proc Natl Acad Sci U S A","volume":"113","issue":"45","page":"E7030-E7038","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27775650","title":"The Role of TAM Family Receptors in Immune Cell Function: Implications for Cancer Therapy.","abstract":"The TAM receptor protein tyrosine kinases-Tyro3, Axl, and Mer-are essential regulators of immune homeostasis. Guided by their cognate ligands Growth arrest-specific gene 6 (Gas6) and Protein S (Pros1), these receptors ensure the resolution of inflammation by dampening the activation of innate cells as well as by restoring tissue function through promotion of tissue repair and clearance of apoptotic cells. Their central role as negative immune regulators is highlighted by the fact that deregulation of TAM signaling has been linked to the pathogenesis of autoimmune, inflammatory, and infectious diseases. Importantly, TAM receptors have also been associated with cancer development and progression. In a cancer setting, TAM receptors have a dual regulatory role, controlling the initiation and progression of tumor development and, at the same time, the associated anti-tumor responses of diverse immune cells. Thus, modulation of TAM receptors has emerged as a potential novel strategy for cancer treatment. In this review, we discuss our current understanding of how TAM receptors control immunity, with a particular focus on the regulation of anti-tumor responses and its implications for cancer immunotherapy.","authors":"Paolino, M., Penninger, JM.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Cancers (Basel)","volume":"8","issue":"10","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27734929","title":"Prioritizing cancer-related microRNAs by integrating microRNA and mRNA datasets.","abstract":"MicroRNAs (miRNAs) are small non-coding RNAs regulating the expression of target genes, and they are involved in cancer initiation and progression. Even though many cancer-related miRNAs were identified, their functional impact may vary, depending on their effects on the regulation of other miRNAs and genes. In this study, we propose a novel method for the prioritization of candidate cancer-related miRNAs that may affect the expression of other miRNAs and genes across the entire biological network. For this, we propose three important features: the average expression of a miRNA in multiple cancer samples, the average of the absolute correlation values between the expression of a miRNA and expression of all genes, and the number of predicted miRNA target genes. These three features were integrated using order statistics. By applying the proposed approach to four cancer types, glioblastoma, ovarian cancer, prostate cancer, and breast cancer, we prioritized candidate cancer-related miRNAs and determined their functional roles in cancer-related pathways. The proposed approach can be used to identify miRNAs that play crucial roles in driving cancer development, and the elucidation of novel potential therapeutic targets for cancer treatment.","authors":"Jin, D., Lee, H.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Sci Rep","volume":"6","issue":"","page":"35350","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27703274","title":"Cross-inhibition of pathogenic agents and the host proteins they exploit.","abstract":"The major limitations of pathogen-directed therapies are the emergence of drug-resistance and their narrow spectrum of coverage. A recently applied approach directs therapies against host proteins exploited by pathogens in order to circumvent these limitations. However, host-oriented drugs leave the pathogens unaffected and may result in continued pathogen dissemination. In this study we aimed to discover drugs that could simultaneously cross-inhibit pathogenic agents, as well as the host proteins that mediate their lethality. We observed that many pathogenic and host-assisting proteins belong to the same functional class. In doing so we targeted a protease component of anthrax toxin as well as host proteases exploited by this toxin. We identified two approved drugs, ascorbic acid 6-palmitate and salmon sperm protamine, that effectively inhibited anthrax cytotoxic protease and demonstrated that they also block proteolytic activities of host furin, cathepsin B, and caspases that mediate toxin's lethality in cells. We demonstrated that these drugs are broad-spectrum and reduce cellular sensitivity to other bacterial toxins that require the same host proteases. This approach should be generally applicable to the discovery of simultaneous pathogen and host-targeting inhibitors of many additional pathogenic agents.","authors":"Zilbermintz, L., Leonardi, W., Tran, SH., Zozaya, J., Mathew-Joseph, A., Liem, S., Levitin, A., Martchenko, M.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Sci Rep","volume":"6","issue":"","page":"34846","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27627128","title":"A Genome-Wide siRNA Screen Implicates Spire1\/2 in SipA-Driven Salmonella Typhimurium Host Cell Invasion.","abstract":"Salmonella Typhimurium (S. Tm) is a leading cause of diarrhea. The disease is triggered by pathogen invasion into the gut epithelium. Invasion is attributed to the SPI-1 type 3 secretion system (T1). T1 injects effector proteins into epithelial cells and thereby elicits rearrangements of the host cellular actin cytoskeleton and pathogen invasion. The T1 effector proteins SopE, SopB, SopE2 and SipA are contributing to this. However, the host cell factors contributing to invasion are still not completely understood. To address this question comprehensively, we used Hela tissue culture cells, a genome-wide siRNA library, a modified gentamicin protection assay and S. TmSipA, a sopBsopE2sopE mutant which strongly relies on the T1 effector protein SipA to invade host cells. We found that S. TmSipA invasion does not elicit membrane ruffles, nor promote the entry of non-invasive bacteria \"in trans\". However, SipA-mediated infection involved the SPIRE family of actin nucleators, besides well-established host cell factors (WRC, ARP2\/3, RhoGTPases, COPI). Stage-specific follow-up assays and knockout fibroblasts indicated that SPIRE1 and SPIRE2 are involved in different steps of the S. Tm infection process. Whereas SPIRE1 interferes with bacterial binding, SPIRE2 influences intracellular replication of S. Tm. Hence, these two proteins might fulfill non-redundant functions in the pathogen-host interaction. The lack of co-localization hints to a short, direct interaction between S. Tm and SPIRE proteins or to an indirect effect.","authors":"Andritschke, D., Dilling, S., Emmenlauer, M., Welz, T., Schmich, F., Misselwitz, B., R\u00e4m\u00f6, P., Rottner, K., Kerkhoff, E., Wada, T., Penninger, JM., Beerenwinkel, N., Horvath, P., Dehio, C., Hardt, WD.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"PLoS One","volume":"11","issue":"9","page":"e0161965","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12656746","title":"Squamous cutaneous epithelial cell carcinoma in two CML patients with progressive disease under imatinib treatment.","abstract":"Imatinib (glivec), formerly known as STI571) effectively blocks the ATP-binding site of the bcr\/abl fusion protein thereby inactivating selectively the tyrosine kinase activity of bcr\/abl. Therefore, it is a promising drug in Philadelphia chromosome positive chronic myeloid leukemia showing high hematologic and cytogenetic response rates combined with a mild toxicity profile. Here we report two cases of squamous cell carcinoma of the skin, which appeared in the photo-exposed areas in two elderly patients treated for advanced chronic myeloid leukemia with imatinib. The role of chemotherapy, chronic sun exposure and of possible additional risk factors such as human papillomavirus infection is discussed.","authors":"Baskaynak, G., Kreuzer, KA., Schwarz, M., Zuber, J., Audring, H., Riess, H., D\u00f6rken, B., le Coutre, P.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Eur J Haematol","volume":"70","issue":"4","page":"231-4","pdf":null,"JrId":"3673","fulltextlink":null,"preprintlink":null,"articledate":"2003-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27591191","title":"Polo-like kinase phosphorylation determines Caenorhabditis elegans centrosome size and density by biasing SPD-5 toward an assembly-competent conformation.","abstract":"Centrosomes are major microtubule-organizing centers composed of centrioles surrounded by an extensive proteinacious layer called the pericentriolar material (PCM). In Caenorhabditis elegans embryos, the mitotic PCM expands by Polo-like kinase 1 (PLK-1) phosphorylation-accelerated assembly of SPD-5 molecules into supramolecular scaffolds. However, how PLK-1 phosphorylation regulates SPD-5 assembly is not known. We found that a mutant version of SPD-5 that is insensitive to PLK-1 phosphorylation (SPD-5<sup>4A<\/sup>) could localize to PCM but was unable to rescue the reduction in PCM size and density when wild-type SPD-5 levels were decreased. In vitro, purified SPD-5<sup>4A<\/sup> self-assembled into functional supramolecular scaffolds over long time scales, suggesting that phosphorylation only controls the rate of SPD-5 scaffold assembly. Furthermore, the SPD-5 scaffold, once assembled, remained intact and supported microtubule nucleation in the absence of PLK-1 activity in vivo We conclude that PLK-1 is required for rapid assembly of the PCM scaffold but not for scaffold maintenance or function. Based on this idea, we developed a theoretical model that adequately predicted PCM growth rates in different mutant conditions in vivo We propose that PLK-1 phosphorylation-dependent conversion of SPD-5 into an assembly-competent form underlies PCM formation in vivo and that the rate of this conversion determines final PCM size and density.","authors":"Wueseke, O., Zwicker, D., Schwager, A., Wong, YL., Oegema, K., J\u00fclicher, F., Hyman, AA., Woodruff, JB.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Biol Open","volume":"5","issue":"10","page":"1431-1440","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27575958","title":"Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation.","abstract":"Hox homeodomain transcription factors are key regulators of animal development. They specify the identity of segments along the anterior-posterior body axis in metazoans by controlling the expression of diverse downstream targets, including transcription factors and signaling pathway components. The Drosophila melanogaster Hox factor Ultrabithorax (Ubx) directs the development of thoracic and abdominal segments and appendages, and loss of Ubx function can lead for example to the transformation of third thoracic segment appendages (e.g. halters) into second thoracic segment appendages (e.g. wings), resulting in a characteristic four-wing phenotype. Here we present a Drosophila melanogaster strain with a V5-epitope tagged Ubx allele, which we employed to obtain a high quality genome-wide map of Ubx binding sites using ChIP-seq. We confirm the sensitivity of the V5 ChIP-seq by recovering 7\/8 of well-studied Ubx-dependent cis-regulatory regions. Moreover, we show that Ubx binding is predictive of enhancer activity as suggested by comparison with a genome-scale resource of in vivo tested enhancer candidates. We observed densely clustered Ubx binding sites at 12 extended genomic loci that included ANTP-C, BX-C, Polycomb complex genes, and other regulators and the clustered binding sites were frequently active enhancers. Furthermore, Ubx binding was detected at known Polycomb response elements (PREs) and was associated with significant enrichments of Pc and Pho ChIP signals in contrast to binding sites of other developmental TFs. Together, our results show that Ubx targets developmental regulators via strongly clustered binding sites and allow us to hypothesize that regulation by Ubx might involve Polycomb group proteins to maintain specific regulatory states in cooperative or mutually exclusive fashion, an attractive model that combines two groups of proteins with prominent gene regulatory roles during animal development.","authors":"Shlyueva, D., Meireles-Filho, AC., Pagani, M., Stark, A.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"PLoS One","volume":"11","issue":"8","page":"e0161997","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27549742","title":"Topology and structure of an engineered human cohesin complex bound to Pds5B.","abstract":"The cohesin subunits Smc1, Smc3 and Scc1 form large tripartite rings which mediate sister chromatid cohesion and chromatin structure. These are thought to entrap DNA with the help of the associated proteins SA1\/2 and Pds5A\/B. Structural information is available for parts of cohesin, but analyses of entire cohesin complexes are limited by their flexibility. Here we generated a more rigid 'bonsai' cohesin by truncating the coiled coils of Smc1 and Smc3 and used single-particle electron microscopy, chemical crosslinking-mass spectrometry and in silico modelling to generate three-dimensional models of cohesin bound to Pds5B. The HEAT-repeat protein Pds5B forms a curved structure around the nucleotide-binding domains of Smc1 and Smc3 and bridges the Smc3-Scc1 and SA1-Scc1 interfaces. These results indicate that Pds5B forms an integral part of the cohesin ring by contacting all other cohesin subunits, a property that may reflect the complex role of Pds5 proteins in controlling cohesin-DNA interactions.","authors":"Hons, MT., Huis In 't Veld, PJ., Kaesler, J., Rombaut, P., Schleiffer, A., Herzog, F., Stark, H., Peters, JM.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Nat Commun","volume":"7","issue":null,"page":"12523","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27461342","title":"Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">27461342<\/PMID><DateCompleted><Year>2017<\/Year><Month>10<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1479-7364<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>10 Suppl 2<\/Volume><PubDate><Year>2016<\/Year><Month>07<\/Month><Day>25<\/Day><\/PubDate><\/JournalIssue><Title>Human genomics<\/Title><ISOAbbreviation>Hum Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia.<\/ArticleTitle><Pagination><MedlinePgn>18<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s40246-016-0071-5<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Methylation changes are frequent in cancers, but understanding how hyper- and hypomethylated region changes coordinate, associate with genomic features, and affect gene expression is needed to better understand their biological significance. The functional significance of hypermethylation is well studied, but that of hypomethylation remains limited. Here, with paired expression and methylation samples gathered from a patient\/control cohort, we attempt to better characterize the gene expression and methylation changes that take place in cancer from B cell chronic lymphocyte leukemia (B-CLL) samples.","authors":"Kushwaha, G., Dozmorov, M., Wren, JD., Qiu, J., Shi, H., Xu, D.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Hum Genomics","volume":"10 Suppl 2","issue":"","page":"18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27434854","title":"Direct detection of a single photon by humans.","abstract":"Despite investigations for over 70 years, the absolute limits of human vision have remained unclear. Rod cells respond to individual photons, yet whether a single-photon incident on the eye can be perceived by a human subject has remained a fundamental open question. Here we report that humans can detect a single-photon incident on the cornea with a probability significantly above chance. This was achieved by implementing a combination of a psychophysics procedure with a quantum light source that can generate single-photon states of light. We further discover that the probability of reporting a single photon is modulated by the presence of an earlier photon, suggesting a priming process that temporarily enhances the effective gain of the visual system on the timescale of seconds.","authors":"Tinsley, JN., Molodtsov, MI., Prevedel, R., Wartmann, D., Espigul\u00e9-Pons, J., Lauwers, M., Vaziri, A.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Nat Commun","volume":"7","issue":null,"page":"12172","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27304859","title":"Dbl2 Regulates Rad51 and DNA Joint Molecule Metabolism to Ensure Proper Meiotic Chromosome Segregation.","abstract":"To identify new proteins required for faithful meiotic chromosome segregation, we screened a Schizosaccharomyces pombe deletion mutant library and found that deletion of the dbl2 gene led to missegregation of chromosomes during meiosis. Analyses of both live and fixed cells showed that dbl2\u0394 mutant cells frequently failed to segregate homologous chromosomes to opposite poles during meiosis I. Removing Rec12 (Spo11 homolog) to eliminate meiotic DNA double-strand breaks (DSBs) suppressed the segregation defect in dbl2\u0394 cells, indicating that Dbl2 acts after the initiation of meiotic recombination. Analyses of DSBs and Holliday junctions revealed no significant defect in their formation or processing in dbl2\u0394 mutant cells, although some Rec12-dependent DNA joint molecules persisted late in meiosis. Failure to segregate chromosomes in the absence of Dbl2 correlated with persistent Rad51 foci, and deletion of rad51 or genes encoding Rad51 mediators also suppressed the segregation defect of dbl2\u0394. Formation of foci of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments, was impaired in dbl2\u0394 cells. Our results suggest that Dbl2 is a novel regulator of Fbh1 and thereby Rad51-dependent DSB repair required for proper meiotic chromosome segregation and viable sex cell formation. The wide conservation of these proteins suggests that our results apply to many species.","authors":"Polakova, S., Molnarova, L., Hyppa, RW., Benko, Z., Misova, I., Schleiffer, A., Smith, GR., Gregan, J.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"PLoS Genet","volume":"12","issue":"6","page":"e1006102","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27280787","title":"A Combination of CRISPR\/Cas9 and Standardized RNAi as a Versatile Platform for the Characterization of Gene Function.","abstract":"Traditional loss-of-function studies in Drosophila suffer from a number of shortcomings, including off-target effects in the case of RNA interference (RNAi) or the stochastic nature of mosaic clonal analysis. Here, we describe minimal in vivo GFP interference (miGFPi) as a versatile strategy to characterize gene function and to conduct highly stringent, cell type-specific loss-of-function experiments in Drosophila miGFPi combines CRISPR\/Cas9-mediated tagging of genes at their endogenous locus with an immunotag and an exogenous 21 nucleotide RNAi effector sequence with the use of a single reagent, highly validated RNAi line targeting this sequence. We demonstrate the utility and time effectiveness of this method by characterizing the function of the Polymerase I (Pol I)-associated transcription factor Tif-1a, and the previously uncharacterized gene MESR4, in the Drosophila female germline stem cell lineage. In addition, we show that miGFPi serves as a powerful technique to functionally characterize individual isoforms of a gene. We exemplify this aspect of miGFPi by studying isoform-specific loss-of-function phenotypes of the longitudinals lacking (lola) gene in neural stem cells. Altogether, the miGFPi strategy constitutes a generalized loss-of-function approach that is amenable to the study of the function of all genes in the genome in a stringent and highly time effective manner.","authors":"Wissel, S., Kieser, A., Yasugi, T., Duchek, P., Roitinger, E., Gokcezade, J., Steinmann, V., Gaul, U., Mechtler, K., F\u00f6rstemann, K., Knoblich, JA., Neum\u00fcller, RA.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"G3 (Bethesda)","volume":"6","issue":"8","page":"2467-78","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27222228","title":"Regulation of two motor patterns enables the gradual adjustment of locomotion strategy in Caenorhabditis elegans.","abstract":"In animal locomotion a tradeoff exists between stereotypy and flexibility: fast long-distance travelling (LDT) requires coherent regular motions, while local sampling and area-restricted search (ARS) rely on flexible movements. We report here on a posture control system in C. elegans that coordinates these needs. Using quantitative posture analysis we explain worm locomotion as a composite of two modes: regular undulations versus flexible turning. Graded reciprocal regulation of both modes allows animals to flexibly adapt their locomotion strategy under sensory stimulation along a spectrum ranging from LDT to ARS. Using genetics and functional imaging of neural activity we characterize the counteracting interneurons AVK and DVA that utilize FLP-1 and NLP-12 neuropeptides to control both motor modes. Gradual regulation of behaviors via this system is required for spatial navigation during chemotaxis. This work shows how a nervous system controls simple elementary features of posture to generate complex movements for goal-directed locomotion strategies.","authors":"Hums, I., Riedl, J., Mende, F., Kato, S., Kaplan, HS., Latham, R., Sonntag, M., Traunm\u00fcller, L., Zimmer, M.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Elife","volume":"5","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27216465","title":"Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish.","abstract":"Upstream open reading frames (uORFs) are ubiquitous repressive genetic elements in vertebrate mRNAs. While much is known about the regulation of individual genes by their uORFs, the range of uORF-mediated translational repression in vertebrate genomes is largely unexplored. Moreover, it is unclear whether the repressive effects of uORFs are conserved across species. To address these questions, we analyse transcript sequences and ribosome profiling data from human, mouse and zebrafish. We find that uORFs are depleted near coding sequences (CDSes) and have initiation contexts that diminish their translation. Linear modelling reveals that sequence features at both uORFs and CDSes modulate the translation of CDSes. Moreover, the ratio of translation over 5' leaders and CDSes is conserved between human and mouse, and correlates with the number of uORFs. These observations suggest that the prevalence of vertebrate uORFs may be explained by their conserved role in repressing CDS translation.","authors":"Chew, GL., Pauli, A., Schier, AF.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Nat Commun","volume":"7","issue":null,"page":"11663","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27103580","title":"VirB8-like protein TraH is crucial for DNA transfer in Enterococcus faecalis.","abstract":"Untreatable bacterial infections caused by a perpetual increase of antibiotic resistant strains represent a serious threat to human healthcare in the 21(st) century. Conjugative DNA transfer is the most important mechanism for antibiotic resistance and virulence gene dissemination among bacteria and is mediated by a protein complex, known as type IV secretion system (T4SS). The core of the T4SS is a multiprotein complex that spans the bacterial envelope as a channel for macromolecular secretion. We report the NMR structure and functional characterization of the transfer protein TraH encoded by the conjugative Gram-positive broad-host range plasmid pIP501. The structure exhibits a striking similarity to VirB8 proteins of Gram-negative secretion systems where they play an essential role in the scaffold of the secretion machinery. Considering TraM as the first VirB8-like protein discovered in pIP501, TraH represents the second protein affiliated with this family in the respective transfer operon. A markerless traH deletion in pIP501 resulted in a total loss of transfer in Enterococcus faecalis as compared with the pIP501 wild type (wt) plasmid, demonstrating that TraH is essential for pIP501 mediated conjugation. Moreover, oligomerization state and topology of TraH in the native membrane were determined providing insights in molecular organization of a Gram-positive T4SS.","authors":"Fercher, C., Probst, I., Kohler, V., Goessweiner-Mohr, N., Arends, K., Grohmann, E., Zangger, K., Meyer, NH., Keller, W.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Sci Rep","volume":"6","issue":null,"page":"24643","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27070147","title":"Genetic Deletion of ACE2 Induces Vascular Dysfunction in C57BL\/6 Mice: Role of Nitric Oxide Imbalance and Oxidative Stress.","abstract":"Accumulating evidence indicates that angiotensin-converting enzyme 2 (ACE2) plays a critical role in cardiovascular homeostasis, and its altered expression is associated with major cardiac and vascular disorders. The aim of this study was to evaluate the regulation of vascular function and assess the vascular redox balance in ACE2-deficient (ACE2-\/y) animals. Experiments were performed in 20-22 week-old C57BL\/6 and ACE2-\/y male mice. Evaluation of endothelium-dependent and -independent relaxation revealed an impairment of in vitro and in vivo vascular function in ACE2-\/y mice. Drastic reduction in eNOS expression at both protein and mRNA levels, and a decrease in \u2022NO concentrations were observed in aortas of ACE2-\/y mice in comparison to controls. Consistently, these mice presented a lower plasma and urine nitrite concentration, confirming reduced \u2022NO availability in ACE2-deficient animals. Lipid peroxidation was significantly increased and superoxide dismutase activity was decreased in aorta homogenates of ACE2-\/y mice, indicating impaired antioxidant capacity. Taken together, our data indicate, that ACE2 regulates vascular function by modulating nitric oxide release and oxidative stress. In conclusion, we elucidate mechanisms by which ACE2 is involved in the maintenance of vascular homeostasis. Furthermore, these findings provide insights into the role of the renin-angiotensin system in both vascular and systemic redox balance.","authors":"Rabelo, LA., Todiras, M., Nunes-Souza, V., Qadri, F., Szij\u00e1rt\u00f3, IA., Gollasch, M., Penninger, JM., Bader, M., Santos, RA., Alenina, N.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"PLoS One","volume":"11","issue":"4","page":"e0150255","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27010503","title":"The GIY-YIG Type Endonuclease Ankyrin Repeat and LEM Domain-Containing Protein 1 (ANKLE1) Is Dispensable for Mouse Hematopoiesis.","abstract":"Ankyrin repeat and LEM-domain containing protein 1 (ANKLE1) is a GIY-YIG endonuclease with unknown functions, mainly expressed in mouse hematopoietic tissues. To test its potential role in hematopoiesis we generated Ankle1-deficient mice. Ankle1\u0394\/\u0394 mice are viable without any detectable phenotype in hematopoiesis. Neither hematopoietic progenitor cells, myeloid and lymphoid progenitors, nor B and T cell development in bone marrow, spleen and thymus, are affected in Ankle1\u0394\/\u0394-mice. Similarly embryonic stress erythropoiesis in liver and adult erythropoiesis in bone marrow and spleen appear normal. To test whether ANKLE1, like the only other known GIY-YIG endonuclease in mammals, SLX1, may contribute to Holliday junction resolution during DNA repair, Ankle1-deficient cells were exposed to various DNA-damage inducing agents. However, lack of Ankle1 did not affect cell viability and, unlike depletion of Slx1, Ankle1-deficiency did not increase sister chromatid exchange in Bloom helicase-depleted cells. Altogether, we show that lack of Ankle1 does neither affect mouse hematopoiesis nor DNA damage repair in mouse embryonic fibroblasts, indicating a redundant or non-essential function of ANKLE1 in mouse.","authors":"Braun, J., Meixner, A., Brachner, A., Foisner, R.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"PLoS One","volume":"11","issue":"3","page":"e0152278","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27001307","title":"Intercellular Communication between Keratinocytes and Fibroblasts Induces Local Osteoclast Differentiation: a Mechanism Underlying Cholesteatoma-Induced Bone Destruction.","abstract":"Bone homeostasis is maintained by a balance in activity between bone-resorbing osteoclasts and bone-forming osteoblasts. Shifting the balance toward bone resorption causes osteolytic bone diseases such as rheumatoid arthritis and periodontitis. Osteoclast differentiation is regulated by receptor activator of nuclear factor \u03baB ligand (RANKL), which, under some pathological conditions, is produced by T and B lymphocytes and synoviocytes. However, the mechanism underlying bone destruction in other diseases is little understood. Bone destruction caused by cholesteatoma, an epidermal cyst in the middle ear resulting from hyperproliferation of keratinizing squamous epithelium, can lead to lethal complications. In this study, we succeeded in generating a model for cholesteatoma, epidermal cyst-like tissue, which has the potential for inducing osteoclastogenesis in mice. Furthermore, an in vitro coculture system composed of keratinocytes, fibroblasts, and osteoclast precursors was used to demonstrate that keratinocytes stimulate osteoclast differentiation through the induction of RANKL in fibroblasts. Thus, this study demonstrates that intercellular communication between keratinocytes and fibroblasts is involved in the differentiation and function of osteoclasts, which may provide the molecular basis of a new therapeutic strategy for cholesteatoma-induced bone destruction.","authors":"Iwamoto, Y., Nishikawa, K., Imai, R., Furuya, M., Uenaka, M., Ohta, Y., Morihana, T., Itoi-Ochi, S., Penninger, JM., Katayama, I., Inohara, H., Ishii, M.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Mol Cell Biol","volume":"36","issue":"11","page":"1610-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26871722","title":"Intact Cohesion, Anaphase, and Chromosome Segregation in Human Cells Harboring Tumor-Derived Mutations in STAG2.","abstract":"Somatic mutations of the cohesin complex subunit STAG2 are present in diverse tumor types. We and others have shown that STAG2 inactivation can lead to loss of sister chromatid cohesion and alterations in chromosome copy number in experimental systems. However, studies of naturally occurring human tumors have demonstrated little, if any, correlation between STAG2 mutational status and aneuploidy, and have further shown that STAG2-deficient tumors are often euploid. In an effort to provide insight into these discrepancies, here we analyze the effect of tumor-derived STAG2 mutations on the protein composition of cohesin and the expected mitotic phenotypes of STAG2 mutation. We find that many mutant STAG2 proteins retain their ability to interact with cohesin; however, the presence of mutant STAG2 resulted in a reduction in the ability of regulatory subunits WAPL, PDS5A, and PDS5B to interact with the core cohesin ring. Using AAV-mediated gene targeting, we then introduced nine tumor-derived mutations into the endogenous allele of STAG2 in cultured human cells. While all nonsense mutations led to defects in sister chromatid cohesion and a subset induced anaphase defects, missense mutations behaved like wild-type in these assays. Furthermore, only one of nine tumor-derived mutations tested induced overt alterations in chromosome counts. These data indicate that not all tumor-derived STAG2 mutations confer defects in cohesion, chromosome segregation, and ploidy, suggesting that there are likely to be other functional effects of STAG2 inactivation in human cancer cells that are relevant to cancer pathogenesis.","authors":"Kim, JS., He, X., Orr, B., Wutz, G., Hill, V., Peters, JM., Compton, DA., Waldman, T.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"PLoS Genet","volume":"12","issue":"2","page":"e1005865","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26768888","title":"Semi-automated quantification of living cells with internalized nanostructures.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">26768888<\/PMID><DateCompleted><Year>2016<\/Year><Month>10<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1477-3155<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>14<\/Volume><PubDate><Year>2016<\/Year><Month>Jan<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Journal of nanobiotechnology<\/Title><ISOAbbreviation>J Nanobiotechnology<\/ISOAbbreviation><\/Journal><ArticleTitle>Semi-automated quantification of living cells with internalized nanostructures.<\/ArticleTitle><Pagination><MedlinePgn>4<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12951-015-0153-x<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Nanostructures fabricated by different methods have become increasingly important for various applications in biology and medicine, such as agents for medical imaging or cancer therapy. In order to understand their interaction with living cells and their internalization kinetics, several attempts have been made in tagging them. Although methods have been developed to measure the number of nanostructures internalized by the cells, there are only few approaches aimed to measure the number of cells that internalize the nanostructures, and they are usually limited to fixed-cell studies. Flow cytometry can be used for live-cell assays on large populations of cells, however it is a single time point measurement, and does not include any information about cell morphology. To date many of the observations made on internalization events are limited to few time points and cells.","authors":"Margineanu, MB., Julfakyan, K., Sommer, C., Perez, JE., Contreras, MF., Khashab, N., Kosel, J., Ravasi, T.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"J Nanobiotechnology","volume":"14","issue":"","page":"4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26673895","title":"A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning.","abstract":"CRM1 is a highly conserved, RanGTPase-driven exportin that carries proteins and RNPs from the nucleus to the cytoplasm. We now explored the cargo-spectrum of CRM1 in depth and identified surprisingly large numbers, namely &gt;700 export substrates from the yeast S. cerevisiae, \u22481000 from Xenopus oocytes and &gt;1050 from human cells. In addition, we quantified the partitioning of \u22485000 unique proteins between nucleus and cytoplasm of Xenopus oocytes. The data suggest new CRM1 functions in spatial control of vesicle coat-assembly, centrosomes, autophagy, peroxisome biogenesis, cytoskeleton, ribosome maturation, translation, mRNA degradation, and more generally in precluding a potentially detrimental action of cytoplasmic pathways within the nuclear interior. There are also numerous new instances where CRM1 appears to act in regulatory circuits. Altogether, our dataset allows unprecedented insights into the nucleocytoplasmic organisation of eukaryotic cells, into the contributions of an exceedingly promiscuous exportin and it provides a new basis for NES prediction.","authors":"K\u0131rl\u0131, K., Karaca, S., Dehne, HJ., Samwer, M., Pan, KT., Lenz, C., Urlaub, H., G\u00f6rlich, D.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Elife","volume":"4","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26647066","title":"Cellular dynamics underlying regeneration of appropriate segment number during axolotl tail regeneration.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">26647066<\/PMID><DateCompleted><Year>2016<\/Year><Month>08<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-213X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>15<\/Volume><PubDate><Year>2015<\/Year><Month>Dec<\/Month><Day>09<\/Day><\/PubDate><\/JournalIssue><Title>BMC developmental biology<\/Title><ISOAbbreviation>BMC Dev Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Cellular dynamics underlying regeneration of appropriate segment number during axolotl tail regeneration.<\/ArticleTitle><Pagination><MedlinePgn>48<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12861-015-0098-1<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Salamanders regenerate their tails after amputation anywhere along their length. How the system faithfully reconstitutes the original number of segments and length is not yet known.","authors":"Vincent, CD., Rost, F., Masselink, W., Brusch, L., Tanaka, EM.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"BMC Dev Biol","volume":"15","issue":null,"page":"48","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26588211","title":"Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals.","abstract":"The Piwi pathway is deeply conserved amongst animals because one of its essential functions is to repress transposons. However, many Piwi-interacting RNAs (piRNAs) do not base-pair to transposons and remain mysterious in their targeting function. The sheer number of piRNA cluster (piC) loci in animal genomes and infrequent piRNA sequence conservation also present challenges in determining which piC loci are most important for development. To address this question, we determined the piRNA expression patterns of piC loci across a wide phylogenetic spectrum of animals, and reveal that most genic and intergenic piC loci evolve rapidly in their capacity to generate piRNAs, regardless of known transposon silencing function. Surprisingly, we also uncovered a distinct set of piC loci with piRNA expression conserved deeply in Eutherian mammals. We name these loci Eutherian-Conserved piRNA cluster (ECpiC) loci. Supporting the hypothesis that conservation of piRNA expression across ~100 million years of Eutherian evolution implies function, we determined that one ECpiC locus generates abundant piRNAs antisense to the STOX1 transcript, a gene clinically associated with preeclampsia. Furthermore, we confirmed reduced piRNAs in existing mouse mutations at ECpiC-Asb1 and -Cbl, which also display spermatogenic defects. The Asb1 mutant testes with strongly reduced Asb1 piRNAs also exhibit up-regulated gene expression profiles. These data indicate ECpiC loci may be specially adapted to support Eutherian reproduction.","authors":"Chirn, GW., Rahman, R., Sytnikova, YA., Matts, JA., Zeng, M., Gerlach, D., Yu, M., Berger, B., Naramura, M., Kile, BT., Lau, NC.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"PLoS Genet","volume":"11","issue":"11","page":"e1005652","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26583753","title":"Burst muscle performance predicts the speed, acceleration, and turning performance of Anna's hummingbirds.","abstract":"Despite recent advances in the study of animal flight, the biomechanical determinants of maneuverability are poorly understood. It is thought that maneuverability may be influenced by intrinsic body mass and wing morphology, and by physiological muscle capacity, but this hypothesis has not yet been evaluated because it requires tracking a large number of free flight maneuvers from known individuals. We used an automated tracking system to record flight sequences from 20 Anna's hummingbirds flying solo and in competition in a large chamber. We found that burst muscle capacity predicted most performance metrics. Hummingbirds with higher burst capacity flew with faster velocities, accelerations, and rotations, and they used more demanding complex turns. In contrast, body mass did not predict variation in maneuvering performance, and wing morphology predicted only the use of arcing turns and high centripetal accelerations. Collectively, our results indicate that burst muscle capacity is a key predictor of maneuverability.","authors":"Segre, PS., Dakin, R., Zordan, VB., Dickinson, MH., Straw, AD., Altshuler, DL.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Elife","volume":"4","issue":null,"page":"e11159","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26568310","title":"Planar cell polarity-mediated induction of neural stem cell expansion during axolotl spinal cord regeneration.","abstract":"Axolotls are uniquely able to mobilize neural stem cells to regenerate all missing regions of the spinal cord. How a neural stem cell under homeostasis converts after injury to a highly regenerative cell remains unknown. Here, we show that during regeneration, axolotl neural stem cells repress neurogenic genes and reactivate a transcriptional program similar to embryonic neuroepithelial cells. This dedifferentiation includes the acquisition of rapid cell cycles, the switch from neurogenic to proliferative divisions, and the re-expression of planar cell polarity (PCP) pathway components. We show that PCP induction is essential to reorient mitotic spindles along the anterior-posterior axis of elongation, and orthogonal to the cell apical-basal axis. Disruption of this property results in premature neurogenesis and halts regeneration. Our findings reveal a key role for PCP in coordinating the morphogenesis of spinal cord outgrowth with the switch from a homeostatic to a regenerative stem cell that restores missing tissue.","authors":"Rodrigo Albors, A., Tazaki, A., Rost, F., Nowoshilow, S., Chara, O., Tanaka, EM.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Elife","volume":"4","issue":null,"page":"e10230","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26449415","title":"KCNJ15\/Kir4.2 couples with polyamines to sense weak extracellular electric fields in galvanotaxis.","abstract":"Weak electric fields guide cell migration, known as galvanotaxis\/electrotaxis. The sensor(s) cells use to detect the fields remain elusive. Here we perform a large-scale screen using an RNAi library targeting ion transporters in human cells. We identify 18 genes that show either defective or increased galvanotaxis after knockdown. Knockdown of the KCNJ15 gene (encoding inwardly rectifying K(+) channel Kir4.2) specifically abolishes galvanotaxis, without affecting basal motility and directional migration in a monolayer scratch assay. Depletion of cytoplasmic polyamines, highly positively charged small molecules that regulate Kir4.2 function, completely inhibits galvanotaxis, whereas increase of intracellular polyamines enhances galvanotaxis in a Kir4.2-dependent manner. Expression of a polyamine-binding defective mutant of KCNJ15 significantly decreases galvanotaxis. Knockdown or inhibition of KCNJ15 prevents phosphatidylinositol 3,4,5-triphosphate (PIP3) from distributing to the leading edge. Taken together these data suggest a previously unknown two-molecule sensing mechanism in which KCNJ15\/Kir4.2 couples with polyamines in sensing weak electric fields.","authors":"Nakajima, KI., Zhu, K., Sun, YH., Hegyi, B., Zeng, Q., Murphy, CJ., Small, JV., Chen-Izu, Y., Izumiya, Y., Penninger, JM., Zhao, M.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Nat Commun","volume":"6","issue":null,"page":"8532","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26436892","title":"Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish.","abstract":"Antisense oligonucleotides (ASOs) are synthetic, single-strand RNA-DNA hybrids that induce catalytic degradation of complementary cellular RNAs via RNase H. ASOs are widely used as gene knockdown reagents in tissue culture and in Xenopus and mouse model systems. To test their effectiveness in zebrafish, we targeted 20 developmental genes and compared the morphological changes with mutant and morpholino (MO)-induced phenotypes. ASO-mediated transcript knockdown reproduced the published loss-of-function phenotypes for oep, chordin, dnd, ctnnb2, bmp7a, alk8, smad2 and smad5 in a dosage-sensitive manner. ASOs knocked down both maternal and zygotic transcripts, as well as the long noncoding RNA (lncRNA) MALAT1. ASOs were only effective within a narrow concentration range and were toxic at higher concentrations. Despite this drawback, quantitation of knockdown efficiency and the ability to degrade lncRNAs make ASOs a useful knockdown reagent in zebrafish.","authors":"Pauli, A., Montague, TG., Lennox, KA., Behlke, MA., Schier, AF.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"PLoS One","volume":"10","issue":"10","page":"e0139504","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26423723","title":"SiR-Hoechst is a far-red DNA stain for live-cell nanoscopy.","abstract":"Cell-permeable DNA stains are popular markers in live-cell imaging. Currently used DNA stains for live-cell imaging are either toxic, require illumination with blue light or are not compatible with super-resolution microscopy, thereby limiting their utility. Here we describe a far-red DNA stain, SiR-Hoechst, which displays minimal toxicity, is applicable in different cell types and tissues, and is compatible with super-resolution microscopy. The combination of these properties makes this probe a powerful tool for live-cell imaging.","authors":"Lukinavi\u010dius, G., Blaukopf, C., Pershagen, E., Schena, A., Reymond, L., Derivery, E., Gonzalez-Gaitan, M., D'Este, E., Hell, SW., Wolfram Gerlich, D., Johnsson, K.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Nat Commun","volume":"6","issue":null,"page":"8497","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26355343","title":"Autophagy regulates hepatocyte identity and epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions promoting Snail degradation.","abstract":"Epithelial-to-mesenchymal transition (EMT) and the reverse process mesenchymal-to-epithelial transition (MET) are events involved in development, wound healing and stem cell behaviour and contribute pathologically to cancer progression. The identification of the molecular mechanisms underlying these phenotypic conversions in hepatocytes are fundamental to design specific therapeutic strategies aimed at optimising liver repair. The role of autophagy in EMT\/MET processes of hepatocytes was investigated in liver-specific autophagy-deficient mice (Alb-Cre;ATG7(fl\/fl)) and using the nontumorigenic immortalised hepatocytes cell line MMH. Autophagy deficiency in vivo reduces epithelial markers' expression and increases the levels of mesenchymal markers. These alterations are associated with an increased protein level of the EMT master regulator Snail, without transcriptional induction. Interestingly, we found that autophagy degrades Snail in a p62\/SQSTM1 (Sequestosome-1)-dependent manner. Moreover, accordingly to a pro-epithelial function, we observed that autophagy stimulation strongly affects EMT progression, whereas it is necessary for MET. Finally, we found that the EMT induced by TGF\u03b2 affects the autophagy flux, indicating that these processes regulate each other. Overall, we found that autophagy regulates the phenotype plasticity of hepatocytes promoting their epithelial identity through the inhibition of the mesenchymal programme.","authors":"Grassi, G., Di Caprio, G., Santangelo, L., Fimia, GM., Cozzolino, AM., Komatsu, M., Ippolito, G., Tripodi, M., Alonzi, T.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Cell Death Dis","volume":"6","issue":"","page":"e1880","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26327695","title":"Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome.","abstract":"Proteasomes are central regulators of protein homeostasis in eukaryotes. Proteasome function is vulnerable to environmental insults, cellular protein imbalance and targeted pharmaceuticals. Yet, mechanisms that cells deploy to counteract inhibition of this central regulator are little understood. To find such mechanisms, we reduced flux through the proteasome to the point of toxicity with specific inhibitors and performed genome-wide screens for mutations that allowed cells to survive. Counter to expectation, reducing expression of individual subunits of the proteasome's 19S regulatory complex increased survival. Strong 19S reduction was cytotoxic but modest reduction protected cells from inhibitors. Protection was accompanied by an increased ratio of 20S to 26S proteasomes, preservation of protein degradation capacity and reduced proteotoxic stress. While compromise of 19S function can have a fitness cost under basal conditions, it provided a powerful survival advantage when proteasome function was impaired. This means of rebalancing proteostasis is conserved from yeast to humans.","authors":"Tsvetkov, P., Mendillo, ML., Zhao, J., Carette, JE., Merrill, PH., Cikes, D., Varadarajan, M., van Diemen, FR., Penninger, JM., Goldberg, AL., Brummelkamp, TR., Santagata, S., Lindquist, S.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Elife","volume":"4","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22139419","title":"New gene functions in megakaryopoiesis and platelet formation.","abstract":"Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes controlling both traits. Here we carried out a high-powered meta-analysis of genome-wide association studies (GWAS) in up to 66,867 individuals of European ancestry, followed by extensive biological and functional assessment. We identified 68 genomic loci reliably associated with platelet count and volume mapping to established and putative novel regulators of megakaryopoiesis and platelet formation. These genes show megakaryocyte-specific gene expression patterns and extensive network connectivity. Using gene silencing in Danio rerio and Drosophila melanogaster, we identified 11 of the genes as novel regulators of blood cell formation. Taken together, our findings advance understanding of novel gene functions controlling fate-determining events during megakaryopoiesis and platelet formation, providing a new example of successful translation of GWAS to function.","authors":"Gieger, C., Radhakrishnan, A., Cvejic, A., Tang, W., Porcu, E., Pistis, G., Serbanovic-Canic, J., Elling, U., Goodall, AH., Labrune, Y., Lopez, LM., M\u00e4gi, R., Meacham, S., Okada, Y., Pirastu, N., Sorice, R., Teumer, A., Voss, K., Zhang, W., Ramirez-Solis, R., Bis, JC., Ellinghaus, D., G\u00f6gele, M., Hottenga, JJ., Langenberg, C., Kovacs, P., O'Reilly, PF., Shin, SY., Esko, T., Hartiala, J., Kanoni, S., Murgia, F., Parsa, A., Stephens, J., van der Harst, P., Ellen van der Schoot, C., Allayee, H., Attwood, A., Balkau, B., Bastardot, F., Basu, S., Baumeister, SE., Biino, G., Bomba, L., Bonnefond, A., Cambien, F., Chambers, JC., Cucca, F., D'Adamo, P., Davies, G., de Boer, RA., de Geus, EJ., D\u00f6ring, A., Elliott, P., Erdmann, J., Evans, DM., Falchi, M., Feng, W., Folsom, AR., Frazer, IH., Gibson, QD., Glazer, NL., Hammond, C., Hartikainen, AL., Heckbert, SR., Hengstenberg, C., Hersch, M., Illig, T., Loos, RJ., Jolley, J., Khaw, KT., K\u00fchnel, B., Kyrtsonis, MC., Lagou, V., Lloyd-Jones, H., Lumley, T., Mangino, M., Maschio, A., Mateo Leach, I., McKnight, B., Memari, Y., Mitchell, BD., Montgomery, GW., Nakamura, Y., Nauck, M., Navis, G., N\u00f6thlings, U., Nolte, IM., Porteous, DJ., Pouta, A., Pramstaller, PP., Pullat, J., Ring, SM., Rotter, JI., Ruggiero, D., Ruokonen, A., Sala, C., Samani, NJ., Sambrook, J., Schlessinger, D., Schreiber, S., Schunkert, H., Scott, J., Smith, NL., Snieder, H., Starr, JM., Stumvoll, M., Takahashi, A., Tang, WH., Taylor, K., Tenesa, A., Lay Thein, S., T\u00f6njes, A., Uda, M., Ulivi, S., van Veldhuisen, DJ., Visscher, PM., V\u00f6lker, U., Wichmann, HE., Wiggins, KL., Willemsen, G., Yang, TP., Hua Zhao, J., Zitting, P., Bradley, JR., Dedoussis, GV., Gasparini, P., Hazen, SL., Metspalu, A., Pirastu, M., Shuldiner, AR., Joost van Pelt, L., Zwaginga, JJ., Boomsma, DI., Deary, IJ., Franke, A., Froguel, P., Ganesh, SK., Jarvelin, MR., Martin, NG., Meisinger, C., Psaty, BM., Spector, TD., Wareham, NJ., Akkerman, JW., Ciullo, M., Deloukas, P., Greinacher, A., Jupe, S., Kamatani, N., Khadake, J., Kooner, JS., Penninger, J., Prokopenko, I., Stemple, D., Toniolo, D., Wernisch, L., Sanna, S., Hicks, AA., Rendon, A., Ferreira, MA., Ouwehand, WH., Soranzo, N.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nature","volume":"480","issue":"7376","page":"201-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26201077","title":"Chromosome Missegregation Associated with RUVBL1 Deficiency.","abstract":"RUVBL1 (RuvB-like1) and RUVBL2 (RuvB-like 2) are integral components of multisubunit protein complexes involved in processes ranging from cellular metabolism, transcription and chromatin remodeling to DNA repair. Here, we show that although RUVBL1 and RUVBL2 are known to form heterodimeric complexes in which they stabilize each other, the subunits separate during cytokinesis. In anaphase-to-telophase transition, RUVBL1 localizes to structures of the mitotic spindle apparatus, where it partially co-localizes with polo-like kinase 1 (PLK1). The ability of PLK1 to phosphorylate RUVBL1-but not RUVBL2-in vitro and their physical association in vivo suggest that this kinase differentially regulates the function of the RuvB-like proteins during mitosis. We further show that siRNA-mediated knock-down of RuvB-like proteins causes severe defects in chromosome alignment and segregation. In addition, we show that the ATPase activity of RUVBL1 is indispensable for cell proliferation. Our data thus demonstrate that RUVBL1 is essential for efficient mitosis and proliferation.","authors":"Gentili, C., Castor, D., Kaden, S., Lauterbach, D., Gysi, M., Steigemann, P., Gerlich, DW., Jiricny, J., Ferrari, S.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"PLoS One","volume":"10","issue":"7","page":"e0133576","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26182244","title":"Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers.","abstract":"Meiotic chromosomes are organized into linear looped chromatin arrays by a protein axis localized along the loop-bases. Programmed remodelling of the axis occurs during prophase I of meiosis. Structured illumination microscopy (SIM) has revealed dynamic changes in the chromosome axis in Arabidopsis thaliana and Brassica oleracea. We show that the axis associated protein ASY1 is depleted during zygotene concomitant with synaptonemal complex (SC) formation. Study of an Atpch2 mutant demonstrates this requires the conserved AAA+ ATPase, PCH2, which localizes to the sites of axis remodelling. Loss of PCH2 leads to a failure to deplete ASY1 from the axes and compromizes SC polymerisation. Immunolocalization of recombination proteins in Atpch2 indicates that recombination initiation and CO designation during early prophase I occur normally. Evidence suggests that CO interference is initially functional in the mutant but there is a defect in CO maturation following designation. This leads to a reduction in COs and a failure to form COs between some homologous chromosome pairs leading to univalent chromosomes at metaphase I. Genetic analysis reveals that CO distribution is also affected in some chromosome regions. Together these data indicate that the axis remodelling defect in Atpch2 disrupts normal patterned formation of COs.","authors":"Lambing, C., Osman, K., Nuntasoontorn, K., West, A., Higgins, JD., Copenhaver, GP., Yang, J., Armstrong, SJ., Mechtler, K., Roitinger, E., Franklin, FC.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"PLoS Genet","volume":"11","issue":"7","page":"e1005372","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25993311","title":"Casein Kinase 1 and Phosphorylation of Cohesin Subunit Rec11 (SA3) Promote Meiotic Recombination through Linear Element Formation.","abstract":"Proper meiotic chromosome segregation, essential for sexual reproduction, requires timely formation and removal of sister chromatid cohesion and crossing-over between homologs. Early in meiosis cohesins hold sisters together and also promote formation of DNA double-strand breaks, obligate precursors to crossovers. Later, cohesin cleavage allows chromosome segregation. We show that in fission yeast redundant casein kinase 1 homologs, Hhp1 and Hhp2, previously shown to regulate segregation via phosphorylation of the Rec8 cohesin subunit, are also required for high-level meiotic DNA breakage and recombination. Unexpectedly, these kinases also mediate phosphorylation of a different meiosis-specific cohesin subunit Rec11. This phosphorylation in turn leads to loading of linear element proteins Rec10 and Rec27, related to synaptonemal complex proteins of other species, and thereby promotes DNA breakage and recombination. Our results provide novel insights into the regulation of chromosomal features required for crossing-over and successful reproduction. The mammalian functional homolog of Rec11 (STAG3) is also phosphorylated during meiosis and appears to be required for fertility, indicating wide conservation of the meiotic events reported here.","authors":"Phadnis, N., Cipak, L., Polakova, S., Hyppa, RW., Cipakova, I., Anrather, D., Karvaiova, L., Mechtler, K., Smith, GR., Gregan, J.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"PLoS Genet","volume":"11","issue":"5","page":"e1005225","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25977730","title":"MicroRNA-375 plays a dual role in prostate carcinogenesis.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">25977730<\/PMID><DateCompleted><Year>2015<\/Year><Month>05<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Print\">1868-7075<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>7<\/Volume><PubDate><Year>2015<\/Year><\/PubDate><\/JournalIssue><Title>Clinical epigenetics<\/Title><ISOAbbreviation>Clin Epigenetics<\/ISOAbbreviation><\/Journal><ArticleTitle>MicroRNA-375 plays a dual role in prostate carcinogenesis.<\/ArticleTitle><Pagination><MedlinePgn>42<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13148-015-0076-2<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Prostate cancer (PCa), a highly incident and heterogeneous malignancy, mostly affects men from developed countries. Increased knowledge of the biological mechanisms underlying PCa onset and progression are critical for improved clinical management. MicroRNAs (miRNAs) deregulation is common in human cancers, and understanding how it impacts in PCa is of major importance. MiRNAs are mostly downregulated in cancer, although some are overexpressed, playing a critical role in tumor initiation and progression. We aimed to identify miRNAs overexpressed in PCa and subsequently determine its impact in tumorigenesis.","authors":"Costa-Pinheiro, P., Ramalho-Carvalho, J., Vieira, FQ., Torres-Ferreira, J., Oliveira, J., Gon\u00e7alves, CS., Costa, BM., Henrique, R., Jer\u00f3nimo, C.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Clin Epigenetics","volume":"7","issue":"","page":"42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25890286","title":"Cationic nanoparticles directly bind angiotensin-converting enzyme 2 and induce acute lung injury in mice.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">25890286<\/PMID><DateCompleted><Year>2016<\/Year><Month>01<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1743-8977<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>12<\/Volume><PubDate><Year>2015<\/Year><Month>Mar<\/Month><Day>07<\/Day><\/PubDate><\/JournalIssue><Title>Particle and fibre toxicology<\/Title><ISOAbbreviation>Part Fibre Toxicol<\/ISOAbbreviation><\/Journal><ArticleTitle>Cationic nanoparticles directly bind angiotensin-converting enzyme 2 and induce acute lung injury in mice.<\/ArticleTitle><Pagination><MedlinePgn>4<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12989-015-0080-x<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Nanoparticles have become a key technology in multiple industries. However, there are growing reports of the toxicity of nanomaterials to humans. In particular, nanomaterials have been linked to lung diseases. The molecular mechanisms of nanoparticle toxicity are largely unexplored.","authors":"Sun, Y., Guo, F., Zou, Z., Li, C., Hong, X., Zhao, Y., Wang, C., Wang, H., Liu, H., Yang, P., Han, Z., Liu, K., Kuba, K., Song, B., Gao, J., Mo, Z., Li, D., Li, B., Li, Q., Zhong, N., Wang, C., Penninger, JM., Jiang, C.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Part Fibre Toxicol","volume":"12","issue":"","page":"4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25851096","title":"Rio1 promotes rDNA stability and downregulates RNA polymerase I to ensure rDNA segregation.","abstract":"The conserved protein kinase Rio1 localizes to the cytoplasm and nucleus of eukaryotic cells. While the roles of Rio1 in the cytoplasm are well characterized, its nuclear function remains unknown. Here we show that nuclear Rio1 promotes rDNA array stability and segregation in Saccharomyces cerevisiae. During rDNA replication in S phase, Rio1 downregulates RNA polymerase I (PolI) and recruits the histone deacetylase Sir2. Both interventions ensure rDNA copy-number homeostasis and prevent the formation of extrachromosomal rDNA circles, which are linked to accelerated ageing in yeast. During anaphase, Rio1 downregulates PolI by targeting its subunit Rpa43, causing PolI to dissociate from the rDNA. By stimulating the processing of PolI-generated transcripts at the rDNA, Rio1 allows for rDNA condensation and segregation in late anaphase. These events finalize the genome transmission process. We identify Rio1 as an essential nucleolar housekeeper that integrates rDNA replication and segregation with ribosome biogenesis.","authors":"Iacovella, MG., Golfieri, C., Massari, LF., Busnelli, S., Pagliuca, C., Dal Maschio, M., Infantino, V., Visintin, R., Mechtler, K., Ferreira-Cerca, S., De Wulf, P.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Nat Commun","volume":"6","issue":null,"page":"6643","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25780729","title":"Optimizing and extending light-sculpting microscopy for fast functional imaging in neuroscience.","abstract":"A number of questions in system biology such as understanding how dynamics of neuronal networks are related to brain function require the ability to capture the functional dynamics of large cellular populations at high speed. Recently, this has driven the development of a number of parallel and high speed imaging techniques such as light-sculpting microscopy, which has been used to capture neuronal dynamics at the whole brain and single cell level in small model organisms. However, the broader applicability of light-sculpting microcopy is limited by the size of volumes for which high speed imaging can be obtained and scattering in brain tissue. Here, we present strategies for optimizing the present tradeoffs in light-sculpting microscopy. Various scanning modalities in light-sculpting microscopy are theoretically and experimentally evaluated, and strategies to maximize the obtainable volume speeds, and depth penetration in brain tissue using different laser systems are provided. Design-choices, important parameters and their trade-offs are experimentally demonstrated by performing calcium-imaging in acute mouse-brain slices. We further show that synchronization of line-scanning techniques with rolling-shutter read-out of the camera can reduce scattering effects and enhance image contrast at depth.","authors":"Rupprecht, P., Prevedel, R., Groessl, F., Haubensak, WE., Vaziri, A.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Biomed Opt Express","volume":"6","issue":"2","page":"353-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25734337","title":"Disruption of STAT3 signalling promotes KRAS-induced lung tumorigenesis.","abstract":"STAT3 is considered to play an oncogenic role in several malignancies including lung cancer; consequently, targeting STAT3 is currently proposed as therapeutic intervention. Here we demonstrate that STAT3 plays an unexpected tumour-suppressive role in KRAS mutant lung adenocarcinoma (AC). Indeed, lung tissue-specific inactivation of Stat3 in mice results in increased Kras(G12D)-driven AC initiation and malignant progression leading to markedly reduced survival. Knockdown of STAT3 in xenografted human AC cells increases tumour growth. Clinically, low STAT3 expression levels correlate with poor survival and advanced malignancy in human lung AC patients with smoking history, which are prone to KRAS mutations. Consistently, KRAS mutant lung tumours exhibit reduced STAT3 levels. Mechanistically, we demonstrate that STAT3 controls NF-\u03baB-induced IL-8 expression by sequestering NF-\u03baB within the cytoplasm, thereby inhibiting IL-8-mediated myeloid tumour infiltration and tumour vascularization and hence tumour progression. These results elucidate a novel STAT3-NF-\u03baB-IL-8 axis in KRAS mutant AC with therapeutic and prognostic relevance.","authors":"Grabner, B., Schramek, D., Mueller, KM., Moll, HP., Svinka, J., Hoffmann, T., Bauer, E., Blaas, L., Hruschka, N., Zboray, K., Stiedl, P., Nivarthi, H., Bogner, E., Gruber, W., Mohr, T., Zwick, RH., Kenner, L., Poli, V., Aberger, F., Stoiber, D., Egger, G., Esterbauer, H., Zuber, J., Moriggl, R., Eferl, R., Gy\u0151rffy, B., Penninger, JM., Popper, H., Casanova, E.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Nat Commun","volume":"6","issue":null,"page":"6285","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25628765","title":"Combining the differentiating effect of panobinostat with the apoptotic effect of arsenic trioxide leads to significant survival benefit in a model of t(8;21) acute myeloid leukemia.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">25628765<\/PMID><DateCompleted><Year>2015<\/Year><Month>01<\/Month><Day>28<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>11<\/Month><Day>19<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Print\">1868-7075<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>7<\/Volume><PubDate><Year>2015<\/Year><\/PubDate><\/JournalIssue><Title>Clinical epigenetics<\/Title><ISOAbbreviation>Clin Epigenetics<\/ISOAbbreviation><\/Journal><ArticleTitle>Combining the differentiating effect of panobinostat with the apoptotic effect of arsenic trioxide leads to significant survival benefit in a model of t(8;21) acute myeloid leukemia.<\/ArticleTitle><Pagination><MedlinePgn>2<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13148-014-0034-4<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">One of the most frequently found abnormalities in acute myeloid leukemia (AML) is the t(8;21)(q22;q22) translocation, which is seen in around 15% of patients. This translocation results in the production of the AML1\/ETO (A\/E) fusion protein and commonly involves cooperating activating mutations of RAS. AE9a encodes a C-terminally truncated A\/E protein of 575 amino acids that retains the ability to recruit histone deacetylases (HDACs). Expression of AE9a leads to rapid development of leukemia in experimental mouse systems. We have recently shown that treatment of mice bearing A\/E9a;Nras (G12D) tumors with the histone deacetylase inhibitor (HDACi) panobinostat leads to degradation of the A\/E9a fusion protein, cell cycle arrest, differentiation of AML blasts into mature granulocytes and prolonged survival. Herein, we sought to enhance this therapeutic effect.","authors":"Salmon, JM., Bots, M., Vidacs, E., Stanley, KL., Atadja, P., Zuber, J., Johnstone, RW.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Clin Epigenetics","volume":"7","issue":"","page":"2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25626168","title":"Non-catalytic motor domains enable processive movement and functional diversification of the kinesin-14 Kar3.","abstract":"Motor proteins of the conserved kinesin-14 family have important roles in mitotic spindle organization and chromosome segregation. Previous studies have indicated that kinesin-14 motors are non-processive enzymes, working in the context of multi-motor ensembles that collectively organize microtubule networks. In this study, we show that the yeast kinesin-14 Kar3 generates processive movement as a heterodimer with the non-motor proteins Cik1 or Vik1. By analyzing the single-molecule properties of engineered motors, we demonstrate that the non-catalytic domain has a key role in the motility mechanism by acting as a 'foothold' that allows Kar3 to bias translocation towards the minus end. This mechanism rivals the speed and run length of conventional motors, can support transport of the Ndc80 complex in vitro and is critical for Kar3 function in vivo. Our findings provide an example for a non-conventional translocation mechanism and can explain how Kar3 substitutes for key functions of Dynein in the yeast nucleus.","authors":"Mieck, C., Molodtsov, MI., Drzewicka, K., van der Vaart, B., Litos, G., Schmauss, G., Vaziri, A., Westermann, S.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Elife","volume":"4","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24800963","title":"Angiotensin II plasma levels are linked to disease severity and predict fatal outcomes in H7N9-infected patients.","abstract":"A novel influenza A (H7N9) virus of avian origin emerged in eastern China in the spring of 2013. This virus causes severe disease in humans, including acute and often lethal respiratory failure. As of January 2014, 275 cases of H7N9-infected patients had been reported, highlighting the urgency of identifying biomarkers for predicting disease severity and fatal outcomes. Here, we show that plasma levels of angiotensin II, a major regulatory peptide of the renin-angiotensin system, are markedly elevated in H7N9 patients and are associated with disease progression. Moreover, the sustained high levels of angiotensin II in these patients are strongly correlated with mortality. The predictive value of angiotensin II is higher than that of C-reactive protein and some clinical parameters such as the PaO2\/FiO2 ratio (partial pressure of arterial oxygen to the fraction of inspired oxygen). Our findings indicate that angiotensin II is a biomarker for lethality in flu infections.","authors":"Huang, F., Guo, J., Zou, Z., Liu, J., Cao, B., Zhang, S., Li, H., Wang, W., Sheng, M., Liu, S., Pan, J., Bao, C., Zeng, M., Xiao, H., Qian, G., Hu, X., Chen, Y., Chen, Y., Zhao, Y., Liu, Q., Zhou, H., Zhu, J., Gao, H., Yang, S., Liu, X., Zheng, S., Yang, J., Diao, H., Cao, H., Wu, Y., Zhao, M., Tan, S., Guo, D., Zhao, X., Ye, Y., Wu, W., Xu, Y., Penninger, JM., Li, D., Gao, GF., Jiang, C., Li, L.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Nat Commun","volume":"5","issue":null,"page":"3595","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25505873","title":"Neurogenesis in the embryonic and adult brain: same regulators, different roles.","abstract":"Neurogenesis persists in adult mammals in specific brain areas, known as neurogenic niches. Adult neurogenesis is highly dynamic and is modulated by multiple physiological stimuli and pathological states. There is a strong interest in understanding how this process is regulated, particularly since active neuronal production has been demonstrated in both the hippocampus and the subventricular zone (SVZ) of adult humans. The molecular mechanisms that control neurogenesis have been extensively studied during embryonic development. Therefore, we have a broad knowledge of the intrinsic factors and extracellular signaling pathways driving proliferation and differentiation of embryonic neural precursors. Many of these factors also play important roles during adult neurogenesis, but essential differences exist in the biological responses of neural precursors in the embryonic and adult contexts. Because adult neural stem cells (NSCs) are normally found in a quiescent state, regulatory pathways can affect adult neurogenesis in ways that have no clear counterpart during embryogenesis. BMP signaling, for instance, regulates NSC behavior both during embryonic and adult neurogenesis. However, this pathway maintains stem cell proliferation in the embryo, while it promotes quiescence to prevent stem cell exhaustion in the adult brain. In this review, we will compare and contrast the functions of transcription factors (TFs) and other regulatory molecules in the embryonic brain and in adult neurogenic regions of the adult brain in the mouse, with a special focus on the hippocampal niche and on the regulation of the balance between quiescence and activation of adult NSCs in this region.","authors":"Urb\u00e1n, N., Guillemot, F.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Front Cell Neurosci","volume":"8","issue":null,"page":"396","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25443631","title":"Sharpin prevents skin inflammation by inhibiting TNFR1-induced keratinocyte apoptosis.","abstract":"Linear Ubiquitin chain Assembly Complex (LUBAC) is an E3 ligase complex that generates linear ubiquitin chains and is important for tumour necrosis factor (TNF) signaling activation. Mice lacking Sharpin, a critical subunit of LUBAC, spontaneously develop inflammatory lesions in the skin and other organs. Here we show that TNF receptor 1 (TNFR1)-associated death domain (TRADD)-dependent TNFR1 signaling in epidermal keratinocytes drives skin inflammation in Sharpin-deficient mice. Epidermis-restricted ablation of Fas-associated protein with death domain (FADD) combined with receptor-interacting protein kinase 3 (RIPK3) deficiency fully prevented skin inflammation, while single RIPK3 deficiency only delayed and partly ameliorated lesion development in Sharpin-deficient mice, showing that inflammation is primarily driven by TRADD- and FADD-dependent keratinocyte apoptosis while necroptosis plays a minor role. At the cellular level, Sharpin deficiency sensitized primary murine keratinocytes, human keratinocytes, and mouse embryonic fibroblasts to TNF-induced apoptosis. Depletion of FADD or TRADD in Sharpin-deficient HaCaT cells suppressed TNF-induced apoptosis, indicating the importance of FADD and TRADD in Sharpin-dependent anti-apoptosis signaling in keratinocytes.","authors":"Kumari, S., Redouane, Y., Lopez-Mosqueda, J., Shiraishi, R., Romanowska, M., Lutzmayer, S., Kuiper, J., Martinez, C., Dikic, I., Pasparakis, M., Ikeda, F.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Elife","volume":"3","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25391767","title":"Angiotensin-converting enzyme 2 (ACE2) mediates influenza H7N9 virus-induced acute lung injury.","abstract":"Since March 2013, the emergence of an avian-origin influenza A (H7N9) virus has raised concern in China. Although most infections resulted in respiratory illness, some severe cases resulted in acute respiratory distress syndrome (ARDS), which is a severe form of acute lung injury (ALI) that further contributes to morbidity. To date, no effective drugs that improve the clinical outcome of influenza A (H7N9) virus-infected patients have been identified. Angiotensin-converting enzyme (ACE) and ACE2 are involved in several pathologies such as cardiovascular functions, renal disease, and acute lung injury. In the current study, we report that ACE2 could mediate the severe acute lung injury induced by influenza A (H7N9) virus infection in an experimental mouse model. Moreover, ACE2 deficiency worsened the disease pathogenesis markedly, mainly by targeting the angiotensin II type 1 receptor (AT1). The current findings demonstrate that ACE2 plays a critical role in influenza A (H7N9) virus-induced acute lung injury, and suggest that might be a useful potential therapeutic target for future influenza A (H7N9) outbreaks.","authors":"Yang, P., Gu, H., Zhao, Z., Wang, W., Cao, B., Lai, C., Yang, X., Zhang, L., Duan, Y., Zhang, S., Chen, W., Zhen, W., Cai, M., Penninger, JM., Jiang, C., Wang, X.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Sci Rep","volume":"4","issue":null,"page":"7027","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25369922","title":"Versatile in vitro system to study translocation and functional integration of bacterial outer membrane proteins.","abstract":"Gram-negative bacteria use the type-V secretion pathway to expose proteins at their cell surface, many of which have virulence functions. Translocation of those proteins across the outer membrane occurs either by means of dedicated translocator proteins (two-partner secretion) or covalently fused translocator domains (autotransporters). Translocator proteins and translocator domains are \u03b2-barrels requiring the \u03b2-barrel assembly machinery (BAM) for membrane integration. However, the molecular details of their passage across the envelope and insertion into the outer membrane remain enigmatic, owing in part to the fact that in vitro systems are not available. Here we describe a versatile in vitro reconstitution system that faithfully reproduces both branches of the type-V secretion pathway and the assembly of \u03b2-barrel outer membrane proteins. This system will allow an in-depth analysis of protein secretion across and integration into outer membranes.","authors":"Norell, D., Heuck, A., Tran-Thi, TA., G\u00f6tzke, H., Jacob-Dubuisson, F., Clausen, T., Daley, DO., Braun, V., M\u00fcller, M., Fan, E.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Nat Commun","volume":"5","issue":null,"page":"5396","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25236734","title":"Efficient CRISPR\/Cas9 plasmids for rapid and versatile genome editing in Drosophila.","abstract":"The CRISPR-associated RNA-guided nuclease Cas9 has emerged as a powerful tool for genome engineering in a variety of organisms. To achieve efficient gene targeting rates in Drosophila, current approaches require either injection of in vitro transcribed RNAs or injection into transgenic Cas9-expressing embryos. We report a simple and versatile alternative method for CRISPR-mediated genome editing in Drosophila using bicistronic Cas9\/sgRNA expression vectors. Gene targeting with this single-plasmid injection approach is as efficient as in transgenic nanos-Cas9 embryos and allows the isolation of targeted knock-out and knock-in alleles by molecular screening within 2 months. Our strategy is independent of genetic background and does not require prior establishment of transgenic flies.","authors":"Gokcezade, J., Sienski, G., Duchek, P.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"G3 (Bethesda)","volume":"4","issue":"11","page":"2279-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25103259","title":"Characterization of a mouse model with complete RPE loss and its use for RPE cell transplantation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">25103259<\/PMID><DateCompleted><Year>2014<\/Year><Month>10<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2014<\/Year><Month>08<\/Month><Day>29<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1552-5783<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>55<\/Volume><Issue>8<\/Issue><PubDate><Year>2014<\/Year><Month>Aug<\/Month><Day>07<\/Day><\/PubDate><\/JournalIssue><Title>Investigative ophthalmology &amp; visual science<\/Title><ISOAbbreviation>Invest Ophthalmol Vis Sci<\/ISOAbbreviation><\/Journal><ArticleTitle>Characterization of a mouse model with complete RPE loss and its use for RPE cell transplantation.<\/ArticleTitle><Pagination><MedlinePgn>5431-44<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1167\/iovs.14-14325<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE\" NlmCategory=\"OBJECTIVE\">Age-related macular degeneration (AMD) is a major leading cause of visual impairment and blindness with no cure currently established. Cell replacement of RPE is discussed as a potential therapy for AMD. Previous studies were performed in animal models with severe limitations in recapitulating the disease progression. In detail, we describe the effect of systemic injection of sodium iodate in the mouse retina. We further evaluate the usefulness of this animal model to analyze cell-specific effects following transplantation of human embryonic stem cell (hESC)-derived RPE cells.","authors":"Carido, M., Zhu, Y., Postel, K., Benkner, B., Cimalla, P., Karl, MO., Kurth, T., Paquet-Durand, F., Koch, E., M\u00fcnch, TA., Tanaka, EM., Ader, M.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Invest Ophthalmol Vis Sci","volume":"55","issue":"8","page":"5431-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24988319","title":"Reversible suppression of cyclooxygenase 2 (COX-2) expression in vivo by inducible RNA interference.","abstract":"Prostaglandin-endoperoxide synthase 2 (PTGS2), also known as cyclooxygenase 2 (COX-2), plays a critical role in many normal physiological functions and modulates a variety of pathological conditions. The ability to turn endogenous COX-2 on and off in a reversible fashion, at specific times and in specific cell types, would be a powerful tool in determining its role in many contexts. To achieve this goal, we took advantage of a recently developed RNA interference system in mice. An shRNA targeting the Cox2 mRNA 3'untranslated region was inserted into a microRNA expression cassette, under the control of a tetracycline response element (TRE) promoter. Transgenic mice containing the COX-2-shRNA were crossed with mice encoding a CAG promoter-driven reverse tetracycline transactivator, which activates the TRE promoter in the presence of tetracycline\/doxycycline. To facilitate testing the system, we generated a knockin reporter mouse in which the firefly luciferase gene replaces the Cox2 coding region. Cox2 promoter activation in cultured cells from triple transgenic mice containing the luciferase allele, the shRNA and the transactivator transgene resulted in robust luciferase and COX-2 expression that was reversibly down-regulated by doxycycline administration. In vivo, using a skin inflammation-model, both luciferase and COX-2 expression were inhibited over 80% in mice that received doxycycline in their diet, leading to a significant reduction of infiltrating leukocytes. In summary, using inducible RNA interference to target COX-2 expression, we demonstrate potent, reversible Cox2 gene silencing in vivo. This system should provide a valuable tool to analyze cell type-specific roles for COX-2.","authors":"Zaiss, AK., Zuber, J., Chu, C., Machado, HB., Jiao, J., Catapang, AB., Ishikawa, TO., Gil, JS., Lowe, SW., Herschman, HR.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"PLoS One","volume":"9","issue":"7","page":"e101263","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24890513","title":"Epigenetic control of immunity.","abstract":"Immunity relies on the heterogeneity of immune cells and their ability to respond to pathogen challenges. In the adaptive immune system, lymphocytes display a highly diverse antigen receptor repertoire that matches the vast diversity of pathogens. In the innate immune system, the cell's heterogeneity and phenotypic plasticity enable flexible responses to changes in tissue homeostasis caused by infection or damage. The immune responses are calibrated by the graded activity of immune cells that can vary from yeast-like proliferation to lifetime dormancy. This article describes key epigenetic processes that contribute to the function of immune cells during health and disease.","authors":"Busslinger, M., Tarakhovsky, A.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Cold Spring Harb Perspect Biol","volume":"6","issue":"6","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24873830","title":"Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs.","abstract":"The CRISPR\/Cas9 system has been implemented in a variety of model organisms to mediate site-directed mutagenesis. A wide range of mutation rates has been reported, but at a limited number of genomic target sites. To uncover the rules that govern effective Cas9-mediated mutagenesis in zebrafish, we targeted over a hundred genomic loci for mutagenesis using a streamlined and cloning-free method. We generated mutations in 85% of target genes with mutation rates varying across several orders of magnitude, and identified sequence composition rules that influence mutagenesis. We increased rates of mutagenesis by implementing several novel approaches. The activities of poor or unsuccessful single-guide RNAs (sgRNAs) initiating with a 5' adenine were improved by rescuing 5' end homogeneity of the sgRNA. In some cases, direct injection of Cas9 protein\/sgRNA complex further increased mutagenic activity. We also observed that low diversity of mutant alleles led to repeated failure to obtain frame-shift mutations. This limitation was overcome by knock-in of a stop codon cassette that ensured coding frame truncation. Our improved methods and detailed protocols make Cas9-mediated mutagenesis an attractive approach for labs of all sizes.","authors":"Gagnon, JA., Valen, E., Thyme, SB., Huang, P., Akhmetova, L., Ahkmetova, L., Pauli, A., Montague, TG., Zimmerman, S., Richter, C., Schier, AF.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"PLoS One","volume":"9","issue":"5","page":"e98186","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24804774","title":"A regulatory transcriptional loop controls proliferation and differentiation in Drosophila neural stem cells.","abstract":"Neurogenesis is initiated by a set of basic Helix-Loop-Helix (bHLH) transcription factors that specify neural progenitors and allow them to generate neurons in multiple rounds of asymmetric cell division. The Drosophila Daughterless (Da) protein and its mammalian counterparts (E12\/E47) act as heterodimerization factors for proneural genes and are therefore critically required for neurogenesis. Here, we demonstrate that Da can also be an inhibitor of the neural progenitor fate whose absence leads to stem cell overproliferation and tumor formation. We explain this paradox by demonstrating that Da induces the differentiation factor Prospero (Pros) whose asymmetric segregation is essential for differentiation in one of the two daughter cells. Da co-operates with the bHLH transcription factor Asense, whereas the other proneural genes are dispensible. After mitosis, Pros terminates Asense expression in one of the two daughter cells. In da mutants, pros is not expressed, leading to the formation of lethal transplantable brain tumors. Our results define a transcriptional feedback loop that regulates the balance between self-renewal and differentiation in Drosophila optic lobe neuroblasts. They indicate that initiation of a neural differentiation program in stem cells is essential to prevent tumorigenesis.","authors":"Yasugi, T., Fischer, A., Jiang, Y., Reichert, H., Knoblich, JA.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"PLoS One","volume":"9","issue":"5","page":"e97034","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24800825","title":"Angiotensin-converting enzyme 2 protects from lethal avian influenza A H5N1 infections.","abstract":"The potential for avian influenza H5N1 outbreaks has increased in recent years. Thus, it is paramount to develop novel strategies to alleviate death rates. Here we show that avian influenza A H5N1-infected patients exhibit markedly increased serum levels of angiotensin II. High serum levels of angiotensin II appear to be linked to the severity and lethality of infection, at least in some patients. In experimental mouse models, infection with highly pathogenic avian influenza A H5N1 virus results in downregulation of angiotensin-converting enzyme 2 (ACE2) expression in the lung and increased serum angiotensin II levels. Genetic inactivation of ACE2 causes severe lung injury in H5N1-challenged mice, confirming a role of ACE2 in H5N1-induced lung pathologies. Administration of recombinant human ACE2 ameliorates avian influenza H5N1 virus-induced lung injury in mice. Our data link H5N1 virus-induced acute lung failure to ACE2 and provide a potential treatment strategy to address future flu pandemics.","authors":"Zou, Z., Yan, Y., Shu, Y., Gao, R., Sun, Y., Li, X., Ju, X., Liang, Z., Liu, Q., Zhao, Y., Guo, F., Bai, T., Han, Z., Zhu, J., Zhou, H., Huang, F., Li, C., Lu, H., Li, N., Li, D., Jin, N., Penninger, JM., Jiang, C.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Nat Commun","volume":"5","issue":null,"page":"3594","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24632752","title":"MTSS1 is a metastasis driver in a subset of human melanomas.","abstract":"In cancers with a highly altered genome, distinct genetic alterations drive subsets rather than the majority of individual tumours. Here we use a sequential search across human tumour samples for transcript outlier data points with associated gene copy number variations that correlate with patient's survival to identify genes with pro-invasive functionality. Employing loss and gain of function approaches in vitro and in vivo, we show that one such gene, MTSS1, promotes the ability of melanocytic cells to metastasize and engages actin dynamics via Rho-GTPases and cofilin in this process. Indeed, high MTSS1 expression defines a subgroup of primary melanomas with unfavourable prognosis. These data underscore the biological, clinical and potential therapeutic implications of molecular subsets within genetically complex cancers.","authors":"Mertz, KD., Pathria, G., Wagner, C., Saarikangas, J., Sboner, A., Romanov, J., Gschaider, M., Lenz, F., Neumann, F., Schreiner, W., Nemethova, M., Glassmann, A., Lappalainen, P., Stingl, G., Small, JV., Fink, D., Chin, L., Wagner, SN.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Nat Commun","volume":"5","issue":null,"page":"3465","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24614889","title":"HACE1-dependent protein degradation provides cardiac protection in response to haemodynamic stress.","abstract":"The HECT E3 ubiquitin ligase HACE1 is a tumour suppressor known to regulate Rac1 activity under stress conditions. HACE1 is increased in the serum of patients with heart failure. Here we show that HACE1 protects the heart under pressure stress by controlling protein degradation. Hace1 deficiency in mice results in accelerated heart failure and increased mortality under haemodynamic stress. Hearts from Hace1(-\/-) mice display abnormal cardiac hypertrophy, left ventricular dysfunction, accumulation of LC3, p62 and ubiquitinated proteins enriched for cytoskeletal species, indicating impaired autophagy. Our data suggest that HACE1 mediates p62-dependent selective autophagic turnover of ubiquitinated proteins by its ankyrin repeat domain through protein-protein interaction, which is independent of its E3 ligase activity. This would classify HACE1 as a dual-function E3 ligase. Our finding that HACE1 has a protective function in the heart in response to haemodynamic stress suggests that HACE1 may be a potential diagnostic and therapeutic target for heart disease.","authors":"Zhang, L., Chen, X., Sharma, P., Moon, M., Sheftel, AD., Dawood, F., Nghiem, MP., Wu, J., Li, RK., Gramolini, AO., Sorensen, PH., Penninger, JM., Brumell, JH., Liu, PP.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Nat Commun","volume":"5","issue":null,"page":"3430","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24586900","title":"Human adipose tissue-derived stromal\/stem cells promote migration and early metastasis of triple negative breast cancer xenografts.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24586900<\/PMID><DateCompleted><Year>2014<\/Year><Month>11<\/Month><Day>04<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><Issue>2<\/Issue><PubDate><Year>2014<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Human adipose tissue-derived stromal\/stem cells promote migration and early metastasis of triple negative breast cancer xenografts.<\/ArticleTitle><Pagination><MedlinePgn>e89595<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0089595<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Fat grafting is used to restore breast defects after surgical resection of breast tumors. Supplementing fat grafts with adipose tissue-derived stromal\/stem cells (ASCs) is proposed to improve the regenerative\/restorative ability of the graft and retention. However, long term safety for ASC grafting in proximity of residual breast cancer cells is unknown. The objective of this study was to determine the impact of human ASCs derived from abdominal lipoaspirates of three donors, on a human breast cancer model that exhibits early metastasis.","authors":"Rowan, BG., Gimble, JM., Sheng, M., Anbalagan, M., Jones, RK., Frazier, TP., Asher, M., Lacayo, EA., Friedlander, PL., Kutner, R., Chiu, ES.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"PLoS One","volume":"9","issue":"2","page":"e89595","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24510288","title":"Retroviral gene expression control in primary organoid cultures.","abstract":"In this unit, we describe a protocol for regulated gene expression in primary endodermal organoid culture using retroviral vectors. The study of gene function in endodermal epithelia such as those lining the stomach, small intestine, and colon has so far mainly relied on the generation of transgenic mouse lines. Establishing such animal models is laborious, expensive, and time-consuming. Ever-expanding endodermal organoids, grown in an in vitro 3-D epithelial culture system, faithfully recapitulate the in vivo counterpart and represent a sustainable alternative. Gene overexpression and knockdown can be achieved in organoids by retroviral transduction. The technique can also be applied to organoids derived from pre-established mutant mouse lines or used in combination with chemical and biological inhibitors or activators. This method provides a novel, versatile tool for phenotypic analysis of endodermal epithelium in vitro.","authors":"Koo, BK., Sasselli, V., Clevers, H.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"Curr Protoc Stem Cell Biol","volume":"27","issue":null,"page":"Unit 5A.6.","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24296171","title":"Epigenetics of ciliates.","abstract":"Research using ciliates revealed early examples of epigenetic phenomena and continues to provide novel findings. These protozoans maintain separate germline and somatic nuclei that carry transcriptionally silent and active genomes, respectively. Examining the differences in chromatin within distinct nuclei of Tetrahymena identified histone variants and established that transcriptional regulators act by modifying histones. Formation of somatic nuclei requires both transcriptional activation of silent chromatin and large-scale DNA elimination. This somatic genome remodeling is directed by homologous RNAs, acting with an RNA interference (RNAi)-related machinery. Furthermore, the content of the parental somatic genome provides a homologous template to guide this genome restructuring. The mechanisms regulating ciliate DNA rearrangements reveal the surprising power of homologous RNAs to remodel the genome and transmit information transgenerationally.","authors":"Chalker, DL., Meyer, E., Mochizuki, K.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"Cold Spring Harb Perspect Biol","volume":"5","issue":"12","page":"a017764","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24289286","title":"Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24289286<\/PMID><DateCompleted><Year>2015<\/Year><Month>05<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>14<\/Volume><Issue>11<\/Issue><PubDate><Year>2013<\/Year><Month>Nov<\/Month><Day>30<\/Day><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation.<\/ArticleTitle><Pagination><MedlinePgn>r133<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/gb-2013-14-11-r133<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Genome-wide transcriptome analyses have given systems-level insights into gene regulatory networks. Due to the limited depth of quantitative proteomics, however, our understanding of post-transcriptional gene regulation and its effects on protein-complex stoichiometry are lagging behind.","authors":"J\u00fcschke, C., Dohnal, I., Pichler, P., Harzer, H., Swart, R., Ammerer, G., Mechtler, K., Knoblich, JA.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"Genome Biol","volume":"14","issue":"11","page":"r133","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24260257","title":"Long-term live cell imaging and automated 4D analysis of drosophila neuroblast lineages.","abstract":"The developing Drosophila brain is a well-studied model system for neurogenesis and stem cell biology. In the Drosophila central brain, around 200 neural stem cells called neuroblasts undergo repeated rounds of asymmetric cell division. These divisions typically generate a larger self-renewing neuroblast and a smaller ganglion mother cell that undergoes one terminal division to create two differentiating neurons. Although single mitotic divisions of neuroblasts can easily be imaged in real time, the lack of long term imaging procedures has limited the use of neuroblast live imaging for lineage analysis. Here we describe a method that allows live imaging of cultured Drosophila neuroblasts over multiple cell cycles for up to 24 hours. We describe a 4D image analysis protocol that can be used to extract cell cycle times and growth rates from the resulting movies in an automated manner. We use it to perform lineage analysis in type II neuroblasts where clonal analysis has indicated the presence of a transit-amplifying population that potentiates the number of neurons. Indeed, our experiments verify type II lineages and provide quantitative parameters for all cell types in those lineages. As defects in type II neuroblast lineages can result in brain tumor formation, our lineage analysis method will allow more detailed and quantitative analysis of tumorigenesis and asymmetric cell division in the Drosophila brain.","authors":"Homem, CC., Reichardt, I., Berger, C., Lendl, T., Knoblich, JA.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"PLoS One","volume":"8","issue":"11","page":"e79588","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24148528","title":"Genetic control of renal tumorigenesis by the mouse Rtm1 locus.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24148528<\/PMID><DateCompleted><Year>2014<\/Year><Month>12<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>14<\/Volume><PubDate><Year>2013<\/Year><Month>Oct<\/Month><Day>22<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Genetic control of renal tumorigenesis by the mouse Rtm1 locus.<\/ArticleTitle><Pagination><MedlinePgn>724<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-14-724<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The genetic basis of susceptibility to renal tumorigenesis has not yet been established in mouse strains. Mouse lines derived by bidirectional phenotypic selection on the basis of their maximal (AIRmax) or minimal (AIRmin) acute inflammatory responsiveness differ widely in susceptibility to spontaneous and urethane-induced renal tumorigenesis. To map the functional loci modulating renal tumor susceptibility in these mice, we carried out a genome-wide genetic linkage study, using SNP arrays, in an (AIRmax x AIRmin)F2 intercross population treated with a single urethane dose at 1 week of age and phenotyped for renal tumors at 35 weeks of age.","authors":"Jensen, JR., Galvan, A., Borrego, A., Cabrera, WH., Ribeiro, OG., Starobinas, N., De Franco, M., Colecchia, M., Bertolotti, A., Dragani, TA., Iba\u00f1ez, OC.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"BMC Genomics","volume":"14","issue":"","page":"724","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24090483","title":"Quantitative trait loci analysis reveals candidate genes implicated in regulating functional deficit and CNS vascular permeability in CD8 T cell-initiated blood-brain barrier disruption.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24090483<\/PMID><DateCompleted><Year>2014<\/Year><Month>06<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>14<\/Volume><PubDate><Year>2013<\/Year><Month>Oct<\/Month><Day>03<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Quantitative trait loci analysis reveals candidate genes implicated in regulating functional deficit and CNS vascular permeability in CD8 T cell-initiated blood-brain barrier disruption.<\/ArticleTitle><Pagination><MedlinePgn>678<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-14-678<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Blood-brain barrier (BBB) disruption is an integral feature of numerous neurological disorders. However, there is a relative lack of knowledge regarding the underlying molecular mechanisms of immune-mediated BBB disruption. We have previously shown that CD8 T cells and perforin play critical roles in initiating altered permeability of the BBB in the peptide-induced fatal syndrome (PIFS) model developed by our laboratory. Additionally, despite having indistinguishable CD8 T cell responses, C57BL\/6J (B6) mice are highly susceptible to PIFS, exhibiting functional motor deficits, increased astrocyte activation, and severe CNS vascular permeability, while 129S1\/SvImJ (129S1) mice remain resistant. Therefore, to investigate the potential role of genetic factors, we performed a comprehensive genetic analysis of (B6 x 129S1) F2 progeny to define quantitative trait loci (QTL) linked to the phenotypic characteristics stated above that mediate CD8 T cell-initiated BBB disruption.","authors":"Johnson, HL., Hanson, LM., Chen, Y., Bieber, AJ., Buono, RJ., Ferraro, TN., Pirko, I., Johnson, AJ.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"BMC Genomics","volume":"14","issue":"","page":"678","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24086725","title":"Analysis of transduction efficiency, tropism and axonal transport of AAV serotypes 1, 2, 5, 6, 8 and 9 in the mouse brain.","abstract":"Recombinant Adeno-associated virus vectors (rAAV) are widely used for gene delivery and multiple naturally occurring serotypes have been harnessed to target cells in different tissues and organs including the brain. Here, we provide a detailed and quantitative analysis of the transduction profiles of rAAV vectors based on six of the most commonly used serotypes (AAV1, AAV2, AAV5, AAV6, AAV8, AAV9) that allows systematic comparison and selection of the optimal vector for a specific application. In our studies we observed marked differences among serotypes in the efficiency to transduce three different brain regions namely the striatum, hippocampus and neocortex of the mouse. Despite the fact that the analyzed serotypes have the general ability to transduce all major cell types in the brain (neurons, microglia, astrocytes and oligodendrocytes), the expression level of a reporter gene driven from a ubiquitous promoter varies significantly for specific cell type \/ serotype combinations. For example, rAAV8 is particularly efficient to drive transgene expression in astrocytes while rAAV9 appears well suited for the transduction of cortical neurons. Interestingly, we demonstrate selective retrograde transport of rAAV5 along axons projecting from the ventral part of the entorhinal cortex to the dentate gyrus. Furthermore, we show that self-complementing rAAV can be used to significantly decrease the time required for the onset of transgene expression in the mouse brain.","authors":"Aschauer, DF., Kreuz, S., Rumpel, S.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"PLoS One","volume":"8","issue":"9","page":"e76310","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28065321","title":"Studying cytokinesis in Drosophila epithelial tissues.","abstract":"Epithelial tissue cohesiveness is ensured through cell-cell junctions that maintain both adhesion and mechanical coupling between neighboring cells. During development, epithelial tissues undergo intensive cell proliferation. Cell division, and particularly cytokinesis, is coupled to the formation of new adhesive contacts, thereby preserving tissue integrity and propagating cell polarity. Remarkably, the geometry of the new interfaces is determined by the combined action of the dividing cell and its neighbors. To further understand the interplay between the dividing cell and its neighbors, as well as the role of cell division for tissue morphogenesis, it is important to analyze cytokinesis in vivo. Here we present methods to perform live imaging of cell division in Drosophila epithelial tissues and discuss some aspects of image processing and analysis.","authors":"Pinheiro, D., Bella\u00efche, Y.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Methods Cell Biol","volume":"137","issue":null,"page":"73-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24067190","title":"Cardiac protective effects of irbesartan via the PPAR-gamma signaling pathway in angiotensin-converting enzyme 2-deficient mice.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24067190<\/PMID><DateCompleted><Year>2014<\/Year><Month>07<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1479-5876<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>11<\/Volume><PubDate><Year>2013<\/Year><Month>Sep<\/Month><Day>25<\/Day><\/PubDate><\/JournalIssue><Title>Journal of translational medicine<\/Title><ISOAbbreviation>J Transl Med<\/ISOAbbreviation><\/Journal><ArticleTitle>Cardiac protective effects of irbesartan via the PPAR-gamma signaling pathway in angiotensin-converting enzyme 2-deficient mice.<\/ArticleTitle><Pagination><MedlinePgn>229<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1479-5876-11-229<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Angiotensin-converting enzyme 2 (ACE2), a monocarboxypeptidase which metabolizes angiotensin II (Ang II) to generate Ang-(1-7), has been shown to prevent cardiac hypertrophy and injury but the mechanism remains elusive. Irbesartan has the dual actions of angiotensin receptor blockade and peroxisome proliferator-activated receptor-\u03b3 (PPAR\u03b3) activation. We hypothesized that irbesartan would exert its protective effects on ACE2 deficiency-mediated myocardial fibrosis and cardiac injury via the PPAR\u03b3 signaling.","authors":"Zhang, ZZ., Shang, QH., Jin, HY., Song, B., Oudit, GY., Lu, L., Zhou, T., Xu, YL., Gao, PJ., Zhu, DL., Penninger, JM., Zhong, JC.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"J Transl Med","volume":"11","issue":"","page":"229","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23817469","title":"Loss of Apelin exacerbates myocardial infarction adverse remodeling and ischemia-reperfusion injury: therapeutic potential of synthetic Apelin analogues.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23817469<\/PMID><DateCompleted><Year>2014<\/Year><Month>05<\/Month><Day>02<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">2047-9980<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>2<\/Volume><Issue>4<\/Issue><PubDate><Year>2013<\/Year><Month>Jul<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Journal of the American Heart Association<\/Title><ISOAbbreviation>J Am Heart Assoc<\/ISOAbbreviation><\/Journal><ArticleTitle>Loss of Apelin exacerbates myocardial infarction adverse remodeling and ischemia-reperfusion injury: therapeutic potential of synthetic Apelin analogues.<\/ArticleTitle><Pagination><MedlinePgn>e000249<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/JAHA.113.000249<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Coronary artery disease leading to myocardial ischemia is the most common cause of heart failure. Apelin (APLN), the endogenous peptide ligand of the APJ receptor, has emerged as a novel regulator of the cardiovascular system.","authors":"Wang, W., McKinnie, SM., Patel, VB., Haddad, G., Wang, Z., Zhabyeyev, P., Das, SK., Basu, R., McLean, B., Kandalam, V., Penninger, JM., Kassiri, Z., Vederas, JC., Murray, AG., Oudit, GY.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"J Am Heart Assoc","volume":"2","issue":"4","page":"e000249","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23762309","title":"The role of the e3 ligase cbl-B in murine dendritic cells.","abstract":"Dendritic cells (DCs) are potent antigen-presenting cells with a promising potential in cancer immunotherapy. Cbl proteins are E3 ubiquitin ligases and have been implicated in regulating the functional activity of various immune cells. As an example, c-Cbl negatively affects DC activation. We here describe that another member of the Cbl-protein family (i.e. Cbl-b) is highly expressed in murine bone-marrow-derived DCs (BMDCs). Differentiation of cblb-\/- bone marrow mononuclear cells into classical BMDCs is unaltered, except enhanced induction of DEC-205 (CD205) expression. When tested in mixed-lymphocyte reaction (MLR), cblb-\/- BMDCs exhibit increased allo-stimulatory capacity in vitro. BMDCs were next in vitro stimulated by various toll like receptor (TLR)-agonists (LPS, Poly(I:C), CpG) and exposed to FITC-labeled dextran. Upon TLR-stimulation, cblb-\/- BMDCs produce higher levels of proinflammatory cytokines (IL-1\u03b1, IL-6 and TNF-\u03b1) and exhibit a slightly higher level of FITC-dextran uptake. To further characterize the functional significance of cblb-\/- BMDCs we tested them in antigen-specific T cell responses against ovalbumin (OVA) protein and peptides, activating either CD8(+) OT-I or CD4(+) OT-II transgenic T cells. However, cblb-\/- BMDCs are equally effective in inducing antigen-specific T cell responses when compared to wildtype BMDCs both in vitro and in vivo. The migratory capacity into lymph nodes during inflammation was similarly not affected by the absence of Cbl-b. In line with these observations, cblb-\/- peptide-pulsed BMDCs are equally effective vaccines against OVA-expressing B16 tumors in vivo when compared to wildtype BMDCs. We conclude that in contrast to c-Cbl, Cbl-b plays only a limited role in the induction of Ag-specific T cell responses by murine BMDCs in vitro and in vivo.","authors":"Wallner, S., Lutz-Nicoladoni, C., Tripp, CH., Gastl, G., Baier, G., Penninger, JM., Stoitzner, P., Wolf, D.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"PLoS One","volume":"8","issue":"6","page":"e65178","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23758845","title":"Linking cytoarchitecture to metabolism: sarcolemma-associated plectin affects glucose uptake by destabilizing microtubule networks in mdx myofibers.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23758845<\/PMID><DateCompleted><Year>2013<\/Year><Month>07<\/Month><Day>02<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Print\">2044-5040<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>3<\/Volume><Issue>1<\/Issue><PubDate><Year>2013<\/Year><Month>Jun<\/Month><Day>12<\/Day><\/PubDate><\/JournalIssue><Title>Skeletal muscle<\/Title><ISOAbbreviation>Skelet Muscle<\/ISOAbbreviation><\/Journal><ArticleTitle>Linking cytoarchitecture to metabolism: sarcolemma-associated plectin affects glucose uptake by destabilizing microtubule networks in mdx myofibers.<\/ArticleTitle><Pagination><MedlinePgn>14<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/2044-5040-3-14<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Duchenne muscular dystrophy (DMD) is one of the most frequent forms of muscular disorders. It is caused by the absence of dystrophin, a core component of the sarcolemma-associated junctional complex that links the cytoskeleton to the extracellular matrix. We showed previously that plectin 1f (P1f), one of the major muscle-expressed isoforms of the cytoskeletal linker protein plectin, accumulates at the sarcolemma of DMD patients as well as of mdx mice, a widely studied animal model for DMD.Based on plectin's dual role as structural protein and scaffolding platform for signaling molecules, we speculated that the dystrophic phenotype observed after loss of dystrophin was caused, at least to some extent, by excess plectin. Thus, we hypothesized that elimination of plectin expression in mdx skeletal muscle, while probably resulting in an overall more severe phenotype, may lead to a partial phenotype rescue. In particular, we wanted to assess whether excess sarcolemmal plectin contributes to the dysregulation of sugar metabolism in mdx myofibers.","authors":"Raith, M., Valencia, RG., Fischer, I., Orthofer, M., Penninger, JM., Spuler, S., Rezniczek, GA., Wiche, G.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"Skelet Muscle","volume":"3","issue":"1","page":"14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23043155","title":"Sister chromatid cohesion.","abstract":"During S phase, not only does DNA have to be replicated, but also newly synthesized DNA molecules have to be connected with each other. This sister chromatid cohesion is essential for the biorientation of chromosomes on the mitotic or meiotic spindle, and is thus an essential prerequisite for chromosome segregation. Cohesion is mediated by cohesin complexes that are thought to embrace sister chromatids as large rings. Cohesin binds to DNA dynamically before DNA replication and is converted into a stably DNA-bound form during replication. This conversion requires acetylation of cohesin, which in vertebrates leads to recruitment of sororin. Sororin antagonizes Wapl, a protein that is able to release cohesin from DNA, presumably by opening the cohesin ring. Inhibition of Wapl by sororin therefore \"locks\" cohesin rings on DNA and allows them to maintain cohesion for long periods of time in mammalian oocytes, possibly for months or even years.","authors":"Peters, JM., Nishiyama, T.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Cold Spring Harb Perspect Biol","volume":"4","issue":"11","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23758785","title":"ATR-FTIR spectroscopy reveals genomic loci regulating the tissue response in high fat diet fed BXD recombinant inbred mouse strains.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23758785<\/PMID><DateCompleted><Year>2013<\/Year><Month>10<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>14<\/Volume><PubDate><Year>2013<\/Year><Month>Jun<\/Month><Day>10<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>ATR-FTIR spectroscopy reveals genomic loci regulating the tissue response in high fat diet fed BXD recombinant inbred mouse strains.<\/ArticleTitle><Pagination><MedlinePgn>386<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-14-386<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Obesity-associated organ-specific pathological states can be ensued from the dysregulation of the functions of the adipose tissues, liver and muscle. However, the influence of genetic differences underlying gross-compositional differences in these tissues is largely unknown. In the present study, the analytical method of ATR-FTIR spectroscopy has been combined with a genetic approach to identify genetic differences responsible for phenotypic alterations in adipose, liver and muscle tissues.","authors":"Dogan, A., Lasch, P., Neuschl, C., Millrose, MK., Alberts, R., Schughart, K., Naumann, D., Brockmann, GA.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"BMC Genomics","volume":"14","issue":"","page":"386","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23723983","title":"Spatial distribution of prominin-1 (CD133)-positive cells within germinative zones of the vertebrate brain.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23723983<\/PMID><DateCompleted><Year>2014<\/Year><Month>02<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic-Print\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>8<\/Volume><Issue>5<\/Issue><PubDate><Year>2013<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Spatial distribution of prominin-1 (CD133)-positive cells within germinative zones of the vertebrate brain.<\/ArticleTitle><Pagination><MedlinePgn>e63457<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0063457<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">In mammals, embryonic neural progenitors as well as adult neural stem cells can be prospectively isolated based on the cell surface expression of prominin-1 (CD133), a plasma membrane glycoprotein. In contrast, characterization of neural progenitors in non-mammalian vertebrates endowed with significant constitutive neurogenesis and inherent self-repair ability is hampered by the lack of suitable cell surface markers. Here, we have investigated whether prominin-1-orthologues of the major non-mammalian vertebrate model organisms show any degree of conservation as for their association with neurogenic geminative zones within the central nervous system (CNS) as they do in mammals or associated with activated neural progenitors during provoked neurogenesis in the regenerating CNS.","authors":"J\u00e1szai, J., Graupner, S., Tanaka, EM., Funk, RH., Huttner, WB., Brand, M., Corbeil, D.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"PLoS One","volume":"8","issue":"5","page":"e63457","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23658691","title":"Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program.","abstract":"Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression - early wound healing followed by a transition-phase leading to establishment of the limb development program, which correspond to the three phases of limb regeneration that had been defined by morphological criteria. By focusing on the transition-phase, we identified 93 strictly amputation-associated genes many of which are implicated in oxidative-stress response, chromatin modification, epithelial development or limb development. We further classified the genes based on whether they were or were not significantly expressed in the developing limb bud. The specific localization of 53 selected candidates within the blastema was investigated by in situ hybridization. In summary, we identified a set of genes that are expressed specifically during regeneration and are therefore, likely candidates for the regulation of blastema formation.","authors":"Knapp, D., Schulz, H., Rascon, CA., Volkmer, M., Scholz, J., Nacu, E., Le, M., Novozhilov, S., Tazaki, A., Protze, S., Jacob, T., Hubner, N., Habermann, B., Tanaka, EM.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"PLoS One","volume":"8","issue":"5","page":"e61352","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23641815","title":"Foamy virus for efficient gene transfer in regeneration studies.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23641815<\/PMID><DateCompleted><Year>2013<\/Year><Month>10<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-213X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>13<\/Volume><PubDate><Year>2013<\/Year><Month>May<\/Month><Day>03<\/Day><\/PubDate><\/JournalIssue><Title>BMC developmental biology<\/Title><ISOAbbreviation>BMC Dev Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Foamy virus for efficient gene transfer in regeneration studies.<\/ArticleTitle><Pagination><MedlinePgn>17<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-213X-13-17<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Molecular studies of appendage regeneration have been hindered by the lack of a stable and efficient means of transferring exogenous genes. We therefore sought an efficient integrating virus system that could be used to study limb and tail regeneration in salamanders.","authors":"Khattak, S., Sandoval-Guzm\u00e1n, T., Stanke, N., Protze, S., Tanaka, EM., Lindemann, D.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"BMC Dev Biol","volume":"13","issue":null,"page":"17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23626779","title":"Transgenic mouse models enabling photolabeling of individual neurons in vivo.","abstract":"One of the biggest tasks in neuroscience is to explain activity patterns of individual neurons during behavior by their cellular characteristics and their connectivity within the neuronal network. To greatly facilitate linking in vivo experiments with a more detailed molecular or physiological analysis in vitro, we have generated and characterized genetically modified mice expressing photoactivatable GFP (PA-GFP) that allow conditional photolabeling of individual neurons. Repeated photolabeling at the soma reveals basic morphological features due to diffusion of activated PA-GFP into the dendrites. Neurons photolabeled in vivo can be re-identified in acute brain slices and targeted for electrophysiological recordings. We demonstrate the advantages of PA-GFP expressing mice by the correlation of in vivo firing rates of individual neurons with their expression levels of the immediate early gene c-fos. Generally, the mouse models described in this study enable the combination of various analytical approaches to characterize living cells, also beyond the neurosciences.","authors":"Peter, M., Bathellier, B., Fontinha, B., Pliota, P., Haubensak, W., Rumpel, S.","publication_status":"epublish","journalpubyear":"2013","journaltitle":"PLoS One","volume":"8","issue":"4","page":"e62132","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22935085","title":"SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT\/t driven mice breast cancer.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22935085<\/PMID><DateCompleted><Year>2013<\/Year><Month>07<\/Month><Day>22<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2407<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>12<\/Volume><PubDate><Year>2012<\/Year><Month>Aug<\/Month><Day>31<\/Day><\/PubDate><\/JournalIssue><Title>BMC cancer<\/Title><ISOAbbreviation>BMC Cancer<\/ISOAbbreviation><\/Journal><ArticleTitle>SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT\/t driven mice breast cancer.<\/ArticleTitle><Pagination><MedlinePgn>380<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2407-12-380<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Tumor development is known to be a stepwise process involving dynamic changes that affect cellular integrity and cellular behavior. This complex interaction between genomic organization and gene, as well as protein expression is not yet fully understood. Tumor characterization by gene expression analyses is not sufficient, since expression levels are only available as a snapshot of the cell status. So far, research has mainly focused on gene expression profiling or alterations in oncogenes, even though DNA microarray platforms would allow for high-throughput analyses of copy number alterations (CNAs).","authors":"Standfuss, C., Pospisil, H., Klein, A.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"BMC Cancer","volume":"12","issue":"","page":"380","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22837003","title":"ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation.","abstract":"Malnutrition affects up to one billion people in the world and is a major cause of mortality. In many cases, malnutrition is associated with diarrhoea and intestinal inflammation, further contributing to morbidity and death. The mechanisms by which unbalanced dietary nutrients affect intestinal homeostasis are largely unknown. Here we report that deficiency in murine angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 (Ace2), which encodes a key regulatory enzyme of the renin-angiotensin system (RAS), results in highly increased susceptibility to intestinal inflammation induced by epithelial damage. The RAS is known to be involved in acute lung failure, cardiovascular functions and SARS infections. Mechanistically, ACE2 has a RAS-independent function, regulating intestinal amino acid homeostasis, expression of antimicrobial peptides, and the ecology of the gut microbiome. Transplantation of the altered microbiota from Ace2 mutant mice into germ-free wild-type hosts was able to transmit the increased propensity to develop severe colitis. ACE2-dependent changes in epithelial immunity and the gut microbiota can be directly regulated by the dietary amino acid tryptophan. Our results identify ACE2 as a key regulator of dietary amino acid homeostasis, innate immunity, gut microbial ecology, and transmissible susceptibility to colitis. These results provide a molecular explanation for how amino acid malnutrition can cause intestinal inflammation and diarrhoea.","authors":"Hashimoto, T., Perlot, T., Rehman, A., Trichereau, J., Ishiguro, H., Paolino, M., Sigl, V., Hanada, T., Hanada, R., Lipinski, S., Wild, B., Camargo, SM., Singer, D., Richter, A., Kuba, K., Fukamizu, A., Schreiber, S., Clevers, H., Verrey, F., Rosenstiel, P., Penninger, JM.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nature","volume":"487","issue":"7408","page":"477-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22797726","title":"The Blk pathway functions as a tumor suppressor in chronic myeloid leukemia stem cells.","abstract":"A therapeutic strategy for treating cancer is to target and eradicate cancer stem cells (CSCs) without harming their normal stem cell counterparts. The success of this approach relies on the identification of molecular pathways that selectively regulate CSC function. Using BCR-ABL-induced chronic myeloid leukemia (CML) as a disease model for CSCs, we show that BCR-ABL downregulates the Blk gene (encoding B-lymphoid kinase) through c-Myc in leukemic stem cells (LSCs) in CML mice and that Blk functions as a tumor suppressor in LSCs but does not affect normal hematopoietic stem cells (HSCs) or hematopoiesis. Blk suppresses LSC function through a pathway involving an upstream regulator, Pax5, and a downstream effector, p27. Inhibition of this Blk pathway accelerates CML development, whereas increased activity of the Blk pathway delays CML development. Blk also suppresses the proliferation of human CML stem cells. Our results show the feasibility of selectively targeting LSCs, an approach that should be applicable to other cancers.","authors":"Zhang, H., Peng, C., Hu, Y., Li, H., Sheng, Z., Chen, Y., Sullivan, C., Cerny, J., Hutchinson, L., Higgins, A., Miron, P., Zhang, X., Brehm, MA., Li, D., Green, MR., Li, S.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nat Genet","volume":"44","issue":"8","page":"861-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22740833","title":"Astrocytes as a source for extracellular matrix molecules and cytokines.","abstract":"Research of the past 25\u2009years has shown that astrocytes do more than participating and building up the blood-brain barrier and detoxify the active synapse by reuptake of neurotransmitters and ions. Indeed, astrocytes express neurotransmitter receptors and, as a consequence, respond to stimuli. Within the tripartite synapse, the astrocytes owe more and more importance. Besides the functional aspects the differentiation of astrocytes has gained a more intensive focus. Deeper knowledge of the differentiation processes during development of the central nervous system might help explaining and even help treating neurological diseases like Alzheimer's disease, Amyotrophic lateral sclerosis, Parkinsons disease, and psychiatric disorders in which astrocytes have been shown to play a role. Specific differentiation of neural stem cells toward the astroglial lineage is performed as a multi-step process. Astrocytes and oligodendrocytes develop from a multipotent stem cell that prior to this has produced primarily neuronal precursor cells. This switch toward the more astroglial differentiation is regulated by a change in receptor composition on the cell surface and responsiveness to Fibroblast growth factor and Epidermal growth factor (EGF). The glial precursor cell is driven into the astroglial direction by signaling molecules like Ciliary neurotrophic factor, Bone Morphogenetic Proteins, and EGF. However, the early astrocytes influence their environment not only by releasing and responding to diverse soluble factors but also express a wide range of extracellular matrix (ECM) molecules, in particular proteoglycans of the lectican family and tenascins. Lately these ECM molecules have been shown to participate in glial development. In this regard, especially the matrix protein Tenascin C (Tnc) proved to be an important regulator of astrocyte precursor cell proliferation and migration during spinal cord development. Nevertheless, ECM molecules expressed by reactive astrocytes are also known to act mostly in an inhibitory fashion under pathophysiological conditions. Thus, we further summarize resent data concerning the role of chondroitin sulfate proteoglycans and Tnc under pathological conditions.","authors":"Wiese, S., Karus, M., Faissner, A.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Front Pharmacol","volume":"3","issue":"","page":"120","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23102583","title":"Deciphering the transcriptional cis-regulatory code.","abstract":"Information about developmental gene expression resides in defined regulatory elements, called enhancers, in the non-coding part of the genome. Although cells reliably utilize enhancers to orchestrate gene expression, a cis-regulatory code that would allow their interpretation has remained one of the greatest challenges of modern biology. In this review, we summarize studies from the past three decades that describe progress towards revealing the properties of enhancers and discuss how recent approaches are providing unprecedented insights into regulatory elements in animal genomes. Over the next years, we believe that the functional characterization of regulatory sequences in entire genomes, combined with recent computational methods, will provide a comprehensive view of genomic regulatory elements and their building blocks and will enable researchers to begin to understand the sequence basis of the cis-regulatory code.","authors":"Y\u00e1\u00f1ez-Cuna, JO., Kvon, EZ., Stark, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Trends Genet","volume":"29","issue":"1","page":"11-22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22721355","title":"Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22721355<\/PMID><DateCompleted><Year>2013<\/Year><Month>04<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>13<\/Volume><PubDate><Year>2012<\/Year><Month>Jun<\/Month><Day>21<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice.<\/ArticleTitle><Pagination><MedlinePgn>264<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-13-264<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">MicroRNAs (miRNAs) modulate gene expression in different tissues and at diverse developmental stages, including grain development in japonica rice. To identify novel miRNAs in indica rice and to study their expression patterns during the entire grain filling process, small RNAs from all stages of grain development were sequenced and their expression patterns were studied using customized miRNA chips.","authors":"Lan, Y., Su, N., Shen, Y., Zhang, R., Wu, F., Cheng, Z., Wang, J., Zhang, X., Guo, X., Lei, C., Wang, J., Jiang, L., Mao, L., Wan, J.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"BMC Genomics","volume":"13","issue":"","page":"264","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22692129","title":"The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers.","abstract":"Two types of stem cells are currently defined in small intestinal crypts: cycling crypt base columnar (CBC) cells and quiescent '+4' cells. Here, we combine transcriptomics with proteomics to define a definitive molecular signature for Lgr5(+) CBC cells. Transcriptional profiling of FACS-sorted Lgr5(+) stem cells and their daughters using two microarray platforms revealed an mRNA stem cell signature of 384 unique genes. Quantitative mass spectrometry on the same cell populations identified 278 proteins enriched in intestinal stem cells. The mRNA and protein data sets showed a high level of correlation and a combined signature of 510 stem cell-enriched genes was defined. Spatial expression patterns were further characterized by mRNA in-situ hybridization, revealing that approximately half of the genes were expressed in a gradient with highest levels at the crypt bottom, while the other half was expressed uniquely in Lgr5(+)stem cells. Lineage tracing using a newly established knock-in mouse for one of the signature genes, Smoc2, confirmed its stem cell specificity. Using this resource, we find-and confirm by independent approaches-that the proposed quiescent\/'+4' stem cell markers Bmi1, Tert, Hopx and Lrig1 are robustly expressed in CBC cells.","authors":"Mu\u00f1oz, J., Stange, DE., Schepers, AG., van de Wetering, M., Koo, BK., Itzkovitz, S., Volckmann, R., Kung, KS., Koster, J., Radulescu, S., Myant, K., Versteeg, R., Sansom, OJ., van Es, JH., Barker, N., van Oudenaarden, A., Mohammed, S., Heck, AJ., Clevers, H.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"EMBO J","volume":"31","issue":"14","page":"3079-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22679446","title":"Dynamic evolution of toll-like receptor multigene families in echinoderms.","abstract":"The genome sequence of the purple sea urchin, Strongylocentrotus purpuratus, a large and long-lived invertebrate, provides a new perspective on animal immunity. Analysis of this genome uncovered a highly complex immune system in which the gene families that encode homologs of the pattern recognition receptors that form the core of vertebrate innate immunity are encoded in large multigene families. The sea urchin genome contains 253 Toll-like receptor (TLR) sequences, more than 200 Nod-like receptors and 1095 scavenger receptor cysteine-rich domains, a 10-fold expansion relative to vertebrates. Given their stereotypic protein structure and simple intron-exon architecture, the TLRs are the most tractable of these families for more detailed analysis. A role for these receptors in immune defense is suggested by their similarity to TLRs in other organisms, sequence diversity, and expression in immunologically active tissues, including phagocytes. The complexity of the sea urchin TLR multigene families is largely derived from expansions independent of those in vertebrates and protostomes, although a small family of TLRs with structure similar to that of Drosophila Toll can be traced to an ancient eumetazoan ancestor. Several other echinoderm sequences are now available, including Lytechinus variegatus, as well as partial sequences from two other sea urchin species. Here, we present an analysis of the invertebrate deuterostome TLRs with emphasis on the echinoderms. Representatives of most of the S. purpuratus TLR subfamilies and homologs of the mccTLR sequences are found in L. variegatus, although the L. variegatus TLR gene family is notably smaller (68 TLR sequences). The phylogeny of these genes within sea urchins highlights lineage-specific expansions at higher resolution than is evident at the phylum level. These analyses identify quickly evolving TLR subfamilies that are likely to have novel immune recognition functions and other, more stable, subfamilies that may function more similarly to those of vertebrates.","authors":"Buckley, KM., Rast, JP.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Front Immunol","volume":"3","issue":"","page":"136","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22669466","title":"The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis.","abstract":"Pax5 controls the identity and development of B cells by repressing lineage-inappropriate genes and activating B-cell-specific genes. Here, we used genome-wide approaches to identify Pax5 target genes in pro-B and mature B cells. In these cell types, Pax5 bound to 40% of the cis-regulatory elements defined by mapping DNase I hypersensitive (DHS) sites, transcription start sites and histone modifications. Although Pax5 bound to 8000 target genes, it regulated only 4% of them in pro-B and mature B cells by inducing enhancers at activated genes and eliminating DHS sites at repressed genes. Pax5-regulated genes in pro-B cells account for 23% of all expression changes occurring between common lymphoid progenitors and committed pro-B cells, which identifies Pax5 as an important regulator of this developmental transition. Regulated Pax5 target genes minimally overlap in pro-B and mature B cells, which reflects massive expression changes between these cell types. Hence, Pax5 controls B-cell identity and function by regulating distinct target genes in early and late B lymphopoiesis.","authors":"Revilla-I-Domingo, R., Bilic, I., Vilagos, B., Tagoh, H., Ebert, A., Tamir, IM., Smeenk, L., Trupke, J., Sommer, A., Jaritz, M., Busslinger, M.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"EMBO J","volume":"31","issue":"14","page":"3130-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22635062","title":"Unsupervised modeling of cell morphology dynamics for time-lapse microscopy.","abstract":"Analysis of cellular phenotypes in large imaging data sets conventionally involves supervised statistical methods, which require user-annotated training data. This paper introduces an unsupervised learning method, based on temporally constrained combinatorial clustering, for automatic prediction of cell morphology classes in time-resolved images. We applied the unsupervised method to diverse fluorescent markers and screening data and validated accurate classification of human cell phenotypes, demonstrating fully objective data labeling in image-based systems biology.","authors":"Zhong, Q., Busetto, AG., Fededa, JP., Buhmann, JM., Gerlich, DW.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nat Methods","volume":"9","issue":"7","page":"711-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38467876","title":"Structural basis of human U5 snRNP late biogenesis and recycling.","abstract":"Pre-mRNA splicing by the spliceosome requires the biogenesis and recycling of its small nuclear ribonucleoprotein (snRNP) complexes, which are consumed in each round of splicing. The human U5 snRNP is the ~1&#x2009;MDa 'heart' of the spliceosome and is recycled through an unknown mechanism involving major architectural rearrangements and the dedicated chaperones CD2BP2 and TSSC4. Late steps in U5 snRNP biogenesis similarly involve these chaperones. Here we report cryo-electron microscopy structures of four human U5 snRNP-CD2BP2-TSSC4 complexes, revealing how a series of molecular events primes the U5 snRNP to generate the ~2&#x2009;MDa U4\/U6.U5 tri-snRNP, the largest building block of the spliceosome.","authors":"Riabov Bassat, D., Visanpattanasin, S., Vorl\u00e4nder, MK., Fin, L., Phillips, AW., Plaschka, C.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Nat Struct Mol Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-04-19","doi":"10.1038\/s41594-024-01243-4","first_author":null,"corresponding_authors":null},{"pmid":"22607633","title":"Demasculinization of the Anopheles gambiae X chromosome.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22607633<\/PMID><DateCompleted><Year>2012<\/Year><Month>11<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2148<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>12<\/Volume><PubDate><Year>2012<\/Year><Month>May<\/Month><Day>18<\/Day><\/PubDate><\/JournalIssue><Title>BMC evolutionary biology<\/Title><ISOAbbreviation>BMC Evol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Demasculinization of the Anopheles gambiae X chromosome.<\/ArticleTitle><Pagination><MedlinePgn>69<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2148-12-69<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">In a number of organisms sex-biased genes are non-randomly distributed between autosomes and the shared sex chromosome X (or Z). Studies on Anopheles gambiae have produced conflicting results regarding the underrepresentation of male-biased genes on the X chromosome and it is unclear to what extent sexual antagonism, dosage compensation or X-inactivation in the male germline, the evolutionary forces that have been suggested to affect the chromosomal distribution of sex-biased genes, are operational in Anopheles.","authors":"Magnusson, K., Lycett, GJ., Mendes, AM., Lynd, A., Papathanos, PA., Crisanti, A., Windbichler, N.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"BMC Evol Biol","volume":"12","issue":"","page":"69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22589448","title":"Immunopathologic processes in sympathetic ophthalmia as signified by microRNA profiling.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22589448<\/PMID><DateCompleted><Year>2012<\/Year><Month>09<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1552-5783<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>53<\/Volume><Issue>7<\/Issue><PubDate><Year>2012<\/Year><Month>Jun<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>Investigative ophthalmology &amp; visual science<\/Title><ISOAbbreviation>Invest Ophthalmol Vis Sci<\/ISOAbbreviation><\/Journal><ArticleTitle>Immunopathologic processes in sympathetic ophthalmia as signified by microRNA profiling.<\/ArticleTitle><Pagination><MedlinePgn>4197-204<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1167\/iovs.12-9465<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE\" NlmCategory=\"OBJECTIVE\">Recent discovery of microRNAs and their negative gene regulation have provided new understanding in the pathogenesis of inflammatory diseases. This study demonstrated microRNA expression profiling and their likely role in sympathetic ophthalmia, using formalin-fixed, paraffin embedded samples.","authors":"Kaneko, Y., Wu, GS., Saraswathy, S., Vasconcelos-Santos, DV., Rao, NA.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Invest Ophthalmol Vis Sci","volume":"53","issue":"7","page":"4197-204","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22589437","title":"ER stress is involved in T17M rhodopsin-induced retinal degeneration.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22589437<\/PMID><DateCompleted><Year>2012<\/Year><Month>09<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1552-5783<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>53<\/Volume><Issue>7<\/Issue><PubDate><Year>2012<\/Year><Month>Jun<\/Month><Day>20<\/Day><\/PubDate><\/JournalIssue><Title>Investigative ophthalmology &amp; visual science<\/Title><ISOAbbreviation>Invest Ophthalmol Vis Sci<\/ISOAbbreviation><\/Journal><ArticleTitle>ER stress is involved in T17M rhodopsin-induced retinal degeneration.<\/ArticleTitle><Pagination><MedlinePgn>3792-800<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1167\/iovs.11-9235<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE\" NlmCategory=\"OBJECTIVE\">The human rhodopsin (Rho) mutation T17M leads to autosomal dominant retinitis pigmentosa (adRP). The goal of our study was to elucidate the role of endoplasmic reticulum (ER) stress in retinal degeneration in hT17M Rho mice and identify potential candidates for adRP gene therapy.","authors":"Kunte, MM., Choudhury, S., Manheim, JF., Shinde, VM., Miura, M., Chiodo, VA., Hauswirth, WW., Gorbatyuk, OS., Gorbatyuk, MS.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Invest Ophthalmol Vis Sci","volume":"53","issue":"7","page":"3792-800","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22561346","title":"CENP-T proteins are conserved centromere receptors of the Ndc80 complex.","abstract":"Centromeres direct the assembly of kinetochores, microtubule-attachment sites that allow chromosome segregation on the mitotic spindle. Fundamental differences in size and organization between evolutionarily distant eukaryotic centromeres have in many cases obscured general principles of their function. Here we demonstrate that centromere-binding proteins are highly conserved between budding yeast and humans. We identify the histone-fold protein Cnn1(CENP-T) as a direct centromere receptor of the microtubule-binding Ndc80 complex. The amino terminus of Cnn1 contains a conserved peptide motif that mediates stoichiometric binding to the Spc24-25 domain of the Ndc80 complex. Consistent with the critical role of this interaction, artificial tethering of the Ndc80 complex through Cnn1 allows mini-chromosomes to segregate in the absence of a natural centromere. Our results reveal the molecular function of CENP-T proteins and demonstrate how the Ndc80 complex is anchored to centromeres in a manner that couples chromosome movement to spindle dynamics.","authors":"Schleiffer, A., Maier, M., Litos, G., Lampert, F., Hornung, P., Mechtler, K., Westermann, S.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nat Cell Biol","volume":"14","issue":"6","page":"604-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22552143","title":"Molecular control of animal cell cytokinesis.","abstract":"Cytokinesis is the process by which mitotic cells physically split in two following chromosome segregation. Dividing animal cells first ingress a cytokinetic furrow and then separate the plasma membrane by abscission. The general cytological events and several conserved molecular factors involved in cytokinesis have been known for many years. However, recent progress in microscopy, chemical genetics, biochemical reconstitution and biophysical methodology has tremendously increased our understanding of the underlying molecular mechanisms. We discuss how recent insights have led to refined models of the distinct steps of animal cell cytokinesis, including anaphase spindle reorganization, division plane specification, actomyosin ring assembly and contraction, and abscission. We highlight how molecular signalling pathways coordinate the individual events to ensure faithful partitioning of the genome to emerging daughter cells.","authors":"Fededa, JP., Gerlich, DW.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nat Cell Biol","volume":"14","issue":"5","page":"440-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22580403","title":"The regulation of the development and function of dendritic cell subsets by GM-CSF: more than a hematopoietic growth factor.","abstract":"Granulocyte-macrophage colony stimulating factor (GM-CSF) is a cytokine that functions as a hematopoietic growth factor for the generation of white blood cells and is used clinically to stimulate hematopoiesis following chemotherapy. Apart from stimulating production of granulocytes and monocytes\/macrophages, GM-CSF has also long been used for in vitro survival\/generation of dendritic cells (DCs) from monocytes and bone marrow cells. Evidence has emerged pointing to an additional role for GM-CSF in regulating the function and differential development of several DC subsets. These newly ascribed functions of GM-CSF may underscore its importance in immunity against pathogens as well as initiating\/mediating immunopathology in chronic inflammation. Here we summarize recent advances on the role of GM-CSF in regulating the development and function of DC subsets and discuss the biological significance of these new findings.","authors":"Zhan, Y., Xu, Y., Lew, AM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Mol Immunol","volume":"52","issue":"1","page":"30-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22500922","title":"The evolution of Dscam genes across the arthropods.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22500922<\/PMID><DateCompleted><Year>2012<\/Year><Month>09<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2148<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>12<\/Volume><PubDate><Year>2012<\/Year><Month>Apr<\/Month><Day>13<\/Day><\/PubDate><\/JournalIssue><Title>BMC evolutionary biology<\/Title><ISOAbbreviation>BMC Evol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The evolution of Dscam genes across the arthropods.<\/ArticleTitle><Pagination><MedlinePgn>53<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2148-12-53<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">One way of creating phenotypic diversity is through alternative splicing of precursor mRNAs. A gene that has evolved a hypervariable form is Down syndrome cell adhesion molecule (Dscam-hv), which in Drosophila melanogaster can produce thousands of isoforms via mutually exclusive alternative splicing. The extracellular region of this protein is encoded by three variable exon clusters, each containing multiple exon variants. The protein is vital for neuronal wiring where the extreme variability at the somatic level is required for axonal guidance, and it plays a role in immunity where the variability has been hypothesised to relate to recognition of different antigens. Dscam-hv has been found across the Pancrustacea. Additionally, three paralogous non-hypervariable Dscam-like genes have also been described for D. melanogaster. Here we took a bioinformatics approach, building profile Hidden Markov Models to search across species for putative orthologs to the Dscam genes and for hypervariable alternatively spliced exons, and inferring the phylogenetic relationships among them. Our aims were to examine whether Dscam orthologs exist outside the Bilateria, whether the origin of Dscam-hv could lie outside the Pancrustacea, when the Dscam-like orthologs arose, how many alternatively spliced exons of each exon cluster were present in the most common recent ancestor, and how these clusters evolved.","authors":"Armitage, SA., Freiburg, RY., Kurtz, J., Bravo, IG.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"BMC Evol Biol","volume":"12","issue":"","page":"53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22498708","title":"Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS\/MS using ultralong gradients.","abstract":"The majority of proteome-wide studies rely on the high separation power of two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS\/MS), often combined with protein prefractionation. Alternative approaches would be advantageous in order to reduce the analysis time and the amount of sample required. On the basis of the recent advances in chromatographic and mass spectrometric instrumentation, thousands of proteins can be identified in a single-run LC-MS\/MS experiment using ultralong gradients. Consequently, the analysis of simple proteomes or clinical samples in adequate depth becomes possible by performing single-run LC-MS\/MS experiments. Here we present a generally applicable protocol for protein analysis from unseparated whole-cell extracts and discuss its potential and limitations. Demonstrating the practical applicability of the method, we identified 2,761 proteins from a HeLa cell lysate, requiring around 10 h of nanoLC-MS\/MS measurement time.","authors":"K\u00f6cher, T., Pichler, P., Swart, R., Mechtler, K.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nat Protoc","volume":"7","issue":"5","page":"882-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22495303","title":"Clusters of iron-rich cells in the upper beak of pigeons are macrophages not magnetosensitive neurons.","abstract":"Understanding the molecular and cellular mechanisms that mediate magnetosensation in vertebrates is a formidable scientific problem. One hypothesis is that magnetic information is transduced into neuronal impulses by using a magnetite-based magnetoreceptor. Previous studies claim to have identified a magnetic sense system in the pigeon, common to avian species, which consists of magnetite-containing trigeminal afferents located at six specific loci in the rostral subepidermis of the beak. These studies have been widely accepted in the field and heavily relied upon by both behavioural biologists and physicists. Here we show that clusters of iron-rich cells in the rostro-medial upper beak of the pigeon Columbia livia are macrophages, not magnetosensitive neurons. Our systematic characterization of the pigeon upper beak identified iron-rich cells in the stratum laxum of the subepidermis, the basal region of the respiratory epithelium and the apex of feather follicles. Using a three-dimensional blueprint of the pigeon beak created by magnetic resonance imaging and computed tomography, we mapped the location of iron-rich cells, revealing unexpected variation in their distribution and number--an observation that is inconsistent with a role in magnetic sensation. Ultrastructure analysis of these cells, which are not unique to the beak, showed that their subcellular architecture includes ferritin-like granules, siderosomes, haemosiderin and filopodia, characteristics of iron-rich macrophages. Our conclusion that these cells are macrophages and not magnetosensitive neurons is supported by immunohistological studies showing co-localization with the antigen-presenting molecule major histocompatibility complex class II. Our work necessitates a renewed search for the true magnetite-dependent magnetoreceptor in birds.","authors":"Treiber, CD., Salzer, MC., Riegler, J., Edelman, N., Sugar, C., Breuss, M., Pichler, P., Cadiou, H., Saunders, M., Lythgoe, M., Shaw, J., Keays, DA.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nature","volume":"484","issue":"7394","page":"367-70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22439699","title":"Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22439699<\/PMID><DateCompleted><Year>2012<\/Year><Month>09<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>02<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>13<\/Volume><PubDate><Year>2012<\/Year><Month>Mar<\/Month><Day>22<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans.<\/ArticleTitle><Pagination><MedlinePgn>109<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-13-109<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.","authors":"Zhou, Q., Zhu, HM., Huang, QF., Zhao, L., Zhang, GJ., Roy, SW., Vicoso, B., Xuan, ZL., Ruan, J., Zhang, Y., Zhao, RP., Ye, C., Zhang, XQ., Wang, J., Wang, W., Bachtrog, D.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"BMC Genomics","volume":"13","issue":"","page":"109","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22429863","title":"A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22429863<\/PMID><DateCompleted><Year>2012<\/Year><Month>07<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>10<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>13<\/Volume><PubDate><Year>2012<\/Year><Month>Mar<\/Month><Day>19<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses.<\/ArticleTitle><Pagination><MedlinePgn>99<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-13-99<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Sugar beet (Beta vulgaris sp. vulgaris) crops account for about 30% of world sugar. Sugar yield is compromised by reproductive growth hence crops must remain vegetative until harvest. Prolonged exposure to cold temperature (vernalization) in the range 6 \u00b0C to 12 \u00b0C induces reproductive growth, leading to bolting (rapid elongation of the main stem) and flowering. Spring cultivation of crops in cool temperate climates makes them vulnerable to vernalization and hence bolting, which is initiated in the apical shoot meristem in processes involving interaction between gibberellin (GA) hormones and vernalization. The underlying mechanisms are unknown and genome scale next generation sequencing approaches now offer comprehensive strategies to investigate them; enabling the identification of novel targets for bolting control in sugar beet crops. In this study, we demonstrate the application of an mRNA-Seq based strategy for this purpose.","authors":"Mutasa-G\u00f6ttgens, ES., Joshi, A., Holmes, HF., Hedden, P., G\u00f6ttgens, B.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"BMC Genomics","volume":"13","issue":"","page":"99","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22388288","title":"Long-term, efficient inhibition of microRNA function in mice using rAAV vectors.","abstract":"Understanding the function of individual microRNA (miRNA) species in mice would require the production of hundreds of loss-of-function strains. To accelerate analysis of miRNA biology in mammals, we combined recombinant adeno-associated virus (rAAV) vectors with miRNA 'tough decoys' (TuDs) to inhibit specific miRNAs. Intravenous injection of rAAV9 expressing anti-miR-122 or anti-let-7 TuDs depleted the corresponding miRNA and increased its mRNA targets. rAAV producing anti-miR-122 TuD but not anti-let-7 TuD reduced serum cholesterol by &gt;30% for 25 weeks in wild-type mice. High-throughput sequencing of liver miRNAs from the treated mice confirmed that the targeted miRNAs were depleted and revealed that TuDs induced miRNA tailing and trimming in vivo. rAAV-mediated miRNA inhibition thus provides a simple way to study miRNA function in adult mammals and a potential therapy for dyslipidemia and other diseases caused by miRNA deregulation.","authors":"Xie, J., Ameres, SL., Friedline, R., Hung, JH., Zhang, Y., Xie, Q., Zhong, L., Su, Q., He, R., Li, M., Li, H., Mu, X., Zhang, H., Broderick, JA., Kim, JK., Weng, Z., Flotte, TR., Zamore, PD., Gao, G.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nat Methods","volume":"9","issue":"4","page":"403-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22301776","title":"A pipeline for the generation of shRNA transgenic mice.","abstract":"RNA interference (RNAi) is an extremely effective tool for studying gene function in almost all metazoan and eukaryotic model systems. RNAi in mice, through the expression of short hairpin RNAs (shRNAs), offers something not easily achieved with traditional genetic approaches-inducible and reversible gene silencing. However, technical variability associated with the production of shRNA transgenic strains has so far limited their widespread use. Here we describe a pipeline for the generation of miR30-based shRNA transgenic mice that enables efficient and consistent targeting of doxycycline-regulated, fluorescence-linked shRNAs to the Col1a1 locus. Notably, the protocol details crucial steps in the design and testing of miR30-based shRNAs to maximize the potential for developing effective transgenic strains. In all, this 14-week procedure provides a fast and cost-effective way for any laboratory to investigate gene function in vivo in the mouse.","authors":"Dow, LE., Premsrirut, PK., Zuber, J., Fellmann, C., McJunkin, K., Miething, C., Park, Y., Dickins, RA., Hannon, GJ., Lowe, SW.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nat Protoc","volume":"7","issue":"2","page":"374-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22245966","title":"Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ.","abstract":"The HtrA protein family combines chaperone and protease activities and is essential for protein quality control in many organisms. Whereas the mechanisms underlying the proteolytic function of HtrA proteins are well characterized, their chaperone activity remains poorly understood. Here we describe cryo-EM structures of Escherichia coli DegQ in its 12- and 24-mer states in complex with model substrates, providing a structural model of HtrA chaperone action. Up to six lysozyme substrates bind inside the DegQ 12-mer cage and are visualized in a close-to-native state. An asymmetric reconstruction reveals the binding of a well-ordered lysozyme to four DegQ protomers. DegQ PDZ domains are located adjacent to substrate density and their presence is required for chaperone activity. The substrate-interacting regions appear conserved in 12- and 24-mer cages, suggesting a common mechanism of chaperone function.","authors":"Malet, H., Canellas, F., Sawa, J., Yan, J., Thalassinos, K., Ehrmann, M., Clausen, T., Saibil, HR.","publication_status":"epublish","journalpubyear":"2012","journaltitle":"Nat Struct Mol Biol","volume":"19","issue":"2","page":"152-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22179591","title":"A computational pipeline for comparative ChIP-seq analyses.","abstract":"Chromatin immunoprecipitation (ChIP) followed by deep sequencing can now easily be performed across different conditions, time points and even species. However, analyzing such data is not trivial and standard methods are as yet unavailable. Here we present a protocol to systematically compare ChIP-sequencing (ChIP-seq) data across conditions. We first describe technical guidelines for data preprocessing, read mapping, read-density visualization and peak calling. We then describe methods and provide code with specific examples to compare different data sets across species and across conditions, including a threshold-free approach to measure global similarity, a strategy to assess the binary conservation of binding events and measurements for quantitative changes of binding. We discuss how differences in binding can be related to gene functions, gene expression and sequence changes. Once established, this protocol should take about 2 d to complete and be generally applicable to many data sets.","authors":"Bardet, AF., He, Q., Zeitlinger, J., Stark, A.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Protoc","volume":"7","issue":"1","page":"45-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22158248","title":"Predicting mutation outcome from early stochastic variation in genetic interaction partners.","abstract":"Many mutations, including those that cause disease, only have a detrimental effect in a subset of individuals. The reasons for this are usually unknown, but may include additional genetic variation and environmental risk factors. However, phenotypic discordance remains even in the absence of genetic variation, for example between monozygotic twins, and incomplete penetrance of mutations is frequent in isogenic model organisms in homogeneous environments. Here we propose a model for incomplete penetrance based on genetic interaction networks. Using Caenorhabditis elegans as a model system, we identify two compensation mechanisms that vary among individuals and influence mutation outcome. First, feedback induction of an ancestral gene duplicate differs across individuals, with high expression masking the effects of a mutation. This supports the hypothesis that redundancy is maintained in genomes to buffer stochastic developmental failure. Second, during normal embryonic development we find that there is substantial variation in the induction of molecular chaperones such as Hsp90 (DAF-21). Chaperones act as promiscuous buffers of genetic variation, and embryos with stronger induction of Hsp90 are less likely to be affected by an inherited mutation. Simultaneously quantifying the variation in these two independent responses allows the phenotypic outcome of a mutation to be more accurately predicted in individuals. Our model and methodology provide a framework for dissecting the causes of incomplete penetrance. Further, the results establish that inter-individual variation in both specific and more general buffering systems combine to determine the outcome inherited mutations in each individual.","authors":"Burga, A., Casanueva, MO., Lehner, B.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nature","volume":"480","issue":"7376","page":"250-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21639788","title":"Protein quality control in the bacterial periplasm.","abstract":"Protein quality control involves sensing and treatment of defective or incomplete protein structures. Misfolded or mislocalized proteins trigger dedicated signal transduction cascades that upregulate the production of protein quality-control factors. Corresponding proteases and chaperones either degrade or repair damaged proteins, thereby reducing the level of aggregation-prone molecules. Because the periplasm of gram-negative bacteria is particularly exposed to environmental changes and respective protein-folding stresses connected with the presence of detergents, low or high osmolarity of the medium, elevated temperatures, and the host's immune response, fine-tuned protein quality control systems are essential for survival under these unfavorable conditions. This review discusses recent advances in the identification and characterization of the key cellular factors and the emerging general principles of the underlying molecular mechanisms.","authors":"Merdanovic, M., Clausen, T., Kaiser, M., Huber, R., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Annu Rev Microbiol","volume":"65","issue":null,"page":"149-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22094701","title":"Spalt mediates an evolutionarily conserved switch to fibrillar muscle fate in insects.","abstract":"Flying insects oscillate their wings at high frequencies of up to 1,000 Hz and produce large mechanical forces of 80 W per kilogram of muscle. They utilize a pair of perpendicularly oriented indirect flight muscles that contain fibrillar, stretch-activated myofibres. In contrast, all other, more slowly contracting, insect body muscles have a tubular muscle morphology. Here we identify the transcription factor Spalt major (Salm) as a master regulator of fibrillar flight muscle fate in Drosophila. salm is necessary and sufficient to induce fibrillar muscle fate. salm switches the entire transcriptional program from tubular to fibrillar fate by regulating the expression and splicing of key sarcomeric components specific to each muscle type. Spalt function is conserved in insects evolutionarily separated by 280 million years. We propose that Spalt proteins switch myofibres from tubular to fibrillar fate during development, a function potentially conserved in the vertebrate heart--a stretch-activated muscle sharing features with insect flight muscle.","authors":"Sch\u00f6nbauer, C., Distler, J., J\u00e4hrling, N., Radolf, M., Dodt, HU., Frasch, M., Schnorrer, F.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nature","volume":"479","issue":"7373","page":"406-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22067460","title":"Systematic phosphorylation analysis of human mitotic protein complexes.","abstract":"Progression through mitosis depends on a large number of protein complexes that regulate the major structural and physiological changes necessary for faithful chromosome segregation. Most, if not all, of the mitotic processes are regulated by a set of mitotic protein kinases that control protein activity by phosphorylation. Although many mitotic phosphorylation events have been identified in proteome-scale mass spectrometry studies, information on how these phosphorylation sites are distributed within mitotic protein complexes and which kinases generate these phosphorylation sites is largely lacking. We used systematic protein-affinity purification combined with mass spectrometry to identify 1818 phosphorylation sites in more than 100 mitotic protein complexes. In many complexes, the phosphorylation sites were concentrated on a few subunits, suggesting that these subunits serve as \"switchboards\" to relay the kinase-regulatory signals within the complexes. Consequent bioinformatic analyses identified potential kinase-substrate relationships for most of these sites. In a subsequent in-depth analysis of key mitotic regulatory complexes with the Aurora kinase B (AURKB) inhibitor Hesperadin and a new Polo-like kinase (PLK1) inhibitor, BI 4834, we determined the kinase dependency for 172 phosphorylation sites on 41 proteins. Combination of the results of the cellular studies with Scansite motif prediction enabled us to identify 14 sites on six proteins as direct candidate substrates of AURKB or PLK1.","authors":"Hegemann, B., Hutchins, JR., Hudecz, O., Novatchkova, M., Rameseder, J., Sykora, MM., Liu, S., Mazanek, M., L\u00e9n\u00e1rt, P., H\u00e9rich\u00e9, JK., Poser, I., Kraut, N., Hyman, AA., Yaffe, MB., Mechtler, K., Peters, JM.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Sci Signal","volume":"4","issue":"198","page":"rs12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21993624","title":"A high-resolution map of human evolutionary constraint using 29 mammals.","abstract":"The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering \u223c4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for \u223c60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.","authors":"Lindblad-Toh, K., Garber, M., Zuk, O., Lin, MF., Parker, BJ., Washietl, S., Kheradpour, P., Ernst, J., Jordan, G., Mauceli, E., Ward, LD., Lowe, CB., Holloway, AK., Clamp, M., Gnerre, S., Alf\u00f6ldi, J., Beal, K., Chang, J., Clawson, H., Cuff, J., Di Palma, F., Fitzgerald, S., Flicek, P., Guttman, M., Hubisz, MJ., Jaffe, DB., Jungreis, I., Kent, WJ., Kostka, D., Lara, M., Martins, AL., Massingham, T., Moltke, I., Raney, BJ., Rasmussen, MD., Robinson, J., Stark, A., Vilella, AJ., Wen, J., Xie, X., Zody, MC., Baldwin, J., Bloom, T., Chin, CW., Heiman, D., Nicol, R., Nusbaum, C., Young, S., Wilkinson, J., Worley, KC., Kovar, CL., Muzny, DM., Gibbs, RA., Cree, A., Dihn, HH., Fowler, G., Jhangiani, S., Joshi, V., Lee, S., Lewis, LR., Nazareth, LV., Okwuonu, G., Santibanez, J., Warren, WC., Mardis, ER., Weinstock, GM., Wilson, RK., Delehaunty, K., Dooling, D., Fronik, C., Fulton, L., Fulton, B., Graves, T., Minx, P., Sodergren, E., Birney, E., Margulies, EH., Herrero, J., Green, ED., Haussler, D., Siepel, A., Goldman, N., Pollard, KS., Pedersen, JS., Lander, ES., Kellis, M.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nature","volume":"478","issue":"7370","page":"476-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21909113","title":"CTCF-binding elements mediate control of V(D)J recombination.","abstract":"Immunoglobulin heavy chain (IgH) variable region exons are assembled from V(H), D and J(H) gene segments in developing B lymphocytes. Within the 2.7-megabase mouse Igh locus, V(D)J recombination is regulated to ensure specific and diverse antibody repertoires. Here we report in mice a key Igh V(D)J recombination regulatory region, termed intergenic control region 1 (IGCR1), which lies between the V(H) and D clusters. Functionally, IGCR1 uses CTCF looping\/insulator factor-binding elements and, correspondingly, mediates Igh loops containing distant enhancers. IGCR1 promotes normal B-cell development and balances antibody repertoires by inhibiting transcription and rearrangement of D(H)-proximal V(H) gene segments and promoting rearrangement of distal V(H) segments. IGCR1 maintains ordered and lineage-specific V(H)(D)J(H) recombination by suppressing V(H) joining to D segments not joined to J(H) segments, and V(H) to DJ(H) joins in thymocytes, respectively. IGCR1 is also required for feedback regulation and allelic exclusion of proximal V(H)-to-DJ(H) recombination. Our studies elucidate a long-sought Igh V(D)J recombination control region and indicate a new role for the generally expressed CTCF protein.","authors":"Guo, C., Yoon, HS., Franklin, A., Jain, S., Ebert, A., Cheng, HL., Hansen, E., Despo, O., Bossen, C., Vettermann, C., Bates, JG., Richards, N., Myers, D., Patel, H., Gallagher, M., Schlissel, MS., Murre, C., Busslinger, M., Giallourakis, CC., Alt, FW.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nature","volume":"477","issue":"7365","page":"424-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21909105","title":"Evidence for osteocyte regulation of bone homeostasis through RANKL expression.","abstract":"Osteocytes embedded in bone have been postulated to orchestrate bone homeostasis by regulating both bone-forming osteoblasts and bone-resorbing osteoclasts. We find here that purified osteocytes express a much higher amount of receptor activator of nuclear factor-\u03baB ligand (RANKL) and have a greater capacity to support osteoclastogenesis in vitro than osteoblasts and bone marrow stromal cells. Furthermore, the severe osteopetrotic phenotype that we observe in mice lacking RANKL specifically in osteocytes indicates that osteocytes are the major source of RANKL in bone remodeling in vivo.","authors":"Nakashima, T., Hayashi, M., Fukunaga, T., Kurata, K., Oh-Hora, M., Feng, JQ., Bonewald, LF., Kodama, T., Wutz, A., Wagner, EF., Penninger, JM., Takayanagi, H.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Med","volume":"17","issue":"10","page":"1231-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"42704963","title":"Generation of high-quality reference control panels of human induced pluripotent stem cell clones from PBMCs.","abstract":"High-quality, standardized iPSC reference lines are crucial for disease modeling and regenerative medicine. We generated and extensively characterized thirteen iPSC clones from PBMCs of five healthy donors (three female, two male) using non-integrating Sendai virus. This resource is distinguished by its standardized derivation and deep characterization and the deliberate generation of multiple clones per donor to capture and control for clonal variation. These validated lines are available to academic and commercial researchers to accelerate advances in stem cell biology and tissue engineering.","authors":"Stein, E., Mosca, E., John, J., Kinzer, M., Novatchkova, M., Scheuch, H., Agu, C., Stary, G., Penninger, JM., Meixner, A., Volz-Glaser, J.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Stem Cell Res","volume":"96","issue":null,"page":"104097","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-09-07","doi":"10.1016\/j.scr.2026.104097","first_author":"Stein, E.","corresponding_authors":"Volz-Glaser, J."},{"pmid":"21874003","title":"Germline mutations in BAP1 predispose to melanocytic tumors.","abstract":"Common acquired melanocytic nevi are benign neoplasms that are composed of small, uniform melanocytes and are typically present as flat or slightly elevated pigmented lesions on the skin. We describe two families with a new autosomal dominant syndrome characterized by multiple, skin-colored, elevated melanocytic tumors. In contrast to common acquired nevi, the melanocytic neoplasms in affected family members ranged histopathologically from epithelioid nevi to atypical melanocytic proliferations that showed overlapping features with melanoma. Some affected individuals developed uveal or cutaneous melanomas. Segregating with this phenotype, we found inactivating germline mutations of BAP1, which encodes a ubiquitin carboxy-terminal hydrolase. The majority of melanocytic neoplasms lost the remaining wild-type allele of BAP1 by various somatic alterations. In addition, we found BAP1 mutations in a subset of sporadic melanocytic neoplasms showing histological similarities to the familial tumors. These findings suggest that loss of BAP1 is associated with a clinically and morphologically distinct type of melanocytic neoplasm.","authors":"Wiesner, T., Obenauf, AC., Murali, R., Fried, I., Griewank, KG., Ulz, P., Windpassinger, C., Wackernagel, W., Loy, S., Wolf, I., Viale, A., Lash, AE., Pirun, M., Socci, ND., R\u00fctten, A., Palmedo, G., Abramson, D., Offit, K., Ott, A., Becker, JC., Cerroni, L., Kutzner, H., Bastian, BC., Speicher, MR.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Genet","volume":"43","issue":"10","page":"1018-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-11-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21863019","title":"A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors.","abstract":"PIWI proteins and their bound PIWI-interacting RNAs (piRNAs) form the core of a gonad-specific small RNA silencing pathway that protects the animal genome against the deleterious activity of transposable elements. Recent studies linked the piRNA pathway to TUDOR biology as TUDOR domains of various proteins bind symmetrically methylated Arginine residues in PIWI proteins. We systematically analysed the Drosophila TUDOR protein family and identified four previously not characterized TUDOR domain-containing proteins (CG4771, CG14303, CG11133 and CG31755) as essential piRNA pathway factors. We characterized CG4771 (Vreteno) in detail and demonstrate a critical role for this protein in primary piRNA biogenesis. Vreteno physically and\/or genetically interacts with the primary pathway components Piwi, Armitage, Yb and Zucchini. Vreteno also interacts with the Tdrd12 orthologues CG11133 (Brother of Yb) and CG31755 (Sister of Yb), which are essential for the primary piRNA pathway in the germline and probably replace the function of the related but soma-specific factor Yb.","authors":"Handler, D., Olivieri, D., Novatchkova, M., Gruber, FS., Meixner, K., Mechtler, K., Stark, A., Sachidanandam, R., Brennecke, J.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"EMBO J","volume":"30","issue":"19","page":"3977-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21857667","title":"The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.","abstract":"In Drosophila, defects in asymmetric cell division often result in the formation of stem-cell-derived tumours. Here, we show that very similar terminal brain tumour phenotypes arise through a fundamentally different mechanism. We demonstrate that brain tumours in l(3)mbt mutants originate from overproliferation of neuroepithelial cells in the optic lobes caused by derepression of target genes in the Salvador-Warts-Hippo (SWH) pathway. We use ChIP-sequencing to identify L(3)mbt binding sites and show that L(3)mbt binds to chromatin insulator elements. Mutating l(3)mbt or inhibiting expression of the insulator protein gene mod(mdg4) results in upregulation of SWH pathway reporters. As l(3)mbt tumours are rescued by mutations in bantam or yorkie or by overexpression of Expanded, the deregulation of SWH pathway target genes is an essential step in brain tumour formation. Therefore, very different primary defects result in the formation of brain tumours, which behave quite similarly in their advanced stages.","authors":"Richter, C., Oktaba, K., Steinmann, J., M\u00fcller, J., Knoblich, JA.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Cell Biol","volume":"13","issue":"9","page":"1029-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21832993","title":"A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation.","abstract":"Cohesin enables post-replicative DNA repair and chromosome segregation by holding sister chromatids together from the time of DNA replication in S phase until mitosis. There is growing evidence that cohesin also forms long-range chromosomal cis-interactions and may regulate gene expression in association with CTCF, mediator or tissue-specific transcription factors. Human cohesinopathies such as Cornelia de Lange syndrome are thought to result from impaired non-canonical cohesin functions, but a clear distinction between the cell-division-related and cell-division-independent functions of cohesion--as exemplified in Drosophila--has not been demonstrated in vertebrate systems. To address this, here we deleted the cohesin locus Rad21 in mouse thymocytes at a time in development when these cells stop cycling and rearrange their T-cell receptor (TCR) \u03b1 locus (Tcra). Rad21-deficient thymocytes had a normal lifespan and retained the ability to differentiate, albeit with reduced efficiency. Loss of Rad21 led to defective chromatin architecture at the Tcra locus, where cohesion-binding sites flank the TEA promoter and the E\u03b1 enhancer, and demarcate Tcra from interspersed Tcrd elements and neighbouring housekeeping genes. Cohesin was required for long-range promoter-enhancer interactions, Tcra transcription, H3K4me3 histone modifications that recruit the recombination machinery and Tcra rearrangement. Provision of pre-rearranged TCR transgenes largely rescued thymocyte differentiation, demonstrating that among thousands of potential target genes across the genome, defective Tcra rearrangement was limiting for the differentiation of cohesin-deficient thymocytes. These findings firmly establish a cell-division-independent role for cohesin in Tcra locus rearrangement and provide a comprehensive account of the mechanisms by which cohesin enables cellular differentiation in a well-characterized mammalian system.","authors":"Seitan, VC., Hao, B., Tachibana-Konwalski, K., Lavagnolli, T., Mira-Bontenbal, H., Brown, KE., Teng, G., Carroll, T., Terry, A., Horan, K., Marks, H., Adams, DJ., Schatz, DG., Aragon, L., Fisher, AG., Krangel, MS., Nasmyth, K., Merkenschlager, M.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nature","volume":"476","issue":"7361","page":"467-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21814200","title":"RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia.","abstract":"Epigenetic pathways can regulate gene expression by controlling and interpreting chromatin modifications. Cancer cells are characterized by altered epigenetic landscapes, and commonly exploit the chromatin regulatory machinery to enforce oncogenic gene expression programs. Although chromatin alterations are, in principle, reversible and often amenable to drug intervention, the promise of targeting such pathways therapeutically has been limited by an incomplete understanding of cancer-specific dependencies on epigenetic regulators. Here we describe a non-biased approach to probe epigenetic vulnerabilities in acute myeloid leukaemia (AML), an aggressive haematopoietic malignancy that is often associated with aberrant chromatin states. By screening a custom library of small hairpin RNAs (shRNAs) targeting known chromatin regulators in a genetically defined AML mouse model, we identify the protein bromodomain-containing 4 (Brd4) as being critically required for disease maintenance. Suppression of Brd4 using shRNAs or the small-molecule inhibitor JQ1 led to robust antileukaemic effects in vitro and in vivo, accompanied by terminal myeloid differentiation and elimination of leukaemia stem cells. Similar sensitivities were observed in a variety of human AML cell lines and primary patient samples, revealing that JQ1 has broad activity in diverse AML subtypes. The effects of Brd4 suppression are, at least in part, due to its role in sustaining Myc expression to promote aberrant self-renewal, which implicates JQ1 as a pharmacological means to suppress MYC in cancer. Our results establish small-molecule inhibition of Brd4 as a promising therapeutic strategy in AML and, potentially, other cancers, and highlight the utility of RNA interference (RNAi) screening for revealing epigenetic vulnerabilities that can be exploited for direct pharmacological intervention.","authors":"Zuber, J., Shi, J., Wang, E., Rappaport, AR., Herrmann, H., Sison, EA., Magoon, D., Qi, J., Blatt, K., Wunderlich, M., Taylor, MJ., Johns, C., Chicas, A., Mulloy, JC., Kogan, SC., Brown, P., Valent, P., Bradner, JE., Lowe, SW., Vakoc, CR.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nature","volume":"478","issue":"7370","page":"524-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21727895","title":"Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling.","abstract":"The adult stem cell marker Lgr5 and its relative Lgr4 are often co-expressed in Wnt-driven proliferative compartments. We find that conditional deletion of both genes in the mouse gut impairs Wnt target gene expression and results in the rapid demise of intestinal crypts, thus phenocopying Wnt pathway inhibition. Mass spectrometry demonstrates that Lgr4 and Lgr5 associate with the Frizzled\/Lrp Wnt receptor complex. Each of the four R-spondins, secreted Wnt pathway agonists, can bind to Lgr4, -5 and -6. In HEK293 cells, RSPO1 enhances canonical WNT signals initiated by WNT3A. Removal of LGR4 does not affect WNT3A signalling, but abrogates the RSPO1-mediated signal enhancement, a phenomenon rescued by re-expression of LGR4, -5 or -6. Genetic deletion of Lgr4\/5 in mouse intestinal crypt cultures phenocopies withdrawal of Rspo1 and can be rescued by Wnt pathway activation. Lgr5 homologues are facultative Wnt receptor components that mediate Wnt signal enhancement by soluble R-spondin proteins. These results will guide future studies towards the application of R-spondins for regenerative purposes of tissues expressing Lgr5 homologues.","authors":"de Lau, W., Barker, N., Low, TY., Koo, BK., Li, VS., Teunissen, H., Kujala, P., Haegebarth, A., Peters, PJ., van de Wetering, M., Stange, DE., van Es, JE., Guardavaccaro, D., Schasfoort, RB., Mohri, Y., Nishimori, K., Mohammed, S., Heck, AJ., Clevers, H.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nature","volume":"476","issue":"7360","page":"293-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21724824","title":"Immersion freezing of biological specimens: rationale, principles, and instrumentation.","abstract":"","authors":"Resch, GP., Brandstetter, M., Pickl-Herk, AM., K\u00f6nigsmaier, L., Wonesch, VI., Urban, E.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Cold Spring Harb Protoc","volume":"2011","issue":"7","page":"778-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21712545","title":"Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling.","abstract":"The timing and localization of events during mitosis are controlled by the regulated phosphorylation of proteins by the mitotic kinases, which include Aurora A, Aurora B, Nek2 (never in mitosis kinase 2), Plk1 (Polo-like kinase 1), and the cyclin-dependent kinase complex Cdk1\/cyclin B. Although mitotic kinases can have overlapping subcellular localizations, each kinase appears to phosphorylate its substrates on distinct sites. To gain insight into the relative importance of local sequence context in kinase selectivity, identify previously unknown substrates of these five mitotic kinases, and explore potential mechanisms for substrate discrimination, we determined the optimal substrate motifs of these major mitotic kinases by positional scanning oriented peptide library screening (PS-OPLS). We verified individual motifs with in vitro peptide kinetic studies and used structural modeling to rationalize the kinase-specific selection of key motif-determining residues at the molecular level. Cross comparisons among the phosphorylation site selectivity motifs of these kinases revealed an evolutionarily conserved mutual exclusion mechanism in which the positively and negatively selected portions of the phosphorylation motifs of mitotic kinases, together with their subcellular localizations, result in proper substrate targeting in a coordinated manner during mitosis.","authors":"Alexander, J., Lim, D., Joughin, BA., Hegemann, B., Hutchins, JR., Ehrenberger, T., Ivins, F., Sessa, F., Hudecz, O., Nigg, EA., Fry, AM., Musacchio, A., Stukenberg, PT., Mechtler, K., Peters, JM., Smerdon, SJ., Yaffe, MB.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Sci Signal","volume":"4","issue":"179","page":"ra42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21685890","title":"Differential requirement for the dual functions of \u03b2-catenin in embryonic stem cell self-renewal and germ layer formation.","abstract":"Canonical Wnt signalling has been implicated in mouse and human embryonic stem cell (ESC) maintenance; however, its requirement is controversial. \u03b2-catenin is the key component in this highly conserved Wnt pathway, acting as a transcriptional transactivator. However, \u03b2-catenin has additional roles at the plasma membrane regulating cell-cell adhesion, complicating the analyses of cells\/tissues lacking \u03b2-catenin. We report here the generation of a Ctnnb1 (\u03b2-catenin)-deficient mouse ESC (mESC) line and show that self-renewal is maintained in the absence of \u03b2-catenin. Cell adhesion is partially rescued by plakoglobin upregulation, but fails to be maintained during differentiation. When differentiated as aggregates, wild-type mESCs form descendants of all three germ layers, whereas mesendodermal germ layer formation and neuronal differentiation are defective in Ctnnb1-deficient mESCs. A Tcf\/Lef-signalling-defective \u03b2-catenin variant, which re-establishes cadherin-mediated cell adhesion, rescues definitive endoderm and neuroepithelial formation, indicating that the \u03b2-catenin cell-adhesion function is more important than its signalling function for these processes.","authors":"Lyashenko, N., Winter, M., Migliorini, D., Biechele, T., Moon, RT., Hartmann, C.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Cell Biol","volume":"13","issue":"7","page":"753-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21633384","title":"A blueprint for kinetochores - new insights into the molecular mechanics of cell division.","abstract":"Kinetochores are large proteinaceous complexes that physically link centromeric DNA to the plus ends of spindle microtubules. Stable kinetochore-microtubule attachments are a prerequisite for the accurate and efficient distribution of genetic material over multiple generations. In the past decade, concerted research has resulted in the identification of the individual kinetochore building blocks, the characterization of critical microtubule-interacting components, such as the NDC80 complex, and the development of an approximate model of the architecture of this sophisticated biological machine.","authors":"Lampert, F., Westermann, S.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Nat Rev Mol Cell Biol","volume":"12","issue":"7","page":"407-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21552207","title":"The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells.","abstract":"Pax5 is a critical regulator of B-cell commitment. Here, we identified direct Pax5 target genes by streptavidin-mediated ChIP-chip analysis of pro-B cells expressing in vivo biotinylated Pax5. By binding to promoters and enhancers, Pax5 directly regulates the expression of multiple transcription factor, cell surface receptor and signal transducer genes. One of the newly identified enhancers was shown by transgenic analysis to confer Pax5-dependent B-cell-specific activity to the Nedd9 gene controlling B-cell trafficking. Profiling of histone modifications in Pax5-deficient and wild-type pro-B cells demonstrated that Pax5 induces active chromatin at activated target genes, while eliminating active chromatin at repressed genes in committed pro-B cells. Pax5 rapidly induces these chromatin and transcription changes by recruiting chromatin-remodelling, histone-modifying and basal transcription factor complexes to its target genes. These data provide novel insight into the regulatory network and epigenetic regulation, by which Pax5 controls B-cell commitment.","authors":"McManus, S., Ebert, A., Salvagiotto, G., Medvedovic, J., Sun, Q., Tamir, I., Jaritz, M., Tagoh, H., Busslinger, M.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"EMBO J","volume":"30","issue":"12","page":"2388-404","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-223","title":"Adaptive brain rewiring after brain injury via adult neurogenesis","abstract":null,"authors":"Chakraborty O, Maturi S,  Zabolocki M, Muhia M, Villar-Pazos S, Decroocq M,  Horenkamp S, Gonz\u00e1lez  Alvarado MN, Piszczek L, Schlachter M,  Oppelt Duranova T,  Skibbe H,  Knoblich JA,   Grade S","publication_status":"preprint","journalpubyear":"2026","journaltitle":"bioRixv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.09.22.753668v1","preprintlink":"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.09.22.753668v1","articledate":"2026-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21410956","title":"Quantitative analysis of polycomb response elements (PREs) at identical genomic locations distinguishes contributions of PRE sequence and genomic environment.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21410956<\/PMID><DateCompleted><Year>2011<\/Year><Month>07<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1756-8935<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>4<\/Volume><PubDate><Year>2011<\/Year><Month>Mar<\/Month><Day>16<\/Day><\/PubDate><\/JournalIssue><Title>Epigenetics &amp; chromatin<\/Title><ISOAbbreviation>Epigenetics Chromatin<\/ISOAbbreviation><\/Journal><ArticleTitle>Quantitative analysis of polycomb response elements (PREs) at identical genomic locations distinguishes contributions of PRE sequence and genomic environment.<\/ArticleTitle><Pagination><MedlinePgn>4<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1756-8935-4-4<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Polycomb\/Trithorax response elements (PREs) are cis-regulatory elements essential for the regulation of several hundred developmentally important genes. However, the precise sequence requirements for PRE function are not fully understood, and it is also unclear whether these elements all function in a similar manner. Drosophila PRE reporter assays typically rely on random integration by P-element insertion, but PREs are extremely sensitive to genomic position.","authors":"Okulski, H., Druck, B., Bhalerao, S., Ringrose, L.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"Epigenetics Chromatin","volume":"4","issue":"","page":"4","pdf":null,"JrId":"34457","fulltextlink":null,"preprintlink":null,"articledate":"2011-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21407811","title":"Distinct and conserved prominin-1\/CD133-positive retinal cell populations identified across species.","abstract":"Besides being a marker of various somatic stem cells in mammals, prominin-1 (CD133) plays a role in maintaining the photoreceptor integrity since mutations in the PROM1 gene are linked with retinal degeneration. In spite of that, little information is available regarding its distribution in eyes of non-mammalian vertebrates endowed with high regenerative abilities. To address this subject, prominin-1 cognates were isolated from axolotl, zebrafish and chicken, and their retinal compartmentalization was investigated and compared to that of their mammalian orthologue. Interestingly, prominin-1 transcripts--except for the axolotl--were not strictly restricted to the outer nuclear layer (i.e., photoreceptor cells), but they also marked distinct subdivisions of the inner nuclear layer (INL). In zebrafish, where the prominin-1 gene is duplicated (i.e., prominin-1a and prominin-1b), a differential expression was noted for both paralogues within the INL being localized either to its vitreal or scleral subdivision, respectively. Interestingly, expression of prominin-1a within the former domain coincided with Pax-6-positive cells that are known to act as progenitors upon injury-induced retino-neurogenesis. A similar, but minute population of prominin-1-positive cells located at the vitreal side of the INL was also detected in developing and adult mice. In chicken, however, prominin-1-positive cells appeared to be aligned along the scleral side of the INL reminiscent of zebrafish prominin-1b. Taken together our data indicate that in addition to conserved expression of prominin-1 in photoreceptors, significant prominin-1-expressing non-photoreceptor retinal cell populations are present in the vertebrate eye that might represent potential sources of stem\/progenitor cells for regenerative therapies.","authors":"J\u00e1szai, J., Fargeas, CA., Graupner, S., Tanaka, EM., Brand, M., Huttner, WB., Corbeil, D.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"PLoS One","volume":"6","issue":"3","page":"e17590","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21245904","title":"Epigenetic regulation of learning and memory by Drosophila EHMT\/G9a.","abstract":"The epigenetic modification of chromatin structure and its effect on complex neuronal processes like learning and memory is an emerging field in neuroscience. However, little is known about the \"writers\" of the neuronal epigenome and how they lay down the basis for proper cognition. Here, we have dissected the neuronal function of the Drosophila euchromatin histone methyltransferase (EHMT), a member of a conserved protein family that methylates histone 3 at lysine 9 (H3K9). EHMT is widely expressed in the nervous system and other tissues, yet EHMT mutant flies are viable. Neurodevelopmental and behavioral analyses identified EHMT as a regulator of peripheral dendrite development, larval locomotor behavior, non-associative learning, and courtship memory. The requirement for EHMT in memory was mapped to 7B-Gal4 positive cells, which are, in adult brains, predominantly mushroom body neurons. Moreover, memory was restored by EHMT re-expression during adulthood, indicating that cognitive defects are reversible in EHMT mutants. To uncover the underlying molecular mechanisms, we generated genome-wide H3K9 dimethylation profiles by ChIP-seq. Loss of H3K9 dimethylation in EHMT mutants occurs at 5% of the euchromatic genome and is enriched at the 5' and 3' ends of distinct classes of genes that control neuronal and behavioral processes that are corrupted in EHMT mutants. Our study identifies Drosophila EHMT as a key regulator of cognition that orchestrates an epigenetic program featuring classic learning and memory genes. Our findings are relevant to the pathophysiological mechanisms underlying Kleefstra Syndrome, a severe form of intellectual disability caused by mutations in human EHMT1, and have potential therapeutic implications. Our work thus provides novel insights into the epigenetic control of cognition in health and disease.","authors":"Kramer, JM., Kochinke, K., Oortveld, MA., Marks, H., Kramer, D., de Jong, EK., Asztalos, Z., Westwood, JT., Stunnenberg, HG., Sokolowski, MB., Keleman, K., Zhou, H., van Bokhoven, H., Schenck, A.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"PLoS Biol","volume":"9","issue":"1","page":"e1000569","pdf":null,"JrId":"30470","fulltextlink":null,"preprintlink":null,"articledate":"2011-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21173847","title":"How do RNA sequence, DNA sequence, and chromatin properties regulate splicing?","abstract":"Recent genome-wide studies have revealed a remarkable correspondence between nucleosome positions and exon-intron boundaries, and several studies have implicated specific histone modifications in regulating alternative splicing. In addition, recent progress in cracking the 'splicing code' shows that sequence motifs carried on the nascent RNA molecule itself are sufficient to accurately predict tissue-specific alternative splicing patterns. Together, these studies shed light on the complex interplay between RNA sequence, DNA sequence, and chromatin properties in regulating splicing.","authors":"Ringrose, L.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"F1000 Biol Rep","volume":"2","issue":null,"page":"74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21124984","title":"Photounbinding of calmodulin from a family of CaM binding peptides.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21124984<\/PMID><DateCompleted><Year>2011<\/Year><Month>04<\/Month><Day>27<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>5<\/Volume><Issue>11<\/Issue><PubDate><Year>2010<\/Year><Month>Nov<\/Month><Day>18<\/Day><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Photounbinding of calmodulin from a family of CaM binding peptides.<\/ArticleTitle><Pagination><MedlinePgn>e14050<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0014050<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Recent studies have shown that fluorescently labeled antibodies can be dissociated from their antigen by illumination with laser light. The mechanism responsible for the photounbinding effect, however, remains elusive. Here, we give important insights into the mechanism of photounbinding and show that the effect is not restricted to antibody\/antigen binding.","authors":"Neum\u00fcller, KG., Elsayad, K., Reisecker, JM., Waxham, MN., Heinze, KG.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"PLoS One","volume":"5","issue":"11","page":"e14050","pdf":null,"JrId":null,"fulltextlink":"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0014050","preprintlink":null,"articledate":"2011-04-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21124819","title":"Leptotene\/zygotene chromosome movement via the SUN\/KASH protein bridge in Caenorhabditis elegans.","abstract":"The Caenorhabditis elegans inner nuclear envelope protein matefin\/SUN-1 plays a conserved, pivotal role in the process of genome haploidization. CHK-2-dependent phosphorylation of SUN-1 regulates homologous chromosome pairing and interhomolog recombination in Caenorhabditis elegans. Using time-lapse microscopy, we characterized the movement of matefin\/SUN-1::GFP aggregates (the equivalent of chromosomal attachment plaques) and showed that the dynamics of matefin\/SUN-1 aggregates remained unchanged throughout leptonene\/zygotene, despite the progression of pairing. Movement of SUN-1 aggregates correlated with chromatin polarization. We also analyzed the requirements for the formation of movement-competent matefin\/SUN-1 aggregates in the context of chromosome structure and found that chromosome axes were required to produce wild-type numbers of attachment plaques. Abrogation of synapsis led to a deceleration of SUN-1 aggregate movement. Analysis of matefin\/SUN-1 in a double-strand break deficient mutant revealed that repair intermediates influenced matefin\/SUN-1 aggregate dynamics. Investigation of movement in meiotic regulator mutants substantiated that proper orchestration of the meiotic program and effective repair of DNA double-strand breaks were necessary for the wild-type behavior of matefin\/SUN-1 aggregates.","authors":"Baudrimont, A., Penkner, A., Woglar, A., Machacek, T., Wegrostek, C., Gloggnitzer, J., Fridkin, A., Klein, F., Gruenbaum, Y., Pasierbek, P., Jantsch, V.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"PLoS Genet","volume":"6","issue":"11","page":"e1001219","pdf":null,"JrId":"32385","fulltextlink":null,"preprintlink":null,"articledate":"2011-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21087492","title":"From an electrophoretic mobility shift assay to isolated transcription factors: a fast genomic-proteomic approach.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21087492<\/PMID><DateCompleted><Year>2011<\/Year><Month>03<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>11<\/Volume><PubDate><Year>2010<\/Year><Month>Nov<\/Month><Day>18<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>From an electrophoretic mobility shift assay to isolated transcription factors: a fast genomic-proteomic approach.<\/ArticleTitle><Pagination><MedlinePgn>644<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-11-644<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Hypocrea jecorina (anamorph Trichoderma reesei) is a filamentous ascomycete of industrial importance due to its hydrolases (e.g., xylanases and cellulases). The regulation of gene expression can influence the composition of the hydrolase cocktail, and thus, transcription factors are a major target of current research. Here, we design an approach for identifying a repressor of a xylanase-encoding gene.","authors":"Mach-Aigner, AR., Grosstessner-Hain, K., Po\u00e7as-Fonseca, MJ., Mechtler, K., Mach, RL.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"BMC Genomics","volume":"11","issue":"","page":"644","pdf":null,"JrId":"21855","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20735826","title":"Nolz1 promotes striatal neurogenesis through the regulation of retinoic acid signaling.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20735826<\/PMID><DateCompleted><Year>2011<\/Year><Month>01<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1749-8104<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>5<\/Volume><PubDate><Year>2010<\/Year><Month>Aug<\/Month><Day>24<\/Day><\/PubDate><\/JournalIssue><Title>Neural development<\/Title><ISOAbbreviation>Neural Dev<\/ISOAbbreviation><\/Journal><ArticleTitle>Nolz1 promotes striatal neurogenesis through the regulation of retinoic acid signaling.<\/ArticleTitle><Pagination><MedlinePgn>21<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1749-8104-5-21<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Nolz1 is a zinc finger transcription factor whose expression is enriched in the lateral ganglionic eminence (LGE), although its function is still unknown.","authors":"Urb\u00e1n, N., Mart\u00edn-Ib\u00e1\u00f1ez, R., Herranz, C., Esgleas, M., Crespo, E., Pardo, M., Crespo-Enr\u00edquez, I., M\u00e9ndez-G\u00f3mez, HR., Waclaw, R., Chatzi, C., Alvarez, S., Alvarez, R., Duester, G., Campbell, K., de Lera, AR., Vicario-Abej\u00f3n, C., Martinez, S., Alberch, J., Canals, JM.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"Neural Dev","volume":"5","issue":null,"page":"21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20727173","title":"Pax2 and Pax8 cooperate in mouse inner ear morphogenesis and innervation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20727173<\/PMID><DateCompleted><Year>2010<\/Year><Month>11<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>14<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-213X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>10<\/Volume><PubDate><Year>2010<\/Year><Month>Aug<\/Month><Day>20<\/Day><\/PubDate><\/JournalIssue><Title>BMC developmental biology<\/Title><ISOAbbreviation>BMC Dev Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Pax2 and Pax8 cooperate in mouse inner ear morphogenesis and innervation.<\/ArticleTitle><Pagination><MedlinePgn>89<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-213X-10-89<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Pax2;5;8 transcription factors play diverse roles in vertebrate and invertebrate organogenesis, including the development of the inner ear. Past research has suggested various cochlear defects and some vestibular defects in Pax2 null mice but the details of the cochlear defects and the interaction with other Pax family members in ear development remain unclear.","authors":"Bouchard, M., de Caprona, D., Busslinger, M., Xu, P., Fritzsch, B.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"BMC Dev Biol","volume":"10","issue":"","page":"89","pdf":null,"JrId":"21975","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20668550","title":"Enhanced food anticipatory activity associated with enhanced activation of extrahypothalamic neural pathways in serotonin2C receptor null mutant mice.","abstract":"The ability to entrain circadian rhythms to food availability is important for survival. Food-entrained circadian rhythms are characterized by increased locomotor activity in anticipation of food availability (food anticipatory activity). However, the molecular components and neural circuitry underlying the regulation of food anticipatory activity remain unclear. Here we show that serotonin(2C) receptor (5-HT2CR) null mutant mice subjected to a daytime restricted feeding schedule exhibit enhanced food anticipatory activity compared to wild-type littermates, without phenotypic differences in the impact of restricted feeding on food consumption, body weight loss, or blood glucose levels. Moreover, we show that the enhanced food anticipatory activity in 5-HT2CR null mutant mice develops independent of external light cues and persists during two days of total food deprivation, indicating that food anticipatory activity in 5-HT2CR null mutant mice reflects the locomotor output of a food-entrainable oscillator. Whereas restricted feeding induces c-fos expression to a similar extent in hypothalamic nuclei of wild-type and null mutant animals, it produces enhanced expression in the nucleus accumbens and other extrahypothalamic regions of null mutant mice relative to wild-type subjects. These data suggest that 5-HT2CRs gate food anticipatory activity through mechanisms involving extrahypothalamic neural pathways.","authors":"Hsu, JL., Yu, L., Sullivan, E., Bowman, M., Mistlberger, RE., Tecott, LH.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"PLoS One","volume":"5","issue":"7","page":"e11802","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20626890","title":"Establishment of a Cre\/loxP recombination system for N-terminal epitope tagging of genes in Tetrahymena.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20626890<\/PMID><DateCompleted><Year>2010<\/Year><Month>11<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2180<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>10<\/Volume><PubDate><Year>2010<\/Year><Month>Jul<\/Month><Day>13<\/Day><\/PubDate><\/JournalIssue><Title>BMC microbiology<\/Title><ISOAbbreviation>BMC Microbiol<\/ISOAbbreviation><\/Journal><ArticleTitle>Establishment of a Cre\/loxP recombination system for N-terminal epitope tagging of genes in Tetrahymena.<\/ArticleTitle><Pagination><MedlinePgn>191<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2180-10-191<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Epitope tagging is a powerful strategy to study the function of proteins. Although tools for C-terminal protein tagging in the ciliated protozoan Tetrahymena thermophila have been developed, N-terminal protein tagging in this organism is still technically demanding.","authors":"Busch, CJ., Vogt, A., Mochizuki, K.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"BMC Microbiol","volume":"10","issue":null,"page":"191","pdf":null,"JrId":"21992","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20492666","title":"Characterization of a naturally-occurring p27 mutation predisposing to multiple endocrine tumors.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20492666<\/PMID><DateCompleted><Year>2010<\/Year><Month>07<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1476-4598<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><PubDate><Year>2010<\/Year><Month>May<\/Month><Day>21<\/Day><\/PubDate><\/JournalIssue><Title>Molecular cancer<\/Title><ISOAbbreviation>Mol Cancer<\/ISOAbbreviation><\/Journal><ArticleTitle>Characterization of a naturally-occurring p27 mutation predisposing to multiple endocrine tumors.<\/ArticleTitle><Pagination><MedlinePgn>116<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1476-4598-9-116<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">p27Kip1 (p27) is an important negative regulator of the cell cycle and a putative tumor suppressor. The finding that a spontaneous germline frameshift mutation in Cdkn1b (encoding p27) causes the MENX multiple endocrine neoplasia syndrome in the rat provided the first evidence that Cdkn1b is a tumor susceptibility gene for endocrine tumors. Noteworthy, germline p27 mutations were also identified in human patients presenting with endocrine tumors. At present, it is not clear which features of p27 are crucial for this tissue-specific tumor predisposition in both rats and humans. It was shown that the MENX-associated Cdkn1b mutation causes reduced expression of the encoded protein, but the molecular mechanisms are unknown. To better understand the role of p27 in tumor predisposition and to characterize the MENX animal model at the molecular level, a prerequisite for future preclinical studies, we set out to assess the functional properties of the MENX-associated p27 mutant protein (named p27fs177) in vitro and in vivo.","authors":"Molatore, S., Kiermaier, E., Jung, CB., Lee, M., Pulz, E., H\u00f6fler, H., Atkinson, MJ., Pellegata, NS.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"Mol Cancer","volume":"9","issue":null,"page":"116","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20485517","title":"The Set3\/Hos2 histone deacetylase complex attenuates cAMP\/PKA signaling to regulate morphogenesis and virulence of Candida albicans.","abstract":"Candida albicans, like other pleiomorphic fungal pathogens, is able to undergo a reversible transition between single yeast-like cells and multicellular filaments. This morphogenetic process has long been considered as a key fungal virulence factor. Here, we identify the evolutionarily conserved Set3\/Hos2 histone deacetylase complex (Set3C) as a crucial repressor of the yeast-to-filament transition. Cells lacking core components of the Set3C are able to maintain all developmental phases, but are hypersusceptible to filamentation-inducing signals, because of a hyperactive cAMP\/Protein Kinase A signaling pathway. Strikingly, Set3C-mediated control of filamentation is required for virulence in vivo, since set3Delta\/Delta cells display strongly attenuated virulence in a mouse model of systemic infection. Importantly, the inhibition of histone deacetylase activity by trichostatin A exclusively phenocopies the absence of a functional Set3C, but not of any other histone deacetylase gene. Hence, our work supports a paradigm for manipulating morphogenesis in C. albicans through alternative antifungal therapeutic strategies.","authors":"Hnisz, D., Majer, O., Frohner, IE., Komnenovic, V., Kuchler, K.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"PLoS Pathog","volume":"6","issue":"5","page":"e1000889","pdf":null,"JrId":"32532","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20368966","title":"Topology and organization of the Salmonella typhimurium type III secretion needle complex components.","abstract":"The correct organization of single subunits of multi-protein machines in a three dimensional context is critical for their functionality. Type III secretion systems (T3SS) are molecular machines with the capacity to deliver bacterial effector proteins into host cells and are fundamental for the biology of many pathogenic or symbiotic bacteria. A central component of T3SSs is the needle complex, a multiprotein structure that mediates the passage of effector proteins through the bacterial envelope. We have used cryo electron microscopy combined with bacterial genetics, site-specific labeling, mutational analysis, chemical derivatization and high-resolution mass spectrometry to generate an experimentally validated topographic map of a Salmonella typhimurium T3SS needle complex. This study provides insights into the organization of this evolutionary highly conserved nanomachinery and is the basis for further functional analysis.","authors":"Schraidt, O., Lefebre, MD., Brunner, MJ., Schmied, WH., Schmidt, A., Radics, J., Mechtler, K., Gal\u00e1n, JE., Marlovits, TC.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"PLoS Pathog","volume":"6","issue":"4","page":"e1000824","pdf":null,"JrId":"32532","fulltextlink":null,"preprintlink":null,"articledate":"2010-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20230614","title":"Riding in silence: a little snowboarding, a lot of small RNAs.","abstract":"The recent symposium, RNA silencing: Mechanism, Biology and Applications, organized by Phillip D. Zamore (University of Massachusetts Medical School) and Beverly Davidson (University of Iowa), and held in Keystone, Colorado, brought together scientists working on diverse aspects of RNA silencing, a field that comprises a multitude of gene regulatory pathways guided by microRNAs, small interfering RNAs and PIWI-interacting RNAs.","authors":"Ameres, SL., Fukunaga, R.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"Silence","volume":"1","issue":"1","page":"8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20195357","title":"A comprehensive resource of interacting protein regions for refining human transcription factor networks.","abstract":"Large-scale data sets of protein-protein interactions (PPIs) are a valuable resource for mapping and analysis of the topological and dynamic features of interactome networks. The currently available large-scale PPI data sets only contain information on interaction partners. The data presented in this study also include the sequences involved in the interactions (i.e., the interacting regions, IRs) suggested to correspond to functional and structural domains. Here we present the first large-scale IR data set obtained using mRNA display for 50 human transcription factors (TFs), including 12 transcription-related proteins. The core data set (966 IRs; 943 PPIs) displays a verification rate of 70%. Analysis of the IR data set revealed the existence of IRs that interact with multiple partners. Furthermore, these IRs were preferentially associated with intrinsic disorder. This finding supports the hypothesis that intrinsically disordered regions play a major role in the dynamics and diversity of TF networks through their ability to structurally adapt to and bind with multiple partners. Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function.","authors":"Miyamoto-Sato, E., Fujimori, S., Ishizaka, M., Hirai, N., Masuoka, K., Saito, R., Ozawa, Y., Hino, K., Washio, T., Tomita, M., Yamashita, T., Oshikubo, T., Akasaka, H., Sugiyama, J., Matsumoto, Y., Yanagawa, H.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"PLoS One","volume":"5","issue":"2","page":"e9289","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20179753","title":"PI3Kgamma protects from myocardial ischemia and reperfusion injury through a kinase-independent pathway.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20179753<\/PMID><DateCompleted><Year>2010<\/Year><Month>09<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>5<\/Volume><Issue>2<\/Issue><PubDate><Year>2010<\/Year><Month>Feb<\/Month><Day>22<\/Day><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>PI3Kgamma protects from myocardial ischemia and reperfusion injury through a kinase-independent pathway.<\/ArticleTitle><Pagination><MedlinePgn>e9350<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0009350<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">PI3Kgamma functions in the immune compartment to promote inflammation in response to G-protein-coupled receptor (GPCR) agonists and PI3Kgamma also acts within the heart itself both as a negative regulator of cardiac contractility and as a pro-survival factor. Thus, PI3Kgamma has the potential to both promote and limit M I\/R injury.","authors":"Haubner, BJ., Neely, GG., Voelkl, JG., Damilano, F., Kuba, K., Imai, Y., Komnenovic, V., Mayr, A., Pachinger, O., Hirsch, E., Penninger, JM., Metzler, B.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"PLoS One","volume":"5","issue":"2","page":"e9350","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20158870","title":"Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS\/MS spectra and noise reduction.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20158870<\/PMID><DateCompleted><Year>2010<\/Year><Month>04<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>11 Suppl 1<\/Volume><PubDate><Year>2010<\/Year><Month>Feb<\/Month><Day>10<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS\/MS spectra and noise reduction.<\/ArticleTitle><Pagination><MedlinePgn>S13<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-11-S1-S13<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Tandem mass spectrometry (MS\/MS) has become a standard method for identification of proteins extracted from biological samples but the huge number and the noise contamination of MS\/MS spectra obstruct swift and reliable computer-aided interpretation. Typically, a minor fraction of the spectra per sample (most often, only a few %) and about 10% of the peaks per spectrum contribute to the final result if protein identification is not prevented by the noise at all.","authors":"Mujezinovic, N., Schneider, G., Wildpaner, M., Mechtler, K., Eisenhaber, F.","publication_status":"epublish","journalpubyear":"2010","journaltitle":"BMC Genomics","volume":"11 Suppl 1","issue":null,"page":"S13","pdf":null,"JrId":"21855","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19956608","title":"Defining a superlens operating regime for imaging fluorescent molecules.","abstract":"It has been shown that thin metal-based films can at certain frequencies act as planar near-field lenses for certain polarization components. A desirable property of such \"lenses\" is that they can also enhance and focus some large transverse spatial frequency components which contain sub-diffraction limit details. Over the last decade there has been much work in optimizing designs to reduce effects (such as material losses and surface roughness) that are detrimental to image reconstruction. One design that can reduce some of these undesirable effects, and which has received a fair amount of attention recently, is the stacked metal-dielectric superlens. Here we theoretically explore the imaging ability of such a design for the specific purpose of imaging a fluorescent dye (the common bio-marker GFP) in the vicinity of the superlens surface. Our calculations take into consideration the interaction (damping) of an oscillating electric dipole with the metallic layers in the superlens. We also assume a Gaussian frequency distribution spectrum for the dipole. We treat the metallic-alloy and dielectric-alloy layers separately using an appropriate effective medium theory. The transmission properties are evaluated via Transfer matrix (-matrix) calculations that were performed in the MatLab and MathCad environments. Our study shows that it is in principle possible to image fluorescent molecules using a simple bilayer planar superlens. We find that optimal parameters for such a superlens occur when the peak dipole emission-frequency is slightly offset from the Surface Plasmon resonance frequency of the metal-dielectric interfaces. The best resolution is obtained when the fluorescent molecules are not too close (&gt;\/ approximately 10 nm) or too far (&gt;\/approximately 30 nm) from the superlens surface. The realization and application of a superlens with the specified design is possible using current nanofabrication techniques. When combined with e.g. a sub-wavelength grating structure (such as in the far-field superlens design previously proposed [1]) or a fast near-field scanning probe, it could provide a means for fast fluorescent imaging with sub-diffraction limit resolution.","authors":"Elsayad, K., Heinze, KG.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"PLoS One","volume":"4","issue":"12","page":"e7963","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19765287","title":"Dynamic localisation of Ran GTPase during the cell cycle.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19765287<\/PMID><DateCompleted><Year>2009<\/Year><Month>12<\/Month><Day>03<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2121<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>10<\/Volume><PubDate><Year>2009<\/Year><Month>Sep<\/Month><Day>18<\/Day><\/PubDate><\/JournalIssue><Title>BMC cell biology<\/Title><ISOAbbreviation>BMC Cell Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Dynamic localisation of Ran GTPase during the cell cycle.<\/ArticleTitle><Pagination><MedlinePgn>66<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2121-10-66<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Ran GTPase has multiple functions during the cell division cycle, including nucleocytoplasmic transport, mitotic spindle assembly and nuclear envelope formation. The activity of Ran is determined by both its guanine nucleotide-bound state and its subcellular localization.","authors":"Hutchins, JR., Moore, WJ., Clarke, PR.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"BMC Cell Biol","volume":"10","issue":null,"page":"66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19624853","title":"Motmot, an open-source toolkit for realtime video acquisition and analysis.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19624853<\/PMID><DateCompleted><Year>2011<\/Year><Month>07<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>09<\/Month><Day>30<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1751-0473<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>4<\/Volume><PubDate><Year>2009<\/Year><Month>Jul<\/Month><Day>22<\/Day><\/PubDate><\/JournalIssue><Title>Source code for biology and medicine<\/Title><ISOAbbreviation>Source Code Biol Med<\/ISOAbbreviation><\/Journal><ArticleTitle>Motmot, an open-source toolkit for realtime video acquisition and analysis.<\/ArticleTitle><Pagination><MedlinePgn>5<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1751-0473-4-5<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Video cameras sense passively from a distance, offer a rich information stream, and provide intuitively meaningful raw data. Camera-based imaging has thus proven critical for many advances in neuroscience and biology, with applications ranging from cellular imaging of fluorescent dyes to tracking of whole-animal behavior at ecologically relevant spatial scales.","authors":"Straw, AD., Dickinson, MH.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"Source Code Biol Med","volume":"4","issue":null,"page":"5","pdf":null,"JrId":"32959","fulltextlink":null,"preprintlink":null,"articledate":"2011-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19549985","title":"PKC-theta modulates the strength of T cell responses by targeting Cbl-b for ubiquitination and degradation.","abstract":"The E3 ubiquitin ligase Casitas B-lineage lymphoma (Cbl-b) is central to antigen-induced immune tolerance and regulates the CD28 dependence of T cell activation. Cbl-b undergoes ubiquitination and proteasomal degradation after adequate costimulation of T cells; however, the mechanism involved is unknown. Here, we identified protein kinase C-theta (PKC-theta) as the critical intermediary for the inactivation of Cbl-b in response to costimulation of T cells through CD28. PKC-theta associated with Cbl-b on stimulation of the T cell receptor. After costimulation of T cells through CD28, Cbl-b was ubiquitinated and degraded through a mechanism that depended on the kinase activity of PKC-theta. Consistent with this mechanism, the impaired responses of PKCtheta-deficient T cells were at least partially restored by the concomitant genetic loss of cblb. Thus, our data establish a nonredundant antagonism between PKC-theta and Cbl-b that regulates T cell activation responses.","authors":"Gruber, T., Hermann-Kleiter, N., Hinterleitner, R., Fresser, F., Schneider, R., Gastl, G., Penninger, JM., Baier, G.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"Sci Signal","volume":"2","issue":"76","page":"ra30","pdf":null,"JrId":"34171","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19482689","title":"CTGF and chronic kidney fibrosis.","abstract":"Chronic kidney fibrosis is the unifying pathological feature of diverse renal disease leading to a progressive decline in renal function and eventually end-stage kidney failure. Many growth factors are able to induce an imbalance of extracellular matrix production and degradation, leading to excessive matrix and fibrosis in both glomeruli and in the tubulointerstitium. Over the last decade the role of connective tissue growth factor (CTGF) in renal fibrosis has been intensively studied. CTGF participates in cell proliferation, migration, and differentiation and mediates profibrotic activity by acting either directly, or as a co-factor for TGF beta 1, which is well characterised as a key cytokine mediating both the induction and promotion of fibrogenesis. CTGF also has the potential to modulate factors such as VEGF and bone morphogenic proteins, which are integral to both the development and repair process inherent in renal fibrogenesis. This review focuses on the role of CTGF in renal fibrosis and specifically its role in inducing fibrosis by factors integrally involved in the development of diabetic nephropathy, namely high glucose, angiotensin II, TGF beta 1 and AGEs.","authors":"Chen, XM., Qi, W., Pollock, CA.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"Front Biosci (Schol Ed)","volume":"1","issue":"","page":"132-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19400936","title":"Origin and evolution of the RIG-I like RNA helicase gene family.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19400936<\/PMID><DateCompleted><Year>2009<\/Year><Month>06<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2148<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><PubDate><Year>2009<\/Year><Month>Apr<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>BMC evolutionary biology<\/Title><ISOAbbreviation>BMC Evol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Origin and evolution of the RIG-I like RNA helicase gene family.<\/ArticleTitle><Pagination><MedlinePgn>85<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2148-9-85<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The DExD\/H domain containing RNA helicases such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are key cytosolic pattern recognition receptors (PRRs) for detecting nucleotide pathogen associated molecular patterns (PAMPs) of invading viruses. The RIG-I and MDA5 proteins differentially recognise conserved PAMPs in double stranded or single stranded viral RNA molecules, leading to activation of the interferon system in vertebrates. They share three core protein domains including a RNA helicase domain near the C terminus (HELICc), one or more caspase activation and recruitment domains (CARDs) and an ATP dependent DExD\/H domain. The RIG-I\/MDA5 directed interferon response is negatively regulated by laboratory of genetics and physiology 2 (LGP2) and is believed to be controlled by the mitochondria antiviral signalling protein (MAVS), a CARD containing protein associated with mitochondria.","authors":"Zou, J., Chang, M., Nie, P., Secombes, CJ.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"BMC Evol Biol","volume":"9","issue":"","page":"85","pdf":null,"JrId":"22312","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19393099","title":"FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19393099<\/PMID><DateCompleted><Year>2009<\/Year><Month>06<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2105<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>10<\/Volume><PubDate><Year>2009<\/Year><Month>Apr<\/Month><Day>25<\/Day><\/PubDate><\/JournalIssue><Title>BMC bioinformatics<\/Title><ISOAbbreviation>BMC Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families.<\/ArticleTitle><Pagination><MedlinePgn>123<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2105-10-123<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The availability of 12 fully sequenced Drosophila species genomes provides an excellent opportunity to explore the evolutionary mechanism, structure and function of gene families in Drosophila. Currently, several important resources, such as FlyBase, FlyMine and DroSpeGe, have been devoted to integrating genetic, genomic, and functional data of Drosophila into a well-organized form. However, all of these resources are gene-centric and lack the information of the gene families in Drosophila.","authors":"Wu, J., Xu, X., Xiao, J., Xu, L., Yi, H., Gao, S., Liu, J., Bao, Q., Zhao, F., Li, X.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"BMC Bioinformatics","volume":"10","issue":"","page":"123","pdf":null,"JrId":"21854","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19383157","title":"Meiosis genes in Daphnia pulex and the role of parthenogenesis in genome evolution.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19383157<\/PMID><DateCompleted><Year>2009<\/Year><Month>05<\/Month><Day>27<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2148<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><PubDate><Year>2009<\/Year><Month>Apr<\/Month><Day>21<\/Day><\/PubDate><\/JournalIssue><Title>BMC evolutionary biology<\/Title><ISOAbbreviation>BMC Evol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Meiosis genes in Daphnia pulex and the role of parthenogenesis in genome evolution.<\/ArticleTitle><Pagination><MedlinePgn>78<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2148-9-78<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Thousands of parthenogenetic animal species have been described and cytogenetic manifestations of this reproductive mode are well known. However, little is understood about the molecular determinants of parthenogenesis. The Daphnia pulex genome must contain the molecular machinery for different reproductive modes: sexual (both male and female meiosis) and parthenogenetic (which is either cyclical or obligate). This feature makes D. pulex an ideal model to investigate the genetic basis of parthenogenesis and its consequences for gene and genome evolution. Here we describe the inventory of meiotic genes and their expression patterns during meiotic and parthenogenetic reproduction to help address whether parthenogenesis uses existing meiotic and mitotic machinery, or whether novel processes may be involved.","authors":"Schurko, AM., Logsdon, JM., Eads, BD.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"BMC Evol Biol","volume":"9","issue":"","page":"78","pdf":null,"JrId":"22312","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19368711","title":"Evolutionary history of the iroquois\/Irx genes in metazoans.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19368711<\/PMID><DateCompleted><Year>2009<\/Year><Month>05<\/Month><Day>01<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2148<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><PubDate><Year>2009<\/Year><Month>Apr<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>BMC evolutionary biology<\/Title><ISOAbbreviation>BMC Evol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Evolutionary history of the iroquois\/Irx genes in metazoans.<\/ArticleTitle><Pagination><MedlinePgn>74<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2148-9-74<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The iroquois (iro\/Irx) genes encode transcriptional regulators that belong to the TALE superclass of homeodomain proteins and have key functions during development in both vertebrates and insects. The Irx genes occur in one or two genomic clusters containing three genes each within the Drosophila and several vertebrate genomes, respectively. The similar genomic organization in Drosophila and vertebrates is widely considered as a result of convergent evolution, due to independent tandem gene duplications. In this study, we investigate the evolutionary history of the Irx genes at the scale of the whole metazoan kingdom.","authors":"Kerner, P., Ikmi, A., Coen, D., Vervoort, M.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"BMC Evol Biol","volume":"9","issue":"","page":"74","pdf":null,"JrId":"22312","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19323841","title":"Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss-of-function phenotypes in Drosophila.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19323841<\/PMID><DateCompleted><Year>2009<\/Year><Month>06<\/Month><Day>01<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2199<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>10<\/Volume><PubDate><Year>2009<\/Year><Month>Mar<\/Month><Day>26<\/Day><\/PubDate><\/JournalIssue><Title>BMC molecular biology<\/Title><ISOAbbreviation>BMC Mol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss-of-function phenotypes in Drosophila.<\/ArticleTitle><Pagination><MedlinePgn>26<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2199-10-26<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The Arthropods are a diverse group of organisms including Chelicerata (ticks, mites, spiders), Crustacea (crabs, shrimps), and Insecta (flies, mosquitoes, beetles, silkworm). The cattle tick, Rhipicephalus (Boophilus) microplus, is an economically significant ectoparasite of cattle affecting cattle industries world wide. With the availability of sequence reads from the first Chelicerate genome project (the Ixodes scapularis tick) and extensive R. microplus ESTs, we investigated evidence for putative RNAi proteins and studied RNA interference in tick cell cultures and adult female ticks targeting Drosophila homologues with known cell viability phenotype.","authors":"Kurscheid, S., Lew-Tabor, AE., Rodriguez Valle, M., Bruyeres, AG., Doogan, VJ., Munderloh, UG., Guerrero, FD., Barrero, RA., Bellgard, MI.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"BMC Mol Biol","volume":"10","issue":"","page":"26","pdf":null,"JrId":"21887","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19292915","title":"Ancient diversification of eukaryotic MCM DNA replication proteins.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19292915<\/PMID><DateCompleted><Year>2009<\/Year><Month>04<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2148<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><PubDate><Year>2009<\/Year><Month>Mar<\/Month><Day>17<\/Day><\/PubDate><\/JournalIssue><Title>BMC evolutionary biology<\/Title><ISOAbbreviation>BMC Evol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Ancient diversification of eukaryotic MCM DNA replication proteins.<\/ArticleTitle><Pagination><MedlinePgn>60<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2148-9-60<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Yeast and animal cells require six mini-chromosome maintenance proteins (Mcm2-7) for pre-replication complex formation, DNA replication initiation and DNA synthesis. These six individual MCM proteins form distinct heterogeneous subunits within a hexamer which is believed to form the replicative helicase and which associates with the essential but non-homologous Mcm10 protein during DNA replication. In contrast Archaea generally only possess one MCM homologue which forms a homohexameric MCM helicase. In some eukaryotes Mcm8 and Mcm9 paralogues also appear to be involved in DNA replication although their exact roles are unclear.","authors":"Liu, Y., Richards, TA., Aves, SJ.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"BMC Evol Biol","volume":"9","issue":"","page":"60","pdf":null,"JrId":"22312","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19273247","title":"The dark and the bright side of Stat3: proto-oncogene and tumor-suppressor.","abstract":"Stat transcription factors have been implicated in tumorigenesis in mice and men. Stat3 and Stat5 are considered powerful proto-oncogenes, whereas Stat1 has been demonstrated to suppress tumor formation. We demonstrate here for the first time that a constitutive active version of Stat3alpha (Stat3alphaC) may also suppress transformation. Mouse embryonic fibroblasts (MEFs) deficient for p53 can be transformed with either c-myc or with rasV12 alone. Interestingly, transformation by c-myc is efficiently suppressed by co-expression of Stat3alphaC, but Stat3alphaC does not interfere with transformation by the rasV12-oncogene. In contrast, transplantation of bone marrow cells expressing Stat3alphaC induces the formation of a highly aggressive T cell leukemia in mice. The leukemic cells invaded multiple organs including lung, heart, salivary glands, liver and kidney. Interestingly, transplanted mice developed a similar leukemia when the bone marrow cells were transduced with Stat3beta, which is also constitutively active when expressed at significant levels. Our experiments demonstrate that Stat3 has both - tumor suppressing and tumor promoting properties.","authors":"Ecker, A., Simma, O., Hoelbl, A., Kenner, L., Beug, H., Moriggl, R., Sexl, V.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"Front Biosci (Landmark Ed)","volume":"14","issue":null,"page":"2944-58","pdf":null,"JrId":"29838","fulltextlink":null,"preprintlink":null,"articledate":"2009-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31802445","title":"Developments in Artificial Platelet and Erythroid Transfusion Products.","abstract":"Platelet and blood transfusions have vital importance to the lives of many patients. Platelet transfusions are a life-saving intervention by reducing risk of bleeding in thrombocytopenic patients. Due to the short shelf life of platelets and their limited availability, researchers have developed various platelet transfusion production technologies. Understanding the cellular and biophysical mechanisms of platelet release is particularly important for development of platelet transfusion products (PTPs) and to translate them to clinical applications in patients requiring platelet infusion. Similarly, due to donor dependence and increased clinical need of blood transfusions, studies on the erythroid transfusion products (ETPs) have recently gained momentum. This led to development of ETP technologies involving differentiation of stem cells to fully functional erythrocytes in vitro. During megakaryopoiesis or erythropoiesis, various stimulatory factors, growth factors, transcription factors, and biophysical conditions have been shown to play a crucial role in the formation final blood products. Thus, understanding of the in vivo mechanisms of platelet release and erythrocyte maturation is particularly important for mimicking these conditions in vitro. This review focuses on latest and up-to-date information about the innovations in PTP and ETP technologies. We also discuss some of the recent fundamental findings that have changed our understanding of in vivo platelet release and blood formation. Human bone marrow acts as a source of cells required for erythropoiesis and megakaryopoeiesis. Understanding of molecular mechanism and physiology of these vital and curitial events allowed us to mimic these conditions ex vivo and to develop artificial platelet and erythroid transfusion production technologies.","authors":"Meric, N., Guney Esken, G., Uslu, M., Kocabas, F.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Adv Exp Med Biol","volume":"1247","issue":"","page":"65-87","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19239685","title":"A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19239685<\/PMID><DateCompleted><Year>2009<\/Year><Month>06<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>09<\/Month><Day>29<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1748-7188<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>4<\/Volume><PubDate><Year>2009<\/Year><Month>Feb<\/Month><Day>24<\/Day><\/PubDate><\/JournalIssue><Title>Algorithms for molecular biology : AMB<\/Title><ISOAbbreviation>Algorithms Mol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data.<\/ArticleTitle><Pagination><MedlinePgn>5<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1748-7188-4-5<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networks from transcript profiling data remains an important yet challenging endeavor. A transcript profile specifies the abundances of many genes in a biological sample of interest. Prevailing strategies for learning the structure of a genetic network from high-dimensional transcript profiling data assume sparsity and linearity. Many methods consider relatively small directed graphs, inferring graphs with up to a few hundred nodes. This work examines large undirected graphs representations of genetic networks, graphs with many thousands of nodes where an undirected edge between two nodes does not indicate the direction of influence, and the problem of estimating the structure of such a sparse linear genetic network (SLGN) from transcript profiling data.","authors":"Bhadra, S., Bhattacharyya, C., Chandra, NR., Mian, IS.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"Algorithms Mol Biol","volume":"4","issue":"","page":"5","pdf":null,"JrId":"32753","fulltextlink":null,"preprintlink":null,"articledate":"2009-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19223600","title":"The role of calsenilin\/DREAM\/KChIP3 in contextual fear conditioning.","abstract":"Potassium channel interacting proteins (KChIPs) are members of a family of calcium binding proteins that interact with Kv4 potassium (K(+)) channel primary subunits and also act as transcription factors. The Kv4 subunit is a primary K(+) channel pore-forming subunit, which contributes to the somatic and dendritic A-type currents throughout the nervous system. These A-type currents play a key role in the regulation of neuronal excitability and dendritic processing of incoming synaptic information. KChIP3 is also known as calsenilin and as the transcription factor, downstream regulatory element antagonist modulator (DREAM), which regulates a number of genes including prodynorphin. KChIP3 and Kv4 primary channel subunits are highly expressed in hippocampus, an area of the brain important for learning and memory. Through its various functions, KChIP3 may play a role in the regulation of synaptic plasticity and learning and memory. We evaluated the role of KChIP3 in a hippocampus-dependent memory task, contextual fear conditioning. Male KChIP3 knockout (KO) mice showed significantly enhanced memory 24 hours after training as measured by percent freezing. In addition, we found that membrane association and interaction with Kv4.2 of KChIP3 protein was significantly decreased and nuclear KChIP3 expression was increased six hours after the fear conditioning training paradigm with no significant change in KChIP3 mRNA. In addition, prodynorphin mRNA expression was significantly decreased six hours after fear conditioning training in wild-type (WT) but not in KO animals. These data suggest a role for regulation of gene expression by KChIP3\/DREAM\/calsenilin in consolidation of contextual fear conditioning memories.","authors":"Alexander, JC., McDermott, CM., Tunur, T., Rands, V., Stelly, C., Karhson, D., Bowlby, MR., An, WF., Sweatt, JD., Schrader, LA.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"Learn Mem","volume":"16","issue":"3","page":"167-77","pdf":null,"JrId":"20827","fulltextlink":null,"preprintlink":null,"articledate":"2009-05-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19154605","title":"Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19154605<\/PMID><DateCompleted><Year>2009<\/Year><Month>03<\/Month><Day>19<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2148<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><PubDate><Year>2009<\/Year><Month>Jan<\/Month><Day>20<\/Day><\/PubDate><\/JournalIssue><Title>BMC evolutionary biology<\/Title><ISOAbbreviation>BMC Evol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers.<\/ArticleTitle><Pagination><MedlinePgn>18<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2148-9-18<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs.","authors":"Finnerty, JR., Mazza, ME., Jezewski, PA.","publication_status":"epublish","journalpubyear":"2009","journaltitle":"BMC Evol Biol","volume":"9","issue":"","page":"18","pdf":null,"JrId":"22312","fulltextlink":null,"preprintlink":null,"articledate":"2009-03-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19050754","title":"Vision egg: an open-source library for realtime visual stimulus generation.","abstract":"Modern computer hardware makes it possible to produce visual stimuli in ways not previously possible. Arbitrary scenes, from traditional sinusoidal gratings to naturalistic 3D scenes can now be specified on a frame-by-frame basis in realtime. A programming library called the Vision Egg that aims to make it easy to take advantage of these innovations. The Vision Egg is a free, open-source library making use of OpenGL and written in the high-level language Python with extensions in C. Careful attention has been paid to the issues of luminance and temporal calibration, and several interfacing techniques to input devices such as mice, movement tracking systems, and digital triggers are discussed. Together, these make the Vision Egg suitable for many psychophysical, electrophysiological, and behavioral experiments. This software is available for free download at visionegg.org.","authors":"Straw, AD.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"Front Neuroinform","volume":"2","issue":null,"page":"4","pdf":null,"JrId":"34630","fulltextlink":null,"preprintlink":null,"articledate":"2011-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18776931","title":"Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system.","abstract":"Genome-wide identification of mRNAs regulated by RNA-binding proteins is crucial to uncover post-transcriptional gene regulatory systems. The conserved PUF family RNA-binding proteins repress gene expression post-transcriptionally by binding to sequence elements in 3'-UTRs of mRNAs. Despite their well-studied implications for development and neurogenesis in metazoa, the mammalian PUF family members are only poorly characterized and mRNA targets are largely unknown. We have systematically identified the mRNAs associated with the two human PUF proteins, PUM1 and PUM2, by the recovery of endogenously formed ribonucleoprotein complexes and the analysis of associated RNAs with DNA microarrays. A largely overlapping set comprised of hundreds of mRNAs were reproducibly associated with the paralogous PUM proteins, many of them encoding functionally related proteins. A characteristic PUF-binding motif was highly enriched among PUM bound messages and validated with RNA pull-down experiments. Moreover, PUF motifs as well as surrounding sequences exhibit higher conservation in PUM bound messages as opposed to transcripts that were not found to be associated, suggesting that PUM function may be modulated by other factors that bind conserved elements. Strikingly, we found that PUF motifs are enriched around predicted miRNA binding sites and that high-confidence miRNA binding sites are significantly enriched in the 3'-UTRs of experimentally determined PUM1 and PUM2 targets, strongly suggesting an interaction of human PUM proteins with the miRNA regulatory system. Our work suggests extensive connections between the RBP and miRNA post-transcriptional regulatory systems and provides a framework for deciphering the molecular mechanism by which PUF proteins regulate their target mRNAs.","authors":"Galgano, A., Forrer, M., Jaskiewicz, L., Kanitz, A., Zavolan, M., Gerber, AP.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"PLoS One","volume":"3","issue":"9","page":"e3164","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-11-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11567140","title":"Positive regulation of T cell activation and integrin adhesion by the adapter Fyb\/Slap.","abstract":"The molecular adapter Fyb\/Slap regulates signaling downstream of the T cell receptor (TCR), but whether it plays a positive or negative role is controversial. We demonstrate that Fyb\/Slap-deficient T cells exhibit defective proliferation and cytokine production in response to TCR stimulation. Fyb\/Slap is also required in vivo for T cell-dependent immune responses. Functionally, Fyb\/Slap has no apparent role in the activation of known TCR signaling pathways, F-actin polymerization, or TCR clustering. Rather, Fyb\/Slap regulates TCR-induced integrin clustering and adhesion. Thus, Fyb\/Slap is the first molecular adapter to be identified that couples TCR stimulation to the avidity modulation of integrins governing T cell adhesion.","authors":"Griffiths, EK., Krawczyk, C., Kong, YY., Raab, M., Hyduk, SJ., Bouchard, D., Chan, VS., Kozieradzki, I., Oliveira-Dos-Santos, AJ., Wakeham, A., Ohashi, PS., Cybulsky, MI., Rudd, CE., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Science","volume":"293","issue":"5538","page":"2260-3","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-10-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18775069","title":"Hen's teeth with enamel cap: from dream to impossibility.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18775069<\/PMID><DateCompleted><Year>2009<\/Year><Month>02<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2148<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>8<\/Volume><PubDate><Year>2008<\/Year><Month>Sep<\/Month><Day>05<\/Day><\/PubDate><\/JournalIssue><Title>BMC evolutionary biology<\/Title><ISOAbbreviation>BMC Evol Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Hen's teeth with enamel cap: from dream to impossibility.<\/ArticleTitle><Pagination><MedlinePgn>246<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2148-8-246<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The ability to form teeth was lost in an ancestor of all modern birds, approximately 100-80 million years ago. However, experiments in chicken have revealed that the oral epithelium can respond to inductive signals from mouse mesenchyme, leading to reactivation of the odontogenic pathway. Recently, tooth germs similar to crocodile rudimentary teeth were found in a chicken mutant. These \"chicken teeth\" did not develop further, but the question remains whether functional teeth with enamel cap would have been obtained if the experiments had been carried out over a longer time period or if the chicken mutants had survived. The next odontogenetic step would have been tooth differentiation, involving deposition of dental proteins.","authors":"Sire, JY., Delgado, SC., Girondot, M.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"BMC Evol Biol","volume":"8","issue":"","page":"246","pdf":null,"JrId":"22312","fulltextlink":null,"preprintlink":null,"articledate":"2009-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18716665","title":"JunB Inhibits ER Stress and Apoptosis in Pancreatic Beta Cells.","abstract":"Cytokines contribute to pancreatic beta-cell apoptosis in type 1 diabetes (T1D) by modulation of beta-cell gene expression networks. The transcription factor Activator Protein-1 (AP-1) is a key regulator of inflammation and apoptosis. We presently evaluated the function of the AP-1 subunit JunB in cytokine-mediated beta-cell dysfunction and death. The cytokines IL-1beta+IFN-gamma induced an early and transitory upregulation of JunB by NF-kappaB activation. Knockdown of JunB by RNA interference increased cytokine-mediated expression of inducible nitric oxide synthase (iNOS) and endoplasmic reticulum (ER) stress markers, leading to increased apoptosis in an insulin-producing cell line (INS-1E) and in purified rat primary beta-cells. JunB knockdown beta-cells and junB(-\/-) fibroblasts were also more sensitive to the chemical ER stressor cyclopiazonic acid (CPA). Conversely, adenoviral-mediated overexpression of JunB diminished iNOS and ER markers expression and protected beta-cells from cytokine-induced cell death. These findings demonstrate a novel and unexpected role for JunB as a regulator of defense mechanisms against cytokine- and ER stress-mediated apoptosis.","authors":"Gurzov, EN., Ortis, F., Bakiri, L., Wagner, EF., Eizirik, DL.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"PLoS One","volume":"3","issue":"8","page":"e3030","pdf":null,"JrId":"33103","fulltextlink":null,"preprintlink":null,"articledate":"2008-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18560542","title":"Perinatal androgens and adult behavior vary with nestling social system in siblicidal boobies.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18560542<\/PMID><DateCompleted><Year>2008<\/Year><Month>08<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>3<\/Volume><Issue>6<\/Issue><PubDate><Year>2008<\/Year><Month>Jun<\/Month><Day>18<\/Day><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Perinatal androgens and adult behavior vary with nestling social system in siblicidal boobies.<\/ArticleTitle><Pagination><MedlinePgn>e2460<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0002460<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Exposure to androgens early in development, while activating adaptive aggressive behavior, may also exert long-lasting effects on non-target components of phenotype. Here we compare these organizational effects of perinatal androgens in closely related Nazca (Sula granti) and blue-footed (S. nebouxii) boobies that differ in neonatal social system. The older of two Nazca booby hatchlings unconditionally attacks and ejects the younger from the nest within days of hatching, while blue-footed booby neonates lack lethal aggression. Both Nazca booby chicks facultatively upregulate testosterone (T) during fights, motivating the prediction that baseline androgen levels differ between obligately siblicidal and other species.","authors":"M\u00fcller, MS., Brennecke, JF., Porter, ET., Ottinger, MA., Anderson, DJ.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"PLoS One","volume":"3","issue":"6","page":"e2460","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18545663","title":"Live imaging at the onset of cortical neurogenesis reveals differential appearance of the neuronal phenotype in apical versus basal progenitor progeny.","abstract":"The neurons of the mammalian brain are generated by progenitors dividing either at the apical surface of the ventricular zone (neuroepithelial and radial glial cells, collectively referred to as apical progenitors) or at its basal side (basal progenitors, also called intermediate progenitors). For apical progenitors, the orientation of the cleavage plane relative to their apical-basal axis is thought to be of critical importance for the fate of the daughter cells. For basal progenitors, the relationship between cell polarity, cleavage plane orientation and the fate of daughter cells is unknown. Here, we have investigated these issues at the very onset of cortical neurogenesis. To directly observe the generation of neurons from apical and basal progenitors, we established a novel transgenic mouse line in which membrane GFP is expressed from the beta-III-tubulin promoter, an early pan-neuronal marker, and crossed this line with a previously described knock-in line in which nuclear GFP is expressed from the Tis21 promoter, a pan-neurogenic progenitor marker. Mitotic Tis21-positive basal progenitors nearly always divided symmetrically, generating two neurons, but, in contrast to symmetrically dividing apical progenitors, lacked apical-basal polarity and showed a nearly randomized cleavage plane orientation. Moreover, the appearance of beta-III-tubulin-driven GFP fluorescence in basal progenitor-derived neurons, in contrast to that in apical progenitor-derived neurons, was so rapid that it suggested the initiation of the neuronal phenotype already in the progenitor. Our observations imply that (i) the loss of apical-basal polarity restricts neuronal progenitors to the symmetric mode of cell division, and that (ii) basal progenitors initiate the expression of neuronal phenotype already before mitosis, in contrast to apical progenitors.","authors":"Attardo, A., Calegari, F., Haubensak, W., Wilsch-Br\u00e4uninger, M., Huttner, WB.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"PLoS One","volume":"3","issue":"6","page":"e2388","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17957245","title":"Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor.","abstract":"Maintaining quiescent cells in G0 phase is achieved in part through the multiprotein subunit complex known as DREAM, and in human cell lines the transcription factor E2F4 directs this complex to its cell cycle targets. We found that E2F4 binds a highly overlapping set of human genes among three diverse primary tissues and an asynchronous cell line, which suggests that tissue-specific binding partners and chromatin structure have minimal influence on E2F4 targeting. To investigate the conservation of these transcription factor binding events, we identified the mouse genes bound by E2f4 in seven primary mouse tissues and a cell line. E2f4 bound a set of mouse genes that was common among mouse tissues, but largely distinct from the genes bound in human. The evolutionarily conserved set of E2F4 bound genes is highly enriched for functionally relevant regulatory interactions important for maintaining cellular quiescence. In contrast, we found minimal mRNA expression perturbations in this core set of E2f4 bound genes in the liver, kidney, and testes of E2f4 null mice. Thus, the regulatory mechanisms maintaining quiescence are robust even to complete loss of conserved transcription factor binding events.","authors":"Conboy, CM., Spyrou, C., Thorne, NP., Wade, EJ., Barbosa-Morais, NL., Wilson, MD., Bhattacharjee, A., Young, RA., Tavar\u00e9, S., Lees, JA., Odom, DT.","publication_status":"epublish","journalpubyear":"2007","journaltitle":"PLoS One","volume":"2","issue":"10","page":"e1061","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18516287","title":"Systematic identification of genes that regulate neuronal wiring in the Drosophila visual system.","abstract":"Forward genetic screens in model organisms are an attractive means to identify those genes involved in any complex biological process, including neural circuit assembly. Although mutagenesis screens are readily performed to saturation, gene identification rarely is, being limited by the considerable effort generally required for positional cloning. Here, we apply a systematic positional cloning strategy to identify many of the genes required for neuronal wiring in the Drosophila visual system. From a large-scale forward genetic screen selecting for visual system wiring defects with a normal retinal pattern, we recovered 122 mutations in 42 genetic loci. For 6 of these loci, the underlying genetic lesions were previously identified using traditional methods. Using SNP-based mapping approaches, we have now identified 30 additional genes. Neuronal phenotypes have not previously been reported for 20 of these genes, and no mutant phenotype has been previously described for 5 genes. The genes encode a variety of proteins implicated in cellular processes such as gene regulation, cytoskeletal dynamics, axonal transport, and cell signalling. We conducted a comprehensive phenotypic analysis of 35 genes, scoring wiring defects according to 33 criteria. This work demonstrates the feasibility of combining large-scale gene identification with large-scale mutagenesis in Drosophila, and provides a comprehensive overview of the molecular mechanisms that regulate visual system wiring.","authors":"Berger, J., Senti, KA., Senti, G., Newsome, TP., Asling, B., Dickson, BJ., Suzuki, T.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"PLoS Genet","volume":"4","issue":"5","page":"e1000085","pdf":null,"JrId":"32385","fulltextlink":null,"preprintlink":null,"articledate":"2008-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18508657","title":"The different functions of Stat5 and chromatin alteration through Stat5 proteins.","abstract":"Stat5 proteins modulate gene transcription upon cytokine- and growth factor action. Stat5a and Stat5b proteins alone are weak activators of transcription. They can modify chromatin organization through oligomerization and they act predominantly in co-operation and interaction with other proteins. The conservative view of exclusively nuclear functions of Stat5 was challenged by the observation of additional Stat5 effects in the cytoplasm, resulting in activation of the PI3K-Akt pathway. We summarize biological consequences of mutations in conserved domains of Stat5 or of deletions in the N- or C-terminal domains with impact on target gene transcription. Formation of higher-order oligomers is dramatically changed upon amino- or carboxyterminal deletions in Stat5 proteins. Mutations in or deletion of the Stat5 N-terminus leads to diminished leukemogenic potential of oncogenic Stat5, probably due to the inability to form Stat5 tetramers. The Stat5 N-terminal domain prevents persistent activation and can act as a DNA-docking platform for the glucocorticoid receptor (GR). The corresponding protocols should facilitate follow-up studies on Stat5 proteins and their contribution to normal physiological versus pathological processes through differential chromatin binding.","authors":"Kornfeld, JW., Grebien, F., Kerenyi, MA., Friedbichler, K., Kovacic, B., Zankl, B., Hoelbl, A., Nivarti, H., Beug, H., Sexl, V., Muller, M., Kenner, L., Mullner, EW., Gouilleux, F., Moriggl, R.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"Front Biosci","volume":"13","issue":null,"page":"6237-54","pdf":null,"JrId":"29838","fulltextlink":null,"preprintlink":null,"articledate":"2008-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18507836","title":"Identification and characteristics of microRNAs from Bombyx mori.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18507836<\/PMID><DateCompleted><Year>2008<\/Year><Month>08<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><PubDate><Year>2008<\/Year><Month>May<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Identification and characteristics of microRNAs from Bombyx mori.<\/ArticleTitle><Pagination><MedlinePgn>248<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-9-248<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression by targeting messenger RNAs (mRNAs) and causing mRNA cleavage or translation blockage. Of the 355 Arthropod miRNAs that have been identified, only 21 are B. mori miRNAs that were predicted computationally; of these, only let-7 has been confirmed by Northern blotting.","authors":"He, PA., Nie, Z., Chen, J., Chen, J., Lv, Z., Sheng, Q., Zhou, S., Gao, X., Kong, L., Wu, X., Jin, Y., Zhang, Y.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"BMC Genomics","volume":"9","issue":"","page":"248","pdf":null,"JrId":"21855","fulltextlink":null,"preprintlink":null,"articledate":"2008-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18484838","title":"Contrast sensitivity of insect motion detectors to natural images.","abstract":"How do animals regulate self-movement despite large variation in the luminance contrast of the environment? Insects are capable of regulating flight speed based on the velocity of image motion, but the mechanisms for this are unclear. The Hassenstein-Reichardt correlator model and elaborations can accurately predict responses of motion detecting neurons under many conditions but fail to explain the apparent lack of spatial pattern and contrast dependence observed in freely flying bees and flies. To investigate this apparent discrepancy, we recorded intracellularly from horizontal-sensitive (HS) motion detecting neurons in the hoverfly while displaying moving images of natural environments. Contrary to results obtained with grating patterns, we show these neurons encode the velocity of natural images largely independently of the particular image used despite a threefold range of contrast. This invariance in response to natural images is observed in both strongly and minimally motion-adapted neurons but is sensitive to artificial manipulations in contrast. Current models of these cells account for some, but not all, of the observed insensitivity to image contrast. We conclude that fly visual processing may be matched to commonalities between natural scenes, enabling accurate estimates of velocity largely independent of the particular scene.","authors":"Straw, AD., Rainsford, T., O'Carroll, DC.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"J Vis","volume":"8","issue":"3","page":"32.1-9","pdf":null,"JrId":"30247","fulltextlink":null,"preprintlink":null,"articledate":"2008-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"14604445","title":"Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">14604445<\/PMID><DateCompleted><Year>2004<\/Year><Month>06<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2105<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>4<\/Volume><PubDate><Year>2003<\/Year><Month>Nov<\/Month><Day>07<\/Day><\/PubDate><\/JournalIssue><Title>BMC bioinformatics<\/Title><ISOAbbreviation>BMC Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses.<\/ArticleTitle><Pagination><MedlinePgn>55<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The genome of the avian adenovirus Chicken Embryo Lethal Orphan (CELO) has two terminal regions without detectable homology in mammalian adenoviruses that are left without annotation in the initial analysis. Since adenoviruses have been a rich source of new insights into molecular cell biology and practical applications of CELO as gene a delivery vector are being considered, this genome appeared worth revisiting. We conducted a systematic reannotation and in-depth sequence analysis of the CELO genome.","authors":"Washietl, S., Eisenhaber, F.","publication_status":"epublish","journalpubyear":"2003","journaltitle":"BMC Bioinformatics","volume":"4","issue":null,"page":"55","pdf":null,"JrId":"21854","fulltextlink":null,"preprintlink":null,"articledate":"2004-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18461144","title":"Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance.","abstract":"microRNAs (miRNAs) are small non-coding RNAs that regulate mRNA stability and translation through the action of the RNAi-induced silencing complex (RISC). Our current understanding of miRNA function is inferred largely from studies of the effects of miRNAs on steady-state mRNA levels and from seed match conservation and context in putative targets. Here we have taken a more direct approach to these issues by comprehensively assessing the miRNAs and mRNAs that are physically associated with Argonaute 2 (Ago2), which is a core RISC component. We transfected HEK293T cells with epitope-tagged Ago2, immunopurified Ago2 together with any associated miRNAs and mRNAs, and quantitatively determined the levels of these RNAs by microarray analyses. We found that Ago2 immunopurified samples contained a representative repertoire of the cell's miRNAs and a select subset of the cell's total mRNAs. Transfection of the miRNAs miR-1 and miR-124 caused significant changes in the association of scores of mRNAs with Ago2. The mRNAs whose association with Ago2 increased upon miRNA expression were much more likely to contain specific miRNA seed matches and to have their overall mRNA levels decrease in response to the miRNA transfection than expected by chance. Hundreds of mRNAs were recruited to Ago2 by each miRNA via seed sequences in 3'-untranslated regions and coding sequences and a few mRNAs appear to be targeted via seed sequences in 5'-untranslated regions. Microarray analysis of Ago2 immunopurified samples provides a simple, direct method for experimentally identifying the targets of miRNAs and for elucidating roles of miRNAs in cellular regulation.","authors":"Hendrickson, DG., Hogan, DJ., Herschlag, D., Ferrell, JE., Brown, PO.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"PLoS One","volume":"3","issue":"5","page":"e2126","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18447903","title":"Comparative analysis of sequence features involved in the recognition of tandem splice sites.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18447903<\/PMID><DateCompleted><Year>2008<\/Year><Month>06<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>9<\/Volume><PubDate><Year>2008<\/Year><Month>Apr<\/Month><Day>30<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>Comparative analysis of sequence features involved in the recognition of tandem splice sites.<\/ArticleTitle><Pagination><MedlinePgn>202<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-9-202<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The splicing of pre-mRNAs is conspicuously often variable and produces multiple alternatively spliced (AS) isoforms that encode different messages from one gene locus. Computational studies uncovered a class of highly similar isoforms, which were related to tandem 5'-splice sites (5'ss) and 3'-splice sites (3'ss), yet with very sparse anecdotal evidence in experimental studies. To compare the types and levels of alternative tandem splice site exons occurring in different human organ systems and cell types, and to study known sequence features involved in the recognition and distinction of neighboring splice sites, we performed large-scale, stringent alignments of cDNA sequences and ESTs to the human and mouse genomes, followed by experimental validation.","authors":"Bortfeldt, R., Schindler, S., Szafranski, K., Schuster, S., Holste, D.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"BMC Genomics","volume":"9","issue":null,"page":"202","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18288631","title":"Engineering vascularised tissues in vitro.","abstract":"Tissue engineering aims at replacing or regenerating tissues lost due to diseases or traumas (Langer and Vacanti, 1993). However, mimicking in vitro the physiological complexity of vascularized tissue is a major obstacle, which possibly contributes to impaired healing in vivo. In higher organisms, native features including the vascular network, the lymphatic networks and interstitial flow promote both mass transport and organ development. Attempts to mimic those features in engineered tissues will lead to more clinically relevant cell-based therapies. Aside from current strategies promoting angiogenesis from the host, an alternative concept termed prevascularization is emerging. It aims at creating a biological vasculature inside an engineered tissue prior to implantation. This vasculature can rapidly anastamose with the host and enhances tissue survival and differentiation. Interestingly, growing evidence supports a role of the vasculature in regulating pattern formation and tissue differentiation. Thus, prevascularized tissues also benefit from an intrinsic contribution of their vascular system to their development. From those early attempts are emerging a body of principles and strategies to grow and maintain, in vitro, those self-assembled biological vascular networks. This could lead to the generation of engineered tissues of more physiologically relevant complexity and improved regenerative potential.","authors":"Rivron, NC., Liu J, J., Rouwkema, J., de Boer, J., van Blitterswijk, CA.","publication_status":"epublish","journalpubyear":"2008","journaltitle":"Eur Cell Mater","volume":"15","issue":null,"page":"27-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"18043734","title":"An obligatory role of mind bomb-1 in notch signaling of mammalian development.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">18043734<\/PMID><DateCompleted><Year>2008<\/Year><Month>08<\/Month><Day>21<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>2<\/Volume><Issue>11<\/Issue><PubDate><Year>2007<\/Year><Month>Nov<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>An obligatory role of mind bomb-1 in notch signaling of mammalian development.<\/ArticleTitle><Pagination><MedlinePgn>e1221<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The Notch signaling pathway is an evolutionarily conserved intercellular signaling module essential for cell fate specification that requires endocytosis of Notch ligands. Structurally distinct E3 ubiquitin ligases, Neuralized (Neur) and Mind bomb (Mib), cooperatively regulate the endocytosis of Notch ligands in Drosophila. However, the respective roles of the mammalian E3 ubiquitin ligases, Neur1, Neur2, Mib1, and Mib2, in mammalian development are poorly understood.","authors":"Koo, BK., Yoon, MJ., Yoon, KJ., Im, SK., Kim, YY., Kim, CH., Suh, PG., Jan, YN., Kong, YY.","publication_status":"epublish","journalpubyear":"2007","journaltitle":"PLoS One","volume":"2","issue":"11","page":"e1221","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1710340","title":"2'-O-methyl, 2'-O-ethyl oligoribonucleotides and phosphorothioate oligodeoxyribonucleotides as inhibitors of the in vitro U7 snRNP-dependent mRNA processing event.","abstract":"We describe the synthesis of 2'-O-methyl, 2'-O-ethyl oligoribonucleotides and phosphorothioate oligodeoxyribonucleotides and demonstrate their utility as inhibitors of the in vitro U7 snRNP-dependent mRNA processing event. These 2'-O-modified compounds were designed to possess the binding affinity of an RNA molecule towards a complementary RNA target with an enhanced stability against nucleases. The 2'-O-methyl and 2'-O-ethyl antisense compounds function as potent inhibitors of the reaction at 1-10 nM, approximately 5-fold more effective than a natural antisense RNA molecule and requiring an approximate 5-fold excess over the target RNA for 80% inhibition of the processing reaction.","authors":"Cotten, M., Oberhauser, B., Brunar, H., Holzner, A., Issakides, G., Noe, CR., Schaffner, G., Wagner, E., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Nucleic Acids Res","volume":"19","issue":"10","page":"2629-35","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1991-07-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17570144","title":"Clustering protein environments for function prediction: finding PROSITE motifs in 3D.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">17570144<\/PMID><DateCompleted><Year>2007<\/Year><Month>07<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2105<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>8 Suppl 4<\/Volume><PubDate><Year>2007<\/Year><Month>May<\/Month><Day>22<\/Day><\/PubDate><\/JournalIssue><Title>BMC bioinformatics<\/Title><ISOAbbreviation>BMC Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Clustering protein environments for function prediction: finding PROSITE motifs in 3D.<\/ArticleTitle><Pagination><MedlinePgn>S10<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Structural genomics initiatives are producing increasing numbers of three-dimensional (3D) structures for which there is little functional information. Structure-based annotation of molecular function is therefore becoming critical. We previously presented FEATURE, a method for describing microenvironments around functional sites in proteins. However, FEATURE uses supervised machine learning and so is limited to building models for sites of known importance and location. We hypothesized that there are a large number of sites in proteins that are associated with function that have not yet been recognized. Toward that end, we have developed a method for clustering protein microenvironments in order to evaluate the potential for discovering novel sites that have not been previously identified.","authors":"Yoon, S., Ebert, JC., Chung, EY., De Micheli, G., Altman, RB.","publication_status":"epublish","journalpubyear":"2007","journaltitle":"BMC Bioinformatics","volume":"8 Suppl 4","issue":"","page":"S10","pdf":null,"JrId":"21854","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17567892","title":"MASPECTRAS: a platform for management and analysis of proteomics LC-MS\/MS data.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">17567892<\/PMID><DateCompleted><Year>2007<\/Year><Month>07<\/Month><Day>31<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2105<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>8<\/Volume><PubDate><Year>2007<\/Year><Month>Jun<\/Month><Day>13<\/Day><\/PubDate><\/JournalIssue><Title>BMC bioinformatics<\/Title><ISOAbbreviation>BMC Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>MASPECTRAS: a platform for management and analysis of proteomics LC-MS\/MS data.<\/ArticleTitle><Pagination><MedlinePgn>197<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The advancements of proteomics technologies have led to a rapid increase in the number, size and rate at which datasets are generated. Managing and extracting valuable information from such datasets requires the use of data management platforms and computational approaches.","authors":"Hartler, J., Thallinger, GG., Stocker, G., Sturn, A., Burkard, TR., K\u00f6rner, E., Rader, R., Schmidt, A., Mechtler, K., Trajanoski, Z.","publication_status":"epublish","journalpubyear":"2007","journaltitle":"BMC Bioinformatics","volume":"8","issue":"","page":"197","pdf":null,"JrId":"21854","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17222345","title":"pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">17222345<\/PMID><DateCompleted><Year>2007<\/Year><Month>07<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1745-6150<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>2<\/Volume><PubDate><Year>2007<\/Year><Month>Jan<\/Month><Day>12<\/Day><\/PubDate><\/JournalIssue><Title>Biology direct<\/Title><ISOAbbreviation>Biol Direct<\/ISOAbbreviation><\/Journal><ArticleTitle>pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model.<\/ArticleTitle><Pagination><MedlinePgn>1<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Protein kinase A (cAMP-dependent kinase, PKA) is a serine\/threonine kinase, for which ca. 150 substrate proteins are known. Based on a refinement of the recognition motif using the available experimental data, we wished to apply the simplified substrate protein binding model for accurate prediction of PKA phosphorylation sites, an approach that was previously successful for the prediction of lipid posttranslational modifications and of the PTS1 peroxisomal translocation signal.","authors":"Neuberger, G., Schneider, G., Eisenhaber, F.","publication_status":"epublish","journalpubyear":"2007","journaltitle":"Biol Direct","volume":"2","issue":null,"page":"1","pdf":null,"JrId":"32601","fulltextlink":null,"preprintlink":null,"articledate":"2007-07-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17149364","title":"Identification of microRNAs and other small RNAs from the adult newt eye.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">17149364<\/PMID><DateCompleted><Year>2007<\/Year><Month>01<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2008<\/Year><Month>12<\/Month><Day>23<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1090-0535<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>12<\/Volume><PubDate><Year>2006<\/Year><Month>Nov<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Molecular vision<\/Title><ISOAbbreviation>Mol Vis<\/ISOAbbreviation><\/Journal><ArticleTitle>Identification of microRNAs and other small RNAs from the adult newt eye.<\/ArticleTitle><Pagination><MedlinePgn>1386-91<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"PURPOSE\" NlmCategory=\"OBJECTIVE\">MicroRNAs (miRNAs) are capable of controlling gene expression by targeting complimentary sequences in many mRNAs. Thus, a small number of miRNAs are capable of regulating expression of many different genes. miRNAs have been found in all animals from Drosophila to human and they are highly conserved. This work was undertaken in order to identify such RNAs in the newt eye.","authors":"Makarev, E., Spence, JR., Del Rio-Tsonis, K., Tsonis, PA.","publication_status":"epublish","journalpubyear":"2006","journaltitle":"Mol Vis","volume":"12","issue":"","page":"1386-91","pdf":null,"JrId":"20659","fulltextlink":null,"preprintlink":null,"articledate":"2007-01-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"17115376","title":"Role of canonical Wnt-signalling in joint formation.","abstract":"The individual elements of the vertebrate skeleton are separated by three different types of joints, fibrous, cartilaginous and synovial joints. Synovial joint formation in the limbs is coupled to the formation of the prechondrogenic condensations, which precede the formation of the joint interzone. We are beginning to understand the signals involved in the formation of prechondrogenic condensations and the subsequent differentiation of cells within the condensations into chondrocytes. However, relatively little is known about the molecules and molecular pathways involved in induction of the early joint interzone and the subsequent formation of the synovial joints. Based on gain-of function studies Wnt-signalling, in particular the canonical pathway, has been implicated in the joint induction process. Here we provide genetic evidence from loss-of function analysis of embryos lacking either the central player of the canonical Wnt-pathway, beta-catenin, in the limb mesenchyme or the two ligands, Wnt9a and Wnt4, demonstrating that canonical Wnt-signalling plays an important role in suppressing the chondrogenic potential of cells in the joint thereby actively allowing joint formation. Furthermore our data show that the beta-catenin activity is not essential for the induction of molecular markers expressed in the joint interzone. Thus, suggesting that canonical Wnt-signalling is not required for the induction, but for the subsequent maintenance of the fate of the joint interzone cells.","authors":"Sp\u00e4ter, D., Hill, TP., Gruber, M., Hartmann, C.","publication_status":"epublish","journalpubyear":"2006","journaltitle":"Eur Cell Mater","volume":"12","issue":null,"page":"71-80","pdf":null,"JrId":"30421","fulltextlink":null,"preprintlink":null,"articledate":"2006-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16551354","title":"Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">16551354<\/PMID><DateCompleted><Year>2006<\/Year><Month>05<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2105<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><PubDate><Year>2006<\/Year><Month>Mar<\/Month><Day>21<\/Day><\/PubDate><\/JournalIssue><Title>BMC bioinformatics<\/Title><ISOAbbreviation>BMC Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases.<\/ArticleTitle><Pagination><MedlinePgn>164<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Manually finding subtle yet statistically significant links to distantly related homologues becomes practically impossible for very populated protein families due to the sheer number of similarity searches to be invoked and analyzed. The unclear evolutionary relationship between classical mammalian lipases and the recently discovered human adipose triglyceride lipase (ATGL; a patatin family member) is an exemplary case for such a problem.","authors":"Schneider, G., Neuberger, G., Wildpaner, M., Tian, S., Berezovsky, I., Eisenhaber, F.","publication_status":"epublish","journalpubyear":"2006","journaltitle":"BMC Bioinformatics","volume":"7","issue":null,"page":"164","pdf":null,"JrId":"21854","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16507103","title":"Farnesylation or geranylgeranylation? Efficient assays for testing protein prenylation in vitro and in vivo.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">16507103<\/PMID><DateCompleted><Year>2007<\/Year><Month>02<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2091<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><PubDate><Year>2006<\/Year><Month>Feb<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>BMC biochemistry<\/Title><ISOAbbreviation>BMC Biochem<\/ISOAbbreviation><\/Journal><ArticleTitle>Farnesylation or geranylgeranylation? Efficient assays for testing protein prenylation in vitro and in vivo.<\/ArticleTitle><Pagination><MedlinePgn>6<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Available in vitro and in vivo methods for verifying protein substrates for posttranslational modifications via farnesylation or geranylgeranylation (for example, autoradiography with 3H-labeled anchor precursors) are time consuming (weeks\/months), laborious and suffer from low sensitivity.","authors":"Benetka, W., Koranda, M., Maurer-Stroh, S., Pittner, F., Eisenhaber, F.","publication_status":"epublish","journalpubyear":"2006","journaltitle":"BMC Biochem","volume":"7","issue":null,"page":"6","pdf":null,"JrId":"21856","fulltextlink":null,"preprintlink":null,"articledate":"2007-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16332694","title":"SNEV is an evolutionarily conserved splicing factor whose oligomerization is necessary for spliceosome assembly.","abstract":"We have isolated the human protein SNEV as downregulated in replicatively senescent cells. Sequence homology to the yeast splicing factor Prp19 suggested that SNEV might be the orthologue of Prp19 and therefore might also be involved in pre-mRNA splicing. We have used various approaches including gene complementation studies in yeast using a temperature sensitive mutant with a pleiotropic phenotype and SNEV immunodepletion from human HeLa nuclear extracts to determine its function. A human-yeast chimera was indeed capable of restoring the wild-type phenotype of the yeast mutant strain. In addition, immunodepletion of SNEV from human nuclear extracts resulted in a decrease of in vitro pre-mRNA splicing efficiency. Furthermore, as part of our analysis of protein-protein interactions within the CDC5L complex, we found that SNEV interacts with itself. The self-interaction domain was mapped to amino acids 56-74 in the protein's sequence and synthetic peptides derived from this region inhibit in vitro splicing by surprisingly interfering with spliceosome formation and stability. These results indicate that SNEV is the human orthologue of yeast PRP19, functions in splicing and that homo-oligomerization of SNEV in HeLa nuclear extract is essential for spliceosome assembly and that it might also be important for spliceosome stability.","authors":"Grillari, J., Ajuh, P., Stadler, G., L\u00f6scher, M., Voglauer, R., Ernst, W., Chusainow, J., Eisenhaber, F., Pokar, M., Fortschegger, K., Grey, M., Lamond, AI., Katinger, H.","publication_status":"epublish","journalpubyear":"2005","journaltitle":"Nucleic Acids Res","volume":"33","issue":"21","page":"6868-83","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"2005-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15698469","title":"Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">15698469<\/PMID><DateCompleted><Year>2006<\/Year><Month>01<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2105<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>6<\/Volume><PubDate><Year>2005<\/Year><Month>Feb<\/Month><Day>07<\/Day><\/PubDate><\/JournalIssue><Title>BMC bioinformatics<\/Title><ISOAbbreviation>BMC Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family.<\/ArticleTitle><Pagination><MedlinePgn>22<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Post-translational modification by Small Ubiquitin-like Modifiers (SUMO) has been implicated in protein targeting, in the maintenance of genomic integrity and in transcriptional control. But the specific molecular effects of SUMO modification on many target proteins remain to be elucidated. Recent findings point at the importance of SUMO-mediated histone NAD-dependent deacetylase (HDAC) recruitment in transcriptional regulation.","authors":"Novatchkova, M., Bachmair, A., Eisenhaber, B., Eisenhaber, F.","publication_status":"epublish","journalpubyear":"2005","journaltitle":"BMC Bioinformatics","volume":"6","issue":null,"page":"22","pdf":null,"JrId":"21854","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15640448","title":"Translation of stable hepadnaviral mRNA cleavage fragments induced by the action of phosphorothioate-modified antisense oligodeoxynucleotides.","abstract":"Phosphorothioate-modified antisense oligodeoxynucleotides (ASOs) are used to suppress gene expression by inducing RNase H-mediated cleavage with subsequent degradation of the target mRNA. However, previous observations suggest that ASO\/RNase H can also result in the generation of stable mRNA cleavage fragments and expression of truncated proteins. Here, we addressed the underlying translational mechanisms in more detail using hepadnavirus-transfected hepatoma cells as a model system of antisense therapy. Generation of stable mRNA cleavage fragments was restricted to the ASO\/RNase H pathway and not observed upon cotransfection of isosequential small interfering RNA or RNase H-incompetent oligonucleotides. Furthermore, direct evidence for translation of mRNA fragments was established by polysome analysis. Polysome-associated RNA contained cleavage fragments devoid of a 5' cap structure indicating that translation was, at least in part, cap-independent. Further analysis of the uncapped cleavage fragments revealed that their 5' terminus and initiation codon were only separated by a few nucleotides suggesting a 5' end-dependent mode of translation, whereas internal initiation could be ruled out. However, the efficiency of translation was moderate compared to uncleaved mRNA and amounted to 13-24% depending on the ASO used. These findings provide a rationale for understanding the translation of mRNA fragments generated by ASO\/RNase H mechanistically.","authors":"Hasselblatt, P., Hockenjos, B., Thoma, C., Blum, HE., Offensperger, WB.","publication_status":"epublish","journalpubyear":"2005","journaltitle":"Nucleic Acids Res","volume":"33","issue":"1","page":"114-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12700068","title":"The role of Smads in BMP signaling.","abstract":"Bone morphogenetic proteins, BMPs, are members of the transforming growth factor-beta (TGF-beta) superfamily, which are implicated in embryogenesis, organogenesis, skeletogenesis, osteogenesis, cellular differentiation and apoptosis by regulating the expression of specific target genes. Recent progresses in studying the BMP signaling reveal that a cytoplasmic protein family, Smad, plays a central role in mediating the biological effects of BMPs. Smad transduces the signal from the cytoplasm to the nucleus where Smad regulates the transcription of the target genes through the direct association with the specific biding elements or with assistance of other transcription factors or co-activators such as p300\/CBP. In addition, the signals mediated by Smad are also positively or negatively controlled by cross-talks with other hormone, growth factor or cytokine signalings, thereby modulating the biological actions of BMPs. Moreover, Smad signaling has negative feedback regulations at the cytoplasmic or nuclear level, which are important to restrict or terminate the biological effect of BMPs. Here we provide an overview of recent knowledge about the roles of Smad family in the regulation of BMP signaling.","authors":"Nishimura, R., Hata, K., Ikeda, F., Matsubara, T., Yamashita, K., Ichida, F., Yoneda, T.","publication_status":"epublish","journalpubyear":"2003","journaltitle":"Front Biosci","volume":"8","issue":null,"page":"s275-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-02-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11943877","title":"ADAP-ting TCR signaling to integrins.","abstract":"Adaptor proteins are essential components of T cell receptor (TCR) signaling cascades regulating gene transcription and cytoskeletal reorganization. The molecular adaptor adhesion- and degranulation-promoting adaptor protein (ADAP), also known as Fyn binding protein (FYB) or Slp-76-associated protein of 130 kilodaltons (SLAP-130), interacts with a number of signaling intermediates including Slp-76, the Src family tyrosine kinase Fyn, vasodilator-stimulated phosphoprotein (VASP), and the actin-nucleating protein WASP. Recently ADAP was shown genetically to positively regulate T cell activation, TCR-induced integrin clustering, and T cell adhesion. The mechanism by which ADAP couples TCR stimulation to integrin clustering remains unclear; however, studies of ADAP, the exchange factor Vav1, and WASP suggest that TCR and integrin clustering may be controlled by distinct signaling pathways.","authors":"Griffiths, EK., Penninger, JM.","publication_status":"epublish","journalpubyear":"2002","journaltitle":"Sci STKE","volume":"2002","issue":"127","page":"re3","pdf":null,"JrId":"22277","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34137250","title":"Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO.","abstract":"In the light of the ongoing single-cell revolution, scientific disciplines are combining forces to retrieve as much relevant data as possible from trace amounts of biological material. For single-cell proteomics, this implies optimizing the entire workflow from initial cell isolation down to sample preparation, liquid chromatography (LC) separation, mass spectrometer (MS) data acquisition, and data analysis. To demonstrate the potential for single-cell and limited sample proteomics, we report on a series of benchmarking experiments where we combine LC separation on a new generation of micropillar array columns with state-of-the-art Orbitrap MS\/MS detection and high-field asymmetric waveform ion mobility spectrometry (FAIMS). This dedicated limited sample column has a reduced cross section and micropillar dimensions that have been further downscaled (interpillar distance and pillar diameter by a factor of 2), resulting in improved chromatography at reduced void times. A dilution series of a HeLa tryptic digest (5-0.05 ng\/\u03bcL) was used to explore the sensitivity that can be achieved. Comparative processing of the MS\/MS data with Sequest HT, MS Amanda, Mascot, and SpectroMine pointed out the benefits of using Sequest HT together with INFERYS when analyzing sample amounts below 1 ng. Here, 2855 protein groups were identified from just 1 ng of HeLa tryptic digest hereby increasing detection sensitivity as compared to a previous contribution by a factor well above 10. By successfully identifying 1486 protein groups from as little as 250 pg of HeLa tryptic digest, we demonstrate outstanding sensitivity with great promise for use in limited sample proteomics workflows.","authors":"Stejskal, K., Op de Beeck, J., D\u00fcrnberger, G., Jacobs, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Anal Chem","volume":"93","issue":"25","page":"8704-8710","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33719859","title":"Selective autophagy receptor SQSTM1\/ p62 inhibits Seneca Valley virus replication by targeting viral VP1 and VP3.","abstract":"Macroautophagy\/autophagy plays a critical role in antiviral immunity through targeting viruses and initiating host immune responses. The receptor protein, SQSTM1\/p62 (sequestosome 1), plays a vital role in selective autophagy. It serves as a receptor targeting ubiquitinated proteins or pathogens to phagophores for degradation. In this study, we explored the reciprocal regulation between selective autophagy receptor SQSTM1 and Seneca Valley virus (SVV). SVV infection induced autophagy. Autophagy promoted SVV infection in pig cells but played opposite functions in human cells. Overexpression of SQSTM1 decreased viral protein production and reduced viral titers. Further study showed that SQSTM1 interacted with SVV VP1 and VP3 independent of its UBA domain. SQSTM1 targeted SVV VP1 and VP3 to phagophores for degradation to inhibit viral replication. To counteract this, SVV evolved strategies to circumvent the host autophagic machinery to promote viral replication. SVV 3C<sup>pro<\/sup> targeted the receptor SQSTM1 for cleavage at glutamic acid 355, glutamine 392, and glutamine 395 and abolished its capacity to mediate selective autophagy. At the same time, the 3C<sup>pro<\/sup>-mediated SQSTM1 cleavage products lost the ability to inhibit viral propagation. Collectively, our results provide evidence for selective autophagy in host against viruses and reveal potential viral strategies to evade autophagic machinery for successful pathogenesis. Abbreviations: Baf.A1: bafilomycin A<sub>1<\/sub>; Co-IP: co-immunoprecipitation; hpi: h post-infection; LIR: LC3-interacting region; MAP1LC3B\/LC3B: microtubule-associated protein 1 light chain 3 beta; MOI: multiplicity of infection; PB1: N-terminal Phox\/Bem1p; Rap.: rapamycin; Seneca Valley virus: SVV; SQSTM1\/p62: sequestosome 1; SQSTM1-N355: residues 1 to 355 of SQSTM1; SQSTM1-C355: residues 355 to 478 of SQSTM1; SQSTM1-N392: residues 1 to 392 of SQSTM1; SQSTM1-C392: residues 392 to 478 of SQSTM1; SQSTM1-N388: residues 1 to 388 of SQSTM1; SQSTM1-N397: residues 1 to 397 of SQSTM1; UBA: ubiquitin association; Ubi: ubiquitin.","authors":"Wen, W., Li, X., Yin, M., Wang, H., Qin, L., Li, H., Liu, W., Zhao, Z., Zhao, Q., Chen, H., Hu, J., Qian, P.","publication_status":"aheadofprint","journalpubyear":"2021","journaltitle":"Autophagy","volume":"","issue":"","page":"1-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12563272","title":"Mitochondria, AIF and caspases--rivaling for cell death execution.","abstract":"","authors":"Penninger, JM., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"Nat Cell Biol","volume":"5","issue":"2","page":"97-9","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2003-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12428186","title":"Cytokines that regulate autoimmune myocarditis.","abstract":"A growing body of evidence suggests that autoimmune responses are involved in the pathogenesis of myocarditis and postinfectious cardiomyopathy. Autoimmunity may also arise after ischaemic or traumatic damage to heart tissue. Myocarditis leading to heart failure can be mimicked in rodents by immunisation with cardiac alpha myosin and peptides derived from it. Cytokines and chemokines, produced mainly by T-cells and antigen-presenting cells, control immune responses by acting as either potentiating or inhibitory agents. Gene targeting and experiments with antibodies and\/or antagonists blocking cytokines and their receptors have uncovered mechanisms whereby such regulatory molecules are involved in the pathogenesis of myocarditis. Identification of regulatory key cytokines and the associated pro- or anti-inflammatory pathways involved in the pathogenesis of cardiac inflammation may have important implications for therapeutic strategies and vaccine design in the future.","authors":"Kurrer, MO., Kopf, M., Penninger, J., Eriksson, U.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Swiss Med Wkly","volume":"132","issue":"29-30","page":"408-13","pdf":null,"JrId":"22290","fulltextlink":null,"preprintlink":null,"articledate":"2003-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-218","title":"Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing","abstract":null,"authors":"Briedis-Gert, KR., Schulze, G., Novatchkova, M., Panser, K., Cabrera Quio, LE., Koller, A., Guo, Y., Cairns, BR., Valen, E., Pauli, A","publication_status":"preprint","journalpubyear":"2026","journaltitle":"bioRxiv ","volume":"10.1101\/2021.11.03.467109","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.11.03.467109v2","preprintlink":null,"articledate":"2026-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12438440","title":"Osteoclasts are essential for TNF-alpha-mediated joint destruction.","abstract":"The detailed cellular and molecular mechanisms leading to joint destruction in rheumatoid arthritis, a disease driven by proinflammatory cytokines, are still unknown. To address the question of whether osteoclasts play a pivotal role in this process, transgenic mice that express human TNF (hTNFtg) and that develop a severe and destructive arthritis were crossed with osteopetrotic, c-fos-deficient mice (c-fos(-\/-)) completely lacking osteoclasts. The resulting mutant mice (c-fos(-\/-)hTNFtg) developed a TNF-dependent arthritis in the absence of osteoclasts. All clinical features of arthritis, such as paw swelling and reduction of grip strength, progressed equally in both groups. Histological evaluation of joint sections revealed no difference in the extent of synovial inflammation, its cellular composition (except for the lack of osteoclasts), and the expression of matrix metalloprotein-ase-3 (MMP-3) and MMP-13. In addition, cartilage damage, proteoglycan loss, and MMP-3, -9, and -13 expression in chondrocytes were similar in hTNFtg and c-fos(-\/-)hTNFtg mice. However, despite the presence of severe inflammatory changes, c-fos(-\/-)hTNFtg mice were fully protected against bone destruction. These data reveal that TNF-dependent bone erosion is mediated by osteoclasts and that the absence of osteoclasts alters TNF-mediated arthritis from a destructive to a nondestructive arthritis. Therefore, in addition to the use of anti-inflammatory therapies, osteoclast inhibition could be beneficial for the treatment of rheumatoid arthritis.","authors":"Redlich, K., Hayer, S., Ricci, R., David, JP., Tohidast-Akrad, M., Kollias, G., Steiner, G., Smolen, JS., Wagner, EF., Schett, G.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Clin Invest","volume":"110","issue":"10","page":"1419-27","pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":"2003-01-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33417886","title":"Ubiquitous Selfish Toxin-Antidote Elements in Caenorhabditis Species.","abstract":"Toxin-antidote elements (TAs) are selfish genetic dyads that spread in populations by selectively killing non-carriers. TAs are common in prokaryotes, but very few examples are known in animals. Here, we report the discovery of maternal-effect TAs in both C.\u00a0tropicalis and C.\u00a0briggsae, two distant relatives of C.\u00a0elegans. In C.\u00a0tropicalis, multiple TAs combine to cause a striking degree of intraspecific incompatibility: five elements reduce the fitness of &gt;70% of the F<sub>2<\/sub> hybrid progeny of two Caribbean isolates. We\u00a0identified the genes underlying one of the novel TAs, slow-1\/grow-1, and found that its toxin, slow-1, is homologous to nuclear hormone receptors. Remarkably, although previously known TAs act during embryonic development, maternal loading of slow-1 in oocytes specifically slows down larval development, delaying the onset of reproduction by several days. Finally, we found that balancing selection acting on linked, conflicting TAs hampers their ability to spread in populations, leading to more stable genetic incompatibilities. Our findings indicate that TAs are widespread in Caenorhabditis species and target a wide range of developmental processes and that antagonism between them may cause lasting\u00a0incompatibilities in natural populations. We expect that similar phenomena exist in other animal species.","authors":"Ben-David, E., Pliota, P., Widen, SA., Koreshova, A., Lemus-Vergara, T., Verpukhovskiy, P., Mandali, S., Braendle, C., Burga, A., Kruglyak, L.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Curr Biol","volume":"31","issue":"5","page":"990-1001.e5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33361811","title":"RANK links thymic regulatory T cells to fetal loss and gestational diabetes in pregnancy.","abstract":"Successful pregnancies rely on adaptations within the mother<sup>1<\/sup>, including marked changes within the immune system<sup>2<\/sup>. It has long been known that the thymus, the central lymphoid organ, changes markedly during pregnancy<sup>3<\/sup>. However, the molecular basis and importance of this process remain largely obscure. Here we show that the osteoclast differentiation receptor RANK<sup>4,5<\/sup> couples female sex hormones to the rewiring of the thymus during pregnancy. Genetic deletion of Rank (also known as Tnfrsf11a) in thymic epithelial cells results in impaired thymic involution and blunted expansion of natural regulatory T (T<sub>reg<\/sub>) cells in pregnant female mice. Sex hormones, in particular progesterone, drive the development of thymic T<sub>reg<\/sub> cells through RANK in a manner that depends on AIRE<sup>+<\/sup> medullary thymic epithelial cells. The depletion of Rank in the mouse thymic epithelium results in reduced accumulation of natural T<sub>reg<\/sub> cells in the placenta, and an increase in the number of miscarriages. Thymic deletion of Rank also results in impaired accumulation of T<sub>reg<\/sub> cells in visceral adipose tissue, and is associated with enlarged adipocyte size, tissue inflammation, enhanced maternal glucose intolerance, fetal macrosomia, and a long-lasting transgenerational alteration in glucose homeostasis, which are all key hallmarks of gestational diabetes. Transplantation of T<sub>reg<\/sub> cells rescued fetal loss, maternal glucose intolerance and fetal macrosomia. In human pregnancies, we found that gestational diabetes also correlates with a reduced number of T<sub>reg<\/sub> cells in the placenta. Our findings show that RANK promotes the hormone-mediated development of thymic T<sub>reg<\/sub> cells during pregnancy, and expand the functional role of maternal T<sub>reg<\/sub> cells to the development of gestational diabetes and the transgenerational metabolic rewiring of glucose homeostasis.","authors":"Paolino, M., Koglgruber, R., Cronin, SJF., Uribesalgo, I., Rauscher, E., Harreiter, J., Schuster, M., Bancher-Todesca, D., Pranjic, B., Novatchkova, M., Fededa, JP., White, AJ., Sigl, V., Dekan, S., Penz, T., Bock, C., Kenner, L., Holl\u00e4nder, GA., Anderson, G., Kautzky-Willer, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature","volume":"589","issue":"7842","page":"442-447","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33505974","title":"Oral and Palatal Dentition of Axolotl Arises From a Common Tooth-Competent Zone Along the Ecto-Endodermal Boundary.","abstract":"Vertebrate dentitions arise at various places within the oropharyngeal cavity including the jaws, the palate, or the pharynx. These dentitions develop in a highly organized way, where new tooth germs are progressively added adjacent to the initiator center, the first tooth. At the same time, the places where dentitions develop house the contact zones between the outer ectoderm and the inner endoderm, and this colocalization has instigated various suggestions on the roles of germ layers for tooth initiation and development. Here, we study development of the axolotl dentition, which is a complex of five pairs of tooth fields arranged into the typically tetrapod outer and inner dental arcades. By tracking the expression patterns of odontogenic genes, we reason that teeth of both dental arcades originate from common tooth-competent zones, one present on the mouth roof and one on the mouth floor. Progressive compartmentalization of these zones and a simultaneous addition of new tooth germs distinct for each prospective tooth field subsequently control the final shape and composition of the axolotl dentition. Interestingly, by following the fate of the GFP-labeled oral ectoderm, we further show that, in three out of five tooth field pairs, the first tooth develops right at the ecto-endodermal boundary. Our results thus indicate that a single tooth-competent zone gives rise to both dental arcades of a complex tetrapod dentition. Further, we propose that the ecto-endodermal boundary running through this zone should be accounted for as a potential source of instruction factors instigating the onset of the odontogenic program.","authors":"Soukup, V., Tazaki, A., Yamazaki, Y., Pospisilova, A., Epperlein, HH., Tanaka, EM., Cerny, R.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Front Cell Dev Biol","volume":"8","issue":null,"page":"622308","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"42449529","title":"Reply: Stem cell-based embryo models: scientific promise clashes with ethical reality.","abstract":null,"authors":"Martinez Arias, A., Rivron, N., Tajbakhsh, S., Johnston, J., Alev, C., Bally-Cuif, L., B\u00f6ke, E., Cavazza, T., Cave, E., Cyranoski, D., David, L., Esteban, MA., Fu, J., Geijsen, N., De Graeff, N., Hanna, JH., Hopwood, N., Inamdar, MS., Lanner, F., Leeners, B., Liu, Z., Maitre, JL., Minchiotti, G., Moris, N., Munsie, M., Niakan, KK., Pourquie, O., Pasque, V., Pera, M., Peng, Y., Petropoulos, S., Ramanathan, S., Rossant, J., Rugg-Gunn, P., Saitou, M., Sermon, K., Silva, J., Theunissen, T., Turco, M., Wallingford, J., Wang, H., Warmflash, A., Wu, J., Yu, L.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Hum Reprod","volume":"41","issue":"9","page":"1624-1626","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-08-01","doi":"10.1093\/humrep\/deag113","first_author":"Martinez Arias, A.","corresponding_authors":"Yu, L."},{"pmid":"16581772","title":"Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster.","abstract":"RNA silencing pathways are conserved gene regulation mechanisms that elicit decay and\/or translational repression of mRNAs complementary to short interfering RNAs and microRNAs (miRNAs). The fraction of the transcriptome regulated by these pathways is not known, but it is thought that each miRNA may have hundreds of targets. To identify transcripts regulated by silencing pathways at the genomic level, we examined mRNA expression profiles in Drosophila melanogaster cells depleted of four Argonaute paralogs (i.e., AGO1, AGO2, PIWI, or Aubergine) that play essential roles in RNA silencing. We also profiled cells depleted of the miRNA-processing enzyme Drosha. The results reveal that transcripts differentially expressed in Drosha-depleted cells have highly correlated expression in the AGO1 knockdown and are significantly enriched in predicted and validated miRNA targets. The levels of a subset of miRNA targets are also regulated by AGO2. Moreover, AGO1 and AGO2 silence the expression of a common set of mobile genetic elements. Together, these results indicate that the functional overlap between AGO1 and AGO2 in Drosophila is more important than previously thought.","authors":"Rehwinkel, J., Natalin, P., Stark, A., Brennecke, J., Cohen, SM., Izaurralde, E.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Mol Cell Biol","volume":"26","issue":"8","page":"2965-75","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33125867","title":"Two MicroRNAs Are Sufficient for Embryonic Patterning in C.\u00a0elegans.","abstract":"MicroRNAs (miRNAs) are a class of post-transcriptional repressors with diverse roles in animal development and physiology [1]. The Microprocessor complex, composed of Drosha and Pasha\/DGCR8, is necessary for the biogenesis of all canonical miRNAs and essential for the early stages of animal embryogenesis [2-8]. However, the cause for this requirement is largely unknown. Animals often express hundreds of miRNAs, and it remains unclear whether the Microprocessor is required to produce one or few essential miRNAs or many individually non-essential miRNAs. Additionally, both Drosha and Pasha\/DGCR8 bind and cleave a variety of non-miRNA substrates [9-15], and it is unknown whether these activities account for the Microprocessor's essential requirement. To distinguish between these possibilities, we developed a system in C.\u00a0elegans to stringently deplete embryos of Microprocessor activity. Using a combination of auxin-inducible degradation (AID) and RNA interference (RNAi), we achieved Drosha and Pasha\/DGCR8 depletion starting in the maternal germline, resulting in Microprocessor and miRNA-depleted embryos, which fail to undergo morphogenesis or form organs. Using a Microprocessor-bypass strategy, we show that this early embryonic arrest is rescued by the addition of just two miRNAs, one miR-35 and one miR-51 family member, resulting in morphologically normal larvae. Thus, just two out of \u223c150 canonical miRNAs are sufficient for morphogenesis and organogenesis, and the processing of these miRNAs accounts for the essential requirement for Drosha and Pasha\/DGCR8 during the early stages of C.\u00a0elegans embryonic development. VIDEO ABSTRACT.","authors":"Dexheimer, PJ., Wang, J., Cochella, L.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Curr Biol","volume":"30","issue":"24","page":"5058-5065.e5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33094674","title":"Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.","abstract":"Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4\/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.","authors":"Garrido-Godino, AI., Gupta, I., Guti\u00e9rrez-Santiago, F., Mart\u00ednez-Padilla, AB., Alekseenko, A., Steinmetz, LM., P\u00e9rez-Ort\u00edn, JE., Pelechano, V., Navarro, F.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"RNA Biol","volume":"18","issue":"8","page":"1206-1220","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32894860","title":"LifeTime and improving European healthcare through cell-based interceptive medicine.","abstract":"Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration\u00a0and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.","authors":"Rajewsky, N., Almouzni, G., Gorski, SA., Aerts, S., Amit, I., Bertero, MG., Bock, C., Bredenoord, AL., Cavalli, G., Chiocca, S., Clevers, H., De Strooper, B., Eggert, A., Ellenberg, J., Fern\u00e1ndez, XM., Figlerowicz, M., Gasser, SM., Hubner, N., Kjems, J., Knoblich, JA., Krabbe, G., Lichter, P., Linnarsson, S., Marine, JC., Marioni, JC., Marti-Renom, MA., Netea, MG., Nickel, D., Nollmann, M., Novak, HR., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, JL., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, FJ., Torres-Padilla, ME., Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M., Voet, T.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nature","volume":"587","issue":"7834","page":"377-386","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-02-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32220807","title":"The emergence of genome architecture and zygotic genome activation.","abstract":"The fusion of two transcriptionally silent gametes, egg and sperm, generates a totipotent zygote that activates zygotic transcription to support further development. Although the molecular details of zygotic genome activation (ZGA)\u00a0are not well understood in most species, an emerging concept is that one or more pioneer transcription factors trigger zygotic transcription. Concomitantly, extensive changes in 3D chromatin organization occur during development. In this review, we discuss recent advances in understanding when and how genome architecture emerges in early metazoan embryos, how the zygotic genome is activated, and how these events might be coordinated. We also highlight some of the unknowns that may be critical to address in the future.","authors":"Vallot, A., Tachibana, K.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Curr Opin Cell Biol","volume":"64","issue":null,"page":"50-57","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32891891","title":"Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell.","abstract":"The small proteins and short open reading frames encoded peptides (SEPs) are of fundamental importance because of their essential roles in biological processes. However, the annotation or identification of them is challenging, in part owing to the limitation of the traditional genome annotation pipeline and their inherent characteristics of low abundance and low molecular weight. To discover and characterize SEPs in Hep3B cell line, we developed an optimized peptidomic assay by combining different peptide extraction and separation methods. The organic solvent precipitation method in peptidomic showed promotion in the enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high-quality MS\/MS spectra. Furthermore, different strategies exhibited good complementarity in improving the total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Results in this work provide robust evidence to date that the human proteome is more complicated than previously appreciated, and this will be a benefit to discoveries of proteins without function annotation. SIGNIFICANCE: In this work, methods were optimized to identify SEPs in Hep3B. The organic solvent precipitation presents promotion in enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high quality MS\/MS spectra. Different strategies exhibited good complementarity in improving total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Furthermore, 22 SEPs generated from the uORF may has potential effect in translation control, and 149 newly identified SEPs have known functional domains or cross-species conservation. Results in this work present robust evidence for the coding potential of the ignored region of human genomes and may provide additional insights into tumor biology.","authors":"Wang, B., Hao, J., Pan, N., Wang, Z., Chen, Y., Wan, C.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Proteomics","volume":"230","issue":"","page":"103965","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32879507","title":"Reflections on the past two decades of neuroscience.","abstract":"The first issue of Nature Reviews Neuroscience was published 20 years ago, in 2000. To mark this anniversary, in this Viewpoint article we asked a selection of researchers from across the field who have authored pieces published in the journal in recent years for their thoughts on notable and interesting developments in neuroscience, and particularly in their areas of the field, over the past two decades. They also provide some thoughts on current lines of research and questions that excite them.","authors":"Bassett, DS., Cullen, KE., Eickhoff, SB., Farah, MJ., Goda, Y., Haggard, P., Hu, H., Hurd, YL., Josselyn, SA., Khakh, BS., Knoblich, JA., Poirazi, P., Poldrack, RA., Prinz, M., Roelfsema, PR., Spires-Jones, TL., Sur, M., Ueda, HR.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Rev Neurosci","volume":"21","issue":"10","page":"524-534","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32848067","title":"Calcium modulates the domain flexibility and function of an \u03b1-actinin similar to the ancestral \u03b1-actinin.","abstract":"The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin-binding proteins, is fundamentally important in eukaryotes. \u03b1-Actinins are major F-actin bundlers that are inhibited by Ca<sup>2+<\/sup> in nonmuscle cells. Here we report the mechanism of Ca<sup>2+<\/sup>-mediated regulation of <i>Entamoeba histolytica<\/i> \u03b1-actinin-2 (<i>Eh<\/i>Actn2) with features expected for the common ancestor of <i>Entamoeba<\/i> and higher eukaryotic \u03b1-actinins. Crystal structures of Ca<sup>2+<\/sup>-free and Ca<sup>2+<\/sup>-bound <i>Eh<\/i>Actn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the <i>Eh<\/i>Actn2 CaMD for Ca<sup>2+<\/sup>, binding of which can only be regulated in the presence of physiological concentrations of Mg<sup>2+<\/sup> Ca<sup>2+<\/sup> binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin-binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that <i>Eh<\/i>Actn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.","authors":"Pinotsis, N., Zielinska, K., Babuta, M., Arolas, JL., Kostan, J., Khan, MB., Schreiner, C., Salmazo, A., Ciccarelli, L., Puchinger, M., Gkougkoulia, EA., Ribeiro, EA., Marlovits, TC., Bhattacharya, A., Djinovic-Carugo, K.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Proc Natl Acad Sci U S A","volume":"117","issue":"36","page":"22101-22112","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32788360","title":"Multicolor 3D MINFLUX nanoscopy of mitochondrial MICOS proteins.","abstract":"The mitochondrial contact site and cristae organizing system (MICOS) is a multisubunit protein complex that is essential for the proper architecture of the mitochondrial inner membrane. MICOS plays a key role in establishing and maintaining crista junctions, tubular or slit-like structures that connect the cristae membrane with the inner boundary membrane, thereby ensuring a contiguous inner membrane. MICOS is enriched at crista junctions, but the detailed distribution of its subunits around crista junctions is unclear because such small length scales are inaccessible with established fluorescence microscopy. By targeting individually activated fluorophores with an excitation beam featuring a central zero-intensity point, the nanoscopy method called MINFLUX delivers single-digit nanometer-scale three-dimensional (3D) resolution and localization precision. We employed MINFLUX nanoscopy to investigate the submitochondrial localization of the core MICOS subunit Mic60 in relation to two other MICOS proteins, Mic10 and Mic19. We demonstrate that dual-color 3D MINFLUX nanoscopy is applicable to the imaging of organellar substructures, yielding a 3D localization precision of \u223c5 nm in human mitochondria. This isotropic precision facilitated the development of an analysis framework that assigns localization clouds to individual molecules, thus eliminating a source of bias when drawing quantitative conclusions from single-molecule localization microscopy data. MINFLUX recordings of Mic60 indicate ringlike arrangements of multiple molecules with a diameter of 40 to 50 nm, suggesting that Mic60 surrounds individual crista junctions. Statistical analysis of dual-color MINFLUX images demonstrates that Mic19 is generally in close proximity to Mic60, whereas the spatial coordination of Mic10 with Mic60 is less regular, suggesting structural heterogeneity of MICOS.","authors":"Pape, JK., Stephan, T., Balzarotti, F., B\u00fcchner, R., Lange, F., Riedel, D., Jakobs, S., Hell, SW.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Proc Natl Acad Sci U S A","volume":"117","issue":"34","page":"20607-20614","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32850393","title":"Targeting the RANKL\/RANK\/OPG Axis for Cancer Therapy.","abstract":"RANKL and RANK are expressed in different cell types and tissues throughout the body. They were originally described for their essential roles in bone remodeling and the immune system but have subsequently been shown to provide essential signals from regulating mammary gland homeostasis during pregnancy to modulating tumorigenesis. The success of RANKL\/RANK research serves as a paragon for translational research from the laboratory to the bedside. The case in point has been the development of Denosumab, a RANKL-blocking monoclonal antibody which has already helped millions of patients suffering from post-menopausal osteoporosis and skeletal related events in cancer. Here we will provide an overview of the pathway from its origins to its clinical relevance in disease, with a special focus on emerging evidence demonstrating the therapeutic value of targeting the RANKL\/RANK\/OPG axis not only in breast cancer but also as an addition to the cancer immunotherapy arsenal.","authors":"Ming, J., Cronin, SJF., Penninger, JM.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Front Oncol","volume":"10","issue":null,"page":"1283","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20211138","title":"The Tetrahymena argonaute-binding protein Giw1p directs a mature argonaute-siRNA complex to the nucleus.","abstract":"Emerging evidence suggests that RNA interference (RNAi)-related processes act both in the cytoplasm and in the nucleus. However, the process by which the RNAi machinery is transported into the nucleus remains poorly understood. The Tetrahymena Argonaute protein Twi1p localizes to the nucleus and is crucial for small RNA-directed programmed DNA elimination. In this study, we identify Giw1p, which binds to Twi1p and is required for its nuclear localization. Furthermore, the endoribonuclease (Slicer) activity of Twi1p plays a vital role in the removal of one of the two strands of Twi1p-associated small interfering RNAs (siRNAs), leading to a functionally mature Twi1p-siRNA complex. Slicer activity is also shown to be required for nuclear localization of Twi1p and for its association with Giw1p. These results suggest that Giw1p senses the state of Twi1p-associated siRNAs and selectively transports the mature Twi1p-siRNA complex into the nucleus.","authors":"Noto, T., Kurth, HM., Kataoka, K., Aronica, L., DeSouza, LV., Siu, KW., Pearlman, RE., Gorovsky, MA., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell","volume":"140","issue":"5","page":"692-703","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32612238","title":"Wapl repression by Pax5 promotes V gene recombination by Igh loop extrusion.","abstract":"Nuclear processes, such as V(D)J recombination, are orchestrated by the three-dimensional organization of chromosomes at multiple levels, including compartments<sup>1<\/sup> and topologically associated domains (TADs)<sup>2,3<\/sup> consisting of chromatin loops<sup>4<\/sup>. TADs are formed by chromatin-loop extrusion<sup>5-7<\/sup>, which depends on the loop-extrusion function of the ring-shaped cohesin complex<sup>8-12<\/sup>. Conversely, the cohesin-release factor Wapl<sup>13,14<\/sup> restricts loop extension<sup>10,15<\/sup>. The generation of a diverse antibody repertoire, providing humoral immunity to pathogens, requires the participation of all V genes in V(D)J recombination<sup>16<\/sup>, which depends on contraction of the 2.8-Mb-long immunoglobulin heavy chain (Igh) locus by Pax5<sup>17,18<\/sup>. However, how Pax5 controls Igh contraction in pro-B cells remains unknown. Here we demonstrate that locus contraction is caused by loop extrusion across the entire Igh locus. Notably, the expression of Wapl is repressed by Pax5 specifically in pro-B and pre-B cells, facilitating extended loop extrusion by increasing the residence time of cohesin on chromatin. Pax5 mediates the transcriptional repression of Wapl through a single Pax5-binding site by recruiting the polycomb repressive complex 2 to induce bivalent chromatin at the Wapl promoter. Reduced Wapl expression causes global alterations in the chromosome architecture, indicating that the potential to recombine all V genes entails structural changes of the entire genome in pro-B cells.","authors":"Hill, L., Ebert, A., Jaritz, M., Wutz, G., Nagasaka, K., Tagoh, H., Kostanova-Poliakova, D., Schindler, K., Sun, Q., B\u00f6nelt, P., Fischer, M., Peters, JM., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nature","volume":"584","issue":"7819","page":"142-147","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32367046","title":"In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states.","abstract":"Following implantation, the naive pluripotent epiblast of the mouse blastocyst generates a rosette, undergoes lumenogenesis and forms the primed pluripotent egg cylinder, which is able to generate the embryonic tissues. How pluripotency progression and morphogenesis are linked and whether intermediate pluripotent states exist remain controversial. We identify here a rosette pluripotent state defined by the co-expression of naive factors with the transcription factor OTX2. Downregulation of blastocyst WNT signals drives the transition into rosette pluripotency by inducing OTX2. The rosette then activates MEK signals that induce lumenogenesis and drive progression to primed pluripotency. Consequently, combined WNT and MEK inhibition supports rosette-like stem cells, a self-renewing naive-primed intermediate. Rosette-like stem cells erase constitutive heterochromatin marks and display a primed chromatin landscape, with bivalently marked primed pluripotency genes. Nonetheless, WNT induces reversion to naive pluripotency. The rosette is therefore a reversible pluripotent intermediate whereby control over both pluripotency progression and morphogenesis pivots from WNT to MEK signals.","authors":"Neagu, A., van Genderen, E., Escudero, I., Verwegen, L., Kurek, D., Lehmann, J., Stel, J., Dirks, RAM., van Mierlo, G., Maas, A., Eleveld, C., Ge, Y., den Dekker, AT., Brouwer, RWW., van IJcken, WFJ., Modic, M., Drukker, M., Jansen, JH., Rivron, NC., Baart, EB., Marks, H., Ten Berge, D.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Nat Cell Biol","volume":"22","issue":"5","page":"534-545","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32780801","title":"Repression of the B cell identity factor Pax5 is not required for plasma cell development.","abstract":"B cell and plasma cell fates are controlled by different transcriptional networks, as exemplified by the mutually exclusive expression and cross-antagonism of the B cell identity factor Pax5 and the plasma cell regulator Blimp1. It has been postulated that repression of Pax5 by Blimp1 is essential for plasma cell development. Here, we challenged this hypothesis by analyzing the IghPax5\/+ mouse, which expressed a Pax5 minigene from the immunoglobulin heavy-chain locus. Despite high Pax5 expression, plasma cells efficiently developed in young IghPax5\/+ mice at steady state and upon immunization, while their number moderately declined in older mice. Although Pax5 significantly deregulated the plasma cell expression program, key plasma cell regulators were normally expressed in IghPax5\/+ plasma cells. While IgM and IgA secretion by IghPax5\/+ plasma cells was normal, IgG secretion was modestly decreased. Hence, Pax5 repression is not essential for robust plasma cell development and antibody secretion, although it is required for optimal IgG production and accumulation of long-lived plasma cells.","authors":"Liu, GJ., Jaritz, M., W\u00f6hner, M., Agerer, B., Bergthaler, A., Malin, SG., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Exp Med","volume":"217","issue":"11","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32483384","title":"Brain organoids: an ensemble of bioassays to investigate human neurodevelopment and disease.","abstract":"Understanding etiology of human neurological and psychiatric diseases is challenging. Genomic changes, protracted development, and histological features unique to human brain development limit the disease aspects that can be investigated using model organisms. Hence, in order to study phenotypes associated with human brain development, function, and disease, it is necessary to use alternative experimental systems that are accessible, ethically justified, and replicate human context. Human pluripotent stem cell (hPSC)-derived brain organoids offer such a system, which recapitulates features of early human neurodevelopment in vitro, including the generation, proliferation, and differentiation of neural progenitors into neurons and glial cells and the complex interactions among the diverse, emergent cell types of the developing brain in three-dimensions (3-D). In recent years, numerous brain organoid protocols and related techniques have been developed to recapitulate aspects of embryonic and fetal brain development in a reproducible and predictable manner. Altogether, these different organoid technologies provide distinct bioassays to unravel novel, disease-associated phenotypes and mechanisms. In this review, we summarize how the diverse brain organoid methods can be utilized to enhance our understanding of brain disorders. FACTS: Brain organoids offer an in vitro approach to study aspects of human brain development and disease. Diverse brain organoid techniques offer bioassays to investigate new phenotypes associated with human brain disorders that are difficult to study in monolayer cultures. Brain organoids have been particularly useful to study phenomena and diseases associated with neural progenitor morphology, survival, proliferation, and differentiation. OPEN QUESTION: Future brain organoid research needs to aim at later stages of neurodevelopment, linked with neuronal activity and connections, to unravel further disease-associated phenotypes. Continued improvement of existing organoid protocols is required to generate standardized methods that recapitulate in vivo-like spatial diversity and complexity.","authors":"Sidhaye, J., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell Death Differ","volume":"28","issue":"1","page":"52-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32333836","title":"Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2.","abstract":"We have previously provided the first genetic evidence that angiotensin converting enzyme 2 (ACE2) is the critical receptor for severe acute respiratory syndrome coronavirus (SARS-CoV), and ACE2 protects the lung from injury, providing a molecular explanation for the severe lung failure and death due to SARS-CoV infections. ACE2 has now also been identified as a key receptor for SARS-CoV-2 infections, and it has been proposed that inhibiting this interaction might be used in treating patients with COVID-19. However, it is not known whether human recombinant soluble ACE2 (hrsACE2) blocks growth of SARS-CoV-2. Here, we show that clinical grade hrsACE2 reduced SARS-CoV-2 recovery from Vero cells by a factor of 1,000-5,000. An equivalent mouse rsACE2 had no effect. We also show that SARS-CoV-2 can directly infect engineered human blood vessel organoids and human kidney organoids, which can be inhibited by hrsACE2. These data demonstrate that hrsACE2 can significantly block early stages of SARS-CoV-2 infections.","authors":"Monteil, V., Kwon, H., Prado, P., Hagelkr\u00fcys, A., Wimmer, RA., Stahl, M., Leopoldi, A., Garreta, E., Hurtado Del Pozo, C., Prosper, F., Romero, JP., Wirnsberger, G., Zhang, H., Slutsky, AS., Conder, R., Montserrat, N., Mirazimi, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell","volume":"181","issue":"4","page":"905-913.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32157739","title":"Sigma-1 receptors control neuropathic pain and macrophage infiltration into the dorsal root ganglion after peripheral nerve injury.","abstract":"Neuron-immune interaction in the dorsal root ganglia (DRG) plays a pivotal role in the neuropathic pain development after nerve injury. Sigma-1 receptor (Sig-1R) is expressed by DRG neurons but its role in neuropathic pain is not fully understood. We investigated the effect of peripheral Sig-1R on neuroinflammation in the DRG after spared (sciatic) nerve injury (SNI) in mice. Nerve injury induced a decrease in NeuN staining along with the nuclear eccentricity and ATF3 expression in the injured DRG. Sig-1R was present in all DRG neurons examined, and after SNI this receptor translocated to the periphery of the soma and the vicinity of the nucleus, especially in injured ATF3\u00a0+\u00a0neurons. In WT mice, injured DRG produced the chemokine CCL2, and this was followed by massive infiltration of macrophages\/monocytes, which clustered mainly around sensory neurons with translocated Sig-1R, accompanied by robust IL-6 increase and mechanical allodynia. In contrast, Sig-1R knockout (Sig-1R-KO) mice showed reduced levels of CCL2, decreased macrophage\/monocyte infiltration into DRG, and less IL-6 and neuropathic mechanical allodynia after SNI. Our findings point to an important role of peripheral Sig-1R in sensory neuron-macrophage\/monocyte communication in the DRG after peripheral nerve injury; thus, these receptors may contribute to the neuropathic pain phenotype.","authors":"Bravo-Caparr\u00f3s, I., Ruiz-Cantero, MC., Perazzoli, G., Cronin, SJF., Vela, JM., Hamed, MF., Penninger, JM., Baeyens, JM., Cobos, EJ., Nieto, FR.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"FASEB J","volume":"34","issue":"4","page":"5951-5966","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32328639","title":"Wapl releases Scc1-cohesin and regulates chromosome structure and segregation in mouse oocytes.","abstract":"Cohesin is essential for genome folding and inheritance. In somatic cells, these functions are both mediated by Scc1-cohesin, which in mitosis is released from chromosomes by Wapl and separase. In mammalian oocytes, cohesion is mediated by Rec8-cohesin. Scc1 is expressed but neither required nor sufficient for cohesion, and its function remains unknown. Likewise, it is unknown whether Wapl regulates one or both cohesin complexes and chromosome segregation in mature oocytes. Here, we show that Wapl is required for accurate meiosis I chromosome segregation, predominantly releases Scc1-cohesin from chromosomes, and promotes production of euploid eggs. Using single-nucleus Hi-C, we found that Scc1 is essential for chromosome organization in oocytes. Increasing Scc1 residence time on chromosomes by Wapl depletion leads to vermicelli formation and intra-loop structures but, unlike in somatic cells, does not increase loop size. We conclude that distinct cohesin complexes generate loops and cohesion in oocytes and propose that the same principle applies to all cell types and species.","authors":"Silva, MCC., Powell, S., Ladst\u00e4tter, S., Gassler, J., Stocsits, R., Tedeschi, A., Peters, JM., Tachibana, K.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Cell Biol","volume":"219","issue":"4","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31955849","title":"Cerebellar Neurodynamics Predict Decision Timing and Outcome on the Single-Trial Level.","abstract":"Goal-directed behavior requires the interaction of multiple brain regions. How these regions and their interactions with brain-wide activity drive action selection is less understood. We have investigated this question by combining whole-brain volumetric calcium imaging using light-field microscopy and an operant-conditioning task in larval zebrafish. We find global, recurring dynamics of brain states to exhibit pre-motor bifurcations toward mutually exclusive decision outcomes. These dynamics arise from a distributed network displaying trial-by-trial functional connectivity changes, especially between cerebellum and habenula, which correlate with decision outcome. Within this network the cerebellum shows particularly strong and predictive pre-motor activity (&gt;10\u00a0s before movement initiation), mainly within the granule cells. Turn directions are determined by the difference neuroactivity between the ipsilateral and contralateral hemispheres, while the rate of bi-hemispheric population ramping quantitatively predicts decision time on the trial-by-trial level. Our results highlight a cognitive role of the cerebellum and its importance in motor planning.","authors":"Lin, Q., Manley, J., Helmreich, M., Schlumm, F., Li, JM., Robson, DN., Engert, F., Schier, A., N\u00f6bauer, T., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell","volume":"180","issue":"3","page":"536-551.e17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31930531","title":"Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells.","abstract":"Somatic cells acclimate to changes in the environment by temporary reprogramming. Much has been learned about transcription factors that induce these cell-state switches in both plants and animals, but how cells rapidly modulate their proteome remains elusive. Here, we show rapid induction of autophagy during temporary reprogramming in plants triggered by phytohormones, immune, and danger signals. Quantitative proteomics following sequential reprogramming revealed that autophagy is required for timely decay of previous cellular states and for tweaking the proteome to acclimate to the new conditions. Signatures of previous cellular programs thus persist in autophagy-deficient cells, affecting cellular decision-making. Concordantly, autophagy-deficient cells fail to acclimatize to dynamic climate changes. Similarly, they have defects in dedifferentiating into pluripotent stem cells, and redifferentiation during organogenesis. These observations indicate that autophagy mediates cell-state switches that underlie somatic cell reprogramming in plants and possibly other organisms, and thereby promotes phenotypic plasticity.","authors":"Rodriguez, E., Chevalier, J., Olsen, J., Ansb\u00f8l, J., Kapousidou, V., Zuo, Z., Svenning, S., Loefke, C., Koemeda, S., Drozdowskyj, PS., Jez, J., Durnberger, G., Kuenzl, F., Schutzbier, M., Mechtler, K., Ebstrup, EN., Lolle, S., Dagdas, Y., Petersen, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"EMBO J","volume":"39","issue":"4","page":"e103315","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31907318","title":"Activation by substoichiometric inhibition.","abstract":"Startling reports described the paradoxical triggering of the human mitogen-activated protein kinase pathway when a small-molecule inhibitor specifically inactivates the BRAF V600E protein kinase but not wt-BRAF. We performed a conceptual analysis of the general phenomenon \"activation by inhibition\" using bacterial and human HtrA proteases as models. Our data suggest a clear explanation that is based on the classic biochemical principles of allostery and cooperativity. Although substoichiometric occupancy of inhibitor binding sites results in partial inhibition, this effect is overrun by a concomitant activation of unliganded binding sites. Therefore, when an inhibitor of a cooperative enzyme does not reach saturating levels, a common scenario during drug administration, it may cause the contrary of the desired effect. The implications for drug development are discussed.","authors":"Merdanovic, M., Burston, SG., Schmitz, AL., K\u00f6cher, S., Knapp, S., Clausen, T., Kaiser, M., Huber, R., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Proc Natl Acad Sci U S A","volume":"117","issue":"3","page":"1414-1418","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31676384","title":"Sonoprinting liposomes on tumor spheroids by microbubbles and ultrasound.","abstract":"Ultrasound-triggered drug-loaded microbubbles have great potential for drug delivery due to their ability to locally release drugs and simultaneously enhance their delivery into the target tissue. We have recently shown that upon applying ultrasound, nanoparticle-loaded microbubbles can deposit nanoparticles onto cells grown in 2D monolayers, through a process that we termed \"sonoprinting\". However, the rigid surfaces on which cell monolayers are typically growing might be a source of acoustic reflections and aspherical microbubble oscillations, which can influence microbubble-cell interactions. In the present study, we aim to reveal whether sonoprinting can also occur in more complex and physiologically relevant tissues, by using free-floating 3D tumor spheroids as a tissue model. We show that both monospheroids (consisting of tumor cells alone) and cospheroids (consisting of tumor cells and fibroblasts, which produce an extracellular matrix) can be sonoprinted. Using doxorubicin-liposome-loaded microbubbles, we show that sonoprinting allows to deposit large amounts of doxorubicin-containing liposomes to the outer cell layers of the spheroids, followed by doxorubicin release into the deeper layers of the spheroids, resulting in a significant reduction in cell viability. Sonoprinting may become an attractive approach to deposit drug patches at the surface of tissues, thereby promoting the delivery of drugs into target tissues.","authors":"Roovers, S., Deprez, J., Priwitaningrum, D., Lajoinie, G., Rivron, N., Declercq, H., De Wever, O., Stride, E., Le Gac, S., Versluis, M., Prakash, J., De Smedt, SC., Lentacker, I.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Control Release","volume":"316","issue":null,"page":"79-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31617949","title":"Deciphering retinal diseases through the generation of three dimensional stem cell-derived organoids: Concise Review.","abstract":"Three-dimensional (3D) retinal organoids, in vitro tissue structures derived from self-organizing cultures of differentiating human embryonic stem cells or induced pluripotent stem cells, could recapitulate some aspects of the cytoarchitectural structure and function of the retina in vivo. 3D retinal organoids display huge potential for the investigation of the pathogenesis of monogenic hereditary eye diseases that are related to the malfunction or degeneration of photoreceptors or retinal ganglion cells by providing an effective in vitro tool with multiple applications. In combination with recent genome editing tools, 3D retinal organoids could also represent a reliable and renewable source of transplantable cells for personalized therapies. In this review, we describe the recent advances in human pluripotent stem cells-derived retinal organoids, determination of their histoarchitecture, complexity, and maturity. We also discuss their application as a means to decipher the pathogenesis of retinal diseases, as well as the main drawbacks and challenges. Stem Cells 2019;37:1496-1504.","authors":"Artero Castro, A., Rodr\u00edguez Jimenez, FJ., Jendelova, P., Erceg, S.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Stem Cells","volume":"37","issue":"12","page":"1496-1504","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31569015","title":"Cancer susceptibility of beta HPV49 E6 and E7 transgenic mice to 4-nitroquinoline 1-oxide treatment correlates with mutational signatures of tobacco exposure.","abstract":"We have previously showed that a transgenic (Tg) mouse model with cytokeratin 14 promoter (K14)-driven expression of E6 and E7 from beta-3 HPV49 in the basal layer of the epidermis and of the mucosal epithelia of the digestive tract (K14 HPV49 E6\/E7 Tg mice) are highly susceptible to upper digestive tract carcinogenesis upon exposure to 4-nitroquinoline 1-oxide (4NQO). Using whole-exome sequencing, we show that in K14 HPV49 E6\/E7 Tg mice, development of 4NQO-induced cancers tightly correlates with the accumulation of somatic mutations in cancer-related genes. The mutational signature in 4NQO-treated mice was similar to the signature observed in humans exposed to tobacco smoking and tobacco chewing. Similar results were obtained with K14 Tg animals expressing mucosal high-risk HPV16 E6 and E7 oncogenes. Thus, beta-3 HPV49 share some functional similarities with HPV16 in Tg animals.","authors":"Viarisio, D., Robitaille, A., M\u00fcller-Decker, K., Flechtenmacher, C., Gissmann, L., Tommasino, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Virology","volume":"538","issue":"","page":"53-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31543265","title":"Organization of Chromatin by Intrinsic and Regulated Phase Separation.","abstract":"Eukaryotic chromatin is highly condensed but dynamically accessible to regulation and organized into subdomains. We demonstrate that reconstituted chromatin undergoes histone tail-driven liquid-liquid phase separation (LLPS) in physiologic salt and when microinjected into cell nuclei, producing dense and dynamic droplets. Linker histone H1 and internucleosome linker lengths shared across eukaryotes promote phase separation of chromatin, tune droplet properties, and coordinate to form condensates of consistent density in manners that parallel chromatin behavior in cells. Histone acetylation by p300 antagonizes chromatin phase separation, dissolving droplets in\u00a0vitro and decreasing droplet formation in nuclei. In the presence of multi-bromodomain proteins, such as BRD4, highly acetylated chromatin forms a new phase-separated state with droplets of distinct physical properties, which can be immiscible with unmodified chromatin droplets, mimicking nuclear chromatin subdomains. Our data suggest a framework, based on intrinsic phase separation of the chromatin polymer, for understanding the organization and regulation of eukaryotic genomes.","authors":"Gibson, BA., Doolittle, LK., Schneider, MWG., Jensen, LE., Gamarra, N., Henry, L., Gerlich, DW., Redding, S., Rosen, MK.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell","volume":"179","issue":"2","page":"470-484.e21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31526867","title":"Gene doubling increases glyoxalase 1 expression in RAGE knockout mice.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31526867<\/PMID><DateCompleted><Year>2020<\/Year><Month>07<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>07<\/Month><Day>07<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1872-8006<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>1864<\/Volume><Issue>1<\/Issue><PubDate><Year>2020<\/Year><Month>01<\/Month><\/PubDate><\/JournalIssue><Title>Biochimica et biophysica acta. General subjects<\/Title><ISOAbbreviation>Biochim Biophys Acta Gen Subj<\/ISOAbbreviation><\/Journal><ArticleTitle>Gene doubling increases glyoxalase 1 expression in RAGE knockout mice.<\/ArticleTitle><Pagination><MedlinePgn>129438<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0304-4165(19)30224-7<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.bbagen.2019.129438<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">The receptor for advanced glycation end-products (RAGE) is a multifunctional protein. Its function as pattern recognition receptor able to interact with various extracellular ligands is well described. Genetically modified mouse models, especially the RAGE knockout (RAGE-KO) mouse, identified the amplification of the immune response as an important function of RAGE. Pro-inflammatory ligands of RAGE are also methylglyoxal-derived advanced glycation end-products, which depend in their quantity, at least in part, on the activity of the methylglyoxal-detoxifying enzyme glyoxalase-1 (Glo1). Therefore, we studied the potential interaction of RAGE and Glo1 by use of RAGE-KO mice.","authors":"Bartling, B., Zunkel, K., Al-Robaiy, S., Dehghani, F., Simm, A.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Biochim Biophys Acta Gen Subj","volume":"1864","issue":"1","page":"129438","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31414712","title":"Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self-renewal and identity.","abstract":"Tissues in multicellular organisms are populated by resident macrophages, which perform both generic and tissue-specific functions. The latter are induced by signals from the microenvironment and rely on unique tissue-specific molecular programs requiring the combinatorial action of tissue-specific and broadly expressed transcriptional regulators. Here, we identify the transcription factors Bhlhe40 and Bhlhe41 as novel regulators of alveolar macrophages (AMs)-a population that provides the first line of immune defense and executes homeostatic functions in lung alveoli. In the absence of these factors, AMs exhibited decreased proliferation that resulted in a severe disadvantage of knockout AMs in a competitive setting. Gene expression analyses revealed a broad cell-intrinsic footprint of Bhlhe40\/Bhlhe41 deficiency manifested by a downregulation of AM signature genes and induction of signature genes of other macrophage lineages. Genome-wide characterization of Bhlhe40 DNA binding suggested that these transcription factors directly repress the expression of lineage-inappropriate genes in AMs. Taken together, these results identify Bhlhe40 and Bhlhe41 as key regulators of AM self-renewal and guardians of their identity.","authors":"Rauschmeier, R., Gustafsson, C., Reinhardt, A., A-Gonzalez, N., Tortola, L., Cansever, D., Subramanian, S., Taneja, R., Rossner, MJ., Sieweke, MH., Greter, M., M\u00e5nsson, R., Busslinger, M., Kreslavsky, T.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"EMBO J","volume":"38","issue":"19","page":"e101233","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31384064","title":"The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation.","abstract":"The PIWI-interacting RNA (piRNA) pathway protects genome integrity in part through establishing repressive heterochromatin at transposon loci. Silencing requires piRNA-guided targeting of nuclear PIWI proteins to nascent transposon transcripts, yet the subsequent molecular events are not understood. Here, we identify SFiNX (silencing factor interacting nuclear export variant), an interdependent protein complex required for Piwi-mediated cotranscriptional silencing in Drosophila. SFiNX consists of Nxf2-Nxt1, a gonad-specific variant of the heterodimeric messenger RNA export receptor Nxf1-Nxt1 and the Piwi-associated protein Panoramix. SFiNX mutant flies are sterile and exhibit transposon derepression because piRNA-loaded Piwi is unable to establish heterochromatin. Within SFiNX, Panoramix recruits heterochromatin effectors, while the RNA binding protein Nxf2 licenses cotranscriptional silencing. Our data reveal how Nxf2 might have evolved from an RNA transport receptor into a cotranscriptional silencing factor. Thus, NXF variants, which are abundant in metazoans, can have diverse molecular functions and might have been coopted for host genome defense more broadly.","authors":"Batki, J., Schnabl, J., Wang, J., Handler, D., Andreev, VI., Stieger, CE., Novatchkova, M., Lampersberger, L., Kauneckaite, K., Xie, W., Mechtler, K., Patel, DJ., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Struct Mol Biol","volume":"26","issue":"8","page":"720-731","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31330507","title":"Identification of Key Genes and Candidated Pathways in Human Autosomal Dominant Polycystic Kidney Disease by Bioinformatics Analysis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31330507<\/PMID><DateCompleted><Year>2020<\/Year><Month>01<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>01<\/Month><Day>29<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1423-0143<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>44<\/Volume><Issue>4<\/Issue><PubDate><Year>2019<\/Year><\/PubDate><\/JournalIssue><Title>Kidney &amp; blood pressure research<\/Title><ISOAbbreviation>Kidney Blood Press Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Identification of Key Genes and Candidated Pathways in Human Autosomal Dominant Polycystic Kidney Disease by Bioinformatics Analysis.<\/ArticleTitle><Pagination><MedlinePgn>533-552<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1159\/000500458<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\/AIMS\" NlmCategory=\"OBJECTIVE\">Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic form of kidney disease. High-throughput microarray analysis has been applied for elucidating key genes and pathways associated with ADPKD. Most genetic profiling data from ADPKD patients have been uploaded to public databases but not thoroughly analyzed. This study integrated 2 human microarray profile datasets to elucidate the potential pathways and protein-protein interactions (PPIs) involved in ADPKD via bioinformatics analysis in order to identify possible therapeutic targets.","authors":"Liu, D., Huo, Y., Chen, S., Xu, D., Yang, B., Xue, C., Fu, L., Bu, L., Song, S., Mei, C.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Kidney Blood Press Res","volume":"44","issue":"4","page":"533-552","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31267692","title":"Apelin inhibition prevents resistance and metastasis associated with anti-angiogenic therapy.","abstract":"Angiogenesis is a hallmark of cancer, promoting growth and metastasis. Anti-angiogenic treatment has limited efficacy due to therapy-induced blood vessel alterations, often followed by local hypoxia, tumor adaptation, progression, and metastasis. It is therefore paramount to overcome therapy-induced resistance. We show that Apelin inhibition potently remodels the tumor microenvironment, reducing angiogenesis, and effectively blunting tumor growth. Functionally, targeting Apelin improves vessel function and reduces polymorphonuclear myeloid-derived suppressor cell infiltration. Importantly, in mammary and lung cancer, Apelin prevents resistance to anti-angiogenic receptor tyrosine kinase (RTK) inhibitor therapy, reducing growth and angiogenesis in lung and breast cancer models without increased hypoxia in the tumor microenvironment. Apelin blockage also prevents RTK inhibitor-induced metastases, and high Apelin levels correlate with poor prognosis of anti-angiogenic therapy patients. These data identify a druggable anti-angiogenic drug target that reduces tumor blood vessel densities and normalizes the tumor vasculature to decrease metastases.","authors":"Uribesalgo, I., Hoffmann, D., Zhang, Y., Kavirayani, A., Lazovic, J., Berta, J., Novatchkova, M., Pai, TP., Wimmer, RA., L\u00e1szl\u00f3, V., Schramek, D., Karim, R., Tortola, L., Deswal, S., Haas, L., Zuber, J., Sz\u0171cs, M., Kuba, K., Dome, B., Cao, Y., Haubner, BJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"EMBO Mol Med","volume":"11","issue":"8","page":"e9266","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30917309","title":"Prdm12 Directs Nociceptive Sensory Neuron Development by Regulating the Expression of the NGF Receptor TrkA.","abstract":"In humans, many cases of congenital insensitivity to pain (CIP) are caused by mutations of components of the NGF\/TrkA signaling pathway, which is required for survival and specification of nociceptors and plays a major role in pain processing. Mutations in PRDM12 have been identified in CIP patients that indicate a putative role for this transcriptional regulator in pain sensing. Here, we show that Prdm12 expression is restricted to developing and adult nociceptors and that its genetic ablation compromises their viability and maturation. Mechanistically, we find that Prdm12 is required for the initiation and maintenance of the expression of TrkA by acting as\u00a0a modulator of Neurogenin1\/2 transcription factor activity, in frogs, mice, and humans. Altogether, our\u00a0results identify Prdm12 as an evolutionarily conserved key regulator of nociceptor specification and as an actionable target for new pain therapeutics.","authors":"Desiderio, S., Vermeiren, S., Van Campenhout, C., Kricha, S., Malki, E., Richts, S., Fletcher, EV., Vanwelden, T., Schmidt, BZ., Henningfeld, KA., Pieler, T., Woods, CG., Nagy, V., Verfaillie, C., Bellefroid, EJ.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell Rep","volume":"26","issue":"13","page":"3522-3536.e5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31133695","title":"AIF-regulated oxidative phosphorylation supports lung cancer development.","abstract":"Cancer is a major and still increasing cause of death in humans. Most cancer cells have a fundamentally different metabolic profile from that of normal tissue. This shift away from mitochondrial ATP synthesis via oxidative phosphorylation towards a high rate of glycolysis, termed Warburg effect, has long been recognized as a paradigmatic hallmark of cancer, supporting the increased biosynthetic demands of tumor cells. Here we show that deletion of apoptosis-inducing factor (AIF) in a Kras<sup>G12D<\/sup>-driven mouse lung cancer model resulted in a marked survival advantage, with delayed tumor onset and decreased malignant progression. Mechanistically, Aif deletion leads to oxidative phosphorylation (OXPHOS) deficiency and a switch in cellular metabolism towards glycolysis in non-transformed pneumocytes and at early stages of tumor development. Paradoxically, although Aif-deficient cells exhibited a metabolic Warburg profile, this bioenergetic change resulted in a growth disadvantage of Kras<sup>G12D<\/sup>-driven as well as Kras wild-type lung cancer cells. Cell-autonomous re-expression of both wild-type and mutant AIF (displaying an intact mitochondrial, but abrogated apoptotic function) in Aif-knockout Kras<sup>G12D<\/sup> mice restored OXPHOS and reduced animal survival to the same level as AIF wild-type mice. In patients with non-small cell lung cancer, high AIF expression was associated with poor prognosis. These data show that AIF-regulated mitochondrial respiration and OXPHOS drive the progression of lung cancer.","authors":"Rao, S., Mondrag\u00f3n, L., Pranjic, B., Hanada, T., Stoll, G., K\u00f6cher, T., Zhang, P., Jais, A., Lercher, A., Bergthaler, A., Schramek, D., Haigh, K., Sica, V., Leduc, M., Modjtahedi, N., Pai, TP., Onji, M., Uribesalgo, I., Hanada, R., Kozieradzki, I., Koglgruber, R., Cronin, SJ., She, Z., Quehenberger, F., Popper, H., Kenner, L., Haigh, JJ., Kepp, O., Rak, M., Cai, K., Kroemer, G., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell Res","volume":"29","issue":"7","page":"579-591","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31113824","title":"Augmin accumulation on long-lived microtubules drives amplification and kinetochore-directed growth.","abstract":"Dividing cells reorganize their microtubule cytoskeleton into a bipolar spindle, which moves one set of sister chromatids to each nascent daughter cell. Early spindle assembly models postulated that spindle pole-derived microtubules search the cytoplasmic space until they randomly encounter a kinetochore to form a stable attachment. More recent work uncovered several additional, centrosome-independent microtubule generation pathways, but the contributions of each pathway to spindle assembly have remained unclear. Here, we combined live microscopy and mathematical modeling to show that most microtubules nucleate at noncentrosomal regions in dividing human cells. Using a live-cell probe that selectively labels aged microtubule lattices, we demonstrate that the distribution of growing microtubule plus ends can be almost entirely explained by Augmin-dependent amplification of long-lived microtubule lattices. By ultrafast 3D lattice light-sheet microscopy, we observed that this mechanism results in a strong directional bias of microtubule growth toward individual kinetochores. Our systematic quantification of spindle dynamics reveals highly coordinated microtubule growth during kinetochore fiber assembly.","authors":"David, AF., Roudot, P., Legant, WR., Betzig, E., Danuser, G., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Cell Biol","volume":"218","issue":"7","page":"2150-2168","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31025257","title":"The ERBB receptor inhibitor dacomitinib suppresses proliferation and invasion of pancreatic ductal adenocarcinoma cells.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">31025257<\/PMID><DateCompleted><Year>2019<\/Year><Month>12<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>02<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">2211-3436<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>42<\/Volume><Issue>4<\/Issue><PubDate><Year>2019<\/Year><Month>Aug<\/Month><\/PubDate><\/JournalIssue><Title>Cellular oncology (Dordrecht)<\/Title><ISOAbbreviation>Cell Oncol (Dordr)<\/ISOAbbreviation><\/Journal><ArticleTitle>The ERBB receptor inhibitor dacomitinib suppresses proliferation and invasion of pancreatic ductal adenocarcinoma cells.<\/ArticleTitle><Pagination><MedlinePgn>491-504<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s13402-019-00448-w<\/ELocationID><Abstract><AbstractText Label=\"PURPOSE\" NlmCategory=\"OBJECTIVE\">Pancreatic ductal adenocarcinoma (PDAC), the most common malignancy of the pancreas, is the fourth most common cause of cancer-related death in the USA. Local progression, early tumor dissemination and low efficacy of current treatments are the major reasons for its high mortality rate. The ERBB family is over-expressed in PDAC and plays essential roles in its tumorigenesis; however, single-targeted ERBB inhibitors have shown limited activity in this disease. Here, we examined the anti-tumor activity of dacomitinib, a pan-ERBB receptor inhibitor, on PDAC cells.","authors":"Momeny, M., Esmaeili, F., Hamzehlou, S., Yousefi, H., Javadikooshesh, S., Vahdatirad, V., Alishahi, Z., Mousavipak, SH., Bashash, D., Dehpour, AR., Tavangar, SM., Tavakkoly-Bazzaz, J., Haddad, P., Kordbacheh, F., Alimoghaddam, K., Ghavamzadeh, A., Ghaffari, SH.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell Oncol (Dordr)","volume":"42","issue":"4","page":"491-504","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31013075","title":"Genome-Wide DNA Methylome and Transcriptome Analysis of Porcine Intestinal Epithelial Cells upon Deoxynivalenol Exposure.","abstract":"Deoxynivalenol (DON) is a type of mycotoxin that is disruptive to intestinal and immune systems. To better understand the molecular effects of DON exposure, we performed genome-wide comparisons of DNA methylation and gene expression from porcine intestinal epithelial cell IPEC-J2 upon DON exposure using reduced representation bisulfite sequencing and RNA-seq technologies. We characterized the methylation pattern changes and found 3030 differentially methylated regions. Moreover, 3226 genes showing differential expression were enriched in pathways of protein and nucleic acid synthesis and ribosome biogenesis. Integrative analysis identified 29 genes showing inverse correlations between promoter methylation and expression. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions upon DON exposure. Our data provided new insights into epigenetic and transcriptomic alterations of intestinal epithelial cells upon DON exposure and may advance the identification of biomarkers and drug targets for predicting and controlling the toxic effects of this common mycotoxin.","authors":"Wang, H., Zong, Q., Wang, S., Zhao, C., Wu, S., Bao, W.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Agric Food Chem","volume":"67","issue":"22","page":"6423-6431","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12113552","title":"The role of LFA-1 in osteoclast development induced by co-cultures of mouse bone marrow cells and MC3T3-G2\/PA6 cells.","abstract":"Interactions between leukocyte function-associated antigen-1 (LFA-1) and intercellular adhesion molecule-1 (ICAM-1) influence the development of osteoclasts. However, little is known about how these adhesion molecules are involved in the process of osteoclast development. This study evaluated the role of LFA-1 and its ligands in osteoclast development and bone resorption. Co-cultures of bone marrow cells from LFA-1-deficient mice and MC3T3-G2\/PA6 (PA6) cells were cultured in the presence of 1alpha,25(OH)2D3 and dexamethasone for 7 days. The number of TRAP-positive cells that were generated by bone marrow cells from LFA-1-deficient mice was smaller than that generated by bone marrow cells from wild-type mice. In addition, the bone-resorbing activity of osteoclast-like cells that were generated from LFA-1-deficient mice was lower than that generated by osteoclast-like cells from wild-type mice. Immunofluorescence flow cytometry showed that osteoclast stromal PA6 cells expressed the cell adhesion molecules, ICAM-1 and VCAM-1. When monoclonal antibodies to mice VCAM-1, CD11b or CD18 were added separately to the co-culture system, the number of TRAP-positive cells that were generated from LFA-1-deficient mice was 20-30% smaller than that generated from wild-type mice. The formation of TRAP-positive cells from both LFA-1 deficient and wild-type mice was especially inhibited by anti-CD18 antibody, in comparison to the addition of normal IgG serum. These results suggest that LFA-1 adhesion molecules play a role in osteoclast development by affecting adhesion between stromal cells and osteoclast progenitors before the occurrence of ODF-ODF receptor signaling. CD18 appears to be a key adhesion molecule in cell-to-cell contacts during the early stage of osteoclast development.","authors":"Tani-Ishii, N., Penninger, JM., Matsumoto, G., Teranaka, T., Umemoto, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Periodontal Res","volume":"37","issue":"3","page":"184-91","pdf":null,"JrId":"5143","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30963785","title":"LncRNA <i>HOXA-AS3<\/i> Sponges <i>miR-29c<\/i> to Facilitate Cell Proliferation, Metastasis, and EMT Process and Activate the MEK\/ERK Signaling Pathway in Hepatocellular Carcinoma.","abstract":"Hepatocellular carcinoma (HCC) is a prevalent malignant tumor with high morbidity and mortality across the world. Recent findings have suggested that long noncoding (lnc)RNA <i>HOXA-AS3<\/i> plays an important role in tumorigenesis and metastasis in a variety of cancers. However, the role of lncRNA <i>HOXA-AS3<\/i> in the initiation and progression of HCC remains largely unclear. In the present study, <i>HOXA-AS3<\/i> was highly expressed in HCC tumor tissues and cell lines. High <i>HOXA-AS3<\/i> expression was correlated with low survival of HCC patients. Loss-of-function experiments showed that knockdown of <i>HOXA-AS3<\/i> inhibited cell proliferation, migration, invasion, the epithelial-mesenchymal transition (EMT) process, and the mitogen-activated protein kinase\/extracellular regulated protein kinase (MEK\/ERK) signaling pathway in HCC. Molecular mechanism exploration uncovered that <i>HOXA-AS3<\/i> could directly interact with and negatively regulate <i>miR-29c<\/i>. BMP1 is a downstream target gene of <i>miR-29c<\/i>, and <i>HOXA-AS3<\/i> could regulate BMP1 expression by targeting <i>miR-29c<\/i>. <i>miR-29c<\/i> negatively regulated and BMP1 promoted the progression of HCC. Rescue experiments revealed that <i>miR-29c<\/i> inhibitor could partially counteract the impact induced by <i>HOXA-AS3<\/i> knockdown in HCC. Taken together, our study is the first to show the interaction of <i>HOXA-AS3<\/i> with <i>miR-29c<\/i> in facilitating cell proliferation, metastasis, EMT process, and MEK\/ERK signaling pathway in HCC.","authors":"Tong, Y., Wang, M., Dai, Y., Bao, D., Zhang, J., Pan, H.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Hum Gene Ther Clin Dev","volume":"30","issue":"3","page":"129-141","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30962626","title":"Structure of McsB, a protein kinase for regulated arginine phosphorylation.","abstract":"Protein phosphorylation regulates key processes in all organisms. In Gram-positive bacteria, protein arginine phosphorylation plays a central role in protein quality control by regulating transcription factors and marking aberrant proteins for degradation. Here, we report structural, biochemical, and in vivo data of the responsible kinase, McsB, the founding member of an arginine-specific class of protein kinases. McsB differs in structure and mechanism from protein kinases that act on serine, threonine, and tyrosine residues and instead has a catalytic domain related to that of phosphagen kinases (PhKs), metabolic enzymes that phosphorylate small guanidino compounds. In McsB, the PhK-like phosphotransferase domain is structurally adapted to target protein substrates and is accompanied by a novel phosphoarginine (pArg)-binding domain that allosterically controls protein kinase activity. The identification of distinct pArg reader domains in this study points to a remarkably complex signaling system, thus challenging simplistic views of bacterial protein phosphorylation.","authors":"Suskiewicz, MJ., Hajdusits, B., Beveridge, R., Heuck, A., Vu, LD., Kurzbauer, R., Hauer, K., Thoeny, V., Rumpel, K., Mechtler, K., Meinhart, A., Clausen, T.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Chem Biol","volume":"15","issue":"5","page":"510-518","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30901730","title":"Characterization of the ERG-regulated Kinome in Prostate Cancer Identifies TNIK as a Potential Therapeutic Target.","abstract":"Approximately 50% of prostate cancers harbor the TMPRSS2:ERG fusion, resulting in elevated expression of the ERG transcription factor. Despite the identification of this subclass of prostate cancers, no personalized therapeutic strategies have achieved clinical implementation. Kinases are attractive therapeutic targets as signaling networks are commonly perturbed in cancers. The impact of elevated ERG expression on kinase signaling networks in prostate cancer has not been investigated. Resolution of this issue may identify novel therapeutic approaches for ERG-positive prostate cancers. In this study, we used quantitative mass spectrometry-based kinomic profiling to identify ERG-mediated changes to cellular signaling networks. We identified 76 kinases that were differentially expressed and\/or phosphorylated in DU145 cells engineered to express ERG. In particular, the Traf2 and Nck-interacting kinase (TNIK) was markedly upregulated and phosphorylated on multiple sites upon ERG overexpression. Importantly, TNIK has not previously been implicated in prostate cancer. To validate the clinical relevance of these findings, we characterized expression of TNIK and TNIK phosphorylated at serine 764 (pS764) in a localized prostate cancer patient cohort and showed that nuclear enrichment of TNIK (pS764) was significantly positively correlated with ERG expression. Moreover, TNIK protein levels were dependent upon ERG expression in VCaP cells and primary cells established from a prostate cancer patient-derived xenograft. Furthermore, reduction of TNIK expression and activity by silencing TNIK expression or using the TNIK inhibitor NCB-0846 reduced cell viability, colony formation and anchorage independent growth. Therefore, TNIK represents a novel and actionable therapeutic target for ERG-positive prostate cancers that could be exploited to develop new treatments for these patients.","authors":"Lee, RS., Zhang, L., Berger, A., Lawrence, MG., Song, J., Niranjan, B., Davies, RG., Lister, NL., Sandhu, SK., Rubin, MA., Risbridger, GP., Taylor, RA., Rickman, DS., Horvath, LG., Daly, RJ.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Neoplasia","volume":"21","issue":"4","page":"389-400","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30718358","title":"Targeting APLN\/APLNR Improves Antiangiogenic Efficiency and Blunts Proinvasive Side Effects of VEGFA\/VEGFR2 Blockade in Glioblastoma.","abstract":"Antiangiogenic therapy of glioblastoma (GBM) with bevacizumab, a VEGFA-blocking antibody, may accelerate tumor cell invasion and induce alternative angiogenic pathways. Here we investigate the roles of the proangiogenic apelin receptor APLNR and its cognate ligand apelin in VEGFA\/VEGFR2 antiangiogenic therapy against distinct subtypes of GBM. In proneural GBM, apelin levels were downregulated by VEGFA or VEGFR2 blockade. A central role for apelin\/APLNR in controlling GBM vascularization was corroborated in a serial implantation model of the angiogenic switch that occurs in human GBM. Apelin and APLNR are broadly expressed in human GBM, and knockdown or knockout of <i>APLN<\/i> in orthotopic models of proneural or classical GBM subtypes significantly reduced GBM vascularization compared with controls. However, reduction in apelin expression led to accelerated GBM cell invasion. Analysis of stereotactic GBM biopsies from patients as well as from <i>in vitro<\/i> and <i>in vivo<\/i> experiments revealed increased dissemination of APLNR-positive tumor cells when apelin levels were reduced. Application of apelin-F13A, a mutant APLNR ligand, blocked tumor angiogenesis and GBM cell invasion. Furthermore, cotargeting VEGFR2 and APLNR synergistically improved survival of mice bearing proneural GBM. In summary, we show that apelin\/APLNR signaling controls GBM angiogenesis and invasion and that both pathologic features are blunted by apelin-F13A. We suggest that apelin-F13A can improve the efficiency and reduce the side effects of established antiangiogenic treatments for distinct GBM subtypes. SIGNIFICANCE: Pharmacologic targeting of the APLNR acts synergistically with established antiangiogenic treatments in glioblastoma and blunts therapy resistance to current strategies for antiangiogenesis.<i>See related commentary by Amoozgar et al., p. 2104<\/i>.","authors":"Mastrella, G., Hou, M., Li, M., Stoecklein, VM., Zdouc, N., Volmar, MNM., Miletic, H., Reinhard, S., Herold-Mende, CC., Kleber, S., Eisenhut, K., Gargiulo, G., Synowitz, M., Vescovi, AL., Harter, PN., Penninger, JM., Wagner, E., Mittelbronn, M., Bjerkvig, R., Hambardzumyan, D., Sch\u00fcller, U., Tonn, JC., Radke, J., Glass, R., K\u00e4lin, RE.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cancer Res","volume":"79","issue":"9","page":"2298-2313","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29775240","title":"Analysis of PNGase F-Resistant N-Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities.","abstract":"SugarQb (www.imba.oeaw.ac.at\/sugarqb) is a freely available collection of computational tools for the automated identification of intact glycopeptides from high-resolution HCD MS\/MS datasets in the Proteome Discoverer environment. We report the migration of SugarQb to the latest and free version of Proteome Discoverer 2.1, and apply it to the analysis of PNGase F-resistant N-glycopeptides from mouse embryonic stem cells. The analysis of intact glycopeptides highlights unexpected technical limitations to PNGase F-dependent glycoproteomic workflows at the proteome level, and warrants a critical reinterpretation of seminal datasets in the context of N-glycosylation-site prediction.","authors":"Stadlmann, J., Hoi, DM., Taubenschmid, J., Mechtler, K., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Proteomics","volume":"18","issue":"13","page":"e1700436","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30693776","title":"Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents.","abstract":"Cross-linking mass spectrometry is becoming increasingly popular, and current advances are widening the applicability of the technique so that it can be utilized by nonspecialist laboratories. Specifically, the use of novel mass-spectrometry-cleavable (MS-cleavable) reagents dramatically reduces the complexity of the data by providing (i) characteristic reporter ions and (ii) the mass of the individual peptides rather than that of the cross-linked moiety. However, optimum acquisition strategies to obtain the best-quality data for such cross-linkers with higher energy C-trap dissociation (HCD) alone are yet to be achieved. Therefore, we have carefully investigated and optimized MS parameters to facilitate the identification of disuccinimidyl-sulfoxide-based cross-links on HCD-equipped mass spectrometers. From the comparison of nine different fragmentation energies, we chose several stepped-HCD fragmentation methods that were evaluated on a variety of cross-linked proteins. The optimal stepped-HCD method was then directly compared with previously described methods using an Orbitrap Fusion Lumos Tribrid instrument using a high-complexity sample. The final results indicate that our stepped-HCD method is able to identify more cross-links than other methods, mitigating the need for multistage MS-enabled (MS<sup>n<\/sup>) instrumentation and alternative dissociation techniques. Data are available via ProteomeXchange with identifier PXD011861.","authors":"Stieger, CE., Doppler, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Proteome Res","volume":"18","issue":"3","page":"1363-1370","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30651639","title":"Human blood vessel organoids as a\u00a0model of\u00a0diabetic vasculopathy.","abstract":"The increasing prevalence of diabetes has resulted in a global epidemic<sup>1<\/sup>. Diabetes is a major cause of blindness, kidney failure, heart attacks, stroke and amputation of lower limbs. These are often caused by changes in blood vessels, such as the expansion of the basement membrane and a loss of vascular cells<sup>2-4<\/sup>. Diabetes also impairs the functions of endothelial cells<sup>5<\/sup> and disturbs the communication between endothelial cells and pericytes<sup>6<\/sup>. How dysfunction of endothelial cells and\/or pericytes leads to diabetic vasculopathy remains largely unknown. Here we report the development of self-organizing three-dimensional human blood vessel organoids from pluripotent stem cells. These human blood vessel organoids contain endothelial cells and pericytes that self-assemble into capillary networks that are enveloped by a basement membrane. Human blood vessel organoids transplanted into mice form a stable, perfused vascular tree, including arteries, arterioles and venules. Exposure of blood vessel organoids to hyperglycaemia and inflammatory cytokines in vitro induces thickening of the vascular basement membrane. Human blood vessels, exposed in vivo to a diabetic milieu in mice, also mimic the microvascular changes found in patients with diabetes. DLL4 and NOTCH3 were identified as key drivers of diabetic vasculopathy in human blood vessels. Therefore, organoids derived from human stem cells faithfully recapitulate the structure and function of human blood vessels and are amenable systems for modelling and identifying the regulators of diabetic vasculopathy, a disease that affects hundreds of millions of patients worldwide.","authors":"Wimmer, RA., Leopoldi, A., Aichinger, M., Wick, N., Hantusch, B., Novatchkova, M., Taubenschmid, J., H\u00e4mmerle, M., Esk, C., Bagley, JA., Lindenhofer, D., Chen, G., Boehm, M., Agu, CA., Yang, F., Fu, B., Zuber, J., Knoblich, JA., Kerjaschki, D., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nature","volume":"565","issue":"7740","page":"505-510","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30633834","title":"RANK deletion in neuropeptide Y neurones attenuates oestrogen deficiency-related bone loss.","abstract":"The RANKL pathway is known to be an important aspect of the pathogenesis of oestrogen deficiency-induced bone loss. RANK deletion specifically in neuropeptide Y (NPY) neurones has been shown to enhance the ability of the skeleton to match increases in body weight caused by high-fat diet feeding, likely via the modulation of NPY levels. In the present study, we used ovariectomy in female mice to show that RANK deletion in NPY neurones attenuates bone loss caused by long-term oestrogen deficiency, particularly in the vertebral compartment. Ovariectomy led to a reduction in NPY expression levels in the arcuate nucleus of NPY<sup>cre\/+<\/sup> ;RANK<sup>lox\/lox<\/sup> mice compared to NPY<sup>cre\/+<\/sup> ;RANK<sup>lox\/+<\/sup> controls. Because NPY deficient mice also displayed a similar protection against ovariectomy-induced bone loss, modulation of hypothalamic NPY signalling is the likely mechanism behind the protection from bone loss in the NPY<sup>cre\/+<\/sup> ;RANK<sup>lox\/lox<\/sup> mice.","authors":"Lee, NJ., Clarke, IM., Zengin, A., Enriquez, RF., Nagy, V., Penninger, JM., Baldock, PA., Herzog, H.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Neuroendocrinol","volume":"31","issue":"2","page":"e12687","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30608810","title":"Salt-Dependent Rheology and Surface Tension of Protein Condensates Using Optical Traps.","abstract":"An increasing number of proteins with intrinsically disordered domains have been shown to phase separate in buffer to form liquidlike phases. These protein condensates serve as simple models for the investigation of the more complex membraneless organelles in cells. To understand the function of such proteins in cells, the material properties of the condensates they form are important. However, these material properties are not well understood. Here, we develop a novel method based on optical traps to study the frequency-dependent rheology and the surface tension of P-granule protein PGL-3 condensates as a function of salt concentration. We find that PGL-3 droplets are predominantly viscous but also exhibit elastic properties. As the salt concentration is reduced, their elastic modulus, viscosity, and surface tension increase. Our findings show that salt concentration has a strong influence on the rheology and dynamics of protein condensates suggesting an important role of electrostatic interactions for their material properties.","authors":"Jawerth, LM., Ijavi, M., Ruer, M., Saha, S., Jahnel, M., Hyman, AA., J\u00fclicher, F., Fischer-Friedrich, E.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Phys Rev Lett","volume":"121","issue":"25","page":"258101","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30607549","title":"CD73 expression in normal and pathological human hepatobiliopancreatic tissues.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30607549<\/PMID><DateCompleted><Year>2019<\/Year><Month>03<\/Month><Day>28<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>03<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1432-0851<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>68<\/Volume><Issue>3<\/Issue><PubDate><Year>2019<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>Cancer immunology, immunotherapy : CII<\/Title><ISOAbbreviation>Cancer Immunol Immunother<\/ISOAbbreviation><\/Journal><ArticleTitle>CD73 expression in normal and pathological human hepatobiliopancreatic tissues.<\/ArticleTitle><Pagination><MedlinePgn>467-478<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s00262-018-2290-1<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The tumor-expressed CD73 ectonucleotidase generates immune tolerance and promotes invasiveness via adenosine production from degradation of AMP. While anti-CD73 blockade treatment is a promising tool in cancer immunotherapy, a characterization of CD73 expression in human hepatobiliopancreatic system is lacking.","authors":"Sciarra, A., Monteiro, I., M\u00e9n\u00e9trier-Caux, C., Caux, C., Gilbert, B., Halkic, N., La Rosa, S., Romero, P., Sempoux, C., de Leval, L.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cancer Immunol Immunother","volume":"68","issue":"3","page":"467-478","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29346747","title":"Sensorimotor Integration for Decision Making: How the Worm Steers.","abstract":"Animals' movements actively shape their perception and subsequent decision making. In this issue of Neuron, Liu et\u00a0al. (2018) show how C.\u00a0elegans nematodes steer toward an odorant: a dedicated interneuron class integrates oscillatory olfactory signals, generated by head swings, with corollary discharge motor signals.","authors":"Kaplan, HS., Zimmer, M.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Neuron","volume":"97","issue":"2","page":"258-260","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30449657","title":"Mutations in MAST1 Cause Mega-Corpus-Callosum Syndrome with Cerebellar Hypoplasia and Cortical Malformations.","abstract":"Corpus callosum malformations are associated with a broad range of neurodevelopmental diseases. We report that de novo mutations in MAST1 cause mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations (MCC-CH-CM) in the absence of megalencephaly. We show that MAST1 is a microtubule-associated protein that is predominantly expressed in post-mitotic neurons and is present in both dendritic and axonal compartments. We further show that Mast1 null animals are phenotypically normal, whereas the deletion of a single amino acid (L278del) recapitulates the distinct neurological phenotype observed in patients. In animals harboring Mast1 microdeletions, we find that the PI3K\/AKT3\/mTOR pathway is unperturbed, whereas Mast2 and Mast3 levels are diminished, indicative of a dominant-negative mode of action. Finally, we report that de novo MAST1 substitutions are present in patients with autism and microcephaly, raising the prospect that mutations in this gene give rise to a spectrum of neurodevelopmental diseases.","authors":"Tripathy, R., Leca, I., van Dijk, T., Weiss, J., van Bon, BW., Sergaki, MC., Gstrein, T., Breuss, M., Tian, G., Bahi-Buisson, N., Paciorkowski, AR., Pagnamenta, AT., Wenninger-Weinzierl, A., Martinez-Reza, MF., Landler, L., Lise, S., Taylor, JC., Terrone, G., Vitiello, G., Del Giudice, E., Brunetti-Pierri, N., D'Amico, A., Reymond, A., Voisin, N., Bernstein, JA., Farrelly, E., Kini, U., Leonard, TA., Valence, S., Burglen, L., Armstrong, L., Hiatt, SM., Cooper, GM., Aldinger, KA., Dobyns, WB., Mirzaa, G., Pierson, TM., Baas, F., Chelly, J., Cowan, NJ., Keays, DA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Neuron","volume":"100","issue":"6","page":"1354-1368.e5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30427222","title":"SGLT2 inhibition and renal urate excretion: role of luminal glucose, GLUT9, and URAT1.","abstract":"Inhibitors of the Na<sup>+<\/sup>-glucose cotransporter SGLT2 enhance urinary glucose and urate excretion and lower plasma urate levels. The mechanisms remain unclear, but a role for enhanced glucose in the tubular fluid, which may interact with tubular urate transporters, such as the glucose transporter GLUT9 or the urate transporter URAT1, has been proposed. Studies were performed in nondiabetic mice treated with the SGLT2 inhibitor canagliflozin and in gene-targeted mice lacking the urate transporter Glut9 in the tubule or in mice with whole body knockout of Sglt2, Sglt1, or Urat1. Renal urate handling was assessed by analysis of urate in spontaneous plasma and urine samples and normalization to creatinine concentrations or by renal clearance studies with assessment of glomerular filtration rate by FITC-sinistrin. The experiments confirmed the contribution of URAT1 and GLUT9 to renal urate reabsorption, showing a greater contribution of the latter and additive effects. Genetic and pharmacological inhibition of SGLT2 enhanced fractional renal urate excretion (FE-urate), indicating that a direct effect of the SGLT2 inhibitor on urate transporters is not absolutely necessary. Consistent with a proposed role of increased luminal glucose delivery, the absence of Sglt1, which by itself had no effect on FE-urate, enhanced the glycosuric and uricosuric effects of the SGLT2 inhibitor. The SGLT2 inhibitor enhanced renal mRNA expression of Glut9 in wild-type mice, but tubular GLUT9 seemed dispensable for the increase in FE-urate in response to canagliflozin. First evidence is presented that URAT1 is required for the acute uricosuric effect of the SGLT2 inhibitor in mice.","authors":"Novikov, A., Fu, Y., Huang, W., Freeman, B., Patel, R., van Ginkel, C., Koepsell, H., Busslinger, M., Onishi, A., Nespoux, J., Vallon, V.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Am J Physiol Renal Physiol","volume":"316","issue":"1","page":"F173-F185","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30405245","title":"The metabolite BH4 controls T\u00a0cell proliferation in autoimmunity and cancer.","abstract":"Genetic regulators and environmental stimuli modulate T\u00a0cell activation in autoimmunity and cancer. The enzyme co-factor tetrahydrobiopterin (BH4) is involved in the production of monoamine neurotransmitters, the generation of nitric oxide, and pain<sup>1,2<\/sup>. Here we uncover a link between these processes, identifying a fundamental role for BH4 in T\u00a0cell biology. We find that genetic inactivation of GTP cyclohydrolase 1 (GCH1, the rate-limiting enzyme in the synthesis of BH4) and inhibition of sepiapterin reductase (the terminal enzyme in the synthetic pathway\u00a0for BH4) severely impair the proliferation of mature mouse and human T cells. BH4 production in activated T cells is linked to alterations in iron metabolism and mitochondrial bioenergetics. In vivo blockade of BH4 synthesis abrogates T-cell-mediated autoimmunity and allergic inflammation, and enhancing BH4 levels through GCH1 overexpression augments responses by CD4- and CD8-expressing T cells, increasing their antitumour activity in vivo. Administration of BH4 to mice markedly reduces tumour growth and expands the population of intratumoral effector T cells. Kynurenine-a tryptophan metabolite that blocks antitumour immunity-inhibits T\u00a0cell proliferation in a manner that can be rescued by BH4. Finally, we report the development of a potent SPR antagonist for possible clinical use. Our data uncover GCH1, SPR and their downstream metabolite BH4 as critical regulators of T\u00a0cell biology that can be readily manipulated to either block autoimmunity or enhance anticancer immunity.","authors":"Cronin, SJF., Seehus, C., Weidinger, A., Talbot, S., Reissig, S., Seifert, M., Pierson, Y., McNeill, E., Longhi, MS., Turnes, BL., Kreslavsky, T., Kogler, M., Hoffmann, D., Ticevic, M., da Luz Scheffer, D., Tortola, L., Cikes, D., Jais, A., Rangachari, M., Rao, S., Paolino, M., Novatchkova, M., Aichinger, M., Barrett, L., Latremoliere, A., Wirnsberger, G., Lametschwandtner, G., Busslinger, M., Zicha, S., Latini, A., Robson, SC., Waisman, A., Andrews, N., Costigan, M., Channon, KM., Weiss, G., Kozlov, AV., Tebbe, M., Johnsson, K., Woolf, CJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"563","issue":"7732","page":"564-568","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30372795","title":"PTEN and miR-26b: Promising prognostic biomarkers in initiation and progression of Oral Squamous Cell Carcinoma.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">30372795<\/PMID><DateCompleted><Year>2019<\/Year><Month>05<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>05<\/Month><Day>17<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1600-0714<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>48<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>Jan<\/Month><\/PubDate><\/JournalIssue><Title>Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology<\/Title><ISOAbbreviation>J Oral Pathol Med<\/ISOAbbreviation><\/Journal><ArticleTitle>PTEN and miR-26b: Promising prognostic biomarkers in initiation and progression of Oral Squamous Cell Carcinoma.<\/ArticleTitle><Pagination><MedlinePgn>31-35<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/jop.12794<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUNDS\" NlmCategory=\"BACKGROUND\">Oral Squamous Cell Carcinoma (OSCC) is the most common malignancy of the oral cavity. Phosphatase and TENsin homolog (PTEN) is a well-known tumor suppressive gene regulated by several biomarkers including a small single-stranded molecule, microRNA26b (miR-26b). Here, we studied the expression of PTEN and miR-26b in OSCC specimens in comparison with adjacent normal mucosa.","authors":"Baghaei, F., Abdollahi, A., Mohammadpour, H., Jahanbin, M., Naseri Taheri, F., Aminishakib, P., Emami Razavi, A., Kharazifard, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Oral Pathol Med","volume":"48","issue":"1","page":"31-35","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35020831","title":"Single-cell analysis reveals immune dysfunction from the earliest stages of CLL that can be reversed by ibrutinib.","abstract":null,"authors":"Purroy, N., Tong, YE., Lemvigh, CK., Cieri, N., Li, S., Parry, EM., Zhang, W., Rassenti, LZ., Kipps, TJ., Slager, SL., Kay, NE., Lesnick, C., Shanafelt, TD., Ghia, P., Scarf\u00f2, L., Livak, KJ., Kharchenko, PV., Neuberg, DS., Olsen, LR., Fan, J., Gohil, SH., Wu, CJ.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Blood","volume":"139","issue":"14","page":"2252-2256","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-11","doi":"10.1182\/blood.2021013926","first_author":"Purroy, N.","corresponding_authors":"Wu, CJ."},{"pmid":"30357530","title":"Role of miRNA-210, miRNA-21 and miRNA-126 as diagnostic biomarkers in colorectal carcinoma: impact of HIF-1\u03b1-VEGF signaling pathway.","abstract":"Colorectal cancer (CRC) is a major cause of death worldwide. Novel non-invasive, high diagnostic value screening test is urgently needed to improve survival rate, treatment and prognosis. Stable, small, circulating microRNA (miRNA) offers unique opportunities for the early diagnosis of several diseases. It acts as tumor oncogenes or suppressors and involve in cell death, survival, and metastasis. Communication between miRNA and carcinogenesis is critical but it still not clear and needs further investigation. The aim of our study is to evaluate the role of miR-210, miR-21, miR-126, as non-invasive diagnostic biomarkers for screening, early detection of CRC, studying their correlation with prognostic variables, and clarifying the roles of miRNAs on HIF-1\u03b1-VEGF signaling pathway. The expression of miR-210, miR-21 and miR-126 was performed using qRT-PCR in adenocarcinoma (no\u2009=\u200935), adenomas (no\u2009=\u200951), and neoplasm free controls (no\u2009=\u2009101). Serum levels of VEGF and HIF-1\u03b1 was determined by ELISA Kit. The results show that the expression of miR-210, miR-21, VEGF, HIF-1\u03b1 was significantly up-regulated while that miRNA-126 was down-regulated in both adenocarcinoma and adenomas compared with controls (p\u2009&lt;\u20090.001 for each). No significant difference was noted comparing patients with adenocarcinoma and adenomas. The three miRNAs correlated with VEGF, HIF-\u03b1. The miR-210 and miR-21 associated with TNM classification and clinical staging of adenocarcinoma (p\u2009&lt;\u20090.001) and they show high diagnostic value with sensitivity and specificity 88.6%, 90.1% and 91.4%, 95.0% respectively. Our study revealed that circulating miR-210, miR-21 were up-regulated while miR-126 was down-regulated in CRC and adenomas patients, they all correlated with TNM staging and they had high diagnostic value. HIF-1\u03b1 VEGF signaling pathways regulated by miRNAs played a role in colon cancer initiation. To the best of our knowledge, this is the first study of this miRNAs panel in CRC in our community. These data suggested that these biomarkers could be a potential novel, non-invasive marker for early diagnosis, screening and predicting prognosis of CRC. Understanding the molecular functions by which miRNAs affect cancer and understanding its roles in modulating the signaling output of VEGF might be fruitful in reducing the incidence and slowing the progression of this dark malignancy.","authors":"Sabry, D., El-Deek, SEM., Maher, M., El-Baz, MAH., El-Bader, HM., Amer, E., Hassan, EA., Fathy, W., El-Deek, HEM.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Mol Cell Biochem","volume":"454","issue":"1-2","page":"177-189","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30311406","title":"Tumor-driven like macrophages induced by conditioned media from pancreatic ductal adenocarcinoma promote tumor metastasis via secreting IL-8.","abstract":"Tumor-associated macrophages (TAMs) are abundant population of inflammatory cells which play an essential role in remodeling tumor microenvironment and tumor progression. Previously, we found the high density of TAMs was correlated with lymph node metastasis and poor prognosis in pancreatic ductal adenocarcinoma (PDAC). Therefore, this study was designed to investigate the mechanisms of interaction between TAMs and PDAC. THP-1 monocytes were the exposure to conditioned media (CM) produced by PDAC cells; then, monocyte recruitment and macrophage differentiation were assessed. CM from PDAC attracted and polarized THP-1 monocytes to tumor-driven like macrophages. mRNA expression cytokine profiling and ELISA identified the IL-8 secretion was increasing in tumor-driven like macrophages, and STAT3 pathway was involved. Addition of exogenous recombinant human IL-8 promoted PDAC cells motility in vitro and metastasis in vivo via upregulating Twist expression, which mediated epithelial-mesenchymal transition in cancer cells. What is more, IL-8 expression level in tumor stroma by immunohistochemical analysis was related to lymph node metastasis, the number of tumor CD68 but not CD163 positive macrophages and patient outcome. Taken together, these findings shed light on the important interplay between cancer cells and TAMs in tumor microenvironment and suggested that IL-8 signaling might be a potential therapeutic target for PDAC.","authors":"Chen, SJ., Lian, GD., Li, JJ., Zhang, QB., Zeng, LJ., Yang, KG., Huang, CM., Li, YQ., Chen, YT., Huang, KH.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cancer Med","volume":"7","issue":"11","page":"5679-5690","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30262634","title":"Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration.","abstract":"Amputation of the axolotl forelimb results in the formation of a blastema, a transient tissue where progenitor cells accumulate prior to limb regeneration. However, the molecular understanding of blastema formation had previously been hampered by the inability to identify and isolate blastema precursor cells in the adult tissue. We have used a combination of Cre-loxP reporter lineage tracking and single-cell messenger RNA sequencing (scRNA-seq) to molecularly track mature connective tissue (CT) cell heterogeneity and its transition to a limb blastema state. We have uncovered a multiphasic molecular program where CT cell types found in the uninjured adult limb revert to a relatively homogenous progenitor state that recapitulates an embryonic limb bud-like phenotype including multipotency within the CT lineage. Together, our data illuminate molecular and cellular reprogramming during complex organ regeneration in a vertebrate.","authors":"Gerber, T., Murawala, P., Knapp, D., Masselink, W., Schuez, M., Hermann, S., Gac-Santel, M., Nowoshilow, S., Kageyama, J., Khattak, S., Currie, JD., Camp, JG., Tanaka, EM., Treutlein, B.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Science","volume":"362","issue":"6413","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30257850","title":"Genomic insights into chromatin reprogramming to totipotency in embryos.","abstract":"The early embryo is the natural prototype for the acquisition of totipotency, which is the potential of a cell to produce a whole organism. Generation of a totipotent embryo involves chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications. Understanding embryonic chromatin architecture and how this is related to the epigenome and transcriptome will provide invaluable insights into cell fate decisions. Recently emerging low-input genomic assays allow the exploration of regulatory networks in the sparsely available mammalian embryo. Thus, the field of developmental biology is transitioning from microscopy to genome-wide chromatin descriptions. Ultimately, the prototype becomes a unique model for studying fundamental principles of development, epigenetic reprogramming, and cellular plasticity. In this review, we discuss chromatin reprogramming in the early mouse embryo, focusing on DNA methylation, chromatin accessibility, and higher-order chromatin structure.","authors":"Ladst\u00e4tter, S., Tachibana, K.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"J Cell Biol","volume":"218","issue":"1","page":"70-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30307926","title":"Publisher Correction: Guided self-organization and cortical plate formation in human brain organoids.","abstract":"This corrects the article DOI: 10.1038\/nbt.3906.","authors":"Lancaster, MA., Corsini, NS., Wolfinger, S., Gustafson, EH., Phillips, AW., Burkard, TR., Otani, T., Livesey, FJ., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Biotechnol","volume":"36","issue":"10","page":"1016","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29335676","title":"Behavioral Assays to Study Oxygen and Carbon Dioxide Sensing in <i>Caenorhabditis elegans<\/i>.","abstract":"Animals use behavioral strategies to seek optimal environments. Population behavioral assays provide a robust means to determine the effect of genetic perturbations on the ability of animals to sense and respond to changes in the environment. Here, we describe a <i>C. elegans<\/i> population behavioral assay used to measure locomotory responses to changes in environmental oxygen (O<sub>2<\/sub>) and carbon dioxide (CO<sub>2<\/sub>) concentrations. These behavioral assays are high-throughput and enable examination of genetic, neuronal and circuit function.","authors":"Rojo Romanos, T., Ng, L., Pocock, R.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Bio Protoc","volume":"8","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-00-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38847119","title":"Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023.","abstract":"BackgroundThe COVID-19 pandemic was largely driven by genetic mutations of SARS-CoV-2, leading in some instances to enhanced infectiousness of the virus or its capacity to evade the host immune system. To closely monitor SARS-CoV-2 evolution and resulting variants at genomic-level, an innovative pipeline termed SARSeq was developed in Austria.AimWe discuss technical aspects of the SARSeq pipeline, describe its performance and present noteworthy results it enabled during the pandemic in Austria.MethodsThe SARSeq pipeline was set up as a collaboration between private and public clinical diagnostic laboratories, a public health agency, and an academic institution. Representative SARS-CoV-2 positive specimens from each of the nine Austrian provinces were obtained from SARS-CoV-2 testing laboratories and processed centrally in an academic setting for S-gene sequencing and analysis.ResultsSARS-CoV-2 sequences from up to 2,880 cases weekly resulted in 222,784 characterised case samples in January 2021-March 2023. Consequently, Austria delivered the fourth densest genomic surveillance worldwide in a very resource-efficient manner. While most SARS-CoV-2 variants during the study showed comparable kinetic behaviour in all of Austria, some, like Beta, had a more focused spread. This highlighted multifaceted aspects of local population-level acquired immunity. The nationwide surveillance system enabled reliable nowcasting. Measured early growth kinetics of variants were predictive of later incidence peaks.ConclusionWith low automation, labour, and cost requirements, SARSeq is adaptable to monitor other pathogens and advantageous even for resource-limited countries. This multiplexed genomic surveillance system has potential as a rapid response tool for future emerging threats.","authors":"Frank, O., Balboa, DA., Novatchkova, M., \u00d6zkan, E., Strobl, MM., Yelagandula, R., Albanese, TG., Endler, L., Amman, F., Felsenstein, V., Gavrilovic, M., Acosta, M., Patocka, T., Vogt, A., Tamir, I., Klikovits, J., Zoufaly, A., Seitz, T., F\u00f6dinger, M., Bergthaler, A., Indra, A., Schmid, D., Klimek, P., Stark, A., Allerberger, F., Benka, B., Reich, K., Cochella, L., Elling, U.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Euro Surveill","volume":"29","issue":"23","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-07","doi":"10.2807\/1560-7917.ES.2024.29.23.2300542","first_author":null,"corresponding_authors":null},{"pmid":"30209397","title":"Necroptosis microenvironment directs lineage commitment in liver cancer.","abstract":"Primary liver cancer represents a major health problem. It comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC), which differ markedly with regards to their morphology, metastatic potential and responses to therapy. However, the regulatory molecules and tissue context that commit transformed hepatic cells towards HCC or ICC are largely unknown. Here we show that the hepatic microenvironment epigenetically shapes lineage commitment in mosaic mouse models of liver tumorigenesis. Whereas a necroptosis-associated hepatic cytokine microenvironment determines ICC outgrowth from oncogenically transformed hepatocytes, hepatocytes containing identical oncogenic drivers give rise to HCC if they are surrounded by apoptotic hepatocytes. Epigenome and transcriptome profiling of mouse HCC and ICC singled out Tbx3 and Prdm5 as major microenvironment-dependent and epigenetically regulated lineage-commitment factors, a function that is conserved in humans. Together, our results provide insight into lineage commitment in liver tumorigenesis, and explain molecularly why common liver-damaging risk factors can lead to either HCC or ICC.","authors":"Seehawer, M., Heinzmann, F., D'Artista, L., Harbig, J., Roux, PF., Hoenicke, L., Dang, H., Klotz, S., Robinson, L., Dor\u00e9, G., Rozenblum, N., Kang, TW., Chawla, R., Buch, T., Vucur, M., Roth, M., Zuber, J., Luedde, T., Sipos, B., Longerich, T., Heikenw\u00e4lder, M., Wang, XW., Bischof, O., Zender, L.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"562","issue":"7725","page":"69-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30202089","title":"Experimental and computational framework for a dynamic protein atlas of human cell division.","abstract":"Essential biological functions, such as mitosis, require tight coordination of hundreds of proteins in space and time. Localization, the timing of interactions and changes in cellular structure are all crucial to ensure the correct assembly, function and regulation of protein complexes<sup>1-4<\/sup>. Imaging of live cells can reveal protein distributions and dynamics but experimental and theoretical challenges have prevented the collection of quantitative data, which are necessary for the formulation of a model of mitosis that comprehensively integrates information and enables the analysis of the dynamic interactions between the molecular parts of the mitotic machinery within changing cellular boundaries. Here we generate a canonical model of the morphological changes during the mitotic progression of human cells on the basis of four-dimensional image data. We use this model to integrate dynamic three-dimensional concentration data of many fluorescently knocked-in mitotic proteins, imaged by fluorescence correlation spectroscopy-calibrated microscopy<sup>5<\/sup>. The approach taken here to generate a dynamic protein atlas of human cell division is generic; it can be applied to systematically map and mine dynamic protein localization networks that drive cell division in different cell types, and can be conceptually transferred to other cellular functions.","authors":"Cai, Y., Hossain, MJ., H\u00e9rich\u00e9, JK., Politi, AZ., Walther, N., Koch, B., Wachsmuth, M., Nijmeijer, B., Kueblbeck, M., Martinic-Kavur, M., Ladurner, R., Alexander, S., Peters, JM., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"561","issue":"7723","page":"411-415","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30185903","title":"Coupling of bone resorption and formation by RANKL reverse signalling.","abstract":"Receptor activator of nuclear factor-kappa B (RANK) ligand (RANKL) binds RANK on the surface of osteoclast precursors to trigger osteoclastogenesis. Recent studies have indicated that osteocytic RANKL has an important role in osteoclastogenesis during bone remodelling; however, the role of osteoblastic RANKL remains unclear. Here we show that vesicular RANK, which is secreted from the maturing osteoclasts, binds osteoblastic RANKL and promotes bone formation by triggering RANKL reverse signalling, which activates Runt-related transcription factor 2 (Runx2). The proline-rich motif in the RANKL cytoplasmic tail is required for reverse signalling, and a\u00a0RANKL(Pro29Ala) point mutation reduces activation of the reverse signalling pathway. The coupling of bone resorption and formation is disrupted in RANKL(Pro29Ala) mutant mice, indicating that osteoblastic RANKL functions as a coupling signal acceptor that recognizes vesicular RANK. RANKL reverse signalling is therefore a potential pharmacological target for avoiding the reduced bone formation associated with inhibition of osteoclastogenesis.","authors":"Ikebuchi, Y., Aoki, S., Honma, M., Hayashi, M., Sugamori, Y., Khan, M., Kariya, Y., Kato, G., Tabata, Y., Penninger, JM., Udagawa, N., Aoki, K., Suzuki, H.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"561","issue":"7722","page":"195-200","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30038414","title":"Genetically engineered cerebral organoids model brain tumor formation.","abstract":"Brain tumors are among the most lethal and devastating cancers. Their study is limited by genetic heterogeneity and the incompleteness of available laboratory models. Three-dimensional organoid culture models offer innovative possibilities for the modeling of human disease. Here we establish a 3D in vitro model called a neoplastic cerebral organoid (neoCOR), in which we recapitulate brain tumorigenesis by introducing oncogenic mutations in cerebral organoids via transposon- and CRISPR-Cas9-mediated mutagenesis. By screening clinically relevant mutations identified in cancer genome projects, we defined mutation combinations that result in glioblastoma-like and central nervous system primitive neuroectodermal tumor (CNS-PNET)-like neoplasms. We demonstrate that neoCORs are suitable for use in investigations of aspects of tumor biology such as invasiveness, and for evaluation of drug effects in the context of specific DNA aberrations. NeoCORs will provide a valuable complement to the current basic and preclinical models used to study brain tumor biology.","authors":"Bian, S., Repic, M., Guo, Z., Kavirayani, A., Burkard, T., Bagley, JA., Krauditsch, C., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Methods","volume":"15","issue":"8","page":"631-639","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29951776","title":"Histone deacetylase 1 expression is inversely correlated with age in the short-lived fish Nothobranchius furzeri.","abstract":"Aging is associated with profound changes in the epigenome, resulting in alterations of gene expression, epigenetic landscape, and genome architecture. Class I Histone deacetylases (HDACs), consisting of HDAC1, HDAC2, HDAC3, and HDAC8, play a major role in epigenetic regulation of chromatin structure and transcriptional control, and have been implicated as key players in the pathogenesis of age-dependent diseases and disorders affecting health and longevity. Here, we report the identification of class I Hdac orthologs and their detailed spatio-temporal expression profile in the short-lived fish Nothobranchius furzeri from the onset of embryogenesis until old age covering the entire lifespan of the organism. Database search of the recently annotated N. furzeri genomes retrieved four distinct genes: two copies of hdac1 and one copy of each hdac3 and hdac8. However, no hdac2 ortholog could be identified. Phylogenetic analysis grouped the individual killifish class I Hdacs within the well-defined terminal clades. We find that upon aging, Hdac1 is significantly down-regulated in muscle, liver, and brain, and this age-dependent down-regulation in brain clearly correlates with increased mRNA levels of the cyclin-dependent kinase inhibitor cdkn1a (p21). Furthermore, this apparent reduction of class I HDACs in transcript and protein levels is mirrored in the mouse brain, highlighting an evolutionarily conserved role of class I HDACs during normal development and in the aging process.","authors":"Zupkovitz, G., Lagger, S., Martin, D., Steiner, M., Hagelkruys, A., Seiser, C., Sch\u00f6fer, C., Pusch, O.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Histochem Cell Biol","volume":"150","issue":"3","page":"255-269","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29930102","title":"The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion.","abstract":"Chromosome segregation depends on sister chromatid cohesion which is established by cohesin during DNA replication. Cohesive cohesin complexes become acetylated to prevent their precocious release by WAPL before cells have reached mitosis. To obtain insight into how DNA replication, cohesion establishment and cohesin acetylation are coordinated, we analysed the interaction partners of 55 human proteins implicated in these processes by mass spectrometry. This proteomic screen revealed that on chromatin the cohesin acetyltransferase ESCO2 associates with the MCM2-7 subcomplex of the replicative Cdc45-MCM-GINS helicase. The analysis of ESCO2 mutants defective in MCM binding indicates that these interactions are required for proper recruitment of ESCO2 to chromatin, cohesin acetylation during DNA replication, and centromeric cohesion. We propose that MCM binding enables ESCO2 to travel with replisomes to acetylate cohesive cohesin complexes in the vicinity of replication forks so that these complexes can be protected from precocious release by WAPL Our results also indicate that ESCO1 and ESCO2 have distinct functions in maintaining cohesion between chromosome arms and centromeres, respectively.","authors":"Ivanov, MP., Ladurner, R., Poser, I., Beveridge, R., Rampler, E., Hudecz, O., Novatchkova, M., H\u00e9rich\u00e9, JK., Wutz, G., van der Lelij, P., Kreidl, E., Hutchins, JR., Axelsson-Ekker, H., Ellenberg, J., Hyman, AA., Mechtler, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"EMBO J","volume":"37","issue":"15","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29929453","title":"The anti-apoptotic ubiquitin conjugating enzyme BIRC6\/BRUCE regulates autophagosome-lysosome fusion.","abstract":"The Inhibitor of Apoptosis (IAP) family member, Baculoviral IAP Repeat Containing 6 (BIRC6)\/BRUCE is a ubiquitin conjugating E2 enzyme and a well-established anti-apoptosis regulator. However, its role in mammalian autophagy has not been shown. We identified BIRC6 as an important positive regulator of macroautophagy\/autophagy by performing an siRNA screen targeting enzymes in the ubiquitin pathway. Compared to wild-type cells, BIRC6-deficient cells show accumulation of lipidated LC3B both at basal and starved conditions. Furthermore, BIRC6 deficiency blocks starvation-induced autophagic flux monitored by a tandem fluorescent autophagy sensor, mCherry-GFP-LC3B. Most strikingly, fusion of autophagosomes and lysosomes is blocked in BIRC6-deficient cells. BIRC6 colocalizes with the lysosomal protein LAMP2 in cells, and biochemically interacts with STX17 (syntaxin 17), which is a marker for completed autophagosomes. These data collectively suggest that BIRC6 bridges lysosomes and autophagosomes by interacting with these proteins. Because a deletion mutant of BIRC6 lacking the UBC domain partially rescues the autophagosome-lysosome fusion defect in BIRC6-deficient cells, a role of BIRC6 in this event is independent of its E2 catalytic activity.","authors":"Ikeda, F.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Autophagy","volume":"14","issue":"7","page":"1283-1284","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29844182","title":"MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution.","abstract":"Compared with localization schemes solely based on evaluating patterns of molecular emission, the recently introduced single-molecule localization concept called MINFLUX and the fluorescence nanoscopies derived from it require up to orders of magnitude fewer emissions to attain single-digit nanometer resolution. Here, we demonstrate that the lower number of required fluorescence photons enables MINFLUX to detect molecular movements of a few nanometers at a temporal sampling of well below 1 millisecond. Using fluorophores attached to thermally fluctuating DNA strands as model systems, we demonstrate that measurement times as short as 400 microseconds suffice to localize fluorescent molecules with \u223c2-nm precision. Such performance is out of reach for popular camera-based localization by centroid calculation of emission diffraction patterns. Since theoretical limits have not been reached, our results show that emerging MINFLUX nanoscopy bears great potential for dissecting the motions of individual (macro)molecules at hitherto-unattained combinations of spatial and temporal resolution.","authors":"Eilers, Y., Ta, H., Gwosch, KC., Balzarotti, F., Hell, SW.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Proc Natl Acad Sci U S A","volume":"115","issue":"24","page":"6117-6122","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29942006","title":"Reply to 'Defining distance restraints in HADDOCK'.","abstract":null,"authors":"Orb\u00e1n-N\u00e9meth, Z., Beveridge, R., Hollenstein, DM., Rampler, E., Stranzl, T., Hudecz, O., Doblmann, J., Schl\u00f6gelhofer, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Protoc","volume":"13","issue":"7","page":"1503-1505","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29779899","title":"Signaling-Dependent Control of Apical Membrane Size and Self-Renewal in Rosette-Stage Human Neuroepithelial Stem Cells.","abstract":"In the developing nervous system, neural stem cells are polarized and maintain an apical domain facing a central lumen. The presence of apical membrane is thought to have a profound influence on maintaining the stem cell state. With the onset of neurogenesis, cells lose their polarization, and the concomitant loss of the apical domain coincides with a loss of the stem cell identity. Little is known about the molecular signals controlling apical membrane size. Here, we use two neuroepithelial cell systems, one derived from regenerating axolotl spinal cord and the other from human embryonic stem cells, to identify a molecular signaling pathway initiated by lysophosphatidic acid that controls apical membrane size and consequently controls and maintains epithelial organization and lumen size in neuroepithelial rosettes. This apical domain size increase occurs independently of effects on proliferation and involves a serum response factor-dependent transcriptional induction of junctional and apical membrane components.","authors":"Medelnik, JP., Roensch, K., Okawa, S., Del Sol, A., Chara, O., Mchedlishvili, L., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Stem Cell Reports","volume":"10","issue":"6","page":"1751-1765","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29779889","title":"Epithelial Sodium Channel Regulates Adult Neural Stem Cell Proliferation in a Flow-Dependent Manner.","abstract":"One hallmark of adult neurogenesis is its adaptability to environmental influences. Here, we uncovered the epithelial sodium channel (ENaC) as a key regulator of adult neurogenesis as its deletion in neural stem cells (NSCs) and their progeny in the murine subependymal zone (SEZ) strongly impairs their proliferation and neurogenic output in the olfactory bulb. Importantly, alteration of fluid flow promotes proliferation of SEZ cells in an ENaC-dependent manner, eliciting sodium and calcium signals that regulate proliferation via calcium-release-activated channels and phosphorylation of ERK. Flow-induced calcium signals are restricted to NSCs in contact with the ventricular fluid, thereby providing a highly specific mechanism to regulate NSC behavior at this special interface with the cerebrospinal fluid. Thus, ENaC plays a central role in regulating adult neurogenesis, and among multiple modes of ENaC function, flow-induced changes in sodium signals are critical for NSC biology.","authors":"Petrik, D., Myoga, MH., Grade, S., Gerkau, NJ., Pusch, M., Rose, CR., Grothe, B., G\u00f6tz, M.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell Stem Cell","volume":"22","issue":"6","page":"865-878.e8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38843779","title":"Making sense of Timothy syndrome with 3D human neuronal models.","abstract":"In a recent issue of Nature, Chen and colleagues<sup>1<\/sup> reveal the potential for antisense oligonucleotides (ASOs) to rescue the neuropathological mechanisms underlying Timothy syndrome (TS) using three-dimensional neuronal models. Combining in&#xa0;vitro and in&#xa0;vivo approaches, the authors present a strategy to translate disease biology findings into potential therapeutics.","authors":"Najm, R., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Neuron","volume":"112","issue":"11","page":"1730-1732","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-06","doi":"10.1016\/j.neuron.2024.05.016","first_author":null,"corresponding_authors":null},{"pmid":"29720634","title":"Blastocyst-like structures generated solely from stem cells.","abstract":"The blastocyst (the early mammalian embryo) forms all embryonic and extra-embryonic tissues, including the placenta. It consists of a spherical thin-walled layer, known as the trophectoderm, that surrounds a fluid-filled cavity sheltering the embryonic cells <sup>1<\/sup> . From mouse blastocysts, it is possible to derive both trophoblast <sup>2<\/sup> and embryonic stem-cell lines <sup>3<\/sup> , which are in vitro analogues of the trophectoderm and embryonic compartments, respectively. Here we report that trophoblast and embryonic stem cells cooperate in vitro to form structures that morphologically and transcriptionally resemble embryonic day 3.5 blastocysts, termed blastoids. Like blastocysts, blastoids form from inductive signals that originate from the inner embryonic cells and drive the development of the outer trophectoderm. The nature and function of these signals have been largely unexplored. Genetically and physically uncoupling the embryonic and trophectoderm compartments, along with single-cell transcriptomics, reveals the extensive inventory of embryonic inductions. We specifically show that the embryonic cells maintain trophoblast proliferation and self-renewal, while fine-tuning trophoblast epithelial morphogenesis in part\u00a0via a BMP4\/Nodal-KLF6 axis. Although blastoids do not support the development of bona fide embryos, we demonstrate that embryonic inductions are crucial to form a trophectoderm state that robustly implants and triggers decidualization in utero. Thus, at this stage, the nascent embryo fuels trophectoderm development and implantation.","authors":"Rivron, NC., Frias-Aldeguer, J., Vrij, EJ., Boisset, JC., Korving, J., Vivi\u00e9, J., Truckenm\u00fcller, RK., van Oudenaarden, A., van Blitterswijk, CA., Geijsen, N.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"557","issue":"7703","page":"106-111","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29703791","title":"Human gastric cancer modelling using organoids.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">29703791<\/PMID><DateCompleted><Year>2019<\/Year><Month>01<\/Month><Day>18<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>02<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1468-3288<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>68<\/Volume><Issue>2<\/Issue><PubDate><Year>2019<\/Year><Month>02<\/Month><\/PubDate><\/JournalIssue><Title>Gut<\/Title><ISOAbbreviation>Gut<\/ISOAbbreviation><\/Journal><ArticleTitle>Human gastric cancer modelling using organoids.<\/ArticleTitle><Pagination><MedlinePgn>207-217<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1136\/gutjnl-2017-314549<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\">Gastric cancer is the second leading cause of cancer-related deaths and the fifth most common malignancy worldwide. In this study, human and mouse gastric cancer organoids were generated to model the disease and perform drug testing to delineate treatment strategies.","authors":"Seidlitz, T., Merker, SR., Rothe, A., Zakrzewski, F., von Neubeck, C., Gr\u00fctzmann, K., Sommer, U., Schweitzer, C., Sch\u00f6lch, S., Uhlemann, H., Gaebler, AM., Werner, K., Krause, M., Baretton, GB., Welsch, T., Koo, BK., Aust, DE., Klink, B., Weitz, J., Stange, DE.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Gut","volume":"68","issue":"2","page":"207-217","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29695489","title":"Dynamics of sister chromatid resolution during cell cycle progression.","abstract":"Faithful genome transmission in dividing cells requires that the two copies of each chromosome's DNA package into separate but physically linked sister chromatids. The linkage between sister chromatids is mediated by cohesin, yet where sister chromatids are linked and how they resolve during cell cycle progression has remained unclear. In this study, we investigated sister chromatid organization in live human cells using dCas9-mEGFP labeling of endogenous genomic loci. We detected substantial sister locus separation during G2 phase irrespective of the proximity to cohesin enrichment sites. Almost all sister loci separated within a few hours after their respective replication and then rapidly equilibrated their average distances within dynamic chromatin polymers. Our findings explain why the topology of sister chromatid resolution in G2 largely reflects the DNA replication program. Furthermore, these data suggest that cohesin enrichment sites are not persistent cohesive sites in human cells. Rather, cohesion might occur at variable genomic positions within the cell population.","authors":"Stanyte, R., Nuebler, J., Blaukopf, C., Hoefler, R., Stocsits, R., Peters, JM., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"J Cell Biol","volume":"217","issue":"6","page":"1985-2004","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29691655","title":"Loss of function mutations in VARS encoding cytoplasmic valyl-tRNA synthetase cause microcephaly, seizures, and progressive cerebral atrophy.","abstract":"Progressive microcephaly and neurodegeneration are genetically heterogenous conditions, largely associated with genes that are essential for the survival of neurons. In this study, we interrogate the genetic etiology of two siblings from a non-consanguineous family with severe early onset of neurological manifestations. Whole exome sequencing identified novel compound heterozygous mutations in VARS that segregated with the proband: a missense (c.3192G&gt;A; p.Met1064Ile) and a splice site mutation (c.1577-2A&gt;G).\u00a0The VARS gene encodes cytoplasmic valyl-tRNA synthetase (ValRS), an enzyme that is essential during eukaryotic translation. cDNA analysis on patient derived fibroblasts revealed that the splice site acceptor variant allele led to nonsense mediated decay, thus resulting in a\u00a0null allele. Three-dimensional modeling of ValRS predicts that the missense mutation lies in a highly conserved region and could alter side chain packing, thus affecting tRNA binding or destabilizing the interface between the catalytic and tRNA binding domains. Further quantitation of the expression of VARS showed remarkably reduced levels of mRNA and protein in skin derived fibroblasts. Aminoacylation experiments on patient derived cells showed markedly reduced enzyme activity of ValRS suggesting the mutations to be loss of function. Bi-allelic mutations in cytoplasmic amino acyl tRNA synthetases are well-known for their role in neurodegenerative disorders, yet human disorders associated with VARS mutations have not yet been clinically well characterized. Our study describes the phenotype associated with recessive VARS mutations and further functional delineation of the pathogenicity of novel variants identified, which widens the clinical and genetic spectrum of patients with progressive microcephaly.","authors":"Stephen, J., Nampoothiri, S., Banerjee, A., Tolman, NJ., Penninger, JM., Elling, U., Agu, CA., Burke, JD., Devadathan, K., Kannan, R., Huang, Y., Steinbach, PJ., Martinis, SA., Gahl, WA., Malicdan, MCV.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Hum Genet","volume":"137","issue":"4","page":"293-303","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16546096","title":"Gene repression by Pax5 in B cells is essential for blood cell homeostasis and is reversed in plasma cells.","abstract":"The transcription factor Pax5 represses lineage-inappropriate genes and activates B cell-specific genes in B lymphocytes. By identifying 110 Pax5-repressed genes, we now demonstrate that Pax5 downregulates diverse biological activities including receptor signaling, cell adhesion, migration, transcriptional control, and cellular metabolism at B cell commitment. The T lymphoid or myeloid expression of these genes demonstrates that Pax5(-\/-) pro-B cells and common lymphoid progenitors display lymphoid and myeloid promiscuity of gene expression. These lineage-inappropriate genes require continuous Pax5 activity for their repression, as they are reactivated in committed pro-B cells and mature B cells following conditional Pax5 deletion. Pax5-repressed genes are also reexpressed in plasma cells, which depend for normal function on Cd28 and Ccr2 reactivation. The loss of Pax5 during terminal differentiation thus contributes to the plasma cell transcription program. Finally, ectopic expression of the Pax5-repressed chemokine gene Ccl3 in B cells results in increased osteoclast formation and bone loss, demonstrating that Pax5-mediated gene repression is essential for normal homeostasis of hematopoietic development.","authors":"Delogu, A., Schebesta, A., Sun, Q., Aschenbrenner, K., Perlot, T., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Immunity","volume":"24","issue":"3","page":"269-81","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2006-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12096341","title":"Novel colon cancer cell lines leading to better understanding of the diversity of respective primary cancers.","abstract":"A major obstacle to obtaining more detailed insights into the diversity of phenotypic and molecular changes occurring in colon cancer cells is the lack of low-passage colon cancer cell lines, which would still closely reflect the phenotype of the colon cancer cells in vivo. Here, we characterize eight novel, low passage number human colon carcinoma cell lines, originating from colorectal cancers extensively characterized in the clinics. All cell lines closely resemble the original tumors with respect to phenotype, markers and detectable genetic changes. Cell morphology and marker expression is highly variable, ranging from fully polarized cells correctly expressing all basolateral epithelial markers, to cells with mesenchymal characteristics and a complete loss of polarity due to delocalization or loss of junction complex proteins. The alterations in phenotype and epithelial marker expression correspond to changes already detectable in the primary tumor in vivo. Seven of the cell lines show chromosomal instability, while one cell line is characterized by microsatellite instability. p53 associated with K-ras mutations were detected in three cell lines. Hitherto non-described E-cadherin mutations were found at both alleles in one cell line whereas in another cell line the E-cadherin protein was down-regulated. A stabilizing beta-catenin mutation (S45F) appears in the same cell line that carried the mutated E-cadherin gene. Six cell lines carried APC mutations, which in five of the lines led to an activated beta-catenin\/Tcf\/LEF signaling pathway. In accordance with beta-catenin\/Tcf\/LEF activation, the cell lines show increased migration and invasiveness. Our results show that the characterized, low-passage cell lines mirror the diversity of the individual tumors from which they were derived. Through molecular analyses of these cell lines we demonstrate that tumorgenicity events are much more diverse in human colon cancer than expected, despite the common origin of the tumors from a small patient group with similar tumor grading and clinical prognosis.","authors":"V\u00e9csey-Semj\u00e9n, B., Becker, KF., Sinski, A., Blennow, E., Vietor, I., Zatloukal, K., Beug, H., Wagner, E., Huber, LA.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Oncogene","volume":"21","issue":"30","page":"4646-62","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29514850","title":"Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation.","abstract":"Spt5 is a highly conserved RNA polymerase II (Pol II)-associated pausing and elongation factor. However, its impact on global elongation and Pol II processivity in mammalian cells has not been clarified. Here, we show that depleting Spt5 in mouse embryonic fibroblasts (MEFs) does not cause global elongation defects or decreased elongation rates. Instead, in Spt5-depleted cells, a fraction of Pol II molecules are dislodged during elongation, thus decreasing the number of Pol II complexes that complete the transcription cycle. Most strikingly, this decrease is restricted to a narrow window between 15 and 20\u00a0kb from the promoter, a distance which coincides with the stage where accelerating Pol II attains maximum elongation speed. Consequently, long genes show a greater dependency on Spt5 for optimal elongation efficiency and overall gene expression than short genes. We propose that an important role of Spt5 in mammalian elongation is to promote the processivity of those Pol II complexes that are transitioning toward maximum elongation speed 15-20\u00a0kb from the promoter.","authors":"Fitz, J., Neumann, T., Pavri, R.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"EMBO J","volume":"37","issue":"8","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29489750","title":"The SMAD2\/3 interactome reveals that TGF\u03b2 controls m<sup>6<\/sup>A mRNA methylation in pluripotency.","abstract":"The TGF\u03b2 pathway has essential roles in embryonic development, organ homeostasis, tissue repair and disease. These diverse effects are mediated through the intracellular effectors SMAD2 and SMAD3 (hereafter SMAD2\/3), whose canonical function is to control the activity of target genes by interacting with transcriptional regulators. Therefore, a complete description of the factors that interact with SMAD2\/3 in a given cell type would have broad implications for many areas of cell biology. Here we describe the interactome of SMAD2\/3 in human pluripotent stem cells. This analysis reveals that SMAD2\/3 is involved in multiple molecular processes in addition to its role in transcription. In particular, we identify a functional interaction with the METTL3-METTL14-WTAP complex, which mediates the conversion of adenosine to N<sup>6<\/sup>-methyladenosine (m<sup>6<\/sup>A) on RNA. We show that SMAD2\/3 promotes binding of the m<sup>6<\/sup>A methyltransferase complex to a subset of transcripts involved in early cell fate decisions. This mechanism destabilizes specific SMAD2\/3 transcriptional targets, including the pluripotency factor gene NANOG, priming them for rapid downregulation upon differentiation to enable timely exit from pluripotency. Collectively, these findings reveal the mechanism by which extracellular signalling can induce rapid cellular responses through regulation of the epitranscriptome. These aspects of TGF\u03b2 signalling could have far-reaching implications in many other cell types and in diseases such as cancer.","authors":"Bertero, A., Brown, S., Madrigal, P., Osnato, A., Ortmann, D., Yiangou, L., Kadiwala, J., Hubner, NC., de Los Mozos, IR., Sad\u00e9e, C., Lenaerts, AS., Nakanoh, S., Grandy, R., Farnell, E., Ule, J., Stunnenberg, HG., Mendjan, S., Vallier, L.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"555","issue":"7695","page":"256-259","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29477253","title":"Central RANK signalling in NPY neurons alters bone mass in male mice.","abstract":"RANKL signalling known to be important for the control of bone mass, has recently also been implicated in the brain to control thermoregulation, however, it is not known which neuronal pathways are involved and whether other aspects of energy homeostasis are also affected. Here we show that selective deletion of RANK from NPY neurons down-regulated NPY mRNA expression in the hypothalamus. While comprehensive phenotyping of germline-induced NPY neuron specific RANK deficient mice revealed no significant changes in physical or metabolic parameters, adult onset deletion of RANK from NPY neurons led to a significant increase in fat mass and a decrease in whole body bone mineral content and bone mineral density. Intriguingly, when these conditional knockout mice were placed on a high fat diet, body weight and fat mass did not differ to control mice. However, they were able to significantly increase their bone mass to match their increased body weight, an ability that was lacking in control mice. Taken together, results from this study demonstrate that RANK signalling in NPY neurons is involved in modulating NPY levels and through that matching bone mass to body weight.","authors":"Lee, NJ., Clarke, IM., Enriquez, RF., Nagy, V., Penninger, J., Baldock, PA., Herzog, H.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Neuropeptides","volume":"68","issue":null,"page":"75-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29311744","title":"Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans.","abstract":"The formation of the vertebrate brain requires the generation, migration, differentiation and survival of neurons. Genetic mutations that perturb these critical cellular events can result in malformations of the telencephalon, providing a molecular window into brain development. Here we report the identification of an N-ethyl-N-nitrosourea-induced mouse mutant characterized by a fractured hippocampal pyramidal cell layer, attributable to defects in neuronal migration. We show that this is caused by a hypomorphic mutation in Vps15 that perturbs endosomal-lysosomal trafficking and autophagy, resulting in an upregulation of Nischarin, which inhibits Pak1 signaling. The complete ablation of Vps15 results in the accumulation of autophagic substrates, the induction of apoptosis and severe cortical atrophy. Finally, we report that mutations in VPS15 are associated with cortical atrophy and epilepsy in humans. These data highlight the importance of the Vps15-Vps34 complex and the Nischarin-Pak1 signaling hub in the development of the telencephalon.","authors":"Gstrein, T., Edwards, A., P\u0159istoupilov\u00e1, A., Leca, I., Breuss, M., Pilat-Carotta, S., Hansen, AH., Tripathy, R., Traunbauer, AK., Hochstoeger, T., Rosoklija, G., Repic, M., Landler, L., Str\u00e1neck\u00fd, V., D\u00fcrnberger, G., Keane, TM., Zuber, J., Adams, DJ., Flint, J., Honzik, T., Gut, M., Beltran, S., Mechtler, K., Sherr, E., Kmoch, S., Gut, I., Keays, DA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Neurosci","volume":"21","issue":"2","page":"207-217","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29419372","title":"SNARE-Encoding Genes VdSec22 and VdSso1 Mediate Protein Secretion Required for Full Virulence in Verticillium dahliae.","abstract":"Proteins that mediate cellular and subcellular membrane fusion are key factors in vesicular trafficking in all eukaryotic cells, including the secretion and transport of plant pathogen virulence factors. In this study, we identified vesicle-fusion components that included 22 soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), four Sec1\/Munc18 (SM) family proteins, and 10 Rab GTPases encoded in the genome of the vascular wilt pathogen Verticillium dahliae Vd991. Targeted deletion of two SNARE-encoding genes in V. dahliae, VdSec22 and VdSso1, significantly reduced virulence of both mutants on cotton, relative to the wild-type Vd991 strain. Comparative analyses of the secreted protein content (exoproteome) revealed that many enzymes involved in carbohydrate hydrolysis were regulated by VdSec22 or VdSso1. Consistent with a role of these enzymes in plant cell-wall degradation, pectin, cellulose, and xylan utilization were reduced in the VdSec22 or VdSso1 mutant strains along with a loss of exoproteome cytotoxic activity on cotton leaves. Comparisons with a pathogenicity-related exoproteome revealed that several known virulence factors were not regulated by VdSec22 or VdSso1, but some of the proteins regulated by VdSec22 or VdSso1 displayed different characteristics, including the lack of a typical signal peptide, suggesting that V. dahliae employs more than one secretory route to transport proteins to extracellular sites during infection.","authors":"Wang, J., Tian, L., Zhang, DD., Short, DPG., Zhou, L., Song, SS., Liu, Y., Wang, D., Kong, ZQ., Cui, WY., Ma, XF., Klosterman, SJ., Subbarao, KV., Chen, JY., Dai, XF.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Mol Plant Microbe Interact","volume":"31","issue":"6","page":"651-664","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29386137","title":"Energy Scarcity Promotes a Brain-wide Sleep State Modulated by Insulin Signaling in C.\u00a0elegans.","abstract":"Neural information processing entails a high energetic cost, but its maintenance is crucial for animal survival. However, the brain's energy conservation strategies are incompletely understood. Employing functional brain-wide imaging and quantitative behavioral assays, we describe a neuronal strategy in Caenorhabditis elegans that balances energy availability and expenditure. Upon acute food deprivation, animals exhibit a transiently elevated state of arousal, indicated by foraging behaviors and increased responsiveness to food-related cues. In contrast, long-term starvation suppresses these behaviors and biases animals to intermittent sleep episodes. Brain-wide neuronal population dynamics, which are likely energetically costly but important for behavior, are robust to starvation while animals are awake. However, during starvation-induced sleep, brain dynamics are systemically downregulated. Neuromodulation via insulin-like signaling is required to transiently maintain the animals' arousal state upon acute food deprivation. Our data suggest that the regulation of sleep and wakefulness supports optimal energy allocation.","authors":"Skora, S., Mende, F., Zimmer, M.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell Rep","volume":"22","issue":"4","page":"953-966","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29364872","title":"The axolotl genome and the evolution of key tissue formation regulators.","abstract":"Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new genome assembler (MARVEL). We observed a size expansion of introns and intergenic regions, largely attributable to multiplication of long terminal repeat retroelements. We provide evidence that intron size in developmental genes is under constraint and that species-restricted genes may contribute to limb regeneration. The axolotl genome assembly does not contain the essential developmental gene Pax3. However, mutation of the axolotl Pax3 paralogue Pax7 resulted in an axolotl phenotype that was similar to those seen in Pax3<sup>-\/-<\/sup> and Pax7<sup>-\/-<\/sup> mutant mice. The axolotl genome provides a rich biological resource for developmental and evolutionary studies.","authors":"Nowoshilow, S., Schloissnig, S., Fei, JF., Dahl, A., Pang, AWC., Pippel, M., Winkler, S., Hastie, AR., Young, G., Roscito, JG., Falcon, F., Knapp, D., Powell, S., Cruz, A., Cao, H., Habermann, B., Hiller, M., Tanaka, EM., Myers, EW.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"554","issue":"7690","page":"50-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29362479","title":"Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.","abstract":"Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field.","authors":"Galluzzi, L., Vitale, I., Aaronson, SA., Abrams, JM., Adam, D., Agostinis, P., Alnemri, ES., Altucci, L., Amelio, I., Andrews, DW., Annicchiarico-Petruzzelli, M., Antonov, AV., Arama, E., Baehrecke, EH., Barlev, NA., Bazan, NG., Bernassola, F., Bertrand, MJM., Bianchi, K., Blagosklonny, MV., Blomgren, K., Borner, C., Boya, P., Brenner, C., Campanella, M., Candi, E., Carmona-Gutierrez, D., Cecconi, F., Chan, FK., Chandel, NS., Cheng, EH., Chipuk, JE., Cidlowski, JA., Ciechanover, A., Cohen, GM., Conrad, M., Cubillos-Ruiz, JR., Czabotar, PE., D'Angiolella, V., Dawson, TM., Dawson, VL., De Laurenzi, V., De Maria, R., Debatin, KM., DeBerardinis, RJ., Deshmukh, M., Di Daniele, N., Di Virgilio, F., Dixit, VM., Dixon, SJ., Duckett, CS., Dynlacht, BD., El-Deiry, WS., Elrod, JW., Fimia, GM., Fulda, S., Garc\u00eda-S\u00e1ez, AJ., Garg, AD., Garrido, C., Gavathiotis, E., Golstein, P., Gottlieb, E., Green, DR., Greene, LA., Gronemeyer, H., Gross, A., Hajnoczky, G., Hardwick, JM., Harris, IS., Hengartner, MO., Hetz, C., Ichijo, H., J\u00e4\u00e4ttel\u00e4, M., Joseph, B., Jost, PJ., Juin, PP., Kaiser, WJ., Karin, M., Kaufmann, T., Kepp, O., Kimchi, A., Kitsis, RN., Klionsky, DJ., Knight, RA., Kumar, S., Lee, SW., Lemasters, JJ., Levine, B., Linkermann, A., Lipton, SA., Lockshin, RA., L\u00f3pez-Ot\u00edn, C., Lowe, SW., Luedde, T., Lugli, E., MacFarlane, M., Madeo, F., Malewicz, M., Malorni, W., Manic, G., Marine, JC., Martin, SJ., Martinou, JC., Medema, JP., Mehlen, P., Meier, P., Melino, S., Miao, EA., Molkentin, JD., Moll, UM., Mu\u00f1oz-Pinedo, C., Nagata, S., Nu\u00f1ez, G., Oberst, A., Oren, M., Overholtzer, M., Pagano, M., Panaretakis, T., Pasparakis, M., Penninger, JM., Pereira, DM., Pervaiz, S., Peter, ME., Piacentini, M., Pinton, P., Prehn, JHM., Puthalakath, H., Rabinovich, GA., Rehm, M., Rizzuto, R., Rodrigues, CMP., Rubinsztein, DC., Rudel, T., Ryan, KM., Sayan, E., Scorrano, L., Shao, F., Shi, Y., Silke, J., Simon, HU., Sistigu, A., Stockwell, BR., Strasser, A., Szabadkai, G., Tait, SWG., Tang, D., Tavernarakis, N., Thorburn, A., Tsujimoto, Y., Turk, B., Vanden Berghe, T., Vandenabeele, P., Vander Heiden, MG., Villunger, A., Virgin, HW., Vousden, KH., Vucic, D., Wagner, EF., Walczak, H., Wallach, D., Wang, Y., Wells, JA., Wood, W., Yuan, J., Zakeri, Z., Zhivotovsky, B., Zitvogel, L., Melino, G., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell Death Differ","volume":"25","issue":"3","page":"486-541","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29314711","title":"MiR-492 regulates metastatic properties of hepatoblastoma via CD44.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">29314711<\/PMID><DateCompleted><Year>2019<\/Year><Month>04<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>04<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1478-3231<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>38<\/Volume><Issue>7<\/Issue><PubDate><Year>2018<\/Year><Month>07<\/Month><\/PubDate><\/JournalIssue><Title>Liver international : official journal of the International Association for the Study of the Liver<\/Title><ISOAbbreviation>Liver Int<\/ISOAbbreviation><\/Journal><ArticleTitle>MiR-492 regulates metastatic properties of hepatoblastoma via CD44.<\/ArticleTitle><Pagination><MedlinePgn>1280-1291<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/liv.13687<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\">MicroRNAs are important genetic regulators of physiological and pathophysiological processes including cancer initiation and progression of hepatoblastoma, the most common liver tumour in childhood. We aimed to identify malignant and metastasis promoting effects of miR-492, a miRNA, previously reported to be overexpressed in metastatic hepatoblastoma. Furthermore, we intended to evaluate its diagnostic and prognostic potential.","authors":"von Frowein, J., Hauck, SM., Kappler, R., Pagel, P., Fleischmann, KK., Magg, T., Cairo, S., Roscher, A., von Schweinitz, D., Schmid, I.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Liver Int","volume":"38","issue":"7","page":"1280-1291","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29311336","title":"Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy.","abstract":"The adult mouse subependymal zone provides a niche for mammalian neural stem cells (NSCs). However, the molecular signature, self-renewal potential, and fate behavior of NSCs remain poorly defined. Here we propose a model in which the fate of active NSCs is coupled to the total number of neighboring NSCs in a shared niche. Using knock-in reporter alleles and single-cell RNA sequencing, we show that the Wnt target <i>Tnfrsf19\/<\/i>Troy identifies both active and quiescent NSCs. Quantitative analysis of genetic lineage tracing of individual NSCs under homeostasis or in response to injury reveals rapid expansion of stem-cell number before some return to quiescence. This behavior is best explained by stochastic fate decisions, where stem-cell number within a shared niche fluctuates over time. Fate mapping proliferating cells using a Ki67<sup>iresCreER<\/sup> allele confirms that active NSCs reversibly return to quiescence, achieving long-term self-renewal. Our findings suggest a niche-based mechanism for the regulation of NSC fate and number.","authors":"Basak, O., Krieger, TG., Muraro, MJ., Wiebrands, K., Stange, DE., Frias-Aldeguer, J., Rivron, NC., van de Wetering, M., van Es, JH., van Oudenaarden, A., Simons, BD., Clevers, H.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Proc Natl Acad Sci U S A","volume":"115","issue":"4","page":"E610-E619","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29258294","title":"Senescence-associated reprogramming promotes cancer stemness.","abstract":"Cellular senescence is a stress-responsive cell-cycle arrest program that terminates the further expansion of (pre-)malignant cells. Key signalling components of the senescence machinery, such as p16<sup>INK4a<\/sup>, p21<sup>CIP1<\/sup> and p53, as well as trimethylation of lysine 9 at histone H3 (H3K9me3), also operate as critical regulators of stem-cell functions (which are collectively termed 'stemness'). In cancer cells, a gain of stemness may have profound implications for tumour aggressiveness and clinical outcome. Here we investigated whether chemotherapy-induced senescence could change stem-cell-related properties of malignant cells. Gene expression and functional analyses comparing senescent and non-senescent B-cell lymphomas from E\u03bc-Myc transgenic mice revealed substantial upregulation of an adult tissue stem-cell signature, activated Wnt signalling, and distinct stem-cell markers in senescence. Using genetically switchable models of senescence targeting H3K9me3 or p53 to mimic spontaneous escape from the arrested condition, we found that cells released from senescence re-entered the cell cycle with strongly enhanced and Wnt-dependent clonogenic growth potential compared to virtually identical populations that had been equally exposed to chemotherapy but had never been senescent. In vivo, these previously senescent cells presented with a much higher tumour initiation potential. Notably, the temporary enforcement of senescence in p53-regulatable models of acute lymphoblastic leukaemia and acute myeloid leukaemia was found to reprogram non-stem bulk leukaemia cells into self-renewing, leukaemia-initiating stem cells. Our data, which are further supported by consistent results in human cancer cell lines and primary samples of human haematological malignancies, reveal that senescence-associated stemness is an unexpected, cell-autonomous feature that exerts its detrimental, highly aggressive growth potential upon escape from cell-cycle blockade, and is enriched in relapse tumours. These findings have profound implications for cancer therapy, and provide new mechanistic insights into the plasticity of cancer cells.","authors":"Milanovic, M., Fan, DNY., Belenki, D., D\u00e4britz, JHM., Zhao, Z., Yu, Y., D\u00f6rr, JR., Dimitrova, L., Lenze, D., Monteiro Barbosa, IA., Mendoza-Parra, MA., Kanashova, T., Metzner, M., Pardon, K., Reimann, M., Trumpp, A., D\u00f6rken, B., Zuber, J., Gronemeyer, H., Hummel, M., Dittmar, G., Lee, S., Schmitt, CA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"553","issue":"7686","page":"96-100","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29312250","title":"Identification of New Degrons in <i>Streptococcus mutans<\/i> Reveals a Novel Strategy for Engineering Targeted, Controllable Proteolysis.","abstract":"Recently, controllable, targeted proteolysis has emerged as one of the most promising new strategies to study essential genes and otherwise toxic mutations. One of the principal limitations preventing the wider adoption of this approach is due to the lack of easily identifiable species-specific degrons that can be used to trigger the degradation of target proteins. Here, we report new advancements in the targeted proteolysis concept by creating the first prokaryotic N-terminal targeted proteolysis system. We demonstrate how proteins from the LexA-like protein superfamily can be exploited as species-specific reservoirs of N- and\/or C-degrons, which are easily identifiable due to their proximity to strictly conserved residues found among LexA-like proteins. Using the LexA-like regulator HdiR of <i>Streptococcus mutans<\/i>, we identified two separate N-degrons derived from HdiR that confer highly efficient constitutive proteolysis upon target proteins when added as N-terminal peptide tags. Both degrons mediate degradation via AAA+ family housekeeping proteases with one degron primarily targeting FtsH and the other targeting the ClpP-dependent proteases. To modulate degron activity, our approach incorporates a hybrid N-terminal protein tag consisting of the ubiquitin-like protein NEDD8 fused to an HdiR degron. The NEDD8 fusion inhibits degron function until the NEDD8-specific endopeptidase NEDP1 is heterologously expressed to expose the N-degron. By fusing the NEDD8-degron tag onto GFP, luciferase, and the pleiotropic regulator RNase J2, we demonstrate that the N-terminal proteolysis approach exhibits far superior performance compared to the classic transcriptional depletion approach and is similarly applicable for the study of highly toxic mutations.","authors":"Liu, N., Chaudhry, MT., Xie, Z., Kreth, J., Merritt, J.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Front Microbiol","volume":"8","issue":"","page":"2572","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29249817","title":"Drug-induced inhibition of phosphorylation of STAT5 overrides drug resistance in neoplastic mast cells.","abstract":"Systemic mastocytosis (SM) is a mast cell (MC) neoplasm with complex pathology and a variable clinical course. In aggressive SM (ASM) and MC leukemia (MCL), responses to conventional drugs are poor and the prognosis is dismal. R763 is a multi-kinase inhibitor that blocks the activity of Aurora-kinase-A\/B, ABL1, AKT and FLT3. We examined the effects of R763 on proliferation and survival of neoplastic MC. R763 produced dose-dependent inhibition of proliferation in the human MC lines HMC-1.1 (IC<sub>50<\/sub> 5-50\u2009nM), HMC-1.2 (IC<sub>50<\/sub> 1-10\u2009nM), ROSA<sup>KIT WT<\/sup> (IC<sub>50<\/sub> 1-10\u2009nM), ROSA<sup>KIT D816V<\/sup> (IC<sub>50<\/sub> 50-500\u2009nM) and MCPV-1.1 (IC<sub>50<\/sub> 100-1000\u2009nM). Moreover, R763 induced growth inhibition in primary neoplastic MC in patients with ASM and MCL. Growth-inhibitory effects of R763 were accompanied by signs of apoptosis and a G2\/M cell cycle arrest. R763 also inhibited phosphorylation of KIT, BTK, AKT and STAT5 in neoplastic MC. The most sensitive target appeared to be STAT5. In fact, tyrosine phosphorylation of STAT5 was inhibited by R763 at 10\u2009nM. At this low concentration, R763 produced synergistic growth-inhibitory effects on neoplastic MC when combined with midostaurin or dasatinib. Together, R763 is a novel promising multi-kinase inhibitor that blocks STAT5 activation and thereby overrides drug-resistance in neoplastic MC.","authors":"Peter, B., Bibi, S., Eisenwort, G., Wingelhofer, B., Berger, D., Stefanzl, G., Blatt, K., Herrmann, H., Hadzijusufovic, E., Hoermann, G., Hoffmann, T., Schwaab, J., Jawhar, M., Willmann, M., Sperr, WR., Zuber, J., Sotlar, K., Horny, HP., Moriggl, R., Reiter, A., Arock, M., Valent, P.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Leukemia","volume":"32","issue":"4","page":"1016-1022","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29241686","title":"RANKL and RANK: From Mammalian Physiology to Cancer Treatment.","abstract":"The tumor necrosis factor (TNF) receptor RANK (TNFRSF11A) and its ligand RANKL (TNFSF11) regulate osteoclast development and bone metabolism. They also control stem cell expansion and proliferation of mammary epithelial cells via the sex hormone progesterone. As such, RANKL and RANK have been implicated in the onset of hormone-induced breast cancer. Recently, RANK\/RANKL were identified as crucial regulators for BRCA1 mutation-driven breast cancer. Current prevention strategies for BRCA1 mutation carriers are associated with wide-ranging risks; therefore, the search for alternative, non-invasive strategies is of paramount importance. We summarize here the functions of the RANKL\/RANK pathway in mammalian physiology and focus on its recently uncovered role in breast cancer. We propose that anti-RANKL therapy should be pursued as a preventative strategy for breast cancer.","authors":"Rao, S., Cronin, SJF., Sigl, V., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Trends Cell Biol","volume":"28","issue":"3","page":"213-223","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29217590","title":"A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.","abstract":"Fertilization triggers assembly of higher-order chromatin structure from a condensed maternal and a na\u00efve paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single-nucleus Hi-C (snHi-C), but not bulk Hi-C. It is therefore unclear when and how embryonic chromatin conformations are assembled. Here, we investigated whether a mechanism of cohesin-dependent loop extrusion generates higher-order chromatin structures within the one-cell embryo. Using snHi-C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically depend on Scc1-cohesin and that are regulated in size and linear density by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting differences in loop extrusion dynamics and epigenetic reprogramming. Dynamic polymer models of chromosomes reproduce changes in snHi-C, suggesting a mechanism where cohesin locally compacts chromatin by active loop extrusion, whose processivity is controlled by Wapl. Our simulations and experimental data provide evidence that cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell embryo onward.","authors":"Gassler, J., Brand\u00e3o, HB., Imakaev, M., Flyamer, IM., Ladst\u00e4tter, S., Bickmore, WA., Peters, JM., Mirny, LA., Tachibana, K.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"EMBO J","volume":"36","issue":"24","page":"3600-3618","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29198566","title":"Pseudotyped baculovirus is an effective gene expression tool for studying molecular function during axolotl limb regeneration.","abstract":"Axolotls can regenerate complex structures through recruitment and remodeling of cells within mature tissues. Accessing the underlying mechanisms at a molecular resolution is crucial to understand how injury triggers regeneration and how it proceeds. However, gene transformation in adult tissues can be challenging. Here we characterize the use of pseudotyped baculovirus (BV) as an effective gene transfer method both for cells within mature limb tissue and within the blastema. These cells remain competent to participate in regeneration after transduction. We further characterize the effectiveness of BV for gene overexpression studies by overexpressing Shh in the blastema, which yields a high penetrance of classic polydactyly phenotypes. Overall, our work establishes BV as a powerful tool to access gene function in axolotl limb regeneration.","authors":"Oliveira, CR., Lemaitre, R., Murawala, P., Tazaki, A., Drechsel, DN., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Dev Biol","volume":"433","issue":"2","page":"262-275","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29191977","title":"The tumor suppressor Brat controls neuronal stem cell lineages by inhibiting Deadpan and Zelda.","abstract":"The TRIM-NHL protein Brain tumor (Brat) acts as a tumor suppressor in the <i>Drosophila<\/i> brain, but how it suppresses tumor formation is not completely understood. Here, we combine temperature-controlled <i>brat<\/i> RNAi with transcriptome analysis to identify the immediate Brat targets in <i>Drosophila<\/i> neuroblasts. Besides the known target Deadpan (Dpn), our experiments identify the transcription factor Zelda (Zld) as a critical target of Brat. Our data show that Zld is expressed in neuroblasts and required to allow re-expression of Dpn in transit-amplifying intermediate neural progenitors. Upon neuroblast division, Brat is enriched in one daughter cell where its NHL domain directly binds to specific motifs in the 3'UTR of <i>dpn<\/i> and <i>zld<\/i> mRNA to mediate their degradation. In <i>brat<\/i> mutants, both Dpn and Zld continue to be expressed, but inhibition of either transcription factor prevents tumorigenesis. Our genetic and biochemical data indicate that Dpn inhibition requires higher Brat levels than Zld inhibition and suggest a model where stepwise post-transcriptional inhibition of distinct factors ensures sequential generation of fates in a stem cell lineage.","authors":"Reichardt, I., Bonnay, F., Steinmann, V., Loedige, I., Burkard, TR., Meister, G., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"EMBO Rep","volume":"19","issue":"1","page":"102-117","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29180814","title":"The crystal structure of Deg9 reveals a novel octameric-type HtrA protease.","abstract":"The high temperature requirement A (HtrA) proteases (also termed Deg proteases) play important roles in diverse organisms by regulating protein quality and quantity. One of the 16 Arabidopsis homologs, Deg9, is located in the nucleus where it modulates cytokinin- and light-mediated signalling via degrading the ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4). To uncover the structural features underlying the proteolytic activity of Deg9, we determined its crystal structure. Unlike the well-established trimeric building block of HtrAs, Deg9 displays a novel octameric structure consisting of two tetrameric rings that have distinct conformations. Based on the structural architecture, we generated several mutant variants of Deg9, determined their structure and tested their proteolytic activity towards ARR4. The results of the structural and biochemical analyses allowed us to propose a model for a novel mechanism of substrate recognition and activity regulation of Deg9. In this model, protease activation of one tetramer is mediated by en-bloc reorientation of the protease domains to open an entrance for the substrate in the opposite (inactive) tetramer. This study provides the structural basis for understanding how the levels of nuclear signal components are regulated by a plant protease.","authors":"Ouyang, M., Li, X., Zhao, S., Pu, H., Shen, J., Adam, Z., Clausen, T., Zhang, L.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Plants","volume":"3","issue":"12","page":"973-982","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29141958","title":"DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">29141958<\/PMID><DateCompleted><Year>2018<\/Year><Month>12<\/Month><Day>31<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1468-3288<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>68<\/Volume><Issue>1<\/Issue><PubDate><Year>2019<\/Year><Month>01<\/Month><\/PubDate><\/JournalIssue><Title>Gut<\/Title><ISOAbbreviation>Gut<\/ISOAbbreviation><\/Journal><ArticleTitle>DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.<\/ArticleTitle><Pagination><MedlinePgn>49-61<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1136\/gutjnl-2017-314817<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\">Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular characteristics and behaviour in culture remains limited.","authors":"Kraiczy, J., Nayak, KM., Howell, KJ., Ross, A., Forbester, J., Salvestrini, C., Mustata, R., Perkins, S., Andersson-Rolf, A., Leenen, E., Liebert, A., Vallier, L., Rosenstiel, PC., Stegle, O., Dougan, G., Heuschkel, R., Koo, BK., Zilbauer, M.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Gut","volume":"68","issue":"1","page":"49-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28656981","title":"Promoting transcription over long distances.","abstract":"Promoters and enhancers have long been regarded as distinct elements, a notion that has been challenged more recently. Two new studies now identify promoters that function as long-range enhancers in vivo to regulate the transcription of distal genes.","authors":"Catarino, RR., Neumayr, C., Stark, A.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Genet","volume":"49","issue":"7","page":"972-973","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29138277","title":"Coupling shRNA screens with single-cell RNA-seq identifies a dual role for mTOR in reprogramming-induced senescence.","abstract":"Expression of the transcription factors OCT4, SOX2, KLF4, and cMYC (OSKM) reprograms somatic cells into induced pluripotent stem cells (iPSCs). Reprogramming is a slow and inefficient process, suggesting the presence of safeguarding mechanisms that counteract cell fate conversion. One such mechanism is senescence. To identify modulators of reprogramming-induced senescence, we performed a genome-wide shRNA screen in primary human fibroblasts expressing OSKM. In the screen, we identified novel mediators of OSKM-induced senescence and validated previously implicated genes such as <i>CDKN1A<\/i> We developed an innovative approach that integrates single-cell RNA sequencing (scRNA-seq) with the shRNA screen to investigate the mechanism of action of the identified candidates. Our data unveiled regulation of senescence as a novel way by which mechanistic target of rapamycin (mTOR) influences reprogramming. On one hand, mTOR inhibition blunts the induction of cyclin-dependent kinase (CDK) inhibitors (CDKIs), including p16<sup>INK4a<\/sup>, p21<sup>CIP1<\/sup>, and p15<sup>INK4b<\/sup>, preventing OSKM-induced senescence. On the other hand, inhibition of mTOR blunts the senescence-associated secretory phenotype (SASP), which itself favors reprogramming. These contrasting actions contribute to explain the complex effect that mTOR has on reprogramming. Overall, our study highlights the advantage of combining functional screens with scRNA-seq to accelerate the discovery of pathways controlling complex phenotypes.","authors":"Aarts, M., Georgilis, A., Beniazza, M., Beolchi, P., Banito, A., Carroll, T., Kulisic, M., Kaemena, DF., Dharmalingam, G., Martin, N., Reik, W., Zuber, J., Kaji, K., Chandra, T., Gil, J.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Genes Dev","volume":"31","issue":"20","page":"2085-2098","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29137925","title":"Polycomb repression complex 2 is required for the maintenance of retinal progenitor cells and balanced retinal differentiation.","abstract":"Polycomb repressive complexes maintain transcriptional repression of genes encoding crucial developmental regulators through chromatin modification. Here we investigated the role of Polycomb repressive complex 2 (PRC2) in retinal development by inactivating its key components Eed and Ezh2. Conditional deletion of Ezh2 resulted in a partial loss of PRC2 function and accelerated differentiation of M\u00fcller glial cells. In contrast, inactivation of Eed led to the ablation of PRC2 function at early postnatal stage. Cell proliferation was reduced and retinal progenitor cells were significantly decreased in this mutant, which subsequently caused depletion of M\u00fcller glia, bipolar, and rod photoreceptor cells, primarily generated from postnatal retinal progenitor cells. Interestingly, the proportion of amacrine cells was dramatically increased at postnatal stages in the Eed-deficient retina. In accordance, multiple transcription factors controlling amacrine cell differentiation were upregulated. Furthermore, ChIP-seq analysis showed that these deregulated genes contained bivalent chromatin (H3K27me3<sup>+<\/sup> H3K4me3<sup>+<\/sup>). Our results suggest that PRC2 is required for proliferation in order to maintain the retinal progenitor cells at postnatal stages and for retinal differentiation by controlling amacrine cell generation.","authors":"Fujimura, N., Kuzelova, A., Ebert, A., Strnad, H., Lachova, J., Machon, O., Busslinger, M., Kozmik, Z.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Dev Biol","volume":"433","issue":"1","page":"47-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29109121","title":"Glycogen Synthase Kinase-3 Modulates Cbl-b and Constrains T Cell Activation.","abstract":"The decision between T cell activation and tolerance is governed by the spatial and temporal integration of diverse molecular signals and events occurring downstream of TCR and costimulatory or coinhibitory receptor engagement. The PI3K-protein kinase B (PKB; also known as Akt) signaling pathway is a central axis in mediating proximal signaling events of TCR and CD28 engagement in T cells. Perturbation of the PI3K-PKB pathway, or the loss of negative regulators of T cell activation, such as the E3 ubiquitin ligase Cbl-b, have been reported to lead to increased susceptibility to autoimmunity. In this study, we further examined the molecular pathway linking PKB and Cbl-b in murine models. Our data show that the protein kinase GSK-3, one of the first targets identified for PKB, catalyzes two previously unreported phosphorylation events at Ser<sup>476<\/sup> and Ser<sup>480<\/sup> of Cbl-b. GSK-3 inactivation by PKB abrogates phosphorylation of Cbl-b at these two sites and results in reduced Cbl-b protein levels. We further show that constitutive activation of PKB in vivo results in a loss of tolerance that is mediated through the downregulation of Cbl-b. Altogether, these data indicate that the PI3K-PKB-GSK-3 pathway is a novel regulatory axis that is important for controlling the decision between T cell activation and tolerance via Cbl-b.","authors":"Tran, CW., Saibil, SD., Le Bihan, T., Hamilton, SR., Lang, KS., You, H., Lin, AE., Garza, KM., Elford, AR., Tai, K., Parsons, ME., Wigmore, K., Vainberg, MG., Penninger, JM., Woodgett, JR., Mak, TW., Ohashi, PS.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"J Immunol","volume":"199","issue":"12","page":"4056-4065","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29057658","title":"PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search.","abstract":"Standard proteomics workflows use tandem mass spectrometry followed by sequence database search to analyze complex biological samples. The identification of proteins carrying post-translational modifications, for example, phosphorylation, is typically addressed by allowing variable modifications in the searched sequences. Accounting for these variations exponentially increases the combinatorial space in the database, which leads to increased processing times and more false positive identifications. The here-presented tool PhoStar identifies spectra that originate from phosphorylated peptides before database search using a supervised machine learning approach. The model for the prediction of phosphorylation was trained and validated with an accuracy of 97.6% on a large set of high-confidence spectra collected from publicly available experimental data. Its power was further validated by predicting phosphorylation in the complete NIST human and mouse high collision-dissociation spectral libraries, achieving an accuracy of 98.2 and 97.9%, respectively. We demonstrate the application of PhoStar by using it for spectra filtering before database search. In database search of HeLa samples the peptide search space was reduced by 27-66% while finding at least 97% of total peptide identifications (at 1% FDR) compared with a standard workflow.","authors":"Dorl, S., Winkler, S., Mechtler, K., Dorfer, V.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"J Proteome Res","volume":"17","issue":"1","page":"290-295","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11498575","title":"Translating the histone code.","abstract":"Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins, which in turn dictate dynamic transitions between transcriptionally active or transcriptionally silent chromatin states. The combinatorial nature of histone amino-terminal modifications thus reveals a \"histone code\" that considerably extends the information potential of the genetic code. We propose that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.","authors":"Jenuwein, T., Allis, CD.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Science","volume":"293","issue":"5532","page":"1074-80","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29039415","title":"CRISPR-UMI: single-cell lineage tracing of pooled CRISPR-Cas9 screens.","abstract":"Pooled CRISPR screens are a powerful tool for assessments of gene function. However, conventional analysis is based exclusively on the relative abundance of integrated single guide RNAs (sgRNAs) between populations, which does not discern distinct phenotypes and editing outcomes generated by identical sgRNAs. Here we present CRISPR-UMI, a single-cell lineage-tracing methodology for pooled screening to account for cell heterogeneity. We generated complex sgRNA libraries with unique molecular identifiers (UMIs) that allowed for screening of clonally expanded, individually tagged cells. A proof-of-principle CRISPR-UMI negative-selection screen provided increased sensitivity and robustness compared with conventional analysis by accounting for underlying cellular and editing-outcome heterogeneity and detection of outlier clones. Furthermore, a CRISPR-UMI positive-selection screen uncovered new roadblocks in reprogramming mouse embryonic fibroblasts as pluripotent stem cells, distinguishing reprogramming frequency and speed (i.e., effect size and probability). CRISPR-UMI boosts the predictive power, sensitivity, and information content of pooled CRISPR screens.","authors":"Michlits, G., Hubmann, M., Wu, SH., Vainorius, G., Budusan, E., Zhuk, S., Burkard, TR., Novatchkova, M., Aichinger, M., Lu, Y., Reece-Hoyes, J., Nitsch, R., Schramek, D., Hoepfner, D., Elling, U.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Methods","volume":"14","issue":"12","page":"1191-1197","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29030146","title":"Salamander spinal cord regeneration: The ultimate positive control in vertebrate spinal cord regeneration.","abstract":"Repairing injured tissues \/ organs is one of the major challenges for the maintenance of proper organ function in adulthood. In mammals, the central nervous system including the spinal cord, once established during embryonic development, has very limited capacity to regenerate. In contrast, salamanders such as axolotls can fully regenerate the injured spinal cord, making this a very powerful vertebrate model system for studying this process. Here we discuss the cellular and molecular requirements for spinal cord regeneration in the axolotl. The recent development of tools to test molecular function, including CRISPR-mediated gene editing, has lead to the identification of key players involved in the cell response to injury that ultimately leads to outgrowth of neural stem cells that are competent to replay the process of spinal cord development to replace the damaged\/missing tissue.","authors":"Tazaki, A., Tanaka, EM., Fei, JF.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Dev Biol","volume":"432","issue":"1","page":"63-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28974565","title":"Apelin Is a Negative Regulator of Angiotensin II-Mediated Adverse Myocardial Remodeling and Dysfunction.","abstract":"The apelin pathway has emerged as a critical regulator of cardiovascular homeostasis and disease. However, the exact role of pyr1-apelin-13 in angiotensin (Ang) II-mediated heart disease remains unclear. We used apelin-deficient (APLN<sup>-\/y<\/sup>) and apolipoprotein E knockout mice to evaluate the regulatory roles of pyr1-apelin-13. The 1-year aged APLN<sup>-\/y<\/sup> mice developed myocardial hypertrophy and dysfunction with reduced angiotensin-converting enzyme 2 levels. Ang II infusion (1.5 mg kg<sup>-1<\/sup> d<sup>-1<\/sup>) for 4 weeks potentiated oxidative stress, pathological hypertrophy, and myocardial fibrosis in young APLN<sup>-\/y<\/sup> hearts resulting in exacerbation of cardiac dysfunction. Importantly, daily administration of 100 \u03bcg\/kg pyr1-apelin-13 resulted in upregulated angiotensin-converting enzyme 2 levels, decreased superoxide production and expression of hypertrophy- and fibrosis-related genes leading to attenuated myocardial hypertrophy, fibrosis, and dysfunction in the Ang II-infused apolipoprotein E knockout mice. In addition, pyr1-apelin-13 treatment largely attenuated Ang II-induced apoptosis and ultrastructural injury in the apolipoprotein E knockout mice by activating Akt and endothelial nitric oxide synthase phosphorylation signaling. In cultured neonatal rat cardiomyocytes and cardiofibroblasts, exposure of Ang II decreased angiotensin-converting enzyme 2 protein and increased superoxide generation, cellular proliferation, and migration, which were rescued by pyr1-apelin-13, and Akt and endothelial nitric oxide synthase agonist stimulation. The increased superoxide generation and apoptosis in cultured cardiofibroblasts in response to Ang II were strikingly prevented by pyr1-apelin-13 which was partially reversed by cotreatment with the Akt inhibitor MK2206. In conclusion, pyr1-apelin-13 peptide pathway is a negative regulator of aging-mediated and Ang II-mediated adverse myocardial remodeling and dysfunction and represents a potential candidate to prevent and treat heart disease.","authors":"Zhang, ZZ., Wang, W., Jin, HY., Chen, X., Cheng, YW., Xu, YL., Song, B., Penninger, JM., Oudit, GY., Zhong, JC.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Hypertension","volume":"70","issue":"6","page":"1165-1175","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28959962","title":"Comparative glycoproteomics of stem cells identifies new players in ricin toxicity.","abstract":"Glycosylation, the covalent attachment of carbohydrate structures onto proteins, is the most abundant post-translational modification. Over 50% of human proteins are glycosylated, which alters their activities in diverse fundamental biological processes. Despite the importance of glycosylation in biology, the identification and functional validation of complex glycoproteins has remained largely unexplored. Here we develop a novel quantitative approach to identify intact glycopeptides from comparative proteomic data sets, allowing us not only to infer complex glycan structures but also to directly map them to sites within the associated proteins at the proteome scale. We apply this method to human and mouse embryonic stem cells to illuminate the stem cell glycoproteome. This analysis nearly doubles the number of experimentally confirmed glycoproteins, identifies previously unknown glycosylation sites and multiple glycosylated stemness factors, and uncovers evolutionarily conserved as well as species-specific glycoproteins in embryonic stem cells. The specificity of our method is confirmed using sister stem cells carrying repairable mutations in enzymes required for fucosylation, Fut9 and Slc35c1. Ablation of fucosylation confers resistance to the bioweapon ricin, and we discover proteins that carry a fucosylation-dependent sugar code for ricin toxicity. Mutations disrupting a subset of these proteins render cells ricin resistant, revealing new players that orchestrate ricin toxicity. Our comparative glycoproteomics platform, SugarQb, enables genome-wide insights into protein glycosylation and glycan modifications in complex biological systems.","authors":"Stadlmann, J., Taubenschmid, J., Wenzel, D., Gattinger, A., D\u00fcrnberger, G., Dusberger, F., Elling, U., Mach, L., Mechtler, K., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"549","issue":"7673","page":"538-542","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28953874","title":"A reversible haploid mouse embryonic stem cell biobank resource for functional genomics.","abstract":"The ability to directly uncover the contributions of genes to a given phenotype is fundamental for biology research. However, ostensibly homogeneous cell populations exhibit large clonal variance that can confound analyses and undermine reproducibility. Here we used genome-saturated mutagenesis to create a biobank of over 100,000 individual haploid mouse embryonic stem (mES) cell lines targeting 16,970 genes with genetically barcoded, conditional and reversible mutations. This Haplobank is, to our knowledge, the largest resource of hemi\/homozygous mutant mES cells to date and is available to all researchers. Reversible mutagenesis overcomes clonal variance by permitting functional annotation of the genome directly in sister cells. We use the Haplobank in reverse genetic screens to investigate the temporal resolution of essential genes in mES cells, and to identify novel genes that control sprouting angiogenesis and lineage specification of blood vessels. Furthermore, a genome-wide forward screen with Haplobank identified PLA2G16 as a host factor that is required for cytotoxicity by rhinoviruses, which cause the common cold. Therefore, clones from the Haplobank combined with the use of reversible technologies enable high-throughput, reproducible, functional annotation of the genome.","authors":"Elling, U., Wimmer, RA., Leibbrandt, A., Burkard, T., Michlits, G., Leopoldi, A., Micheler, T., Abdeen, D., Zhuk, S., Aspalter, IM., Handl, C., Liebergesell, J., Hubmann, M., Husa, AM., Kinzer, M., Schuller, N., Wetzel, E., van de Loo, N., Martinez, JAZ., Estoppey, D., Riedl, R., Yang, F., Fu, B., Dechat, T., Ivics, Z., Agu, CA., Bell, O., Blaas, D., Gerhardt, H., Hoepfner, D., Stark, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"550","issue":"7674","page":"114-118","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28945705","title":"Thiol-linked alkylation of RNA to assess expression dynamics.","abstract":"Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM seq), an orthogonal-chemistry-based RNA sequencing technology that detects 4-thiouridine (s<sup>4<\/sup>U) incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM seq enabled rapid access to RNA-polymerase-II-dependent gene expression dynamics in the context of total RNA. We validated the method in mouse embryonic stem cells by showing that the RNA-polymerase-II-dependent transcriptional output scaled with Oct4\/Sox2\/Nanog-defined enhancer activity, and we provide quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N<sup>6<\/sup>-methyladenosine. SLAM seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective and scalable manner.","authors":"Herzog, VA., Reichholf, B., Neumann, T., Rescheneder, P., Bhat, P., Burkard, TR., Wlotzka, W., von Haeseler, A., Zuber, J., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Methods","volume":"14","issue":"12","page":"1198-1204","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28935704","title":"The splicing co-factor Barricade\/Tat-SF1 is required for cell cycle and lineage progression in <i>Drosophila<\/i> neural stem cells.","abstract":"Stem cells need to balance self-renewal and differentiation for correct tissue development and homeostasis. Defects in this balance can lead to developmental defects or tumor formation. In recent years, mRNA splicing has emerged as an important mechanism regulating cell fate decisions. Here we address the role of the evolutionarily conserved splicing co-factor Barricade (Barc)\/Tat-SF1\/CUS2 in <i>Drosophila<\/i> neural stem cell (neuroblast) lineage formation. We show that Barc is required for the generation of neurons during <i>Drosophila<\/i> brain development by ensuring correct neural progenitor proliferation and differentiation. Barc associates with components of the U2 small nuclear ribonucleoprotein (snRNP) complex, and its depletion causes alternative splicing in the form of intron retention in a subset of genes. Using bioinformatics analysis and a cell culture-based splicing assay, we found that Barc-dependent introns share three major traits: they are short, GC rich and have weak 3' splice sites. Our results show that Barc, together with the U2 snRNP complex, plays an important role in regulating neural stem cell lineage progression during brain development and facilitates correct splicing of a subset of introns.","authors":"Abramczuk, MK., Burkard, TR., Rolland, V., Steinmann, V., Duchek, P., Jiang, Y., Wissel, S., Reichert, H., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Development","volume":"144","issue":"21","page":"3932-3945","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28925387","title":"A vital sugar code for ricin toxicity.","abstract":"Ricin is one of the most feared bioweapons in the world due to its extreme toxicity and easy access. Since no antidote exists, it is of paramount importance to identify the pathways underlying ricin toxicity. Here, we demonstrate that the Golgi GDP-fucose transporter Slc35c1 and fucosyltransferase Fut9 are key regulators of ricin toxicity. Genetic and pharmacological inhibition of fucosylation renders diverse cell types resistant to ricin via deregulated intracellular trafficking. Importantly, cells from a patient with SLC35C1 deficiency are also resistant to ricin. Mechanistically, we confirm that reduced fucosylation leads to increased sialylation of Lewis X structures and thus masking of ricin-binding sites. Inactivation of the sialyltransferase responsible for modifications of Lewis X (St3Gal4) increases the sensitivity of cells to ricin, whereas its overexpression renders cells more resistant to the toxin. Thus, we have provided unprecedented insights into an evolutionary conserved modular sugar code that can be manipulated to control ricin toxicity.","authors":"Taubenschmid, J., Stadlmann, J., Jost, M., Klokk, TI., Rillahan, CD., Leibbrandt, A., Mechtler, K., Paulson, JC., Jude, J., Zuber, J., Sandvig, K., Elling, U., Marquardt, T., Thiel, C., Koerner, C., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell Res","volume":"27","issue":"11","page":"1351-1364","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16543150","title":"Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila.","abstract":"Dosage compensation in Drosophila is dependent on MSL proteins and involves hypertranscription of the male X chromosome, which ensures equal X-linked gene expression in both sexes. Here, we report the purification of enzymatically active MSL complexes from Drosophila embryos, Schneider cells, and human HeLa cells. We find a stable association of the histone H4 lysine 16-specific acetyltransferase MOF with the RNA\/protein containing MSL complex as well as with an evolutionary conserved complex. We show that the MSL complex interacts with several components of the nuclear pore, in particular Mtor\/TPR and Nup153. Strikingly, knockdown of Mtor or Nup153 results in loss of the typical MSL X-chromosomal staining and dosage compensation in Drosophila male cells but not in female cells. These results reveal an unexpected physical and functional connection between nuclear pore components and chromatin regulation through MSL proteins, highlighting the role of nucleoporins in gene regulation in higher eukaryotes.","authors":"Mendjan, S., Taipale, M., Kind, J., Holz, H., Gebhardt, P., Schelder, M., Vermeulen, M., Buscaino, A., Duncan, K., Mueller, J., Wilm, M., Stunnenberg, HG., Saumweber, H., Akhtar, A.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Mol Cell","volume":"21","issue":"6","page":"811-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28877513","title":"Predicting functional neuroanatomical maps from fusing brain networks with genetic information.","abstract":"Functional neuroanatomical maps provide a mesoscale reference framework for studies from molecular to systems neuroscience and psychiatry. The underlying structure-function relationships are typically derived from functional manipulations or imaging approaches. Although highly informative, these are experimentally costly. The increasing amount of publicly available brain and genetic data offers a rich source that could be mined to address this problem computationally. Here, we developed an algorithm that fuses gene expression and connectivity data with functional genetic meta data and exploits cumulative effects to derive neuroanatomical maps related to multi-genic functions. We validated the approach by using public available mouse and human data. The generated neuroanatomical maps recapture known functional anatomical annotations from literature and functional MRI data. When applied to multi-genic meta data from mouse quantitative trait loci (QTL) studies and human neuropsychiatric databases, this method predicted known functional maps underlying behavioral or psychiatric traits. Taken together, genetically weighted connectivity analysis (GWCA) allows for high throughput functional exploration of brain anatomy in silico. It maps functional genetic associations onto brain circuitry for refining functional neuroanatomy, or identifying trait-associated brain circuitry, from genetic data.","authors":"Ganglberger, F., Kaczanowska, J., Penninger, JM., Hess, A., B\u00fchler, K., Haubensak, W.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Neuroimage","volume":"170","issue":null,"page":"113-120","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28792605","title":"Single-cell Hi-C bridges microscopy and genome-wide sequencing approaches to study 3D chromatin organization.","abstract":"Recent years have witnessed an explosion of the single-cell biochemical toolbox including chromosome conformation capture (3C)-based methods that provide novel insights into chromatin spatial organization in individual cells. The observations made with these techniques revealed that topologically associating domains emerge from cell population averages and do not exist as static structures in individual cells. Stochastic nature of the genome folding is likely to be biologically relevant and may reflect the ability of chromatin fibers to adopt a number of alternative configurations, some of which could be transiently stabilized and serve regulatory purposes. Single-cell Hi-C approaches provide an opportunity to analyze chromatin folding in rare cell types such as stem cells, tumor progenitors, oocytes, and totipotent cells, contributing to a deeper understanding of basic mechanisms in development and disease. Here, we review key findings of single-cell Hi-C and discuss possible biological reasons and consequences of the inferred dynamic chromatin spatial organization.","authors":"Ulianov, SV., Tachibana-Konwalski, K., Razin, SV.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Bioessays","volume":"39","issue":"10","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28678782","title":"Transcription elongation factors represent in vivo cancer dependencies in glioblastoma.","abstract":"Glioblastoma is a universally lethal cancer with a median survival time of approximately 15 months. Despite substantial efforts to define druggable targets, there are no therapeutic options that notably extend the lifespan of patients with glioblastoma. While previous work has largely focused on in vitro cellular models, here we demonstrate a more physiologically relevant approach to target discovery in glioblastoma. We adapted pooled RNA interference (RNAi) screening technology for use in orthotopic patient-derived xenograft models, creating a high-throughput negative-selection screening platform in a functional in vivo tumour microenvironment. Using this approach, we performed parallel in vivo and in vitro screens and discovered that the chromatin and transcriptional regulators needed for cell survival in vivo are non-overlapping with those required in vitro. We identified transcription pause-release and elongation factors as one set of in vivo-specific cancer dependencies, and determined that these factors are necessary for enhancer-mediated transcriptional adaptations that enable cells to survive the tumour microenvironment. Our lead hit, JMJD6, mediates the upregulation of in vivo stress and stimulus response pathways through enhancer-mediated transcriptional pause-release, promoting cell survival specifically in vivo. Targeting JMJD6 or other identified elongation factors extends survival in orthotopic xenograft mouse models, suggesting that targeting transcription elongation machinery may be an effective therapeutic strategy for glioblastoma. More broadly, this study demonstrates the power of in vivo phenotypic screening to identify new classes of 'cancer dependencies' not identified by previous in vitro approaches, and could supply new opportunities for therapeutic intervention.","authors":"Miller, TE., Liau, BB., Wallace, LC., Morton, AR., Xie, Q., Dixit, D., Factor, DC., Kim, LJY., Morrow, JJ., Wu, Q., Mack, SC., Hubert, CG., Gillespie, SM., Flavahan, WA., Hoffmann, T., Thummalapalli, R., Hemann, MT., Paddison, PJ., Horbinski, CM., Zuber, J., Scacheri, PC., Bernstein, BE., Tesar, PJ., Rich, JN.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"547","issue":"7663","page":"355-359","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28650477","title":"Video rate volumetric Ca<sup>2+<\/sup> imaging across cortex using seeded iterative demixing (SID) microscopy.","abstract":"Light-field microscopy (LFM) is a scalable approach for volumetric Ca<sup>2+<\/sup> imaging with high volumetric acquisition rates (up to 100 Hz). Although the technology has enabled whole-brain Ca<sup>2+<\/sup> imaging in semi-transparent specimens, tissue scattering has limited its application in the rodent brain. We introduce seeded iterative demixing (SID), a computational source-extraction technique that extends LFM to the mammalian cortex. SID can capture neuronal dynamics in vivo within a volume of 900 \u00d7 900 \u00d7 260 \u03bcm located as deep as 380 \u03bcm in the mouse cortex or hippocampus at a 30-Hz volume rate while discriminating signals from neurons as close as 20 \u03bcm apart, at a computational cost three orders of magnitude less than that of frame-by-frame image reconstruction. We expect that the simplicity and scalability of LFM, coupled with the performance of SID, will open up a range of applications including closed-loop experiments.","authors":"N\u00f6bauer, T., Skocek, O., Pern\u00eda-Andrade, AJ., Weilguny, L., Traub, FM., Molodtsov, MI., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Methods","volume":"14","issue":"8","page":"811-818","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28599149","title":"An optimized lentiviral vector system for conditional RNAi and efficient cloning of microRNA embedded short hairpin RNA libraries.","abstract":"RNA interference (RNAi) and CRISPR-Cas9-based screening systems have emerged as powerful and complementary tools to unravel genetic dependencies through systematic gain- and loss-of-function studies. In recent years, a series of technical advances helped to enhance the performance of virally delivered RNAi. For instance, the incorporation of short hairpin RNAs (shRNAs) into endogenous microRNA contexts (shRNAmiRs) allows the use of Tet-regulated promoters for synchronous onset of gene knockdown and precise interrogation of gene dosage effects. However, remaining challenges include lack of efficient cloning strategies, inconsistent knockdown potencies and leaky expression. Here, we present a simple, one-step cloning approach for rapid and efficient cloning of miR-30 shRNAmiR libraries. We combined a human miR-30 backbone retaining native flanking sequences with an optimized all-in-one lentiviral vector system for conditional RNAi to generate a versatile toolbox characterized by higher doxycycline sensitivity, reduced leakiness and enhanced titer. Furthermore, refinement of existing shRNA design rules resulted in substantially improved prediction of powerful shRNAs. Our approach was validated by accurate quantification of the knockdown potency of over 250 single shRNAmiRs. To facilitate access and use by the scientific community, an online tool was developed for the automated design of refined shRNA-coding oligonucleotides ready for cloning into our system.","authors":"Adams, FF., Heckl, D., Hoffmann, T., Talbot, SR., Kloos, A., Thol, F., Heuser, M., Zuber, J., Schambach, A., Schwarzer, A.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Biomaterials","volume":"139","issue":null,"page":"102-115","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28581519","title":"Autophagy suppresses Ras-driven epithelial tumourigenesis by limiting the accumulation of reactive oxygen species.","abstract":"Activation of Ras signalling occurs in ~30% of human cancers; however, activated Ras alone is not sufficient for tumourigenesis. In a screen for tumour suppressors that cooperate with oncogenic Ras (Ras<sup>V12<\/sup>) in Drosophila, we identified genes involved in the autophagy pathway. Bioinformatic analysis of human tumours revealed that several core autophagy genes, including GABARAP, correlate with oncogenic KRAS mutations and poor prognosis in human pancreatic cancer, supporting a potential tumour-suppressive effect of the pathway in Ras-driven human cancers. In Drosophila, we demonstrate that blocking autophagy at any step of the pathway enhances Ras<sup>V12<\/sup>-driven epithelial tissue overgrowth via the accumulation of reactive oxygen species and activation of the Jun kinase stress response pathway. Blocking autophagy in Ras<sup>V12<\/sup> clones also results in non-cell-autonomous effects with autophagy, cell proliferation and caspase activation induced in adjacent wild-type cells. Our study has implications for understanding the interplay between perturbations in Ras signalling and autophagy in tumourigenesis, which might inform the development of novel therapeutics targeting Ras-driven cancers.","authors":"Manent, J., Banerjee, S., de Matos Simoes, R., Zoranovic, T., Mitsiades, C., Penninger, JM., Simpson, KJ., Humbert, PO., Richardson, HE.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Oncogene","volume":"36","issue":"40","page":"5576-5592","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28562594","title":"Guided self-organization and cortical plate formation in human brain organoids.","abstract":"Three-dimensional cell culture models have either relied on the self-organizing properties of mammalian cells or used bioengineered constructs to arrange cells in an organ-like configuration. While self-organizing organoids excel at recapitulating early developmental events, bioengineered constructs reproducibly generate desired tissue architectures. Here, we combine these two approaches to reproducibly generate human forebrain tissue while maintaining its self-organizing capacity. We use poly(lactide-co-glycolide) copolymer (PLGA) fiber microfilaments as a floating scaffold to generate elongated embryoid bodies. Microfilament-engineered cerebral organoids (enCORs) display enhanced neuroectoderm formation and improved cortical development. Furthermore, reconstitution of the basement membrane leads to characteristic cortical tissue architecture, including formation of a polarized cortical plate and radial units. Thus, enCORs model the distinctive radial organization of the cerebral cortex and allow for the study of neuronal migration. Our data demonstrate that combining 3D cell culture with bioengineering can increase reproducibility and improve tissue architecture.","authors":"Lancaster, MA., Corsini, NS., Wolfinger, S., Gustafson, EH., Phillips, AW., Burkard, TR., Otani, T., Livesey, FJ., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Biotechnol","volume":"35","issue":"7","page":"659-666","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28530653","title":"Structure of a pre-catalytic spliceosome.","abstract":"Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-catalytic B complex spliceosome at near-atomic resolution. The mobile U2 small nuclear ribonucleoprotein particle (snRNP) associates with U4\/U6.U5 tri-snRNP through the U2\/U6 helix II and an interface between U4\/U6 di-snRNP and the U2 snRNP SF3b-containing domain, which also transiently contacts the helicase Brr2. The 3' region of the U2 snRNP is flexibly attached to the SF3b-containing domain and protrudes over the concave surface of tri-snRNP, where the U1 snRNP may reside before its release from the pre-mRNA 5' splice site. The U6 ACAGAGA sequence forms a hairpin that weakly tethers the 5' splice site. The B complex proteins Prp38, Snu23 and Spp381 bind the Prp8 N-terminal domain and stabilize U6 ACAGAGA stem-pre-mRNA and Brr2-U4 small nuclear RNA interactions. These results provide important insights into the events leading to active site formation.","authors":"Plaschka, C., Lin, PC., Nagai, K.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"546","issue":"7660","page":"617-621","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28383256","title":"Phosphoproteomics with Activated Ion Electron Transfer Dissociation.","abstract":"The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion manuscript ( Anal. Chem. 2017 , DOI: 10.1021\/acs.analchem.7b00213 ), we described a new implementation of activated ion electron transfer dissociation (AI-ETD) on a quadrupole-Orbitrap-linear ion trap hybrid MS system (Orbitrap Fusion Lumos), which greatly improved peptide fragmentation and identification over ETD and other supplemental activation methods. Here we present the performance of AI-ETD for identifying and localizing sites of phosphorylation in both phosphopeptides and intact phosphoproteins. Using 90 min analyses we show that AI-ETD can identify 24,503 localized phosphopeptide spectral matches enriched from mouse brain lysates, which more than triples identifications from standard ETD experiments and outperforms ETcaD and EThcD as well. AI-ETD achieves these gains through improved quality of fragmentation and MS\/MS success rates for all precursor charge states, especially for doubly protonated species. We also evaluate the degree to which phosphate neutral loss occurs from phosphopeptide product ions due to the infrared photoactivation of AI-ETD and show that modifying phosphoRS (a phosphosite localization algorithm) to include phosphate neutral losses can significantly improve localization in AI-ETD spectra. Finally, we demonstrate the utility of AI-ETD in localizing phosphosites in \u03b1-casein, an \u223c23.5 kDa phosphoprotein that showed eight of nine known phosphorylation sites occupied upon intact mass analysis. AI-ETD provided the greatest sequence coverage for all five charge states investigated and was the only fragmentation method to localize all eight phosphosites for each precursor. Overall, this work highlights the analytical value AI-ETD can bring to both bottom-up and top-down phosphoproteomics.","authors":"Riley, NM., Hebert, AS., D\u00fcrnberger, G., Stanek, F., Mechtler, K., Westphall, MS., Coon, JJ.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Anal Chem","volume":"89","issue":"12","page":"6367-6376","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"12052899","title":"Promoter specificity and biological activity of tethered AP-1 dimers.","abstract":"Activator protein 1 (AP-1) is a group of dimeric transcription factors composed of Jun, Fos, and ATF family proteins. Both gain- and loss-of-function studies have revealed specific roles for individual AP-1 components in cell proliferation, differentiation, apoptosis, and other biological processes. However, little is known about the functions of specific AP-1 dimers. To test the importance of AP-1 composition in transcriptional activation, AP-1 monomers were joined via a flexible polypeptide tether to force specific pairing. The resultant single-chain AP-1 molecules showed DNA binding specificity and transcriptional activation potentials similar to those of untethered dimers, even in the presence of dominant-negative AP-1 monomers. c-Jun-containing dimers showed distinct promoter specificity in transient-transfection experiments, depending on the Fos, Fra, or ATF partner. When stably expressed in NIH 3T3 cells, c-Jun tethered dimer Fra2, but not c-Jun tethered dimer Fra1 and c-Jun tethered dimer cFos (the tilde indicates a tethered dimer), inhibited G(0) arrest at confluency and under low-serum conditions and specifically activated cyclin A expression. These data suggest that the choice of dimerization partner defines the role of c-Jun in gene activation and cell cycle regulation and that single-chain AP-1 molecules provide a powerful tool for assessing the role of specific AP-1 dimers.","authors":"Bakiri, L., Matsuo, K., Wisniewska, M., Wagner, EF., Yaniv, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Mol Cell Biol","volume":"22","issue":"13","page":"4952-64","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28283582","title":"Self-organized developmental patterning and differentiation in cerebral organoids.","abstract":"Cerebral organoids recapitulate human brain development at a considerable level of detail, even in the absence of externally added signaling factors. The patterning events driving this self-organization are currently unknown. Here, we examine the developmental and differentiative capacity of cerebral organoids. Focusing on forebrain regions, we demonstrate the presence of a variety of discrete ventral and dorsal regions. Clearing and subsequent 3D reconstruction of entire organoids reveal that many of these regions are interconnected, suggesting that the entire range of dorso-ventral identities can be generated within continuous neuroepithelia. Consistent with this, we demonstrate the presence of forebrain organizing centers that express secreted growth factors, which may be involved in dorso-ventral patterning within organoids. Furthermore, we demonstrate the timed generation of neurons with mature morphologies, as well as the subsequent generation of astrocytes and oligodendrocytes. Our work provides the methodology and quality criteria for phenotypic analysis of brain organoids and shows that the spatial and temporal patterning events governing human brain development can be recapitulated <i>in\u00a0vitro<\/i>.","authors":"Renner, M., Lancaster, MA., Bian, S., Choi, H., Ku, T., Peer, A., Chung, K., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"EMBO J","volume":"36","issue":"10","page":"1316-1329","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"39217332","title":"Joint single-cell genetic and transcriptomic analysis reveal pre-malignant SCP-like subclones in human neuroblastoma.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">39217332<\/PMID><DateCompleted><Year>2024<\/Year><Month>08<\/Month><Day>31<\/Day><\/DateCompleted><DateRevised><Year>2026<\/Year><Month>09<\/Month><Day>22<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1476-4598<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>23<\/Volume><Issue>1<\/Issue><PubDate><Year>2024<\/Year><Month>Aug<\/Month><Day>31<\/Day><\/PubDate><\/JournalIssue><Title>Molecular cancer<\/Title><ISOAbbreviation>Mol Cancer<\/ISOAbbreviation><\/Journal><ArticleTitle>Joint single-cell genetic and transcriptomic analysis reveal pre-malignant SCP-like subclones in human neuroblastoma.<\/ArticleTitle><Pagination><StartPage>180<\/StartPage><MedlinePgn>180<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">180<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12943-024-02091-y<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Neuroblastoma (NB) is a heterogeneous embryonal malignancy and the deadliest tumor of infancy. It is a complex disease that can result in diverse clinical outcomes. In some children, tumors regress spontaneously. Others respond well to existing treatments. But for the high-risk group, which constitutes approximately 40% of all patients, the prognosis remains dire despite collaborative efforts in basic and clinical research. While its exact cellular origin is still under debate, NB is assumed to arise from the neural crest cell lineage including multipotent Schwann cell precursors (SCPs), which differentiate into sympatho-adrenal cell states eventually producing chromaffin cells and sympathoblasts.","authors":"Olsen, TK., Otte, J., Mei, S., Embaie, BT., Kameneva, P., Cheng, H., Gao, T., Zachariadis, V., Tsea, I., Bj\u00f6rklund, \u00c5., Kryukov, E., Hou, Z., Johansson, A., Sundstr\u00f6m, E., Martinsson, T., Fransson, S., Stenman, J., Fard, SS., Johnsen, JI., Kogner, P., Adameyko, I., Enge, M., Kharchenko, PV., Baryawno, N.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Mol Cancer","volume":"23","issue":"1","page":"180","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-31","doi":"10.1186\/s12943-024-02091-y","first_author":"Olsen, TK.","corresponding_authors":"Baryawno, N."},{"pmid":"28250425","title":"Essential role for the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells.","abstract":"Innate-like B-1a cells provide a first line of defense against pathogens, yet little is known about their transcriptional control. Here we identified an essential role for the transcription factor Bhlhe41, with a lesser contribution by Bhlhe40, in controlling B-1a cell differentiation. Bhlhe41<sup>-\/-<\/sup>Bhlhe40<sup>-\/-<\/sup> B-1a cells were present at much lower abundance than were their wild-type counterparts. Mutant B-1a cells exhibited an abnormal cell-surface phenotype and altered B cell receptor (BCR) repertoire exemplified by loss of the phosphatidylcholine-specific V<sub>H<\/sub>12V<sub>\u03ba<\/sub>4 BCR. Expression of a pre-rearranged V<sub>H<\/sub>12V<sub>\u03ba<\/sub>4 BCR failed to 'rescue' the mutant phenotype and revealed enhanced proliferation accompanied by increased cell death. Bhlhe41 directly repressed the expression of cell-cycle regulators and inhibitors of BCR signaling while enabling pro-survival cytokine signaling. Thus, Bhlhe41 controls the development, BCR repertoire and self-renewal of B-1a cells.","authors":"Kreslavsky, T., Vilagos, B., Tagoh, H., Poliakova, DK., Schwickert, TA., W\u00f6hner, M., Jaritz, M., Weiss, S., Taneja, R., Rossner, MJ., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Immunol","volume":"18","issue":"4","page":"442-455","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28041881","title":"Nipbl Interacts with Zfp609 and the Integrator Complex to Regulate Cortical Neuron Migration.","abstract":"Mutations in NIPBL are the most frequent cause of Cornelia de Lange syndrome (CdLS), a developmental disorder encompassing several neurological defects, including intellectual disability and seizures. How NIPBL mutations affect brain development is not understood. Here we identify Nipbl as a functional interaction partner of the neural transcription factor Zfp609 in brain development. Depletion of Zfp609 or Nipbl from cortical neural progenitors in\u00a0vivo is detrimental to neuronal migration. Zfp609 and Nipbl overlap at genomic binding sites independently of cohesin and regulate genes that control cortical neuron migration. We find that Zfp609 and\u00a0Nipbl interact with the Integrator complex, which\u00a0functions in RNA polymerase 2 pause release. Indeed, Zfp609 and Nipbl co-localize at gene promoters containing paused RNA polymerase 2, and Integrator similarly regulates neuronal migration. Our data provide a rationale and mechanistic insights for the role of Nipbl in the neurological defects associated with CdLS.","authors":"van den Berg, DLC., Azzarelli, R., Oishi, K., Martynoga, B., Urb\u00e1n, N., Dekkers, DHW., Demmers, JA., Guillemot, F.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Neuron","volume":"93","issue":"2","page":"348-361","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28003466","title":"Ultrastructural anatomy of nodes of Ranvier in the peripheral nervous system as revealed by STED microscopy.","abstract":"We used stimulated emission depletion (STED) superresolution microscopy to analyze the nanoscale organization of 12 glial and axonal proteins at the nodes of Ranvier of teased sciatic nerve fibers. Cytoskeletal proteins of the axon (betaIV spectrin, ankyrin G) exhibit a high degree of one-dimensional longitudinal order at nodal gaps. In contrast, axonal and glial nodal adhesion molecules [neurofascin-186, neuron glial-related cell adhesion molecule (NrCAM)] can arrange in a more complex, 2D hexagonal-like lattice but still feature a \u223c190-nm periodicity. Such a lattice-like organization is also found for glial actin. Sodium and potassium channels exhibit a one-dimensional periodicity, with the Na<sub>v<\/sub> channels appearing to have a lower degree of organization. At paranodes, both axonal proteins (betaII spectrin, Caspr) and glial proteins (neurofascin-155, ankyrin B) form periodic quasi-one-dimensional arrangements, with a high degree of interdependence between the position of the axonal and the glial proteins. The results indicate the presence of mechanisms that finely align the cytoskeleton of the axon with the one of the Schwann cells, both at paranodal junctions (with myelin loops) and at nodal gaps (with microvilli). Taken together, our observations reveal the importance of the lateral organization of proteins at the nodes of Ranvier and pave the way for deeper investigations of the molecular ultrastructural mechanisms involved in action potential propagation, the formation of the nodes, axon-glia interactions, and demyelination diseases.","authors":"D'Este, E., Kamin, D., Balzarotti, F., Hell, SW.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Proc Natl Acad Sci U S A","volume":"114","issue":"2","page":"E191-E199","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27939316","title":"Mechanical Constraints on Flight at High Elevation Decrease Maneuvering Performance of Hummingbirds.","abstract":"High-elevation habitats offer ecological advantages including reduced competition, predation, and parasitism [1]. However, flying organisms at high elevation also face physiological challenges due to lower air density and oxygen availability [2]. These constraints are expected to affect the flight maneuvers that are required to compete with rivals, capture prey, and evade threats [3-5]. To test how individual maneuvering performance is affected by elevation, we measured the free-flight maneuvers of male Anna's hummingbirds in a large chamber translocated to a high-elevation site and then measured their performance at low elevation. We used a multi-camera tracking system to identify thousands of maneuvers based on body position and orientation [6]. At high elevation, the birds' translational velocities, accelerations, and rotational velocities were reduced, and they used less demanding turns. To determine how mechanical and metabolic constraints independently affect performance, we performed a second experiment to evaluate flight maneuvers in an airtight chamber infused with either normoxic heliox, to lower air density, or nitrogen, to lower oxygen availability. The hypodense treatment caused the birds to reduce their accelerations and rotational velocities, whereas the hypoxic treatment had no significant effect on maneuvering performance. Collectively, these experiments reveal how aerial maneuvering performance changes with elevation, demonstrating that as birds move up in elevation, air density constrains their maneuverability prior to any influence of oxygen availability. Our results support the hypothesis that changes in competitive ability at high elevations are the result of mechanical limits to flight performance [7].","authors":"Segre, PS., Dakin, R., Read, TJG., Straw, AD., Altshuler, DL.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Curr Biol","volume":"26","issue":"24","page":"3368-3374","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27374225","title":"Id2 and E Proteins Orchestrate the Initiation and Maintenance of MLL-Rearranged Acute Myeloid Leukemia.","abstract":"E proteins and their antagonists, the Id proteins, are transcriptional regulators important for normal hematopoiesis. We found that Id2 acts as a key regulator of leukemia stem cell (LSC) potential in MLL-rearranged acute myeloid leukemia (AML). Low endogenous Id2 expression is associated with LSC enrichment while Id2 overexpression impairs MLL-AF9-leukemia initiation and growth. Importantly, MLL-AF9 itself controls the E-protein pathway by suppressing Id2 while directly activating E2-2 expression, and E2-2 depletion phenocopies Id2 overexpression in MLL-AF9-AML cells. Remarkably, Id2 tumor-suppressive function is conserved in t(8;21) AML. Low expression of Id2 and its associated gene signature are associated with poor prognosis in MLL-rearranged and t(8;21) AML patients, identifying the Id2\/E-protein axis as a promising new therapeutic target in AML.","authors":"Ghisi, M., Kats, L., Masson, F., Li, J., Kratina, T., Vidacs, E., Gilan, O., Doyle, MA., Newbold, A., Bolden, JE., Fairfax, KA., de Graaf, CA., Firth, M., Zuber, J., Dickins, RA., Corcoran, LM., Dawson, MA., Belz, GT., Johnstone, RW.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cancer Cell","volume":"30","issue":"1","page":"59-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-03-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27856463","title":"CCL2 is a KIT D816V-dependent modulator of the bone marrow microenvironment in systemic mastocytosis.","abstract":"Systemic mastocytosis (SM) is characterized by abnormal accumulation of neoplastic mast cells harboring the activating KIT mutation D816V in the bone marrow and other internal organs. As found in other myeloproliferative neoplasms, increased production of profibrogenic and angiogenic cytokines and related alterations of the bone marrow microenvironment are commonly found in SM. However, little is known about mechanisms and effector molecules triggering fibrosis and angiogenesis in SM. Here we show that KIT D816V promotes expression of the proangiogenic cytokine CCL2 in neoplastic mast cells. Correspondingly, the KIT-targeting drug midostaurin and RNA interference-mediated knockdown of KIT reduced expression of CCL2. We also found that nuclear factor \u03baB contributes to KIT-dependent upregulation of CCL2 in mast cells. In addition, CCL2 secreted by KIT D816V<sup>+<\/sup> mast cells was found to promote the migration of human endothelial cells in vitro. Furthermore, knockdown of CCL2 in neoplastic mast cells resulted in reduced microvessel density and reduced tumor growth in vivo compared with CCL2-expressing cells. Finally, we measured CCL2 serum concentrations in patients with SM and found that CCL2 levels were significantly increased in mastocytosis patients compared with controls. CCL2 serum levels were higher in patients with advanced SM and were found to correlate with poor survival. In summary, we have identified CCL2 as a novel KIT D816V-dependent key regulator of vascular cell migration and angiogenesis in SM. CCL2 expression correlates with disease severity and prognosis. Whether CCL2 may serve as a therapeutic target in advanced SM remains to be determined in forthcoming studies.","authors":"Greiner, G., Witzeneder, N., Berger, A., Schmetterer, K., Eisenwort, G., Schiefer, AI., Roos, S., Popow-Kraupp, T., M\u00fcllauer, L., Zuber, J., Sexl, V., Kenner, L., Sperr, WR., Valent, P., Mayerhofer, M., Hoermann, G.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Blood","volume":"129","issue":"3","page":"371-382","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27851737","title":"Genetic and mechanistic diversity of piRNA 3'-end formation.","abstract":"Small regulatory RNAs guide Argonaute (Ago) proteins in a sequence-specific manner to their targets and therefore have important roles in eukaryotic gene silencing. Of the three small RNA classes, microRNAs and short interfering RNAs are processed from double-stranded precursors into defined 21- to 23-mers by Dicer, an endoribonuclease with intrinsic ruler function. PIWI-interacting RNAs (piRNAs)-the 22-30-nt-long guides for PIWI-clade Ago proteins that silence transposons in animal gonads-are generated independently of Dicer from single-stranded precursors. piRNA 5' ends are defined either by Zucchini, the Drosophila homologue of mitoPLD-a mitochondria-anchored endonuclease, or by piRNA-guided target cleavage. Formation of piRNA 3' ends is poorly understood. Here we report that two genetically and mechanistically distinct pathways generate piRNA 3' ends in Drosophila. The initiating nucleases are either Zucchini or the PIWI-clade proteins Aubergine (Aub) or Ago3. While Zucchini-mediated cleavages directly define mature piRNA 3' ends, Aub\/Ago3-mediated cleavages liberate pre-piRNAs that require extensive resection by the 3'-to-5' exoribonuclease Nibbler (Drosophila homologue of Mut-7). The relative activity of these two pathways dictates the extent to which piRNAs are directed to cytoplasmic or nuclear PIWI-clade proteins and thereby sets the balance between post-transcriptional and transcriptional silencing. Notably, loss of both Zucchini and Nibbler reveals a minimal, Argonaute-driven small RNA biogenesis pathway in which piRNA 5' and 3' ends are directly produced by closely spaced Aub\/Ago3-mediated cleavage events. Our data reveal a coherent model for piRNA biogenesis, and should aid the mechanistic dissection of the processes that govern piRNA 3'-end formation.","authors":"Hayashi, R., Schnabl, J., Handler, D., Mohn, F., Ameres, SL., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nature","volume":"539","issue":"7630","page":"588-592","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27840105","title":"Live Imaging of Axolotl Digit Regeneration Reveals Spatiotemporal Choreography of Diverse Connective Tissue Progenitor Pools.","abstract":"Connective tissues-skeleton, dermis, pericytes, fascia-are a key cell source for regenerating the patterned skeleton during axolotl appendage regeneration. This complexity has made it difficult to identify the cells that regenerate skeletal tissue. Inability to identify these cells has impeded a mechanistic understanding of blastema formation. By tracing cells during digit tip regeneration using brainbow transgenic axolotls, we show that cells from each connective tissue compartment have distinct spatial and temporal profiles of proliferation, migration, and differentiation. Chondrocytes proliferate but do not migrate into the regenerate. In contrast, pericytes proliferate, then migrate into the blastema and give rise solely to pericytes. Periskeletal cells and fibroblasts contribute the bulk of digit blastema cells and acquire diverse fates according to successive waves of migration that choreograph their proximal-distal and tissue contributions. We further show that platelet-derived growth factor signaling is a potent inducer of fibroblast migration, which is required to form the blastema.","authors":"Currie, JD., Kawaguchi, A., Traspas, RM., Schuez, M., Chara, O., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Dev Cell","volume":"39","issue":"4","page":"411-423","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27783592","title":"Transplanted embryonic neurons integrate into adult neocortical circuits.","abstract":"The ability of the adult mammalian brain to compensate for neuronal loss caused by injury or disease is very limited. Transplantation aims to replace lost neurons, but the extent to which new neurons can integrate into existing circuits is unknown. Here, using chronic in vivo two-photon imaging, we show that embryonic neurons transplanted into the visual cortex of adult mice mature into bona fide pyramidal cells with selective pruning of basal dendrites, achieving adult-like densities of dendritic spines and axonal boutons within 4-8 weeks. Monosynaptic tracing experiments reveal that grafted neurons receive area-specific, afferent inputs matching those of pyramidal neurons in the normal visual cortex, including topographically organized geniculo-cortical connections. Furthermore, stimulus-selective responses refine over the course of many weeks and finally become indistinguishable from those of host neurons. Thus, grafted neurons can integrate with great specificity into neocortical circuits that normally never incorporate new neurons in the adult brain.","authors":"Falkner, S., Grade, S., Dimou, L., Conzelmann, KK., Bonhoeffer, T., G\u00f6tz, M., H\u00fcbener, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nature","volume":"539","issue":"7628","page":"248-253","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27775702","title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of\u00a0leukocytes.","abstract":"Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2\/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion.","authors":"Leithner, A., Eichner, A., M\u00fcller, J., Reversat, A., Brown, M., Schwarz, J., Merrin, J., de Gorter, DJ., Schur, F., Bayerl, J., de Vries, I., Wieser, S., Hauschild, R., Lai, FP., Moser, M., Kerjaschki, D., Rottner, K., Small, JV., Stradal, TE., Sixt, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Cell Biol","volume":"18","issue":"11","page":"1253-1259","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27741509","title":"MEK1 is required for the development of NRAS-driven leukemia.","abstract":"The dual-specificity kinases MEK1 and MEK2 act downstream of RAS\/RAF to induce ERK activation, which is generally considered protumorigenic. Activating MEK mutations have not been discovered in leukemia, in which pathway activation is caused by mutations in upstream components such as RAS or Flt3. The anti-leukemic potential of MEK inhibitors is being tested in clinical trials; however, downregulation of MEK1 promotes E\u03bc-Myc-driven lymphomagenesis and MEK1 ablation induces myeloproliferative disease in mice, raising the concern that MEK inhibitors may be inefficient or counterproductive in this context. We investigated the role of MEK1 in the proliferation of human leukemic cell lines and in retroviral models of leukemia. Our data show that MEK1 suppression via RNA interference and genomic engineering does not affect the proliferation of human leukemic cell lines in culture; similarly, MEK1 ablation does not impact the development of MYC-driven leukemia in vivo. In contrast, MEK1 ablation significantly reduces tumorigenesis driven by Nras alone or in combination with Myc. Thus, while MEK1 restricts proliferation and tumorigenesis in some cellular and genetic contexts, it cannot be considered a tumor suppressor in the context of leukemogenesis. On the contrary, its role in NRAS-driven leukemogenesis advocates the use of MEK inhibitors, particularly in combination with PI3K\/AKT inhibitors, in hematopoietic malignancies involving RAS activation.","authors":"Nowacka, JD., Baumgartner, C., Pelorosso, C., Roth, M., Zuber, J., Baccarini, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Oncotarget","volume":"7","issue":"49","page":"80113-80130","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27653700","title":"The Tumor Suppressor Hace1 Is a Critical Regulator of TNFR1-Mediated Cell Fate.","abstract":null,"authors":"Tortola, L., Nitsch, R., Bertrand, MJM., Kogler, M., Redouane, Y., Kozieradzki, I., Uribesalgo, I., Fennell, LM., Daugaard, M., Klug, H., Wirnsberger, G., Wimmer, R., Perlot, T., Sarao, R., Rao, S., Hanada, T., Takahashi, N., Kernbauer, E., Demir\u00f6z, D., Lang, M., Superti-Furga, G., Decker, T., Pichler, A., Ikeda, F., Kroemer, G., Vandenabeele, P., Sorensen, PH., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Rep","volume":"16","issue":"12","page":"3414","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27621061","title":"\u03b2-catenin activity in late hypertrophic chondrocytes locally orchestrates osteoblastogenesis and osteoclastogenesis.","abstract":"Trabecular bone formation is the last step in endochondral ossification. This remodeling process of cartilage into bone involves blood vessel invasion and removal of hypertrophic chondrocytes (HTCs) by chondroclasts and osteoclasts. Periosteal- and chondrocyte-derived osteoprogenitors utilize the leftover mineralized HTC matrix as a scaffold for primary spongiosa formation. Here, we show genetically that \u03b2-catenin (encoded by Ctnnb1), a key component of the canonical Wnt pathway, orchestrates this remodeling process at multiple levels. Conditional inactivation or stabilization of \u03b2-catenin in HTCs by a Col10a1-Cre line locally modulated osteoclastogenesis by altering the Rankl:Opg ratio in HTCs. Lack of \u03b2-catenin resulted in a severe decrease of trabecular bone in the embryonic long bones. Gain of \u03b2-catenin activity interfered with removal of late HTCs and bone marrow formation, leading to a continuous mineralized hypertrophic core in the embryo and resulting in an osteopetrotic-like phenotype in adult mice. Furthermore, \u03b2-catenin activity in late HTCs is required for chondrocyte-derived osteoblastogenesis at the chondro-osseous junction. The latter contributes to the severe trabecular bone phenotype in mutants lacking \u03b2-catenin activity in HTCs.","authors":"Houben, A., Kostanova-Poliakova, D., Weissenb\u00f6ck, M., Graf, J., Teufel, S., von der Mark, K., Hartmann, C.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Development","volume":"143","issue":"20","page":"3826-3838","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27666825","title":"MuSK Kinase Activity is Modulated By A Serine Phosphorylation Site in The Kinase Loop.","abstract":"The neuromuscular junction (NMJ) forms when a motor neuron contacts a muscle fibre. A reciprocal exchange of signals initiates a cascade of signalling events that result in pre- and postsynaptic differentiation. At the centre of these signalling events stands muscle specific kinase (MuSK). MuSK activation, kinase activity and subsequent downstream signalling are crucial for NMJ formation as well as maintenance. Therefore MuSK kinase activity is tightly regulated to ensure proper NMJ development. We have identified a novel serine phosphorylation site at position 751 in MuSK that is increasingly phosphorylated upon agrin stimulation. S751 is also phosphorylated in muscle tissue and its phosphorylation depends on MuSK kinase activity. A phosphomimetic mutant of S751 increases MuSK kinase activity in response to non-saturating agrin concentrations . In addition, basal MuSK and AChR phosphorylation as well as AChR cluster size are increased. We believe that the phosphorylation of S751 provides a novel mechanism to relief the autoinhibition of the MuSK activation loop. Such a lower autoinhibition could foster or stabilize MuSK kinase activation, especially during stages when no or low level of agrin are present. Phosphorylation of S751 might therefore represent a novel mechanism to modulate MuSK kinase activity during prepatterning or NMJ maintenance.","authors":"Camurdanoglu, BZ., Hrovat, C., D\u00fcrnberger, G., Madalinski, M., Mechtler, K., Herbst, R.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Sci Rep","volume":"6","issue":null,"page":"33583","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11984857","title":"Distinct gene expression signatures in the striata of wild-type and heterozygous c-fos knockout mice following methamphetamine administration: evidence from cDNA array analyses.","abstract":"Methamphetamine (METH) is a drug of abuse which can cause apoptosis and degeneration of monoaminergic terminals in the mammalian brain. c-fos appears to play a protective role against METH-induced damage because METH toxicity is exacerbated in c-fos heterozygous knockout mice. In the present study, we used the comprehensive technique of cDNA array to test the idea that heterozygous c-fos knockout mice might show differential METH-induced molecular responses in comparison to wild-type (WT) animals. Of 1,176 genes examined, the expression of 195 genes in either of the two groups of mice was affected by at least 2-fold at 2 or 12 h after METH treatment. More genes were either up- or downregulated in the WT mice. Moreover, there were substantial differences in the pattern of responses between the two genotypes, with more genes involved in DNA repair and protective processes being upregulated in WT mice after METH administration. These results support the idea that the c-fos knockout genotype may render the animals unable to trigger multicomponent responses in order to protect against the multifaceted toxic effects of this illicit neurotoxin.","authors":"Cadet, JL., McCoy, MT., Ladenheim, B.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Synapse","volume":"44","issue":"4","page":"211-26","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1730263","title":"Thymic nurse cell lymphocytes react against self major histocompatibility complex.","abstract":"It has been postulated that thymic nurse cells (TNC), lymphoid-epithelial complexes composed of thymocytes enclosed within major histocompatibility complex (MHC) class I+ and class II+ cortical epithelial cells, may provide an optimal microenvironment for the process of T cell selection. By transplanting single TNC in the avian chorionallantoic membrane assay we demonstrate that a significant portion of intra-TNC lymphocytes (TNC-L) possess reactivity against self-MHC molecules. The frequency of these autoreactive cells among TNC-L exceeds by far that of thymocytes or peripheral blood lymphocytes of the same donor. These results indicate that TNC-L constitute a T cell population enriched for self-MHC reactivity, i.e. cells that have undergone positive selection, but not yet deletion and\/or deactivation.","authors":"Penninger, J., Wick, G.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Eur J Immunol","volume":"22","issue":"1","page":"79-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1992-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27615452","title":"Decrease in newly generated oligodendrocytes leads to motor dysfunctions and changed myelin structures that can be rescued by transplanted cells.","abstract":"NG2-glia in the adult brain are known to proliferate and differentiate into mature and myelinating oligodendrocytes throughout lifetime. However, the role of these newly generated oligodendrocytes in the adult brain still remains little understood. Here we took advantage of the Sox10-iCreER<sup>T2<\/sup> x CAG-eGFP x Esco2<sup>fl\/fl<\/sup> mouse line in which we can specifically ablate proliferating NG2-glia in adult animals. Surprisingly, we observed that the generation of new oligodendrocytes in the adult brain was severely affected, although the number of NG2-glia remained stable due to the enhanced proliferation of non-recombined cells. This lack of oligodendrogenesis led to the elongation of the nodes of Ranvier as well as the associated paranodes, which could be locally rescued by myelinating oligodendrocytes differentiated from transplanted NG2-glia deriving from wildtype mice. Repetitive measurements of conduction velocity in the corpus callosum of awake animals revealed a progressive deceleration specifically in the mice lacking adult oligodendrogenesis that resulted in progressive motor deficits. In summary, here we demonstrated for the first time that axon function is not only controlled by the reliable organization of myelin, but also requires a dynamic and continuous generation of new oligodendrocytes in the adult brain. GLIA 2016;64:2201-2218.","authors":"Schneider, S., Gruart, A., Grade, S., Zhang, Y., Kr\u00f6ger, S., Kirchhoff, F., Eichele, G., Delgado Garc\u00eda, JM., Dimou, L.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Glia","volume":"64","issue":"12","page":"2201-2218","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27606829","title":"LOX Fails to Substitute for RANKL in Osteoclastogenesis.","abstract":"Osteoclasts are the exclusive bone-resorbing cells that have a central role in bone homeostasis as well as bone destruction in cancer and autoimmune disease. Both mouse and human genetic studies have clearly proven that receptor activator of NF-\u03baB ligand (RANKL; encoded by the Tnfsf11 gene) and its receptor RANK are essential for osteoclastogenesis. Although there have been several reports on RANKL-independent osteoclastogenesis, previous studies have never provided in vivo evidence showing RANKL can be substituted by other molecules using RANKL- or RANK-deficient genetic backgrounds. Thus, to date, there is no clear evidence of RANKL-independent osteoclastogenesis and no molecule has ever been proven capable of inducing osteoclast differentiation more efficiently than RANKL. Recently, lysyl oxidase (LOX), the enzyme that mediates collagen cross-linking, has been shown to induce human osteoclasts in the absence of RANKL and has a stronger osteoclastogenic activity than RANKL. Here, we investigated the effect of LOX on osteoclast differentiation using RANKL- and RANK-deficient cells to strictly explore RANKL-independent osteoclastogenesis. CD14<sup>+<\/sup> human peripheral blood cells as well as osteoclast precursor cells derived from wild-type, RANKL- and RANK-deficient mice were treated with RANKL and\/or LOX in short-term (3 days) or long-term (3 weeks) experimental settings. LOX treatment alone did not result in the formation of tartrate-resistant acid phosphatase (TRAP)<sup>+<\/sup> cells or resorption pits in either short-term or long-term culture. In combination with RANKL, long-term treatment with LOX synergistically promoted osteoclastogenesis in cells derived from wild-type mice; however, this was abrogated in RANKL-deficient cells. Long-term treatment with LOX stimulated RANKL expression in mouse bone marrow stromal cells via the production of reactive oxygen species (ROS). Furthermore, LOX injection failed to rescue the phenotype of RANKL-deficient mice. These results suggest that LOX has the ability to induce RANKL expression on stromal cells; however, it fails to substitute for RANKL in osteoclastogenesis. \u00a9 2016 American Society for Bone and Mineral Research.","authors":"Tsukasaki, M., Hamada, K., Okamoto, K., Nagashima, K., Terashima, A., Komatsu, N., Win, SJ., Okamura, T., Nitta, T., Yasuda, H., Penninger, JM., Takayanagi, H.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"J Bone Miner Res","volume":"32","issue":"3","page":"434-439","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27601672","title":"Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6-Bre1.","abstract":"Cotranscriptional ubiquitination of histone H2B is key to gene regulation. The yeast E3 ubiquitin ligase Bre1 (human RNF20\/40) pairs with the E2 ubiquitin conjugating enzyme Rad6 to monoubiquitinate H2B at Lys123. How this single lysine residue on the nucleosome core particle (NCP) is targeted by the Rad6-Bre1 machinery is unknown. Using chemical cross-linking and mass spectrometry, we identified the functional interfaces of Rad6, Bre1, and NCPs in a defined in vitro system. The Bre1 RING domain cross-links exclusively with distinct regions of histone H2B and H2A, indicating a spatial alignment of Bre1 with the NCP acidic patch. By docking onto the NCP surface in this distinct orientation, Bre1 positions the Rad6 active site directly over H2B Lys123. The Spt-Ada-Gcn5 acetyltransferase (SAGA) H2B deubiquitinase module competes with Bre1 for binding to the NCP acidic patch, indicating regulatory control. Our study reveals a mechanism that ensures site-specific NCP ubiquitination and fine-tuning of opposing enzymatic activities.","authors":"Gallego, LD., Ghodgaonkar Steger, M., Polyansky, AA., Schubert, T., Zagrovic, B., Zheng, N., Clausen, T., Herzog, F., K\u00f6hler, A.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Proc Natl Acad Sci U S A","volume":"113","issue":"38","page":"10553-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27524485","title":"CCAN Assembly Configures Composite Binding Interfaces to Promote Cross-Linking of Ndc80 Complexes at the Kinetochore.","abstract":"Partitioning of the genome requires kinetochores, large protein complexes that mediate dynamic attachment of chromosomes to the spindle. Kinetochores contain two supramolecular protein assemblies. The ten-protein KMN network harbors key microtubule-binding sites in the Ndc80 complex and mediates assembly of checkpoint complexes via the KNL-1\/Spc105 protein [1, 2]. As KMN does not contact DNA directly, it relies on different centromere-binding proteins for recruitment and cell-cycle-dependent assembly. These proteins are collectively referred to as the CCAN (constitutive centromere-associated network) [2-4]. The molecular mechanisms by which CCAN subunits associate, however, have remained incompletely defined. In particular, it is unclear how CCAN subunits facilitate the assembly of a microtubule-binding interface that contains multiple Ndc80 molecules bound to different receptors [5]. Here, we dissect molecular mechanisms that underlie targeting of the CCAN subunit Cnn1\/CENP-T to the sequence-determined point centromeres of budding yeast. Systematic quantitative mass spectrometry experiments reveal association dependencies within the yeast CCAN network. We show that evolutionarily conserved residues in the histone-fold domain of Cnn1 are required for the formation of a stable five-subunit CCAN subassembly with the Ctf3 complex. Cnn1 localizes in a Ctf3-dependent manner to the core of the yeast point centromere, overlapping with the yeast CENP-A protein Cse4. By arranging the N-terminal domains of the CCAN subunits Mcm16, Mcm22, and Cnn1 into close proximity, the Ctf3c-Cnn1-Wip1 complex configures a composite interaction site for two molecules of the Ndc80 complex. Our experiments show how cooperative assembly mechanisms organize the microtubule-binding interface of the kinetochore.","authors":"Pekg\u00f6z Altunkaya, G., Malvezzi, F., Demianova, Z., Zimniak, T., Litos, G., Weissmann, F., Mechtler, K., Herzog, F., Westermann, S.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Curr Biol","volume":"26","issue":"17","page":"2370-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27522463","title":"Cryo-EM of Mitotic Checkpoint Complex-Bound APC\/C Reveals Reciprocal and Conformational Regulation of Ubiquitin Ligation.","abstract":"The mitotic checkpoint complex (MCC) coordinates proper chromosome biorientation on the spindle with ubiquitination activities of CDC20-activated anaphase-promoting complex\/cyclosome (APC\/C(CDC20)). APC\/C(CDC20) and two E2s, UBE2C and UBE2S, catalyze ubiquitination through distinct architectures for linking ubiquitin (UB) to substrates and elongating polyUB chains, respectively. MCC, which contains a second molecule of CDC20, blocks APC\/C(CDC20)-UBE2C-dependent ubiquitination of Securin and Cyclins, while differentially determining or inhibiting CDC20 ubiquitination to regulate spindle surveillance, checkpoint activation, and checkpoint\u00a0termination. Here electron microscopy reveals conformational variation of APC\/C(CDC20)-MCC underlying this multifaceted regulation. MCC binds APC\/C-bound CDC20 to inhibit substrate access. However, rotation about the CDC20-MCC assembly and\u00a0conformational variability of APC\/C modulate UBE2C-catalyzed ubiquitination of MCC's CDC20 molecule. Access of UBE2C is limiting for subsequent\u00a0polyubiquitination by UBE2S. We propose that conformational dynamics of APC\/C(CDC20)-MCC modulate E2 activation and determine distinctive ubiquitination activities as part of a response mechanism ensuring accurate sister chromatid segregation.","authors":"Yamaguchi, M., VanderLinden, R., Weissmann, F., Qiao, R., Dube, P., Brown, NG., Haselbach, D., Zhang, W., Sidhu, SS., Peters, JM., Stark, H., Schulman, BA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Mol Cell","volume":"63","issue":"4","page":"593-607","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27487330","title":"CXCR5(+) follicular cytotoxic T cells control viral infection in B cell follicles.","abstract":"During unresolved infections, some viruses escape immunological control and establish a persistant reservoir in certain cell types, such as human immunodeficiency virus (HIV), which persists in follicular helper T cells (TFH cells), and Epstein-Barr virus (EBV), which persists in B cells. Here we identified a specialized group of cytotoxic T cells (TC cells) that expressed the chemokine receptor CXCR5, selectively entered B cell follicles and eradicated infected TFH cells and B cells. The differentiation of these cells, which we have called 'follicular cytotoxic T cells' (TFC cells), required the transcription factors Bcl6, E2A and TCF-1 but was inhibited by the transcriptional regulators Blimp1, Id2 and Id3. Blimp1 and E2A directly regulated Cxcr5 expression and, together with Bcl6 and TCF-1, formed a transcriptional circuit that guided TFC cell development. The identification of TFC cells has far-reaching implications for the development of strategies to control infections that target B cells and TFH cells and to treat B cell-derived malignancies.","authors":"Leong, YA., Chen, Y., Ong, HS., Wu, D., Man, K., Deleage, C., Minnich, M., Meckiff, BJ., Wei, Y., Hou, Z., Zotos, D., Fenix, KA., Atnerkar, A., Preston, S., Chipman, JG., Beilman, GJ., Allison, CC., Sun, L., Wang, P., Xu, J., Toe, JG., Lu, HK., Tao, Y., Palendira, U., Dent, AL., Landay, AL., Pellegrini, M., Comerford, I., McColl, SR., Schacker, TW., Long, HM., Estes, JD., Busslinger, M., Belz, GT., Lewin, SR., Kallies, A., Yu, D.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Immunol","volume":"17","issue":"10","page":"1187-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27466409","title":"Phosphorylation of an HP1-like protein is a prerequisite for heterochromatin body formation in Tetrahymena DNA elimination.","abstract":"Multiple heterochromatic loci are often clustered into a higher order nuclear architecture called a heterochromatin body in diverse eukaryotes. Although phosphorylation of Heterochromatin Protein 1 (HP1) family proteins regulates heterochromatin dynamics, its role in heterochromatin bodies remains unknown. We previously reported that dephosphorylation of the HP1-like protein Pdd1p is required for the formation of heterochromatin bodies during the process of programmed DNA elimination in the ciliated protozoan Tetrahymena Here, we show that the heterochromatin body component Jub4p is required for Pdd1p phosphorylation, heterochromatin body formation, and DNA elimination. Moreover, our analyses of unphosphorylatable Pdd1p mutants demonstrate that Pdd1p phosphorylation is required for heterochromatin body formation and DNA elimination, whereas it is dispensable for local heterochromatin assembly. Therefore, both phosphorylation and the following dephosphorylation of Pdd1p are necessary to facilitate the formation of heterochromatin bodies. We suggest that Jub4p-mediated phosphorylation of Pdd1p creates a chromatin environment that is a prerequisite for subsequent heterochromatin body assembly and DNA elimination.","authors":"Kataoka, K., Noto, T., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Proc Natl Acad Sci U S A","volume":"113","issue":"32","page":"9027-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27428901","title":"Inhibition of CBLB protects from lethal Candida albicans sepsis.","abstract":"Fungal infections claim an estimated 1.5 million lives each year. Mechanisms that protect from fungal infections are still elusive. Recognition of fungal pathogens relies on C-type lectin receptors (CLRs) and their downstream signaling kinase SYK. Here we report that the E3 ubiquitin ligase CBLB controls proximal CLR signaling in macrophages and dendritic cells. We show that CBLB associates with SYK and ubiquitinates SYK, dectin-1, and dectin-2 after fungal recognition. Functionally, CBLB deficiency results in increased inflammasome activation, enhanced reactive oxygen species production, and increased fungal killing. Genetic deletion of Cblb protects mice from morbidity caused by cutaneous infection and markedly improves survival after a lethal systemic infection with Candida albicans. On the basis of these findings, we engineered a cell-permeable CBLB inhibitory peptide that protects mice from lethal C. albicans infections. We thus describe a key role for Cblb in the regulation of innate antifungal immunity and establish a novel paradigm for the treatment of fungal sepsis.","authors":"Wirnsberger, G., Zwolanek, F., Asaoka, T., Kozieradzki, I., Tortola, L., Wimmer, RA., Kavirayani, A., Fresser, F., Baier, G., Langdon, WY., Ikeda, F., Kuchler, K., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nat Med","volume":"22","issue":"8","page":"915-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27426516","title":"Automatic Segmentation of Drosophila Neural Compartments Using GAL4 Expression Data Reveals Novel Visual Pathways.","abstract":"Identifying distinct anatomical structures within the brain and developing genetic tools to target them are fundamental steps for understanding brain function. We hypothesize that enhancer expression patterns can be used to automatically identify functional units such as neuropils and fiber tracts. We used two recent, genome-scale Drosophila GAL4 libraries and associated confocal image datasets to segment large brain regions into smaller subvolumes. Our results (available at https:\/\/strawlab.org\/braincode) support this hypothesis because regions with well-known anatomy, namely the antennal lobes and central complex, were automatically segmented into familiar compartments. The basis for the structural assignment is clustering of voxels based on patterns of enhancer expression. These initial clusters are agglomerated to make hierarchical predictions of structure. We applied the algorithm to central brain regions receiving input from the optic lobes. Based on the automated segmentation and manual validation, we can identify and provide promising driver lines for 11 previously identified and 14 novel types of visual projection neurons and their associated optic glomeruli. The same strategy can be used in other brain regions and likely other species, including vertebrates.","authors":"Panser, K., Tirian, L., Schulze, F., Villalba, S., Jefferis, GSXE., B\u00fchler, K., Straw, AD.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Curr Biol","volume":"26","issue":"15","page":"1943-1954","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27401343","title":"Identification of embryonic precursor cells that differentiate into thymic epithelial cells expressing autoimmune regulator.","abstract":"Medullary thymic epithelial cells (mTECs) expressing autoimmune regulator (Aire) are critical for preventing the onset of autoimmunity. However, the differentiation program of Aire-expressing mTECs (Aire(+) mTECs) is unclear. Here, we describe novel embryonic precursors of Aire(+) mTECs. We found the candidate precursors of Aire(+) mTECs (pMECs) by monitoring the expression of receptor activator of nuclear factor-\u03baB (RANK), which is required for Aire(+) mTEC differentiation. pMECs unexpectedly expressed cortical TEC molecules in addition to the mTEC markers UEA-1 ligand and RANK and differentiated into mTECs in reaggregation thymic organ culture. Introduction of pMECs in the embryonic thymus permitted long-term maintenance of Aire(+) mTECs and efficiently suppressed the onset of autoimmunity induced by Aire(+) mTEC deficiency. Mechanistically, pMECs differentiated into Aire(+) mTECs by tumor necrosis factor receptor-associated factor 6-dependent RANK signaling. Moreover, nonclassical nuclear factor-\u03baB activation triggered by RANK and lymphotoxin-\u03b2 receptor signaling promoted pMEC induction from progenitors exhibiting lower RANK expression and higher CD24 expression. Thus, our findings identified two novel stages in the differentiation program of Aire(+) mTECs.","authors":"Akiyama, N., Takizawa, N., Miyauchi, M., Yanai, H., Tateishi, R., Shinzawa, M., Yoshinaga, R., Kurihara, M., Demizu, Y., Yasuda, H., Yagi, S., Wu, G., Matsumoto, M., Sakamoto, R., Yoshida, N., Penninger, JM., Kobayashi, Y., Inoue, J., Akiyama, T.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Exp Med","volume":"213","issue":"8","page":"1441-58","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27362226","title":"Ki-67 acts as a biological surfactant to disperse mitotic chromosomes.","abstract":"Eukaryotic genomes are partitioned into chromosomes that form compact and spatially well-separated mechanical bodies during mitosis. This enables chromosomes to move independently of each other for segregation of precisely one copy of the genome to each of the nascent daughter cells. Despite insights into the spatial organization of mitotic chromosomes and the discovery of proteins at the chromosome surface, the molecular and biophysical bases of mitotic chromosome structural individuality have remained unclear. Here we report that the proliferation marker protein Ki-67 (encoded by the MKI67 gene), a component of the mitotic chromosome periphery, prevents chromosomes from collapsing into a single chromatin mass after nuclear envelope disassembly, thus enabling independent chromosome motility and efficient interactions with the mitotic spindle. The chromosome separation function of human Ki-67 is not confined within a specific protein domain, but correlates with size and net charge of truncation mutants that apparently lack secondary structure. This suggests that Ki-67 forms a steric and electrostatic charge barrier, similar to surface-active agents (surfactants) that disperse particles or phase-separated liquid droplets in solvents. Fluorescence correlation spectroscopy showed a high surface density of Ki-67 and dual-colour labelling of both protein termini revealed an extended molecular conformation, indicating brush-like arrangements that are characteristic of polymeric surfactants. Our study thus elucidates a biomechanical role of the mitotic chromosome periphery in mammalian cells and suggests that natural proteins can function as surfactants in intracellular compartmentalization.","authors":"Cuylen, S., Blaukopf, C., Politi, AZ., M\u00fcller-Reichert, T., Neumann, B., Poser, I., Ellenberg, J., Hyman, AA., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nature","volume":"535","issue":"7611","page":"308-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27212245","title":"Role of epithelial to mesenchymal transition in hepatocellular carcinoma.","abstract":"The epithelial to mesenchymal transition (EMT) is a multistep biological process whereby epithelial cells change in plasticity by transient de-differentiation into a mesenchymal phenotype. EMT and its reversal, mesenchymal to epithelial transition (MET), essentially occur during embryogenetic morphogenesis and have been increasingly described in fibrosis and cancer during the last decade. In carcinoma progression, EMT plays a crucial role in early steps of metastasis when cells lose cell-cell contacts due to ablation of E-cadherin and acquire increased motility to spread into surrounding or distant tissues. Epithelial plasticity has become a hot issue in hepatocellular carcinoma (HCC), as strong inducers of EMT such as transforming growth factor-\u03b2 are able to orchestrate both fibrogenesis and carcinogenesis, showing rising cytokine levels in cirrhosis and late stage HCC. In this review, we consider the significance of EMT-MET in malignant hepatocytes as well as changes in the plasticity of hepatic stellate cells for cellular heterogeneity of HCC, and further aim at explaining the current limiting insights into EMT by snapshot analyses of HCC tissues. Recent advances in the identification of clinically relevant mechanisms that impinge on important EMT-transcription factors, as well as on miRNAs causing EMT signatures and HCC progression are highlighted. In addition, we draw particular attention to framing EMT in the context of potential clinical relevance for HCC patients. We conclude that some aspects of EMT are still elusive and further studies are required to better link the clinical management of HCC with biomarkers and targeted therapies related to EMT.","authors":"Giannelli, G., Koudelkova, P., Dituri, F., Mikulits, W.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Hepatol","volume":"65","issue":"4","page":"798-808","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27193681","title":"Transcription initiation complex structures elucidate DNA opening.","abstract":"Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8\u2009\u00c5 and 3.6\u2009\u00c5, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.","authors":"Plaschka, C., Hantsche, M., Dienemann, C., Burzinski, C., Plitzko, J., Cramer, P.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Nature","volume":"533","issue":"7603","page":"353-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27165042","title":"The enigmatic meiotic dense body and its newly discovered component, SCML1, are dispensable for fertility and gametogenesis in mice.","abstract":"Meiosis is a critical phase in the life cycle of sexually reproducing organisms. Chromosome numbers are halved during meiosis, which requires meiosis-specific modification of chromosome behaviour. Furthermore, suppression of transposons is particularly important during meiosis to allow the transmission of undamaged genomic information between generations. Correspondingly, specialized genome defence mechanisms and nuclear structures characterize the germ line during meiosis. Survival of mammalian spermatocytes requires that the sex chromosomes form a distinct silenced chromatin domain, called the sex body. An enigmatic spherical DNA-negative structure, called the meiotic dense body, forms in association with the sex body. The dense body contains small non-coding RNAs including microRNAs and PIWI-associated RNAs. These observations gave rise to speculations that the dense body may be involved in sex body formation and or small non-coding RNA functions, e.g. the silencing of transposons. Nevertheless, the function of the dense body has remained mysterious because no protein essential for dense body formation has been reported yet. We discovered that the polycomb-related sex comb on midleg-like 1 (SCML1) is a meiosis-specific protein and is an essential component of the meiotic dense body. Despite abolished dense body formation, Scml1-deficient mice are fertile and proficient in sex body formation, transposon silencing and in timely progression through meiosis and gametogenesis. Thus, we conclude that dense body formation is not an essential component of the gametogenetic program in the mammalian germ line.","authors":"Papanikos, F., Daniel, K., Goercharn-Ramlal, A., Fei, JF., Kurth, T., Wojtasz, L., Dereli, I., Fu, J., Penninger, J., Habermann, B., Surani, A., Stewart, AF., Toth, A.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Chromosoma","volume":"126","issue":"3","page":"399-415","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38467877","title":"Structure of the human 20S U5 snRNP.","abstract":"The 20S U5 small nuclear ribonucleoprotein particle (snRNP) is a 17-subunit RNA-protein complex and a precursor of the U4\/U6.U5 tri-snRNP, the major building block of the precatalytic spliceosome. CD2BP2 is a hallmark protein of the 20S U5 snRNP, absent from the mature tri-snRNP. Here we report a high-resolution cryogenic electron microscopy structure of the 20S U5 snRNP, shedding light on the mutually exclusive interfaces utilized during tri-snRNP assembly and the role of the CD2BP2 in facilitating this process.","authors":"Schneider, S., Brandina, I., Peter, D., Lagad, S., Fraudeau, A., Portell-Montserrat, J., Tholen, J., Zhao, J., Galej, WP.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nat Struct Mol Biol","volume":"31","issue":"5","page":"752-756","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-05-19","doi":"10.1038\/s41594-024-01250-5","first_author":null,"corresponding_authors":null},{"pmid":"11980884","title":"Amino-terminal phosphorylation of c-Jun regulates apoptosis in the retinal ganglion cells by optic nerve transection.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11980884<\/PMID><DateCompleted><Year>2002<\/Year><Month>06<\/Month><Day>03<\/Day><\/DateCompleted><DateRevised><Year>2015<\/Year><Month>11<\/Month><Day>19<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0146-0404<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>43<\/Volume><Issue>5<\/Issue><PubDate><Year>2002<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>Investigative ophthalmology &amp; visual science<\/Title><ISOAbbreviation>Invest Ophthalmol Vis Sci<\/ISOAbbreviation><\/Journal><ArticleTitle>Amino-terminal phosphorylation of c-Jun regulates apoptosis in the retinal ganglion cells by optic nerve transection.<\/ArticleTitle><Pagination><MedlinePgn>1631-5<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"PURPOSE\" NlmCategory=\"OBJECTIVE\">To examine the involvement of c-Jun and c-Jun N-terminal phosphorylation (JNP) in apoptosis of retinal ganglion cells (RGCs) after the optic nerve (ON) transection.","authors":"Yoshida, K., Behrens, A., Le-Niculescu, H., Wagner, EF., Harada, T., Imaki, J., Ohno, S., Karin, M.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Invest Ophthalmol Vis Sci","volume":"43","issue":"5","page":"1631-5","pdf":null,"JrId":"4371","fulltextlink":null,"preprintlink":null,"articledate":"2002-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27114506","title":"biGBac enables rapid gene assembly for the expression of large multisubunit protein complexes.","abstract":"Analyses of protein complexes are facilitated by methods that enable the generation of recombinant complexes via coexpression of their subunits from multigene DNA constructs. However, low experimental throughput limits the generation of such constructs in parallel. Here we describe a method that allows up to 25 cDNAs to be assembled into a single baculoviral expression vector in only two steps. This method, called biGBac, uses computationally optimized DNA linker sequences that enable the efficient assembly of linear DNA fragments, using reactions developed by Gibson for the generation of synthetic genomes. The biGBac method uses a flexible and modular \"mix and match\" approach and enables the generation of baculoviruses from DNA constructs at any assembly stage. Importantly, it is simple, efficient, and fast enough to allow the manual generation of many multigene expression constructs in parallel. We have used this method to generate and characterize recombinant forms of the anaphase-promoting complex\/cyclosome, cohesin, and kinetochore complexes.","authors":"Weissmann, F., Petzold, G., VanderLinden, R., Huis In 't Veld, PJ., Brown, NG., Lampert, F., Westermann, S., Stark, H., Schulman, BA., Peters, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Proc Natl Acad Sci U S A","volume":"113","issue":"19","page":"E2564-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27102484","title":"Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes.","abstract":"Tissue-resident memory T (Trm) cells permanently localize to portals of pathogen entry, where they provide immediate protection against reinfection. To enforce tissue retention, Trm cells up-regulate CD69 and down-regulate molecules associated with tissue egress; however, a Trm-specific transcriptional regulator has not been identified. Here, we show that the transcription factor Hobit is specifically up-regulated in Trm cells and, together with related Blimp1, mediates the development of Trm cells in skin, gut, liver, and kidney in mice. The Hobit-Blimp1 transcriptional module is also required for other populations of tissue-resident lymphocytes, including natural killer T (NKT) cells and liver-resident NK cells, all of which share a common transcriptional program. Our results identify Hobit and Blimp1 as central regulators of this universal program that instructs tissue retention in diverse tissue-resident lymphocyte populations.","authors":"Mackay, LK., Minnich, M., Kragten, NA., Liao, Y., Nota, B., Seillet, C., Zaid, A., Man, K., Preston, S., Freestone, D., Braun, A., Wynne-Jones, E., Behr, FM., Stark, R., Pellicci, DG., Godfrey, DI., Belz, GT., Pellegrini, M., Gebhardt, T., Busslinger, M., Shi, W., Carbone, FR., van Lier, RA., Kallies, A., van Gisbergen, KP.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Science","volume":"352","issue":"6284","page":"459-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27053009","title":"Effects of ACE2 deficiency on physical performance and physiological adaptations of cardiac and skeletal muscle to exercise.","abstract":"The renin-angiotensin system (RAS) is related to physiological adaptations induced by exercise. Angiotensin-converting enzyme (ACE) 2 is a major regulator of the RAS in tissues, as it metabolizes angiotensin (Ang) II to Ang-(1-7). The aim of this study was to determine the effects of ACE2 deficiency on physical performance and physiological adaptations induced by voluntary running. Physical performance, body composition and plasma angiotensin levels, as well as tissue morphology and gene expression of RAS components in the left ventricle (LV) and skeletal muscle (gastrocnemius), were evaluated in ACE2-deficient (ACE2(-\/y)) and wild-type (ACE2(+\/y)) mice after 6 weeks of voluntary wheel running. ACE2(-\/y) mice run less than ACE2(+\/y) mice (19\u00b14.7 vs. 26\u00b112.6 revolutions per day \u00d7 100, P&lt;0.01). The ACE2(+\/y) group presented a lower fat mass (15\u00b11.1%) and higher muscle mass (76.6\u00b11.6%) after 6 weeks of voluntary running compared with the sedentary control group (fat mass: 18.3\u00b12.1%; muscle mass: 72.7\u00b12.2). However, no change in body composition was observed in ACE2(-\/y) mice after exercise. Heart and skeletal muscle hypertrophy was observed only in trained ACE2(+\/y) mice. Besides a small decrease in Ang I in ACE2(-\/y) mice, plasma levels of angiotensin peptides remained unchanged by exercise or ACE2 deficiency. In the LV of trained animals, AT2 gene expression was higher in ACE2(+\/y) compared with ACE2(-\/y) mice. ACE2 deficiency leads to an increase in AT1 gene expression in skeletal muscle. ACE expression in soleus was increased in all exercised groups. ACE2 deficiency affects physical performance and impairs cardiac and skeletal muscle adaptations to exercise.","authors":"Motta-Santos, D., Dos Santos, RA., Oliveira, M., Qadri, F., Poglitsch, M., Mosienko, V., Kappes Becker, L., Campagnole-Santos, MJ., M Penninger, J., Alenina, N., Bader, M.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Hypertens Res","volume":"39","issue":"7","page":"506-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27000493","title":"Directed Assembly and Development of Material-Free Tissues with Complex Architectures.","abstract":"Material-free tissues are assembled using solely cells. Microstructured hydrogel templates and high content screening allow the formation of centimeter-scale tissues with precise architectures. Similar to developing tissues, these contract autonomously, controllably shift shape, self-scaffold by secreting extracellular matrix, and undergo morphogenesis.","authors":"Vrij, E., Rouwkema, J., LaPointe, V., van Blitterswijk, C., Truckenm\u00fcller, R., Rivron, N.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Adv Mater","volume":"28","issue":"21","page":"4032-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11967150","title":"Drosophila Aurora-A is required for centrosome maturation and actin-dependent asymmetric protein localization during mitosis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11967150<\/PMID><DateCompleted><Year>2002<\/Year><Month>10<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>12<\/Volume><Issue>8<\/Issue><PubDate><Year>2002<\/Year><Month>Apr<\/Month><Day>16<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Drosophila Aurora-A is required for centrosome maturation and actin-dependent asymmetric protein localization during mitosis.<\/ArticleTitle><Pagination><MedlinePgn>640-7<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">During asymmetric cell division in the Drosophila nervous system, Numb segregates into one of two daughter cells where it is required for the establishment of the correct cell fate. Numb is uniformly cortical in interphase, but in late prophase, the protein concentrates in the cortical area overlying one of two centrosomes in an actin\/myosin-dependent manner. What triggers the asymmetric localization of Numb at the onset of mitosis is unclear.","authors":"Berdnik, D., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"8","page":"640-7","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-10-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26954065","title":"A de novo frameshift in HNRNPK causing a Kabuki-like syndrome with nodular heterotopia.","abstract":"Kabuki syndrome is a heterogeneous condition characterized by distinctive facial features, intellectual disability, growth retardation, skeletal abnormalities and a range of organ malformations. Although at least two major causative genes have been identified, these do not explain all cases. Here we describe a patient with a complex Kabuki-like syndrome that included nodular heterotopia, in whom testing for several single-gene disorders had proved negative. Exome sequencing uncovered a de novo c.931_932insTT variant in HNRNPK (heterogeneous nuclear ribonucleoprotein K). Although this variant was identified in March 2012, its clinical relevance could only be confirmed following the August 2015 publication of two cases with HNRNPK mutations and an overlapping phenotype that included intellectual disability, distinctive facial dysmorphism and skeletal\/connective tissue abnormalities. Whilst we had attempted (unsuccessfully) to identify additional cases through existing collaborators, the two published cases were 'matched' using GeneMatcher, a web-based tool for connecting researchers and clinicians working on identical genes. Our report therefore exemplifies the importance of such online tools in clinical genetics research and the benefits of periodically reviewing cases with variants of unproven significance. Our study also suggests that loss of function variants in HNRNPK should be considered as a molecular basis for patients with Kabuki-like syndrome.","authors":"Lange, L., Pagnamenta, AT., Lise, S., Clasper, S., Stewart, H., Akha, ES., Quaghebeur, G., Knight, SJ., Keays, DA., Taylor, JC., Kini, U.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Clin Genet","volume":"90","issue":"3","page":"258-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26903504","title":"Mutations in the murine homologue of TUBB5 cause microcephaly by perturbing cell cycle progression and inducing p53-associated apoptosis.","abstract":"Microtubules play a crucial role in the generation, migration and differentiation of nascent neurons in the developing vertebrate brain. Mutations in the constituents of microtubules, the tubulins, are known to cause an array of neurological disorders, including lissencephaly, polymicrogyria and microcephaly. In this study we explore the genetic and cellular mechanisms that cause TUBB5-associated microcephaly by exploiting two new mouse models: a conditional E401K knock-in, and a conditional knockout animal. These mice present with profound microcephaly due to a loss of upper-layer neurons that correlates with massive apoptosis and upregulation of p53. This phenotype is associated with a delay in cell cycle progression and ectopic DNA elements in progenitors, which is dependent on the dosage of functional Tubb5. Strikingly, we report ectopic Sox2-positive progenitors and defects in spindle orientation in our knock-in mouse line, which are absent in knockout animals. This work sheds light on the functional repertoire of Tubb5, reveals that the E401K mutation acts by a complex mechanism, and demonstrates that the cellular pathology driving TUBB5-associated microcephaly is cell death.","authors":"Breuss, M., Fritz, T., Gstrein, T., Chan, K., Ushakova, L., Yu, N., Vonberg, FW., Werner, B., Elling, U., Keays, DA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Development","volume":"143","issue":"7","page":"1126-33","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26876168","title":"C.\u00a0elegans Body Cavity Neurons Are Homeostatic Sensors that Integrate Fluctuations in Oxygen Availability and Internal Nutrient Reserves.","abstract":"It is known that internal physiological state, or interoception, influences CNS function and behavior. However, the neurons and mechanisms that integrate sensory information with internal physiological state remain largely unknown. Here, we identify C.\u00a0elegans body cavity neurons called URX(L\/R) as central homeostatic sensors that integrate fluctuations in oxygen availability with internal metabolic state. We show that depletion of internal body fat reserves increases the tonic activity of URX neurons, which influences the magnitude of the evoked sensory response to oxygen. These responses are integrated via intracellular cGMP and Ca(2+). The extent of neuronal activity thus reflects the balance between the perception of oxygen and available fat reserves. The URX homeostatic sensor ensures that neural signals that stimulate fat loss are only deployed when there are sufficient fat reserves to do so. Our results uncover an interoceptive neuroendocrine axis that relays internal state information to the nervous system.","authors":"Witham, E., Comunian, C., Ratanpal, H., Skora, S., Zimmer, M., Srinivasan, S.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Rep","volume":"14","issue":"7","page":"1641-1654","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26659640","title":"Functional Recovery of a Human Neonatal Heart After Severe Myocardial Infarction.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">26659640<\/PMID><DateCompleted><Year>2016<\/Year><Month>06<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2016<\/Year><Month>02<\/Month><Day>03<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4571<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>118<\/Volume><Issue>2<\/Issue><PubDate><Year>2016<\/Year><Month>Jan<\/Month><Day>22<\/Day><\/PubDate><\/JournalIssue><Title>Circulation research<\/Title><ISOAbbreviation>Circ Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Functional Recovery of a Human Neonatal Heart After Severe Myocardial Infarction.<\/ArticleTitle><Pagination><MedlinePgn>216-21<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/CIRCRESAHA.115.307017<\/ELocationID><Abstract><AbstractText Label=\"RATIONALE\" NlmCategory=\"BACKGROUND\">Cardiac remodeling and subsequent heart failure remain critical issues after myocardial infarction despite improved treatment and reperfusion strategies. Recently, cardiac regeneration has been demonstrated in fish and newborn mice after apex resection or cardiac infarctions. Two key issues remain to translate findings in model organisms to future therapies in humans: what is the mechanism and can cardiac regeneration indeed occur in newborn humans?","authors":"Haubner, BJ., Schneider, J., Schweigmann, U., Schuetz, T., Dichtl, W., Velik-Salchner, C., Stein, JI., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Circ Res","volume":"118","issue":"2","page":"216-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26644564","title":"Human cerebral organoids recapitulate gene expression programs of fetal neocortex development.","abstract":"Cerebral organoids-3D cultures of human cerebral tissue derived from pluripotent stem cells-have emerged as models of human cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed in vivo remains unclear. Here we use single-cell RNA sequencing (scRNA-seq) to dissect and compare cell composition and progenitor-to-neuron lineage relationships in human cerebral organoids and fetal neocortex. Covariation network analysis using the fetal neocortex data reveals known and previously unidentified interactions among genes central to neural progenitor proliferation and neuronal differentiation. In the organoid, we detect diverse progenitors and differentiated cell types of neuronal and mesenchymal lineages and identify cells that derived from regions resembling the fetal neocortex. We find that these organoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue to organize into cerebral cortex-like regions. Our comparison of in vivo and in vitro cortical single-cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures.","authors":"Camp, JG., Badsha, F., Florio, M., Kanton, S., Gerber, T., Wilsch-Br\u00e4uninger, M., Lewitus, E., Sykes, A., Hevers, W., Lancaster, M., Knoblich, JA., Lachmann, R., P\u00e4\u00e4bo, S., Huttner, WB., Treutlein, B.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Proc Natl Acad Sci U S A","volume":"112","issue":"51","page":"15672-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26535604","title":"Comprehensive Cross-Linking Mass Spectrometry Reveals Parallel Orientation and Flexible Conformations of Plant HOP2-MND1.","abstract":"The HOP2-MND1 heterodimer is essential for meiotic homologous recombination in plants and other eukaryotes and promotes the repair of DNA double-strand breaks. We investigated the conformational flexibility of HOP2-MND1, important for understanding the mechanistic details of the heterodimer, with chemical cross-linking in combination with mass spectrometry (XL-MS). The final XL-MS workflow encompassed the use of complementary cross-linkers, quenching, digestion, size exclusion enrichment, and HCD-based LC-MS\/MS detection prior to data evaluation. We applied two different homobifunctional amine-reactive cross-linkers (DSS and BS(2)G) and one zero-length heterobifunctional cross-linker (EDC). Cross-linked peptides of four biological replicates were analyzed prior to 3D structure prediction by protein threading and protein-protein docking for cross-link-guided molecular modeling. Miniaturization of the size-exclusion enrichment step reduced the required starting material, led to a high amount of cross-linked peptides, and allowed the analysis of replicates. The major interaction site of HOP2-MND1 was identified in the central coiled-coil domains, and an open colinear parallel arrangement of HOP2 and MND1 within the complex was predicted. Moreover, flexibility of the C-terminal capping helices of both complex partners was observed, suggesting the coexistence of a closed complex conformation in solution.","authors":"Rampler, E., Stranzl, T., Orban-Nemeth, Z., Hollenstein, DM., Hudecz, O., Schl\u00f6gelhofer, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Proteome Res","volume":"14","issue":"12","page":"5048-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26477366","title":"Spatial Regulation of V-(D)J Recombination at Antigen Receptor Loci.","abstract":"Lymphocytes express a diverse repertoire of antigen receptors, which are able to recognize a large variety of foreign pathogens. Functional antigen receptor genes are assembled by V(D)J recombination in immature B cells (Igh and Igk) and T cells (Tcr b and Tcra\/d). V(D)J recombination takes place in the 3' proximal domain containing the D, J, and C gene segments, whereas 31 (Tcrb) to 200 (Igh) V genes are spread over a large region of 0.67 (Tcrb) to 3 (Igk) megabase pairs. The spatial regulation of V(D)J recombination has been best studied for the Igh locus, which undergoes reversible contraction by long-range looping in pro-B cells. This large-scale contraction brings distantly located VH genes into close proximity of the DJH-rearranged gene segment, which facilitates VH-DJH recombination. The B-cell-specific Pax5, ubiquitous YY1, and architectural CTCF\/cohesin proteins regulate Igh locus contraction in pro-B cells by binding to multiple sites in the VH gene cluster. These regulators also control the pro-B-cell-specific activity of the distally located PAIR elements, which may be involved in the regulation of VH-DJH recombination by promoting locus contraction. Moreover, the large VH gene cluster of the Igh locus undergoes flexible long-range looping, which guarantees similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire. Importantly, long-range looping is a more general regulatory principle, as other antigen receptor loci also undergo reversible contraction at the developmental stage, where they engage in V-(D)J recombination.","authors":"Ebert, A., Hill, L., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Adv Immunol","volume":"128","issue":null,"page":"93-121","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26460345","title":"Exploring the emerging complexity in transcriptional regulation of energy homeostasis.","abstract":"Obesity and its associated diseases are expected to affect more than 1 billion people by the year 2030. These figures have sparked intensive research into the molecular control of food intake, nutrient distribution, storage and metabolism--processes that are collectively termed energy homeostasis. Recent decades have also seen dramatic developments in our understanding of gene regulation at the signalling, chromatin and post-transcriptional levels. The seemingly exponential growth in this complexity now poses a major challenge for translational researchers in need of simplified but accurate paradigms for clinical use. In this Review, we consider the current understanding of transcriptional control of energy homeostasis, including both transcriptional and epigenetic regulators, and crosstalk between pathways. We also provide insights into emerging developments and challenges in this field.","authors":"Lempradl, A., Pospisilik, JA., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Rev Genet","volume":"16","issue":"11","page":"665-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26637975","title":"Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type.","abstract":"Circumferential skin creases Kunze type (CSC-KT) is a specific congenital entity with an unknown genetic cause. The disease phenotype comprises characteristic circumferential skin creases accompanied by intellectual disability, a cleft palate, short stature, and dysmorphic features. Here, we report that mutations in either MAPRE2 or TUBB underlie the genetic origin of this syndrome. MAPRE2 encodes a member of the microtubule end-binding family of proteins that bind to the guanosine triphosphate cap at growing microtubule plus ends, and TUBB encodes a \u03b2-tubulin isotype that is expressed abundantly in the developing brain. Functional analyses of the TUBB mutants show multiple defects in the chaperone-dependent tubulin heterodimer folding and assembly pathway that leads to a compromised yield of native heterodimers. The TUBB mutations also have an impact on microtubule dynamics. For MAPRE2, we show that the mutations result in enhanced MAPRE2 binding to microtubules, implying an increased dwell time at microtubule plus ends. Further, in vivo analysis of MAPRE2 mutations in a zebrafish model of craniofacial development shows that the variants most likely perturb the patterning of branchial arches, either through excessive activity (under a recessive paradigm) or through haploinsufficiency (dominant de novo paradigm). Taken together, our data add CSC-KT to the growing list of tubulinopathies and highlight how multiple inheritance paradigms can affect dosage-sensitive biological systems so as to result in the same clinical defect.","authors":"Isrie, M., Breuss, M., Tian, G., Hansen, AH., Cristofoli, F., Morandell, J., Kupchinsky, ZA., Sifrim, A., Rodriguez-Rodriguez, CM., Dapena, EP., Doonanco, K., Leonard, N., Tinsa, F., Moortgat, S., Ulucan, H., Koparir, E., Karaca, E., Katsanis, N., Marton, V., Vermeesch, JR., Davis, EE., Cowan, NJ., Keays, DA., Van Esch, H.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Am J Hum Genet","volume":"97","issue":"6","page":"790-800","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26444240","title":"Alternative transcription initiation leads to expression of a novel ALK isoform in cancer.","abstract":"Activation of oncogenes by mechanisms other than genetic aberrations such as mutations, translocations, or amplifications is largely undefined. Here we report a novel isoform of the anaplastic lymphoma kinase (ALK) that is expressed in \u223c11% of melanomas and sporadically in other human cancer types, but not in normal tissues. The novel ALK transcript initiates from a de novo alternative transcription initiation (ATI) site in ALK intron 19, and was termed ALK(ATI). In ALK(ATI)-expressing tumours, the ATI site is enriched for H3K4me3 and RNA polymerase II, chromatin marks characteristic of active transcription initiation sites. ALK(ATI) is expressed from both ALK alleles, and no recurrent genetic aberrations are found at the ALK locus, indicating that the transcriptional activation is independent of genetic aberrations at the ALK locus. The ALK(ATI) transcript encodes three proteins with molecular weights of 61.1, 60.8 and 58.7 kilodaltons, consisting primarily of the intracellular tyrosine kinase domain. ALK(ATI) stimulates multiple oncogenic signalling pathways, drives growth-factor-independent cell proliferation in vitro, and promotes tumorigenesis in vivo in mouse models. ALK inhibitors can suppress the kinase activity of ALK(ATI), suggesting that patients with ALK(ATI)-expressing tumours may benefit from ALK inhibitors. Our findings suggest a novel mechanism of oncogene activation in cancer through de novo alternative transcription initiation.","authors":"Wiesner, T., Lee, W., Obenauf, AC., Ran, L., Murali, R., Zhang, QF., Wong, EW., Hu, W., Scott, SN., Shah, RH., Landa, I., Button, J., Lailler, N., Sboner, A., Gao, D., Murphy, DA., Cao, Z., Shukla, S., Hollmann, TJ., Wang, L., Borsu, L., Merghoub, T., Schwartz, GK., Postow, MA., Ariyan, CE., Fagin, JA., Zheng, D., Ladanyi, M., Busam, KJ., Berger, MF., Chen, Y., Chi, P.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nature","volume":"526","issue":"7573","page":"453-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38906097","title":"Developmental and stem cell biology's bright future.","abstract":"The next 50 years of developmental biology will illuminate exciting new discoveries but are also poised to provide solutions to important problems society faces. Ten scientists whose work intersects with developmental biology in various capacities tell us about their vision for the future.","authors":"Lewis, J., Schuh, M., Hanna, JH., Zernicka-Goetz, M., Srivastava, M., Tan, T., Behjati, S., Liu, Z., Petridou, NI., Mendjan, S.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Cell","volume":"187","issue":"13","page":"3224-3228","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-21","doi":"10.1016\/j.cell.2024.05.037","first_author":null,"corresponding_authors":null},{"pmid":"26317470","title":"A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation.","abstract":"Many proteins contain disordered regions of low-sequence complexity, which cause aging-associated diseases because they are prone to aggregate. Here, we study FUS, a prion-like protein containing intrinsically disordered domains associated with the neurodegenerative disease ALS. We show that, in cells, FUS forms liquid compartments at sites of DNA damage and in the cytoplasm upon stress. We confirm this by reconstituting liquid FUS compartments in vitro. Using an in vitro \"aging\" experiment, we demonstrate that liquid droplets of FUS protein convert with time from a liquid to an aggregated state, and this conversion is accelerated by patient-derived mutations. We conclude that the physiological role of FUS requires forming dynamic liquid-like compartments. We propose that liquid-like compartments carry the trade-off between functionality and risk of aggregation and that aberrant phase transitions within liquid-like compartments lie at the heart of ALS and, presumably, other age-related diseases.","authors":"Patel, A., Lee, HO., Jawerth, L., Maharana, S., Jahnel, M., Hein, MY., Stoynov, S., Mahamid, J., Saha, S., Franzmann, TM., Pozniakovski, A., Poser, I., Maghelli, N., Royer, LA., Weigert, M., Myers, EW., Grill, S., Drechsel, D., Hyman, AA., Alberti, S.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell","volume":"162","issue":"5","page":"1066-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26350455","title":"G0\/G1 Switch Gene 2 Regulates Cardiac Lipolysis.","abstract":"The anabolism and catabolism of myocardial triacylglycerol (TAG) stores are important processes for normal cardiac function. TAG synthesis detoxifies and stockpiles fatty acids to prevent lipotoxicity, whereas TAG hydrolysis (lipolysis) remobilizes fatty acids from endogenous storage pools as energy substrates, signaling molecules, or precursors for complex lipids. This study focused on the role of G0\/G1 switch 2 (G0S2) protein, which was previously shown to inhibit the principal TAG hydrolase adipose triglyceride lipase (ATGL), in the regulation of cardiac lipolysis. Using wild-type and mutant mice, we show the following: (i) G0S2 is expressed in the heart and regulated by the nutritional status with highest expression levels after re-feeding. (ii) Cardiac-specific overexpression of G0S2 inhibits cardiac lipolysis by direct protein-protein interaction with ATGL. This leads to severe cardiac steatosis. The steatotic hearts caused by G0S2 overexpression are less prone to fibrotic remodeling or cardiac dysfunction than hearts with a lipolytic defect due to ATGL deficiency. (iii) Conversely to the phenotype of transgenic mice, G0S2 deficiency results in a de-repression of cardiac lipolysis and decreased cardiac TAG content. We conclude that G0S2 acts as a potent ATGL inhibitor in the heart modulating cardiac substrate utilization by regulating cardiac lipolysis.","authors":"Heier, C., Radner, FP., Moustafa, T., Schreiber, R., Grond, S., Eichmann, TO., Schweiger, M., Schmidt, A., Cerk, IK., Oberer, M., Theussl, HC., Wojciechowski, J., Penninger, JM., Zimmermann, R., Zechner, R.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Biol Chem","volume":"290","issue":"43","page":"26141-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26315885","title":"New Insights into the Role of Ubiquitin Networks in the Regulation of Antiapoptosis Pathways.","abstract":"Ubiquitin is a small modifier protein that conjugates on lysine (Lys) residues of substrates, and it can be targeted by another ubiquitin molecule to form chains through conjugation on the intrinsic Lys residues and methionine (Met) 1 residue. Ubiquitination of substrates by such chains determines the fate of substrates, thereby influencing various biological processes. In this chapter, we focus on apoptosis with an emphasis on the regulation by ubiquitination. The signal transduction of apoptosis is governed not only by the classical function of ubiquitin, which is proteasome-dependent degradation of substrates, but also by the apoptosis signaling complex formation guided by different types of ubiquitin chains. Ubiquitinations of pro- and antiapoptotic proteins are tightly regulated by particular sets of enzymes, such as ubiquitin E3 ligases and deubiquitinases (DUBs). We further discuss ubiquitination in the tumor necrosis factor (TNF) signaling pathway as an example for the ubiquitin-dependent regulation of apoptosis and cell survival.","authors":"Asaoka, T., Ikeda, F.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Int Rev Cell Mol Biol","volume":"318","issue":null,"page":"121-58","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26254932","title":"Measuring APC\/C-Dependent Ubiquitylation In Vitro.","abstract":"The anaphase-promoting complex\/cyclosome (APC\/C) is a 1.2 MDa ubiquitin ligase complex with important functions in both proliferating and post-mitotic differentiated cells. In proliferating cells, APC\/C controls cell cycle progression by targeting inhibitors of chromosome segregation and mitotic exit for degradation by the 26S proteasome. To understand how APC\/C recruits and ubiquitylates its substrate proteins and how these processes are controlled, it is essential to analyze APC\/C activity in vitro. In the past, such experiments have been limited by the fact that large quantities of purified APC\/C were difficult to obtain and that mutated versions of the APC\/C could not be easily generated. In this chapter we review recent advances in generating and purifying recombinant forms of the human APC\/C and its co-activators, using methods that are scalable and compatible with mutagenesis. We also describe a method that allows the quantitative analysis of APC\/C activity using fluorescently labeled substrate proteins.","authors":"Jarvis, MA., Brown, NG., Watson, ER., VanderLinden, R., Schulman, BA., Peters, JM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Methods Mol Biol","volume":"1342","issue":null,"page":"287-303","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26299517","title":"The Deubiquitinase USP37 Regulates Chromosome Cohesion and Mitotic Progression.","abstract":"A bipolar mitotic spindle facilitates the equal segregation of chromosomes to two daughter cells. To achieve bipolar attachment of microtubules to kinetochores of sister chromatids, chromatids must remain paired after replication. This cohesion is mediated by the conserved cohesin complex comprised of SMC1, SMC3, SCC1, and either SA1 or SA2 in humans. Because defects in spindle assembly or sister chromatid cohesion can lead to aneuploidy in daughter cells, proper regulation of these processes is essential for fidelity in chromosome segregation. In an RNAi screen for regulators of spindle assembly, we identify the deubiquitinase USP37 as a regulator of mitotic progression, centrosome integrity, and chromosome alignment. USP37 associates with cohesin and contributes to sister chromatid resolution. Cohesion defects are rescued by expression of an RNAi-resistant USP37, but not the catalytically impaired USP37(C350A) mutant. Further, USP37 associates with WAPL, a negative regulator of cohesion necessary for cohesin release in prophase, in a manner dependent on USP37's second and third ubiquitin-interacting motifs. Depletion of USP37 reduces the stability of chromatin-associated WAPL and increases the fraction of WAPL that is more heavily ubiquitylated in mitosis. Consistently, overexpression of USP37(C350A) results in increased modification of WAPL, and addition of purified USP37(WT), but not USP37(C350A), to WAPL immunoprecipitates results in a reduction of ubiquitylated products. Taken together, our results ascribe a novel function for USP37 in mitotic progression and further suggest that USP37 positively regulates the stability of chromatin-associated WAPL to facilitate sister chromatid resolution.","authors":"Yeh, C., Coyaud, \u00c9., Bashkurov, M., van der Lelij, P., Cheung, SW., Peters, JM., Raught, B., Pelletier, L.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Curr Biol","volume":"25","issue":"17","page":"2290-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26317468","title":"The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression.","abstract":"Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription, and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31\/Med7N submodule. TREX-2 regulates assembly of Mediator with the Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent at specific genes. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing. Our data provide mechanistic insight into how an NPC-associated adaptor complex accesses the core transcription machinery.","authors":"Schneider, M., Hellerschmied, D., Schubert, T., Amlacher, S., Vinayachandran, V., Reja, R., Pugh, BF., Clausen, T., K\u00f6hler, A.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell","volume":"162","issue":"5","page":"1016-28","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26237227","title":"ProteoPlex: stability optimization of macromolecular complexes by sparse-matrix screening of chemical space.","abstract":"Molecular machines or macromolecular complexes are supramolecular assemblies of biomolecules with a variety of functions. Structure determination of these complexes in a purified state is often tedious owing to their compositional complexity and the associated relative structural instability. To improve the stability of macromolecular complexes in vitro, we present a generic method that optimizes the stability, homogeneity and solubility of macromolecular complexes by sparse-matrix screening of their thermal unfolding behavior in the presence of various buffers and small molecules. The method includes the automated analysis of thermal unfolding curves based on a biophysical unfolding model for complexes. We found that under stabilizing conditions, even large multicomponent complexes reveal an almost ideal two-state unfolding behavior. We envisage an improved biochemical understanding of purified macromolecules as well as a substantial boost in successful macromolecular complex structure determination by both X-ray crystallography and cryo-electron microscopy.","authors":"Chari, A., Haselbach, D., Kirves, JM., Ohmer, J., Paknia, E., Fischer, N., Ganichkin, O., M\u00f6ller, V., Frye, JJ., Petzold, G., Jarvis, M., Tietzel, M., Grimm, C., Peters, JM., Schulman, BA., Tittmann, K., Markl, J., Fischer, U., Stark, H.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Methods","volume":"12","issue":"9","page":"859-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26208905","title":"Metastatic Competence Can Emerge with Selection of Preexisting Oncogenic Alleles without a Need of New Mutations.","abstract":"Several experimental models faithfully recapitulate many important facets of human metastatic disease. Here, we have performed whole-exome sequencing in five widely used experimental metastasis models that were independently derived through in vivo selection from heterogeneous human cancer cell lines. In addition to providing an important characterization of these model systems, our study examines the genetic evolution of metastatic phenotypes. We found that in vivo selected highly metastatic cell populations showed little genetic divergence from the corresponding parental population. However, selection of genetic variations that preexisted in parental populations, including the well-established oncogenic mutations KRAS(G13D) and BRAF(G464V), was associated with increased metastatic capability. Conversely, expression of the wild-type BRAF allele in metastatic cells inhibited metastatic outgrowth as well as tumor initiation in mice. Our findings establish that metastatic competence can arise from heterogeneous cancer cell populations without the need for acquisition of additional mutations and that such competence can benefit from further selection of tumor-initiating mutations that seed primary tumorigenesis.","authors":"Jacob, LS., Vanharanta, S., Obenauf, AC., Pirun, M., Viale, A., Socci, ND., Massagu\u00e9, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cancer Res","volume":"75","issue":"18","page":"3713-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26195726","title":"CHMP5 controls bone turnover rates by dampening NF-\u03baB activity in osteoclasts.","abstract":"Physiological bone remodeling requires that bone formation by osteoblasts be tightly coupled to bone resorption by osteoclasts. However, relatively little is understood about how this coupling is regulated. Here, we demonstrate that modulation of NF-\u03baB signaling in osteoclasts via a novel activity of charged multivesicular body protein 5 (CHMP5) is a key determinant of systemic rates of bone turnover. A conditional deletion of CHMP5 in osteoclasts leads to increased bone resorption by osteoclasts coupled with exuberant bone formation by osteoblasts, resembling an early onset, polyostotic form of human Paget's disease of bone (PDB). These phenotypes are reversed by haploinsufficiency for Rank, as well as by antiresorptive treatments, including alendronate, zolendronate, and OPG-Fc. Accordingly, CHMP5-deficient osteoclasts display increased RANKL-induced NF-\u03baB activation and osteoclast differentiation. Biochemical analysis demonstrated that CHMP5 cooperates with the PDB genetic risk factor valosin-containing protein (VCP\/p97) to stabilize the inhibitor of NF-\u03baB\u03b1 (I\u03baB\u03b1), down-regulating ubiquitination of I\u03baB\u03b1 via the deubiquitinating enzyme USP15. Thus, CHMP5 tunes NF-\u03baB signaling downstream of RANK in osteoclasts to dampen osteoclast differentiation, osteoblast coupling and bone turnover rates, and disruption of CHMP5 activity results in a PDB-like skeletal disorder.","authors":"Greenblatt, MB., Park, KH., Oh, H., Kim, JM., Shin, DY., Lee, JM., Lee, JW., Singh, A., Lee, KY., Hu, D., Xiao, C., Charles, JF., Penninger, JM., Lotinun, S., Baron, R., Ghosh, S., Shim, JH.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Exp Med","volume":"212","issue":"8","page":"1283-301","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26160380","title":"MUCOSAL IMMUNOLOGY. The microbiota regulates type 2 immunity through ROR\u03b3t\u207a T cells.","abstract":"Changes to the symbiotic microbiota early in life, or the absence of it, can lead to exacerbated type 2 immunity and allergic inflammations. Although it is unclear how the microbiota regulates type 2 immunity, it is a strong inducer of proinflammatory T helper 17 (T(H)17) cells and regulatory T cells (T(regs)) in the intestine. Here, we report that microbiota-induced T(regs) express the nuclear hormone receptor ROR\u03b3t and differentiate along a pathway that also leads to T(H)17 cells. In the absence of ROR\u03b3t(+) T(regs), T(H)2-driven defense against helminths is more efficient, whereas T(H)2-associated pathology is exacerbated. Thus, the microbiota regulates type 2 responses through the induction of type 3 ROR\u03b3t(+) T(regs) and T(H)17 cells and acts as a key factor in balancing immune responses at mucosal surfaces.","authors":"Ohnmacht, C., Park, JH., Cording, S., Wing, JB., Atarashi, K., Obata, Y., Gaboriau-Routhiau, V., Marques, R., Dulauroy, S., Fedoseeva, M., Busslinger, M., Cerf-Bensussan, N., Boneca, IG., Voehringer, D., Hase, K., Honda, K., Sakaguchi, S., Eberl, G.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Science","volume":"349","issue":"6251","page":"989-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26145176","title":"Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila.","abstract":"Uridylation of RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small RNA biogenesis and stability in plants, worms, and mammals. Here, we report Tailor, an uridylyltransferase that is required for the majority of 3' end modifications of microRNAs in Drosophila and predominantly targets precursor hairpins. Uridylation modulates the characteristic two-nucleotide 3' overhang of microRNA hairpins, which regulates processing by Dicer-1 and destabilizes RNA hairpins. Tailor preferentially uridylates mirtron hairpins, thereby impeding the production of non-canonical microRNAs. Mirtron selectivity is explained by primary sequence specificity of Tailor, selecting substrates ending with a 3' guanosine. In contrast to mirtrons, conserved Drosophila precursor microRNAs are significantly depleted in 3' guanosine, thereby escaping regulatory uridylation. Our data support the hypothesis that evolutionary adaptation to Tailor-directed uridylation shapes the nucleotide composition of precursor microRNA 3' ends. Hence, hairpin uridylation may serve as a barrier for the de novo creation of microRNAs in Drosophila.","authors":"Reim\u00e3o-Pinto, MM., Ignatova, V., Burkard, TR., Hung, JH., Manzenreither, RA., Sowemimo, I., Herzog, VA., Reichholf, B., Fari\u00f1a-Lopez, S., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Mol Cell","volume":"59","issue":"2","page":"203-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26124239","title":"Xanthomonas campestris pv. vesicatoria Secretes Proteases and Xylanases via the Xps Type II Secretion System and Outer Membrane Vesicles.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">26124239<\/PMID><DateCompleted><Year>2015<\/Year><Month>10<\/Month><Day>27<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>12<\/Month><Day>02<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1098-5530<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>197<\/Volume><Issue>17<\/Issue><PubDate><Year>2015<\/Year><Month>Sep<\/Month><\/PubDate><\/JournalIssue><Title>Journal of bacteriology<\/Title><ISOAbbreviation>J Bacteriol<\/ISOAbbreviation><\/Journal><ArticleTitle>Xanthomonas campestris pv. vesicatoria Secretes Proteases and Xylanases via the Xps Type II Secretion System and Outer Membrane Vesicles.<\/ArticleTitle><Pagination><MedlinePgn>2879-93<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1128\/JB.00322-15<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Many plant-pathogenic bacteria utilize type II secretion (T2S) systems to secrete degradative enzymes into the extracellular milieu. T2S substrates presumably mediate the degradation of plant cell wall components during the host-pathogen interaction and thus promote bacterial virulence. Previously, the Xps-T2S system from Xanthomonas campestris pv. vesicatoria was shown to contribute to extracellular protease activity and the secretion of a virulence-associated xylanase. The identities and functions of additional T2S substrates from X. campestris pv. vesicatoria, however, are still unknown. In the present study, the analysis of 25 candidate proteins from X. campestris pv. vesicatoria led to the identification of two type II secreted predicted xylanases, a putative protease and a lipase which was previously identified as a virulence factor of X. campestris pv. vesicatoria. Studies with mutant strains revealed that the identified xylanases and the protease contribute to virulence and in planta growth of X. campestris pv. vesicatoria. When analyzed in the related pathogen X. campestris pv. campestris, several T2S substrates from X. campestris pv. vesicatoria were secreted independently of the T2S systems, presumably because of differences in the T2S substrate specificities of the two pathogens. Furthermore, in X. campestris pv. vesicatoria T2S mutants, secretion of T2S substrates was not completely absent, suggesting the contribution of additional transport systems to protein secretion. In line with this hypothesis, T2S substrates were detected in outer membrane vesicles, which were frequently observed for X. campestris pv. vesicatoria. We, therefore, propose that extracellular virulence-associated enzymes from X. campestris pv. vesicatoria are targeted to the Xps-T2S system and to outer membrane vesicles.","authors":"Sol\u00e9, M., Scheibner, F., Hoffmeister, AK., Hartmann, N., Hause, G., Rother, A., Jordan, M., Lautier, M., Arlat, M., B\u00fcttner, D.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Bacteriol","volume":"197","issue":"17","page":"2879-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26095658","title":"Small-RNA-Mediated Genome-wide trans-Recognition Network in Tetrahymena DNA Elimination.","abstract":"Small RNAs are used to silence transposable elements (TEs) in many eukaryotes, which use diverse evolutionary solutions to identify TEs. In ciliated protozoans, small-RNA-mediated comparison of the germline and somatic genomes underlies identification of TE-related sequences, which are then eliminated from the soma. Here, we describe an additional mechanism of small-RNA-mediated identification of TE-related sequences in the ciliate Tetrahymena. We show that a limited set of internal eliminated sequences (IESs) containing potentially active TEs produces a class of small RNAs that recognize not only the IESs from which they are derived, but also other IESs in trans. This trans recognition triggers the expression of yet another class of small RNAs that identify other IESs. Therefore, TE-related sequences in Tetrahymena are robustly targeted for elimination by a genome-wide trans-recognition network accompanied by a chain reaction of small RNA production.","authors":"Noto, T., Kataoka, K., Suhren, JH., Hayashi, A., Woolcock, KJ., Gorovsky, MA., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Mol Cell","volume":"59","issue":"2","page":"229-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26094891","title":"Osteoprotegerin and Denosumab Stimulate Human Beta Cell Proliferation through Inhibition of the Receptor Activator of NF-\u03baB Ligand Pathway.","abstract":"Diabetes results from a reduction of pancreatic \u03b2-cells. Stimulating replication could normalize \u03b2-cell mass. However, adult human \u03b2-cells are recalcitrant to proliferation. We identified osteoprotegerin, a bone-related decoy receptor, as a \u03b2-cell mitogen. Osteoprotegerin was induced by and required for lactogen-mediated rodent \u03b2-cell replication. Osteoprotegerin enhanced \u03b2-cell proliferation in young, aged, and diabetic mice. This resulted in increased \u03b2-cell mass in young mice and significantly delayed hyperglycemia in diabetic mice. Osteoprotegerin stimulated replication of adult human \u03b2-cells, without causing dedifferentiation. Mechanistically, osteoprotegerin induced human and rodent \u03b2-cell replication by modulating CREB and GSK3 pathways, through binding Receptor Activator of NF-\u03baB (RANK) Ligand (RANKL), a brake in \u03b2-cell proliferation. Denosumab, an FDA-approved osteoporosis drug, and RANKL-specific antibody induced human \u03b2-cell proliferation in vitro, and in vivo, in humanized mice. Thus, osteoprotegerin and Denosumab prevent RANKL\/RANK interaction to stimulate \u03b2-cell replication, highlighting the potential for repurposing an osteoporosis drug to treat diabetes.","authors":"Kondegowda, NG., Fenutria, R., Pollack, IR., Orthofer, M., Garcia-Oca\u00f1a, A., Penninger, JM., Vasavada, RC.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell Metab","volume":"22","issue":"1","page":"77-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26070482","title":"Thymic B Cells Are Licensed to Present Self Antigens for Central T Cell Tolerance Induction.","abstract":"Thymic antigen-presenting cells (APCs) such as dendritic cells and medullary thymic epithelial cells (mTECs) use distinct strategies of self-antigen expression and presentation to mediate central tolerance. The thymus also harbors B cells; whether they also display unique tolerogenic features and how they genealogically relate to peripheral B cells is unclear. Here, we found that Aire is expressed in thymic but not peripheral B cells. Aire expression in thymic B cells coincided with major histocompatibility class II (MHCII) and CD80 upregulation and immunoglobulin class-switching. These features were recapitulated upon immigration of naive peripheral B cells into the thymus, whereby this intrathymic licensing required CD40 signaling in the context of cognate interactions with autoreactive CD4(+) thymocytes. Moreover, a licensing-dependent neo-antigen selectively upregulated in immigrating B cells mediated negative selection through direct presentation. Thus, autoreactivity within the nascent T cell repertoire fuels a feed forward loop that endows thymic B cells with tolerogenic features.","authors":"Yamano, T., Nedjic, J., Hinterberger, M., Steinert, M., Koser, S., Pinto, S., Gerdes, N., Lutgens, E., Ishimaru, N., Busslinger, M., Brors, B., Kyewski, B., Klein, L.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Immunity","volume":"42","issue":"6","page":"1048-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26015544","title":"Brachyury and SMAD signalling collaboratively orchestrate distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells.","abstract":"The transcription factor brachyury (T, BRA) is one of the first markers of gastrulation and lineage specification in vertebrates. Despite its wide use and importance in stem cell and developmental biology, its functional genomic targets in human cells are largely unknown. Here, we use differentiating human embryonic stem cells to study the role of BRA in activin A-induced endoderm and BMP4-induced mesoderm progenitors. We show that BRA has distinct genome-wide binding landscapes in these two cell populations, and that BRA interacts and collaborates with SMAD1 or SMAD2\/3 signalling to regulate the expression of its target genes in a cell-specific manner. Importantly, by manipulating the levels of BRA in cells exposed to different signalling environments, we demonstrate that BRA is essential for mesoderm but not for endoderm formation. Together, our data illuminate the function of BRA in the context of human embryonic development and show that the regulatory role of BRA is context dependent. Our study reinforces the importance of analysing the functions of a transcription factor in different cellular and signalling environments.","authors":"Faial, T., Bernardo, AS., Mendjan, S., Diamanti, E., Ortmann, D., Gentsch, GE., Mascetti, VL., Trotter, MW., Smith, JC., Pedersen, RA.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Development","volume":"142","issue":"12","page":"2121-35","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25946522","title":"Laser-induced acoustic desorption of natural and functionalized biochromophores.","abstract":"Laser-induced acoustic desorption (LIAD) has recently been established as a tool for analytical chemistry. It is capable of launching intact, neutral, or low charged molecules into a high vacuum environment. This makes it ideally suited to mass spectrometry. LIAD can be used with fragile biomolecules and very massive compounds alike. Here, we apply LIAD time-of-flight mass spectrometry (TOF-MS) to the natural biochromophores chlorophyll, hemin, bilirubin, and biliverdin and to high mass fluoroalkyl-functionalized porphyrins. We characterize the variation in the molecular fragmentation patterns as a function of the desorption and the VUV postionization laser intensity. We find that LIAD can produce molecular beams an order of magnitude slower than matrix-assisted laser desorption (MALD), although this depends on the substrate material. Using titanium foils we observe a most probable velocity of 20 m\/s for functionalized molecules with a mass m = 10,000 Da.","authors":"Sezer, U., W\u00f6rner, L., Horak, J., Felix, L., T\u00fcxen, J., G\u00f6tz, C., Vaziri, A., Mayor, M., Arndt, M.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Anal Chem","volume":"87","issue":"11","page":"5614-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25912690","title":"Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern.","abstract":"A large subset of mammalian imprinted genes show extra-embryonic lineage (EXEL) specific imprinted expression that is restricted to placental trophectoderm lineages and to visceral yolk sac endoderm (ysE). Isolated ysE provides a homogenous in vivo model of a mid-gestation extra-embryonic tissue to examine the mechanism of EXEL-specific imprinted gene silencing, but an in vitro model of ysE to facilitate more rapid and cost-effective experiments is not available. Reports indicate that ES cells differentiated into cystic embryoid bodies (EBs) contain ysE, so here we investigate if cystic EBs model ysE imprinted expression. The imprinted expression pattern of cystic EBs is shown to resemble fetal liver and not ysE. To investigate the reason for this we characterized the methylome and transcriptome of cystic EBs in comparison to fetal liver and ysE, by whole genome bisulphite sequencing and RNA-seq. Cystic EBs show a fetal liver pattern of global hypermethylation and low expression of repeats, while ysE shows global hypomethylation and high expression of IAPEz retroviral repeats, as reported for placenta. Transcriptome analysis confirmed that cystic EBs are more similar to fetal liver than ysE and express markers of early embryonic endoderm. Genome-wide analysis shows that ysE shares epigenetic and repeat expression features with placenta. Contrary to previous reports, we show that cystic EBs do not contain ysE, but are more similar to the embryonic endoderm of fetal liver. This explains why cystic EBs reproduce the imprinted expression seen in the embryo but not that seen in the ysE.","authors":"Kulinski, TM., Casari, MR., Guenzl, PM., Wenzel, D., Andergassen, D., Hladik, A., Datlinger, P., Farlik, M., Theussl, HC., Penninger, JM., Knapp, S., Bock, C., Barlow, DP., Hudson, QJ.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Dev Biol","volume":"402","issue":"2","page":"291-305","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25977553","title":"Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis.","abstract":"In animal gonads, PIWI-clade Argonaute proteins repress transposons sequence-specifically via bound Piwi-interacting RNAs (piRNAs). These are processed from single-stranded precursor RNAs by largely unknown mechanisms. Here we show that primary piRNA biogenesis is a 3'-directed and phased process that, in the Drosophila germ line, is initiated by secondary piRNA-guided transcript cleavage. Phasing results from consecutive endonucleolytic cleavages catalyzed by Zucchini, implying coupled formation of 3' and 5' ends of flanking piRNAs. Unexpectedly, Zucchini also participates in 3' end formation of secondary piRNAs. Its function can, however, be bypassed by downstream piRNA-guided precursor cleavages coupled to exonucleolytic trimming. Our data uncover an evolutionarily conserved piRNA biogenesis mechanism in which Zucchini plays a central role in defining piRNA 5' and 3' ends.","authors":"Mohn, F., Handler, D., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Science","volume":"348","issue":"6236","page":"812-817","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25861001","title":"Visualizing KcsA conformational changes upon ion binding by infrared spectroscopy and atomistic modeling.","abstract":"The effect of ion binding in the selectivity filter of the potassium channel KcsA is investigated by combining amide I Fourier-transform infrared spectroscopy with structure-based spectral modeling. Experimental difference IR spectra between K(+)-bound KcsA and Na(+)-bound KcsA are in good qualitative agreement with spectra modeled from structural ensembles generated from molecular dynamics simulations. The molecular origins of the vibrational modes contributing to differences in these spectra are determined not only from structural differences in the selectivity filter but also from the pore helices surrounding this region. Furthermore, the coordination of K(+) or Na(+) to carbonyls in the selectivity filter effectively decouples the vibrations of those carbonyls from the rest of the protein, creating local probes of the electrostatic environment. The results suggest that it is necessary to include the influence of the surrounding helices in discussing selectivity and transport in KcsA and, on a more general level, that IR spectroscopy offers a nonperturbative route to studying the structure and dynamics of ion channels.","authors":"Stevenson, P., G\u00f6tz, C., Baiz, CR., Akerboom, J., Tokmakoff, A., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Phys Chem B","volume":"119","issue":"18","page":"5824-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25825779","title":"RING E3 mechanism for ubiquitin ligation to a disordered substrate visualized for human anaphase-promoting complex.","abstract":"For many E3 ligases, a mobile RING (Really Interesting New Gene) domain stimulates ubiquitin (Ub) transfer from a thioester-linked E2\u223cUb intermediate to a lysine on a remotely bound disordered substrate. One such E3 is the gigantic, multisubunit 1.2-MDa anaphase-promoting complex\/cyclosome (APC), which controls cell division by ubiquitinating cell cycle regulators to drive their timely degradation. Intrinsically disordered substrates are typically recruited via their KEN-box, D-box, and\/or other motifs binding to APC and a coactivator such as CDH1. On the opposite side of the APC, the dynamic catalytic core contains the cullin-like subunit APC2 and its RING partner APC11, which collaborates with the E2 UBCH10 (UBE2C) to ubiquitinate substrates. However, how dynamic RING-E2\u223cUb catalytic modules such as APC11-UBCH10\u223cUb collide with distally tethered disordered substrates remains poorly understood. We report structural mechanisms of UBCH10 recruitment to APC(CDH1) and substrate ubiquitination. Unexpectedly, in addition to binding APC11's RING, UBCH10 is corecruited via interactions with APC2, which we visualized in a trapped complex representing an APC(CDH1)-UBCH10\u223cUb-substrate intermediate by cryo-electron microscopy, and in isolation by X-ray crystallography. To our knowledge, this is the first structural view of APC, or any cullin-RING E3, with E2 and substrate juxtaposed, and it reveals how tripartite cullin-RING-E2 interactions establish APC's specificity for UBCH10 and harness a flexible catalytic module to drive ubiquitination of lysines within an accessible zone. We propose that multisite interactions reduce the degrees of freedom available to dynamic RING E3-E2\u223cUb catalytic modules, condense the search radius for target lysines, increase the chance of active-site collision with conformationally fluctuating substrates, and enable regulation.","authors":"Brown, NG., VanderLinden, R., Watson, ER., Qiao, R., Grace, CR., Yamaguchi, M., Weissmann, F., Frye, JJ., Dube, P., Ei Cho, S., Actis, ML., Rodrigues, P., Fujii, N., Peters, JM., Stark, H., Schulman, BA.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Proc Natl Acad Sci U S A","volume":"112","issue":"17","page":"5272-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25807485","title":"Therapy-induced tumour secretomes promote resistance and tumour progression.","abstract":"Drug resistance invariably limits the clinical efficacy of targeted therapy with kinase inhibitors against cancer. Here we show that targeted therapy with BRAF, ALK or EGFR kinase inhibitors induces a complex network of secreted signals in drug-stressed human and mouse melanoma and human lung adenocarcinoma cells. This therapy-induced secretome stimulates the outgrowth, dissemination and metastasis of drug-resistant cancer cell clones and supports the survival of drug-sensitive cancer cells, contributing to incomplete tumour regression. The tumour-promoting secretome of melanoma cells treated with the kinase inhibitor vemurafenib is driven by downregulation of the transcription factor FRA1. In situ transcriptome analysis of drug-resistant melanoma cells responding to the regressing tumour microenvironment revealed hyperactivation of several signalling pathways, most prominently the AKT pathway. Dual inhibition of RAF and the PI(3)K\/AKT\/mTOR intracellular signalling pathways blunted the outgrowth of the drug-resistant cell population in BRAF mutant human melanoma, suggesting this combination therapy as a strategy against tumour relapse. Thus, therapeutic inhibition of oncogenic drivers induces vast secretome changes in drug-sensitive cancer cells, paradoxically establishing a tumour microenvironment that supports the expansion of drug-resistant clones, but is susceptible to combination therapy.","authors":"Obenauf, AC., Zou, Y., Ji, AL., Vanharanta, S., Shu, W., Shi, H., Kong, X., Bosenberg, MC., Wiesner, T., Rosen, N., Lo, RS., Massagu\u00e9, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nature","volume":"520","issue":"7547","page":"368-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25708645","title":"Osteoprotegerin protects against muscular dystrophy.","abstract":"Receptor-activator of NF-\u03baB, its ligand RANKL, and the soluble decoy receptor osteoprotegerin are the key regulators of osteoclast differentiation and bone remodeling. Although there is a strong association between osteoporosis and skeletal muscle atrophy\/dysfunction, the functional relevance of a particular biological pathway that synchronously regulates bone and skeletal muscle physiopathology still is elusive. Here, we show that muscle cells can produce and secrete osteoprotegerin and pharmacologic treatment of dystrophic mdx mice with recombinant osteoprotegerin muscles. (Recombinant osteoprotegerin-Fc mitigates the loss of muscle force in a dose-dependent manner and preserves muscle integrity, particularly in fast-twitch extensor digitorum longus.) Our data identify osteoprotegerin as a novel protector of muscle integrity, and it potentially represents a new therapeutic avenue for both muscular diseases and osteoporosis.","authors":"Dufresne, SS., Dumont, NA., Bouchard, P., Lavergne, \u00c9., Penninger, JM., Frenette, J.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Am J Pathol","volume":"185","issue":"4","page":"920-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25707030","title":"Atomic-accuracy models from 4.5-\u00c5 cryo-electron microscopy data with density-guided iterative local refinement.","abstract":"We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-\u00c5 resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.","authors":"DiMaio, F., Song, Y., Li, X., Brunner, MJ., Xu, C., Conticello, V., Egelman, E., Marlovits, T., Cheng, Y., Baker, D.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Methods","volume":"12","issue":"4","page":"361-365","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25655195","title":"Activated Notch counteracts Ikaros tumor suppression in mouse and human T-cell acute lymphoblastic leukemia.","abstract":"Activating NOTCH1 mutations occur in ~60% of human T-cell acute lymphoblastic leukemias (T-ALLs), and mutations disrupting the transcription factor IKZF1 (IKAROS) occur in ~5% of cases. To investigate the regulatory interplay between these driver genes, we have used a novel transgenic RNA interference mouse model to produce primary T-ALLs driven by reversible Ikaros knockdown. Restoring endogenous Ikaros expression in established T-ALL in vivo acutely represses Notch1 and its oncogenic target genes including Myc, and in multiple primary leukemias causes disease regression. In contrast, leukemias expressing high levels of endogenous or engineered forms of activated intracellular Notch1 (ICN1) resembling those found in human T-ALL rapidly relapse following Ikaros restoration, indicating that ICN1 functionally antagonizes Ikaros in established disease. Furthermore, we find that IKAROS mRNA expression is significantly reduced in a cohort of primary human T-ALL patient samples with activating NOTCH1\/FBXW7 mutations, but is upregulated upon acute inhibition of aberrant NOTCH signaling across a panel of human T-ALL cell lines. These results demonstrate for the first time that aberrant NOTCH activity compromises IKAROS function in mouse and human T-ALL, and provide a potential explanation for the relative infrequency of IKAROS gene mutations in human T-ALL.","authors":"Witkowski, MT., Cimmino, L., Hu, Y., Trimarchi, T., Tagoh, H., McKenzie, MD., Best, SA., Tuohey, L., Willson, TA., Nutt, SL., Busslinger, M., Aifantis, I., Smyth, GK., Dickins, RA.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Leukemia","volume":"29","issue":"6","page":"1301-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25620640","title":"Ascl2 acts as an R-spondin\/Wnt-responsive switch to control stemness in intestinal crypts.","abstract":"The Wnt signaling pathway controls stem cell identity in the intestinal epithelium and in many other adult organs. The transcription factor Ascl2 (a Wnt target gene) is a master regulator of intestinal stem cell identity. It is unclear how the continuous Wnt gradient along the crypt axis is translated into discrete expression of Ascl2 and discrete specification of stem cells at crypt bottoms. We show that (1) Ascl2 is regulated in a direct autoactivatory loop, leading to a distinct on\/off expression pattern, and (2) Wnt\/R-spondin can activate this regulatory loop. This mechanism interprets the Wnt levels in the intestinal crypt and translates the continuous Wnt signal into a discrete Ascl2 \"on\" or \"off\" decision. In turn, Ascl2, together with \u03b2-catenin\/Tcf, activates the genes fundamental to the stem cell state. In this manner, Ascl2 forms a transcriptional switch that is both Wnt responsive and Wnt dependent to define stem cell identity.","authors":"Schuijers, J., Junker, JP., Mokry, M., Hatzis, P., Koo, BK., Sasselli, V., van der Flier, LG., Cuppen, E., van Oudenaarden, A., Clevers, H.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell Stem Cell","volume":"16","issue":"2","page":"158-70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25588944","title":"A Tetrahymena Hsp90 co-chaperone promotes siRNA loading by ATP-dependent and ATP-independent mechanisms.","abstract":"The loading of small interfering RNAs (siRNAs) and microRNAs into Argonaute proteins is enhanced by Hsp90 and ATP in diverse eukaryotes. However, whether this loading also occurs independently of Hsp90 and ATP remains unclear. We show that the Tetrahymena Hsp90 co-chaperone Coi12p promotes siRNA loading into the Argonaute protein Twi1p in both ATP-dependent and ATP-independent manners in vitro. The ATP-dependent activity requires Hsp90 and the tetratricopeptide repeat (TPR) domain of Coi12p, whereas these factors are dispensable for the ATP-independent activity. Both activities facilitate siRNA loading by counteracting the Twi1p-binding protein Giw1p, which is important to specifically sort the 26- to 32-nt siRNAs to Twi1p. Although Coi12p lacking its TPR domain does not bind to Hsp90, it can partially restore the siRNA loading and DNA elimination defects of COI12 knockout cells, suggesting that Hsp90- and ATP-independent loading of siRNA occurs in vivo and plays a physiological role in Tetrahymena.","authors":"Woehrer, SL., Aronica, L., Suhren, JH., Busch, CJ., Noto, T., Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"EMBO J","volume":"34","issue":"4","page":"559-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25561503","title":"Quantitative phosphoproteomics of the ataxia telangiectasia-mutated (ATM) and ataxia telangiectasia-mutated and rad3-related (ATR) dependent DNA damage response in Arabidopsis thaliana.","abstract":"The reversible phosphorylation of proteins on serine, threonine, and tyrosine residues is an important biological regulatory mechanism. In the context of genome integrity, signaling cascades driven by phosphorylation are crucial for the coordination and regulation of DNA repair. The two serine\/threonine protein kinases ataxia telangiectasia-mutated (ATM) and Ataxia telangiectasia-mutated and Rad3-related (ATR) are key factors in this process, each specific for different kinds of DNA lesions. They are conserved across eukaryotes, mediating the activation of cell-cycle checkpoints, chromatin modifications, and regulation of DNA repair proteins. We designed a novel mass spectrometry-based phosphoproteomics approach to study DNA damage repair in Arabidopsis thaliana. The protocol combines filter aided sample preparation, immobilized metal affinity chromatography, metal oxide affinity chromatography, and strong cation exchange chromatography for phosphopeptide generation, enrichment, and separation. Isobaric labeling employing iTRAQ (isobaric tags for relative and absolute quantitation) was used for profiling the phosphoproteome of atm atr double mutants and wild type plants under either regular growth conditions or challenged by irradiation. A total of 10,831 proteins were identified and 15,445 unique phosphopeptides were quantified, containing 134 up- and 38 down-regulated ATM\/ATR dependent phosphopeptides. We identified known and novel ATM\/ATR targets such as LIG4 and MRE11 (needed for resistance against ionizing radiation), PIE1 and SDG26 (implicated in chromatin remodeling), PCNA1, WAPL, and PDS5 (implicated in DNA replication), and ASK1 and HTA10 (involved in meiosis).","authors":"Roitinger, E., Hofer, M., K\u00f6cher, T., Pichler, P., Novatchkova, M., Yang, J., Schl\u00f6gelhofer, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Mol Cell Proteomics","volume":"14","issue":"3","page":"556-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25535350","title":"No evidence for intracellular magnetite in putative vertebrate magnetoreceptors identified by magnetic screening.","abstract":"The cellular basis of the magnetic sense remains an unsolved scientific mystery. One theory that aims to explain how animals detect the magnetic field is the magnetite hypothesis. It argues that intracellular crystals of the iron oxide magnetite (Fe3O4) are coupled to mechanosensitive channels that elicit neuronal activity in specialized sensory cells. Attempts to find these primary sensors have largely relied on the Prussian Blue stain that labels cells rich in ferric iron. This method has proved problematic as it has led investigators to conflate iron-rich macrophages with magnetoreceptors. An alternative approach developed by Eder et al. [Eder SH, et al. (2012) Proc Natl Acad Sci USA 109(30):12022-12027] is to identify candidate magnetoreceptive cells based on their magnetic moment. Here, we explore the utility of this method by undertaking a screen for magnetic cells in the pigeon. We report the identification of a small number of cells (1 in 476,000) with large magnetic moments (8-106 fAm(2)) from various tissues. The development of single-cell correlative light and electron microscopy (CLEM) coupled with electron energy loss spectroscopy (EELS) and energy-filtered transmission electron microscopy (EFTEM) permitted subcellular analysis of magnetic cells. This revealed the presence of extracellular structures composed of iron, titanium, and chromium accounting for the magnetic properties of these cells. Application of single-cell CLEM to magnetic cells from the trout failed to identify any intracellular structures consistent with biogenically derived magnetite. Our work illustrates the need for new methods to test the magnetite hypothesis of magnetosensation.","authors":"Edelman, NB., Fritz, T., Nimpf, S., Pichler, P., Lauwers, M., Hickman, RW., Papadaki-Anastasopoulou, A., Ushakova, L., Heuser, T., Resch, GP., Saunders, M., Shaw, JA., Keays, DA.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Proc Natl Acad Sci U S A","volume":"112","issue":"1","page":"262-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25532219","title":"The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle.","abstract":"In Drosophila, fibrillar flight muscles (IFMs) enable flight, while tubular muscles mediate other body movements. Here, we use RNA-sequencing and isoform-specific reporters to show that spalt major (salm) determines fibrillar muscle physiology by regulating transcription and alternative splicing of a large set of sarcomeric proteins. We identify the RNA-binding protein Arrest (Aret, Bruno) as downstream of salm. Aret shuttles between the cytoplasm and nuclei and is essential for myofibril maturation and sarcomere growth of IFMs. Molecularly, Aret regulates IFM-specific splicing of various salm-dependent sarcomeric targets, including Stretchin and wupA (TnI), and thus maintains muscle fiber integrity. As Aret and its sarcomeric targets are evolutionarily conserved, similar principles may regulate mammalian muscle morphogenesis.","authors":"Spletter, ML., Barz, C., Yeroslaviz, A., Sch\u00f6nbauer, C., Ferreira, IR., Sarov, M., Gerlach, D., Stark, A., Habermann, BH., Schnorrer, F.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"EMBO Rep","volume":"16","issue":"2","page":"178-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25497548","title":"High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.","abstract":"Cells control dynamic transitions in transcript levels by regulating transcription, processing, and\/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing sites; and transcription, processing, and degradation rates of each transcript at a splice junction resolution during the LPS response of mouse dendritic cells. Four key regulatory strategies, dominated by RNA transcription changes, generate most temporal gene expression patterns. Noncanonical strategies that also employ dynamic posttranscriptional regulation control only a minority of genes, but provide unique signal processing features. We validate Tristetraprolin (TTP) as a major regulator of RNA degradation in one noncanonical strategy. Applying DRiLL to the regulation of noncoding RNAs and to zebrafish embryogenesis demonstrates its broad utility. Our study provides a new quantitative approach to discover transcriptional and posttranscriptional events that control dynamic changes in transcript levels using RNA sequencing data.","authors":"Rabani, M., Raychowdhury, R., Jovanovic, M., Rooney, M., Stumpo, DJ., Pauli, A., Hacohen, N., Schier, AF., Blackshear, PJ., Friedman, N., Amit, I., Regev, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell","volume":"159","issue":"7","page":"1698-710","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25454634","title":"3D reconstitution of the patterned neural tube from embryonic stem cells.","abstract":"Inducing organogenesis in 3D culture is an important aspect of stem cell research. Anterior neural structures have been produced from large embryonic stem cell (ESC) aggregates, but the steps involved in patterning such complex structures have been ill defined, as embryoid bodies typically contained many cell types. Here we show that single mouse ESCs directly embedded in Matrigel or defined synthetic matrices under neural induction conditions can clonally form neuroepithelial cysts containing a single lumen in 3D. Untreated cysts were uniformly dorsal and could be ventralized to floor plate (FP). Retinoic acid posteriorized cysts to cervical levels and induced localize FP formation yielding full patterning along the dorsal\/ventral (DV) axis. Correct spatial organization of motor neurons, interneurons, and dorsal interneurons along the DV axis was observed. This system serves as a valuable tool for studying morphogen action in 3D and as a source of patterned spinal cord tissue.","authors":"Meinhardt, A., Eberle, D., Tazaki, A., Ranga, A., Niesche, M., Wilsch-Br\u00e4uninger, M., Stec, A., Schackert, G., Lutolf, M., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Stem Cell Reports","volume":"3","issue":"6","page":"987-99","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25378478","title":"The mammalian tRNA ligase complex mediates splicing of XBP1 mRNA and controls antibody secretion in plasma cells.","abstract":"The unfolded protein response (UPR) is a conserved stress-signaling pathway activated after accumulation of unfolded proteins within the endoplasmic reticulum (ER). Active UPR signaling leads to unconventional, enzymatic splicing of XBP1 mRNA enabling expression of the transcription factor XBP1s to control ER homeostasis. While IRE1 has been identified as the endoribonuclease required for cleavage of this mRNA, the corresponding ligase in mammalian cells has remained elusive. Here, we report that RTCB, the catalytic subunit of the tRNA ligase complex, and its co-factor archease mediate XBP1 mRNA splicing both in vitro and in vivo. Depletion of RTCB in plasma cells of Rtcb(fl\/fl) Cd23-Cre mice prevents XBP1s expression, which normally is strongly induced during plasma cell development. RTCB-depleted plasma cells show reduced and disorganized ER structures as well as severe defects in antibody secretion. Targeting RTCB and\/or archease thus represents a promising strategy for the treatment of a growing number of diseases associated with elevated expression of XBP1s.","authors":"Jurkin, J., Henkel, T., Nielsen, AF., Minnich, M., Popow, J., Kaufmann, T., Heindl, K., Hoffmann, T., Busslinger, M., Martinez, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"EMBO J","volume":"33","issue":"24","page":"2922-36","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25361812","title":"Preclinical efficacy of MEK inhibition in Nras-mutant AML.","abstract":"Oncogenic NRAS mutations are highly prevalent in acute myeloid leukemia (AML). Genetic analysis supports the hypothesis that NRAS mutations cooperate with antecedent molecular lesions in leukemogenesis, but have limited independent prognostic significance. Using short hairpin RNA-mediated knockdown in human cell lines and primary mouse leukemias, we show that AML cells with NRAS\/Nras mutations are dependent on continued oncogene expression in vitro and in vivo. Using the Mx1-Cre transgene to inactivate a conditional mutant Nras allele, we analyzed hematopoiesis and hematopoietic stem and progenitor cells (HSPCs) under normal and stressed conditions and found that HSPCs lacking Nras expression are functionally equivalent to normal HSPCs in the adult mouse. Treating recipient mice transplanted with primary Nras(G12D) AMLs with 2 potent allosteric mitogen-activated protein kinase kinase (MEK) inhibitors (PD0325901 or trametinib\/GlaxoSmithKline 1120212) significantly prolonged survival and reduced proliferation but did not induce apoptosis, promote differentiation, or drive clonal evolution. The phosphatidylinositol 3-kinase inhibitor GDC-0941 was ineffective as a single agent and did not augment the activity of PD0325901. All mice ultimately succumbed to progressive leukemia. Together, these data validate oncogenic N-Ras signaling as a therapeutic target in AML and support testing combination regimens that include MEK inhibitors.","authors":"Burgess, MR., Hwang, E., Firestone, AJ., Huang, T., Xu, J., Zuber, J., Bohin, N., Wen, T., Kogan, SC., Haigis, KM., Sampath, D., Lowe, S., Shannon, K., Li, Q.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Blood","volume":"124","issue":"26","page":"3947-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25344531","title":"The AAA-ATPase molecular chaperone Cdc48\/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes.","abstract":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)\/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin\/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48A(NPL4) complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.","authors":"M\u00e9rai, Z., Chumak, N., Garc\u00eda-Aguilar, M., Hsieh, TF., Nishimura, T., Schoft, VK., Bindics, J., Slusarz, L., Arnoux, S., Opravil, S., Mechtler, K., Zilberman, D., Fischer, RL., Tamaru, H.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Proc Natl Acad Sci U S A","volume":"111","issue":"45","page":"16166-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25241743","title":"CRISPR-mediated genomic deletion of Sox2 in the axolotl shows a requirement in spinal cord neural stem cell amplification during tail regeneration.","abstract":"The salamander is the only tetrapod that functionally regenerates all cell types of the limb and spinal cord (SC) and thus represents an important regeneration model, but the lack of gene-knockout technology has limited molecular analysis. We compared transcriptional activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPRs) in the knockout of three loci in the axolotl and find that CRISPRs show highly penetrant knockout with less toxic effects compared to TALENs. Deletion of Sox2 in up to 100% of cells yielded viable F0 larvae with normal SC organization and ependymoglial cell marker expression such as GFAP and ZO-1. However, upon tail amputation, neural stem cell proliferation was inhibited, resulting in spinal-cord-specific regeneration failure. In contrast, the mesodermal blastema formed normally. Sox3 expression during development, but not regeneration, most likely allowed embryonic survival and the regeneration-specific phenotype. This analysis represents the first tissue-specific regeneration phenotype from the genomic deletion of a gene in the axolotl.","authors":"Fei, JF., Schuez, M., Tazaki, A., Taniguchi, Y., Roensch, K., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Stem Cell Reports","volume":"3","issue":"3","page":"444-59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25236395","title":"Essential versus accessory aspects of cell death: recommendations of the NCCD 2015.","abstract":"Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as 'accidental cell death' (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. 'Regulated cell death' (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death.","authors":"Galluzzi, L., Bravo-San Pedro, JM., Vitale, I., Aaronson, SA., Abrams, JM., Adam, D., Alnemri, ES., Altucci, L., Andrews, D., Annicchiarico-Petruzzelli, M., Baehrecke, EH., Bazan, NG., Bertrand, MJ., Bianchi, K., Blagosklonny, MV., Blomgren, K., Borner, C., Bredesen, DE., Brenner, C., Campanella, M., Candi, E., Cecconi, F., Chan, FK., Chandel, NS., Cheng, EH., Chipuk, JE., Cidlowski, JA., Ciechanover, A., Dawson, TM., Dawson, VL., De Laurenzi, V., De Maria, R., Debatin, KM., Di Daniele, N., Dixit, VM., Dynlacht, BD., El-Deiry, WS., Fimia, GM., Flavell, RA., Fulda, S., Garrido, C., Gougeon, ML., Green, DR., Gronemeyer, H., Hajnoczky, G., Hardwick, JM., Hengartner, MO., Ichijo, H., Joseph, B., Jost, PJ., Kaufmann, T., Kepp, O., Klionsky, DJ., Knight, RA., Kumar, S., Lemasters, JJ., Levine, B., Linkermann, A., Lipton, SA., Lockshin, RA., L\u00f3pez-Ot\u00edn, C., Lugli, E., Madeo, F., Malorni, W., Marine, JC., Martin, SJ., Martinou, JC., Medema, JP., Meier, P., Melino, S., Mizushima, N., Moll, U., Mu\u00f1oz-Pinedo, C., Nu\u00f1ez, G., Oberst, A., Panaretakis, T., Penninger, JM., Peter, ME., Piacentini, M., Pinton, P., Prehn, JH., Puthalakath, H., Rabinovich, GA., Ravichandran, KS., Rizzuto, R., Rodrigues, CM., Rubinsztein, DC., Rudel, T., Shi, Y., Simon, HU., Stockwell, BR., Szabadkai, G., Tait, SW., Tang, HL., Tavernarakis, N., Tsujimoto, Y., Vanden Berghe, T., Vandenabeele, P., Villunger, A., Wagner, EF., Walczak, H., White, E., Wood, WG., Yuan, J., Zakeri, Z., Zhivotovsky, B., Melino, G., Kroemer, G.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell Death Differ","volume":"22","issue":"1","page":"58-73","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25220052","title":"Cohesin's ATPase activity couples cohesin loading onto DNA with Smc3 acetylation.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">25220052<\/PMID><DateCompleted><Year>2015<\/Year><Month>06<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>24<\/Volume><Issue>19<\/Issue><PubDate><Year>2014<\/Year><Month>Oct<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Cohesin's ATPase activity couples cohesin loading onto DNA with Smc3 acetylation.<\/ArticleTitle><Pagination><MedlinePgn>2228-37<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2014.08.011<\/ELocationID><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0960-9822(14)00989-0<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Cohesin mediates sister chromatid cohesion by topologically entrapping sister DNA molecules inside its ring structure. Cohesin is loaded onto DNA by the Scc2\/NIPBL-Scc4\/MAU2-loading complex in a manner that depends on the adenosine triphosphatase (ATPase) activity of cohesin's Smc1 and Smc3 subunits. Subsequent cohesion establishment during DNA replication depends on Smc3 acetylation by Esco1 and Esco2 and on recruitment of sororin, which \"locks\" cohesin on DNA by inactivating the cohesin release factor Wapl.","authors":"Ladurner, R., Bhaskara, V., Huis in 't Veld, PJ., Davidson, IF., Kreidl, E., Petzold, G., Peters, JM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Biol","volume":"24","issue":"19","page":"2228-37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25218586","title":"3DSpectra: A 3-dimensional quantification algorithm for LC-MS labeled profile data.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">25218586<\/PMID><DateCompleted><Year>2015<\/Year><Month>08<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2016<\/Year><Month>05<\/Month><Day>18<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1876-7737<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>112<\/Volume><PubDate><Year>2015<\/Year><Month>Jan<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Journal of proteomics<\/Title><ISOAbbreviation>J Proteomics<\/ISOAbbreviation><\/Journal><ArticleTitle>3DSpectra: A 3-dimensional quantification algorithm for LC-MS labeled profile data.<\/ArticleTitle><Pagination><MedlinePgn>156-65<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.jprot.2014.08.017<\/ELocationID><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S1874-3919(14)00416-3<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Mass spectrometry-based proteomics can generate highly informative datasets, as profile three-dimensional (3D) LC-MS data: LC-MS separates peptides in two dimensions (time, m\/z) minimizing their overlap, and profile acquisition enhances quantification. To exploit both data features, we developed 3DSpectra, a 3D approach embedding a statistical method for peptide border recognition. 3DSpectra efficiently accesses profile data by means of mzRTree, and makes use of a priori metadata, provided by search engines, to quantify the identified peptides. An isotopic distribution model, shaped by a bivariate Gaussian Mixture Model (GMM), which includes a noise component, is fitted to the peptide peaks using the expectation-maximization (EM) approach. The EM starting parameters, i.e., the centers and shapes of the Gaussians, are retrieved from the metadata. The borders of the peaks are delimited by the GMM iso-density curves, and noisy or outlying data are discarded from subsequent analysis. The 3DSpectra program was compared to ASAPRatio for a controlled mixture of Isotope-Coded Protein Labels (ICPL) labeled proteins, which were mixed at predefined ratios and acquired in enhanced profile mode, in triplicate. The 3DSpectra software showed significantly higher linearity, quantification accuracy, and precision than did ASAPRatio in this real use case simulation where the true ratios are known, and it also achieved wider peptide coverage and dynamic range.","authors":"Nasso, S., Hartler, J., Trajanoski, Z., Di Camillo, B., Mechtler, K., Toffolo, GM.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"J Proteomics","volume":"112","issue":null,"page":"156-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25216638","title":"In vivo RNAi screening identifies a mechanism of sorafenib resistance in liver cancer.","abstract":"In solid tumors, resistance to therapy inevitably develops upon treatment with cytotoxic drugs or molecularly targeted therapies. Here, we describe a system that enables pooled shRNA screening directly in mouse hepatocellular carcinomas (HCC) in vivo to identify genes likely to be involved in therapy resistance. Using a focused shRNA library targeting genes located within focal genomic amplifications of human HCC, we screened for genes whose inhibition increased the therapeutic efficacy of the multikinase inhibitor sorafenib. Both shRNA-mediated and pharmacological silencing of Mapk14 (p38\u03b1) were found to sensitize mouse HCC to sorafenib therapy and prolong survival by abrogating Mapk14-dependent activation of Mek-Erk and Atf2 signaling. Elevated Mapk14-Atf2 signaling predicted poor response to sorafenib therapy in human HCC, and sorafenib resistance of p-Mapk14-expressing HCC cells could be reverted by silencing Mapk14. Our results suggest that a combination of sorafenib and Mapk14 blockade is a promising approach to overcoming therapy resistance of human HCC.","authors":"Rudalska, R., Dauch, D., Longerich, T., McJunkin, K., Wuestefeld, T., Kang, TW., Hohmeyer, A., Pesic, M., Leibold, J., von Thun, A., Schirmacher, P., Zuber, J., Weiss, KH., Powers, S., Malek, NP., Eilers, M., Sipos, B., Lowe, SW., Geffers, R., Laufer, S., Zender, L.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Med","volume":"20","issue":"10","page":"1138-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"69","title":"Purification and some enzymatic properties of the chitosanase from Bacillus R-4 which lyses Rhizopus cell walls.","abstract":"A strain of Bacillus sp (Bacillus R-4) produces a protease and a carbohydrolase both of which have the ability to lyse Rhizopus cell walls. Of the enzymes, the carbohydrolase has been purified to an ultracentrifugally and electrophoretically homogeneous state, and identified as a chitosanase. The enzyme was active on glycol chitosan as well as chitosan. Molecular weight of the purified enzyme was estimated as 31 000 and isoelectric point as pH 8.30. The enzyme was most active at pH 5.6 and at 40 degrees C with either Rhizopus cell wall or glycol chitosan as substrate, and was stable over a range of pH 4.5 to 7.5 at 40 degrees C for 3 h. The activity was lost by sulfhydryl reagents and restored by either reduced glutathione of L-cysteine. An abrupt decrease in viscosity of the reaction mixture suggested an endowise cleavage of chitosan by this enzyme.","authors":"Tominaga, Y., Tsujisaka, Y.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"145-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25199833","title":"Alternative 3' UTR selection controls PAR-5 homeostasis and cell polarity in C. elegans embryos.","abstract":"Cell polarity in one-cell C. elegans embryos guides asymmetric cell division and cell-fate specification. Shortly after fertilization, embryos establish two antagonistic cortical domains of PAR proteins. Here, we find that the conserved polarity factor PAR-5 regulates PAR domain size in a dose-dependent manner. Using quantitative imaging and controlled genetic manipulation, we find that PAR-5 protein levels reflect the cumulative output of three mRNA isoforms with different translational efficiencies mediated by their 3' UTRs. 3' UTR selection is regulated, influencing PAR-5 protein abundance. Alternative splicing underlies the selection of par-5 3' UTR isoforms. 3' UTR splicing is enhanced by the SR protein kinase SPK-1, and accordingly, SPK-1 is required for wild-type PAR-5 levels and PAR domain size. Precise regulation of par-5 isoform selection is essential for polarization when the posterior PAR network is compromised. Together, strict control of PAR-5 protein levels and feedback from polarity to par-5 3' UTR selection confer robustness to embryo polarization.","authors":"Mikl, M., Cowan, CR.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell Rep","volume":"8","issue":"5","page":"1380-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25157418","title":"Deep and precise quantification of the mouse synaptosomal proteome reveals substantial remodeling during postnatal maturation.","abstract":"During postnatal murine maturation, behavioral patterns emerge and become shaped by experience-dependent adaptations. During the same period, the morphology of dendritic spines, the morphological correlates of excitatory synapses, is known to change, and there is evidence of concurrent alterations of the synaptosomal protein machinery. To obtain comprehensive and quantitative insights in the developmental regulation of the proteome of synapses, we prepared cortical synaptosomal fractions from a total of 16 individual juvenile and adult mouse brains (age 3 or 8 weeks, respectively). We then applied peptide-based iTRAQ labeling (four pools of 4 animals) and high-resolution two-dimensional peptide fractionation (99 SCX fractions and 3 h reversed-phase gradients) using a hybrid CID-HCD acquisition method on a Velos Orbitrap mass spectrometer to identify a comprehensive set of synaptic proteins and to quantify changes in protein expression. We obtained a data set tracking expression levels of 3500 proteins mapping to 3427 NCBI GeneIDs during development with complete quantification data available for 3422 GeneIDs, which, to the best of our knowledge, constitutes the deepest coverage of the synaptosome proteome to date. The inclusion of biological replicates in a single mass spectrometry analysis demonstrated both high reproducibility of our synaptosome preparation method as well as high precision of our quantitative data (correlation coefficient R = 0.87 for the biological replicates). To evaluate the validity of our data, the developmental regulation of eight proteins identified in our analysis was confirmed independently using western blotting. A gene ontology analysis confirmed the synaptosomal nature of a large fraction of identified proteins. Of note, the set of the most strongly regulated proteins revealed candidates involved in neurological processes in health and disease states. This highlights the fact that developmentally regulated proteins can play additional roles in neurological disease processes. All data have been deposited to the ProteomeXchange with identifier PXD000552.","authors":"Moczulska, KE., Pichler, P., Schutzbier, M., Schleiffer, A., Rumpel, S., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Proteome Res","volume":"13","issue":"10","page":"4310-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25135956","title":"H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress.","abstract":"The selectivity of transcriptional responses to extracellular cues is reflected by the deposition of stimulus-specific chromatin marks. Although histone H3 phosphorylation is a target of numerous signaling pathways, its role in transcriptional regulation remains poorly understood. Here, for the first time, we report a genome-wide analysis of H3S28 phosphorylation in a mammalian system in the context of stress signaling. We found that this mark targets as many as 50% of all stress-induced genes, underlining its importance in signal-induced transcription. By combining ChIP-seq, RNA-seq, and mass spectrometry we identified the factors involved in the biological interpretation of this histone modification. We found that MSK1\/2-mediated phosphorylation of H3S28 at stress-responsive promoters contributes to the dissociation of HDAC corepressor complexes and thereby to enhanced local histone acetylation and subsequent transcriptional activation of stress-induced genes. Our data reveal a novel function of the H3S28ph mark in the activation of mammalian genes in response to MAP kinase pathway activation.","authors":"Sawicka, A., Hartl, D., Goiser, M., Pusch, O., Stocsits, RR., Tamir, IM., Mechtler, K., Seiser, C.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genome Res","volume":"24","issue":"11","page":"1808-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25108384","title":"A strand-specific switch in noncoding transcription switches the function of a Polycomb\/Trithorax response element.","abstract":"Polycomb\/Trithorax response elements (PRE\/TREs) can switch their function reversibly between silencing and activation by mechanisms that are poorly understood. Here we show that a switch in forward and reverse noncoding transcription from the Drosophila melanogaster vestigial (vg) PRE\/TRE switches the status of the element between silencing (induced by the forward strand) and activation (induced by the reverse strand). In vitro, both noncoding RNAs inhibit PRC2 histone methyltransferase activity, but, in vivo, only the reverse strand binds PRC2. Overexpression of the reverse strand evicts PRC2 from chromatin and inhibits its enzymatic activity. We propose that the interaction of RNAs with PRC2 is differentially regulated in vivo, allowing regulated inhibition of local PRC2 activity. Genome-wide analysis shows that strand switching of noncoding RNAs occurs at several hundred Polycomb-binding sites in fly and vertebrate genomes. This work identifies a previously unreported and potentially widespread class of PRE\/TREs that switch function by switching the direction of noncoding RNA transcription.","authors":"Herzog, VA., Lempradl, A., Trupke, J., Okulski, H., Altmutter, C., Ruge, F., Boidol, B., Kubicek, S., Schmauss, G., Aumayr, K., Ruf, M., Pospisilik, A., Dimond, A., Senergin, HB., Vargas, ML., Simon, JA., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Genet","volume":"46","issue":"9","page":"973-981","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25123281","title":"Mi-2\/NuRD chromatin remodeling complexes regulate B and T-lymphocyte development and function.","abstract":"Mi-2\/nucleosomal remodeling and deacetylase (NuRD) complexes are important epigenetic regulators of chromatin structure and gene expression. Mi-2\/NuRD complexes are an assemblage of proteins that combine key epigenetic regulators necessary for (i) histone deacetylation and demethylation, (ii) binding to methylated DNA, (iii) mobilization of nucleosomes, and (iv) recruitment of additional regulatory proteins. Depending on their context in chromatin, Mi-2\/NuRD complexes either activate or repress gene transcription. In this regard, they are important regulators of hematopoiesis and lymphopoiesis. Mi-2\/NuRD complexes maintain pools of hematopoietic stem cells. Specifically, components of these complexes control multiple stages of B-cell development by regulating B-cell specific transcription. With one set of components, they inhibit terminal differentiation of germinal center B cells into plasma B cells. They also mediate gene repression together with Blimp-1 during plasma cell differentiation. In cooperation with Ikaros, Mi-2\/NuRD complexes also play important roles in T-cell development, including CD4 versus CD8 fate decisions and peripheral T-cell responses. Dysregulation of NuRD during lymphopoiesis promotes leukemogenesis. Here, we review general properties of Mi-2\/NuRD complexes and focus on their functions in gene regulation and development of lymphocytes.","authors":"Dege, C., Hagman, J.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Immunol Rev","volume":"261","issue":"1","page":"126-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25088559","title":"The conserved discs-large binding partner Banderuola regulates asymmetric cell division in Drosophila.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">25088559<\/PMID><DateCompleted><Year>2015<\/Year><Month>04<\/Month><Day>21<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>05<\/Month><Day>20<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>24<\/Volume><Issue>16<\/Issue><PubDate><Year>2014<\/Year><Month>Aug<\/Month><Day>18<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The conserved discs-large binding partner Banderuola regulates asymmetric cell division in Drosophila.<\/ArticleTitle><Pagination><MedlinePgn>1811-25<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2014.06.059<\/ELocationID><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0960-9822(14)00775-1<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Asymmetric cell division (ACD) is a key process that allows different cell types to be generated at precisely defined times and positions. In Drosophila, neural precursor cells rely heavily on ACD to generate the different cell types in the nervous system. A conserved protein machinery that regulates ACD has been identified in Drosophila, but how this machinery acts to allow the establishment of differential cell fates is not entirely understood.","authors":"Mauri, F., Reichardt, I., Mummery-Widmer, JL., Yamazaki, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Biol","volume":"24","issue":"16","page":"1811-25","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25016959","title":"Par3-mInsc and G\u03b1i3 cooperate to promote oriented epidermal cell divisions through LGN.","abstract":"Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and G\u03b1i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and G\u03b1i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation.","authors":"Williams, SE., Ratliff, LA., Postiglione, MP., Knoblich, JA., Fuchs, E.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Cell Biol","volume":"16","issue":"8","page":"758-69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25002086","title":"Bacterial type III secretion systems: specialized nanomachines for protein delivery into target cells.","abstract":"One of the most exciting developments in the field of bacterial pathogenesis in recent years is the discovery that many pathogens utilize complex nanomachines to deliver bacterially encoded effector proteins into target eukaryotic cells. These effector proteins modulate a variety of cellular functions for the pathogen's benefit. One of these protein-delivery machines is the type III secretion system (T3SS). T3SSs are widespread in nature and are encoded not only by bacteria pathogenic to vertebrates or plants but also by bacteria that are symbiotic to plants or insects. A central component of T3SSs is the needle complex, a supramolecular structure that mediates the passage of the secreted proteins across the bacterial envelope. Working in conjunction with several cytoplasmic components, the needle complex engages specific substrates in sequential order, moves them across the bacterial envelope, and ultimately delivers them into eukaryotic cells. The central role of T3SSs in pathogenesis makes them great targets for novel antimicrobial strategies.","authors":"Gal\u00e1n, JE., Lara-Tejero, M., Marlovits, TC., Wagner, S.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Annu Rev Microbiol","volume":"68","issue":null,"page":"415-38","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24964966","title":"\"Uno, nessuno e centomila\": the different faces of the budding yeast kinetochore.","abstract":"\"One, no one and one hundred thousand\" is a masterpiece of Italian literature, written by Luigi Pirandello. The central theme is that in each individual there are multiple personalities, since one's perception of one's self differs from the view of others. As a consequence, a unique identity does not exist, but rather one hundred thousand. This concept can be very well applied to the kinetochore, one of the largest macromolecular complexes conserved in eukaryotes. The kinetochore is essential during cell division and fulfills different sophisticated functions, including linking chromosomes to spindle microtubules and delaying anaphase onset in case of incorrect bi-orientation. In order to perform these tasks, the kinetochore shapes its structure by recruiting different subunits, such as the components of the spindle assembly checkpoint (SAC) or the monopolin complex during meiosis. It also modifies its internal organization by rearranging intramolecular connections and acquiring a distinct identity at different time points of cell division. In this review, we describe recent insights into the changes in composition and configuration of the kinetochore in mitosis and meiosis, focusing on the kinetochore of Saccharomyces cerevisiae.","authors":"Malvezzi, F., Westermann, S.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Chromosoma","volume":"123","issue":"5","page":"447-57","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24920484","title":"Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up.","abstract":"LC-MS\/MS is the most commonly used technique for the identification and characterization of proteins. The efficiency of the electrospray process is a critical factor in LC-MS\/MS. Despite the benefits associated with very low flow rates for the ionization efficiency, most LC-MS\/MS platforms are operated at relatively high flow rates. The purpose of this work was to develop a nano LC system operable at a flow rate of 20 nL\/min, applicable for routine analysis in proteomics laboratories. Peptide separation was performed with an analytical column packed with 2 \u03bcm porous chromatographic beads, a length of 25 cm and an inner diameter (i.d.) of 25 \u03bcm. Practical usability, reproducibility, and overall performance of the system were evaluated with a tryptic peptide mixture generated from HeLa cells. Using 100 ng of sample, we identified on average 3721 protein groups based on 25,699 peptides. We demonstrate that the number of peptides identified with this system increases with decreasing flow rates. Probing the sensitivity of the set-up we analyzed only 10 ng of the sample, identifying an average number of 2042 protein groups based on 11 424 peptides. All MS data have been deposited in the ProteomeXchange with identifier PXD000396 (http:\/\/proteomecentral.proteomexchange.org\/dataset\/PXD000396).","authors":"K\u00f6cher, T., Pichler, P., De Pra, M., Rieux, L., Swart, R., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Proteomics","volume":"14","issue":"17-18","page":"1999-2007","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24909410","title":"MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.","abstract":"Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most widely used search engines were developed when high-resolution mass spectrometry data were not readily available for fragment ion masses, we have designed a scoring algorithm particularly suitable for high mass accuracy. Our algorithm, MS Amanda, is generally applicable to HCD, ETD, and CID fragmentation type data. The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification for most spectra also explained by Mascot or SEQUEST. MS Amanda, available at http:\/\/ms.imp.ac.at\/?goto=msamanda , is provided free of charge both as standalone version for integration into custom workflows and as a plugin for the Proteome Discoverer platform.","authors":"Dorfer, V., Pichler, P., Stranzl, T., Stadlmann, J., Taus, T., Winkler, S., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Proteome Res","volume":"13","issue":"8","page":"3679-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24908439","title":"Automated image-based tracking and its application in ecology.","abstract":"The behavior of individuals determines the strength and outcome of ecological interactions, which drive population, community, and ecosystem organization. Bio-logging, such as telemetry and animal-borne imaging, provides essential individual viewpoints, tracks, and life histories, but requires capture of individuals and is often impractical to scale. Recent developments in automated image-based tracking offers opportunities to remotely quantify and understand individual behavior at scales and resolutions not previously possible, providing an essential supplement to other tracking methodologies in ecology. Automated image-based tracking should continue to advance the field of ecology by enabling better understanding of the linkages between individual and higher-level ecological processes, via high-throughput quantitative analysis of complex ecological patterns and processes across scales, including analysis of environmental drivers.","authors":"Dell, AI., Bender, JA., Branson, K., Couzin, ID., de Polavieja, GG., Noldus, LP., P\u00e9rez-Escudero, A., Perona, P., Straw, AD., Wikelski, M., Brose, U.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Trends Ecol Evol","volume":"29","issue":"7","page":"417-28","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24908250","title":"Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution.","abstract":"Phenotypic differences between closely related species are thought to arise primarily from changes in gene expression due to mutations in cis-regulatory sequences (enhancers). However, it has remained unclear how frequently mutations alter enhancer activity or create functional enhancers de novo. Here we use STARR-seq, a recently developed quantitative enhancer assay, to determine genome-wide enhancer activity profiles for five Drosophila species in the constant trans-regulatory environment of Drosophila melanogaster S2 cells. We find that the functions of a large fraction of D. melanogaster enhancers are conserved for their orthologous sequences owing to selection and stabilizing turnover of transcription factor motifs. Moreover, hundreds of enhancers have been gained since the D. melanogaster-Drosophila yakuba split about 11 million years ago without apparent adaptive selection and can contribute to changes in gene expression in vivo. Our finding that enhancer activity is often deeply conserved and frequently gained provides functional insights into regulatory evolution.","authors":"Arnold, CD., Gerlach, D., Spies, D., Matts, JA., Sytnikova, YA., Pagani, M., Lau, NC., Stark, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Genet","volume":"46","issue":"7","page":"685-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24899341","title":"Global analysis of muscle-specific kinase signaling by quantitative phosphoproteomics.","abstract":"The development of the neuromuscular synapse depends on signaling processes that involve protein phosphorylation as a crucial regulatory event. Muscle-specific kinase (MuSK) is the key signaling molecule at the neuromuscular synapse whose activity is required for the formation of a mature and functional synapse. However, the signaling cascade downstream of MuSK and the regulation of the different components are still poorly understood. In this study we used a quantitative phosphoproteomics approach to study the phosphorylation events and their temporal regulation downstream of MuSK. We identified a total of 10,183 phosphopeptides, of which 203 were significantly up- or down-regulated. Regulated phosphopeptides were classified into four different clusters according to their temporal profiles. Within these clusters we found an overrepresentation of specific protein classes associated with different cellular functions. In particular, we found an enrichment of regulated phosphoproteins involved in posttranscriptional mechanisms and in cytoskeletal organization. These findings provide novel insights into the complex signaling network downstream of MuSK and form the basis for future mechanistic studies.","authors":"D\u00fcrnberger, G., Camurdanoglu, BZ., Tomschik, M., Schutzbier, M., Roitinger, E., Hudecz, O., Mechtler, K., Herbst, R.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mol Cell Proteomics","volume":"13","issue":"8","page":"1993-2003","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24859206","title":"Stem cells marked by the R-spondin receptor LGR5.","abstract":"Since the discovery of LGR5 as a marker of intestinal stem cells, the field has developed explosively and led to many new avenues of research. The inner workings of the intestinal crypt stem cell niche are now well understood. The study of stem cell-enriched genes has uncovered some previously unknown aspects of the Wnt signaling pathway, the major driver of crypt dynamics. LGR5(+) stem cells can now be cultured over long periods in vitro as epithelial organoids or \"mini-guts.\" This technology opens new possibilities of using cultured adult stem cells for drug development, disease modeling, gene therapy, and regenerative medicine. This review describes the rediscovery of crypt base columnar cells as LGR5(+) adult stem cells and summarizes subsequent progress, promises, unresolved issues, and challenges of the field.","authors":"Koo, BK., Clevers, H.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Gastroenterology","volume":"147","issue":"2","page":"289-302","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24813946","title":"RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase Clp1.","abstract":"RNA-specific polynucleotide kinases of the Clp1 subfamily are key components of various RNA maturation pathways. However, the structural basis explaining their substrate specificity and the enzymatic mechanism is elusive. Here, we report crystal structures of Clp1 from Caenorhabditis elegans (ceClp1) in a number of nucleotide- and RNA-bound states along the reaction pathway. The combined structural and biochemical analysis of ceClp1 elucidates the RNA specificity and lets us derive a general model for enzyme catalysis of RNA-specific polynucleotide kinases. We identified an RNA binding motif referred to as \"clasp\" as well as a conformational switch that involves the essential Walker A lysine (Lys127) and regulates the enzymatic activity of ceClp1. Structural comparison with other P loop proteins, such as kinases, adenosine triphosphatases (ATPases), and guanosine triphosphatases (GTPases), suggests that the observed conformational switch of the Walker A lysine is a broadly relevant mechanistic feature.","authors":"Dikfidan, A., Loll, B., Zeymer, C., Magler, I., Clausen, T., Meinhart, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mol Cell","volume":"54","issue":"6","page":"975-86","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24728465","title":"Heterozygote loss of ACE2 is sufficient to increase the susceptibility to heart disease.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24728465<\/PMID><DateCompleted><Year>2015<\/Year><Month>03<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1432-1440<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>92<\/Volume><Issue>8<\/Issue><PubDate><Year>2014<\/Year><Month>Aug<\/Month><\/PubDate><\/JournalIssue><Title>Journal of molecular medicine (Berlin, Germany)<\/Title><ISOAbbreviation>J Mol Med (Berl)<\/ISOAbbreviation><\/Journal><ArticleTitle>Heterozygote loss of ACE2 is sufficient to increase the susceptibility to heart disease.<\/ArticleTitle><Pagination><MedlinePgn>847-58<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007\/s00109-014-1149-y<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Angiotensin-converting enzyme 2 (ACE2) metabolizes Ang II into Ang 1-7 thereby negatively regulating the renin-angiotensin system. However, heart disease in humans and in animal models is associated with only a partial loss of ACE2. ACE2 is an X-linked gene; and as such, we tested the clinical relevance of a partial loss of ACE2 by using female ACE2(+\/+) (wildtype) and ACE2(+\/-) (heterozygote) mice. Pressure overload in ACE2(+\/-) mice resulted in greater LV dilation and worsening systolic and diastolic dysfunction. These changes were associated with increased myocardial fibrosis, hypertrophy, and upregulation of pathological gene expression. In response to Ang II infusion, there was increased NADPH oxidase activity and myocardial fibrosis resulting in the worsening of Ang II-induced diastolic dysfunction with a preserved systolic function. Ang II-mediated cellular effects in cultured adult ACE2(+\/-) cardiomyocytes and cardiofibroblasts were exacerbated. Ang II-mediated pathological signaling worsened in ACE2(+\/-) hearts characterized by an increase in the phosphorylation of ERK1\/2 and JNK1\/2 and STAT-3 pathways. The ACE2(+\/-) mice showed an exacerbated pressor response with increased vascular fibrosis and stiffness. Vascular superoxide and nitrotyrosine levels were increased in ACE2(+\/-) vessels consistent with increased vascular oxidative stress. These changes occurred with increased renal fibrosis and superoxide production. Partial heterozygote loss of ACE2 is sufficient to increase the susceptibility to heart disease secondary to pressure overload and Ang II infusion.","authors":"Wang, W., Patel, VB., Parajuli, N., Fan, D., Basu, R., Wang, Z., Ramprasath, T., Kassiri, Z., Penninger, JM., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Mol Med (Berl)","volume":"92","issue":"8","page":"847-58","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24700552","title":"Micro-aggregates do not influence bone marrow stromal cell chondrogenesis.","abstract":"Although bone marrow stromal cells (BMSCs) appear promising for cartilage repair, current clinical results are suboptimal and the success of BMSC-based therapies relies on a number of methodological improvements, among which is better understanding and control of their differentiation pathways. We investigated here the role of the cellular environment (paracrine vs juxtacrine signalling) in the chondrogenic differentiation of BMSCs. Bovine BMSCs were encapsulated in alginate beads, as dispersed cells or as small micro-aggregates, to create different paracrine and juxtacrine signalling conditions. BMSCs were then cultured for 21 days with TGF\u03b2<sub>3<\/sub> added for 0, 7 or 21 days. Chondrogenic differentiation was assessed at the gene (type II and X collagens, aggrecan, TGF\u03b2, sp7) and matrix (biochemical assays and histology) levels. The results showed that micro-aggregates had no beneficial effects over dispersed cells: matrix production was similar, whereas chondrogenic marker gene expression was lower for the micro-aggregates, under all TGF\u03b2 conditions tested. This weakened chondrogenic differentiation might be explained by a different cytoskeleton organization at day 0 in the micro-aggregates. Copyright \u00a9 2014 John Wiley &amp; Sons, Ltd.","authors":"Potier, E., Rivron, NC., Van Blitterswijk, CA., Ito, K.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"J Tissue Eng Regen Med","volume":"10","issue":"12","page":"1021-1032","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-11-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24700286","title":"Gain-of-function mutation in Gnao1: a murine model of epileptiform encephalopathy (EIEE17)?","abstract":"G protein-coupled receptors strongly modulate neuronal excitability but there has been little evidence for G protein mechanisms in genetic epilepsies. Recently, four patients with epileptic encephalopathy (EIEE17) were found to have mutations in GNAO1, the most abundant G protein in brain, but the mechanism of this effect is not known. The GNAO1 gene product, G\u03b1o, negatively regulates neurotransmitter release. Here, we report a dominant murine model of Gnao1-related seizures and sudden death. We introduced a genomic gain-of-function knock-in mutation (Gnao1 (+\/G184S)) that prevents Go turnoff by Regulators of G protein signaling proteins. This results in rare seizures, strain-dependent death between 15 and 40\u00a0weeks of age, and a markedly increased frequency of interictal epileptiform discharges. Mutants on a C57BL\/6J background also have faster sensitization to pentylenetetrazol (PTZ) kindling. Both premature lethality and PTZ kindling effects are suppressed in the 129SvJ mouse strain. We have mapped a 129S-derived modifier locus on Chromosome 17 (within the region 41-70\u00a0MB) as a Modifer of G protein Seizures (Mogs1). Our mouse model suggests a novel gain-of-function mechanism for the newly defined subset of epileptic encephalopathy (EIEE17). Furthermore, it reveals a new epilepsy susceptibility modifier Mogs1 with implications for the complex genetics of human epilepsy as well as sudden death in epilepsy.","authors":"Kehrl, JM., Sahaya, K., Dalton, HM., Charbeneau, RA., Kohut, KT., Gilbert, K., Pelz, MC., Parent, J., Neubig, RR.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mamm Genome","volume":"25","issue":"5-6","page":"202-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24685159","title":"Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin.","abstract":"Steroid hormones act as important developmental switches, and their nuclear receptors regulate many genes. However, few hormone-dependent enhancers have been characterized, and important aspects of their sequence architecture, cell-type-specific activating and repressing functions, or the regulatory roles of their chromatin structure have remained unclear. We used STARR-seq, a recently developed enhancer-screening assay, and ecdysone signaling in two different Drosophila cell types to derive genome-wide hormone-dependent enhancer-activity maps. We demonstrate that enhancer activation depends on cis-regulatory motif combinations that differ between cell types and can predict cell-type-specific ecdysone targeting. Activated enhancers are often not accessible prior to induction. Enhancer repression following hormone treatment seems independent of receptor motifs and receptor binding to the enhancer, as we show using ChIP-seq, but appears to rely on motifs for other factors, including Eip74. Our strategy is applicable to study signal-dependent\u00a0enhancers for different pathways and across organisms.","authors":"Shlyueva, D., Stelzer, C., Gerlach, D., Y\u00e1\u00f1ez-Cuna, JO., Rath, M., Bory\u0144, \u0141M., Arnold, CD., Stark, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Mol Cell","volume":"54","issue":"1","page":"180-192","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24407481","title":"Toddler: an embryonic signal that promotes cell movement via Apelin receptors.","abstract":"It has been assumed that most, if not all, signals regulating early development have been identified. Contrary to this expectation, we identified 28 candidate signaling proteins expressed during zebrafish embryogenesis, including Toddler, a short, conserved, and secreted peptide. Both absence and overproduction of Toddler reduce the movement of mesendodermal cells during zebrafish gastrulation. Local and ubiquitous production of Toddler promote cell movement, suggesting that Toddler is neither an attractant nor a repellent but acts globally as a motogen. Toddler drives internalization of G protein-coupled APJ\/Apelin receptors, and activation of APJ\/Apelin signaling rescues toddler mutants. These results indicate that Toddler is an activator of APJ\/Apelin receptor signaling, promotes gastrulation movements, and might be the first in a series of uncharacterized developmental signals.","authors":"Pauli, A., Norris, ML., Valen, E., Chew, GL., Gagnon, JA., Zimmerman, S., Mitchell, A., Ma, J., Dubrulle, J., Reyon, D., Tsai, SQ., Joung, JK., Saghatelian, A., Schier, AF.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Science","volume":"343","issue":"6172","page":"1248636","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24639532","title":"Flying Drosophila stabilize their vision-based velocity controller by sensing wind with their antennae.","abstract":"Flies and other insects use vision to regulate their groundspeed in flight, enabling them to fly in varying wind conditions. Compared with mechanosensory modalities, however, vision requires a long processing delay (~100 ms) that might introduce instability if operated at high gain. Flies also sense air motion with their antennae, but how this is used in flight control is unknown. We manipulated the antennal function of fruit flies by ablating their aristae, forcing them to rely on vision alone to regulate groundspeed. Arista-ablated flies in flight exhibited significantly greater groundspeed variability than intact flies. We then subjected them to a series of controlled impulsive wind gusts delivered by an air piston and experimentally manipulated antennae and visual feedback. The results show that an antenna-mediated response alters wing motion to cause flies to accelerate in the same direction as the gust. This response opposes flying into a headwind, but flies regularly fly upwind. To resolve this discrepancy, we obtained a dynamic model of the fly's velocity regulator by fitting parameters of candidate models to our experimental data. The model suggests that the groundspeed variability of arista-ablated flies is the result of unstable feedback oscillations caused by the delay and high gain of visual feedback. The antenna response drives active damping with a shorter delay (~20 ms) to stabilize this regulator, in exchange for increasing the effect of rapid wind disturbances. This provides insight into flies' multimodal sensory feedback architecture and constitutes a previously unknown role for the antennae.","authors":"Fuller, SB., Straw, AD., Peek, MY., Murray, RM., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Proc Natl Acad Sci U S A","volume":"111","issue":"13","page":"E1182-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24614317","title":"Transcriptional enhancers: from properties to genome-wide predictions.","abstract":"Cellular development, morphology and function are governed by precise patterns of gene expression. These are established by the coordinated action of genomic regulatory elements known as enhancers or cis-regulatory modules. More than 30 years after the initial discovery of enhancers, many of their properties have been elucidated; however, despite major efforts, we only have an incomplete picture of enhancers in animal genomes. In this Review, we discuss how properties of enhancer sequences and chromatin are used to predict enhancers in genome-wide studies. We also cover recently developed high-throughput methods that allow the direct testing and identification of enhancers on the basis of their activity. Finally, we discuss recent technological advances and current challenges in the field of regulatory genomics.","authors":"Shlyueva, D., Stampfel, G., Stark, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nat Rev Genet","volume":"15","issue":"4","page":"272-86","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24584058","title":"Control of antigen receptor diversity through spatial regulation of V(D)J recombination.","abstract":"Lymphocytes recognize a vast variety of pathogens by expressing a diverse repertoire of antigen receptor genes that are assembled by V(D)J recombination in immature B cells (Igh, Igk) and T cells (Tcrb, Tcra\/d). V(D)J recombination takes place in the 3' proximal domain containing the D, J, and C gene segments, whereas 31 (Tcrb) to 200 (Igh) V genes are spread over a large region of 0.67 (Tcrb) to 3 (Igk) Mb pairs. All antigen receptor loci undergo reversible contraction at the developmental stage, where they engage in V-(D)J recombination. This long-range looping promotes the participation of all V genes in V-(D)J recombination by juxtaposing distant V genes next to (D)J segments in the proximal recombination center. The B-cell-specific Pax5, ubiquitous YY1, and architectural CTCF\/cohesin proteins promote Igh locus contraction in pro-B cells by binding to multiple sites in the VH gene cluster. These regulators also control the pro-B-cell-specific activity of the distally located PAIR elements, which are likely involved in the regulation of VH-DJH recombination by mediating locus contraction. Notably, the large VH gene cluster of the Igh locus undergoes flexible long-range looping that ensures similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire.","authors":"Ebert, A., Medvedovic, J., Tagoh, H., Schwickert, TA., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cold Spring Harb Symp Quant Biol","volume":"78","issue":null,"page":"11-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24630726","title":"SWI\/SNF complex prevents lineage reversion and induces temporal patterning in neural stem cells.","abstract":"Members of the SWI\/SNF chromatin-remodeling complex are among the most frequently mutated genes in human cancer, but how they suppress tumorigenesis is currently unclear. Here, we use Drosophila neuroblasts to demonstrate that the SWI\/SNF component Osa (ARID1) prevents tumorigenesis by ensuring correct lineage progression in stem cell lineages. We show that Osa induces a transcriptional program in the transit-amplifying population that initiates temporal patterning, limits self-renewal, and prevents dedifferentiation. We identify the Prdm protein Hamlet as a key component of this program. Hamlet is directly induced by Osa and regulates the progression of progenitors through distinct transcriptional states to limit the number of transit-amplifying divisions. Our data provide a mechanistic explanation for the widespread tumor suppressor activity of SWI\/SNF. Because the Hamlet homologs Evi1 and Prdm16 are frequently mutated in cancer, this mechanism could well be conserved in human stem cell lineages. PAPERCLIP:","authors":"Eroglu, E., Burkard, TR., Jiang, Y., Saini, N., Homem, CCF., Reichert, H., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell","volume":"156","issue":"6","page":"1259-1273","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24583019","title":"Cdk1 inactivation terminates mitotic checkpoint surveillance and stabilizes kinetochore attachments in anaphase.","abstract":"Two mechanisms safeguard the bipolar attachment of chromosomes in mitosis. A correction mechanism destabilizes erroneous attachments that do not generate tension across sister kinetochores [1]. In response to unattached kinetochores, the mitotic checkpoint delays anaphase onset by inhibiting the anaphase-promoting complex\/cyclosome (APC\/C(Cdc20)) [2]. Upon satisfaction of both pathways, the APC\/C(Cdc20) elicits the degradation of securin and cyclin B [3]. This liberates separase triggering sister chromatid disjunction and inactivates cyclin-dependent kinase 1 (Cdk1) causing mitotic exit. How eukaryotic cells avoid the engagement of attachment monitoring mechanisms when sister chromatids split and tension is lost at anaphase is poorly understood [4]. Here we show that Cdk1 inactivation disables mitotic checkpoint surveillance at anaphase onset in human cells. Preventing cyclin B1 proteolysis at the time of sister chromatid disjunction destabilizes kinetochore-microtubule attachments and triggers the engagement of the mitotic checkpoint. As a consequence, mitotic checkpoint proteins accumulate at anaphase kinetochores, the APC\/C(Cdc20) is inhibited, and securin reaccumulates. Conversely, acute pharmacological inhibition of Cdk1 abrogates the engagement and maintenance of the mitotic checkpoint upon microtubule depolymerization. We propose that the simultaneous destruction of securin and cyclin B elicited by the APC\/C(Cdc20) couples chromosome segregation to the dissolution of attachment monitoring mechanisms during mitotic exit.","authors":"V\u00e1zquez-Novelle, MD., Sansregret, L., Dick, AE., Smith, CA., McAinsh, AD., Gerlich, DW., Petronczki, M.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Biol","volume":"24","issue":"6","page":"638-45","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24553136","title":"The E3 ligase Cbl-b and TAM receptors regulate cancer metastasis via natural killer cells.","abstract":"Tumour metastasis is the primary cause of mortality in cancer patients and remains the key challenge for cancer therapy. New therapeutic approaches to block inhibitory pathways of the immune system have renewed hopes for the utility of such therapies. Here we show that genetic deletion of the E3 ubiquitin ligase Cbl-b (casitas B-lineage lymphoma-b) or targeted inactivation of its E3 ligase activity licenses natural killer (NK) cells to spontaneously reject metastatic tumours. The TAM tyrosine kinase receptors Tyro3, Axl and Mer (also known as Mertk) were identified as ubiquitylation substrates for Cbl-b. Treatment of wild-type NK cells with a newly developed small molecule TAM kinase inhibitor conferred therapeutic potential, efficiently enhancing anti-metastatic NK cell activity in vivo. Oral or intraperitoneal administration using this TAM inhibitor markedly reduced murine mammary cancer and melanoma metastases dependent on NK cells. We further report that the anticoagulant warfarin exerts anti-metastatic activity in mice via Cbl-b\/TAM receptors in NK cells, providing a molecular explanation for a 50-year-old puzzle in cancer biology. This novel TAM\/Cbl-b inhibitory pathway shows that it might be possible to develop a 'pill' that awakens the innate immune system to kill cancer metastases.","authors":"Paolino, M., Choidas, A., Wallner, S., Pranjic, B., Uribesalgo, I., Loeser, S., Jamieson, AM., Langdon, WY., Ikeda, F., Fededa, JP., Cronin, SJ., Nitsch, R., Schultz-Fademrecht, C., Eickhoff, J., Menninger, S., Unger, A., Torka, R., Gruber, T., Hinterleitner, R., Baier, G., Wolf, D., Ullrich, A., Klebl, BM., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nature","volume":"507","issue":"7493","page":"508-12","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24516159","title":"HACE1 reduces oxidative stress and mutant Huntingtin toxicity by promoting the NRF2 response.","abstract":"Oxidative stress plays a key role in late onset diseases including cancer and neurodegenerative diseases such as Huntington disease. Therefore, uncovering regulators of the antioxidant stress responses is important for understanding the course of these diseases. Indeed, the nuclear factor erythroid 2-related factor 2 (NRF2), a master regulator of the cellular antioxidative stress response, is deregulated in both cancer and neurodegeneration. Similar to NRF2, the tumor suppressor Homologous to the E6-AP Carboxyl Terminus (HECT) domain and Ankyrin repeat containing E3 ubiquitin-protein ligase 1 (HACE1) plays a protective role against stress-induced tumorigenesis in mice, but its roles in the antioxidative stress response or its involvement in neurodegeneration have not been investigated. To this end we examined Hace1 WT and KO mice and found that Hace1 KO animals exhibited increased oxidative stress in brain and that the antioxidative stress response was impaired. Moreover, HACE1 was found to be essential for optimal NRF2 activation in cells challenged with oxidative stress, as HACE1 depletion resulted in reduced NRF2 activity, stability, and protein synthesis, leading to lower tolerance against oxidative stress triggers. Strikingly, we found a reduction of HACE1 levels in the striatum of Huntington disease patients, implicating HACE1 in the pathology of Huntington disease. Moreover, ectopic expression of HACE1 in striatal neuronal progenitor cells provided protection against mutant Huntingtin-induced redox imbalance and hypersensitivity to oxidative stress, by augmenting NRF2 functions. These findings reveal that the tumor suppressor HACE1 plays a role in the NRF2 antioxidative stress response pathway and in neurodegeneration.","authors":"Rotblat, B., Southwell, AL., Ehrnhoefer, DE., Skotte, NH., Metzler, M., Franciosi, S., Leprivier, G., Somasekharan, SP., Barokas, A., Deng, Y., Tang, T., Mathers, J., Cetinbas, N., Daugaard, M., Kwok, B., Li, L., Carnie, CJ., Fink, D., Nitsch, R., Galpin, JD., Ahern, CA., Melino, G., Penninger, JM., Hayden, MR., Sorensen, PH.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Proc Natl Acad Sci U S A","volume":"111","issue":"8","page":"3032-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24554530","title":"Accelerated Three-Dimensional Neuroepithelium Formation from Human Embryonic Stem Cells and Its Use for Quantitative Differentiation to Human Retinal Pigment Epithelium.","abstract":"Successful applications of pluripotent stem cells to cell-based therapies will rely on rapid and efficient methods to differentiate cells toward the target cell type. While methods have been developed for the generation of some medically relevant cell types including retinal pigment epithelium (RPE) cells, such protocols are lengthy and result in a heterogeneous cell mixture of RPE and non-RPE cells, requiring manual subselection and expansion. Such considerations have significant limiting impact of therapeutic applicability. Here we describe the accelerated three-dimensional neuroepithelial cyst culture of human embryonic stem cells (hESCs) and its utility to achieve quantitative production of RPE cell sheet with no manual selection in 30 days.","authors":"Zhu, Y., Schreiter, S., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Methods Mol Biol","volume":"1307","issue":null,"page":"345-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24453943","title":"Electron tomography and simulation of baculovirus actin comet tails support a tethered filament model of pathogen propulsion.","abstract":"Several pathogens induce propulsive actin comet tails in cells they invade to disseminate their infection. They achieve this by recruiting factors for actin nucleation, the Arp2\/3 complex, and polymerization regulators from the host cytoplasm. Owing to limited information on the structural organization of actin comets and in particular the spatial arrangement of filaments engaged in propulsion, the underlying mechanism of pathogen movement is currently speculative and controversial. Using electron tomography we have resolved the three-dimensional architecture of actin comet tails propelling baculovirus, the smallest pathogen yet known to hijack the actin motile machinery. Comet tail geometry was also mimicked in mixtures of virus capsids with purified actin and a minimal inventory of actin regulators. We demonstrate that propulsion is based on the assembly of a fishbone-like array of actin filaments organized in subsets linked by branch junctions, with an average of four filaments pushing the virus at any one time. Using an energy-minimizing function we have simulated the structure of actin comet tails as well as the tracks adopted by baculovirus in infected cells in vivo. The results from the simulations rule out gel squeezing models of propulsion and support those in which actin filaments are continuously tethered during branch nucleation and polymerization. Since Listeria monocytogenes, Shigella flexneri, and Vaccinia virus among other pathogens use the same common toolbox of components as baculovirus to move, we suggest they share the same principles of actin organization and mode of propulsion.","authors":"Mueller, J., Pfanzelter, J., Winkler, C., Narita, A., Le Clainche, C., Nemethova, M., Carlier, MF., Maeda, Y., Welch, MD., Ohkawa, T., Schmeiser, C., Resch, GP., Small, JV.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"PLoS Biol","volume":"12","issue":"1","page":"e1001765","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24381158","title":"Analysis and modeling of mitotic spindle orientations in three dimensions.","abstract":"The orientation of the mitotic spindle determines the relative size and position of the daughter cells and influences the asymmetric inheritance of localized cell fate determinants. The onset of mammalian neurogenesis, for example, coincides with changes in spindle orientation. To address the functional implications of this and related phenomena, precise methods for determining the orientation of the mitotic spindle in complex tissues are needed. Here, we present methodology for the analysis of spindle orientation in 3D. Our method allows statistical analysis and modeling of spindle orientation and involves two parameters for horizontal and vertical bias that can unambiguously describe the distribution of spindle orientations in an experimental sample. We find that 3D analysis leads to systematically different results from 2D analysis and, surprisingly, truly random spindle orientations do not result in equal numbers of horizontal and vertical orientations. We show that our method can describe the distribution of spindle orientation angles under different biological conditions. As an example of biological application we demonstrate that the adapter protein Inscuteable (mInsc) can actively promote vertical spindle orientation in apical progenitors during mouse neurogenesis.","authors":"J\u00fcschke, C., Xie, Y., Postiglione, MP., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Proc Natl Acad Sci U S A","volume":"111","issue":"3","page":"1014-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24452333","title":"Transgenic expression of Map3k4 rescues T-associated sex reversal (Tas) in mice.","abstract":"Disorders of sex development in the human population range in severity from mild genital defects to gonadal sex reversal. XY female development has been associated with heterozygous mutations in several genes, including SOX9, WT1 and MAP3K1. In contrast, XY sex reversal in mice usually requires complete absence of testis-determining gene products. One exception to this involves T-associated sex reversal (Tas), a phenomenon characterized by the formation of ovotestes or ovaries in XY mice hemizygous for the hairpin-tail (T(hp)) or T-Orleans (T(Orl)) deletions on proximal mouse chromosome 17. We recently reported that mice heterozygous for a null allele of Map3k4, which resides in the T(hp) deletion, exhibit XY ovotestis development and occasional gonadal sex reversal on the sensitized C57BL\/6J-Y(AKR) (B6-Y(AKR)) genetic background, reminiscent of the Tas phenotype. However, these experiments did not exclude the possibility that loss of other loci in the T(hp) deletion, or other effects of the deletion itself, might contribute to Tas. Here, we show that disruption to Sry expression underlies XY gonadal defects in B6-Y(AKR) embryos harbouring the T(hp) deletion and that a functional Map3k4 bacterial artificial chromosome rescues these abnormalities by re-establishing a normal Sry expression profile. These data demonstrate that Map3k4 haploinsufficiency is the cause of T-associated sex reversal and that levels of this signalling molecule are a major determinant of the expression profile of Sry.","authors":"Warr, N., Siggers, P., Carr\u00e9, GA., Bogani, D., Brixey, R., Akiyoshi, M., Tachibana, M., Teboul, L., Wells, S., Sanderson, J., Greenfield, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Hum Mol Genet","volume":"23","issue":"11","page":"3035-44","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24440450","title":"Myosin chaperones.","abstract":"The folding and assembly of myosin motor proteins is essential for most movement processes at the cellular, but also at the organism level. Importantly, myosins, which represent a very diverse family of proteins, require the activity of general and specialized folding factors to develop their full motor function. The activities of the myosin-specific UCS (UNC-45\/Cro1\/She4) chaperones range from assisting acto-myosin dependent transport processes to scaffolding multi-subunit chaperone complexes, which are required to assemble myofilaments. Recent structure-function studies revealed the structural organization of TPR (tetratricopeptide repeat)-containing and TPR-less UCS chaperones. The observed structural differences seem to reflect the specialized and remarkably versatile working mechanisms of myosin-directed chaperones, as will be discussed in this review.","authors":"Hellerschmied, D., Clausen, T.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Opin Struct Biol","volume":"25","issue":null,"page":"9-15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11919638","title":"Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine.","abstract":"Molecular chaperones and proteases monitor the folded state of other proteins. In addition to recognizing non-native conformations, these quality control factors distinguish substrates that can be refolded from those that need to be degraded. To investigate the molecular basis of this process, we have solved the crystal structure of DegP (also known as HtrA), a widely conserved heat shock protein that combines refolding and proteolytic activities. The DegP hexamer is formed by staggered association of trimeric rings. The proteolytic sites are located in a central cavity that is only accessible laterally. The mobile side-walls are constructed by twelve PDZ domains, which mediate the opening and closing of the particle and probably the initial binding of substrate. The inner cavity is lined by several hydrophobic patches that may act as docking sites for unfolded polypeptides. In the chaperone conformation, the protease domain of DegP exists in an inactive state, in which substrate binding in addition to catalysis is abolished.","authors":"Krojer, T., Garrido-Franco, M., Huber, R., Ehrmann, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Nature","volume":"416","issue":"6879","page":"455-9","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2002-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24440391","title":"Cellular and behavioral functions of fruitless isoforms in Drosophila courtship.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">24440391<\/PMID><DateCompleted><Year>2014<\/Year><Month>08<\/Month><Day>28<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>24<\/Volume><Issue>3<\/Issue><PubDate><Year>2014<\/Year><Month>Feb<\/Month><Day>03<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Cellular and behavioral functions of fruitless isoforms in Drosophila courtship.<\/ArticleTitle><Pagination><MedlinePgn>242-51<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2013.12.015<\/ELocationID><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0960-9822(13)01534-0<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Male-specific products of the fruitless (fru) gene control the development and function of neuronal circuits that underlie male-specific behaviors in Drosophila, including courtship. Alternative splicing generates at least three distinct Fru isoforms, each containing a different zinc-finger domain. Here, we examine the expression and function of each of these isoforms.","authors":"von Philipsborn, AC., J\u00f6rchel, S., Tirian, L., Demir, E., Morita, T., Stern, DL., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Curr Biol","volume":"24","issue":"3","page":"242-51","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24413397","title":"Cell-autonomous correction of ring chromosomes in human induced pluripotent stem cells.","abstract":"Ring chromosomes are structural aberrations commonly associated with birth defects, mental disabilities and growth retardation. Rings form after fusion of the long and short arms of a chromosome, and are sometimes associated with large terminal deletions. Owing to the severity of these large aberrations that can affect multiple contiguous genes, no possible therapeutic strategies for ring chromosome disorders have been proposed. During cell division, ring chromosomes can exhibit unstable behaviour leading to continuous production of aneuploid progeny with low viability and high cellular death rate. The overall consequences of this chromosomal instability have been largely unexplored in experimental model systems. Here we generated human induced pluripotent stem cells (iPSCs) from patient fibroblasts containing ring chromosomes with large deletions and found that reprogrammed cells lost the abnormal chromosome and duplicated the wild-type homologue through the compensatory uniparental disomy (UPD) mechanism. The karyotypically normal iPSCs with isodisomy for the corrected chromosome outgrew co-existing aneuploid populations, enabling rapid and efficient isolation of patient-derived iPSCs devoid of the original chromosomal aberration. Our results suggest a fundamentally different function for cellular reprogramming as a means of 'chromosome therapy' to reverse combined loss-of-function across many genes in cells with large-scale aberrations involving ring structures. In addition, our work provides an experimentally tractable human cellular system for studying mechanisms of chromosomal number control, which is of critical relevance to human development and disease.","authors":"Bershteyn, M., Hayashi, Y., Desachy, G., Hsiao, EC., Sami, S., Tsang, KM., Weiss, LA., Kriegstein, AR., Yamanaka, S., Wynshaw-Boris, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nature","volume":"507","issue":"7490","page":"99-103","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24361693","title":"Two distinct types of neuronal asymmetries are controlled by the Caenorhabditis elegans zinc finger transcription factor die-1.","abstract":"Left\/right asymmetric features of animals are either randomly distributed on either the left or right side within a population (\"antisymmetries\") or found stereotypically on one particular side of an animal (\"directional asymmetries\"). Both types of asymmetries can be found in nervous systems, but whether the regulatory programs that establish these asymmetries share any mechanistic features is not known. We describe here an unprecedented molecular link between these two types of asymmetries in Caenorhabditis elegans. The zinc finger transcription factor die-1 is expressed in a directionally asymmetric manner in the gustatory neuron pair ASE left (ASEL) and ASE right (ASER), while it is expressed in an antisymmetric manner in the olfactory neuron pair AWC left (AWCL) and AWC right (AWCR). Asymmetric die-1 expression is controlled in a fundamentally distinct manner in these two neuron pairs. Importantly, asymmetric die-1 expression controls the directionally asymmetric expression of gustatory receptor proteins in the ASE neurons and the antisymmetric expression of olfactory receptor proteins in the AWC neurons. These asymmetries serve to increase the ability of the animal to discriminate distinct chemosensory inputs.","authors":"Cochella, L., Tursun, B., Hsieh, YW., Galindo, S., Johnston, RJ., Chuang, CF., Hobert, O.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genes Dev","volume":"28","issue":"1","page":"34-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24325444","title":"Is salamander hindlimb regeneration similar to that of the forelimb? Anatomical and morphogenetic analysis of hindlimb muscle regeneration in GFP-transgenic axolotls as a basis for regenerative and developmental studies.","abstract":"The axolotl Ambystoma mexicanum is one of the most used model organisms in developmental and regenerative studies because it is commonly said that it can reconstitute a normal and fully functional forelimb\/hindlimb after amputation. However, there is not a publication that has described in detail the regeneration of the axolotl hindlimb muscles. Here we describe and illustrate, for the first time, the regeneration of the thigh, leg and foot muscles in transgenic axolotls that express green fluorescent protein in muscle fibers and compare our results with data obtained by us and by other authors about axolotl forelimb regeneration and about fore- and hindlimb ontogeny in axolotls, frogs and other tetrapods. Our observations and comparisons point out that: (1) there are no muscle anomalies in any regenerated axolotl hindlimbs, in clear contrast to our previous study of axolotl forelimb regeneration, where we found muscle anomalies in 43% of the regenerated forelimbs; (2) during axolotl hindlimb regeneration there is a proximo-distal and a tibio-fibular morphogenetic gradient in the order of muscle regeneration and differentiation, but not a ventro-dorsal gradient, whereas our previous studies showed that in axolotl forelimb muscle regeneration there are proximo-distal, radio-ulnar and ventro-dorsal morphogenetic gradients. We discuss the broader implications of these observations for regenerative, evolutionary, developmental and morphogenetic studies.","authors":"Diogo, R., Murawala, P., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Anat","volume":"224","issue":"4","page":"459-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24302552","title":"Development of fore- and hindlimb muscles in GFP-transgenic axolotls: morphogenesis, the tetrapod bauplan, and new insights on the forelimb-hindlimb enigma.","abstract":"The axolotl is becoming one of the most used model organisms in developmental and regenerative studies but no publication has described in detail the development of its forelimb and hindlimb muscles. We describe and illustrate the ontogeny of these muscles in transgenic axolotls that express GFP in muscle fibers and discuss our results and data previously obtained by us and by other authors about limb regeneration in axolotls and ontogeny in frogs and other tetrapods. Our observations and comparisons: (1) demonstrate radio-ulnar and ventro-dorsal morphogenetic gradients in the order of axolotl forelimb muscle formation and differentiation, while in axolotl hindlimb ontogeny there are only proximo-distal and tibio-fibular gradients; some of the axolotl gradients are therefore different from the ulno-radial\/fibulo-tibial fore- and hindlimb and the dorso-ventral hindimb ontogenetic morphogenetic gradients seen in frogs and amniotes such as chickens; (2) provide a potential explanation for the usual presence, in both limbs of taxa from all major tetrapod groups, of more radial\/tibial muscles than ulnar\/fibular muscles; (3) support the \"in-out\" developmental mechanism of appendicular muscle formation; (4) offer new insights about the ancestral Bauplan of tetrapod limbs, including the striking similarity of the zeugopodial (forearm\/leg) and autopodial (hand\/foot) muscles of the two limbs and the ventro-dorsal symmetry of the zeugopodial muscles of a same limb; and (5) provide further evidence to corroborate the hypothesis that these similarities are due to derived homoplastic events that occurred during the fins-limbs transition and not due to forelimb-hindlimb serial homology.","authors":"Diogo, R., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"J Exp Zool B Mol Dev Evol","volume":"322","issue":"2","page":"106-27","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24292673","title":"ZRF1 controls the retinoic acid pathway and regulates leukemogenic potential in acute myeloid leukemia.","abstract":"Acute myeloid leukemia (AML) is frequently linked to epigenetic abnormalities and deregulation of gene transcription, which lead to aberrant cell proliferation and accumulation of undifferentiated precursors. ZRF1, a recently characterized epigenetic factor involved in transcriptional regulation, is highly overexpressed in human AML, but it is not known whether it plays a role in leukemia progression. Here, we demonstrate that ZRF1 depletion decreases cell proliferation, induces apoptosis and enhances cell differentiation in human AML cells. Treatment with retinoic acid (RA), a differentiating agent currently used to treat certain AMLs, leads to a functional switch of ZRF1 from a negative regulator to an activator of differentiation. At the molecular level, ZRF1 controls the RA-regulated gene network through its interaction with the RA receptor \u03b1 (RAR\u03b1) and its binding to RA target genes. Our genome-wide expression study reveals that ZRF1 regulates the transcription of nearly half of RA target genes. Consistent with our in vitro observations that ZRF1 regulates proliferation, apoptosis, and differentiation, ZRF1 depletion strongly inhibits leukemia progression in a xenograft mouse model. Finally, ZRF1 knockdown cooperates with RA treatment in leukemia suppression in vivo. Taken together, our data reveal that ZRF1 is a key transcriptional regulator in leukemia progression and suggest that ZRF1 inhibition could be a novel strategy to be explored for AML treatment.","authors":"Demajo, S., Uribesalgo, I., Guti\u00e9rrez, A., Ballar\u00e9, C., Capdevila, S., Roth, M., Zuber, J., Mart\u00edn-Caballero, J., Di Croce, L.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Oncogene","volume":"33","issue":"48","page":"5501-10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34750578","title":"Cell type ontologies of the Human Cell Atlas.","abstract":"Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body while at the same time raising the need to formalize this new knowledge. Here, we discuss current efforts to harmonize and integrate different sources of annotations of cell types and states into a reference cell ontology. We illustrate with examples how a unified ontology can consolidate and advance our understanding of cell types across scientific communities and biological domains.","authors":"Osumi-Sutherland, D., Xu, C., Keays, M., Levine, AP., Kharchenko, PV., Regev, A., Lein, E., Teichmann, SA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Cell Biol","volume":"23","issue":"11","page":"1129-1135","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-12-29","doi":"10.1038\/s41556-021-00787-7","first_author":"Osumi-Sutherland, D.","corresponding_authors":"Teichmann, SA."},{"pmid":"24291092","title":"Spindle assembly checkpoint of oocytes depends on a kinetochore structure determined by cohesin in meiosis I.","abstract":"Since the dissolution of sister chromatid cohesion by separase and cyclin B destruction is irreversible, it is essential to delay both until all chromosomes have bioriented on the mitotic spindle. Kinetochores that are not correctly attached to the spindle generate the mitotic checkpoint complex (MCC), which inhibits the anaphase-promoting complex\/cyclosome (APC\/C) and blocks anaphase onset. This process is known as the spindle assembly checkpoint (SAC). The SAC is especially important in meiosis I, where bivalents consisting of homologous chromosomes held together by chiasmata biorient. Since the first meiotic division is unaffected by rare achiasmatic chromosomes or misaligned bivalents, it is thought that several tensionless kinetochores are required to produce sufficient MCC for APC\/C inhibition. Consistent with this, univalents lacking chiasmata elicit a SAC-mediated arrest in Mlh1(-\/-) oocytes. In contrast, chromatids generated by TEV protease-induced cohesin cleavage in Rec8(TEV\/TEV) oocytes merely delay APC\/C activation. Since the arrest of Mlh1(-\/-)Rec8(TEV\/TEV) oocytes is alleviated by TEV protease, even when targeted to kinetochores, we conclude that their SAC depends on cohesin as well as dedicated kinetochore proteins. This has important implications for aging oocytes, where cohesin deterioration will induce sister kinetochore biorientation and compromise MCC production, leading to chromosome missegregation and aneuploid fetuses.","authors":"Tachibana-Konwalski, K., Godwin, J., Borsos, M., Rattani, A., Adams, DJ., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Curr Biol","volume":"23","issue":"24","page":"2534-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24285721","title":"Canonical nucleosome organization at promoters forms during genome activation.","abstract":"The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of histone H3 lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.","authors":"Zhang, Y., Vastenhouw, NL., Feng, J., Fu, K., Wang, C., Ge, Y., Pauli, A., van Hummelen, P., Schier, AF., Liu, XS.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genome Res","volume":"24","issue":"2","page":"260-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24268695","title":"Fundamental differences in dedifferentiation and stem cell recruitment during skeletal muscle regeneration in two salamander species.","abstract":"Salamanders regenerate appendages via a progenitor pool called the blastema. The cellular mechanisms underlying regeneration of muscle have been much debated but have remained unclear. Here we applied Cre-loxP genetic fate mapping to skeletal muscle during limb regeneration in two salamander species, Notophthalmus viridescens (newt) and Ambystoma mexicanum (axolotl). Remarkably, we found that myofiber dedifferentiation is an integral part of limb regeneration in the newt, but not in axolotl. In the newt, myofiber fragmentation results in proliferating, PAX7(-) mononuclear cells in the blastema that give rise to the skeletal muscle in the new limb. In contrast, myofibers in axolotl do not generate proliferating cells, and do not contribute to newly regenerated muscle; instead, resident PAX7(+) cells provide the regeneration activity. Our results therefore show significant diversity in limb muscle regeneration mechanisms among salamanders and suggest that multiple strategies may be feasible for inducing regeneration in other species, including mammals.","authors":"Sandoval-Guzm\u00e1n, T., Wang, H., Khattak, S., Schuez, M., Roensch, K., Nacu, E., Tazaki, A., Joven, A., Tanaka, EM., Simon, A.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cell Stem Cell","volume":"14","issue":"2","page":"174-87","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24259662","title":"Machine learning in cell biology - teaching computers to recognize phenotypes.","abstract":"Recent advances in microscope automation provide new opportunities for high-throughput cell biology, such as image-based screening. High-complex image analysis tasks often make the implementation of static and predefined processing rules a cumbersome effort. Machine-learning methods, instead, seek to use intrinsic data structure, as well as the expert annotations of biologists to infer models that can be used to solve versatile data analysis tasks. Here, we explain how machine-learning methods work and what needs to be considered for their successful application in cell biology. We outline how microscopy images can be converted into a data representation suitable for machine learning, and then introduce various state-of-the-art machine-learning algorithms, highlighting recent applications in image-based screening. Our Commentary aims to provide the biologist with a guide to the application of machine learning to microscopy assays and we therefore include extensive discussion on how to optimize experimental workflow as well as the data analysis pipeline.","authors":"Sommer, C., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Cell Sci","volume":"126","issue":"Pt 24","page":"5529-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24255115","title":"A multiplicative reinforcement learning model capturing learning dynamics and interindividual variability in mice.","abstract":"Both in humans and in animals, different individuals may learn the same task with strikingly different speeds; however, the sources of this variability remain elusive. In standard learning models, interindividual variability is often explained by variations of the learning rate, a parameter indicating how much synapses are updated on each learning event. Here, we theoretically show that the initial connectivity between the neurons involved in learning a task is also a strong determinant of how quickly the task is learned, provided that connections are updated in a multiplicative manner. To experimentally test this idea, we trained mice to perform an auditory Go\/NoGo discrimination task followed by a reversal to compare learning speed when starting from naive or already trained synaptic connections. All mice learned the initial task, but often displayed sigmoid-like learning curves, with a variable delay period followed by a steep increase in performance, as often observed in operant conditioning. For all mice, learning was much faster in the subsequent reversal training. An accurate fit of all learning curves could be obtained with a reinforcement learning model endowed with a multiplicative learning rule, but not with an additive rule. Surprisingly, the multiplicative model could explain a large fraction of the interindividual variability by variations in the initial synaptic weights. Altogether, these results demonstrate the power of multiplicative learning rules to account for the full dynamics of biological learning and suggest an important role of initial wiring in the brain for predispositions to different tasks.","authors":"Bathellier, B., Tee, SP., Hrovat, C., Rumpel, S.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proc Natl Acad Sci U S A","volume":"110","issue":"49","page":"19950-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24243021","title":"CtpB assembles a gated protease tunnel regulating cell-cell signaling during spore formation in Bacillus subtilis.","abstract":"Spore formation in Bacillus subtilis relies on a regulated intramembrane proteolysis (RIP) pathway that synchronizes mother-cell and forespore development. To address the molecular basis of this SpoIV transmembrane signaling, we carried out a structure-function analysis of the activating protease CtpB. Crystal structures reflecting distinct functional states show that CtpB constitutes a ring-like protein scaffold penetrated by two narrow tunnels. Access to the proteolytic sites sequestered within these tunnels is controlled by PDZ domains that rearrange upon substrate binding. Accordingly, CtpB resembles a minimal version of a self-compartmentalizing protease regulated by a unique allosteric mechanism. Moreover, biochemical analysis of the PDZ-gated channel combined with sporulation assays reveal that activation of the SpoIV RIP pathway is induced by the concerted activity of CtpB and a second signaling protease, SpoIVB. This proteolytic mechanism is of broad relevance for cell-cell communication, illustrating how distinct signaling pathways can be integrated into a single RIP module.","authors":"Mastny, M., Heuck, A., Kurzbauer, R., Heiduk, A., Boisguerin, P., Volkmer, R., Ehrmann, M., Rodrigues, CD., Rudner, DZ., Clausen, T.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell","volume":"155","issue":"3","page":"647-58","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24177423","title":"Apelin is a positive regulator of ACE2 in failing hearts.","abstract":"Angiotensin converting enzyme 2 (ACE2) is a negative regulator of the renin-angiotensin system (RAS), catalyzing the conversion of Angiotensin II to Angiotensin 1-7. Apelin is a second catalytic substrate for ACE2 and functions as an inotropic and cardioprotective peptide. While an antagonistic relationship between the RAS and apelin has been proposed, such functional interplay remains elusive. Here we found that ACE2 was downregulated in apelin-deficient mice. Pharmacological or genetic inhibition of angiotensin II type 1 receptor (AT1R) rescued the impaired contractility and hypertrophy of apelin mutant mice, which was accompanied by restored ACE2 levels. Importantly, treatment with angiotensin 1-7 rescued hypertrophy and heart dysfunctions of apelin-knockout mice. Moreover, apelin, via activation of its receptor, APJ, increased ACE2 promoter activity in vitro and upregulated ACE2 expression in failing hearts in vivo. Apelin treatment also increased cardiac contractility and ACE2 levels in AT1R-deficient mice. These data demonstrate that ACE2 couples the RAS to the apelin system, adding a conceptual framework for the apelin-ACE2-angiotensin 1-7 axis as a therapeutic target for cardiovascular diseases.","authors":"Sato, T., Suzuki, T., Watanabe, H., Kadowaki, A., Fukamizu, A., Liu, PP., Kimura, A., Ito, H., Penninger, JM., Imai, Y., Kuba, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Clin Invest","volume":"123","issue":"12","page":"5203-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24151334","title":"Dynamics of dendritic spines in the mouse auditory cortex during memory formation and memory recall.","abstract":"Long-lasting changes in synaptic connections induced by relevant experiences are believed to represent the physical correlate of memories. Here, we combined chronic in vivo two-photon imaging of dendritic spines with auditory-cued classical conditioning to test if the formation of a fear memory is associated with structural changes of synapses in the mouse auditory cortex. We find that paired conditioning and unpaired conditioning induce a transient increase in spine formation or spine elimination, respectively. A fraction of spines formed during paired conditioning persists and leaves a long-lasting trace in the network. Memory recall triggered by the reexposure of mice to the sound cue did not lead to changes in spine dynamics. Our findings provide a synaptic mechanism for plasticity in sound responses of auditory cortex neurons induced by auditory-cued fear conditioning; they also show that retrieval of an auditory fear memory does not lead to a recapitulation of structural plasticity in the auditory cortex as observed during initial memory consolidation.","authors":"Moczulska, KE., Tinter-Thiede, J., Peter, M., Ushakova, L., Wernle, T., Bathellier, B., Rumpel, S.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proc Natl Acad Sci U S A","volume":"110","issue":"45","page":"18315-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24132237","title":"Inhibitory signalling to the Arp2\/3 complex steers cell migration.","abstract":"Cell migration requires the generation of branched actin networks that power the protrusion of the plasma membrane in lamellipodia. The actin-related proteins 2 and 3 (Arp2\/3) complex is the molecular machine that nucleates these branched actin networks. This machine is activated at the leading edge of migrating cells by Wiskott-Aldrich syndrome protein (WASP)-family verprolin-homologous protein (WAVE, also known as SCAR). The WAVE complex is itself directly activated by the small GTPase Rac, which induces lamellipodia. However, how cells regulate the directionality of migration is poorly understood. Here we identify a new protein, Arpin, that inhibits the Arp2\/3 complex in vitro, and show that Rac signalling recruits and activates Arpin at the lamellipodial tip, like WAVE. Consistently, after depletion of the inhibitory Arpin, lamellipodia protrude faster and cells migrate faster. A major role of this inhibitory circuit, however, is to control directional persistence of migration. Indeed, Arpin depletion in both mammalian cells and Dictyostelium discoideum amoeba resulted in straighter trajectories, whereas Arpin microinjection in fish keratocytes, one of the most persistent systems of cell migration, induced these cells to turn. The coexistence of the Rac-Arpin-Arp2\/3 inhibitory circuit with the Rac-WAVE-Arp2\/3 activatory circuit can account for this conserved role of Arpin in steering cell migration.","authors":"Dang, I., Gorelik, R., Sousa-Blin, C., Derivery, E., Gu\u00e9rin, C., Linkner, J., Nemethova, M., Dumortier, JG., Giger, FA., Chipysheva, TA., Ermilova, VD., Vacher, S., Campanacci, V., Herrada, I., Planson, AG., Fetics, S., Henriot, V., David, V., Oguievetskaia, K., Lakisic, G., Pierre, F., Steffen, A., Boyreau, A., Peyri\u00e9ras, N., Rottner, K., Zinn-Justin, S., Cherfils, J., Bi\u00e8che, I., Alexandrova, AY., David, NB., Small, JV., Faix, J., Blanchoin, L., Gautreau, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nature","volume":"503","issue":"7475","page":"281-4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24096243","title":"Kinetic framework of spindle assembly checkpoint signalling.","abstract":"The mitotic spindle assembly checkpoint (SAC) delays anaphase onset until all chromosomes have attached to both spindle poles. Here, we investigated SAC signalling kinetics in response to acute detachment of individual chromosomes using laser microsurgery. Most detached chromosomes delayed anaphase until they had realigned to the metaphase plate. A substantial fraction of cells, however, entered anaphase in the presence of unaligned chromosomes. We identify two mechanisms by which cells can bypass the SAC: first, single unattached chromosomes inhibit the anaphase-promoting complex\/cyclosome (APC\/C) less efficiently than a full complement of unattached chromosomes; second, because of the relatively slow kinetics of re-imposing APC\/C inhibition during metaphase, cells were unresponsive to chromosome detachment up to several minutes before anaphase onset. Our study defines when cells irreversibly commit to enter anaphase and shows that the SAC signal strength correlates with the number of unattached chromosomes. Detailed knowledge about SAC signalling kinetics is important for understanding the emergence of aneuploidy and the response of cancer cells to chemotherapeutics targeting the mitotic spindle.","authors":"Dick, AE., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Cell Biol","volume":"15","issue":"11","page":"1370-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24056535","title":"Periventricular heterotopia in 6q terminal deletion syndrome: role of the C6orf70 gene.","abstract":"Periventricular nodular heterotopia is caused by defective neuronal migration that results in heterotopic neuronal nodules lining the lateral ventricles. Mutations in filamin A (FLNA) or ADP-ribosylation factor guanine nucleotide-exchange factor 2 (ARFGEF2) cause periventricular nodular heterotopia, but most patients with this malformation do not have a known aetiology. Using comparative genomic hybridization, we identified 12 patients with developmental brain abnormalities, variably combining periventricular nodular heterotopia, corpus callosum dysgenesis, colpocephaly, cerebellar hypoplasia and polymicrogyria, harbouring a common 1.2 Mb minimal critical deletion in 6q27. These anatomic features were mainly associated with epilepsy, ataxia and cognitive impairment. Using whole exome sequencing in 14 patients with isolated periventricular nodular heterotopia but no copy number variants, we identified one patient with periventricular nodular heterotopia, developmental delay and epilepsy and a de novo missense mutation in the chromosome 6 open reading frame 70 (C6orf70) gene, mapping in the minimal critical deleted region. Using immunohistochemistry and western blots, we demonstrated that in human cell lines, C6orf70 shows primarily a cytoplasmic vesicular puncta-like distribution and that the mutation affects its stability and subcellular distribution. We also performed in utero silencing of C6orf70 and of Phf10 and Dll1, the two additional genes mapping in the 6q27 minimal critical deleted region that are expressed in human and rodent brain. Silencing of C6orf70 in the developing rat neocortex produced periventricular nodular heterotopia that was rescued by concomitant expression of wild-type human C6orf70 protein. Silencing of the contiguous Phf10 or Dll1 genes only produced slightly delayed migration but not periventricular nodular heterotopia. The complex brain phenotype observed in the 6q terminal deletion syndrome likely results from the combined haploinsufficiency of contiguous genes mapping to a small 1.2 Mb region. Our data suggest that, of the genes within this minimal critical region, C6orf70 plays a major role in the control of neuronal migration and its haploinsufficiency or mutation causes periventricular nodular heterotopia.","authors":"Conti, V., Carabalona, A., Pallesi-Pocachard, E., Parrini, E., Leventer, RJ., Buhler, E., McGillivray, G., Michel, FJ., Striano, P., Mei, D., Watrin, F., Lise, S., Pagnamenta, AT., Taylor, JC., Kini, U., Clayton-Smith, J., Novara, F., Zuffardi, O., Dobyns, WB., Scheffer, IE., Robertson, SP., Berkovic, SF., Represa, A., Keays, DA., Cardoso, C., Guerrini, R.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Brain","volume":"136","issue":"Pt 11","page":"3378-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24009038","title":"Limb regeneration.","abstract":"Limb regeneration is observed in certain members of the animal phyla. Some animals keep this ability during their entire life while others lose it at some time during development. How do animals regenerate limbs? Is it possible to find unifying, conserved mechanisms of limb regeneration or have different species evolved distinct means of replacing a lost limb? How is limb regeneration similar or different to limb development? Studies on many organisms, including echinoderms, arthropods, and chordates have provided significant knowledge about limb regeneration. In this focus article, we concentrate on tetrapod limb regeneration as studied in three model amphibians: newts, axolotls, and frogs. We review recent progress on tissue interactions during limb regeneration, and place those findings into an evolutionary context.","authors":"Simon, A., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Wiley Interdiscip Rev Dev Biol","volume":"2","issue":"2","page":"291-300","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24002445","title":"Transcriptional regulation of the Ikzf1 locus.","abstract":"Ikaros is a critical regulator of lymphocyte development and homeostasis; thus, understanding its transcriptional regulation is important from both developmental and clinical perspectives. Using a mouse transgenic reporter approach, we functionally characterized a network of highly conserved cis-acting elements at the Ikzf1 locus. We attribute B-cell and myeloid but not T-cell specificity to the main Ikzf1 promoter. Although this promoter was unable to counter local chromatin silencing effects, each of the 6 highly conserved Ikzf1 intronic enhancers alleviated silencing. Working together, the Ikzf1 enhancers provided locus control region activity, allowing reporter expression in a position and copy-independent manner. Only 1 of the Ikzf1 enhancers was responsible for the progressive upregulation of Ikaros expression from hematopoietic stem cells to lymphoid-primed multipotent progenitors to T-cell precursors, which are stages of differentiation dependent on Ikaros for normal outcome. Thus, Ikzf1 is regulated by both epigenetic and transcriptional factors that target its enhancers in both redundant and specific fashions to provide an expression profile supportive of normal lymphoid lineage progression and homeostasis. Mutations in the Ikzf1 regulatory elements and their interacting factors are likely to have adverse effects on lymphopoiesis and contribute to leukemogenesis.","authors":"Yoshida, T., Landhuis, E., Dose, M., Hazan, I., Zhang, J., Naito, T., Jackson, AF., Wu, J., Perotti, EA., Kaufmann, C., Gounari, F., Morgan, BA., Georgopoulos, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Blood","volume":"122","issue":"18","page":"3149-59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23995685","title":"Cerebral organoids model human brain development and microcephaly.","abstract":"The complexity of the human brain has made it difficult to study many brain disorders in model organisms, highlighting the need for an in vitro model of human brain development. Here we have developed a human pluripotent stem cell-derived three-dimensional organoid culture system, termed cerebral organoids, that develop various discrete, although interdependent, brain regions. These include a cerebral cortex containing progenitor populations that organize and produce mature cortical neuron subtypes. Furthermore, cerebral organoids are shown to recapitulate features of human cortical development, namely characteristic progenitor zone organization with abundant outer radial glial stem cells. Finally, we use RNA interference and patient-specific induced pluripotent stem cells to model microcephaly, a disorder that has been difficult to recapitulate in mice. We demonstrate premature neuronal differentiation in patient organoids, a defect that could help to explain the disease phenotype. Together, these data show that three-dimensional organoids can recapitulate development and disease even in this most complex human tissue.","authors":"Lancaster, MA., Renner, M., Martin, CA., Wenzel, D., Bicknell, LS., Hurles, ME., Homfray, T., Penninger, JM., Jackson, AP., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nature","volume":"501","issue":"7467","page":"373-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23925246","title":"A directional tuning map of Drosophila elementary motion detectors.","abstract":"The extraction of directional motion information from changing retinal images is one of the earliest and most important processing steps in any visual system. In the fly optic lobe, two parallel processing streams have been anatomically described, leading from two first-order interneurons, L1 and L2, via T4 and T5 cells onto large, wide-field motion-sensitive interneurons of the lobula plate. Therefore, T4 and T5 cells are thought to have a pivotal role in motion processing; however, owing to their small size, it is difficult to obtain electrical recordings of T4 and T5 cells, leaving their visual response properties largely unknown. We circumvent this problem by means of optical recording from these cells in Drosophila, using the genetically encoded calcium indicator GCaMP5 (ref. 2). Here we find that specific subpopulations of T4 and T5 cells are directionally tuned to one of the four cardinal directions; that is, front-to-back, back-to-front, upwards and downwards. Depending on their preferred direction, T4 and T5 cells terminate in specific sublayers of the lobula plate. T4 and T5 functionally segregate with respect to contrast polarity: whereas T4 cells selectively respond to moving brightness increments (ON edges), T5 cells only respond to moving brightness decrements (OFF edges). When the output from T4 or T5 cells is blocked, the responses of postsynaptic lobula plate neurons to moving ON (T4 block) or OFF edges (T5 block) are selectively compromised. The same effects are seen in turning responses of tethered walking flies. Thus, starting with L1 and L2, the visual input is split into separate ON and OFF pathways, and motion along all four cardinal directions is computed separately within each pathway. The output of these eight different motion detectors is then sorted such that ON (T4) and OFF (T5) motion detectors with the same directional tuning converge in the same layer of the lobula plate, jointly providing the input to downstream circuits and motion-driven behaviours.","authors":"Maisak, MS., Haag, J., Ammer, G., Serbe, E., Meier, M., Leonhardt, A., Schilling, T., Bahl, A., Rubin, GM., Nern, A., Dickson, BJ., Reiff, DF., Hopp, E., Borst, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nature","volume":"500","issue":"7461","page":"212-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23940826","title":"High resolution anatomical mapping confirms the absence of a magnetic sense system in the rostral upper beak of pigeons.","abstract":"The cells that are responsible for detecting magnetic fields in animals remain undiscovered. Previous studies have proposed that pigeons employ a magnetic sense system that consists of six bilateral patches of magnetite containing dendrites located in the rostral subepidermis of the upper beak. We have challenged this hypothesis arguing that clusters of iron-rich cells in this region are macrophages, not magnetosensitive neurons. Here we present additional data in support of this conclusion. We have undertaken high resolution anatomical mapping of iron-rich cells in the rostral upper beak of pigeons, excluding the possibility that a conserved six-loci magnetic sense system exists. In addition we have extended our immunohistochemical studies to a second cohort of pigeons, confirming that iron rich cells in the upper beak are positive for MHCII and CD44, which are expressed by macrophages. We argue that it is important to critically assess conclusions that have been made in the past, while keeping an open mind as the search for the magnetoreceptor continues.","authors":"Treiber, CD., Salzer, M., Breuss, M., Ushakova, L., Lauwers, M., Edelman, N., Keays, DA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Commun Integr Biol","volume":"6","issue":"4","page":"e24859","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11911819","title":"Vav1 controls integrin clustering and MHC\/peptide-specific cell adhesion to antigen-presenting cells.","abstract":"Integrin-mediated adhesion is essential for the formation of stable contacts between T cells and antigen-presenting cells (APCs). We show that Vav1 controls integrin-mediated adhesion of thymocytes and T cells to ECM proteins and ICAM1 following TCR stimulation. In a peptide-specific system, Vav1 is required for T cell adhesion to peptide-loaded APCs. Intriguingly, TCR-induced cell adhesion and aggregation of integrins occurs independent of WASP. Whereas LFA-1 and actin caps colocalize in wasp(-\/-) T cells in response to TCR stimulation, loss of WASP uncouples TCR caps from actin patches. Our data reveal a novel role for Vav1 and WASP in the regulation of TCR-induced integrin clustering and cell adhesion and show that integrin and TCR clustering are controlled by distinct pathways.","authors":"Krawczyk, C., Oliveira-dos-Santos, A., Sasaki, T., Griffiths, E., Ohashi, PS., Snapper, S., Alt, F., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Immunity","volume":"16","issue":"3","page":"331-43","pdf":null,"JrId":"8591","fulltextlink":null,"preprintlink":null,"articledate":"2002-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23901111","title":"Aurora B and Cdk1 mediate Wapl activation and release of acetylated cohesin from chromosomes by phosphorylating Sororin.","abstract":"Sister chromatid cohesion depends on Sororin, a protein that stabilizes acetylated cohesin complexes on DNA by antagonizing the cohesin release factor Wings-apart like protein (Wapl). Cohesion is essential for chromosome biorientation but has to be dissolved to enable sister chromatid separation. To achieve this, the majority of cohesin is removed from chromosome arms in prophase and prometaphase in a manner that depends on Wapl and phosphorylation of cohesin's subunit stromal antigen 2 (SA2), whereas centromeric cohesin is cleaved in metaphase by the protease separase. Here we show that the mitotic kinases Aurora B and Cyclin-dependent kinase 1 (Cdk1) destabilize interactions between Sororin and the cohesin subunit precocious dissociation of sisters protein 5 (Pds5) by phosphorylating Sororin, leading to release of acetylated cohesin from chromosome arms and loss of cohesion. At centromeres, the cohesin protector shugoshin (Sgo1)-protein phosphatase 2A (PP2A) antagonizes Aurora B and Cdk1 partly by dephosphorylating Sororin and thus maintains cohesion until metaphase. We propose that the stepwise loss of cohesion between chromosome arms and centromeres is caused by local regulation of Wapl activity, which is controlled by the phosphorylation state of Sororin.","authors":"Nishiyama, T., Sykora, MM., Huis in 't Veld, PJ., Mechtler, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proc Natl Acad Sci U S A","volume":"110","issue":"33","page":"13404-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23891001","title":"FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis.","abstract":"FOXO transcription factors are central regulators of longevity from worms to humans. FOXO3, the FOXO isoform associated with exceptional human longevity, preserves adult neural stem cell pools. Here, we identify FOXO3 direct targets genome-wide in primary cultures of adult neural progenitor cells (NPCs). Interestingly, FOXO3-bound sites are enriched for motifs for bHLH transcription factors, and FOXO3 shares common targets with the proneuronal bHLH transcription factor ASCL1\/MASH1 in NPCs. Analysis of the chromatin landscape reveals that FOXO3 and ASCL1 are particularly enriched at the enhancers of genes involved in neurogenic pathways. Intriguingly, FOXO3 inhibits ASCL1-dependent neurogenesis in NPCs and direct neuronal conversion in fibroblasts. FOXO3 also restrains neurogenesis in vivo. Our study identifies a genome-wide interaction between the prolongevity transcription factor FOXO3 and the cell-fate determinant ASCL1 and raises the possibility that FOXO3's ability to restrain ASCL1-dependent neurogenesis may help preserve the neural stem cell pool.","authors":"Webb, AE., Pollina, EA., Vierbuchen, T., Urb\u00e1n, N., Ucar, D., Leeman, DS., Martynoga, B., Sewak, M., Rando, TA., Guillemot, F., Wernig, M., Brunet, A.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Rep","volume":"4","issue":"3","page":"477-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16514079","title":"Angiotensin-converting enzyme II in the heart and the kidney.","abstract":"The renin-angiotensin system (RAS) has been recognized for many years as critical pathway for blood pressure control and kidney functions. Although most of the well-known cardiovascular and renal effects of RAS are attributed to angiotensin-converting enzyme (ACE), much less is known about the function of ACE2. Experiments using genetically modified mice and inhibitor studies have shown that ACE2 counterbalances the functions of ACE and that the balance between these two proteases determines local and systemic levels of RAS peptides such as angiotensin II and angiotensin1-7. Ace2 mutant mice exhibit progressive impairment of heart contractility at advanced ages, a phenotype that can be reverted by loss of ACE, suggesting that these enzymes directly control heart function. Moreover, ACE2 is also found to be upregulated in failing hearts. In the kidney, ACE2 protein levels are significantly decreased in hypertensive rats, suggesting a negative regulatory role of ACE2 in blood pressure control. Moreover, ACE2 expression is downregulated in the kidneys of diabetic and pregnant rats and ACE2 mutant mice develop late onset glomerulonephritis resembling diabetic nephropathy. Importantly, ACE2 not only controls angiotensin II levels but functions as a protease on additional molecular targets that could contribute to the observed in vivo phenotypes of ACE2 mutant mice. Thus, ACE2 seems to be a molecule that has protective roles in heart and kidney. The development of drugs that could activate ACE2 function would allow extending our treatment options in diabetic nephropathy, heart failure, or hypertension.","authors":"Danilczyk, U., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Circ Res","volume":"98","issue":"4","page":"463-71","pdf":null,"JrId":"2974","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-199","title":"TRIM52 is a primate-specific player in the DNA repair process under tight proteolytic control by a triad of giant E3 ligases","abstract":null,"authors":"Shulkina, A., Hacker, K., Ehrmann, J. F., Budroni, V., Mandlbauer, A., Bock, J., Grabarczyk, D. B., Cochella, L., Clausen, T., Versteeg, G.A. ","publication_status":"preprint","journalpubyear":"2024","journaltitle":"bioRxiv ","volume":"10.1101\/2024.05.16.594269","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.05.16.594269v1","preprintlink":null,"articledate":"2024-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11137006","title":"Pds5 cooperates with cohesin in maintaining sister chromatid cohesion.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11137006<\/PMID><DateCompleted><Year>2001<\/Year><Month>06<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>10<\/Volume><Issue>24<\/Issue><PubDate><MedlineDate>2000 Dec 14-28<\/MedlineDate><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Pds5 cooperates with cohesin in maintaining sister chromatid cohesion.<\/ArticleTitle><Pagination><MedlinePgn>1557-64<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Sister chromatid cohesion depends on a complex called cohesin, which contains at least four subunits: Smc1, Smc3, Scc1 and Scc3. Cohesion is established during DNA replication, is partially dismantled in many, but not all, organisms during prophase, and is finally destroyed at the metaphase-to-anaphase transition. A quite separate protein called Spo76 is required for sister chromatid cohesion during meiosis in the ascomycete Sordaria. Spo76-like proteins are highly conserved amongst eukaryotes and a homologue in Aspergillus nidulans, called BimD, is required for the completion of mitosis. The isolation of the cohesin subunit Smc3 as a suppressor of BimD mutations suggests that Spo76\/BimD might function in the same process as cohesin.","authors":"Panizza, S., Tanaka, T., Hochwagen, A., Eisenhaber, F., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Curr Biol","volume":"10","issue":"24","page":"1557-64","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2001-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23864022","title":"Hace1 controls ROS generation of vertebrate Rac1-dependent NADPH oxidase complexes.","abstract":"The Hace1-HECT E3 ligase is a tumor suppressor that ubiquitylates the activated GTP-bound form of the Rho family GTPase Rac1, leading to Rac1 proteasomal degradation. Here we show that, in vertebrates, Hace1 targets Rac1 for degradation when Rac1 is localized to the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase holoenzyme. This event blocks de novo reactive oxygen species generation by Rac1-dependent NADPH oxidases, and thereby confers cellular protection from reactive oxygen species-induced DNA damage and cyclin D1-driven hyper-proliferation. Genetic inactivation of Hace1 in mice or zebrafish, as well as Hace1 loss in human tumor cell lines or primary murine or human tumors, leads to chronic NADPH oxidase-dependent reactive oxygen species elevation, DNA damage responses and enhanced cyclin D1 expression. Our data reveal a conserved ubiquitin-dependent molecular mechanism that controls the activity of Rac1-dependent NADPH oxidase complexes, and thus constitutes the first known example of a tumor suppressor protein that directly regulates reactive oxygen species production in vertebrates.","authors":"Daugaard, M., Nitsch, R., Razaghi, B., McDonald, L., Jarrar, A., Torrino, S., Castillo-Lluva, S., Rotblat, B., Li, L., Malliri, A., Lemichez, E., Mettouchi, A., Berman, JN., Penninger, JM., Sorensen, PH.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Commun","volume":"4","issue":null,"page":"2180","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23841592","title":"Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics.","abstract":"Reversed-phase liquid chromatography has become the preferred method for separating peptides in most of the mass spectrometry-based proteomics workflows of today. In the way the technique is typically applied, the peptides are released from the chromatography column by the gradual addition of an organic buffer according to a linear function. However, when applied to complex peptide mixtures, this approach leads to unequal spreads of the peptides over the chromatography time. To address this, we investigated the use of nonlinear gradients, customized for each setup at hand. We developed an algorithm to generate optimized gradient functions for shotgun proteomics experiments and evaluated it for two data sets consisting each of four replicate runs of a human complex sample. Our results show that the optimized gradients produce a more even spread of the peptides over the chromatography run, while leading to increased numbers of confident peptide identifications. In addition, the list of peptides identified using nonlinear gradients differed considerably from those found with the linear ones, suggesting that such gradients can be a valuable tool for increasing the proteome coverage of mass spectrometry-based experiments.","authors":"Moruz, L., Pichler, P., Stranzl, T., Mechtler, K., K\u00e4ll, L.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Anal Chem","volume":"85","issue":"16","page":"7777-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23816468","title":"Angiotensin-converting enzyme 2 attenuates oxidative stress and VSMC proliferation via the JAK2\/STAT3\/SOCS3 and profilin-1\/MAPK signaling pathways.","abstract":"Angiotensin (Ang) II plays a vital role in vascular smooth muscle cell (VSMC) growth and proliferation. Angiotensin-converting enzyme 2 (ACE2) is a specific Ang II-degrading enzyme but its role in VSMC proliferation remains largely unknown. We hypothesized that ACE2 might suppress Ang II-mediated oxidative stress and VSMC proliferation. Human umbilical artery smooth muscle cells (HUASMCs) were pretreated with Ang II (100nM) for 6h and 24h, respectively. Exposure to Ang II resulted in significant increases in suppressor of cytokine signaling 3 (SOCS3) expression and phosphorylation levels of JAK2, STAT3 and ERK1\/2 linked with elevated superoxide production and cell proliferation in HUASMCs. These changes were strikingly prevented by administration of ERK1\/2 inhibitor PD98059 (10\u03bcM) and JAK\/STAT inhibitor WP1066 (5 \u03bcM) but were largely aggravated by ACE2 inhibitor DX600 (0.5 \u03bcM). More importantly, treatment with human recombinant ACE2 (hrACE2; 1mg\/ml) dramatically prevented Ang II-mediated SOCS3 expression and the JAK2-STAT3 and ERK1\/2 signaling, and resulted in attenuation of superoxide production and cell proliferation in HUASMCs. Intriguingly, downregulation of profilin-1 with profilin-1 siRNA (50 nM) was able to abolish Ang II-induced upregulations of profilin-1 expression, ERK1\/2 phosphorylation and superoxide production with attenuation of VSMC proliferation. In conclusion, treatment with hrACE2 prevents Ang II-mediated activation of the JAK2\/STAT3\/SOCS3 and profilin-1\/MAPK signaling pathways, contributing to attenuation of superoxide generation and cell proliferation in HUASMCs, suggesting a protective mechanism of ACE2 against Ang II-mediated oxidative stress and VSMC proliferation. ACE2 may represent a potential candidate to prevent and treat vascular disorders.","authors":"Song, B., Jin, H., Yu, X., Zhang, Z., Yu, H., Ye, J., Xu, Y., Zhou, T., Oudit, GY., Ye, JY., Chen, C., Gao, P., Zhu, D., Penninger, JM., Zhong, JC.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Regul Pept","volume":"185","issue":null,"page":"44-51","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23770242","title":"Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria.","abstract":"Many cellular pathways are regulated by the competing activity of protein kinases and phosphatases. The recent identification of arginine phosphorylation as a protein modification in bacteria prompted us to analyze the molecular basis of targeting phospho-arginine. In this work, we characterize an annotated tyrosine phosphatase, YwlE, that counteracts the protein arginine kinase McsB. Strikingly, structural studies of YwlE reaction intermediates provide a direct view on a captured arginine residue. Together with biochemical data, the crystal structures depict the evolution of a highly specific phospho-arginine phosphatase, with the use of a size-and-polarity filter for distinguishing phosphorylated arginine from other phosphorylated side chains. To confirm the proposed mechanism, we performed bioinformatic searches for phosphatases, employing a similar selectivity filter, and identified a protein in Drosophila melanogaster exhibiting robust arginine phosphatase activity. In sum, our findings uncover the molecular framework for specific targeting of phospho-arginine and suggest that protein arginine (de)phosphorylation may be relevant in eukaryotes.","authors":"Fuhrmann, J., Mierzwa, B., Trentini, DB., Spiess, S., Lehner, A., Charpentier, E., Clausen, T.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Rep","volume":"3","issue":"6","page":"1832-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23763294","title":"Genetic resistance to liver fibrosis on A\/J mouse chromosome 17.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23763294<\/PMID><DateCompleted><Year>2014<\/Year><Month>05<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1530-0277<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>37<\/Volume><Issue>10<\/Issue><PubDate><Year>2013<\/Year><Month>Oct<\/Month><\/PubDate><\/JournalIssue><Title>Alcoholism, clinical and experimental research<\/Title><ISOAbbreviation>Alcohol Clin Exp Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Genetic resistance to liver fibrosis on A\/J mouse chromosome 17.<\/ArticleTitle><Pagination><MedlinePgn>1668-79<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/acer.12157<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Because the histological and biochemical progression of liver disease is similar in alcoholic steatohepatitis (ASH) and nonalcoholic steatohepatitis (NASH), we hypothesized that the genetic susceptibility to these liver diseases would be similar. To identify potential candidate genes that regulate the development of liver fibrosis, we studied a chromosome substitution strain (CSS-17) that contains chromosome 17 from the A\/J inbred strain substituted for the corresponding chromosome on the C57BL\/6J (B6) genetic background. Previously, we identified quantitative trait loci (QTLs) in CSS-17, namely obesity-resistant QTL 13 and QTL 15 (Obrq13 and Obrq15, respectively), that were associated with protection from diet-induced obesity and hepatic steatosis on a high-fat diet.","authors":"DeSantis, DA., Lee, P., Doerner, SK., Ko, CW., Kawasoe, JH., Hill-Baskin, AE., Ernest, SR., Bhargava, P., Hur, KY., Cresci, GA., Pritchard, MT., Lee, CH., Nagy, LE., Nadeau, JH., Croniger, CM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Alcohol Clin Exp Res","volume":"37","issue":"10","page":"1668-79","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23721814","title":"Transgenic expression of the FTDP-17 tauV337M mutation in brain dissociates components of executive function in mice.","abstract":"Frontotemporal lobe dementia (FTD) is a heterogeneous range of disorders, a subset of which arise from fully penetrant, autosomal dominant point mutations in the gene coding for the microtubule associated protein tau. These genetic tauopathies are associated with complex behavioural\/cognitive disturbances, including compromised executive function. In the present study, we modelled the effects of the FTD with Parkinsonism linked to chromosome 17 (FTDP-17) tauV337M mutation (known as the Seattle Family A mutation) expressed in mice on executive processes using a novel murine analogue of the Stroop task. Employing biconditional discrimination procedures, Experiment 1 showed that normal mice, but not mice with excitotoxic lesions of the medial prefrontal cortex, were able to use context cues to resolve response conflict generated by incongruent stimulus compounds. In contrast to predictions, response conflict resolution was not disrupted by the tauV337M mutation (Experiment 2). However, while context appropriate actions were goal-directed in wild-type mice, performance of tauV337M mice was not goal-directed (Experiment 3). The results indicate that the tauV337M mutation in mice disrupts, selectively, a subset of processes related to executive function.","authors":"Reichelt, AC., Killcross, S., Wilkinson, LS., Humby, T., Good, MA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Neurobiol Learn Mem","volume":"104","issue":"","page":"73-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23708605","title":"Electron microscopy structure of human APC\/C(CDH1)-EMI1 reveals multimodal mechanism of E3 ligase shutdown.","abstract":"The anaphase-promoting complex\/cyclosome (APC\/C) is a ~1.5-MDa multiprotein E3 ligase enzyme that regulates cell division by promoting timely ubiquitin-mediated proteolysis of key cell-cycle regulatory proteins. Inhibition of human APC\/C(CDH1) during interphase by early mitotic inhibitor 1 (EMI1) is essential for accurate coordination of DNA synthesis and mitosis. Here, we report a hybrid structural approach involving NMR, electron microscopy and enzymology, which reveal that EMI1's 143-residue C-terminal domain inhibits multiple APC\/C(CDH1) functions. The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC\/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation. The functional importance of intrinsic structural disorder is explained by enabling a small inhibitory domain to bind multiple sites to shut down various functions of a 'molecular machine' nearly 100 times its size.","authors":"Frye, JJ., Brown, NG., Petzold, G., Watson, ER., Grace, CR., Nourse, A., Jarvis, MA., Kriwacki, RW., Peters, JM., Stark, H., Schulman, BA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Struct Mol Biol","volume":"20","issue":"7","page":"827-35","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23671427","title":"EGL-13\/SoxD specifies distinct O2 and CO2 sensory neuron fates in Caenorhabditis elegans.","abstract":"Animals harbor specialized neuronal systems that are used for sensing and coordinating responses to changes in oxygen (O2) and carbon dioxide (CO2). In Caenorhabditis elegans, the O2\/CO2 sensory system comprises functionally and morphologically distinct sensory neurons that mediate rapid behavioral responses to exquisite changes in O2 or CO2 levels via different sensory receptors. How the diversification of the O2- and CO2-sensing neurons is established is poorly understood. We show here that the molecular identity of both the BAG (O2\/CO2-sensing) and the URX (O2-sensing) neurons is controlled by the phylogenetically conserved SoxD transcription factor homolog EGL-13. egl-13 mutant animals fail to fully express the distinct terminal gene batteries of the BAG and URX neurons and, as such, are unable to mount behavioral responses to changes in O2 and CO2. We found that the expression of egl-13 is regulated in the BAG and URX neurons by two conserved transcription factors-ETS-5(Ets factor) in the BAG neurons and AHR-1(bHLH factor) in the URX neurons. In addition, we found that EGL-13 acts in partially parallel pathways with both ETS-5 and AHR-1 to direct BAG and URX neuronal fate respectively. Finally, we found that EGL-13 is sufficient to induce O2- and CO2-sensing cell fates in some cellular contexts. Thus, the same core regulatory factor, egl-13, is required and sufficient to specify the distinct fates of O2- and CO2-sensing neurons in C. elegans. These findings extend our understanding of mechanisms of neuronal diversification and the regulation of molecular factors that may be conserved in higher organisms.","authors":"Gramstrup Petersen, J., Rojo Romanos, T., Juozaityte, V., Redo Riveiro, A., Hums, I., Traunm\u00fcller, L., Zimmer, M., Pocock, R.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"PLoS Genet","volume":"9","issue":"5","page":"e1003511","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11402330","title":"AP-1--Introductory remarks.","abstract":"This issue attempts to give a 'state of the art' overview of the AP-1 transcription factor family, a fundamental class of transcriptional regulators. The AP-1 family consists of several bZIP (basic region leucine zipper) domain proteins, the Jun, the Fos, and the ATF subfamilies, which all have to dimerize before they can bind to their DNA target sites. AP-1 has been a paradigm for transcription factors that regulate many aspects of cell physiology in response to environmental changes such as stress, radiation, or to growth factor signals thereby acting like an environmental biosensor. Although we have come a long way from discovering its major components, the heterodimer between c-Fos and c-Jun, it is daunting to realize that we still lack a detailed molecular knowledge of how these factors interact with DNA to activate or repress genes in the nucleus. It is also not clear how the response of AP-1 to growth factor signaling from the cell surface to the nucleus is interpreted at the molecular level and whether AP-1 is relevant for human disease.","authors":"Wagner, EF.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Oncogene","volume":"20","issue":"19","page":"2334-5","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23665231","title":"The genetic makeup of the Drosophila piRNA pathway.","abstract":"The piRNA (PIWI-interacting RNA) pathway is a small RNA silencing system that acts in animal gonads and protects the genome against the deleterious influence of transposons. A major bottleneck in the field is the lack of comprehensive knowledge of the factors and molecular processes that constitute this pathway. We conducted an RNAi screen in Drosophila and identified ~50 genes that strongly impact the ovarian somatic piRNA pathway. Many identified genes fall into functional categories that indicate essential roles for mitochondrial metabolism, RNA export, the nuclear pore, transcription elongation, and chromatin regulation in the pathway. Follow-up studies on two factors demonstrate that components acting at distinct hierarchical levels of the pathway were identified. Finally, we define CG2183\/Gasz as an essential primary piRNA biogenesis factor in somatic and germline cells. Based on the similarities between insect and vertebrate piRNA pathways, our results have far-reaching implications for the understanding of this conserved genome defense system.","authors":"Handler, D., Meixner, K., Pizka, M., Lauss, K., Schmied, C., Gruber, FS., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Mol Cell","volume":"50","issue":"5","page":"762-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23660757","title":"FACS purification of Drosophila larval neuroblasts for next-generation sequencing.","abstract":"Elegant tools are available for the genetic analysis of neural stem cell lineages in Drosophila, but a methodology for purifying stem cells and their differentiated progeny for transcriptome analysis is currently missing. Previous attempts to overcome this problem either involved using RNA isolated from whole larval brain tissue or co-transcriptional in vivo mRNA tagging. As both methods have limited cell type specificity, we developed a protocol for the isolation of Drosophila neural stem cells (neuroblasts, NBs) and their differentiated sibling cells by FACS. We dissected larval brains from fly strains expressing GFP under the control of a NB lineage-specific GAL4 line. Upon dissociation, we made use of differences in GFP intensity and cell size to separate NBs and neurons. The resulting cell populations are over 98% pure and can readily be used for live imaging or gene expression analysis. Our method is optimized for neural stem cells, but it can also be applied to other Drosophila cell types. Primary cell suspensions and sorted cell populations can be obtained within 1 d; material for deep-sequencing library preparation can be obtained within 4 d.","authors":"Harzer, H., Berger, C., Conder, R., Schmauss, G., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Protoc","volume":"8","issue":"6","page":"1088-1099","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23595665","title":"CellH5: a format for data exchange in high-content screening.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Curated\" Owner=\"NLM\"><PMID Version=\"1\">23595665<\/PMID><DateCompleted><Year>2013<\/Year><Month>11<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>12<\/Month><Day>02<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1367-4811<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>29<\/Volume><Issue>12<\/Issue><PubDate><Year>2013<\/Year><Month>Jun<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>CellH5: a format for data exchange in high-content screening.<\/ArticleTitle><Pagination><MedlinePgn>1580-2<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/bioinformatics\/btt175<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">High-throughput microscopy data require a diversity of analytical approaches. However, the construction of workflows that use algorithms from different software packages is difficult owing to a lack of interoperability. To overcome this limitation, we present CellH5, an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional image data along with inter-object relations in graphs. CellH5Browser, an interactive gallery image browser, demonstrates the versatility and performance of the file format on live imaging data of dividing human cells. CellH5 provides new opportunities for integrated data analysis by multiple software platforms.","authors":"Sommer, C., Held, M., Fischer, B., Huber, W., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Bioinformatics","volume":"29","issue":"12","page":"1580-2","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23545496","title":"ER stress causes rapid loss of intestinal epithelial stemness through activation of the unfolded protein response.","abstract":"Stem cells generate rapidly dividing transit-amplifying cells that have lost the capacity for self-renewal but cycle for a number of times until they exit the cell cycle and undergo terminal differentiation. We know very little of the type of signals that trigger the earliest steps of stem cell differentiation and mediate a stem cell to transit-amplifying cell transition. We show that in normal intestinal epithelium, endoplasmic reticulum (ER) stress and activity of the unfolded protein response (UPR) are induced at the transition from stem cell to transit-amplifying cell. Induction of ER stress causes loss of stemness in a Perk-eIF2\u03b1-dependent manner. Inhibition of Perk-eIF2\u03b1 signaling results in stem cell accumulation in organoid culture of primary intestinal epithelium. Our findings show that the UPR plays an important role in the regulation of intestinal epithelial stem cell differentiation.","authors":"Heijmans, J., van Lidth de Jeude, JF., Koo, BK., Rosekrans, SL., Wielenga, MC., van de Wetering, M., Ferrante, M., Lee, AS., Onderwater, JJ., Paton, JC., Paton, AW., Mommaas, AM., Kodach, LL., Hardwick, JC., Hommes, DW., Clevers, H., Muncan, V., van den Brink, GR.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Rep","volume":"3","issue":"4","page":"1128-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23540420","title":"Predicting phenotypic variation from genotypes, phenotypes and a combination of the two.","abstract":"A central challenge for medicine is to predict disease risk and treatment outcomes for individuals. But what kind of information should be used to make useful predictions in biology? One important cause of phenotypic variation is of course genetics. However genetic predictions have both practical and fundamental limitations: most genetic influences on a trait are usually unknown, and phenotypic variation is not just due to genetics. A pragmatic alternative is to use intermediate phenotypes such as gene expression and other molecular measurements to make predictions about later trait variation such as disease risk. Intermediate phenotypes are useful because they capture both genetic and non-genetic influences on a system, and can reflect both the current state of a system and its history. Here we discuss examples of both genetic and non-genetic approaches to predicting phenotypic variation. Moreover, we argue that it will be by combining these two sources of information-genetics and intermediate molecular phenotypes-that it will be possible to make accurate predictions about variation in many phenotypic traits, even if we will not always mechanistically understand why this is the case. In particular, we encourage the human genetics community to focus more on combining genetics with intermediate phenotypes when attempting to predict clinically relevant traits such as disease risk.","authors":"Burga, A., Lehner, B.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Curr Opin Biotechnol","volume":"24","issue":"4","page":"803-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23474986","title":"CLP1 links tRNA metabolism to progressive motor-neuron loss.","abstract":"CLP1 was the first mammalian RNA kinase to be identified. However, determining its in vivo function has been elusive. Here we generated kinase-dead Clp1 (Clp1(K\/K)) mice that show a progressive loss of spinal motor neurons associated with axonal degeneration in the peripheral nerves and denervation of neuromuscular junctions, resulting in impaired motor function, muscle weakness, paralysis and fatal respiratory failure. Transgenic rescue experiments show that CLP1 functions in motor neurons. Mechanistically, loss of CLP1 activity results in accumulation of a novel set of small RNA fragments, derived from aberrant processing of tyrosine pre-transfer RNA. These tRNA fragments sensitize cells to oxidative-stress-induced p53 (also known as TRP53) activation and p53-dependent cell death. Genetic inactivation of p53 rescues Clp1(K\/K) mice from the motor neuron loss, muscle denervation and respiratory failure. Our experiments uncover a mechanistic link between tRNA processing, formation of a new RNA species and progressive loss of lower motor neurons regulated by p53.","authors":"Hanada, T., Weitzer, S., Mair, B., Bernreuther, C., Wainger, BJ., Ichida, J., Hanada, R., Orthofer, M., Cronin, SJ., Komnenovic, V., Minis, A., Sato, F., Mimata, H., Yoshimura, A., Tamir, I., Rainer, J., Kofler, R., Yaron, A., Eggan, KC., Woolf, CJ., Glatzel, M., Herbst, R., Martinez, J., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nature","volume":"495","issue":"7442","page":"474-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23468601","title":"Discriminating external and internal causes for heading changes in freely flying Drosophila.","abstract":"As animals move through the world in search of resources, they change course in reaction to both external sensory cues and internally-generated programs. Elucidating the functional logic of complex search algorithms is challenging because the observable actions of the animal cannot be unambiguously assigned to externally- or internally-triggered events. We present a technique that addresses this challenge by assessing quantitatively the contribution of external stimuli and internal processes. We apply this technique to the analysis of rapid turns (\"saccades\") of freely flying Drosophila melanogaster. We show that a single scalar feature computed from the visual stimulus experienced by the animal is sufficient to explain a majority (93%) of the turning decisions. We automatically estimate this scalar value from the observable trajectory, without any assumption regarding the sensory processing. A posteriori, we show that the estimated feature field is consistent with previous results measured in other experimental conditions. The remaining turning decisions, not explained by this feature of the visual input, may be attributed to a combination of deterministic processes based on unobservable internal states and purely stochastic behavior. We cannot distinguish these contributions using external observations alone, but we are able to provide a quantitative bound of their relative importance with respect to stimulus-triggered decisions. Our results suggest that comparatively few saccades in free-flying conditions are a result of an intrinsic spontaneous process, contrary to previous suggestions. We discuss how this technique could be generalized for use in other systems and employed as a tool for classifying effects into sensory, decision, and motor categories when used to analyze data from genetic behavioral screens.","authors":"Censi, A., Straw, AD., Sayaman, RW., Murray, RM., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"PLoS Comput Biol","volume":"9","issue":"2","page":"e1002891","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23396210","title":"Blockade of receptor activator of nuclear factor-\u03baB (RANKL) signaling improves hepatic insulin resistance and prevents development of diabetes mellitus.","abstract":"Hepatic insulin resistance is a driving force in the pathogenesis of type 2 diabetes mellitus (T2DM) and is tightly coupled with excessive storage of fat and the ensuing inflammation within the liver. There is compelling evidence that activation of the transcription factor nuclear factor-\u03baB (NF-\u03baB) and downstream inflammatory signaling pathways systemically and in the liver are key events in the etiology of hepatic insulin resistance and \u03b2-cell dysfunction, although the molecular mechanisms involved are incompletely understood. We here test the hypothesis that receptor activator of NF-\u03baB ligand (RANKL), a prototypic activator of NF-\u03baB, contributes to this process using both an epidemiological and experimental approach. In the prospective population-based Bruneck Study, a high serum concentration of soluble RANKL emerged as a significant (P&lt;0.001) and independent risk predictor of T2DM manifestation. In close agreement, systemic or hepatic blockage of RANKL signaling in genetic and nutritional mouse models of T2DM resulted in a marked improvement of hepatic insulin sensitivity and amelioration or even normalization of plasma glucose concentrations and glucose tolerance. Overall, this study provides evidence for a role of RANKL signaling in the pathogenesis of T2DM. If so, translation to the clinic may be feasible given current pharmacological strategies to lower RANKL activity to treat osteoporosis.","authors":"Kiechl, S., Wittmann, J., Giaccari, A., Knoflach, M., Willeit, P., Bozec, A., Moschen, AR., Muscogiuri, G., Sorice, GP., Kireva, T., Summerer, M., Wirtz, S., Luther, J., Mielenz, D., Billmeier, U., Egger, G., Mayr, A., Oberhollenzer, F., Kronenberg, F., Orthofer, M., Penninger, JM., Meigs, JB., Bonora, E., Tilg, H., Willeit, J., Schett, G.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Med","volume":"19","issue":"3","page":"358-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23382200","title":"8-CPT-cAMP\/all-trans retinoic acid targets t(11;17) acute promyelocytic leukemia through enhanced cell differentiation and PLZF\/RAR\u03b1 degradation.","abstract":"The refractoriness of acute promyelocytic leukemia (APL) with t(11;17)(q23;q21) to all-trans retinoic acid (ATRA)-based therapy concerns clinicians and intrigues basic researchers. By using a murine leukemic model carrying both promyelocytic leukemia zinc finger\/retinoic acid receptor-\u03b1 (PLZF\/RAR\u03b1) and RAR\u03b1\/PLZF fusion genes, we discovered that 8-chlorophenylthio adenosine-3', 5'-cyclic monophosphate (8-CPT-cAMP) enhances cellular differentiation and improves gene trans-activation by ATRA in leukemic blasts. Mechanistically, in combination with ATRA, 8-CPT-cAMP activates PKA, causing phosphorylation of PLZF\/RAR\u03b1 at Ser765 and resulting in increased dissociation of the silencing mediator for retinoic acid and thyroid hormone receptors\/nuclear receptor corepressor from PLZF\/RAR\u03b1. This process results in changes of local chromatin and transcriptional reactivation of the retinoic acid pathway in leukemic cells. Meanwhile, 8-CPT-cAMP also potentiated ATRA-induced degradation of PLZF\/RAR\u03b1 through its Ser765 phosphorylation. In vivo treatment of the t(11;17) APL mouse model demonstrated that 8-CPT-cAMP could significantly improve the therapeutic effect of ATRA by targeting a leukemia-initiating cell activity. This combined therapy, which induces enhanced differentiation and oncoprotein degradation, may benefit t(11;17) APL patients.","authors":"Jiao, B., Ren, ZH., Liu, P., Chen, LJ., Shi, JY., Dong, Y., Ablain, J., Shi, L., Gao, L., Hu, JP., Ren, RB., de Th\u00e9, H., Chen, Z., Chen, SJ.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proc Natl Acad Sci U S A","volume":"110","issue":"9","page":"3495-500","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35349341","title":"An allosteric HTRA1-calpain 2 complex with restricted activation profile.","abstract":"SignificanceClassic serine proteases are synthesized as inactive precursors that are proteolytically processed, resulting in irreversible activation. We report an alternative and reversible mechanism of activation that is executed by an inactive protease. This mechanism involves a protein complex between the serine protease HTRA1 and the cysteine protease calpain 2. Surprisingly, activation is restricted as it improves the proteolysis of soluble tau protein but not the dissociation and degradation of its amyloid fibrils, a task that free HTRA1 is efficiently performing. These data exemplify a challenge for protein quality control proteases in the clearing of pathogenic fibrils and suggest a potential for unexpected side effects of chemical modulators targeting PDZ or other domains located at a distance to the active site.","authors":"Rey, J., Breiden, M., Lux, V., Bluemke, A., Steindel, M., Ripkens, K., M\u00f6llers, B., Bravo Rodriguez, K., Boisguerin, P., Volkmer, R., Mieres-Perez, J., Clausen, T., Sanchez-Garcia, E., Ehrmann, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Proc Natl Acad Sci U S A","volume":"119","issue":"14","page":"e2113520119","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23361909","title":"Erythropoiesis and globin switching in compound Klf1::Bcl11a mutant mice.","abstract":"B-cell lymphoma 11A (BCL11A) downregulation in human primary adult erythroid progenitors results in elevated expression of fetal \u03b3-globin. Recent reports showed that BCL11A expression is activated by KLF1, leading to \u03b3-globin repression. To study regulation of erythropoiesis and globin expression by KLF1 and BCL11A in an in vivo model, we used mice carrying a human \u03b2-globin locus transgene with combinations of Klf1 knockout, Bcl11a floxed, and EpoR(Cre) knockin alleles. We found a higher percentage of reticulocytes in adult Klf1(wt\/ko) mice and a mild compensated anemia in Bcl11a(cko\/cko) mice. These phenotypes were more pronounced in compound Klf1(wt\/ko)::Bcl11a(cko\/cko) mice. Analysis of Klf1(wt\/ko), Bcl11a(cko\/cko), and Klf1(wt\/ko)::Bcl11a(cko\/cko) mutant embryos demonstrated increased expression of mouse embryonic globins during fetal development. Expression of human \u03b3-globin remained high in Bcl11a(cko\/cko) embryos during fetal development, and this was further augmented in Klf1(wt\/ko)::Bcl11a(cko\/cko) embryos. After birth, expression of human \u03b3-globin and mouse embryonic globins decreased in Bcl11a(cko\/cko) and Klf1(wt\/ko)::Bcl11a(cko\/cko) mice, but the levels remained much higher than those observed in control animals. Collectively, our data support an important role for the KLF1-BCL11A axis in erythroid maturation and developmental regulation of globin expression.","authors":"Esteghamat, F., Gillemans, N., Bilic, I., van den Akker, E., Cant\u00f9, I., van Gent, T., Klingm\u00fcller, U., van Lom, K., von Lindern, M., Grosveld, F., Bryn van Dijk, T., Busslinger, M., Philipsen, S.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Blood","volume":"121","issue":"13","page":"2553-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23358448","title":"Three-dimensional neuroepithelial culture from human embryonic stem cells and its use for quantitative conversion to retinal pigment epithelium.","abstract":"A goal in human embryonic stem cell (hESC) research is the faithful differentiation to given cell types such as neural lineages. During embryonic development, a basement membrane surrounds the neural plate that forms a tight, apico-basolaterally polarized epithelium before closing to form a neural tube with a single lumen. Here we show that the three-dimensional epithelial cyst culture of hESCs in Matrigel combined with neural induction results in a quantitative conversion into neuroepithelial cysts containing a single lumen. Cells attain a defined neuroepithelial identity by 5 days. The neuroepithelial cysts naturally generate retinal epithelium, in part due to IGF-1\/insulin signaling. We demonstrate the utility of this epithelial culture approach by achieving a quantitative production of retinal pigment epithelial (RPE) cells from hESCs within 30 days. Direct transplantation of this RPE into a rat model of retinal degeneration without any selection or expansion of the cells results in the formation of a donor-derived RPE monolayer that rescues photoreceptor cells. The cyst method for neuroepithelial differentiation of pluripotent stem cells is not only of importance for RPE generation but will also be relevant to the production of other neuronal cell types and for reconstituting complex patterning events from three-dimensional neuroepithelia.","authors":"Zhu, Y., Carido, M., Meinhardt, A., Kurth, T., Karl, MO., Ader, M., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"PLoS One","volume":"8","issue":"1","page":"e54552","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-09-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23347405","title":"Unambiguous phosphosite localization using electron-transfer\/higher-energy collision dissociation (EThcD).","abstract":"We recently introduced a novel scheme combining electron-transfer and higher-energy collision dissociation (termed EThcD), for improved peptide ion fragmentation and identification. We reasoned that phosphosite localization, one of the major hurdles in high-throughput phosphoproteomics, could also highly benefit from the generation of such EThcD spectra. Here, we systematically assessed the impact on phosphosite localization utilizing EThcD in comparison to methods employing either ETD or HCD, respectively, using a defined synthetic phosphopeptide mixture and also using a larger data set of Ti(4+)-IMAC enriched phosphopeptides from a tryptic human cell line digest. In combination with a modified version of phosphoRS, we observed that in the majority of cases EThcD generated richer and more confidently identified spectra, resulting in superior phosphosite localization scores. Our data demonstrates the distinctive potential of EThcD for PTM localization, also beyond protein phosphorylation.","authors":"Frese, CK., Zhou, H., Taus, T., Altelaar, AF., Mechtler, K., Heck, AJ., Mohammed, S.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Proteome Res","volume":"12","issue":"3","page":"1520-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23336996","title":"Spheroid culture as a tool for creating 3D complex tissues.","abstract":"3D cell culture methods confer a high degree of clinical and biological relevance to in vitro models. This is specifically the case with the spheroid culture, where a small aggregate of cells grows free of foreign materials. In spheroid cultures, cells secrete the extracellular matrix (ECM) in which they reside, and they can interact with cells from their original microenvironment. The value of spheroid cultures is increasing quickly due to novel microfabricated platforms amenable to high-throughput screening (HTS) and advances in cell culture. Here, we review new possibilities that combine the strengths of spheroid culture with new microenvironment fabrication methods that allow for the creation of large numbers of highly reproducible, complex tissues.","authors":"Fennema, E., Rivron, N., Rouwkema, J., van Blitterswijk, C., de Boer, J.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Trends Biotechnol","volume":"31","issue":"2","page":"108-15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23328447","title":"Multiple functions of angiotensin-converting enzyme 2 and its relevance in cardiovascular diseases.","abstract":"Angiotensin-converting enzyme 2 (ACE2) is a negative regulator of the renin-angiotensin system, and functions as the key SARS coronavirus receptor and stabilizer of neutral amino acid transporters. ACE2 catalyzes the conversion of angiotensin II to angiotensin 1-7, thereby counterbalancing ACE activity. Accumulating evidence indicates that the enzymatic activity of ACE2 has a protective role in cardiovascular diseases. Loss of ACE2 can be detrimental, as it leads to functional deterioration of the heart and progression of cardiac, renal, and vascular pathologies. Recombinant soluble human ACE2 protein has been demonstrated to exhibit beneficial effects in various animal models, including cardiovascular diseases. ACE2 is a multifunctional enzyme and thus potentially acts on other vasoactive peptides, such as Apelin, a vital regulator of blood pressure and myocardium contractility. In addition, ACE2 is structurally a chimeric protein that has emerged from the duplication of 2 genes: homology with ACE at the carboxypeptidase domain and homology with Collectrin in the transmembrane C-terminal domain. ACE2 has been implicated in the pathology of Hartnup's disease, a disorder of amino acid homeostasis, and, via its function in amino acid transport, it has been recently revealed that ACE2 controls intestinal inflammation and diarrhea, thus regulating the gut microbiome. This review summarizes and discusses the structure and multiple functions of ACE2 and the relevance of this key enzyme in disease pathogenesis.","authors":"Kuba, K., Imai, Y., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Circ J","volume":"77","issue":"2","page":"301-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-200","title":"Multiple ubiquitin ligases protect human genome integrity by targeting cancer-associated APOBEC3 deaminases for degradation","abstract":null,"authors":"Schwartz, I. Budroni, V., Meyenberg, M., Hornegger H., Hacker, K., Schwartz, S., Hodakova, Z., Grabarczyk, D. B., Ehrmann, J. F., Scinicariello, S., Haselbach, D., Menche, J., Clausen, T., Karag\u00f6z, G. E., Versteeg, G. A.","publication_status":"preprint","journalpubyear":"2024","journaltitle":"bioRxiv ","volume":"10.1101\/2024.04.23.590688 ","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.04.23.590688v1","preprintlink":null,"articledate":"2024-04-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23307892","title":"Systems genetics implicates cytoskeletal genes in oocyte control of cloned embryo quality.","abstract":"Cloning by somatic cell nuclear transfer is an important technology, but remains limited due to poor rates of success. Identifying genes supporting clone development would enhance our understanding of basic embryology, improve applications of the technology, support greater understanding of establishing pluripotent stem cells, and provide new insight into clinically important determinants of oocyte quality. For the first time, a systems genetics approach was taken to discover genes contributing to the ability of an oocyte to support early cloned embryo development. This identified a primary locus on mouse chromosome 17 and potential loci on chromosomes 1 and 4. A combination of oocyte transcriptome profiling data, expression correlation analysis, and functional and network analyses yielded a short list of likely candidate genes in two categories. The major category-including two genes with the strongest genetic associations with the traits (Epb4.1l3 and Dlgap1)-encodes proteins associated with the subcortical cytoskeleton and other cytoskeletal elements such as the spindle. The second category encodes chromatin and transcription regulators (Runx1t1, Smchd1, and Chd7). Smchd1 promotes X chromosome inactivation, whereas Chd7 regulates expression of pluripotency genes. Runx1t1 has not been associated with these processes, but acts as a transcriptional repressor. The finding that cytoskeleton-associated proteins may be key determinants of early clone development highlights potential roles for cytoplasmic components of the oocyte in supporting nuclear reprogramming. The transcriptional regulators identified may contribute to the overall process as downstream effectors.","authors":"Cheng, Y., Gaughan, J., Midic, U., Han, Z., Liang, CG., Patel, BG., Latham, KE.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Genetics","volume":"193","issue":"3","page":"877-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23300623","title":"Neural crest does not contribute to the neck and shoulder in the axolotl (Ambystoma mexicanum).","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23300623<\/PMID><DateCompleted><Year>2013<\/Year><Month>07<\/Month><Day>02<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><Issue>12<\/Issue><PubDate><Year>2012<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Neural crest does not contribute to the neck and shoulder in the axolotl (Ambystoma mexicanum).<\/ArticleTitle><Pagination><MedlinePgn>e52244<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0052244<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">A major step during the evolution of tetrapods was their transition from water to land. This process involved the reduction or complete loss of the dermal bones that made up connections to the skull and a concomitant enlargement of the endochondral shoulder girdle. In the mouse the latter is derived from three separate embryonic sources: lateral plate mesoderm, somites, and neural crest. The neural crest was suggested to sustain the muscle attachments. How this complex composition of the endochondral shoulder girdle arose during evolution and whether it is shared by all tetrapods is unknown. Salamanders that lack dermal bone within their shoulder girdle were of special interest for a possible contribution of the neural crest to the endochondral elements and muscle attachment sites, and we therefore studied them in this context.","authors":"Epperlein, HH., Khattak, S., Knapp, D., Tanaka, EM., Malashichev, YB.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"12","page":"e52244","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23277578","title":"Structural basis for cooperativity of CRM1 export complex formation.","abstract":"In eukaryotes, the nucleocytoplasmic transport of macromolecules is mainly mediated by soluble nuclear transport receptors of the karyopherin-\u03b2 superfamily termed importins and exportins. The highly versatile exportin chromosome region maintenance 1 (CRM1) is essential for nuclear depletion of numerous structurally and functionally unrelated protein and ribonucleoprotein cargoes. CRM1 has been shown to adopt a toroidal structure in several functional transport complexes and was thought to maintain this conformation throughout the entire nucleocytoplasmic transport cycle. We solved crystal structures of free CRM1 from the thermophilic eukaryote Chaetomium thermophilum. Surprisingly, unbound CRM1 exhibits an overall extended and pitched superhelical conformation. The two regulatory regions, namely the acidic loop and the C-terminal \u03b1-helix, are dramatically repositioned in free CRM1 in comparison with the ternary CRM1-Ran-Snurportin1 export complex. Single-particle EM analysis demonstrates that, in a noncrystalline environment, free CRM1 exists in equilibrium between extended, superhelical and compact, ring-like conformations. Molecular dynamics simulations show that the C-terminal helix plays an important role in regulating the transition from an extended to a compact conformation and reveal how the binding site for nuclear export signals of cargoes is modulated by different CRM1 conformations. Combining these results, we propose a model for the cooperativity of CRM1 export complex assembly involving the long-range allosteric communication between the distant binding sites of GTP-bound Ran and cargo.","authors":"Monecke, T., Haselbach, D., Vo\u00df, B., Russek, A., Neumann, P., Thomson, E., Hurt, E., Zachariae, U., Stark, H., Grubm\u00fcller, H., Dickmanns, A., Ficner, R.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proc Natl Acad Sci U S A","volume":"110","issue":"3","page":"960-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23277429","title":"Molecular requirements for the formation of a kinetochore-microtubule interface by Dam1 and Ndc80 complexes.","abstract":"Kinetochores are large protein complexes that link sister chromatids to the spindle and transduce microtubule dynamics into chromosome movement. In budding yeast, the kinetochore-microtubule interface is formed by the plus end-associated Dam1 complex and the kinetochore-resident Ndc80 complex, but how they work in combination and whether a physical association between them is critical for chromosome segregation is poorly understood. Here, we define structural elements required for the Ndc80-Dam1 interaction and probe their function in vivo. A novel ndc80 allele, selectively impaired in Dam1 binding, displayed growth and chromosome segregation defects. Its combination with an N-terminal truncation resulted in lethality, demonstrating essential but partially redundant roles for the Ndc80 N-tail and Ndc80-Dam1 interface. In contrast, mutations in the calponin homology domain of Ndc80 abrogated kinetochore function and were not compensated by the presence of Dam1. Our experiments shed light on how microtubule couplers cooperate and impose important constraints on structural models for outer kinetochore assembly.","authors":"Lampert, F., Mieck, C., Alushin, GM., Nogales, E., Westermann, S.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"J Cell Biol","volume":"200","issue":"1","page":"21-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34435732","title":"RNA velocity-current challenges and future perspectives.","abstract":"RNA velocity has enabled the recovery of directed dynamic information from single-cell transcriptomics by connecting measurements to the underlying kinetics of gene expression. This approach has opened up new ways of studying cellular dynamics. Here, we review the current state of RNA velocity modeling approaches, discuss various examples illustrating limitations and potential pitfalls, and provide guidance on how the ensuing challenges may be addressed. We then outline future directions on how to generalize the concept of RNA velocity to a wider variety of biological systems and modalities.","authors":"Bergen, V., Soldatov, RA., Kharchenko, PV., Theis, FJ.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Mol Syst Biol","volume":"17","issue":"8","page":"e10282","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-13","doi":"10.15252\/msb.202110282","first_author":"Bergen, V.","corresponding_authors":"Theis, FJ."},{"pmid":"23275436","title":"Yeast protein phosphatase 2A-Cdc55 regulates the transcriptional response to hyperosmolarity stress by regulating Msn2 and Msn4 chromatin recruitment.","abstract":"We have identified Cdc55, a regulatory B subunit of protein phosphatase 2A (PP2A), as an essential activating factor for stress gene transcription in Saccharomyces cerevisiae. The presence of PP2A-Cdc55 is required for full activation of the environmental stress response mediated by the transcription factors Msn2 and Msn4. We show that PP2A-Cdc55 contributes to sustained nuclear accumulation of Msn2 and Msn4 during hyperosmolarity stress. PP2A-Cdc55 also enhances Msn2-dependent transactivation, required for extended chromatin recruitment of the transcription factor. We analyzed a possible direct regulatory role for PP2A-Cdc55 on the phosphorylation status of Msn2. Detailed mass spectrometric and genetic analysis of Msn2 showed that stress exposure causes immediate transient dephosphorylation of Msn2 which is not dependent on PP2A-Cdc55 activity. Furthermore, the Hog1 mitogen-activated protein kinase pathway activity is not influenced by PP2A-Cdc55. We therefore propose that the PP2A-Cdc55 phosphatase is not involved in cytosolic stress signal perception but is involved in a specific intranuclear mechanism to regulate Msn2 and Msn4 nuclear accumulation and chromatin association under stress conditions.","authors":"Reiter, W., Klopf, E., De Wever, V., Anrather, D., Petryshyn, A., Roetzer, A., Niederacher, G., Roitinger, E., Dohnal, I., G\u00f6rner, W., Mechtler, K., Brocard, C., Sch\u00fcller, C., Ammerer, G.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Mol Cell Biol","volume":"33","issue":"5","page":"1057-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23248301","title":"Transcription factor YY1 is essential for regulation of the Th2 cytokine locus and for Th2 cell differentiation.","abstract":"The Th2 locus control region (LCR) has been shown to be important in efficient and coordinated cytokine gene regulation during Th2 cell differentiation. However, the molecular mechanism for this is poorly understood. To study the molecular mechanism of the Th2 LCR, we searched for proteins binding to it. We discovered that transcription factor YY1 bound to the LCR and the entire Th2 cytokine locus in a Th2-specific manner. Retroviral overexpression of YY1 induced Th2 cytokine expression. CD4-specific knockdown of YY1 in mice caused marked reduction in Th2 cytokine expression, repressed chromatin remodeling, decreased intrachromosomal interactions, and resistance in an animal model of asthma. YY1 physically associated with GATA-binding protein-3 (GATA3) and is required for GATA3 binding to the locus. YY1 bound to the regulatory elements in the locus before GATA3 binding. Thus, YY1 cooperates with GATA3 and is required for regulation of the Th2 cytokine locus and Th2 cell differentiation.","authors":"Hwang, SS., Kim, YU., Lee, S., Jang, SW., Kim, MK., Koh, BH., Lee, W., Kim, J., Souabni, A., Busslinger, M., Lee, GR.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proc Natl Acad Sci U S A","volume":"110","issue":"1","page":"276-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23239499","title":"Association analysis reveals genetic variation altering bleomycin-induced pulmonary fibrosis in mice.","abstract":"Pulmonary fibrosis is a disease of significant morbidity, with an incompletely defined genetic basis. Here, we combine linkage and association studies to identify genetic variations associated with pulmonary fibrosis in mice. Mice were treated with bleomycin by osmotic minipump, and pulmonary fibrosis was histologically assessed 6 weeks later. Fibrosis was mapped in C57BL6\/J (fibrosis-susceptible) \u00d7 A\/J (fibrosis-resistant) F2 mice, and the major identified linkage intervals were evaluated in consomic mice. Genome-wide and linkage-interval genes were assessed for their association with fibrosis, using phenotypic data from 23 inbred strains and the murine single-nucleotide polymorphism map. Susceptibility to pulmonary fibrosis mapped to a locus on chromosome 17, which was verified with consomic mice, and to three additional suggestive loci that may interact with alleles on chromosome 17 to affect the trait in F2 mice. Two of the loci, including the region on chromosome 17, are homologous to previously mapped loci of human idiopathic fibrosis. Of the 23 phenotyped murine strains, four developed significant fibrosis, and the majority presented minimal disease. Genome-wide and linkage region-specific association studies revealed 11 pulmonary expressed genes (including the autophagy gene Cep55, and Masp2, which is a complement component) to contain polymorphisms significantly associated with bleomycin-induced fibrotic lung disease. In conclusion, genomic approaches were used to identify linkage intervals and specific genetic variations associated with pulmonary fibrosis in mice. The common loci and similarities in phenotype suggest these findings to be of relevance to clinical pulmonary fibrosis.","authors":"Paun, A., Lemay, AM., Tomko, TG., Haston, CK.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Am J Respir Cell Mol Biol","volume":"48","issue":"3","page":"330-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23239737","title":"Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing.","abstract":"Mammalian imprinted genes often cluster with long noncoding (lnc) RNAs. Three lncRNAs that induce parental-specific silencing show hallmarks indicating that their transcription is more important than their product. To test whether Airn transcription or product silences the Igf2r gene, we shortened the endogenous lncRNA to different lengths. The results excluded a role for spliced and unspliced Airn lncRNA products and for Airn nuclear size and location in silencing Igf2r. Instead, silencing only required Airn transcriptional overlap of the Igf2r promoter, which interferes with RNA polymerase II recruitment in the absence of repressive chromatin. Such a repressor function for lncRNA transcriptional overlap reveals a gene silencing mechanism that may be widespread in the mammalian genome, given the abundance of lncRNA transcripts.","authors":"Latos, PA., Pauler, FM., Koerner, MV., \u015eenergin, HB., Hudson, QJ., Stocsits, RR., Allhoff, W., Stricker, SH., Klement, RM., Warczok, KE., Aumayr, K., Pasierbek, P., Barlow, DP.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Science","volume":"338","issue":"6113","page":"1469-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23236295","title":"A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis.","abstract":"Despite their classical role as transcriptional repressors, several histone deacetylases, including the baker's yeast Set3\/Hos2 complex (Set3C), facilitate gene expression. In the dimorphic human pathogen Candida albicans, the homologue of the Set3C inhibits the yeast-to-filament transition, but the precise molecular details of this function have remained elusive. Here, we use a combination of ChIP-Seq and RNA-Seq to show that the Set3C acts as a transcriptional co-factor of metabolic and morphogenesis-related genes in C. albicans. Binding of the Set3C correlates with gene expression during fungal morphogenesis; yet, surprisingly, deletion of SET3 leaves the steady-state expression level of most genes unchanged, both during exponential yeast-phase growth and during the yeast-filament transition. Fine temporal resolution of transcription in cells undergoing this transition revealed that the Set3C modulates transient expression changes of key morphogenesis-related genes. These include a transcription factor cluster comprising of NRG1, EFG1, BRG1, and TEC1, which form a regulatory circuit controlling hyphal differentiation. Set3C appears to restrict the factors by modulating their transcription kinetics, and the hyperfilamentous phenotype of SET3-deficient cells can be reverted by mutating the circuit factors. These results indicate that the chromatin status at coding regions represents a dynamic platform influencing transcription kinetics. Moreover, we suggest that transcription at the coding sequence can be transiently decoupled from potentially conflicting promoter information in dynamic environments.","authors":"Hnisz, D., Bardet, AF., Nobile, CJ., Petryshyn, A., Glaser, W., Sch\u00f6ck, U., Stark, A., Kuchler, K.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"12","page":"e1003118","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23236288","title":"Construction of a global pain systems network highlights phospholipid signaling as a regulator of heat nociception.","abstract":"The ability to perceive noxious stimuli is critical for an animal's survival in the face of environmental danger, and thus pain perception is likely to be under stringent evolutionary pressure. Using a neuronal-specific RNAi knock-down strategy in adult Drosophila, we recently completed a genome-wide functional annotation of heat nociception that allowed us to identify \u03b12\u03b43 as a novel pain gene. Here we report construction of an evolutionary-conserved, system-level, global molecular pain network map. Our systems map is markedly enriched for multiple genes associated with human pain and predicts a plethora of novel candidate pain pathways. One central node of this pain network is phospholipid signaling, which has been implicated before in pain processing. To further investigate the role of phospholipid signaling in mammalian heat pain perception, we analysed the phenotype of PIP5K\u03b1 and PI3K\u03b3 mutant mice. Intriguingly, both of these mice exhibit pronounced hypersensitivity to noxious heat and capsaicin-induced pain, which directly mapped through PI3K\u03b3 kinase-dead knock-in mice to PI3K\u03b3 lipid kinase activity. Using single primary sensory neuron recording, PI3K\u03b3 function was mechanistically linked to a negative regulation of TRPV1 channel transduction. Our data provide a systems map for heat nociception and reinforces the extraordinary conservation of molecular mechanisms of nociception across different species.","authors":"Neely, GG., Rao, S., Costigan, M., Mair, N., Racz, I., Milinkeviciute, G., Meixner, A., Nayanala, S., Griffin, RS., Belfer, I., Dai, F., Smith, S., Diatchenko, L., Marengo, S., Haubner, BJ., Novatchkova, M., Gibson, D., Maixner, W., Pospisilik, JA., Hirsch, E., Whishaw, IQ., Zimmer, A., Gupta, V., Sasaki, J., Kanaho, Y., Sasaki, T., Kress, M., Woolf, CJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"12","page":"e1003071","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23160880","title":"Impact of ACE2 deficiency and oxidative stress on cerebrovascular function with aging.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23160880<\/PMID><DateCompleted><Year>2013<\/Year><Month>02<\/Month><Day>05<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4628<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>43<\/Volume><Issue>12<\/Issue><PubDate><Year>2012<\/Year><Month>Dec<\/Month><\/PubDate><\/JournalIssue><Title>Stroke<\/Title><ISOAbbreviation>Stroke<\/ISOAbbreviation><\/Journal><ArticleTitle>Impact of ACE2 deficiency and oxidative stress on cerebrovascular function with aging.<\/ArticleTitle><Pagination><MedlinePgn>3358-63<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/STROKEAHA.112.667063<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND AND PURPOSE\" NlmCategory=\"OBJECTIVE\">Angiotensin II produces oxidative stress and endothelial dysfunction in cerebral arteries, and angiotensin II type I receptors may play a role in longevity and vascular aging. Angiotensin-converting enzyme type 2 (ACE2) converts angiotensin II to angiotensin (1-7) and thus, may protect against effects of angiotensin II. We hypothesized that ACE2 deficiency increases oxidative stress and endothelial dysfunction in cerebral arteries and examined the role of ACE2 in age-related cerebrovascular dysfunction.","authors":"Pe\u00f1a Silva, RA., Chu, Y., Miller, JD., Mitchell, IJ., Penninger, JM., Faraci, FM., Heistad, DD.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Stroke","volume":"43","issue":"12","page":"3358-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23144331","title":"CXCL10-CXCR3 enhances the development of neutrophil-mediated fulminant lung injury of viral and nonviral origin.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">23144331<\/PMID><DateCompleted><Year>2013<\/Year><Month>03<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>09<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1535-4970<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>187<\/Volume><Issue>1<\/Issue><PubDate><Year>2013<\/Year><Month>Jan<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>American journal of respiratory and critical care medicine<\/Title><ISOAbbreviation>Am J Respir Crit Care Med<\/ISOAbbreviation><\/Journal><ArticleTitle>CXCL10-CXCR3 enhances the development of neutrophil-mediated fulminant lung injury of viral and nonviral origin.<\/ArticleTitle><Pagination><MedlinePgn>65-77<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1164\/rccm.201203-0508OC<\/ELocationID><Abstract><AbstractText Label=\"RATIONALE\" NlmCategory=\"BACKGROUND\">Patients who developed acute respiratory distress syndrome (ARDS) after infection with severe respiratory viruses (e.g., severe acute respiratory syndrome-coronavirus, H5N1 avian influenza virus), exhibited unusually high levels of CXCL10, which belongs to the non-ELR (glutamic-leucine-arginine) CXC chemokine superfamily. CXCL10 may not be a bystander to the severe virus infection but may directly contribute to the pathogenesis of neutrophil-mediated, excessive pulmonary inflammation.","authors":"Ichikawa, A., Kuba, K., Morita, M., Chida, S., Tezuka, H., Hara, H., Sasaki, T., Ohteki, T., Ranieri, VM., dos Santos, CC., Kawaoka, Y., Akira, S., Luster, AD., Lu, B., Penninger, JM., Uhlig, S., Slutsky, AS., Imai, Y.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Am J Respir Crit Care Med","volume":"187","issue":"1","page":"65-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23123849","title":"Structure of the Mediator head module.","abstract":"Gene transcription by RNA polymerase (Pol) II requires the coactivator complex Mediator. Mediator connects transcriptional regulators and Pol II, and is linked to human disease. Mediator from the yeast Saccharomyces cerevisiae has a molecular mass of 1.4\u2009megadaltons and comprises 25\u2009subunits that form the head, middle, tail and kinase modules. The head module constitutes one-half of the essential Mediator core, and comprises the conserved subunits Med6, Med8, Med11, Med17, Med18, Med20 and Med22. Recent X-ray analysis of the S. cerevisiae head module at 4.3\u2009\u00c5 resolution led to a partial architectural model with three submodules called neck, fixed jaw and moveable jaw. Here we determine de novo the crystal structure of the head module from the fission yeast Schizosaccharomyces pombe at 3.4\u2009\u00c5 resolution. Structure solution was enabled by new structures of Med6 and the fixed jaw, and previous structures of the moveable jaw and part of the neck, and required deletion of Med20. The S. pombe head module resembles the head of a crocodile with eight distinct elements, of which at least four are mobile. The fixed jaw comprises tooth and nose domains, whereas the neck submodule contains a helical spine and one limb, with shoulder, arm and finger elements. The arm and the essential shoulder contact other parts of Mediator. The jaws and a central joint are implicated in interactions with Pol\u2009II and its carboxy-terminal domain, and the joint is required for transcription in vitro. The S. pombe head module structure leads to a revised model of the S. cerevisiae module, reveals a high conservation and flexibility, explains known mutations, and provides the basis for unravelling a central mechanism of gene regulation.","authors":"Larivi\u00e8re, L., Plaschka, C., Seizl, M., Wenzeck, L., Kurth, F., Cramer, P.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nature","volume":"492","issue":"7429","page":"448-51","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23093776","title":"A misplaced lncRNA causes brachydactyly in humans.","abstract":"Translocations are chromosomal rearrangements that are frequently associated with a variety of disease states and developmental disorders. We identified 2 families with brachydactyly type E (BDE) resulting from different translocations affecting chromosome 12p. Both translocations caused downregulation of the parathyroid hormone-like hormone (PTHLH) gene by disrupting the cis-regulatory landscape. Using chromosome conformation capturing, we identified a regulator on chromosome 12q that interacts in cis with PTHLH over a 24.4-megabase distance and in trans with the sex-determining region Y-box 9 (SOX9) gene on chromosome 17q. The element also harbored a long noncoding RNA (lncRNA). Silencing of the lncRNA, PTHLH, or SOX9 revealed a feedback mechanism involving an expression-dependent network in humans. In the BDE patients, the human lncRNA was upregulated by the disrupted chromosomal association. Moreover, the lncRNA occupancy at the PTHLH locus was reduced. Our results document what we believe to be a novel in cis- and in trans-acting DNA and lncRNA regulatory feedback element that is reciprocally regulated by coding genes. Furthermore, our findings provide a systematic and combinatorial view of how enhancers encoding lncRNAs may affect gene expression in normal development.","authors":"Maass, PG., Rump, A., Schulz, H., Stricker, S., Schulze, L., Platzer, K., Aydin, A., Tinschert, S., Goldring, MB., Luft, FC., B\u00e4hring, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Clin Invest","volume":"122","issue":"11","page":"3990-4002","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23083744","title":"Discrete neocortical dynamics predict behavioral categorization of sounds.","abstract":"The ability to group stimuli into perceptual categories is essential for efficient interaction with the environment. Discrete dynamics that emerge in brain networks are believed to be the neuronal correlate of category formation. Observations of such dynamics have recently been made; however, it is still unresolved if they actually match perceptual categories. Using in\u00a0vivo two-photon calcium imaging in\u00a0the auditory cortex of mice, we show that local network activity evoked by sounds is constrained to few response modes. Transitions between response modes are characterized by an abrupt switch, indicating attractor-like, discrete dynamics. Moreover, we show that local cortical responses quantitatively predict discrimination performance and spontaneous categorization of sounds in behaving mice. Our results therefore demonstrate that local nonlinear dynamics in the auditory cortex generate spontaneous sound categories which can be selected for behavioral or perceptual decisions.","authors":"Bathellier, B., Ushakova, L., Rumpel, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Neuron","volume":"76","issue":"2","page":"435-49","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23082122","title":"The lipid phenotype of breast cancer cells characterized by Raman microspectroscopy: towards a stratification of malignancy.","abstract":"Although molecular classification brings interesting insights into breast cancer taxonomy, its implementation in daily clinical care is questionable because of its expense and the information supplied in a single sample allocation is not sufficiently reliable. New approaches, based on a panel of small molecules derived from the global or targeted analysis of metabolic profiles of cells, have found a correlation between activation of de novo lipogenesis and poorer prognosis and shorter disease-free survival for many tumors. We hypothesized that the lipid content of breast cancer cells might be a useful indirect measure of a variety of functions coupled to breast cancer progression. Raman microspectroscopy was used to characterize metabolism of breast cancer cells with different degrees of malignancy. Raman spectra from MDA-MB-435, MDA-MB-468, MDA-MB-231, SKBR3, MCF7 and MCF10A cells were acquired with an InVia Raman microscope (Renishaw) with a backscattered configuration. We used Principal Component Analysis and Partial Least Squares Discriminant Analyses to assess the different profiling of the lipid composition of breast cancer cells. Characteristic bands related to lipid content were found at 3014, 2935, 2890 and 2845 cm(-1), and related to lipid and protein content at 2940 cm(-1). A classificatory model was generated which segregated metastatic cells and non-metastatic cells without basal-like phenotype with a sensitivity of 90% and a specificity of 82.1%. Moreover, expression of SREBP-1c and ABCA1 genes validated the assignation of the lipid phenotype of breast cancer cells. Indeed, changes in fatty acid unsaturation were related with the epithelial-to-mesenchymal transition phenotype. Raman microspectroscopy is a promising technique for characterizing and classifying the malignant phenotype of breast cancer cells on the basis of their lipid profiling. The algorithm for the discrimination of metastatic ability is a first step towards stratifying breast cancer cells using this rapid and reagent-free tool.","authors":"Nieva, C., Marro, M., Santana-Codina, N., Rao, S., Petrov, D., Sierra, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"10","page":"e46456","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23081890","title":"Traumatic nonanastomotic pseudoaneurysm of axillofemoral bypass graft: a case report and review of the literature.","abstract":"Traumatic nonanastomtic disruption of an axillofemoral bypass graft (AFBG) is a relatively rare entity. However, we are reporting on an 82-year-old female who presented with a pulsating mass on her left side, which was noticed about 2 weeks after she fell on her side. The patient had undergone an ABFG about 15 years earlier for limb revascularization, and she had an occluded aortobifemoral bypass graft. A diagnosis of localized rupture with pseudoaneurysm (PSA) was confirmed with arterial duplex ultrasound and computed tomograph (CT) angiogram scans. A 7-cm PSA with partial disruption of the polytetrafluoroethylene (PTFE) graft at the level of the fifth thoracic vertebrae was noted. An initial work-up to eliminate the possibility of sepsis and localized mycotic seeding was negative. The patient was taken to the hybrid angiogram room, and a percutaneous cut down of the AFBG was performed with local dissection below the site of rupture. A limited angiogram showed a focal PSA of the AFBG. An intravascular ultrasound (IVUS) was performed to calibrate the diameter of the AFBG, and a covered stent was deployed across the area of the disrupted graft. A completion angiogram showed complete exclusion of the PSA with good runoff throughout the graft. The authors will review the management of the traumatic PSA with an endovascular approach.","authors":"Mousa, AY., Nanjundappa, A., Abu-Halimah, S., Aburahma, AF.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Vasc Endovascular Surg","volume":"47","issue":"1","page":"57-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23081728","title":"Modelling cell migration and adhesion during development.","abstract":"Cell-cell adhesion is essential for biological development: cells migrate to their target sites, where cell-cell adhesion enables them to aggregate and form tissues. Here, we extend analysis of the model of cell migration proposed by Anguige and Schmeiser (J. Math. Biol. 58(3):395-427, 2009) that incorporates both cell-cell adhesion and volume filling. The stochastic space-jump model is compared to two deterministic counterparts (a system of stochastic mean equations and a non-linear partial differential equation), and it is shown that the results of the deterministic systems are, in general, qualitatively similar to the mean behaviour of multiple stochastic simulations. However, individual stochastic simulations can give rise to behaviour that varies significantly from that of the mean. In particular, individual simulations might admit cell clustering when the mean behaviour does not. We also investigate the potential of this model to display behaviour predicted by the differential adhesion hypothesis by incorporating a second cell species, and present a novel approach for implementing models of cell migration on a growing domain.","authors":"Thompson, RN., Yates, CA., Baker, RE.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Bull Math Biol","volume":"74","issue":"12","page":"2793-809","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-202","title":"A dual ribosomal system in the zebrafish soma and germline","abstract":null,"authors":"Shah, AN., Leesch, F., Lorenzo-Orts, L., Grundmann, L., Novatchkova, M., Haselbach, D., Calo, E., Pauli, A.","publication_status":"preprint","journalpubyear":"2024","journaltitle":"bioRxiv","volume":"doi:10.1101\/2024.08.29.610041","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.08.29.610041v1","preprintlink":null,"articledate":"2024-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23081670","title":"Long-term hearing result using Kurz titanium ossicular implants.","abstract":"Titanium implants in middle ear surgery were introduced in the late 90s and are now frequently used in middle ear surgery. However, long-term studies of patient outcome are few and have only been published in subgroups of patients. We report the long-term effect of titanium middle ear implants for ossicular reconstruction in chronic ear disease investigated in a Norwegian tertiary otological referral centre. Retrospective chart reviews were performed for procedures involving 76 titanium implants between 2000 and 2007. All patients who underwent surgery using the Kurz Vario titanium implant were included in the study. Audiological parameters using four frequencies, 0.5, 1, 2, and 3 kHz, according to AAO-HNS guidelines, was assessed pre and postoperatively. Otosurgical procedures, complications, revisions, and extrusion rates were analyzed. The study had no dropouts. The partial ossicular replacement prosthesis (PORP) was used in 44 procedures and the total ossicular replacement prosthesis (TORP) in 32 procedures, respectively. Mean follow-up was 5.2 years (62 months). The ossiculoplasties were performed as staging procedures or in combination with other chronic ear surgery. The same surgeon performed all the procedures. A postoperative air-bone gap of \u2264 20 dB was obtained in 74 % of the patients, 82 % for the Bell (PORP) prosthesis, and 63 % for the Arial (TORP) prosthesis. The extrusion rate was 5 %. We conclude that titanium ossicular implants give stable and excellent long-term hearing results.","authors":"Hess-Erga, J., M\u00f8ller, P., Vassbotn, FS.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Eur Arch Otorhinolaryngol","volume":"270","issue":"6","page":"1817-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23080431","title":"Effects of cadmium on the sub-cellular localization of \u03b2-catenin and \u03b2-catenin-regulated gene expression in NRK-52E cells.","abstract":"The E-cadherin\/\u03b2-catenin complex is a structural component of adherens-type junctions in epithelial cells. Moreover, \u03b2-catenin acts as an intracellular signaling molecule that can influence the expression of a variety of genes that regulate apoptosis and cell cycle control. Cadmium (Cd) is an environmental toxicant that causes renal dysfunction and disrupts cadherin-dependent cell-cell adhesion in various types of epithelial cells. In this study, we examined the effects of Cd on the subcellular localization of \u03b2-catenin, the cadherin\/\u03b2-catenin complex and \u03b2-catenin-mediated gene transcription in rat proximal tubule NRK-52E cells. Exposure to 5-10\u00a0\u03bcM Cd for 4\u00a0h caused the NRK cells to separate from each other without killing the cells or causing them to detach from the growing surface. This effect was associated with the loss of \u03b2-catenin and E-cadherin from the cell-cell contacts and apparent changes in the accumulation of \u03b2-catenin in the nuclear cell subfraction. The expression of the \u03b2-catenin-sensitive gene, c-jun was significantly increased in cells exposed to 5\u00a0\u03bcM Cd. However, there was no change in the expression of several other \u03b2-catenin-regulated genes including: c-myc, cyclin D1 and matrilysin. Additional studies utilizing the TOPFLASH \u03b2-catenin reporter gene construct showed that Cd caused a 2-3 fold increase in the expression of the luciferase reporter gene. Overall, these results indicate that Cd disrupts the cadherin\/\u03b2-catenin complex in NRK-52E cells, but this effect leads to only partial activation of \u03b2-catenin-mediated gene transcription.","authors":"Edwards, JR., Kolman, K., Lamar, PC., Chandar, N., Fay, MJ., Prozialeck, WC.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Biometals","volume":"26","issue":"1","page":"33-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23023663","title":"Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster.","abstract":"Researchers have now had access to the fully sequenced Drosophila melanogaster genome for over a decade, and the sequenced genomes of 11 additional Drosophila species have been available for almost 5 years, with more species' genomes becoming available every year [Adams MD, Celniker SE, Holt RA, et al. The genome sequence of Drosophila melanogaster. Science 2000;287:2185-95; Clark AG, Eisen MB, Smith DR, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007;450:203-18]. Although the best studied of the D. melanogaster transcription factors (TFs) were cloned before sequencing of the genome, the availability of sequence data promised to transform our understanding of TFs and gene regulatory networks. Sequenced genomes have allowed researchers to generate tools for high-throughput characterization of gene expression levels, genome-wide TF localization and analyses of evolutionary constraints on DNA elements across multiple species. With an estimated 700 DNA-binding proteins in the Drosophila genome, it will be many years before each potential sequence-specific TF is studied in detail, yet the last decade of functional genomics research has already impacted our view of gene regulatory networks and TF DNA recognition.","authors":"Slattery, M., N\u00e8gre, N., White, KP.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Brief Funct Genomics","volume":"11","issue":"5","page":"336-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23053744","title":"Behaviour of mesenchymal stem cells from bone marrow of untreated advanced breast and lung cancer patients without bone osteolytic metastasis.","abstract":"Tumour cells can find in bone marrow (BM) a niche rich in growth factors and cytokines that promote their self-renewal, proliferation and survival. In turn, tumour cells affect the homeostasis of the BM and bone, as well as the balance among haematopoiesis, osteogenesis, osteoclastogenesis and bone-resorption. As a result, growth and survival factors normally sequestered in the bone matrix are released, favouring tumour development. Mesenchymal stem cells (MSCs) from BM can become tumour-associated fibroblasts, have immunosuppressive function, and facilitate metastasis by epithelial-to-mesenchymal transition. Moreover, MSCs generate osteoblasts and osteocytes and regulate osteoclastogenesis. Therefore, MSCs can play an important pro-tumorigenic role in the formation of a microenvironment that promotes BM and bone metastasis. In this study we showed that BM MSCs from untreated advanced breast and lung cancer patients, without bone metastasis, had low osteogenic and adipogenic differentiation capacity compared to that of healthy volunteers. In contrast, chondrogenic differentiation was increased. Moreover, MSCs from patients had lower expression of CD146. Finally, our data showed higher levels of Dkk-1 in peripheral blood plasma from patients compared with healthy volunteers. Because no patient had any bone disorder by the time of the study we propose that the primary tumour altered the plasticity of MSCs. As over 70 % of advanced breast cancer patients and 30-40 % of lung cancer patients will develop osteolytic bone metastasis for which there is no total cure, our findings could possibly be used as predictive tools indicating the first signs of future bone disease. In addition, as the MSCs present in the BM of these patients may not be able to regenerate bone after the tumour cells invasion into BM\/bone, it is possible that they promote the cycle between tumour cell growth and bone destruction.","authors":"Fern\u00e1ndez Vallone, VB., Hofer, EL., Choi, H., Bordenave, RH., Batagelj, E., Feldman, L., La Russa, V., Caramutti, D., Dimase, F., Labovsky, V., Mart\u00ednez, LM., Chasseing, NA.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Clin Exp Metastasis","volume":"30","issue":"3","page":"317-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36171373","title":"A nomenclature consensus for nervous system organoids and assembloids.","abstract":"Self-organizing three-dimensional cellular models derived from human pluripotent stem cells or primary tissue have great potential to provide insights into how the human nervous system develops, what makes it unique and how disorders of the nervous system arise, progress and could be treated. Here, to facilitate progress and improve communication with the scientific community and the public, we clarify and provide a basic framework for the nomenclature of human multicellular models of nervous system development and disease, including organoids, assembloids and transplants.","authors":"Pa\u0219ca, SP., Arlotta, P., Bateup, HS., Camp, JG., Cappello, S., Gage, FH., Knoblich, JA., Kriegstein, AR., Lancaster, MA., Ming, GL., Muotri, AR., Park, IH., Reiner, O., Song, H., Studer, L., Temple, S., Testa, G., Treutlein, B., Vaccarino, FM.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nature","volume":"609","issue":"7929","page":"907-910","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23051844","title":"Cancer stem cell definitions and terminology: the devil is in the details.","abstract":"The cancer stem cell (CSC) concept has important therapeutic implications, but its investigation has been hampered both by a lack of consistency in the terms used for these cells and by how they are defined. Evidence of their heterogeneous origins, frequencies and their genomic, as well as their phenotypic and functional, properties has added to the confusion and has fuelled new ideas and controversies. Participants in The Year 2011 Working Conference on CSCs met to review these issues and to propose a conceptual and practical framework for CSC terminology. More precise reporting of the parameters that are used to identify CSCs and to attribute responses to them is also recommended as key to accelerating an understanding of their biology and developing more effective methods for their eradication in patients.","authors":"Valent, P., Bonnet, D., De Maria, R., Lapidot, T., Copland, M., Melo, JV., Chomienne, C., Ishikawa, F., Schuringa, JJ., Stassi, G., Huntly, B., Herrmann, H., Soulier, J., Roesch, A., Schuurhuis, GJ., W\u00f6hrer, S., Arock, M., Zuber, J., Cerny-Reiterer, S., Johnsen, HE., Andreeff, M., Eaves, C.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nat Rev Cancer","volume":"12","issue":"11","page":"767-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23050044","title":"Oncostatin m promotes mammary tumor metastasis to bone and osteolytic bone degradation.","abstract":"Oncostatin M (OSM) is an interleukin-6 (IL-6) family cytokine that has been implicated in a number of biological processes including inflammation, hematopoiesis, immune responses, development, and bone homeostasis. Recent evidence suggests that OSM may promote breast tumor invasion and metastasis. We investigated the role of OSM in the formation of bone metastases in vivo using the 4T1.2 mouse mammary tumor model in which OSM expression was knocked down using shRNA (4T1.2-OSM). 4T1.2-OSM cells were injected orthotopically into Balb\/c mice, resulting in a greater than 97% decrease in spontaneous metastasis to bone compared to control cells. Intratibial injection of these same 4T1.2-OSM cells also dramatically reduced the osteolytic destruction of trabecular bone volume compared to control cells. Furthermore, in a tumor resection model, mice bearing 4T1.2-OSM tumors showed an increase in survival by a median of 10 days. To investigate the specific cellular mechanisms important for OSM-induced osteolytic metastasis to bone, an in vitro model was developed using the RAW 264.7 preosteoclast cell line co-cultured with 4T1.2 mouse mammary tumor cells. Treatment of co-cultures with OSM resulted in a 3-fold induction of osteoclastogenesis using the TRAP assay. We identified several tumor cell-induced factors including vascular endothelial growth factor, IL-6, and a previously uncharacterized OSM-regulated bone metastasis factor, amphiregulin (AREG), which increased osteoclast differentiation by 4.5-fold. In addition, pretreatment of co-cultures with an anti-AREG neutralizing antibody completely reversed OSM-induced osteoclastogenesis. Our results suggest that one mechanism for OSM-induced osteoclast differentiation is via an AREG autocrine loop, resulting in decreased osteoprotegerin secretion by the 4T1.2 cells. These data provide evidence that OSM might be an important therapeutic target for the prevention of breast cancer metastasis to bone.","authors":"Bolin, C., Tawara, K., Sutherland, C., Redshaw, J., Aranda, P., Moselhy, J., Anderson, R., Jorcyk, CL.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genes Cancer","volume":"3","issue":"2","page":"117-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22984523","title":"Novel small noncoding RNAs in mouse spermatozoa, zygotes and early embryos.","abstract":"The recent discovery of a significant amount of RNA in spermatozoa contradicted the previously held belief that paternal contribution was limited to one copy of the genome. Furthermore, detection of RNA in sperm raised the intriguing question of its possible role in embryonic development. The possibility that RNAs may serve as epigenetic determinants was supported by experiments showing inheritance of epigenetic traits in mice mediated by RNA. We used high-throughput, large-scale sequencing technology to analyze sperm RNA. The RNA sequences generated were diverse in terms of length and included mRNAs, rRNAs, piRNAs, and miRNAs. We studied two small noncoding RNAs enriched in mature sperm, designated sperm RNAs (spR) -12 and -13. They are both encoded in a piRNA locus on chromosome 17, but neither their length (20-21 nt), nor their sequences correspond to known piRNAs or miRNAs. They are resistant to periodate-oxidation-mediated reaction, implying that they undergo terminal post-transcriptional modification. Both were detected in sperm and ovulated unfertilized oocytes, present in one-cell embryos and maintained in preimplantation stages, but not at later differentiation stages. These findings offer a new perspective regarding a possibly important role for gamete-specific small RNAs in early embryogenesis.","authors":"Kawano, M., Kawaji, H., Grandjean, V., Kiani, J., Rassoulzadegan, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"9","page":"e44542","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22973548","title":"Mitochondrial genome evolution in a single protoploid yeast species.","abstract":"Mitochondria are organelles, which play a key role in some essential functions, including respiration, metabolite biosynthesis, ion homeostasis, and apoptosis. The vast numbers of mitochondrial DNA (mtDNA) sequences of various yeast species, which have recently been published, have also helped to elucidate the structural diversity of these genomes. Although a large corpus of data are now available on the diversity of yeast species, little is known so far about the mtDNA diversity in single yeast species. To study the genetic variations occurring in the mtDNA of wild yeast isolates, we performed a genome-wide polymorphism survey on the mtDNA of 18 Lachancea kluyveri (formerly Saccharomyces kluyveri) strains. We determined the complete mt genome sequences of strains isolated from various geographical locations (in North America, Asia, and Europe) and ecological niches (Drosophila, tree exudates, soil). The mt genome of the NCYC 543 reference strain is 51,525 bp long. It contains the same core of genes as Lachancea thermotolerans, the nearest relative to L. kluyveri. To explore the mt genome variations in a single yeast species, we compared the mtDNAs of the 18 isolates. The phylogeny and population structure of L. kluyveri provide clear-cut evidence for the existence of well-defined geographically isolated lineages. Although these genomes are completely syntenic, their size and the intron content were found to vary among the isolates studied. These genomes are highly polymorphic, showing an average diversity of 28.5 SNPs\/kb and 6.6 indels\/kb. Analysis of the SNP and indel patterns showed the existence of a particularly high overall level of polymorphism in the intergenic regions. The dN\/dS ratios obtained are consistent with purifying selection in all these genes, with the noteworthy exception of the VAR1 gene, which gave a very high ratio. These data suggest that the intergenic regions have evolved very fast in yeast mitochondrial genomes.","authors":"Jung, PP., Friedrich, A., Reisser, C., Hou, J., Schacherer, J.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"G3 (Bethesda)","volume":"2","issue":"9","page":"1103-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22963334","title":"Experimental identification and theoretical analysis of a thermally stabilized green fluorescent protein variant.","abstract":"In this study, we aim to relate experimentally measured macroscopic properties to dynamic and structural changes as calculated by molecular dynamics (MD) simulations. We performed the analysis on four GFP (green fluorescent protein) variants, which have amino acid replacements or insertion in a flexible region on the protein surface and which resulted from a previous protein splicing reaction optimization experiment. The variants are a reference GFP (CEGFP), GFP-N144C, GFP-N144C\/Y145F, and a GFP with five residues inserted between Y145 and N146 (GFP-5ins). As a result, we identified a single Y145F mutation that increased the thermal stability of GFP-N144C\/Y145F by 3-4 \u00b0C. Because circular dichroism measurements indicated that the overall GFP \u03b2-barrel fold was maintained in all variants, we presumed that the fluorescence activity and thermal stability related to local changes that could be detected by standard MD simulations. The 60 ns MD simulations indicated that the Y145's hydroxyl group, which is straight and buried in the crystal structure, was bent avoiding the hydrophobic core during the simulation in both CEGFP and GFP-N144C. This local strain was relieved in GFP-N144C\/Y145F, where the tyrosine's hydroxyl group was replaced with the F145 hydrophobic aliphatic carbon. F145 remained indeed buried during the simulation maintaining local compactness, which presumably reflected the improved thermal stability of GFP-N144C\/Y145F. Furthermore, the analysis of internal water molecules localized within the GFP's \u03b2-barrel suggested that a change in the local hydrogen bonding pattern around the chromophore correlated with a strong fluorescence activity decrease in GFP-5ins. Although relating experimental observation with calculated molecular features proved to be delicate, this study suggested that some microscopic features could be useful reporters for redesigning GFPs and other proteins. The newly identified GFP-N144C\/Y145F was among the most stable GFP variant and demonstrates the potential of such computer-aided design.","authors":"Akiyama, S., Suenaga, A., Kobayashi, T., Kamioka, T., Taiji, M., Kuroda, Y.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Biochemistry","volume":"51","issue":"40","page":"7974-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22962608","title":"Adoptive transfer of siRNA Cblb-silenced CD8+ T lymphocytes augments tumor vaccine efficacy in a B16 melanoma model.","abstract":"The ubiquitin ligase Cbl-b is an established regulator of T cell immune response thresholds. We recently showed that adoptive cell transfer (ACT) of cblb(-\/-) CD8(+) T cells enhances dendritic cell (DC) immunization-mediated anti-tumor effects in immune-competent recipients. However, translation of cblb targeting to clinically applicable concepts requires that inhibition of cblb activity be transient and reversible. Here we provide experimental evidence that inhibition of cblb using chemically synthesized siRNA has such potential. Silencing cblb expression by ex vivo siRNA transfection of polyclonal CD8(+) T cells prior to ACT increased T cell tumor infiltration, significantly delayed tumor outgrowth, and increased survival rates of tumor-bearing mice. As shown by ex vivo recall assays, cblb silencing resulted in significant augmentation of intratumoral T cell cytokine response. ACT of cblb-silenced polyclonal CD8(+) T cells combined with DC-based tumor vaccines predominantly mediated anti-tumor immune responses, whereas no signs of autoimmunity could be detected. Importantly, CBLB silencing in human CD8(+) T cells mirrored the effects observed for cblb-silenced and cblb-deficient murine T cells. Our data validate the concept of enhanced anti-tumor immunity by repetitive ACT of ex vivo cblb siRNA-silenced hyper-reactive CD8(+) T cells as add-on adjuvant therapy to augment the efficacy of existing cancer immunotherapy regimens in clinical practice.","authors":"Hinterleitner, R., Gruber, T., Pfeifhofer-Obermair, C., Lutz-Nicoladoni, C., Tzankov, A., Schuster, M., Penninger, JM., Loibner, H., Lametschwandtner, G., Wolf, D., Baier, G.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"9","page":"e44295","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22952758","title":"Comparative transcript profiling of a male sterile cybrid pummelo and its fertile type revealed altered gene expression related to flower development.","abstract":"Male sterile and seedless characters are highly desired for citrus cultivar improvement. In our breeding program, a male sterile cybrid pummelo, which could be considered as a variant of male fertile pummelo, was produced by protoplast fusion. Herein, ecotopic stamen primordia initiation and development were detected in this male sterile cybrid pummelo. Histological studies revealed that the cybrid showed reduced petal development in size and width, and retarded stamen primordia development. Additionally, disorganized cell proliferation was also detected in stamen-like structures (fused to petals and\/or carpel). To gain new insight into the underlying mechanism, we compared, by RNA-Seq analysis, the nuclear gene expression profiles of floral buds of the cybrid with that of fertile pummelo. Gene expression profiles which identified a large number of differentially expressed genes (DEGs) between the two lines were captured at both petal primordia and stamen primordia distinguishable stages. For example, nuclear genes involved in nucleic acid binding and response to hormone synthesis and metabolism, genes required for floral bud identification and expressed in particular floral whorls. Furthermore, in accordance with flower morphology of the cybrid, expression of PISTILLATA (PI) was reduced in stamen-like structures, even though it was restricted to correct floral whorls. Down-regulated expression of APETALA3 (AP3) coincided with that of PI. These finding indicated that, due to their whorl specific effects in flower development, citrus class-B MADS-box genes likely constituted 'perfect targets' for CMS retrograde signaling, and that dysfunctional mitochondria seemed to cause male sterile phenotype in the cybrid pummelo.","authors":"Zheng, BB., Wu, XM., Ge, XX., Deng, XX., Grosser, JW., Guo, WW.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"8","page":"e43758","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22932803","title":"NKT cell adjuvant-based tumor vaccine for treatment of myc oncogene-driven mouse B-cell lymphoma.","abstract":"Immunomodulators are effective in controlling hematologic malignancy by initiating or reactivating host antitumor immunity to otherwise poorly immunogenic and immune suppressive cancers. We aimed to boost antitumor immunity in B-cell lymphoma by developing a tumor cell vaccine incorporating \u03b1-galactosylceramide (\u03b1-GalCer) that targets the immune adjuvant properties of NKT cells. In the E\u03bc-myc transgenic mouse model, single therapeutic vaccination of irradiated, \u03b1-GalCer-loaded autologous tumor cells was sufficient to significantly inhibit growth of established tumors and prolong survival. Vaccine-induced antilymphoma immunity required NKT cells, NK cells, and CD8 T cells, and early IL-12-dependent production of IFN-\u03b3. CD4 T cells, gamma\/delta T cells, and IL-18 were not critical. Vaccine treatment induced a large systemic spike of IFN-\u03b3 and transient peripheral expansion of both NKT cells and NK cells, the major sources of IFN-\u03b3. Furthermore, this vaccine approach was assessed in several other hematopoietic tumor models and was also therapeutically effective against AML-ETO9a acute myeloid leukemia. Replacing \u03b1-GalCer with \u03b2-mannosylceramide resulted in prolonged protection against E\u03bc-myc lymphoma. Overall, our results demonstrate a potent immune adjuvant effect of NKT cell ligands in therapeutic anticancer vaccination against oncogene-driven lymphomas, and this work supports clinical investigation of NKT cell-based immunotherapy in patients with hematologic malignancies.","authors":"Mattarollo, SR., West, AC., Steegh, K., Duret, H., Paget, C., Martin, B., Matthews, GM., Shortt, J., Chesi, M., Bergsagel, PL., Bots, M., Zuber, J., Lowe, SW., Johnstone, RW., Smyth, MJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Blood","volume":"120","issue":"15","page":"3019-29","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22911103","title":"Epigenetics meets mathematics: towards a quantitative understanding of chromatin biology.","abstract":"How fast? How strong? How many? So what? Why do numbers matter in biology? Chromatin binding proteins are forever in motion, exchanging rapidly between bound and free pools. How do regulatory systems whose components are in constant flux ensure stability and flexibility? This review explores the application of quantitative and mathematical approaches to mechanisms of epigenetic regulation. We discuss methods for measuring kinetic parameters and protein quantities in living cells, and explore the insights that have been gained by quantifying and modelling dynamics of chromatin binding proteins.","authors":"Steffen, PA., Fonseca, JP., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Bioessays","volume":"34","issue":"10","page":"901-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22903061","title":"A novel molecular mechanism involved in multiple myeloma development revealed by targeting MafB to haematopoietic progenitors.","abstract":"Understanding the cellular origin of cancer can help to improve disease prevention and therapeutics. Human plasma cell neoplasias are thought to develop from either differentiated B cells or plasma cells. However, when the expression of Maf oncogenes (associated to human plasma cell neoplasias) is targeted to mouse B cells, the resulting animals fail to reproduce the human disease. Here, to explore early cellular changes that might take place in the development of plasma cell neoplasias, we engineered transgenic mice to express MafB in haematopoietic stem\/progenitor cells (HS\/PCs). Unexpectedly, we show that plasma cell neoplasias arise in the MafB-transgenic mice. Beyond their clinical resemblance to human disease, these neoplasias highly express genes that are known to be upregulated in human multiple myeloma. Moreover, gene expression profiling revealed that MafB-expressing HS\/PCs were more similar to B cells and tumour plasma cells than to any other subset, including wild-type HS\/PCs. Consistent with this, genome-scale DNA methylation profiling revealed that MafB imposes an epigenetic program in HS\/PCs, and that this program is preserved in mature B cells of MafB-transgenic mice, demonstrating a novel molecular mechanism involved in tumour initiation. Our findings suggest that, mechanistically, the haematopoietic progenitor population can be the target for transformation in MafB-associated plasma cell neoplasias.","authors":"Vicente-Due\u00f1as, C., Romero-Camarero, I., Gonz\u00e1lez-Herrero, I., Alonso-Escudero, E., Abollo-Jim\u00e9nez, F., Jiang, X., Gutierrez, NC., Orfao, A., Mar\u00edn, N., Villar, LM., Criado, MC., Pintado, B., Flores, T., Alonso-L\u00f3pez, D., De Las Rivas, J., Jim\u00e9nez, R., Criado, FJ., Cenador, MB., Lossos, IS., Cobaleda, C., S\u00e1nchez-Garc\u00eda, I.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"EMBO J","volume":"31","issue":"18","page":"3704-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22902557","title":"The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila.","abstract":"In animal gonads, PIWI proteins and their bound 23-30 nt piRNAs guard genome integrity by the sequence specific silencing of transposons. Two branches of piRNA biogenesis, namely primary processing and ping-pong amplification, have been proposed. Despite an overall conceptual understanding of piRNA biogenesis, identity and\/or function of the involved players are largely unknown. Here, we demonstrate an essential role for the female sterility gene shutdown in piRNA biology. Shutdown, an evolutionarily conserved cochaperone collaborates with Hsp90 during piRNA biogenesis, potentially at the loading step of RNAs into PIWI proteins. We demonstrate that Shutdown is essential for both primary and secondary piRNA populations in Drosophila. An extension of our study to previously described piRNA pathway members revealed three distinct groups of biogenesis factors. Together with data on how PIWI proteins are wired into primary and secondary processing, we propose a unified model for piRNA biogenesis.","authors":"Olivieri, D., Senti, KA., Subramanian, S., Sachidanandam, R., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Mol Cell","volume":"47","issue":"6","page":"954-69","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11864574","title":"Eco1 is a novel acetyltransferase that can acetylate proteins involved in cohesion.","abstract":"Cohesion between sister chromatids is established during S phase and maintained through G2 phase until it is resolved in anaphase (for review, see [1-3]). In Saccharomyces cerevisiae, a complex consisting of Scc1, Smc1, Smc3, and Scc3 proteins, called \"cohesin,\" mediates the connection between sister chromatids. The evolutionary conserved yeast protein Eco1 is required for establishment of sister chromatid cohesion during S phase but not for its further maintenance during G2 or M phases or for loading the cohesin complex onto DNA. We address the molecular functions of Eco1 with sensitive sequence analytic techniques, including hidden Markov model domain fragment searches. We found a two-domain architecture with an N-terminal C2H2 Zn finger-like domain and an approximately 150 residue C-terminal domain with an apparent acetyl coenzyme A binding motif (http:\/\/mendel.imp.univie.ac.at\/SEQUENCES\/ECO1\/). Biochemical tests confirm that Eco1 has the acetyltransferase activity in vitro. In vitro Eco1 acetylates itself and components of the cohesin complex but not histones. Thus, the establishment of cohesion between sister chromatids appears to be regulated, directly or indirectly, by a specific acetyltransferase.","authors":"Ivanov, D., Schleiffer, A., Eisenhaber, F., Mechtler, K., Haering, CH., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Curr Biol","volume":"12","issue":"4","page":"323-8","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2002-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22892394","title":"Epigenetic mechanisms in stroke and epilepsy.","abstract":"Epigenetic remodeling and modifications of chromatin structure by DNA methylation and histone modifications represent central mechanisms for the regulation of neuronal gene expression during brain development, higher-order processing, and memory formation. Emerging evidence implicates epigenetic modifications not only in normal brain function, but also in neuropsychiatric disorders. This review focuses on recent findings that disruption of chromatin modifications have a major role in the neurodegeneration associated with ischemic stroke and epilepsy. Although these disorders differ in their underlying causes and pathophysiology, they share a common feature, in that each disorder activates the gene silencing transcription factor REST (repressor element 1 silencing transcription factor), which orchestrates epigenetic remodeling of a subset of 'transcriptionally responsive targets' implicated in neuronal death. Although ischemic insults activate REST in selectively vulnerable neurons in the hippocampal CA1, seizures activate REST in CA3 neurons destined to die. Profiling the array of genes that are epigenetically dysregulated in response to neuronal insults is likely to advance our understanding of the mechanisms underlying the pathophysiology of these disorders and may lead to the identification of novel therapeutic strategies for the amelioration of these serious human conditions.","authors":"Hwang, JY., Aromolaran, KA., Zukin, RS.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Neuropsychopharmacology","volume":"38","issue":"1","page":"167-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-05-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22887808","title":"A novel nonsense CDK5RAP2 mutation in a Somali child with primary microcephaly and sensorineural hearing loss.","abstract":"Primary microcephaly is a genetically heterogeneous condition characterized by reduced head circumference (-3 SDS or more) and mild-to-moderate learning disability. Here, we describe clinical and molecular investigations of a microcephalic child with sensorineural hearing loss. Although consanguinity was unreported initially, detection of 13.7 Mb of copy neutral loss of heterozygosity (cnLOH) on chromosome 9 implicated the CDK5RAP2 gene. Targeted sequencing identified a homozygous E234X mutation, only the third mutation to be described in CDK5RAP2, the first in an individual of non-Pakistani descent. Sensorineural hearing loss is not generally considered to be consistent with autosomal recessive microcephaly and therefore it seems likely that the deafness in this individual is caused by the co-occurrence of a further gene mutation, independent of CDK5RAP2. Nevertheless, further detailed clinical descriptions of rare CDK5RAP2 patients, including hearing assessments will be needed to resolve fully the phenotypic range associated with mutations in this gene. This study also highlights the utility of SNP-array testing to guide disease gene identification where an autosomal recessive condition is plausible.","authors":"Pagnamenta, AT., Murray, JE., Yoon, G., Sadighi Akha, E., Harrison, V., Bicknell, LS., Ajilogba, K., Stewart, H., Kini, U., Taylor, JC., Keays, DA., Jackson, AP., Knight, SJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Am J Med Genet A","volume":"158A","issue":"10","page":"2577-82","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22885737","title":"Stress-induced GSK3 regulates the redox stress response by phosphorylating glucose-6-phosphate dehydrogenase in Arabidopsis.","abstract":"Diverse stresses such as high salt conditions cause an increase in reactive oxygen species (ROS), necessitating a redox stress response. However, little is known about the signaling pathways that regulate the antioxidant system to counteract oxidative stress. Here, we show that a Glycogen Synthase Kinase3 from Arabidopsis thaliana (ASK\u03b1) regulates stress tolerance by activating Glc-6-phosphate dehydrogenase (G6PD), which is essential for maintaining the cellular redox balance. Loss of stress-activated ASK\u03b1 leads to reduced G6PD activity, elevated levels of ROS, and enhanced sensitivity to salt stress. Conversely, plants overexpressing ASK\u03b1 have increased G6PD activity and low levels of ROS in response to stress and are more tolerant to salt stress. ASK\u03b1 stimulates the activity of a specific cytosolic G6PD isoform by phosphorylating the evolutionarily conserved Thr-467, which is implicated in cosubstrate binding. Our results reveal a novel mechanism of G6PD adaptive regulation that is critical for the cellular stress response.","authors":"Dal Santo, S., Stampfl, H., Krasensky, J., Kempa, S., Gibon, Y., Petutschnig, E., Rozhon, W., Heuck, A., Clausen, T., Jonak, C.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Plant Cell","volume":"24","issue":"8","page":"3380-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-185","title":"Composition can buffer protein dynamics within liquid-like condensates","abstract":null,"authors":"Stela Jelenic, Janos Bindics, Philipp Czermak, Balashankar R Pillai, Martine Ruer, Alex S Holehouse, Shambaditya Saha","publication_status":"preprint","journalpubyear":"2022","journaltitle":"BioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.05.16.492059v1","preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.05.16.492059v1","articledate":"2022-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22884370","title":"FACS purification and transcriptome analysis of drosophila neural stem cells reveals a role for Klumpfuss in self-renewal.","abstract":"Drosophila neuroblasts (NBs) have emerged as a model for stem cell biology that is ideal for genetic analysis but is limited by the lack of cell-type-specific gene expression data. Here, we describe a method for isolating large numbers of pure NBs and differentiating neurons that retain both cell-cycle and lineage characteristics. We determine transcriptional profiles by mRNA sequencing and identify 28 predicted\u00a0NB-specific transcription factors that can be arranged in a network containing hubs for Notch signaling, growth control, and chromatin regulation. Overexpression and RNA interference for these factors identify Klumpfuss as a regulator of self-renewal. We show that loss of Klumpfuss function causes premature differentiation and that overexpression results in the formation of transplantable brain tumors. Our data represent a valuable resource for investigating Drosophila developmental neurobiology, and the described method can be applied to other invertebrate stem cell lineages as well.","authors":"Berger, C., Harzer, H., Burkard, TR., Steinmann, J., van der Horst, S., Laurenson, AS., Novatchkova, M., Reichert, H., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Rep","volume":"2","issue":"2","page":"407-18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22874558","title":"Stimulation of autophagy is neuroprotective in a mouse model of human tauopathy.","abstract":"The most common neurodegenerative diseases are characterized by the accumulation of misfolded proteins. Tauopathies, which include Alzheimer disease, progressive supranuclear palsy, corticobasal degeneration, Pick disease and cases of frontotemporal dementia and parkinsonism linked to chromosome 17, are characterized by the accumulation of hyperphosphorylated and filamentous MAPT\/tau protein. The pathological mechanisms involved in MAPT protein accumulation are not well understood, but a possible impairment of protein degradation pathways has been suggested. We investigated the effects of autophagy stimulation on MAPT pathology in a model tauopathy, the human mutant P301S MAPT transgenic mouse line. In the brain of the trehalose-treated mutant mice, autophagy is activated and a reduced number of neurons containing MAPT inclusions, as well as a decreased amount of insoluble MAPT, are observed. The improvement of MAPT pathology is associated with increased nerve cell survival. Moreover, MAPT inclusions colocalize with SQSTM1\/p62- and LC3-positive puncta, suggesting the colocalization of MAPT aggregates with autophagic vacuoles. Autophagy is not activated in the spinal cord of the human P301S MAPT transgenic mice and neuronal survival, as well as MAPT pathology, is unaffected. This study supports a role for autophagy stimulation in the degradation of MAPT aggregates and opens new perspectives for the investigation of autophagy as a pathological mechanism involved in neurodegenerative diseases.","authors":"Schaeffer, V., Goedert, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Autophagy","volume":"8","issue":"11","page":"1686-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-07-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22863881","title":"A mouse model to identify cooperating signaling pathways in cancer.","abstract":"We here establish a mouse cancer model called Multi-Hit that allows for the evaluation of oncogene cooperativities in tumor development. The model is based on the stochastic expression of oncogene combinations ('hits') that are mediated by Cre in a given tissue. Cells with cooperating hits are positively selected and give rise to tumors. We used this approach to evaluate the requirement of Ras downstream effector pathways in tumorigenesis.","authors":"Musteanu, M., Blaas, L., Zenz, R., Svinka, J., Hoffmann, T., Grabner, B., Schramek, D., Kantner, HP., M\u00fcller, M., Kolbe, T., R\u00fclicke, T., Moriggl, R., Kenner, L., Stoiber, D., Penninger, JM., Popper, H., Casanova, E., Eferl, R.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nat Methods","volume":"9","issue":"9","page":"897-900","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22863622","title":"Notch1 counteracts WNT\/\u03b2-catenin signaling through chromatin modification in colorectal cancer.","abstract":"Crosstalk between the Notch and wingless-type MMTV integration site (WNT) signaling pathways has been investigated for many developmental processes. However, this negative correlation between Notch and WNT\/\u03b2-catenin signaling activity has been studied primarily in normal developmental and physiological processes in which negative feedback loops for both signaling pathways are intact. We found that Notch1 signaling retained the capability of suppressing the expression of WNT target genes in colorectal cancers even when \u03b2-catenin destruction by the adenomatous polyposis coli (APC) complex was disabled. Activation of Notch1 converted high-grade adenoma into low-grade adenoma in an Apcmin mouse colon cancer model and suppressed the expression of WNT target genes in human colorectal cancer cells through epigenetic modification recruiting histone methyltransferase SET domain bifurcated 1 (SETDB1). Extensive microarray analysis of human colorectal cancers also showed a negative correlation between the Notch1 target gene, Notch-regulated ankyrin repeat protein 1 (NRARP), and WNT target genes. Notch is known to be a strong promoter of tumor initiation, but here we uncovered an unexpected suppressive role of Notch1 on WNT\/\u03b2-catenin target genes involved in colorectal cancer.","authors":"Kim, HA., Koo, BK., Cho, JH., Kim, YY., Seong, J., Chang, HJ., Oh, YM., Stange, DE., Park, JG., Hwang, D., Kong, YY.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Clin Invest","volume":"122","issue":"9","page":"3248-59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22858987","title":"Gab2 signaling in chronic myeloid leukemia cells confers resistance to multiple Bcr-Abl inhibitors.","abstract":"Grb2-associated binder 2 (Gab2) serves as a critical amplifier in the signaling network of Bcr-Abl, the driver of chronic myeloid leukemia (CML). Despite the success of tyrosine kinase inhibitors (TKIs) in CML treatment, TKI resistance, caused by mutations in Bcr-Abl or aberrant activity of its network partners, remains a clinical problem. Using inducible expression and knockdown systems, we analyzed the role of Gab2 in Bcr-Abl signaling in human CML cells, especially with respect to TKI sensitivity. We show for the first time that Gab2 signaling protects CML cells from various Bcr-Abl inhibitors (imatinib, nilotinib, dasatinib and GNF-2), whereas Gab2 knockdown or haploinsufficiency leads to increased TKI sensitivity. We dissected the underlying molecular mechanism using various Gab2 mutants and kinase inhibitors and identified the Shp2\/Ras\/ERK and the PI3K\/AKT\/mTOR axes as the two critical signaling pathways. Gab2-mediated TKI resistance was associated with persistent phosphorylation of Gab2 Y452, a PI3K recruitment site, and consistent with this finding, the protective effect of Gab2 was completely abolished by the combination of dasatinib with the dual PI3K\/mTOR inhibitor NVP-BEZ235. The identification of Gab2 as a novel modulator of TKI sensitivity in CML suggests that Gab2 could be exploited as a biomarker and therapeutic target in TKI-resistant disease.","authors":"W\u00f6hrle, FU., Halbach, S., Aumann, K., Schwemmers, S., Braun, S., Auberger, P., Schramek, D., Penninger, JM., La\u00dfmann, S., Werner, M., Waller, CF., Pahl, HL., Zeiser, R., Daly, RJ., Brummer, T.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Leukemia","volume":"27","issue":"1","page":"118-29","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"39163854","title":"Hallmarks of regeneration.","abstract":"Regeneration is a heroic biological process that restores tissue architecture and function in the face of day-to-day cell loss or the aftershock of injury. Capacities and mechanisms for regeneration can vary widely among species, organs, and injury contexts. Here, we describe \"hallmarks\" of regeneration found in diverse settings of the animal kingdom, including activation of a cell source, initiation of regenerative programs in the source, interplay with supporting cell types, and control of tissue size and function. We discuss these hallmarks with an eye toward major challenges and applications of regenerative biology.","authors":"Poss, KD., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Cell Stem Cell","volume":"31","issue":"9","page":"1244-1261","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-09-06","doi":"10.1016\/j.stem.2024.07.007","first_author":null,"corresponding_authors":null},{"pmid":"22847449","title":"Functional epialleles at an endogenous human centromere.","abstract":"Human centromeres are defined by megabases of homogenous alpha-satellite DNA arrays that are packaged into specialized chromatin marked by the centromeric histone variant, centromeric protein A (CENP-A). Although most human chromosomes have a single higher-order repeat (HOR) array of alpha satellites, several chromosomes have more than one HOR array. Homo sapiens chromosome 17 (HSA17) has two juxtaposed HOR arrays, D17Z1 and D17Z1-B. Only D17Z1 has been linked to CENP-A chromatin assembly. Here, we use human artificial chromosome assembly assays to show that both D17Z1 and D17Z1-B can support de novo centromere assembly independently. We extend these in vitro studies and demonstrate, using immunostaining and chromatin analyses, that in human cells the centromere can be assembled at D17Z1 or D17Z1-B. Intriguingly, some humans are functional heterozygotes, meaning that CENP-A is located at a different HOR array on the two HSA17 homologs. The site of CENP-A assembly on HSA17 is stable and is transmitted through meiosis, as evidenced by inheritance of CENP-A location through multigenerational families. Differences in histone modifications are not linked clearly with active and inactive D17Z1 and D17Z1-B arrays; however, we detect a correlation between the presence of variant repeat units of D17Z1 and CENP-A assembly at the opposite array, D17Z1-B. Our studies reveal the presence of centromeric epialleles on an endogenous human chromosome and suggest genomic complexities underlying the mechanisms that determine centromere identity in humans.","authors":"Maloney, KA., Sullivan, LL., Matheny, JE., Strome, ED., Merrett, SL., Ferris, A., Sullivan, BA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Proc Natl Acad Sci U S A","volume":"109","issue":"34","page":"13704-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22844466","title":"Identification of galectin-1 as a critical factor in function of mouse mesenchymal stromal cell-mediated tumor promotion.","abstract":"Bone marrow derived mesenchymal stromal cells (MSCs) have recently been implicated as one source of the tumor-associated stroma, which plays essential role in regulating tumor progression. In spite of the intensive research, the individual factors in MSCs controlling tumor progression have not been adequately defined. In the present study we have examined the role of galectin-1 (Gal-1), a protein highly expressed in tumors with poor prognosis, in MSCs in the course of tumor development. Co-transplantation of wild type MSCs with 4T1 mouse breast carcinoma cells enhances the incidence of palpable tumors, growth, vascularization and metastasis. It also reduces survival compared to animals treated with tumor cells alone or in combination with Gal-1 knockout MSCs. In vitro studies show that the absence of Gal-1 in MSCs does not affect the number of migrating MSCs toward the tumor cells, which is supported by the in vivo migration of intravenously injected MSCs into the tumor. Moreover, differentiation of endothelial cells into blood vessel-like structures strongly depends on the expression of Gal-1 in MSCs. Vital role of Gal-1 in MSCs has been further verified in Gal-1 knockout mice. By administering B16F10 melanoma cells into Gal-1 deficient animals, tumor growth is highly reduced compared to wild type animals. Nevertheless, co-injection of wild type but not Gal-1 deficient MSCs results in dramatic tumor growth and development.These results confirm that galectin-1 is one of the critical factors in MSCs regulating tumor progression.","authors":"Szebeni, GJ., Kriston-P\u00e1l, \u00c9., Blazs\u00f3, P., Katona, RL., Nov\u00e1k, J., Szab\u00f3, E., Czibula, \u00c1., Fajka-Boja, R., Hegyi, B., Uher, F., Kren\u00e1cs, L., Jo\u00f3, G., Monostori, \u00c9.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"7","page":"e41372","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22844245","title":"The Arabidopsis HEI10 is a new ZMM protein related to Zip3.","abstract":"In numerous species, the formation of meiotic crossovers is largely under the control of a group of proteins known as ZMM. Here, we identified a new ZMM protein, HEI10, a RING finger-containing protein that is well conserved among species. We show that HEI10 is structurally and functionally related to the yeast Zip3 ZMM and that it is absolutely required for class I crossover (CO) formation in Arabidopsis thaliana. Furthermore, we show that it is present as numerous foci on the chromosome axes and the synaptonemal complex central element until pachytene. Then, from pachytene to diakinesis, HEI10 is retained at a limited number of sites that correspond to class I COs, where it co-localises with MLH1. Assuming that HEI10 early staining represents an early selection of recombination intermediates to be channelled into the ZMM pathway, HEI10 would therefore draw a continuity between early chosen recombination intermediates and final class I COs.","authors":"Chelysheva, L., Vezon, D., Chambon, A., Gendrot, G., Pereira, L., Lemhemdi, A., Vrielynck, N., Le Guin, S., Novatchkova, M., Grelon, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"7","page":"e1002799","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22801782","title":"Sds22 and Repo-Man stabilize chromosome segregation by counteracting Aurora B on anaphase kinetochores.","abstract":"During mitotic spindle assembly, Aurora B kinase is part of an error correction mechanism that detaches microtubules from kinetochores that are under low mechanical tension. During anaphase, however, kinetochore-microtubule attachments must be maintained despite a drop of tension after removal of sister chromatid cohesion. Consistent with this requirement, Aurora B relocates away from chromosomes to the central spindle at the metaphase-anaphase transition. By ribonucleic acid interference screening using a phosphorylation biosensor, we identified two PP1-targeting subunits, Sds22 and Repo-Man, which counteracted Aurora B-dependent phosphorylation of the outer kinetochore component Dsn1 during anaphase. Sds22 or Repo-Man depletion induced transient pauses during poleward chromosome movement and a high incidence of chromosome missegregation. Thus, our study identifies PP1-targeting subunits that regulate the microtubule-kinetochore interface during anaphase for faithful chromosome segregation.","authors":"Wurzenberger, C., Held, M., Lampson, MA., Poser, I., Hyman, AA., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Cell Biol","volume":"198","issue":"2","page":"173-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22753893","title":"Bnip3 and AIF cooperate to induce apoptosis and cavitation during epithelial morphogenesis.","abstract":"Apoptosis is an essential step in cavitation during embryonic epithelial morphogenesis, but its mechanisms are largely unknown. In this paper, we used embryonic stem cell-differentiated embryoid bodies (EBs) as a model and found that Bnip3 (Bcl-2\/adenovirus E1B 19-kD interacting protein), a BH3-only proapoptotic protein, was highly up-regulated during cavitation in a hypoxia-dependent manner. Short hairpin RNA silencing of Bnip3 inhibited apoptosis of the core cells and delayed cavitation. We show that the Bnip3 up-regulation was mediated mainly by hypoxia-inducible factor (HIF)-2. Ablation of HIF-2\u03b1 or HIF-1\u03b2, the common \u03b2 subunit of HIF-1 and -2, suppressed Bnip3 up-regulation and inhibited apoptosis and cavitation. We further show that apoptosis-inducing factor (AIF) cooperated with Bnip3 to promote lumen clearance. Bnip3 silencing in AIF-null EBs nearly blocked apoptosis and cavitation. Moreover, AIF also regulated Bnip3 expression through mitochondrial production of reactive oxygen species and consequent HIF-2\u03b1 stabilization. These results uncover a mechanism of cavitation through hypoxia-induced apoptosis of the core cells mediated by HIFs, Bnip3, and AIF.","authors":"Qi, Y., Tian, X., Liu, J., Han, Y., Graham, AM., Simon, MC., Penninger, JM., Carmeliet, P., Li, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Cell Biol","volume":"198","issue":"1","page":"103-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22750422","title":"Angiotensin-converting enzyme 2 antagonizes angiotensin II-induced pressor response and NADPH oxidase activation in Wistar-Kyoto rats and spontaneously hypertensive rats.","abstract":"Angiotensin-converting enzyme 2 (ACE2), a monocarboxypeptidase capable of metabolizing angiotensin II (Ang II) into angiotensin-(1-7) [Ang-(1-7)], has emerged as a potential therapeutic target. We hypothesized that ACE2 is a negative regulator of Ang II-mediated pathological effects in vivo. In Wistar-Kyoto (WKY) rats, Ang II infusion (0.1 \u03bcg min(-1) kg(-1)) induced a pressor response, activation of NADPH oxidase and generation of superoxide in the heart, kidney and blood vessels; these effects were significantly blunted by recombinant human ACE2 (rhACE2; 2 mg kg(-1)), in association with a lowering of plasma Ang II and elevation of Ang-(1-7) levels. In the spontaneously hypertensive rat (SHR) model, rhACE2 (2 mg kg(-1) day(-1)) delivered over a 14 day period partly corrected the hypertension, the NADPH oxidase activation and the increased superoxide generation in the heart, kidney and blood vessels. Treatment with rhACE2 inhibited Ang II-mediated phosphorylation of the myocardial extracellular signal-regulated kinase 1\/2 pathway in WKY rats, with congruent results seen in SHR hearts. Hence, rhACE2 is an important negative regulator of the Ang II-induced pressor response and NADPH oxidase activation and suppresses pathological myocardial signalling, thereby providing a novel therapeutic agent with which to antagonize an activated renin-angiotesin system.","authors":"Lo, J., Patel, VB., Wang, Z., Levasseur, J., Kaufman, S., Penninger, JM., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Exp Physiol","volume":"98","issue":"1","page":"109-22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22737970","title":"Transgenic nude mouse with green fluorescent protein expression-based human glioblastoma multiforme animal model with EGFR expression and invasiveness.","abstract":"Previously, we developed an orthotopic xenograft model of human glioblastoma multiforme (GBM) with high EGFR expression and invasiveness in Balb\/c nu\/nu nude mice. Now we also developed the same orthotopic xenograft model in transgenic nude mice with green fluorescent protein (GFP) expression. The present orthotopic xenografts labeled by phycoerythrin fluorescing red showed high EGFR expression profile, and invasive behavior under a bright green-red dual-color fluorescence background. A striking advantage in the present human GBM model is that the change of tumor growth can be observed visually instead of sacrificing animals in our further antitumor therapy studies.","authors":"Tan, GW., Lan, FL., Gao, JG., Jiang, CM., Zhang, Y., Huang, XH., Ma, YH., Shao, HD., He, XY., Chen, JL., Long, JW., Xiao, HS., Guo, ZT., Diao, Y.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cancer Invest","volume":"30","issue":"7","page":"537-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11859094","title":"Cutting edge: Attenuated experimental autoimmune encephalomyelitis in eta-1\/osteopontin-deficient mice.","abstract":"Recent studies indicate that early T lymphocyte activation 1 (Eta-1), also known as osteopontin, is a cytokine contributing to the development of Th1 immunity. In the present report, the role of Eta-1 in experimental autoimmune encephalomyelitis (EAE), a disease associated with Th1 immunity, was examined by analysis of disease progression in Eta-1-deficient (Eta-1-\/-) mice. Although incidence and onset of peptide-induced EAE were found to be similar in Eta-1-\/- and Eta-1+\/+ mice, Eta-1-\/- mice displayed significantly lower mean maximal clinical score and faster recovery without spontaneous relapses. Accordingly, decreased inflammatory infiltration and demyelination were observed in the spinal cords of Eta-1-\/- mice. Furthermore, in comparison to Eta-1+\/+, Eta-1-\/- CD4+ T cells had reduced expression of IFN-gamma and TNF-alpha upon ex vivo restimulation. Taken together, these results suggest that Eta-1 may sustain autoimmune responses by assisting in maintenance of Th1 immunity during EAE.","authors":"Jansson, M., Panoutsakopoulou, V., Baker, J., Klein, L., Cantor, H.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"J Immunol","volume":"168","issue":"5","page":"2096-9","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11858838","title":"Genetic analysis of the mammalian cell death machinery.","abstract":"Programmed cell death is used by multicellular organisms to eliminate excess, damaged or harmful cells. This process of cell suicide, defined in morphological terms as apoptosis, is crucial for developmental morphogenesis, tissue homeostasis and defense against pathogens. Over the past decade, our understanding of the genetic basis of the cell death machinery has grown exponentially using genetically modified organisms. In particular, inactivation of genes involved in cell death using homologous recombination in mice has provided an invaluable tool to understand the mechanisms, as well as the structural and functional consequences, of programmed cell death in mammals. This review discusses recent insights into the cellular death program as revealed by these mutant animals.","authors":"Joza, N., Kroemer, G., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Trends Genet","volume":"18","issue":"3","page":"142-9","pdf":null,"JrId":"7839","fulltextlink":null,"preprintlink":null,"articledate":"2002-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22737079","title":"Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family.","abstract":"Heterochromatin is the gene-poor, satellite-rich eukaryotic genome compartment that supports many essential cellular processes. The functional diversity of proteins that bind and often epigenetically define heterochromatic DNA sequence reflects the diverse functions supported by this enigmatic genome compartment. Moreover, heterogeneous signatures of selection at chromosomal proteins often mirror the heterogeneity of evolutionary forces that act on heterochromatic DNA. To identify new such surrogates for dissecting heterochromatin function and evolution, we conducted a comprehensive phylogenomic analysis of the Heterochromatin Protein 1 gene family across 40 million years of Drosophila evolution. Our study expands this gene family from 5 genes to at least 26 genes, including several uncharacterized genes in Drosophila melanogaster. The 21 newly defined HP1s introduce unprecedented structural diversity, lineage-restriction, and germline-biased expression patterns into the HP1 family. We find little evidence of positive selection at these HP1 genes in both population genetic and molecular evolution analyses. Instead, we find that dynamic evolution occurs via prolific gene gains and losses. Despite this dynamic gene turnover, the number of HP1 genes is relatively constant across species. We propose that karyotype evolution drives at least some HP1 gene turnover. For example, the loss of the male germline-restricted HP1E in the obscura group coincides with one episode of dramatic karyotypic evolution, including the gain of a neo-Y in this lineage. This expanded compendium of ovary- and testis-restricted HP1 genes revealed by our study, together with correlated gain\/loss dynamics and chromosome fission\/fusion events, will guide functional analyses of novel roles supported by germline chromatin.","authors":"Levine, MT., McCoy, C., Vermaak, D., Lee, YC., Hiatt, MA., Matsen, FA., Malik, HS.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"6","page":"e1002729","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22628617","title":"Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis.","abstract":"Nonalchoholic fatty liver disease (NAFLD) is the most common cause of liver dysfunction and is associated with metabolic diseases, including obesity, insulin resistance, and type 2 diabetes. We mapped a quantitative trait locus (QTL) for NAFLD to chromosome 17 in a cross between C57BL\/6 (B6) and BTBR mouse strains made genetically obese with the Lep(ob\/ob) mutation. We identified Tsc2 as a gene underlying the chromosome 17 NAFLD QTL. Tsc2 functions as an inhibitor of mammalian target of rapamycin, which is involved in many physiological processes, including cell growth, proliferation, and metabolism. We found that Tsc2(+\/-) mice have increased lipogenic gene expression in the liver in an insulin-dependent manner. The coding single nucleotide polymorphism between the B6 and BTBR strains leads to a change in the ability to inhibit the expression of lipogenic genes and de novo lipogenesis in AML12 cells and to promote the proliferation of Ins1 cells. This difference is due to a different affinity of binding to Tsc1, which affects the stability of Tsc2.","authors":"Wang, CY., Stapleton, DS., Schueler, KL., Rabaglia, ME., Oler, AT., Keller, MP., Kendziorski, CM., Broman, KW., Yandell, BS., Schadt, EE., Attie, AD.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Lipid Res","volume":"53","issue":"8","page":"1493-501","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22693641","title":"ACE2 deficiency enhances angiotensin II-mediated aortic profilin-1 expression, inflammation and peroxynitrite production.","abstract":"Inflammation and oxidative stress play a crucial role in angiotensin (Ang) II-mediated vascular injury. Angiotensin-converting enzyme 2 (ACE2) has recently been identified as a specific Ang II-degrading enzyme but its role in vascular biology remains elusive. We hypothesized that loss of ACE2 would facilitate Ang II-mediated vascular inflammation and peroxynitrite production. 10-week wildtype (WT, Ace2(+\/y)) and ACE2 knockout (ACE2KO, Ace2(-\/y)) mice received with mini-osmotic pumps with Ang II (1.5 mg.kg\u207b\u00b9.d\u207b\u00b9) or saline for 2 weeks. Aortic ACE2 protein was obviously reduced in WT mice in response to Ang II related to increases in profilin-1 protein and plasma levels of Ang II and Ang-(1-7). Loss of ACE2 resulted in greater increases in Ang II-induced mRNA expressions of inflammatory cytokines monocyte chemoattractant protein-1 (MCP-1), interleukin (IL)-1\u03b2, and IL-6 without affecting tumor necrosis factor-\u03b1 in aortas of ACE2KO mice. Furthermore, ACE2 deficiency led to greater increases in Ang II-mediated profilin-1 expression, NADPH oxidase activity, and superoxide and peroxynitrite production in the aortas of ACE2KO mice associated with enhanced phosphorylated levels of Akt, p70S6 kinase, extracellular signal-regulated kinases (ERK1\/2) and endothelial nitric oxide synthase (eNOS). Interestingly, daily treatment with AT1 receptor blocker irbesartan (50 mg\/kg) significantly prevented Ang II-mediated aortic profilin-1 expression, inflammation, and peroxynitrite production in WT mice with enhanced ACE2 levels and the suppression of the Akt-ERK-eNOS signaling pathways. Our findings reveal that ACE2 deficiency worsens Ang II-mediated aortic inflammation and peroxynitrite production associated with the augmentation of profilin-1 expression and the activation of the Akt-ERK-eNOS signaling, suggesting potential therapeutic approaches by enhancing ACE2 action for patients with vascular diseases.","authors":"Jin, HY., Song, B., Oudit, GY., Davidge, ST., Yu, HM., Jiang, YY., Gao, PJ., Zhu, DL., Ning, G., Kassiri, Z., Penninger, JM., Zhong, JC.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"6","page":"e38502","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22688123","title":"Identification and characterization of microRNAs and their target genes in Brassica oleracea.","abstract":"The microRNAs are a new class of small non-coding endogenous RNAs with lengths of approximately ~21 nt. MicroRNAs perform their biological function via the degradation of the target mRNAs or by inhibiting protein translation. Until recently, only limited numbers of miRNAs were identified in Brassica oleracea, a vegetable widely cultivated around the world. In present study, 193 potential miRNA candidates were identified from 17 expressed sequence tag (ESTs) and 152 genome survey sequences (GSSs) in B. oleracea. These miRNA candidates were classified into 70 families using a well-defined comparative genome-based computational analysis. Most miRNAs belong to the miRNA169, miR5021, miR156 and miR158 families. Of these, 36 miRNA families are firstly found in Brassica species. Around 1393 B. oleracea genes were predicted as candidate targets of 175 miRNAs. The mutual relationship between miRNAs and the candidate target genes was verified by checking differentially expression levels using quantitative real-time polymerase chain reaction (qRT-PCR) and 5' RLM-RACE analyses. These target genes participate in multiple biological and metabolic processes, including signal transduction, stress response, and plant development. Gene Ontology analysis shows that the 818, 514, and 265 target genes are involved in molecular functions, biological processes, and cellular component respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis suggests that these miRNAs might regulate 186 metabolic pathways, including those of lipid, energy, starch and sucrose, fatty acid and nitrogen.","authors":"Wang, J., Yang, X., Xu, H., Chi, X., Zhang, M., Hou, X.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Gene","volume":"505","issue":"2","page":"300-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22670054","title":"Spleen serves as a reservoir of osteoclast precursors through vitamin D-induced IL-34 expression in osteopetrotic op\/op mice.","abstract":"Osteoclasts are generated from monocyte\/macrophage-lineage precursors in response to colony-stimulating factor 1 (CSF-1) and receptor activator of nuclear factor-\u03baB ligand (RANKL). CSF-1-mutated CSF-1(op\/op) mice as well as RANKL(-\/-) mice exhibit osteopetrosis (OP) caused by osteoclast deficiency. We previously identified RANKL receptor (RANK)\/CSF-1 receptor (CSF-1R) double-positive cells as osteoclast precursors (OCPs), which existed in bone in RANKL(-\/-) mice. Here we show that OCPs do not exist in bone but in spleen in CSF-1(op\/op) mice, and spleen acts as their reservoir. IL-34, a newly discovered CSF-1R ligand, was highly expressed in vascular endothelial cells in spleen in CSF-1(op\/op) mice. Vascular endothelial cells in bone also expressed IL-34, but its expression level was much lower than in spleen, suggesting a role of IL-34 in the splenic generation of OCPs. Splenectomy (SPX) blocked CSF-1-induced osteoclastogenesis in CSF-1(op\/op) mice. Osteoclasts appeared in aged CSF-1(op\/op) mice with up-regulation of IL-34 expression in spleen and bone. Splenectomy blocked the age-associated appearance of osteoclasts. The injection of 2-methylene-19-nor-(20S)-1\u03b1,25(OH)(2)D(3) (2MD), a potent analog of 1\u03b1,25-dihidroxyvitamin D(3), into CSF-1(op\/op) mice induced both hypercalcemia and osteoclastogenesis. Administration of 2MD enhanced IL-34 expression not only in spleen but also in bone through a vitamin D receptor-mediated mechanism. Either splenectomy or siRNA-mediated knockdown of IL-34 suppressed 2MD-induced osteoclastogenesis. These results suggest that IL-34 plays a pivotal role in maintaining the splenic reservoir of OCPs, which are transferred to bone in response to diverse stimuli, in CSF-1(op\/op) mice. The present study also suggests that the IL-34 gene in vascular endothelial cells is a unique target of vitamin D.","authors":"Nakamichi, Y., Mizoguchi, T., Arai, A., Kobayashi, Y., Sato, M., Penninger, JM., Yasuda, H., Kato, S., DeLuca, HF., Suda, T., Udagawa, N., Takahashi, N.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Proc Natl Acad Sci U S A","volume":"109","issue":"25","page":"10006-11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22654675","title":"EMT inducers catalyze malignant transformation of mammary epithelial cells and drive tumorigenesis towards claudin-low tumors in transgenic mice.","abstract":"The epithelial-mesenchymal transition (EMT) is an embryonic transdifferentiation process consisting of conversion of polarized epithelial cells to motile mesenchymal ones. EMT-inducing transcription factors are aberrantly expressed in multiple tumor types and are known to favor the metastatic dissemination process. Supporting oncogenic activity within primary lesions, the TWIST and ZEB proteins can prevent cells from undergoing oncogene-induced senescence and apoptosis by abolishing both p53- and RB-dependent pathways. Here we show that they also downregulate PP2A phosphatase activity and efficiently cooperate with an oncogenic version of H-RAS in malignant transformation of human mammary epithelial cells. Thus, by down-regulating crucial tumor suppressor functions, EMT inducers make cells particularly prone to malignant conversion. Importantly, by analyzing transformed cells generated in vitro and by characterizing novel transgenic mouse models, we further demonstrate that cooperation between an EMT inducer and an active form of RAS is sufficient to trigger transformation of mammary epithelial cells into malignant cells exhibiting all the characteristic features of claudin-low tumors, including low expression of tight and adherens junction genes, EMT traits, and stem cell-like characteristics. Claudin-low tumors are believed to be the most primitive breast malignancies, having arisen through transformation of an early epithelial precursor with inherent stemness properties and metaplastic features. Challenging this prevailing view, we propose that these aggressive tumors arise from cells committed to luminal differentiation, through a process driven by EMT inducers and combining malignant transformation and transdifferentiation.","authors":"Morel, AP., Hinkal, GW., Thomas, C., Fauvet, F., Courtois-Cox, S., Wierinckx, A., Devouassoux-Shisheboran, M., Treilleux, I., Tissier, A., Gras, B., Pourchet, J., Puisieux, I., Browne, GJ., Spicer, DB., Lachuer, J., Ansieau, S., Puisieux, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"5","page":"e1002723","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22653755","title":"Maternal genetic effect in DNA analysis: egg on your traits.","abstract":"A dilemma of penetrance parallels the uncertainty principle as array analyses uncover a disturbing continuity of human molecular variation. Among mechanisms for altered penetrance is maternal genetic effect, hypothesized to explain mother-offspring discordance from 12\/13 translocation [Wilson et al., 1991] and important to consider when confronting identical genetic changes in normal mothers and their abnormal children. A boy with developmental delays, autistic features, minimal dysmorphology, and maternally inherited 17p13.3 microduplication could exemplify maternal genetic effect, as could a boy with altered brain pattern and maternally inherited Sonic Hedgehog mutation reported by Schell-Apacik et al. [2009]. Maternal genetic effects, characterized in fly, fish, and mouse, are important to consider in human DNA analysis so that identical findings in mother and child are not routinely dismissed as benign variations. Suspect families can define relevant maternal-zygote transition (MZT) genes, provide assays for oocyte function and disruption, and shift anomaly emphasis from pattern recognition to pattern restoration.","authors":"Wilson, GN.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Am J Med Genet A","volume":"158A","issue":"7","page":"1589-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22627767","title":"Sox4 cooperates with CREB in myeloid transformation.","abstract":"The cAMP response element-binding protein (CREB) is a nuclear transcription factor that is critical for normal and neoplastic hematopoiesis. Previous studies have demonstrated that CREB is a proto-oncogene whose overexpression promotes cellular proliferation in hematopoietic cells. Transgenic mice that overexpress CREB in myeloid cells develop a myeloproliferative disease with splenomegaly and aberrant myelopoiesis. However, CREB overexpressing mice do not spontaneously develop acute myeloid leukemia. In this study, we used retroviral insertional mutagenesis to identify genes that accelerate leukemia in CREB transgenic mice. Our mutagenesis screen identified several integration sites, including oncogenes Gfi1, Myb, and Ras. The Sox4 transcription factor was identified by our screen as a gene that cooperates with CREB in myeloid leukemogenesis. We show that the transduction of CREB transgenic mouse bone marrow cells with a Sox4 retrovirus increases survival and self-renewal of cells in vitro. Furthermore, leukemic blasts from the majority of acute myeloid leukemia patients have higher CREB, phosphorylated CREB, and Sox 4 protein expression. Sox4 transduction of mouse bone marrow cells results in increased expression of CREB target genes. We also demonstrate that CREB is a direct target of Sox4 by chromatin immunoprecipitation assays. These results indicate that Sox4 and CREB cooperate and contribute to increased proliferation of hematopoietic progenitor cells.","authors":"Sandoval, S., Kraus, C., Cho, EC., Cho, M., Bies, J., Manara, E., Accordi, B., Landaw, EM., Wolff, L., Pigazzi, M., Sakamoto, KM.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Blood","volume":"120","issue":"1","page":"155-65","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22615579","title":"Inactivation of a novel FGF23 regulator, FAM20C, leads to hypophosphatemic rickets in mice.","abstract":"Family with sequence similarity 20,-member C (FAM20C) is highly expressed in the mineralized tissues of mammals. Genetic studies showed that the loss-of-function mutations in FAM20C were associated with human lethal osteosclerotic bone dysplasia (Raine Syndrome), implying an inhibitory role of this molecule in bone formation. However, in vitro gain- and loss-of-function studies suggested that FAM20C promotes the differentiation and mineralization of mouse mesenchymal cells and odontoblasts. Recently, we generated Fam20c conditional knockout (cKO) mice in which Fam20c was globally inactivated (by crossbreeding with Sox2-Cre mice) or inactivated specifically in the mineralized tissues (by crossbreeding with 3.6 kb Col 1a1-Cre mice). Fam20c transgenic mice were also generated and crossbred with Fam20c cKO mice to introduce the transgene in the knockout background. In vitro gain- and loss-of-function were examined by adding recombinant FAM20C to MC3T3-E1 cells and by lentiviral shRNA-mediated knockdown of FAM20C in human and mouse osteogenic cell lines. Surprisingly, both the global and mineralized tissue-specific cKO mice developed hypophosphatemic rickets (but not osteosclerosis), along with a significant downregulation of osteoblast differentiation markers and a dramatic elevation of fibroblast growth factor 23 (FGF23) in the serum and bone. The mice expressing the Fam20c transgene in the wild-type background showed no abnormalities, while the expression of the Fam20c transgene fully rescued the skeletal defects in the cKO mice. Recombinant FAM20C promoted the differentiation and mineralization of MC3T3-E1 cells. Knockdown of FAM20C led to a remarkable downregulation of DMP1, along with a significant upregulation of FGF23 in both human and mouse osteogenic cell lines. These results indicate that FAM20C is a bone formation \"promoter\" but not an \"inhibitor\" in mouse osteogenesis. We conclude that FAM20C may regulate osteogenesis through its direct role in facilitating osteoblast differentiation and its systemic regulation of phosphate homeostasis via the mediation of FGF23.","authors":"Wang, X., Wang, S., Li, C., Gao, T., Liu, Y., Rangiani, A., Sun, Y., Hao, J., George, A., Lu, Y., Groppe, J., Yuan, B., Feng, JQ., Qin, C.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"5","page":"e1002708","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22607481","title":"Drug discovery technologies and strategies for Machupo virus and other New World arenaviruses.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22607481<\/PMID><DateCompleted><Year>2012<\/Year><Month>10<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1746-045X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><Issue>7<\/Issue><PubDate><Year>2012<\/Year><Month>Jul<\/Month><\/PubDate><\/JournalIssue><Title>Expert opinion on drug discovery<\/Title><ISOAbbreviation>Expert Opin Drug Discov<\/ISOAbbreviation><\/Journal><ArticleTitle>Drug discovery technologies and strategies for Machupo virus and other New World arenaviruses.<\/ArticleTitle><Pagination><MedlinePgn>613-32<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1517\/17460441.2012.687719<\/ELocationID><Abstract><AbstractText Label=\"INTRODUCTION\" NlmCategory=\"BACKGROUND\">Seven arenaviruses cause viral hemorrhagic fever in humans: the Old World arenaviruses Lassa and Lujo, and the New World Clade B arenaviruses Machupo (MACV), Jun\u00edn (JUNV), Guanarito (GTOV), Sabi\u00e1 (SABV), and Chapare (CHPV). All of these viruses are Risk Group 4 biosafety pathogens. MACV causes human disease outbreak with high case-fatality rates. To date, at least 1,200 cases with \u2248200 fatalities have been recorded.","authors":"Radoshitzky, SR., Kuhn, JH., de Kok-Mercado, F., Jahrling, PB., Bavari, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Expert Opin Drug Discov","volume":"7","issue":"7","page":"613-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11792319","title":"DREAM is a critical transcriptional repressor for pain modulation.","abstract":"Control and treatment of chronic pain remain major clinical challenges. Progress may be facilitated by a greater understanding of the mechanisms underlying pain processing. Here we show that the calcium-sensing protein DREAM is a transcriptional repressor involved in modulating pain. dream(-\/-) mice displayed markedly reduced responses in models of acute thermal, mechanical, and visceral pain. dream(-\/-) mice also exhibited reduced pain behaviors in models of chronic neuropathic and inflammatory pain. However, dream(-\/-) mice showed no major defects in motor function or learning and memory. Mice lacking DREAM had elevated levels of prodynorphin mRNA and dynorphin A peptides in the spinal cord, and the reduction of pain behaviors in dream(-\/-) mice was mediated through dynorphin-selective kappa (kappa)-opiate receptors. Thus, DREAM appears to be a critical transcriptional repressor in pain processing.","authors":"Cheng, HY., Pitcher, GM., Laviolette, SR., Whishaw, IQ., Tong, KI., Kockeritz, LK., Wada, T., Joza, NA., Crackower, M., Goncalves, J., Sarosi, I., Woodgett, JR., Oliveira-dos-Santos, AJ., Ikura, M., van der Kooy, D., Salter, MW., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2002","journaltitle":"Cell","volume":"108","issue":"1","page":"31-43","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2002-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22605335","title":"Analysis of nuclear factor-\u03baB (NF-\u03baB) essential modulator (NEMO) binding to linear and lysine-linked ubiquitin chains and its role in the activation of NF-\u03baB.","abstract":"Nuclear factor-\u03baB (NF-\u03baB) essential modulator (NEMO), a component of the inhibitor of \u03baB kinase (IKK) complex, controls NF-\u03baB signaling by binding to ubiquitin chains. Structural studies of NEMO provided a rationale for the specific binding between the UBAN (ubiquitin binding in ABIN and NEMO) domain of NEMO and linear (Met-1-linked) di-ubiquitin chains. Full-length NEMO can also interact with Lys-11-, Lys-48-, and Lys-63-linked ubiquitin chains of varying length in cells. Here, we show that purified full-length NEMO binds preferentially to linear ubiquitin chains in competition with lysine-linked ubiquitin chains of defined length, including long Lys-63-linked deca-ubiquitins. Linear di-ubiquitins were sufficient to activate both the IKK complex in vitro and to trigger maximal NF-\u03baB activation in cells. In TNF\u03b1-stimulated cells, NEMO chimeras engineered to bind exclusively to Lys-63-linked ubiquitin chains mediated partial NF-\u03baB activation compared with cells expressing NEMO that binds to linear ubiquitin chains. We propose that NEMO functions as a high affinity receptor for linear ubiquitin chains and a low affinity receptor for long lysine-linked ubiquitin chains. This phenomenon could explain quantitatively distinct NF-\u03baB activation patterns in response to numerous cell stimuli.","authors":"Kensche, T., Tokunaga, F., Ikeda, F., Goto, E., Iwai, K., Dikic, I.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Biol Chem","volume":"287","issue":"28","page":"23626-34","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22579702","title":"Tacrolimus potently inhibits human osteoclastogenesis induced by IL-17 from human monocytes alone and suppresses human Th17 differentiation.","abstract":"Tacrolimus (FK506, Prograf\u00ae) is an orally available, T cell specific and anti-inflammatory agent that has been proposed as a therapeutic drug in rheumatoid arthritis (RA) patients. It has been known that T cells have a critical role in the pathogenesis of RA. Recent studies suggest that Th17 cells, which mainly produce IL-17, are involved in many autoimmune inflammatory disease including RA. The present study was undertaken to assess the effect of tacrolimus on IL-17-induced human osteoclastogenesis and human Th17 differentiation. Human CD14(+) monocytes were cultured in the presence of macrophage-colony stimulating factor (M-CSF) and IL-17. From day 4, tacrolimus was added to these cultures. Osteoclasts were immunohistologically stained for vitronectin receptor 10days later. IL-17 production from activated T cells stimulated with IL-23 was measured by enzyme-linked immunosorbent assay (ELISA). Th17 differentiation from na\u00efve T cells was assayed by flow cytometry. Tacrolimus potently inhibited IL-17-induced osteoclastogenesis from human monocytes and osteoclast activation. Addition of tacrolimus also reduced production of IL-17 in human activated T cells stimulated with IL-23. Interestingly, the population of human IL-17(+)IFN-\u03b3(-) CD4 T cells or IL-17(+)TNF-\u03b1(+) CD4 T cells were decreased by adding of tacrolimus. The present study demonstrates that the inhibitory effect of tacrolimus on IL-17-induced osteoclastogenesis from human monocytes. Tacrolimus also inhibited expression of IL-17 or TNF-\u03b1 by reducing the proportion of Th17, suggesting that therapeutic effect on Th17-associated disease such as RA, inflammatory bowel disease, multiple sclerosis, psoriasis, or allograft rejection.","authors":"Yago, T., Nanke, Y., Kawamoto, M., Yamanaka, H., Kotake, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cytokine","volume":"59","issue":"2","page":"252-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22576691","title":"Haploinsufficiency of the Nijmegen breakage syndrome 1 gene increases             mammary tumor latency and metastasis.","abstract":"Human diseases such as Nijmegen breakage syndrome due to mutations in the             NBS1 gene result in defects in resection of double strand breaks. NBS1 functions             as part of the MRN complex which functions in homologous recombination and non-homologous             end joining. NBS is a rare human autosomal recessive disorder caused by hypomorphic             mutations. At the cellular level, NBS is characterized by radiosensitivity, chromosomal             breakage and defective cell cycle checkpoints. NBS1 null mutations result in early             embryonic lethality in mice, but NBS1 hypomorphic mutants are viable. Cells from             these mice are defective in S phase and G2\/M checkpoints. In humans, NBS1 polymorphisms             have been associated with increased risk of breast cancer. MRN expression was             reduced in the majority of breast tumors, and low expression of MRN correlated             with increased histologic grade and estrogen receptor negativity. While these             studies have shown NBS1 to be important in clinical outcomes of patients with             breast cancer, mammary tumors are rare in the NBS1 haploinsufficient mouse. To             better understand the role of NBS1 in mammary tumorigenesis, we examined the NBS1+\/-;MMTV-neu             mouse model. Mammary tumor latency was markedly increased in NBS1+\/-;neu mice             compared to NBS1+\/+;neu control animals. This effect was due to increased apoptosis             in early NBS1+\/-;neu mammary tumors. However, NBS1+\/-;neu mammary tumors were             highly metastatic and demonstrated clear differences in gene expression profiles             compared to control tumors. We concluded that NBS1 haploinsufficiency results             in increased mammary tumor latency and metastasis.","authors":"Wan, R., Crowe, DL.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Int J Oncol","volume":"41","issue":"1","page":"345-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22573614","title":"Failure of extra-embryonic progenitor maintenance in the absence of dosage compensation.","abstract":"Proper regulation of X-linked gene expression, termed dosage compensation, is required for the normal development of mammalian embryos. Through the process of X chromosome inactivation (XCI), somatic cells of mammalian females inactivate one of their two X chromosomes in order to balance X-linked gene dosage with their male counterparts. The process of XCI is dependent upon the long non-coding RNA Xist, which is expressed from and coats the inactivated X chromosome (Xi) in cis. During mouse embryogenesis, imprinted XCI inactivates the paternally inherited X chromosome (Xp) within the extra-embryonic lineages. Consequently, females harboring a paternally derived Xist mutation (X\/X(Xist-)) die owing to failure of imprinted XCI and, presumably, poor trophoblast development. Here, we investigate the consequence of two active X chromosomes in the extra-embryonic ectoderm (ExE) of X\/X(Xist-) female embryos. At embryonic day (E) 6.5, we find that the X\/X(Xist-) ExE lacks the transcriptional regulator CDX2, a factor required to maintain the ExE in a progenitor state. In addition, spongiotrophoblast progenitors are not maintained. Surprisingly, we observe evidence of an Xi in a subpopulation of X\/X(Xist-) ExE cells. We demonstrate further that trophectodermal stem cells derived from X\/X(Xist-) embryos completely reverse normal imprinted XCI patterns. Taken together, our data suggest that, much like in the cells of the epiblast, the initial imprint that establishes imprinted XCI is probably erased in ExE cells. Conversely, unlike the epiblast, in which XCI is not required for progenitor cell maintenance, we demonstrate that dosage compensation is indispensable for the maintenance of trophoblast progenitors.","authors":"Mugford, JW., Yee, D., Magnuson, T.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Development","volume":"139","issue":"12","page":"2130-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22566646","title":"A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions.","abstract":"The large chromosomal deletions frequently observed in cancer genomes are often thought to arise as a \"two-hit\" mechanism in the process of tumor-suppressor gene (TSG) inactivation. Using a murine model system of hepatocellular carcinoma (HCC) and in vivo RNAi, we test an alternative hypothesis, that such deletions can arise from selective pressure to attenuate the activity of multiple genes. By targeting the mouse orthologs of genes frequently deleted on human 8p22 and adjacent regions, which are lost in approximately half of several other major epithelial cancers, we provide evidence suggesting that multiple genes on chromosome 8p can cooperatively inhibit tumorigenesis in mice, and that their cosuppression can synergistically promote tumor growth. In addition, in human HCC patients, the combined down-regulation of functionally validated 8p TSGs is associated with poor survival, in contrast to the down-regulation of any individual gene. Our data imply that large cancer-associated deletions can produce phenotypes distinct from those arising through loss of a single TSG, and as such should be considered and studied as distinct mutational events.","authors":"Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., Revill, K., Weissmueller, S., Rappaport, AR., Simon, J., Zhang, J., Luo, W., Hicks, J., Zender, L., Wang, XW., Powers, S., Wigler, M., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Proc Natl Acad Sci U S A","volume":"109","issue":"21","page":"8212-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34890555","title":"Xist nucleates local protein gradients to propagate silencing across the X chromosome.","abstract":null,"authors":"Markaki, Y., Chong, JG., Wang, Y., Jacobson, EC., Luong, C., Tan, SYX., Jachowicz, JW., Strehle, M., Maestrini, D., Banerjee, AK., Mistry, BA., Dror, I., Dossin, F., Sch\u04e7neberg, J., Heard, E., Guttman, M., Chou, T., Plath, K.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell","volume":"184","issue":"25","page":"6212","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"39223372","title":"Criteria for the standardization of stem-cell-based embryo models.","abstract":null,"authors":"Martinez Arias, A., Rivron, N., Moris, N., Tam, P., Alev, C., Fu, J., Hadjantonakis, AK., Hanna, JH., Minchiotti, G., Pourquie, O., Sheng, G., Solnica Krezel, L., Veenvliet, JV., Warmflash, A.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nat Cell Biol","volume":"26","issue":"10","page":"1625-1628","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-10-11","doi":"10.1038\/s41556-024-01492-x","first_author":null,"corresponding_authors":null},{"pmid":"33930313","title":"Evolutionary switch in expression of key markers between mouse and human leads to mis-assignment of cell types in developing adrenal medulla.","abstract":null,"authors":"Kameneva, P., V Artemov, A., Kastriti, ME., Sundstr\u00f6m, E., Kharchenko, PV., Adameyko, I.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cancer Cell","volume":"39","issue":"5","page":"590-591","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-11","doi":"10.1016\/j.ccell.2021.04.009","first_author":"Kameneva, P.","corresponding_authors":"Kharchenko, PV., Adameyko, I."},{"pmid":"22556267","title":"A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2\/Src-2 in liver cancer.","abstract":"The Sleeping Beauty (SB) transposon mutagenesis system is a powerful tool that facilitates the discovery of mutations that accelerate tumorigenesis. In this study, we sought to identify mutations that cooperate with MYC, one of the most commonly dysregulated genes in human malignancy. We performed a forward genetic screen with a mouse model of MYC-induced liver cancer using SB-mediated mutagenesis. We sequenced insertions in 63 liver tumor nodules and identified at least 16 genes\/loci that contribute to accelerated tumor development. RNAi-mediated knockdown in a liver progenitor cell line further validate three of these genes, Ncoa2\/Src-2, Zfx, and Dtnb, as tumor suppressors in liver cancer. Moreover, deletion of Ncoa2\/Src-2 in mice predisposes to diethylnitrosamine-induced liver tumorigenesis. These findings reveal genes and pathways that functionally restrain MYC-mediated liver tumorigenesis and therefore may provide targets for cancer therapy.","authors":"O'Donnell, KA., Keng, VW., York, B., Reineke, EL., Seo, D., Fan, D., Silverstein, KA., Schrum, CT., Xie, WR., Mularoni, L., Wheelan, SJ., Torbenson, MS., O'Malley, BW., Largaespada, DA., Boeke, JD.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Proc Natl Acad Sci U S A","volume":"109","issue":"21","page":"E1377-86","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22536455","title":"The DNA glycosylases Ogg1 and Nth1 do not contribute to Ig class switching in activated mouse splenic B cells.","abstract":"During activation of B cells to undergo class switching, B cell metabolism is increased, and levels of reactive oxygen species (ROS) are increased. ROS can oxidize DNA bases resulting in substrates for the DNA glycosylases Ogg1 and Nth1. Ogg1 and Nth1 excise oxidized bases, and nick the resulting abasic sites, forming single-strand DNA breaks (SSBs) as intermediates during the repair process. In this study, we asked whether splenic B cells from mice deficient in these two enzymes would show altered class switching and decreased DNA breaks in comparison with wild-type mice. As the c-myc gene frequently recombines with the IgH S region in B cells induced to undergo class switching, we also analyzed the effect of deletion of these two glycosylases on DSBs in the c-myc gene. We did not detect a reduction in S region or c-myc DSBs or in class switching in splenic B cells from Ogg1- or Nth1-deficient mice or from mice deficient in both enzymes.","authors":"Ucher, AJ., Linehan, EK., Teebor, GW., Schrader, CE., Stavnezer, J.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"4","page":"e36061","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22535371","title":"JDP2 inhibits the epithelial-to-mesenchymal transition in pancreatic cancer BxPC3 cells.","abstract":"Pancreatic carcinoma is one of the most malignant and aggressive cancers. Increased motility and invasiveness of pancreatic cancer cells are believed to be associated with epithelial-to-mesenchymal transition (EMT). However, the molecular basis of EMT in pancreatic cancer cells is poorly understood. In this study, we examined the relationship between Jun dimerization protein 2 (JDP2), which is an AP-1 inhibitor, and EMT in human pancreatic carcinoma cells. We demonstrated that transforming growth factor-\u03b21 (TGF-\u03b21) promoted epidermal growth factor (EGF)-induced EMT in co-treated human pancreatic BxPC3 cells and that JDP2 overexpression reversed the EMT that was induced by co-treatment with TGF-\u03b21 and EGF. These results suggest that EGF plays a principal role in EMT through its association with TGF-\u03b21 in human pancreatic BxPC3 cells and that JDP2 may be a molecular target for pancreatic carcinoma intervention.","authors":"Liu, Z., Du, R., Long, J., Dong, A., Fan, J., Guo, K., Xu, Y.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Tumour Biol","volume":"33","issue":"5","page":"1527-34","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22534400","title":"Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.","abstract":"The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is encoded in the cis-regulatory DNA sequence has, however, remained unclear. We computationally dissect context-specific TF binding sites in Drosophila, Caenorhabditis elegans, mouse, and human and find distinct combinations of sequence motifs for partner factors, which are predictive and reveal specific motif requirements of individual binding sites. We predict that TF binding in the early Drosophila embryo depends on motifs for the early zygotic TFs Vielfaltig (also known as Zelda) and Tramtrack. We validate experimentally that the activity of Twist-bound enhancers and Twist binding itself depend on Vielfaltig motifs, suggesting that Vielfaltig is more generally important for early transcription. Our finding that the motif content can predict context-specific binding and that the predictions work across different Drosophila species suggests that characteristic motif combinations are shared between sites, revealing context-specific motif codes (cis-regulatory signatures), which appear to be conserved during evolution. Taken together, this study establishes a novel approach to derive predictive cis-regulatory motif requirements for individual TF binding sites and enhancers. Importantly, the method is generally applicable across different cell types and organisms to elucidate cis-regulatory sequence determinants and the corresponding trans-acting factors from the increasing number of tissue- and cell-type-specific TF binding studies.","authors":"Y\u00e1\u00f1ez-Cuna, JO., Dinh, HQ., Kvon, EZ., Shlyueva, D., Stark, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genome Res","volume":"22","issue":"10","page":"2018-30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22521784","title":"Spatiotemporal regulation of Ipl1\/Aurora activity by direct Cdk1 phosphorylation.","abstract":"Oscillating cyclin-dependent kinase 1 (Cdk1) activity is the major regulator of cell-cycle progression, whereas the Aurora B kinase, as part of the chromosome passenger complex (CPC), controls critical aspects of mitosis such as chromosome condensation and biorientation on the spindle. How these kinases mechanistically coordinate their important functions is only partially understood. Here, using budding yeast, we identify a regulatory mechanism by which the Cdk1 kinase Cdc28 directly controls the Aurora kinase Ipl1. We show that Cdk1 phosphorylates Ipl1 on two serine residues in the N-terminal domain, thereby suppressing its association with the microtubule plus-end tracking protein Bim1 until the onset of anaphase. Failure to phosphorylate Ipl1 leads to its premature targeting to the metaphase spindle and results in constitutive Bim1 phosphorylation, which is normally restricted to anaphase. Cells expressing an Ipl1-Sli15 complex that cannot be phosphorylated by Cdk1 display a severe growth defect. Our work shows that Ipl1\/Aurora is not only the catalytic subunit of the CPC but also an important regulatory target that allows Cdk1 to coordinate chromosome biorientation with spindle morphogenesis.","authors":"Zimniak, T., Fitz, V., Zhou, H., Lampert, F., Opravil, S., Mechtler, K., Stolt-Bergner, P., Westermann, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Curr Biol","volume":"22","issue":"9","page":"787-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22511716","title":"Tissue deformation spatially modulates VEGF signaling and angiogenesis.","abstract":"Physical forces play a major role in the organization of developing tissues. During vascular development, physical forces originating from a fluid phase or from cells pulling on their environment can alter cellular signaling and the behavior of cells. Here, we observe how tissue deformation spatially modulates angiogenic signals and angiogenesis. Using soft lithographic templates, we assemble three-dimensional, geometric tissues. The tissues contract autonomously, change shape stereotypically and form patterns of vascular structures in regions of high deformations. We show that this emergence correlates with the formation of a long-range gradient of Vascular Endothelial Growth Factor (VEGF) in interstitial cells, the local overexpression of the corresponding receptor VEGF receptor 2 (VEGFR-2) and local differences in endothelial cells proliferation. We suggest that tissue contractility and deformation can induce the formation of gradients of angiogenic microenvironments which could contribute to the long-range patterning of the vascular system.","authors":"Rivron, NC., Vrij, EJ., Rouwkema, J., Le Gac, S., van den Berg, A., Truckenm\u00fcller, RK., van Blitterswijk, CA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Proc Natl Acad Sci U S A","volume":"109","issue":"18","page":"6886-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22499593","title":"HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature.","abstract":"HOT (highly occupied target) regions bound by many transcription factors are considered to be one of the most intriguing findings of the recent modENCODE reports, yet their functions have remained unclear. We tested 108 Drosophila melanogaster HOT regions in transgenic embryos with site-specifically integrated transcriptional reporters. In contrast to prior expectations, we found 102 (94%) to be active enhancers during embryogenesis and to display diverse spatial and temporal patterns, reminiscent of expression patterns for important developmental genes. Remarkably, HOT regions strongly activate nearby genes and are required for endogenous gene expression, as we show using bacterial artificial chromosome (BAC) transgenesis. HOT enhancers have a distinct cis-regulatory signature with enriched sequence motifs for the global activators Vielfaltig, also known as Zelda, and Trithorax-like, also known as GAGA. This signature allows the prediction of HOT versus control regions from the DNA sequence alone.","authors":"Kvon, EZ., Stampfel, G., Y\u00e1\u00f1ez-Cuna, JO., Dickson, BJ., Stark, A.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genes Dev","volume":"26","issue":"9","page":"908-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22473956","title":"Essential role of EBF1 in the generation and function of distinct mature B cell types.","abstract":"The transcription factor EBF1 is essential for lineage specification in early B cell development. In this study, we demonstrate by conditional mutagenesis that EBF1 is required for B cell commitment, pro-B cell development, and subsequent transition to the pre-B cell stage. Later in B cell development, EBF1 was essential for the generation and maintenance of several mature B cell types. Marginal zone and B-1 B cells were lost, whereas follicular (FO) and germinal center (GC) B cells were reduced in the absence of EBF1. Activation of the B cell receptor resulted in impaired intracellular signaling, proliferation and survival of EBF1-deficient FO B cells. Immune responses were severely reduced upon Ebf1 inactivation, as GCs were formed but not maintained. ChIP- and RNA-sequencing of FO B cells identified EBF1-activated genes that encode receptors, signal transducers, and transcriptional regulators implicated in B cell signaling. Notably, ectopic expression of EBF1 efficiently induced the development of B-1 cells at the expense of conventional B cells. These gain- and loss-of-function analyses uncovered novel important functions of EBF1 in controlling B cell immunity.","authors":"Vilagos, B., Hoffmann, M., Souabni, A., Sun, Q., Werner, B., Medvedovic, J., Bilic, I., Minnich, M., Axelsson, E., Jaritz, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Exp Med","volume":"209","issue":"4","page":"775-92","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22467211","title":"PAREsnip: a tool for rapid genome-wide discovery of small RNA\/target interactions evidenced through degradome sequencing.","abstract":"Small RNAs (sRNAs) are a class of short (20-25\u2009nt) non-coding RNAs that play important regulatory roles in gene expression. An essential first step in understanding their function is to confidently identify sRNA targets. In plants, several classes of sRNAs such as microRNAs (miRNAs) and trans-acting small interfering RNAs have been shown to bind with near-perfect complementarity to their messenger RNA (mRNA) targets, generally leading to cleavage of the mRNA. Recently, a high-throughput technique known as Parallel Analysis of RNA Ends (PARE) has made it possible to sequence mRNA cleavage products on a large-scale. Computational methods now exist to use these data to find targets of conserved and newly identified miRNAs. Due to speed limitations such methods rely on the user knowing which sRNA sequences are likely to target a transcript. By limiting the search to a tiny subset of sRNAs it is likely that many other sRNA\/mRNA interactions will be missed. Here, we describe a new software tool called PAREsnip that allows users to search for potential targets of all sRNAs obtained from high-throughput sequencing experiments. By searching for targets of a complete 'sRNAome' we can facilitate large-scale identification of sRNA targets, allowing us to discover regulatory interaction networks.","authors":"Folkes, L., Moxon, S., Woolfenden, HC., Stocks, MB., Szittya, G., Dalmay, T., Moulton, V.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nucleic Acids Res","volume":"40","issue":"13","page":"e103","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22459261","title":"Direct determination of actin polarity in the cell.","abstract":"Actin filaments are polar structures that exhibit a fast growing plus end and a slow growing minus end. According to their organization in cells, in parallel or antiparallel arrays, they can serve, respectively, in protrusions or in contractions. The determination of actin filament polarity in subcellular compartments is therefore required to establish their local function. Myosin binding has previously been the sole method of polarity determination. Here, we report the first direct determination of actin filament polarity in the cell without myosin binding. Negatively stained cytoskeletons of lamellipodia were analyzed by adapting electron tomography and a single particle analysis for filamentous complexes. The results of the stained cytoskeletons confirmed that all actin filament ends facing the cell membrane were the barbed ends. In general, this approach should be applicable to the analysis of actin polarity in tomograms of the actin cytoskeleton.","authors":"Narita, A., Mueller, J., Urban, E., Vinzenz, M., Small, JV., Ma\u00e9da, Y.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Mol Biol","volume":"419","issue":"5","page":"359-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-186","title":"Multi-chamber cardioids unravel human heart development and cardiac defects","abstract":null,"authors":"Clara Schmidt, Alison Deyett, Tobias Ilmer, Aranxa Torres Caballero, Simon Haendeler, Lokesh Pimpale, Michael A. Netzer, Lavinia Ceci Ginistrelli, Martina Cirigliano, Estela Juncosa Mancheno, Daniel Reumann, Katherina Tavernini, Steffen Hering, Pablo Hofbauer,  Sasha Mendjan","publication_status":"preprint","journalpubyear":"2022","journaltitle":"BioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.07.14.499699v1","preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.07.14.499699v1","articledate":"2022-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22454522","title":"Fos plays an essential role in the upregulation of RANK expression in osteoclast precursors within the bone microenvironment.","abstract":"Fos plays essential roles in the osteoclastic differentiation of precursor cells generated by colony-stimulating factor 1 (CSF-1) and receptor activator of NF-\u03baB ligand (RANKL; also known as tumor necrosis factor ligand superfamily member 11, Tnsf11). RANKL-deficient (RANKL(-\/-)) mice and Fos(-\/-) mice exhibit osteopetrosis due to an osteoclast deficiency. We previously reported that RANK-positive osteoclast precursors are present in bone of RANKL(-\/-) mice but not Fos(-\/-) mice. Here we report the role of Fos in RANK expression in osteoclast precursors. Medullary thymic epithelial cells and intestinal antigen-sampling microfold cells have been shown to express RANK. High expression of RANK was observed in some epithelial cells in the thymic medulla and intestine but not in osteoclast precursors in Fos(-\/-) mice. RANK mRNA and protein levels in bone were lower in Fos(-\/-) mice than RANKL(-\/-) mice, suggesting that Fos-regulated RANK expression is tissue specific. When wild-type bone marrow cells were inoculated into Fos(-\/-) mice, RANK-positive cells appeared along bones. RANK expression in wild-type macrophages was upregulated by coculturing with RANKL(-\/-) osteoblasts as well as wild-type osteoblasts, suggesting that cytokines other than RANKL expressed by osteoblasts upregulate RANK expression in osteoclast precursors. CSF-1 receptor-positive cells were detected near CSF-1-expressing osteoblastic cells in bone in Fos(-\/-) mice. CSF-1 upregulated RANK expression in wild-type macrophages but not Fos(-\/-) macrophages. Overexpression of Fos in Fos(-\/-) macrophages resulted in the upregulation of RANK expression. Overexpression of RANK in Fos(-\/-) macrophages caused RANKL-induced signals, but failed to recover the RANKL-induced osteoclastogenesis. These results suggest that Fos plays essential roles in the upregulation of RANK expression in osteoclast precursors within the bone environment.","authors":"Arai, A., Mizoguchi, T., Harada, S., Kobayashi, Y., Nakamichi, Y., Yasuda, H., Penninger, JM., Yamada, K., Udagawa, N., Takahashi, N.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Cell Sci","volume":"125","issue":"Pt 12","page":"2910-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22445448","title":"Random roots and lineage sorting.","abstract":"Lineage sorting has been suggested as a major force in generating incongruent phylogenetic signal when multiple gene partitions are examined. The degree of lineage sorting can be estimated using the coalescent process and simulation studies have also pointed to a major role for incomplete lineage sorting as a factor in phylogenetic inference. Some recent empirical studies point to an extreme role for this phenomenon with up to 50-60% of all informative genes showing incongruence as a result of lineage sorting. Here, we examine seven large multi-partition genome level data sets over a large range of taxonomic representation. We took the approach of examining outgroup choice and its impact on tree topology, by swapping outgroups into analyses with successively larger genetics distances to the ingroup. Our results indicate a linear relationship of outgroup distance with incongruence in the data sets we examined suggesting a strong random rooting effect. In addition, we attempted to estimate the degree of lineage sorting in several large genome level data sets by examining triads of very closely related taxa. This exercise resulted in much lower estimates of incongruent genes that could be the result of lineage sorting, with an overall estimate of around 10% of the total number of genes in a genome showing incongruence as a result of true lineage sorting. Finally we examined the behavior of likelihood and parsimony approaches on the random rooting phenomenon. Likelihood tends to stabilize incongruence as outgroups get further and further away from the ingroup. In one extreme case, likelihood overcompensates for sequence divergence but increases random rooting causing long branch repulsion.","authors":"Rosenfeld, JA., Payne, A., DeSalle, R.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Mol Phylogenet Evol","volume":"64","issue":"1","page":"12-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22432004","title":"Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22432004<\/PMID><DateCompleted><Year>2012<\/Year><Month>07<\/Month><Day>13<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>11<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1932-6203<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><Issue>3<\/Issue><PubDate><Year>2012<\/Year><\/PubDate><\/JournalIssue><Title>PloS one<\/Title><ISOAbbreviation>PLoS One<\/ISOAbbreviation><\/Journal><ArticleTitle>Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis.<\/ArticleTitle><Pagination><MedlinePgn>e33174<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1371\/journal.pone.0033174<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Pandemic and seasonal respiratory viruses are a major global health concern. Given the genetic diversity of respiratory viruses and the emergence of drug resistant strains, the targeted disruption of human host-virus interactions is a potential therapeutic strategy for treating multi-viral infections. The availability of large-scale genomic datasets focused on host-pathogen interactions can be used to discover novel drug targets as well as potential opportunities for drug repositioning.","authors":"Smith, SB., Dampier, W., Tozeren, A., Brown, JR., Magid-Slav, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"3","page":"e33174","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22431015","title":"Actin branching in the initiation and maintenance of lamellipodia.","abstract":"Using correlated live-cell imaging and electron tomography we found that actin branch junctions in protruding and treadmilling lamellipodia are not concentrated at the front as previously supposed, but link actin filament subsets in which there is a continuum of distances from a junction to the filament plus ends, for up to at least 1 \u03bcm. When branch sites were observed closely spaced on the same filament their separation was commonly a multiple of the actin helical repeat of 36 nm. Image averaging of branch junctions in the tomograms yielded a model for the in vivo branch at 2.9 nm resolution, which was comparable with that derived for the in vitro actin-Arp2\/3 complex. Lamellipodium initiation was monitored in an intracellular wound-healing model and was found to involve branching from the sides of actin filaments oriented parallel to the plasmalemma. Many filament plus ends, presumably capped, terminated behind the lamellipodium tip and localized on the dorsal and ventral surfaces of the actin network. These findings reveal how branching events initiate and maintain a network of actin filaments of variable length, and provide the first structural model of the branch junction in vivo. A possible role of filament capping in generating the lamellipodium leaflet is discussed and a mathematical model of protrusion is also presented.","authors":"Vinzenz, M., Nemethova, M., Schur, F., Mueller, J., Narita, A., Urban, E., Winkler, C., Schmeiser, C., Koestler, SA., Rottner, K., Resch, GP., Maeda, Y., Small, JV.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Cell Sci","volume":"125","issue":"Pt 11","page":"2775-85","pdf":null,"JrId":null,"fulltextlink":"","preprintlink":null,"articledate":"2012-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19893034","title":"Expression of activated STAT5 in neoplastic mast cells in systemic mastocytosis: subcellular distribution and role of the transforming oncoprotein KIT D816V.","abstract":"Recent data suggest that the signal transducer and activator of transcription (STAT)5 contributes to differentiation and growth of mast cells. It has also been described that constitutively phosphorylated STAT5 (pSTAT5) plays a pro-oncogenic role in various myeloid neoplasms. We examined the expression of pSTAT5 in neoplastic mast cells in systemic mastocytosis and asked whether the disease-related oncoprotein KIT D816V is involved in STAT5 activation. As assessed by immunohistochemistry using the anti-pSTAT5 antibody AX1, neoplastic mast cells were found to display pSTAT5 in all SM patients examined (n = 40). Expression of pSTAT5 was also demonstrable in the KIT D816V-positive mast cell leukemia cell line HMC-1. Using various staining-protocols, pSTAT5 was found to be located in both the cytoplasmic and nuclear compartment of mast cells. To define the functional role of KIT D816V in STAT5-activation, Ba\/F3 cells with doxycycline-inducible expression of KIT D816V were used. In these cells, induction of KIT D816V resulted in an increased expression of pSTAT5 without substantial increase in total STAT5. Moreover, the KIT D816V-targeting kinase-inhibitor PKC412 was found to counteract expression of pSTAT5 in HMC-1 cells as well as doxycycline-induced expression of pSTAT5 in Ba\/F3 cells. Finally, a dominant negative STAT5-construct was found to inhibit growth of HMC-1 cells. Together, our data show that neoplastic mast cells express cytoplasmic and nuclear pSTAT5, that KIT D816V promotes STAT5-activation, and that STAT5-activation contributes to growth of neoplastic mast cells.","authors":"Baumgartner, C., Cerny-Reiterer, S., Sonneck, K., Mayerhofer, M., Gleixner, KV., Fritz, R., Kerenyi, M., Boudot, C., Gouilleux, F., Kornfeld, JW., Sillaber, C., Moriggl, R., Valent, P.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Am J Pathol","volume":"175","issue":"6","page":"2416-29","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22430937","title":"Genetic identification and functional validation of Fc\u03b3RIV as key molecule in autoantibody-induced tissue injury.","abstract":"Autoantibody-mediated diseases are clinically heterogeneous and often fail conventional therapeutic strategies. Gene expression profiling has helped to identify new molecular pathways in these diseases, although their potential as treatment targets largely remains to be functionally validated. Based on weighted gene co-expression network analysis, we determined the transcriptional network in experimental epidermolysis bullosa acquisita (EBA), a paradigm of an antibody-mediated organ-specific autoimmune disease characterized by autoantibodies directed against type VII collagen. We identified 33 distinct and differentially expressed modules, including Fc\u03b3 receptor (Fc\u03b3R) IV and components of the neutrophil-associated enzyme system in autoantibody transfer-induced EBA. Validation experiments, including functional analysis, demonstrated that Fc\u03b3RIV expression on neutrophils crucially contributes to autoantibody-induced tissue injury in the transfer model of EBA. Mice lacking the common \u03b3-chain of activating Fc\u03b3Rs, deficient in Fc\u03b3RIV or treated with Fc\u03b3RIV function blocking antibody, but not mice deficient in Fc\u03b3RI, Fc\u03b3RIIB, Fc\u03b3RIII or both Fc\u03b3RI and Fc\u03b3RIII, were effectively protected from EBA. Skin disease was restored in \u03b3-chain-deficient mice locally reconstituted with neutrophils from wild-type, but not from \u03b3-chain-deficient, mice. Our findings both genetically and functionally identify a novel disease-related molecule, Fc\u03b3RIV, in an autoantibody-mediated disorder, which may be of importance for the development of novel targeted therapies.","authors":"Kasperkiewicz, M., Nimmerjahn, F., Wende, S., Hirose, M., Iwata, H., Jonkman, MF., Samavedam, U., Gupta, Y., M\u00f6ller, S., Rentz, E., Hellberg, L., Kalies, K., Yu, X., Schmidt, E., H\u00e4sler, R., Laskay, T., Westermann, J., K\u00f6hl, J., Zillikens, D., Ludwig, RJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Pathol","volume":"228","issue":"1","page":"8-19","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22427741","title":"Combinatorial activation and repression by seven transcription factors specify Drosophila odorant receptor expression.","abstract":"The mechanism that specifies olfactory sensory neurons to express only one odorant receptor (OR) from a large repertoire is critical for odor discrimination but poorly understood. Here, we describe the first comprehensive analysis of OR expression regulation in Drosophila. A systematic, RNAi-mediated knock down of most of the predicted transcription factors identified an essential function of acj6, E93, Fer1, onecut, sim, xbp1, and zf30c in the regulation of more than 30 ORs. These regulatory factors are differentially expressed in antennal sensory neuron classes and specifically required for the adult expression of ORs. A systematic analysis reveals not only that combinations of these seven factors are necessary for receptor gene expression but also a prominent role for transcriptional repression in preventing ectopic receptor expression. Such regulation is supported by bioinformatics and OR promoter analyses, which uncovered a common promoter structure with distal repressive and proximal activating regions. Thus, our data provide insight into how combinatorial activation and repression can allow a small number of transcription factors to specify a large repertoire of neuron classes in the olfactory system.","authors":"Jafari, S., Alkhori, L., Schleiffer, A., Brochtrup, A., Hummel, T., Alenius, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Biol","volume":"10","issue":"3","page":"e1001280","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22426497","title":"Diversity and roles of (t)RNA ligases.","abstract":"The discovery of discontiguous tRNA genes triggered studies dissecting the process of tRNA splicing. As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins. In addition to the elucidation of tRNA processing, these studies facilitated the discovery of additional functions of RNA ligases such as RNA repair and non-conventional mRNA splicing events. Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing. This review summarizes past and recent findings in the field of tRNA splicing with a focus on RNA ligation as it preferentially occurs in archaea and humans. In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.","authors":"Popow, J., Schleiffer, A., Martinez, J.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Mol Life Sci","volume":"69","issue":"16","page":"2657-70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22425250","title":"Rank signaling links the development of invariant \u03b3\u03b4 T cell progenitors and Aire(+) medullary epithelium.","abstract":"The thymic medulla provides a specialized microenvironment for the negative selection of T cells, with the presence of autoimmune regulator (Aire)-expressing medullary thymic epithelial cells (mTECs) during the embryonic-neonatal period being both necessary and sufficient to establish long-lasting tolerance. Here we showed that emergence of the first cohorts of Aire(+) mTECs at this key developmental stage, prior to \u03b1\u03b2 T cell repertoire selection, was jointly directed by Rankl(+) lymphoid tissue inducer cells and invariant V\u03b35(+) dendritic epidermal T cell (DETC) progenitors that are the first thymocytes to express the products of gene rearrangement. In turn, generation of Aire(+) mTECs then fostered Skint-1-dependent, but Aire-independent, DETC progenitor maturation and the emergence of an invariant DETC repertoire. Hence, our data attributed a functional importance to the temporal development of V\u03b35(+) \u03b3\u03b4 T cells during thymus medulla formation for \u03b1\u03b2 T cell tolerance induction and demonstrated a Rank-mediated reciprocal link between DETC and Aire(+) mTEC maturation.","authors":"Roberts, NA., White, AJ., Jenkinson, WE., Turchinovich, G., Nakamura, K., Withers, DR., McConnell, FM., Desanti, GE., Benezech, C., Parnell, SM., Cunningham, AF., Paolino, M., Penninger, JM., Simon, AK., Nitta, T., Ohigashi, I., Takahama, Y., Caamano, JH., Hayday, AC., Lane, PJ., Jenkinson, EJ., Anderson, G.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Immunity","volume":"36","issue":"3","page":"427-37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22387240","title":"Actin filament tracking in electron tomograms of negatively stained lamellipodia using the localized radon transform.","abstract":"The aim of this work was to develop a protocol for automated tracking of actin filaments in electron tomograms of lamellipodia embedded in negative stain. We show that a localized version of the Radon transform for the detection of filament directions enables three-dimensional visualizations of filament network architecture, facilitating extraction of statistical information including orientation profiles. We discuss the requirements for parameter selection set by the raw image data in the context of other, similar tracking protocols.","authors":"Winkler, C., Vinzenz, M., Small, JV., Schmeiser, C.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Struct Biol","volume":"178","issue":"1","page":"19-28","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11600886","title":"Promiscuous gene expression in medullary thymic epithelial cells mirrors the peripheral self.","abstract":"Expression of peripheral antigens in the thymus has been implicated in T cell tolerance and autoimmunity. Here we identified medullary thymic epithelial cells as being a unique cell type that expresses a diverse range of tissue-specific antigens. We found that this promiscuous gene expression was a cell-autonomous property of medullary epithelial cells and was maintained during the entire period of thymic T cell output. It may facilitate tolerance induction to self-antigens that would otherwise be temporally or spatially secluded from the immune system. However, the array of promiscuously expressed self-antigens appeared random rather than selected and was not confined to secluded self-antigens.","authors":"Derbinski, J., Schulte, A., Kyewski, B., Klein, L.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Immunol","volume":"2","issue":"11","page":"1032-9","pdf":null,"JrId":"21750","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22384097","title":"3T3 cell lines stably expressing Pax6 or Pax6(5a)--a new tool used for identification of common and isoform specific target genes.","abstract":"Pax6 and Pax6(5a) are two isoforms of the evolutionary conserved Pax6 gene often co-expressed in specific stochiometric relationship in the brain and the eye during development. The Pax6(5a) protein differs from Pax6 by having a 14 amino acid insert in the paired domain, causing the two proteins to have different DNA binding specificities. Difference in functions during development is proven by the fact that mutations in the 14 amino acid insertion for Pax6(5a) give a slightly different eye phenotype than the one described for Pax6. Whereas quite many Pax6 target genes have been published during the last years, few Pax6(5a) specific target genes have been reported on. However, target genes identified by Pax6 knockout studies can probably be Pax6(5a) targets as well, since this isoform also will be affected by the knockout. In order to identify new Pax6 target genes, and to try to distinguish between genes regulated by Pax6 and Pax6(5a), we generated FlpIn-3T3 cell lines stably expressing Pax6 or Pax6(5a). RNA was harvested from these cell lines and used in gene expression microarrays where we identified a number of genes differentially regulated by Pax6 and Pax6(5a). A majority of these were associated with the extracellular region. By qPCR we verified that Ncam1, Ngef, Sphk1, Dkk3 and Crtap are Pax6(5a) specific target genes, while Tgfbi, Vegfa, EphB2, Klk8 and Edn1 were confirmed as Pax6 specific target genes. Nbl1, Ngfb and seven genes encoding different glycosyl transferases appeared to be regulated by both. Direct binding to the promoters of Crtap, Ctgf, Edn1, Dkk3, Pdgfb and Ngef was verified by ChIP. Furthermore, a change in morphology of the stably transfected Pax6 and Pax6(5a) cells was observed, and the Pax6 expressing cells were shown to have increased proliferation and migration capacities.","authors":"Kiselev, Y., Eriksen, TE., Forsdahl, S., Nguyen, LH., Mikkola, I.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"2","page":"e31915","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22333576","title":"Distinct activities of the anaphase-promoting complex\/cyclosome (APC\/C) in mouse embryonic cells.","abstract":"The first differentiation event in mammalian development gives rise to the blastocyst, consisting of two cell lineages that have also segregated in how the cell cycle is structured. Pluripotent cells of the inner cell mass divide mitotically to retain a diploid DNA content, but the outer trophoblast cells can amplify their genomes more than 500-fold by undergoing multiple rounds of DNA replication, completely bypassing mitosis. Central to this striking divergence in cell cycle control is the E3 ubiquitin-ligase activity of the anaphase-promoting complex or cyclosome (APC\/C). Extended suppression of APC\/C activity during interphase of mouse pluripotent cells promotes rapid cell cycle progression by allowing stabilization of cyclins, whereas unopposed APC\/C activity during S phase of mouse trophoblast cells triggers proteasomal-mediated degradation of geminin and giant cell formation. While differential APC\/C activity might govern the atypical cell cycles observed in pre-implantation mouse embryos, geminin is a critical APC\/C substrate that: (1) escapes degradation in pluripotent cells to maintain expression of Oct4, Sox2 and Nanog; and (2) mediates specification and endoreduplication when targeted for ectopic destruction in trophoblast. Thus, in contrast to trophoblast giant cells that lack geminin, geminin is preserved in both mouse pluripotent cells and non-endoreduplicating human cytotrophoblast cells.","authors":"Yang, VS., Carter, SA., Ng, Y., Hyland, SJ., Tachibana-Konwalski, K., Fisher, RA., Sebire, NJ., Seckl, MJ., Pedersen, RA., Laskey, RA., Gonzalez, MA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Cell Cycle","volume":"11","issue":"5","page":"846-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22246130","title":"Angiotensin converting enzyme 2 abrogates bleomycin-induced lung injury.","abstract":"Despite substantial progress, mortality and morbidity of the acute respiratory distress syndrome (ARDS), a severe form of acute lung injury (ALI), remain unacceptably high. There is no effective treatment for ARDS\/ALI. The renin-angiotensin system (RAS) through Angiotensin-converting enzyme (ACE)-generated Angiotensin II contributes to lung injury. ACE2, a recently discovered ACE homologue, acts as a negative regulator of the RAS and counterbalances the function of ACE. We hypothesized that ACE2 prevents Bleomycin (BLM)-induced lung injury. Fourteen to 16-week-old ACE2 knockout mice-male (ACE2(-\/y)) and female (ACE2(-\/-))-and age-matched wild-type (WT) male mice received intratracheal BLM (1.5U\/kg). Male ACE2(-\/y) BLM injured mice exhibited poorer exercise capacity, worse lung function and exacerbated lung fibrosis and collagen deposition compared with WT. These changes were associated with increased expression of the profibrotic genes \u03b1-smooth muscle actin (\u03b1-SMA) and Transforming Growth Factor \u00df1. Compared with ACE2(-\/y) exposed to BLM, ACE2(-\/-) exhibited better lung function and architecture and decreased collagen deposition. Treatment with intraperitoneal recombinant human (rh) ACE2 (2\u00a0mg\/kg) for 21\u00a0days improved survival, exercise capacity, and lung function and decreased lung inflammation and fibrosis in male BLM-WT mice. Female BLM WT mice had mild fibrosis and displayed a possible compensatory upregulation of the AT2 receptor. We conclude that ACE2 gene deletion worsens BLM-induced lung injury and more so in males than females. Conversely, ACE2 protects against BLM-induced fibrosis. rhACE2 may have therapeutic potential to attenuate respiratory morbidity in ALI\/ARDS.","authors":"Rey-Parra, GJ., Vadivel, A., Coltan, L., Hall, A., Eaton, F., Schuster, M., Loibner, H., Penninger, JM., Kassiri, Z., Oudit, GY., Th\u00e9baud, B.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"J Mol Med (Berl)","volume":"90","issue":"6","page":"637-47","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22212853","title":"Induction of immediate early genes in the mouse auditory cortex after auditory cued fear conditioning to complex sounds.","abstract":"Immediate early genes (IEGs) are widely used as markers to delineate neuronal circuits because they show fast and transient expression induced by various behavioral paradigms. In this study, we investigated the expression of the IEGs c-fos and Arc in the auditory cortex of the mouse after auditory cued fear conditioning using quantitative polymerase chain reaction and microarray analysis. To test for the specificity of the IEG induction, we included several control groups that allowed us to test for factors other than associative learning to sounds that could lead to an induction of IEGs. We found that both c-fos and Arc showed strong and robust induction after auditory fear conditioning. However, we also observed increased expression of both genes in any control paradigm that involved shocks, even when no sounds were presented. Using mRNA microarrays and comparing the effect of the various behavioral paradigms on mRNA expression levels, we did not find genes being selectively upregulated in the auditory fear conditioned group. In summary, our results indicate that the use of IEGs to identify neuronal circuits involved specifically in processing of sound cues in the fear conditioning paradigm can be limited by the effects of the aversive unconditional stimulus and that activity levels in a particular primary sensory cortical area can be strongly influenced by stimuli mediated by other modalities.","authors":"Peter, M., Scheuch, H., Burkard, TR., Tinter, J., Wernle, T., Rumpel, S.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genes Brain Behav","volume":"11","issue":"3","page":"314-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28247050","title":"Role of Cdc6 During Oogenesis and Early Embryo Development in Mouse and Xenopus laevis.","abstract":"Cdc6 is an important player in cell cycle regulation. It is involved in the regulation of both S-phase and M-phase. Its role during oogenesis is crucial for repression of the S-phase between the first and the second meiotic M-phases, and it also regulates, via CDK1 inhibition, the M-phase entry and exit. This is of special importance for the reactivation of the major M-phase-regulating kinase CDK1 (Cyclin-Dependent Kinase 1) in oocytes entering metaphase II of meiosis and in embryo cleavage divisions, in which precise timing allows coordination between cell cycle events and developmental program of the embryo. In this chapter, we discuss the role of Cdc6 protein in oocytes and early embryos.","authors":"Borsuk, E., Jachowicz, J., Kloc, M., Tassan, JP., Kubiak, JZ.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Results Probl Cell Differ","volume":"59","issue":null,"page":"201-211","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22210322","title":"Apelin treatment increases complete Fatty Acid oxidation, mitochondrial oxidative capacity, and biogenesis in muscle of insulin-resistant mice.","abstract":"Both acute and chronic apelin treatment have been shown to improve insulin sensitivity in mice. However, the effects of apelin on fatty acid oxidation (FAO) during obesity-related insulin resistance have not yet been addressed. Thus, the aim of the current study was to determine the impact of chronic treatment on lipid use, especially in skeletal muscles. High-fat diet (HFD)-induced obese and insulin-resistant mice treated by an apelin injection (0.1 \u03bcmol\/kg\/day i.p.) during 4 weeks had decreased fat mass, glycemia, and plasma levels of triglycerides and were protected from hyperinsulinemia compared with HFD PBS-treated mice. Indirect calorimetry experiments showed that apelin-treated mice had a better use of lipids. The complete FAO, the oxidative capacity, and mitochondrial biogenesis were increased in soleus of apelin-treated mice. The action of apelin was AMP-activated protein kinase (AMPK) dependent since all the effects studied were abrogated in HFD apelin-treated mice with muscle-specific inactive AMPK. Finally, the apelin-stimulated improvement of oxidative capacity led to decreased levels of acylcarnitines and enhanced insulin-stimulated glucose uptake in soleus. Thus, by promoting complete lipid use in muscle of insulin-resistant mice through mitochondrial biogenesis and tighter matching between FAO and the tricarboxylic acid cycle, apelin treatment could contribute to insulin sensitivity improvement.","authors":"Attan\u00e9, C., Foussal, C., Le Gonidec, S., Benani, A., Daviaud, D., Wanecq, E., Guzm\u00e1n-Ruiz, R., Dray, C., Bezaire, V., Rancoule, C., Kuba, K., Ruiz-Gayo, M., Levade, T., Penninger, J., Burcelin, R., P\u00e9nicaud, L., Valet, P., Castan-Laurell, I.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Diabetes","volume":"61","issue":"2","page":"310-20","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22140377","title":"Sixteen New Cases Contributing to the Characterization of Patients with Distal 22q11.2 Microduplications.","abstract":"The chromosome region 22q11.2 has long been recognized to be susceptible to genomic rearrangement. More recently, this genomic instability has been shown to extend distally (involving LCR22E-H) to the commonly deleted\/duplicated region. To date, 21 index cases with 'distal' 22q11.2 duplications have been reported. We report on the clinical and molecular characterization of 16 individuals with distal 22q11.2 duplications identified by DNA microarray analysis. Two of the individuals have been partly described previously. The clinical phenotype varied among the patients in this study, although the majority displayed various degrees of developmental delay and speech disturbances. Other clinical features included behavioral problems, hypotonia, and dysmorphic facial features. Notably, none of the patients was diagnosed with a congenital heart defect. We found a high degree of inherited duplications. Additional copy number changes of unclear clinical significance were identified in 5 of our patients, and it is possible that these may contribute to the phenotypic expression in these patients as has been suggested recently in a 2-hit 'digenic' model for 16p12.1 deletions. The varied phenotypic expression and incomplete penetrance observed for distal 22q11.2 duplications makes it exceedingly difficult to ascribe pathogenicity for these duplications. Given the observed enrichment of the duplication in patient samples versus healthy controls, it is likely that distal 22q11.2 duplications represent a susceptibility\/risk locus for speech and mild developmental delay.","authors":"Wincent, J., Bruno, DL., van Bon, BW., Bremer, A., Stewart, H., Bongers, EM., Ockeloen, CW., Willemsen, MH., Keays, DD., Baird, G., Newbury, DF., Kleefstra, T., Marcelis, C., Kini, U., Stark, Z., Savarirayan, R., Sheffield, LJ., Zuffardi, O., Slater, HR., de Vries, BB., Knight, SJ., Anderlid, BM., Schoumans, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Mol Syndromol","volume":"1","issue":"5","page":"246-254","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22110045","title":"Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.","abstract":"Long noncoding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in humans and the mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time-series of RNA-seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1133 noncoding multi-exonic transcripts expressed during embryogenesis. These include long intergenic ncRNAs (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for small RNAs (sRNAs). Zebrafish lncRNAs share many of the characteristics of their mammalian counterparts: relatively short length, low exon number, low expression, and conservation levels comparable to that of introns. Subsets of lncRNAs carry chromatin signatures characteristic of genes with developmental functions. The temporal expression profile of lncRNAs revealed two novel properties: lncRNAs are expressed in narrower time windows than are protein-coding genes and are specifically enriched in early-stage embryos. In addition, several lncRNAs show tissue-specific expression and distinct subcellular localization patterns. Integrative computational analyses associated individual lncRNAs with specific pathways and functions, ranging from cell cycle regulation to morphogenesis. Our study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies.","authors":"Pauli, A., Valen, E., Lin, MF., Garber, M., Vastenhouw, NL., Levin, JZ., Fan, L., Sandelin, A., Rinn, JL., Regev, A., Schier, AF.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genome Res","volume":"22","issue":"3","page":"577-91","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22102886","title":"An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.","abstract":"Imprinted macro non-protein-coding (nc) RNAs are cis-repressor transcripts that silence multiple genes in at least three imprinted gene clusters in the mouse genome. Similar macro or long ncRNAs are abundant in the mammalian genome. Here we present the full coding and non-coding transcriptome of two mouse tissues: differentiated ES cells and fetal head using an optimized RNA-Seq strategy. The data produced is highly reproducible in different sequencing locations and is able to detect the full length of imprinted macro ncRNAs such as Airn and Kcnq1ot1, whose length ranges between 80-118 kb. Transcripts show a more uniform read coverage when RNA is fragmented with RNA hydrolysis compared with cDNA fragmentation by shearing. Irrespective of the fragmentation method, all coding and non-coding transcripts longer than 8 kb show a gradual loss of sequencing tags towards the 3' end. Comparisons to published RNA-Seq datasets show that the strategy presented here is more efficient in detecting known functional imprinted macro ncRNAs and also indicate that standardization of RNA preparation protocols would increase the comparability of the transcriptome between different RNA-Seq datasets.","authors":"Huang, R., Jaritz, M., Guenzl, P., Vlatkovic, I., Sommer, A., Tamir, IM., Marks, H., Klampfl, T., Kralovics, R., Stunnenberg, HG., Barlow, DP., Pauler, FM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"PLoS One","volume":"6","issue":"11","page":"e27288","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29203171","title":"The NLRP3 Inflammasome Renders Cell Death Pro-inflammatory.","abstract":"NLRP3 is the most studied inflammasome sensor due to its crucial involvement in sterile and infection-triggered inflammation. Although its molecular mode of activation remains to be defined, it is well established that low intracellular potassium concentrations result in its activation. This functionality allows the classical NLRP3 pathway to serve as a highly sensitive, but non-specific surveillance mechanism responding to any type of perturbation that breaches plasma membrane integrity and the associated potassium gradient across the membrane. Here, we review our current knowledge on potassium efflux-dependent NLRP3 activation, with a special focus on how major cell death programs are rendered pro-inflammatory by secondary NLRP3 activation. Apart from the \"alternative inflammasome\" as the major exception to the rule, this connection explains the fundamental importance of NLRP3 in cell death-associated inflammation and firmly establishes NLRP3 as a principal surveillance mechanism of cellular integrity.","authors":"Gaidt, MM., Hornung, V.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"J Mol Biol","volume":"430","issue":"2","page":"133-141","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11751226","title":"Taxonomy workbench.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11751226<\/PMID><DateCompleted><Year>2002<\/Year><Month>03<\/Month><Day>01<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>05<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">1367-4803<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>17<\/Volume><Issue>12<\/Issue><PubDate><Year>2001<\/Year><Month>Dec<\/Month><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Taxonomy workbench.<\/ArticleTitle><Pagination><MedlinePgn>1179-82<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"UNLABELLED\">At advanced stages of working with user-defined protein and gene sequence collections, it is frequently necessary to link these data to the taxonomic tree and to extract subsets in accordance with taxonomic considerations. Since no general automatic tools had been available, this was a tedious manual effort. Our taxonomy workbench allows processing of sequence sets, mapping of these sets onto the taxonomic tree, collection of taxonomic subsets from them and printing of the whole tree or some part of it. As a side effect, the system enables queries to and navigation within the taxonomy database.","authors":"Wildpaner, M., Schneider, G., Schleiffer, A., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Bioinformatics","volume":"17","issue":"12","page":"1179-82","pdf":null,"JrId":"20940","fulltextlink":null,"preprintlink":null,"articledate":"2002-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22055293","title":"The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">22055293<\/PMID><DateCompleted><Year>2012<\/Year><Month>08<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>20<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>21<\/Volume><Issue>22<\/Issue><PubDate><Year>2011<\/Year><Month>Nov<\/Month><Day>22<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1.<\/ArticleTitle><Pagination><MedlinePgn>1878-87<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2011.09.034<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">MicroRNAs (miRNAs) are ~22 nucleotide (nt) small RNAs that control development, physiology, and pathology in animals and plants. Production of miRNAs involves the sequential processing of primary hairpin-containing RNA polymerase II transcripts by the RNase III enzymes Drosha in the nucleus and Dicer in the cytoplasm. miRNA duplexes then assemble into Argonaute proteins to form the RNA-induced silencing complex (RISC). In mature RISC, a single-stranded miRNA directs the Argonaute protein to bind partially complementary sequences, typically in the 3' untranslated regions of messenger RNAs, repressing their expression.","authors":"Han, BW., Hung, JH., Weng, Z., Zamore, PD., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Curr Biol","volume":"21","issue":"22","page":"1878-87","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22006978","title":"Osteoclasts are dispensable for hematopoietic stem cell maintenance and mobilization.","abstract":"Hematopoietic stem cells (HSCs) are maintained in a specific bone marrow (BM) niche in cavities formed by osteoclasts. Osteoclast-deficient mice are osteopetrotic and exhibit closed BM cavities. Osteoclast activity is inversely correlated with hematopoietic activity; however, how osteoclasts and the BM cavity potentially regulate hematopoiesis is not well understood. To investigate this question, we evaluated hematopoietic activity in three osteopetrotic mouse models: op\/op, c-Fos-deficient, and RANKL (receptor activator of nuclear factor kappa B ligand)-deficient mice. We show that, although osteoclasts and, by consequence, BM cavities are absent in these animals, hematopoietic stem and progenitor cell (HSPC) mobilization after granulocyte colony-stimulating factor injection was comparable or even higher in all three lines compared with wild-type mice. In contrast, osteoprotegerin-deficient mice, which have increased numbers of osteoclasts, showed reduced HSPC mobilization. BM-deficient patients and mice reportedly maintain hematopoiesis in extramedullary spaces, such as spleen; however, splenectomized op\/op mice did not show reduced HSPC mobilization. Interestingly, we detected an HSC population in osteopetrotic bone of op\/op mice, and pharmacological ablation of osteoclasts in wild-type mice did not inhibit, and even increased, HSPC mobilization. These results suggest that osteoclasts are dispensable for HSC mobilization and may function as negative regulators in the hematopoietic system.","authors":"Miyamoto, K., Yoshida, S., Kawasumi, M., Hashimoto, K., Kimura, T., Sato, Y., Kobayashi, T., Miyauchi, Y., Hoshi, H., Iwasaki, R., Miyamoto, H., Hao, W., Morioka, H., Chiba, K., Kobayashi, T., Yasuda, H., Penninger, JM., Toyama, Y., Suda, T., Miyamoto, T.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Exp Med","volume":"208","issue":"11","page":"2175-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21977972","title":"Temporal and spatial regulation of microRNA activity with photoactivatable cantimirs.","abstract":"MicroRNAs (miRNAs) are small non-coding RNAs that play numerous important roles in physiology and human diseases. During animal development, many miRNAs are expressed continuously from early embryos throughout adults, yet it is unclear whether these miRNAs are actually required at all the stages of development. Current techniques of manipulating microRNA function lack the required spatial and temporal resolution to adequately address the functionality of a given microRNA at a specific time or at single-cell resolution. To examine stage- or cell-specific function of miRNA during development and to achieve precise control of miRNA activity, we have developed photoactivatable antisense oligonucleotides against miRNAs. These caged oligonucleotides can be activated with 365 nm light with extraordinarily high efficiency to release potent antisense reagents to inhibit miRNAs. Initial application of these caged antimirs in a model organism (C. elegans) revealed that the activity of a miRNA (lsy-6) is required specifically around the comma stage during embryonic development to control a left\/right asymmetric differentiation program in the C. elegans nervous system. This suggests that a transient input of lsy-6 during development is sufficient to specify the neuronal cell fate.","authors":"Zheng, G., Cochella, L., Liu, J., Hobert, O., Li, WH.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"ACS Chem Biol","volume":"6","issue":"12","page":"1332-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22000011","title":"Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis.","abstract":"Chronic myelogenous leukemia (CML) is caused by the constitutively active tyrosine kinase Bcr-Abl and treated with the tyrosine kinase inhibitor (TKI) imatinib. However, emerging TKI resistance prevents complete cure. Therefore, alternative strategies targeting regulatory modules of Bcr-Abl in addition to the kinase active site are strongly desirable. Here, we show that an intramolecular interaction between the SH2 and kinase domains in Bcr-Abl is both necessary and sufficient for high catalytic activity of the enzyme. Disruption of this interface led to inhibition of downstream events critical for CML signaling and, importantly, completely abolished leukemia formation in mice. Furthermore, disruption of the SH2-kinase interface increased sensitivity of imatinib-resistant Bcr-Abl mutants to TKI inhibition. An engineered Abl SH2-binding fibronectin type III monobody inhibited Bcr-Abl kinase activity both in vitro and in primary CML cells, where it induced apoptosis. This work validates the SH2-kinase interface as an allosteric target for therapeutic intervention.","authors":"Grebien, F., Hantschel, O., Wojcik, J., Kaupe, I., Kovacic, B., Wyrzucki, AM., Gish, GD., Cerny-Reiterer, S., Koide, A., Beug, H., Pawson, T., Valent, P., Koide, S., Superti-Furga, G.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Cell","volume":"147","issue":"2","page":"306-19","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21940796","title":"Cofilin cooperates with fascin to disassemble filopodial actin filaments.","abstract":"Cells use a large repertoire of proteins to remodel the actin cytoskeleton. Depending on the proteins involved, F-actin is organized in specialized protrusions such as lamellipodia or filopodia, which serve diverse functions in cell migration and sensing. Although factors responsible for directed filament assembly in filopodia have been extensively characterized, the mechanisms of filament disassembly in these structures are mostly unknown. We investigated how the actin-depolymerizing factor cofilin-1 affects the dynamics of fascincrosslinked actin filaments in vitro and in live cells. By multicolor total internal reflection fluorescence microscopy and fluorimetric assays, we found that cofilin-mediated severing is enhanced in fascin-crosslinked bundles compared with isolated filaments, and that fascin and cofilin act synergistically in filament severing. Immunolabeling experiments demonstrated for the first time that besides its known localization in lamellipodia and membrane ruffles, endogenous cofilin can also accumulate in the tips and shafts of filopodia. Live-cell imaging of fluorescently tagged proteins revealed that cofilin is specifically targeted to filopodia upon stalling of protrusion and during their retraction. Subsequent electron tomography established filopodial actin filament and\/or bundle fragmentation to precisely correlate with cofilin accumulation. These results identify a new mechanism of filopodium disassembly involving both fascin and cofilin.","authors":"Breitsprecher, D., Koestler, SA., Chizhov, I., Nemethova, M., Mueller, J., Goode, BL., Small, JV., Rottner, K., Faix, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Cell Sci","volume":"124","issue":"Pt 19","page":"3305-18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21947283","title":"Survival and differentiation of mammary epithelial cells in mammary gland development require nuclear retention of Id2 due to RANK signaling.","abstract":"RANKL plays an essential role in mammary gland development during pregnancy. However, the molecular mechanism by which RANK signaling leads to mammary gland development is largely unknown. We report here that RANKL stimulation induces phosphorylation of Id2 at serine 5, which leads to nuclear retention of Id2. In lactating Id2Tg; RANKL(-\/-) mice, Id2 was not phosphorylated and was localized in the cytoplasm. In addition, in lactating Id2(S5A)Tg mice, Id2(S5A) (with serine 5 mutated to alanine) was exclusively localized in the cytoplasm of mammary epithelial cells (MECs), while endogenous Id2 was localized in the nucleus. Intriguingly, nuclear expression of Id2(S5A) rescued increased apoptosis and defective differentiation of MECs in RANKL(-\/-) mice. Our results demonstrate that nuclear retention of Id2 due to RANK signaling plays a decisive role in the survival and differentiation of MECs during mammary gland development.","authors":"Kim, NS., Kim, HT., Kwon, MC., Choi, SW., Kim, YY., Yoon, KJ., Koo, BK., Kong, MP., Shin, J., Cho, Y., Kong, YY.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mol Cell Biol","volume":"31","issue":"23","page":"4775-88","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21942411","title":"Connecting rare DNA conformations and surface dynamics using single-molecule resonance energy transfer.","abstract":"A mechanistic understanding of single-stranded DNA (ssDNA) behavior in the near-surface environment is critical to advancing DNA-directed self-assembled nanomaterials. A new approach is described that uses total internal reflection fluorescence microscopy to measure resonance energy transfer at the single-molecule level, providing a mechanistic understanding of the connection between molecular conformation and interfacial dynamics near amine-modified surfaces. Large numbers (&gt;10(5)) of ssDNA trajectories were observed, permitting dynamic correlation of molecular conformation with desorption and surface mobility. On the basis of dynamic behavior, molecules could be designated as members of the more common coiled population or a rare, weakly bound conformation. Molecules in the coiled state generally exhibited slow diffusion and conformational fluctuations that decreased with increasing average end-to-end distance. Lattice simulations of adsorbed self-avoiding polymers successfully predicted these trends. In contrast, the weakly bound conformation, observed in about 5% of molecules, had a large end-to-end distance but demonstrated conformational fluctuations that were much higher than predicted by simulations for adsorbed flexible chains. This conformation correlated positively with desorption events and led to fast diffusion, indicating weak surface associations. Understanding the role of the weakly bound conformation in DNA hybridization, and how solution conditions and surface properties may favor it, could lead to improved self-assembled nanomaterials.","authors":"Kastantin, M., Schwartz, DK.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"ACS Nano","volume":"5","issue":"12","page":"9861-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21956937","title":"DNA rearrangements directed by non-coding RNAs in ciliates.","abstract":"Extensive programmed rearrangement of DNA, including DNA elimination, chromosome fragmentation, and DNA unscrambling, takes place in the newly developed macronucleus during the sexual reproduction of ciliated protozoa. Recent studies have revealed that two distant classes of ciliates use distinct types of non-coding RNAs to regulate such DNA rearrangement events. DNA elimination in Tetrahymena is regulated by small non-coding RNAs that are produced and utilized in an RNA interference (RNAi)-related process. It has been proposed that the small RNAs produced from the micronuclear genome are used to identify eliminated DNA sequences by whole-genome comparison between the parental macronucleus and the micronucleus. In contrast, DNA unscrambling in Oxytricha is guided by long non-coding RNAs that are produced from the parental macronuclear genome. These long RNAs are proposed to act as templates for the direct unscrambling events that occur in the developing macronucleus. Both cases provide useful examples to study epigenetic chromatin regulation by non-coding RNAs.","authors":"Mochizuki, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Wiley Interdiscip Rev RNA","volume":"1","issue":"3","page":"376-87","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16407844","title":"Erythroid progenitor renewal versus differentiation: genetic evidence for cell autonomous, essential functions of EpoR, Stat5 and the GR.","abstract":"The balance between hematopoietic progenitor commitment and self-renewal versus differentiation is controlled by various transcriptional regulators cooperating with cytokine receptors. Disruption of this balance is increasingly recognized as important in the development of leukemia, by causing enhanced renewal and differentiation arrest. We studied regulation of renewal versus differentiation in primary murine erythroid progenitors that require cooperation of erythropoietin receptor (EpoR), the receptor tyrosine kinase c-Kit and a transcriptional regulator (glucocorticoid receptor; GR) for sustained renewal. However, mice defective for GR- (GR(dim\/dim)), EpoR- (EpoR(H)) or STAT5ab function (Stat5ab(-\/-)) show no severe erythropoiesis defects in vivo. Using primary erythroblast cultures from these mutants, we present genetic evidence that functional GR, EpoR, and Stat5 are essential for erythroblast renewal in vitro. Cells from GR(dim\/dim), EpoR(H), and Stat5ab(-\/-) mice showed enhanced differentiation instead of renewal, causing accumulation of mature cells and gradual proliferation arrest. Stat5ab was additionally required for Epo-induced terminal differentiation: differentiating Stat5ab(-\/-) erythroblasts underwent apoptosis instead of erythrocyte maturation, due to absent induction of the antiapoptotic protein Bcl-X(L). This defect could be fully rescued by exogenous Bcl-X(L). These data suggest that signaling molecules driving leukemic proliferation may also be essential for prolonged self-renewal of normal erythroid progenitors.","authors":"Dolznig, H., Grebien, F., Deiner, EM., Stangl, K., Kolbus, A., Habermann, B., Kerenyi, MA., Kieslinger, M., Moriggl, R., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Oncogene","volume":"25","issue":"20","page":"2890-900","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2006-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21930791","title":"Gab2 promotes colony-stimulating factor 1-regulated macrophage expansion via alternate effectors at different stages of development.","abstract":"Colony-stimulating factor 1 (CSF-1) receptor (CSF-1R, or macrophage CSF receptor [M-CSFR]) is the primary regulator of the proliferation, survival, and differentiation of mononuclear phagocytes (MNPs), but the critical CSF-1 signals for these functions are unclear. The scaffold protein Gab2 is a major tyrosyl phosphoprotein in the CSF-1R signaling network. Here we demonstrate that Gab2 deficiency results in profoundly defective expansion of CSF-1R-dependent MNP progenitors in the bone marrow, through decreased proliferation and survival. Reconstitution and phospho-flow studies show that downstream of CSF-1R, Gab2 uses phosphatidylinositol 3-kinase (PI3K)-Akt and extracellular signal-regulated kinase (Erk) to regulate MNP progenitor expansion. Unexpectedly, Gab2 ablation enhances Jun N-terminal protein kinase 1 (JNK1) phosphorylation in differentiated MNPs but reduces their proliferation; inhibition of JNK signaling or reduction of JNK1 levels restores proliferation. MNP recruitment to inflammatory sites and the corresponding bone marrow response is strongly impaired in Gab2-deficient mice. Our data provide genetic and biochemical evidence that CSF-1R, through Gab2, utilizes different effectors at different stages of MNP development to promote their expansion.","authors":"Lee, AW., Mao, Y., Penninger, JM., Yu, S.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mol Cell Biol","volume":"31","issue":"22","page":"4563-81","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21925573","title":"Microarray analysis of gene expression changes in the brains of NR2B-induced memory-enhanced mice.","abstract":"Glutamate N-methyl-D-aspartate (NMDA) receptors play a pivotal role in different forms of memory. The dysfunction of NMDA receptors contributes to the pathology of central nervous system (CNS) disorders. To further investigate the role of the NMDA receptors in brain processes, we analyzed and compared the gene expression profiles in the hippocampus of NR2B overexpression-induced memory-enhanced mice (Tg mice) with those of their wild-type littermates. Results reveal that 249 genes, which are mainly involved in neurotransmission, signal transduction, cytoskeletal structure, hormone activity, and transcription, were significantly affected in Tg mice. Interestingly, the intracellular calcium channel proteins ryanodine receptor (RyR) 1 and 3, as well as functionally related proteins such as the histidine-rich calcium-binding protein and triadin 2, were upregulated. The Homer-1c protein was also increased in Tg mice and formed a complex with the RyR protein in the mouse brain, suggesting that Homer-1c is an important modulator in both intracellular calcium signaling and overall neuronal signaling by simultaneously interacting with the NMDA receptors and RyR. Western blot and real-time PCR results show that the expression of phospho-CREB, c-fos, and the immediate-early genes Egr2 and Egr4 were also upregulated in Tg mice. The current study demonstrates that a chronic increase in the activation of NMDA receptors affected the expression of a large number of genes and may provide important clues for a better understanding of the molecular mechanism of NMDA receptor-modulated learning and memory, as well as of CNS disorders.","authors":"Li, C., Dong, S., Wang, H., Hu, Y.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Neuroscience","volume":"197","issue":"","page":"121-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21909389","title":"TrpA1 regulates thermal nociception in Drosophila.","abstract":"Pain is a significant medical concern and represents a major unmet clinical need. The ability to perceive and react to tissue-damaging stimuli is essential in order to maintain bodily integrity in the face of environmental danger. To prevent damage the systems that detect noxious stimuli are therefore under strict evolutionary pressure. We developed a high-throughput behavioral method to identify genes contributing to thermal nociception in the fruit fly and have reported a large-scale screen that identified the Ca\u00b2\u207a channel straightjacket (stj) as a conserved regulator of thermal nociception. Here we present the minimal anatomical and neuronal requirements for Drosophila to avoid noxious heat in our novel behavioral paradigm. Bioinformatics analysis of our whole genome data set revealed 23 genes implicated in Ca\u00b2\u207a signaling that are required for noxious heat avoidance. One of these genes, the conserved thermoreceptor TrpA1, was confirmed as a bona fide \"pain\" gene in both adult and larval fly nociception paradigms. The nociceptive function of TrpA1 required expression within the Drosophila nervous system, specifically within nociceptive multi-dendritic (MD) sensory neurons. Therefore, our analysis identifies the channel TRPA1 as a conserved regulator of nociception.","authors":"Neely, GG., Keene, AC., Duchek, P., Chang, EC., Wang, QP., Aksoy, YA., Rosenzweig, M., Costigan, M., Woolf, CJ., Garrity, PA., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"PLoS One","volume":"6","issue":"8","page":"e24343","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16400644","title":"Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells.","abstract":"Transgenic and gene-targeted mutant mice provide powerful tools for analysis of the cellular processes involved in early development and in the pathogenesis of many diseases. Here we describe a transgene integration strategy mediated by site-specific recombination that allows establishment of multiple embryonic stem (ES) cell lines carrying tetracycline-inducible genes targeted to a specific locus to assure predictable temporal and spatial expression in ES cells and mice. Using homologous recombination we inserted an frt homing site into which tetracycline-inducible transgenes can be integrated efficiently in the presence of FLPe recombinase. This strategy and the vectors described here are generally applicable to any locus in ES cells and should allow for the rapid production of mice with transgenes efficiently targeted to a defined site.","authors":"Beard, C., Hochedlinger, K., Plath, K., Wutz, A., Jaenisch, R.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Genesis","volume":"44","issue":"1","page":"23-8","pdf":null,"JrId":"21590","fulltextlink":null,"preprintlink":null,"articledate":"2006-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21834641","title":"Loss of dexras1 alters nonphotic circadian phase shifts and reveals a role for the intergeniculate leaflet (IGL) in gene-targeted mice.","abstract":"Loss of Dexras1 in gene-targeted mice impairs circadian entrainment to light cycles and produces complex changes to phase-dependent resetting responses (phase shifts) to light. The authors now describe greatly enhanced and phase-specific nonphotic responses induced by arousal in dexras1(-\/-) mice. In constant conditions, mutant mice exhibited significant arousal-induced phase shifts throughout the subjective day. Unusual phase advances in the late subjective night were also produced when arousal has little effect in mice. Bilateral lesions of the intergeniculate leaflet (IGL) completely eliminated both the nonphotic as well as the light-induced phase shifts of circadian locomotor rhythms during the subjective day, but had no effect on nighttime phase shifts. The expression of FOS-like protein in the suprachiasmatic nucleus (SCN) was not affected by either photic or nonphotic stimulation in the subjective day in either genotype. Therefore, the loss of Dexras1 (1) enhances nonphotic phase shifts in a phase-dependent manner, and (2) demonstrates that the IGL in mice is a primary mediator of circadian phase-resetting responses to both photic and nonphotic events during the subjective day, but plays a different functional role in the subjective night. Furthermore, (3) the change in FOS level does not appear to be a critical step in the entrainment pathways for either light or arousal during the subjective day. The cumulative evidence suggests that Dexras1 regulates multiple photic and nonphotic signal-transduction pathways, thereby playing an essential role modulating species-specific characteristics of circadian entrainment.","authors":"Koletar, MM., Cheng, HY., Penninger, JM., Ralph, MR.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Chronobiol Int","volume":"28","issue":"7","page":"553-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21748764","title":"Promotion of tumor cell metastasis and vasculogenic mimicry by way of transcription coactivation by Bcl-2 and Twist1: a study of hepatocellular carcinoma.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21748764<\/PMID><DateCompleted><Year>2012<\/Year><Month>01<\/Month><Day>09<\/Day><\/DateCompleted><DateRevised><Year>2016<\/Year><Month>11<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1527-3350<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>54<\/Volume><Issue>5<\/Issue><PubDate><Year>2011<\/Year><Month>Nov<\/Month><\/PubDate><\/JournalIssue><Title>Hepatology (Baltimore, Md.)<\/Title><ISOAbbreviation>Hepatology<\/ISOAbbreviation><\/Journal><ArticleTitle>Promotion of tumor cell metastasis and vasculogenic mimicry by way of transcription coactivation by Bcl-2 and Twist1: a study of hepatocellular carcinoma.<\/ArticleTitle><Pagination><MedlinePgn>1690-706<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/hep.24543<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">The antiapoptotic protein Bcl-2 plays multiple roles in apoptosis, immunity, and autophagy. Its expression in tumors correlates with tumor grade and malignancy. The recapitulation of the normal developmental process of epithelial-mesenchymal transition (EMT) contributes to tumor cell plasticity. This process is also a characteristic of metastatic cells and vasculogenic mimicry. In the present study we report functional and structural interactions between Bcl-2 and the EMT-regulating transcription factor Twist1 and the relationship with metastasis and vascular mimicry. Bcl-2 and Twist1 are coexpressed under hypoxia conditions. The Bcl-2 can bind to Twist1 in vivo and in vitro. This interaction involves basic helix-loop-helix DNA binding domain within Twist1 and through two separate domains within Bcl-2 protein. Formation of the Bcl-2\/Twist1 complex facilitates the nuclear transport of Twist1 and leads to transcriptional activation of wide ranges of genes that can increase the tumor cell plasticity, metastasis, and vasculogenic mimicry. Finally, nuclear expression of Bcl-2 and Twist1 is correlated with poor survival of these patients in a cohort of 97 cases of human hepatocellular carcinoma.","authors":"Sun, T., Sun, BC., Zhao, XL., Zhao, N., Dong, XY., Che, N., Yao, Z., Ma, YM., Gu, Q., Zong, WK., Liu, ZY.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Hepatology","volume":"54","issue":"5","page":"1690-706","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21763617","title":"The cellular basis for animal regeneration.","abstract":"The ability of animals to regenerate missing parts is a dramatic and poorly understood aspect of biology. The sources of new cells for these regenerative phenomena have been sought for decades. Recent advances involving cell fate tracking in complex tissues have shed new light on the cellular underpinnings of regeneration in Hydra, planarians, zebrafish, Xenopus, and Axolotl. Planarians accomplish regeneration with use of adult pluripotent stem cells, whereas several vertebrates utilize a collection of lineage-restricted progenitors from different tissues. Together, an array of cellular strategies-from pluripotent stem cells to tissue-specific stem cells and dedifferentiation-are utilized for regeneration.","authors":"Tanaka, EM., Reddien, PW.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Dev Cell","volume":"21","issue":"1","page":"172-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21779445","title":"BI 5700, a Selective Chemical Inhibitor of I\u03baB Kinase 2, Specifically Suppresses Epithelial-Mesenchymal Transition and Metastasis in Mouse Models of Tumor Progression.","abstract":"Increasing evidence suggests that processes termed epithelial-mesenchymal transitions (EMTs) play a key role in therapeutic resistance, tumor recurrence, and metastatic progression. NF-\u03baB signaling has been previously identified as an important pathway in the regulation of EMT in a mouse model of tumor progression. However, it remains unclear whether there is a broad requirement for this pathway to govern EMT and what the relative contribution of IKK family members acting as upstream NF-\u03baB activators is toward promoting EMT and metastasis. To address this question, we have used a novel, small-molecule inhibitor of I\u03baB kinase 2 (IKK2\/IKK\u03b2), termed BI 5700. We investigated the role of IKK2 in a number of mouse models of EMT, including TGF\u03b2-induced EMT in the mammary epithelial cell line EpRas, CT26 colon carcinoma cells, and 4T1 mammary carcinoma cells. The latter model was also used to evaluate in vivo activities of BI 5700.We found that BI 5700 inhibits IKK2 with an IC(50) of 9 nM and was highly selective as compared to other IKK family members (IKK1, IKK\u03b5, and TBK1) and other kinases. BI 5700 effectively blocks NF-\u03baB activity in EpRas cells and prevents TGF\u03b2-induced EMT. In addition, BI 5700 reverts EMT in mesenchymal CT26 cells and prevents EMT in the 4T1 model. Oral application of BI 5700 significantly interferes with metastasis after mammary fat-pad injection of 4T1 cells, yielding fewer, smaller, and more differentiated metastases as compared to vehicle-treated control animals. We conclude that IKK2 is a key regulator of both the induction and maintenance of EMT in a panel of mouse tumor progression models and that the IKK2 inhibitor BI 5700 constitutes a promising candidate for the treatment of metastatic cancers.","authors":"Huber, MA., Maier, HJ., Alacakaptan, M., Wiedemann, E., Braunger, J., Boehmelt, G., Madwed, JB., Young, ER., Marshall, DR., Pehamberger, H., Wirth, T., Kraut, N., Beug, H.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Genes Cancer","volume":"1","issue":"2","page":"101-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21698137","title":"A Genome-Wide RNAi Screen for Factors Involved in Neuronal Specification in Caenorhabditis elegans.","abstract":"One of the central goals of developmental neurobiology is to describe and understand the multi-tiered molecular events that control the progression of a fertilized egg to a terminally differentiated neuron. In the nematode Caenorhabditis elegans, the progression from egg to terminally differentiated neuron has been visually traced by lineage analysis. For example, the two gustatory neurons ASEL and ASER, a bilaterally symmetric neuron pair that is functionally lateralized, are generated from a fertilized egg through an invariant sequence of 11 cellular cleavages that occur stereotypically along specific cleavage planes. Molecular events that occur along this developmental pathway are only superficially understood. We take here an unbiased, genome-wide approach to identify genes that may act at any stage to ensure the correct differentiation of ASEL. Screening a genome-wide RNAi library that knocks-down 18,179 genes (94% of the genome), we identified 245 genes that affect the development of the ASEL neuron, such that the neuron is either not generated, its fate is converted to that of another cell, or cells from other lineage branches now adopt ASEL fate. We analyze in detail two factors that we identify from this screen: (1) the proneural gene hlh-14, which we find to be bilaterally expressed in the ASEL\/R lineages despite their asymmetric lineage origins and which we find is required to generate neurons from several lineage branches including the ASE neurons, and (2) the COMPASS histone methyltransferase complex, which we find to be a critical embryonic inducer of ASEL\/R asymmetry, acting upstream of the previously identified miRNA lsy-6. Our study represents the first comprehensive, genome-wide analysis of a single neuronal cell fate decision. The results of this analysis provide a starting point for future studies that will eventually lead to a more complete understanding of how individual neuronal cell types are generated from a single-cell embryo.","authors":"Poole, RJ., Bashllari, E., Cochella, L., Flowers, EB., Hobert, O.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"PLoS Genet","volume":"7","issue":"6","page":"e1002109","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21685389","title":"Molecular adaptation of the DegQ protease to exert protein quality control in the bacterial cell envelope.","abstract":"To react to distinct stress situations and to prevent the accumulation of misfolded proteins, all cells employ a number of proteases and chaperones, which together set up an efficient protein quality control system. The functionality of proteins in the cell envelope of Escherichia coli is monitored by the HtrA proteases DegS, DegP, and DegQ. In contrast with DegP and DegS, the structure and function of DegQ has not been addressed in detail. Here, we show that substrate binding triggers the conversion of the resting DegQ hexamer into catalytically active 12- and 24-mers. Interestingly, substrate-induced oligomer reassembly and protease activation depends on the first PDZ domain but not on the second. Therefore, the regulatory mechanism originally identified in DegP should be a common feature of HtrA proteases, most of which encompass only a single PDZ domain. Using a DegQ mutant lacking the second PDZ domain, we determined the high resolution crystal structure of a dodecameric HtrA complex. The nearly identical domain orientation of protease and PDZ domains within 12- and 24-meric HtrA complexes reveals a conserved PDZ1 \u2192 L3 \u2192 LD\/L1\/L2 signaling cascade, in which loop L3 senses the repositioned PDZ1 domain of higher order, substrate-engaged particles and activates protease function. Furthermore, our in vitro and in vivo data imply a pH-related function of DegQ in the bacterial cell envelope.","authors":"Sawa, J., Malet, H., Krojer, T., Canellas, F., Ehrmann, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Biol Chem","volume":"286","issue":"35","page":"30680-30690","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35895833","title":"Mechanism-based combination therapies for metastatic cancer.","abstract":"Functional interrogation of cancer and immune cells during tumor evolution reveals cancer drivers and informs mechanism-based combination therapies.","authors":"Obenauf, AC.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Sci Transl Med","volume":"14","issue":"655","page":"eadd0887","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21613549","title":"A system for imaging the regulatory noncoding Xist RNA in living mouse embryonic stem cells.","abstract":"In mammals, silencing of one of the two X chromosomes in female cells compensates for the different number of X chromosomes between the sexes. The noncoding Xist RNA initiates X chromosome inactivation. Xist spreads from its transcription site over the X chromosome territory and triggers the formation of a repressive chromatin domain. To understand localization of Xist over one X chromosome we aimed to develop a system for investigating Xist in living cells. Here we report successful visualization of transgenically expressed MS2-tagged Xist in mouse embryonic stem cells. Imaging of Xist during an entire cell cycle shows that Xist spreads from a single point to a steady state when the chromosome is covered with a constant amount of Xist. Photobleaching experiments of the established Xist cluster indicate that chromosome-bound Xist is dynamic and turns over on the fully Xist covered chromosome. It appears that in interphase the loss of bound Xist and newly produced Xist are in equilibrium. We also show that the turnover of bound Xist requires transcription, and Xist binding becomes stable when transcription is inhibited. Our data reveal a strategy for visualizing Xist and indicate that spreading over the chromosome might involve dynamic binding and displacement.","authors":"Ng, K., Daigle, N., Bancaud, A., Ohhata, T., Humphreys, P., Walker, R., Ellenberg, J., Wutz, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mol Biol Cell","volume":"22","issue":"14","page":"2634-45","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-11-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21603613","title":"Microtubules as platforms for assaying actin polymerization in vivo.","abstract":"The actin cytoskeleton is continuously remodeled through cycles of actin filament assembly and disassembly. Filaments are born through nucleation and shaped into supramolecular structures with various essential functions. These range from contractile and protrusive assemblies in muscle and non-muscle cells to actin filament comets propelling vesicles or pathogens through the cytosol. Although nucleation has been extensively studied using purified proteins in vitro, dissection of the process in cells is complicated by the abundance and molecular complexity of actin filament arrays. We here describe the ectopic nucleation of actin filaments on the surface of microtubules, free of endogenous actin and interfering membrane or lipid. All major mechanisms of actin filament nucleation were recapitulated, including filament assembly induced by Arp2\/3 complex, formin and Spir. This novel approach allows systematic dissection of actin nucleation in the cytosol of live cells, its genetic re-engineering as well as screening for new modifiers of the process.","authors":"Oelkers, JM., Vinzenz, M., Nemethova, M., Jacob, S., Lai, FP., Block, J., Szczodrak, M., Kerkhoff, E., Backert, S., Schl\u00fcter, K., Stradal, TE., Small, JV., Koestler, SA., Rottner, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"PLoS One","volume":"6","issue":"5","page":"e19931","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21545157","title":"Molecular conformations in the pentasaccharide LNF-1 derived from NMR spectroscopy and molecular dynamics simulations.","abstract":"The conformational dynamics of the human milk oligosaccharide lacto-N-fucopentaose (LNF-1), \u03b1-L-Fucp-(1 \u2192 2)-\u03b2-D-Galp-(1 \u2192 3)-\u03b2-D-GlcpNAc-(1 \u2192 3)-\u03b2-D-Galp-(1 \u2192 4)-D-Glcp, has been analyzed using NMR spectroscopy and molecular dynamics (MD) computer simulations. Employing the Hadamard (13)C-excitation technique and the J-HMBC experiment, (1)H,(13)C trans-glycosidic J coupling constants were obtained, and from one- and two-dimensional (1)H,(1)H T-ROESY experiments, proton-proton cross-relaxation rates were determined in isotropic D(2)O solution. In the lyotropic liquid-crystalline medium consisting of ditetradecylphosphatidylcholine, dihexylphosphatidylcholine, N-cetyl-N,N,N-trimethylammonium bromide, and D(2)O, (1)H, (1)H and one-bond (1)H, (13)C residual dipolar couplings (RDCs), as well as relative sign information on homonuclear RDCs, were determined for the pentasaccharide. Molecular dynamics simulations with explicit water were carried out from which the internal isomerization relaxation time constant, \u03c4(N), was calculated for transitions at the \u03c8 torsion angle of the \u03b2-(1 \u2192 3) linkage to the lactosyl group in LNF-1. Compared to the global reorientation time, \u03c4(M), of \u223c0.6 ns determined experimentally in D(2)O solution, the time constant for the isomerization relaxation process, \u03c4(N(scaled)), is about one-third as large. The NMR parameters derived from the isotropic solution show very good agreement with those calculated from the MD simulations. The only notable difference occurs at the reducing end, which should be more flexible than observed by the molecular simulation, a conclusion in complete agreement with previous (13)C NMR relaxation data. A hydrogen-bond analysis of the MD simulation revealed that inter-residue hydrogen bonds on the order of \u223c30% were present across the glycosidic linkages to sugar ring oxygens. This finding highlights that intramolecular hydrogen bonds might be important in preserving well-defined structures in otherwise flexible molecules. An analysis including generalized order parameters obtained from nuclear spin relaxation experiments was performed and successfully shown to limit the conformational space accessible to the molecule when the number of experimental data are too scarce for a complete conformational analysis.","authors":"S\u00e4w\u00e9n, E., Stevensson, B., Ostervall, J., Maliniak, A., Widmalm, G.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Phys Chem B","volume":"115","issue":"21","page":"7109-21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21549331","title":"Genome-wide analysis of self-renewal in Drosophila neural stem cells by transgenic RNAi.","abstract":"The balance between stem cell self-renewal and differentiation is precisely controlled to ensure tissue homeostasis and prevent tumorigenesis. Here we use genome-wide transgenic RNAi to identify 620 genes potentially involved in controlling this balance in Drosophila neuroblasts. We quantify all phenotypes and derive measurements for proliferation, lineage, cell size, and cell shape. We identify a set of transcriptional regulators essential for self-renewal and use hierarchical clustering and integration with interaction data to create functional networks for the control of neuroblast self-renewal and differentiation. Our data identify key roles for the chromatin remodeling Brm complex, the spliceosome, and the TRiC\/CCT-complex and show that the alternatively spliced transcription factor Lola and the transcriptional elongation factors Ssrp and Barc control self-renewal in neuroblast lineages. As our data are strongly enriched for genes highly expressed in murine neural stem cells, they are likely to provide valuable insights into mammalian stem cell biology as well.","authors":"Neum\u00fcller, RA., Richter, C., Fischer, A., Novatchkova, M., Neum\u00fcller, KG., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Cell Stem Cell","volume":"8","issue":"5","page":"580-93","pdf":null,"JrId":"34100","fulltextlink":null,"preprintlink":null,"articledate":"2011-10-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21540552","title":"The WNT antagonist Dickkopf2 promotes angiogenesis in rodent and human endothelial cells.","abstract":"Neovessel formation is a complex process governed by the orchestrated action of multiple factors that regulate EC specification and dynamics within a growing vascular tree. These factors have been widely exploited to develop therapies for angiogenesis-related diseases such as diabetic retinopathy and tumor growth and metastasis. WNT signaling has been implicated in the regulation and development of the vascular system, but the detailed mechanism of this process remains unclear. Here, we report that Dickkopf1 (DKK1) and Dickkopf2 (DKK2), originally known as WNT antagonists, play opposite functional roles in regulating angiogenesis. DKK2 induced during EC morphogenesis promoted angiogenesis in cultured human endothelial cells and in in vivo assays using mice. Its structural homolog, DKK1, suppressed angiogenesis and was repressed upon induction of morphogenesis. Importantly, local injection of DKK2 protein significantly improved tissue repair, with enhanced neovascularization in animal models of both hind limb ischemia and myocardial infarction. We further showed that DKK2 stimulated filopodial dynamics and angiogenic sprouting of ECs via a signaling cascade involving LRP6-mediated APC\/Asef2\/Cdc42 activation. Thus, our findings demonstrate the distinct functions of DKK1 and DKK2 in controlling angiogenesis and suggest that DKK2 may be a viable therapeutic target in the treatment of ischemic vascular diseases.","authors":"Min, JK., Park, H., Choi, HJ., Kim, Y., Pyun, BJ., Agrawal, V., Song, BW., Jeon, J., Maeng, YS., Rho, SS., Shim, S., Chai, JH., Koo, BK., Hong, HJ., Yun, CO., Choi, C., Kim, YM., Hwang, KC., Kwon, YG.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Clin Invest","volume":"121","issue":"5","page":"1882-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520487","title":"Genotoxicity of dietary, environmental and therapeutic topoisomerase II poisons is uniformly correlated to prolongation of enzyme DNA residence.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520487<\/PMID><DateCompleted><Year>2011<\/Year><Month>08<\/Month><Day>04<\/Day><\/DateCompleted><DateRevised><Year>2013<\/Year><Month>11<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1613-4133<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>55 Suppl 1<\/Volume><PubDate><Year>2011<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>Molecular nutrition &amp; food research<\/Title><ISOAbbreviation>Mol Nutr Food Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Genotoxicity of dietary, environmental and therapeutic topoisomerase II poisons is uniformly correlated to prolongation of enzyme DNA residence.<\/ArticleTitle><Pagination><MedlinePgn>S127-42<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/mnfr.201000509<\/ELocationID><Abstract><AbstractText Label=\"SCOPE\" NlmCategory=\"METHODS\">DNA damage by genistein and etoposide is determined by the half-life of topoisomerase II-DNA linkage induced [Bandele O. J. and Osheroff N., Biochemistry 2008, 47, 11900]. Here, we test whether this applies generally to dietary flavonoids and therapeutic compounds enhancing topoisomerase II-DNA cleavage (Topo II poisons).","authors":"Kalfalah, FM., Mielke, C., Christensen, MO., Baechler, S., Marko, D., Boege, F.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mol Nutr Food Res","volume":"55 Suppl 1","issue":"","page":"S127-42","pdf":null,"JrId":"32150","fulltextlink":null,"preprintlink":null,"articledate":"2011-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520472","title":"Evaluation of Turkish seaweeds for antiprotozoal, antimycobacterial and cytotoxic activities.","abstract":"As part of our continuing research on seaweeds, crude MeOH extracts of two green, three brown and six red algae collected from Marmara, Black, Aegean and Mediterranean Seas were screened. Four parasitic protozoa, i.e. Plasmodium falciparum, Trypanosoma brucei rhodesiense, T. cruzi, Leishmania donovani and the tubercle bacillus Mycobacterium tuberculosis were used as test organisms for the in vitro assays. The selective toxicity of the extracts was also determined against mammalian L6 cells. All seaweed extracts were active against T. brucei rhodesiense; the Dasya pedicellata extract was the most potent (IC(50) value 0.37\u2009\u00b5g\/mL). The same extract also weakly inhibited the growth of T. cruzi (IC(50) 62.02\u2009\u00b5g\/mL). All seaweed extracts also showed leishmanicidal activity (IC(50) values 16.76-69.98\u2009\u00b5g\/mL). The majority of the extracts also exhibited antiplasmodial potential and the most potent extracts were those from D. pedicellata (IC(50) 0.38\u2009\u00b5g\/mL), Codium bursa (IC(50) 1.38\u2009\u00b5g\/mL) and Caulerpa rasemosa (IC(50) 3.12\u2009\u00b5g\/mL). One brown and two red algal extracts showed some weak activity against Mycobacterium tuberculosis (MIC values 125-256\u2009\u00b5g\/mL). Except for the extract of Dasya pedicellata, none of the extracts displayed any cytotoxicity. This is the second study investigating the antiprotozoal activities of Turkish marine algae and identifies Dasya pedicellata, an understudied algal species, as a candidate for further studies.","authors":"S\u00fczge\u00e7-Sel\u00e7uk, S., Meri\u00e7li, AH., G\u00fcven, KC., Kaiser, M., Casey, R., Hingley-Wilson, S., Lalvani, A., Tasdemir, D.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Phytother Res","volume":"25","issue":"5","page":"778-83","pdf":null,"JrId":"21098","fulltextlink":null,"preprintlink":null,"articledate":"2012-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520442","title":"Physical activity, fitness, and dyspnea perception in children with congenital diaphragmatic hernia.","abstract":"We assessed whether physical activity could influence the performance and perception of dyspnea in children who were operated on for high risk congenital diaphragmatic hernia (CDH). We hypothesized that CDH children with normal activity would have better lung function and exercise performance level when compared to sedentary CDH subjects. We studied 18 children (11 males and 7 females, mean age 6.6\u2009\u00b1\u20092.6 years) who were surgically corrected. All children underwent physical examination, ECG at rest, and a maximal exercise stress test on a treadmill to measure the duration of exercise, maximal heart rate and blood pressure, maximal oxygen uptake (VO(2) \u2009max and VO(2) \u2009ml\/kg\/min). Lung function testing to measure forced vital capacity (FVC), forced expiratory volume in 1\u2009sec (FEV(1) ), and peak expiratory flow (PEF) was also performed. Following the stress test, the Dalhousie dyspnea and effort scale was shown to children as a pictorial panel with three groups of increasing (from 1 to 7) levels of effort perception, throat discomfort, and chest dyspnea. Children were divided into group A (sedentary) and group B (regular physical participation). There was no difference in CDH severity between the two groups. Group A had a statistically significant lower duration of exercise (P\u2009&lt;\u20090.01), maximal oxygen consumption (VO(2) \u2009max P\u2009&lt;\u20090.0001), VO(2) \u2009ml\/kg\/min (P\u2009&lt;\u20090.001), higher throat closing feeling (P\u2009&lt;\u20090.004), chest dyspnea (P\u2009&lt;\u20090.001), and effort perception (P\u2009&lt;\u20090.04) compared to group B. No differences were found in lung function tests. In conclusion, our data may suggest that children with a history of CDH who are active maintain a higher level of performance with less perception of dyspnea and effort.","authors":"Turchetta, A., Fintini, D., Cafiero, G., Calzolari, A., Giordano, U., Cutrera, R., Morini, F., Braguglia, A., Bagolan, P.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Pediatr Pulmonol","volume":"46","issue":"10","page":"1000-6","pdf":null,"JrId":"6398","fulltextlink":null,"preprintlink":null,"articledate":"2012-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520440","title":"Descriptive analysis of central sleep apnea in childhood at a single center.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520440<\/PMID><DateCompleted><Year>2012<\/Year><Month>01<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2011<\/Year><Month>09<\/Month><Day>19<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1099-0496<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>46<\/Volume><Issue>10<\/Issue><PubDate><Year>2011<\/Year><Month>Oct<\/Month><\/PubDate><\/JournalIssue><Title>Pediatric pulmonology<\/Title><ISOAbbreviation>Pediatr Pulmonol<\/ISOAbbreviation><\/Journal><ArticleTitle>Descriptive analysis of central sleep apnea in childhood at a single center.<\/ArticleTitle><Pagination><MedlinePgn>1023-30<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/ppul.21469<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Data on central sleep apnea (CSA) and its significance in children are limited. Our objectives were to describe the polysomnogram (PSG) characteristics and clinical features of children with significant CSA at a single pediatric sleep center.","authors":"Kritzinger, FE., Al-Saleh, S., Narang, I.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Pediatr Pulmonol","volume":"46","issue":"10","page":"1023-30","pdf":null,"JrId":"6398","fulltextlink":null,"preprintlink":null,"articledate":"2012-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21486945","title":"Cdc48\/p97-Ufd1-Npl4 antagonizes Aurora B during chromosome segregation in HeLa cells.","abstract":"During exit from mitosis in Xenopus laevis egg extracts, the AAA+ ATPase Cdc48\/p97 (also known as VCP in vertebrates) and its adapter Ufd1-Npl4 remove the kinase Aurora B from chromatin to allow nucleus formation. Here, we show that in HeLa cells Ufd1-Npl4 already antagonizes Aurora B on chromosomes during earlier mitotic stages and that this is crucial for proper chromosome segregation. Depletion of Ufd1-Npl4 by small interfering RNA (siRNA) caused chromosome alignment and anaphase defects resulting in missegregated chromosomes and multi-lobed nuclei. Ufd1-Npl4 depletion also led to increased levels of Aurora B on prometaphase and metaphase chromosomes. This increase was associated with higher Aurora B activity, as evidenced by the partial resistance of CENP-A phosphorylation to the Aurora B inhibitor hesperadin. Furthermore, low concentrations of hesperadin partially rescued chromosome alignment in Ufd1-depleted cells, whereas, conversely, Ufd1-depletion partially restored congression in the presence of hesperadin. These data establish Cdc48\/p97-Ufd1-Npl4 as a crucial negative regulator of Aurora B early in mitosis of human somatic cells and suggest that the activity of Aurora B on chromosomes needs to be restrained to ensure faithful chromosome segregation.","authors":"Dobrynin, G., Popp, O., Romer, T., Bremer, S., Schmitz, MH., Gerlich, DW., Meyer, H.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Cell Sci","volume":"124","issue":"Pt 9","page":"1571-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520294","title":"XRCC1 and hOGG1 genes and risk of nasopharyngeal carcinoma in North African countries.","abstract":"Although genetic susceptibility to nasopharyngeal carcinoma (NPC) has been recognized for a long time, little is known about the responsible genes. X-Ray repair cross-complementing protein 1 (XRCC1) and human 8-oxo-guanine glycosylase 1 (hOGG1) genes are involved in deoxyribonucleic acid (DNA) repair and were found associated with NPC risk in three Asian case-control studies. The objective of the present study was to test these genes in a sample from North Africa, one of the major NPC endemic regions in the world. Three single nucleotide polymorphisms (SNPs) in the XRCC1 gene and one SNP in the hOGG1 gene were genotyped in 598 NPC cases from Morocco, Algeria, and Tunisia and 545 controls frequency matched by recruitment center, age, sex, and urban\/rural household. The genotype and allelic distributions for the hOGG1 (326)Ser\/Cys SNP and for the XRCC1 (399)Arg\/Trp, (280)Arg\/His, and (194)Arg\/Trp SNPs did not differ significantly among NPC cases and controls. The XRCC1 (194)Trp allele frequency was significantly lower in the North African population than in Asian population (f = 0.04 vs. 0.31 in Cantonese Chinese and 0.21 Han Chinese). The hOGG1 (326)Ser allele frequency was significantly higher in the North African population (f = 0.73) than in Asian populations (f = 0.39 in Taiwanese). The results of the present study obtained from a large sample indicate that the XRCC1 and hOGG1 genes are unlikely to play a role in the susceptibility to NPC in North Africans. Our results do not corroborate those found in Asian population on smaller samples.","authors":"Laantri, N., Jalbout, M., Khyatti, M., Ayoub, WB., Dahmoul, S., Ayad, M., Bedadra, W., Abdoun, M., Mesli, S., Kandil, M., Hamdi-Cherif, M., Boualga, K., Bouaouina, N., Chouchane, L., Benider, A., Ben-Ayed, F., Goldgar, D., Corbex, M.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mol Carcinog","volume":"50","issue":"9","page":"732-7","pdf":null,"JrId":"1399","fulltextlink":null,"preprintlink":null,"articledate":"2011-09-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21520278","title":"Prevalence of small intestinal bacterial overgrowth in Parkinson's disease.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">21520278<\/PMID><DateCompleted><Year>2011<\/Year><Month>08<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2011<\/Year><Month>04<\/Month><Day>26<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1531-8257<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>26<\/Volume><Issue>5<\/Issue><PubDate><Year>2011<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>Movement disorders : official journal of the Movement Disorder Society<\/Title><ISOAbbreviation>Mov Disord<\/ISOAbbreviation><\/Journal><ArticleTitle>Prevalence of small intestinal bacterial overgrowth in Parkinson's disease.<\/ArticleTitle><Pagination><MedlinePgn>889-92<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/mds.23566<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Parkinson's disease (PD) is associated with gastrointestinal motility abnormalities that could favor the occurrence of small intestinal bacterial overgrowth. The aim of the study was to assess the prevalence of small intestinal bacterial overgrowth in PD patients.","authors":"Gabrielli, M., Bonazzi, P., Scarpellini, E., Bendia, E., Lauritano, EC., Fasano, A., Ceravolo, MG., Capecci, M., Rita Bentivoglio, A., Provinciali, L., Tonali, PA., Gasbarrini, A.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Mov Disord","volume":"26","issue":"5","page":"889-92","pdf":null,"JrId":"5937","fulltextlink":null,"preprintlink":null,"articledate":"2011-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21497086","title":"Geminin escapes degradation in G1 of mouse pluripotent cells and mediates the expression of Oct4, Sox2, and Nanog.","abstract":"Geminin is an essential cell-cycle protein that is only present from S phase to early mitosis in metazoan somatic cells. Genetic ablation of geminin in the mouse results in preimplantation embryonic lethality because pluripotent cells fail to form and all cells differentiate to trophoblast. Here we show that geminin is present in G1 phase of mouse pluripotent cells in contrast to somatic cells, where anaphase-promoting complex\/cyclosome (APC\/C)-mediated proteasomal destruction removes geminin in G1. Silencing geminin directly or by depleting the APC\/C inhibitor Emi1 causes loss of stem cell identity and trophoblast differentiation of mouse embryonal carcinoma and embryonic stem cells. Depletion of cyclins A2 or B1 does not induce this effect, even though both of these APC\/C substrates are also present during G1 of pluripotent cells. Crucially, geminin antagonizes the chromatin-remodeling protein Brg1 to maintain expression of Oct4, Sox2, and Nanog. Our results define a pluripotency pathway by which suppressed APC\/C activity protects geminin from degradation in G1, allowing sustained expression of core pluripotency factors. Collectively, these findings link the cell cycle to the pluripotent state but also raise an unexplained paradox: How is cell-cycle progression possible in pluripotent cells when oscillations of key regulatory proteins are lost?","authors":"Yang, VS., Carter, SA., Hyland, SJ., Tachibana-Konwalski, K., Laskey, RA., Gonzalez, MA.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Curr Biol","volume":"21","issue":"8","page":"692-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21490297","title":"Robo-3--mediated repulsive interactions guide R8 axons during Drosophila visual system development.","abstract":"The formation of neuronal connections requires the precise guidance of developing axons toward their targets. In the Drosophila visual system, photoreceptor neurons (R cells) project from the eye into the brain. These cells are grouped into some 750 clusters comprised of eight photoreceptors or R cells each. R cells fall into three classes: R1 to R6, R7, and R8. Posterior R8 cells are the first to project axons into the brain. How these axons select a specific pathway is not known. Here, we used a microarray-based approach to identify genes expressed in R8 neurons as they extend into the brain. We found that Roundabout-3 (Robo3), an axon-guidance receptor, is expressed specifically and transiently in R8 growth cones. In wild-type animals, posterior-most R8 axons extend along a border of glial cells demarcated by the expression of Slit, the secreted ligand of Robo3. In contrast, robo3 mutant R8 axons extend across this border and fasciculate inappropriately with other axon tracts. We demonstrate that either Robo1 or Robo2 rescues the robo3 mutant phenotype when each is knocked into the endogenous robo3 locus separately, indicating that R8 does not require a function unique to the Robo3 paralog. However, persistent expression of Robo3 in R8 disrupts the layer-specific targeting of R8 growth cones. Thus, the transient cell-specific expression of Robo3 plays a crucial role in establishing neural circuits in the Drosophila visual system by selectively regulating pathway choice for posterior-most R8 growth cones.","authors":"Pappu, KS., Morey, M., Nern, A., Spitzweck, B., Dickson, BJ., Zipursky, SL.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Proc Natl Acad Sci U S A","volume":"108","issue":"18","page":"7571-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2011-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27842238","title":"Alternative inflammasome activation enables IL-1\u03b2 release from living cells.","abstract":"Classical modes of NLRP3 activation entail a priming step that enables its activation (signal 1) and a potassium efflux-dependent activation signal (signal 2) that triggers pyroptosome formation and pyroptosis, a lytic cell death necessary for IL-1\u03b2 release. Opposing to that, human monocytes engage an alternative NLRP3 inflammasome pathway in response to LPS that proceeds in the absence of signal 2 activation and enables IL-1\u03b2 secretion without pyroptosis. This specifically relies on Caspase-8 to propagate signaling to NLRP3, leading to inflammasome activation in absence of pyroptosome formation. Here, we summarize the current knowledge about alternative inflammasome activation, discuss potential extensions of this signaling entity beyond LPS-dependent activation, speculate about its role in tissue homeostasis and sterile inflammation and highlight the implications of pyroptosis-independent IL-1\u03b2 secretion.","authors":"Gaidt, MM., Hornung, V.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Curr Opin Immunol","volume":"44","issue":null,"page":"7-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-03-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21482754","title":"Reversible suppression of an essential gene in adult mice using transgenic RNA interference.","abstract":"RNAi has revolutionized loss-of-function genetics by enabling sequence-specific suppression of virtually any gene. Furthermore, tetracycline response elements (TRE) can drive expression of short hairpin RNAs (shRNAs) for inducible and reversible target gene suppression. Here, we demonstrate the feasibility of transgenic inducible RNAi for suppression of essential genes. We set out to directly target cell proliferation by screening an RNAi library against DNA replication factors and identified multiple shRNAs against Replication Protein A, subunit 3 (RPA3). We generated transgenic mice with TRE-driven Rpa3 shRNAs whose expression enforced a reversible cell cycle arrest. In adult mice, the block in cell proliferation caused rapid atrophy of the intestinal epithelium which led to weight loss and lethality within 8-11 d of shRNA induction. Upon shRNA withdrawal, villus atrophy and weight loss were fully reversible. Thus, shRpa3 transgenic mice provide an interesting tool to study tissue maintenance and regeneration. Overall, we have established a robust system that serves the purpose of temperature-sensitive alleles in other model organisms, enabling inducible and reversible suppression of essential genes in a mammalian system.","authors":"McJunkin, K., Mazurek, A., Premsrirut, PK., Zuber, J., Dow, LE., Simon, J., Stillman, B., Lowe, SW.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Proc Natl Acad Sci U S A","volume":"108","issue":"17","page":"7113-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21478888","title":"High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.","abstract":"The binding of some transcription factors has been shown to diverge substantially between closely related species. Here we show that the binding of the developmental transcription factor Twist is highly conserved across six Drosophila species, revealing strong functional constraints at its enhancers. Conserved binding correlates with sequence motifs for Twist and its partners, permitting the de novo discovery of their combinatorial binding. It also includes over 10,000 low-occupancy sites near the detection limit, which tend to mark enhancers of later developmental stages. These results suggest that developmental enhancers can be highly evolutionarily constrained, presumably because of their complex combinatorial nature.","authors":"He, Q., Bardet, AF., Patton, B., Purvis, J., Johnston, J., Paulson, A., Gogol, M., Stark, A., Zeitlinger, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Genet","volume":"43","issue":"5","page":"414-20","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"2011-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21470874","title":"RANKL and RANK in sex hormone-induced breast cancer and breast cancer metastasis.","abstract":"The receptor activator of nuclear factor-\u03baB (RANK) and its ligand RANKL are best known for their essential function in bone remodeling and bone-related pathologies such as osteoporosis and arthritis. In humans, dysregulation of the RANK-RANKL system is the major cause of osteoporosis in postmenopausal women. Furthermore, appropriate RANKL signaling is also required for the formation of a lactating mammary gland. Both RANKL and RANK are expressed by mammary epithelial cells under the control of sex hormones. Recent data also indicate that RANK and RANKL control the preferential metastasis of breast cancer cells to the bone as well as sex hormone-driven primary mammary cancer. Here we critically review these data with special attention on mammary cancer development.","authors":"Schramek, D., Sigl, V., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Trends Endocrinol Metab","volume":"22","issue":"5","page":"188-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21460824","title":"A genome-scale shRNA resource for transgenic RNAi in Drosophila.","abstract":"Existing transgenic RNAi resources in Drosophila melanogaster based on long double-stranded hairpin RNAs are powerful tools for functional studies, but they are ineffective in gene knockdown during oogenesis, an important model system for the study of many biological questions. We show that shRNAs, modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress toward building a genome-wide shRNA resource.","authors":"Ni, JQ., Zhou, R., Czech, B., Liu, LP., Holderbaum, L., Yang-Zhou, D., Shim, HS., Tao, R., Handler, D., Karpowicz, P., Binari, R., Booker, M., Brennecke, J., Perkins, LA., Hannon, GJ., Perrimon, N.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Methods","volume":"8","issue":"5","page":"405-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21445556","title":"RANKL\/RANK-beyond bones.","abstract":"Receptor-activator of NF-\u03baB ligand (TNFSF11, also known as RANKL, OPGL, TRANCE, and ODF) and its tumor necrosis factor (TNF)-family receptor RANK are essential regulators of bone remodeling, lymph node formation, establishment of the thymic microenvironment, mammary gland development during pregnancy, and bone metastasis in cancer. We have recently also reported that the RANKL\/RANK system controls the incidence and onset of sex hormone, progestin-driven breast cancer. RANKL and RANK are also expressed in the central nervous systems where they play an essential role in body temperature regulation. RANKL activates brain regions involved in thermoregulation and induces fever via the COX2-PGE(2)\/EP3R pathway. Moreover, female mice with a RANK gene deleted in neurons and astrocytes exhibit increased basal body temperature, suggesting that the RANKL\/RANK system also controls physiological thermoregulation in females under the control of sex hormones. This review will summarize the recently emerging role of the RANKL\/RANK signaling axis in mammary gland development, cancer metastasis, hormone-derived breast cancer development, and thermal regulation. Furthermore, we will highlight the striking therapeutic potential of this pathway and provide a molecular rationale for consideration of targeting RANKL\/RANK in diseases such as breast cancer.","authors":"Hanada, R., Hanada, T., Sigl, V., Schramek, D., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Mol Med (Berl)","volume":"89","issue":"7","page":"647-56","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21415365","title":"Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners.","abstract":"The maintenance of specific gene expression patterns during cellular proliferation is crucial for the identity of every cell type and the development of tissues in multicellular organisms. Such a cellular memory function is conveyed by the complex interplay of the Polycomb and Trithorax groups of proteins (PcG\/TrxG). These proteins exert their function at the level of chromatin by establishing and maintaining repressed (PcG) and active (TrxG) chromatin domains. Past studies indicated that a core PcG protein complex is potentially associated with cell type or even cell stage-specific sets of accessory proteins. In order to better understand the dynamic aspects underlying PcG composition and function we have established an inducible version of the biotinylation tagging approach to purify Polycomb and associated factors from Drosophila embryos. This system enabled fast and efficient isolation of Polycomb containing complexes under near physiological conditions, thereby preserving substoichiometric interactions. Novel interacting proteins were identified by highly sensitive mass spectrometric analysis. We found many TrxG related proteins, suggesting a previously unrecognized extent of molecular interaction of the two counteracting chromatin regulatory protein groups. Furthermore, our analysis revealed an association of PcG protein complexes with the cohesin complex and showed that Polycomb-dependent silencing of a transgenic reporter depends on cohesin function.","authors":"Str\u00fcbbe, G., Popp, C., Schmidt, A., Pauli, A., Ringrose, L., Beisel, C., Paro, R.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Proc Natl Acad Sci U S A","volume":"108","issue":"14","page":"5572-7","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2011-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21455181","title":"SHARPIN forms a linear ubiquitin ligase complex regulating NF-\u03baB activity and apoptosis.","abstract":"SHARPIN is a ubiquitin-binding and ubiquitin-like-domain-containing protein which, when mutated in mice, results in immune system disorders and multi-organ inflammation. Here we report that SHARPIN functions as a novel component of the linear ubiquitin chain assembly complex (LUBAC) and that the absence of SHARPIN causes dysregulation of NF-\u03baB and apoptotic signalling pathways, explaining the severe phenotypes displayed by chronic proliferative dermatitis (cpdm) in SHARPIN-deficient mice. Upon binding to the LUBAC subunit HOIP (also known as RNF31), SHARPIN stimulates the formation of linear ubiquitin chains in vitro and in vivo. Coexpression of SHARPIN and HOIP promotes linear ubiquitination of NEMO (also known as IKBKG), an adaptor of the I\u03baB kinases (IKKs) and subsequent activation of NF-\u03baB signalling, whereas SHARPIN deficiency in mice causes an impaired activation of the IKK complex and NF-\u03baB in B cells, macrophages and mouse embryonic fibroblasts (MEFs). This effect is further enhanced upon concurrent downregulation of HOIL-1L (also known as RBCK1), another HOIP-binding component of LUBAC. In addition, SHARPIN deficiency leads to rapid cell death upon tumour-necrosis factor \u03b1 (TNF-\u03b1) stimulation via FADD- and caspase-8-dependent pathways. SHARPIN thus activates NF-\u03baB and inhibits apoptosis via distinct pathways in vivo.","authors":"Ikeda, F., Deribe, YL., Sk\u00e5nland, SS., Stieglitz, B., Grabbe, C., Franz-Wachtel, M., van Wijk, SJ., Goswami, P., Nagy, V., Terzic, J., Tokunaga, F., Androulidaki, A., Nakagawa, T., Pasparakis, M., Iwai, K., Sundberg, JP., Schaefer, L., Rittinger, K., Macek, B., Dikic, I.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nature","volume":"471","issue":"7340","page":"637-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-05-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21402940","title":"Receptor activator of NF-kappaB (RANK) stimulates the proliferation of epithelial cells of the epidermo-pilosebaceous unit.","abstract":"Receptor activator of NF-\u03baB (RANK), known for controlling bone mass, has been recognized for its role in epithelial cell activation of the mammary gland. Because bone and the epidermo-pilosebaceous unit of the skin share a lifelong renewal activity where similar molecular players operate, and because mammary glands and hair follicles are both skin appendages, we have addressed the function of RANK in the hair follicle and the epidermis. Here, we show that mice deficient in RANK ligand (RANKL) are unable to initiate a new growth phase of the hair cycle and display arrested epidermal homeostasis. However, transgenic mice overexpressing RANK in the hair follicle or administration of recombinant RANKL both activate the hair cycle and epidermal growth. RANK is expressed by the hair follicle germ and bulge stem cells and the epidermal basal cells, cell types implicated in the renewal of the epidermo-pilosebaceous unit. RANK signaling is dispensable for the formation of the stem cell compartment and the inductive hair follicle mesenchyme, and the hair cycle can be rescued by Rankl knockout skin transplantation onto nude mice. RANKL is actively transcribed by the hair follicle at initiation of its growth phase, providing a mechanism for stem cell RANK engagement and hair-cycle entry. Thus, RANK-RANKL regulates hair renewal and epidermal homeostasis and provides a link between these two activities.","authors":"Duheron, V., Hess, E., Duval, M., Decossas, M., Castaneda, B., Kl\u00f6pper, JE., Amoasii, L., Barbaroux, JB., Williams, IR., Yagita, H., Penninger, J., Choi, Y., L\u00e9zot, F., Groves, R., Paus, R., Mueller, CG.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Proc Natl Acad Sci U S A","volume":"108","issue":"13","page":"5342-7","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21388192","title":"Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides.","abstract":"Currently, unbiased protein identification is mostly performed by directly coupling reversed-phase liquid chromatography (RPLC) via electrospray ionization to a mass spectrometer. In contrast to the innovations in mass spectrometric instrumentation, cutting-edge technology in RPLC has generally not been well adopted. Here, we describe the effects of increased peak capacities on the number of identified proteins and peptides in complex mixtures utilizing collision-induced dissociation on an LTQ-Orbitrap Velos, providing a rationale for using advanced RPLC technology in LC-MS\/MS. Using two different column lengths and gradient times between 1 and 10 h, we found a linear relation between the obtained peak capacities and the number of identified peptides. We identified on average 2516 proteins in the tryptic digest of 1 \u03bcg of HeLa lysate using an 8 h gradient on a 50 cm column packed with 2 \u03bcm C18 reversed-phase chromatographic material.","authors":"K\u00f6cher, T., Swart, R., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Anal Chem","volume":"83","issue":"7","page":"2699-704","pdf":null,"JrId":"519","fulltextlink":null,"preprintlink":null,"articledate":"2011-07-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21383769","title":"Reinforcement of cancer immunotherapy by adoptive transfer of cblb-deficient CD8+ T cells combined with a DC vaccine.","abstract":"The success of cancer immunotherapy is limited by potent endogenous immune-evasion mechanisms, which are at least in part mediated by transforming growth factor-\u03b2 (TGF-\u03b2). The E3 ubiquitin ligase Cbl-b is a key regulator of T cell activation and is established to regulate TGF-\u03b2 sensitivity. cblb-deficient animals reject tumors via CD8(+) T cells, which make Cbl-b an ideal target for improvement of adoptive T-cell transfer (ATC) therapy. In this study, we show that cblb-deficient CD8(+) T cells are hyper-responsive to T-cell receptor (TCR)\/CD28-stimulation and are in part protected against the negative cues induced by TGF-\u03b2 in vitro. Notably, adoptive transfer of polyclonal, non-TCR transgenic cblb-deficient CD8(+) T cells is not sufficient to reject B16-ova or EG7 tumors in vivo. Thus, cblb-deficient ATC requires proper in vivo re-activation by a dendritic cell (DC) vaccine. In strict contrast to ATC monotherapy, this approach delayed tumor outgrowth and significantly increased survival rates, which is paralleled by increased CD8(+) T-cells infiltration to the tumor site and enrichment of ova-specific and interferon-\u03b3 (IFN-\u03b3)-secreting CD8(+) T cell in the draining lymph node (LN). Moreover, CD8(+) T cells from cblb-deficient mice vaccinated with the DC vaccine show increased cytolytic activity in vivo. In summary, our data using cblb-deficient polyclonal, non-TCR-transgenic adoptively transferred CD8(+) T cells into immuno-competent non-lymphodepleted recipients suggest that targeting Cbl-b might serve as a novel 'adjuvant approach', suitable to augment the effectiveness of established anti-cancer immunotherapies.","authors":"Lutz-Nicoladoni, C., Wallner, S., Stoitzner, P., Pircher, M., Gruber, T., Wolf, AM., Gastl, G., Penninger, JM., Baier, G., Wolf, D.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Immunol Cell Biol","volume":"90","issue":"1","page":"130-4","pdf":null,"JrId":"4179","fulltextlink":null,"preprintlink":null,"articledate":"2012-06-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36595951","title":"Protocol for SARS-CoV-2 infection of kidney organoids derived from human pluripotent stem cells.","abstract":"This protocol presents the use of SARS-CoV-2 isolates to infect human kidney organoids, enabling exploration of the impact of SARS-CoV-2 infection in a human multicellular in&#xa0;vitro system. We detail steps to generate kidney organoids from human pluripotent stem cells (hPSCs) and emulate a diabetic milieu via organoids exposure to diabetogenic-like cell culture conditions. We further describe preparation and titration steps of SARS-CoV-2 virus stocks, their subsequent use to infect the kidney organoids, and assessment of the infection via immunofluorescence. For complete details on the use and execution of this protocol, please refer to Garreta et&#xa0;al. (2022).<sup>1<\/sup>.","authors":"Garreta, E., Moya-Rull, D., Stanifer, ML., Monteil, V., Prado, P., Marco, A., Tarantino, C., Gallo, M., Jonsson, G., Hagelkruys, A., Mirazimi, A., Boulant, S., Penninger, JM., Montserrat, N.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"STAR Protoc","volume":"3","issue":"4","page":"101872","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21307874","title":"Essential role of the keratinocyte-specific endonuclease DNase1L2 in the removal of nuclear DNA from hair and nails.","abstract":"Degradation of nuclear DNA is a hallmark of programmed cell death. Epidermal keratinocytes die in the course of cornification to function as the dead building blocks of the cornified layer of the epidermis, nails, and hair. Here, we investigated the mechanism and physiological function of DNA degradation during cornification in vivo. Targeted deletion of the keratinocyte-specific endonuclease DNase1-like 2 (DNase1L2) in the mouse resulted in the aberrant retention of DNA in hair and nails, as well as in epithelia of the tongue and the esophagus. In contrast to our previous studies in human keratinocytes, ablation of DNase1L2 did not compromise the cornified layer of the epidermis. Quantitative PCRs showed that the amount of nuclear DNA was dramatically increased in both hair and nails, and that mitochondrial DNA was increased in the nails of DNase1L2-deficient mice. The presence of nuclear DNA disturbed the normal arrangement of structural proteins in hair corneocytes and caused a significant decrease in the resistance of hair to mechanical stress. These data identify DNase1L2 as an essential and specific regulator of programmed cell death in skin appendages, and demonstrate that the breakdown of nuclear DNA is crucial for establishing the full mechanical stability of hair.","authors":"Fischer, H., Szabo, S., Scherz, J., Jaeger, K., Rossiter, H., Buchberger, M., Ghannadan, M., Hermann, M., Theussl, HC., Tobin, DJ., Wagner, EF., Tschachler, E., Eckhart, L.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Invest Dermatol","volume":"131","issue":"6","page":"1208-15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21305683","title":"Improving FRET-based monitoring of single chemomechanical rotary motors at work.","abstract":"Protein dynamics are observable in real time using internal distance measurements of reference positions. Based on F\u00f6rster resonance energy transfer (FRET) as the distance ruler between two fluorescent markers, investigations of single molecules one at a time have modified our views of protein conformational changes. X-ray crystallography provides trapped conformations at atomic resolution and NMR can add information about flexible parts of proteins, but the pathways between these structures including unknown conformations are often not directly accessible. Especially for membrane enzymes comprising multiple subunits, limited structural information requires alternative experimental methods to follow conformational pathways. Herein we summarize the knowledge gathered from single-molecule FRET studies of the membrane-embedded rotary nanomotor F(o)F(1)-ATP synthase. In addition, new ideas and concepts to shift and extend the current limitations of the confocal FRET detection approach using freely diffusing, liposome-reconstituted, individual enzymes are discussed: nanodiamonds as new fluorophores, optimized laser excitation schemes, Hidden Markov Models for software-based FRET trajectory analysis, and application of the anti-Brownian electrokinetic trap (ABELtrap) to keep the single enzyme in focus.","authors":"B\u00f6rsch, M., Wrachtrup, J.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Chemphyschem","volume":"12","issue":"3","page":"542-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-08-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21303690","title":"Modification of the conformational skin structure by treatment with liposomal formulations and its correlation to the penetration depth of aciclovir.","abstract":"The stratum corneum (SC), top layer of the epidermis, is comprised mostly of lipids that are responsible for the permeability properties of the SC and which protect the body from external agents. Changes in these skin microconstituents can be understood by instrumental methods such as attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy. The present work shows that different types of analyzed skin, dermatomed abdominal porcine skin, pig ear skin, and human heat separated skin, influenced both the shape and the intensity of recorded spectra. The typical FTIR spectral bands of the conformation of the lipid aliphatic chains in the skin samples were altered after treatment with pure DPPC liposomes and chitosan (CS) coated DPPC liposomes, but not with aqueous CS-solution. The conformational change could be the reason for the variable permeability of the skin. This was confirmed by tape stripping on pig ear skin (imitating in vivo studies): the amount of aciclovir penetrating from polymer coated and polymer free liposomes was significantly higher under the skin surface in comparison with the aqueous CS-solution. Moreover, the addition of the polymer to liposomes induced a higher skin penetration than pure liposomes. One explanation might be the CS's stronger adhesion to the skin.","authors":"Hasanovic, A., Winkler, R., Resch, GP., Valenta, C.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Eur J Pharm Biopharm","volume":"79","issue":"1","page":"76-81","pdf":null,"JrId":"21026","fulltextlink":null,"preprintlink":null,"articledate":"2012-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21297619","title":"Flybow: genetic multicolor cell labeling for neural circuit analysis in Drosophila melanogaster.","abstract":"To facilitate studies of neural network architecture and formation, we generated three Drosophila melanogaster variants of the mouse Brainbow-2 system, called Flybow. Sequences encoding different membrane-tethered fluorescent proteins were arranged in pairs within cassettes flanked by recombination sites. Flybow combines the Gal4-upstream activating sequence binary system to regulate transgene expression and an inducible modified Flp-FRT system to drive inversions and excisions of cassettes. This provides spatial and temporal control over the stochastic expression of one of two or four reporters within one sample. Using the visual system, the embryonic nervous system and the wing imaginal disc, we show that Flybow in conjunction with specific Gal4 drivers can be used to visualize cell morphology with high resolution. Finally, we demonstrate that this labeling approach is compatible with available Flp-FRT-based techniques, such as mosaic analysis with a repressible cell marker; this could further support the genetic analysis of neural circuit assembly and function.","authors":"Hadjieconomou, D., Rotkopf, S., Alexandre, C., Bell, DM., Dickson, BJ., Salecker, I.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nat Methods","volume":"8","issue":"3","page":"260-6","pdf":null,"JrId":"32338","fulltextlink":null,"preprintlink":null,"articledate":"2011-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11714830","title":"Involvement of phosphoinositide 3-kinases in neutrophil activation and the development of acute lung injury.","abstract":"Activated neutrophils contribute to the development and severity of acute lung injury (ALI). Phosphoinositide 3-kinases (PI3-K) and the downstream serine\/threonine kinase Akt\/protein kinase B have a central role in modulating neutrophil function, including respiratory burst, chemotaxis, and apoptosis. In the present study, we found that exposure of neutrophils to endotoxin resulted in phosphorylation of Akt, activation of NF-kappaB, and expression of the proinflammatory cytokines IL-1beta and TNF-alpha through PI3-K-dependent pathways. In vivo, endotoxin administration to mice resulted in activation of PI3-K and Akt in neutrophils that accumulated in the lungs. The severity of endotoxemia-induced ALI was significantly diminished in mice lacking the p110gamma catalytic subunit of PI3-K. In PI3-Kgamma(-\/-) mice, lung edema, neutrophil recruitment, nuclear translocation of NF-kappaB, and pulmonary levels of IL-1beta and TNF-alpha were significantly lower after endotoxemia as compared with PI3-Kgamma(+\/+) controls. Among neutrophils that did accumulate in the lungs of the PI3-Kgamma(-\/-) mice after endotoxin administration, activation of NF-kappaB and expression of proinflammatory cytokines was diminished compared with levels present in lung neutrophils from PI3-Kgamma(+\/+) mice. These results show that PI3-K, and particularly PI3-Kgamma, occupies a central position in regulating endotoxin-induced neutrophil activation, including that involved in ALI.","authors":"Yum, HK., Arcaroli, J., Kupfner, J., Shenkar, R., Penninger, JM., Sasaki, T., Yang, KY., Park, JS., Abraham, E.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Immunol","volume":"167","issue":"11","page":"6601-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2002-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21275378","title":"Improved precision of iTRAQ and TMT quantification by an axial extraction field in an Orbitrap HCD cell.","abstract":"Improving analytical precision is a major goal in quantitative differential proteomics as high precision ensures low numbers of outliers, a source of false positives with regard to quantification. In addition, higher precision increases statistical power, i.e., the probability to detect significant differences. With chemical labeling using isobaric tags for relative and absolute quantitation (iTRAQ) or tandem mass tag (TMT) reagents, quantification is based on the extraction of reporter ions from tandem mass spectrometry (MS\/MS) spectra. We compared the performance of two versions of the LTQ Orbitrap higher energy collisional dissociation (HCD) cell with and without an axial electric field with regard to reporter ion quantification. The HCD cell with the axial electric field was designed to push fragment ions into the C-trap and this version is mounted in current Orbitrap XL ETD and Orbitrap Velos instruments. Our goal was to evaluate whether the purported improvement in ion transmission had a measurable impact on the precision of MS\/MS based quantification using peptide labeling with isobaric tags. We show that the axial electric field led to an increased percentage of HCD spectra in which the complete set of reporter ions was detected and, even more important, to a reduction in overall variance, i.e., improved analytical precision of the acquired data. Notably, adequate precision of HCD-based quantification was maintained even for low precursor ion intensities of a complex biological sample. These findings may help researchers in their design of quantitative proteomics studies using isobaric tags and establish HCD-based quantification on the LTQ Orbitrap as a highly precise approach in quantitative proteomics.","authors":"Pichler, P., K\u00f6cher, T., Holzmann, J., M\u00f6hring, T., Ammerer, G., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Anal Chem","volume":"83","issue":"4","page":"1469-74","pdf":null,"JrId":"519","fulltextlink":null,"preprintlink":null,"articledate":"2011-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21262518","title":"Entry of a heparan sulphate-binding HRV8 variant strictly depends on dynamin but not on clathrin, caveolin, and flotillin.","abstract":"The major group human rhinovirus type 8 can enter cells via heparan sulphate. When internalized into ICAM-1 negative rhabdomyosarcoma (RD) cells, HRV8 accumulated in the cells but caused CPE only after 3 days when used at high MOI. Adaptation by three blind passages alternating between RD and HeLa cells resulted in variant HRV8v with decreased stability at acidic pH allowing for productive infection in the absence of ICAM-1. HRV8v produced CPE at 10 times lower MOI within 1 day. Confocal fluorescence microscopy colocalization and the use of pharmacological and dominant negative inhibitors revealed that viral uptake is clathrin, caveolin, and flotillin independent. However, it is blocked by dynasore, amiloride, and EIPA. Furthermore, HRV8v induced FITC-dextran uptake and colocalized with this fluid phase marker. Except for the complete inhibition by dynasore, the entry pathway of HRV8v via HS is similar to that of HRV14 in RD cells that overexpress ICAM-1.","authors":"Khan, AG., Pickl-Herk, A., Gajdzik, L., Marlovits, TC., Fuchs, R., Blaas, D.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Virology","volume":"412","issue":"1","page":"55-67","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"2011-05-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21236263","title":"Augmenting \u03b2-augmentation: structural basis of how BamB binds BamA and may support folding of outer membrane proteins.","abstract":"\u03b2-Barrel proteins are frequently found in the outer membrane of mitochondria, chloroplasts and Gram-negative bacteria. In Escherichia coli, these proteins are inserted in the outer membrane by the Bam (\u03b2-barrel assembly machinery) complex, a multiprotein machinery formed by the \u03b2-barrel protein BamA and the four peripheral membrane proteins BamB, BamC, BamD and BamE. The periplasmic part of BamA binds prefolded \u03b2-barrel proteins by a \u03b2-augmentation mechanism, thereby stabilizing the precursors prior to their membrane insertion. However, the role of the associated proteins within the Bam complex remains unknown. Here, we describe the crystal structure of BamB, a nonessential component of the Bam complex. The structure shows a typical eight-bladed \u03b2-propeller fold. Two sequence stretches of BamB were previously identified to be important for interaction with BamA. In our structure, both motifs are located in close proximity to each other and contribute to a conserved region forming a narrow groove on the top of the propeller. Moreover, crystal contacts reveal two interaction modes of how BamB might bind unfolded \u03b2-barrel proteins. In the crystal lattice, BamB binds to exposed \u03b2-strands by \u03b2-augmentation, whereas peptide stretches rich in aromatic residues can be accommodated in hydrophobic pockets located at the bottom of the propeller. Thus, BamB could simultaneously bind to BamA and prefolded \u03b2-barrel proteins, thereby enhancing the folding and membrane insertion capability of the Bam complex.","authors":"Heuck, A., Schleiffer, A., Clausen, T.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J Mol Biol","volume":"406","issue":"5","page":"659-66","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2011-04-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21189404","title":"Prevention of angiotensin II-mediated renal oxidative stress, inflammation, and fibrosis by angiotensin-converting enzyme 2.","abstract":"Angiotensin-converting enzyme 2 (ACE2) is a monocarboxypeptidase capable of metabolizing angiotensin (Ang) II into Ang 1 to 7. We hypothesized that ACE2 is a negative regulator of Ang II signaling and its adverse effects on the kidneys. Ang II infusion (1.5 mg\/kg\u207b\u00b9\/d\u207b\u00b9) for 4 days resulted in higher renal Ang II levels and increased nicotinamide adenine dinucleotide phosphate oxidase activity in ACE2 knockout (Ace2(-\/y)) mice compared to wild-type mice. Expression of proinflammatory cytokines, interleukin-1\u03b2 and chemokine (C-C motif) ligand 5, were increased in association with greater activation of extracellular-regulated kinase 1\/2 and increase of protein kinase C-\u03b1 levels. These changes were associated with increased expression of fibrosis-associated genes (\u03b1-smooth muscle actin, transforming growth factor-\u03b2, procollagen type I\u03b11) and increased protein levels of collagen I with histological evidence of increased tubulointerstitial fibrosis. Ang II-infused wild-type mice were then treated with recombinant human ACE2 (2 mg\/kg\u207b\u00b9\/d\u207b\u00b9, intraperitoneal). Daily treatment with recombinant human ACE2 reduced Ang II-induced pressor response and normalized renal Ang II levels and oxidative stress. These changes were associated with a suppression of Ang II-mediated activation of extracellular-regulated kinase 1\/2 and protein kinase C pathway and Ang II-mediated renal fibrosis and T-lymphocyte-mediated inflammation. We conclude that loss of ACE2 enhances renal Ang II levels and Ang II-induced renal oxidative stress, resulting in greater renal injury, whereas recombinant human ACE2 prevents Ang II-induced hypertension, renal oxidative stress, and tubulointerstitial fibrosis. ACE2 is an important negative regulator of Ang II-induced renal disease and enhancing ACE2 action may have therapeutic potential for patients with kidney disease.","authors":"Zhong, J., Guo, D., Chen, CB., Wang, W., Schuster, M., Loibner, H., Penninger, JM., Scholey, JW., Kassiri, Z., Oudit, GY.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Hypertension","volume":"57","issue":"2","page":"314-22","pdf":null,"JrId":"4217","fulltextlink":null,"preprintlink":null,"articledate":"2011-04-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7760809","title":"Cell cycle-regulated transcription of the CLB2 gene is dependent on Mcm1 and a ternary complex factor.","abstract":"Clb2 is the major B-type mitotic cyclin required for entry into mitosis in the budding yeast Saccharomyces cerevisiae. We showed that accumulation of CLB2 transcripts in G2 cells is controlled at the transcriptional level and identified a 55-bp upstream activating sequence (UAS) containing an Mcm1 binding site as being necessary and sufficient for cell cycle regulation. Sequences within the cell cycle-regulated UAS were shown to bind Mcm1 in vitro, and mutation which abolished Mcm1-dependent DNA binding activity eliminated cell cycle-regulated transcription in vivo. A second protein with no autonomous DNA binding activity was also recruited into Mcm1-UAS complexes, generating a ternary complex. A point mutation in the CLB2 UAS which blocked ternary complex formation, but still allowed Mcm1 to bind, resulted in loss of cell cycle regulation in vivo, suggesting that the ternary complex factor is also important in control of CLB2 transcription. We discuss the possibility that the CLB2 gene is coregulated with other genes known to be regulated with the same periodicity and suggest that Mcm1 and the ternary complex factor may coordinately regulate several other G2-regulated transcripts.","authors":"Maher, M., Cong, F., Kindelberger, D., Nasmyth, K., Dalton, S.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Mol Cell Biol","volume":"15","issue":"6","page":"3129-37","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21136591","title":"Proteomic analysis of the outer membrane of Protochlamydia amoebophila elementary bodies.","abstract":"Chlamydiae are obligate intracellular bacteria, comprising some of the most important bacterial pathogens of animals and humans. During their unique developmental cycle they have to attach to and enter their eukaryotic host cells, a process mediated by proteins in the chlamydial outer membrane. So far the only experimental data for chlamydial outer membrane proteins are available from members of the Chlamydiaceae, a family comprising exclusively human and animal pathogens. To get further insights into the evolution of the protein composition of the chlamydial outer membrane and into host-dependent differences, we performed an extensive experimental analysis of outer membrane fractions of Protochlamydia amoebophila elementary bodies, which constitute the infectious form of this non-pathogenic member of the Chlamydiae that thrives as a symbiont in Acanthamoeba spp. We used 1-D and 2-DE in combination with MALDI-TOF, MALDI-TOF\/TOF and nanoLC-ESI-MS\/MS, and compared our experimental results with a previously published in silico analysis of chlamydial outer membrane proteins. This resulted in the identification of 38 proteins supported by both studies and therefore very likely to be located in the P. amoebophila outer membrane. The obtained experimental data provide the first comprehensive overview of outer membrane proteins of a chlamydial organism outside the Chlamydiaceae. They reveal both fundamental differences and convergent evolution between pathogenic and symbiotic chlamydiae.","authors":"Heinz, E., Pichler, P., Heinz, C., Op den Camp, HJ., Toenshoff, ER., Ammerer, G., Mechtler, K., Wagner, M., Horn, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proteomics","volume":"10","issue":"24","page":"4363-76","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21119595","title":"Functions of Fos phosphorylation in bone homeostasis, cytokine response and tumourigenesis.","abstract":"Mice lacking c-fos develop osteopetrosis due to a block in osteoclast differentiation. Carboxy-terminal phosphorylation of Fos on serine 374 by ERK1\/2 and serine 362 by RSK1\/2 regulates Fos stability and transactivation potential in vitro. To assess the physiological relevance of Fos phosphorylation in vivo, serine 362 and\/or serine 374 was replaced by alanine (Fos362A, Fos374A and FosAA) or by phospho-mimetic aspartic acid (FosDD). Homozygous mutants were healthy and skeletogenesis was largely unaffected. Fos C-terminal phosphorylation, predominantly on serine 374, was found important for osteoclast differentiation in vitro and affected lipopolysaccharide (LPS)-induced cytokine response in vitro and in vivo. Importantly, skin papilloma development was delayed in FosAA, Fos362A and Rsk2-deficient mice, accelerated in FosDD mice and unaffected in Fos374A mutants. Furthermore, the related Fos protein and putative RSK2 target Fra1 failed to substitute for Fos in papilloma development. This indicates that phosphorylation of serines 362 and 374 exerts context-dependent roles in modulating Fos activity in vivo. Inhibition of Fos C-terminal phosphorylation on serine 362 by targeting RSK2 might be of therapeutic relevance for skin tumours.","authors":"Bakiri, L., Reschke, MO., Gefroh, HA., Idarraga, MH., Polzer, K., Zenz, R., Schett, G., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Oncogene","volume":"30","issue":"13","page":"1506-17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21113133","title":"RNAi-based screening identifies the Mms22L-Nfkbil2 complex as a novel regulator of DNA replication in human cells.","abstract":"Cullin 4 (Cul4)-based ubiquitin ligases emerged as critical regulators of DNA replication and repair. Over 50 Cul4-specific adaptors (DNA damage-binding 1 (Ddb1)-Cul4-associated factors; DCAFs) have been identified and are thought to assemble functionally distinct Cul4 complexes. Using a live-cell imaging-based RNAi screen, we analysed the function of DCAFs and Cul4-linked proteins, and identified specific subsets required for progression through G1 and S phase. We discovered C6orf167\/Mms22-like protein (Mms22L) as a putative human orthologue of budding yeast Mms22, which, together with cullin Rtt101, regulates genome stability by promoting DNA replication through natural pause sites and damaged templates. Loss of Mms22L function in human cells results in S phase-dependent genomic instability characterised by spontaneous double-strand breaks and DNA damage checkpoint activation. Unlike yeast Mms22, human Mms22L does not stably bind to Cul4, but is degraded in a Cul4-dependent manner and upon replication stress. Mms22L physically and functionally interacts with the scaffold-like protein Nfkbil2 that co-purifies with histones, several chromatin remodelling and DNA replication\/repair factors. Together, our results strongly suggest that the Mms22L-Nfkbil2 complex contributes to genome stability by regulating the chromatin state at stalled replication forks.","authors":"Piwko, W., Olma, MH., Held, M., Bianco, JN., Pedrioli, PG., Hofmann, K., Pasero, P., Gerlich, DW., Peter, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"EMBO J","volume":"29","issue":"24","page":"4210-22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21092738","title":"PI3K mediated electrotaxis of embryonic and adult neural progenitor cells in the presence of growth factors.","abstract":"Correct guidance of the migration of neural progenitor cells (NPCs) is essential for the development and repair of the central nervous system (CNS). Electric field (EF)-guided migration, electrotaxis, has been observed in many cell types. We report here that, in applied EFs of physiological magnitude, embryonic and adult NPCs show marked electrotaxis, which is dependent on the PI3K\/Akt pathway. The electrotaxis was also evidenced by ex vivo investigation that transplanted NPCs migrated directionally towards cathode in organotypic spinal cord slice model when treated with EFs. Genetic disruption or pharmacological inhibition of phosphoinositide 3-kinase (PI3K) impaired electrotaxis, whereas EF exposure increased Akt phosphorylation in a growth factor-dependent manner and increased phosphatidylinositol-3,4,5-trisphosphate (PIP3) levels. EF treatments also induced asymmetric redistribution of PIP3, growth factor receptors, and actin cytoskeleton. Electrotaxis in both embryonic and adult NPCs requires epidermal growth factor (EGF) and fibroblast growth factor (FGF). Our results demonstrate the importance of the PI3K\/Akt pathway in directed migration of NPCs driven by EFs and growth factors and highlight the potential of EFs to enhance the guidance of various NPC populations in CNS repair therapies.","authors":"Meng, X., Arocena, M., Penninger, J., Gage, FH., Zhao, M., Song, B.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Exp Neurol","volume":"227","issue":"1","page":"210-7","pdf":null,"JrId":"3660","fulltextlink":null,"preprintlink":null,"articledate":"2011-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11590065","title":"Ubiquitylation in plants: a post-genomic look at a post-translational modification.","abstract":"In this article, we summarize Arabidopsis genes encoding ubiquitin, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzymes (E2s) and an additional selected set of proteins related to ubiquitylation. We emphasize comparisons to components from Saccharomyces cerevisiae, with occasional reference to animals. Among the E1 and E2s, Arabidopsis usually has two to four probable orthologs to one yeast gene. Also, Arabidopsis has genes with no likely ortholog in yeast, although they often have potential orthologs in animals. The large number of components with known function in ubiquitylation indicates that this process plays a complex role in cellular physiology.","authors":"Bachmair, A., Novatchkova, M., Potuschak, T., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Trends Plant Sci","volume":"6","issue":"10","page":"463-70","pdf":null,"JrId":"20950","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21080497","title":"Proteomic analysis of endosomes from genetically modified p14\/MP1 mouse embryonic fibroblasts.","abstract":"The p14\/MP1 scaffold complex binds MEK1 and ERK1\/2 on late endosomes, thus regulating the strength, duration and intracellular location of MAPK signaling. By organelle proteomics we have compared the protein composition of endosomes purified from genetically modified p14\u207b\/\u207b, p14+\/\u207b and p14(rev) mouse embryonic fibroblasts. The latter ones were reconstituted retrovirally from p14\u207b\/\u207b mouse embryonic fibroblasts by reexpression of pEGFP-p14 at equimolar ratios with its physiological binding partner MP1, as shown here by absolute quantification of MP1 and p14 proteins on endosomes by quantitative MS using the Equimolarity through Equalizer Peptide strategy. A combination of subcellular fractionation, 2-D DIGE and MALDI-TOF\/TOF MS revealed 31 proteins differentially regulated in p14\u207b\/\u207b organelles, which were rescued by reexpression of pEGFP-p14 in p14\u207b\/\u207b endosomes. Regulated proteins are known to be involved in actin remodeling, endosomal signal transduction and trafficking. Identified proteins and their in silico interaction networks suggested that endosomal signaling might regulate such major cellular functions such as proliferation, differentiation, migration and survival.","authors":"Stasyk, T., Holzmann, J., Stumberger, S., Ebner, HL., Hess, MW., Bonn, GK., Mechtler, K., Huber, LA.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proteomics","volume":"10","issue":"22","page":"4117-27","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2011-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"21041996","title":"The role of Tuba1a in adult hippocampal neurogenesis and the formation of the dentate gyrus.","abstract":"The multitubulin hypothesis holds that each tubulin isotype serves a unique role with respect to microtubule function. Here we investigate the role of the \u03b1-tubulin subunit Tuba1a in adult hippocampal neurogenesis and the formation of the dentate gyrus. Employing birth date labelling and immunohistological markers, we show that mice harbouring an S140G mutation in Tuba1a present with normal neurogenic potential, but that this neurogenesis is often ectopic. Morphological analysis of the dentate gyrus in adulthood revealed a disorganised subgranular zone and a dispersed granule cell layer. We have shown that these anatomical abnormalities are due to defective migration of prospero-homeobox-1-positive neurons and T-box-brain-2-positive progenitors during development. Such migratory defects may also be responsible for the cytoarchitectural defects observed in the dentate gyrus of patients with mutations in TUBA1A.","authors":"Keays, DA., Cleak, J., Huang, GJ., Edwards, A., Braun, A., Treiber, CD., Pidsley, R., Flint, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Dev Neurosci","volume":"32","issue":"4","page":"268-77","pdf":null,"JrId":"3455","fulltextlink":null,"preprintlink":null,"articledate":"2011-03-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20971813","title":"Rec8-containing cohesin maintains bivalents without turnover during the growing phase of mouse oocytes.","abstract":"During female meiosis, bivalent chromosomes are thought to be held together from birth until ovulation by sister chromatid cohesion mediated by cohesin complexes whose ring structure depends on kleisin subunits, either Rec8 or Scc1. Because cohesion is established at DNA replication in the embryo, its maintenance for such a long time may require cohesin turnover. To address whether Rec8- or Scc1-containing cohesin holds bivalents together and whether it turns over, we created mice whose kleisin subunits can be cleaved by TEV protease. We show by microinjection experiments and confocal live-cell imaging that Rec8 cleavage triggers chiasmata resolution during meiosis I and sister centromere disjunction during meiosis II, while Scc1 cleavage triggers sister chromatid disjunction in the first embryonic mitosis, demonstrating a dramatic transition from Rec8- to Scc1-containing cohesin at fertilization. Crucially, activation of an ectopic Rec8 transgene during the growing phase of Rec8(TEV)(\/TEV) oocytes does not prevent TEV-mediated bivalent destruction, implying little or no cohesin turnover for \u22652 wk during oocyte growth. We suggest that the inability of oocytes to regenerate cohesion may contribute to age-related meiosis I errors.","authors":"Tachibana-Konwalski, K., Godwin, J., van der Weyden, L., Champion, L., Kudo, NR., Adams, DJ., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Genes Dev","volume":"24","issue":"22","page":"2505-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20971646","title":"Protein kinases: evolution of dynamic regulatory proteins.","abstract":"Eukayotic protein kinases evolved as a family of highly dynamic molecules with strictly organized internal architecture. A single hydrophobic F-helix serves as a central scaffold for assembly of the entire molecule. Two non-consecutive hydrophobic structures termed \"spines\" anchor all the elements important for catalysis to the F-helix. They make firm, but flexible, connections within the molecule, providing a high level of internal dynamics of the protein kinase. During the course of evolution, protein kinases developed a universal regulatory mechanism associated with a large activation segment that can be dynamically folded and unfolded in the course of cell functioning. Protein kinases thus represent a unique, highly dynamic, and precisely regulated set of switches that control most biological events in eukaryotic cells.","authors":"Taylor, SS., Kornev, AP.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Trends Biochem Sci","volume":"36","issue":"2","page":"65-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-04-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20929728","title":"Mcl-1 is essential for germinal center formation and B cell memory.","abstract":"Lymphocyte survival during immune responses is controlled by the relative expression of pro- and anti-apoptotic molecules, regulating the magnitude, quality, and duration of the response. We investigated the consequences of deleting genes encoding the anti-apoptotic molecules Mcl1 and Bcl2l1 (Bcl-x(L)) from B cells using an inducible system synchronized with expression of activation-induced cytidine deaminase (Aicda) after immunization. This revealed Mcl1 and not Bcl2l1 to be indispensable for the formation and persistence of germinal centers (GCs). Limiting Mcl1 expression reduced the magnitude of the GC response with an equivalent, but not greater, effect on memory B cell formation and no effect on persistence. Our results identify Mcl1 as the main anti-apoptotic regulator of activated B cell survival and suggest distinct mechanisms controlling survival of GC and memory B cells.","authors":"Vikstrom, I., Carotta, S., L\u00fcthje, K., Peperzak, V., Jost, PJ., Glaser, S., Busslinger, M., Bouillet, P., Strasser, A., Nutt, SL., Tarlinton, DM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Science","volume":"330","issue":"6007","page":"1095-9","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20818334","title":"An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila.","abstract":"In Drosophila, PIWI proteins and bound PIWI-interacting RNAs (piRNAs) form the core of a small RNA-mediated defense system against selfish genetic elements. Within germline cells, piRNAs are processed from piRNA clusters and transposons to be loaded into Piwi\/Aubergine\/AGO3 and a subset of piRNAs undergoes target-dependent amplification. In contrast, gonadal somatic support cells express only Piwi, lack signs of piRNA amplification and exhibit primary piRNA biogenesis from piRNA clusters. Neither piRNA processing\/loading nor Piwi-mediated target silencing is understood at the genetic, cellular or molecular level. We developed an in vivo RNAi assay for the somatic piRNA pathway and identified the RNA helicase Armitage, the Tudor domain containing RNA helicase Yb and the putative nuclease Zucchini as essential factors for primary piRNA biogenesis. Lack of any of these proteins leads to transposon de-silencing, to a collapse in piRNA levels and to a failure in Piwi-nuclear accumulation. We show that Armitage and Yb interact physically and co-localize in cytoplasmic Yb bodies, which flank P bodies. Loss of Zucchini leads to an accumulation of Piwi and Armitage in Yb bodies, indicating that Yb bodies are sites of primary piRNA biogenesis.","authors":"Olivieri, D., Sykora, MM., Sachidanandam, R., Mechtler, K., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"EMBO J","volume":"29","issue":"19","page":"3301-17","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2010-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20881962","title":"Osteoclast differentiation factor RANKL controls development of progestin-driven mammary cancer.","abstract":"Breast cancer is one of the most common cancers in humans and will on average affect up to one in eight women in their lifetime in the United States and Europe. The Women's Health Initiative and the Million Women Study have shown that hormone replacement therapy is associated with an increased risk of incident and fatal breast cancer. In particular, synthetic progesterone derivatives (progestins) such as medroxyprogesterone acetate (MPA), used in millions of women for hormone replacement therapy and contraceptives, markedly increase the risk of developing breast cancer. Here we show that the in vivo administration of MPA triggers massive induction of the key osteoclast differentiation factor RANKL (receptor activator of NF-\u03baB ligand) in mammary-gland epithelial cells. Genetic inactivation of the RANKL receptor RANK in mammary-gland epithelial cells prevents MPA-induced epithelial proliferation, impairs expansion of the CD49f(hi) stem-cell-enriched population, and sensitizes these cells to DNA-damage-induced cell death. Deletion of RANK from the mammary epithelium results in a markedly decreased incidence and delayed onset of MPA-driven mammary cancer. These data show that the RANKL\/RANK system controls the incidence and onset of progestin-driven breast cancer.","authors":"Schramek, D., Leibbrandt, A., Sigl, V., Kenner, L., Pospisilik, JA., Lee, HJ., Hanada, R., Joshi, PA., Aliprantis, A., Glimcher, L., Pasparakis, M., Khokha, R., Ormandy, CJ., Widschwendter, M., Schett, G., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nature","volume":"468","issue":"7320","page":"98-102","pdf":null,"JrId":"6011","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20849823","title":"Transcriptional repression of ceramide kinase in LPS-challenged macrophages.","abstract":"Ceramide kinase (CERK) produces the bioactive lipid ceramide 1-phosphate (C1P). Both CERK and C1P have been identified as mediators of cell growth and survival. Recent evidence showed that CERK is down-regulated during M1-type macrophage activation, which is known to promote cell growth arrest. However, the mechanism has not been investigated yet and, in particular, whether growth arrest might be the signal for down-regulation of CERK is currently unknown. Here, we found that LPS-mediated TLR-4 engagement reduces Cerk mRNA levels in mouse primary macrophages. Reporter gene assays in RAW264.7 macrophages showed that LPS inhibits the transcriptional activity of the Cerk proximal promoter. The G1-cell cycle blocker mimosine did not inhibit Cerk transcription, suggesting that transcriptional repression of Cerk by LPS is not a primary consequence of LPS-induced cell cycle blockade.","authors":"Rovina, P., Jaritz, M., Bornancin, F.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Biochem Biophys Res Commun","volume":"401","issue":"1","page":"164-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20869539","title":"Correlative time-lapse imaging and electron microscopy to study abscission in HeLa cells.","abstract":"HeLa cells are widely used as a model system to study cell division. The last step of cell division, abscission, occurs at an about 1 \u03bcm wide intercellular bridge that connects the post-mitotic sister cells. Abscission often occurs long after ingression of the cleavage furrow, and no efficient methods to synchronize cells to this stage are available. Here, we have developed a correlative fluorescence time-lapse imaging and electron microscopic approach using Aclar sheets with engraved grid patterns. This grid pattern, leaving a negative imprint on thin-layer embedded samples, allows identification of cells selected from the time-lapse imaging for serial-section electron microscopy. This method facilitates the ultrastructural analysis of specific stages of abscission.","authors":"Guizetti, J., M\u00e4ntler, J., M\u00fcller-Reichert, T., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Methods Cell Biol","volume":"96","issue":null,"page":"591-601","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-01-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20821804","title":"Annexin A1 attenuates EMT and metastatic potential in breast cancer.","abstract":"Metastasis is the major cause of carcinoma-induced death, but mechanisms involved are poorly understood. Metastasis crucially involves epithelial-to-mesenchymal transition (EMT), causing loss of epithelial polarity. Here we identify Annexin A1 (AnxA1), a protein with important functions in intracellular vesicle trafficking, as an efficient suppressor of EMT and metastasis in breast cancer. AnxA1 levels were strongly reduced in EMT of mammary epithelial cells, in metastatic murine and human cell lines and in metastatic mouse and human carcinomas. RNAi-mediated AnxA1 knockdown cooperated with oncogenic Ras to induce TGF\u03b2-independent EMT and metastasis in non-metastatic cells. Strikingly, forced AnxA1 expression in metastatic mouse and human mammary carcinoma cells reversed EMT and abolished metastasis. AnxA1 knockdown stimulated multiple signalling pathways but only Tyk2\/Stat3 and Erk1\/2 signalling were essential for EMT.","authors":"Maschler, S., Gebeshuber, CA., Wiedemann, EM., Alacakaptan, M., Schreiber, M., Custic, I., Beug, H.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"EMBO Mol Med","volume":"2","issue":"10","page":"401-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20832311","title":"Sexual dimorphism in the fly brain.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20832311<\/PMID><DateCompleted><Year>2011<\/Year><Month>01<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>10<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0445<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>20<\/Volume><Issue>18<\/Issue><PubDate><Year>2010<\/Year><Month>Sep<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Sexual dimorphism in the fly brain.<\/ArticleTitle><Pagination><MedlinePgn>1589-601<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.cub.2010.07.045<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Sex-specific behavior may originate from differences in brain structure or function. In Drosophila, the action of the male-specific isoform of fruitless in about 2000 neurons appears to be necessary and sufficient for many aspects of male courtship behavior. Initial work found limited evidence for anatomical dimorphism in these fru+ neurons. Subsequently, three discrete anatomical differences in central brain fru+ neurons have been reported, but the global organization of sex differences in wiring is unclear.","authors":"Cachero, S., Ostrovsky, AD., Yu, JY., Dickson, BJ., Jefferis, GS.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Curr Biol","volume":"20","issue":"18","page":"1589-601","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20581825","title":"HtrA proteases have a conserved activation mechanism that can be triggered by distinct molecular cues.","abstract":"HtrA proteases are tightly regulated proteolytic assemblies that are essential for maintaining protein homeostasis in extracytosolic compartments. Though HtrA proteases have been characterized in detail, their precise molecular mechanism for switching between different functional states is still unknown. To address this, we carried out biochemical and structural studies of DegP from Escherichia coli. We show that effector-peptide binding to the PDZ domain of DegP induces oligomer conversion from resting hexameric DegP6 into proteolytically active 12-mers and 24-mers (DegP12\/24). Moreover, our data demonstrate that a specific protease loop (L3) functions as a conserved molecular switch of HtrA proteases. L3 senses the activation signal-that is, the repositioned PDZ domain of substrate-engaged DegP12\/24 or the binding of allosteric effectors to regulatory HtrA proteases such as DegS-and transmits this information to the active site. Implications for protein quality control and regulation of oligomeric enzymes are discussed.","authors":"Krojer, T., Sawa, J., Huber, R., Clausen, T.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Struct Mol Biol","volume":"17","issue":"7","page":"844-52","pdf":null,"JrId":"31761","fulltextlink":null,"preprintlink":null,"articledate":"2010-07-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16323424","title":"Chlamydia and antigenic mimicry.","abstract":"Chlamydial infections are among the most common human infections. Every year, in millions of humans, they cause infections of the eyes, the respiratory tract, the genital tract, joints, and the vasculature. Chlamydiae are obligate intracellular prokaryotic pathogens. Chlamydiae promote, in susceptible host cells that include mucosal epithelial cells, vascular endothelial cells, smooth muscle cells, and monocytes and macrophages, their survival while causing disease of varying clinical importance and consequence in their hosts. Chlamydia infections often precede the initiation of autoimmune diseases, and Chlamydiae are often found within autoimmune lesions. Thus, they have been suspected in the etiology and pathogenesis of autoimmune diseases. Autoimmune diseases have many causes. Genes, notably genes encoding cell-surface proteins that display peptides for immune recognition, the major histocompatibility complex (MHC), the environment, and the microbial diversity within the human body determine the susceptibility to autoimmune diseases. One mechanism by which infection is linked to the initiation of autoimmunity is termed molecular mimicry. Molecular mimicry describes the phenomenon of protein products from dissimilar genes sharing similar structures that elicit an immune response to both self and microbial proteins. Molecular mimicry might thus be a mechanism by which infections trigger autoimmune diseases. For the purpose of this chapter, we will focus on chlamydial proteins that mimic host self-proteins and thus contribute to initiation and maintenance of autoimmune diseases. Thus far, the strongest cases for molecular mimicry seem to have been made for chlamydial heat shock proteins 60, the DNA primase of Chlamydia trachomatis, and chlamydial OmcB proteins.","authors":"Bachmaier, K., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Curr Top Microbiol Immunol","volume":"296","issue":"","page":"153-63","pdf":null,"JrId":"3237","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20738317","title":"Cbl-b regulates airway mucosal tolerance to aeroallergen.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20738317<\/PMID><DateCompleted><Year>2011<\/Year><Month>05<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>04<\/Month><Day>12<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1365-2222<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>41<\/Volume><Issue>3<\/Issue><PubDate><Year>2011<\/Year><Month>Mar<\/Month><\/PubDate><\/JournalIssue><Title>Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology<\/Title><ISOAbbreviation>Clin Exp Allergy<\/ISOAbbreviation><\/Journal><ArticleTitle>Cbl-b regulates airway mucosal tolerance to aeroallergen.<\/ArticleTitle><Pagination><MedlinePgn>434-42<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/j.1365-2222.2010.03593.x<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">As an E3 ubiquitin ligase and a molecular adaptor, Cbl-b controls the activation threshold of the antigen receptor and negatively regulates CD28 costimulation, functioning as an intrinsic mediator of T cell anergy that maintains tolerance. However, the role of Cbl-b in the airway immune response to aeroallergens is unclear.","authors":"Oh, SY., Park, JU., Zheng, T., Kim, YK., Wu, F., Cho, SH., Barber, D., Penninger, J., Zhu, Z.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Clin Exp Allergy","volume":"41","issue":"3","page":"434-42","pdf":null,"JrId":"2701","fulltextlink":null,"preprintlink":null,"articledate":"2011-05-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20729470","title":"Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRs.","abstract":"MicroRNAs (miRNAs) are a class of short noncoding RNAs that regulate protein-coding genes posttranscriptionally. In animals, most known miRNA targeting occurs within the 3'UTR of mRNAs, but the extent of biologically relevant targeting in the ORF or 5'UTR of mRNAs remains unknown. Here, we develop an algorithm (MinoTar-miRNA ORF Targets) to identify conserved regulatory motifs within protein-coding regions and use it to estimate the number of preferentially conserved miRNA-target sites in ORFs. We show that, in Drosophila, preferentially conserved miRNA targeting in ORFs is as widespread as it is in 3'UTRs and that, while far less abundant, conserved targets in Drosophila 5'UTRs number in the hundreds. Using our algorithm, we predicted a set of high-confidence ORF targets and selected seven miRNA-target pairs from among these for experimental validation. We observed down-regulation by the miRNA in five out of seven cases, indicating our approach can recover functional sites with high confidence. Additionally, we observed additive targeting by multiple sites within a single ORF. Altogether, our results demonstrate that the scale of biologically important miRNA targeting in ORFs is extensive and that computational tools such as ours can aid in the identification of such targets. Further evidence suggests that our results extend to mammals, but that the extent of ORF and 5'UTR targeting relative to 3'UTR targeting may be greater in Drosophila.","authors":"Schnall-Levin, M., Zhao, Y., Perrimon, N., Berger, B.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc Natl Acad Sci U S A","volume":"107","issue":"36","page":"15751-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2010-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20727759","title":"Visual control of altitude in flying Drosophila.","abstract":"Unlike creatures that walk, flying animals need to control their horizontal motion as well as their height above the ground. Research on insects, the first animals to evolve flight, has revealed several visual reflexes that are used to govern horizontal course. For example, insects orient toward prominent vertical features in their environment [1-5] and generate compensatory reactions to both rotations [6, 7] and translations [1, 8-11] of the visual world. Insects also avoid impending collisions by veering away from visual expansion [9, 12-14]. In contrast to this extensive understanding of the visual reflexes that regulate horizontal course, the sensory-motor mechanisms that animals use to control altitude are poorly understood. Using a 3D virtual reality environment, we found that Drosophila utilize three reflexes--edge tracking, wide-field stabilization, and expansion avoidance--to control altitude. By implementing a dynamic visual clamp, we found that flies do not regulate altitude by maintaining a fixed value of optic flow beneath them, as suggested by a recent model [15]. The results identify a means by which insects determine their absolute height above the ground and uncover a remarkable correspondence between the sensory-motor algorithms used to regulate motion in the horizontal and vertical domains.","authors":"Straw, AD., Lee, S., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Curr Biol","volume":"20","issue":"17","page":"1550-6","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2011-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20383150","title":"The zinc-finger protein MAZR is part of the transcription factor network that controls the CD4 versus CD8 lineage fate of double-positive thymocytes.","abstract":"The CD4 versus CD8 lineage specification of thymocytes is linked to coreceptor expression. The transcription factor MAZR has been identified as an important regulator of Cd8 expression. Here we show that variegated CD8 expression by loss of Cd8 enhancers was reverted in MAZR-deficient mice, which confirms that MAZR negatively regulates the Cd8 loci during the transition to the double-positive (DP) stage. Moreover, loss of MAZR led to partial redirection of major histocompatibility complex (MHC) class I-restricted thymocytes into CD4(+) helper-like T cells, which correlated with derepression of Th-POK, a central transcription factor for helper-lineage development. MAZR bound the silencer of the gene encoding Th-POK, which indicated direct regulation of this locus by MAZR. Thus, MAZR is part of the transcription factor network that regulates the CD8 lineage differentiation of DP thymocytes.","authors":"Sakaguchi, S., Hombauer, M., Bilic, I., Naoe, Y., Schebesta, A., Taniuchi, I., Ellmeier, W.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Immunol","volume":"11","issue":"5","page":"442-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20711181","title":"Live-cell imaging RNAi screen identifies PP2A-B55alpha and importin-beta1 as key mitotic exit regulators in human cells.","abstract":"When vertebrate cells exit mitosis various cellular structures are re-organized to build functional interphase cells. This depends on Cdk1 (cyclin dependent kinase 1) inactivation and subsequent dephosphorylation of its substrates. Members of the protein phosphatase 1 and 2A (PP1 and PP2A) families can dephosphorylate Cdk1 substrates in biochemical extracts during mitotic exit, but how this relates to postmitotic reassembly of interphase structures in intact cells is not known. Here, we use a live-cell imaging assay and RNAi knockdown to screen a genome-wide library of protein phosphatases for mitotic exit functions in human cells. We identify a trimeric PP2A-B55alpha complex as a key factor in mitotic spindle breakdown and postmitotic reassembly of the nuclear envelope, Golgi apparatus and decondensed chromatin. Using a chemically induced mitotic exit assay, we find that PP2A-B55alpha functions downstream of Cdk1 inactivation. PP2A-B55alpha isolated from mitotic cells had reduced phosphatase activity towards the Cdk1 substrate, histone H1, and was hyper-phosphorylated on all subunits. Mitotic PP2A complexes co-purified with the nuclear transport factor importin-beta1, and RNAi depletion of importin-beta1 delayed mitotic exit synergistically with PP2A-B55alpha. This demonstrates that PP2A-B55alpha and importin-beta1 cooperate in the regulation of postmitotic assembly mechanisms in human cells.","authors":"Schmitz, MH., Held, M., Janssens, V., Hutchins, JR., Hudecz, O., Ivanova, E., Goris, J., Trinkle-Mulcahy, L., Lamond, AI., Poser, I., Hyman, AA., Mechtler, K., Peters, JM., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Cell Biol","volume":"12","issue":"9","page":"886-93","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2010-10-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20708087","title":"Cytokinetic abscission in animal cells.","abstract":"Cytokinesis leads to the separation of dividing cells, which in animal cells involves the contraction of an actin-myosin ring and subsequent fission during abscission. Abscission requires a series of dynamic events, including midbody-targeted vesicle secretion, specialization of plasma membrane domains, disassembly of midbody-associated microtubule bundles and plasma membrane fission. A large number of molecular factors required for abscission have been identified through localization, loss-of-function and proteomics studies, but their coordinate function in abscission is still poorly understood. Here, we review the structural elements and molecular factors known to contribute to abscission, and discuss their potential role in the context of proposed models for the abscission mechanism.","authors":"Guizetti, J., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Semin Cell Dev Biol","volume":"21","issue":"9","page":"909-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20699302","title":"Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.","abstract":"Conservation is often used to define essential sequences within RNA sites. However, conservation finds only invariant sequence elements that are necessary for function, rather than finding a set of sequence elements sufficient for function. Biochemical studies in several systems-including the hammerhead ribozyme and the purine riboswitch-find additional elements, such as loop-loop interactions, required for function yet not phylogenetically conserved. Here we define a critical test of sufficiency: We embed a minimal, apparently sufficient motif for binding the amino acid tryptophan in a random-sequence background and ask whether we obtain functional molecules. After a negative result, we use a combination of three-dimensional structural modeling, selection, designed mutations, high-throughput sequencing, and bioinformatics to explore functional insufficiency. This reveals an essential unpaired G in a diverse structural context, varied sequence, and flexible distance from the invariant internal loop binding site identified previously. Addition of the new element yields a sufficient binding site by the insertion criterion, binding tryptophan in 22 out of 23 tries. Random insertion testing for site sufficiency seems likely to be broadly revealing.","authors":"Majerfeld, I., Chocholousova, J., Malaiya, V., Widmann, J., McDonald, D., Reeder, J., Iyer, M., Illangasekare, M., Yarus, M., Knight, R.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"RNA","volume":"16","issue":"10","page":"1915-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-10-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20697156","title":"Prkar1a is an osteosarcoma tumor suppressor that defines a molecular subclass in mice.","abstract":"Some cancers have been stratified into subclasses based on their unique involvement of specific signaling pathways. The mapping of human cancer genomes is revealing a vast number of somatic alterations; however, the identification of clinically relevant molecular tumor subclasses and their respective driver genes presents challenges. This information is key to developing more targeted and personalized cancer therapies. Here, we generate a new mouse model of genomically unstable osteosarcoma (OSA) that phenocopies the human disease. Integrative oncogenomics pinpointed cAMP-dependent protein kinase type I, alpha regulatory subunit (Prkar1a) gene deletions at 11qE1 as a recurrent genetic trait for a molecularly distinct subclass of mouse OSA featuring RANKL overexpression. Using mouse genetics, we established that Prkar1a is a bone tumor suppressor gene capable of directing subclass development and driving RANKL overexpression during OSA tumorigenesis. Finally, we uncovered evidence for a PRKAR1A-low subset of human OSA with distinct clinical behavior. Thus, tumor subclasses develop in mice and can potentially provide information toward the molecular stratification of human cancers.","authors":"Molyneux, SD., Di Grappa, MA., Beristain, AG., McKee, TD., Wai, DH., Paderova, J., Kashyap, M., Hu, P., Maiuri, T., Narala, SR., Stambolic, V., Squire, J., Penninger, J., Sanchez, O., Triche, TJ., Wood, GA., Kirschner, LS., Khokha, R.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Clin Invest","volume":"120","issue":"9","page":"3310-25","pdf":null,"JrId":"4632","fulltextlink":null,"preprintlink":null,"articledate":"2010-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20693996","title":"CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging.","abstract":"Fluorescence time-lapse imaging has become a powerful tool to investigate complex dynamic processes such as cell division or intracellular trafficking. Automated microscopes generate time-resolved imaging data at high throughput, yet tools for quantification of large-scale movie data are largely missing. Here we present CellCognition, a computational framework to annotate complex cellular dynamics. We developed a machine-learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states. Incorporation of time information into the annotation scheme was essential to suppress classification noise at state transitions and confusion between different functional states with similar morphology. We demonstrate generic applicability in different assays and perturbation conditions, including a candidate-based RNA interference screen for regulators of mitotic exit in human cells. CellCognition is published as open source software, enabling live-cell imaging-based screening with assays that directly score cellular dynamics.","authors":"Held, M., Schmitz, MH., Fischer, B., Walter, T., Neumann, B., Olma, MH., Peter, M., Ellenberg, J., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Methods","volume":"7","issue":"9","page":"747-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-10-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32163288","title":"National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions.","abstract":"A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts' opinion on the development and application of multiomic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, and prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular, and functional aberrations within the lesion and within individual cells. Single-cell proteomic data will be essential for the establishment of new tools with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included (i) The best way\/s to analyze single-cells from fresh and preserved tissue; (ii) Detection and analysis of secreted molecules and from single cells, especially from a tissue slice; (iii) Detection of new, previously undocumented cell type\/s in the premalignant and early stage cancer tissue microenvironment; (iv) Multiomic integration of data to support and inform proteomic measurements; (v) Subcellular organelles-identifying abnormal structure, function, distribution, and location within individual premalignant and malignant cells; (vi) How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post-translational modifications (PTM); (vii) The depth of coverage measured concurrently using single-cell techniques; (viii) Quantitation - absolute or semiquantitative? (ix) Single methodology or multiplexed combinations? (x) Application of analytical methods for identification of biologically significant subsets; (xi) Data visualization of <i>N<\/i>-dimensional data sets; (xii) How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME); (xiii) Associations between intrinsic cellular processes and extrinsic stimuli; (xiv) How to predict cellular responses to stress-inducing stimuli; (xv) Identification of new markers for prediction of progression from precursor, benign, and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells; (xvi) Identification of new targets for immunoprevention or immunotherapy-identification of neoantigens and surfactome of individual cells within a lesion.","authors":"Kagan, J., Moritz, RL., Mazurchuk, R., Lee, JH., Kharchenko, PV., Rozenblatt-Rosen, O., Ruppin, E., Edfors, F., Ginty, F., Goltsev, Y., Wells, JA., LaCava, J., Riesterer, JL., Germain, RN., Shi, T., Chee, MS., Budnik, BA., Yates, JR., Chait, BT., Moffitt, JR., Smith, RD., Srivastava, S.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Proteome Res","volume":"19","issue":"5","page":"1900-1912","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-17","doi":"10.1021\/acs.jproteome.0c00021","first_author":"Kagan, J.","corresponding_authors":"Srivastava, S."},{"pmid":"20668237","title":"T-cell regulation by casitas B-lineage lymphoma (Cblb) is a critical failsafe against autoimmune disease due to autoimmune regulator (Aire) deficiency.","abstract":"Autoimmune polyendocrinopathy syndrome type 1 (APS1) results from homozygous Aire mutations that cripple thymic deletion of organ-specific T cells. The clinical course in man and mouse is characterized by high variability both in the latent period before onset of autoimmune disease and in the specific organs affected, but the reasons for this are unknown. Here we test the hypothesis that the latent period reflects the failsafe action of discrete postthymic mechanisms for imposing self-tolerance in peripheral T cells. Aire-deficient mice were crossed with mice of a uniform major histocompatibility complex (MHC) haplotype and genetic background carrying specific genetic defects in one of four distinct peripheral tolerance mechanisms: activation-induced cell death (Fasl(gld\/gld)), anergy and requirement for CD28 costimulation (Cblb(-\/-)), inhibition of ICOS and T(FH) cells (Rc3h1(san\/san)), or decreased numbers of Foxp3(+) T regulatory cells (Card11(unm\/unm)). Cblb-deficiency was unique among these four in precipitating rapid clinical autoimmune disease when combined with Aire-deficiency, resulting in autoimmune exocrine pancreatitis with median age of survival of only 25 d. Massive lymphocytic infiltration selectively destroyed most of the exocrine acinar cells of the pancreas and submandibular salivary gland, and CD4(+) and CD8(+) subsets were necessary and sufficient to transfer the disease. Intrinsic regulation of peripheral T cells by CBL-B thus serves a uniquely critical role as a failsafe against clinical onset of autoimmune disease in AIRE deficiency, and multiple peripheral tolerance mechanisms may need to fail before onset of clinical autoimmunity to many organs.","authors":"Teh, CE., Daley, SR., Enders, A., Goodnow, CC.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc Natl Acad Sci U S A","volume":"107","issue":"33","page":"14709-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20630879","title":"Multi-camera real-time three-dimensional tracking of multiple flying animals.","abstract":"Automated tracking of animal movement allows analyses that would not otherwise be possible by providing great quantities of data. The additional capability of tracking in real time--with minimal latency--opens up the experimental possibility of manipulating sensory feedback, thus allowing detailed explorations of the neural basis for control of behaviour. Here, we describe a system capable of tracking the three-dimensional position and body orientation of animals such as flies and birds. The system operates with less than 40 ms latency and can track multiple animals simultaneously. To achieve these results, a multi-target tracking algorithm was developed based on the extended Kalman filter and the nearest neighbour standard filter data association algorithm. In one implementation, an 11-camera system is capable of tracking three flies simultaneously at 60 frames per second using a gigabit network of nine standard Intel Pentium 4 and Core 2 Duo computers. This manuscript presents the rationale and details of the algorithms employed and shows three implementations of the system. An experiment was performed using the tracking system to measure the effect of visual contrast on the flight speed of Drosophila melanogaster. At low contrasts, speed is more variable and faster on average than at high contrasts. Thus, the system is already a useful tool to study the neurobiology and behaviour of freely flying animals. If combined with other techniques, such as 'virtual reality'-type computer graphics or genetic manipulation, the tracking system would offer a powerful new way to investigate the biology of flying animals.","authors":"Straw, AD., Branson, K., Neumann, TR., Dickinson, MH.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"J R Soc Interface","volume":"8","issue":"56","page":"395-409","pdf":null,"JrId":"32845","fulltextlink":null,"preprintlink":null,"articledate":"2011-04-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20599443","title":"Trilogy of ACE2: a peptidase in the renin-angiotensin system, a SARS receptor, and a partner for amino acid transporters.","abstract":"Angiotensin-converting enzyme (ACE) 2 is a homolog to the carboxypeptidase ACE, which generates angiotensin II, the main active peptide of renin-angiotensin system (RAS). After the cloning of ACE2 in 2000, three major ACE2 functions have been described so far. First ACE2 has emerged as a potent negative regulator of the RAS counterbalancing the multiple functions of ACE. By targeting angiotensin II ACE2 exhibits a protective role in the cardiovascular system and many other organs. Second ACE2 was identified as an essential receptor for the SARS coronavirus that causes severe acute lung failure. Downregulation of ACE2 strongly contributes to the pathogenesis of severe lung failure. Third, both ACE2 and its homologue Collectrin can associate with amino acid transporters and play essential role in the absorption of amino acids in the kidney and gut. In this review, we will discuss the multiple biological functions of ACE2.","authors":"Kuba, K., Imai, Y., Ohto-Nakanishi, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Pharmacol Ther","volume":"128","issue":"1","page":"119-28","pdf":null,"JrId":"6445","fulltextlink":null,"preprintlink":null,"articledate":"2011-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16287843","title":"Muscle-specific loss of apoptosis-inducing factor leads to mitochondrial dysfunction, skeletal muscle atrophy, and dilated cardiomyopathy.","abstract":"Cardiac and skeletal muscle critically depend on mitochondrial energy metabolism for their normal function. Recently, we showed that apoptosis-inducing factor (AIF), a mitochondrial protein implicated in programmed cell death, plays a role in mitochondrial respiration. However, the in vivo consequences of AIF-regulated mitochondrial respiration resulting from a loss-of-function mutation in Aif are not known. Here, we report tissue-specific deletion of Aif in the mouse. Mice in which Aif has been inactivated specifically in cardiac and skeletal muscle exhibit impaired activity and protein expression of respiratory chain complex I. Mutant animals develop severe dilated cardiomyopathy, heart failure, and skeletal muscle atrophy accompanied by lactic acidemia consistent with defects in the mitochondrial respiratory chain. Isolated hearts from mutant animals exhibit poor contractile performance in response to a respiratory chain-dependent energy substrate, but not in response to glucose, supporting the notion that impaired heart function in mutant animals results from defective mitochondrial energy metabolism. These data provide genetic proof that the previously defined cell death promoter AIF has a second essential function in mitochondrial respiration and aerobic energy metabolism required for normal heart function and skeletal muscle homeostasis.","authors":"Joza, N., Oudit, GY., Brown, D., B\u00e9nit, P., Kassiri, Z., Vahsen, N., Benoit, L., Patel, MM., Nowikovsky, K., Vassault, A., Backx, PH., Wada, T., Kroemer, G., Rustin, P., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Mol Cell Biol","volume":"25","issue":"23","page":"10261-72","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2005-12-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26443227","title":"Designer Nuclease-Mediated Generation of Knockout THP1 Cells.","abstract":"Recent developments in the field of designer nucleases allow the efficient and specific manipulation of genomic architectures in eukaryotic cell lines. To this end, it has become possible to introduce DNA double strand breaks (DSBs) at user-defined genomic loci. If located in critical coding regions of genes, thus induced DSBs can lead to insertions or deletions (indels) that result in frameshift mutations and thereby the knockout of the target gene. In this chapter, we describe a step-by-step workflow for establishing knockout cell clones of the difficult-to-transfect suspension cell line THP1. The here described protocol encompasses electroporation, cell cloning, and a deep sequencing-based genotyping step that allows the in-parallel analysis of 96 cell clones per gene of interest. Furthermore, we describe the use of the analysis tool OutKnocker that allows rapid identification of cell clones with all-allelic frameshift mutations.","authors":"Schmidt, T., Schmid-Burgk, JL., Ebert, TS., Gaidt, MM., Hornung, V.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Methods Mol Biol","volume":"1338","issue":null,"page":"261-72","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20543137","title":"Two-photon single-cell optogenetic control of neuronal activity by sculpted light.","abstract":"Recent advances in optogenetic techniques have generated new tools for controlling neuronal activity, with a wide range of neuroscience applications. The most commonly used approach has been the optical activation of the light-gated ion channel channelrhodopsin-2 (ChR2). However, targeted single-cell-level optogenetic activation with temporal precessions comparable to the spike timing remained challenging. Here we report fast (&lt; or = 1 ms), selective, and targeted control of neuronal activity with single-cell resolution in hippocampal slices. Using temporally focused laser pulses (TEFO) for which the axial beam profile can be controlled independently of its lateral distribution, large numbers of channels on individual neurons can be excited simultaneously, leading to strong (up to 15 mV) and fast (&lt; or = 1 ms) depolarizations. Furthermore, we demonstrated selective activation of cellular compartments, such as dendrites and large presynaptic terminals, at depths up to 150 microm. The demonstrated spatiotemporal resolution and the selectivity provided by TEFO allow manipulation of neuronal activity, with a large number of applications in studies of neuronal microcircuit function in vitro and in vivo.","authors":"Andrasfalvy, BK., Zemelman, BV., Tang, J., Vaziri, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc Natl Acad Sci U S A","volume":"107","issue":"26","page":"11981-6","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2010-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20508164","title":"Stat5a serine 725 and 779 phosphorylation is a prerequisite for hematopoietic transformation.","abstract":"Stat5 transcription factors are essential gene regulators promoting proliferation, survival, and differentiation of all hematopoietic cell types. Mutations or fusions of oncogenic tyrosine kinases often result in constitutive Stat5 activation. We have modeled persistent Stat5 activity by using an oncogenic Stat5a variant (cS5). To analyze the hitherto unrecognized role of Stat5 serine phosphorylation in this context, we have generated cS5 constructs with mutated C-terminal serines 725 and 779, either alone or in combination. Genetic complementation assays in primary Stat5(null\/null) mast cells and Stat5(DeltaN) T cells demonstrated reconstitution of proliferation with these mutants. Similarly, an in vivo reconstitution experiment of transduced Stat5(null\/null) fetal liver cells transplanted into irradiated wild-type recipients revealed that these mutants exhibit biologic activity in lineage differentiation. By contrast, the leukemogenic potential of cS5 in bone marrow transplants decreased dramatically in cS5 single-serine mutants or was completely absent upon loss of both serine phosphorylation sites. Our data suggest that Stat5a serine phosphorylation is a prerequisite for cS5-mediated leukemogenesis. Hence, interference with Stat5a serine phosphorylation might provide a new therapeutic option for leukemia and myeloid dysplasias without affecting major functions of Stat5 in normal hematopoiesis.","authors":"Friedbichler, K., Kerenyi, MA., Kovacic, B., Li, G., Hoelbl, A., Yahiaoui, S., Sexl, V., M\u00fcllner, EW., Fajmann, S., Cerny-Reiterer, S., Valent, P., Beug, H., Gouilleux, F., Bunting, KD., Moriggl, R.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Blood","volume":"116","issue":"9","page":"1548-58","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2010-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20498068","title":"B-lymphoid cells with attributes of dendritic cells regulate T cells via indoleamine 2,3-dioxygenase.","abstract":"A discrete population of splenocytes with attributes of dendritic cells (DCs) and coexpressing the B-cell marker CD19 is uniquely competent to express the T-cell regulatory enzyme indoleamine 2,3-dioxygenase (IDO) in mice treated with TLR9 ligands (CpGs). Here we show that IDO-competent cells express the B-lineage commitment factor Pax5 and surface immunoglobulins. CD19 ablation abrogated IDO-dependent T-cell suppression by DCs, even though cells with phenotypic attributes matching IDO-competent cells developed normally and expressed IDO in response to interferon gamma. Consequently, DCs and regulatory T cells (Tregs) did not acquire T-cell regulatory functions after TLR9 ligation, providing an alternative perspective on the known T-cell regulatory defects of CD19-deficient mice. DCs from B-cell-deficient mice expressed IDO and mediated T-cell suppression after TLR9 ligation, indicating that B-cell attributes were not essential for B-lymphoid IDO-competent cells to regulate T cells. Thus, IDO-competent cells constitute a distinctive B-lymphoid cell type with quintessential T-cell regulatory attributes and phenotypic features of both B cells and DCs.","authors":"Johnson, BA., Kahler, DJ., Baban, B., Chandler, PR., Kang, B., Shimoda, M., Koni, PA., Pihkala, J., Vilagos, B., Busslinger, M., Munn, DH., Mellor, AL.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc Natl Acad Sci U S A","volume":"107","issue":"23","page":"10644-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2010-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11713286","title":"Antisense transcription through the Xist locus mediates Tsix function in embryonic stem cells.","abstract":"Expression of the Xist gene, a key player in mammalian X inactivation, has been proposed to be controlled by the antisense Tsix transcript. Targeted deletion of the Tsix promoter encompassing the DPXas34 locus leads to nonrandom inactivation of the mutant X, but it remains unresolved whether this phenotype is caused by loss of Tsix transcription or by deletion of a crucial DNA element. In this study we determined the role of Tsix transcription in random X inactivation by using mouse embryonic stem (ES) cells as a model system. Two approaches were chosen to modulate Tsix transcription with minimal disturbance of genomic sequences. First, Tsix transcription was functionally inhibited by introducing a transcriptional stop signal into the transcribed region of Tsix. In the second approach, an inducible system for Tsix expression was created. We found that the truncation of the Tsix transcript led to complete nonrandom inactivation of the targeted X chromosome. Induction of Tsix transcription during ES cell differentiation, on the other hand, caused the targeted chromosome always to be chosen as the active chromosome. These results for the first time establish a function for antisense transcription in the regulation of X inactivation.","authors":"Luikenhuis, S., Wutz, A., Jaenisch, R.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Mol Cell Biol","volume":"21","issue":"24","page":"8512-20","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20471950","title":"Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination.","abstract":"How polycomb group proteins repress gene expression in vivo is not known. While histone-modifying activities of the polycomb repressive complexes (PRCs) have been studied extensively, in vitro data have suggested a direct activity of the PRC1 complex in compacting chromatin. Here, we investigate higher-order chromatin compaction of polycomb targets in vivo. We show that PRCs are required to maintain a compact chromatin state at Hox loci in embryonic stem cells (ESCs). There is specific decompaction in the absence of PRC2 or PRC1. This is due to a PRC1-like complex, since decompaction occurs in Ring1B null cells that still have PRC2-mediated H3K27 methylation. Moreover, we show that the ability of Ring1B to restore a compact chromatin state and to repress Hox gene expression is not dependent on its histone ubiquitination activity. We suggest that Ring1B-mediated chromatin compaction acts to directly limit transcription in vivo.","authors":"Eskeland, R., Leeb, M., Grimes, GR., Kress, C., Boyle, S., Sproul, D., Gilbert, N., Fan, Y., Skoultchi, AI., Wutz, A., Bickmore, WA.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Mol Cell","volume":"38","issue":"3","page":"452-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20463759","title":"BDNF regulation under GFAP promoter provides engineered astrocytes as a new approach for long-term protection in Huntington's disease.","abstract":"Brain-derived neurotrophic factor (BDNF) is the main candidate for neuroprotective therapeutic strategies for Huntington's disease. However, the administration system and the control over the dosage are still important problems to be solved. Here we generated transgenic mice overexpressing BDNF under the promoter of the glial fibrillary acidic protein (GFAP) (pGFAP-BDNF mice). These mice are viable and have a normal phenotype. However, intrastriatal administration of quinolinate increased the number of reactive astrocytes and enhanced the release of BDNF in pGFAP-BDNF mice compared with wild-type mice. Coincidentally, pGFAP-BDNF mice are more resistant to quinolinate than wild-type mice, suggesting a protective effect of astrocyte-derived BDNF. To verify this, we next cultured astrocytes from pGFAP-BDNF and wild-type mice for grafting. Wild-type and pGFAP-BDNF-derived astrocytes behave similarly in nonlesioned mice. However, pGFAP-BDNF-derived astrocytes showed higher levels of BDNF and larger neuroprotective effects than the wild-type ones when quinolinate was injected 30 days after grafting. Interestingly, mice grafted with pGFAP-BDNF astrocytes showed important and sustained behavioral improvements over time after quinolinate administration as compared with mice grafted with wild-type astrocytes. These findings show that astrocytes engineered to release BDNF can constitute a therapeutic approach for Huntington's disease.","authors":"Giralt, A., Friedman, HC., Caneda-Ferr\u00f3n, B., Urb\u00e1n, N., Moreno, E., Rubio, N., Blanco, J., Peterson, A., Canals, JM., Alberch, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Gene Ther","volume":"17","issue":"10","page":"1294-308","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20445021","title":"Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells.","abstract":"Polycomb group (PcG) proteins are transcriptional repressors with a central role in the establishment and maintenance of gene expression patterns during development. We have investigated the role of polycomb repressive complexes (PRCs) in hematopoietic stem cells (HSCs) and progenitor populations. We show that mice with loss of function mutations in PRC2 components display enhanced HSC\/progenitor population activity, whereas mutations that disrupt PRC1 or pleiohomeotic repressive complex are associated with HSC\/progenitor cell defects. Because the hierarchical model of PRC action would predict synergistic effects of PRC1 and PRC2 mutation, these opposing effects suggest this model does not hold true in HSC\/progenitor cells. To investigate the molecular targets of each complex in HSC\/progenitor cells, we measured genome-wide expression changes associated with PRC deficiency, and identified transcriptional networks that are differentially regulated by PRC1 and PRC2. These studies provide new insights into the mechanistic interplay between distinct PRCs and have important implications for approaching PcG proteins as therapeutic targets.","authors":"Majewski, IJ., Ritchie, ME., Phipson, B., Corbin, J., Pakusch, M., Ebert, A., Busslinger, M., Koseki, H., Hu, Y., Smyth, GK., Alexander, WS., Hilton, DJ., Blewitt, ME.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Blood","volume":"116","issue":"5","page":"731-9","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20421298","title":"Xenin-25 potentiates glucose-dependent insulinotropic polypeptide action via a novel cholinergic relay mechanism.","abstract":"The intestinal peptides GLP-1 and GIP potentiate glucose-mediated insulin release. Agents that increase GLP-1 action are effective therapies in type 2 diabetes mellitus (T2DM). However, GIP action is blunted in T2DM, and GIP-based therapies have not been developed. Thus, it is important to increase our understanding of the mechanisms of GIP action. We developed mice lacking GIP-producing K cells. Like humans with T2DM, \"GIP\/DT\" animals exhibited a normal insulin secretory response to exogenous GLP-1 but a blunted response to GIP. Pharmacologic doses of xenin-25, another peptide produced by K cells, restored the GIP-mediated insulin secretory response and reduced hyperglycemia in GIP\/DT mice. Xenin-25 alone had no effect. Studies with islets, insulin-producing cell lines, and perfused pancreata indicated xenin-25 does not enhance GIP-mediated insulin release by acting directly on the beta-cell. The in vivo effects of xenin-25 to potentiate insulin release were inhibited by atropine sulfate and atropine methyl bromide but not by hexamethonium. Consistent with this, carbachol potentiated GIP-mediated insulin release from in situ perfused pancreata of GIP\/DT mice. In vivo, xenin-25 did not activate c-fos expression in the hind brain or paraventricular nucleus of the hypothalamus indicating that central nervous system activation is not required. These data suggest that xenin-25 potentiates GIP-mediated insulin release by activating non-ganglionic cholinergic neurons that innervate the islets, presumably part of an enteric-neuronal-pancreatic pathway. Xenin-25, or molecules that increase acetylcholine receptor signaling in beta-cells, may represent a novel approach to overcome GIP resistance and therefore treat humans with T2DM.","authors":"Wice, BM., Wang, S., Crimmins, DL., Diggs-Andrews, KA., Althage, MC., Ford, EL., Tran, H., Ohlendorf, M., Griest, TA., Wang, Q., Fisher, SJ., Ladenson, JH., Polonsky, KS.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Biol Chem","volume":"285","issue":"26","page":"19842-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20418872","title":"Electron tomography reveals unbranched networks of actin filaments in lamellipodia.","abstract":"Eukaryotic cells can initiate movement using the forces exerted by polymerizing actin filaments to extend lamellipodial and filopodial protrusions. In the current model, actin filaments in lamellipodia are organized in a branched, dendritic network. We applied electron tomography to vitreously frozen 'live' cells, fixed cells and cytoskeletons, embedded in vitreous ice or in deep-negative stain. In lamellipodia from four cell types, including rapidly migrating fish keratocytes, we found that actin filaments are almost exclusively unbranched. The vast majority of apparent filament junctions proved to be overlapping filaments, rather than branched end-to-side junctions. Analysis of the tomograms revealed that actin filaments terminate at the membrane interface within a zone several hundred nanometres wide at the lamellipodium front, and yielded the first direct measurements of filament densities. Actin filament pairs were also identified as lamellipodium components and bundle precursors. These data provide a new structural basis for understanding actin-driven protrusion during cell migration.","authors":"Urban, E., Jacob, S., Nemethova, M., Resch, GP., Small, JV.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Cell Biol","volume":"12","issue":"5","page":"429-35","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2010-07-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20407207","title":"Sphingosine kinase 1 and sphingosine-1-phosphate receptor 2 are vital to recovery from anaphylactic shock in mice.","abstract":"Sphingosine kinase 1 (SphK1) and SphK2 are ubiquitous enzymes that generate sphingosine-1-phosphate (S1P), a ligand for a family of G protein-coupled receptors (S1PR1-S1PR5) with important functions in the vascular and immune systems. Here we explore the role of these kinases and receptors in recovery from anaphylaxis in mice. We found that Sphk2-\/- mice had a rapid recovery from anaphylaxis. In contrast, Sphk1-\/- mice showed poor recovery from anaphylaxis and delayed histamine clearance. Injection of S1P into Sphk1-\/- mice increased histamine clearance and promoted recovery from anaphylaxis. Adoptive cell transfer experiments demonstrated that SphK1 activity was required in both the hematopoietic and nonhematopoietic compartments for recovery from anaphylaxis. Mice lacking the S1P receptor S1PR2 also showed a delay in plasma histamine clearance and a poor recovery from anaphylaxis. However, S1P did not promote the recovery of S1pr2-\/- mice from anaphylaxis, whereas S1pr2+\/- mice showed partial recovery. Unlike Sphk2-\/- mice, Sphk1-\/- and S1pr2-\/- mice had severe hypotension during anaphylaxis. Thus, SphK1-produced S1P regulates blood pressure, histamine clearance, and recovery from anaphylaxis in a manner that involves S1PR2. This suggests that specific S1PR2 agonists may serve to counteract the vasodilation associated with anaphylactic shock.","authors":"Olivera, A., Eisner, C., Kitamura, Y., Dillahunt, S., Allende, L., Tuymetova, G., Watford, W., Meylan, F., Diesner, SC., Li, L., Schnermann, J., Proia, RL., Rivera, J.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Clin Invest","volume":"120","issue":"5","page":"1429-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-05-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20360068","title":"Systematic analysis of human protein complexes identifies chromosome segregation proteins.","abstract":"Chromosome segregation and cell division are essential, highly ordered processes that depend on numerous protein complexes. Results from recent RNA interference screens indicate that the identity and composition of these protein complexes is incompletely understood. Using gene tagging on bacterial artificial chromosomes, protein localization, and tandem-affinity purification-mass spectrometry, the MitoCheck consortium has analyzed about 100 human protein complexes, many of which had not or had only incompletely been characterized. This work has led to the discovery of previously unknown, evolutionarily conserved subunits of the anaphase-promoting complex and the gamma-tubulin ring complex--large complexes that are essential for spindle assembly and chromosome segregation. The approaches we describe here are generally applicable to high-throughput follow-up analyses of phenotypic screens in mammalian cells.","authors":"Hutchins, JR., Toyoda, Y., Hegemann, B., Poser, I., H\u00e9rich\u00e9, JK., Sykora, MM., Augsburg, M., Hudecz, O., Buschhorn, BA., Bulkescher, J., Conrad, C., Comartin, D., Schleiffer, A., Sarov, M., Pozniakovsky, A., Slabicki, MM., Schloissnig, S., Steinmacher, I., Leuschner, M., Ssykor, A., Lawo, S., Pelletier, L., Stark, H., Nasmyth, K., Ellenberg, J., Durbin, R., Buchholz, F., Mechtler, K., Hyman, AA., Peters, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Science","volume":"328","issue":"5978","page":"593-9","pdf":null,"JrId":"7473","fulltextlink":null,"preprintlink":null,"articledate":"2010-05-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20356927","title":"Evidence that the tumor-suppressor protein BRCA2 does not regulate cytokinesis in human cells.","abstract":"Germline mutations in the tumor-suppressor gene BRCA2 predispose to breast and ovarian cancer. BRCA2 plays a well-established role in maintaining genome stability by regulating homologous recombination. BRCA2 has more recently been implicated in cytokinesis, the final step of cell division, but the molecular basis for this remains unknown. We have used time-lapse microscopy, recently developed cytokinesis assays and BAC recombineering (bacterial artificial chromosome recombinogenic engineering) to investigate the function and localization of BRCA2 during cell division. Our analysis suggests that BRCA2 does not regulate cytokinesis in human cells. Thus, cytokinesis defects are unlikely to contribute to chromosomal instability and tumorigenesis in BRCA2-related cancers.","authors":"Lekomtsev, S., Guizetti, J., Pozniakovsky, A., Gerlich, DW., Petronczki, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Cell Sci","volume":"123","issue":"Pt 9","page":"1395-400","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20352235","title":"Novel insights into the mechanisms mediating the local antihypertrophic effects of cardiac atrial natriuretic peptide: role of cGMP-dependent protein kinase and RGS2.","abstract":"Cardiac atrial natriuretic peptide (ANP) locally counteracts cardiac hypertrophy via the guanylyl cyclase-A (GC-A) receptor and cGMP production, but the downstream signalling pathways are unknown. Here, we examined the influence of ANP on beta-adrenergic versus Angiotensin II (Ang II)-dependent (G(s) vs. G(alphaq) mediated) modulation of Ca(2+) (i)-handling in cardiomyocytes and of hypertrophy in intact hearts. L-type Ca(2+) currents and Ca(2+) (i) transients in adult isolated murine ventricular myocytes were studied by voltage-clamp recordings and fluorescence microscopy. ANP suppressed Ang II-stimulated Ca(2+) currents and transients, but had no effect on isoproterenol stimulation. Ang II suppression by ANP was abolished in cardiomyocytes of mice deficient in GC-A, in cyclic GMP-dependent protein kinase I (PKG I) or in the regulator of G protein signalling (RGS) 2, a target of PKG I. Cardiac hypertrophy in response to exogenous Ang II was significantly exacerbated in mice with conditional, cardiomyocyte-restricted GC-A deletion (CM GC-A KO). This was concomitant to increased activation of the Ca(2+)\/calmodulin-dependent prohypertrophic signal transducer CaMKII. In contrast, beta-adrenoreceptor-induced hypertrophy was not enhanced in CM GC-A KO mice. Lastly, while the stimulatory effects of Ang II on Ca(2+)-handling were absent in myocytes of mice deficient in TRPC3\/TRPC6, the effects of isoproterenol were unchanged. Our data demonstrate a direct myocardial role for ANP\/GC-A\/cGMP to antagonize the Ca(2+) (i)-dependent hypertrophic growth response to Ang II, but not to beta-adrenergic stimulation. The selectivity of this interaction is determined by PKG I and RGS2-dependent modulation of Ang II\/AT(1) signalling. Furthermore, they strengthen published observations in neonatal cardiomyocytes showing that TRPC3\/TRPC6 channels are essential for Ang II, but not for beta-adrenergic Ca(2+) (i)-stimulation in adult myocytes.","authors":"Klaiber, M., Kruse, M., V\u00f6lker, K., Schr\u00f6ter, J., Feil, R., Freichel, M., Gerling, A., Feil, S., Dietrich, A., Londo\u00f1o, JE., Baba, HA., Abramowitz, J., Birnbaumer, L., Penninger, JM., Pongs, O., Kuhn, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Basic Res Cardiol","volume":"105","issue":"5","page":"583-95","pdf":null,"JrId":"954","fulltextlink":null,"preprintlink":null,"articledate":"2010-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20308537","title":"MIPs are ancestral ligands for the sex peptide receptor.","abstract":"Upon mating, females of many animal species undergo dramatic changes in their behavior. In Drosophila melanogaster, postmating behaviors are triggered by sex peptide (SP), which is produced in the male seminal fluid and transferred to female during copulation. SP modulates female behaviors via sex peptide receptor (SPR) located in a small subset of internal sensory neurons that innervate the female uterus and project to the CNS. Although required for postmating responses only in these female sensory neurons, SPR is expressed broadly in the CNS of both sexes. Moreover, SPR is also encoded in the genomes of insects that lack obvious SP orthologs. These observations suggest that SPR may have additional ligands and functions. Here, we identify myoinhibitory peptides (MIPs) as a second family of SPR ligands that is conserved across a wide range of invertebrate species. MIPs are potent agonists for Drosophila, Aedes, and Aplysia SPRs in vitro, yet are unable to trigger postmating responses in vivo. In contrast to SP, MIPs are not produced in male reproductive organs, and are not required for postmating behaviors in Drosophila females. We conclude that MIPs are evolutionarily conserved ligands for SPR, which are likely to mediate functions other than the regulation of female reproductive behaviors.","authors":"Kim, YJ., Bartalska, K., Audsley, N., Yamanaka, N., Yapici, N., Lee, JY., Kim, YC., Markovic, M., Isaac, E., Tanaka, Y., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Proc Natl Acad Sci U S A","volume":"107","issue":"14","page":"6520-5","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2010-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20208542","title":"PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1\/2 demethylation.","abstract":"Histone lysine methylation is dynamically regulated by lysine methyltransferases and lysine demethylases. Here we show that PHD finger protein 8 (PHF8), a protein containing a PHD finger and a Jumonji C (JmjC) domain, is associated with hypomethylated rRNA genes (rDNA). PHF8 interacts with the RNA polymerase I transcription machinery and with WD repeat-containing protein 5 (WDR5)-containing H3K4 methyltransferase complexes. PHF8 exerts a positive effect on rDNA transcription, with transcriptional activation requiring both the JmjC domain and the PHD finger. PHF8 demethylates H3K9me1\/2, and its catalytic activity is stimulated by adjacent H3K4me3. A point mutation within the JmjC domain that is linked to mental retardation with cleft lip and palate (XLMR-CL\/P) abolishes demethylase activity and transcriptional activation. Though further work is needed to unravel the contribution of PHF8 activity to mental retardation and cleft lip\/palate, our results reveal a functional interplay between H3K4 methylation and H3K9me1\/2 demethylation, linking dynamic histone methylation to rDNA transcription and neural disease.","authors":"Feng, W., Yonezawa, M., Ye, J., Jenuwein, T., Grummt, I.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Struct Mol Biol","volume":"17","issue":"4","page":"445-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30267714","title":"Intestinal Inflammation and Dysregulated Immunity in Patients With Inherited Caspase-8 Deficiency.","abstract":null,"authors":"Lehle, AS., Farin, HF., Marquardt, B., Michels, BE., Magg, T., Li, Y., Liu, Y., Ghalandary, M., Lammens, K., Hollizeck, S., Rohlfs, M., Hauck, F., Conca, R., Walz, C., Weiss, B., Lev, A., Simon, AJ., Gro\u00df, O., Gaidt, MM., Hornung, V., Clevers, H., Yazbeck, N., Hanna-Wakim, R., Shouval, DS., Warner, N., Somech, R., Muise, AM., Snapper, SB., Bufler, P., Koletzko, S., Klein, C., Kotlarz, D.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Gastroenterology","volume":"156","issue":"1","page":"275-278","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20201521","title":"Probing the phosphoproteome of HeLa cells using nanocast metal oxide microspheres for phosphopeptide enrichment.","abstract":"Metal oxide affinity chromatography (MOAC) has become a prominent method to enrich phosphopeptides prior to their analysis by liquid chromatography-mass spectrometry. To overcome limitations in material design, we have previously reported the use of nanocasting as a means to generate metal oxide spheres with tailored properties. Here, we report on the application of two oxides, tin dioxide (stannia) and titanium dioxide (titania), for the analysis of the HeLa phosphoproteome. In combination with nanoflow LC-MS\/MS analysis on a linear ion trap-Fourier transform ion cyclotron resonance instrument, we identified 619 phosphopeptides using the new stannia material, and 896 phosphopeptides using titania prepared in house. We also compared the newly developed materials to commercial titania material using an established enrichment protocol. Both titania materials yielded a comparable total number of phosphopeptides, but the overlap of the two data sets was less than one-third. Although fewer peptides were identified using stannia, the complementarity of SnO(2)-based MOAC could be shown as more than 140 phosphopeptides were exclusively identified by this material.","authors":"Leitner, A., Sturm, M., Hudecz, O., Mazanek, M., Sm\u00e5tt, JH., Lind\u00e9n, M., Lindner, W., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Anal Chem","volume":"82","issue":"7","page":"2726-33","pdf":null,"JrId":"519","fulltextlink":null,"preprintlink":null,"articledate":"2010-06-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20190740","title":"Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia.","abstract":"MicroRNAs (miRNAs) have emerged as novel cancer genes. In particular, the miR-17-92 cluster, containing six individual miRNAs, is highly expressed in haematopoietic cancers and promotes lymphomagenesis in vivo. Clinical use of these findings hinges on isolating the oncogenic activity within the 17-92 cluster and defining its relevant target genes. Here we show that miR-19 is sufficient to promote leukaemogenesis in Notch1-induced T-cell acute lymphoblastic leukaemia (T-ALL) in vivo. In concord with the pathogenic importance of this interaction in T-ALL, we report a novel translocation that targets the 17-92 cluster and coincides with a second rearrangement that activates Notch1. To identify the miR-19 targets responsible for its oncogenic action, we conducted a large-scale short hairpin RNA screen for genes whose knockdown can phenocopy miR-19. Strikingly, the results of this screen were enriched for miR-19 target genes, and include Bim (Bcl2L11), AMP-activated kinase (Prkaa1) and the phosphatases Pten and PP2A (Ppp2r5e). Hence, an unbiased, functional genomics approach reveals a coordinate clampdown on several regulators of phosphatidylinositol-3-OH kinase-related survival signals by the leukaemogenic miR-19.","authors":"Mavrakis, KJ., Wolfe, AL., Oricchio, E., Palomero, T., de Keersmaecker, K., McJunkin, K., Zuber, J., James, T., Khan, AA., Leslie, CS., Parker, JS., Paddison, PJ., Tam, W., Ferrando, A., Wendel, HG.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Nat Cell Biol","volume":"12","issue":"4","page":"372-9","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20179086","title":"CD271 antigen defines a subset of multipotent stromal cells with immunosuppressive and lymphohematopoietic engraftment-promoting properties.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20179086<\/PMID><DateCompleted><Year>2010<\/Year><Month>08<\/Month><Day>24<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>12<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1592-8721<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>95<\/Volume><Issue>4<\/Issue><PubDate><Year>2010<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>Haematologica<\/Title><ISOAbbreviation>Haematologica<\/ISOAbbreviation><\/Journal><ArticleTitle>CD271 antigen defines a subset of multipotent stromal cells with immunosuppressive and lymphohematopoietic engraftment-promoting properties.<\/ArticleTitle><Pagination><MedlinePgn>651-9<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.3324\/haematol.2009.015065<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Background In vitro proliferative and differentiation potential of mesenchymal stromal cells generated from CD271(+) bone marrow mononuclear cells (CD271-mesenchymal stromal cells) has been demonstrated in several earlier and recent reports. In the present study we focused, in addition to proliferative and differentiation potential, on in vitro and in vivo immunosuppressive and lymphohematopoietic engraftment-promoting potential of these mesenchymal stromal cells compared to bone marrow-derived mesenchymal stromal cells generated by plastic adherence (plastic adherence-mesenchymal stromal cells).","authors":"Ku\u00e7i, S., Ku\u00e7i, Z., Kreyenberg, H., Deak, E., P\u00fctsch, K., Huenecke, S., Amara, C., Koller, S., Rettinger, E., Grez, M., Koehl, U., Latifi-Pupovci, H., Henschler, R., Tonn, T., von Laer, D., Klingebiel, T., Bader, P.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Haematologica","volume":"95","issue":"4","page":"651-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16228011","title":"Drosophila Ric-8 is essential for plasma-membrane localization of heterotrimeric G proteins.","abstract":"Heterotrimeric G proteins act during signal transduction in response to extracellular ligands. They are also required for spindle orientation and cell polarity during asymmetric cell division. We show here that, in Drosophila, both functions require the Galpha interaction partner Ric-8. Drosophila Ric-8 is a cytoplasmic protein that binds both the GDP- and GTP-bound form of the G-protein alpha-subunit Galphai. In ric-8 mutants, neither Galphai nor its associated beta-subunit Gbeta13F are localized at the plasma membrane, which leads to their degradation in the cytosol. During asymmetric cell division, this leads to various defects: apico-basal polarity is not maintained, mitotic spindles are misoriented and the size of the two daughter cells becomes nearly equal. ric-8 mutants also have defects in gastrulation that resemble mutants in the Galpha protein concertina or the extracellular ligand foldedgastrulation. Our results indicate a model in which both receptor-dependent and receptor-independent G-protein functions are executed at the plasma membrane and require the Ric-8 protein.","authors":"Hampoelz, B., Hoeller, O., Bowman, SK., Dunican, D., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nat Cell Biol","volume":"7","issue":"11","page":"1099-105","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2006-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19898465","title":"TAp63 induces senescence and suppresses tumorigenesis in vivo.","abstract":"p63 is distinct from its homologue p53 in that its role as a tumour suppressor is controversial, an issue complicated by the existence of two classes of p63 isoforms. Here we show that TAp63 isoforms are robust mediators of senescence that inhibit tumorigenesis in vivo. Whereas gain of TAp63 induces senescence, loss of p63 enhances sarcoma development in mice lacking p53. Using a new TAp63-specific conditional mouse model, we demonstrate that TAp63 isoforms are essential for Ras-induced senescence, and that TAp63 deficiency increases proliferation and enhances Ras-mediated oncogenesis in the context of p53 deficiency in vivo. TAp63 induces senescence independently of p53, p19(Arf) and p16(Ink4a), but requires p21(Waf\/Cip1) and Rb. TAp63-mediated senescence overrides Ras-driven transformation of p53-deficient cells, preventing tumour initiation, and doxycycline-regulated expression of TAp63 activates p21(Waf\/Cip1), induces senescence and inhibits progression of established tumours in vivo. Our findings demonstrate that TAp63 isoforms function as tumour suppressors by regulating senescence through p53-independent pathways. The ability of TAp63 to trigger senescence and halt tumorigenesis irrespective of p53 status identifies TAp63 as a potential target of anti-cancer therapy for human malignancies with compromised p53.","authors":"Guo, X., Keyes, WM., Papazoglu, C., Zuber, J., Li, W., Lowe, SW., Vogel, H., Mills, AA.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Cell Biol","volume":"11","issue":"12","page":"1451-7","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2009-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20150277","title":"The Trithorax group protein Ash2l and Saf-A are recruited to the inactive X chromosome at the onset of stable X inactivation.","abstract":"Mammals compensate X chromosome gene dosage between the sexes by silencing of one of the two female X chromosomes. X inactivation is initiated in the early embryo and requires the non-coding Xist RNA, which encompasses the inactive X chromosome (Xi) and triggers its silencing. In differentiated cells, several factors including the histone variant macroH2A and the scaffold attachment factor SAF-A are recruited to the Xi and maintain its repression. Consequently, in female somatic cells the Xi remains stably silenced independently of Xist. Here, we identify the Trithorax group protein Ash2l as a novel component of the Xi. Ash2l is recruited by Xist concomitantly with Saf-A and macroH2A at the transition to Xi maintenance. Recruitment of these factors characterizes a developmental transition point for the chromatin composition of the Xi. Surprisingly, expression of a mutant Xist RNA that does not cause gene repression can trigger recruitment of Ash2l, Saf-A and macroH2A to the X chromosome, and can cause chromosome-wide histone H4 hypoacetylation. This suggests that a chromatin configuration is established on non-genic chromatin on the Xi by Xist to provide a repressive compartment that could be used for maintaining gene silencing. Gene silencing is mechanistically separable from the formation of this repressive compartment and, thus, requires additional pathways. This observation highlights a crucial role for spatial organization of chromatin changes in the maintenance of X inactivation.","authors":"Pullirsch, D., H\u00e4rtel, R., Kishimoto, H., Leeb, M., Steiner, G., Wutz, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Development","volume":"137","issue":"6","page":"935-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20134095","title":"Angiotensin-converting enzyme 2 (ACE2) in disease pathogenesis.","abstract":"Angiotensin-converting enzyme 2 (ACE2), a first homolog of ACE, regulates the renin-angiotensin system by counterbalancing ACE activity. Accumulating evidence in recent years has demonstrated a physiological and pathological role of ACE2 in the cardiovascular, renal and respiratory systems. For instance, in the acute respiratory distress syndrome (ARDS), ACE, AngII, and AT1R promote the disease pathogenesis, whereas ACE2 and the AT2R protect from ARDS. Importantly, ACE2 has been identified as a key SARS-coronavirus receptor and plays a protective role in SARS pathogenesis. Furthermore, the recent explosion of research into the ACE2 homolog, collectrin, has revealed a new physiological function of ACE2 as an amino acid transporter, which explains the pathogenic role of gene mutations in Hartnup disorder. This review summarizes and discusses the recently unveiled roles for ACE2 in disease pathogenesis.","authors":"Imai, Y., Kuba, K., Ohto-Nakanishi, T., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Circ J","volume":"74","issue":"3","page":"405-10","pdf":null,"JrId":"27033","fulltextlink":null,"preprintlink":null,"articledate":"2010-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20118233","title":"G9a and Glp methylate lysine 373 in the tumor suppressor p53.","abstract":"The tumor suppressor p53 is regulated by numerous post-translational modifications. Lysine methylation has recently emerged as a key post-translational modification that alters the activity of p53. Here, we describe a novel lysine methylation site in p53 that is carried out by two homologous histone methyltransferases, G9a and Glp. G9a and Glp specifically methylate p53 at Lys(373), resulting mainly in dimethylation. During DNA damage, the overall level of p53 modified at Lys(373)me2 does not increase, despite the dramatic increase in total p53, indicating that Lys(373)me2 correlates with inactive p53. Further, reduction of G9a and\/or Glp levels leads to a larger population of apoptotic cells. Examination of the Oncomine data base shows that G9a and Glp are overexpressed in various cancers compared with corresponding normal tissues, suggesting that they are putative oncogenes. These data reveal a new methylation site within p53 mediated by the methylases G9a and Glp and indicate that G9a is a potential inhibitory target for cancer treatment.","authors":"Huang, J., Dorsey, J., Chuikov, S., Zhang, X., Jenuwein, T., Reinberg, D., Berger, SL.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Biol Chem","volume":"285","issue":"13","page":"9636-9641","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20068589","title":"Mechanistic concepts in X inactivation underlying dosage compensation in mammals.","abstract":"Mammals inactivate one of the two female X chromosomes to compensate for the unequal copy number of X-linked genes between males and females. This process of X inactivation entails the silencing of one X chromosome in a developmentally regulated manner. In this work, we review recent findings in X inactivation and discuss how these advance the mechanistic understanding. Recent results provide an insight how the cell counts and chooses the appropriate number of X chromosomes to inactivate, how chromosome-wide gene repression is coordinated and how a stable inactive X chromosome is established. Key components of this complex regulatory system have now been identified and provide entry points for understanding epigenetic regulation in mammals. A majority of the data has been obtained from studying mice. It is presently not clear how general these findings can be applied to other mammalian species. We try to assess this aspect from data, which has become available.","authors":"Leeb, M., Wutz, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Heredity (Edinb)","volume":"105","issue":"1","page":"64-70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20144763","title":"Distinct protein domains and expression patterns confer divergent axon guidance functions for Drosophila Robo receptors.","abstract":"The orthogonal array of axon pathways in the Drosophila CNS is constructed in part under the control of three Robo family axon guidance receptors: Robo1, Robo2 and Robo3. Each of these receptors is responsible for a distinct set of guidance decisions. To determine the molecular basis for these functional specializations, we used homologous recombination to create a series of 9 \"robo swap\" alleles: expressing each of the three Robo receptors from each of the three robo loci. We demonstrate that the lateral positioning of longitudinal axon pathways relies primarily on differences in gene regulation, not distinct combinations of Robo proteins as previously thought. In contrast, specific features of the Robo1 and Robo2 proteins contribute to their distinct functions in commissure formation. These specializations allow Robo1 to prevent crossing and Robo2 to promote crossing. These data demonstrate how diversification of expression and structure within a single family of guidance receptors can shape complex patterns of neuronal wiring.","authors":"Spitzweck, B., Brankatschk, M., Dickson, BJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell","volume":"140","issue":"3","page":"409-20","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"41","title":"Stabilization of the globular structure of ferricytochrome c by chloride in acidic solvents.","abstract":"Increasing concentrations of chloride were found to increase the resolution between two visible absorbance spectral transitions associated with acidification of ferricytochrome c. Analysis of a variety of spectral and viscosity measurements indicates that protonation of a single group having an apparent pK of 2.1 +\/- 0.2 and an intrinsic pK of about 5.3 displaces the methionine ligand without significantly perturbing the native globular conformation. Analysis of methylated ferricytochrome c suggests that protonation of a carboxylate ion, most likely a heme propionate residue, is responsible for displacement of the methionine ligand. Addition of a proton to a second group having an apparent pK of 1.2 +\/- 0.1 displaces the histidine ligand and unfolds the protein from a globular conformation into a random coil. It is most likely that the second protonation occurs on the imidazole ring of the histidine ligand itself. Chloride is proposed to perturb these transitions by ligation in the fifth coordination position of the heme ion. Such ligation stabilizes a globular conformation of ferricytochrome c at pH 0.0 and 25 degrees.","authors":"Stellwagen, E., Babul, J.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"23","page":"5135-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20060835","title":"The structure of the Salmonella typhimurium type III secretion system needle shows divergence from the flagellar system.","abstract":"The type III secretion system (T3SS) is essential for the infectivity of many pathogenic Gram-negative bacteria. The T3SS contains proteins that form a channel in the inner and outer bacterial membranes, as well as an extracellular needle that is used for transporting and injecting effector proteins into a host cell. The homology between the T3SS and the bacterial flagellar system has been firmly established, based upon both sequence similarities between respective proteins in the two systems and the structural homology of higher-order assemblies. It has previously been shown that the Shigella flexneri needle has a helical symmetry of approximately 5.6 subunits\/turn, which is quite similar to that of the most intensively studied flagellar filament (from Salmonella typhimurium), which has approximately 5.5 subunits\/turn. We now show that the Sa. typhimurium needle, expected by homology arguments to be more similar to the Sa. typhimurium flagellar filament than is the needle from Shigella, actually has approximately 6.3 subunits\/turn. It is not currently understood how host cell contact, made at the tip of the needle, is communicated to the secretory system at the base. In contrast to the Sa. typhimurium flagellar filament, which shows a nearly crystalline order, the Sa. typhimurium needle has a highly variable symmetry, which could be used to transmit information about host cell contact.","authors":"Galkin, VE., Schmied, WH., Schraidt, O., Marlovits, TC., Egelman, EH.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Mol Biol","volume":"396","issue":"5","page":"1392-7","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20053868","title":"Replicative senescence-associated gene expression changes in mesenchymal stromal cells are similar under different culture conditions.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">20053868<\/PMID><DateCompleted><Year>2011<\/Year><Month>08<\/Month><Day>08<\/Day><\/DateCompleted><DateRevised><Year>2018<\/Year><Month>12<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1592-8721<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>95<\/Volume><Issue>6<\/Issue><PubDate><Year>2010<\/Year><Month>Jun<\/Month><\/PubDate><\/JournalIssue><Title>Haematologica<\/Title><ISOAbbreviation>Haematologica<\/ISOAbbreviation><\/Journal><ArticleTitle>Replicative senescence-associated gene expression changes in mesenchymal stromal cells are similar under different culture conditions.<\/ArticleTitle><Pagination><MedlinePgn>867-74<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.3324\/haematol.2009.011692<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Research on mesenchymal stromal cells has created high expectations for a variety of therapeutic applications. Extensive propagation to yield enough mesenchymal stromal cells for therapy may result in replicative senescence and thus hamper long-term functionality in vivo. Highly variable proliferation rates of mesenchymal stromal cells in the course of long-term expansions under varying culture conditions may already indicate different propensity for cellular senescence. We hypothesized that senescence-associated regulated genes differ in mesenchymal stromal cells propagated under different culture conditions.","authors":"Schallmoser, K., Bartmann, C., Rohde, E., Bork, S., Guelly, C., Obenauf, AC., Reinisch, A., Horn, P., Ho, AD., Strunk, D., Wagner, W.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Haematologica","volume":"95","issue":"6","page":"867-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20045679","title":"Developmental gene regulation in the era of genomics.","abstract":"Genetic experiments over the last few decades have identified many developmental control genes critical for pattern formation and cell fate specification during the development of multicellular organisms. A large fraction of these genes encode transcription factors and signaling molecules, show highly dynamic expression patterns during development, and are deeply evolutionarily conserved and deregulated in various human diseases such as cancer. Because of their importance in development, evolution, and disease, a fundamental question in biology is how these developmental control genes are regulated in such an extensive and precise fashion. Using genomics methods, it has become clear that developmental control genes are a distinct group of genes with special regulatory characteristics. However, a systematic analysis of these characteristics has not been presented. Here we review how developmental control genes were discovered, evaluate their genome-wide regulation and gene structure, discuss emerging evidence for their mode of regulation, and estimate their overall abundance in the genome. Understanding the global regulation of developmental control genes may provide a new perspective on development in the era genomics.","authors":"Zeitlinger, J., Stark, A.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Dev Biol","volume":"339","issue":"2","page":"230-9","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"2010-05-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20040592","title":"Neuron-type specific regulation of a 3'UTR through redundant and combinatorially acting cis-regulatory elements.","abstract":"3' Untranslated region (UTR)-dependent post-transcriptional regulation has emerged as a critical mechanism of controlling gene expression in various physiological contexts, including cellular differentiation events. Here, we examine the regulation of the 3'UTR of the die-1 transcription factor in a single neuron of the nematode C. elegans. This 3'UTR shows the intriguing feature of being differentially regulated across the animal's left\/right axis. In the left gustatory neuron, ASEL, in which DIE-1 protein is normally expressed in adult animals, the 3'UTR confers no regulatory information, while in the right gustatory neuron, ASER, where DIE-1 is normally not expressed, this 3'UTR confers negative regulatory information. Here, we systematically analyze the cis-regulatory architecture of the die-1 3'UTR using a transgenic, in vivo assay system. Through extensive mutagenesis and sequence insertions into heterologous 3'UTR contexts, we describe three 25-base-pair (bp) sequence elements that are both required and sufficient to mediate the ASER-specific down-regulation of the die-1 3'UTR. These three 25-bp sequence elements operate in both a redundant and combinatorial manner. Moreover, there are not only redundant elements within the die-1 3'UTR regulating its left\/right asymmetric activity but asymmetric 3'UTR regulation is itself redundant with other regulatory mechanisms to achieve asymmetric DIE-1 protein expression and function in ASEL versus ASER. The features of 3'UTR regulation we describe here may apply to some of the vast number of genes in animal genomes whose expression is predicted to be regulated through their 3'UTR.","authors":"Didiano, D., Cochella, L., Tursun, B., Hobert, O.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"RNA","volume":"16","issue":"2","page":"349-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27572465","title":"Pore formation by GSDMD is the effector mechanism of pyroptosis.","abstract":null,"authors":"Gaidt, MM., Hornung, V.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"EMBO J","volume":"35","issue":"20","page":"2167-2169","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35337465","title":"The Axolotl's journey to the modern molecular era.","abstract":"The salamander Ambystoma mexicanum, commonly called \"the axolotl\" has a long, illustrious history as a model organism, perhaps with one of the longest track records as a laboratory-bred vertebrate, yet it also holds a prominent place among the emerging model organisms. Or rather it is by now an \"emerged\" model organism, boasting a full cohort molecular genetic tools that allows an expanding community of researchers in the field to explore the remarkable traits of this animal including regeneration, at cellular and molecular precision-which had been a dream for researchers over the years. This chapter describes the journey to this status, that could be helpful for those developing their respective animal or plant models.","authors":"Echeverri, K., Fei, J., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Curr Top Dev Biol","volume":"147","issue":null,"page":"631-658","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"20023287","title":"Growth retardation, impaired triacylglycerol catabolism, hepatic steatosis, and lethal skin barrier defect in mice lacking comparative gene identification-58 (CGI-58).","abstract":"Comparative gene identification-58 (CGI-58), also designated as alpha\/beta-hydrolase domain containing-5 (ABHD-5), is a lipid droplet-associated protein that activates adipose triglyceride lipase (ATGL) and acylates lysophosphatidic acid. Activation of ATGL initiates the hydrolytic catabolism of cellular triacylglycerol (TG) stores to glycerol and nonesterified fatty acids. Mutations in both ATGL and CGI-58 cause \"neutral lipid storage disease\" characterized by massive accumulation of TG in various tissues. The analysis of CGI-58-deficient (Cgi-58(-\/-)) mice, presented in this study, reveals a dual function of CGI-58 in lipid metabolism. First, systemic TG accumulation and severe hepatic steatosis in newborn Cgi-58(-\/-) mice establish a limiting role for CGI-58 in ATGL-mediated TG hydrolysis and supply of nonesterified fatty acids as energy substrate. Second, a severe skin permeability barrier defect uncovers an essential ATGL-independent role of CGI-58 in skin lipid metabolism. The neonatal lethal skin barrier defect is linked to an impaired hydrolysis of epidermal TG. As a consequence, sequestration of fatty acids in TG prevents the synthesis of acylceramides, which are essential lipid precursors for the formation of a functional skin permeability barrier. This mechanism may also underlie the pathogenesis of ichthyosis in neutral lipid storage disease patients lacking functional CGI-58.","authors":"Radner, FP., Streith, IE., Schoiswohl, G., Schweiger, M., Kumari, M., Eichmann, TO., Rechberger, G., Koefeler, HC., Eder, S., Schauer, S., Theussl, HC., Preiss-Landl, K., Lass, A., Zimmermann, R., Hoefler, G., Zechner, R., Haemmerle, G.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Biol Chem","volume":"285","issue":"10","page":"7300-11","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19995970","title":"Systemic anti-VEGF treatment strongly reduces skin inflammation in a mouse model of psoriasis.","abstract":"Although(,) vascular remodeling is a hallmark of many chronic inflammatory disorders such as rheumatoid arthritis, inflammatory bowel disease, and psoriasis, anti-vascular strategies to treat these conditions have received little attention to date. We investigated the anti-inflammatory activity of systemic blockade of VEGF-A by the inhibitory monoclonal antibody G6-31, employing a therapeutic trial in a mouse model of psoriasis. Simultaneous deletion of JunB and c-Jun (DKO*) in the epidermis of adult mice leads to a psoriasis-like phenotype with hyper- and parakeratosis and increased subepidermal vascularization. Moreover, an inflammatory infiltrate and elevated levels of cytokines\/chemokines including TNFalpha, IL-1alpha\/beta, IL-6, and the innate immune mediators IL-22, IL-23, IL-23R, and IL-12p40 are detected. Here we show that anti-VEGF antibody treatment of mice already displaying disease symptoms resulted in an overall improvement of the psoriatic lesions leading to a reduction in the number of blood vessels and a significant decrease in the size of dermal blood and lymphatic vessels. Importantly, anti-VEGF-treated mice showed a pronounced reduction of inflammatory cells within the dermis and a normalization of epidermal differentiation. These results demonstrate that systemic blockade of VEGF by an inhibitory antibody might be used to treat patients who have inflammatory skin disorders such as psoriasis.","authors":"Schonthaler, HB., Huggenberger, R., Wculek, SK., Detmar, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Proc Natl Acad Sci U S A","volume":"106","issue":"50","page":"21264-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19995937","title":"The Cul3-KLHL21 E3 ubiquitin ligase targets aurora B to midzone microtubules in anaphase and is required for cytokinesis.","abstract":"Cul3 (Cullin3)-based E3 ubiquitin ligases recently emerged as critical regulators of mitosis. In this study, we identify two mammalian BTB (Bric-a-brac-Tramtrack-Broad complex)-Kelch proteins, KLHL21 and KLHL22, that interact with Cul3 and are required for efficient chromosome alignment. Interestingly, KLHL21 but not KLHL22 is necessary for cytokinesis and regulates translocation of the chromosomal passenger complex (CPC) from chromosomes to the spindle midzone in anaphase, similar to the previously described BTB-Kelch proteins KLHL9 and KLHL13. KLHL21 directly binds to aurora B and mediates ubiquitination of aurora B in vitro. In contrast to KLHL9 and KLHL13, KLHL21 localizes to midzone microtubules in anaphase and recruits aurora B and Cul3 to this region. Together, our results suggest that different Cul3 adaptors nonredundantly regulate aurora B during mitosis, possibly by ubiquitinating different pools of aurora B at distinct subcellular localizations.","authors":"Maerki, S., Olma, MH., Staubli, T., Steigemann, P., Gerlich, DW., Quadroni, M., Sumara, I., Peter, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Biol","volume":"187","issue":"6","page":"791-800","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19939982","title":"Differential epigenomic and transcriptomic responses in subcutaneous adipose tissue between low and high responders to caloric restriction.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19939982<\/PMID><DateCompleted><Year>2010<\/Year><Month>02<\/Month><Day>22<\/Day><\/DateCompleted><DateRevised><Year>2015<\/Year><Month>07<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1938-3207<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>91<\/Volume><Issue>2<\/Issue><PubDate><Year>2010<\/Year><Month>Feb<\/Month><\/PubDate><\/JournalIssue><Title>The American journal of clinical nutrition<\/Title><ISOAbbreviation>Am J Clin Nutr<\/ISOAbbreviation><\/Journal><ArticleTitle>Differential epigenomic and transcriptomic responses in subcutaneous adipose tissue between low and high responders to caloric restriction.<\/ArticleTitle><Pagination><MedlinePgn>309-20<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.3945\/ajcn.2009.28085<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Caloric restriction is recommended for the treatment of obesity, but it is generally characterized by large interindividual variability in responses. The factors affecting the magnitude of weight loss remain poorly understood. Epigenetic factors (ie, heritable but reversible changes to genomic function that regulate gene expression independently of DNA sequence) may explain some of the interindividual variability seen in weight-loss responses.","authors":"Bouchard, L., Rabasa-Lhoret, R., Faraj, M., Lavoie, ME., Mill, J., P\u00e9russe, L., Vohl, MC.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Am J Clin Nutr","volume":"91","issue":"2","page":"309-20","pdf":null,"JrId":"412","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19934646","title":"Frequent epigenetic inactivation of RASSF10 in thyroid cancer.","abstract":"The Ras association domain family (RASSF) encodes for distinct tumor suppressors and several members are frequently silenced in human cancer. In our study, we analyzed the role of a novel RASSF member termed RASSF10 in thyroid carcinogenesis. The RASSF10 CpG island promoter was intensively methylated in nine thyroid cancer cell lines and in 66% of primary thyroid carcinomas. RASSF10 methylation was significantly increased in primary thyroid carcinoma compared to normal thyroid and follicular adenoma (0 and 10%, respectively; p &lt; 0.004). Patients with cancerous lymph nodes were significantly hypermethylated for RASSF10 in primary thyroid tumors compared to those with non-affected lymph nodes (79 vs. 36%; p = 0.047). RASSF10 promoter hypermethylation correlated with a reduced expression and treatment with a DNA methylation inhibitor reactivated RASSF10 transcription. In summary, our data show frequent epigenetic inactivation of RASSF10 in thyroid cancer. These results suggest that RASSF10 may encode a novel epigenetically inactivated candidate tumor suppressor gene in thyroid carcinogenesis.","authors":"Schagdarsurengin, U., Richter, AM., W\u00f6hler, C., Dammann, RH.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Epigenetics","volume":"4","issue":"8","page":"571-6","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19934035","title":"Regulation of hippocampal H3 histone methylation by acute and chronic stress.","abstract":"The hippocampal formation is a brain region noted for its plasticity in response to stressful events and adrenal steroid hormones. Recent work has shown that chromatin remodeling in various brain regions, including the hippocampus, is associated with the effects of stress in a variety of models. We chose to examine the effects of stress, stress duration, corticosterone administration, and fluoxetine treatment on the levels of hippocampal histone H3 methylation at lysines 4, 9, and 27, marks associated, respectively, with active transcription, heterochromatin formation, and transcriptional repression. We found that acute stress increased the levels of H3K9 tri-methylation (H3K9me3) in the dentate gyrus (DG) and CA1, while it reduced levels of H3K9 mono-methylation (H3K9me1) and H3K27 tri-methylation (H3K27me3) in the same regions, and had no effect on levels of H3K4 tri-methylation (H3K4me3). Seven days of restraint stress reduced levels of H3K4me3 in the CA1 and H3K27me3 in the DG and CA1, while increasing basal levels of H3K9me3. Chronic restraint stress (CRS) for 21 days mildly increased levels of H3K4me3 and reduced H3K9me3 levels in the DG. Treatment with fluoxetine during CRS reversed the decrease in DG H3K9me3, but had no effect on the other marks. These results show a complex, surprisingly rapid, and regionally specific pattern of chromatin remodeling within hippocampus produced by stress and anti-depressant treatment that may open an avenue of understanding the interplay of stress and hippocampal gene expression, and reveal the outlines of a potential chromatin stress response that may be diminished or degraded by chronic stress.","authors":"Hunter, RG., McCarthy, KJ., Milne, TA., Pfaff, DW., McEwen, BS.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Proc Natl Acad Sci U S A","volume":"106","issue":"49","page":"20912-7","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"2010-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11700297","title":"Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis.","abstract":"The separation of sister chromatids at the metaphase to anaphase transition is one of the most dramatic of all cellular events and is a crucial aspect of all sexual and asexual reproduction. The molecular basis for this process has until recently remained obscure. New research has identified proteins that hold sisters together while they are aligned on the metaphase plate. It has also shed insight into the mechanisms that dissolve sister chromatid cohesion during both mitosis and meiosis. These findings promise to provide insights into defects in chromosome segregation that occur in cancer cells and into the pathological pathways by which aneuploidy arises during meiosis.","authors":"Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Annu Rev Genet","volume":"35","issue":null,"page":"673-745","pdf":null,"JrId":"668","fulltextlink":null,"preprintlink":null,"articledate":"2002-01-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19924135","title":"Alterations of the cell-cycle inhibitors p27(KIP1) and p16(INK4a) are frequent in blastic plasmacytoid dendritic cell neoplasms.","abstract":"Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare, clinically aggressive malignancy with a median survival of 12-14 months. To identify pathogenetic relevant genomic aberrations and molecular targets for therapy, we analyzed skin biopsy samples obtained from 14 patients using high-resolution array-based comparative genomic hybridization and immunostaining. Losses of chromosomes 9, 12, 13, and 15 were detected most frequently. Loss of the CDKN1B locus was the most common finding and was detected in 64% of tumors. In all but one case, the dose-dependent haploinsufficient cell-cycle inhibitor p27(KIP1), encoded by CDKN1B, was weakly expressed in the nuclei of tumor cells. Losses of the CDKN2A-ARF-CDKN2B locus occurred in 50% of patients, and in one case a distinct biallelic loss was identified. The cell-cycle inhibitor p16(INK4a), which is encoded by CDKN2A, was not expressed in tumor cells, suggesting a complete loss of function. Loss of chromosome 13, including the RB1 gene, was observed in 43% of tumors. These results imply that alterations of the cell-cycle checkpoint controlling proteins p27(KIP1), p16(INK4a), and RB1 may exert a profound effect in malignant transformation in BPDCN. The elucidation of the affected pathways may guide the development of new treatments specifically designed for this aggressive disease entity.","authors":"Wiesner, T., Obenauf, AC., Cota, C., Fried, I., Speicher, MR., Cerroni, L.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Invest Dermatol","volume":"130","issue":"4","page":"1152-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19923891","title":"The Mi-2\/NuRD complex: a critical epigenetic regulator of hematopoietic development, differentiation and cancer.","abstract":"The Mi-2\/NuRD chromatin remodeling complex links multiple transcriptional regulatory processes including histone deacetylation, histone demethylation, nucleosome mobilization and recruitment of other regulatory proteins. In some contexts, Mi-2\/NuRD functions as a barrier to transcriptional activation by working in opposition to other chromatin remodelers such as SWI\/SNF. Alternatively, the Mi-2beta ATPase subunit of Mi-2\/NuRD can promote transcription. Together, these gatekeeper functions of Mi-2\/NuRD influence cell fate decisions by modulating transcriptional activity. Recent studies have shown the importance of Mi-2\/NuRD both in maintaining hematopoietic stem cell (HSC) pools and in normal lineage progression. Furthermore, components of Mi-2\/NuRD complexes are modular co-repressors\/co-activators comprising multiple protein subunits that have been linked directly to oncogenesis and have potential as therapeutic targets for cancer treatment. Mi-2\/NuRD's essential functions in metazoan cell fates and activities underscore its importance as a focal point of epigenetic research.","authors":"Ram\u00edrez, J., Hagman, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Epigenetics","volume":"4","issue":"8","page":"532-6","pdf":null,"JrId":"33241","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19920814","title":"Learning the transcriptional regulatory code.","abstract":null,"authors":"Stark, A.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Mol Syst Biol","volume":"5","issue":null,"page":"329","pdf":null,"JrId":"32538","fulltextlink":null,"preprintlink":null,"articledate":"2010-05-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19918778","title":"Spatial (Tbata) expression in mature medullary thymic epithelial cells.","abstract":"The Spatial gene is expressed in highly polarized cell types such as testis germ cells, brain neurons and thymic epithelial cells (TEC). Its expression was documented in testis and brain but poorly characterized in thymus. Here, we characterize for the first time Spatial-expressing TEC throughout ontogeny and adult mouse thymus. Spatial is expressed in thymic-fated domain by embryonic day E10.5 and persists in subcapsular, cortical, medullary epithelial cells and in MTS24(+) progenitor TEC. Using mouse strains in which thymocyte development is blocked at various stages, we show that Spatial expression is independent of thymocyte-derived signals during thymus organogenesis. Analyses on purified thymic cell subsets show that Spatial short isoforms are expressed in cortical TEC (cTEC) and mature medullary TEC (mTEC). Spatial long isoforms were detected in the same TEC population. Spatial presents a nuclear distribution specific to mature mTEC expressing UEA1 and Aire. Aire- and RANKL-deficient mice revealed that Spatial expression is drastically reduced in the thymus of these mutants. These findings reveal a critical function of Aire in regulating Spatial expression, which is compatible with promiscuous Spatial gene expression.","authors":"Saade, M., Irla, M., Yammine, M., Boulanger, N., Victorero, G., Vincentelli, R., Penninger, JM., Holl\u00e4nder, GA., Chauvet, S., Nguyen, C.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Eur J Immunol","volume":"40","issue":"2","page":"530-8","pdf":null,"JrId":"3613","fulltextlink":null,"preprintlink":null,"articledate":"2010-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19874196","title":"Cbp recruitment of Csk into lipid rafts is critical to c-Src kinase activity and bone resorption in osteoclasts.","abstract":"A tyrosine kinase, c-Src, that plays an indispensable role in ruffled border formation and bone resorption is constitutively active in osteoclasts. However, to date, the molecular mechanism underlying increased c-Src activity in osteoclasts is unknown. To address this, we first examined the expression levels and subcellular localization of Csk, a negative regulatory kinase for c-Src. We found that the expression level of Csk in osteoclasts was comparable with that of other tissues. However, in osteoclasts, Csk was hardly localized in lipid rafts, where c-Src is highly expressed. Interestingly, expression of Cbp, which recruits Csk into lipid rafts through physical interaction with Csk, was very low in osteoclasts compared with other tissues. To understand the importance of Cbp in osteoclasts, we introduced Cbp into osteoclasts using an adenovirus gene delivery system. Introduction of Cbp stimulated recruitment of Csk into lipid rafts and suppressed c-Src activity in a dose-dependent manner. Furthermore, introduction of Cbp markedly inhibited formation of actin rings and bone-resorbing activity in osteoclasts. In addition, treatment with RANKL and overexpression of TRAF6 or NFAT2 inhibited Cbp expression in the osteoclastogenic cell line RAW264.7 along with osteoclastic differentiation. NFAT2 overexpression also inhibited Cbp expression in spleen macrophages. Collectively, our results indicate that reduction in Cbp expression is responsible for maintaining high c-Src activity in osteoclasts. These findings contribute to an understanding of the unique regulatory system for c-Src in osteoclasts.","authors":"Matsubara, T., Ikeda, F., Hata, K., Nakanishi, M., Okada, M., Yasuda, H., Nishimura, R., Yoneda, T.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"J Bone Miner Res","volume":"25","issue":"5","page":"1068-76","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19855135","title":"Inactivation of Notch signaling in the renal collecting duct causes nephrogenic diabetes insipidus in mice.","abstract":"The heterogeneous cellular composition of the mammalian renal collecting duct enables regulation of fluid, electrolytes, and acid-base homeostasis, but the molecular mechanism of its development has yet to be elucidated. The Notch signaling pathway is involved in cell fate determination and has been implicated in proximal-distal patterning in the mammalian kidney. To investigate the role of Notch signaling in renal collecting duct development, we generated mice in which Mind bomb-1 (Mib1), an E3 ubiquitin ligase required for the initiation of Notch signaling, was specifically inactivated in the ureteric bud of the developing kidney. Mice lacking Mib1 in the renal collecting duct displayed increased urinary production, decreased urinary osmolality, progressive hydronephrosis, sodium wasting, and a severe urinary concentrating defect manifested as nephrogenic diabetes insipidus. Histological analysis revealed a diminished number of principal cells and corresponding increase in the number of intercalated cells. Transgenic overexpression of Notch intracellular domain reversed the altered cellular composition of mutant renal collecting duct, with principal cells occupying the entire region. Our data demonstrate that Notch signaling is required for the development of the mammalian renal collecting duct and principal cell differentiation and indicate that pathway dysregulation may contribute to distal renal tubular disorders.","authors":"Jeong, HW., Jeon, US., Koo, BK., Kim, WY., Im, SK., Shin, J., Cho, Y., Kim, J., Kong, YY.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Clin Invest","volume":"119","issue":"11","page":"3290-300","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19843582","title":"Reprogramming of Xist against the pluripotent state in fusion hybrids.","abstract":"The fusion of somatic cells with pluripotent cells results in the generation of pluripotent hybrid cells. Because the ;memory' of somatic cells seems to be erased during fusion-induced reprogramming, genetic reprogramming is thought to be a largely unidirectional process. Here we show that fusion-induced reprogramming, which brings about the formation of pluripotent hybrids, does not always follow a unidirectional route. Xist is a unique gene in that it is reprogrammed to the state of somatic cells in fusion-induced pluripotent hybrids. In hybrids formed from the cell fusion of embryonal carcinoma cells (ECCs) with male neural stem cells (mNSCs), the Xist gene was found to be reprogrammed to the somatic cell state, whereas the pluripotency-related and tissue-specific marker genes were reprogrammed to the pluripotent cell state. Specifically, Xist is not expressed in hybrids, because the ;memory' of the somatic cell has been retained (i.e. mNSCs do not exhibit Xist expression) and that of the pluripotent cell erased (i.e. inactivation of the partially active Xist gene of ECCs, complete methylation of the Xist region). The latter phenomenon is induced by male, but not by female, NSCs.","authors":"Do, JT., Han, DW., Gentile, L., Sobek-Klocke, I., Wutz, A., Sch\u00f6ler, HR.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Cell Sci","volume":"122","issue":"Pt 22","page":"4122-9","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"2010-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19801644","title":"Essential role of CR6-interacting factor 1 (Crif1) in E74-like factor 3 (ELF3)-mediated intestinal development.","abstract":"Although terminal differentiation of intestinal epithelium is essential for the efficient digestion and absorption of nutrients, little is known about the molecular mechanisms underlying this process. Recent studies have shown that Elf3 (E74-like factor 3), a member of the ETS transcription factor family, has an essential role in the terminal differentiation of absorptive enterocytes and mucus-secreting goblet cells. Here, we demonstrated that Crif1 (CR6-interacting factor 1) functions as transcriptional coactivator of Elf3 in intestinal epithelium differentiation. The intestinal epithelium-specific Crif1-deficient mice died soon after birth and displayed severe alterations of tissue architecture in the small intestine, including poor microvillus formation and abnormal differentiation of absorptive enterocytes. Strikingly, these phenotypes are largely similar to that of Elf3-deficient mice, suggesting that Elf3 signaling in the intestinal epithelium depends on the Crif1 expression. We dissected this relationship further and found that Crif1 indeed interacted with Elf3 through its ETS DNA binding domain and enhanced the transcriptional activity of Elf3 by regulating the DNA binding activity. Knockdown of Crif1 by RNA interference conversely attenuated the transcriptional activity of Elf3. Consistently, the expression level of Tgf-betaRII (transforming growth factor beta type II receptor), a critical target gene of Elf3, was dramatically reduced in the Crif1-deficient mice. Our results reveal that Crif1 is a novel and essential transcriptional coactivator of Elf3 for the terminal differentiation of absorptive enterocytes.","authors":"Kwon, MC., Koo, BK., Kim, YY., Lee, SH., Kim, NS., Kim, JH., Kong, YY.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"J Biol Chem","volume":"284","issue":"48","page":"33634-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36600611","title":"Going high and low: on pluralism and neutrality in human embryology policy-making.","abstract":"Formulating sound and acceptable embryo research policy remains challenging especially in a pluralistic world. This challenge has acquired a new dimension of complexity with the advent of so-called embryo models, which are derived from stem cells. In this article, we present a normative strategy to facilitate the process of sound policy-making in the field of human embryology. This strategy involves seeking neutral agreements on higher level theories and doctrines as well as seeking agreements on the level of concrete policy proposals. We call this strategy: going high and low. By going high and low, the plurality of reasonable moral and epistemic convictions of stakeholders involved in the domain of human embryology is respected while the process of policy-making in this area is improved.","authors":"Ismaili M'hamdi, H., Rivron, NC., Asscher, EC.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"J Med Ethics","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19782426","title":"Blood monocytes stimulate migration of human pancreatic carcinoma cells in vitro: the role of tumour necrosis factor - alpha.","abstract":"In some types of cancers, tumour-infiltrating monocytes\/macrophages (TIM) may be responsible for the formation of an invasive microenvironment in a manner dependent on the secretion of soluble mediators such as tumour necrosis factor-alpha (TNF). Human pancreatic carcinoma (HPC-4) cells are able to induce TNF production by monocytes. Here, the effect of human peripheral blood monocytes, precursors of TIM, on the motility of co-cultured HPC-4 cells, was directly analysed in vitro. A phenotypic transition, i.e., the appearance of rear-front polarised HPC-4 cells paralleled by their increased motility, and increased motility of monocytes, were observed. This effect was attenuated when HPC-4 cells and monocytes were co-cultured in the presence of inhibitors of TNF production and anti-TNF monoclonal antibodies, indicating the specific role of this cytokine in determining paracrine loops between monocytes and cancer cells. Moreover, exogenous TNF induced HPC-4 cell motility concomitantly to the appearance of cellular features characteristic for epithelial-mesenchymal transition (EMT) such as rear-front polarisation, rearrangements of the actin cytoskeleton characteristic for motile cells and the induction of Snail-1 expression. Since cell movement is crucial for cancer invasion and the formation of metastases, these findings demonstrate an EMT-dependent mechanism of cancer progression which acts through the phenotypic transition of pancreatic cancer cells dependent on monocyte-derived TNF.","authors":"Baran, B., Bechyne, I., Siedlar, M., Szpak, K., Mytar, B., Sroka, J., Laczna, E., Madeja, Z., Zembala, M., Czyz, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Eur J Cell Biol","volume":"88","issue":"12","page":"743-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19770394","title":"Survival and cardiac remodeling after myocardial infarction are critically dependent on the host innate immune interleukin-1 receptor-associated kinase-4 signaling: a regulator of bone marrow-derived dendritic cells.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19770394<\/PMID><DateCompleted><Year>2009<\/Year><Month>10<\/Month><Day>23<\/Day><\/DateCompleted><DateRevised><Year>2009<\/Year><Month>11<\/Month><Day>19<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4539<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>120<\/Volume><Issue>14<\/Issue><PubDate><Year>2009<\/Year><Month>Oct<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>Survival and cardiac remodeling after myocardial infarction are critically dependent on the host innate immune interleukin-1 receptor-associated kinase-4 signaling: a regulator of bone marrow-derived dendritic cells.<\/ArticleTitle><Pagination><MedlinePgn>1401-14<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/CIRCULATIONAHA.109.865956<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The innate immune system greatly contributes to the inflammatory process after myocardial infarction (MI). Interleukin-1 receptor-associated kinase-4 (IRAK-4), downstream of Toll\/interleukin-1 receptor signaling, has an essential role in regulating the innate immune response. The present study was designed to determine the mechanism by which IRAK-4 is responsible for the cardiac inflammatory process, which consequently affects left ventricular remodeling after MI.","authors":"Maekawa, Y., Mizue, N., Chan, A., Shi, Y., Liu, Y., Dawood, S., Chen, M., Dawood, F., de Couto, G., Li, GH., Suzuki, N., Yeh, WC., Gramolini, A., Medin, JA., Liu, PP.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Circulation","volume":"120","issue":"14","page":"1401-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19750511","title":"An improved strategy for tandem affinity purification-tagging of Schizosaccharomyces pombe genes.","abstract":"Tandem affinity purification (TAP) is a method that allows rapid purification of native protein complexes. We developed an improved technique to fuse the fission yeast genes with a TAP tag. Our technique is based on tagging constructs that contain regions homologous to the target gene cloned into vectors carrying a TAP tag. We used this technique to design strategies for TAP-tagging of predicted Schizosaccharomyces pombe genes (http:\/\/mendel.imp.ac.at\/Pombe_tagging\/). To validate the approach, we purified the proteins, which associated with two evolutionarily conserved proteins Swi5 and Sfr1 as well as three protein kinases Ksg1, Orb6 and Sid1.","authors":"Cipak, L., Spirek, M., Novatchkova, M., Chen, Z., Rumpf, C., Lugmayr, W., Mechtler, K., Ammerer, G., Csaszar, E., Gregan, J.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Proteomics","volume":"9","issue":"20","page":"4825-8","pdf":null,"JrId":"22472","fulltextlink":null,"preprintlink":null,"articledate":"2010-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19772521","title":"ESCI award lecture: from a little mouse to rationale medicine for bone loss.","abstract":"Completion of the human genome is one of the many significant milestones in the new era of systems biology. The current phase of genomic studies is focused upon parsing this new found genetic data with respect to scientific interest, and economic and health impact applications. As the sequences are now available and whole genome single nucleotide polymorphism maps for multiple human diseases will be available with the advent of modern genomics, the big challenge is to determine the function of these genes in the context of the entire organism. The emphasis is therefore on functional genomic analysis that represents the new front-line and limiting factor for realizing potential benefits of genome-based science. Defined gene targeting has been proven to be particularly useful as loss of expression mutants can reveal essential functions of molecules and the pathogenesis of disease. Using gene-targeted mice, my group has over the years identified genes that control heart and lung functions; apoptosis; lymphocyte activation; cancer; pain; diabetes; fertility or wound healing . In this study, I would like to review our work on RANKL in more detail.","authors":"Leibbrandt, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Eur J Clin Invest","volume":"39","issue":"10","page":"842-50","pdf":null,"JrId":"3611","fulltextlink":null,"preprintlink":null,"articledate":"2010-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11571634","title":"Differential utilization and localization of ErbB receptor tyrosine kinases in skin compared to normal and malignant keratinocytes.","abstract":"Induction of heparin-binding epidermal growth factor-like growth factor (HB-EGF) mRNA in mouse skin organ culture was blocked by two pan-ErbB receptor tyrosine kinase (RTK) inhibitors but not by genetic ablation of ErbB1, suggesting involvement of multiple ErbB species in skin physiology. Human skin, cultured normal keratinocytes, and A431 skin carcinoma cells expressed ErbB1, ErbB2, and ErbB3, but not ErbB4. Skin and A431 cells expressed more ErbB3 than did keratinocytes. Despite strong expression of ErbB2 and ErbB3, heregulin was inactive in stimulating tyrosine phosphorylation in A431 cells. In contrast, it was highly active in MDA-MB-453 breast carcinoma cells. ErbB2 displayed punctate cytoplasmic staining in A431 and keratinocytes, compared to strong cell surface staining in MDA-MB-453. In skin, ErbB2 was cytoplasmic in basal keratinocytes, assuming a cell surface pattern in the upper suprabasal layers. In contrast, ErbB1 retained a cell surface distribution in all epidermal layers. Keratinocyte proliferation in culture was found to be ErbB1-RTK-dependent, using a selective inhibitor. These results suggest that in skin keratinocytes, ErbB2 transduces ligand-dependent differentiation signals, whereas ErbB1 transduces ligand-dependent proliferation\/survival signals. Intracellular sequestration of ErbB2 may contribute to the malignant phenotype of A431 cells, by allowing them to respond to ErbB1-dependent growth\/survival signals, while evading ErbB2-dependent differentiation signals.","authors":"Stoll, SW., Kansra, S., Peshick, S., Fry, DW., Leopold, WR., Wiesen, JF., Sibilia, M., Zhang, T., Werb, Z., Derynck, R., Wagner, EF., Elder, JT.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Neoplasia","volume":"3","issue":"4","page":"339-50","pdf":null,"JrId":"21648","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19730683","title":"The variant rs1867277 in FOXE1 gene confers thyroid cancer susceptibility through the recruitment of USF1\/USF2 transcription factors.","abstract":"In order to identify genetic factors related to thyroid cancer susceptibility, we adopted a candidate gene approach. We studied tag- and putative functional SNPs in genes involved in thyroid cell differentiation and proliferation, and in genes found to be differentially expressed in thyroid carcinoma. A total of 768 SNPs in 97 genes were genotyped in a Spanish series of 615 cases and 525 controls, the former comprising the largest collection of patients with this pathology from a single population studied to date. SNPs in an LD block spanning the entire FOXE1 gene showed the strongest evidence of association with papillary thyroid carcinoma susceptibility. This association was validated in a second stage of the study that included an independent Italian series of 482 patients and 532 controls. The strongest association results were observed for rs1867277 (OR[per-allele] = 1.49; 95%CI = 1.30-1.70; P = 5.9x10(-9)). Functional assays of rs1867277 (NM_004473.3:c.-283G&gt;A) within the FOXE1 5' UTR suggested that this variant affects FOXE1 transcription. DNA-binding assays demonstrated that, exclusively, the sequence containing the A allele recruited the USF1\/USF2 transcription factors, while both alleles formed a complex in which DREAM\/CREB\/alphaCREM participated. Transfection studies showed an allele-dependent transcriptional regulation of FOXE1. We propose a FOXE1 regulation model dependent on the rs1867277 genotype, indicating that this SNP is a causal variant in thyroid cancer susceptibility. Our results constitute the first functional explanation for an association identified by a GWAS and thereby elucidate a mechanism of thyroid cancer susceptibility. They also attest to the efficacy of candidate gene approaches in the GWAS era.","authors":"Landa, I., Ruiz-Llorente, S., Montero-Conde, C., Inglada-P\u00e9rez, L., Schiavi, F., Leskel\u00e4, S., Pita, G., Milne, R., Maravall, J., Ramos, I., And\u00eda, V., Rodr\u00edguez-Poyo, P., Jara-Albarr\u00e1n, A., Meoro, A., del Peso, C., Arribas, L., Iglesias, P., Caballero, J., Serrano, J., Pic\u00f3, A., Pomares, F., Gim\u00e9nez, G., L\u00f3pez-Mond\u00e9jar, P., Castello, R., Merante-Boschin, I., Pelizzo, MR., Mauricio, D., Opocher, G., Rodr\u00edguez-Antona, C., Gonz\u00e1lez-Neira, A., Mat\u00edas-Guiu, X., Santisteban, P., Robledo, M.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"PLoS Genet","volume":"5","issue":"9","page":"e1000637","pdf":null,"JrId":"32385","fulltextlink":null,"preprintlink":null,"articledate":"2009-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19684577","title":"A Dam1-based artificial kinetochore is sufficient to promote chromosome segregation in budding yeast.","abstract":"Kinetochores are large multiprotein complexes that mediate chromosome segregation in all eukaryotes by dynamically connecting specialized chromosome regions, termed centromeres, to the plus-ends of spindle microtubules. Even the relatively simple kinetochores of the budding yeast Saccharomyces cerevisiae consist of more than 80 proteins, making analysis of their respective roles a daunting task. Here, we have developed a system that allows us to artificially recruit proteins to DNA sequences and determine whether they can provide any aspect of kinetochore function in vivo. We show that artificial recruitment of the microtubule-binding Dam1 complex to a plasmid lacking any centromere DNA is sufficient to confer mitotic stabilization. The Dam1-based artificial kinetochores are able to attach, bi-orient and segregate mini-chromosomes on the mitotic spindle, and they bypass the requirement for essential DNA-binding components of natural kinetochores. Thus, we have built a simplified chromosome segregation system by directly recruiting a microtubule force-transducing component to DNA.","authors":"Kiermaier, E., Woehrer, S., Peng, Y., Mechtler, K., Westermann, S.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Nat Cell Biol","volume":"11","issue":"9","page":"1109-15","pdf":null,"JrId":"21417","fulltextlink":null,"preprintlink":null,"articledate":"2009-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19680290","title":"Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin.","abstract":"Centromeric constitutive heterochromatin is marked by DNA methylation and dimethylated histone H3 Lys 9 (H3K9me2) in Arabidopsis. RNA-directed DNA methylation (RdDM) is a process that uses 24-nucleotide (nt) small interfering RNAs (siRNAs) to induce de novo methylation to its homologous DNA sequences. Despite the presence of centromeric 24-nt siRNAs, mutations in genes required for RdDM do not appreciably influence the methylation of centromeric repeats. The mechanism by which constitutive heterochromatin is protected from RdDM remains puzzling. Here, we report that the vegetative cell nuclei (VN) of the male gametophyte (pollen) invariably undergo extensive decondensation of centromeric heterochromatin and lose centromere identity. VN show greatly reduced H3K9me2, phenocopying nuclei carrying a mutation in the chromatin remodeller DECREASE IN DNA METHYLATION 1 (DDM1). However, unlike the situation in ddm1 nuclei, the decondensed heterochromatin retains dense CG methylation and transcriptional silencing, and, unexpectedly, is subjected to RdDM-dependent hypermethylation in non-CG contexts. These findings reveal two assembly orders of silent heterochromatin and implicate the condensed form in blocking the RdDM machinery.","authors":"Schoft, VK., Chumak, N., Mosiolek, M., Slusarz, L., Komnenovic, V., Brownfield, L., Twell, D., Kakutani, T., Tamaru, H.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"EMBO Rep","volume":"10","issue":"9","page":"1015-21","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2009-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"19679828","title":"Liver X receptor-mediated induction of cholesteryl ester transfer protein expression is selectively impaired in inflammatory macrophages.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">19679828<\/PMID><DateCompleted><Year>2010<\/Year><Month>02<\/Month><Day>04<\/Day><\/DateCompleted><DateRevised><Year>2016<\/Year><Month>11<\/Month><Day>25<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1524-4636<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>29<\/Volume><Issue>11<\/Issue><PubDate><Year>2009<\/Year><Month>Nov<\/Month><\/PubDate><\/JournalIssue><Title>Arteriosclerosis, thrombosis, and vascular biology<\/Title><ISOAbbreviation>Arterioscler Thromb Vasc Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Liver X receptor-mediated induction of cholesteryl ester transfer protein expression is selectively impaired in inflammatory macrophages.<\/ArticleTitle><Pagination><MedlinePgn>1923-9<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1161\/ATVBAHA.109.193201<\/ELocationID><Abstract><AbstractText Label=\"OBJECTIVE\" NlmCategory=\"OBJECTIVE\">Cholesteryl ester transfer protein (CETP) is a target gene for the liver X receptor (LXR). The aim of this study was to further explore this regulation in the monocyte-macrophage lineage and its modulation by lipid loading and inflammation, which are key steps in the process of atherogenesis.","authors":"Lakomy, D., R\u00e9b\u00e9, C., Sberna, AL., Masson, D., Gautier, T., Chevriaux, A., Raveneau, M., Ogier, N., Nguyen, AT., Gambert, P., Grober, J., Bonnotte, B., Solary, E., Lagrost, L.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Arterioscler Thromb Vasc Biol","volume":"29","issue":"11","page":"1923-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11672526","title":"Heterotrimeric G proteins direct two modes of asymmetric cell division in the Drosophila nervous system.","abstract":"In Drosophila, distinct mechanisms orient asymmetric cell division along the apical-basal axis in neuroblasts and along the anterior-posterior axis in sensory organ precursor (SOP) cells. Here, we show that heterotrimeric G proteins are essential for asymmetric cell division in both cell types. The G protein subunit G(alpha)i localizes apically in neuroblasts and anteriorly in SOP cells before and during mitosis. Interfering with G protein function by G(alpha)i overexpression or depletion of heterotrimeric G protein complexes causes defects in spindle orientation and asymmetric localization of determinants. G(alpha)i is colocalized and associated with Pins, a protein that induces the release of the betagamma subunit and might act as a receptor-independent G protein activator. Thus, asymmetric activation of heterotrimeric G proteins by a receptor-independent mechanism may orient asymmetric cell divisions in different cell types.","authors":"Schaefer, M., Petronczki, M., Dorner, D., Forte, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell","volume":"107","issue":"2","page":"183-94","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11564756","title":"E-cadherin regulates cell growth by modulating proliferation-dependent beta-catenin transcriptional activity.","abstract":"beta-Catenin is essential for E-cadherin-mediated cell adhesion in epithelial cells, but it also forms nuclear complexes with high mobility group transcription factors. Using a mouse mammary epithelial cell system, we have shown previously that conversion of epithelial cells to a fibroblastoid phenotype (epithelial-mesenchymal transition) involves downregulation of E-cadherin and upregulation of beta-catenin transcriptional activity. Here, we demonstrate that transient expression of exogenous E-cadherin in both epithelial and fibroblastoid cells arrested cell growth or caused apoptosis, depending on the cellular E-cadherin levels. By expressing E-cadherin subdomains, we show that the growth-suppressive effect of E-cadherin required the presence of its cytoplasmic beta-catenin interaction domain and\/or correlated strictly with the ability to negatively interfere with beta-catenin transcriptional activity. Furthermore, coexpression of beta-catenin or lymphoid enhancer binding factor-1 or T cell factor 3 with E-cadherin rescued beta-catenin transcriptional activity and counteracted E-cadherin-mediated cell cycle arrest. Stable expression of E-cadherin in fibroblastoid cells decreased beta-catenin activity and reduced cell growth. Since proliferating cells had a higher beta-catenin activity than G1 phase-arrested or contact-inhibited cells, we conclude that beta-catenin transcriptional activity is essential for cell proliferation and can be controlled by E-cadherin in a cell adhesion-independent manner.","authors":"Stockinger, A., Eger, A., Wolf, J., Beug, H., Foisner, R.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Cell Biol","volume":"154","issue":"6","page":"1185-96","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2001-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2806699","title":"Intra-thymic nurse cell lymphocytes can induce a graft-versus-host reaction with high efficiency.","abstract":"Thymic nurse cells (TNC) are multicellular complexes composed of morphologically intact thymocytes internalized within epithelial cells. Due to their unusual features, they have been suspected to provide an appropriate microenvironment for T-cell repertoire acquisition. In recent functional studies in the chicken system, we have shown that intra-thymic nurse cell-lymphocytes (TNC-L) are highly efficient inducers of a graft-versus-host reaction (GvHR) in an allogeneic chorionallantoic membrane (CAM) assay, manifested by the formation of visible colonies, so-called pocks. Immunohistochemical and electron microscopical assessment of pocks revealed no differences between the cellular components and ultrastructural features of GvHR induced by TNC-L or peripheral blood lymphocytes (PBL). In addition, the stimulation of this local GvHR by interleukin 2 (IL-2) was demonstrated.","authors":"Penninger, J., Klima, J., Kroemer, G., Dietrich, H., Hala, K., Wick, G.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Dev Comp Immunol","volume":"13","issue":"4","page":"313-27","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1989-12-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2758464","title":"Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs.","abstract":"The effects of DNA methylation on transcription and chromatin structure require that nuclear factors be able to distinguish methylated and nonmethylated DNA. We describe a methyl-CpG binding protein (MeCP) that complexes with a variety of unrelated DNA sequences when they are methylated at CpG. Fifteen or more symmetrically methylated CpG moieties per molecule are required for strong binding under our conditions. Competition experiments show that vertebrate DNAs bind to MeCP, whereas naturally nonmethylated genomes or cloned vertebrate genomes do not bind. Cross-linking experiments detect a 120 kd protein that correlates stringently with MeCP activity. Species and tissue comparisons show that MeCP is widely distributed in mammals except in embryonal carcinoma cell lines, which have very low levels.","authors":"Meehan, RR., Lewis, JD., McKay, S., Kleiner, EL., Bird, AP.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Cell","volume":"58","issue":"3","page":"499-507","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1989-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11560992","title":"The stress kinase mitogen-activated protein kinase kinase (MKK)7 is a negative regulator of antigen receptor and growth factor receptor-induced proliferation in hematopoietic cells.","abstract":"The dual specificity kinases mitogen-activated protein kinase (MAPK) kinase (MKK)7 and MKK4 are the only molecules known to directly activate the stress kinases stress-activated protein kinases (SAPKs)\/c-Jun N-terminal kinases (JNKs) in response to environmental or mitogenic stimuli. To examine the physiological role of MKK7 in hematopoietic cells, we used a gene targeting strategy to mutate MKK7 in murine T and B cells and non-lymphoid mast cells. Loss of MKK7 in thymocytes and mature B cells results in hyperproliferation in response to growth factor and antigen receptor stimulation and increased thymic cellularity. Mutation of mkk7 in mast cells resulted in hyperproliferation in response to the cytokines interleukin (IL)-3 and stem cell factor (SCF). SAPK\/JNK activation was completely abolished in the absence of MKK7, even though expression of MKK4 was strongly upregulated in mkk7(-\/-) mast cell lines, and phosphorylation of MKK4 occurred normally in response to multiple stress stimuli. Loss of MKK7 did not affect activation of extracellular signal-regulated kinase (ERK)1\/2 or p38 MAPK. mkk7(-\/-) mast cells display reduced expression of JunB and the cell cycle inhibitor p16INK4a and upregulation of cyclinD1. Reexpression of p16INK4a in mkk7(-\/-) mast cells abrogates the hyperproliferative response. Apoptotic responses to a variety of stimuli were not affected. Thus, MKK7 is an essential and specific regulator of stress-induced SAPK\/JNK activation in mast cells and MKK7 negatively regulates growth factor and antigen receptor-driven proliferation in hematopoietic cells. These results indicate that the MKK7-regulated stress signaling pathway can function as negative regulator of cell growth in multiple hematopoietic lineages.","authors":"Sasaki, T., Wada, T., Kishimoto, H., Irie-Sasaki, J., Matsumoto, G., Goto, T., Yao, Z., Wakeham, A., Mak, TW., Suzuki, A., Cho, SK., Zuniga-Pflucker, JC., Oliveira-dos-Santos, AJ., Katada, T., Nishina, H., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Exp Med","volume":"194","issue":"6","page":"757-68","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2249770","title":"Activity and tissue-specific expression of the transcription factor NF-E1 multigene family.","abstract":"NF-E1, a DNA-binding protein that recognizes the general consensus motif WGATAR, is the first tissue-specific factor to be identified in erythroid cells. Using a probe from the murine GF-1 (NF-E1) cDNA clone, we isolated three homologous chicken cDNAs: One of these corresponds to an mRNA (NF-E1a) that is abundantly and exclusively expressed in erythroid cells; a second mRNA (NF-E1b) is also expressed in all developmental stages of erythroid cells but is additionally found in a limited subset of other chicken tissues; mRNA representative of a third gene (NF-E1c) is expressed only in definitive (adult) erythrocytes within the red cell lineage but is also abundantly expressed in T lymphocytes and brain. All NF-E1 proteins are highly conserved within the DNA-binding domain and bind to the consensus motif with similar affinities in vitro; they are also all stimulatory trans-acting factors in vivo. The factors differ quantitatively in their ability to trans-activate reporter genes in which the number and position of cognate binding sites is varied relative to the transcriptional initiation site. These data suggest that the NF-E1 consensus motif directs a broader and more complicated array of developmental transcriptional regulatory processes than has been assumed and that NF-E1c may play a unique regulatory role in the developing chicken brain and in T lymphocytes.","authors":"Yamamoto, M., Ko, LJ., Leonard, MW., Beug, H., Orkin, SH., Engel, JD.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Genes Dev","volume":"4","issue":"10","page":"1650-62","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1991-01-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36229914","title":"On the essentiality of the angiotensin converting enzyme 2 receptor for SARS-CoV-2 infection and the potential of soluble angiotensin converting enzyme 2 proteins as universal approach for variants causing COVID-19.","abstract":null,"authors":"Hassler, L., Penninger, J., Batlle, D.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Clin Transl Med","volume":"12","issue":"10","page":"e1080","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11533667","title":"Four-dimensional imaging and quantitative reconstruction to analyse complex spatiotemporal processes in live cells.","abstract":"Live-cell imaging technology using fluorescent proteins (green fluorescent protein and its homologues) has revolutionized the study of cellular dynamics. But tools that can quantitatively analyse complex spatiotemporal processes in live cells remain lacking. Here we describe a new technique--fast multi-colour four-dimensional imaging combined with automated and quantitative time-space reconstruction--to fill this gap. As a proof of principle, we apply this method to study the re-formation of the nuclear envelope in live cells. Four-dimensional imaging of three spectrally distinct fluorescent proteins is used to simultaneously visualize three different cellular compartments at high speed and with high spatial resolution. The highly complex data, comprising several thousand images from a single cell, were quantitatively reconstructed in time-space by software developed in-house. This analysis reveals quantitative and qualitative insights into the highly ordered topology of nuclear envelope formation, in correlation with chromatin expansion - results that would have been impossible to achieve by manual inspection alone. Our new technique will greatly facilitate study of the highly ordered dynamic architecture of eukaryotic cells.","authors":"Gerlich, D., Beaudouin, J., Gebhard, M., Ellenberg, J., Eils, R.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Nat Cell Biol","volume":"3","issue":"9","page":"852-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-10-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2333290","title":"Transferrin-polycation conjugates as carriers for DNA uptake into cells.","abstract":"We have developed a high-efficiency nucleic acid delivery system that uses receptor-mediated endocytosis to carry DNA macromolecules into cells. We accomplished this by conjugating the iron-transport protein transferrin to polycations that bind nucleic acids. Human transferrin, as well as the chicken homologue conalbumin, has been covalently linked to the small DNA-binding protein protamine or to polylysines of various sizes through a disulfide linkage. These modified transferrin molecules maintain their ability to bind their cognate receptor and to mediate efficient iron transport into the cell. The transferrin-polycation molecules form electrophoretically stable complexes with double-stranded DNA, single-stranded DNA, and modified RNA molecules independent of nucleic acid size (from short oligonucleotides to DNA of 21 kilobase pairs). When complexes of transferrin-polycation and a bacterial plasmid DNA containing the gene for Photinus pyralis luciferase are supplied to eukaryotic cells, high-level expression of the luciferase gene occurs, demonstrating transferrin receptor-mediated endocytosis and expression of the imported DNA. We refer to this delivery system as \"transferrinfection.\"","authors":"Wagner, E., Zenke, M., Cotten, M., Beug, H., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Proc Natl Acad Sci U S A","volume":"87","issue":"9","page":"3410-4","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1990-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11532394","title":"Genetic control of skeletal development.","abstract":"The skeleton is a single organ composed of &gt;200 different elements spread throughout the body. These skeletal elements comprise two tissues: cartilage and bone. Both tissues contain specific cell type(s): chondrocytes in cartilage and osteoblasts and osteoclasts in bone. We are beginning to understand the genetic control of the differentiation and function of these cells through recent developments in mouse and human genetics, and also through the use of molecular biological and biochemical techniques. The most recent advances in terms of cell differentiation in the skeleton are presented in this review.","authors":"Wagner, EF., Karsenty, G.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Curr Opin Genet Dev","volume":"11","issue":"5","page":"527-32","pdf":null,"JrId":"2199","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2088499","title":"Mouse genetics meets molecular biology at Cold Spring Harbor. Mouse Molecular Genetics sponsored by the Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA, August 29-September 2, 1990.","abstract":"As stated earlier, the digestion of roughly 100 short talks delivered within a few days and containing very condensed information is, even for experts, quite demanding. Sometimes one felt in danger of becoming \"psyched out\" by all the experiments described; perhaps smaller group discussions dealing with experiments that have not worked, as well as the elimination of redundancies in the presentations, would have added to the flavor of the meeting. But what is the \"take home message\" from the 1990 CSH Mouse Meeting? With all the described breakthroughs, has mouse molecular genetics and development arrived at a turning point? I am inclined to answer this question with a \"yes\" on the basis of the following considerations: The elegant studies of development in Drosophila and Caenorhabditis elegans were made possible by the power of genetics with the use of developmental mutations. These studies taught us that the sequential activation of a hierarchy of regulatory genes dictates the temporal and spatial patterns of expression of proteins that define cell phenotypes and the body plan, and thereby control development. With the identification of important regulatory genes responsible for many classical as well as experimentally induced mouse mutations, in conjunction with traditional transgenic studies and the power of deleting and altering genes via ES cell chimeras, the study of mouse development has now gained an important new dimension. It is feasible that the consequences of subtle but precise genetic changes, such as the modification of regulatory elements or DNA-binding domains, can be studied in the whole organism by use of ES cells.(ABSTRACT TRUNCATED AT 250 WORDS)","authors":"Wagner, EF.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"New Biol","volume":"2","issue":"12","page":"1071-4","pdf":null,"JrId":"1880","fulltextlink":null,"preprintlink":null,"articledate":"1991-05-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11526439","title":"AP-1 mediated retinal photoreceptor apoptosis is independent of N-terminal phosphorylation of c-Jun.","abstract":"Apoptosis is essential for retinal development but it is also a major mode of cell loss in many human retinal dystrophies. High levels of visible light induce retinal apoptosis in mice and rats. This process is dependent on the induction of the transcription factor AP-1, a dimeric complex composed of c-Fos and c-Jun\/JunD phosphoproteins. While c-Fos is essential, JunD is dispensable for light-induced photoreceptor apoptosis. Here we show that N-terminal phosphorylation of c-Jun, the other main partner of c-Fos in induced AP-1 complexes is not required for programmed cell death during retinal development in vivo and is also dispensable for photoreceptor apoptosis induced by the exogenous stimuli \"excessive light\" and N-nitroso-N-methylurea (MNU). Mice expressing a mutant c-Jun protein (JunAA) that cannot be phosphorylated at its N-terminus are apoptosis competent and their retina is not distinguishable from wild-type mice. Accordingly, Jun kinase, responsible for phosphorylation of wild-type c-Jun protein is at best only marginally induced by the apoptotic stimuli \"light\" and MNU. Complex composition of light-induced AP-1 complexes is similar in wild-type and JunAA mice. This shows that the mutant c-Jun protein can be part of the DNA binding complex AP-1 and demonstrates that induction of the DNA binding activity of AP-1 after light insult does not depend on N-terminal phosphorylation of c-Jun. Our results suggest that transactivation of target genes by phosphorylated c-jun\/AP-1 is not required for MNU- or light-induced apoptosis of photoreceptor cells.","authors":"Grimm, C., Wenzel, A., Behrens, A., Hafezi, F., Wagner, EF., Rem\u00e9, CE.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell Death Differ","volume":"8","issue":"8","page":"859-67","pdf":null,"JrId":"20326","fulltextlink":null,"preprintlink":null,"articledate":"2001-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2004552","title":"Painting of defined chromosomal regions by in situ suppression hybridization of libraries from laser-microdissected chromosomes.","abstract":"\"Painting\" of defined chromosomal regions provides a powerful tool for cytogenetic analyses. Here, we demonstrate that chromosomal in situ suppression (CISS)-hybridization of DNA libraries derived by microcloning laser-microdissected chromosomal regions can be applied to achieve this goal. As an example, we used unbanded metaphase spreads from a female patient carrying a balanced translocation. t(1;7)(1qter----1p36::7q11----7qter). Fragments from the long arms of 130 translocation chromosomes were microdissected. After microcloning, human inserts with an average size of about 3 kb were pooled from 400 recombinant bacteriophage DNA clones and used as a complex probe set in CISS-hybridization experiments. This resulted in painting of the translocation chromosome along the region 7q35 to 1p31. Painted chromosomal subregions in normal chromosomes 1 and 7 were consistent with this finding. This approach may be used to perform painting of any chromosome regions for which microlibraries can be established. Possible applications include the definition of marker chromosomes in clinical and tumor cytogenetics and studies of chromosomal evolution, as well as studies of nuclear chromosome topography in animal and plant species.","authors":"Lengauer, C., Eckelt, A., Weith, A., Endlich, N., Ponelies, N., Lichter, P., Greulich, KO., Cremer, T.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Cytogenet Cell Genet","volume":"56","issue":"1","page":"27-30","pdf":null,"JrId":"3248","fulltextlink":null,"preprintlink":null,"articledate":"1991-04-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11520670","title":"Over-expression of the SUV39H1 histone methyltransferase induces altered proliferation and differentiation in transgenic mice.","abstract":"The development of multi-cellular organisms is regulated by the ordered definition of gene expression programmes that govern cell proliferation and differentiation. Although differential gene activity is mainly controlled by transcription factors, it is also dependent upon the underlying chromatin structure, which can stabilize transcriptional \"on\" or \"off\" states. We have recently isolated human (SUV39H1) and mouse (Suv39h1) histone methyltransferases (HMTases) and shown that they are important regulators for the organization of repressive chromatin domains. To investigate whether a SUV39H1-induced modulation of heterochromatin would affect mammalian development, we generated transgenic mice that over-express the SUV39H1 HMTase early during embryogenesis. SUV39H1 transgenic mice are growth retarded, display a weak penetrance of skeletal transformations and are largely characterized by impaired erythroid differentiation, consistent with highest transgene expression in foetal liver. Ex vivo transgenic foetal liver cultures initially contain reduced numbers of cells in G1 but progress to immortalized erythroblasts that are compromised in executing an erythroid differentiation programme. The outgrowing SUV39H1-immortalized erythroblasts can maintain a diploid karyotype despite deregulation of several tumour suppressor proteins and dispersed distribution of the heterochromatin component HP1. Together, these data provide evidence for a role of the SUV39H1 HMTase during the mammalian development and indicate a possible function for higher-order chromatin in contributing to the balance between proliferation and differentiation potentials of progenitor cells.","authors":"Czvitkovich, S., Sauer, S., Peters, AH., Deiner, E., Wolf, A., Laible, G., Opravil, S., Beug, H., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Mech Dev","volume":"107","issue":"1-2","page":"141-53","pdf":null,"JrId":"1825","fulltextlink":null,"preprintlink":null,"articledate":"2001-12-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1893868","title":"Expression of v-src induces aberrant development and twinning in chimaeric mice.","abstract":"The role of the proto-oncogene c-src in mouse development has been investigated by studying the consequences of expressing its viral homologue, v-src. Embryonic stem (ES) cell lines with differing levels of v-src tyrosine kinase activity have been used to generate chimaeric mice. Whereas a low level of v-src expression is compatible with embryogenesis, chimaeras derived from ES clones with high levels of v-src activity develop abnormally and die on the 8th-9th day of gestation. These abnormalities are characterized by the formation of twin or multiple embryos within the same Reichert's membrane, and by the arrest of embryonic development at the late egg cylinder stage, accompanied by relative expansion of the visceral yolk sac (VYS) and hyperplasia of the VYS endoderm. These results demonstrate for the first time that deregulated expression of the src protooncogene product can induce developmental abnormalities during early embryogenesis.","authors":"Boulter, CA., Aguzzi, A., Williams, RL., Wagner, EF., Evans, MJ., Beddington, R.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Development","volume":"111","issue":"2","page":"357-66","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"1991-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1849457","title":"The role of CDC28 and cyclins during mitosis in the budding yeast S. cerevisiae.","abstract":"cdc28-1N is a conditional allele that has normal G1 (Start) function but confers a mitotic defect. We have isolated seven genes that in high dosage suppress the growth defect of cdc28-1N cells but not of Start-defective cdc28-4 cells. Three of these (CLB1, CLB2, and CLB4) encode proteins strongly homologous to G2-specific B-type cyclins. Another gene, CLB3, was cloned using PCR, CLB1 and CLB2 encode a pair of closely related proteins; CLB3 and CLB4 encode a second pair. Neither CLB1 nor CLB2 is essential; however, disruption of both is lethal and causes a mitotic defect. Furthermore, the double mutant cdc28-1N clb2::LEU2 is nonviable, whereas cdc28-4 clb2::LEU2 is viable, suggesting that the cdc28-1N protein may be defective in its interaction with B-type cyclins. Our results are consistent with CDC28 function being required in both G1 and mitosis. Its mitotic role, we believe, involves interaction with a family of at least four G2-specific cyclins.","authors":"Surana, U., Robitsch, H., Price, C., Schuster, T., Fitch, I., Futcher, AB., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Cell","volume":"65","issue":"1","page":"145-61","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1991-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11504463","title":"The IGF\/IGF-1 receptor signaling pathway as a potential target for cancer therapy.","abstract":"Expression of insulin-like growth factors (IGFs) and their cognate receptor, the IGF-1 receptor, is frequently upregulated during the development of many types of cancer. Besides stimulating cell cycle progression and the transformation status of tumor cells, a wealth of recent experimental data suggests that IGF-mediated signaling exerts a central tumor-promoting function through the repression of tumor cell apoptosis. These functions are all conveyed by the IGF-1 receptor, thus making it an attractive target for therapeutic intervention. Notably, inhibition of IGF-mediated survival function appears to synergize with conventional chemotherapeutic ablation of tumor cells, raising the possibility of combinatorial cancer therapies with significantly reduced side-effects. Copyright 1999 Harcourt Publishers Ltd.","authors":"Burtscher, I., Christofori, G.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Drug Resist Updat","volume":"2","issue":"1","page":"3-8","pdf":null,"JrId":"25462","fulltextlink":null,"preprintlink":null,"articledate":"1999-01-","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31597973","title":"The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.","abstract":"Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions.","authors":"","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nature","volume":"574","issue":"7777","page":"187-192","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-18","doi":"10.1038\/s41586-019-1629-x","first_author":null,"corresponding_authors":null},{"pmid":"1682217","title":"v-erbA overexpression is required to extinguish c-erbA function in erythroid cell differentiation and regulation of the erbA target gene CAII.","abstract":"The v-erbA oncoprotein represents a retrovirus-transduced oncogenic version of the thyroid hormone (T3\/T4) receptor c-erbA (type alpha). It contributes to virus-induced erythroleukemia by efficiently arresting differentiation of red cell progenitors and by suppressing transcription of erythrocyte-specific genes. Here, we show that v-erbA and c-erbA bind directly to sequences within the promoter of the erythrocyte-specific carbonic anhydrase II (CAII), a gene whose transcription is efficiently suppressed by v-erbA. This erbA-binding site confers thyroid hormone responsiveness to a heterologous promoter in transient expression experiments and is a target for efficient down-regulation of CAII transcription by the v-erbA oncoprotein. In stably transformed erythroblasts coexpressing the v-erbA oncoprotein and the c-erbA\/T3 receptor at an approximately equimolar ratio, c-erbA activity is dominant over v-erbA. T3 efficiently induced erythroid differentiation in these cells, thus overcoming the v-erbA-mediated differentiation arrest. Likewise, T3 activated CAII transcription as well as transient expression of a T3-responsive reporter gene containing the CAII-specific erbA-binding site. The c-erbA-dependent activation of this CAII reporter construct could only be suppressed by very high amounts of v-erbA. Our results suggest that overexpression of v-erbA is required for its function as an oncoprotein.","authors":"Disela, C., Glineur, C., Bugge, T., Sap, J., Stengl, G., Dodgson, J., Stunnenberg, H., Beug, H., Zenke, M.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Genes Dev","volume":"5","issue":"11","page":"2033-47","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1991-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1638115","title":"The SRF and MCM1 transcription factors.","abstract":"The mammalian transcription factor SRF (serum-response factor) and the related Saccharomyces cerevisiae transcription factor MCM1 are the prototypes of a new class of dimeric DNA-binding proteins. Their function is regulated in part by the interactions of their DNA-binding domains with accessory proteins. Recent work has advanced the functional characterization of the contributions of SRF and MCM1, and their accessory proteins to transcriptional activation.","authors":"Treisman, R., Ammerer, G.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Curr Opin Genet Dev","volume":"2","issue":"2","page":"221-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1992-09-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1637288","title":"Lipid utilization by human lymphocytes is correlated with high-density-lipoprotein binding site activity.","abstract":"The nature and physiological importance of high-density lipoprotein (HDL) binding sites on unstimulated (resting) and mitogen-activated (blast) human peripheral blood lymphocytes were investigated. Specific HDL binding on resting and blast T-lymphocytes was saturable at 50 micrograms of 125I-HDL\/ml and of high affinity, with Kd values of 8.1 x 10(-8) M and 6.5 x 10(-8) M, respectively, and Bmax. values of 79 ng and 180 ng\/mg of cell protein respectively at 4 degrees C. Binding of HDL double-labelled with fluorescent dioctadecylindocarbocyanine (Dil) and isotope (125I) as well as of single fluorescence- or isotope-labelled HDL was inhibited competitively by HDL apoproteins. Studies of the cholesterol flux between the cells and HDL showed that HDL, low-density lipoprotein (LDL) or BSA at a concentration of 100 micrograms\/ml in the tissue culture medium did not result in a significant difference in exogenous [3H]cholesterol efflux from the cell membrane at 37 degrees C. Proliferating T-blasts incorporated more cholesterol from HDL or LDL than did resting lymphocytes. When the cells were pulsed with 125I-HDL and chased in fresh lipid-free medium, up to 80% of the radioactivity released was not precipitable with trichloroacetic acid. This percentage decreased in a competitive manner when unlabelled HDL was present in the chase incubation medium. Finally, cultivation of lymphocytes with conditioned medium from macrophages increased Dil-HDL binding\/uptake, while it was decreased by mevinolin-induced inhibition of hydroxymethylglutaryl-coA reductase. In conclusion, human lymphocytes possess a HDL binding site (receptor) responsible for lipid binding\/uptake and concomitant internalization and degradation of apoproteins from HDL, but not for reverse cell membrane cholesterol transport. The activity of the binding site is up-regulated during cell proliferation and down-regulated during cell growth suppression.","authors":"Xu, Q., J\u00fcrgens, G., Huber, LA., B\u00f6ck, G., Wolf, H., Wick, G.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Biochem J","volume":"285 ( Pt 1)","issue":null,"page":"105-12","pdf":null,"JrId":"1011","fulltextlink":null,"preprintlink":null,"articledate":"1992-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11464286","title":"G1-Cdk activity is required for both proliferation and viability of cytokine-dependent myeloid and erythroid cells.","abstract":"Hematopoietic cytokines are critically required for survival and cell proliferation of myeloid and erythroid progenitors. It is poorly understood how the apoptotic machinery of progenitor cells senses the absence of specific cytokines. Here we show that G1-Cdk activity is essential for cytokine-mediated viability of myeloid and erythroid progenitors. Cytokine deprivation is associated with rapid downregulation of G1-Cdk activity, cell cycle arrest, and apoptosis. Specific inhibition of G1-Cdk activity results in apoptotic cell death in the presence of saturating cytokine levels. In contrast, specific cell cycle arrest in G2\/M does not affect viability. When cell proliferation is arrested by cytokine withdrawal, primary erythroid progenitors expressing v-ErbA maintain G1-Cdk activity and undergo delayed apoptosis. Cdk-inhibitors strongly enhance apoptosis in starved v-ErbA cells, indicating that sustained Cdk activity is required for protection from apoptosis by v-ErbA.","authors":"Hofmann, JF., Sykora, M., Redemann, N., Beug, H.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Oncogene","volume":"20","issue":"31","page":"4198-208","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"2001-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11440973","title":"Temporally regulated and tissue-specific gene manipulations in the adult and embryonic heart using a tamoxifen-inducible Cre protein.","abstract":"The advent of conditional and tissue-specific recombination systems in gene-targeted or transgenic mice has permitted an assessment of single gene function in a temporally regulated and cell-specific manner. Here we generated transgenic mice expressing a tamoxifen-inducible Cre recombinase protein fused to two mutant estrogen-receptor ligand-binding domains (MerCreMer) under the control of the alpha-myosin heavy chain promoter. These transgenic mice were crossed with the ROSA26 lacZ-flox-targeted mice to examine Cre recombinase activity and the fidelity of the system. The data demonstrate essentially no Cre-mediated recombination in the embryonic, neonatal, or adult heart in the absence of inducing agent but &gt;80% recombination after only four tamoxifen injections. Expression of the MerCreMer fusion protein within the adult heart did not affect cardiac performance, cellular architecture, or expression of hypertrophic marker genes, demonstrating that the transgene-encoded protein is relatively innocuous. In summary, MerCreMer transgenic mice represent a tool for temporally regulated inactivation of any loxP-targeted gene within the developing and adult heart or for specifically directing recombination and expression of a loxP-inactivated cardiac transgene in the heart.","authors":"Sohal, DS., Nghiem, M., Crackower, MA., Witt, SA., Kimball, TR., Tymitz, KM., Penninger, JM., Molkentin, JD.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Circ Res","volume":"89","issue":"1","page":"20-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25186908","title":"OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines.","abstract":"The application of designer nucleases allows the induction of DNA double-strand breaks (DSBs) at user-defined genomic loci. Due to imperfect DNA repair mechanisms, DSBs can lead to alterations in the genomic architecture, such as the disruption of the reading frame of a critical exon. This can be exploited to generate somatic knockout cell lines. While high genome editing activities can be achieved in various cellular systems, obtaining cell clones that contain all-allelic frameshift mutations at the target locus of interest remains a laborious task. To this end, we have developed an easy-to-follow deep sequencing workflow and the evaluation tool OutKnocker (www.OutKnocker.org), which allows convenient, reliable, and cost-effective identification of knockout cell lines.","authors":"Schmid-Burgk, JL., Schmidt, T., Gaidt, MM., Pelka, K., Latz, E., Ebert, TS., Hornung, V.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genome Res","volume":"24","issue":"10","page":"1719-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1516825","title":"Pax-5 encodes the transcription factor BSAP and is expressed in B lymphocytes, the developing CNS, and adult testis.","abstract":"BSAP has been identified previously as a transcription factor that is expressed at early, but not late, stages of B-cell differentiation. Biochemical purification and cDNA cloning has now revealed that BSAP belongs to the family of paired domain proteins. BSAP is encoded by the Pax-5 gene and has been highly conserved between human and mouse. An intact paired domain was shown to be both necessary and sufficient for DNA binding of BSAP. Binding studies with several BSAP recognition sequences demonstrated that the sequence specificity of BSAP differs from that of the distantly related paired domain protein Pax-1. During embryogenesis, the BSAP gene is transiently expressed in the mesencephalon and spinal cord with a spatial and temporal expression pattern that is distinct from that of other Pax genes in the developing central nervous system (CNS). Later, the expression of the BSAP gene shifts to the fetal liver where it correlates with the onset of B lymphopoiesis. BSAP expression persists in B lymphocytes and is also seen in the testis of the adult mouse. All of this evidence indicates that the transcription factor BSAP may not only play an important role in B-cell differentiation but also in neural development and spermatogenesis.","authors":"Adams, B., D\u00f6rfler, P., Aguzzi, A., Kozmik, Z., Urb\u00e1nek, P., Maurer-Fogy, I., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Genes Dev","volume":"6","issue":"9","page":"1589-607","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1992-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1425574","title":"Reversible phosphorylation--dephosphorylation determines the localization of rab4 during the cell cycle.","abstract":"The ras-like GTP binding protein rab4 is the only known rab protein on endosomes that is phosphorylated during mitosis. Since a large fraction of rab4 accumulates in the cytosol in mitotic cells, we investigated the molecular mechanism controlling membrane association of rab4. We first show that human rab4 is phosphorylated by recombinant mammalian p34cdc2 kinase in vitro. Next, the actual site of phosphorylation and its functional significance were determined using stably transfected CHO cell lines producing high levels of wild type rab4 or rab4 mutants bearing alterations at Ser196, which occurs within a consensus site for p34cdc2 kinase phosphorylation (S196PRR). Mutation of Ser196 to glutamine or aspartic acid completely prevented rab4 phosphorylation in mitotic cells and also blocked its appearance in the cytosol. Neither C-terminal isoprenylation nor carboxymethylation of rab4 was affected by the mutations or by phosphorylation. Finally, dephosphorylation and reassociation of soluble rab4 with membranes occurred upon exit of cells from mitosis. Thus, phosphorylation of Ser196 is directly responsible for the reversible translocation of rab4 into the cytosol of mitotic cells.","authors":"van der Sluijs, P., Hull, M., Huber, LA., M\u00e2le, P., Goud, B., Mellman, I.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"EMBO J","volume":"11","issue":"12","page":"4379-89","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1992-12-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1463783","title":"Gene transfer into hepatocytes using asialoglycoprotein receptor mediated endocytosis of DNA complexed with an artificial tetra-antennary galactose ligand.","abstract":"We have constructed an artificial ligand for the hepatocyte-specific asialoglycoprotein receptor for the purpose of generating a synthetic delivery system for DNA. This ligand has a tetra-antennary structure, containing four terminal galactose residues on a branched carrier peptide. The carbohydrate residues of this glycopeptide were introduced by reductive coupling of lactose to the alpha- and epsilon-amino groups of the two N-terminal lysines on the carrier peptide. The C-terminus of the peptide, containing a cysteine separated from the branched N-terminus by a 10 amino acid spacer sequence, was used for conjugation to 3-(2-pyridyldithio)propionate-modified polylysine via disulfide bond formation. Complexes containing plasmid DNA bound to these galactose-polylysine conjugates have been used for asialoglycoprotein receptor-mediated transfer of a luciferase gene into human (HepG2) and murine (BNL CL.2) hepatocyte cell lines. Gene transfer was strongly promoted when amphipathic peptides with pH-controlled membrane-disruption activity, derived from the N-terminal sequence of influenza virus hemagglutinin HA-2, were also present in these DNA complexes. Thus, we have essentially borrowed the small functional domains of two large proteins, asialoglycoprotein and hemagglutinin, and assembled them into a supramolecular complex to generate an efficient gene-transfer system.","authors":"Plank, C., Zatloukal, K., Cotten, M., Mechtler, K., Wagner, E.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Bioconjug Chem","volume":"3","issue":"6","page":"533-9","pdf":null,"JrId":"1061","fulltextlink":null,"preprintlink":null,"articledate":"1993-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1391034","title":"High-efficiency gene transfer mediated by adenovirus coupled to DNA-polylysine complexes.","abstract":"Employment of recombinant viruses as gene transfer vectors is limited by constraints on the size and functional design of the genetic material to be transferred as well as potential safety hazards deriving from obligatory co-transfer of viral genetic elements. As an alternative strategy that capitalizes on the efficient cellular entry mechanisms of viruses, we have derived adenovirus-polylysine-DNA complexes whereby foreign DNA is transferred bound to the exterior of the virion. This linkage was accomplished utilizing an antibody bridge in which a monoclonal antibody was rendered competent to carry DNA by the attachment of a polylysine residue. Attachment of the antibody-polylysine to the virus was by virtue of the antibody's specificity for the virion. The resulting vector system mediates high-efficiency gene transfer to target cells in vitro. In addition, this vector design allows greatly enhanced flexibility in terms of the size and design of heterologous sequences that can be transferred. Since this strategy selectively exploits viral entry functions, which are independent of viral gene expression, the potential exists to derive vectors that avoid the hazards deriving from transfer of parent virus genome.","authors":"Curiel, DT., Wagner, E., Cotten, M., Birnstiel, ML., Agarwal, S., Li, CM., Loechel, S., Hu, PC.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Hum Gene Ther","volume":"3","issue":"2","page":"147-54","pdf":null,"JrId":"1041","fulltextlink":null,"preprintlink":null,"articledate":"1992-10-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1375717","title":"Angiogenic activity of the K-fgf\/hst oncogene in neural transplants.","abstract":"Using retrovirus-mediated gene transfer into neural transplants, we have expressed the human K-fgf\/hst oncogene in the central nervous system. Single-cell suspensions of fetal rat brains were removed at embryonic days 13 and 14, exposed to a retroviral vector encoding the K-fgf oncogene and stereotaxically implanted into the caudate putamen of syngenic adult Fisher rats. Recipient animals were sacrificed at intervals of 6-16 months without evidence of neurological impairment. Mock-infected grafts showed the characteristic histopathological appearance of organotypically differentiated neural transplants. In contrast, grafts exposed to the K-fgf gene exhibited abundant capillary proliferation and capillary angiomas. By in situ hybridization analysis and immunohistochemistry, expression of K-fgf was detected in neural cells adjacent to vascular proliferations. Neurons and glia with abundant K-fgf transcripts were morphologically unaffected. In order to examine the transforming potential of the K-fgf gene in the nervous system, we combined retrovirus-mediated transfer of the K-fgf oncogene with a single transplacental exposure of the donor animals to the neurotropic carcinogen N-ethyl-N-nitrosourea (NEU). However, this combination of transforming agents did not result in tumor formation in the grafts. These results provide evidence for a powerful angiogenic effect of K-fgf on the developing brain in vivo.","authors":"Br\u00fcstle, O., Aguzzi, A., Talarico, D., Basilico, C., Kleihues, P., Wiestler, OD.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Oncogene","volume":"7","issue":"6","page":"1177-83","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1992-07-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1347913","title":"The v-erbA oncogene requires cooperation with tyrosine kinases to arrest erythroid differentiation induced by ligand-activated endogenous c-erbA and retinoic acid receptor.","abstract":"The v-erbA oncogene, a mutated version of the thyroid hormone receptor alpha (c-erbA\/TR-alpha), cooperates with tyrosine kinase oncogenes in erythroblast transformation. Here we show that the ligand-activated, endogenous retinoic acid receptor (RAR-alpha), in cooperation with c-erbA\/TR-alpha, efficiently reverses the transforming effect of kinase oncogenes, overcoming oncogene-induced self-renewal by triggering terminal differentiation of the transformed cells into healthy erythrocytes. This differentiation induction was accompanied by up-regulation of erythrocyte gene expression. Similarly, RAR-alpha and over-expressed exogenous c-erbA\/TR-alpha efficiently abolished the differentiation arrest caused by v-erbA, while the low levels of endogenous TR-alpha had no effect. In contrast, transformation by v-erbA plus a kinase oncogene was not affected at all by ligand-activated endogenous or over-expressed exogenous TR-alpha and RAR-alpha. These results suggest that oncogene cooperation is required to protect leukemic erythroblasts from differentiation induction via endogenous, nuclear hormone receptors. Endogenous c-erbA\/TR-alpha and RAR-alpha apparently cooperated in abolishing erythroblast self-renewal and inducing differentiation, since the respective ligands acted in a synergistic fashion, and overexpressed, non-ligand-bound c-erbA\/TR-alpha suppressed endogenous RAR-alpha function in differentiation induction. Genetic evidence is presented that this functional cooperation requires the receptor dimerization domain, suggesting that TR-alpha\/RAR-alpha heterodimers play a role in regulation of erythroid differentiation.","authors":"Schroeder, C., Gibson, L., Beug, H.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Oncogene","volume":"7","issue":"2","page":"203-16","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1992-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1343834","title":"Dominant and recessive molecular changes in neuroblastomas.","abstract":"Of all human tumors, neuroblastomas bear the most prominent genetic changes. Amplifications and deletions of chromosomal DNA can be identified by light microscopy on chromosomal spreads of neuroblastoma cells with remarkable frequency and consistency. Consequently, extensive studies have been undertaken to elucidate the molecular basis of these cytogenetic changes. A rich body of information has accumulated on the role played by dominant oncogenes and recessive tumor suppressor genes in the pathogenesis of this disease. Most notably, it was found that amplification of N-myc is responsible for the presence of double minutes and homogeneously staining regions in neuroblastoma chromosomes. It has also been discovered that N-myc amplification is a prognostic sign of malignancy. More recently, recessive genetic alterations in neuroblastoma, such as deletion of putative tumor-suppressing genes have received increasing attention, and considerable efforts are being made to identify such genetic elements. Finally, the susceptibility of neuroblastoma cells to differentiating stimuli has made them a popular in vitro system for neurobiological and pharmacological research. The need for suitable in vivo systems has spurred the development of several animal models employing tumor viruses and transgenic technologies.","authors":"Aguzzi, A., Ellmeier, W., Weith, A.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Brain Pathol","volume":"2","issue":"3","page":"195-208","pdf":null,"JrId":"2602","fulltextlink":null,"preprintlink":null,"articledate":"1994-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"393804","title":"Is the DNA of virus T7 methylated?","abstract":"DNA modification of T7 wild type and of T7 M-mutants was studied by determining the percentage of 5-methylcytosine (5MC)\/cytosine (C) and N6-aminopurine (6MA)\/adenine (A) and by evaluating the plating efficiencies of restriction-sensitive T7 M-mutants on modifying and non-modifying host strains. Only 0.03% adenine and 0.02% cytosine were methylated in the DNA of T7 wild type as well as in T7 M-mutants, which was independent of the host DNA methylation (30- to 50-fold higher). The restriction of T7 M-mutants, determined from the plating efficiencies, was not altered on modifying or non-modifying hosts. These results indicate that host-specific modification is blocked during T7 development and that this is not due to the M-protein.","authors":"Auer, B., G\u00fcnthert, U., Wagner, EF., Schweiger, M.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"J Gen Virol","volume":"44","issue":"3","page":"609-13","pdf":null,"JrId":"4747","fulltextlink":null,"preprintlink":null,"articledate":"1980-04-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"229419","title":"Mutant avian erythroblastosis virus with restricted target cell specificity.","abstract":"Avian erythroblastosis virus (AEV) induces a fatal erythroblastosis within 2 weeks of intravenous injection in chicks in virtually 100% of cases. In chicks injected intramuscularly, sarcomas frequently develop at the site of injection before the animals die from erythroblastosis. In vitro, AEV transforms both erythroblasts, derived from bone marrow cultures, and fibroblasts. These effects have been shown to be a general property of AEV and not of separate leukaemia- and sarcoma-inducing forms of the virus. AEV is defective for replication and can be propagated only in the prewence of helper virus. Its transformation specificity is independent of the helper virus used. It is not clear whether AEV has two different genes controlling transformation of the two types of target cell or whether it has only one gene coding for both. To investigate this question, we looked for mutants of AEV unable to transform one of the two types of target cell. We now describe such a mutant, which is defective for erythroblast transformation but which can still transform fibroblasts.","authors":"Royer-Pokora, B., Grieser, S., Beug, H., Graf, T.","publication_status":"ppublish","journalpubyear":"1979","journaltitle":"Nature","volume":"282","issue":"5740","page":"750-2","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1980-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"156","title":"Effect of coronary blood flow on glycolytic flux and intracellular pH in isolated rat hearts.","abstract":"The rate of coronary blood flow was varied in isolated working rat heart preparations to determine its influence on the rate of glocose utilization, tissue high-energy phosphates, and intracellular pH. A 60% reduction in coronary blood flow resulted in a 30% reduction in oxygen consumption, an accelerated rate of glusoe utilization, lower tissue levels of high-energy phosphate, and higher tissue levels of lactate and H+. Ventricular performance deteriorated as reflected by a decrease in heart rate and peak systolic pressure. Further reductions in coronary blood flow resulted in inhibition of glycolysis, a greater decrease in tissue levels of high-energy phosphates, and higher tissue levels of both lactate and H+. These changes in glycolytic flux, tissue metabolites, and ventricular performance were proportional to the degree of restriction in coronary blood flow. The importance of coronary blood flow and washout of the interstitial space in the maintenance of accelerated glycolytic flux in oxygen-deficient hearts is emphasized. It is concluded that acceleration of ATP production from glycolysis can occur only in the marginally ischemic tissue in the peripheral area of tissue supplied by an occluded artery. The central area of tissue which receives a low rate of coronary blood flow will have a reduced rate of ATP production due to both a lack of oxygen and an inhibition of glycolysis.","authors":"Neely, JR., Whitmer, JT., Rovetto, MJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Circ Res","volume":"37","issue":"6","page":"733-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"138","title":"Temperature and pH optima for 21 species of thermophilic and thermotolerant fungi.","abstract":"A glucose-containing mineral medium supplemented with 0.01% yeast extract is described upon which all the species of thermophilic and thermotolerant fungi tested will grow. Thirteen of the 21 species do not require the yeast extract supplement for growth. Using this solid, supplemented mineral medium, the pH and temperature optima for growth of all strains were measured. No correlation was found between temperature optimum and pH optimum among members of the group tested.","authors":"Rosenberg, SL.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Microbiol","volume":"21","issue":"10","page":"1535-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16163348","title":"Psoriasis-like skin disease and arthritis caused by inducible epidermal deletion of Jun proteins.","abstract":"Psoriasis is a frequent, inflammatory disease of skin and joints with considerable morbidity. Here we report that in psoriatic lesions, epidermal keratinocytes have decreased expression of JunB, a gene localized in the psoriasis susceptibility region PSORS6. Likewise, inducible epidermal deletion of JunB and its functional companion c-Jun in adult mice leads (within two weeks) to a phenotype resembling the histological and molecular hallmarks of psoriasis, including arthritic lesions. In contrast to the skin phenotype, the development of arthritic lesions requires T and B cells and signalling through tumour necrosis factor receptor 1 (TNFR1). Prior to the disease onset, two chemotactic proteins (S100A8 and S100A9) previously mapped to the psoriasis susceptibility region PSORS4, are strongly induced in mutant keratinocytes in vivo and in vitro. We propose that the abrogation of JunB\/activator protein 1 (AP-1) in keratinocytes triggers chemokine\/cytokine expression, which recruits neutrophils and macrophages to the epidermis thereby contributing to the phenotypic changes observed in psoriasis. Thus, these data support the hypothesis that epidermal alterations are sufficient to initiate both skin lesions and arthritis in psoriasis.","authors":"Zenz, R., Eferl, R., Kenner, L., Florin, L., Hummerich, L., Mehic, D., Scheuch, H., Angel, P., Tschachler, E., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nature","volume":"437","issue":"7057","page":"369-75","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2005-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"150","title":"Mercury inhibition of avian fatty acid synthetase complex.","abstract":"(1) Subcutaneous or intra-abdominal injections of 8 mg of HgCl2\/100 g body weight markedly depressed hepatic fatty acid synthetase activity of chicks at 1 h post-injection. The depression occurred despite the fact that the chicks continued to eat up until the time they were killed. Under these same conditions, the hepatic activity of acetyl-CoA carboxylase (EC 6.4.1.2) was not affected by HgCl2, while the activity of the mitochondrial system of fatty acid elongation was stimulated. (2) When 2-mercaptoethanol was included in the incubation medium for a highly purified preparation of fatty acid synthetase, 500 muM HgCl2 was required to show definite inhibition of the enzyme. When 2-mercaptoethanol was omitted, 50 muM HgCl2 was inhibitory and 100 muM HgCl2 abolished enzyme activity. (3) 2 mM dithiothreitol completely protected the purified fatty acid synthetase preparation from inhibition by 100 muM HgCl2. When dithiothreitol was added after the addition of enzyme to the mercury-containing medium, protection of the enzyme was not complete. (4) Dialysis of cytosol fractions from chicks injected with HgCl2 against 500 vol. of 0.2 M potassium phosphate buffer (pH 7.0) containing 1 mM EDTA and 10 mM dithiothreitol for 4 h at 4 degrees stimulated the fatty acid synthetase activity of the fractions. Dialysis of cytosol fractions from noninjected chicks under the same conditions was without effect on fatty acid synthetase activity. (5) These data support the hypothesis that the inhibitory effect of HgCl2 administered in vivo on hepatic fatty acid synthetase activity in chicks is mediated through the interaction of mercury with the sulfhydryl groups of the enzyme.","authors":"Donaldson, WE.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Chem Biol Interact","volume":"11","issue":"5","page":"343-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16135822","title":"The RASSF1A isoform of RASSF1 promotes microtubule stability and suppresses tumorigenesis.","abstract":"The RASSF1A isoform of RASSF1 is frequently inactivated by epigenetic alterations in human cancers, but it remains unclear if and how it acts as a tumor suppressor. RASSF1A overexpression reduces in vitro colony formation and the tumorigenicity of cancer cell lines in vivo. Conversely, RASSF1A knockdown causes multiple mitotic defects that may promote genomic instability. Here, we have used a genetic approach to address the function of RASSF1A as a tumor suppressor in vivo by targeted deletion of Rassf1A in the mouse. Rassf1A null mice were viable and fertile and displayed no pathological abnormalities. Rassf1A null embryonic fibroblasts displayed an increased sensitivity to microtubule depolymerizing agents. No overtly altered cell cycle parameters or aberrations in centrosome number were detected in Rassf1A null fibroblasts. Rassf1A null fibroblasts did not show increased sensitivity to microtubule poisons or DNA-damaging agents and showed no evidence of gross genomic instability, suggesting that cellular responses to genotoxins were unaffected. Rassf1A null mice showed an increased incidence of spontaneous tumorigenesis and decreased survival rate compared with wild-type mice. Irradiated Rassf1A null mice also showed increased tumor susceptibility, particularly to tumors associated with the gastrointestinal tract, compared with wild-type mice. Thus, our results demonstrate that Rassf1A acts as a tumor suppressor gene.","authors":"van der Weyden, L., Tachibana, KK., Gonzalez, MA., Adams, DJ., Ng, BL., Petty, R., Venkitaraman, AR., Arends, MJ., Bradley, A.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Mol Cell Biol","volume":"25","issue":"18","page":"8356-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2005-10-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16113648","title":"Numb and alpha-Adaptin regulate Sanpodo endocytosis to specify cell fate in Drosophila external sensory organs.","abstract":"During asymmetric cell division in Drosophila sensory organ precursors (SOPs), the Numb protein segregates into one of the two daughter cells, in which it inhibits Notch signalling to specify pIIb cell fate. We show here that Numb acts in SOP cells by inducing the endocytosis of Sanpodo, a four-pass transmembrane protein that has previously been shown to regulate Notch signalling in the central nervous system. In sanpodo mutants, SOP cells divide symmetrically into two pIIb cells. We show that Sanpodo is cortical in pIIa, but colocalizes with Notch and Delta in Rab5- and Rab7-positive endocytic vesicles in pIIb. Sanpodo endocytosis requires alpha-Adaptin, a Numb-binding partner involved in clathrin-mediated endocytosis. In numb or alpha-adaptin mutants, Sanpodo is not endocytosed. Surprisingly, this defect is observed already before and during mitosis, which suggests that Numb not only acts in pIIb, but also regulates endocytosis throughout the cell cycle. Numb binds to Sanpodo by means of its phosphotyrosine-binding domain, a region that is essential for Numb function. Our results establish numb- and alpha-adaptin-dependent endocytosis of Sanpodo as the mechanism by which Notch is regulated during external sensory organ development.","authors":"Hutterer, A., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"EMBO Rep","volume":"6","issue":"9","page":"836-42","pdf":null,"JrId":"22272","fulltextlink":null,"preprintlink":null,"articledate":"2006-03-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11430824","title":"Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF.","abstract":"Activation of HO in yeast involves recruitment of transcription factors in two waves. The first is triggered by inactivation of Cdk1 at the end of mitosis, which promotes import into the nucleus of the Swi5 transcription factor. Swi5 recruits the Swi\/Snf chromatin-remodeling complex, which then facilitates recruitment of the SAGA histone acetylase, which in turn permits the binding of the SBF transcription factor. We show here that SBF then recruits the SRB\/mediator complex and that this process occurs in the absence of Cdk1 activity. The second wave is triggered by reactivation of Cdk1, which leads to recruitment of PolII, TFIIB, and TFIIH. RNA polymerase is, therefore, recruited to HO in two steps and not as a holoenzyme. A similar sequence of events occurs at other SBF-regulated promoters, such as CLN1, CLN2, and PCL1.","authors":"Cosma, MP., Panizza, S., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Mol Cell","volume":"7","issue":"6","page":"1213-20","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11390661","title":"The polycomb-group gene Ezh2 is required for early mouse development.","abstract":"Polycomb-group (Pc-G) genes are required for the stable repression of the homeotic selector genes and other developmentally regulated genes, presumably through the modulation of chromatin domains. Among the Drosophila Pc-G genes, Enhancer of zeste [E(z)] merits special consideration since it represents one of the Pc-G genes most conserved through evolution. In addition, the E(Z) protein family contains the SET domain, which has recently been linked with histone methyltransferase (HMTase) activity. Although E(Z)-related proteins have not (yet) been directly associated with HMTase activity, mammalian Ezh2 is a member of a histone deacetylase complex. To investigate its in vivo function, we generated mice deficient for Ezh2. The Ezh2 null mutation results in lethality at early stages of mouse development. Ezh2 mutant mice either cease developing after implantation or initiate but fail to complete gastrulation. Moreover, Ezh2-deficient blastocysts display an impaired potential for outgrowth, preventing the establishment of Ezh2-null embryonic stem cells. Interestingly, Ezh2 is up-regulated upon fertilization and remains highly expressed at the preimplantation stages of mouse development. Together, these data suggest an essential role for Ezh2 during early mouse development and genetically link Ezh2 with eed and YY1, the only other early-acting Pc-G genes.","authors":"O'Carroll, D., Erhardt, S., Pagani, M., Barton, SC., Surani, MA., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Mol Cell Biol","volume":"21","issue":"13","page":"4330-6","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"75","title":"Characteristics of the dephosphorylated form of phosphorylase purified from rat liver and measurement of its activity in crude liver preparations.","abstract":"The phosphorylated form of liver glycogen phosphorylase (alpha-1,4-glucan : orthophosphate alpha-glucosyl-transferase, EC 2.4.1.1) (phosphorylase a) is active and easily measured while the dephosphorylated form (phosphorylase b), in contrast to the muscle enzyme, has been reported to be essentially inactive even in the presence of AMP. We have purified both forms of phosphorylase from rat liver and studied the characteristics of each. Phosphorylase b activity can be measured with our assay conditions. The phosphorylase b we obtained was stimulated by high concentrations of sulfate, and was a substrate for muscle phosphorylase kinase whereas phosphorylase a was inhibited by sulfate, and was a substrate for liver phosphorylase phosphatase. Substrate binding to phosphorylase b was poor (KM glycogen = 2.5 mM, glucose-1-P = 250 mM) compared to phosphorylase a (KM glycogen = 1.8 mM, KM glucose-1-P = 0.7 mM). Liver phosphorylase b was active in the absence of AMP. However, AMP lowered the KM for glucose-1-P to 80 mM for purified phosphorylase b and to 60 mM for the enzyme in crude extract (Ka = 0.5 mM). Using appropriate substrate, buffer and AMP concentrations, assay conditions have been developed which allow determination of phosphorylase a and 90% of the phosphorylase b activity in liver extracts. Interconversion of the two forms can be demonstrated in vivo (under acute stimulation) and in vitro with little change in total activity. A decrease in total phosphorylase activity has been observed after prolonged starvation and in diabetes.","authors":"Tan, AW., Nuttall, FQ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"45-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11389891","title":"Arginine kinase of the flagellate protozoa Trypanosoma cruzi. Regulation of its expression and catalytic activity.","abstract":"In epimastigotes of Trypanosoma cruzi, the etiological agent of Chagas' disease, arginine kinase activity increased continuously during the exponential phase of growth. A correlation between growth rate, enzyme-specific activity and enzyme protein was observed. Arginine kinase-specific activity, expressed as a function of enzyme protein, remains roughly constant up to 18 days of culture. In the whole range of the culture time mRNA levels showed minor changes indicating that the enzyme activity is post-transcriptionally regulated. Arginine kinase could be proposed as a modulator of energetic reserves under starvation stress condition.","authors":"Alonso, GD., Pereira, CA., Remedi, MS., Paveto, MC., Cochella, L., Ivaldi, MS., Gerez de Burgos, NM., Torres, HN., Flawi\u00e1, MM.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"FEBS Lett","volume":"498","issue":"1","page":"22-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"49","title":"The interaction of bovine erythrocyte superoxide dismutase with hydrogen peroxide: inactivation of the enzyme.","abstract":"Bovine erythrocyte superoxide dismutase was slowly and irreversibly inactivated by hydrogen peroxide. The rate of this inactivation was directly dependent upon the concentrations of both H2O2 and of enzyme, and its second-order rate constant at pH 10.0 and 25 degrees was 6.7 M-1 sec-1. Inactivation was preceded by a bleaching due to rapid reduction of Cu2+ on the enzyme, and following this there was a gradual reappearance of a new absorption in the visible region, which was coincident with the loss of catalytic activity. Inactivation of the enzyme was pH-dependent and indicated an essential ionization whose pKa was approximately 10.2. Replacement of H2O by D2O raised this pKa but did not diminish the catalytic activity of superoxide dismutase, measured at pH 10.0. Several compounds, including xanthine, urate, formate, and azide, protected the enzyme against inactivation by H2O2. Alcohols and benzoate, which scavenge hydroxyl radical, did not protect. Compounds with special affinity for singlet oxygen were similarly ineffective. The data were interpreted in terms of the reduction of the enzyme-bound Cu2+ to Cu+, by H2O2, followed by a Fenton's type reaction of the Cu+ with additional H2O2. This would generate Cu2+-OH- or its ionized equivalent, Cu2+-O--, which could then oxidatively attack an adjacent histidine and thus inactivate the enzyme. Compounds which protected the enzyme could have done so by reacting with the bound oxidant, in competition with the adjacent histidine.","authors":"Hodgson, EK., Fridovich, I.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"24","page":"5294-9","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38","title":"Effect of pH on substrate and inhibitor kinetic constants of human liver alanine aminopeptidase. Evidence for two ionizable active center groups.","abstract":"The presence of at least two ionizable active center groups has been detected by a study of the effect of pH upon catalysis of hydrolysis of L-alanyl-beta-naphthylamide by human liver alanine aminopeptidase and upon the inhibition of hydrolysis by inhibitors and substrate analogs. Octanoic acid, octylamine, and peptide inhibitors have been found to be competitive inhibitors and are therefore thought to bind the active center. L-Phe was previously shown to bind the active center since it was found to be a competitive inhibitor of the hydrolysis of tripeptide substrates (Garner, C. W., and Behal, F. J. (1975), Biochemistry 14, 3208). A plot of pKm vs. pH for the substrate L-Ala-beta-naphthylamide showed that binding decreased below pH 5.9 and above 7.5, the points at which the theoretical curve undergoes an integral change in slope. These points are interpreted as the pKa either of substrate ionizable groups or binding-dependent enzyme active center groups. Similar plots of pKm vs. pH for L-alanyl-p-nitroanilide (as substrate) and pKi vs. pH for L-Leu-L-Leu-L-Leu and D-Leu-L-Tyr (as inhibitors) gave pairs fo pKa values of 5.8 and 7.4, 6.0 and 7.5, and 5.7 and 7.5, respectively. All the above substrates (and D-Leu-L-Tyr) have pKa values near 7.5; therefore, the binding-dependent group with a pKa value near 7.5 is possibly this substrate group. Similar plots of pKi vs. pH for the inhibitors L-Phe, L-Met, L-Leu, octylamine, and octanoic acid had only one bending point at 7.7, 7.6, 7.4, 6.3, and 5.9, respectively. Amino acid inhibitors, octylamine, and octanoic acid have no groups with pKa values between 5 and 9. These data indicate that there are two active center ionizable groups with pKa values of approximately 6.0 and 7.5 which are involved in substrate binding or inhibitory amino acid binding but not in catalysis since Vmax was constant at all pH values tested.","authors":"Garner, CW., Behal, FJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"23","page":"5084-8","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36727294","title":"The paradox of the life sciences: How to address climate change in the lab: How to address climate change in the lab.","abstract":"Addressing climate change and sustainability starts with individuals and moves up to institutional change. Here is what we as scientists in the life sciences can do to enact change.","authors":"Winter, N., Marchand, R., Lehmann, C., Nehlin, L., Trapannone, R., Rokvi\u0107, D., Dobbelaere, J.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"EMBO Rep","volume":"24","issue":"3","page":"e56683","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37","title":"Poly(8-aminoguanylic acid): formation of ordered self-structures and interaction with poly(cytidylic acid).","abstract":"Poly(8-aminoguanylic acid) has in neutral solution a novel ordered structure of high stability. The 8-amino group permits formation of three hydrogen bonds between two residues along the \"top\", or long axis, of the purines. The usual hydrogen bonding protons and Watson-Crick pairing sites are not involved in the association. The bonding scheme has a twofold rotation axis and is hemiprotonated at N(7). Poly(8NH2G) is converted by alkaline titration (pK = 9.7) to a quite different ordered structure, which is the favored form over the range approximately pH 10-11. The bonding scheme appears to be composed of a planar, tetrameric array of guanine residues, in which the 8-amino group does not participate in interbase hydrogen bonding. Poly (8NH2G) does not interact with poly(C) in neutral solution because of the high stability of the hemiprotonated G-G self-structure. Titration to the alkaline plateau, however, permits ready formation of a two-stranded Watson-Crick helix. In contrast to the monomer 8NH2GMP, poly(8NH2G) does not form a triple helix with poly(C) under any conditions. The properties of the ordered structures are interpreted in terms of a strong tendency of the 8-amino group to form a third interbase hydrogen bond, when this possibility is not prevented by high pH.","authors":"Hattori, M., Frazier, J., Miles, HT.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"23","page":"5033-45","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"16079837","title":"Oncogene-induced senescence as an initial barrier in lymphoma development.","abstract":"Acute induction of oncogenic Ras provokes cellular senescence involving the retinoblastoma (Rb) pathway, but the tumour suppressive potential of senescence in vivo remains elusive. Recently, Rb-mediated silencing of growth-promoting genes by heterochromatin formation associated with methylation of histone H3 lysine 9 (H3K9me) was identified as a critical feature of cellular senescence, which may depend on the histone methyltransferase Suv39h1. Here we show that Emicro-N-Ras transgenic mice harbouring targeted heterozygous lesions at the Suv39h1, or the p53 locus for comparison, succumb to invasive T-cell lymphomas that lack expression of Suv39h1 or p53, respectively. By contrast, most N-Ras-transgenic wild-type ('control') animals develop a non-lymphoid neoplasia significantly later. Proliferation of primary lymphocytes is directly stalled by a Suv39h1-dependent, H3K9me-related senescent growth arrest in response to oncogenic Ras, thereby cancelling lymphomagenesis at an initial step. Suv39h1-deficient lymphoma cells grow rapidly but, unlike p53-deficient cells, remain highly susceptible to adriamycin-induced apoptosis. In contrast, only control, but not Suv39h1-deficient or p53-deficient, lymphomas senesce after drug therapy when apoptosis is blocked. These results identify H3K9me-mediated senescence as a novel Suv39h1-dependent tumour suppressor mechanism whose inactivation permits the formation of aggressive but apoptosis-competent lymphomas in response to oncogenic Ras.","authors":"Braig, M., Lee, S., Loddenkemper, C., Rudolph, C., Peters, AH., Schlegelberger, B., Stein, H., D\u00f6rken, B., Jenuwein, T., Schmitt, CA.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Nature","volume":"436","issue":"7051","page":"660-5","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"2005-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11371355","title":"T cell-specific loss of Pten leads to defects in central and peripheral tolerance.","abstract":"PTEN, a tumor suppressor gene, is essential for embryogenesis. We used the Cre-loxP system to generate a T cell-specific deletion of the Pten gene (Pten(flox\/-) mice). All Pten(flox\/-) mice develop CD4+ T cell lymphomas by 17 weeks. Pten(flox\/-) mice show increased thymic cellularity due in part to a defect in thymic negative selection. Pten(flox\/-) mice exhibit elevated levels of B cells and CD4+ T cells in the periphery, spontaneous activation of CD4+ T cells, autoantibody production, and hypergammaglobulinemia. Pten(flox\/-) T cells hyperproliferate, are autoreactive, secrete increased levels of Th1\/Th2 cytokines, resist apoptosis, and show increased phosphorylation of PKB\/Akt and ERK. Peripheral tolerance to SEB is also impaired in Pten(flox\/-) mice. PTEN is thus an important regulator of T cell homeostasis and self-tolerance.","authors":"Suzuki, A., Yamaguchi, MT., Ohteki, T., Sasaki, T., Kaisho, T., Kimura, Y., Yoshida, R., Wakeham, A., Higuchi, T., Fukumoto, M., Tsubata, T., Ohashi, PS., Koyasu, S., Penninger, JM., Nakano, T., Mak, TW.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Immunity","volume":"14","issue":"5","page":"523-34","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"15","title":"Increase in acetyl CoA synthetase activity after phenobarbital treatment.","abstract":"","authors":"Akamatsu, N., Nakajima, H., Ono, M., Miura, Y.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochem Pharmacol","volume":"24","issue":"18","page":"1725-7","pdf":null,"JrId":"1015","fulltextlink":null,"preprintlink":null,"articledate":"1976-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8932381","title":"Different thermostabilities of FLP and Cre recombinases: implications for applied site-specific recombination.","abstract":"Genomic manipulations using site-specific recombinases rely on their applied characteristics in living systems. To understand their applied properties so that they can be optimally deployed, we compared the recombinases FLP and Cre in two assays. In both Escherichia coli and in vitro, FLP shows a different temperature optimum than Cre. FLP is more thermolabile, having an optimum near 30 degrees C and little detectable activity above 39 degrees C. Cre is optimally efficient at 37 degrees C and above. Consistent with FLP thermolability, recombination in a mammalian cell line mediated by a ligand- regulated FLP-androgen receptor fusion protein is more efficient at 35 degrees C than at higher temperatures. We also document a mutation in a commercially available FLP plasmid (FLP-F70L) which renders this recombinase even more thermolabile. The different temperature optima of FLP, FLP-F70L and Cre influence their strategies of usage. Our results recommend the use of Cre for applications in mice that require efficient recombination. The thermolabilities of FLP and FLP-F70L can be usefully exploited for gain of function and cell culture applications.","authors":"Buchholz, F., Ringrose, L., Angrand, PO., Rossi, F., Stewart, AF.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Nucleic Acids Res","volume":"24","issue":"21","page":"4256-62","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1996-12-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1346334","title":"Anti-oncogenic activity of signalling-defective epidermal growth factor receptor mutants.","abstract":"Overexpression and autocrine activation of the epidermal growth factor receptor (EGF-R) cause transformation of cultured cells and correlate with tumor progression in cancer patients. Dimerization and transphosphorylation are crucial events in the process by which receptors with tyrosine kinase activity generate normal and transforming cellular signals. Interruption of this process by inactive receptor mutants offers the potential to inhibit ligand-induced cellular responses. Using recombinant retroviruses, we have examined the effects of signalling-incompetent EGF-R mutants on the growth-promoting and transforming potential of ligand-activated, overexpressed wild-type EGF-R and the v-erbB oncogene product. Expression of a soluble extracellular EGF-R domain had little if any effect on the growth and transformation of NIH 3T3 cells by either tyrosine kinase. However, both a kinase-negative EGF-R point mutant (HERK721A) and an EGF-R lacking 533 C-terminal amino acids efficiently inhibited wild-type EGF-R-mediated, de novo DNA synthesis and cell transformation in a dose-dependent manner. Furthermore, coexpression with the v-erbBES4 oncogene product in NIH 3T3 cells resulted in transphosphorylation of the HERK721A mutant receptor and reduced soft-agar colony growth but had no effect in a focus formation assay. These results demonstrate that signalling-defective receptor tyrosine kinase mutants differentially interfere with oncogenic signals generated by either overexpressed EGF-R or the retroviral v-erbBES4 oncogene product.","authors":"Redemann, N., Holzmann, B., von R\u00fcden, T., Wagner, EF., Schlessinger, J., Ullrich, A.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Mol Cell Biol","volume":"12","issue":"2","page":"491-8","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1992-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8521421","title":"c-fos-induced osteosarcoma formation in transgenic mice: cooperativity with c-jun and the role of endogenous c-fos.","abstract":"Transgenic mice overexpressing the c-fos proto-oncogene in bone develop osteosarcomas, whereas mice overexpressing c-Jun are normal. In this study, we investigated whether Fos and Jun would cooperate in vivo and whether the threshold levels of Fos are important in osteosarcoma formation. Fos-Jun double-transgenic mice develop osteosarcomas at a higher frequency than single-Fos transgenic mice with no differences in the time of onset of tumor formation. Histological and histochemical analyses indicated that Fos-Jun tumors contained greater quantities of neoplastic bone, were more remodeled, and contained a greater number of multinucleated osteoclast-like cells than tumors isolated from age-matched, single transgenic littermates. In contrast, overexpression of Fos in knockout mice that lack endogenous Fos resulted in a decrease in the number of tumor-bearing mice; osteosarcomas were almost absent in c-fos -\/- mice, whereas tumor incidence was reduced to approximately 50% in c-fos +\/- mice. Cell lines isolated from Fos-Jun transgenic tumors expressed high levels of both transgenes but significantly lower levels of the jun-related gene junB compared with cells expressing only a c-fos transgene. Osteoblastic marker genes were expressed at varying levels in different cell lines, but expression of interstitial collagenase (matrix metalloproteinase-1) was enhanced in cells derived from Fos-Jun tumors. These studies demonstrate that coexpression of a c-jun transgene can enhance Fos-induced oncogenesis in vivo and suggest that a critical level of Fos is necessary for osteosarcoma development.","authors":"Wang, ZQ., Liang, J., Schellander, K., Wagner, EF., Grigoriadis, AE.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cancer Res","volume":"55","issue":"24","page":"6244-51","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"1996-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11371342","title":"Securin is required for chromosomal stability in human cells.","abstract":"Abnormalities of chromosome number are the most common genetic aberrations in cancer. The mechanisms regulating the fidelity of mitotic chromosome transmission in mammalian cells are therefore of great interest. Here we show that human cells without an hSecurin gene lose chromosomes at a high frequency. This loss was linked to abnormal anaphases during which cells underwent repetitive unsuccessful attempts to segregate their chromosomes. The abnormal mitoses were associated with biochemical defects in the activation of separin, the sister-separating protease, rendering it unable to cleave the cohesin subunit Scc1 efficiently. These results illuminate the function of mammalian securin and show that it is essential for the maintenance of euploidy.","authors":"Jallepalli, PV., Waizenegger, IC., Bunz, F., Langer, S., Speicher, MR., Peters, JM., Kinzler, KW., Vogelstein, B., Lengauer, C.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell","volume":"105","issue":"4","page":"445-57","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11369892","title":"Defining CAR as a cellular receptor for the avian adenovirus CELO using a genetic analysis of the two viral fibre proteins.","abstract":"The coxsackievirus and adenovirus receptor (CAR) is a high affinity receptor used by adenoviruses, including adenovirus type 5 (Ad5). The adenovirus fibre molecule bears the high affinity cell binding domain of Ad5, allowing virions to attach to CAR. The avian adenovirus CELO displays two fibre molecules on its capsid and it was logical to expect that the cell binding functions of CELO might also reside in one or both of these fibres. We had previously shown that the cell binding properties of CELO resemble Ad5, suggesting that the two viruses use similar receptors. Experiments with CAR-deficient CHO cells and CHO cells modified to express CAR demonstrated that CELO has CAR-dependent transduction behaviour like Ad5. Mutations were introduced into the CELO genome to disrupt either the long fibre 1 or the short fibre 2. A CELO genome with fibre 2 disrupted did not generate virus, demonstrating that fibre 2 is essential for some stage in virus growth, assembly or spread. However, a CELO genome with disrupted fibre 1 gene produced virus (CELOdF1) that was capable of entering chicken cells, but had lost both the ability to efficiently transduce human cells and the CAR-specific transduction displayed by wild-type CELO. The ability of CELOdF1 to transduce chicken cells suggests that CELOdF1 may still bind, probably via fibre 2, to a receptor expressed on avian but not mammalian cells. CELOdF1 replication was dramatically impaired in chicken embryos, demonstrating that fibre 1 is important for the in vivo biology of CELO.","authors":"Tan, PK., Michou, AI., Bergelson, JM., Cotten, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Gen Virol","volume":"82","issue":"Pt 6","page":"1465-1472","pdf":null,"JrId":"4747","fulltextlink":null,"preprintlink":null,"articledate":"2001-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11348591","title":"The Drosophila tuberous sclerosis complex gene homologs restrict cell growth and cell proliferation.","abstract":"The inherited human disease tuberous sclerosis, characterized by hamartomatous tumors, results from mutations in either TSC1 or TSC2. We have characterized mutations in the Drosophila Tsc1 and Tsc2\/gigas genes. Inactivating mutations in either gene cause an identical phenotype characterized by enhanced growth and increased cell size with no change in ploidy. Overall, mutant cells spend less time in G1. Coexpression of both Tsc1 and Tsc2 restricts tissue growth and reduces cell size and cell proliferation. This phenotype is modulated by manipulations in cyclin levels. In postmitotic mutant cells, levels of Cyclin E and Cyclin A are elevated. This correlates with a tendency for these cells to reenter the cell cycle inappropriately as is observed in the human lesions.","authors":"Tapon, N., Ito, N., Dickson, BJ., Treisman, JE., Hariharan, IK.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Cell","volume":"105","issue":"3","page":"345-55","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"2001-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11313828","title":"MHC class II presentation of endogenously expressed antigens by transfected dendritic cells.","abstract":"Dendritic cells (DC) present immunogenic epitopes of antigens in the context of MHC class I and class II molecules in association with costimulatory molecules, and efficiently activate both cytotoxic T cells and T helper cells. Gene modified DC expressing antigen encoding cDNA represent a particularly attractive approach for the immunotherapy of disease. We previously described a gene delivery system for DC based on receptor-mediated endocytosis of ligand\/polyethylenimine (PEI) DNA transfer complexes that target cell surface receptors which are abundantly expressed on DC. Employing this gene delivery system, DC were generated that express chicken ovalbumin (OVA) cDNA as a model antigen and introduce antigen into the MHC class I presentation pathway. We demonstrate here that modification of OVA cDNA as transferrin receptor (TfR) or invariant chain (Ii) fusions effectively generate MHC class II specific immune responses in addition to MHC class I responses. TfR-OVA contains the membrane anchoring region of transferrin receptor and represents a membrane-bound form of OVA for access to the MHC class II compartment. Ii-OVA fusions directly target the MHC class II processing pathway. Thus, modification of antigen encoding cDNA represents a convenient and effective means to direct antigens to MHC class II presentation and thus to generate T cell help.","authors":"Diebold, SS., Cotten, M., Koch, N., Zenke, M.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"Gene Ther","volume":"8","issue":"6","page":"487-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2001-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11134081","title":"Transgenic activation of Ras in neurons promotes hypertrophy and protects from lesion-induced degeneration.","abstract":"Ras is a universal eukaryotic intracellular protein integrating extracellular signals from multiple receptor types. To investigate its role in the adult central nervous system, constitutively activated V12-Ha-Ras was expressed selectively in neurons of transgenic mice via a synapsin promoter. Ras-transgene protein expression increased postnatally, reaching a four- to fivefold elevation at day 40 and persisting at this level, thereafter. Neuronal Ras was constitutively active and a corresponding activating phosphorylation of mitogen-activated kinase was observed, but there were no changes in the activity of phosphoinositide 3-kinase, the phosphorylation of its target kinase Akt\/PKB, or expression of the anti-apoptotic proteins Bcl-2 or Bcl-X(L). Neuronal Ras activation did not alter the total number of neurons, but induced cell soma hypertrophy, which resulted in a 14.5% increase of total brain volume. Choline acetyltransferase and tyrosine hydroxylase activities were increased, as well as neuropeptide Y expression. Degeneration of motorneurons was completely prevented after facial nerve lesion in Ras-transgenic mice. Furthermore, neurotoxin-induced degeneration of dopaminergic substantia nigra neurons and their striatal projections was greatly attenuated. Thus, the Ras signaling pathway mimics neurotrophic effects and triggers neuroprotective mechanisms in adult mice. Neuronal Ras activation might become a tool to stabilize donor neurons for neural transplantation and to protect neuronal populations in neurodegenerative diseases.","authors":"Heumann, R., Goemans, C., Bartsch, D., Lingenh\u00f6hl, K., Waldmeier, PC., Hengerer, B., Allegrini, PR., Schellander, K., Wagner, EF., Arendt, T., Kamdem, RH., Obst-Pernberg, K., Narz, F., Wahle, P., Berns, H.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Cell Biol","volume":"151","issue":"7","page":"1537-48","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2001-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11123325","title":"Listeria monocytogenes modulates macrophage cytokine responses through STAT serine phosphorylation and the induction of suppressor of cytokine signaling 3.","abstract":"Macrophage activation as part of natural resistance to infection is caused by stimulation with IFN-gamma and by the invading microorganisms or microbial products. Infection of macrophages with the Gram-positive bacterium Listeria monocytogenes for short periods before activation with IFN-gamma increased the phosphorylation of transcription factor STAT1 at S727 and thereby the expression of IFN-gamma-induced genes. By contrast, persistent infection with viable bacteria or treatment with heat-killed Listeria diminished IFN-gamma-stimulated transcription and the phosphorylation of STAT1 at Y701. Decreased IFN-gamma signaling correlated with the induction of suppressor of cytokine signaling 3 (SOCS3) mRNA and protein. Contrasting our previous findings with LPS, maximal synthesis of SOCS3 required both the immediate signals from Listeria receptors on the cell surface and the activity of a polypeptide secreted in response to bacterial infection. SOCS3 induction by the secreted protein could not be blocked by neutralizing Abs to IL-10 and it did not require the presence of STAT1. Consistent with the induction of SOCS3 activity, Listeria also inhibited activation of STAT5 by GM-CSF. The p38 mitogen-activated protein kinase was rapidly activated upon infection of macrophages with L. monocytogenes. Inhibition of p38 mitogen-activated protein kinase with the pyridinyl imidazol SB203580 abrogated both STAT1 S727 phosphorylation and the expression of SOCS3. The data suggest that STAT1 serine kinase and SOCS3 activity are hallmarks of immediate and delayed phases of influence by bacterial signals on signal transduction in response to IFN-gamma.","authors":"Stoiber, D., Stockinger, S., Steinlein, P., Kovarik, J., Decker, T.","publication_status":"ppublish","journalpubyear":"2001","journaltitle":"J Immunol","volume":"166","issue":"1","page":"466-72","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"2001-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11118376","title":"Expression and folding of human very-low-density lipoprotein receptor fragments: neutralization capacity toward human rhinovirus HRV2.","abstract":"Minor group human rhinoviruses (HRVs) use members of the low-density lipoprotein receptor family for cell entry. To investigate the utility of receptor fragments as viral inhibitors, various polypeptide segments derived from the ligand binding domain of human very-low-density lipoprotein receptor (VLDLR) were expressed in a soluble form in bacteria. Whereas none of the fragments was active in virus binding immediately after recovery from the cell lysates, constructs encompassing complement type repeats 1-3, 1-6, and 1-8 spontaneously acquired virus binding activity by incubation at 4 degrees C in buffer containing Ca(2+) ions and lacking any redox system. When immobilized receptor-associated protein (RAP), a specific chaperone for VLDLR, was present during the incubation, the yield of protein active in ligand binding was substantially increased. A VLDLR fragment with repeats 4-6 failed to bind virus; however, it bound RAP. Bacterial expression of truncated VLDLR 1-3 at high yield, easy purification, and folding together with high inhibitory activity toward HRV2 makes this protein a promising starting point for the development of an oligopeptide-based antiviral agent. Using sucrose density gradient centrifugation, we demonstrate the formation of virus-receptor complexes. The recombinant receptors can thus be used for structure determination by electron cryo-microscopy.","authors":"Ronacher, B., Marlovits, TC., Moser, R., Blaas, D.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Virology","volume":"278","issue":"2","page":"541-50","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"2001-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11101504","title":"The cellular receptor to human rhinovirus 2 binds around the 5-fold axis and not in the canyon: a structural view.","abstract":"Human rhinovirus serotype 2 (HRV2) belongs to the minor group of HRVs that bind to members of the LDL-receptor family including the very low density lipoprotein (VLDL)-receptor (VLDL-R). We have determined the structures of the complex between HRV2 and soluble fragments of the VLDL-R to 15 A resolution by cryo-electron microscopy. The receptor fragments, which include the first three ligand-binding repeats of the VLDL-R (V1-3), bind to the small star-shaped dome on the icosahedral 5-fold axis. This is in sharp contrast to the major group of HRVs where the receptor site for ICAM-1 is located at the base of a depression around each 5-fold axis. Homology models of the three domains of V1-3 were used to explore the virus-receptor interaction. The footprint of VLDL-R on the viral surface covers the BC- and HI-loops on VP1.","authors":"Hewat, EA., Neumann, E., Conway, JF., Moser, R., Ronacher, B., Marlovits, TC., Blaas, D.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"EMBO J","volume":"19","issue":"23","page":"6317-25","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"2001-01-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11094092","title":"Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression.","abstract":"Higher-order chromatin has been implicated in epigenetic gene control and in the functional organization of chromosomes. We have recently discovered mouse (Suv39h1) and human (SUV39H1) histone H3 lysine 9-selective methyltransferases (Suv39h HMTases) and shown that they modulate chromatin dynamics in somatic cells. We describe here the isolation, chromosomal assignment, and characterization of a second murine gene, Suv39h2. Like Suv39h1, Suv39h2 encodes an H3 HMTase that shares 59% identity with Suv39h1 but which differs by the presence of a highly basic N terminus. Using fluorescent in situ hybridization and haplotype analysis, the Suv39h2 locus was mapped to the subcentromeric region of mouse chromosome 2, whereas the Suv39h1 locus resides at the tip of the mouse X chromosome. Notably, although both Suv39h loci display overlapping expression profiles during mouse embryogenesis, Suv39h2 transcripts remain specifically expressed in adult testes. Immunolocalization of Suv39h2 protein during spermatogenesis indicates enriched distribution at the heterochromatin from the leptotene to the round spermatid stage. Moreover, Suv39h2 specifically accumulates with chromatin of the sex chromosomes (XY body) which undergo transcriptional silencing during the first meiotic prophase. These data are consistent with redundant enzymatic roles for Suv39h1 and Suv39h2 during mouse development and suggest an additional function of the Suv39h2 HMTase in organizing meiotic heterochromatin that may even impart an epigenetic imprint to the male germ line.","authors":"O'Carroll, D., Scherthan, H., Peters, AH., Opravil, S., Haynes, AR., Laible, G., Rea, S., Schmid, M., Lebersorger, A., Jerratsch, M., Sattler, L., Mattei, MG., Denny, P., Brown, SD., Schweizer, D., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Cell Biol","volume":"20","issue":"24","page":"9423-33","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2001-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11076961","title":"Characterization of vertebrate cohesin complexes and their regulation in prophase.","abstract":"In eukaryotes, sister chromatids remain connected from the time of their synthesis until they are separated in anaphase. This cohesion depends on a complex of proteins called cohesins. In budding yeast, the anaphase-promoting complex (APC) pathway initiates anaphase by removing cohesins from chromosomes. In vertebrates, cohesins dissociate from chromosomes already in prophase. To study their mitotic regulation we have purified two 14S cohesin complexes from human cells. Both complexes contain SMC1, SMC3, SCC1, and either one of the yeast Scc3p orthologs SA1 and SA2. SA1 is also a subunit of 14S cohesin in Xenopus. These complexes interact with PDS5, a protein whose fungal orthologs have been implicated in chromosome cohesion, condensation, and recombination. The bulk of SA1- and SA2-containing complexes and PDS5 are chromatin-associated until they become soluble from prophase to telophase. Reconstitution of this process in mitotic Xenopus extracts shows that cohesin dissociation does neither depend on cyclin B proteolysis nor on the presence of the APC. Cohesins can also dissociate from chromatin in the absence of cyclin-dependent kinase 1 activity. These results suggest that vertebrate cohesins are regulated by a novel prophase pathway which is distinct from the APC pathway that controls cohesins in yeast.","authors":"Sumara, I., Vorlaufer, E., Gieffers, C., Peters, BH., Peters, JM.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Cell Biol","volume":"151","issue":"4","page":"749-62","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2000-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11069892","title":"Characterization of fission yeast cohesin: essential anaphase proteolysis of Rad21 phosphorylated in the S phase.","abstract":"Cohesin complex acts in the formation and maintenance of sister chromatid cohesion during and after S phase. Budding yeast Scc1p\/Mcd1p, an essential subunit, is cleaved and dissociates from chromosomes in anaphase, leading to sister chromatid separation. Most cohesin in higher eukaryotes, in contrast, is dissociated from chromosomes well before anaphase. The universal role of cohesin during anaphase thus remains to be determined. We report here initial characterization of four putative cohesin subunits, Psm1, Psm3, Rad21, and Psc3, in fission yeast. They are essential for sister chromatid cohesion. Immunoprecipitation demonstrates stable complex formation of Rad21 with Psm1 and Psm3 but not with Psc3. Chromatin immunoprecipitation shows that cohesin subunits are enriched in broad centromere regions and that the level of centromere-associated Rad21 did not change from metaphase to anaphase, very different from budding yeast. In contrast, Rad21 containing similar cleavage sites to those of Scc1p\/Mcd1p is cleaved specifically in anaphase. This cleavage is essential, although the amount of cleaved product is very small (&lt;5%). Mis4, another sister chromatid cohesion protein, plays an essential role for loading Rad21 on chromatin. A simple model is presented to explain the specific behavior of fission yeast cohesin and why only a tiny fraction of Rad21 is sufficient to be cleaved for normal anaphase.","authors":"Tomonaga, T., Nagao, K., Kawasaki, Y., Furuya, K., Murakami, A., Morishita, J., Yuasa, T., Sutani, T., Kearsey, SE., Uhlmann, F., Nasmyth, K., Yanagida, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Genes Dev","volume":"14","issue":"21","page":"2757-70","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2000-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11069886","title":"Fra-1 replaces c-Fos-dependent functions in mice.","abstract":"Structure-function analysis as well as studies with knock-out and transgenic mice have assigned distinct functions to c-Fos and Fra-1, two components of the transcription factor AP-1 (activator protein-1). To test whether Fra-1 could substitute for c-Fos, we generated knock-in mice that express Fra-1 in place of c-Fos. Fra-1 rescues c-Fos-dependent functions such as bone development and light-induced photoreceptor apoptosis. Importantly, rescue of bone cell differentiation, but not photoreceptor apoptosis, is gene-dosage dependent. Moreover, Fra-1 fails to substitute for c-Fos in inducing expression of target genes in fibroblasts. These results show that c-Fos and Fra-1 have maintained functional equivalence during vertebrate evolution.","authors":"Fleischmann, A., Hafezi, F., Elliott, C., Rem\u00e9, CE., R\u00fcther, U., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Genes Dev","volume":"14","issue":"21","page":"2695-700","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"2000-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"11050385","title":"Incenp and an aurora-like kinase form a complex essential for chromosome segregation and efficient completion of cytokinesis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">11050385<\/PMID><DateCompleted><Year>2000<\/Year><Month>11<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>10<\/Volume><Issue>19<\/Issue><PubDate><Year>2000<\/Year><Month>Oct<\/Month><Day>05<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Incenp and an aurora-like kinase form a complex essential for chromosome segregation and efficient completion of cytokinesis.<\/ArticleTitle><Pagination><MedlinePgn>1172-81<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">In animal cells, cytokinesis begins shortly after the sister chromatids move to the spindle poles. The inner centromere protein (Incenp)has been implicated in both chromosome segregation and cytokinesis, but it is not known exactly how it mediates these two distinct processes.","authors":"Kaitna, S., Mendoza, M., Jantsch-Plunger, V., Glotzer, M.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Curr Biol","volume":"10","issue":"19","page":"1172-81","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"2000-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10779362","title":"Structure-function analysis of SUV39H1 reveals a dominant role in heterochromatin organization, chromosome segregation, and mitotic progression.","abstract":"SUV39H1, a human homologue of the Drosophila position effect variegation modifier Su(var)3-9 and of the Schizosaccharomyces pombe silencing factor clr4, encodes a novel heterochromatic protein that transiently accumulates at centromeric positions during mitosis. Using a detailed structure-function analysis of SUV39H1 mutant proteins in transfected cells, we now show that deregulated SUV39H1 interferes at multiple levels with mammalian higher-order chromatin organization. First, forced expression of full-length SUV39H1 (412 amino acids) redistributes endogenous M31 (HP1beta) and induces abundant associations with inter- and metaphase chromatin. These properties depend on the C-terminal SET domain, although the major portion of the SUV39H1 protein (amino acids 89 to 412) does not display affinity for nuclear chromatin. By contrast, the M31 interaction surface, which was mapped to the first 44 N-terminal amino acids, together with the immediately adjacent chromo domain, directs specific accumulation at heterochromatin. Second, cells overexpressing full-length SUV39H1 display severe defects in mitotic progression and chromosome segregation. Surprisingly, whereas localization of centromere proteins is unaltered, the focal, G(2)-specific distribution of phosphorylated histone H3 at serine 10 (phosH3) is dispersed in these cells. This phosH3 shift is not observed with C-terminally truncated mutant SUV39H1 proteins or with deregulated M31. Together, our data reveal a dominant role(s) for the SET domain of SUV39H1 in the distribution of prominent heterochromatic proteins and suggest a possible link between a chromosomal SU(VAR) protein and histone H3.","authors":"Melcher, M., Schmid, M., Aagaard, L., Selenko, P., Laible, G., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Cell Biol","volume":"20","issue":"10","page":"3728-41","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2000-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10777580","title":"Cloning and characterization of the murine glucosamine-6-phosphate acetyltransferase EMeg32. Differential expression and intracellular membrane association.","abstract":"N-Linked glycosylation is a post-translational modification occurring in many eukaryotic secreted and surface-bound proteins and has impact on diverse physiological and pathological processes. Similarly important is the generation of glycosylphosphatidylinositol linkers, which anchor membrane proteins to the cell. Both protein modifications depend on the central nucleotide sugar UDP-N-acetylglucosamine (UDP-GlcNAc). The enzymatic reactions leading to generation of nucleotide sugars are established, yet most of the respective genes still await cloning. We describe the characterization of such a gene, EMeg32, which we identified based on its differential expression in murine hematopoietic precursor cells. We further demonstrate regulated expression during embryogenesis. EMeg32 codes for a 184-amino acid protein exhibiting glucosamine-6-phosphate acetyltransferase activity. It thereby holds a key position in the pathway toward de novo UDP-GlcNAc synthesis. Surprisingly, the protein associates with the cytoplasmic side of various intracellular membranes, accumulates prior to mitosis, and copurifies with the cdc48 homolog p97\/valosin-containing protein.","authors":"Boehmelt, G., Fialka, I., Brothers, G., McGinley, MD., Patterson, SD., Mo, R., Hui, CC., Chung, S., Huber, LA., Mak, TW., Iscove, NN.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Biol Chem","volume":"275","issue":"17","page":"12821-32","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"2000-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10704390","title":"Conditional inactivation of VEGF-A in areas of collagen2a1 expression results in embryonic lethality in the heterozygous state.","abstract":"VEGF-A has been implicated in regulating the initial angiogenic invasion events that are essential for endochondral bone formation. VEGF-A mRNA expression was indeed found in the sclerotome of the developing somite and in the limb-bud mesenchyme at E10.5 in mouse development but declined during chondrogenesis and became upregulated in hypertrophic chondrocytes prior to angiogenic invasion. To determine the functional importance of VEGF-A expression in the developing chondrogenic tissues, VEGF-A was conditionally inactivated during early embryonic development using Collagen2a1-Cre transgenic lines. Deletion of a single VEGF-A allele in Collagen2a1-Cre-expressing cells results in embryonic lethality around E10.5. This lethality is characterized by aberrant development of the dorsal aorta and intersomitic blood vessels, along with defects in the developing endocardial and myocardial layers of the heart. A small percentage of VEGF(Flox)\/+, Collagen2a1-Cre fetuses survive until E17.5, show aberrant endochondral bone formation and develop a heart phenotype resembling a dilated form of ischemic cardiomyopathy. These results provide insights into the function of VEGF-A in heart and endochondral bone formation and underscore the importance of tightly controlled levels of VEGF-A during development.","authors":"Haigh, JJ., Gerber, HP., Ferrara, N., Wagner, EF.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Development","volume":"127","issue":"7","page":"1445-53","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"2000-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10694822","title":"Cell cycle dependence of gene transfer by lipoplex, polyplex and recombinant adenovirus.","abstract":"The aim of this study was to investigate the influence of cell cycle on transfection efficiency. Counterflow centrifugal elutriation was used which avoids possible side-effects from chemical treatment of cells. With this method, cell populations were fractionated by means of size and density, and fractions corresponding to discrete cell cycle phase-specific populations were transfected with various nonviral methods (Lipofectamine, TfpLys and TfPEI), adenovirus-enhanced transferrinfection (AVET system) and recombinant adenovirus. Transfection efficiency was found to be strongly dependent on the cell cycle stage at the time of transfection. Luciferase activity from cells transfected with polycation- or lipid-based transfection systems was 30- to more than 500-fold higher when transfection was performed during S or G2 phase compared with cells in G1 phase which have the lowest expression levels. In contrast, this effect was not observed with recombinant adenovirus which varied only four-fold. Our results indicate that mitotic activity enhances transfection not only by lipoplexes but also by polyplexes, but not a viral system which has an efficient nuclear entry machinery, suggesting that transfection close to M phase is facilitated perhaps by nuclear membrane breakdown. Furthermore, low transfection success into G1 cells indicates that DNA complexes deposited in G1 cells are probably not retained long enough to take advantage of mitosis effects or that passage of transfected cells through S phase is inhibitory. Gene Therapy (2000) 7, 401-407.","authors":"Brunner, S., Sauer, T., Carotta, S., Cotten, M., Saltik, M., Wagner, E.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Gene Ther","volume":"7","issue":"5","page":"401-7","pdf":null,"JrId":"8603","fulltextlink":null,"preprintlink":null,"articledate":"2000-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"24240232","title":"Heterochromatin establishment at pericentromeres depends on nuclear position.","abstract":"Mammalian development begins with fertilization of an oocyte by the sperm followed by genome-wide epigenetic reprogramming. This involves de novo establishment of chromatin domains, including the formation of pericentric heterochromatin. We dissected the spatiotemporal kinetics of the first acquisition of heterochromatic signatures of pericentromeric chromatin and found that the heterochromatic marks follow a temporal order that depends on a specific nuclear localization. We addressed whether nuclear localization of pericentric chromatin is required for silencing by tethering it to the nuclear periphery and show that this results in defective silencing and impaired development. Our results indicate that reprogramming of pericentromeric heterochromatin is functionally linked to its nuclear localization.","authors":"Jachowicz, JW., Santenard, A., Bender, A., Muller, J., Torres-Padilla, ME.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Genes Dev","volume":"27","issue":"22","page":"2427-32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10629227","title":"Epithelial mesenchymal transition by c-Fos estrogen receptor activation involves nuclear translocation of beta-catenin and upregulation of beta-catenin\/lymphoid enhancer binding factor-1 transcriptional activity.","abstract":"Mouse mammary epithelial cells expressing a fusion protein of c-Fos and the estrogen receptor (FosER) formed highly polarized epithelial cell sheets in the absence of estradiol. Beta-catenin and p120(ctn) were exclusively located at the lateral plasma membrane in a tight complex with the adherens junction protein, E-cadherin. Upon activation of FosER by estradiol addition, cells lost epithelial polarity within two days, giving rise to a uniform distribution of junctional proteins along the entire plasma membrane. Most of the beta-catenin and p120(ctn) remained in a complex with E-cadherin at the membrane, but a minor fraction of uncomplexed cytoplasmic beta-catenin increased significantly. The epithelial-mesenchymal cell conversion induced by prolonged estradiol treatment was accompanied by a complete loss of E-cadherin expression, a 70% reduction in beta-catenin protein level, and a change in the expression pattern of p120(ctn) isoforms. In these mesenchymal cells, beta-catenin and p120(ctn) were localized in the cytoplasm and in defined intranuclear structures. Furthermore, beta-catenin colocalized with transcription factor LEF-1 in the nucleus, and coprecipitated with LEF-1-related proteins from cell extracts. Accordingly, beta-catenin- dependent reporter activity was upregulated in mesenchymal cells and could be reduced by transient expression of exogenous E-cadherin. Thus, epithelial mesenchymal conversion in FosER cells may involve beta-catenin signaling.","authors":"Eger, A., Stockinger, A., Schaffhauser, B., Beug, H., Foisner, R.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"J Cell Biol","volume":"148","issue":"1","page":"173-88","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"2000-03-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10611236","title":"c-Jun-dependent CD95-L expression is a rate-limiting step in the induction of apoptosis by alkylating agents.","abstract":"Mouse 3T3 fibroblasts derived from fetuses lacking c-Jun were used to define an essential role of c-Jun, a main component of the transcription factor AP-1, in the cellular response to the alkylating agent methyl methanesulfonate (MMS). MMS represents the most potent and selective activator of the stress-induced kinases JNK\/SAPK and p38, resulting in very efficient induction of c-Jun hyperphosphorylation and c-jun transcription. This agent induced apoptosis with high efficiency in wild-type cells but not in c-jun(-\/-) cells. Resistance to apoptosis was accompanied by impaired expression of CD95 ligand (CD95-L), a well-known inducer of apoptosis. The addition of recombinant CD95-L restored apoptosis sensitivity in c-jun(-\/-) fibroblasts. MMS-induced apoptosis in wild-type fibroblasts or human lymphocytes was strongly reduced by neutralizing CD95-L antibodies or transdominant negative FADD, confirming the importance of CD95 signalling in MMS-induced apoptosis. The loss-of-function approach in fibroblasts allowed the identification and dissection of c-Jun-dependent and -independent processes upstream or downstream of CD95 activation. We have found that c-Jun can act as a proapoptotic regulator in cells exposed to DNA damage via induction of CD95-L. Once activated, CD95-induced death signalling is not affected by the loss of c-Jun, demonstrating that only the initiation and not the execution of stress-induced apoptosis depends on c-Jun.","authors":"Kolbus, A., Herr, I., Schreiber, M., Debatin, KM., Wagner, EF., Angel, P.","publication_status":"ppublish","journalpubyear":"2000","journaltitle":"Mol Cell Biol","volume":"20","issue":"2","page":"575-82","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"2000-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10592329","title":"Post-transcriptional control via iron-responsive elements: the impact of aberrations in hereditary disease.","abstract":"Tight regulation of iron metabolism is crucial to avoid formation of deleterious radicals and is mainly executed at the post-transcriptional level. The regulatory loops are exerted by trans-acting iron regulatory proteins (IRPs) and cis-acting stem-loop motifs, termed iron-responsive elements (IREs), located in the untranslated regions (UTRs) of target mRNAs. Iron scarcity induces binding of IRPs to a single IRE in the 5'-UTR of ferritin, eALAS, aconitase and SDHb mRNAs, which specifically suppresses translation initiation. Simultaneous interaction of IRPs with multiple IREs in the 3'-UTR of transferrin receptor (TfR) mRNA selectively causes its stabilization. The pattern is reverted under iron overload: IRP-mRNA binding affinity is reduced, which results in efficient protein synthesis of target transcripts harboring IREs in the 5'-UTR and rapid degradation of TfR mRNA. Although multiple evidences support this model, several studies reported massive alterations in the regulation of iron homeostasis under specific physiological conditions, raising the possibility for additional regulatory events. Intensive analysis of the palindromic IRE consensus sequence revealed the critical elements for the formation of a functional structure and demonstrated the consequences of IRE mutations in IRP binding. Recent investigations indicated the involvement of naturally occurring IRE mutations of the ferritin L subunit in the hyperferritinemia-cataract syndrome, a hereditary disorder. This review summarizes the apparent links between iron-dependent post-transcriptional control and its abnormalities, governed by the properties of a single mRNA stem-loop structure.","authors":"Mikulits, W., Schranzhofer, M., Beug, H., M\u00fcllner, EW.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Mutat Res","volume":"437","issue":"3","page":"219-30","pdf":null,"JrId":"5976","fulltextlink":null,"preprintlink":null,"articledate":"2000-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10591217","title":"Bazooka recruits Inscuteable to orient asymmetric cell divisions in Drosophila neuroblasts.","abstract":"Asymmetric cell divisions can be generated by the segregation of determinants into one of the two daughter cells. In Drosophila, neuroblasts divide asymmetrically along the apical-basal axis shortly after their delamination from the neuroectodermal epithelium. Several proteins, including Numb and Miranda, segregate into the basal daughter cell and are needed for the determination of its correct cell fate. Both the apical-basal orientation of the mitotic spindle and the localization of Numb and Miranda to the basal cell cortex are directed by Inscuteable, a protein that localizes to the apical cell cortex before and during neuroblast mitosis. Here we show that the apical localizaton of Inscuteable requires Bazooka, a protein containing a PDZ domain that is essential for apical-basal polarity in epithelial cells. Bazooka localizes with Inscuteable in neuroblasts and binds to the Inscuteable localization domain in vitro and in vivo. In embryos lacking both maternal and zygotic bazooka function, Inscuteable no longer localizes asymmetrically in neuroblasts and is instead uniformly distributed in the cytoplasm. Mitotic spindles in neuroblasts are misoriented in these embryos, and the proteins Numb and Miranda fail to localize asymmetrically in metaphase. Our results suggest that direct binding to Bazooka mediates the asymmetric localization of Inscuteable and connects the asymmetric division of neuroblasts to the axis of epithelial apical-basal polarity.","authors":"Schober, M., Schaefer, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nature","volume":"402","issue":"6761","page":"548-51","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1999-12-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10580503","title":"Activated T cells regulate bone loss and joint destruction in adjuvant arthritis through osteoprotegerin ligand.","abstract":"Bone remodelling and bone loss are controlled by a balance between the tumour necrosis factor family molecule osteoprotegerin ligand (OPGL) and its decoy receptor osteoprotegerin (OPG). In addition, OPGL regulates lymph node organogenesis, lymphocyte development and interactions between T cells and dendritic cells in the immune system. The OPGL receptor, RANK, is expressed on chondrocytes, osteoclast precursors and mature osteoclasts. OPGL expression in T cells is induced by antigen receptor engagement, which suggests that activated T cells may influence bone metabolism through OPGL and RANK. Here we report that activated T cells can directly trigger osteoclastogenesis through OPGL. Systemic activation of T cells in vivo leads to an OPGL-mediated increase in osteoclastogenesis and bone loss. In a T-cell-dependent model of rat adjuvant arthritis characterized by severe joint inflammation, bone and cartilage destruction and crippling, blocking of OPGL through osteoprotegerin treatment at the onset of disease prevents bone and cartilage destruction but not inflammation. These results show that both systemic and local T-cell activation can lead to OPGL production and subsequent bone loss, and they provide a novel paradigm for T cells as regulators of bone physiology.","authors":"Kong, YY., Feige, U., Sarosi, I., Bolon, B., Tafuri, A., Morony, S., Capparelli, C., Li, J., Elliott, R., McCabe, S., Wong, T., Campagnuolo, G., Moran, E., Bogoch, ER., Van, G., Nguyen, LT., Ohashi, PS., Lacey, DL., Fish, E., Boyle, WJ., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nature","volume":"402","issue":"6759","page":"304-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10548110","title":"Accumulation of cyclin B1 requires E2F and cyclin-A-dependent rearrangement of the anaphase-promoting complex.","abstract":"In mammalian somatic-cell cycles, progression through the G1-phase restriction point and initiation of DNA replication are controlled by the ability of the retinoblastoma tumour-suppressor protein (pRb) family to regulate the E2F\/DP transcription factors. Continuing transcription of E2F target genes beyond the G1\/S transition is required for coordinating S-phase progression with cell division, a process driven by cyclin-B-dependent kinase and anaphase-promoting complex (APC)-mediated proteolysis. How E2F-dependent events at G1\/S transition are orchestrated with cyclin B and APC activity remains unknown. Here, using an in vivo assay to measure protein stability in real time during the cell cycle, we show that repression of E2F activity or inhibition of cyclin-A-dependent kinase in S phase triggers the destruction of cyclin B1 through the re-assembly of APC, the ubiquitin ligase that is essential for mitotic cyclin proteolysis, with its activatory subunit Cdh1. Phosphorylation-deficient mutant Cdh1 or immunodepletion of cyclin A resulted in assembly of active Cdh1-APC even in S-phase cells. These results implicate an E2F-dependent, cyclin A\/Cdk2-mediated phosphorylation of Cdh1 in the timely accumulation of cyclin B1 and the coordination of cell-cycle progression during the post-restriction point period.","authors":"Lukas, C., S\u00f8rensen, CS., Kramer, E., Santoni-Rugiu, E., Lindeneg, C., Peters, JM., Bartek, J., Lukas, J.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nature","volume":"401","issue":"6755","page":"815-8","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1999-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10524629","title":"Long-term in vivo reconstitution of T-cell development by Pax5-deficient B-cell progenitors.","abstract":"The mechanisms controlling the commitment of haematopoietic progenitors to the B-lymphoid lineage are poorly understood. The observations that mice deficient in E2A and EBF lack B-lineage cells have implicated these two transcription factors in the commitment process. Moreover, the expression of genes encoding components of the rearrangement machinery (RAG1, RAG2, TdT) or pre-B-cell receptor (lambda5, VpreB, Igalpha, Igbeta) has been considered to indicate B-lineage commitment. All these genes including E2A and EBF are expressed in pro-B cells lacking the transcription factor Pax5. Here we show that cloned Pax5-deficient pro-B cells transferred into RAG2-deficient mice provide long-term reconstitution of the thymus and give rise to mature T cells expressing alpha\/beta-T-cell receptors. The bone marrow of these mice contains a population of cells of Pax5-\/- origin with the same phenotype as the donor pro-B cells. When transferred into secondary recipients, these pro-B cells again home to the bone marrow and reconstitute the thymus. Hence, B-lineage commitment is determined neither by immunoglobulin DJ rearrangement nor by the expression of E2A, EBF, lambda5, VpreB, Igalpha and Igbeta. Instead, our data implicate Pax5 in the control of B-lineage commitment.","authors":"Rolink, AG., Nutt, SL., Melchers, F., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nature","volume":"401","issue":"6753","page":"603-6","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1999-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10510209","title":"A putative role for c-Fos in the pathophysiology of Paget's disease.","abstract":"The molecular mechanisms underlying Paget's disease and subsequent osteosarcoma formation are not well understood. In this study, we aim to delineate the function of the c-Fos oncogene in Paget's disease using transgenic mice, based on previous findings that c-Fos is highly expressed in Pagetic osteoclasts and that c-Fos is an essential gene for osteoclast differentiation and skeletal neoplasia. We have generated transgenic mice in which c-Fos is overexpressed specifically in osteoclasts using the tartrate-resistant acid phosphatase (TRAP) promoter, and five founder mice have been identified. All transgene-expressing animals developed severe bone remodeling lesions, some of which progressed to large bone tumors. Histopathologic analysis indicated that the lesions contained a marked increase in the number of osteoclasts that contained a large number of nuclei. Osteoclasts were identified by histochemical staining for TRAP and by in situ hybridization for matrix metalloproteinase-9 (MMP-9) expression. Moreover, transgenic osteoclasts, and in some cases, osteoblasts and chondrocytes, expressed high levels of c-Fos protein as judged by immunocytochemistry. This phenotype of increased osteoclast number and activity, together with an apparently high rate of bone turnover, resembles some characteristics of Paget's disease. These data therefore support an important function for c-Fos in the Pagetic phenotype, and further support the notion that this gene is important in osteoclastogenesis and in bone remodeling disorders.","authors":"Beedles, KE., Sharpe, PT., Wagner, EF., Grigoriadis, AE.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Bone Miner Res","volume":"14 Suppl 2","issue":null,"page":"21-8","pdf":null,"JrId":"104","fulltextlink":null,"preprintlink":null,"articledate":"1999-11-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34927585","title":"Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor.","abstract":"Infection and viral entry of SARS-CoV-2 crucially depends on the binding of its Spike protein to angiotensin converting enzyme 2 (ACE2) presented on host cells. Glycosylation of both proteins is critical for this interaction. Recombinant soluble human ACE2 can neutralize SARS-CoV-2 and is currently undergoing clinical tests for the treatment of COVID-19. We used 3D structural models and molecular dynamics simulations to define the ACE2 N-glycans that critically influence Spike-ACE2 complex formation. Engineering of ACE2 N-glycosylation by site-directed mutagenesis or glycosidase treatment resulted in enhanced binding affinities and improved virus neutralization without notable deleterious effects on the structural stability and catalytic activity of the protein. Importantly, simultaneous removal of all accessible N-glycans from recombinant soluble human ACE2 yields a superior SARS-CoV-2 decoy receptor with promise as effective treatment for COVID-19 patients.","authors":"Capraz, T., Kienzl, NF., Laurent, E., Perthold, JW., F\u00f6derl-H\u00f6benreich, E., Gr\u00fcnwald-Gruber, C., Maresch, D., Monteil, V., Niederh\u00f6fer, J., Wirnsberger, G., Mirazimi, A., Zatloukal, K., Mach, L., Penninger, JM., Oostenbrink, C., Stadlmann, J.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Elife","volume":"10","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10502110","title":"Molecular cloning and expression of the human and mouse homologues of the Drosophila dachshund gene.","abstract":"Recent genetic analysis of the Drosophila dachshund (dac) gene has established that dac encodes a novel nuclear protein that is involved in both eye and leg development. In the Drosophila eye, dac expression appears to be controlled by the product of the eyeless\/Pax6 gene. In order to analyze the Pax6 pathway in vertebrates we have isolated and characterized the cDNA and genomic clones corresponding to the human and mouse homologues of Drosophila dac. A full-length human cDNA encoding dachshund (DACH) encodes the 706 amino acids protein with predicted molecular weight of 73 kDa. A 109 amino acid domain located at the N-terminus of the DACH showed significant sequence and secondary structure homologies to the ski\/sno oncogene products. Northern blot analysis found human DACH predominantly in adult kidney, heart, and placenta, with less expression detected in the brain, lung, skeletal muscle and pancreas. A panel of human cell lines was studied and most notably a large proportion of neuroblastomas expressed DACH mRNA. Mouse Dach encodes a protein of 751 amino acids with predicted molecular weight of 78 kDa that is 95% identical to the human DACH. RNase protection analysis showed the highest Dach mRNA expression in the adult mouse kidney and lung, whereas lower expression was detected in the brain and testis. RT\/PCR analysis readily detected Dach mRNA in the adult mouse cornea and retina. Dach mRNA expression in the mouse E11.5 embryo was observed primarily in the fore and hind limbs, as well as in the somites.","authors":"Kozmik, Z., Pfeffer, P., Kralova, J., Paces, J., Paces, V., Kalousova, A., Cvekl, A.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Dev Genes Evol","volume":"209","issue":"9","page":"537-45","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10498898","title":"Gene expression profiling of fibroblasts resistant toward oncogene-mediated transformation reveals preferential transcription of negative growth regulators.","abstract":"The signal-transducing Ras proteins are important driving forces of diverse cellular processes such as proliferation, neoplastic transformation, differentiation and growth inhibition. As a step toward understanding the complex mechanisms underlying cellular responses, gene expression patterns were examined in two phenotypically normal fibroblast lines which differ in their sensitivity toward oncogene-mediated transformation. Suppression subtractive hybridization (SSH) was used to establish a subtracted cDNA library specific for the REF52 cell line which, like normal diploid fibroblasts, is refractory toward neoplastic transformation induced by mutated HRAS oncogenes. In contrast, rat 208F control cells can be efficiently transformed by HRAS. The nucleotide sequence of 549 subtracted cDNA clones ('REF52 minus 208F') was determined. We identified 93 preferentially expressed gene fragments in resistant REF52 cells as compared to 208F cells. Seventeen of the 52 known genes (32.6%) are capable of inhibiting cell proliferation or of adversely affecting oncogenic signal transduction pathways. These results suggest that the anti-oncogenic properties of resistant REF52 cells are determined by multiple negative growth regulators. The preneoplastic state expressed in 208F cells is characterized by impairment of unexpectedly redundant control mechanisms. Our results also demonstrate that SSH is a powerful method for identifying specific transcriptional patterns in closely related cell types.","authors":"Tchernitsa, OI., Zuber, J., Sers, C., Brinckmann, R., Britsch, SK., Adams, V., Sch\u00e4fer, R.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Oncogene","volume":"18","issue":"39","page":"5448-54","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1999-10-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10473577","title":"Identification of syntenin as a protein of the apical early endocytic compartment in Madin-Darby canine kidney cells.","abstract":"We used flow cytometry to sort and analyze apical and basolateral endocytic vesicles from filter-grown Madin-Darby canine kidney (MDCK) cells after membrane internalization of the lipophilic fluorescent probe trimethylamino-diphenylhexatriene. Western blot analysis of sorted fractions showed enrichment of the early endosomal markers transferrin receptor and the small GTPase Rab5. Two-dimensional gel analysis indicated that the apical and basolateral early endosomes differed significantly in their protein composition. We found nine polypeptides to be specifically enriched in apical or basolateral endocytic vesicles. An apical protein identified by microsequencing was the adaptor molecule syntenin. This protein contains two PDZ domains (PSD-95, Dlg, and ZO-1 homology) that bind syndecan and ephrin-B2 cytoplasmic domains. In MDCK cells, transiently overexpressed Myc-tagged syntenin localized to both plasma membrane domains and to an intracellular vesicular compartment. Syntenin positive vesicles colocalized with internalized transferrin in the perinuclear region. In addition, syntenin colocalized in the apical supranuclear region with Rab5 and Rab11; the latter is a marker for the apical recycling endosomes in MDCK cells.","authors":"Fialka, I., Steinlein, P., Ahorn, H., B\u00f6ck, G., Burbelo, PD., Haberfellner, M., Lottspeich, F., Paiha, K., Pasquali, C., Huber, LA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Biol Chem","volume":"274","issue":"37","page":"26233-9","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1999-10-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10469562","title":"Thrombin regulates S-phase re-entry by cultured newt myotubes.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">10469562<\/PMID><DateCompleted><Year>1999<\/Year><Month>11<\/Month><Day>01<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>9<\/Volume><Issue>15<\/Issue><PubDate><MedlineDate>1999 Jul 29-Aug 12<\/MedlineDate><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Thrombin regulates S-phase re-entry by cultured newt myotubes.<\/ArticleTitle><Pagination><MedlinePgn>792-9<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Adult urodele amphibians such as the newt have remarkable regenerative ability, and a critical aspect of this is the ability of differentiated cells to re-enter the cell cycle and lose their differentiated characteristics. Unlike mammalian myotubes, cultured newt myotubes are able to enter and traverse S phase, following serum stimulation, by a pathway leading to phosphorylation of the retinoblastoma protein. The extracellular regulation of this pathway is unknown.","authors":"Tanaka, EM., Drechsel, DN., Brockes, JP.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Curr Biol","volume":"9","issue":"15","page":"792-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-11-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35035550","title":"Highlights of the ERS Lung Science Conference and Sleep and Breathing Conference 2021 and the new ECMC members.","abstract":"<b>This article provides a brief description of some of the most remarkable sessions of the @EuroRespSoc Lung Science Conference and the Sleep and Breathing Conference 2021 and presents the new incoming members of the ECMC (@EarlyCareerERS)<\/b> https:\/\/bit.ly\/2RSDP40.","authors":"Goodwin, AT., Karado\u011fan, D., De Santis, MM., Alsafadi, HN., Hawthorne, I., Bradicich, M., Siciliano, M., \u015eahin Duyar, S., Targa, A., Meszaros, M., Fanaridis, M., Gille, T., Keir, HR., Moor, CC., Lichtblau, M., Ubags, ND., Cruz, J.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Breathe (Sheff)","volume":"17","issue":"3","page":"210080","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10384109","title":"The guanine-nucleotide exchange factor Vav is a crucial regulator of B cell receptor activation and B cell responses to nonrepetitive antigens.","abstract":"The proto-oncogene product Vav is required for receptor clustering, proliferation, and differentiation of T cells, and Vav was identified as a substrate in the TCR and B cell receptor signaling pathway. The role of Vav in B cell responses to Ag challenge in vivo is not known. In this study, we show that Vav regulates B cell proliferation following in vitro activation of Ag receptors, but Vav has no apparent role in CD40-, IL-4-, or LPS-induced B cell activation. Increased degrees of Ag receptor cross-linking can partially reverse the proliferative defect in the anti-IgM response of vav-\/- B cells. In vivo, vav-\/- mice mounted protective antiviral IgM and IgG responses to infections with vesicular stomatitis virus and recombinant vaccinia virus expressing the vesicular stomatitis virus glycoprotein, which harbor repetitive surface epitopes that directly cross-link the Ag receptor and activate B cells in the absence of T cell help. vav-\/- B cells also responded normally to the polyvalent, repetitive hapten Ag trinitrophenyl (TNP)-Ficoll that effectively cross-links B cell receptors. However, vav-\/- mice failed to mount immune responses to the nonrepetitive, T cell-dependent hapten Ag (4-hydroxy-5-iodo-3-nitrophenyl)acetyl (NIP)-OVA. These results provide the first genetic evidence on the role of the guanine exchange factor Vav in immune responses to viral infections and antigenic challenge in vivo, and suggest that Vav adjusts the threshold for Ag receptor-mediated B cell activation depending on the nature of the Ag.","authors":"Bachmann, MF., Nitschke, L., Krawczyk, C., Tedford, K., Ohashi, PS., Fischer, KD., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"J Immunol","volume":"163","issue":"1","page":"137-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10381654","title":"Apoptosis inducing factor (AIF): a phylogenetically old, caspase-independent effector of cell death.","abstract":"Although much emphasis has been laid on the role of caspase in cell death, recent data indicate that, in many instances, mammalian cell death is caspase-independent. Thus, in many examples of mammalian cell death the 'decision' between death and life is upstream or independent of caspase activation. Similarly, it is unclear whether PCD of plants and fungi involves the activation of caspase-like enzymes, and no caspase-like gene has thus far been cloned in these phyla. Apoptosis inducing factor (AIF) is a new mammalian, caspase-independent death effector which, upon apoptosis induction, translocates from its normal localization, the mitochondrial intermembrane space, to the nucleus. Once in the nucleus, AIF causes chromatin condensation and large scale DNA fragmentation to fragments of approximately 50 kbp. The AIF cDNA from mouse and man codes for a protein which possesses three domains (i) an amino-terminal presequence which is removed upon import into the intermembrane space of mitochondria; (ii) a spacer sequence of approximately 27 amino acids; and (iii) a carboxyterminal 484 amino acid oxidoreductase domain with strong homology to oxidoreductases from other vertebrates (X. laevis), non-vertebrate animals (C. elegans, D. melanogaster), plants, fungi, eubacteria, and archaebacteria. Functionally important amino acids involved in the interaction with the prosthetic groups flavin adenine nucleotide and nicotinamide adenine nucleotide are strongly conserved between AIF and bacterial oxidoreductase. Several eukaryotes possess a similar domain organisation in their AIF homologs, making them candidates to be mitochondrial oxidoreductases as well as caspase-independent death effectors. The phylogenetic implications of these findings are discussed.","authors":"Lorenzo, HK., Susin, SA., Penninger, J., Kroemer, G.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Cell Death Differ","volume":"6","issue":"6","page":"516-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10360979","title":"PSIC: profile extraction from sequence alignments with position-specific counts of independent observations.","abstract":"Sequence weighting techniques are aimed at balancing redundant observed information from subsets of similar sequences in multiple alignments. Traditional approaches apply the same weight to all positions of a given sequence, hence equal efficiency of phylogenetic changes is assumed along the whole sequence. This restrictive assumption is not required for the new method PSIC (position-specific independent counts) described in this paper. The number of independent observations (counts) of an amino acid type at a given alignment position is calculated from the overall similarity of the sequences that share the amino acid type at this position with the help of statistical concepts. This approach allows the fast computation of position-specific sequence weights even for alignments containing hundreds of sequences. The PSIC approach has been applied to profile extraction and to the fold family assignment of protein sequences with known structures. Our method was shown to be very productive in finding distantly related sequences and more powerful than Hidden Markov Models or the profile methods in WiseTools and PSI-BLAST in many cases. The profile extraction routine is available on the WWW (http:\/\/www.bork.embl-heidelberg. de\/PSIC or http:\/\/www.imb.ac.ru\/PSIC).","authors":"Sunyaev, SR., Eisenhaber, F., Rodchenkov, IV., Eisenhaber, B., Tumanyan, VG., Kuznetsov, EN.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Protein Eng","volume":"12","issue":"5","page":"387-94","pdf":null,"JrId":"6619","fulltextlink":null,"preprintlink":null,"articledate":"1999-07-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10354469","title":"Pax2\/5 and Pax6 subdivide the early neural tube into three domains.","abstract":"The nested expression patterns of the paired-box containing transcription factors Pax2\/5 and Pax6 demarcate the midbrain and forebrain primordium at the neural plate stage. We demonstrate that, in Pax2\/5 deficient mice, the mesencephalon\/metencephalon primordium is completely missing, resulting in a fusion of the forebrain to the hindbrain. Morphologically, in the alar plate the deletion is characterized by the substitution of the tectum (dorsal midbrain) and cerebellum (dorsal metencephalon) by the caudal diencephalon and in the basal plate by the replacement of the midbrain tegmentum by the ventral metencephalon (pons). Molecularly, the loss of the tectum is demonstrated by an expanded expression of Pax6, (the molecular determinant of posterior commissure), and a rostral shift of the territory of expression of Gbx2 and Otp (markers for the pons), towards the caudal diencephalon. Our results suggest that an intact territory of expression of Pax2\/5 in the neural plate, nested between the rostral and caudal territories of expression of Pax6, is necessary for defining the midbrain vesicle.","authors":"Schwarz, M., Alvarez-Bolado, G., Dressler, G., Urb\u00e1nek, P., Busslinger, M., Gruss, P.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Mech Dev","volume":"82","issue":"1-2","page":"29-39","pdf":null,"JrId":"1825","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35672347","title":"Neuropeptide Neuromedin B does not alter body weight and glucose homeostasis nor does it act as an insulin-releasing peptide.","abstract":"Neuromedin\u00a0B (NMB)\u00a0is a member of\u00a0the neuromedin\u00a0family of neuropeptides with a high level of region-specific expression in the brain. Several GWAS studies on non-obese and obese patients suggested that polymorphisms in\u00a0NMB\u00a0predispose to obesity by affecting appetite control and feeding preference. Furthermore, several studies proposed that NMB can act as an insulin releasing peptide. Since the functional study has never been done, the in vivo role of NMB as modulator of weight gain or glucose metabolism remains unclear. Here, we generated Nmb conditional mice and nervous system deficient NmB mice. We then performed olfactory and food preference analysis, as well as metabolic analysis under standard and high fat diet. Additionally, in direct islet studies we evaluated the role of NMB on basal and glucose-stimulated insulin secretion in mouse and humans.","authors":"Cikes, D., Atanes, P., Cronin, SJF., Hagelkr\u00fcys, A., Huang, GC., Persaud, SJ., Penninger, JM.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Sci Rep","volume":"12","issue":"1","page":"9383","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10332744","title":"Gene delivery mediated by cationic liposomes: from biophysical aspects to enhancement of transfection.","abstract":"Cationic liposomes complexed with DNA have been used extensively as non-viral vectors for the intracellular delivery of reporter or therapeutic genes in culture and in vivo. However, the relationship between the features of the lipid-DNA complexes ('lipoplexes') and their mode of interaction with cells, the efficiency of gene transfer and gene expression remain to be clarified. To gain insights into these aspects, the size and zeta potential of cationic liposomes (composed of 1,2-dioleoyl-3- (trimethylammonium) propane (DOTAP) and its mixture with phosphatidylethanolamine (PE)), and their complexes with DNA at different (+\/-) charge ratios were determined. A lipid mixing assay was used to assess the interaction of liposomes and lipoplexes with monocytic leukaemia cells. The use of inhibitors of endocytosis indicated that fusion of the cationic liposomes with cells occurred mainly at the plasma membrane level. However, very limited transfection of these cells was achieved using the above complexes. It is possible that the topology of the cationic liposome-DNA complexes does not allow the entry of DNA into cells through a fusion process at the plasma membrane. In an attempt to enhance transfection mediated by lipoplexes composed of DOTAP and its equimolar mixture with dioleoylphosphatidylethanolamine (DOPE) two different strategies were explored: (i) association of a targeting ligand (transferrin) to the complexes to promote their internalization, presumably by receptor-mediated endocytosis; and (ii) association of synthetic fusogenic peptides (GALA or the influenza haemagglutinin N-terminal peptide HA-2) to the complexes to promote endosomal destabilization and release of the genetic material into the cytoplasm. These strategies were effective in enhancing transfection in a large variety of cells, including epithelial and lymphoid cell lines, as well as human macrophages, especially with the use of optimized lipid\/DNA (+\/-) charge ratios. Besides leading to high levels of transfection, the ternary complexes of cationic liposomes, DNA, and protein or peptide, have the advantages of being active in the presence of serum and being non-toxic. Moreover, such ternary complexes present a net negative charge and, thus, are likely to alleviate the problems associated with the use of highly positively charged complexes in vivo, such as avid complexation with serum proteins. Overall, the results indicate that these complexes, and their future derivatives, may constitute viable alternatives to viral vectors for gene delivery in vivo.","authors":"de Lima, MC., Sim\u00f5es, S., Pires, P., Gaspar, R., Slepushkin, V., D\u00fczg\u00fcne\u015f, N.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Mol Membr Biol","volume":"16","issue":"1","page":"103-9","pdf":null,"JrId":"2480","fulltextlink":null,"preprintlink":null,"articledate":"1999-08-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10329623","title":"TGF-beta cooperates with TGF-alpha to induce the self-renewal of normal erythrocytic progenitors: evidence for an autocrine mechanism.","abstract":"Simultaneous addition of both TGF-alpha and TGF-beta induces the sustained, long-term outgrowth of chicken erythrocytic progenitor cells, referred to as T2ECs from both chick bone marrow and 2-day-old chicken embryos. By analysis for differentiation antigens and gene expression, these cells were shown to represent very immature haematopoietic progenitors committed to the erythrocytic lineage. T2ECs differentiate into almost pure populations of fully mature erythrocytes within 6 days, when TGF-alpha and TGF-beta are withdrawn and the cells exposed to anaemic chicken serum plus insulin. Outgrowth of these cells from various sources invariably required both TGF-alpha and TGF-beta, as well as glucocorticoids. Proliferating, established T2ECs still require TGF-alpha, but are independent of exogenous TGF-beta. Using a TGF-beta-neutralizing antibody or expressing a dominant-negative TGF-beta receptor II, we demonstrate that T2ECs generate an autocrine loop involving TGF-beta during their establishment, which is required for sustained proliferation. Using specific inhibitors, we also show that signalling via Mek-1 is specifically required for induction and maintenance of cell proliferation driven by cooperation between the TGF-alpha and -beta receptors. These results establish a novel mechanism by which self-renewal of erythrocytic progenitors is induced and establish avian T2ECs as a new, quasi-optimal model system to study erythrocytic progenitors.","authors":"Gandrillon, O., Schmidt, U., Beug, H., Samarut, J.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"EMBO J","volume":"18","issue":"10","page":"2764-81","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1999-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10223732","title":"Immunotherapy of metastatic malignant melanoma by a vaccine consisting of autologous interleukin 2-transfected cancer cells: outcome of a phase I study.","abstract":"We performed a phase I trial to evaluate the safety and tolerability of repeated skin injections of IL-2-transfected autologous melanoma cells into patients with advanced disease. Cell suspensions, propagated from excised metastases, were IL-2 gene transfected by adenovirus-enhanced transferrinfection and X-irradiated prior to injection. Vaccine production was successful in 54% of the patients. Fifteen patients (37%) received two to eight skin vaccinations of either 3 x 10(6) (intradermal) or 1 x 10(7) (half intradermal, half subcutaneous) transfected melanoma cells per vaccination (secreting 140-17,060 biological response modifier program units of IL-2\/10(6) cells\/24 hr). Analyses of safety and efficacy were carried out in 15 and 14 patients, respectively. Overall, the vaccine was well tolerated. All patients displayed modest local reactions (erythema, induration, and pruritus) and some experienced flu-like symptoms. Apart from newly appearing (4 of 14) and increasing (5 of 14) anti-adenovirus and newly detectable anti-nuclear antibody titers (1 of 15), recipients developed de novo or exhibited increased melanoma cell-specific delayed-type hypersensitivity (DTH) reactions (8 of 15) and vitiligo (3 of 15) and showed signs of tumor regression (3 of 15). This supports the idea of a vaccine-induced or -amplified anti-cancer immune response. None of the patients exhibited complete or partial regressions, but five of them experienced periods of disease stabilization. Three of these individuals received more than the four planned vaccinations and their mean survival time was 15.7 +\/- 3.5 months as compared to 7.8 +\/- 4.6 months for the entire patient cohort. These data indicate that IL-2-producing, autologous cancer cells can be safely administered to stage IV melanoma patients and could conceivably be of benefit to patients with less advanced disease.","authors":"Schreiber, S., K\u00e4mpgen, E., Wagner, E., Pirkhammer, D., Trcka, J., Korschan, H., Lindemann, A., Dorffner, R., Kittler, H., Kasteliz, F., K\u00fcpc\u00fc, Z., Sinski, A., Zatloukal, K., Buschle, M., Schmidt, W., Birnstiel, M., Kempe, RE., Voigt, T., Weber, HA., Pehamberger, H., Mertelsmann, R., Br\u00f6cker, EB., Wolff, K., Stingl, G.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Hum Gene Ther","volume":"10","issue":"6","page":"983-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10209099","title":"ASH1 mRNA localization in yeast involves multiple secondary structural elements and Ash1 protein translation.","abstract":"Localization of ASH1 mRNA to the distal cortex of daughter but not mother cells at the end of anaphase is responsible for the two cells' differential mating-type switching during the subsequent cell cycle. This localization depends on actin filaments and a type V myosin (She1\/Myo4). The 3' untranslated region (3' UTR) of ASH1 mRNA is reportedly capable of directing heterologous RNAs to a mother cell's bud [1] [2]. Surprisingly, however, its replacement has little or no effect on the localisation of ASH1 mRNA. We show here that, unlike all other known localization sequences that have been found in 3' UTRs, all the elements involved in ASH1 mRNA localization are located at least partly within its coding region. A 77 nucleotide region stretching from 7 nucleotides 5' to 67 nucleotides 3' of the stop codon of ASH1 mRNA is sufficient to localize mRNAs to buds; the secondary structure of this region, in particular two stems, is important for its localizing activity. Two regions entirely within coding sequences, both sufficient to localize green fluorescent protein (GFP) mRNA to growing buds, are necessary for ASH1 mRNA localization during anaphase. These three regions can anchor GFP mRNA to the distal cortex of daughter cells only inefficiently. The tight anchoring of ASH1 mRNA to the cortex of the daughter cell depends on translation of the carboxy-terminal sequences of Ash1 protein.","authors":"Gonzalez, I., Buonomo, SB., Nasmyth, K., von Ahsen, U.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Curr Biol","volume":"9","issue":"6","page":"337-40","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10202156","title":"Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31.","abstract":"The chromo and SET domains are conserved sequence motifs present in chromosomal proteins that function in epigenetic control of gene expression, presumably by modulating higher order chromatin. Based on sequence information from the SET domain, we have isolated human (SUV39H1) and mouse (Suv39h1) homologues of the dominant Drosophila modifier of position-effect-variegation (PEV) Su(var)3-9. Mammalian homologues contain, in addition to the SET domain, the characteristic chromo domain, a combination that is also preserved in the Schizosaccharyomyces pombe silencing factor clr4. Chromatin-dependent gene regulation is demonstrated by the potential of human SUV39H1 to increase repression of the pericentromeric white marker gene in transgenic flies. Immunodetection of endogenous Suv39h1\/SUV39H1 proteins in a variety of mammalian cell lines reveals enriched distribution at heterochromatic foci during interphase and centromere-specific localization during metaphase. In addition, Suv39h1\/SUV39H1 proteins associate with M31, currently the only other characterized mammalian SU(VAR) homologue. These data indicate the existence of a mammalian SU(VAR) complex and define Suv39h1\/SUV39H1 as novel components of mammalian higher order chromatin.","authors":"Aagaard, L., Laible, G., Selenko, P., Schmid, M., Dorn, R., Schotta, G., Kuhfittig, S., Wolf, A., Lebersorger, A., Singh, PB., Reuter, G., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"EMBO J","volume":"18","issue":"7","page":"1923-38","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10198632","title":"twin of eyeless, a second Pax-6 gene of Drosophila, acts upstream of eyeless in the control of eye development.","abstract":"The Drosophila Pax-6 gene eyeless (ey) plays a key role in eye development. Here we show tht Drosophila contains a second Pax-6 gene, twin of eyeless (toy), due to a duplication during insect evolution. Toy is more similar to vertebrate Pax-6 proteins than Ey with regard to overall sequence conservation, DNA-binding function, and early expression in the embryo, toy and ey share a similar expression pattern in the developing visual system, and targeted expression of Toy, like Ey, induces the formation of ectopic eyes. Genetic and biochemical evidence indicates, however, that Toy functions upstream of ey by directly regulating the eye-specific enhancer of ey. Toy is therefore required for initiation of ey expression in the embryo and acts through Ey to activate the eye developmental program.","authors":"Czerny, T., Halder, G., Kloter, U., Souabni, A., Gehring, WJ., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Mol Cell","volume":"3","issue":"3","page":"297-307","pdf":null,"JrId":"20730","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10197440","title":"Loss of epithelial polarity is accompanied by differential association of proteins with intracellular membranes.","abstract":"Cellular membranes play an important role in the formation and maintenance of epithelial polarity, which is lost early during carcinogenesis. We set out to identify membrane proteins which are altered during loss of cell polarity in mammary epithelium. As a model system we used murine mammary epithelial cells expressing the conditional oncoprotein c-JunER, which induces a reversible loss of polarity upon beta-estradiol-driven activation [1]. When grown either in the absence or presence of hormone, these cells exhibit a polarized or unpolarized phenotype, respectively. Different membrane fractions of polarized or unpolarized cells were analyzed by two-dimensional electrophoresis (2-DE) and differentially expressed membrane proteins were identified. To distinguish between transmembrane orientation and peripheral attachment of these proteins, were performed extractions with carbonate at high pH or with Triton X-114. In addition, cytosolic proteins of both states were analyzed to investigate their differential association with distinct membrane fractions. We found ten protein spots preferentially or exclusively in polarized cells and 17 other proteins as being upregulated during loss of polarity. Some of the peripheral membrane proteins were identified by microsequencing. The resident Golgi protein nucleobindin and fructose-bisphosphate aldolase were preferentially associated with membranes of polarized cells, whereas alphaB crystallin was detected exclusively and in high amounts in unpolarized cells.","authors":"Fialka, I., Pasquali, C., Kurzbauer, R., Lottspeich, F., Huber, LA.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Electrophoresis","volume":"20","issue":"2","page":"331-43","pdf":null,"JrId":"3579","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10195427","title":"An unexpected role for p53 in augmenting SV40 large T antigen-mediated tumorigenesis.","abstract":"Simian virus 40 large T antigen transforms cells by sequestration and inactivation of the tumor suppressor proteins p53, retinoblastoma gene product (pRb), and the pRb-related proteins p107 and p130. Thus, the absence of functional p53 is expected to promote T antigen-mediated tumorigenesis. However, in a transgenic mouse model of T antigen-mediated beta cell carcinogenesis (Rip1Tag2), tumor volumes are significantly diminished when these mice are intercrossed with p53-deficient mice. Whereas the incidence of beta tumor cell apoptosis is unaffected, their proliferation rate is reduced in p53-deficient beta cell tumors in vivo and in cell lines established from these tumors in vitro. Biochemical analyses reveal higher levels of T antigen in wild-type tumor cells as compared to p53-deficient tumor cells. The data indicate that p53 stabilizes SV40 large T antigen, thereby augmenting its oncogenic potential as manifested by increased proliferation rates in wild-type beta tumor cells as compared to p53-deficient beta tumor cells.","authors":"Herzig, M., Novatchkova, M., Christofori, G.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Biol Chem","volume":"380","issue":"2","page":"203-11","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"1999-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10098216","title":"Model scenarios for evolution of the eukaryotic cell cycle.","abstract":"Progress through the division cycle of present day eukaryotic cells is controlled by a complex network consisting of (i) cyclin-dependent kinases (CDKs) and their associated cyclins, (ii) kinases and phosphatases that regulate CDK activity, and (iii) stoichiometric inhibitors that sequester cyclin-CDK dimers. Presumably regulation of cell division in the earliest ancestors of eukaryotes was a considerably simpler affair. Nasmyth (1995) recently proposed a mechanism for control of a putative, primordial, eukaryotic cell cycle, based on antagonistic interactions between a cyclin-CDK and the anaphase promoting complex (APC) that labels the cyclin subunit for proteolysis. We recast this idea in mathematical form and show that the model exhibits hysteretic behaviour between alternative steady states: a Gl-like state (APC on, CDK activity low, DNA unreplicated and replication complexes assembled) and an S\/M-like state (APC off, CDK activity high, DNA replicated and replication complexes disassembled). In our model, the transition from G1 to S\/M ('Start') is driven by cell growth, and the reverse transition ('Finish') is driven by completion of DNA synthesis and proper alignment of chromosomes on the metaphase plate. This simple and effective mechanism for coupling growth and division and for accurately copying and partitioning a genome consisting of numerous chromosomes, each with multiple origins of replication, could represent the core of the eukaryotic cell cycle. Furthermore, we show how other controls could be added to this core and speculate on the reasons why stoichiometric inhibitors and CDK inhibitory phosphorylation might have been appended to the primitive alternation between cyclin accumulation and degradation.","authors":"Novak, B., Csikasz-Nagy, A., Gyorffy, B., Nasmyth, K., Tyson, JJ.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Philos Trans R Soc Lond B Biol Sci","volume":"353","issue":"1378","page":"2063-76","pdf":null,"JrId":"8277","fulltextlink":null,"preprintlink":null,"articledate":"1999-04-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"10080190","title":"Amino-terminal phosphorylation of c-Jun regulates stress-induced apoptosis and cellular proliferation.","abstract":"c-Jun is a major component of the heterodimeric transcription factor AP-1 and is essential for embryonic development, as fetuses lacking Jun die at mid-gestation with impaired hepatogenesis and primary Jun-\/- fibroblasts have a severe proliferation defect and undergo premature senescence in vitro. c-Jun and AP-1 activities are regulated by c-Jun N-terminal phosphorylation (JNP) at serines 63 and 73 through Jun N-terminal kinases(JNKs). JNP is thought to be required for the anti-apoptotic function of c-Jun during hepatogenesis, as mice lacking the JNK kinase SEK1 exhibit liver defects similar to those seen in Jun-\/- fetuses. To investigate the physiological relevance of JNP, we replaced endogenous Jun by a mutant Jun allele with serines 63 and 73 mutated to alanines (Jun(tm1wag); hereafter referred to as JunAA). Here we show that primary JunAA fibroblasts have proliferation- and stress-induced apoptotic defects, accompanied by reduced AP-1 activity. JunAA mice are viable and fertile, smaller than controls and resistant to epileptic seizures and neuronal apoptosis induced by the excitatory amino acid kainate. Primary mutant neurons are also protected from apoptosis and exhibit unaltered JNK activity. Our results provide evidence that JNP is dispensable for mouse development, and identify c-Jun as the essential substrate of JNK signalling during kainate-induced neuronal apoptosis.","authors":"Behrens, A., Sibilia, M., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Nat Genet","volume":"21","issue":"3","page":"326-9","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"1999-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9933353","title":"GRC5 and NMD3 function in translational control of gene expression and interact genetically.","abstract":"The yeast gene, GRC5 (growth control), is a member of the highly conserved QM gene family, the human member of which has been associated with the suppression of Wilms' tumor. GRC5 encodes ribosomal protein L10, which is thought to play a regulatory role in the translational control of gene expression. A revertant screen identified four spontaneous revertants of the mutant grc5-1ts allele. Genetic and phenotypic analysis showed that these represent one gene, NMD3, and that the interaction of NMD3 and GRC5 is gene-specific. NMD3 was previously identified as a component of the nonsense-mediated mRNA decay pathway. The point mutations within NMD3 reported here may define a domain important for the functional interaction of Grc5p and Nmd3p.","authors":"Karl, T., Onder, K., Kodzius, R., Pichov\u00e1, A., Wimmer, H., Th r, A., Hundsberger, H., L\u00f6ffler, M., Klade, T., Beyer, A., Breitenbach, M., Koller, L.","publication_status":"ppublish","journalpubyear":"1999","journaltitle":"Curr Genet","volume":"34","issue":"6","page":"419-29","pdf":null,"JrId":"2877","fulltextlink":null,"preprintlink":null,"articledate":"1999-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9930665","title":"Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase.","abstract":"Glycosylphosphatidylinositol (GPI) anchoring is a common post-translational modification of extracellular eukaryotic proteins. Attachment of the GPI moiety to the carboxyl terminus (omega-site) of the polypeptide occurs after proteolytic cleavage of a C-terminal propeptide. In this work, the sequence pattern for GPI-modification was analyzed in terms of physical amino acid properties based on a database analysis of annotated proprotein sequences. In addition to a refinement of previously described sequence signals, we report conserved sequence properties in the regions omega - 11...omega - 1 and omega + 4...omega + 5. We present statistical evidence for volume-compensating residue exchanges with respect to the positions omega - 1...omega + 2. Differences between protozoan and metazoan GPI-modification motifs consist mainly in variations of preferences to amino acid types at the positions near the omega-site and in the overall motif length. The variations of polypeptide substrates are exploited to suggest a model of the polypeptide binding site of the putative transamidase, the enzyme catalyzing the GPI-modification. The volume of the active site cleft accommodating the four residues omega - 1...omega + 2 appears to be approximately 540 A3.","authors":"Eisenhaber, B., Bork, P., Eisenhaber, F.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Protein Eng","volume":"11","issue":"12","page":"1155-61","pdf":null,"JrId":"6619","fulltextlink":null,"preprintlink":null,"articledate":"1999-03-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9930349","title":"The size of DNA\/transferrin-PEI complexes is an important factor for gene expression in cultured cells.","abstract":"Under physiological salt concentration, plasmid DNA complexed with transferrin-conjugated or unmodified polyethylenimine (PEI, 800 kDa) forms huge (up to &gt; 1000 nm) aggregates, unless the individual components are mixed at a highly positive nitrogen\/phosphate (N\/P) charge ratio. At low ionic strengths, however, small particles with an average size of 40 nm are formed over a broad range of N\/P ratios. Interestingly, in transfection experiments these small particles result in a 10-fold (B16F10 cells) to more than 100-fold (Neuro2A cells, K562 cells) reduced luciferase gene expression efficiency in comparison to the large complexes formed in physiological salt solutions. Limited transport of the small particles to the cell surfaces is one possible reason for this effect. Application of the small particles in more concentrated form and over extended periods of time improves transfection activity. Reduced intracellular release may be another explanation for the decreased transfection efficiency; incubation with chloroquine or incorporation of the endosomolytic peptide INF5 into the small complexes enhances gene expression approximately 10-fold. Analysis of gene expression at the cellular level using a green fluorescence protein reporter gene and flow cytometry revealed that the differences in overall gene expression largely result from different intensities per expressing cell, while the difference in the percentage of expressing cells is less substantial.","authors":"Ogris, M., Steinlein, P., Kursa, M., Mechtler, K., Kircheis, R., Wagner, E.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Gene Ther","volume":"5","issue":"10","page":"1425-33","pdf":null,"JrId":"8603","fulltextlink":null,"preprintlink":null,"articledate":"1999-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9889159","title":"How representative are the known structures of the proteins in a complete genome? A comprehensive structural census.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9889159<\/PMID><DateCompleted><Year>1999<\/Year><Month>04<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2006<\/Year><Month>11<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">1359-0278<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>3<\/Volume><Issue>6<\/Issue><PubDate><Year>1998<\/Year><\/PubDate><\/JournalIssue><Title>Folding &amp; design<\/Title><ISOAbbreviation>Fold Des<\/ISOAbbreviation><\/Journal><ArticleTitle>How representative are the known structures of the proteins in a complete genome? A comprehensive structural census.<\/ArticleTitle><Pagination><MedlinePgn>497-512<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Determining how representative the known structures are of the proteins encoded by a complete genome is important for assessing to what extent our current picture of protein stability and folding is overly influenced by biases in the structure databank (PDB). It is also important for improving database-based methods of structure prediction and genome annotation.","authors":"Gerstein, M.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Fold Des","volume":"3","issue":"6","page":"497-512","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33947960","title":null,"abstract":null,"authors":"","publication_status":null,"journalpubyear":null,"journaltitle":null,"volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35623327","title":"Evidence in favor of the essentiality of human cell membrane-bound ACE2 and against soluble ACE2 for SARS-CoV-2 infectivity.","abstract":null,"authors":"Batlle, D., Monteil, V., Garreta, E., Hassler, L., Wysocki, J., Chandar, V., Schwartz, RE., Mirazimi, A., Montserrat, N., Bader, M., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cell","volume":"185","issue":"11","page":"1837-1839","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9857194","title":"Leukemic transformation by the v-ErbA oncoprotein entails constitutive binding to and repression of an erythroid enhancer in vivo.","abstract":"v-ErbA, a mutated thyroid hormone receptor alpha (TRalpha), is thought to contribute to avian erythroblastosis virus (AEV)-induced leukemic transformation by constitutively repressing transcription of target genes. However, the binding of v-ErbA or any unliganded nuclear receptor to a chromatin-embedded response element as well as the role of the N-CoR-SMRT-HDAC co-repressor complex in mediating repression remain hypothetical. Here we identify a v-ErbA-response element, VRE, in an intronic DNase I hypersensitive site (HS2) of the chicken erythroid carbonic anhydrase II (CAII) gene. In vivo footprinting shows that v-ErbA is constitutively bound to this HS2-VRE in transformed, undifferentiated erythroblasts along with other transcription factors like GATA-1. Transfection assays show that the repressed HS2 region can be turned into a potent enhancer in v-ErbA-expressing cells by mutation of the VRE. Differentiation of transformed cells alleviates v-ErbA binding concomitant with activation of CAII transcription. Co-expression of a gag-TRalpha fusion protein in AEV-transformed cells and addition of ligand derepresses CAII transcription. Treatment of transformed cells with the histone deacetylase inhibitor, trichostatin A, derepresses the endogenous, chromatin-embedded CAII gene, while a transfected HS2-enhancer construct remains repressed. Taken together, our data suggest that v-ErbA prevents CAII activation by 'neutralizing' in cis the activity of erythroid transcription factors.","authors":"Ciana, P., Braliou, GG., Demay, FG., von Lindern, M., Barettino, D., Beug, H., Stunnenberg, HG.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"EMBO J","volume":"17","issue":"24","page":"7382-94","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1999-02-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9850859","title":"Thymocyte selection in Vav and IRF-1 gene-deficient mice.","abstract":"T cells undergo a defined program of phenotypic and genetic changes during differentiation within the thymus. These changes define commitment of T-cell receptor (TCR) gamma delta and TCR alpha beta cells and lineage differentiation into CD4+ T helper and CD8+ cytotoxic T cells. T-cell differentiation and selection in the thymus constitute a tightly co-ordinated multistep journey through a network that can be envisaged as a three-dimensional informational highway made up of stromal cells and extracellular matrix molecules. This intrathymic journey is controlled by information exchange, with thymocytes depending on two-way cellular interactions with thymic stromal cells in order to receive essential signals for maturation and selection. Genetic inactivation of surface receptors, signal transduction molecules, and transcription factors using homologous recombination has provided novel insight into the signaling cascades that relay surface receptor engagement to gene transcription and subsequent progression of the developmental program. In this review we discuss molecular mechanisms of T lymphocyte development in mice that harbour genetic mutations in the guanine nucleotide exchange factor Vav and the interferon regulatory transcription factor 1 (IRF-1). We also propose a novel model of T-cell selection based on TCR alpha chain-directed signals for allelic exclusion and TCR alpha-based selection for single receptor usage.","authors":"Penninger, JM., Mak, TW.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Immunol Rev","volume":"165","issue":null,"page":"149-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1999-03-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9813124","title":"Comparative kinetic analysis of FLP and cre recombinases: mathematical models for DNA binding and recombination.","abstract":"The integrase class site specific recombinases FLP from Saccharomyces cerevisiae, and Cre from bacteriophage P1, have been extensively used to direct DNA rearrangements in heterologous organisms. Although their reaction mechanisms have been relatively well characterised, little comparative analysis of the two enzymes has been published. We present a comparative kinetic analysis of FLP and Cre, which identifies important differences. Gel mobility shift assays show that Cre has a higher affinity for its target, loxP (7. 4x10(10) M-1), than FLP for its target, FRT (8.92x10(8) M-1). We show that both recombinases bind the two halves of their target sites cooperatively, and that Cre shows approximately threefold higher cooperativity than FLP. Using a mathematical model describing the sequential binding of recombinase monomers to DNA, we have determined values for the association and dissociation rate constants for FLP and Cre.FLP and Cre also showed different characteristics in in vitro recombination assays. In particular, approximately tenfold more active FLP was required than Cre to optimally recombine a given quantity of excision substrate. FLP was able to reach maximum excision levels approaching 100%, whilst Cre-mediated excision did not exceed 75%. To investigate possible reasons for these differences a mathematical model describing the excision recombination reaction was established. Using measured DNA binding parameters for FLP and Cre in the model, and comparing simulated and experimental recombination data, the values of the remaining unknown parameters were determined. This analysis indicates that the synaptic complex is more stable for Cre than for FLP.","authors":"Ringrose, L., Lounnas, V., Ehrlich, L., Buchholz, F., Wade, R., Stewart, AF.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Mol Biol","volume":"284","issue":"2","page":"363-84","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1998-12-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9811769","title":"Very-low-density lipoprotein receptor fragment shed from HeLa cells inhibits human rhinovirus infection.","abstract":"The large family of human rhinoviruses, the main causative agents of the common cold, is divided into the major and the minor group based on receptor specificity. Major group viruses attach to intercellular adhesion molecule 1 (ICAM-1), a member of the immunoglobulin superfamily, whereas minor group viruses use low-density lipoprotein receptors (LDLR) for cell entry. During early attempts aimed at isolating the minor group receptor, we discovered that a protein with virus binding activity was released from HeLa cells upon incubation with buffer at 37 degreesC (F. Hofer, B. Berger, M. Gruenberger, H. Machat, R. Dernick, U. Tessmer, E. Kuechler, and D. Blaas, J. Gen. Virol. 73:627-632, 1992). In light of the recent discovery of several new members of the LDLR family, we reinvestigated the nature of this protein and present evidence for its being derived from the human very-low density lipoprotein receptor (VLDLR). A soluble VLDLR fragment encompassing the eight complement type repeats and representing the N-terminal part of the receptor was then expressed in the baculovirus system; both the shed protein and the recombinant soluble VLDLR bind minor group viruses and inhibit viral infection of HeLa cells in a concentration-dependent manner.","authors":"Marlovits, TC., Abrahamsberg, C., Blaas, D.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Virol","volume":"72","issue":"12","page":"10246-50","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1998-11-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-178","title":"The Sperm Protein Spaca6 is Essential for Fertilization in Zebrafish.","abstract":null,"authors":"Binner, MI., Kogan, A., Panser, K., Schleiffer, A., Deneke, VE., Pauli, A.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Front Cell Dev Biol","volume":"9","issue":null,"page":"806982","pdf":null,"JrId":null,"fulltextlink":"https:\/\/pubmed.ncbi.nlm.nih.gov\/35047514\/","preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.11.19.469324v1","articledate":"2022-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-206","title":"A regulatory module driving the recurrent evolution of irreducible molecular complexes","abstract":null,"authors":"Tikanova, P., Ross, JJ., Hahm\u00fcller, A., P\u00fchringer, F., Pliota, P., Krogull, D., Stefania, V., Hunold, M., Ostapchuk, I., Gokcezade, J., Duchek, P., Dong, G., Ben-David, E.; Burga, A  ","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"BioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.09.16.613340v1","articledate":"2024-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9687498","title":"The thyroid hormone receptor functions as a ligand-operated developmental switch between proliferation and differentiation of erythroid progenitors.","abstract":"The avian erythroblastosis virus (AEV) oncoprotein v-ErbA represents a mutated, oncogenic thyroid hormone receptor alpha (c-ErbA\/ TRalpha). v-ErbA cooperates with the stem cell factor-activated, endogenous receptor tyrosine kinase c-Kit to induce self-renewal and to arrest differentiation of primary avian erythroblasts, the AEV transformation target cells. In this cooperation, v-ErbA substitutes for endogenous steroid hormone receptor function required for sustained proliferation of non-transformed erythroid progenitors. In this paper, we propose a novel concept of how v-ErbA transforms erythroblasts. Using culture media strictly depleted from thyroid hormone (T3) and retinoids, the ligands for c-ErbA\/TRalpha and its co-receptor RXR, we show that overexpressed, unliganded c-ErbA\/ TRalpha closely resembles v-ErbA in its activity on primary erythroblasts. In cooperation with ligand-activated c-Kit, c-ErbA\/ TRalpha causes steroid-independent, long-term proliferation and tightly blocks differentiation. Activation of c-ErbA\/ TRalpha by physiological T3 levels causes the loss of self-renewal capacity and induces synchronous, terminal differentiation under otherwise identical conditions. This T3-induced switch in erythroid progenitor development is correlated with a decrease of c-ErbA-associated histone deacetylase activity. Our results suggest that the crucial role of the mutations activating v-erbA as an oncogene is to 'freeze' c-ErbA\/ TRalpha in its non-liganded, repressive conformation and to facilitate its overexpression.","authors":"Bauer, A., Mikulits, W., Lagger, G., Stengl, G., Brosch, G., Beug, H.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"EMBO J","volume":"17","issue":"15","page":"4291-303","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1998-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9671580","title":"Characterization of three novel members of the zebrafish Pax2\/5\/8 family: dependency of Pax5 and Pax8 expression on the Pax2.1 (noi) function.","abstract":"The mammalian Pax2, Pax5 and Pax8 genes code for highly related transcription factors, which play important roles in embryonic development and organogenesis. Here we report the characterization of all members of the zebrafish Pax2\/5\/8 family. These genes have arisen by duplications before or at the onset of vertebrate evolution. Due to an additional genome amplification in the fish lineage, the zebrafish contains two Pax2 genes, the previously known Pax[b] gene (here renamed as Pax2.1) and a novel Pax2.2 gene. The zebrafish Pax2.1 gene most closely resembles the mammalian Pax2 gene in its expression pattern, as it is transcribed first in the midbrain-hindbrain boundary region, then in the optic stalk, otic system, pronephros and nephric ducts, and lastly in specific interneurons of the hindbrain and spinal cord. Pax2.2 differs from Pax2.1 by the absence of expression in the nephric system and by a delayed onset of transcription in other Pax2.1 expession domains. Pax8 is also expressed in the same domains as Pax2.1, but its transcription is already initiated during gastrulation in the primordia of the otic placode and pronephric anlage, thus identifying Pax8 as the earliest developmental marker of these structures. The zebrafish Pax5 gene, in contrast to its mouse orthologue, is transcribed in the otic system in addition to its prominent expression at the midbrain-hindbrain boundary. The no isthmus (noi) mutation is known to inactivate the Pax2.1 gene, thereby affecting the development of the midbrain-hindbrain boundary region, pronephric system, optic stalk and otic region. Although the different members of the Pax2\/5\/8 family may potentially compensate for the loss of Pax2.1 function, we demonstrate here that only the expression of the Pax2.2 gene remains unaffected in noi mutant embryos. The expression of Pax5 and Pax8 is either not initiated at the midbrain-hindbrain boundary or is later not maintained in other expression domains. Consequently, the noi mutation of zebrafish is equivalent to combined inactivation of the mouse Pax2 and Pax5 genes with regard to the loss of midbrain-hindbrain boundary development.","authors":"Pfeffer, PL., Gerster, T., Lun, K., Brand, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Development","volume":"125","issue":"16","page":"3063-74","pdf":null,"JrId":"3468","fulltextlink":null,"preprintlink":null,"articledate":"1998-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9665839","title":"Homology-based fold predictions for Mycoplasma genitalium proteins.","abstract":"Homology search techniques based on the iterative PSI-BLAST method in combination with various filters for low sequence complexity are applied to assign folds to all Mycoplasma genitalium proteins. The resulting procedure (implemented as a web server) is able to predict at least one domain in 37% of these proteins automatically, with an estimated accuracy higher than 98%. Taking structural features such as coiled coil or transmembrane regions aside, folds can be assigned to more than half of the globular proteins in a bacterium just by iterative sequence comparison.","authors":"Huynen, M., Doerks, T., Eisenhaber, F., Orengo, C., Sunyaev, S., Yuan, Y., Bork, P.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Mol Biol","volume":"280","issue":"3","page":"323-6","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1998-08-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9663658","title":"recessive spotting: a linked locus that interacts with W\/Kit but is not allelic.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9663658<\/PMID><DateCompleted><Year>1998<\/Year><Month>10<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>11<\/Month><Day>02<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">1356-9597<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>3<\/Volume><Issue>4<\/Issue><PubDate><Year>1998<\/Year><Month>Apr<\/Month><\/PubDate><\/JournalIssue><Title>Genes to cells : devoted to molecular &amp; cellular mechanisms<\/Title><ISOAbbreviation>Genes Cells<\/ISOAbbreviation><\/Journal><ArticleTitle>recessive spotting: a linked locus that interacts with W\/Kit but is not allelic.<\/ArticleTitle><Pagination><MedlinePgn>235-44<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The murine coat-colour mutation recessive spotting (rs) maps very closely to the W\/Kit locus, encoding the proto-oncoprotein Kit, the protein tyrosine kinase receptor for stem cell factor. Kit is important in the development of melanocytes, germ cells, interstitial cells of Cajal (ICC) and haemopoietic lineages, including mast cells. rs has never been genetically separated from Kit, and interacts with Kit mutations, suggesting that it is a recessive allele of Kit. Here we have tested this possibility. We have shown previously that diploid rs\/rs melanocytes proliferated more slowly than did +\/+ melanocytes, as did an immortal line of rs\/rs melanocytes, melan-rs.","authors":"Bennett, DC., Trayner, ID., Piao, X., Easty, DJ., Kl\u00fcppel, M., Alexander, WS., Wagner, EF., Bernstein, A.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Genes Cells","volume":"3","issue":"4","page":"235-44","pdf":null,"JrId":"20533","fulltextlink":null,"preprintlink":null,"articledate":"1998-10-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9653174","title":"Evidence for multiclonality in multicentric Kaposi's sarcoma.","abstract":"Kaposi's sarcoma (KS) develops in a variety of clinical states and is the most common tumor seen in patients with HIV-1 infection. KS develops as a multifocal mucocutaneous disease with subsequent spread to visceral organs, and it has been argued to be a benign proliferation caused by its multifocality at initial presentation, lack of aneuploidy, and spontaneous regression upon withdrawal of immunosuppressive agents in iatrogenically induced disease. We wished to determine whether KS lesions are clonal, indicative of a true neoplasm. Also, we tested whether multifocal KS lesions are clonally related, derived from a common progenitor cell or of independent cellular origin. We studied the X-chromosome inactivation pattern of the human androgen receptor gene in tumor biopsies of women with KS. This procedure tests for the clonality of a tissue specimen, a hallmark of neoplasia. Each specimen was microdissected to minimize normal cell contamination. Of 12 evaluable cases, 10 were HIV-seropositive and 2 were HIV-seronegative. Twenty-four biopsies from the 12 patients were examined. Five cases were consistent with individual KS lesions being clonal. In two cases, multiple KS specimens derived from the individual patients had different androgen receptor alleles inactivated, proving unequivocally that these KS lesions arose independently from distinct transformed cells. In seven cases, only a polyclonal pattern of inactivation was observed, whereas two others had tumor areas of both clonal and polyclonal inactivation patterns. These findings suggest that KS can be a clonal neoplasm, and in some of the cases multiple KS lesions in a given patient can arise from independent cellular origins and acquire clonal characteristics. The polyclonal inactivation pattern observed in other KS lesions may represent a premalignant stage or false negative results.","authors":"Gill, PS., Tsai, YC., Rao, AP., Spruck, CH., Zheng, T., Harrington, WA., Cheung, T., Nathwani, B., Jones, PA.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Proc Natl Acad Sci U S A","volume":"95","issue":"14","page":"8257-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-08-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9601639","title":"Vav is a regulator of cytoskeletal reorganization mediated by the T-cell receptor.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9601639<\/PMID><DateCompleted><Year>1998<\/Year><Month>08<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2020<\/Year><Month>12<\/Month><Day>12<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>8<\/Volume><Issue>10<\/Issue><PubDate><Year>1998<\/Year><Month>May<\/Month><Day>07<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Vav is a regulator of cytoskeletal reorganization mediated by the T-cell receptor.<\/ArticleTitle><Pagination><MedlinePgn>554-62<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Vav is a guanine-nucleotide exchange factor for the Rho-like small GTPases RhoA, Rac1 and Cdc42, which regulate cytoskeletal reorganization and activation of stress-activated protein kinases (SAPK\/JNKs). Vav is expressed in hematopoietic cells and is phosphorylated in T and B cells following activation of various growth factor or antigen receptors. Vav interacts with several signaling molecules in T cells, but the functional relevance of these interactions is established only for Slp76: they cooperate to induce activity of the transcription factor NF-AT and interleukin-2 expression. We have investigated the role of Vav in T cells by generating vav-\/- mice.","authors":"Fischer, KD., Kong, YY., Nishina, H., Tedford, K., Mareng\u00e8re, LE., Kozieradzki, I., Sasaki, T., Starr, M., Chan, G., Gardener, S., Nghiem, MP., Bouchard, D., Barbacid, M., Bernstein, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Curr Biol","volume":"8","issue":"10","page":"554-62","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9593195","title":"Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?","abstract":"The parametric description of residue environments through solvent accessibility, backbone conformation, or pairwise residue-residue distances is the key to the comparison between amino acid types at protein sequence positions and residue locations in structural templates (condition of protein sequence-structure match). For the first time, the research results presented in this study clarify and allow to quantify, on a rigorous statistical basis, to what extent the amino acid type-specific distributions of commonly used environment parameters are discriminative with respect to the 20 amino acid types. Relying on the Bahadur theory, we estimate the probability of error in a single-sequence-structure alignment based on weak or absent discriminative power in a learning database of protein structure. We present the results for many residue environment variables and demonstrate that each fold description parameter is sensitive with respect to only a few amino acid types while indifferent to most of the other amino acid types. Even complex structural characteristics combining solvent-accessible surface area, backbone conformation, and pairwise distances distinguish only some amino acid types, whereas the others remain nondiscriminated. We find that the knowledge-based potentials currently in use treat especially Ala, Asp, Gln, His, Ser, Thr, and Tyr as essentially \"average\" amino acids. Thus, highly discriminative amino acid types define the alignment register in gapless sequence-structure alignments. The introduction of gaps leads to alignment ambiguities at sequence positions occupied by nondiscriminated amino acid types. Therefore, local sequence-structure alignments produced by techniques with gaps cannot be reliable. Conceptionally new and more sensitive environment parameters must be invented.","authors":"Sunyaev, SR., Eisenhaber, F., Argos, P., Kuznetsov, EN., Tumanyan, VG.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Proteins","volume":"31","issue":"3","page":"225-46","pdf":null,"JrId":"6646","fulltextlink":null,"preprintlink":null,"articledate":"1998-07-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9590296","title":"PAX8 mutations associated with congenital hypothyroidism caused by thyroid dysgenesis.","abstract":"Permanent congenital hypothyroidism (CH) is a common disease that occurs in 1 of 3,000-4,000 newborns. Except in rare cases due to hypothalamic or pituitary defects, CH is characterized by elevated levels of thyroid-stimulating hormone (TSH) resulting from reduced thyroid function. When thyroid hormone therapy is not initiated within the first two months of life, CH can cause severe neurological, mental and motor damage. In 80-85% of cases, CH is associated with and presumably is a consequence of thyroid dysgenesis (TD). In these cases, the thyroid gland can be absent (agenesis, 35-40%), ectopically located (30-45%) and\/or severely reduced in size (hypoplasia, 5%). Familial cases of TD are rare, even though ectopic or absent thyroid has been occasionally observed in siblings. The pathogenesis of TD is still largely unknown. Although a genetic component has been suggested, mutations in the gene encoding the receptor for the thyroid-stimulating hormone (TSHR) have been identified in only two cases of TD with hypoplasia. We report mutations in the coding region of PAX8 in two sporadic patients and one familial case of TD. All three point mutations are located in the paired domain of PAX8 and result in severe reduction of the DNA-binding activity of this transcription factor. These genetic alterations implicate PAX8 in the pathogenesis of TD and in normal thyroid development.","authors":"Macchia, PE., Lapi, P., Krude, H., Pirro, MT., Missero, C., Chiovato, L., Souabni, A., Baserga, M., Tassi, V., Pinchera, A., Fenzi, G., Gr\u00fcters, A., Busslinger, M., Di Lauro, R.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Nat Genet","volume":"19","issue":"1","page":"83-6","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"1998-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9585421","title":"Mammalian granulocyte-macrophage colony-stimulating factor receptor expressed in primary avian hematopoietic progenitors: lineage-specific regulation of proliferation and differentiation.","abstract":"The cytokine Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) regulates proliferation, differentiation, and apoptosis during myelopoiesis and erythropoiesis. Structure-function relationships of GM-CSF interactions with its receptor (GM-R), the biochemistry of GM-R signal transduction, and GM-CSF action in vivo are relatively well understood. Much less is known, however, about GM-R function in primary hematopoietic cells. In this paper we show that expression of the human GM-R in a heterologous cell system (primary avian erythroid and myeloid cells) confirms respective results in murine or human cell lines, but also provides new insights how the GM-R regulates progenitor proliferation and differentiation. As expected, the hGM-CSF stimulated myeloid progenitor proliferation and differentiation and enhanced erythroid progenitor proliferation during terminal differentiation. In the latter cells, however, the hGM-R only partially substituted for the activities of the erythropoietin receptor (EpoR). It failed to replace the EpoR in its cooperation with c-Kit to induce long-term proliferation of erythroid progenitors. Furthermore, the hGM-R alpha chain specifically interfered with EpoR signaling, an activity neither seen for the betac subunit of the receptor complex alone, nor for the alpha chain of the closely related Interleukin-3 receptor. These results point to a novel role of the GM-R alpha chain in defining cell type-specific functions of the GM-R.","authors":"Wessely, O., Deiner, EM., Lim, KC., Mellitzer, G., Steinlein, P., Beug, H.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"J Cell Biol","volume":"141","issue":"4","page":"1041-51","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1998-06-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35868278","title":"Human organoids: New strategies and methods for analyzing human development and disease.","abstract":"For decades, insight into fundamental principles of human biology and disease has been obtained primarily by experiments in animal models. While this has allowed researchers to understand many human biological processes in great detail, some developmental and disease mechanisms have proven difficult to study due to inherent species differences. The advent of organoid technology more than 10 years ago has established laboratory-grown organ tissues as an additional model system to recapitulate human-specific aspects of biology. The use of human 3D organoids, as well as other advances in single-cell technologies, has revealed unprecedented insights into human biology and disease mechanisms, especially those that distinguish humans from other species. This review highlights novel advances in organoid biology with a focus on how organoid technology has generated a better understanding of human-specific processes in development and disease.","authors":"Corsini, NS., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cell","volume":"185","issue":"15","page":"2756-2769","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9577414","title":"Embryonic overexpression of the c-Fos protooncogene. A murine stem cell chimera applicable to the study of fibrodysplasia ossificans progressiva in humans.","abstract":"Murine embryonic overexpression of the c-fos protooncogene leads to early postnatal heterotopic chondrogenesis and osteogenesis with phenotypic features similar to those seen in children who have the disabling heritable disease fibrodysplasia ossificans progressiva. The overexpression of Fos in embryonic stem cell chimeras leads to heterotopic endochondral osteogenesis at least in part through a bone morphogenetic protein 4 mediated signal transduction pathway. In contrast, early fibrodysplasia ossificans progressiva lesions express abundant bone morphogenetic protein 4, without abundant expression of c-Fos, suggesting that the primary molecular defect in fibrodysplasia ossificans progressiva may be independent of the sustained Fos effects on chondrogenesis and osteogenesis. Comparisons of the clinical, molecular, and pathogenetic features of the c-Fos embryonic stem cell chimeras with those of fibrodysplasia ossificans progressiva provide insight into the earliest events in the molecular pathogenesis of genetically induced heterotopic chondrogenesis and osteogenesis. The relevance of the c-Fos embryonic stem cell chimera to the study of the currently untreatable human disease fibrodysplasia ossificans progressiva demonstrates the power of using embryonic stem cell technology for generating gain of function mutations in the study of human bone disease.","authors":"Olmsted, EA., Gannon, FH., Wang, ZQ., Grigoriadis, AE., Wagner, EF., Zasloff, MA., Shore, EM., Kaplan, FS.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Clin Orthop Relat Res","volume":null,"issue":"346","page":"81-94","pdf":null,"JrId":"3046","fulltextlink":null,"preprintlink":null,"articledate":"1998-05-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9545244","title":"Identification of BSAP (Pax-5) target genes in early B-cell development by loss- and gain-of-function experiments.","abstract":"The Pax-5 gene codes for the transcription factor BSAP which is essential for the progression of adult B lymphopoiesis beyond an early progenitor (pre-BI) cell stage. Although several genes have been proposed to be regulated by BSAP, CD19 is to date the only target gene which has been genetically confirmed to depend on this transcription factor for its expression. We have now taken advantage of cultured pre-BI cells of wild-type and Pax-5 mutant bone marrow to screen a large panel of B lymphoid genes for additional BSAP target genes. Four differentially expressed genes were shown to be under the direct control of BSAP, as their expression was rapidly regulated in Pax-5-deficient pre-BI cells by a hormone-inducible BSAP-estrogen receptor fusion protein. The genes coding for the B-cell receptor component Ig-alpha (mb-1) and the transcription factors N-myc and LEF-1 are positively regulated by BSAP, while the gene coding for the cell surface protein PD-1 is efficiently repressed. Distinct regulatory mechanisms of BSAP were revealed by reconstituting Pax-5-deficient pre-BI cells with full-length BSAP or a truncated form containing only the paired domain. IL-7 signalling was able to efficiently induce the N-myc gene only in the presence of full-length BSAP, while complete restoration of CD19 synthesis was critically dependent on the BSAP protein concentration. In contrast, the expression of the mb-1 and LEF-1 genes was already reconstituted by the paired domain polypeptide lacking any transactivation function, suggesting that the DNA-binding domain of BSAP is sufficient to recruit other transcription factors to the regulatory regions of these two genes. In conclusion, these loss- and gain-of-function experiments demonstrate that BSAP regulates four newly identified target genes as a transcriptional activator, repressor or docking protein depending on the specific regulatory sequence context.","authors":"Nutt, SL., Morrison, AM., D\u00f6rfler, P., Rolink, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"EMBO J","volume":"17","issue":"8","page":"2319-33","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1998-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9541201","title":"Pax genes and organogenesis: Pax9 meets tooth development.","abstract":"Pax genes encode a family of transcription factors that play key roles during embryogenesis. They are required for the development of a variety of organs including the nervous and muscular system, skeleton, eye, ear, kidney, thymus, and pancreas. Whereas the developmental roles of many of the nine known Pax genes have been analyzed in great detail, a functional analysis of Pax9 has just begun. During mouse embryogenesis, Pax9 exhibits a highly specific expression pattern in derivatives of the foregut endoderm, somites, limb mesenchyme, midbrain, and the cephalic neural crest. In the mandibular arch mesenchyme, the expression of Pax9 marks the prospective sites of tooth development prior to any morphological signs of odontogenesis and is maintained in the developing tooth mesenchyme thereafter. To understand the function of Pax9 during mouse embryogenesis, we recently have created a null allele by gene targeting. Preliminary analyses show that Pax9 is essential for the formation of teeth, and we conclude that Pax9 is required for tooth development to proceed beyond the bud stage. Here, we briefly summarize our current knowledge about Pax genes and introduce Pax9 to the growing family of factors which are involved in tooth development.","authors":"Peters, H., Neub\u00fcser, A., Balling, R.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Eur J Oral Sci","volume":"106 Suppl 1","issue":null,"page":"38-43","pdf":null,"JrId":"8729","fulltextlink":null,"preprintlink":null,"articledate":"1998-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9527490","title":"Two-dimensional mapping of the endogenous proteins of the rat hepatocyte Golgi complex cleared of proteins in transit.","abstract":"The discovery of additional endogenous Golgi proteins will lead to significant new insights into Golgi function. To this end, stacked Golgi fractions (SGFs) were isolated from rat liver before (CTL SGF) and after molecules in transit through the Golgi were cleared by pre-treatment with cycloheximide (CHX SGF). Electron microscopic (EM) morphometric and biochemical analyses showed that the in vivo stacked morphology is retained, that &gt; 90% of the elements can be positively identified as Golgi stacks and cisternae, and that transmembrane protein markers of the Golgi complex are enriched 300- to 800-fold over starting postnuclear supernatant (PNS). High-resolution two-dimensional (2-D) gel mapping has been carried out on the CTL PNS, CTL SII (an intermediate fraction), CTL SGF, CHX SGF, CHX SGF - high pH supernatant, and CHX SGF - high pH pellet. This analysis, coupled with immunoblotting and alignment of the 2-D gels with master gels, has allowed the identification of a number of known proteins and the preliminary characterization of the most abundant 173 Golgi-specific proteins. These 173 proteins have been placed into three categories: cargo, cytosolic Golgi-associated, and resident Golgi proteins. These categories are tentative and will be modified as more data are acquired from immunoblotting and protein sequencing.","authors":"Taylor, RS., Fialka, I., Jones, SM., Huber, LA., Howell, KE.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Electrophoresis","volume":"18","issue":"14","page":"2601-12","pdf":null,"JrId":"3579","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9527488","title":"Subcellular fractionation of polarized epithelial cells and identification of organelle-specific proteins by two-dimensional gel electrophoresis.","abstract":"Protein targeting and sorting is accomplished by complex vesicular transport processes that are tightly regulated within a cell. This is especially important for epithelial cells because correct delivery of newly synthesized proteins as well as recycling and sorting of internalized membrane proteins is essential for the establishment and preservation of cellular polarity. Many transport events, linking various subcellular compartments, have been analyzed, but many transport mechanisms still remain unresolved. In this study we attempted to identify proteins specifically associated with distinct organelles in murine mammary epithelial cells (EpH4). We isolated subcellular compartments by continuous sucrose gradient centrifugation in order to further analyze their protein composition by high-resolution two-dimensional gel electrophoresis (2-DE). The successful separation of late endosomes (LE), early endosomes (EE) and most of the rough endoplasmic reticulum (RER) was confirmed by subsequent analysis of gradient fractions for compartment-specific enzymes and marker proteins. Both Golgi and plasma membrane (PM) were found to partially co-purify with EE in such gradients. Characteristic polypeptide patterns were revealed on 2-DE gels for fractions enriched in membranes of different origin. Based on improved sample preparation and loading techniques (this issue, C. Pasquali et al., Electrophoresis, 1997, 18, 2573-2581), we were able to identify several proteins by immunoblotting or microsequencing of Coomassie-stained spots. This will be the basis for a further characterization of organelle-specific molecules in epithelial cells as well as for the establishment of a 2-DE reference map of membrane proteins from murine mammary epithelium.","authors":"Fialka, I., Pasquali, C., Lottspeich, F., Ahorn, H., Huber, LA.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Electrophoresis","volume":"18","issue":"14","page":"2582-90","pdf":null,"JrId":"3579","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9502417","title":"Binding of RANTES, MCP-1, MCP-3, and MIP-1alpha to cells in human skin.","abstract":"Based on their ability to induce leukocyte chemotaxis and adhesion to endothelial cells (ECs), chemokines have been implicated in driving inflammatory leukocyte emigration. Recently, it was suggested that chemokines can accomplish their pro-emigratory role more effectively while being bound to the luminal surface of the ECs. Previously, such binding was demonstrated in situ in human skin for the prototype alpha-chemokine interleukin (IL)-8. Here we used an in situ binding assay to investigate the binding characteristics of several beta-chemokines in intact human skin. RANTES, MCP-1, and MCP-3 bound, similar to IL-8, in a specific saturable manner to the ECs of venules and small veins but not arteries or capillaries. RANTES inhibited MCP-1 and MCP-3 binding and vice versa, indicating that the EC binding sites are shared among these beta-chemokines; moreover, IL-8 and RANTES cross-competed for each other's binding, suggesting that the same chemokine binding sites are used by members of alpha- and beta-chemokine subfamilies. Conversely, MIP-1alpha did not bind to the ECs and did not compete for binding of RANTES. Analogous to IL-8, all of the tested beta-chemokines bound to the resident dermal cells. As a novel aspect of chemokine interaction with cells in normal skin, we observed specific, saturable binding of RANTES, MCP-1, and MCP-3 but not MIP-1alpha or IL-8 to the ECs of dermal afferent lymphatic vessels. RANTES, MCP-1, and MCP-3 also cross-competed for each other's binding to lymphatics, suggesting a common binding site with a novel chemokine binding profile. We suggest that the chemokine binding to the ECs of lymphatics may be involved in the process of leukocyte entry into the afferent lymphatic vessels.","authors":"Hub, E., Rot, A.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Am J Pathol","volume":"152","issue":"3","page":"749-57","pdf":null,"JrId":"449","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9487389","title":"SET domain proteins modulate chromatin domains in eu- and heterochromatin.","abstract":"The SET domain is a 130-amino acid, evolutionarily conserved sequence motif present in chromosomal proteins that function in modulating gene activities from yeast to mammals. Initially identified as members of the Polycomb- and trithorax-group (Pc-G and trx-G) gene families, which are required to maintain expression boundaries of homeotic selector (HOM-C) genes, SET domain proteins are also involved in position-effect-variegation (PEV), telomeric and centromeric gene silencing, and possibly in determining chromosome architecture. These observations implicate SET domain proteins as multifunctional chromatin regulators with activities in both eu- and heterochromatin--a role consistent with their modular structure, which combines the SET domain with additional sequence motifs of either a cysteine-rich region\/zinc-finger type or the chromo domain. Multiple functions for chromatin regulators are not restricted to the SET protein family, since many trx-G (but only very few Pc-G) genes are also modifiers of PEV. Together, these data establish a model in which the modulation of chromatin domains is mechanistically linked with the regulation of key developmental loci (e.g. HOM-C).","authors":"Jenuwein, T., Laible, G., Dorn, R., Reuter, G.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Cell Mol Life Sci","volume":"54","issue":"1","page":"80-93","pdf":null,"JrId":"20436","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9485038","title":"Impairment of survival factor function potentiates chemotherapy-induced apoptosis in tumor cells.","abstract":"The balance between tumor cell proliferation and apoptosis is a critical determinant of malignant tumor outgrowth. In a transgenic mouse model of beta cell tumorigenesis (Rip1Tag2), insulin-like growth factor II (IGF-II) is up-regulated during the onset of tumor cell proliferation. Disruption of IGF-II expression in these transgenic mice causes a dramatic increase of beta tumor cell (betaTC) apoptosis, indicating that IGF-II acts as a survival factor. Here we report that beta tumor cell lines derived from IGF-II-deficient Rip1Tag2 mice show a higher incidence of apoptosis than their wild-type counterparts. In particular, IGF-II-deficient betaTCs are more sensitive to apoptotic stimuli, such as serum deprivation and staurosporine, and to chemotherapeutic agents, such as daunomycin, etoposide, or vincristine. Thus, the lack of the survival factor IGF-II potentiates chemotherapeutic treatment of betaTCs. Furthermore, normal betaTCs can be sensitized to chemotherapy when transfected with a dominant-negative mutant of the IGF-I receptor. These results demonstrate a pivotal role for IGF-mediated signaling in the survival of tumor cells and, thus, raise the possibility of novel approaches toward cancer therapy by interfering with survival factor function.","authors":"Lamm, GM., Christofori, G.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Cancer Res","volume":"58","issue":"4","page":"801-7","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9482731","title":"The Polo-like kinase Cdc5p and the WD-repeat protein Cdc20p\/fizzy are regulators and substrates of the anaphase promoting complex in Saccharomyces cerevisiae.","abstract":"Proteolysis mediated by the anaphase promoting complex (APC) has a crucial role in regulating the passage of cells through anaphase. Destruction of the anaphase inhibitor Pds1p is necessary for separation of sister chromatids, whereas destruction of the mitotic cyclin Clb2p is important for disassembly of the mitotic spindle, cytokinesis and re-replication of the genome. Pds1p proteolysis precedes that of Clb2p by at least 15 min, which helps to ensure that cells never re-replicate their genome before they have separated sister chromatids at the previous mitosis. What triggers Pds1p proteolysis and why does it not also trigger that of Clb2p? Apart from sharing a dependence on the APC, these two proteolytic events differ in their dependence on other cofactors. Pds1p proteolysis depends on a WD-repeat protein called Cdc20p, whereas Clb2p proteolysis depends on another, related WD protein called Hct1\/Cdh1p. On the other hand, destruction of Clb2p, but not that of Pds1p, depends on the Polo-like kinase, Cdc5p. Cdc20p is essential for separation of sister chromatids, whereas Cdc5p is not. We show that both Cdc5p and Cdc20p are unstable proteins whose proteolysis is regulated by the APC. Both proteins accumulate during late G2\/M phase and disappear at a late stage of anaphase. Accumulation of Cdc20p contributes to activation of Pds1p proteolysis in metaphase, whereas accumulation of Cdc5p facilitates the activation of Clb2p proteolysis.","authors":"Shirayama, M., Zachariae, W., Ciosk, R., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"EMBO J","volume":"17","issue":"5","page":"1336-49","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1998-04-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"157","title":"Mechanisms of glycolytic inhibition in ischemic rat hearts.","abstract":"The mechanisms of glycolytic inhibition in ischemic myocardium were investigated in the isolated, perfused rat heart. Glycolysis was inhibited at the level of glyceraldehyde-3-phosphate dehydrogenase. The major factors that accounted for the glycolytic inhibition in the ischemic heart compared with the anoxic heart appeared to be higher tissue levels of lactate and H+ in the ischemic tissue. Increased extracellular pH inhibited glycolysis in anoxic and hypoxic hearts much more readily than it did in aerobic hearts. However, maintenance of both extracellular and intracellular pH caused only a modest acceleration of glycolysis in ischemic hearts. Accumulation of tissue lactate and inhibition of glycolysis were directly proportional to the reduction in coronary bloow flow in both anoxic and ischemic hearts. At intracellular lactate concentrations between 15 and 20 mM, glycolysis was inhibited under both conditions. Addition of either 10, 20, or 40 mM lactate to the perfusate inhibited glycolysis in aerobic, anoxic, and ischemic hearts. The effect of lactate did not appear to be mediated through changes in intracellular pH. It is concluded that accumulation of lactate represents a major factor in the inhibition of glycolysis that develops in ischemic hearts.","authors":"Rovetto, MJ., Lamberton, WF., Neely, JR.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Circ Res","volume":"37","issue":"6","page":"742-51","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9482667","title":"The transactivation domain AF-2 but not the DNA-binding domain of the estrogen receptor is required to inhibit differentiation of avian erythroid progenitors.","abstract":"Earlier work demonstrated that an activated estrogen receptor (ER) is required for long-term self-renewal of c-ErbB-expressing avian erythroid progenitors. Here, we demonstrate that activation of the ER does not only arrest or retard differentiation of early progenitors but that it affects erythroid differentiation at all stages of erythroid maturation. A search for genes whose expression is affected by the ER showed that the 17beta-estradiol-activated receptor suppressed the differentiation-associated up-regulation of Gata-1, SCL-1, and globin genes in partially mature cells. In the same cells, the expression of carbonic anhydrase II (CAII) and histone H5 was enhanced. This led to premature expression of CAII, a possible explanation for the toxic effects of overexpressed ER. Repression specifically required the transactivation domain AF-2, but neither an intact DNA-binding domain (DBD) nor the AF-1 domain. The transcriptional activation of CAII, however, required both an intact AF-2 and a functional DBD. The requirement for the AF-2, but not the DBD, suggested that the ER may compete with other nuclear hormone receptors for transcriptional coactivators that bind AF-2, a domain well conserved within this family of transcription factors. We show, however, that this model does not apply for the most likely candidate, the avian thyroid hormone receptor.","authors":"von Lindern, M., Boer, L., Wessely, O., Parker, M., Beug, H.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Mol Endocrinol","volume":"12","issue":"2","page":"263-77","pdf":null,"JrId":"5920","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9462517","title":"The transcription factor NF-ATc1 regulates lymphocyte proliferation and Th2 cytokine production.","abstract":"NF-ATc1 is a member of a family of genes that encodes the cytoplasmic component of the nuclear factor of activated T cells (NF-AT). In activated T cells, nuclear NF-AT binds to the promoter regions of multiple cytokine genes and induces their transcription. The role of NF-ATc1 was investigated in recombination activating gene-1 (RAG-1)-deficient blastocyst complementation assays using homozygous NF-ATc1-\/- mutant ES cell lines. NF-ATc1-\/-\/RAG-1-\/- chimeric mice showed reduced numbers of thymocytes and impaired proliferation of peripheral lymphocytes, but normal production of IL-2. Induction in vitro of Th2 responses, as demonstrated by a decrease in IL-4 and IL-6 production, was impaired in mutant T cells. These data indicate that NF-ATc1 plays roles in the development of T lymphocytes and in the differentiation of the Th2 response.","authors":"Yoshida, H., Nishina, H., Takimoto, H., Mareng\u00e8re, LE., Wakeham, AC., Bouchard, D., Kong, YY., Ohteki, T., Shahinian, A., Bachmann, M., Ohashi, PS., Penninger, JM., Crabtree, GR., Mak, TW.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"Immunity","volume":"8","issue":"1","page":"115-24","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9450997","title":"A strain-independent postnatal neurodegeneration in mice lacking the EGF receptor.","abstract":"Mice lacking the epidermal growth factor receptor (EGFR) exhibit strain-dependent phenotypes ranging from placental to postnatal skin, lung and brain defects. After birth, all mutant mice develop a progressive neurodegeneration in the frontal cortex, olfactory bulb and thalamus, characterized by massive apoptosis and upregulation of c-fos. These defects occur in a strain-independent manner, since neither rescue of the placental phenotype by aggregation of diploid 129\/Sv EGFR mutant and tetraploid wild-type embryos, nor promotion of lung maturation by transplacental dexamethasone administration alters the course of neurodegeneration. VEGF is not induced during the degenerative process, excluding hypoxia and ischemia as causes of cell death. A migratory disorder is detected in the hippocampus with nests of ectopic neurons, which are also apoptotic. Cerebral cortices from EGFR mutants contain lower numbers of GFAP positive astrocytes, which display reduced proliferation in vitro. Since EGFR is expressed in the affected cell-types, these results define a specific function for EGFR in the proliferation and\/or differentiation of astrocytes and in the survival of postmitotic neurons.","authors":"Sibilia, M., Steinbach, JP., Stingl, L., Aguzzi, A., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1998","journaltitle":"EMBO J","volume":"17","issue":"3","page":"719-31","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9442394","title":"Essential functions of Pax-5 (BSAP) in pro-B cell development.","abstract":"Pax-5 codes for the transcription factor BSAP which is expressed in all B-lymphoid tissues in addition to the developing central nervous system and testis. Within the B-lymphoid lineage, Pax-5 expression is already detected in the earliest B cell progenitors and persists up to the mature B cell stage. Targeted inactivation of the Pax-5 gene in the mouse germline revealed a differential dependency of fetal and adult B-lymphopoiesis on this transcription factor. Pax-5 is required for the differentiation of the earliest B-lineage-committed precursor cells in the fetal liver. In contrast, B cell development in the adult bone marrow progresses up to an early pro-B cell stage in the absence of Pax-5 function. The expression of CD19, Ig alpha (mb-1) and N-myc is severely reduced in Pax-5-deficient pro-B cells. These BSAP target genes are, however, unlikely to explain the early developmental block based on their known function in B cell development. Moreover, VH-to-DHJH rearrangements at the immunoglobulin heavy-chain locus are approximately 50-fold reduced in Pax-5-deficient pro B-cells, while the DH-to-JH rearrangements occur at a normal frequency. However, the expression of rearranged mu heavy-chain transgenes does not allow Pax-5-deficient pro-B cells to develop further to the pre-B cell stage. Together these data demonstrate therefore that B cell development in the Pax-5 deficient bone marrow is arrested at an early pro-B cell stage which is not yet responsive to pre-B cell receptor signaling.","authors":"Nutt, SL., Th\u00e9venin, C., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Immunobiology","volume":"198","issue":"1-3","page":"227-35","pdf":null,"JrId":"4174","fulltextlink":null,"preprintlink":null,"articledate":"1998-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9434125","title":"In search of differentially expressed genes and proteins.","abstract":"A great challenge for modern cell biology is the successful examination of the co-expression of thousands of genes under physiological or pathological conditions and how the expression patterns define the different states of a single cell, tissue or a microorganism. Gene expression can be analyzed today on a large scale by advanced technical approaches for differential screening of proteins and mRNAs. The identification of differentially expressed mRNAs has been successfully applied to understand gene function and the underlying molecular mechanism(-s) of differentiation, development and disease state. Analysis of gene expression by the systematic mapping of thousands of proteins present in a cell or tissue can be achieved by the use of two-dimensional (2D) gel electrophoresis, quantitative computer image analysis, and protein identification techniques. In this article, we comment on some of these techniques and try to stress their advantages and drawbacks. We show how data from RNA\/DNA mapping, sequence information from genome projects and protein pattern profiling can be linked with each other and annotated. These comprehensive approaches permit the study of differential gene and protein expressions in cells or tissues.","authors":"Vietor, I., Huber, LA.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Biochim Biophys Acta","volume":"1359","issue":"3","page":"187-99","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1998-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9405645","title":"Conserved biological function between Pax-2 and Pax-5 in midbrain and cerebellum development: evidence from targeted mutations.","abstract":"The development of two major subdivisions of the vertebrate nervous system, the midbrain and the cerebellum, is controlled by signals emanating from a constriction in the neural primordium called the midbrain\/hindbrain organizer (Joyner, A. L. (1996) Trends Genet. 12, 15-201). The closely related transcription factors Pax-2 and Pax-5 exhibit an overlapping expression pattern very early in the developing midbrain\/hindbrain junction. Experiments carried out in fish (Krauss, S., Maden, M., Holder, N. &amp; Wilson, S. W. (1992) Nature (London) 360, 87-89) with neutralizing antibodies against Pax-b, the orthologue of Pax-2 in mouse, placed this gene family in an regulatory cascade necessary for the development of the midbrain and the cerebellum. The targeted mutation of Pax-5 has been reported to have only slight effects in the development of structures derived from the isthmic constriction, whereas the Pax-2 null mutant mice show a background-dependent phenotype with varying penetrance. To test a possible redundant function between Pax-2 and Pax-5 we analyzed the brain phenotypes of mice expressing different dosages of both genes. Our results demonstrate a conserved biological function of both proteins in midbrain\/hindbrain regionalization. Additionally, we show that one allele of Pax-2, but not Pax-5, is necessary and sufficient for midbrain and cerebellum development in C57BL\/6 mice.","authors":"Schwarz, M., Alvarez-Bolado, G., Urb\u00e1nek, P., Busslinger, M., Gruss, P.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Proc Natl Acad Sci U S A","volume":"94","issue":"26","page":"14518-23","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1998-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9405446","title":"Activation of stress-activated protein kinases\/c-Jun N-terminal protein kinases (SAPKs\/JNKs) by a novel mitogen-activated protein kinase kinase.","abstract":"Mitogen-activated protein kinase (MAPK) kinases (MKKs) are dual-specificity protein kinases that phosphorylate and activate MAPK. We have isolated a cDNA encoding a novel protein kinase that has significant homology to MKKs. The novel kinase MKK7 has a nucleotide sequence that encodes an open reading frame of 347 amino acids with 11 kinase subdomains. MKK7 is ubiquitously expressed in all adult and embryonic organs but displays high expression in epithelial tissues at later stages of fetal development. When transiently expressed in 293 cells, MKK7 specifically activated stress-activated protein kinases (SAPKs)\/c-Jun N-terminal protein kinases (JNKs) but not extracellular-regulated kinase or p38 kinase. A kinase-negative mutant of MKK7 inhibits interleukin-1beta, lipopolysaccharide, and MEKK1-induced SAPK\/JNK activation. Thus, MKK7 is a new member of the MAPK kinase family that functions upstream of SAPK\/JNK in the SAPK\/JNK signaling pathway.","authors":"Yao, Z., Diener, K., Wang, XS., Zukowski, M., Matsumoto, G., Zhou, G., Mo, R., Sasaki, T., Nishina, H., Hui, CC., Tan, TH., Woodgett, JP., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Biol Chem","volume":"272","issue":"51","page":"32378-83","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1998-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9398855","title":"Genetic interaction between PARP and DNA-PK in V(D)J recombination and tumorigenesis.","abstract":"Poly(ADP-ribose) polymerase (PARP) and DNA-dependent protein kinase (DNA-PK) are DNA break-activated molecules, Although mice that lack PARP display no gross phenotype and normal DNA excision repair, they exhibit high levels of sister chromatid exchange, indicative of elevated recombination rates. Mutation of the gene for DNA-PK catalytic subunit (Prkdc) cases defective antigen receptor V(D)J recombination and arrests B- and T-lymphocyte development in severe combined immune-deficiency (SCID) mice. SCID V(D)J recombination can be partly rescued in T-lymphocytes by either DNA-damaging agents (gamma-irradiation and bieomycin) or a null mutation of the p53 gene, possibly because of transiently elevated DNA repair activity in response to DNA damage or to delayed apoptosis in the absence of p53. To determine whether the increased chromosomal recombination observed in PARP-deficient cells affects SCID V(D)J recombination, we generated mice lacking both PARP and DNA-PK. Here, we show that thymocytes of SCID mice express both CD4 and CD8 co-receptors, bypassing the SCID block. Double-mutant T-cells in the periphery express TCR beta, which is attributable to productive TCR beta joints. Double-mutant mice develop a high frequency of T-cell lymphoma. These results demonstrate that increased recombination activity after the loss of PARP anti-recombinogenic function can rescue V(D)J recombination in SCID mice and indicate that PARP and DNA-PK cooperate to minimize genomic damage caused by DNA strand breaks.","authors":"Morrison, C., Smith, GC., Stingl, L., Jackson, SP., Wagner, EF., Wang, ZQ.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Nat Genet","volume":"17","issue":"4","page":"479-82","pdf":null,"JrId":"2419","fulltextlink":null,"preprintlink":null,"articledate":"1997-12-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9371790","title":"The N terminus of the Drosophila Numb protein directs membrane association and actin-dependent asymmetric localization.","abstract":"Drosophila Numb is a membrane associated protein of 557 amino acids (aa) that localizes asymmetrically into a cortical crescent in mitotic neural precursor cells and segregates into one of the daughter cells, where it is required for correct cell fate specification. We demonstrate here that asymmetric localization but not membrane localization of Numb in Drosophila embryos is inhibited by latrunculin A, an inhibitor of actin assembly. We also show that deletion of either the first 41 aa or aa 41-118 of Numb eliminates both localization to the cell membrane and asymmetric localization during mitosis, whereas C-terminal deletions or deletions of central portions of Numb do not affect its subcellular localization. Fusion of the first 76 or the first 119 aa of Numb to beta-galactosidase results in a fusion protein that localizes to the cell membrane, but fails to localize asymmetrically during mitosis. In contrast, a fusion protein containing the first 227 aa of Numb and beta-galactosidase localizes asymmetrically during mitosis and segregates into the same daughter cell as the endogenous Numb protein, demonstrating that the first 227 aa of the Numb protein are sufficient for asymmetric localization.","authors":"Knoblich, JA., Jan, LY., Jan, YN.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Proc Natl Acad Sci U S A","volume":"94","issue":"24","page":"13005-10","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1998-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9362493","title":"Alternatively spliced insertions in the paired domain restrict the DNA sequence specificity of Pax6 and Pax8.","abstract":"Transcription factors of the Pax family bind to their target genes via the paired domain which is known to be composed of two subdomains each recognizing distinct half-sites in adjacent major grooves of the DNA helix. We now demonstrate that the mammalian Pax8 gene gives rise, by alternative mRNA splicing, to a protein isoform containing an extra serine residue in the recognition alpha-helix 3 of the paired domain. This Pax8(S) protein does not interact with bipartite paired domain-binding sites, indicating that inactivation of the N-terminal DNA-binding motif severely restricts the sequence specificity of the paired domain. However, the Pax8(S) protein binds in vitro and in vivo to the 5aCON sequence which was previously identified as a high-affinity binding site for the Pax6(5a) splice variant carrying a 14-amino-acid insertion in the paired domain. The 5aCON sequence is shown to consist of four interdigitated 5' half-sites of the bipartite consensus sequence and is thus bound by four Pax8(S) molecules via the intact C-terminal DNA-binding motif of the paired domain. Together these data suggest that inactivation of the N-terminal region of the paired domain by alternative splicing is used in vivo to selectively target Pax transcription factors to gene regulatory regions containing highly specialized 5aCON-like sequences.","authors":"Kozmik, Z., Czerny, T., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"EMBO J","volume":"16","issue":"22","page":"6793-803","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1998-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9338788","title":"Imprinted expression of the Igf2r gene depends on an intronic CpG island.","abstract":"Gametic imprinting is a developmental process that induces parental-specific expression or repression of autosomal and X-chromosome-linked genes. The mouse Igf2r gene (encoding the receptor for insulin- like growth factor type-2) is imprinted and is expressed from the maternal allele after embryonic implantation. We previously proposed that methylation of region 2, a region rich in cytosine-guanine doublets (a 'CpG island') in the second intron of Igf2r, is the imprinting signal that maintains expression of the maternal allele. Here we use mouse transgenes to test the role of region 2 and the influence of chromosome location on Igf2r imprinting. Yeast artificial chromosome transgenes successfully reproduced the imprinted methylation and expression pattern of the endogenous Igf2r gene; deletion of region 2 from these transgenes caused a loss of imprinting and restored biallelic Igf2r expression. These results define a primary role for region 2 and a negligible role for chromosomal location in Igf2r imprinting; they also show that methylation imprints can maintain allelic expression. Short transgenes containing only region 2 and yeast artificial chromosome transgenes with an inactive Igf2r promoter do not attract parental-specific methylation. All transgenes showing paternal-specific repression of Igf2r produced an antisense RNA whose transcription was dependent on region 2. The production of an antisense RNA by the repressed parental allele is reminiscent of the imprinting of the Igf2\/H19 gene pair and may indicate that expression competition could play a general role in imprinting.","authors":"Wutz, A., Smrzka, OW., Schweifer, N., Schellander, K., Wagner, EF., Barlow, DP.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Nature","volume":"389","issue":"6652","page":"745-9","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1997-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9338005","title":"Polyethylenimine (PEI) is a simple, inexpensive and effective reagent for condensing and linking plasmid DNA to adenovirus for gene delivery.","abstract":"A simple and inexpensive method of condensing and linking plasmid DNA to carrier adenovirus particles is described. The synthetic polycation polyethylenimine is used to condense plasmid DNA into positively charged 100 nm complexes. These PEI-DNA complexes are then bound to adenovirus particles through charge interactions with negative domains on the viral hexon. The resulting transfection complexes deliver plasmid DNA to cells by the adenovirus infectious route without interference from virus gene expression because psoralen-inactivated virus is employed. The PEI-DNA-adenovirus complexes display DNA delivery comparable to more sophisticated DNA virus complexes employing streptavidin\/biotin linkage, but require no special reagents and are much easier to prepare.","authors":"Baker, A., Saltik, M., Lehrmann, H., Killisch, I., Mautner, V., Lamm, G., Christofori, G., Cotten, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Gene Ther","volume":"4","issue":"8","page":"773-82","pdf":null,"JrId":"8603","fulltextlink":null,"preprintlink":null,"articledate":"1997-11-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9335333","title":"Cohesins: chromosomal proteins that prevent premature separation of sister chromatids.","abstract":"Cohesion between sister chromatids opposes the splitting force exerted by microtubules, and loss of this cohesion is responsible for the subsequent separation of sister chromatids during anaphase. We describe three chromosmal proteins that prevent premature separation of sister chromatids in yeast. Two, Smc1p and Smc3p, are members of the SMC family, which are putative ATPases with coiled-coil domains. A third protein, which we call Scc1p, binds to chromosomes during S phase, dissociates from them at the metaphase-to-anaphase transition, and is degraded by the anaphase promoting complex. Association of Scc1p with chromatin depends on Smc1p. Proteins homologous to Scc1p exist in a variety of eukaryotic organisms including humans. A common cohesion apparatus might be used by all eukaryotic cells during both mitosis and meiosis.","authors":"Michaelis, C., Ciosk, R., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Cell","volume":"91","issue":"1","page":"35-45","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1997-11-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9321401","title":"Regulation of ES cell differentiation by functional and conformational modulation of p53.","abstract":"Embryonic stem (ES) cell lines were used to examine the role of p53 during in vitro differentiation. Undifferentiated ES cells express high levels of p53 exclusively in the wild-type conformation, immunoprecipitable by monoclonal antibody PAb246, and p53 was found to be functionally active as determined by its ability to bind DNA specifically and to activate transcription of target genes. Differentiation in vitro resulted in a decrease in the levels of p53 and in a shift in its conformational status to the mutant form, detectable by monoclonal antibody PAb240, with a concomitant loss of functional activity. The presence of functional p53 in the undifferentiated ES cells renders them hypersensitive to UV irradiation, whereas the differentiated cells were resistant to UV treatment. ES cells lacking p53 exhibit enhanced proliferation in both the undifferentiated and differentiated state, and apoptosis accompanying differentiation was found to be reduced. Furthermore, wild-type ES cells undergoing apoptosis expressed functional p53. Expression of the temperature-sensitive p53val135 mutant in wild-type ES cells resulted in a reduction of apoptosis accompanying differentiation when it adopted a mutant conformation at 39 degrees C. These data demonstrate that functional inactivation of p53 allows differentiating cells to escape from apoptosis, and suggest that the conformational switch could regulate the inactivation process.","authors":"Sabapathy, K., Klemm, M., Jaenisch, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"EMBO J","volume":"16","issue":"20","page":"6217-29","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1997-12-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9312056","title":"Is the yeast anaphase promoting complex needed to prevent re-replication during G2 and M phases?","abstract":"The Anaphase Promoting Complex (APC) is required for anaphase progression and B-type cyclin proteolysis. The recent finding that inactivation of the APC allows 'over-replication' of DNA has led to the proposal that the APC might also be required for preventing reduplication of chromosomes during G2 and M phases. In this report we re-investigate the phenotype of apc mutant cells and find that they do not re-replicate their DNA during the period taken for wild-type cells to traverse G2 and M phases. apc mutants do, however, gradually increase their DNA content after long periods of cell cycle arrest. Such DNA synthesis occurs almost exclusively in the cytoplasm and neither occurs in cells lacking mitochondrial DNA nor depends on Cdc6, a protein which is essential for the initiation of chromosomal but not mitochondrial DNA replication. ARS1, a chromosomal replication origin, is not re-fired in cells deprived of APC function, confirming that the 'over-replicated' DNA in apc mutant cells is of mitochondrial origin. Furthermore, we find that APC function is required to promote but not to prevent re-replication in ndc10 mutant cells. We therefore propose that the APC is not involved in preventing re-duplication of chromosomes during G2 and M phases.","authors":"Pichler, S., Piatti, S., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"EMBO J","volume":"16","issue":"19","page":"5988-97","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1997-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35120646","title":"Proteome-scale identification of transcriptional activators in human cells.","abstract":"In this issue of Molecular Cell, Alerasool et\u00a0al. (2022) present a proteome-scale functional screen to systematically uncover human proteins that can activate transcription.","authors":"Nem\u010dko, F., Stark, A.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Mol Cell","volume":"82","issue":"3","page":"497-499","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9294148","title":"Impaired CD28-mediated interleukin 2 production and proliferation in stress kinase SAPK\/ERK1 kinase (SEK1)\/mitogen-activated protein kinase kinase 4 (MKK4)-deficient T lymphocytes.","abstract":"The dual specific kinase SAPK\/ERK1 kinase (SEK1; mitogen-activated protein kinase kinase 4\/Jun NH2 terminal kinase [ JNK] kinase) is a direct activator of stress-activated protein kinases ([SAPKs]\/JNKs) in response to CD28 costimulation, CD40 signaling, or activation of the germinal center kinase. Here we show that SEK1(-\/-) recombination-activating gene (RAG)2(-\/-) chimeric mice have a partial block in B cell maturation. However, peripheral B cells displayed normal responses to IL-4, IgM, and CD40 cross-linking. SEK1(-\/-) peripheral T cells showed decreased proliferation and IL-2 production after CD28 costimulation and PMA\/Ca2+ ionophore activation. Although CD28 expression was absolutely crucial to generate vesicular stomatitis virus (VSV)-specific germinal centers, SEK1(-\/-)RAG2(-\/-) chimeras mounted a protective antiviral B cell response, exhibited normal IgG class switching, and made germinal centers in response to VSV. Interestingly, PMA\/Ca2+ ionophore stimulation, which mimics TCR-CD3 and CD28-mediated signal transduction, induced SAPK\/JNK activation in peripheral T cells, but not in thymocytes, from SEK1(-\/-) mice. These results show that signaling pathways for SAPK activation are developmentally regulated in T cells. Although SEK1(-\/-) thymocytes failed to induce SAPK\/JNK in response to PMA\/Ca2+ ionophore, SEK1(-\/-)RAG2(-\/-) thymocytes proliferated and made IL-2 after PMA\/Ca2+ ionophore and CD3\/CD28 stimulation, albeit at significantly lower levels compared to SEK1(+\/+)RAG2(-\/-) thymocytes, implying that CD28 costimulation and PMA\/Ca2+ ionophore-triggered signaling pathways exist that can mediate proliferation and IL-2 production independently of SAPK activation. Our data provide the first genetic evidence that SEK1 is an important effector molecule that relays CD28 signaling to IL-2 production and T cell proliferation.","authors":"Nishina, H., Bachmann, M., Oliveira-dos-Santos, AJ., Kozieradzki, I., Fischer, KD., Odermatt, B., Wakeham, A., Shahinian, A., Takimoto, H., Bernstein, A., Mak, TW., Woodgett, JR., Ohashi, PS., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Exp Med","volume":"186","issue":"6","page":"941-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9285557","title":"Defective induction but normal activation and function of p53 in mouse cells lacking poly-ADP-ribose polymerase.","abstract":"Poly-ADP-ribose polymerase (PARP) and p53 are both induced by DNA damage and each has been proposed to mediate the normal cellular response to damage. We find that embryo fibroblasts from PARP-null mice have a approximately twofold lower basal level of p53 and that the induction of p53 in response to DNA damage or nucleotide depletion is more than twofold less than in normal mouse cells. These factors combine to decrease the induced level of the p53 protein in PARP-deficient cells by 4-5-fold, compared to normal cells. However, there is virtually no decrease in the induction of p53 activity in PARP-deficient cells, as assayed with a p53-responsive promoter. Furthermore, cells lacking PARP arrest normally in G1 after DNA damage, in contrast to cells lacking p53, where this checkpoint is absent. Other p53-dependent properties, such as the mitotic spindle checkpoint and permissivity for gene amplification, are also normal in PARP-deficient cells. We conclude that the induced level of the p53 protein is governed by a combination of PARP-dependent and PARP-independent pathways and that the activation of p53 is largely PARP-independent. The results are consistent with a model in which the regulation of gene expression by p53 involves both increases in the amount of the protein and activation of p53 as a transcription factor.","authors":"Agarwal, ML., Agarwal, A., Taylor, WR., Wang, ZQ., Wagner, EF., Stark, GR.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Oncogene","volume":"15","issue":"9","page":"1035-41","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1997-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9285409","title":"The interferon regulatory transcription factor IRF-1 controls positive and negative selection of CD8+ thymocytes.","abstract":"Little is known about the molecular mechanisms and transcriptional regulation that govern T cell selection processes and the differentiation of CD4+ and CD8+ T cells. Mice lacking the interferon regulatory transcription factor-1 (IRF-1) have reduced numbers of mature CD8+ cells within the thymus and peripheral lymphatic organs. Here we show that positive and negative T cell selection of two MHC class I-restricted TCR alphabeta transgenes, H-Y and P14, are impaired in IRF-1-\/- mice. The absence of IRF-1 resulted in decreased expression of LMP2, TAP1, and MHC class I on thymic stromal cells. Despite decreased MHC class I expression on IRF-1-\/- thymic stromal cells, the defect in CD8+ T cells development did not reside in the thymic environment, and IRF-1-\/- stromal cells can fully support development of CD8+ thymocytes in in vivo bone marrow chimeras and in vitro reaggregation cultures. Moreover, IRF-1-\/- thymocytes displayed impaired TCR-mediated signal transduction, and the induction of negative selection in TCR Tg thymocytes from IRF-1-\/- mice required a 1000-fold increase in selecting peptide. We also provide evidence that IRF-1 is mainly expressed in mature, but not immature, thymocytes and that expression of IRF-1 in immature thymocytes is induced after peptide-specific TCR activation. These results indicate that IRF-1 regulates gene expression in developing thymocytes required for lineage commitment and selection of CD8+ thymocytes.","authors":"Penninger, JM., Sirard, C., Mittr\u00fccker, HW., Chidgey, A., Kozieradzki, I., Nghiem, M., Hakem, A., Kimura, T., Timms, E., Boyd, R., Taniguchi, T., Matsuyama, T., Mak, TW.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Immunity","volume":"7","issue":"2","page":"243-54","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-09-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9224769","title":"The anaphase-promoting complex is required in G1 arrested yeast cells to inhibit B-type cyclin accumulation and to prevent uncontrolled entry into S-phase.","abstract":"Inactivation of B-type cyclin dependent kinases due to ubiquitin-mediated cyclin proteolysis is necessary for the exit from mitosis. In Saccharomyces cerevisiae, proteolysis is initiated at the onset of anaphase and remains active until Cln1 and Cln2 cyclins appear in late G1 of the subsequent cell cycle. A large particle called the anaphase-promoting complex (APC) which is composed of the TPR proteins Cdc16p\/Cdc23p\/Cdc27p and other proteins is required for B-type cyclin ubiquitination in both anaphase and during G1 phase. The APC has an essential role for the separation of sister chromatids and for the exit from mitosis, but until now it was unclear whether the persistence of APC activity throughout G1 had any physiological role. We show here that the APC is needed in G1 arrested cells to inhibit premature appearance of B-type cyclins and to prevent unscheduled initiation of DNA replication. When pheromone arrested cells of cdc16 and cdc23 mutants were shifted to the restrictive temperature, they underwent DNA replication in the presence of pheromone. DNA replication also occurred in a G1 arrest induced by G1 cyclin (Cln) depletion, indicating that mutant cells with a defective APC initiate DNA replication without the Cln G1 cyclins, which are normally needed for the onset of S-phase. Degradation of Clb2p, Clb3p and Clb5p depends on the APC. This suggests that accumulation of any one of the six B-type cyclin proteins could account for the precocious replication of cdc16 and cdc23 mutants.","authors":"Irniger, S., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Cell Sci","volume":"110 ( Pt 13)","issue":null,"page":"1523-31","pdf":null,"JrId":"4592","fulltextlink":null,"preprintlink":null,"articledate":"1997-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35476527","title":"Cornelia de Lange syndrome mutations in NIPBL can impair cohesin-mediated DNA loop extrusion.","abstract":"Cornelia de Lange syndrome (CdLS) is a developmental multisystem disorder frequently associated with mutations in NIPBL. CdLS is thought to arise from developmental gene regulation defects, but how NIPBL mutations cause these is unknown. Here we show that several NIPBL mutations impair the DNA loop extrusion activity of cohesin. Because this activity is required for the formation of chromatin loops and topologically associating domains, which have important roles in gene regulation, our results suggest that defects in cohesin-mediated loop extrusion contribute to the etiology of CdLS by altering interactions between developmental genes and their enhancers.","authors":"Panarotto, M., Davidson, IF., Litos, G., Schleiffer, A., Peters, JM.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Proc Natl Acad Sci U S A","volume":"119","issue":"18","page":"e2201029119","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9214638","title":"Mammalian homologues of the Polycomb-group gene Enhancer of zeste mediate gene silencing in Drosophila heterochromatin and at S. cerevisiae telomeres.","abstract":"Gene silencing is required to stably maintain distinct patterns of gene expression during eukaryotic development and has been correlated with the induction of chromatin domains that restrict gene activity. We describe the isolation of human (EZH2) and mouse (Ezh1) homologues of the Drosophila Polycomb-group (Pc-G) gene Enhancer of zeste [E(z)], a crucial regulator of homeotic gene expression implicated in the assembly of repressive protein complexes in chromatin. Mammalian homologues of E(z) are encoded by two distinct loci in mouse and man, and the two murine Ezh genes display complementary expression profiles during mouse development. The E(z) gene family reveals a striking functional conservation in mediating gene repression in eukaryotic chromatin: extra gene copies of human EZH2 or Drosophila E(z) in transgenic flies enhance position effect variegation of the heterochromatin-associated white gene, and expression of either human EZH2 or murine Ezh1 restores gene repression in Saccharomyces cerevisiae mutants that are impaired in telomeric silencing. Together, these data provide a functional link between Pc-G-dependent gene repression and inactive chromatin domains, and indicate that silencing mechanism(s) may be broadly conserved in eukaryotes.","authors":"Laible, G., Wolf, A., Dorn, R., Reuter, G., Nislow, C., Lebersorger, A., Popkin, D., Pillus, L., Jenuwein, T.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"EMBO J","volume":"16","issue":"11","page":"3219-32","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1997-07-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9200440","title":"Proto-oncoprotein Vav interacts with c-Cbl in activated thymocytes and peripheral T cells.","abstract":"The molecular adapter c-Cbl is rapidly tyrosine phosphorylated following stimulation through the TCR and associates with Src homology domain-2 (SH2)\/SH3 domain-containing adapters such as Grb2, Crk, and Crk-L, which interact with guanine nucleotide exchange factors specific for the Ras family. This suggests that c-Cbl may link TCR activation to molecules that regulate GTP binding proteins. The SH2\/SH3-containing protein Vav also contains a guanine nucleotide exchange factor domain, and Vav has a crucial role in thymocyte development and activation of peripheral T cells following stimulation through the TCR. Here we show that Vav and c-Cbl form inducible molecular complexes in TCR-activated murine thymocytes and peripheral T cells as well as pervanadate-treated T cells. Vav\/c-Cbl interactions are also detectable in freshly isolated T cells from gene-targeted mice that lack the T cell-specific inhibitory receptor CTLA-4, in which c-Cbl is hyperphosphorylated on tyrosine residues. The interaction between Vav and c-Cbl is directly mediated via the SH2 domain of Vav and is dependent on tyrosine phosphorylation of c-Cbl. In addition, we show that the conserved motif Y699 MTP present in c-Cbl is the binding site for the Vav SH2 domain in vitro. These data imply that c-Cbl is a molecular adapter that regulates the function of Vav in thymocytes and peripheral T cells.","authors":"Mareng\u00e8re, LE., Mirtsos, C., Kozieradzki, I., Veillette, A., Mak, TW., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Immunol","volume":"159","issue":"1","page":"70-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-07-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9191484","title":"Viral myocarditis: balance between viral infection and immune response.","abstract":"Myocarditis is an inflammatory disorder of the heart muscle, and is often underdiagnosed in clinical practice. It presents more dramatically in the young with acute heart failure and more insidiously in adults with chronic dilated cardiomyopathy. The etiology is most often viral in North America, with a wide spectrum of natural history. The majority of patients recover spontaneously, but those with persistent ventricular dysfunction face a 20% one-year mortality. Myocarditis initiates as viral disease, and molecular techniques have confirmed viral persistence. The immune response follows as a two-edged sword-both inadequate and excessive immune responses lead to disease. Finally, the myocyte is the target of the above processes, and expresses molecular, cytokine and vascular changes that lead to dilated cardiomyopathy and heart failure. The gold standard for diagnosis still relies on the overly strict Dallas criteria for evaluating myocardial biopsies. Molecular techniques are playing an increasingly important role in both diagnosis and prognosis. Clinical suspicion is still the key towards an early diagnosis. Treatment must be early and persistent-generally supportive initially, with immunosuppression now playing a secondary role in temporizing those with exuberant immune response. Newer treatments for dilated cardiomyopathy such as amlodipine and carvedilol are equally appropriate for postmyocarditis patients. Future treatment may involve specific biological agents, immune therapy, antiviral strategies and molecular gene therapy.","authors":"Liu, P., Martino, T., Opavsky, MA., Penninger, J.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Can J Cardiol","volume":"12","issue":"10","page":"935-43","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9190940","title":"The transcription factor B cell-specific activator protein (BSAP) enhances both IL-4- and CD40-mediated activation of the human epsilon germline promoter.","abstract":"Induction of isotype switching to a particular C(H) gene correlates with the transcriptional activation of the same gene in germline configuration. Induction of correctly spliced germline transcripts is necessary to target a switch region for recombination and switching. Different cytokines activate transcription at different germline promoters. Because binding sites for the B cell-specific transcription factor BSAP are located upstream of several switch regions in the Ig locus, BSAP might play a role in isotype switching by regulating germline transcription. We investigated whether BSAP plays a role in the transcriptional regulation of the epsilon germline promoter in human B cells. We identified human EBV-negative B cell lines that express epsilon germline transcripts upon stimulation with IL-4. Electrophoretic mobility shift assay analysis showed that the human epsilon germline promoter binds BSAP. BSAP activity was expressed constitutively and was not affected by stimulation with IL-4 and\/or anti-CD40 mAb. Reporter assays with constructs containing a luciferase gene driven by the epsilon germline promoter, with or without mutations in the BSAP binding site, showed that BSAP plays a role in both IL-4-dependent induction and CD40-mediated up-regulation of human epsilon germline transcription. Furthermore, epsilon germline promoter activity was abrogated in REH cells that express a BSAP polypeptide truncated in the trans-activation domain. Among the transcription factors that regulate epsilon germline expression, BSAP is unique, in that it is B cell-specific and is at the merging point of two signaling pathways that are distinct but both critical for the induction of IgE switching.","authors":"Thienes, CP., De Monte, L., Monticelli, S., Busslinger, M., Gould, HJ., Vercelli, D.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Immunol","volume":"158","issue":"12","page":"5874-82","pdf":null,"JrId":"4816","fulltextlink":null,"preprintlink":null,"articledate":"1997-07-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9165088","title":"Mode of action of cystathionine beta-lyase.","abstract":"Cystathionine beta-lyase (CBL) is a member of the gamma-family of pyridoxal-5'-phosphate (PLP)-dependent enzymes (Alexander et al., 1994) that cleave C(beta,gamma)-S bonds of a broad variety of substrates. Recently, we reported the X-ray crystal structures of CBL and the CBL-trifluoroalanine inactivation complex at 1.83 A and 2.3 A resolution, respectively. The structures explicitly reveal the cofactor and substrate binding pockets. Spectral analysis of substrate turnover indicates a change of hydrophobicity in the microenvironment of the aldimine bond. In combination with further spectroscopic data, crystallographic evidence permits the formulation of a likely reaction mechanism.","authors":"Clausen, T., Laber, B., Messerschmidt, A.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Biol Chem","volume":"378","issue":"3-4","page":"321-6","pdf":null,"JrId":"20453","fulltextlink":null,"preprintlink":null,"articledate":"1997-08-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33417858","title":"Angelika Amon (1967-2020).","abstract":null,"authors":"Lehmann, R., Peters, JM.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell","volume":"184","issue":"1","page":"10-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9159136","title":"Cooperation of Pax2 and Pax5 in midbrain and cerebellum development.","abstract":"Midbrain and cerebellum development depends on an organizing center that is located at the midbrain-hindbrain junction of the vertebrate embryo. Expression of the two closely related transcription factors Pax2 and Pax5 overlaps spatially and temporally in this region of the developing central nervous system. To study a possible interaction of these transcription factors in midbrain and cerebellum patterning, we have generated Pax5, Krd double mutant mice. The transgene-induced Krd mutation corresponds to an approximately 7-centimorgan chromosome 19 deletion that eliminates the entire Pax2 locus. The heterozygous Krd mutation deleting one Pax2 allele had no effect on midbrain and cerebellum development. Moreover, only minor developmental defects were previously observed at the midline of the inferior colliculus and anterior cerebellum in mice that were homozygous for a targeted Pax5 mutation. Similar morphological alterations were observed in 80% of all compound heterozygous Pax5 (+\/-) Krd (+\/-) mice. However, in the remaining 20% of compound heterozygotes, the inferior colliculi were missing, and the vermis of the cerebellum was severely disrupted due to the failure of the cerebellar primordia to fuse at the midline. Inactivation of the second Pax5 allele in Pax5 (-\/-) Krd (+\/-) mice resulted in complete loss of the posterior midbrain and cerebellum, as the tissue originating from the midbrain-hindbrain boundary region was deleted in the embryo as early as day 9.5. On the basis of these data, we propose that the cooperation of Pax2 and Pax5 is essential for normal functioning of the organizing center at the midbrain-hindbrain junction.","authors":"Urb\u00e1nek, P., Fetka, I., Meisler, MH., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Proc Natl Acad Sci U S A","volume":"94","issue":"11","page":"5703-8","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9152006","title":"Generation of completely embryonic stem cell-derived mutant mice using tetraploid blastocyst injection.","abstract":"Embryonic stem (ES) cells provide a unique tool for producing specifically designed mutations in mice. Here, we describe an alternative approach toward the generation of mice which are derived completely from ES cells (ES mice), as judged by glucose phosphate isomerase (GPI) analysis, without prior passage through the germline. By injecting wild-type and mutant ES cells into tetraploid blastocysts, viable and fertile ES mice were generated, suggesting that totipotency of ES cells was not affected by long-term culture and experimental manipulation in vitro. When ES cell clones harboring a lacZ reporter gene introduced by either targeted insertion or a gene-trap approach were used, the expression pattern of the lacZ gene in ES fetuses was identical to that of fetuses that were derived from breeding of chimeric mice. Thus, this technique can be considered as a useful and rapid approach to produce fetuses and mice directly from ES cells carrying predetermined genetic changes and offers many applications for studies in molecular genetics and developmental biology.","authors":"Wang, ZQ., Kiefer, F., Urb\u00e1nek, P., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Mech Dev","volume":"62","issue":"2","page":"137-45","pdf":null,"JrId":"1825","fulltextlink":null,"preprintlink":null,"articledate":"1997-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9151696","title":"Polyoma middle T-induced vascular tumor formation: the role of the plasminogen activator\/plasmin system.","abstract":"The middle T antigen of murine Polyomavirus (PymT) rapidly transforms endothelial cells, leading to the formation of vascular tumors in newborn mice. Transformed endothelial (End.) cell lines established from such tumors exhibit altered proteolytic activity as a result of increased expression of urokinase-type plasminogen activator (uPA) and are capable of inducing vascular tumors efficiently when injected into adult mice. In this study we have used mice lacking components of the PA\/plasmin system to analyze the role of this system in the transformation process and in tumor growth. We found that the proteolytic status of the host is not a critical determinant for PymT-induced vascular tumor formation. In addition, the lack of either uPA or tissue-type PA (tPA) activity is not limiting for the establishment and proliferation of End. cells in vitro, although the combined loss of both PA activities leads to a marked reduction in proliferation rates. Furthermore, the in vitro morphogenetic properties of mutant End. cells in fibrin gels could only be correlated with an altered proteolytic status in cells lacking both uPA and tPA. However, in contrast with tumors induced by PymT itself, the tumorigenic potential of mutant and wild-type End. cell lines was found to be highly dependent on the proteolytic status of both the tumor cells and the host. Thus, genetic alterations in the PA\/plasmin system affect vascular tumor development, indicating that this system is a causal component in PymTmediated oncogenesis.","authors":"Sabapathy, KT., Pepper, MS., Kiefer, F., M\u00f6hle-Steinlein, U., Tacchini-Cottier, F., Fetka, I., Breier, G., Risau, W., Carmeliet, P., Montesano, R., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Cell Biol","volume":"137","issue":"4","page":"953-63","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9149900","title":"Distinct roles of the receptor tyrosine kinases c-ErbB and c-Kit in regulating the balance between erythroid cell proliferation and differentiation.","abstract":"In the bone marrow, multipotent and committed hematopoietic progenitors have to closely regulate their balance between sustained proliferation without differentiation (self renewal) and entering a terminal differentiation pathway. A useful model to analyze this regulation at the molecular level is committed avian erythroid progenitors. These are induced to undergo long-term self renewal by the ligand-activated receptor tyrosine kinase (RTK) c-ErbB, in cooperation with steroid hormone receptors. This self-renewal induction by c-ErbB even occurs in the presence of differentiation factors (erythropoietin and insulin). Under the same conditions, the RTK c-Kit is unable to sustain erythroid progenitor self renewal, stimulating cell proliferation without arresting terminal differentiation. Two mechanisms are involved in these differential activities of c-Kit and c-ErbB. The first one, differential regulation of receptor expression, proved to be of minor importance, because c-Kit was unable to induce self renewal, even if exogenously expressed from a retrovirus at high levels. Rather our results support the second mechanism, i.e., that receptor-specific signal transduction is responsible for the differential biological activity of c-Kit and c-ErbB: (a) specific tyrosine kinase inhibitors (tryphostins) were found which selectively inhibited the biological function of either c-Kit or c-ErbB in erythroblasts but did not affect ligand-induced autophosphorylation of either RTK; and (b) c-ErbB selectively induced SHC phosphorylation and STAT5 activation. The Ras pathway was similarly activated by c-Kit and c-ErbB. The c-ErbB-specific tyrphostin AG30 specifically blocked STAT5 activation, implicating this signal transducer in c-ErbB-induced self renewal.","authors":"Wessely, O., Mellitzer, G., von Lindern, M., Levitzki, A., Gazit, A., Ischenko, I., Hayman, MJ., Beug, H.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Cell Growth Differ","volume":"8","issue":"5","page":"481-93","pdf":null,"JrId":"1848","fulltextlink":null,"preprintlink":null,"articledate":"1997-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35084981","title":"Amplification of human interneuron progenitors promotes brain tumors and neurological defects.","abstract":"Evolutionary development of the human brain is characterized by the expansion of various brain regions. Here, we show that developmental processes specific to humans are responsible for malformations of cortical development (MCDs), which result in developmental delay and epilepsy in children. We generated a human cerebral organoid model for tuberous sclerosis complex (TSC) and identified a specific neural stem cell type, caudal late interneuron progenitor (CLIP) cells. In TSC, CLIP cells over-proliferate, generating excessive interneurons, brain tumors, and cortical malformations. Epidermal growth factor receptor inhibition reduces tumor burden, identifying potential treatment options for TSC and related disorders. The identification of CLIP cells reveals the extended interneuron generation in the human brain as a vulnerability for disease. In addition, this work demonstrates that analyzing MCDs can reveal fundamental insights into human-specific aspects of brain development.","authors":"Eichm\u00fcller, OL., Corsini, NS., V\u00e9rtesy, \u00c1., Morassut, I., Scholl, T., Gruber, VE., Peer, AM., Chu, J., Novatchkova, M., Hainfellner, JA., Paredes, MF., Feucht, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Science","volume":"375","issue":"6579","page":"eabf5546","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9148954","title":"Arrest of mycobacterial phagosome maturation is caused by a block in vesicle fusion between stages controlled by rab5 and rab7.","abstract":"Mycobacterium tuberculosis and the closely related organism Mycobacterium bovis can survive and replicate inside macrophages. Intracellular survival is at least in part attributed to the failure of mycobacterial phagosomes to undergo fusion with lysosomes. The transformation of phagosomes into phagolysosomes involves gradual acquisition of markers from the endosomal compartment. Members of the rab family of small GTPases which confer fusion competence in the endocytic pathway are exchanged sequentially onto the phagosomal membranes in the course of their maturation. To identify the step at which the fusion capability of phagosomes containing mycobacteria is compromised, we purified green fluorescent protein-labeled M. bovis BCG phagosomal compartments (MPC) and compared GTP-binding protein profiles of these vesicles with latex bead phagosomal compartments (LBC). We report that the MPC do not acquire rab7, specific for late endosomes, even 7 days postinfection, whereas this GTP-binding protein is present on the LBC within hours after phagocytosis. By contrast, rab5 is retained and enriched with time on the MPC, suggesting fusion competence with an early endosomal compartment. Prior infection of macrophages with M. bovis BCG also affected the dynamics of rab5 and rab7 acquisition by subsequently formed LBC. Selective exclusion of rab7, coupled with the retention of rab5 on the mycobacterial phagosome, may allow organisms from the M. tuberculosis complex to avert the usual physiological destination of phagocytosed material.","authors":"Via, LE., Deretic, D., Ulmer, RJ., Hibler, NS., Huber, LA., Deretic, V.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Biol Chem","volume":"272","issue":"20","page":"13326-31","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9130477","title":"Regulation of human epsilon germline transcription: role of B-cell-specific activator protein.","abstract":"Germline transcripts initiate from promoters upstream of the immunoglobulin switch region, and are necessary to target the appropriate switch region for recombination and switching. Different cytokines activate transcription at the appropriate germline promoter. Because binding sites for B-cell-specific activator protein (BSAP) are located upstream of several switch regions in the immunoglobulin heavy chain gene cluster, BSAP might play a role in the regulation of germline transcription and isotype switching. We investigated whether BSAP plays a role in the transcriptional regulation of the epsilon germline promoter in human B cells. Our results showed that BSAP plays a role in both IL-4-dependent induction and CD40-mediated upregulation of human epsilon germline transcription. BSAP is unique among the transcription factors that regulate epsilon germline expression, because it is B cell specific, and is at the merging point of two signalling pathways that are critical for IgE switching.","authors":"De Monte, L., Thienes, CP., Monticelli, S., Busslinger, M., Gould, HJ., Vercelli, D.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Int Arch Allergy Immunol","volume":"113","issue":"1-3","page":"35-8","pdf":null,"JrId":"2196","fulltextlink":null,"preprintlink":null,"articledate":"1997-05-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9120266","title":"T cell development in mice expressing splice variants of the protein tyrosine phosphatase CD45.","abstract":"The transmembrane protein tyrosine phosphatase CD45 is expressed in multiple isoforms as a result of alternative splicing of variable exons encoding the extracellular domain. CD45 expression is critical for T cell development, and thymocyte maturation is blocked at the immature CD4+ CD8+ double-positive stage in CD45 gene-deficient (CD45 -\/-) mice. Moreover, splicing of variable CD45 exons changes during thymocyte selection. To test the role of CD45 extracellular splice variants in T cell selection and development, we introduced CD45RO (a low-m.w. splice variant lacking exons 4, 5, and 6) and CD45ABC (a high-m.w. isoform containing all exons) transgenes under the control of a thymocyte-specific promoter into a CD45 -\/- background, generating CD45RO transgene-positive CD45 -\/- (CD45RO) and CD45ABC transgene-positive CD45 -\/- (CD45ABC) mice. We demonstrate that both CD45 splice isoforms can rescue development of CD4+ and CD8+ TCR-alphabeta+ thymocytes. Neither CD45 isoform rescued positive selection of H-Y TCR transgene thymocytes, and these cells were blocked at a HSA(high) CD69- CD5(low) stage of development. Peripheral T cells from CD45RO and CD45ABC mice proliferated in response to allogeneic stimulator cells and anti-CD3epsilon cross-linking. However, only CD45RO mice, not CD45ABC mice, generated cytotoxic T cell responses and neutralizing, Th cell-dependent IgG Abs after viral infections. In addition, we show that T cells from CD45RO and CD45ABC mice accumulate in lymph nodes but not in the spleen, liver, or skin, indicating that the CD45 phosphatase may control the homing behavior and trafficking of T cells.","authors":"Kozieradzki, I., K\u00fcndig, T., Kishihara, K., Ong, CJ., Chiu, D., Wallace, VA., Kawai, K., Timms, E., Ionescu, J., Ohashi, P., Marth, JD., Mak, TW., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"J Immunol","volume":"158","issue":"7","page":"3130-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-04-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9096380","title":"Transloading of tumor antigen-derived peptides into antigen-presenting cells.","abstract":"The discovery of a steadily growing number of tumor antigens (TAs) has made generic, cell-free, peptide-based cancer vaccines a possible alternative to cytokine-transfected autologous cellular cancer vaccines. The major drawback of peptide vaccines, however, is the poor immunogenicity of peptides. It is commonly thought that for the induction of an effective anticancer immune response, antigen-presenting cells (APCs) have to display TA-derived peptides to T lymphocytes. Polycationic amino acids have been employed in the past to enhance transport of proteins into cells. In a systematic study, the ability of different cationic polymers to transfer fluorescence-tagged peptides to APCs was investigated. We were able to show that several compounds enhance uptake of fluorescence-labeled peptides by APCs to different degrees. The most efficient compound identified, polyarginine (pArg), enhanced peptide delivery by more than 2 logs as compared with cells treated with peptide alone, whereas polylysine (pLys) treatment resulted in approximately 10-fold increased levels of fluorescence. Augmentation of peptide uptake was concentration-dependent, and the molecular weight of pArg or pLys also influenced peptide delivery. Furthermore, highly negatively charged peptides appear to be delivered with higher efficiency, although neutral peptides were also taken up at enhanced rates. Whereas peptide uptake mediated by pLys appears to be due to an at least transient permeabilization of cell membranes, peptide delivery in the presence of pArg may rely on endocytic processes. TA-derived peptides applied as cancer vaccines in conjunction with polycations afforded antitumor protection in animal models.","authors":"Buschle, M., Schmidt, W., Zauner, W., Mechtler, K., Trska, B., Kirlappos, H., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Proc Natl Acad Sci U S A","volume":"94","issue":"7","page":"3256-61","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1997-05-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31308548","title":"Joint analysis of heterogeneous single-cell RNA-seq dataset collections.","abstract":"Single-cell RNA sequencing is often applied in study designs that include multiple individuals, conditions or tissues. To identify recurrent cell subpopulations in such heterogeneous collections, we developed Conos, an approach that relies on multiple plausible inter-sample mappings to construct a global graph connecting all measured cells. The graph enables identification of recurrent cell clusters and propagation of information between datasets in multi-sample or atlas-scale collections.","authors":"Barkas, N., Petukhov, V., Nikolaeva, D., Lozinsky, Y., Demharter, S., Khodosevich, K., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Nat Methods","volume":"16","issue":"8","page":"695-698","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-08","doi":"10.1038\/s41592-019-0466-z","first_author":"Barkas, N.","corresponding_authors":"Kharchenko, PV."},{"pmid":"9055866","title":"The absence of c-fos prevents light-induced apoptotic cell death of photoreceptors in retinal degeneration in vivo.","abstract":"Apoptotic cell death in the retina was recently demonstrated in animal models of the hereditary human retinal dystrophy known as retinitis pigmentosa. Although recent evidence indicates that the proto-oncogene c-fos is a mediator of apoptosis, its precise role is unclear. In fact, under some conditions, c-fos may even protect against apoptotic cell death. In the retina, c-fos is physiologically expressed in a diurnal manner and is inducible by light. We previously observed a light-elicited, dose-dependent apoptotic response in rat photoreceptors. To determine whether c-fos is involved in the light-induced apoptotic pathway we have used control mice and mice lacking c-fos. We found that following dark adaptation and two hours of light exposure both groups of animals exhibited only a few apoptotic cells. However, at 12 and 24 additional hours after light exposure, apoptosis increased dramatically in controls but was virtually absent in those mice lacking c-fos. Therefore, c-fos is essential for light-induced apoptosis of photoreceptors. Notably, c-fos is continuously upregulated concomitant with apoptotic photoreceptor death in our system and in animal models of retinitis pigmentosa (Agarwal, N. et al., Invest. Ophthalmol. Vis.Sci. Suppl. 36, S638 and Rich, K.A. et al., Invest. Ophthalmol. Vis. Sci. Suppl. 35, 1833). Inhibition of c-fos expression might therefore represent a novel therapeutic strategy to retard the time course of retinal dystrophies and light-induced retinal degeneration.","authors":"Hafezi, F., Steinbach, JP., Marti, A., Munz, K., Wang, ZQ., Wagner, EF., Aguzzi, A., Rem\u00e9, CE.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Nat Med","volume":"3","issue":"3","page":"346-9","pdf":null,"JrId":"8791","fulltextlink":null,"preprintlink":null,"articledate":"1997-04-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9024154","title":"Low-molecular-weight tumor necrosis factor receptor p55 controls induction of autoimmune heart disease.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">9024154<\/PMID><DateCompleted><Year>1997<\/Year><Month>03<\/Month><Day>11<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>06<\/Month><Day>23<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0009-7322<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>95<\/Volume><Issue>3<\/Issue><PubDate><Year>1997<\/Year><Month>Feb<\/Month><Day>04<\/Day><\/PubDate><\/JournalIssue><Title>Circulation<\/Title><ISOAbbreviation>Circulation<\/ISOAbbreviation><\/Journal><ArticleTitle>Low-molecular-weight tumor necrosis factor receptor p55 controls induction of autoimmune heart disease.<\/ArticleTitle><Pagination><MedlinePgn>655-61<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Tumor necrosis factor-alpha (TNF-alpha) is involved in the pathogenesis of myocarditis and can bind to either tumor necrosis factor receptor (TNF-R) p55 or TNF-Rp75. However, it is not known which TNF-R mediates the specific functions of TNF in disease. To determine the role of the TNF\/TNF-R system in chronic heart disease, we used a murine model of cardiac myosin-induced myocarditis that closely resembles the chronic stages of virus-induced myocarditis in humans.","authors":"Bachmaier, K., Pummerer, C., Kozieradzki, I., Pfeffer, K., Mak, TW., Neu, N., Penninger, JM.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Circulation","volume":"95","issue":"3","page":"655-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"9000077","title":"Extension of chromatin accessibility by nuclear matrix attachment regions.","abstract":"Transcription of the variable region of the rearranged immunoglobulin mu gene is dependent on an enhancer sequence situated within one of the introns of the gene. Experiments with transgenic mice have shown that activation of the promoter controlling this transcription also requires the matrix-attachment regions (MARs) that flank the intronic enhancer. As this mu gene enhancer can establish local areas of accessible chromatin, we investigated whether the MARs can extend accessibility to more distal positions. We eliminated interactions between enhancer- and promoter-bound factors by linking mu enhancer\/MAR fragments to the binding sites for bacteriophage RNA polymerases that were either close to or one kilobase distal to the enhancer. The mu enhancer alone mediated chromatin accessibility at the proximal site but required a flanking MAR to confer accessibility upon the distal promoter. This long-range accessibility correlates with extended demethylation of the gene construct but not with whether it is being actively transcribed. MARs thus collaborate with the mu enhancer to generate an extended domain of accessible chromatin.","authors":"Jenuwein, T., Forrester, WC., Fern\u00e1ndez-Herrero, LA., Laible, G., Dull, M., Grosschedl, R.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Nature","volume":"385","issue":"6613","page":"269-72","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1997-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8999996","title":"A requirement for Rho and Cdc42 during cytokinesis in Xenopus embryos.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">8999996<\/PMID><DateCompleted><Year>1997<\/Year><Month>03<\/Month><Day>25<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>7<\/Volume><Issue>1<\/Issue><PubDate><Year>1997<\/Year><Month>Jan<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>A requirement for Rho and Cdc42 during cytokinesis in Xenopus embryos.<\/ArticleTitle><Pagination><MedlinePgn>12-23<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">During cytokinesis in animal cells, an equatorial actomyosin-based contractile ring divides the cell into two daughter cells. The position of the contractile ring is specified by a signal that emanates from the mitotic spindle. This signal has not been identified and it is not understood how the components of the contractile ring assemble. It is also unclear how the ring constricts or how new plasma membrane inserts specifically behind the leading edge of the constricting furrow. The Rho family of small GTPases regulate polarized changes in cell growth and cell shape by affecting the formation of actin structures beneath the plasma membrane, but their role in cytokinesis is unclear.","authors":"Drechsel, DN., Hyman, AA., Hall, A., Glotzer, M.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Curr Biol","volume":"7","issue":"1","page":"12-23","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8982606","title":"Endosomal fractions from viral K-ras-transformed MDCK cells reveal transformation specific changes on two-dimensional gel maps.","abstract":"We have investigated the effects of viral Kirsten ras oncogene expression in Madin-Darby canine kidney (MDCK) II epithelial cell on the differential protein expression of organelle proteins. MDCK cells, stably transformed via infection with a helper-independent retroviral vector construct, were grown on permeable filter supports. Whereas normal cells form highly polarized monolayers, ras-transformed cells display an unpolarized phenotype, detaching from the substratum and developing multilayers (Schoenenberger, C.-A. et al., J. Cell Biol. 1991, 112, 873-889). We postulate that this breakdown of epithelial polarity reflects disturbed intracellular protein transport and sorting, namely, proteins will no longer be sorted correctly in intracellular organelles and will therefore not reach their appropriate target membrane. Here we emphasize the role of endosomes as sorting platform in epithelial cells. We found significant differences in the molecular composition of endosomes from normal vs. oncogenic transformed epithelial cells, strengthening previous evidence indicating that oncogenic transformation results in abnormal expression of normal genes (Celis, J. E., Olsen, E., Electrophoresis 1994, 15, 309-344) as well as the expression of new ones (Huber, L. A. et al., Electrophoresis 1994, 15, 468-473).","authors":"Huber, LA., Pasquali, C., Gagescu, R., Zuk, A., Gruenberg, J., Matlin, KS.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Electrophoresis","volume":"17","issue":"11","page":"1734-40","pdf":null,"JrId":"3579","fulltextlink":null,"preprintlink":null,"articledate":"1997-05-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8955183","title":"Lineage-specific control of superantigen-induced cell death by the protein tyrosine kinase p56(lck).","abstract":"Cell fate decisions in developing T cells depend on signal transduction via the Ag-specific TCR. Although the same TCR can signal for survival or cell death, specific signals that lead to cellular activation or death have not been identified. To study the role of the src tyrosine kinase p56(lck) in cell death of developing T cells, we introduced endogenous mouse mammary tumor retroviruses encoding superantigens (SAG) into p56(lck)-deficient mice. We show that clonal deletion of SAG-reactive CD4+ T cells does occur in p56(lck) -\/- mice. Clonal deletion was also evident in CD4+ cells expressing TCRVbeta7, which has low affinity for Mls-1a. However, clonal deletion did not occur in SAG-reactive CD8+ T cells from p56(lck) -\/- mice. Deletion of cells expressing SAG-reactive TCRVbeta chains was apparent in CD4+ single-positive but not in CD8+ single-positive thymocytes. Both CD4+ and CD8+ peripheral T cells from Mls-1b p56(lck) -\/- mice responded to Mls-1a in vitro. However, CD8+ T cells from Mls-1a p56(lck) -\/- mice that did not undergo deletion could not respond to Mls-1a, indicating that these cells are functionally unresponsive. These data show that p56(lck) is not required for clonal deletion of SAG-reactive CD4+ lymphocytes, including CD4+ cell expressing TCRs with low affinity for the SAG. However, p56(lck) appears to be an important signal transduction molecule involved in deletion of SAG-reactive CD8+ T cells.","authors":"Penninger, JM., Wallace, VA., Molina, T., Mak, TW.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"J Immunol","volume":"157","issue":"12","page":"5359-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1997-01-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8885231","title":"Mutagenic analysis of the destruction signal of mitotic cyclins and structural characterization of ubiquitinated intermediates.","abstract":"Mitotic cyclins are abruptly degraded at the end of mitosis by a cell-cycle-regulated ubiquitin-dependent proteolytic system. To understand how cyclin is recognized for ubiquitin conjugation, we have performed a mutagenic analysis of the destruction signal of mitotic cyclins. We demonstrate that an N-terminal cyclin B segment as short as 27 residues, containing the 9-amino-acid destruction box, is sufficient to destabilize a heterologous protein in mitotic Xenopus extracts. Each of the three highly conserved residues of the cyclin B destruction box is essential for ubiquitination and subsequent degradation. Although an intact destruction box is essential for the degradation of both A- and B-type cyclins, we find that the Xenopus cyclin A1 destruction box cannot functionally substitute for its B-type counterpart, because it does not contain the highly conserved asparagine necessary for cyclin B proteolysis. Physical analysis of ubiquitinated cyclin B intermediates demonstrates that multiple lysine residues function as ubiquitin acceptor sites, and mutagenic studies indicate that no single lysine residue is essential for cyclin B degradation. This study defines the key residues of the destruction box that target cyclin for ubiquitination and suggests there are important differences in the way in which A- and B-type cyclins are recognized by the cyclin ubiquitination machinery.","authors":"King, RW., Glotzer, M., Kirschner, MW.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Mol Biol Cell","volume":"7","issue":"9","page":"1343-57","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"1997-01-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8883534","title":"Function of somite and somitocoele cells in the formation of the vertebral motion segment in avian embryos.","abstract":"We have studied the distribution of thoracic somite and somitocoele-derived cells using homotopical grafting between quail and chicken embryos and reincubation periods of 2-6 days. Serial sections were evaluated with antibodies against quail cells, quail hemangiopoietic cells and desmin. With the exception of neural crest cells in the cranial sclerotome half, all cells of the operated segment are quail cells derived from a single somite. These cells differentiate into sclerotome, myotome and the anlage of the dermis of the back. After longer reincubation periods, the somite-derived quail cells form the neighboring halves of 2 adjacent vertebral bodies and the intervening (disc-homologous) tissue. Resegmentation is furthermore visible in the lamina and the spinous process. Somite cells also form the articular and transverse processes, and the intertransverse muscle including its insertion to the next cranial transverse process. One thoracic somite forms the proximal part of 1 rib. In more distal parts, 1 somite forms the cranial half of 1 rib and the caudal half of the next cranial rib, and the intercostal muscle and part of the connective tissue. Somite-derived quail cells are found in muscle that bridges over 2 segments cranial and caudal from the operated segment. The craniocaudal distribution of endothelial cells is approximately the same. Somitocoele cells that are located centrally in the epithelial somite express the sclerotome-markers Pax-1 and Pax-9. After 2-3 days of reincubation, grafted thoracic somitocoele cells are found mainly in the cranial part of the caudal sclerotome half. They form an area representing the anlagen of the intervertebral disc and the rib. After longer reincubation periods, the grafted quail somitocoele cells form the intervertebral disc-homologous tissue and the proximal part of the rib. In more distal parts of the rib they are located in the cranial half of 1 rib and the caudal half of the next cranial rib. The somitocoele cells also form the surface of the intervertebral joint, and give rise to a small number of endothelial cells that are found up to 1 segment cranial and caudal to the operation site. Our studies show that resegmentation is found in most parts of the vertebra and in the distal ribs. One somite forms the origin and insertion of the segmental muscle. Therefore, the somite can be regarded as the ancestor of the vertebral motion segment. Somitocoele cells are located centrally both in the epithelial somite and in the vertebral motion segment.","authors":"Huang, R., Zhi, Q., Neub\u00fcser, A., M\u00fcller, TS., Brand-Saberi, B., Christ, B., Wilting, J.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Acta Anat (Basel)","volume":"155","issue":"4","page":"231-41","pdf":null,"JrId":"17","fulltextlink":null,"preprintlink":null,"articledate":"1997-01-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8790376","title":"Activation of Stat 5b in erythroid progenitors correlates with the ability of ErbB to induce sustained cell proliferation.","abstract":"Self renewal of normal erythroid progenitors is induced by the receptor tyrosine kinase c-ErbB, whereas other receptors (c-Kit\/Epo-R) regulate erythroid differentiation. To address possible mechanisms that could explain this selective activity of c-ErbB, we analyzed the ability of these receptors to activate the different members of the Stat transcription factor family. Ligand activation of c-ErbB induced the tyrosine phosphorylation, DNA-binding, and reporter gene transcription of Stat 5b in erythroblasts. In contrast, ligand activation of c-Kit was unable to induce any of these effects in the same cells. Activation of the erythropoietin receptor caused specific DNA-binding of Stat 5b, but failed to induce reporter gene transcription. These biochemical findings correlate perfectly with the selective ability of c-ErbB to cause sustained self renewal in erythroid progenitors.","authors":"Mellitzer, G., Wessely, O., Decker, T., Meinke, A., Hayman, MJ., Beug, H.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Proc Natl Acad Sci U S A","volume":"93","issue":"18","page":"9600-5","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1996-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8770593","title":"Mutations Modulating Raf signaling in Drosophila eye development.","abstract":"The R7 fate is specified during Drosophila eye development by an inductive signal transduced intracellularly via the Raf kinase. We have performed a genetic screen for dominant mutations that alter the efficiency with which cells respond to a constitutively activated Raf kinase. Such mutations may affect genes involved in signal transduction downstream of Raf. We have isolated 44 mutations that define eight genes. One of these encodes a mitogen-activated protein kinase homologue: another is a putative target gene of this signaling pathway. We present the results of this screen in detail, as well as a preliminary genetic analysis of the six loci still to be characterized molecularly.","authors":"Dickson, BJ., van der Straten, A., Dominguez, M., Hafen, E.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Genetics","volume":"142","issue":"1","page":"163-71","pdf":null,"JrId":"3871","fulltextlink":null,"preprintlink":null,"articledate":"1996-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8744951","title":"TPR proteins required for anaphase progression mediate ubiquitination of mitotic B-type cyclins in yeast.","abstract":"The abundance of B-type cyclin-CDK complexes is determined by regulated synthesis and degradation of cyclin subunits. Cyclin proteolysis is required for the final exit from mitosis and for the initiation of a new cell cycle. In extracts from frog or clam eggs, degradation is accompanied by ubiquitination of cyclin. Three genes, CDC16, CDC23, and CSE1 have recently been shown to be required specifically for cyclin B proteolysis in yeast. To test whether these genes are required for cyclin ubiquitination, we prepared extracts from G1-arrested yeast cells capable of conjugating ubiquitin to the B-type cyclin Clb2. The ubiquitination activity was cell cycle regulated, required Clb2's destruction box, and was low if not absent in cdc16, cdc23, cdc27, and cse1 mutants. Furthermore all these mutants were also defective in ubiquitination of another mitotic B-type cyclin, Clb3. The Cdc16, Cdc23, and Cdc27 proteins all contain several copies of the tetratricopeptide repeat and are subunits of a complex that is required for the onset of anaphase. The finding that gene products that are required for ubiquitination of Clb2 and Clb3 are also required for cyclin proteolysis in vivo provides the best evidence so far that cyclin B is degraded via the ubiquitin pathway in living cells. Xenopus homologues of Cdc16 and Cdc27 have meanwhile been shown to be associated with a 20S particle that appears to function as a cell cycle-regulated ubiquitin-protein ligase.","authors":"Zachariae, W., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Mol Biol Cell","volume":"7","issue":"5","page":"791-801","pdf":null,"JrId":"1969","fulltextlink":null,"preprintlink":null,"articledate":"1997-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8701076","title":"Genetic analysis of thyroid hormone receptors in development and disease.","abstract":"Thyroid hormone (T3) fulfills diverse functions in vertebrate development and physiology. These functions are thought to be mediated by two genes encoding the related T3 receptors. TR alpha and TR beta. The use of homologous recombination in embryonic stem cells to generate defined, single-gene mutations provides a powerful means to investigate the individual functions of TR alpha and TR beta in mice. We have shown that targeted inactivation of the TR beta gene results in goiter and elevated levels of thyroid hormone. Thyroid stimulating hormone (TSH), which is released by pituitary thyrotropes and is normally suppressed by increased levels of thyroid hormone, was present at elevated levels in homozygous mutant (Thrb-\/-) mice. These findings suggest a unique role for TR beta that cannot be substituted by TR alpha in the T3-dependent feedback regulation of TSH transcription. Thrb-\/- mice provide a recessive model for the human syndrome of resistance to thyroid hormone (RTH). Typically, RTH is associated with dominant mutations in TR beta. It is unknown whether TR alpha, TR beta, or other receptors are targets for inhibition in dominant RTH; however, the analysis of Thrb-\/- mice suggests that antagonism of TR beta-mediated pathways underlies the disorder of the pituitary-thyroid axis. Thrb-\/- mice also display defective maturation of auditory function, demonstrating that TR beta is essential for the development of hearing. Interestingly, hearing defects are generally absent in dominant RTH, indicating that in the auditory system, a dominant TR beta mutant cannot mimic the defect caused by loss of TR beta. This suggests the existence of tissue-specific mechanisms that modulate the activity of TR beta. These results define in vivo functions for TR beta and indicate that specificity in T3 signaling is conferred by distinct receptor genes.","authors":"Forrest, D., Golarai, G., Connor, J., Curran, T.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Recent Prog Horm Res","volume":"51","issue":"","page":"1-22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1996-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8700875","title":"Antiangiogenic therapy of transgenic mice impairs de novo tumor growth.","abstract":"Angiogenesis is activated during multistage tumorigenesis prior to the emergence of solid tumors. Using a transgenic mouse model, we have tested the proposition that treatment with angiogenesis inhibitors can inhibit the progression of tumorigenesis after the switch to the angiogenic phenotype. In this model, islet cell carcinomas develop from multifocal, hyperproliferative nodules that show the histological hallmarks of human carcinoma in situ. Mice were treated with a combination of the angiogenesis inhibitor AGM-1470 (TNP-470), the antibiotic minocycline, and interferon alpha\/beta. The treatment regimen markedly attenuated tumor growth but did not prevent tumor formation; tumor volume was reduced to 11% and capillary density to 40% of controls. The proliferation index of tumor cells in treated and control mice was similar, whereas the apoptotic index was doubled in treated tumors. This study shows that de novo tumor progression can be restricted solely by antiangiogenic therapy. The results suggest that angiogenesis inhibitors represent a valid component of anticancer strategies aimed at progression from discrete stages of tumorigenesis and demonstrate that transgenic mouse models can be used to evaluate efficacy of candidate antiangiogenic agents.","authors":"Parangi, S., O'Reilly, M., Christofori, G., Holmgren, L., Grosfeld, J., Folkman, J., Hanahan, D.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Proc Natl Acad Sci U S A","volume":"93","issue":"5","page":"2002-7","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1996-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8650231","title":"Deregulation of PAX-5 by translocation of the Emu enhancer of the IgH locus adjacent to two alternative PAX-5 promoters in a diffuse large-cell lymphoma.","abstract":"Analyses of the human PAX-5 locus and of the 5' region of the mouse Pax-5 gene revealed that transcription from two distinct promoters results in splicing of two alternative 5' exons to the common coding sequences of exons 2-10. Transcription from the upstream promoter initiates downstream of a TATA box and occurs predominantly in B-lymphocytes, whereas the TATA-less downstream promoter is active in all Pax-5-expressing tissues. The human PAX-5 gene is located on chromosome 9 in region p13, which is involved in t(9;14)(pl3;q32) translocations recurring in small lymphocytic lymphomas of the plasmacytoid subtype and in derived large-cell lymphomas. A previous molecular analysis of a t(9;14) breakpoint from a diffuse large-cell lymphoma (KIS-1) demonstrated that the immunoglobulin heavy-chain (IgH) locus on 14q32 was juxtaposed to chromosome 9p13 sequences of unknown function [Ohno, H., Furukawa, T., Fukuhara, S., Zong, S. Q., Kamesaki, H., Shows, T. B., Le Beau, M. M., McKeithan, T. W., Kawakami, T. &amp; Honjo, T. (1990) Proc. Natl. Acad. Sci. USA 87,628-632]. Here we show that the KIS-1 translocation breakpoint is located 1807 base pairs upstream of exon 1A of PAX-5, thus bringing the potent Emu enhancer of the IgH gene into close proximity of the PAX-5 promoters. These data suggest that deregulation of PAX-5 gene transcription by the t(9;14)(pl3;q32) translocation contributes to the pathogenesis of small lymphocytic lymphomas with plasmacytoid differentiation.","authors":"Busslinger, M., Klix, N., Pfeffer, P., Graninger, PG., Kozmik, Z.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Proc Natl Acad Sci U S A","volume":"93","issue":"12","page":"6129-34","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1996-07-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35243225","title":"Interferons reshape the 3D conformation and accessibility of macrophage chromatin.","abstract":"Engagement of macrophages in innate immune responses is directed by type I and type II interferons (IFN-I and IFN-\u03b3, respectively). IFN triggers drastic changes in cellular transcriptomes, executed by JAK-STAT signal transduction and the transcriptional control of interferon-stimulated genes (ISG) by STAT transcription factors. Here, we study the immediate-early nuclear response to IFN-I and IFN-\u03b3 in murine macrophages. We show that the mechanism of gene control by both cytokines includes a rapid increase of DNA accessibility and rearrangement of the 3D chromatin contacts particularly between open chromatin of ISG loci. IFN-stimulated gene factor 3 (ISGF3), the major transcriptional regulator of ISG, controlled homeostatic and, most notably, induced-state DNA accessibility at a subset of ISG. Increases in DNA accessibility correlated with the appearance of activating histone marks at surrounding nucleosomes. Collectively our data emphasize changes in the three-dimensional nuclear space and epigenome as an important facet of transcriptional control by the IFN-induced JAK-STAT pathway.","authors":"Platanitis, E., Gruener, S., Ravi Sundar Jose Geetha, A., Boccuni, L., Vogt, A., Novatchkova, M., Sommer, A., Barozzi, I., M\u00fcller, M., Decker, T.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"iScience","volume":"25","issue":"3","page":"103840","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-03-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8601589","title":"The estrogen-dependent c-JunER protein causes a reversible loss of mammary epithelial cell polarity involving a destabilization of adherens junctions.","abstract":"Members of the epidermal growth factor (EGF) receptor family are known to be specifically involved in mammary carcinogenesis. As a nuclear target of activated receptors, we examined c-Jun in mammary epithelial cells. For this, we used a c-JunER fusion protein which was tightly controlled by estrogen. Activation of the JunER by hormone resulted in the transcriptional regulation of a variety of AP-1 target genes. Hormone-activated JunER induced the loss of epithelial polarity, a disruption of intercellular junctions and normal barrier function and the formation of irregular multilayers. These changes were completely reversible upon hormone withdrawal. Loss of epithelial polarity involved redistribution of both apical and basolateral proteins to the entire plasma membrane. The redistribution of E-cadherin and beta-catenin was accompanied by a destabilization of complexes formed between these two proteins, leading to an enrichment of beta-catenin in the detergent-soluble fraction. Uninduced cells were able to form three-dimensional tubular structures in collagen I gels which were disrupted upon JunER activation, leading to irregular cell aggregates. The JunER-induced disruption of tubular structures was dependent on active signaling by growth factors. Moreover, the effects of JunER could be mimicked in normal cells by the addition of acidic fibroblast growth factor (aFGF). These data suggest that a possible function of c-Jun in epithelial cells is to modulate epithelial polarity and regulate tissue organization, processes which may be equally important for both normal breast development and as initiating steps in carcinogenesis.","authors":"Fialka, I., Schwarz, H., Reichmann, E., Oft, M., Busslinger, M., Beug, H.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"J Cell Biol","volume":"132","issue":"6","page":"1115-32","pdf":null,"JrId":"4585","fulltextlink":null,"preprintlink":null,"articledate":"1996-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8580840","title":"Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding.","abstract":"Atomic solvation parameters (ASP) are widely used to estimate the solvation contribution to the thermodynamic stability of proteins as well as the free energy of association for protein-ligand complexes. They are also included in several molecular mechanics computer programs. In this work, a total of eight atomic solvation parametric sets has been employed to calculate the solvation contribution to the free energy of folding delta Gs for 17 proteins. A linear correlation between delta Gs and the number of residues in each protein was found for each ASP set. The calculations also revealed a great variety in the absolute value and in the sign of delta Gs values such that certain ASP sets predicted the unfolded state to be more stable than the folded, whereas others yield precisely the opposite. Further, the solvation contribution to the free energy of association of helix pairs and to the disassociation of loops (connection between secondary structural elements in proteins) from the protein tertiary structures were computed for each of the eight ASP sets and discrepancies were evident among them.","authors":"Juffer, AH., Eisenhaber, F., Hubbard, SJ., Walther, D., Argos, P.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Protein Sci","volume":"4","issue":"12","page":"2499-509","pdf":null,"JrId":"2312","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8574583","title":"S-phase-promoting cyclin-dependent kinases prevent re-replication by inhibiting the transition of replication origins to a pre-replicative state.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">8574583<\/PMID><DateCompleted><Year>1996<\/Year><Month>03<\/Month><Day>12<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>07<\/Month><Day>28<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Print\">0960-9822<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>5<\/Volume><Issue>11<\/Issue><PubDate><Year>1995<\/Year><Month>Nov<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Current biology : CB<\/Title><ISOAbbreviation>Curr Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>S-phase-promoting cyclin-dependent kinases prevent re-replication by inhibiting the transition of replication origins to a pre-replicative state.<\/ArticleTitle><Pagination><MedlinePgn>1257-69<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">DNA replication and mitosis are triggered by activation of kinase complexes, each made up of a cyclin and a cyclin-dependent kinase (Cdk). It had seemed possible that the association of Cdks with different classes of cyclins specifies whether S phase (replication) or M phase (mitosis) will occur. The recent finding that individual B-type cyclins (encoded by the genes CLB1-CLB6) can have functions in both processes in the budding yeast Saccharomyces cerevisiae casts doubt on this notion.","authors":"Dahmann, C., Diffley, JF., Nasmyth, KA.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Curr Biol","volume":"5","issue":"11","page":"1257-69","pdf":null,"JrId":"8548","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8566747","title":"Switching transcription on and off during the yeast cell cycle: Cln\/Cdc28 kinases activate bound transcription factor SBF (Swi4\/Swi6) at start, whereas Clb\/Cdc28 kinases displace it from the promoter in G2.","abstract":"When yeast cells reach a critical size in late G1 they simultaneously start budding, initiate DNA synthesis, and activate transcription of a set of genes that includes G1 cyclins CLN1, CLN2, and many DNA synthesis genes. Cell cycle-regulated expression of CLN1, CLN2 genes is attributable to the heteromeric transcription factor complex SBF. SBF is composed of Swi4 and Swi6 and binds to the promoters of CLN1 and CLN2. Different cyclin-Cdc28 complexes have different effects on late G1-specific transcription. Activation of transcription at the G1\/S boundary requires Cdc28 and one of the G1 cyclins Cln1-Cln3, whereas repression of SBF-regulated genes in G2 requires the association of Cdc28 with G2-specific cyclins Clb1-Clb4. Using in vivo genomic footprinting, we show that SBF (Swi4\/Swi6) binding to SCB elements (Swi4\/Swi6 cell cycle box) in the CLN2 promoter is cell cycle regulated. SBF binds to the promoter prior to the activation of transcription in late G1, suggesting that Cln\/Cdc28 kinase regulates the ability of previously bound SBF to activate transcription. In contrast, SBF dissociates from the CLN2 promoter when transcription is repressed during G2 and M phases, suggesting that Clb1-Clb4 repress SBF activity by inhibiting its DNA-binding activity. Switching transcription on and off by different mechanisms could be important to ensure that Clns are activated only once per cell cycle and could be a conserved feature of cell cycle-regulated transcription.","authors":"Koch, C., Schleiffer, A., Ammerer, G., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1996","journaltitle":"Genes Dev","volume":"10","issue":"2","page":"129-41","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1996-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35242010","title":"Editorial: Neurogenesis and Gliogenesis as Potential Contributors to Neurorepair After Brain Damage.","abstract":null,"authors":"Zepeda, A., Encinas-P\u00e9rez, JM., Urb\u00e1n, N.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Front Neurosci","volume":"16","issue":null,"page":"852729","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-03-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-192","title":"Visualization of loop extrusion by DNA nanoscale tracing in single human cells","abstract":null,"authors":"Beckwith, K.S., \u00d8deg\u00e5rd-Fougner, \u00d8., Morero, N.R., Barton, C., Schueder, F., Tang, W., Alexander, S., Peters, J.-M., Jungmann, R., Birney, E., Ellenberg J.","publication_status":"preprint","journalpubyear":"2021","journaltitle":"bioRxiv ","volume":"2021.04.12.439407","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.04.12.439407v3","preprintlink":"","articledate":"2021-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8522068","title":"Maintenance of cell-type-specific cytoskeletal character in epithelial cells out of epithelial context: cytokeratins and other cytoskeletal proteins in the rests of Malassez of the periodontal ligament.","abstract":"We have determined the patterns of synthesis of cytokeratins and other epithelial marker proteins in the \"rests of Malassez\" of the periodontium of rabbits and humans, by immunofluorescence microscopy of cryosections prepared from fixed and decalcified rabbit teeth with attached ligament or from manually isolated human periodontal ligaments. Proteins of the major cell structures characterizing epithelial differentiation are present in Malassez cells: a complex set of cytokeratins as well as desmosomal, hemidesmosomal and basal lamina proteins. In addition, we have shown these cytoskeletal and extracellular matrix structures by electron microscopy. The cytokeratin complement of Malassez cells was found to be highly complex, as 8 of the total of 20 known epithelial cytokeratins were detected (nos. 5, 7, 8, 14, 15, 17, 18, 19). This pattern, together with the presence of the desmosomal cadherins Dsg2 and Dsc2 and the cytoplasmic desmosome plaque-associated protein plakophilin 1, indicates that the cells of the rests of Malassez are derived from the basal cell layer of a stratified squamous epithelium rather than from simple epithelial or neuroendocrine epithelial cells. Our observations show that Malassez cells retain the major characteristics of epithelial cells throughout their differentiation from the root sheath epithelium into the rests of Malassez, even though the surface location and the polar tissue architecture that typify epithelial are lost during this process. From this study we further conclude that the specific cytoskeletal complement of the Malassez cells represents an intrinsic gene expression program that neither depends on nor causes the formation of a stratified epithelium. We also compare the specific cytoskeletal features of Malassez cells with those of other persisting epithelial residues and discuss the potential value of these findings in relation to the histogenesis and diagnostic classification of dental and periodontal cysts and tumors.","authors":"Peters, BH., Peters, JM., Kuhn, C., Z\u00f6ller, J., Franke, WW.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Differentiation","volume":"59","issue":"2","page":"113-26","pdf":null,"JrId":"3402","fulltextlink":null,"preprintlink":null,"articledate":"1996-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8521395","title":"Tumor suppressor loci on mouse chromosomes 9 and 16 are lost at distinct stages of tumorigenesis in a transgenic model of islet cell carcinoma.","abstract":"Techniques that detect loss of genetic heterozygosity (LOH) have helped elucidate genes involved in human cancers. Previously, a genome-wide search using simple sequence length polymorphisms to detect LOH in islet cell tumors arising in a transgenic mouse model of multistage tumorigenesis had revealed two candidate tumor suppressor genes, Loh1 and Loh2, on chromosomes 9 and 16, respectively. We now have analyzed the early stages of tumor development in this model (hyperplastic, early angiogenic, and angiogenic islets) for LOH involving regions of chromosomes 9 and 16. On chromosome 9, hyperplastic and early angiogenic islets reveal a low rate of loss (&lt; 5%) indistinguishable from background; angiogenic islets showed a 9% rate, whereas the final tumor stage had an 18% rate. By contrast, LOH was observed much earlier on chromosome 16. Notably, the LOH rate in angiogenic islets was 29%, comparable to the rate seen in end-stage tumors (32%). The results show that the two loci are lost preferentially at different stages of tumorigenesis. The observation that a high LOH rate at Loh2 is seen in the angiogenic islet stage suggests that this locus may contain an angiogenesis suppressor; in contrast, the later appearance of Loh1 may contribute to the progression from the angiogenic stage to a solid tumor. Tumors containing chromosomes with partial LOH have allowed improved localization of Loh1 to a region of approximately 3.2 centiMorgans on chromosome 9, syntenic with human chromosomes 3q and 15q.","authors":"Parangi, S., Dietrich, W., Christofori, G., Lander, ES., Hanahan, D.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cancer Res","volume":"55","issue":"24","page":"6071-6","pdf":null,"JrId":"2786","fulltextlink":null,"preprintlink":null,"articledate":"1996-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8469988","title":"Requirement for tyrosine kinase p56lck for thymic development of transgenic gamma delta T cells.","abstract":"The Src-related protein tyrosine kinase p56lck is essential for antigen-specific signal transduction and thymic maturation of T cells that have an alpha beta T cell receptor (TCR), presumably by physical association with CD4 or CD8 molecules. To evaluate the requirement for p56lck in the development of T cells that have gamma delta TCRs, which generally do not express CD4 or CD8, p56lck mutant mice were bred with TCR gamma delta transgenic mice. Few peripheral cells that carried the transgenes could be detected in p56lck-\/- mice, although 70 percent of thymocytes were transgenic. Development of transgenic gamma delta+ thymocytes was blocked at an early stage, defined by interleukin-2 receptor alpha expression. However, extrathymic development of CD8 alpha alpha+ TCR gamma delta+ intestinal intraepithelial lymphocytes appeared to be normal. Thus, p56lck is crucial for the thymic, but not intestinal, maturation of gamma delta T cells and may function in thymic development independently of CD4 or CD8.","authors":"Penninger, J., Kishihara, K., Molina, T., Wallace, VA., Timms, E., Hedrick, SM., Mak, TW.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Science","volume":"260","issue":"5106","page":"358-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1993-05-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8386440","title":"Human foamy virus proteins accumulate in neurons and induce multinucleated giant cells in the brain of transgenic mice.","abstract":"Human foamy virus (HFV) is a retrovirus encoding structural genes and, like human immunodeficiency virus and human T cell leukemia virus I, several ancillary reading frames collectively termed the be1 genes. We have previously shown that HFV transgenic mice develop an encephalopathy with neuronal loss in hippocampus and cerebral cortex. We have now raised and characterized rabbit antisera to various recombinant portions of gag, pol, env, and bel-1, the viral trans-activator. Immunoreactivity for gag and bel-1 was observed in nuclei and processes of hippocampal and cortical neurons before the onset of morphological lesions and correlated with the appearance of HFV mRNA. Astrocyte-derived multinucleated giant cells containing HFV proteins were present in the brain of transgenic mice coexpressing full-length HFV genes but not in mice expressing truncated gag and env, suggesting that these genes contain a fusogenic domain. Expression of full-length structural genes decreased the life expectancy of transgenic mice, implying an adjuvant role for these proteins in HFV-induced brain damage.","authors":"Aguzzi, A., Wagner, EF., Netzer, KO., Bothe, K., Anhauser, I., Rethwilm, A.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Am J Pathol","volume":"142","issue":"4","page":"1061-71","pdf":null,"JrId":"449","fulltextlink":null,"preprintlink":null,"articledate":"1993-05-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8335002","title":"Kettin, a large modular protein in the Z-disc of insect muscles.","abstract":"Z-discs of insect flight muscle contain a large protein of 500-700 kDa. Monoclonal antibodies label an epitope in the molecule at the Z-disc in Drosophila and Lethocerus (waterbug). A partial cDNA of 1.6 kb from the Drosophila gene has been cloned and sequenced. The corresponding amino acid sequence has a modular structure composed of four conserved repeats of 95 amino acids homologous to immunoglobulin C2 domains (called class II domains in muscle proteins), separated by less conserved linker sequences of 35 amino acids. An expressed class II domain with flanking linker sequences binds to actin and alpha-actinin but not to myosin. Single molecules of the protein would be large enough to span the Z-disc. We suggest that the protein acts as scaffolding in the Z-disc and we call the protein kettin. The Ca2+ activated protease, calpain, disrupts the Z-disc of striated muscle, releasing alpha-actinin intact. Calpain digests kettin to a series of peptides of between 30 and 170 kDa which are released from the myofibril. Digestion of kettin may cause disintegration of the Z-disc and alpha-actinin release which lead to disassembly of the myofibril.","authors":"Lakey, A., Labeit, S., Gautel, M., Ferguson, C., Barlow, DP., Leonard, K., Bullard, B.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"EMBO J","volume":"12","issue":"7","page":"2863-71","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1993-08-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8291240","title":"Efficient foreign gene expression in Epstein-Barr virus-transformed human B-cells.","abstract":"Epstein-Barr virus (EBV) is a herpesvirus that transforms B-cells (B-LCL) and has undergone intense scrutiny owing to its association with Burkitt's lymphoma, nasopharyngeal carcinoma, and immunoblastic lymphomas. B-LCL have also proven useful in the study of human immunology. We describe a novel system for inducing efficient foreign gene expression in B-LCL using biotinylated adenovirus as an endosome-disrupting agent. Plasmid DNA is coupled to the exterior of viral particles by streptavidin-polylysine chimeric proteins. Up to 67% of B-LCL may be induced to express foreign genes in vitro in transient expression systems, and gene expression lasts for at least 17 days. We have expressed firefly luciferase, beta-galactosidase (beta-gal), chloramphenicol acetyltransferase, HIV gag, and env genes, as well as infectious HIV, and the EBV-specific BZLF gene in B-LCL with this system. In vivo delivery of a beta-gal reporter gene to B-LCL was documented in a SCID mouse model. Potential applications include study of genetic regulation of EBV infection and transformation events, study of potential gene therapies for EBV-related B-cell tumors, and production of antigen-presenting cells for use in immunologic assays. Because of the high percentage of cells transformed and the length of foreign gene expression, the possibility of examining foreign gene expression in transient assays, without selection for clonal populations, exists.","authors":"Curiel, TJ., Cook, DR., Bogedain, C., Jilg, W., Harrison, GS., Cotten, M., Curiel, DT., Wagner, E.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Virology","volume":"198","issue":"2","page":"577-85","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1994-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8264605","title":"Mice lacking c-fos have normal hematopoietic stem cells but exhibit altered B-cell differentiation due to an impaired bone marrow environment.","abstract":"Mice lacking c-fos develop severe osteopetrosis with deficiencies in bone remodeling and exhibit extramedullary hematopoiesis, thymic atrophy, and altered B-cell development. In this study, we have used these mice to characterize in detail the developmental potential of hematopoietic stem cells lacking c-fos and to analyze how the lymphoid differentiation is altered. In c-fos -\/- mice, B-cell numbers are reduced in the spleen, lymph nodes, and the peripheral blood as a result of a marked reduction (&gt; 90%) in the number of clonogenic B-cell precursors. In contrast, the number and lineage distribution of myeloid progenitor cells are not affected. The thymic defects observed in a large number of these mice correlate with their health status, suggesting that this may be an indirect effect of the c-fos mutation. In vitro differentiation and bone marrow reconstitution experiments demonstrated that hematopoietic stem cells lacking c-fos can give rise to all mature myeloid as well as lymphoid cells, suggesting that the observed B lymphopenia in the mutant mice is due to an altered environment. Transplantation of wild-type bone marrow cells into newborn mutant mice resulted in the establishment of a bone marrow space and subsequent correction of the B-cell defect. These results demonstrate that hematopoietic stem cells lacking Fos have full developmental potential and that the observed defect in B-cell development is most likely due to the impaired bone marrow environment as a consequence of osteopetrosis.","authors":"Okada, S., Wang, ZQ., Grigoriadis, AE., Wagner, EF., von R\u00fcden, T.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Mol Cell Biol","volume":"14","issue":"1","page":"382-90","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1994-01-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8232543","title":"Yeast origin recognition complex is involved in DNA replication and transcriptional silencing.","abstract":"The HMR E silencer represses transcription of silent mating-type genes in the budding yeast Saccharomyces cerevisiae and contains three redundant regulatory elements A, E and B (ref. 1). The A element contains the 11 base pair consensus sequence that is essential for the firing of DNA replication origins. A multisubunit protein called the origin recognition complex (ORC) binds specifically to this consensus sequence within yeast origins in vitro and in vivo. We isolated mutants in A element-mediated silencing and report here that one of the genes we identified, RRR1, encodes ORC2, the 72K subunit of ORC. RRR1\/ORC2 is an essential gene, but the rrr1-316 allele, which is viable, is defective in the replication of nuclear DNA and the maintenance of the 2-microns episomal DNA. This is, to our knowledge, the first genetic evidence that ORC is involved in DNA replication and silencing.","authors":"Micklem, G., Rowley, A., Harwood, J., Nasmyth, K., Diffley, JF.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Nature","volume":"366","issue":"6450","page":"87-9","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1993-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8175709","title":"The influence of endosome-disruptive peptides on gene transfer using synthetic virus-like gene transfer systems.","abstract":"The process by which viruses destabilize endosomal membranes in an acidification-dependent manner has been mimicked with synthetic peptides that are able to disrupt liposomes, erythrocytes, or endosomes of cultured cells. Peptides containing the 20 amino-terminal amino acid sequence of influenza virus hemagglutinin as well as acidic derivatives showed erythrocyte lysis activity only when peptides were elongated by an amphipathic helix or by carboxyl-terminal dimerization. Interestingly, peptides consisting of the 23 amino-terminal amino acids of influenza virus hemagglutinin were also active in erythrocyte lysis. When peptides were incorporated into DNA complexes that utilize a receptor-mediated endocytosis pathway for uptake into cultured cells, either by ionic interaction with positively charged polylysine-DNA complexes or by a streptavidin-biotin bridge, a strong correlation between pH-specific erythrocyte disruption activity and gene transfer was observed. A high-level expression of luciferase or interleukin-2 was obtained with optimized gene transfer complexes in human melanoma cells and several cell lines.","authors":"Plank, C., Oberhauser, B., Mechtler, K., Koch, C., Wagner, E.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"J Biol Chem","volume":"269","issue":"17","page":"12918-24","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8101634","title":"Direct transcriptional stimulation of the ornithine decarboxylase gene by Fos in PC12 cells but not in fibroblasts.","abstract":"We have established rat PC12 pheochromocytoma cell lines stably expressing the estrogen-activatable transcription factor FosER to identify genes that can be regulated by c-Fos in this neuronal cell type. Induction of ectopic c-Fos activity in PC12 cells increased the mRNA levels of the ornithine decarboxylase (ODC) and tyrosine hydroxylase genes with similar kinetics and to the same maximal level as nerve growth factor treatment. In both cases the rate of transcription initiation was increased. Induction of the ODC gene occurred even in the absence of protein synthesis, indicating direct regulation by FosER. ODC expression, however, was not induced by a mutant FosER protein containing a proline insertion in the basic region of the c-Fos moiety, demonstrating the requirement for a functional DNA-binding domain. These data show that FosER, and by extrapolation c-Fos, can directly activate transcription of the endogenous ODC gene in PC12 cells by binding to cis-regulatory sequences. Activation of the ODC gene was unexpectedly transient, as transcripts returned to the basal level after prolonged exposure of PC12 cells to FosER activity. Furthermore, ODC transcription was not at all induced by FosER in rat fibroblasts. To account for this cell-specific action of FosER, we propose that stimulation of the ODC gene by FosER requires either (i) cooperation with another transcription factor(s) or (ii) a specific pattern of modification which is present in PC12 cells but not in otherwise unstimulated fibroblasts. One or both of these mechanisms may be employed by cells to achieve selective gene activation in response to apparently stereotyped induction of c-fos.","authors":"Wrighton, C., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Mol Cell Biol","volume":"13","issue":"8","page":"4657-69","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1993-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"8020559","title":"Ultrastructural analysis of thymic nurse cell epithelium.","abstract":"Thymic nurse cells (TNC), a paradigmatic cell type of cortical epithelium, are large lymphoid-epithelial cell complexes of thymocytes enclosed within vacuoles lined by the epithelial cell membrane. TNC express major histocompatibility complex (MHC) class I and class II molecules on their surface and vacuole-lining membranes at high density and it was suggested that TNC provide an optimal microenvironment for positive selection of T cells. In this report we present electron microscopical data demonstrating that chicken TNC display morphological structures of exocytosis previously shown for hormone-secreting cells. In TNC, however, exocytosis is restricted to the capillary cleft between the epithelial cell and engulfed thymocytes. Thus, besides physical contact between the epithelial cell and enclosed thymocytes, TNC may additionally influence the development of thymocytes through release of soluble factors in a restricted microenvironment. By employing the 3-(2,4-dinitroanilino)-3'-amino-N-methyl-propylamine technique which at the ultrastructural level detects acidic organelles involved in processing of antigens presented by MHC class II molecules, we also show that TNC contain acidic compartments similar to classical antigen-presenting cells, i.e. early and late endosomes and lysosomes, albeit in a lower amount than in thymic dendritic cells. This fact provides evidence that TNC not only are capable of antigen presentation but also possess the intracellular machinery for antigen processing.","authors":"Penninger, J., Rieker, T., Romani, N., Klima, J., Salvenmoser, W., Dietrich, H., St\u00f6ssel, H., Wick, G.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Eur J Immunol","volume":"24","issue":"1","page":"222-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1994-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7910953","title":"A second signal supplied by insulin-like growth factor II in oncogene-induced tumorigenesis.","abstract":"Transgenic mice expressing the simian virus-40 large T-antigen (Tag) under the control of the insulin gene regulatory region offer a useful model for tumorigenesis. All the islets of Langerhans express Tag, although there is at first no aberrant proliferation. Over half of the islets become hyperplastic, however, and neovascularization of a further subset (about 10%)3 leads eventually to formation of highly vascularized solid tumours in 1-2% of islets by about 14 weeks of age. Here we show that the initial proliferative switch is correlated with focal activation of insulin-like growth factor II (IGF-II). Transfection with an antisense oligonucleotide to the IGF-II messenger RNA interferes with tumour cell proliferation in vitro, and transgenic mice homozygous for a disruption of the IGF-II gene develop tumours with reduced malignancy and a higher incidence of apoptosis. Several signals, in this case including an oncoprotein and a growth\/survival factor, thus appear to be needed to elicit hyperproliferation.","authors":"Christofori, G., Naik, P., Hanahan, D.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Nature","volume":"369","issue":"6479","page":"414-8","pdf":null,"JrId":"6012","fulltextlink":null,"preprintlink":null,"articledate":"1994-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7815487","title":"Rhinovirus-mediated endosomal release of transfection complexes.","abstract":"Endocytosis is an efficient method for transfer of genes into mammalian cells. Incorporation of adenovirus particles into gene transfer complexes greatly enhances gene delivery, probably by the release of endocytosed DNA into the cytoplasm. We report here that two different serotypes of human rhinovirus (HRV), HRV2 and HRV14, are also able to enhance receptor-mediated gene transfer. The effect of several compounds known to inhibit viral infection on HRV2- and HRV14-enhanced transfection was examined. WIN I(s) and WIN IV, two compounds which inhibit viral uncoating, had different effects on HRV2- and HRV14-enhanced gene transfer to NIH 3T3 cells. While HRV14-enhanced gene transfer was severely reduced in the presence of these compounds, virtually no effects were observed when HRV2 was used. The use of antiviral compounds thus allowed transfection of human cells, which are normally lysed rapidly upon infection with HRV. Viral activity could be mimicked by using a peptide derived from the N terminus of VP1 of HRV2. This peptide possesses pH-dependent membrane-disrupting activity and enhances gene transfer to NIH 3T3 and HeLa cells.","authors":"Zauner, W., Blaas, D., Kuechler, E., Wagner, E.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Virol","volume":"69","issue":"2","page":"1085-92","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1995-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7798218","title":"Molecular characterization of phagosomes.","abstract":"The transformation of newly formed phagosomes into mature phagolysosomes is a process that involves a complex series of interactions between phagosomes and other vacuolar organelles. The machinery required by phagosomes to mediate these interactions is poorly understood. In this study, we allowed human and various rodent cells to take up latex beads whose density facilitates a simple purification of phagosomes using discontinuous sucrose gradients. With this system, we initiated a systematic study of phagosome proteins using two-dimensional gel electrophoresis and the currently available two-dimensional gel protein data bases. By this approach, we were able to recognize a group of polypeptides associated with mouse J774 phagosomes-phagolysosomes including annexin II, annexin VI, the beta-1 and beta-2 subunits of trimeric G proteins, and a group of actin-binding proteins. While the amount of annexin II associated to phagosomes was similar at all times of latex internalization, the levels of annexin VI were higher on late phagosomes. Phospholipid analysis of J774 phagosomes isolated at early and late time points during phagolysosome formation also revealed significant differences in their lipid composition. In the human phagosomes, we resolved over 200 polypeptides on the two-dimensional gels. These included the proteins described in the mouse, as well as 32 polypeptides that were found to be highly enriched in phagosomes, 15 of which are not present in the current data bases. The results demonstrate that the use of latex bead phagosomes is a powerful system to identify key molecules involved in phagolysosome biogenesis.","authors":"Desjardins, M., Celis, JE., van Meer, G., Dieplinger, H., Jahraus, A., Griffiths, G., Huber, LA.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"J Biol Chem","volume":"269","issue":"51","page":"32194-200","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1995-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7705356","title":"Involvement of Tyr24 and Trp108 in substrate binding and substrate specificity of glycolate oxidase.","abstract":"Tyr24 and Trp108 are located in the active site of spinach glycolate oxidase. To elucidate their function in substrate binding and catalysis, they were replaced by phenylalanine and serine, respectively. The [Y24F]glycolate oxidase mutant enzyme showed a tenfold higher Km value for glycolate. L-lactate and DL-2-hydroxybutyrate also showed higher Km values, however, the substrate specificity was unchanged as compared to the wild-type enzyme (Km increases in the order glycolate &lt; DL-2-hydroxybutyrate &lt; L-lactate &lt; L-mandelate). The turnover number and the rate of reduction, found to be rate limiting in catalysis, were only slightly affected by the deletion of the hydroxyl group. These findings suggest that Tyr24 is mostly involved in substrate binding. The spectral features of the [Y24F]glycolate oxidase suggest that a fraction (50-80%) of the protein bears a flavin N(5) adduct instead of the oxidized cofactor. Crystals obtained from the isolated [Y24F]glycolate oxidase mutant protein allowed the determination of the three-dimensional structure. Although the structure was low resolution (0.3 nm), it is evident that the structure determined is that of the N(5) adduct species. In addition to the lacking hydroxyl group of Tyr24, we also observed movements of the amino acid side chains of Arg164 and Trp108, the latter replacing a water molecule in the substrate-binding pocket. Other features predominantly found in the class of flavoprotein oxidases, such as stabilization of the covalent N(5)-sulfite adduct and of the paraquinoid form of 8-mercapto-FMN, were found to be conserved. [W108S]Glycolate oxidase, in contrast, showed dramatic effects on both the Km of substrates as well as the turnover number. The Km for glycolate was increased some hundred fold and the turnover number was decreased 500-fold. In addition, it was found that the higher homologs of glycolate, L-lactate and DL-2-hydroxybutyrate had turnover numbers similar to those found with the wild-type enzyme, although the Km values also increased dramatically. These results indicate that Trp108 is of major importance in catalysis and that this residue is involved in determining the substrate specificity of glycolate oxidase.","authors":"Stenberg, K., Clausen, T., Lindqvist, Y., Macheroux, P.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Eur J Biochem","volume":"228","issue":"2","page":"408-16","pdf":null,"JrId":"3607","fulltextlink":null,"preprintlink":null,"articledate":"1995-05-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7774634","title":"T lymphocyte development in p56lck deficient mice: allelic exclusion of the TcR beta locus is incomplete but thymocyte development is not restored by TcR beta or TcR alpha beta transgenes.","abstract":"The protein tyrosine kinase, p56lck, is involved in signal transduction in mature T cells and in the molecular events controlling early thymocyte differentiation. Thymuses of mice deficient for p56lck expression (p56lck-\/-) consist of immature CD4-CD8- double-negative (DN) and CD4+CD8+ double-positive (DP) thymocytes and are severely reduced in total cell number. In this report we have studied DN thymocytes from p56lck-\/- mice and found an increase in the proportion of the CD44-CD25+ subset, suggesting that transit through this stage, which is known to require T cell receptor (TcR) beta expression, may be delayed in the absence of p56lck expression. In addition, the expression of a transgenic TcR beta chain or TcR alpha beta pair did not restore thymic development in p56lck-\/- mice. However, in contrast to mice expressing a dominant negative isoform of p56lck in which DP thymocytes do not develop, DP thymocytes still develop in nontransgenic and TcR transgenic p56lck-\/- mice. These results demonstrate that expansion of the DP subset is impaired in p56lck-\/- mice. In contrast, allelic exclusion is not severely compromised. Although there was an increase in the number of peripheral T cells expressing more than one V beta chain in TcR transgenic p56lck-\/- mice, we found that inhibition of endogenous TcR beta gene rearrangement was almost complete in thymocytes of V beta transgenic p56lck-\/- mice and we could not detect any peripheral T cells that expressed more than one V beta chain in non-transgenic p56lck-\/- mice.","authors":"Wallace, VA., Kawai, K., Levelt, CN., Kishihara, K., Molina, T., Timms, E., Pircher, H., Penninger, J., Ohashi, PS., Eichmann, K.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Eur J Immunol","volume":"25","issue":"5","page":"1312-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1995-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7744749","title":"Inactivation of the poly(ADP-ribose) polymerase gene affects oxygen radical and nitric oxide toxicity in islet cells.","abstract":"Activation of the nuclear enzyme poly(ADP-ribose) polymerase (PARP) is an early response of cells exposed to DNA-damaging compounds such as nitric oxide (NO) or reactive oxygen intermediates (ROI). Excessive poly-(ADP-ribose) formation by PARP has been assumed to deplete cellular NAD+ pools and to induce the death of several cell types, including the loss of insulin-producing islet cells in type I diabetes. In the present study we used cells from mice with a disrupted and thus inactivated PARP gene to provide direct evidence for a causal relationship between PARP activation, NAD+ depletion, and cell death. We found that mutant islet cells do not show NAD+ depletion after exposure to DNA-damaging radicals and are more resistant to the toxicity of both NO and ROI. These findings directly prove that PARP activation is responsible for most of the loss of NAD+ following such treatment. The ADP-ribosylation inhibitor 3-aminobenzamide partially protected islet cells with intact PARP gene but not mutant cells from lysis following either NO or ROI treatment. Hence the protective action of 3-aminobenzamide must be due to inhibition of PARP and does not result from its other pharmacological properties such as oxygen radical scavenging. Finally, the use of mutant cells an alternative pathway of cell death was discovered which does not require PARP activation and NAD+ depletion. In conclusion, the data prove the causal relationship of PARP activation and subsequent islet cell death and demonstrate the existence of an alternative pathway of cell death independent of PARP activation and NAD+ depletion.","authors":"Heller, B., Wang, ZQ., Wagner, EF., Radons, J., B\u00fcrkle, A., Fehsel, K., Burkart, V., Kolb, H.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Biol Chem","volume":"270","issue":"19","page":"11176-80","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7739038","title":"DNA recognition site analysis of Xenopus winged helix proteins.","abstract":"DNA binding proteins of the winged helix family contain a conserved 110 amino acid region, the fork head\/HNF-3 domain. Three members of the recently described XFD (Xenopus fork head domain related) multigene family in the frog Xenopus laevis that contain this DNA-binding domain have been studied. We determined the in vitro DNA recognition sequences by means of two independent methods: PCR supported site selection with degenerated deoxyoligonucleotides and affinity chromatography of genomic Xenopus DNA fragments. In contrast to a remarkable sequence divergence within their protein sequence of the fork head domains, all three proteins share a similar 7 bp DNA target motif. The protein-DNA interaction has been studied by means of DMS interference and hydroxyl radical footprinting. A region of 18 bp encompassing the 7 bp target motif is sufficient to confer binding and specificity. The specificity of binding could be attributed on the DNA level to residues located 5' to the 7 bp core region, and on the protein level most likely to a region within the first half of the fork head domain. The possible role of specific nucleotides within the target site in binding the protein is discussed in the context of the current crystal structure of the complex of this domain with DNA.","authors":"Kaufmann, E., M\u00fcller, D., Kn\u00f6chel, W.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"J Mol Biol","volume":"248","issue":"2","page":"239-54","pdf":null,"JrId":"4967","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7736785","title":"Direct microdissection and microcloning of a translocation breakpoint region, t(1;11)(q42.2;q21), associated with schizophrenia.","abstract":"We describe the generation of large-fragment microclone libraries from the chromosomal breakpoint of a reciprocal balanced translocation linked to schizophrenia. The abnormality was visible under the phase-contrast microscope, allowing direct dissection from unstained, unbanded metaphases. Two separate microdissection experiments yielded 443 and 672 recombinants, respectively. Following complete EcoRI digestion, inserts with an average size of 0.3 kb (range, 0.2-3 kb) were obtained in the first experiment and 1.5 kb (range, 0.15-6.5 kb) in the second. FISH analysis of pooled clones \"painted\" back onto the derivative chromosome and assignment of microclones to somatic cell hybrids confirmed the fidelity of the method. Microdissection of chromosome regions identified by karyotype rearrangements in unstained, unbanded metaphases is a potentially powerful tool for positional cloning.","authors":"Muir, WJ., Gosden, CM., Brookes, AJ., Fantes, J., Evans, KL., Maguire, SM., Stevenson, B., Boyle, S., Blackwood, DH., St Clair, DM.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cytogenet Cell Genet","volume":"70","issue":"1-2","page":"35-40","pdf":null,"JrId":"3248","fulltextlink":null,"preprintlink":null,"articledate":"1995-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35220288","title":"Organoid Studies in COVID-19 Research.","abstract":"The current COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has completely changed human life for more than two years. Upon the emergence of this new lethal virus, multiple approaches were utilized to gain basic knowledge about its biology. Moreover, modern technologies, such as the organoid model system and next-generation sequencing, enabled us to rapidly establish strategies to tackle the disease, including vaccines and therapeutics. The recently developed organoid technology reflects human physiology more closely than other model systems. Coupled with its rapidness, high efficiency, and outstanding reliability, it has provided an opportunity to develop new drugs and understand the impact of the viral pathogen on the host. Recent findings using organoids have successfully revealed the cellular tropism of the virus in different organs and identified potential drug candidates that impact the disease. This review will summarize current achievements made with organoids in the fight against COVID-19.","authors":"Kim, J., Koo, BK., Clevers, H.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Int J Stem Cells","volume":"15","issue":"1","page":"3-13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7669731","title":"Expression of interstitial collagenase during skeletal development of the mouse is restricted to osteoblast-like cells and hypertrophic chondrocytes.","abstract":"We determined the expression pattern of the matrix metalloproteinase interstitial collagenase (MMP-1) during mouse embryo development using in situ hybridization and immunohistochemistry. Localized MMP-1 mRNA was first detected at 14.5 days postconceptus. The spatial and temporal expression was restricted to areas of endochondral and intramembranous bone formation, such as in the mandibula, maxilla, clavicle, scapula, in the vertebrae, and in the dorsal, but not the ventral part of the ribs. The highest levels of MMP-1 transcripts and MMP-1 protein were found in the metaphyses and diaphyses of the long bones. MMP-1 was expressed by hypertrophic chondrocytes and by osteoblastic cells localized along the newly formed bone trabeculae. No expression was detected in osteoclasts. Two other related members of the MMP family, stromelysin-1 (MMP-3) and stromelysin-2 (MMP-10), were not expressed during days 7.5 and 16.5 of mouse embryogenesis. The tissue-specific expression of MMP-1 and the exclusive ability of interstitial collagenase to digest native collagen of types I, II, III, and X, the major components of bone, cartilage, and tendon, strongly suggests an important and specific function of this enzyme in bone development and remodeling.","authors":"Gack, S., Vallon, R., Schmidt, J., Grigoriadis, A., Tuckermann, J., Schenkel, J., Weiher, H., Wagner, EF., Angel, P.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Cell Growth Differ","volume":"6","issue":"6","page":"759-67","pdf":null,"JrId":"1848","fulltextlink":null,"preprintlink":null,"articledate":"1995-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7649470","title":"Ste20-like protein kinases are required for normal localization of cell growth and for cytokinesis in budding yeast.","abstract":"The yeast Ste20 protein kinase is involved in pheromone response. Mammalian homologs of Ste20 exist, but their function remains unknown. We identified a novel yeast STE20 homolog, CLA4, in a screen for mutations lethal in the absence of the G1 cyclins Cln1 and Cln2. Cla4 is involved in budding and cytokinesis and interacts with Cdc42, a GTPase required for polarized cell growth. Despite a cytokinesis defect, cla4 mutants are viable. However, double cla4 ste20 mutants cannot maintain septin rings at the bud neck and cannot undergo cytokinesis. Mutations in CDC12, which encodes one of the septins, were found in the same screen. Cla4 and Ste20 kinases apparently share a function in localizing cell growth with respect to the septin ring.","authors":"Cvrckov\u00e1, F., De Virgilio, C., Manser, E., Pringle, JR., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Genes Dev","volume":"9","issue":"15","page":"1817-30","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1995-09-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7649395","title":"Characterization and developmental expression of Pax9, a paired-box-containing gene related to Pax1.","abstract":"Pax9, a recently identified mouse paired-box-containing gene, is highly homologous to Pax1 and belongs to the same subfamily as Pax1, Hup48, PAX9, and pox meso. Two overlapping cDNA clones spanning the entire coding region of Pax9 were isolated and sequenced. A comparison of the Pax1 and -9 protein sequences reveals a high degree of similarity even outside the paired box, while the carboxy-terminus of the two proteins diverges completely. We demonstrate that Pax9 can bind to the e5 sequence from the Drosophila even skipped promoter, which is also recognized by Pax1. We analyzed the expression of Pax9 during embryogenesis of wildtype, Undulated short-tail (Uns), and Danforth's short tail (Sd) mice. In wildtype embryos Pax9 is expressed in the pharyngeal pouches and their derivatives, the developing vertebral column, the tail, the head, and the limbs. Expression of Pax9 is unaffected in Uns embryos, in which the Pax1 gene is deleted, arguing that expression of Pax9 is not dependent on Pax1. The expression of Pax9 is lost in the caudal part of Sd homozygous embryos, suggesting that expression of Pax9 in the vertebral column is dependent on the notochord. These results indicate that both Pax9 and -1 may act in parallel during morphogenesis of the vertebral column.","authors":"Neub\u00fcser, A., Koseki, H., Balling, R.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Dev Biol","volume":"170","issue":"2","page":"701-16","pdf":null,"JrId":"3389","fulltextlink":null,"preprintlink":null,"articledate":"1995-09-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7588610","title":"Roles and regulation of Cln-Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae.","abstract":"In budding yeast G1 cells increase in cell mass until they reach a critical cell size, at which point (called Start) they enter S phase, bud and duplicate their spindle pole bodies. Activation of the Cdc28 protein kinase by G1-specific cyclins Cln1, Cln2 or Cln3 is necessary for all three Start events. Transcriptional activation of CLN1 and CLN2 by SBF and MBF transcription factors also requires an active Cln-Cdc28 kinase and it has therefore been proposed that the sudden accumulation of CLN1 and CLN2 transcripts during late G1 occurs via a positive feedback loop. We report that whereas Cln1 and Cln2 are required for the punctual execution of most, if not all, other Start-related events, they are not required for the punctual activation of SBF- or MBF-driven transcription. Cln3, on the other hand, is essential. By turning off cyclin B proteolysis and turning on proteolysis of the cyclin B-Cdc28 inhibitor p40SIC1, Cln1 and Cln2 kinases activate cyclin B-Cdc28 kinases and thereby trigger S phase. Thus the accumulation of Cln1 and Cln2 kinases which starts the yeast cell cycle is set in motion by prior activation of SBF- and MBF-mediated transcription by Cln3-Cdc28 kinase. This dissection of regulatory events during late G1 demands a rethinking of Start as a single process that causes cells to be committed to the mitotic cell cycle.","authors":"Dirick, L., B\u00f6hm, T., Nasmyth, K.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"EMBO J","volume":"14","issue":"19","page":"4803-13","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1995-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7527137","title":"Molecular cloning and characterization of a human PAX-7 cDNA expressed in normal and neoplastic myocytes.","abstract":"The myogenic basic helix-loop-helix proteins are essential components of the regulatory network controlling vertebrate myogenesis. However, determined myoblasts appear in the limb buds which do not initially express any member of this transcription factor family. In a search for potential novel regulators of myogenesis, a human PAX-7 cDNA was isolated from primary myoblasts. Analysis of the DNA-binding properties of the Pax-7 paired domain revealed that it binds DNA in a sequence-specific manner indistinguishable from that of the paralogous Pax-3 protein. Each of the two proteins also binds to palindromic homeodomain-binding sites by cooperative dimerization. Both Pax-3 and Pax-7, which are known to partially overlap in their expression during development, can also efficiently form heterodimers on these sites and stimulate reporter gene transcription in transient transfection experiments which, in the case of Pax-7, is dependent on the transactivation function encoded by the C-terminal sequences. Thus, the formation of heterodimers might have important consequences for target gene recognition and regulation during development. PAX-7 was found to be weakly expressed in normal human myoblasts, while PAX-3 could not be detected in these cells at all. However, transcripts for either PAX-3 and\/or PAX-7 were expressed at elevated levels in tumorigenic rhabdomyosarcoma cell lines. Hence, overexpression of these PAX genes may be involved in the genesis of myogenic tumors.","authors":"Sch\u00e4fer, BW., Czerny, T., Bernasconi, M., Genini, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1994","journaltitle":"Nucleic Acids Res","volume":"22","issue":"22","page":"4574-82","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1995-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35426368","title":"Recalibrating vascular malformations and mechanotransduction by pharmacological intervention.","abstract":null,"authors":"Abdelilah-Seyfried, S., Iruela-Arispe, ML., Penninger, JM., Tournier-Lasserve, E., Vikkula, M., Cleaver, O.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"J Clin Invest","volume":"132","issue":"8","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7510812","title":"Serum glycoprotein hormones and their free alpha-subunit in a healthy elderly population selected according to the SENIEUR protocol. Analyses with ultrasensitive time resolved fluoroimmunoassays.","abstract":"The SENIEUR protocol was elaborated by a working party of European Community's Concerted Action Programme on Aging (EURAGE) to define strict admission criteria for 'healthy' elderly subjects and young controls for immunogerontological studies. This protocol, which is based on case history, laboratory values and drug consumption, intends to limit the influence of underlying disease and\/or medication in order to allow analyses of the aging process per se. In a group of 38 male and 37 female individuals we determined the impact of age and classification according to the SENIEUR protocol on luteinizing hormone (LH), follicle stimulating hormone (FSH), human chorionic gonadotropin (hCG) and free glycoprotein hormone alpha-subunit serum values. Analyses were performed by a set of ultrasensitive time-resolved immunofluorometric assays (IFMA) using our own panel of monoclonal antibodies (MCA). HLH and hFSH, but also hCG and free alpha serum levels increased highly significantly with age in the female population (P &lt; 0.001). In males hFSH, hLH hCG and the free alpha-subunit increased with age. However, only the rise of hFSH and of Free alpha was statistically significant (P &lt; 0.01). The influence of the SENIEUR status on the respective hormone serum levels was determined using two factor analysis of variance, which revealed no statistically significant difference (P &gt; 0.01) between SENIEUR and NON-SENIEUR individuals for all four analytes in both sexes. We conclude that the age related increase of hLH, hFSH, hCG and free alpha is an intrinsic age-dependent phenomen and is not modified by or due to underlying disease or medication as demonstrated by analyses of SENIEUR individuals. Since SENIEUR and NON-SENIEUR individuals had comparable hormone values, a randomly chosen, 'apparently healthy' population seems to be sufficient for physiological studies on serum GPH levels. Lastly, these age related hormonal changes in an extremely well defined healthy population underline the need for age adjusted 'normal' hormone values as elaborated in this communication.","authors":"Madersbacher, S., Stulnig, T., Huber, LA., Sch\u00f6nitzer, D., Dirnhofer, S., Wick, G., Berger, P.","publication_status":"ppublish","journalpubyear":"1993","journaltitle":"Mech Ageing Dev","volume":"71","issue":"3","page":"223-33","pdf":null,"JrId":"5571","fulltextlink":null,"preprintlink":null,"articledate":"1994-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7478542","title":"Spi-1 and mutant p53 regulate different aspects of the proliferation and differentiation control of primary erythroid progenitors.","abstract":"The emergence of leukemic cells in Friend virus complex-induced erythroleukemia is associated with two recurrent genetic alterations, namely the inactivation of the p53 tumor suppressor gene and the overexpression of Spi-1, a member of the Ets family of transcriptional regulators. In order to determine the role of these genetic alterations on the proliferation and differentiation control of erythroblasts, we expressed Spi-1 and the temperature sensitive mutant p53(V135A) in avian primary erythroid progenitors. We show that enforced expression of Spi-1 in erythroblasts obtained from bone marrow cells by expression of the ts-Sea tyrosine kinase inhibits the execution of the differentiation program normally induced in these cells in response to Epo and insulin and following inactivation of ts-Sea function. In contrast, overexpression of p53(V135A) is without effect on the ability of these cells to differentiate into erythrocytes. However, expression of p53(V135A) in erythroid progenitors obtained from bone marrow cells in the presence of SCF, TGF alpha and estradiol, was found to relieve these cells from their absolute TGF alpha requirement for long term proliferation. This phenotype is dependent upon the expression of the mutant form of p53(V135A) as it is not observed at a temperature at which p53(V135A) regains wild type p53 function. Our results show that each of the genetic alterations which characterize Friend erythroleukemic cells affect in a distinct manner the proliferation and differentiation control of primary erythroid progenitors.","authors":"Quang, CT., Pironin, M., von Lindern, M., Beug, H., Ghysdael, J.","publication_status":"ppublish","journalpubyear":"1995","journaltitle":"Oncogene","volume":"11","issue":"7","page":"1229-39","pdf":null,"JrId":"6325","fulltextlink":null,"preprintlink":null,"articledate":"1995-11-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"7443547","title":"Ubiquitous and gene-specific regulatory 5' sequences in a sea urchin histone DNA clone coding for histone protein variants.","abstract":"The DNA sequences of the entire structural H4, H3, H2A and H2B genes and of their 5' flanking regions have been determined in the histone DNA clone h19 of the sea urchin Psammechinus miliaris. In clone h19 the polarity of transcription and the relative arrangement of the histone genes is identical to that in clone h22 of the same species. The histone proteins encoded by h19 DNA differ in their primary structure from those encoded by clone h22 and have been compared to histone protein sequences of other sea urchin species as well as other eukaryotes. A comparative analysis of the 5' flanking DNA sequences of the structural histone genes in both clones revealed four ubiquitous sequence motifs; a pentameric element GATCC, followed at short distance by the Hogness box GTATAAATAG, a conserved sequence PyCATTCPu, in or near which the 5' ends of the mRNAs map in h22 DNA and lastly a sequence A, containing the initiation codon. These sequences are also found, sometimes in modified version, in front of other eukaryotic genes transcribed by polymerase II. When prelude sequences of isocoding histone genes in clone h19 and h22 are compared areas of homology are seen to extend beyond the ubiquitous sequence motifs towards the divergent AT-rich spacer and terminate between approximately 140 and 240 nucleotides away from the structural gene. These prelude regions contain quite large conservative sequence blocks which are specific for each type of histone genes.","authors":"Busslinger, M., Portmann, R., Irminger, JC., Birnstiel, ML.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"Nucleic Acids Res","volume":"8","issue":"5","page":"957-77","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1981-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6297778","title":"Transformation of both erythroid and myeloid cells by E26, an avian leukemia virus that contains the myb gene.","abstract":"E26 and avian myeloblastosis virus are replication-defective avian retroviruses that contain the myb oncogene and cause leukemia in chickens with short periods of latency. Animals infected with E26 develop erythroleukemia and also contain low numbers of transformed myeloid cells, while avian myeloblastosis virus induces a purely myeloid leukemia. In both cases the type of leukemia induced is independent of the subgroup of the helper virus used. E26-transformed erythroid and myeloid cells can each be propagated selectively from explanted leukemic cells with media supplemented with factors that promote the growth either of normal chicken erythroid precursors or of myeloid progenitor cells. E26 also induces the outgrowth of transformed cells from bone marrow cells infected in vitro. These cells are also either erythroid or myeloid, depending on the culture conditions employed. Most of the erythroid cells transformed by E26 are erythroblast-like, but a significant number are more mature, including erythrocyte-like cells as well as some cells that appear to be aberrant in differentiation. Both erythroid and myeloid E26-transformed cells produce infectious virus and express P135 E26, the putative (gag-myb-x) transforming protein of the virus. Thus E26 is a virus that is capable of generating factor-dependent transformed cells in two different hematopoietic lineages.","authors":"Radke, K., Beug, H., Kornfeld, S., Graf, T.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Cell","volume":"31","issue":"3 Pt 2","page":"643-53","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1983-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35417553","title":null,"abstract":null,"authors":"","publication_status":null,"journalpubyear":null,"journaltitle":null,"volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":null,"doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-182","title":"Priming enables a NEK7-independent route of NLRP3 activation","abstract":null,"authors":"Schmacke, NA.*, Gaidt, M.M.*, Szymanska, I., O\u2019Duill, F., Stafford, CA., Chauhan, D., Fr\u00f6hlich, AL., Nagl, D., Pinci, F., Schmid-Burgk, JL., Hornung, V.","publication_status":"preprint","journalpubyear":"2019","journaltitle":"bioRxiv","volume":"10.1101\/799320","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/799320v1","preprintlink":"","articledate":"2019-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6287228","title":"Transfer of nonselectable genes into mouse teratocarcinoma cells and transcription of the transferred human beta-globin gene.","abstract":"Teratocarcinoma (TCC) stem cells can function as vehicles for the introduction of specific recombinant genes into mice. Because most genes do not code for a selectable marker, we investigated the transformation efficiency of vectors with a linked selectable gene. In one series, TCC cells first selected for thymidine kinase deficiency were treated with DNA from the plasmid vector PtkH beta 1 containing the human genomic beta-globin gene and the thymidine kinase gene of herpes simplex virus. A high transformation frequency was obtained after selection in hypoxanthine-aminopterin-thymidine medium. Hybridization tests revealed that the majority of transformants had intact copies of the human gene among three to six total copies per cell. These were associated with cellular DNA sequences as judged from the presence of additional new restriction fragments and from stability of the sequences in tumors produced by injecting the cells subcutaneously. Total polyadenylate-containing RNA from cell cultures of two out of four transformants examined showed hybridization to the human gene probe: one RNA species resembled mature human beta-globin mRNA transcripts; the others were of larger size. In differentiating tumors, various tissues, including hematopoietic cells of TCC provenance could be found. In a second model set of experiments, wild-type TCC cells were used to test a dominant-selection scheme with pSV-gpt vectors. Numerous transformants were isolated, and their transfected DNA was apparently stably integrated. Thus, any gene of choice can be transferred into TCC stem cells even without mutagenesis of the cells, and selected cell clones can be characterized. Cells of interest may then be introduced into early embryos to produce new mouse strains with predetermined genetic changes.","authors":"Wagner, EF., Mintz, B.","publication_status":"ppublish","journalpubyear":"1982","journaltitle":"Mol Cell Biol","volume":"2","issue":"2","page":"190-8","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1982-10-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6272287","title":"The human beta-globin gene and a functional viral thymidine kinase gene in developing mice.","abstract":"Two foreign cloned genes--one encoding a tissue-specific protein and one encoding a constitutive enzyme--were introduced into mouse eggs by microinjection into a pronucleus shortly after fertilization. They were the adult human genomic beta-globin gene and the thymidine kinase (TK; ATP:thymidine 5'-phosphotransferase, EC 2.7.1.21) gene of herpes simplex virus (HSV), ligated in the pBR322 plasmid. Thirty-three developing mice were autopsied in late fetal life; all appeared normal. Blot hybridization tests revealed that the DNA of as many as five (15%) of the fetuses (from separate litters), and of their corresponding placentas, contained copies of the human beta-globin gene and of the HSV tk gene that had been retained and replicated without significant loss or rearrangement. The estimated total numbers of copies per cell were 3-50 for the donor globin gene and 3-20 for the donor tk. In some of the fetuses, these totals included some copies of molecular weight higher than that of the intact sequence; the additional segments may have arisen through changes such as deletions or duplications. The foreign genes in the five positive fetuses appear to be present in high molecular weight DNA. Assays capable of distinguishing between foreign and native TK indicated that at least one of the fetuses with the HSV tk gene had some TK enzyme of the HSV type and, therefore, at least one gene copy that was being accurately transcribed and translated to produce a functional protein, despite the absence of selective pressure. Thus, pure recombinant genes introduced into mice at the onset of their development can remain intact and be stably incorporated and even expressed. These experiments provide a practical basis for novel investigations of the developmental control of normal gene expression in vivo of the causes and possible cures of genetic diseases.","authors":"Wagner, EF., Stewart, TA., Mintz, B.","publication_status":"ppublish","journalpubyear":"1981","journaltitle":"Proc Natl Acad Sci U S A","volume":"78","issue":"8","page":"5016-20","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1982-01-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6109301","title":"Cell transformation by avian defective leukaemia viruses.","abstract":"A comparative study of seven independently isolated defective leukaemia viruses has been carried out. Phenotypic analysis of the chicken bone marrow cells transformed in vitro allowed the separation of these seven viruses into three groups based on the differentiation phenotype of the transformed cell. Nucleic acid hybridization studies revealed that these seven viruses had acquired cellular sequences. Interestingly, these studies also showed that the viruses within the same biological grouping had acquired related sequences. This indicates that viruses that have acquired the same or similar cellular sequences have very similar oncogenic capabilities. Analysis of proteins expressed in cells transformed by these viruses demonstrated that the cellular sequences were usually inserted within the gene for the viral core proteins, gag. Therefore the cellular sequences are expressed as a gag-related fusion protein which has an amino-terminal region derived from the gag gene and a carboxy-terminal half derived from the cellular sequences. Two exceptions to this are discussed. The general conclusion from these studies is that defective leukaemia viruses transform cells by virtue of acquired host cellular sequences. The ability of these viruses to transform cells and the target cell specificity of the transformation depends on these cellular sequences.","authors":"Hayman, MJ., Ramsay, G., Kitchener, G., Graf, T., Beug, H., Roussel, M., Saule, S., Stehelin, D.","publication_status":"ppublish","journalpubyear":"1980","journaltitle":"Proc R Soc Lond B Biol Sci","volume":"210","issue":"1180","page":"397-409","pdf":null,"JrId":"6660","fulltextlink":null,"preprintlink":null,"articledate":"1981-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"6096011","title":"Ts mutants of E26 leukemia virus allow transformed myeloblasts, but not erythroblasts or fibroblasts, to differentiate at the nonpermissive temperature.","abstract":"The myb, ets-containing avian acute leukemia virus E26 transforms myeloblasts, erythroblasts, and fibroblasts in culture and causes a mixed erythroid\/myeloid leukemia in chicks. We report the isolation and characterization of four E26 mutants that are temperature-sensitive (ts) for myeloblast transformation. At the permissive temperature, tsE26-transformed myeloid cells resemble macrophage precursors and proliferate rapidly, provided the growth medium contains chicken myelomonocytic growth factor (cMGF). When shifted to the nonpermissive temperature the cells stop growing and differentiate into macrophage-like cells, as determined by their expression of morphological, functional, and antigenic markers of normal macrophages. They also lose their responsiveness to cMGF and secrete a cMGF-like factor. Ts mutants of E26 retain their leukemogenicity and their ability to transform both erythroblasts and fibroblasts at the nonpermissive temperature, suggesting that the myb oncogene of E26 causes myeloblast transformation and that ets is responsible for erythroblast and fibroblast transformation.","authors":"Beug, H., Leutz, A., Kahn, P., Graf, T.","publication_status":"ppublish","journalpubyear":"1984","journaltitle":"Cell","volume":"39","issue":"3 Pt 2","page":"579-88","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1985-02-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"3658668","title":"OVEC, a versatile system to study transcription in mammalian cells and cell-free extracts.","abstract":"We have developed a vector, OVEC (\"oligonucleotide vector\") to study DNA sequences involved in the regulation of transcription in mammalian cells. This vector is equally suitable for studying expression in vivo after transfection into cells, or for transcription studies in vitro with cell-free extracts. Putative cis-acting DNA segments from enhancers or promoters can be inserted at a position immediately upstream of the TATA box and coding sequence of the rabbit beta-globin gene. A regulatory DNA segment can be tested by itself or in conjunction with an enhancer located either in an adjacent upstream position, or downstream of the beta-globin gene. S1 nuclease mapping can be used to study transcription from circular and linear templates and run-off transcription in vitro is also feasible. Transcripts from a reference globin gene with a small deletion around the transcription initiation site can be measured with the same S1 nuclease probe and thus serve as an internal standard. We demonstrate the usefulness of OVEC by inserting either short oligonucleotides comprising a metal responsive enhancer element, or the SV40 enhancer, directly upstream of the TATA box. Both constructs yield high levels of correctly initiated transcripts in a transient expression assay in HeLa cells. In a HeLa cell nuclear extract the SV40 enhancer stimulates transcription 40-fold.","authors":"Westin, G., Gerster, T., M\u00fcller, MM., Schaffner, G., Schaffner, W.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"Nucleic Acids Res","volume":"15","issue":"17","page":"6787-98","pdf":null,"JrId":"6133","fulltextlink":null,"preprintlink":null,"articledate":"1987-11-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2990891","title":"Effects of inhibitors of glycoprotein processing on the synthesis and biological activity of the erb B oncogene.","abstract":"Three glycoprotein-processing inhibitors were used to resolve whether correct glycosylation was required for the oncogenic activity of erb B. The two glucosidase-I inhibitors, 1-deoxynojirimycin and 2,5-dihydroxymethyl 3,4-dihydroxypyrrolidine, arrested processing of v-erb B at the immature 68-kd form whereas, in the presence of the alpha-mannosidase-II inhibitor (swainsonine), cells synthesised an abnormally processed 70-kd form of v-erb B. Transport of incorrectly processed v-erb B to the cell surface was, however, unaffected, suggesting that correct processing is not a prerequisite for intracellular routing of v-erb B. Two systems were used to assess whether incorrectly processed erb B could maintain the transformed state. The first asked whether inhibitor treatment would release temperature-sensitive avian erythroblastosis virus (AEV) transformed erythroblasts kept at the viral permissive temperature from the erb B-induced block in differentiation, as seen when cells are normally shifted to the non-permissive temperature. The second tested the ability of AEV-transformed fibroblasts to grow in soft agar. In both systems, all three processing inhibitors did not alter the transformed phenotype suggesting that correct carbohydrate processing is not required for the transforming activity of erb B. In addition, none of the three processing inhibitors were found to have any effect on the normal maturation of bone marrow CFU-E or induced differentiation of temperature-sensitive AEV-transformed erythroblasts.","authors":"Schmidt, JA., Beug, H., Hayman, MJ.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"EMBO J","volume":"4","issue":"1","page":"105-12","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1985-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2990096","title":"S13, a rapidly oncogenic replication-defective avian retrovirus.","abstract":"The avian leukemia sarcoma virus S13 transforms chicken and Japanese quail embryo fibroblasts and chicken erythroid cells in tissue culture. S13-induced erythroid transformation requires culture conditions suitable for the growth of normal erythroid precursors (H. Beug and M. J. Hayman (1984), Cell 36, 963-972). S13-transformed erythroid colonies contain a high percentage of cells that differentiate in absence of erythropoietin. S13 is defective in pol and env functions but can code for a complete set of gag proteins. Nonproducer cell clones transformed by S13 release a noninfectious viral particle containing gag but no functional env or pol proteins. They also synthesize a transformation-specific protein of 155,000 molecular weight. This protein reacts with antibody to viral envelope glycoproteins and appears to represent onc as well as env sequences. The 155,000-molecular weight env-linked protein does not cross react immunologically with an antiserum against the v-erb A and v-erb B gene products.","authors":"Beug, H., Hayman, MJ., Graf, T., Benedict, SH., Wallbank, AM., Vogt, PK.","publication_status":"ppublish","journalpubyear":"1985","journaltitle":"Virology","volume":"145","issue":"1","page":"141-53","pdf":null,"JrId":"8015","fulltextlink":null,"preprintlink":null,"articledate":"1985-08-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2884103","title":"A single point mutation in erbA restores the erythroid transforming potential of a mutant avian erythroblastosis virus (AEV) defective in both erbA and erbB oncogenes.","abstract":"We have characterized the v-erbA and v-erbB oncogenes of td359, a transformation-defective mutant of avian erythroblastosis virus (AEV) unable to transform erythroblasts, and the revertant r12, obtained after in vivo passage of the mutant. Molecular cloning, sequencing, construction of chimeric viruses and testing of their oncogenic capacities revealed that both oncogenes of td359 are mutated and biologically defective. The r12 virus, although still containing a mutant v-erbB gene, recovered its erythroid transforming potential by acquiring a highly active gag-erbA gene. These results demonstrate that two co-operating oncogenes, an active v-erbA and a defective v-erbB, can transform a cell type not transformed by either oncogene alone. Furthermore, a single amino acid substitution inactivated the td359 v-erbA protein and we show that its reversion led to the reactivation of the protein. This lesion is located in the same region as several previously described inactivating mutations of glucocorticoid receptors, suggesting that the structure\/function relationship of the virally transduced form of the c-erbA\/thyroid hormone receptor is closely similar to that of steroid hormone receptors.","authors":"Damm, K., Beug, H., Graf, T., Vennstr\u00f6m, B.","publication_status":"ppublish","journalpubyear":"1987","journaltitle":"EMBO J","volume":"6","issue":"2","page":"375-82","pdf":null,"JrId":"3588","fulltextlink":null,"preprintlink":null,"articledate":"1987-07-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2843647","title":"Redundancy of information in enhancers as a principle of mammalian transcription control.","abstract":"In contrast to prokaryotes, in which strong transcriptional signals can be located within very short DNA segments, typical mammalian enhancers are about 200 base-pairs long. We reasoned that a minimal length of enhancer-active DNA is required for a high transcription rate in higher eukaryotes, and that segments from a single enhancer or from different enhancers might be multimerized or combined to satisfy such a requirement. To test this, enhancer fragments from different viruses were joined in a recombinant simian virus 40 (SV40) and screened for efficiency of viral growth. The 48 combinations tested show that the hypothesis is basically correct. For example, two subfunctional heterologous enhancer fragments can together form a functional enhancer. No enhancer shorter than 84 base-pairs could promote SV40 growth, i.e. in no case did we find a short \"superstrong\" enhancer segment. To test whether multimerization of a short fragment would result in a strong enhancer, we have synthesized a 50 base-pair enhancer segment derived from Herpesvirus saimiri. One to six copies of this oligonucleotide gave an incremental increase in enhancer activity. We propose, therefore, that mammalian gene regulation is based on a redundancy of information that can be provided either by a combination of different DNA sequence elements, or by multiple copies of the same element. Also, the finding of strong and weak enhancers suggests that in most cases an enhancer is permanently required for transcription of a gene, rather than acting in an all-or-none fashion to establish a transcription complex, after which it becomes dispensable.","authors":"Schaffner, G., Schirm, S., M\u00fcller-Baden, B., Weber, F., Schaffner, W.","publication_status":"ppublish","journalpubyear":"1988","journaltitle":"J Mol Biol","volume":"201","issue":"1","page":"81-90","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1988-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1824253","title":"Fractionation of mouse bone marrow by adherence separates primitive hematopoietic stem cells from in vitro colony-forming cells and spleen colony-forming cells.","abstract":"Fractionation of mouse bone marrow by adherence to tissue culture plastic was used to characterize the adhesive properties of hematopoietic stem (HS) cells capable of long-term reconstitution. The adherent fraction that represents approximately 13% of the total marrow population was virtually devoid of in vitro colony-forming cells and spleen colony-forming cells but did contain approximately 30% of the total HS cells recovered from the procedure. These cells could be detected by both the competitive repopulation assay and by repopulation of W\/Wv recipients. In approximately 60% of the recipients from the competitive repopulation experiments, the contribution of the adherent marrow cells was relatively low early (8 to 10 weeks) after transplantation. With time, however, the hematopoietic contribution from these cells increased, reaching a stable level 20 to 30 weeks posttransplantation. In the remaining recipients (40%), the contribution from adherent cells was already significant within 8 to 10 weeks of transplantation and did not change dramatically throughout the course of the experiment. Adherent bone marrow containing significant numbers of HS cells was unable to protect mice from radiation death, indicating that these early cells in the absence of later-stage progenitors are unable to provide this function.","authors":"Kiefer, F., Wagner, EF., Keller, G.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Blood","volume":"78","issue":"10","page":"2577-82","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"1992-10-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2548349","title":"[The immunology of aging: immunoregulatory role of lipoproteins].","abstract":"This report deals with immunoregulation by lipoproteins and with age-related changes in immune function. It was investigated whether a diminished immune response during ageing could be caused by a disturbed interaction of lipoproteins with cells of the immune system. The aim of these investigations was to show whether changes in the immune response in the elderly were really age-related, or attributable to other factors (i.e. medication, life style) not related to ageing per se. Therefore, admission criteria for blood donors to take part in these studies of the ageing human immune system were set up by using the Senieur protocol (EURAGE). An immunoregulatory influence of lipoproteins from different density fractions-Low Density Lipoproteins (LDL), High Density Lipoproteins (HDL) and Very Low Density Lipoproteins (VLDL) on the in vitro mitogen response of human peripheral blood lymphocytes (PBL) was shown. Lymphocytes can take up lipoproteins by receptor-mediated (specific binding) and non receptor-mediated (receptor-independent exchange) mechanisms. In this context a HDL-binding site\/receptor was demonstrated and characterised here for the first time on human T-cells. Furthermore, interactions of lipoproteins with lymphocytes were investigated in the elderly and compared with young control groups. The increased LDL uptake during ageing was found to correlate with an increased HDL uptake. The age-related diminished immune response correlated with a decrease in plasma membrane fluidity of human PBL, but not with an enhanced lipoprotein uptake. The Senieur protocol in this present form, used for classifying blood donors, had no influence on distribution and statistical processing of the obtained sets of data, indicating that this protocol needs further modifications.","authors":"Huber, LA.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"Wien Klin Wochenschr","volume":"101","issue":"13","page":"440-6","pdf":null,"JrId":"8079","fulltextlink":null,"preprintlink":null,"articledate":"1989-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2542280","title":"Promotion of lymphocyte growth by high density lipoproteins (HDL). Physiological significance of the HDL binding site.","abstract":"The characteristics and physiological relevance of the high density lipoprotein (HDL) binding site on unstimulated and mitogen activated human peripheral blood lymphocytes have been investigated. At 37 degrees C, specific binding\/uptake of fluorescent (dioctadecylin-docarbocyanine, DiI) HDL was observed by cells from healthy donors as well as by those from low density lipoprotein receptor-defective patients; mitogen activated T-blasts exhibited a markedly elevated DiI-HDL uptake compared to resting T-cells. Binding was saturable at 37 degrees C and of high affinity, with a Kd of 5 x 10(-8) M. It was blocked by anti-apoAI polyclonal antibodies (F(ab)2 fraction), but not by anti-apolipoprotein (apo)E, anti-apoAII, or anti-apoB, and was inhibited competitively by HDL apoproteins and an apoAI-protein A fusion protein. T-cell associated DiI-HDL was increased by trypsin treatment (of the cells) and decreased by activation in the presence of HDL or low density lipoprotein. Comparison of the concentration dependencies of growth promotion and specific cell association of HDL indicated that two mechanisms of lipid exchange may be in operation: one a binding-dependent mechanism of cholesterol exchange, with maximal effect in the HDL concentration range (20-200 micrograms\/ml) in which specific binding increases rapidly, and the other a binding-independent exchange of lipids effective at concentrations in which specific binding is saturated (300-5000 micrograms\/ml).","authors":"J\u00fcrgens, G., Xu, QB., Huber, LA., B\u00f6ck, G., Howanietz, H., Wick, G., Traill, KN.","publication_status":"ppublish","journalpubyear":"1989","journaltitle":"J Biol Chem","volume":"264","issue":"15","page":"8549-56","pdf":null,"JrId":"4559","fulltextlink":null,"preprintlink":null,"articledate":"1989-06-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2379237","title":"Increased proteolytic activity is responsible for the aberrant morphogenetic behavior of endothelial cells expressing the middle T oncogene.","abstract":"Expression of the polyoma virus middle T (mT) oncogene in vivo is associated with a profound subversion of normal vascular development, which results in the formation of endothelial tumors (hemangiomas). In an attempt to understand the molecular mechanisms responsible for this phenomenon, we have investigated, in an in vitro system, the morphogenetic properties of endothelial cells expressing this oncogene. mT-expressing endothelioma (End) cells grown within fibrin gels formed large hemangioma-like cystic structures. All End cell lines examined expressed high levels of fibrinolytic activity resulting from increased production of urokinase-type plasminogen activator and decreased production of plasminogen activator inhibitors. Neutralization of excess proteolytic activity by exogenously added serine protease inhibitors corrected the aberrant in vitro behavior of End cells and allowed the formation of capillary-like tubules. These results suggest that tightly controlled proteolytic activity is essential for vascular morphogenesis and that physiological protease inhibitors play an important regulatory role in angiogenesis.","authors":"Montesano, R., Pepper, MS., M\u00f6hle-Steinlein, U., Risau, W., Wagner, EF., Orci, L.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Cell","volume":"62","issue":"3","page":"435-45","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1990-09-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2173771","title":"Ectopic expression of the erythrocyte band 3 anion exchange protein, using a new avian retrovirus vector.","abstract":"A retrovirus vector was constructed from the genome of avian erythroblastosis virus ES4. The v-erbA sequences of avian erythroblastosis virus were replaced by those coding for neomycin phosphotransferase, creating a gag-neo fusion protein which provides G418 resistance as a selectable marker. The v-erbB sequences following the splice acceptor were replaced by a cloning linker allowing insertion of foreign genes. The vector has been tested in conjunction with several helper viruses for the transmission of G418 resistance, titer, stability, transcription, and the transduction and expression of foreign genes in both chicken embryo fibroblasts and the QT6 quail cell line. The results show that the vector is capable of producing high titers of Neor virus from stably integrated proviruses. These proviruses express a balanced ratio of genome length to spliced transcripts which are efficiently translated into protein. Using the Escherichia coli beta-galactosidase gene cloned into the vector as a test construct, expression of enzyme activity could be detected in 90 to 95% of transfected target cells and in 80 to 85% of subsequently infected cells. In addition, a cDNA encoding the avian erythrocyte band 3 anion exchange protein has been expressed from the vector in both chicken embryo fibroblasts and QT6 cells and appears to function as an active, plasma membrane-based anion transporter. The ectopic expression of band 3 protein provides a visual marker for vector function in these cells.","authors":"Fuerstenberg, S., Beug, H., Introna, M., Khazaie, K., Mu\u00f1oz, A., Ness, S., Nordstr\u00f6m, K., Sap, J., Stanley, I., Zenke, M.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"J Virol","volume":"64","issue":"12","page":"5891-902","pdf":null,"JrId":"5334","fulltextlink":null,"preprintlink":null,"articledate":"1990-12-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"2024527","title":"[Phenotypic and functional analysis of thymic nurse cell (TNC)-lymphocytes].","abstract":"Thymic nurse cells (TNC) are epithelial cells containing intact T-cells engulfed within membrane-lined vacuoles in their cytoplasm. Since thymic epithelial cells strongly express MHC class I and II antigens, these lymphoid-epithelial complexes have been considered to provide an optimal micro-environment for the process of self-recognition and\/or clonal deactivation of thymocytes. The present experiments were designed to further analyze the phenotypical stage of differentiation and the functional properties of intra-TNC lymphocytes (TNC-L) at a single cell level using the chorionallantoic membrane (CAM) assay, which can only be performed in avian species and, thus, presents a unique possibility to circumvent technical problems for the functional study of TNC-L in mammals. In immunofluorescence analyses with monoclonal antibodies (mAb) to the chicken alpha\/beta and gamma\/delta T cell receptors (TCR) and the CD3, CD4, and CD8 equivalents, an enrichment was found of CD3+\/CD4+\/CD8-, CD3+\/CD4-\/CD8+, TCR alpha\/beta + and TCR gamma\/delta + cells inside TNC, as compared with extra-TNC thymocytes. Assessing micromanipulated, single chicken TNC in the CAM assay, we also demonstrated at a clonal level that TNC-L possess a strong graft-versus-host (GvH) reactivity in allogeneic combinations. This reaction showed morphological, phenotypical and functional characteristics of a classical graft-versus-host reaction (GvHR). The efficiency to induce a GvHR was higher for TNC-L than peripheral blood lymphocytes (PBL) or thymocytes from the same donor. Surprisingly, in syngeneic combinations TNC-L also react against self-MHC molecules with high frequency. The frequency in syngeneic combinations is, however, lower than in allogeneic combinations.(ABSTRACT TRUNCATED AT 250 WORDS)","authors":"Penninger, J.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Wien Klin Wochenschr","volume":"103","issue":"2","page":"45-50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1991-06-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1972036","title":"v-erbA oncogene activation entails the loss of hormone-dependent regulator activity of c-erbA.","abstract":"The v-erbA oncogene, one of the two oncogenes of the avian erythroblastosis virus, efficiently blocks erythroid differentiation and suppresses erythrocyte-specific gene transcription. Here we show that the overexpressed thyroid hormone receptor c-erbA effectively modulates erythroid differentiation and erythrocyte-specific gene expression in a T3-dependent fashion, when introduced into erythroid cells via a retrovirus. In contrast, the endogenous thyroid hormone receptor does not detectably affect erythroid differentiation. The analysis of a series of chimeric v-\/c-erbA proteins suggests that the v-erbA oncoprotein has lost one type of thyroid hormone receptor function (regulating erythrocyte gene transcription in response to T3), but constitutively displays another function: it represses transcription in the absence of T3. The region responsible for the loss of hormone-dependent regulator activity of v-erbA has been mapped to the very C-terminus of c-erbA, encompassing a cluster of highly conserved amino acid residues with the potential to form an amphipathic alpha-helix.","authors":"Zenke, M., Mu\u00f1oz, A., Sap, J., Vennstr\u00f6m, B., Beug, H.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Cell","volume":"61","issue":"6","page":"1035-49","pdf":null,"JrId":"2830","fulltextlink":null,"preprintlink":null,"articledate":"1990-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1904384","title":"Complex pattern of immunoglobulin mu gene expression in normal and transgenic mice: nonoverlapping regulatory sequences govern distinct tissue specificities.","abstract":"Analysis of normal mice and transgenic mice carrying a rearranged immunoglobulin mu gene revealed a more complex tissue-specific pattern of mu gene expression than anticipated from previous observations. Expression of the endogenous mu locus and the mu transgene was detected both in lymphoid tissues and in skeletal muscle. Analysis of the expression pattern of mu transgenes containing intragenic deletions or point mutations in binding sites for Oct transcription factors (OCTA sites) indicated that distinct regulatory sequences control lymphoid- and muscle-specific mu gene expression. Consistent with previous transfection experiments, mu gene expression in lymphoid tissues is dependent on the intragenic enhancer and the OCTA site in the promoter. However, neither of these regulatory sequences is required for mu gene expression in skeletal muscle that is governed by a muscle-specific control region located 3' of the enhancer. An \"off-state\" of the mu transgene was observed only in liver and embryonal fibroblasts, whereas enhancer-dependent mu transgene expression was detected at low levels in other nonlymphoid tissues. From these data we suggest a model for the regulation of tissue-specific mu gene expression in which a \"ubiquitous\" competence for basal transcription is up-regulated in lymphoid and muscle tissues by distinct cell type-specific regulatory sequences and down-regulated in liver and fibroblastic cells by putative negative sequence elements.","authors":"Jenuwein, T., Grosschedl, R.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Genes Dev","volume":"5","issue":"6","page":"932-43","pdf":null,"JrId":"3868","fulltextlink":null,"preprintlink":null,"articledate":"1991-07-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1889814","title":"Microclones derived from the mouse chromosome 7 D-E bands map within the proximal region of the c14CoS deletion in albino mutant mice.","abstract":"A group of radiation-induced perinatal-lethal deletions that include the albino (c) locus on mouse chromosome 7 causes failure of expression of various hepatocyte-specific genes when homozygous (S. Gluecksohn-Waelsch, 1979, Cell 16:225-237). The transcription of such genes could be controlled in trans by a regulatory gene(s) located within the proximal region of the C14CoS deletion. To identify this potential regulatory gene, a microclone library was established from microdissected D and E bands of chromosome 7. Three nonoverlapping microclones (E305, E336B, and E453B) hybridizing with wildtype but not with C14CoS\/C14CoS DNA were isolated. E336B represents a single-copy DNA fragment, whereas E305 and E453B hybridized with 3 and 10 EcoRI DNA restriction fragments, respectively. All fragments map exclusively within the deletion. The microclones hybridized to DNA of viable C6H\/C14CoS deletion heterozygotes but not to DNA of homozygotes for the lethal mutation c10R75M, which belongs to the same complementation group as c14CoS. DNA of viable homozygous mutant C62DSD, which carries a deletion breakpoint proximal to that of c6H, hybridized only with E453B. This microclone identified 6 EcoRI restriction fragments in C62DSD\/C62DSD DNA. The results demonstrate that of the isolated microclones, E453B identifies a locus (D7RT453B) that maps closest to the hsdr-1 (hepatocyte-specific developmental regulation) locus (S. Gluecksohn-Waelsch, 1989, Mouse Newslett. 83: 149), which maps between the proximal breakpoints of deletions c10R75M and c62DSD.","authors":"T\u00f6njes, RR., Weith, A., Rinchik, EM., Winking, H., Carnwath, JW., Kaliner, B., Paul, D.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Genomics","volume":"10","issue":"3","page":"686-91","pdf":null,"JrId":"4142","fulltextlink":null,"preprintlink":null,"articledate":"1991-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30399339","title":"Mechanical Force-Driven Adherens Junction Remodeling and Epithelial Dynamics.","abstract":null,"authors":"Pinheiro, D., Bella\u03cache, Y.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Dev Cell","volume":"47","issue":"3","page":"391","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-187","title":"Sororin is an evolutionary conserved antagonist of WAPL ","abstract":null,"authors":"Prusen Mota, I., Galova, M., Schleiffer, A., Nguyen, T.-T., Kovacikova, I., Nishiyama, T., Gregan, J., Peters, J.-M., Schl\u00f6gelhofer, P. ","publication_status":"preprint","journalpubyear":"2022","journaltitle":"bioRxiv ","volume":"2022.10.24.513534","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.10.24.513534v1","preprintlink":"","articledate":"2022-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1802724","title":"Ultrastructure of the approximately 26S complex containing the approximately 20S cylinder particle (multicatalytic proteinase\/proteasome).","abstract":"We have isolated a large protein complex of approximately 26S from Xenopus laevis oocytes and eggs which is composed of the approximately 20S cylinder particle (multicatalytic proteinase\/proteasome) and additional proteinaceous components. In its polypeptide composition and sedimentation coefficient this approximately 26S complex closely resembles the 26S ubiquitin-dependent protease, a high molecular weight multienzyme complex recently described in the literature. Specific antibodies directed against a single subunit of the approximately 20S cylinder particle retain, on affinity columns, the large approximately 26S complex, and on sucrose gradients up to approximately 50% of the approximately 20S cylinder particles present in oocyte extracts sedimented with approximately 26S, suggesting that a large proportion of the approximately 20S particles exists in the cell as a component of the approximately 26S complex. Electron microscopy reveals the approximately 26S complex to be a symmetrical elongated macromolecular assembly of at least three protein particles. The central core of the complex is formed by the approximately 20S cylinder particle to which two other large components are attached at the ends, yielding a dumbbell-shaped complex of approximately 40 nm in length. Dissociation of the approximately 26S complexes releases in addition to approximately 20S cylinder particles a novel type of a disc-shaped particle of approximately 15 nm diameter which may represent the attached components or subcomplexes of them. Based on its structural and biochemical properties we postulate that the approximately 26S complex identified here is identical to the ubiquitin-dependent protease.","authors":"Peters, JM., Harris, JR., Kleinschmidt, JA.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Eur J Cell Biol","volume":"56","issue":"2","page":"422-32","pdf":null,"JrId":"3585","fulltextlink":null,"preprintlink":null,"articledate":"1992-04-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1698589","title":"Nonradioactive in situ nick translation combined with counterstaining: characterization of C-band and silver positive regions in mouse testicular cells.","abstract":"The DNase I sensitivity of three different chromatin regions in mouse testicular cells was analysed by in situ nick translation with biotin-dUTP combined with various counterstaining techniques. The regions were: (i) the constitutive centromeric heterochromatin, (ii) an interstitial C-band positive insertion on chromosome 1, Is(HSR1;C5)1Lub, and (iii) the chromatin containing rDNA (designated nucleolar chromatin herein). Incorporated biotin was detected either by the horseradish peroxidase reaction with diaminobenzidine (DAB) or the alkaline phosphatase reaction with fast red. The latter resulted in a water insoluble red precipitate, which was easily removable by any organic solution thus allowing the application of various counterstaining protocols. DNase I sensitivity of the three chromatin regions was screened in different cell types of the mouse testis. The interstitial Is(HSR) region was highly DNase I sensitive when it was recognizable by strong mithramycin fluorescence. The centromeric heterochromatin was DNase I resistant when it was compacted into microscopically visible chromosomal structures (mitosis, pachytene, metaphase I and II). In interphase nuclei from Sertoli cells and spermatogonia it became highly DNase I sensitive. In round spermatids it displayed medium DNase I sensitivity. Nucleolar chromatin was not labelled by in situ nick translation when silver staining demonstrated strong protein production. Sperm cells were highly DNase I sensitive from stages 11 to 15, but resistant as mature spermatozoa.","authors":"Adolph, S., Klett, C., Weith, A.","publication_status":"ppublish","journalpubyear":"1990","journaltitle":"Chromosoma","volume":"99","issue":"4","page":"251-9","pdf":null,"JrId":"2943","fulltextlink":null,"preprintlink":null,"articledate":"1990-11-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1681545","title":"Adenovirus enhancement of transferrin-polylysine-mediated gene delivery.","abstract":"Gene transfer may be accomplished by the receptor-mediated endocytosis pathway using transferrin-polylysine conjugates. For some target cells, however, gene transfer by this vector is extremely limited, despite the presence of the appropriate surface receptors, a phenomenon attributed to lysosomal degradation of endosome-internalized conjugate-DNA complexes. To enhance DNA escape from the cell vesicle system and thus augment gene transfer by this route, we have used the capacity of adenoviruses to disrupt endosomes as part of their entry mechanism. Adenoviral infection augmented levels of gene transfer by transferrin-polylysine conjugates in a dose-dependent manner: levels of gene transfer of greater than 2000-fold above baseline were achieved. Use of the adenovirus in this context allowed enhanced levels of gene transfer in a variety of target cells, including cell lines otherwise refractory to gene transfer by transferrin-polylysine conjugates. This augmentation was based on adenoviral-mediated vesicle disruption, a process independent of viral gene expression. Thus, the development of specific mechanisms to effect release from the endosome in combination with gene transfer by the receptor-mediated endocytosis pathway will increase the utility of this delivery system by allowing high levels of gene expression in target cells.","authors":"Curiel, DT., Agarwal, S., Wagner, E., Cotten, M.","publication_status":"ppublish","journalpubyear":"1991","journaltitle":"Proc Natl Acad Sci U S A","volume":"88","issue":"19","page":"8850-4","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1991-10-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1495997","title":"Inhibition of leukemia cell proliferation by receptor-mediated uptake of c-myb antisense oligodeoxynucleotides.","abstract":"Exposure of human leukemia HL-60 cells to an oligodeoxynucleotide complementary to an 18-base sequence (codons 2-7) of c-myb-encoded mRNA has previously been shown to result in inhibition of cell proliferation. Because HL-60 cells express high levels of transferrin receptor we adapted a DNA delivery system based on receptor-mediated endocytosis to introduce myb oligomers complexed with a transferrin-polylysine conjugate into those cells. A DNA.RNA duplex resistant to S1 nuclease digestion was detected as early as 12 hr after culture of HL-60 cells in the presence of the myb antisense\/transferrin-polylysine complex. Exposure of HL-60 cells to the myb antisense\/transferrin-polylysine complex resulted in rapid and profound inhibition of proliferation and loss of cell viability much more pronounced than that occurring in cells exposed to free myb antisense oligodeoxynucleotides. The transferrin-polylysine\/myb sense complex or the transferrin-polylysine conjugate alone had no effect on HL-60 cell proliferation and viability. These findings indicate that myb synthetic oligodeoxynucleotides enter efficiently into HL-60 by transferrin receptor-mediated endocytosis and exert a profound biological effect. Such a delivery system could exploit other ligand-receptor interactions for the selective delivery of oncogene-targeted antisense oligodeoxynucleotides.","authors":"Citro, G., Perrotti, D., Cucco, C., D'Agnano, I., Sacchi, A., Zupi, G., Calabretta, B.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Proc Natl Acad Sci U S A","volume":"89","issue":"15","page":"7031-5","pdf":null,"JrId":"6653","fulltextlink":null,"preprintlink":null,"articledate":"1992-09-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-189","title":"Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms","abstract":null,"authors":"Nagasaka, K., Davidson, I.F., Stocsits, R., Tang, W., Wutz, G., Betty, P., Panarotto, M., Litos, G., Schleiffer, A., Gerlich, D. and Peters, J.-M. ","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"bioRxiv ","volume":"2022.09.23.509019","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.09.23.509019v1","preprintlink":"","articledate":"2022-09-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1375324","title":"The promoter of the CD19 gene is a target for the B-cell-specific transcription factor BSAP.","abstract":"The CD19 protein is expressed on the surface of all B-lymphoid cells with the exception of terminally differentiated plasma cells and has been implicated as a signal-transducing receptor in the control of proliferation and differentiation. Here we demonstrate complete correlation between the expression pattern of the CD19 gene and the B-cell-specific transcription factor BSAP in a large panel of B-lymphoid cell lines. The human CD19 gene has been cloned, and several BSAP-binding sites have been mapped by in vitro protein-DNA binding studies. In particular, a high-affinity BSAP-binding site instead of a TATA sequence is located in the -30 promoter region upstream of a cluster of heterogeneous transcription start sites. Moreover, this site is occupied by BSAP in vivo in a CD19-expressing B-cell line but not in plasma or HeLa cells. This high-affinity site has been conserved in the promoters of both human and mouse CD19 genes and was furthermore shown to confer B-cell specificity to a beta-globin reporter gene in transient transfection experiments. In addition, BSAP was found to be the only abundant DNA-binding activity of B-cell nuclear extracts that interacts with the CD19 promoter. Together, this evidence strongly implicates BSAP in the regulation of the CD19 gene.","authors":"Kozmik, Z., Wang, S., D\u00f6rfler, P., Adams, B., Busslinger, M.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Mol Cell Biol","volume":"12","issue":"6","page":"2662-72","pdf":null,"JrId":"5919","fulltextlink":null,"preprintlink":null,"articledate":"1992-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1350740","title":"Development of a lethal mast cell disease in mice reconstituted with bone marrow cells expressing the v-erbB oncogene.","abstract":"An animal model for malignant mastocytosis is described in mice reconstituted with bone marrow cells expressing the v-erbB oncogene. The lethal mast cell disease is characterized by massive infiltration of bone marrow, spleen, and several other visceral organs by connective tissue mast cells, which normally reside in the skin and the peritoneal cavity. As is frequently found in malignant mastocytosis, the v-erbB-induced mast cell disease was accompanied in some primary recipients by an acute myelogenous leukemia (AML) that killed all secondary recipients regardless of whether the AML was already evident in the primary host. The infiltrating mast cells stained strongly positive with berberine sulfate, suggesting that they were terminally differentiated and in vitro they showed only a weak proliferative capacity. The leukemias were clonal but apparently of different origin than the malignant mast cells, implying the transformation of two independent cell populations. Leukemic cells expressed various myeloid-specific markers as well as the B220 antigen, normally associated with the B-cell lineage. However, the Ig heavy chain genes were still in germ line configuration. In culture, these cells proliferated in the absence of exogenous growth factors and had the capacity to differentiate into mature myeloid cells. Preliminary experiments suggest that v-erbB may use parts of a signal transduction pathway normally coupled to the c-kit receptor. The v-erbB-induced malignant mast cell disease should provide a useful animal model for elucidating the cause for malignant mastocytosis in humans and to explore possible therapeutic strategies.","authors":"von R\u00fcden, T., Kandels, S., Radaszkiewicz, T., Ullrich, A., Wagner, EF.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Blood","volume":"79","issue":"12","page":"3145-58","pdf":null,"JrId":"1243","fulltextlink":null,"preprintlink":null,"articledate":"1992-07-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"1341947","title":"Retrovirus-mediated oncogene transfer into neural transplants.","abstract":"A gene transfer model was developed which allows for the identification of transformation pathways in the developing nervous system. Transforming genes were introduced into fetal brain transplants using embryonic CNS as donor tissue and replication-defective retroviral vectors as genetic vehicles. This technique relies on the extraordinary organotypic differentiation capacity of neural grafts and the expression of retrovirally transmitted genes in various cell types of CNS transplants. In contrast to transgenic animals but analogous to sporadic tumor formation, target cells for the retroviral vector develop in an environment of unmodified neural tissue. We have introduced a number of neurotropic oncogenes into fetal brain transplants including genes with an associated tyrosine kinase activity (polyoma medium T, v-src), a novel member of the fibroblast growth factor (fgf) gene family and the SV40 large T antigen. These experiments have demonstrated a significant transformation potential of oncogenes in specific target cells of the brain, provided evidence for a dominant complementary transforming effect of simultaneously expressed ras and myc genes in neural precursor cells and have yielded intriguing model systems for human CNS neoplasms such as the cerebellar medulloblastoma. This review describes the transplantation model, demonstrates several striking phenotypes induced by oncogene expression in neural grafts and elaborates on future prospects of this experimental approach.","authors":"Wiestler, OD., Br\u00fcstle, O., Eibl, RH., Radner, H., Aguzzi, A., Kleihues, P.","publication_status":"ppublish","journalpubyear":"1992","journaltitle":"Brain Pathol","volume":"2","issue":"1","page":"47-59","pdf":null,"JrId":"2602","fulltextlink":null,"preprintlink":null,"articledate":"1994-02-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"158","title":"Comparison of contractile performance of canine atrial and ventricular muscles.","abstract":"This study compared the contractile performance of a canine right atrial trabecula with that of a macroscopically indistinguishable trabecula isolated from the right ventricular apex. The heart was removed from nine mongrel puppies weighing 6-8 kg and placed in Krebs-Ringer's bicarbonate solution. The bathing solution contained only 1.25 mmoles of Ca2+ and was bubbled with a 95% O2-5% CO2 gas mixture. Each atrial trabecula was specially selected from the right atrial appendage. Histologically, these trabeculae showed a remarkable longitudinal orientation of the fibers. At Lmax (the length of the muscle at which developed tension was maximum) under identical conditions of temperature, rate of stimulation, ionic milieu, pH, and O2 and CO2 supply, right atrial trabeculae achieved the same developed and total tensions but in a much shorter time than did ventricular trabeculae. In both muscle groups the maximum developed tension averaged about 2.5 g\/mm2. Since Lo (expressed as a fraction of Lmax) was less in atrial muscle than it was in ventribular muscle, we concluded that atrial muscle can be stretched considerably more than can ventricular muscle before optimum length is reached. At any given initial muscle length, the maximum of tension rise for atrial trabeculae amounted to at least twice that for ventricular trabeculae. At any given load up to 1.5 g\/mm2, the maximum velocity of shortening of an atrial trabecula was about three to four times that of a ventricular trabecula. These results collectively indicate that the contractile performance of the right atrial muscle is in many respects superior to that of the right ventricle, at least under the conditions of these experiments.","authors":"Urthaler, F., Walker, AA., Hefner, LL., James, TN.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Circ Res","volume":"37","issue":"6","page":"762-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"39706570","title":"The evolutionary origin and mechanism of chordate tail regeneration. An ancient tale?","abstract":"Chordate tail regeneration represents the remarkable ability of some chordates to partially or completely regenerate a significant portion of their primary body axis. In this review we will discuss the chordate regenerative ability, what is known about the cellular sources which contribute to the regenerating tail, how various structures such as the spinal cord and vertebral column are re-established, and how scaling of the regenerating tail is regulated. Finally, we propose that tail regeneration is evolutionarily conserved and is fundamentally different from tail development however the origin and mechanism of this process remain elusive.","authors":"Masselink, W., Murawala, P.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Cells Dev","volume":null,"issue":null,"page":"203988","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-12-21","doi":"10.1016\/j.cdev.2024.203988","first_author":null,"corresponding_authors":null},{"pmid":"155","title":"Interaction of the chemoreflex and the pulmonary inflation reflex in the regulation of coronary circulation in conscious dogs.","abstract":"The interaction of chemoreflex and pulmonary inflation reflex control of the coronary circulation was examined in conscious dogs by comparing the responses to chemoreflex stimulation (intracarotid injection of nicotine) when ventilation was allowed to increase with those when ventilation was controlled. The responses were also compared with those elicited by both forced mechanical and spontaneous hyperinflation. When the heart rate was constant, intracarotidly administered nicotine induced an increase in the depth of respiration followed closely by an increase in late diastolic coronary flow from 48 +\/- 2 to 106 +\/- 8 ml\/min and a reduction in late diastolic coronary resistance from 1.62 +\/- 0.08 to 0.78 +\/- 0.06 mm Hg\/ml min-1. After beta-receptor and cholinergic blockade, a similar coronary dilation in response to nicotine occurred only when ventilation was allowed to increase. However, when ventilation was controlled, intracarotidly administered nicotine increased coronary resistance after combined beta-receptor and cholinergic blockade. The reflex coronary dilation was not observed after carotid sinus nerve section or after alpha-receptor blockade. Thus, nicotine stimulation of the carotid chemoreflex results in a striking coronary dilation that has two components. The minor component involves a chemoreflex with its efferent pathway in tthe vagi. The major component of coronary dilation follows an increase in the depth of respiration, and its efferent component appears to involve withdrawal of alpha-adrenergic constrictor tone. An almost identical period of reflex coronary dilation followed either forced mechanical or spontaneous hyperinflation in the conscious dog.","authors":"Vatner, SF., McRitchie, RJ.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Circ Res","volume":"37","issue":"5","page":"664-73","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"149","title":"Some characteristics of two azoreductase systems in rat liver. Relevance to the activity of 2-[4'-di(2\"-bromopropyl)-aminophenylazo]benzoic acid (CB10-252), a compound possessing latent cytotoxic activity.","abstract":"The system involved in the reduction of 2-[4'-di(2''-bromopropyl) aminophenylazolbenzoic acid (CB10-252), an agent designed for treating primary liver cell cancer, has been demonstrated to be localised mainly in the 108 000 X g supernatant fraction of rat liver homogenate. It is also present in other organs particularly in the spleen. DAB-azoreductase as shown previously is present almost entirely in the microsomal fraction and is found in high concentration only in liver. The pH maximum for CB10-252-azoreductase implying the importance of the 2'-carboxyl group in determining substrate specificity. The use of enzyme inhibitors and other additives showed that CB10-252 WAS NOT AXANTHINE OXIDASE OR DIHYDROFOLATE REDUCTASE. Its activity was not affected by carbon monoxide, phenobarbitone (PB), or 3-methylcholanthrene (MC) pretreatment. Enhancement of the activity by ferrous ions and FAD indicated that at least part of the reduction system could involve a flavoprotein with FAD as the prosthetic group. The activity of CB10-252-azoreductase and methylred-azoreductase was reduced by menadione (vitamin K3), cyanide and propylgallate. A diaphorase preparation from pig heart reduced both CB10-252 and methylred with both NADPH- and NADH-generating systems.","authors":"Autrup, H., Warwick, GP.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Chem Biol Interact","volume":"11","issue":"5","page":"329-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"141","title":"Characterization studies on the membrane-bound adenosine triphosphatase (ATPase) of Azotobacter vinelandii.","abstract":"The adenosinetriphosphatase (ATPase) (EC 3.6.1.3) activity in Azotobacter vinelandii concentrates in the membranous R3 fraction that is directly associated with Azotobacter electron transport function. Sonically disrupted Azotobacter cells were examined for distribution of ATPase activity and the highest specific activity (and activity units) was consistently found in the particulate R3 membranous fraction which sediments on ultracentrifugation at 144 000 X g for 2 h. When the sonication time interval was increased, the membrane-bound ATPase activity could neither be solubilized nor released into the supernatant fraction. Optimal ATPase activty occurred at pH 8.0; Mg2+ ion when added to the assay was stimulatory. Maximal activity always occurred when the Mg2+:ATP stoichiometry was 1:1 on a molar ratio at the 5 mM concentration level. Sodium and potassium ions had no stimulatory effect. The reaction kinetics were linear for the time intervals studied (0-60 min). The membrane-bound ATPase in the R3 fraction was stimulated 12-fold by treatment wiTH TRypsin, and fractionation studies showed that trypsin treatment did not solubilize ATPase activity off the membranous R3 electron transport fraction. The ATPase was not cold labile and the temperature during the preparation of the R3 fraction had no effect on activity; overnight refrigeration at 4 degrees C, however, resulted in a 25% loss of activity as compared with a 14% loss when the R3 fraction was stored overnight at 25 degrees C. A marked inactivation (although variable, usually about 60%) did occur by overnight freezing (-20 degrees C), and subsequent sonication failed to restore ATPase activity. This indicates that membrane reaggregation (by freezing) was not responsible for ATPase inactivation. The addition of azide, ouabain, 2,4-dinitrophenol, or oligomycin to the assay system resulted in neither inhibition nor stimulation of the ATPase activity. The property of trypsin activation and that ATPase activity is highest in the R3 electron transport fraction suggests that its probable functional role is in coupling of electron transport to oxidative phosphorylation.","authors":"Jurtshuk, P., McEntire, JE.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Microbiol","volume":"21","issue":"11","page":"1807-14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"139","title":"Physiological differences among isolates of Phytophthora cinnamomi.","abstract":"Significant differences in amylase, beta-glucosidase, and phosphatase activities were observed among four Phytophthora cinnamomi isolates grown in nutrient-amended sterilized soil for 20 days. Amylase pH optima for the four isolates were within a relatively narrow range; at pH 5.5 each isolate was within 90% of its peak activity. Isolates SB-216-1, 1-281, and C-39 each exhibited maximal beta-glucosidase activity at pH 5.0 and maximal phosphatase activity at pH 5.0-5.5. Maximal activity for these two enzymes of isolate A-7725 occurred at pH 3.5. In timed experiments, isolates 1-281 and A-7725 exhibited greater amylase activities than did the other two isolates. For beta-glucosidase, greatest activity was observed for SB-216-1; ACTivity of 1-281 was intermediate and least activity was observed for isolates A-7725 and C-39. Isolates SB-216-1 and 1-281 exhibited greatest phosphatase activities; isolate C-39 was intermediate in activity, and A-7725 was least active. Results indicate that significant differences exist among the isolates tested and that these differences can be quantitatively measured by the methods described.","authors":"Kelley, WD.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Microbiol","volume":"21","issue":"10","page":"1548-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"43","title":"Modification of arginine and lysine in proteins with 2,4-pentanedione.","abstract":"Primary amines react with 2,4-pentanedione at pH 6-9 to form enamines, N-alkyl-4-amino-3-penten-2-ones. The latter compounds readily regenerate the primary amine at low pH or on treatment with hydroxylamine. Guanidine and substituted guanidines react with 2,4-pentanedione to form N-substituted 2-amino-4,6-dimethylpyrimidines at a rate which is lower by at least a factor of 20 than the rate of reaction of 2,4-pentanedione with primary amines. Selective modification of lysine and arginine side chains in proteins can readily be achieved with 2,4-pentanedione. Modification of lysine is favored by reaction at pH 7 or for short reaction times at pH 9. Selective modification of arginine is achieved by reaction with 2,4-pentanedione for long times at pH 9, followed by treatment of the protein with hydroxylamine. The extent of modification of lysine and arginine side chains can readily be measured spectrophotometrically. Modification of lysozyme with 2,4-pentanedione at pH 7 results in modification of 3.8 lysine residues and less than 0.4 arginine residue in 24 hr. Modification of lysozyme with 2,4-pentanedione at pH 9 results in modification of 4 lysine residues and 4.5 arginine residues in 100 hr. Treatment of this modified protein with hydroxylamine regenerated the modified lysine residues but caused no change in the modified arginine residues. One arginine residue seems to be essential for the catalytic activity of the enzyme.","authors":"Gilbert, HF., O'Leary, MH.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"23","page":"5194-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"135","title":"Soil fungistasis: elevation of the exogenous carbon and nitrogen requirements for spore germination by fungistatic volatiles in soils.","abstract":"Axenic, washed conidia of Fusarium solani f. sp. phaseoli, Aspergillus flavus, and Verticillium albo-atrum were placed on washed Difco purified agar discs along with an inorganic salt solution containing various levels of carbon and nitrogen substrates. These discs were exposed to volatiles from six soils (pH 5.1-8.6). Fusarium solani macroconidial germination was inhibited mostly by volatiles from soils of pH 5.1, 6.1, 7.0, and 7.5, but high levels of glucose and NH4Cl reversed this inhibition, raising germination to that of no-soil, no-carbon or nitrogen controls. Conidial germination of A. flavus was inhibited mainly by volatiles from high pH (7.0, 7.8, and 8.6) soils, and increased levels of glucose plus an amino acid mixture nullified this inhibition. Volatiles from soils of pH 5.1, 6.1, and 7.5 stimulated A. flavus conidial germination. Assays after the removal of CO2 from the air above soil of pH 5.1 demonstrated that volatiles inhibitory to A. flavus were produced by this soil. Assays indicated that a KOH-soluble compound was a fungistatic soil volatile to F. solani macroconidial germination. The nullification by carbon and nitrogen substrates of F. solani and A. flavus inhibition caused by soil volatiles parallels that for soil fungistasis. Conidial germination of V. albo-atrum was markedly stimulated by volatiles in all soils tested, and was not affected by removal of CO2. Inhibitory soil volatiles may increase the nutritional requirements for spore germination of certain fungi.","authors":"Griffin, GJ., Hora, TS., Baker, R.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Microbiol","volume":"21","issue":"10","page":"1468-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"133","title":"The prevention of autolysis of stored cornea using steroid as a lysosome membrane stabilizer.","abstract":"Many eyes donated for use in corneal grafting are rejected because of signs of autolysis in the donor material. The purpose of this experimental study was to determine whether hydrocortisone acting as a lysosome membrane stabilizer could prevent or retard autolysis of the corneas under storage, and if so, what was the most efficacious concentration. Different groups of rabbit corneas were placed in saline as controls or in varying concentrations of hydrocortisone (10(-10) M to 10(-4) M at pH 7.4) at 37 degrees C and 4 degrees C. Acid phosphatase released after six hours was measured biochemically. This enzyme was used as a marker enzyme reflecting lysosomal labilization. Results showed a significant stabilization of the lysosomal membrane at 4 degrees C as compared to 37 degrees C. A trend towards stabilization of the lysosomal membrane was seen when 10(-8) M concentration of hydrocortisone at 37 degrees C was used, there being no demonstrable stabilization at 4 degrees C.","authors":"Fook, TJ., Ranadive, NS., Basu, PK.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Can J Ophthalmol","volume":"10","issue":"4","page":"482-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"85","title":"Myosin from arterial smooth muscle: isolation following actin depolymerization.","abstract":"The contractile proteins from arterial smooth muscle are highly soluble, and can be extracted at I = 0.05. However, they can be precipitated by a prolonged dialysis at pH 6 to give an actomyosin with a high, although variable, actin:myosin ratio. The sedimentation behavior of this actomyosin at high ionic strength was examined as a function of pH, protein concentration and composition by preparative ultracentrifugation. Comparisons with synthetic skeletal muscle actomyosins of similar composition demonstrated significant differences in the behaviors of these two systems. It was found that much smooth muscle actomyosin is not dissociated by normally relaxing conditions, and that it sediments at a slower rate than F-actin. The solubility of the supernatant protein (a myosin-enriched actomyosin) in 0.2 M K Cl (pH 7) depended on the pH during centrifugation. A lower solubility was associated only with a higher actin concentration in the supernatant, suggesting a dependence on actin repolymerization. Pure myosin was selectively precipitated from the supernatant by polyethylene glycol-6000, but only when the protein was soluble at low ionic strength. The solubility of purified myosin was similar to that of myosin from striated muscles. A relationship between the presence of depolymerized actin and the high solubility of smooth muscle contractile proteins is suggested.","authors":"Megerman, J., Murphy, RA.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"412","issue":"2","page":"241-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"72","title":"Preparation and characterization of an enzymatically active immobilized derivative of myosin.","abstract":"Purified skeletal muscle myosin (EC 3.6.1.3) has been covalently bound to Sepharose 4B by the cyanogen bromide procedure. The resulting complex, Sepharose-Myosin, possesses adenosine triphosphatase activity and is relatively stable for long periods of time. Under optimal binding conditions, approximately 33% of the specific ATPase activity of the bound myosin is retained. Polyacrylamide gel electrophoresis of polypeptides released from denatured Sepharose-Myosin indicates that 85% of the myosin is attached to the agarose beads through the heavy chains and the remainder through the light chains, in agreement with predictions of binding and release based upon either the lysine contents or molecular weights of themyosin subunits. The adenosine triphosphatase of the immobilized myosin has been investigated under conditions of varying pH, ionic strength, and cation concentration. The ATPase profiles of immobilized myosin are quite similar to those for free myosin, however subtle differences are found. The Sepharose-Myosin ATPase is not as sensitive as myosin to alterations in salt concentration and the apparent KM is approximately two-fold higher than that of myosin. These differences are probably due to chemical modification in the region of the attachment site(s) to the agarose beads and hydration and diffusion limitations imposed by the polymeric agarose matrix.","authors":"Elgart, ES., Gusovsky, T., Rosenberg, MD.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"178-92","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"68","title":"Behavior of soluble and immobilized acid phosphatase in hydro-organic media.","abstract":"The hydrolysis of p-nitrophenyl phosphate by wheat germ acid phosphatase (orthophosphoric monoester phosphohydrolase, EC 3.1.3.2) has been investigated in mixtures of aqueous buffers with acetone, dioxane and acetonitrile. The enzyme was either in free solution or immobilized on a pellicular support which consisted of a porous carbonaceous layer on solid glass beads. The highest enzyme activity was obtained in acetone and acetonitrile mixed with citrate buffer over a wide range of organic solvent concentration. In 50% (v\/v) acetone both V and Km of the immobilized enzyme were about half of the values in the neat aqueous buffer, but the Ki for inorganic phosphate was unchanged. In 50% (v\/v) mixtures of various solvents and citrate buffers of different pH, the enzymic activity was found to depend on the pH of the aqueous buffer component rather than the pH of the hydro-organic mixture as measured with the glass-calomel electrode. The relatively high rates of p-nitrophenol liberation in the presence of glucose even at high organic solvent concentrations suggest that transphosphorylation is facilitated at low water activity.","authors":"Wan, H., Horvath, C.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochim Biophys Acta","volume":"410","issue":"1","page":"135-44","pdf":null,"JrId":"1037","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"56","title":"Kinetic light scattering studies on the dissociation of hemoglobin from Lumbricus terrestris.","abstract":"The kinetics of the pH-induced dissociation of the 3 X 10(6) mol wt hemoglobin from Lumbricus terrestris (the earthworm) have been studied in a light-scattering stopped-flow apparatus. The ligand dependent dissociation data were fit well by a simple sequential model. The data for CO and oxyhemoglobin are consistent with Hb12 leads to 2Hb6 leads to 12Hb. Methemoglobin at pH 7 appears to be hexameric and the dissociation is consistent with the model: Hb6 leads to 6Hb. In a sequential decay scheme for which light-scattering changes are monitored, the relative amounts of rapid and slow phase are determined by the rate constants as well as the molecular weights of intermediate species. Assignment of the hexameric intermediate is supported by an investigation of the sensitivity of the theoretical kinetic curves to the molecular weights of the intermediates. This assignment is further supported by the following: (1) the same model will fit the data for oxy- and CO-hemoglobin at all three temperatures (a 24-29-fold variation in rate constants), (2) evidence from electron microscopy shows hexameric forms, and (3) methemoglobin is apparently stable as a hexamer at pH 7. When CO replaces O2 as the ligand, the dissociation rate increases by a factor of four. The met is about 20 times faster than the initial oxyhemoglobin dissociation rate, but perhaps more relevant for comparing dissociation of the hexamer, the met rate was respectively 100 times and 500 times faster than that for the assumed hexameric forms of CO- and oxy-hemoglobin. The activation energies for the dodecamer to hexamer dissociation and for the dissociation of the hexamer to smaller forms were about 30 kcal\/mol for oxy-, CO-, and methemoglobin.","authors":"Goss, DJ., Parkhurst, LJ., G\u00f6risch, H.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"25","page":"5461-4","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"53","title":"The interaction of phospholipase A2 with micellar interfaces. The role of the N-terminal region.","abstract":"The localization of the previously postulated interface recognition site (IRS) in porcine pancreatic phospholipase A2, required for a specific interaction between the enzyme and organized lipid-water interfaces, was investigated by ultraviolet difference spectroscopy, by measurements of the intrinsic fluorescence of the unique Trp residue, and by protection experiments against specific tryptic hydrolysis. Using the enzymically nondegradable substrate analogues: CnH(2n+1)(0-)OOCH2CH2N+(CH3)3-(H,OH), it is shown that the rather hydrophobic N-terminal sequence of the enzyme, viz., Ala-Leu-Trp-Gln-Phe-Arg, is directly involved in the interaction with the lipid-water interface. Besides hydrophobic probably also polar interactions contribute to the binding process. At neutral or acidic pH the presence of a salt bridge between the N-terminal alpha-NH3+ group and a negatively charged side chain stablizes the interface recognition site and allows the enzyme to penetrate micellar surfaces, even in the absence of metal ion. At alkaline pH, interaction of the enzyme with micellar interfaces requires the presence of Ca2+ (Ba2+) ions.","authors":"van Dam-Mieras, MC., Slotboom, AJ., Pieterson, WA., de Haas, GH.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"25","page":"5387-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"1976-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"52","title":"Evidence of the involvement of a 50S ribosomal protein in several active sites.","abstract":"The functional role of the Bacillus stearothermophilus 50S ribosomal protein B-L3 (probably homologous to the Escherichia coli protein L2) was examined by chemical modification. The complex [B-L3-23S RNA] was photooxidized in the presence of rose bengal and the modified protein incorporated by reconstitution into 50S ribosomal subunits containing all other unmodified components. Particles containing photooxidized B-L3 are defective in several functional assays, including (1) poly(U)-directed poly(Phe) synthesis, (2) peptidyltransferase activity, (3) ability to associate with a [30S-poly(U)-Phe-tRNA] complex, and (4) binding of elongation factor G and GTP. The rates of loss of the partial functional activities during photooxidation of B-L3 indicate that at least two independent inactivating events are occurring, a faster one, involving oxidation of one or more histidine residues, affecting peptidyltransferase and subunit association activities and a slower one affecting EF-G binding. Therefore the protein B-L3 has one or more histidine residues which are essential for peptidyltransferase and subunit association, and another residue which is essential for EF-G-GTP binding. B-L3 may be the ribosomal peptidyltransferase protein, or a part of the active site, and may contribute functional groups to the other active sites as well.","authors":"Fahnestock, SR.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"24","page":"5321-7","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"51","title":"Conformational changes induced in a homogeneous anti-type III pneumococcal antibody by oligosaccharides of increasing size.","abstract":"The circular polarization of luminescence (CPL) emitted by tryptophan residues was used as a sensitive probe for measuring ligand-induced structural changes in a homogeneous type III pneumococcal antibody. A series of oligosaccharide ligands of increasing size derived from type III polysaccharide by partial acid hydrolysis was assayed. Ligand-induced changes in the circular polarization of fluorescence of the antibody were observed for all antigens tested, including tetra-, hexa-, and octasaccharides and a 16-residue oligomer, the largest changes being recorded upon interaction with the intact soluble type III pneumococcal (SIII) polysaccharide. When Fab' or F(ab')2 fragments were used instead of the antibody IgG for binding of SIII polysaccharide, the extent of conformational changes was decreased. This suggests interactions between Fab and Fc portions in the IgG molecule and subsequent conformational changes in Fc part upon antigen binding. Reduction of interchain disulfide bonds abolished the additional spectral changes attributed to the Fc part but not the changes observed in the Fab part, thus suggesting that the presence of the interchain disulfide bond in the hinge region is required for maximal CPL changes to occur. Small monovalent ligands, i.e., the tetra-, hexa-, and octasaccharides, were capable of inducing CPL changes in the Fab part of the antibody molecule as well as CPL changes attributed to the Fc portion. A multivalent ligand containing about 16 sugar residues appears to be the minimal antigenic size required for triggering conformational changes attributed to the Fc part, similar to those seen in the interaction with the whole polysaccharide antigen.","authors":"Jaton, JC., Huser, H., Braun, DG., Givol, D., Pecht, I., Schlessinger, J.","publication_status":"ppublish","journalpubyear":"1975","journaltitle":"Biochemistry","volume":"14","issue":"24","page":"5312-5","pdf":null,"JrId":"1028","fulltextlink":null,"preprintlink":null,"articledate":"1976-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"-180","title":"Somatic hypermutation spectra are independent of the local transcriptional and epigenetic landscape","abstract":null,"authors":"Schoeberl, U. E., Fitz, J., Froussios, K., Valieris, R., Makharova, M., Ourailidis, I., Bauer, B., Neumann, T., Wiedemann, E., Steininger, M., Garcia, A. C., Mastrovito, M., Mouquet, H., Tojal Da Silva, I., Pavri, R. ","publication_status":"preprint","journalpubyear":"2022","journaltitle":"bioRxiv ","volume":"2022.05.21.492925","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.05.21.492925v1","preprintlink":null,"articledate":"2002-05-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36473204","title":"RANKL and RANK in Cancer Therapy.","abstract":"Receptor activator of nuclear factor-&#x3ba;B (RANK) and its ligand (RANKL) are key regulators of mammalian physiology such as bone metabolism, immune tolerance and antitumor immunity, and mammary gland biology. Here, we explore the multiple functions of RANKL\/RANK in physiology and pathophysiology and discuss underlying principles and strategies to modulate the RANKL\/RANK pathway as a therapeutic target in immune-mediated cancer treatment.","authors":"Onji, M., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Physiology (Bethesda)","volume":"38","issue":"3","page":"0","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32969030","title":"Hepatocyte Mitogen-Activated Protein Kinase Kinase 7 Contributes to Restoration of the Liver Parenchyma Following Injury in Mice.","abstract":"on Status=\\\"MEDLINE\\\" Owner=\\\"NLM\\\"><PMID Version=\\\"1\\\">32969030<\/PMID><DateCompleted><Year>2022<\/Year><Month>01<\/Month><Day>07<\/Day><\/DateCompleted><DateRevised><Year>2022<\/Year><Month>01<\/Month><Day>07<\/Day><\/DateRevised><Article PubModel=\\\"Print-Electronic\\\"><Journal><ISSN IssnType=\\\"Electronic\\\">1527-3350<\/ISSN><JournalIssue CitedMedium=\\\"Internet\\\"><Volume>73<\/Volume><Issue>6<\/Issue><PubDate><Year>2021<\/Year><Month>06<\/Month><\/PubDate><\/JournalIssue><Title>Hepatology (Baltimore, Md.)<\/Title><ISOAbbreviation>Hepatology<\/ISOAbbreviation><\/Journal><ArticleTitle>Hepatocyte Mitogen-Activated Protein Kinase Kinase 7 Contributes to Restoration of the Liver Parenchyma Following Injury in Mice.<\/ArticleTitle><Pagination><MedlinePgn>2510-2526<\/MedlinePgn><\/Pagination><ELocationID EIdType=\\\"doi\\\" ValidYN=\\\"Y\\\">10.1002\/hep.31565<\/ELocationID><Abstract><AbstractText Label=\\\"BACKGROUND AND AIMS\\\">Mitogen-activated protein kinase kinase (MKK) 7 and MKK4 are upstream activators of c-Jun NH<sub>2<\/sub> -terminal kinases (JNKs) and have been shown to be required for the early development of the liver. Although it has been suggested that MKK7 might be involved in the regulation of hepatocyte proliferation, the functional role of MKK7 in the liver has remained unclear.","authors":"Ooshio, T., Yamamoto, M., Fujii, K., Xin, B., Watanabe, K., Goto, M., Okada, Y., Suzuki, A., Penninger, JM., Nishina, H., Nishikawa, Y.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Hepatology","volume":"73","issue":"6","page":"2510-2526","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35029322","title":"Transcription factor Mesenchyme Homeobox Protein 2 (MEOX2) modulates nociceptor function.","abstract":"Mesenchyme homeobox protein 2 (MEOX2) is a transcription factor involved in mesoderm differentiation, including development of bones, muscles, vasculature and dermatomes. We have previously identified dysregulation of MEOX2 in fibroblasts from Congenital Insensitivity to Pain (CIP) patients, and confirmed that btn, the Drosophila homologue of MEOX2, plays a role in nocifensive responses to noxious heat stimuli. To determine the importance of MEOX2 in the mammalian peripheral nervous system, we used a Meox2 heterozygous (Meox2<sup>+\/-<\/sup> ) mouse model to characterize its function in the sensory nervous system, and more specifically, in nociception. MEOX2 is expressed in the mouse dorsal root ganglia (DRG) and spinal cord, and localizes in the nuclei of a subset of sensory neurons. Functional studies of the mouse model, including behavioral, cellular and electrophysiological analyses, showed altered nociception encompassing impaired action potential initiation upon depolarization. Mechanistically, we noted decreased expression of Scn9a and Scn11a genes encoding Na<sub>v<\/sub> 1.7 and Na<sub>v<\/sub> 1.9 voltage gated sodium channels, respectively, that are crucial in subthreshold amplification and action potential initiation in nociceptors. Further transcriptomic analyses of Meox2<sup>+\/-<\/sup> DRG revealed downregulation of a specific subset of genes including those previously associated with pain perception, such as PENK and NPY. Based on these observations, we propose a novel role of MEOX2 in primary afferent nociceptor neurons for the maintenance of a transcriptional program required for proper perception of acute and inflammatory noxious stimuli.","authors":"Kokotovi\u0107, T., Lenartowicz, EM., Langeslag, M., Ciotu, CI., Fell, CW., Scaramuzza, A., Fischer, MJM., Kress, M., Penninger, JM., Nagy, V.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"FEBS J","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35023830","title":"ACE2 is the critical in vivo receptor for SARS-CoV-2 in a novel COVID-19 mouse model with TNF- and IFN\u03b3-driven immunopathology.","abstract":"Despite tremendous progress in the understanding of COVID-19, mechanistic insight into immunological, disease-driving factors remains limited. We generated maVie16, a mouse-adapted SARS-CoV-2, by serial passaging of a human isolate. In silico modeling revealed how only three Spike mutations of maVie16 enhanced interaction with murine ACE2. maVie16 induced profound pathology in BALB\/c and C57BL\/6 mice, and the resulting mouse COVID-19 (mCOVID-19) replicated critical aspects of human disease, including early lymphopenia, pulmonary immune cell infiltration, pneumonia, and specific adaptive immunity. Inhibition of the proinflammatory cytokines IFN\u03b3 and TNF substantially reduced immunopathology. Importantly, genetic ACE2-deficiency completely prevented mCOVID-19 development. Finally, inhalation therapy with recombinant ACE2 fully protected mice from mCOVID-19, revealing a novel and efficient treatment. Thus, we here present maVie16 as a new tool to model COVID-19 for the discovery of new therapies and show that disease severity is determined by cytokine-driven immunopathology and critically dependent on ACE2 in vivo.","authors":"Gawish, R., Starkl, P., Pimenov, L., Hladik, A., Lakovits, K., Oberndorfer, F., Cronin, SJ., Ohradanova-Repic, A., Wirnsberger, G., Agerer, B., Endler, L., Capraz, T., Perthold, JW., Cikes, D., Koglgruber, R., Hagelkruys, A., Montserrat, N., Mirazimi, A., Boon, L., Stockinger, H., Bergthaler, A., Oostenbrink, C., Penninger, JM., Knapp, S.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Elife","volume":"11","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35039505","title":"RNF43\/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the\u00a0liver lipid metabolic ground-state.","abstract":"RNF43\/ZNRF3 negatively regulate WNT signalling. Both genes are mutated in several types of cancers, however, their contribution to liver disease is unknown. Here we describe that hepatocyte-specific loss of Rnf43\/Znrf3 results in steatohepatitis and in increase in unsaturated lipids, in the absence of dietary fat supplementation. Upon injury, Rnf43\/Znrf3 deletion results in defective hepatocyte regeneration and liver cancer, caused by an imbalance between differentiation\/proliferation. Using hepatocyte-, hepatoblast- and ductal cell-derived organoids we demonstrate that the differentiation defects and lipid alterations are, in part, cell-autonomous. Interestingly, ZNRF3 mutant liver cancer patients present poorer prognosis, altered hepatic lipid metabolism and steatohepatitis\/NASH signatures. Our results imply that RNF43\/ZNRF3 predispose to liver cancer by controlling the proliferative\/differentiation and lipid metabolic state of hepatocytes. Both mechanisms combined facilitate the progression towards malignancy. Our findings might aid on the management of those RNF43\/ZNRF3 mutated individuals at risk of developing fatty liver and\/or liver cancer.","authors":"Belenguer, G., Mastrogiovanni, G., Pacini, C., Hall, Z., Dowbaj, AM., Arnes-Benito, R., Sljukic, A., Prior, N., Kakava, S., Bradshaw, CR., Davies, S., Vacca, M., Saeb-Parsy, K., Koo, BK., Huch, M.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Nat Commun","volume":"13","issue":"1","page":"334","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35121945","title":"Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumor microenvironment and cross-resistance to immunotherapy in melanoma.","abstract":"How targeted therapies and immunotherapies shape tumors, and thereby influence subsequent therapeutic responses, is poorly understood. In the present study, we show, in melanoma patients and mouse models, that when tumors relapse after targeted therapy with MAPK pathway inhibitors, they are cross-resistant to immunotherapies, despite the different modes of action of these therapies. We find that cross-resistance is mediated by a cancer cell-instructed, immunosuppressive tumor microenvironment that lacks functional CD103<sup>+<\/sup> dendritic cells, precluding an effective T cell response. Restoring the numbers and functionality of CD103<sup>+<\/sup> dendritic cells can re-sensitize cross-resistant tumors to immunotherapy. Cross-resistance does not arise from selective pressure of an immune response during evolution of resistance, but from the MAPK pathway, which not only is reactivated, but also exhibits an increased transcriptional output that drives immune evasion. Our work provides mechanistic evidence for cross-resistance between two unrelated therapies, and a scientific rationale for treating patients with immunotherapy before they acquire resistance to targeted therapy.","authors":"Haas, L., Elewaut, A., Gerard, CL., Umkehrer, C., Leiendecker, L., Pedersen, M., Krecioch, I., Hoffmann, D., Novatchkova, M., Kuttke, M., Neumann, T., da Silva, IP., Witthock, H., Cuendet, MA., Carotta, S., Harrington, KJ., Zuber, J., Scolyer, RA., Long, GV., Wilmott, JS., Michielin, O., Vanharanta, S., Wiesner, T., Obenauf, AC.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Cancer","volume":"2","issue":"7","page":"693-708","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35184157","title":"TSPAN6 is a suppressor of Ras-driven cancer.","abstract":"Oncogenic mutations in the small GTPase RAS contribute to ~30% of human cancers. In a Drosophila genetic screen, we identified novel and evolutionary conserved cancer genes that affect Ras-driven tumorigenesis and metastasis in Drosophila including confirmation of the tetraspanin Tsp29Fb. However, it was not known whether the mammalian Tsp29Fb orthologue, TSPAN6, has any role in RAS-driven human epithelial tumors. Here we show that TSPAN6 suppressed tumor growth and metastatic dissemination of human RAS activating mutant pancreatic cancer xenografts. Whole-body knockout as well as tumor cell autonomous inactivation using floxed alleles of Tspan6 in mice enhanced Kras<sup>G12D<\/sup>-driven lung tumor initiation and malignant progression. Mechanistically, TSPAN6 binds to the EGFR and blocks EGFR-induced RAS activation. Moreover, we show that inactivation of TSPAN6 induces an epithelial-to-mesenchymal transition and inhibits cell migration in vitro and in vivo. Finally, low TSPAN6 expression correlates with poor prognosis of patients with lung and pancreatic cancers with mesenchymal morphology. Our results uncover TSPAN6 as a novel tumor suppressor receptor that controls epithelial cell identify and restrains RAS-driven epithelial cancer.","authors":"Humbert, PO., Pryjda, TZ., Pranjic, B., Farrell, A., Fujikura, K., de Matos Simoes, R., Karim, R., Kozieradzki, I., Cronin, SJF., Neely, GG., Meyer, TF., Hagelkruys, A., Richardson, HE., Penninger, JM.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Oncogene","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35165179","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells.","abstract":"Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow [J.-L. Ma\u00eetre <i>et\u00a0al.<\/i>, <i>Science<\/i> 338, 253-256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension-stabilizing E-cadherin-actin complexes at the contact.","authors":"Slov\u00e1kov\u00e1, J., Sikora, M., Arslan, FN., Caballero-Mancebo, S., Krens, SFG., Kaufmann, WA., Merrin, J., Heisenberg, CP.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Proc Natl Acad Sci U S A","volume":"119","issue":"8","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35241478","title":"NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation.","abstract":"Cell fate transitions depend on balanced rewiring of transcription and translation programs to mediate ordered developmental progression. Components of the nonsense-mediated mRNA decay (NMD) pathway have been implicated in regulating embryonic stem cell (ESC) differentiation, but the exact mechanism is unclear. Here we show that NMD controls expression levels of the translation initiation factor <i>Eif4a2<\/i> and its premature termination codon-encoding isoform (<i>Eif4a2<\/i><sup><i>PTC<\/i><\/sup> ). NMD deficiency leads to translation of the truncated eIF4A2<sup>PTC<\/sup> protein. eIF4A2<sup>PTC<\/sup> elicits increased mTORC1 activity and translation rates and causes differentiation delays. This establishes a previously unknown feedback loop between NMD and translation initiation. Furthermore, our results show a clear hierarchy in the severity of target deregulation and differentiation phenotypes between NMD effector KOs (<i>Smg5<\/i> KO &gt; <i>Smg6<\/i> KO &gt; <i>Smg7<\/i> KO), which highlights heterodimer-independent functions for SMG5 and SMG7. Together, our findings expose an intricate link between mRNA homeostasis and mTORC1 activity that must be maintained for normal dynamics of cell state transitions.","authors":"Huth, M., Santini, L., Galimberti, E., Ramesmayer, J., Titz-Teixeira, F., Sehlke, R., Oberhuemer, M., Stummer, S., Herzog, V., Garmhausen, M., Romeike, M., Chugunova, A., Leesch, F., Holcik, L., Weipoltshammer, K., Lackner, A., Schoefer, C., von Haeseler, A., Buecker, C., Pauli, A., Ameres, SL., Smith, A., Beyer, A., Leeb, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Genes Dev","volume":"36","issue":"5-6","page":"348-367","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.07.07.180133v1","articledate":"2022-04-21","doi":"10.1101\/gad.347690.120","first_author":null,"corresponding_authors":null},{"pmid":"35393517","title":"Sperm membrane proteins DCST1 and DCST2 are required for sperm-egg interaction in mice and fish.","abstract":"The process of sperm-egg fusion is critical for successful fertilization, yet the underlying mechanisms that regulate these steps have remained unclear in vertebrates. Here, we show that both mouse and zebrafish DCST1 and DCST2 are necessary in sperm to fertilize the egg, similar to their orthologs SPE-42 and SPE-49 in C. elegans and Sneaky in D. melanogaster. Mouse Dcst1 and Dcst2 single knockout (KO) sperm are able to undergo the acrosome reaction and show normal relocalization of IZUMO1, an essential factor for sperm-egg fusion, to the equatorial segment. While both single KO sperm can bind to the oolemma, they show the fusion defect, resulting that Dcst1 KO males become almost sterile and Dcst2 KO males become sterile. Similar to mice, zebrafish dcst1 KO males are subfertile and dcst2 and dcst1\/2 double KO males are sterile. Zebrafish dcst1\/2 KO sperm are motile and can approach the egg, but are defective in binding to the oolemma. Furthermore, we find that DCST1 and DCST2 interact with each other and are interdependent. These data demonstrate that DCST1\/2 are essential for male fertility in two vertebrate species, highlighting their crucial role as conserved factors in fertilization.","authors":"Noda, T., Blaha, A., Fujihara, Y., Gert, KR., Emori, C., Deneke, VE., Oura, S., Panser, K., Lu, Y., Berent, S., Kodani, M., Cabrera-Quio, LE., Pauli, A., Ikawa, M.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Commun Biol","volume":"5","issue":"1","page":"332","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.04.18.440256v1","articledate":"2022-04-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35433827","title":"A Rapid, Highly Sensitive and Open-Access SARS-CoV-2 Detection Assay for Laboratory and Home Testing.","abstract":"RT-qPCR-based diagnostic tests play important roles in combating virus-caused pandemics such as Covid-19. However, their dependence on sophisticated equipment and the associated costs often limits their widespread use. Loop-mediated isothermal amplification after reverse transcription (RT-LAMP) is an alternative nucleic acid detection method that overcomes these limitations. Here, we present a rapid, robust, and sensitive RT-LAMP-based SARS-CoV-2 detection assay. Our 40-min procedure bypasses the RNA isolation step, is insensitive to carryover contamination, and uses a colorimetric readout that enables robust SARS-CoV-2 detection from various sample types. Based on this assay, we have increased sensitivity and scalability by adding a nucleic acid enrichment step (Bead-LAMP), developed a version for home testing (HomeDip-LAMP), and identified open-source RT-LAMP enzymes that can be produced in any molecular biology laboratory. On a dedicated website, rtlamp.org (DOI: 10.5281\/zenodo.6033689), we provide detailed protocols and videos. Our optimized, general-purpose RT-LAMP assay is an important step toward population-scale SARS-CoV-2 testing.","authors":"Kellner, MJ., Ross, JJ., Schnabl, J., Dekens, MPS., Matl, M., Heinen, R., Grishkovskaya, I., Bauer, B., Stadlmann, J., Men\u00e9ndez-Arias, L., Straw, AD., Fritsche-Polanz, R., Traugott, M., Seitz, T., Zoufaly, A., F\u00f6dinger, M., Wenisch, C., Zuber, J., Pauli, A., Brennecke, J.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Front Mol Biosci","volume":"9","issue":null,"page":"801309","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.06.23.166397v2","articledate":"2022-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34634810","title":"SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks.","abstract":"Signaling networks represent the molecular mechanisms controlling a cell's response to various internal or external stimuli. Most currently available signaling databases contain only a part of the complex network of intertwining pathways, leaving out key interactions or processes. Hence, we have developed SignaLink3 (http:\/\/signalink.org\/), a value-added knowledge-base that provides manually curated data on signaling pathways and integrated data from several types of databases (interaction, regulation, localisation, disease, etc.) for humans, and three major animal model organisms. SignaLink3 contains over 400 000 newly added human protein-protein interactions resulting in a total of 700 000 interactions for Homo sapiens, making it one of the largest integrated signaling network resources. Next to H. sapiens, SignaLink3 is the only current signaling network resource to provide regulatory information for the model species Caenorhabditis elegans and Danio rerio, and the largest resource for Drosophila melanogaster. Compared to previous versions, we have integrated gene expression data as well as subcellular localization of the interactors, therefore uniquely allowing tissue-, or compartment-specific pathway interaction analysis to create more accurate models. Data is freely available for download in widely used formats, including CSV, PSI-MI TAB or SQL.","authors":"Csabai, L., Fazekas, D., Kadlecsik, T., Szalay-Bek\u0151, M., Boh\u00e1r, B., Madgwick, M., M\u00f3dos, D., \u00d6lbei, M., Gul, L., Sudhakar, P., Kubisch, J., Oyeyemi, OJ., Liska, O., Ari, E., Hotzi, B., Billes, VA., Moln\u00e1r, E., F\u00f6ldv\u00e1ri-Nagy, L., Cs\u00e1lyi, K., Demeter, A., P\u00e1pai, N., Koltai, M., Varga, M., Lenti, K., Farkas, IJ., T\u00fcrei, D., Csermely, P., Vellai, T., Korcsm\u00e1ros, T.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nucleic Acids Res","volume":"50","issue":"D1","page":"D701-D709","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35229715","title":"GFPT2\/GFAT2 and AMDHD2 act in tandem to control the hexosamine pathway.","abstract":"The hexosamine biosynthetic pathway (HBP) produces the essential metabolite UDP-GlcNAc and plays a key role in metabolism, health, and aging. The HBP is controlled by its rate-limiting enzyme glutamine fructose-6-phosphate amidotransferase (GFPT\/GFAT) that is directly inhibited by UDP-GlcNAc in a feedback loop. HBP regulation by GFPT is well studied but other HBP regulators have remained obscure. Elevated UDP-GlcNAc levels counteract the glycosylation toxin tunicamycin (TM), and thus we screened for TM resistance in haploid mouse embryonic stem cells (mESCs) using random chemical mutagenesis to determine alternative HBP regulation. We identified the N-acetylglucosamine deacetylase AMDHD2 that catalyzes a reverse reaction in the HBP and its loss strongly elevated UDP-GlcNAc. To better understand AMDHD2, we solved the crystal structure and found that loss-of-function (LOF) is caused by protein destabilization or interference with its catalytic activity. Finally, we show that mESCs express AMDHD2 together with GFPT2 instead of the more common paralog GFPT1. Compared with GFPT1, GFPT2 had a much lower sensitivity to UDP-GlcNAc inhibition, explaining how AMDHD2 LOF resulted in HBP activation. This HBP configuration in which AMDHD2 serves to balance GFPT2 activity was also observed in other mESCs and, consistently, the GFPT2:GFPT1 ratio decreased with differentiation of human embryonic stem cells. Taken together, our data reveal a critical function of AMDHD2 in limiting UDP-GlcNAc production in cells that use GFPT2 for metabolite entry into the HBP.","authors":"Kroef, V., Ruegenberg, S., Horn, M., Allmeroth, K., Ebert, L., Bozkus, S., Miethe, S., Elling, U., Schermer, B., Baumann, U., Denzel, MS.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Elife","volume":"11","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34331109","title":"The Trithorax group protein ASH1 requires a combination of BAH domain and AT hooks, but not the SET domain, for mitotic chromatin binding and survival.","abstract":"The Drosophila Trithorax group (TrxG) protein ASH1 remains associated with mitotic chromatin through mechanisms that are poorly understood. ASH1 dimethylates histone H3 at lysine 36 via its SET domain. Here, we identify domains of the TrxG protein ASH1 that are required for mitotic chromatin attachment in living Drosophila. Quantitative live imaging demonstrates that ASH1 requires AT hooks and the BAH domain but not the SET domain for full chromatin binding in metaphase, and that none of these domains are essential for interphase binding. Genetic experiments show that disruptions of the AT hooks and the BAH domain together, but not deletion of the SET domain alone, are lethal. Transcriptional profiling demonstrates that intact ASH1 AT hooks and the BAH domain are required to maintain expression levels of a specific set of genes, including several involved in cell identity and survival. This study identifies in vivo roles for specific ASH1 domains in mitotic binding, gene regulation, and survival that are distinct from its functions as a histone methyltransferase.","authors":"Steffen, PA., Altmutter, C., Dworschak, E., Junttila, S., Gyenesei, A., Zhu, X., Kockmann, T., Ringrose, L.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Chromosoma","volume":"130","issue":"2-3","page":"215-234","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-03-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34918496","title":"Multifocal Organoid Capturing of Colon Cancer Reveals Pervasive Intratumoral Heterogenous Drug Responses.","abstract":"Intratumor heterogeneity (ITH) stands as one of the main difficulties in the treatment of colorectal cancer (CRC) as it causes the development of resistant clones and leads to heterogeneous drug responses. Here, 12 sets of patient-derived organoids (PDOs) and cell lines (PDCs) isolated from multiple regions of single tumors from 12 patients, capturing ITH by multiregion sampling of individual tumors, are presented. Whole-exome sequencing and RNA sequencing of the 12 sets are performed. The PDOs and PDCs of the 12 sets are also analyzed with a clinically relevant 24-compound library to assess their drug responses. The results reveal unexpectedly widespread subregional heterogeneity among PDOs and PDCs isolated from a single tumor, which is manifested by genetic and transcriptional heterogeneity and strong variance in drug responses, while each PDO still recapitulates the major histologic, genomic, and transcriptomic characteristics of the primary tumor. The data suggest an imminent drawback of single biopsy-originated PDO-based clinical diagnosis in evaluating CRC patient responses. Instead, the results indicate the importance of targeting common somatic driver mutations positioned in the trunk of all tumor subregional clones in parallel with a comprehensive understanding of the molecular ITH of each tumor.","authors":"Kim, SC., Park, JW., Seo, HY., Kim, M., Park, JH., Kim, GH., Lee, JO., Shin, YK., Bae, JM., Koo, BK., Jeong, SY., Ku, JL.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Adv Sci (Weinh)","volume":"9","issue":"5","page":"e2103360","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35431774","title":"Could a Different View of Quiescence Help Us Understand How Neurogenesis Is Regulated?","abstract":"The majority of adult neural stem cells (aNSCs) are in a distinct metabolic state of reversible cell cycle exit also known as quiescence. The rate of aNSC activation determines the number of new neurons generated and directly influences the long-term maintenance of neurogenesis. Despite its relevance, it is still unclear how aNSC quiescence is regulated. Many factors contribute to this, like aNSC heterogeneity, the lack of reliable quiescence markers, the complexity of the neurogenic niches or the intricacy of the transcriptional and post-transcriptional mechanisms involved. In this perspective article I discuss possible solutions to these problems. But, first and foremost, I believe we require a model that goes beyond a simple transition toward activation. Instead, we must acknowledge the full complexity of aNSC states, which include not only activation but also differentiation and survival as behavioural outcomes. I propose a model where aNSCs dynamically transition through a cloud of highly interlinked cellular states driven by intrinsic and extrinsic cues. I also show how a new perspective enables us to integrate current results into a coherent framework leading to the formulation of new testable hypothesis. This model, like all others, is still far from perfect and will be reshaped by future findings. I believe that having a more complete view of aNSC transitions and embracing their complexity will bring us closer to understand how aNSC activity and neurogenesis are controlled throughout life.","authors":"Urb\u00e1n, N.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Front Neurosci","volume":"16","issue":null,"page":"878875","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35523142","title":"p57<sup>Kip2<\/sup> imposes the reserve stem cell state of gastric chief cells.","abstract":"Adult stem cells constantly react to local changes to ensure tissue homeostasis. In the main body of the stomach, chief cells produce digestive enzymes; however, upon injury, they undergo rapid proliferation for prompt tissue regeneration. Here, we identified p57<sup>Kip2<\/sup> (p57) as a molecular switch for the reserve stem cell state of chief cells in mice. During homeostasis, p57 is constantly expressed in chief cells but rapidly diminishes after injury, followed by robust proliferation. Both single-cell RNA sequencing and dox-induced lineage tracing confirmed the sequential loss of p57 and activation of proliferation within the chief cell lineage. In corpus organoids, p57 overexpression induced a long-term reserve stem cell state, accompanied by altered niche requirements and a mature chief cell\/secretory phenotype. Following the constitutive expression of p57 in\u00a0vivo, chief cells showed an impaired injury response. Thus, p57 is a gatekeeper that imposes the reserve stem cell state of chief cells in homeostasis.","authors":"Lee, JH., Kim, S., Han, S., Min, J., Caldwell, B., Bamford, AD., Rocha, ASB., Park, J., Lee, S., Wu, SS., Lee, H., Fink, J., Pilat-Carotta, S., Kim, J., Josserand, M., Szep-Bakonyi, R., An, Y., Ju, YS., Philpott, A., Simons, BD., Stange, DE., Choi, E., Koo, BK., Kim, JK.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cell Stem Cell","volume":"29","issue":"5","page":"826-839.e9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35478248","title":"Sister chromatid-sensitive Hi-C to map the conformation of replicated genomes.","abstract":"Chromosome conformation capture (Hi-C) techniques map the 3D organization of entire genomes. How sister chromatids fold in replicated chromosomes, however, cannot be determined with conventional Hi-C because of the identical DNA sequences of sister chromatids. Here, we present a protocol for sister chromatid-sensitive Hi-C (scsHi-C) that enables the distinction of DNA contacts within individual sister chromatids (cis sister contacts) from those between sister chromatids (trans sister contacts), thereby allowing investigation of the organization of replicated genomes. scsHi-C is based on live-cell labeling of nascent DNA by the synthetic nucleoside 4-thio-thymidine (4sT), which incorporates into a distinct DNA strand on each sister chromatid because of semi-conservative DNA replication. After purification of genomic DNA and in situ Hi-C library preparation, 4sT is chemically converted into 5-methyl-cytosine in the presence of OsO<sub>4<\/sub>\/NH<sub>4<\/sub>Cl to introduce T-to-C signature point mutations on 4sT-labeled DNA. The Hi-C library is then sequenced, and ligated fragments are assigned to sister chromatids on the basis of strand orientation and the presence of signature mutations. The ensemble of scsHi-C contacts thereby represents genome-wide contact probabilities within and across sister chromatids. scsHi-C can be completed in 2 weeks, has been successfully applied in HeLa cells and can potentially be established for any cell type that allows proper cell cycle synchronization and incorporation of sufficient amounts of 4sT. The genome-wide maps of replicated chromosomes detected by scsHi-C enable investigation of the molecular mechanisms shaping sister chromatid topologies and the relevance of sister chromatid conformation in crucial processes like DNA repair, mitotic chromosome formation and potentially other biological processes.","authors":"Mitter, M., Takacs, Z., K\u00f6cher, T., Micura, R., Langer, CCH., Gerlich, DW.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Nat Protoc","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35576477","title":"Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy.","abstract":"on Status=\\\"Publisher\\\" Owner=\\\"NLM\\\"><PMID Version=\\\"1\\\">35576477<\/PMID><DateRevised><Year>2022<\/Year><Month>05<\/Month><Day>16<\/Day><\/DateRevised><Article PubModel=\\\"Print-Electronic\\\"><Journal><ISSN IssnType=\\\"Electronic\\\">1755-3245<\/ISSN><JournalIssue CitedMedium=\\\"Internet\\\"><PubDate><Year>2022<\/Year><Month>May<\/Month><Day>16<\/Day><\/PubDate><\/JournalIssue><Title>Cardiovascular research<\/Title><ISOAbbreviation>Cardiovasc Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy.<\/ArticleTitle><ELocationID EIdType=\\\"pii\\\" ValidYN=\\\"Y\\\">cvac072<\/ELocationID><ELocationID EIdType=\\\"doi\\\" ValidYN=\\\"Y\\\">10.1093\/cvr\/cvac072<\/ELocationID><Abstract><AbstractText Label=\\\"AIMS\\\" NlmCategory=\\\"OBJECTIVE\\\">Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disorder that is characterized by progressive loss of myocardium that is replaced by fibro-fatty cells, arrhythmias, and sudden cardiac death. While myocardial degeneration and fibro-fatty replacement occur in specific locations, the underlying molecular changes remain poorly characterized. Here we aim to delineate local changes in gene expression to identify new genes and pathways that are relevant for specific remodelling processes occurring during ACM.","authors":"Boogerd, CJ., Lacraz, GPA., V\u00e9rtesy, \u00c1., van Kampen, SJ., Perini, I., de Ruiter, H., Versteeg, D., Brodehl, A., van der Kraak, P., Giacca, M., de Jonge, N., Junker, JP., van Oudenaarden, A., Vink, A., van Rooij, E.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Cardiovasc Res","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35561674","title":"A diabetic milieu increases ACE2 expression and cellular susceptibility to SARS-CoV-2 infections in human kidney organoids and patient cells.","abstract":"It is not well understood why diabetic individuals are more prone to develop severe COVID-19. To this, we here established a human kidney organoid model promoting early hallmarks of diabetic kidney disease development. Upon SARS-CoV-2 infection, diabetic-like kidney organoids exhibited higher viral loads compared with their control counterparts. Genetic deletion of the angiotensin-converting enzyme 2 (ACE2) in kidney organoids under control or diabetic-like conditions prevented viral detection. Moreover, cells isolated from kidney biopsies from diabetic patients exhibited altered mitochondrial respiration and enhanced glycolysis, resulting in higher SARS-CoV-2 infections compared with non-diabetic cells. Conversely, the exposure of patient cells to dichloroacetate (DCA), an inhibitor of aerobic glycolysis, resulted in reduced SARS-CoV-2 infections. Our results provide insights into the identification of diabetic-induced metabolic programming in the kidney as a critical event increasing SARS-CoV-2 infection susceptibility, opening the door to the identification of new interventions in COVID-19 pathogenesis targeting energy metabolism.","authors":"Garreta, E., Prado, P., Stanifer, ML., Monteil, V., Marco, A., Ullate-Agote, A., Moya-Rull, D., Vilas-Zornoza, A., Tarantino, C., Romero, JP., Jonsson, G., Oria, R., Leopoldi, A., Hagelkruys, A., Gallo, M., Gonz\u00e1lez, F., Domingo-Pedrol, P., Gavald\u00e0, A., Del Pozo, CH., Hasan Ali, O., Ventura-Aguiar, P., Campistol, JM., Prosper, F., Mirazimi, A., Boulant, S., Penninger, JM., Montserrat, N.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Cell Metab","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35585235","title":"MCM complexes are barriers that restrict cohesin-mediated loop extrusion.","abstract":"Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)<sup>1-3<\/sup>, which contribute to transcription, recombination and genomic stability<sup>4,5<\/sup>. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered<sup>6-12<\/sup>. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are 'active' barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.","authors":"Dequeker, BJH., Scherr, MJ., Brand\u00e3o, HB., Gassler, J., Powell, S., Gaspar, I., Flyamer, IM., Lalic, A., Tang, W., Stocsits, R., Davidson, IF., Peters, JM., Duderstadt, KE., Mirny, LA., Tachibana, K.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35687687","title":"Brain injury environment critically influences the connectivity of transplanted neurons.","abstract":"Cell transplantation is a promising approach for the reconstruction of neuronal circuits after brain damage. Transplanted neurons integrate with remarkable specificity into circuitries of the mouse cerebral cortex affected by neuronal ablation. However, it remains unclear how neurons perform in a local environment undergoing reactive gliosis, inflammation, macrophage infiltration, and scar formation, as in traumatic brain injury (TBI). To elucidate this, we transplanted cells from the embryonic mouse cerebral cortex into TBI-injured, inflamed-only, or intact cortex of adult mice. Brain-wide quantitative monosynaptic rabies virus (RABV) tracing unraveled graft inputs from correct regions across the brain in all conditions, with pronounced quantitative differences: scarce in intact and inflamed brain versus exuberant after TBI. In the latter, the initial overshoot is followed by pruning, with only a few input neurons persisting at 3 months. Proteomic profiling identifies candidate molecules for regulation of the synaptic yield, a pivotal parameter to tailor for functional restoration of neuronal circuits.","authors":"Grade, S., Thomas, J., Zarb, Y., Thorwirth, M., Conzelmann, KK., Hauck, SM., G\u00f6tz, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Sci Adv","volume":"8","issue":"23","page":"eabg9445","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35662409","title":"BacPROTACs mediate targeted protein degradation in bacteria.","abstract":"Hijacking the cellular protein degradation system offers unique opportunities for drug discovery, as exemplified by proteolysis-targeting chimeras. Despite their great promise for medical chemistry, so far, it has not been possible to reprogram the bacterial degradation machinery to interfere with microbial infections. Here, we develop small-molecule degraders, so-called BacPROTACs, that bind to the substrate receptor of the ClpC:ClpP protease, priming neo-substrates for degradation. In addition to their targeting function, BacPROTACs activate ClpC, transforming the resting unfoldase into its functional state. The induced higher-order oligomer was visualized by cryo-EM analysis, providing a structural snapshot of activated ClpC unfolding a protein substrate. Finally, drug susceptibility and degradation assays performed in mycobacteria demonstrate in\u00a0vivo activity of BacPROTACs, allowing selective targeting of endogenous proteins via fusion to an established degron. In addition to guiding antibiotic discovery, the BacPROTAC technology presents a versatile research tool enabling the inducible degradation of bacterial proteins.","authors":"Morreale, FE., Kleine, S., Leodolter, J., Junker, S., Hoi, DM., Ovchinnikov, S., Okun, A., Kley, J., Kurzbauer, R., Junk, L., Guha, S., Podlesainski, D., Kazmaier, U., Boehmelt, G., Weinstabl, H., Rumpel, K., Schmiedel, VM., Hartl, M., Haselbach, D., Meinhart, A., Kaiser, M., Clausen, T.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cell","volume":"185","issue":"13","page":"2338-2353.e18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.06.09.447781v1","articledate":"2022-06-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35697783","title":"Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction.","abstract":"Human naive pluripotent stem cells have unrestricted lineage potential. Underpinning this property, naive cells are thought to lack chromatin-based lineage barriers. However, this assumption has not been tested. Here we define the chromatin-associated proteome, histone post-translational modifications and transcriptome of human naive and primed pluripotent stem cells. Our integrated analysis reveals differences in the relative abundance and activities of distinct chromatin modules. We identify a strong enrichment of polycomb repressive complex 2 (PRC2)-associated H3K27me3 in the chromatin of naive pluripotent stem cells and H3K27me3 enrichment at promoters of lineage-determining genes, including trophoblast regulators. PRC2 activity acts as a chromatin barrier restricting the differentiation of naive cells towards the trophoblast lineage, whereas inhibition of PRC2 promotes trophoblast-fate induction and cavity formation in human blastoids. Together, our results establish that human naive pluripotent stem cells are not epigenetically unrestricted, but instead possess chromatin mechanisms that oppose the induction of alternative cell fates.","authors":"Zijlmans, DW., Talon, I., Verhelst, S., Bendall, A., Van Nerum, K., Javali, A., Malcolm, AA., van Knippenberg, SSFA., Biggins, L., To, SK., Janiszewski, A., Admiraal, D., Knops, R., Corthout, N., Balaton, BP., Georgolopoulos, G., Panda, A., Bhanu, NV., Collier, AJ., Fabian, C., Allsop, RN., Chappell, J., Pham, TXA., Oberhuemer, M., Ertekin, C., Vanheer, L., Athanasouli, P., Lluis, F., Deforce, D., Jansen, JH., Garcia, BA., Vermeulen, M., Rivron, N., Dhaenens, M., Marks, H., Rugg-Gunn, PJ., Pasque, V.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Cell Biol","volume":"24","issue":"6","page":"858-871","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35661927","title":"Contact-dependent signaling triggers tumor-like proliferation of CCM3 knockout endothelial cells in co-culture with wild-type cells.","abstract":"Cerebral cavernous malformations (CCM) are low-flow vascular lesions prone to cause severe hemorrhage-associated neurological complications. Pathogenic germline variants in CCM1, CCM2, or CCM3 can be identified in nearly 100% of CCM patients with a positive family history. In line with the concept that tumor-like mechanisms are involved in CCM formation and growth, we here demonstrate an abnormally increased proliferation rate of CCM3-deficient endothelial cells in co-culture with wild-type cells and in mosaic human iPSC-derived vascular organoids. The observation that NSC59984, an anticancer drug, blocked the abnormal proliferation of mutant endothelial cells further supports this intriguing concept. Fluorescence-activated cell sorting and RNA sequencing revealed that co-culture induces upregulation of proangiogenic chemokine genes in wild-type endothelial cells. Furthermore, genes known to be significantly downregulated in CCM3<sup>-\/-<\/sup> endothelial cell mono-cultures were upregulated back to normal levels in co-culture with wild-type cells. These results support the hypothesis that wild-type ECs facilitate the formation of a niche that promotes abnormal proliferation of mutant ECs. Thus, targeting the cancer-like features of CCMs is a promising new direction for drug development.","authors":"Rath, M., Schwefel, K., Malinverno, M., Skowronek, D., Leopoldi, A., Pilz, RA., Biedenweg, D., Bekeschus, S., Penninger, JM., Dejana, E., Felbor, U.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Cell Mol Life Sci","volume":"79","issue":"6","page":"340","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35650434","title":"Differential cofactor dependencies define distinct types of human enhancers.","abstract":"All multicellular organisms rely on differential gene transcription regulated by genomic enhancers, which function through cofactors that are recruited by transcription factors<sup>1,2<\/sup>. Emerging evidence suggests that not all cofactors are required at all enhancers<sup>3-5<\/sup>, yet whether these observations reflect more general principles or distinct types of enhancers remained unknown. Here we categorized human enhancers by their cofactor dependencies and show that these categories provide a framework to understand the sequence and chromatin diversity of enhancers and their roles in different gene-regulatory programmes. We quantified enhancer activities along the entire human genome using STARR-seq<sup>6<\/sup> in HCT116 cells, following the rapid degradation of eight cofactors. This analysis identified different types of enhancers with distinct cofactor requirements, sequences and chromatin properties. Some enhancers were insensitive to the depletion of the core Mediator subunit MED14 or the bromodomain protein BRD4 and regulated distinct transcriptional programmes. In particular, canonical Mediator<sup>7<\/sup> seemed dispensable for P53-responsive enhancers, and MED14-depleted cells induced endogenous P53 target genes. Similarly, BRD4 was not required for the transcription of genes that bear CCAAT boxes and a TATA box (including histone genes and LTR12 retrotransposons) or for the induction of heat-shock genes. This categorization of enhancers through cofactor dependencies reveals distinct enhancer types that can bypass broadly utilized cofactors, which illustrates how alternative ways to activate transcription separate gene expression programmes and provide a conceptual framework to understand enhancer function and regulatory specificity.","authors":"Neumayr, C., Haberle, V., Serebreni, L., Karner, K., Hendy, O., Boija, A., Henninger, JE., Li, CH., Stejskal, K., Lin, G., Bergauer, K., Pagani, M., Rath, M., Mechtler, K., Arnold, CD., Stark, A.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nature","volume":"606","issue":"7913","page":"406-413","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35631123","title":"Redirecting Imipramine against Bluetongue Virus Infection: Insights from a Genome-wide Haploid Screening Study.","abstract":"Bluetongue virus (BTV), an arbovirus of ruminants, is a causative agent of numerous epidemics around the world. Due to the emergence of novel reassortant BTV strains and new outbreaks, there is an unmet need for efficacious antivirals. In this study, we used an improved haploid screening platform to identify the relevant host factors for BTV infection. Our screening tool identified and validated the host factor Niemann-Pick C1 (NPC1), a lysosomal membrane protein that is involved in lysosomal cholesterol transport, as a critical factor in BTV infection. This finding prompted us to investigate the possibility of testing imipramine, an antidepressant drug known to inhibit NPC1 function by interfering with intracellular cholesterol trafficking. In this study, we evaluated the sensitivity of BTV to imipramine using in vitro assays. Our results demonstrate that imipramine pretreatment inhibited in vitro replication and progeny release of BTV-4, BTV-8, and BTV-16. Collectively, our findings highlight the importance of NPC1 for BTV infection and recommend the reprofiling of imipramine as a potential antiviral drug against BTV.","authors":"John, L., Vernersson, C., Kwon, H., Elling, U., Penninger, JM., Mirazimi, A.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Pathogens","volume":"11","issue":"5","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35605621","title":"Moyamoya disease: diagnosis and interventions.","abstract":"Moyamoya disease is a rare cause of stroke, radiologically characterised by progressive stenosis of the terminal portion of the internal carotid arteries and compensatory capillary collaterals. The discovery that RNF213, which encodes an unconventional E3 ubiquitin ligase, is the major susceptibility gene for moyamoya disease in people from east Asia has opened new avenues for investigation into the mechanisms of disease and potential treatment targets. The Arg4810Lys variant of the gene is most strongly associated with moyamoya disease, but the penetrance is lower than 1%, suggesting a synergistic relationship with additional environmental and genetic risk factors. White people carry less common non-Arg4810Lys variants of RNF213, which partly explains the lower prevalence of moyamoya disease in European countries and in the USA than in east Asian countries. Several monogenic moyamoya syndromes possess the radiological characteristics of moyamoya disease and have been associated with multiple genes and pathways involved in moyamoya angiopathy pathogenesis. Further clarification of the genetic and environmental factors that contribute to the emergence of moyamoya angiopathy could enable development of new treatment strategies for moyamoya disease.","authors":"Ihara, M., Yamamoto, Y., Hattori, Y., Liu, W., Kobayashi, H., Ishiyama, H., Yoshimoto, T., Miyawaki, S., Clausen, T., Bang, OY., Steinberg, GK., Tournier-Lasserve, E., Koizumi, A.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Lancet Neurol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35000205","title":"Targeted protein degradation: from small molecules to complex organelles-a Keystone Symposia report.","abstract":"Targeted protein degradation is critical for proper cellular function and development. Protein degradation pathways, such as the ubiquitin proteasomes system, autophagy, and endosome-lysosome pathway, must be tightly regulated to ensure proper elimination of misfolded and aggregated proteins and regulate changing protein levels during cellular differentiation, while ensuring that normal proteins remain unscathed. Protein degradation pathways have also garnered interest as a means to selectively eliminate target proteins that may be difficult to inhibit via other mechanisms. On June 7 and 8, 2021, several experts in protein degradation pathways met virtually for the Keystone eSymposium \"Targeting protein degradation: from small molecules to complex organelles.\" The event brought together researchers working in different protein degradation pathways in an effort to begin to develop a holistic, integrated vision of protein degradation that incorporates all the major pathways to understand how changes in them can lead to disease pathology and, alternatively, how they can be leveraged for novel therapeutics.","authors":"Cable, J., Weber-Ban, E., Clausen, T., Walters, KJ., Sharon, M., Finley, DJ., Gu, Y., Hanna, J., Feng, Y., Martens, S., Simonsen, A., Hansen, M., Zhang, H., Goodwin, JM., Reggio, A., Chang, C., Ge, L., Schulman, BA., Deshaies, RJ., Dikic, I., Harper, JW., Wertz, IE., Thom\u00e4, NH., S\u0142abicki, M., Frydman, J., Jakob, U., David, DC., Bennett, EJ., Bertozzi, CR., Sardana, R., Eapen, VV., Carra, S.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Ann N Y Acad Sci","volume":"1510","issue":"1","page":"79-99","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35293761","title":"Potent Bactericidal Antimycobacterials Targeting the Chaperone ClpC1 Based on the Depsipeptide Natural Products Ecumicin and Ohmyungsamycin A.","abstract":"Ohmyungsamycin A and ecumicin are structurally related cyclic depsipeptide natural products that possess activity against <i>Mycobacterium tuberculosis<\/i> (Mtb), the causative agent of tuberculosis (TB). Herein, we describe the design and synthesis of a library of analogues of these two natural products using an efficient solid-phase synthesis and late-stage macrolactamization strategy. Lead analogues possessed potent activity against Mtb in vitro (minimum inhibitory concentration 125-500 nM) and were shown to inhibit protein degradation by the mycobacterial ClpC1-ClpP1P2 protease with an associated enhancement of ClpC1 ATPase activity. The most promising analogue from the series exhibited rapid bactericidal killing activity against Mtb, capable of sterilizing cultures after 7 days, and retained bactericidal activity against hypoxic non-replicating Mtb. This natural product analogue was also active in an in vivo zebrafish model of infection.","authors":"Hawkins, PME., Hoi, DM., Cheung, CY., Wang, T., Quan, D., Sasi, VM., Liu, DY., Linington, RG., Jackson, CJ., Oehlers, SH., Cook, GM., Britton, WJ., Clausen, T., Payne, RJ.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"J Med Chem","volume":"65","issue":"6","page":"4893-4908","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35703121","title":"Nucleome programming is required for the foundation of totipotency in mammalian germline development.","abstract":"Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in\u2009vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia\/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia\/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia\/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres-an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.","authors":"Nagano, M., Hu, B., Yokobayashi, S., Yamamura, A., Umemura, F., Coradin, M., Ohta, H., Yabuta, Y., Ishikura, Y., Okamoto, I., Ikeda, H., Kawahira, N., Nosaka, Y., Shimizu, S., Kojima, Y., Mizuta, K., Kasahara, T., Imoto, Y., Meehan, K., Stocsits, R., Wutz, G., Hiraoka, Y., Murakawa, Y., Yamamoto, T., Tachibana, K., Peters, JM., Mirny, LA., Garcia, BA., Majewski, J., Saitou, M.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"EMBO J","volume":null,"issue":null,"page":"e110600","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35781796","title":"Clinical grade ACE2 as a universal agent to block SARS-CoV-2 variants.","abstract":"The recent emergence of multiple SARS-CoV-2 variants has caused considerable concern due to both reduced vaccine efficacy and escape from neutralizing antibody therapeutics. It is, therefore, paramount to develop therapeutic strategies that inhibit all known and future SARS-CoV-2 variants. Here, we report that all SARS-CoV-2 variants analyzed, including variants of concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron, exhibit enhanced binding affinity to clinical grade and phase 2 tested recombinant human soluble ACE2 (APN01). Importantly, soluble ACE2 neutralized infection of VeroE6 cells and human lung epithelial cells by all current VOC strains with markedly enhanced potency when compared to reference SARS-CoV-2 isolates. Effective inhibition of infections with SARS-CoV-2 variants was validated and confirmed in two independent laboratories. These data show that SARS-CoV-2 variants that have emerged around the world, including current VOC and several variants of interest, can be inhibited by soluble ACE2, providing proof of principle of a pan-SARS-CoV-2 therapeutic.","authors":"Monteil, V., Eaton, B., Postnikova, E., Murphy, M., Braunsfeld, B., Crozier, I., Kricek, F., Niederh\u00f6fer, J., Schwarzb\u00f6ck, A., Breid, H., Devignot, S., Klingstr\u00f6m, J., Th\u00e5lin, C., Kellner, MJ., Christ, W., Havervall, S., Mereiter, S., Knapp, S., Sanchez Jimenez, A., Bugajska-Schretter, A., Dohnal, A., Ruf, C., Gugenberger, R., Hagelkruys, A., Montserrat, N., Kozieradzki, I., Hasan Ali, O., Stadlmann, J., Holbrook, MR., Schmaljohn, C., Oostenbrink, C., Shoemaker, RH., Mirazimi, A., Wirnsberger, G., Penninger, JM.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"EMBO Mol Med","volume":null,"issue":null,"page":"e15230","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34426703","title":"Single-cell measurement of higher-order 3D genome organization with scSPRITE.","abstract":"Although three-dimensional (3D) genome organization is central to many aspects of nuclear function, it has been difficult to measure at the single-cell level. To address this, we developed 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE). scSPRITE uses split-and-pool barcoding to tag DNA fragments in the same nucleus and their 3D spatial arrangement. Because scSPRITE measures multiway DNA contacts, it generates higher-resolution maps within an individual cell than can be achieved by proximity ligation. We applied scSPRITE to thousands of mouse embryonic stem cells and detected known genome structures, including chromosome territories, active and inactive compartments, and topologically associating domains (TADs) as well as long-range inter-chromosomal structures organized around various nuclear bodies. We observe that these structures exhibit different levels of heterogeneity across the population, with TADs representing dynamic units of genome organization across cells. We expect that scSPRITE will be a critical tool for studying genome structure within heterogeneous populations.","authors":"Arrastia, MV., Jachowicz, JW., Ollikainen, N., Curtis, MS., Lai, C., Quinodoz, SA., Selck, DA., Ismagilov, RF., Guttman, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Biotechnol","volume":"40","issue":"1","page":"64-73","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35816490","title":"Development of an aerosol intervention for COVID-19 disease: Tolerability of soluble ACE2 (APN01) administered via nebulizer.","abstract":"As ACE2 is the critical SARS-CoV-2 receptor, we hypothesized that aerosol administration of clinical grade soluble human recombinant ACE2 (APN01) will neutralize SARS-CoV-2 in the airways, limit spread of infection in the lung, and mitigate lung damage caused by deregulated signaling in the renin-angiotensin (RAS) and Kinin pathways. Here, after demonstrating in vitro neutralization of SARS-CoV-2 by APN01, and after obtaining preliminary evidence of its tolerability and preventive efficacy in a mouse model, we pursued development of an aerosol formulation. As a prerequisite to a clinical trial, we evaluated both virus binding activity and enzymatic activity for cleavage of Ang II following aerosolization. We report successful aerosolization for APN01, retaining viral binding as well as catalytic RAS activity. Dose range-finding and IND-enabling repeat-dose aerosol toxicology testing were conducted in dogs. Twice daily aerosol administration for two weeks at the maximum feasible concentration revealed no notable toxicities. Based on these results, a Phase I clinical trial in healthy volunteers has now been initiated (NCT05065645), with subsequent Phase II testing planned for individuals with SARS-CoV-2 infection.","authors":"Shoemaker, RH., Panettieri, RA., Libutti, SK., Hochster, HS., Watts, NR., Wingfield, PT., Starkl, P., Pimenov, L., Gawish, R., Hladik, A., Knapp, S., Boring, D., White, JM., Lawrence, Q., Boone, J., Marshall, JD., Matthews, RL., Cholewa, BD., Richig, JW., Chen, BT., McCormick, DL., Gugensberger, R., H\u00f6ller, S., Penninger, JM., Wirnsberger, G.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"PLoS One","volume":"17","issue":"7","page":"e0271066","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35803948","title":"Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows.","abstract":"Cross-linking mass spectrometry has matured to a frequently used tool for the investigation of protein structures as well as interactome studies up to a system-wide level. The growing community generated a broad spectrum of applications, linker types, acquisition strategies and specialized data analysis tools, which makes it challenging to decide for an appropriate analysis workflow. Here, we report a large and flexible synthetic peptide library as reliable instrument to benchmark crosslink workflows. Additionally, we provide a tool, IMP-X-FDR, that calculates the real, experimentally validated, FDR, compares results across search engine platforms and analyses crosslink properties in an automated manner. We apply the library with 6 commonly used linker reagents and analyse the data with 6 established search engines. We thereby show that the correct algorithm and search setting choice is highly important to improve identification rate and reliability. We reach identification rates of up to ~70 % of the theoretical maximum (i.e. 700 unique lysine-lysine cross-links) while maintaining a real false-discovery-rate of &lt;3 % at cross-link level with high reproducibility, representatively showing that our test system delivers valuable and statistically solid results.","authors":"Matzinger, M., Vasiu, A., Madalinski, M., M\u00fcller, F., Stanek, F., Mechtler, K.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Nat Commun","volume":"13","issue":"1","page":"3975","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35803228","title":"Epiblast inducers capture mouse trophectoderm stem cells in\u00a0vitro and pattern blastoids for implantation in utero.","abstract":"The embryo instructs the allocation of cell states to spatially regulate functions. In the blastocyst, patterning of trophoblast (TR) cells ensures successful implantation and placental development. Here, we defined an optimal set of molecules secreted by the epiblast (inducers) that captures in\u00a0vitro stable, highly self-renewing mouse trophectoderm stem cells (TESCs) resembling the blastocyst stage. When exposed to suboptimal inducers, these stem cells fluctuate to form interconvertible subpopulations with reduced self-renewal and facilitated differentiation, resembling peri-implantation cells, known as TR stem cells (TSCs). TESCs have enhanced capacity to form blastoids that implant more efficiently in utero due to inducers maintaining not only local TR proliferation and self-renewal, but also WNT6\/7B secretion that stimulates uterine decidualization. Overall, the epiblast maintains sustained growth and decidualization potential of abutting TR cells, while, as known, distancing imposed by the blastocyst cavity differentiates TR cells for uterus adhesion, thus patterning the essential functions of implantation.","authors":"Seong, J., Frias-Aldeguer, J., Holzmann, V., Kagawa, H., Sestini, G., Heidari Khoei, H., Scholte Op Reimer, Y., Kip, M., Pradhan, SJ., Verwegen, L., Vivi\u00e9, J., Li, L., Alemany, A., Korving, J., Darmis, F., van Oudenaarden, A., Ten Berge, D., Geijsen, N., Rivron, NC.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cell Stem Cell","volume":"29","issue":"7","page":"1102-1118.e8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35301492","title":"Xist spatially amplifies SHARP\/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome.","abstract":"Although thousands of long non-coding RNAs (lncRNAs) are encoded in mammalian genomes, their mechanisms of action are poorly understood, in part because they are often expressed at lower levels than their proposed targets. One such lncRNA is Xist, which mediates chromosome-wide gene silencing on one of the two X chromosomes (X) to achieve gene expression balance between males and females. How a limited number of Xist molecules can mediate robust silencing of a much larger number of target genes while maintaining specificity exclusively to genes on the X within each cell is not well understood. Here, we show that Xist drives non-stoichiometric recruitment of the essential silencing protein SHARP (also known as SPEN) to amplify its abundance across the inactive X, including at regions not directly occupied by Xist. This amplification is achieved through concentration-dependent homotypic assemblies of SHARP on the X and is required for chromosome-wide silencing. Expression of Xist at higher levels leads to increased localization at autosomal regions, demonstrating that low levels of Xist are critical for ensuring its specificity to the X. We show that Xist (through SHARP) acts to suppress production of its own RNA which may act to constrain overall RNA levels and restrict its ability to spread beyond the X. Together, our results demonstrate a spatial amplification mechanism that allows Xist to achieve two essential but countervailing regulatory objectives: chromosome-wide gene silencing and specificity to the X. This suggests a more general mechanism by which other low-abundance lncRNAs could balance specificity to, and robust control of, their regulatory targets.","authors":"Jachowicz, JW., Strehle, M., Banerjee, AK., Blanco, MR., Thai, J., Guttman, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Struct Mol Biol","volume":"29","issue":"3","page":"239-249","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35013617","title":"SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding.","abstract":"A fundamental question in gene regulation is how cell-type-specific gene expression is influenced by the packaging of DNA within the nucleus of each cell. We recently developed Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which enables mapping of higher-order interactions within the nucleus. SPRITE works by cross-linking interacting DNA, RNA and protein molecules and then mapping DNA-DNA spatial arrangements through an iterative split-and-pool barcoding method. All DNA molecules within a cross-linked complex are barcoded by repeatedly splitting complexes across a 96-well plate, ligating molecules with a unique tag sequence, and pooling all complexes into a single well before repeating the tagging. Because all molecules in a cross-linked complex are covalently attached, they will sort together throughout each round of split-and-pool and will obtain the same series of SPRITE tags, which we refer to as a barcode. The DNA fragments and their associated barcodes are sequenced, and all reads sharing identical barcodes are matched to reconstruct interactions. SPRITE accurately maps pairwise DNA interactions within the nucleus and measures higher-order spatial contacts occurring among up to thousands of simultaneously interacting molecules. Here, we provide a detailed protocol for the experimental steps of SPRITE, including a video ( https:\/\/youtu.be\/6SdWkBxQGlg ). Furthermore, we provide an automated computational pipeline available on GitHub that allows experimenters to seamlessly generate SPRITE interaction matrices starting with raw fastq files. The protocol takes ~5 d from cell cross-linking to high-throughput sequencing for the experimental steps and 1 d for data processing.","authors":"Quinodoz, SA., Bhat, P., Chovanec, P., Jachowicz, JW., Ollikainen, N., Detmar, E., Soehalim, E., Guttman, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Protoc","volume":"17","issue":"1","page":"36-75","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34739832","title":"RNA promotes the formation of spatial compartments in the nucleus.","abstract":"RNA, DNA, and protein molecules are highly organized within three-dimensional (3D) structures in the nucleus. Although RNA has been proposed to play a role in nuclear organization, exploring this has been challenging because existing methods cannot measure higher-order RNA and DNA contacts within 3D structures. To address this, we developed RNA &amp; DNA SPRITE (RD-SPRITE) to comprehensively map the spatial organization of RNA and DNA. These maps reveal higher-order RNA-chromatin structures associated with three major classes of nuclear function: RNA processing, heterochromatin assembly, and gene regulation. These data demonstrate that hundreds of ncRNAs form high-concentration territories throughout the nucleus, that specific RNAs are required to recruit various regulators into these territories, and that these RNAs can shape long-range DNA contacts, heterochromatin assembly, and gene expression. These results demonstrate a mechanism where RNAs form high-concentration territories, bind to diffusible regulators, and guide them into compartments to regulate essential nuclear functions.","authors":"Quinodoz, SA., Jachowicz, JW., Bhat, P., Ollikainen, N., Banerjee, AK., Goronzy, IN., Blanco, MR., Chovanec, P., Chow, A., Markaki, Y., Thai, J., Plath, K., Guttman, M.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell","volume":"184","issue":"23","page":"5775-5790.e30","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33846535","title":"Deletion of LBR N-terminal domains recapitulates Pelger-Huet anomaly phenotypes in mouse without disrupting X chromosome inactivation.","abstract":"Mutations in the gene encoding Lamin B receptor (LBR), a nuclear-membrane protein with sterol reductase activity, have been linked to rare human disorders. Phenotypes range from a benign blood disorder, such as Pelger-Huet anomaly (PHA), affecting the morphology and chromatin organization\u00a0of white blood cells, to embryonic lethality as for Greenberg dysplasia (GRBGD). Existing PHA mouse models do not fully recapitulate the human phenotypes, hindering efforts to understand the molecular etiology of this disorder. Here we show, using CRISPR\/Cas-9 gene editing technology, that a 236bp N-terminal deletion in the mouse Lbr gene, generating a protein missing\u00a0the N-terminal domains of LBR, presents a superior model of human PHA. Further, we address recent reports of a link between Lbr and defects in X chromosome inactivation (XCI) and show that our mouse mutant displays minor X chromosome inactivation defects that do not lead to any overt phenotypes in vivo. We suggest that our N-terminal deletion model provides a valuable pre-clinical tool to the research community and will aid in further understanding the etiology of PHA and the diverse functions of LBR.","authors":"Young, AN., Perlas, E., Ruiz-Blanes, N., Hierholzer, A., Pomella, N., Martin-Martin, B., Liverziani, A., Jachowicz, JW., Giannakouros, T., Cerase, A.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Commun Biol","volume":"4","issue":"1","page":"478","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28846101","title":"LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo.","abstract":"After fertilization, to initiate development, gametes are reprogramed to become totipotent. Approximately half of the mammalian genome consists of repetitive elements, including retrotransposons, some of which are transcribed after fertilization. Retrotransposon activation is generally assumed to be a side effect of the extensive chromatin remodeling underlying the epigenetic reprogramming of gametes. Here, we used a targeted epigenomic approach to address whether specific retrotransposon families play a direct role in chromatin organization and developmental progression. We demonstrate that premature silencing of LINE-1 elements decreases chromatin accessibility, whereas prolonged activation prevents the gradual chromatin compaction that occurs naturally in developmental progression. Preventing LINE-1 activation and interfering with its silencing decreases developmental rates independently of the coding nature of the LINE-1 transcript, thus suggesting that LINE-1 functions primarily at the chromatin level. Our data suggest that activation of LINE-1 regulates global chromatin accessibility at the beginning of development and indicate that retrotransposon activation is integral to the developmental program.","authors":"Jachowicz, JW., Bing, X., Pontabry, J., Bo\u0161kovi\u0107, A., Rando, OJ., Torres-Padilla, ME.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nat Genet","volume":"49","issue":"10","page":"1502-1510","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-10-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25975894","title":"LINEs in mice: features, families, and potential roles in early development.","abstract":"Approximately half of the mammalian genome is composed of repetitive elements, including LINE-1 (L1) elements. Because of their potential ability to transpose and integrate into other regions of the genome, their activation represents a threat to genome stability. Molecular pathways have emerged to tightly regulate and repress their transcriptional activity, including DNA methylation, histone modifications, and RNA pathways. It has become evident that Line-L1 elements are evolutionary diverse and dedicated repression pathways have been recently uncovered that discriminate between evolutionary old and young elements, with RNA-directed silencing mechanisms playing a prominent role. During periods of epigenetic reprogramming in development, specific classes of repetitive elements are upregulated, presumably due to the loss of most heterochromatic marks in this process. While we have learnt a lot on the molecular mechanisms that regulate Line-L1 expression over the last years, it is still unclear whether reactivation of Line-L1 after fertilization serves a functional purpose or it is a simple side effect of reprogramming.","authors":"Jachowicz, JW., Torres-Padilla, ME.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Chromosoma","volume":"125","issue":"1","page":"29-39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34759314","title":"Self-guarding of MORC3 enables virulence factor-triggered immunity.","abstract":"Pathogens use virulence factors to inhibit the immune system<sup>1<\/sup>. The guard hypothesis<sup>2,3<\/sup> postulates that hosts monitor (or 'guard') critical innate immune pathways such that their disruption by virulence factors provokes a secondary immune response<sup>1<\/sup>. Here we describe a 'self-guarded' immune pathway in human monocytes, in which guarding and guarded functions are combined in one protein. We find that this pathway is triggered by ICP0, a key virulence factor of herpes simplex virus type 1, resulting in robust induction of anti-viral type I interferon (IFN). Notably, induction of IFN by ICP0 is independent of canonical immune pathways and the IRF3 and IRF7 transcription factors. A CRISPR screen identified the ICP0 target MORC3<sup>4<\/sup> as an essential negative regulator of IFN. Loss of MORC3 recapitulates the IRF3- and IRF7-independent IFN response induced by ICP0. Mechanistically, ICP0 degrades MORC3, which leads to de-repression of a MORC3-regulated DNA element (MRE) adjacent to the IFNB1 locus. The MRE is required in cis for IFNB1 induction by the MORC3 pathway, but is not required for canonical IFN-inducing pathways. As well as repressing the MRE to regulate IFNB1, MORC3 is also a direct restriction factor of HSV-1<sup>5<\/sup>. Our results thus suggest a model in which the primary anti-viral function of MORC3 is self-guarded by its secondary IFN-repressing function-thus, a virus that degrades MORC3 to avoid its primary anti-viral function will unleash the secondary anti-viral IFN response.","authors":"Gaidt, MM., Morrow, A., Fairgrieve, MR., Karr, JP., Yosef, N., Vance, RE.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature","volume":"600","issue":"7887","page":"138-142","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30591564","title":"Human RIPK1 deficiency causes combined immunodeficiency and inflammatory bowel diseases.","abstract":"Receptor-interacting serine\/threonine-protein kinase 1 (RIPK1) is a critical regulator of cell death and inflammation, but its relevance for human disease pathogenesis remains elusive. Studies of monogenic disorders might provide critical insights into disease mechanisms and therapeutic targeting of RIPK1 for common diseases. Here, we report on eight patients from six unrelated pedigrees with biallelic loss-of-function mutations in <i>RIPK1<\/i> presenting with primary immunodeficiency and\/or intestinal inflammation. Mutations in <i>RIPK1<\/i> were associated with reduced NF-\u03baB activity, defective differentiation of T and B cells, increased inflammasome activity, and impaired response to TNFR1-mediated cell death in intestinal epithelial cells. The characterization of RIPK1-deficient patients highlights the essential role of RIPK1 in controlling human immune and intestinal homeostasis, and might have critical implications for therapies targeting RIPK1.","authors":"Li, Y., F\u00fchrer, M., Bahrami, E., Socha, P., Klaudel-Dreszler, M., Bouzidi, A., Liu, Y., Lehle, AS., Magg, T., Hollizeck, S., Rohlfs, M., Conca, R., Field, M., Warner, N., Mordechai, S., Shteyer, E., Turner, D., Boukari, R., Belbouab, R., Walz, C., Gaidt, MM., Hornung, V., Baumann, B., Pannicke, U., Al Idrissi, E., Ali Alghamdi, H., Sepulveda, FE., Gil, M., de Saint Basile, G., H\u00f6nig, M., Koletzko, S., Muise, AM., Snapper, SB., Schwarz, K., Klein, C., Kotlarz, D.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Proc Natl Acad Sci U S A","volume":"116","issue":"3","page":"970-975","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-03-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"27037191","title":"Human Monocytes Engage an Alternative Inflammasome Pathway.","abstract":"Interleukin-1\u03b2 (IL-1\u03b2) is a cytokine whose bioactivity is controlled by activation of the inflammasome. However, in response to lipopolysaccharide, human monocytes secrete IL-1\u03b2 independently of classical inflammasome stimuli. Here, we report that this constituted a species-specific response that is not observed in the murine system. Indeed, in human monocytes, lipopolysaccharide triggered an \"alternative inflammasome\" that relied on NLRP3-ASC-caspase-1 signaling, yet was devoid of any classical inflammasome characteristics including pyroptosome formation, pyroptosis induction, and K(+) efflux dependency. Genetic dissection of the underlying signaling pathway in a monocyte transdifferentiation system revealed that alternative inflammasome activation was propagated by TLR4-TRIF-RIPK1-FADD-CASP8 signaling upstream of NLRP3. Importantly, involvement of this signaling cascade was limited to alternative inflammasome activation and did not extend to classical NLRP3 activation. Because alternative inflammasome activation embraces both sensitivity and promiscuity of TLR4, we propose a pivotal role for this signaling cascade in TLR4-driven, IL-1\u03b2-mediated immune responses and immunopathology in humans.","authors":"Gaidt, MM., Ebert, TS., Chauhan, D., Schmidt, T., Schmid-Burgk, JL., Rapino, F., Robertson, AA., Cooper, MA., Graf, T., Hornung, V.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Immunity","volume":"44","issue":"4","page":"833-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-09-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29033128","title":"The DNA Inflammasome in Human Myeloid Cells Is Initiated by a STING-Cell Death Program Upstream of NLRP3.","abstract":"Detection of cytosolic DNA constitutes a central event in the context of numerous infectious and sterile inflammatory conditions. Recent studies have uncovered a bipartite mode of cytosolic DNA recognition, in which the cGAS-STING axis triggers antiviral immunity, whereas AIM2 triggers inflammasome activation. Here, we show that AIM2 is dispensable for DNA-mediated inflammasome activation in human myeloid cells. Instead, detection of cytosolic DNA by the cGAS-STING axis induces a cell death program initiating potassium efflux upstream of NLRP3. Forward genetics identified regulators of lysosomal trafficking to modulate this cell death program, and subsequent studies revealed that activated STING traffics to the lysosome, where it triggers membrane permeabilization and thus lysosomal cell death (LCD). Importantly, the cGAS-STING-NLRP3 pathway constitutes the default inflammasome response during viral and bacterial infections in human myeloid cells. We conclude that targeting the cGAS-STING-LCD-NLRP3 pathway will ameliorate pathology in inflammatory conditions that are associated with cytosolic DNA sensing.","authors":"Gaidt, MM., Ebert, TS., Chauhan, D., Ramshorn, K., Pinci, F., Zuber, S., O'Duill, F., Schmid-Burgk, JL., Hoss, F., Buhmann, R., Wittmann, G., Latz, E., Subklewe, M., Hornung, V.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Cell","volume":"171","issue":"5","page":"1110-1124.e18","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-12-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"33082141","title":"C-tag TNF: a reporter system to study TNF shedding.","abstract":"TNF is a highly pro-inflammatory cytokine that contributes not only to the regulation of immune responses but also to the development of severe inflammatory diseases. TNF is synthesized as a transmembrane protein, which is further matured via proteolytic cleavage by metalloproteases such as ADAM17, a process known as shedding. At present, TNF is mainly detected by measuring the precursor or the mature cytokine of bulk cell populations by techniques such as ELISA or immunoblotting. However, these methods do not provide information on the exact timing and extent of TNF cleavage at single-cell resolution and they do not allow the live visualization of shedding events. Here, we generated C-tag TNF as a genetically encoded reporter to study TNF shedding at the single-cell level. The functionality of the C-tag TNF reporter is based on the exposure of a cryptic epitope on the C terminus of the transmembrane portion of pro-TNF on cleavage. In both denatured and nondenatured samples, this epitope can be detected by a nanobody in a highly sensitive and specific manner only upon TNF shedding. As such, C-tag TNF can successfully be used for the detection of TNF cleavage in flow cytometry and live-cell imaging applications. We furthermore demonstrate its applicability in a forward genetic screen geared toward the identification of genetic regulators of TNF maturation. In summary, the C-tag TNF reporter can be employed to gain novel insights into the complex regulation of ADAM-dependent TNF shedding.","authors":"Pinci, F., Gaidt, MM., Jung, C., Kuut, G., Jackson, MA., Bauernfried, S., Hornung, V.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"J Biol Chem","volume":"295","issue":"52","page":"18065-18075","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31778653","title":"TLR8 Is a Sensor of RNase T2 Degradation Products.","abstract":"TLR8 is among the highest-expressed pattern-recognition receptors in the human myeloid compartment, yet its mode of action is poorly understood. TLR8 engages two distinct ligand binding sites to sense RNA degradation products, although it remains unclear how these ligands are formed in cellulo in the context of complex RNA molecule sensing. Here, we identified the lysosomal endoribonuclease RNase T2 as a\u00a0non-redundant upstream component of TLR8-dependent RNA recognition. RNase T2 activity is required for rendering complex single-stranded, exogenous RNA molecules detectable for TLR8. This is due to RNase T2's preferential cleavage of single-stranded RNA molecules between purine and uridine residues, which critically contributes to the supply of catabolic uridine and the generation of purine-2',3'-cyclophosphate-terminated oligoribonucleotides. Thus-generated molecules constitute agonistic ligands for the first and second binding pocket of TLR8. Together, these results establish the identity and origin of the RNA-derived molecular pattern sensed by TLR8.","authors":"Greulich, W., Wagner, M., Gaidt, MM., Stafford, C., Cheng, Y., Linder, A., Carell, T., Hornung, V.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Cell","volume":"179","issue":"6","page":"1264-1275.e13","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-05-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34151776","title":"Role of the transcriptional regulator SP140 in resistance to bacterial infections via repression of type I interferons.","abstract":"Type I interferons (IFNs) are essential for anti-viral immunity, but often impair protective immune responses during bacterial infections. An important question is how type I IFNs are strongly induced during viral infections, and yet are appropriately restrained during bacterial infections. The <i>Super susceptibility to tuberculosis 1<\/i> (<i>Sst1<\/i>) locus in mice confers resistance to diverse bacterial infections. Here we provide evidence that <i>Sp140<\/i> is a gene encoded within the <i>Sst1<\/i> locus that represses type I IFN transcription during bacterial infections. We generated <i>Sp140<\/i><sup>-\/-<\/sup> mice and found that they are susceptible to infection by <i>Legionella pneumophila<\/i> and <i>Mycobacterium tuberculosis<\/i>. Susceptibility of <i>Sp140<\/i><sup>-\/-<\/sup> mice to bacterial infection was rescued by crosses to mice lacking the type I IFN receptor (<i>Ifnar<\/i><sup>-\/-<\/sup>). Our results implicate <i>Sp140<\/i> as an important negative regulator of type I IFNs that is essential for resistance to bacterial infections.","authors":"Ji, DX., Witt, KC., Kotov, DI., Margolis, SR., Louie, A., Chev\u00e9e, V., Chen, KJ., Gaidt, MM., Dhaliwal, HS., Lee, AY., Nishimura, SL., Zamboni, DS., Kramnik, I., Portnoy, DA., Darwin, KH., Vance, RE.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Elife","volume":"10","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30485805","title":"BAX\/BAK-Induced Apoptosis Results in Caspase-8-Dependent IL-1\u03b2 Maturation in Macrophages.","abstract":"IL-1\u03b2 is a cytokine of pivotal importance to the orchestration of inflammatory responses. Synthesized as an inactive pro-cytokine, IL-1\u03b2 requires proteolytic maturation to gain biological activity. Here, we identify intrinsic apoptosis as a non-canonical trigger of IL-1\u03b2 maturation. Guided by the discovery of the immunomodulatory activity of vioprolides, cyclic peptides isolated from myxobacteria, we observe IL-1\u03b2 maturation independent of canonical inflammasome pathways, yet dependent on intrinsic apoptosis. Mechanistically, vioprolides inhibit MCL-1 and BCL2, which in turn triggers BAX\/BAK-dependent mitochondrial outer membrane permeabilization (MOMP). Induction of MOMP results in the release of pro-apoptotic factors initiating intrinsic apoptosis, as well as the depletion of IAPs (inhibitors of apoptosis proteins). IAP depletion, in turn, operates upstream of ripoptosome complex formation, subsequently resulting in caspase-8-dependent IL-1\u03b2 maturation. These results establish the ripoptosome\/caspase-8 complex as a pro-inflammatory checkpoint that senses the perturbation of mitochondrial integrity.","authors":"Chauhan, D., Bartok, E., Gaidt, MM., Bock, FJ., Herrmann, J., Seeger, JM., Broz, P., Beckmann, R., Kashkar, H., Tait, SWG., M\u00fcller, R., Hornung, V.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell Rep","volume":"25","issue":"9","page":"2354-2368.e5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-12-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29177855","title":"Modeling Primary Human Monocytes with the Trans-Differentiation Cell Line BLaER1.","abstract":"Monocytes and macrophages play a pivotal role in the induction and shaping of immune responses. Expressing a broad array of pattern recognition receptors (PRRs), monocytes and macrophages constitute an integral component of the innate branch of the immune system. Traditionally, the majority of innate immune sensing and signaling pathways have been studied in macrophages of the murine system. This is largely due to the fact that genetic loss-of-function studies are amenable in this species. On the other hand, human cell lines of the monocyte-macrophage cell lineage have been widely used to study myeloid cells in vitro. However, commonly utilized models (e.g., THP-1 cells) only mimic a limited spectrum of the immunobiology of primary human myeloid cells. Recently, we have explored the possibility to fill this gap with a human trans-differentiation cell culture system, in which lineage conversion from malignant B-lineage cells to monocytes\/macrophages is caused by the inducible nuclear translocation of a C\/EBP\u03b1 transgene, BLaER1 cells. Using this model, we were able to characterize a novel inflammasome signaling entity that could not have been uncovered in the murine system or THP-1 cells. Here, we describe the handling of BLaER1 cells, providing a detailed protocol for their induced trans-differentiation. We also provide data to demonstrate the applicability of the BLaER1 monocyte\/macrophage system to study phagocytosis and various PRR cascades in human cells.","authors":"Gaidt, MM., Rapino, F., Graf, T., Hornung, V.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Methods Mol Biol","volume":"1714","issue":null,"page":"57-66","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"29290987","title":"ICG-001 affects DRP1 activity and ER stress correlative with its anti-proliferative effect.","abstract":"Mitochondria form a highly dynamic network driven by opposing scission and fusion events. DRP1 is an essential modulator of mitochondrial fission and dynamics within mammalian cells. Its fission activity is regulated by posttranslational modifications such as activating phosphorylation at serine 616. DRP1 activity has recently been implicated as being dysregulated in numerous human disorders such as cancer and neurodegenerative diseases. Here we describe the development of a cell-based screening assay to detect DRP1 activation. We utilized this to undertake focused compound library screening and identified potent modulators that affected DRP1 activity including ICG-001, which is described as WNT\/\u03b2-catenin signaling inhibitor. Our findings elucidate novel details about ICG-001's mechanism of action (MOA) in mediating anti-proliferative activity. We show ICG-001 both inhibits mitochondrial fission and activates an early endoplasmic reticulum (ER) stress response to induce cell death in susceptible colorectal cancer cell lines.","authors":"Zinecker, H., Ouaret, D., Ebner, D., Gaidt, MM., Taylor, S., Aulicino, A., Jagielowicz, M., Hornung, V., Simmons, A.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Oncotarget","volume":"8","issue":"63","page":"106764-106777","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"26174085","title":"Caspase-4 mediates non-canonical activation of the NLRP3 inflammasome in human myeloid cells.","abstract":"Inflammasome activation culminates in activation of caspase-1, which leads to the maturation and subsequent release of cytokines of the interleukin 1 (IL-1) family and results in a particular form of cell death known as pyroptosis. In addition, in the murine system, a so-called non-canonical inflammasome involving caspase-11 has been described that directly responds to cytosolic LPS. Here, we show that the human monocytic cell line THP1 activates the inflammasome in response to cytosolic LPS in a TLR4-independent fashion. This response is mediated by caspase-4 and accompanied by caspase-1 activation, pyroptosis, and IL-1\u03b2 maturation. In addition to caspase-4, efficient IL-1\u03b2 conversion upon intracellular LPS delivery relies on potassium efflux, NLRP3, ASC, and caspase-1, indicating that although caspase-4 activation alone is sufficient to induce pyroptosis, this process depends on the NLRP3 inflammasome activation to drive IL-1\u03b2 maturation. Altogether, this study provides evidence for the presence of a non-canonical inflammasome in humans and its dependence on caspase-4.","authors":"Schmid-Burgk, JL., Gaidt, MM., Schmidt, T., Ebert, TS., Bartok, E., Hornung, V.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Eur J Immunol","volume":"45","issue":"10","page":"2911-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-01-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28902841","title":"cGAS senses long and HMGB\/TFAM-bound U-turn DNA by forming protein-DNA ladders.","abstract":"Cytosolic DNA arising from intracellular pathogens triggers a powerful innate immune response. It is sensed by cyclic GMP-AMP synthase (cGAS), which elicits the production of type I interferons by generating the second messenger 2'3'-cyclic-GMP-AMP (cGAMP). Endogenous nuclear or mitochondrial DNA can also be sensed by cGAS under certain conditions, resulting in sterile inflammation. The cGAS dimer binds two DNA ligands shorter than 20 base pairs side-by-side, but 20-base-pair DNA fails to activate cGAS in vivo and is a poor activator in vitro. Here we show that cGAS is activated in a strongly DNA length-dependent manner both in vitro and in human cells. We also show that cGAS dimers form ladder-like networks with DNA, leading to cooperative sensing of DNA length: assembly of the pioneering cGAS dimer between two DNA molecules is ineffective; but, once formed, it prearranges the flanking DNA to promote binding of subsequent cGAS dimers. Remarkably, bacterial and mitochondrial nucleoid proteins HU and mitochondrial transcription factor A (TFAM), as well as high-mobility group box 1 protein (HMGB1), can strongly stimulate long DNA sensing by cGAS. U-turns and bends in DNA induced by these proteins pre-structure DNA to nucleate cGAS dimers. Our results suggest a nucleation-cooperativity-based mechanism for sensitive detection of mitochondrial DNA and pathogen genomes, and identify HMGB\/TFAM proteins as DNA-structuring host factors. They provide an explanation for the peculiar cGAS dimer structure and suggest that cGAS preferentially binds incomplete nucleoid-like structures or bent DNA.","authors":"Andreeva, L., Hiller, B., Kostrewa, D., L\u00e4ssig, C., de Oliveira Mann, CC., Jan Drexler, D., Maiser, A., Gaidt, M., Leonhardt, H., Hornung, V., Hopfner, KP.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"549","issue":"7672","page":"394-398","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-02-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"25425575","title":"Cytosolic RNA:DNA hybrids activate the cGAS-STING axis.","abstract":"Intracellular recognition of non-self and also self-nucleic acids can result in the initiation of potent pro-inflammatory and antiviral cytokine responses. Most recently, cGAS was shown to be critical for the recognition of cytoplasmic dsDNA. Binding of dsDNA to cGAS results in the synthesis of cGAMP(2'-5'), which then binds to the endoplasmic reticulum resident protein STING. This initiates a signaling cascade that triggers the induction of an antiviral immune response. While most studies on intracellular nucleic acids have focused on dsRNA or dsDNA, it has remained unexplored whether cytosolic RNA:DNA hybrids are also sensed by the innate immune system. Studying synthetic RNA:DNA hybrids, we indeed observed a strong type I interferon response upon cytosolic delivery of this class of molecule. Studies in THP-1 knockout cells revealed that the recognition of RNA:DNA hybrids is completely attributable to the cGAS-STING pathway. Moreover, in vitro studies showed that recombinant cGAS produced cGAMP upon RNA:DNA hybrid recognition. Altogether, our results introduce RNA:DNA hybrids as a novel class of intracellular PAMP molecules and describe an alternative cGAS ligand next to dsDNA.","authors":"Mankan, AK., Schmidt, T., Chauhan, D., Goldeck, M., H\u00f6ning, K., Gaidt, M., Kubarenko, AV., Andreeva, L., Hopfner, KP., Hornung, V.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"EMBO J","volume":"33","issue":"24","page":"2937-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-07-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"22629382","title":"Lack of PPAR\u03b3 in myeloid cells confers resistance to Listeria monocytogenes infection.","abstract":"The peroxisomal proliferator-activated receptor \u03b3 (PPAR\u03b3) is a nuclear receptor that controls inflammation and immunity. Innate immune defense against bacterial infection appears to be compromised by PPAR\u03b3. The relevance of PPAR\u03b3 in myeloid cells, that organize anti-bacterial immunity, for the outcome of immune responses against intracellular bacteria such as Listeria monocytogenes in vivo is unknown. We found that Listeria monocytogenes infection of macrophages rapidly led to increased expression of PPAR\u03b3. This prompted us to investigate whether PPAR\u03b3 in myeloid cells influences innate immunity against Listeria monocytogenes infection by using transgenic mice with myeloid-cell specific ablation of PPAR\u03b3 (LysMCre\u00d7PPAR\u03b3(flox\/flox)). Loss of PPAR\u03b3 in myeloid cells results in enhanced innate immune defense against Listeria monocytogenes infection both, in vitro and in vivo. This increased resistance against infection was characterized by augmented levels of bactericidal factors and inflammatory cytokines: ROS, NO, IFN\u03b3 TNF IL-6 and IL-12. Moreover, myeloid cell-specific loss of PPAR\u03b3 enhanced chemokine and adhesion molecule expression leading to improved recruitment of inflammatory Ly6C(hi) monocytes to sites of infection. Importantly, increased resistance against Listeria infection in the absence of PPAR\u03b3 was not accompanied by enhanced immunopathology. Our results elucidate a yet unknown regulatory network in myeloid cells that is governed by PPAR\u03b3 and restrains both listeriocidal activity and recruitment of inflammatory monocytes during Listeria infection, which may contribute to bacterial immune escape. Pharmacological interference with PPAR\u03b3 activity in myeloid cells might represent a novel strategy to overcome intracellular bacterial infection.","authors":"Abdullah, Z., Geiger, S., Nino-Castro, A., B\u00f6ttcher, JP., Muraliv, E., Gaidt, M., Schildberg, FA., Riethausen, K., Flossdorf, J., Krebs, W., Chakraborty, T., Kurts, C., Schultze, JL., Knolle, PA., Klotz, L.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS One","volume":"7","issue":"5","page":"e37349","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35852463","title":"Transient upregulation of IRF1 during exit from naive pluripotency confers viral protection.","abstract":"Stem cells intrinsically express a subset of genes which are normally associated with interferon stimulation and the innate immune response. However, the expression of these interferon-stimulated genes (ISG) in stem cells is independent from external stimuli such as viral infection. Here, we show that the interferon regulatory factor 1, Irf1, is directly controlled by the murine formative pluripotency gene regulatory network and transiently upregulated during the transition from naive to formative pluripotency. IRF1 binds to regulatory regions of a conserved set of ISGs and is required for their faithful expression upon exit from naive pluripotency. We show that in the absence of IRF1, cells exiting the naive pluripotent stem cell state are more susceptible to viral infection. Irf1 therefore acts as a link between the formative pluripotency network, regulation of innate immunity genes, and defense against viral infections during formative pluripotency.","authors":"Romeike, M., Spach, S., Huber, M., Feng, S., Vainorius, G., Elling, U., Versteeg, GA., Buecker, C.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"EMBO Rep","volume":null,"issue":null,"page":"e55375","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35821636","title":"Targeting Glycans for CAR Therapy: the Advent of Sweet CARs.","abstract":"CAR T cell therapy has created a paradigm shift in the treatment of hematologic malignancies but has not been as effective toward solid tumors. For such tumors, the primary obstacles facing CAR T cells are scarcity of tumor-specific antigens and the hostile and complex tumor microenvironment. Glycosylation, the process by which sugars are post-translationally added to proteins or lipids, is profoundly dysregulated in cancer. Abnormally glycosylated glycoproteins expressed on cancer cells offer unique targets for CAR T therapy as they are specific to tumor cells. Tumor stromal cells also express abnormal glycoproteins and thus also have the potential to be targeted by glycan-binding CAR T cells. This review will discuss the state of CAR T cells in the therapy of solid tumors, the cancer glycoproteome and its potential for use as a therapeutic target, and the landscape and future of glycan-binding CAR T cell therapy.","authors":"Raglow, Z., McKenna, MK., Bonifant, CL., Wang, W., Pasca di Magliano, M., Stadlmann, J., Penninger, JM., Cummings, RD., Brenner, MK., Markovitz, DM.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Mol Ther","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35551305","title":"DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.","abstract":"Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood, and de novo enhancer design has been challenging. Here, we built a deep-learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. The model learned relevant TF motifs and higher-order syntax rules, including functionally nonequivalent instances of the same TF motif that are determined by motif-flanking sequence and intermotif distances. We validated these rules experimentally and demonstrated that they can be generalized to humans by testing more than 40,000 wildtype and mutant Drosophila and human enhancers. Finally, we designed and functionally validated synthetic enhancers with desired activities de novo.","authors":"de Almeida, BP., Reiter, F., Pagani, M., Stark, A.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Genet","volume":"54","issue":"5","page":"613-624","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35867642","title":"ACE2-like enzyme B38-CAP suppresses abdominal sepsis and severe acute lung injury.","abstract":"Angiotensin-converting enzyme 2 (ACE2) is the carboxypeptidase to degrade angiotensin II (Ang II) to angiotensin 1-7 (Ang 1-7) and improves the pathologies of cardiovascular disease and acute respiratory distress syndrome (ARDS)\/acute lung injury. B38-CAP is a bacteria-derived ACE2-like carboxypeptidase as potent as human ACE2 and ameliorates hypertension, heart failure and SARS-CoV-2-induced lung injury in mice. Recombinant B38-CAP is prepared with E. coli protein expression system more efficiently than recombinant soluble human ACE2. Here we show therapeutic effects of B38-CAP on abdominal sepsis- or acid aspiration-induced acute lung injury. ACE2 expression was downregulated in the lungs of mice with cecal ligation puncture (CLP)-induced sepsis or acid-induced lung injury thereby leading to upregulation of Ang II levels. Intraperitoneal injection of B38-CAP significantly decreased Ang II levels while upregulated angiotensin 1-7 levels. B38-CAP improved survival rate of the mice under sepsis. B38-CAP suppressed the pathologies of lung inflammation, improved lung dysfunction and downregulated elevated cytokine mRNA levels in the mice with acute lung injury. Thus, systemic treatment with an ACE2-like enzyme might be a potential therapeutic strategy for the patients with severe sepsis or ARDS.","authors":"Minato, T., Yamaguchi, T., Hoshizaki, M., Nirasawa, S., An, J., Takahashi, S., Penninger, JM., Imai, Y., Kuba, K.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"PLoS One","volume":"17","issue":"7","page":"e0270920","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35864192","title":"Hijacking of transcriptional condensates by endogenous retroviruses.","abstract":"Most endogenous retroviruses (ERVs) in mammals are incapable of retrotransposition; therefore, why ERV derepression is associated with lethality during early development has been a mystery. Here, we report that rapid and selective degradation of the heterochromatin adapter protein TRIM28 triggers dissociation of transcriptional condensates from loci encoding super-enhancer (SE)-driven pluripotency genes and their association with transcribed ERV loci in murine embryonic stem cells. Knockdown of ERV RNAs or forced expression of SE-enriched transcription factors rescued condensate localization at SEs in TRIM28-degraded cells. In a biochemical reconstitution system, ERV RNA facilitated partitioning of RNA polymerase&#x2009;II and the Mediator coactivator into phase-separated droplets. In TRIM28 knockout mouse embryos, single-cell RNA-seq analysis revealed specific depletion of pluripotent lineages. We propose that coding and noncoding nascent RNAs, including those produced by retrotransposons, may facilitate 'hijacking' of transcriptional condensates in various developmental and disease contexts.","authors":"Asimi, V., Sampath Kumar, A., Niskanen, H., Riemenschneider, C., Hetzel, S., Naderi, J., Fasching, N., Popitsch, N., Du, M., Kretzmer, H., Smith, ZD., Weigert, R., Walther, M., Mamde, S., Meierhofer, D., Wittler, L., Buschow, R., Timmermann, B., Cisse, II., Ameres, SL., Meissner, A., Hnisz, D.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Genet","volume":"54","issue":"8","page":"1238-1247","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-09","doi":"10.1038\/s41588-022-01132-w","first_author":null,"corresponding_authors":null},{"pmid":"35922507","title":"A mitotic chromatin phase transition prevents perforation by microtubules.","abstract":"Dividing\u00a0eukaryotic cells package extremely long chromosomal DNA molecules into discrete bodies to enable microtubule-mediated transport of one genome copy to each of the newly forming daughter cells<sup>1-3<\/sup>. Assembly of mitotic chromosomes involves DNA looping by condensin<sup>4-8<\/sup> and chromatin compaction by global histone deacetylation<sup>9-13<\/sup>. Although condensin confers mechanical resistance to spindle pulling forces<sup>14-16<\/sup>, it is not known how histone deacetylation affects material properties and, as a consequence, segregation mechanics of mitotic chromosomes. Here we show how global histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with the physical characteristics necessary for their precise movement during cell division. Deacetylation-mediated compaction of chromatin forms a structure dense in negative charge and allows mitotic chromosomes to resist perforation by microtubules as they are pushed to the metaphase plate. By contrast, hyperacetylated mitotic chromosomes lack a defined surface boundary, are frequently perforated by microtubules and are prone to missegregation. Our study highlights the different contributions of DNA loop formation and chromatin phase separation to genome segregation in dividing cells.","authors":"Schneider, MWG., Gibson, BA., Otsuka, S., Spicer, MFD., Petrovic, M., Blaukopf, C., Langer, CCH., Batty, P., Nagaraju, T., Doolittle, LK., Rosen, MK., Gerlich, DW.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35974295","title":"AIF Overexpression Aggravates Oxidative Stress in Neonatal Male Mice After Hypoxia-Ischemia Injury.","abstract":"There are sex differences in the severity, mechanisms, and outcomes of neonatal hypoxia-ischemia (HI) brain injury, and apoptosis-inducing factor (AIF) may play a critical role in this discrepancy. Based on previous findings that AIF overexpression aggravates neonatal HI brain injury, we further investigated potential sex differences in the severity and molecular mechanisms underlying the injury using mice that overexpress AIF from homozygous transgenes. We found that the male sex significantly aggravated AIF-driven brain damage, as indicated by the injury volume in the gray matter (2.25 times greater in males) and by the lost volume of subcortical white matter (1.71 greater in males) after HI. As compared to females, male mice exhibited more severe brain injury, correlating with reduced antioxidant capacities, more pronounced protein carbonylation and nitration, and increased neuronal cell death. Under physiological conditions (without HI), the doublecortin-positive area in the dentate gyrus of females was 1.15 times larger than in males, indicating that AIF upregulation effectively promoted neurogenesis in females in the long term. We also found that AIF stimulated carbohydrate metabolism in young males. Altogether, these findings corroborate earlier studies and further demonstrate that AIF is involved in oxidative stress, which contributes to the sex-specific differences observed in neonatal HI brain injury.","authors":"Li, T., Sun, Y., Zhang, S., Xu, Y., Li, K., Xie, C., Wang, Y., Wang, Y., Cao, J., Wang, X., Penninger, JM., Kroemer, G., Blomgren, K., Zhu, C.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Mol Neurobiol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35948369","title":"Single-cell multi-omics of human preimplantation embryos demonstrates susceptibility to glucocorticoids.","abstract":"The pre-conceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of Assisted Reproductive Technologies (ART; ~25%), additives and adjuvants, such as glucocorticoids, are utilized to improve the success rate. Considering the dynamic developmental events that occur during this window, these exposures may alter blastocyst formation at a molecular level, and as such, affect not only the viability of the embryo and ability of the blastocyst to implant, but also the developmental trajectory of the first three cell lineages, ultimately influencing the physiology of the embryo. In this study we present a comprehensive single-cell transcriptome, methylome and small RNA atlas in the day 7 human embryo. We demonstrate that, despite no change in morphology and developmental features, preimplantation glucocorticoid exposure reprograms the molecular profile of the TE lineage and these changes are associated with an altered metabolic and inflammatory response. Our data also suggest that glucocorticoids can precociously mature the TE sub-lineages, supported by the presence of extravillous trophoblast markers in the polar sub-lineage and presence of X Chromosome dosage compensation. Further, we have elucidated that epigenetic regulation (DNA methylation and microRNAs (miRNAs)) likely underlie the transcriptional changes observed. This study suggests that exposures to exogenous compounds during preimplantation may unintentionally reprogram the human embryo, possibly leading to suboptimal development and longer-term health outcomes.","authors":"Zhao, C., Biondic, S., Vandal, K., Bjorklund, AK., Hagemann-Jensen, M., Sommer, TM., Canizo, J., Clark, S., Raymond, P., Zenklusen, D., Rivron, N., Reik, W., Petropoulos, S.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Genome Res","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35947077","title":"Biallelic PAX5 mutations cause hypogammaglobulinemia, sensorimotor deficits, and autism spectrum disorder.","abstract":"The genetic causes of primary antibody deficiencies and autism spectrum disorder (ASD) are largely unknown. Here, we report a patient with hypogammaglobulinemia and ASD who carries biallelic mutations in the transcription factor PAX5. A patient-specific Pax5 mutant mouse revealed an early B cell developmental block and impaired immune responses as the cause of hypogammaglobulinemia. Pax5 mutant mice displayed behavioral deficits in all ASD domains. The patient and the mouse model showed aberrant cerebellar foliation and severely impaired sensorimotor learning. PAX5 deficiency also caused profound hypoplasia of the substantia nigra and ventral tegmental area due to loss of GABAergic neurons, thus affecting two midbrain hubs, controlling motor function and reward processing, respectively. Heterozygous Pax5 mutant mice exhibited similar anatomic and behavioral abnormalities. Lineage tracing identified Pax5 as a crucial regulator of cerebellar morphogenesis and midbrain GABAergic neurogenesis. These findings reveal new roles of Pax5 in brain development and unravel the underlying mechanism of a novel immunological and neurodevelopmental syndrome.","authors":"Kaiser, FMP., Gruenbacher, S., Oyaga, MR., Nio, E., Jaritz, M., Sun, Q., van der Zwaag, W., Kreidl, E., Zopf, LM., Dalm, VASH., Pel, J., Gaiser, C., van der Vliet, R., Wahl, L., Rietman, A., Hill, L., Leca, I., Driessen, G., Laffeber, C., Brooks, A., Katsikis, PD., Lebbink, JHG., Tachibana, K., van der Burg, M., De Zeeuw, CI., Badura, A., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"J Exp Med","volume":"219","issue":"9","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35926164","title":"Pulmonary Surfactant Proteins Are Inhibited by Immunoglobulin A Autoantibodies in Severe COVID-19.","abstract":"<b>Rationale:<\/b> Coronavirus disease 2019 (COVID-19) can lead to acute respiratory distress syndrome with fatal outcomes. Evidence suggests that dysregulated immune responses, including autoimmunity, are key pathogenic factors. <b>Objectives:<\/b> To assess whether IgA autoantibodies target lung-specific proteins and contribute to disease severity. <b>Methods:<\/b> We collected 147 blood, 9 lung tissue, and 36 BAL fluid samples from three tertiary hospitals in Switzerland and one in Germany. Severe COVID-19 was defined by the need to administer oxygen. We investigated the presence of IgA autoantibodies and their effects on pulmonary surfactant in COVID-19 using the following methods: immunofluorescence on tissue samples, immunoprecipitations followed by mass spectrometry on BAL fluid samples, enzyme-linked immunosorbent assays on blood samples, and surface tension measurements with medical surfactant. <b>Measurements and Main Results:<\/b> IgA autoantibodies targeting pulmonary surfactant proteins B and C were elevated in patients with severe COVID-19 but not in patients with influenza or bacterial pneumonia. Notably, pulmonary surfactant failed to reduce surface tension after incubation with either plasma or purified IgA from patients with severe COVID-19. <b>Conclusions:<\/b> Our data suggest that patients with severe COVID-19 harbor IgA autoantibodies against pulmonary surfactant proteins B and C and that these autoantibodies block the function of lung surfactant, potentially contributing to alveolar collapse and poor oxygenation.","authors":"Sinnberg, T., Lichtensteiger, C., Ali, OH., Pop, OT., Jochum, AK., Risch, L., Brugger, SD., Velic, A., Bomze, D., Kohler, P., Vernazza, P., Albrich, WC., Kahlert, CR., Abdou, MT., Wyss, N., Hofmeister, K., Niessner, H., Zinner, C., Gilardi, M., Tzankov, A., R\u00f6cken, M., Dulovic, A., Shambat, SM., Ruetalo, N., Buehler, PK., Scheier, TC., Jochum, W., Kern, L., Henz, S., Schneider, T., Kuster, GM., Lampart, M., Siegemund, M., Bingisser, R., Schindler, M., Schneiderhan-Marra, N., Kalbacher, H., McCoy, KD., Spengler, W., Brutsche, MH., Ma\u010dek, B., Twerenbold, R., Penninger, JM., Matter, MS., Flatz, L.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Am J Respir Crit Care Med","volume":"207","issue":"1","page":"38-49","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35919947","title":"Gruffi: an algorithm for computational removal of stressed cells from brain organoid transcriptomic datasets.","abstract":"Organoids enable in\u2009vitro modeling of complex developmental processes and disease pathologies. Like most 3D cultures, organoids lack sufficient oxygen supply and therefore experience cellular stress. These negative effects are particularly prominent in complex models, such as brain organoids, and can affect lineage commitment. Here, we analyze brain organoid and fetal single-cell RNA sequencing (scRNAseq) data from published and new datasets, totaling about 190,000 cells. We identify a unique stress signature in the data from all organoid samples, but not in fetal samples. We demonstrate that cell stress is limited to a defined subpopulation of cells that is unique to organoids and does not affect neuronal specification or maturation. We have developed a computational algorithm, Gruffi, which uses granular functional filtering to identify and remove stressed cells from any organoid scRNAseq dataset in an unbiased manner. We validated our method using six additional datasets from different organoid protocols and early brains, and show its usefulness to other organoid systems including retinal organoids. Our data show that the adverse effects of cell stress can be corrected by bioinformatic analysis for improved delineation of developmental trajectories and resemblance to in\u2009vivo data.","authors":"V\u00e9rtesy, \u00c1., Eichm\u00fcller, OL., Naas, J., Novatchkova, M., Esk, C., Balma\u00f1a, M., Ladstaetter, S., Bock, C., von Haeseler, A., Knoblich, JA.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"EMBO J","volume":null,"issue":null,"page":"e111118","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35156727","title":"The PAX5-JAK2 translocation acts as dual-hit mutation that promotes aggressive B-cell leukemia via nuclear STAT5 activation.","abstract":"While PAX5 is an important tumor suppressor gene in B-cell acute lymphoblastic leukemia (B-ALL), it is also involved in oncogenic translocations coding for diverse PAX5 fusion proteins. PAX5-JAK2 encodes a protein consisting of the PAX5 DNA-binding region fused to the constitutively active JAK2 kinase domain. Here, we studied the oncogenic function of the PAX5-JAK2 fusion protein in a mouse model expressing it from the endogenous Pax5 locus, resulting in inactivation of one of the two Pax5 alleles. Pax5<sup>Jak2\/+<\/sup> mice rapidly developed an aggressive B-ALL in the absence of another cooperating exogenous gene mutation. The DNA-binding function and kinase activity of Pax5-Jak2 as well as IL-7 signaling contributed to leukemia development. Interestingly, all Pax5<sup>Jak2\/+<\/sup> tumors lost the remaining wild-type Pax5 allele, allowing efficient DNA-binding of Pax5-Jak2. While we could not find evidence for a nuclear role of Pax5-Jak2 as an epigenetic regulator, high levels of active phosphorylated STAT5 and increased expression of STAT5 target genes were seen in Pax5<sup>Jak2\/+<\/sup> B-ALL tumors, implying that nuclear Pax5-Jak2 phosphorylates STAT5. Together, these data reveal Pax5-Jak2 as an important nuclear driver of leukemogenesis by maintaining phosphorylated STAT5 levels in the nucleus.","authors":"Jurado, S., Fedl, AS., Jaritz, M., Kostanova-Poliakova, D., Malin, SG., Mullighan, CG., Strehl, S., Fischer, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"EMBO J","volume":"41","issue":"7","page":"e108397","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34919144","title":"Bhlhe40 function in activated B and TFH cells restrains the GC reaction and prevents lymphomagenesis.","abstract":"The generation of high-affinity antibodies against pathogens and vaccines requires the germinal center (GC) reaction, which relies on a complex interplay between specialized effector B and CD4 T lymphocytes, the GC B cells and T follicular helper (TFH) cells. Intriguingly, several positive key regulators of the GC reaction are common for both cell types. Here, we report that the transcription factor Bhlhe40 is a crucial cell-intrinsic negative regulator affecting both the B and T cell sides of the GC reaction. In activated CD4 T cells, Bhlhe40 was required to restrain proliferation, thus limiting the number of TFH cells. In B cells, Bhlhe40 executed its function in the first days after immunization by selectively restricting the generation of the earliest GC B cells but not of early memory B cells or plasmablasts. Bhlhe40-deficient mice with progressing age succumbed to a B cell lymphoma characterized by the accumulation of monoclonal GC B-like cells and polyclonal TFH cells in various tissues.","authors":"Rauschmeier, R., Reinhardt, A., Gustafsson, C., Glaros, V., Artemov, AV., Dunst, J., Taneja, R., Adameyko, I., M\u00e5nsson, R., Busslinger, M., Kreslavsky, T.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"J Exp Med","volume":"219","issue":"2","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35993866","title":"A pendulum of induction between the epiblast and extra-embryonic endoderm supports post-implantation progression.","abstract":"Embryogenesis is supported by dynamic loops of cellular interactions. Here, we create a partial mouse embryo model to elucidate the principles of epiblast (Epi) and extra-embryonic endoderm co-development (XEn). We trigger naive mouse embryonic stem cells to form a blastocyst-stage niche of Epi-like cells and XEn-like cells (3D, hydrogel free and serum free). Once established, these two lineages autonomously progress in minimal medium to form an inner pro-amniotic-like cavity surrounded by polarized Epi-like cells covered with visceral endoderm (VE)-like cells. The progression occurs through reciprocal inductions by which the Epi supports the primitive endoderm (PrE) to produce a basal lamina that subsequently regulates Epi polarization and\/or cavitation, which, in return, channels the transcriptomic progression to VE. This VE then contributes to Epi bifurcation into anterior- and posterior-like states. Similarly, boosting the formation of PrE-like cells within blastoids supports developmental progression. We argue that self-organization can arise from lineage bifurcation followed by a pendulum of induction that propagates over time.","authors":"Vrij, EJ., Scholte Op Reimer, YS., Fuentes, LR., Guerreiro, IM., Holzmann, V., Aldeguer, JF., Sestini, G., Koo, BK., Kind, J., van Blitterswijk, CA., Rivron, NC.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Development","volume":"149","issue":"20","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35993110","title":"Sensitivity towards HDAC inhibition is associated with RTK\/MAPK pathway activation in gastric cancer.","abstract":"Gastric cancer ranks the fifth most common and third leading cause of cancer-related deaths worldwide. Alterations in the RTK\/MAPK, WNT, cell adhesion, TP53, TGF\u03b2, NOTCH, and NF\u03baB signaling pathways could be identified as main oncogenic drivers. A combination of altered pathways can be associated with molecular subtypes of gastric cancer. In order to generate model systems to study the impact of different pathway alterations in a defined genetic background, we generated three murine organoid models: a RAS-activated (Kras<sup>G12D<\/sup> , Tp53<sup>R172H<\/sup> ), a WNT-activated (Apc<sup>fl\/fl<\/sup> , Tp53<sup>R172H<\/sup> ), and a diffuse (Cdh1<sup>fl\/fl<\/sup> , Apc<sup>fl\/fl<\/sup> ) model. These organoid models were morphologically and phenotypically diverse, differed in proteome expression signatures and possessed individual drug sensitivities. A differential vulnerability to RTK\/MAPK pathway interference based on the different mitogenic drivers and according to the level of dependence on the pathway could be uncovered. Furthermore, an association between RTK\/MAPK pathway activity and susceptibility to HDAC inhibition was observed. This finding was further validated in patient-derived organoids from gastric adenocarcinoma, thus identifying a novel treatment approach for RTK\/MAPK pathway altered gastric cancer patients.","authors":"Seidlitz, T., Schm\u00e4che, T., Garc\u03afa, F., Lee, JH., Qin, N., Kochall, S., Fohgrub, J., Pauck, D., Rothe, A., Koo, BK., Weitz, J., Remke, M., Mu\u00f1oz, J., Stange, DE.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"EMBO Mol Med","volume":null,"issue":null,"page":"e15705","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36036618","title":"Protocol for Human Blastoids Modeling Blastocyst Development and Implantation.","abstract":"A model of the human blastocyst formed from stem cells (blastoid) would support scientific and medical advances. However, its predictive power will depend on its ability to efficiently, timely, and faithfully recapitulate the sequences of blastocyst development (morphogenesis, specification, patterning), and to form cells reflecting the blastocyst stage. Here we show that na\u00efve human pluripotent stem cells cultured in PXGL conditions and then triply inhibited for the Hippo, transforming growth factor- \u03b2, and extracellular signal-regulated kinase pathways efficiently undergo morphogenesis to form blastoids (&gt;70%). Matching with developmental timing (~4 days), blastoids unroll the blastocyst sequence of specification by producing analogs of the trophoblast and epiblast, followed by the formation of analogs of the primitive endoderm and the polar trophoblasts. This results in the formation of cells transcriptionally similar to the blastocyst (&gt;96%) and a minority of post-implantation analogs. Blastoids efficiently pattern by forming the embryonic-abembryonic axis marked by the maturation of the polar region (NR2F2+), which acquires the specific potential to directionally attach to hormonally stimulated endometrial cells, as in utero. Such a human blastoid is a scalable, versatile, and ethical model to study human development and implantation in vitro.","authors":"Kagawa, H., Javali, A., Heidari Khoei, H., Sommer, TM., Sestini, G., Novatchkova, M., Scholte Op Reimer, Y., Rivron, N.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"J Vis Exp","volume":null,"issue":"186","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36002576","title":"Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration.","abstract":"The Holliday junction is a key intermediate formed during DNA recombination across all kingdoms of life<sup>1<\/sup>. In bacteria, the Holliday junction is processed by two homo-hexameric AAA+ ATPase RuvB motors, which assemble together with the RuvA-Holliday junction complex to energize the strand-exchange reaction<sup>2<\/sup>. Despite its importance for chromosome maintenance, the structure and mechanism by which this complex facilitates branch migration are unknown. Here, using time-resolved cryo-electron microscopy, we obtained structures of the ATP-hydrolysing RuvAB complex in seven distinct conformational states, captured during assembly and processing of a Holliday junction. Five structures together resolve the complete nucleotide cycle and reveal the spatiotemporal relationship between ATP hydrolysis, nucleotide exchange and context-specific conformational changes in RuvB. Coordinated motions in a converter formed by DNA-disengaged RuvB subunits stimulate hydrolysis and nucleotide exchange. Immobilization of the converter enables RuvB to convert the ATP-contained energy into a lever motion, which generates the pulling force driving the branch migration. We show that RuvB motors rotate together with the DNA substrate, which, together with a progressing nucleotide cycle, forms the mechanistic basis for DNA recombination by continuous branch migration. Together, our data decipher the molecular principles of homologous recombination by the RuvAB complex, elucidate discrete and sequential transition-state intermediates for chemo-mechanical coupling of hexameric AAA+ motors and provide a blueprint for the design of state-specific compounds targeting AAA+ motors.","authors":"Wald, J., Fahrenkamp, D., Goessweiner-Mohr, N., Lugmayr, W., Ciccarelli, L., Vesper, O., Marlovits, TC.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nature","volume":"609","issue":"7927","page":"630-639","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28296858","title":"Transmission of cytokinesis forces via E-cadherin dilution and actomyosin flows.","abstract":"During epithelial cytokinesis, the remodelling of adhesive cell-cell contacts between the dividing cell and its neighbours has profound implications for the integrity, arrangement and morphogenesis of proliferative tissues. In both vertebrates and invertebrates, this remodelling requires the activity of non-muscle myosin II (MyoII) in the interphasic cells neighbouring the dividing cell. However, the mechanisms that coordinate cytokinesis and MyoII activity in the neighbours are unknown. Here we show that in the Drosophila notum epithelium, each cell division is associated with a mechanosensing and transmission event that controls MyoII dynamics in neighbouring cells. We find that the ring pulling forces promote local junction elongation, which results in local E-cadherin dilution at the ingressing adherens junction. In turn, the reduction in E-cadherin concentration and the contractility of the neighbouring cells promote self-organized actomyosin flows, ultimately leading to accumulation of MyoII at the base of the ingressing junction. Although force transduction has been extensively studied in the context of adherens junction reinforcement to stabilize adhesive cell-cell contacts, we propose an alternative mechanosensing mechanism that coordinates actomyosin dynamics between epithelial cells and sustains the remodelling of the adherens junction in response to mechanical forces.","authors":"Pinheiro, D., Hannezo, E., Herszterg, S., Bosveld, F., Gaugue, I., Balakireva, M., Wang, Z., Cristo, I., Rigaud, SU., Markova, O., Bella\u00efche, Y.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Nature","volume":"545","issue":"7652","page":"103-107","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23685359","title":"Drosophila Polo regulates the spindle assembly checkpoint through Mps1-dependent BubR1 phosphorylation.","abstract":"Maintenance of genomic stability during eukaryotic cell division relies on the spindle assembly checkpoint (SAC) that prevents mitotic exit until all chromosomes are properly attached to the spindle. Polo is a mitotic kinase proposed to be involved in SAC function, but its role has remained elusive. We demonstrate that Polo and Aurora B functional interdependency comprises a positive feedback loop that promotes Mps1 kinetochore localization and activity. Expression of constitutively active Polo restores normal Mps1 kinetochore levels even after Aurora B inhibition, highlighting a role for Polo in Mps1 recruitment to unattached kinetochores downstream of Aurora B. We also show that Mps1 kinetochore localization is required for BubR1 hyperphosphorylation and formation of the 3F3\/2 phosphoepitope. This is essential to allow recruitment of Cdc20 to unattached kinetochores and the assembly of anaphase-promoting complex\/cyclosome-inhibitory complexes to levels that ensure long-term SAC activity. We propose a model in which Polo controls Mps1-dependent BubR1 phosphorylation to promote Cdc20 kinetochore recruitment and sustained SAC function.","authors":"Conde, C., Osswald, M., Barbosa, J., Moutinho-Santos, T., Pinheiro, D., Guimar\u00e3es, S., Matos, I., Maiato, H., Sunkel, CE.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"EMBO J","volume":"32","issue":"12","page":"1761-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"32250246","title":"Zebrafish embryonic explants undergo genetically encoded self-assembly.","abstract":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and\/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo <i>bona fide<\/i> self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order.","authors":"Schauer, A., Pinheiro, D., Hauschild, R., Heisenberg, CP.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Elife","volume":"9","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"31959295","title":"Zebrafish gastrulation: Putting fate in motion.","abstract":"Gastrulation entails specification and formation of three embryonic germ layers-ectoderm, mesoderm and endoderm-thereby establishing the basis for the future body plan. In zebrafish embryos, germ layer specification occurs during blastula and early gastrula stages (Ho &amp; Kimmel, 1993), a period when the main morphogenetic movements underlying gastrulation are initiated. Hence, the signals driving progenitor cell fate specification, such as Nodal ligands from the TGF-\u03b2 family, also play key roles in regulating germ layer progenitor cell segregation (Carmany-Rampey &amp; Schier, 2001; David &amp; Rosa, 2001; Feldman et al., 2000; Gritsman et al., 1999; Keller et al., 2008). In this review, we summarize and discuss the main signaling pathways involved in germ layer progenitor cell fate specification and segregation, specifically focusing on recent advances in understanding the interplay between mesoderm and endoderm specification and the internalization movements at the onset of zebrafish gastrulation.","authors":"Pinheiro, D., Heisenberg, CP.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Curr Top Dev Biol","volume":"136","issue":null,"page":"343-375","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"23681663","title":"Selective tracking of template DNA strands after induction of mitosis with unreplicated genomes (MUGs) in Drosophila S2 cells.","abstract":"According to the \"immortal\" DNA strand hypothesis (Cairns Nature 255:197-200, 1975), stem cells would keep their template strands in order to prevent the accumulation of mutations, which could occur during DNA replication. Despite the growing number of studies that attempt to test this hypothesis, the conclusions remain highly controversial. In the base of this controversy lie the current limitations of available methodology to selectively and faithfully track the fate of template DNA strands throughout and upon cell division. Here, we developed a method that allows the unequivocal tracking of single chromatids containing template DNA strands in Drosophila S2 cells in culture. This method consists in the induction of mitosis with unreplicated genomes (MUGs) in which cells are allowed to enter mitosis without prior DNA replication. This is achieved by RNAi-mediated knockdown of Double parked, a conserved protein required for the initiation of DNA replication and post-replication checkpoint response. The advantages of this system when compared with MUGs generated in mammalian cells is the preservation of chromatid morphology, the ease of loss-of-function studies and the possibility of in vivo applications. Altogether, this approach allows for the readily visualization and tracking of template DNA strands by simply monitoring cells stably expressing GFP-fusions with either Histone H2B or the centromeric Histone variant CID\/CENP-A by time-lapse fluorescence microscopy. This might be useful for the dissection of the molecular mechanism behind asymmetric DNA strand segregation.","authors":"Drpic, D., Barisic, M., Pinheiro, D., Maiato, H.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Chromosome Res","volume":"21","issue":"3","page":"329-37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36055191","title":"Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells.","abstract":"A hallmark of primate postimplantation embryogenesis is the specification of extraembryonic mesoderm (EXM) before gastrulation, in contrast to rodents where this tissue is formed only after gastrulation. Here, we discover that naive human pluripotent stem cells (hPSCs) are competent to differentiate into EXM cells (EXMCs). EXMCs are specified by inhibition of Nodal signaling and GSK3B, are maintained by mTOR and BMP4 signaling activity, and their transcriptome and epigenome closely resemble that of human and monkey embryo EXM. EXMCs are mesenchymal, can arise from an epiblast intermediate, and are capable of self-renewal. Thus, EXMCs arising via primate-specific specification between implantation and gastrulation can be modeled in\u00a0vitro. We also find that most of the rare off-target cells within human blastoids formed by triple inhibition (Kagawa et\u00a0al., 2021) correspond to EXMCs. Our study impacts our ability to model and study the molecular mechanisms of early human embryogenesis and related defects.","authors":"Pham, TXA., Panda, A., Kagawa, H., To, SK., Ertekin, C., Georgolopoulos, G., van Knippenberg, SSFA., Allsop, RN., Bruneau, A., Chui, JS., Vanheer, L., Janiszewski, A., Chappell, J., Oberhuemer, M., Tchinda, RS., Talon, I., Khodeer, S., Rossant, J., Lluis, F., David, L., Rivron, N., Balaton, BP., Pasque, V.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cell Stem Cell","volume":"29","issue":"9","page":"1346-1365.e10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36044597","title":"Phenotypic drug screen uncovers the metabolic GCH1\/BH4 pathway as key regulator of EGFR\/KRAS-mediated neuropathic pain and lung cancer.","abstract":"Increased tetrahydrobiopterin (BH4) generated in injured sensory neurons contributes to increased pain sensitivity and its persistence. GTP cyclohydrolase 1 (GCH1) is the rate-limiting enzyme in the de novo BH4 synthetic pathway, and human single-nucleotide polymorphism studies, together with mouse genetic modeling, have demonstrated that decreased GCH1 leads to both reduced BH4 and pain. However, little is known about the regulation of <i>Gch1<\/i> expression upon nerve injury and whether this could be modulated as an analgesic therapeutic intervention. We performed a phenotypic screen using about 1000 bioactive compounds, many of which are target-annotated FDA-approved drugs, for their effect on regulating <i>Gch1<\/i> expression in rodent injured dorsal root ganglion neurons. From this approach, we uncovered relevant pathways that regulate <i>Gch1<\/i> expression in sensory neurons. We report that EGFR\/KRAS signaling triggers increased <i>Gch1<\/i> expression and contributes to neuropathic pain; conversely, inhibiting EGFR suppressed GCH1 and BH4 and exerted analgesic effects, suggesting a molecular link between EGFR\/KRAS and pain perception. We also show that GCH1\/BH4 acts downstream of KRAS to drive lung cancer, identifying a potentially druggable pathway. Our screen shows that pharmacologic modulation of GCH1 expression and BH4 could be used to develop pharmacological treatments to alleviate pain and identified a critical role for EGFR-regulated GCH1\/BH4 expression in neuropathic pain and cancer in rodents.","authors":"Cronin, SJF., Rao, S., Tejada, MA., Turnes, BL., Licht-Mayer, S., Omura, T., Brenneis, C., Jacobs, E., Barrett, L., Latremoliere, A., Andrews, N., Channon, KM., Latini, A., Arvanites, AC., Davidow, LS., Costigan, M., Rubin, LL., Penninger, JM., Woolf, CJ.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Sci Transl Med","volume":"14","issue":"660","page":"eabj1531","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36108018","title":"DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations.","abstract":"Chromosomal translocations result from the joining of DNA double-strand breaks (DSBs) and frequently cause cancer. However, the steps linking DSB formation to DSB ligation remain undeciphered. We report that DNA replication timing (RT) directly regulates lymphomagenic <i>Myc<\/i> translocations during antibody maturation in B cells downstream of DSBs and independently of DSB frequency. Depletion of minichromosome maintenance complexes alters replication origin activity, decreases translocations, and deregulates global RT. Ablating a single origin at <i>Myc<\/i> causes an early-to-late RT switch, loss of translocations, and reduced proximity with the immunoglobulin heavy chain (<i>Igh<\/i>) gene, its major translocation partner. These phenotypes were reversed by restoring early RT. Disruption of early RT also reduced tumorigenic translocations in human leukemic cells. Thus, RT constitutes a general mechanism in translocation biogenesis linking DSB formation to DSB ligation.","authors":"Peycheva, M., Neumann, T., Malzl, D., Nazarova, M., Schoeberl, UE., Pavri, R.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Science","volume":"377","issue":"6612","page":"eabj5502","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36117218","title":"Clone wars: From molecules to cell competition in intestinal stem cell homeostasis and disease.","abstract":"The small intestine is among the fastest self-renewing tissues in adult mammals. This rapid turnover is fueled by the intestinal stem cells residing in the intestinal crypt. Wnt signaling plays a pivotal role in regulating intestinal stem cell renewal and differentiation, and the dysregulation of this pathway leads to cancer formation. Several studies demonstrate that intestinal stem cells follow neutral drift dynamics, as they divide symmetrically to generate other equipotent stem cells. Competition for niche space and extrinsic signals in the intestinal crypt is the governing mechanism that regulates stemness versus cell differentiation, but the underlying molecular mechanisms are still poorly understood, and it is not yet clear how this process changes during disease. In this review, we highlight the mechanisms that regulate stem cell homeostasis in the small intestine, focusing on Wnt signaling and its regulation by RNF43 and ZNRF3, key inhibitors of the Wnt pathway. Furthermore, we summarize the evidence supporting the current model of intestinal stem cell regulation, highlighting the principles of neutral drift at the basis of intestinal stem cell homeostasis. Finally, we discuss recent studies showing how cancer cells bypass this mechanism to gain a competitive advantage against neighboring normal cells.","authors":"Colozza, G., Park, SY., Koo, BK.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Exp Mol Med","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36143426","title":"Urinary Collectrin (TMEM27) as Novel Marker for Acute Kidney Injury.","abstract":"Acute kidney injury (AKI) is a leading complication in hospitalized patients of different disciplines due to various aetiologies and is associated with the risk of chronic kidney disease, the need for dialysis and death. Since nephrons are not supplied with pain signals, kidney injury is mostly diagnosed by serum creatinine with a time delay. Recent work has shown that certain urinary biomarkers are available for early detection of AKI. In total, 155 subjects, including 102 patients with AKI at various stages and 53 subjects without AKI, were enrolled, and their course and laboratory data were recorded. Urinary collectrin (TMEM27) was measured by a commercially available ELISA assay. Changes in serum creatinine were used to determine AKI stage. Patients with AKI presented with significantly lower levels of urinary collectrin compared to patients without AKI (1597 \u00b1 1827 pg\/mL vs. 2855 \u00b1 2073; <i>p<\/i> = 0.001). Collectrin was found to inversely correlate with serum creatinine and stages of AKI. Collectrin levels were lowest in AKI stage III (1576 \u00b1 1686 pg\/mL; <i>p<\/i> = 0.001) and also significantly lower in stage II (1616 \u00b1 2148 pg\/mL; <i>p<\/i> = 0.021) and stage I (1630 \u00b1 1956 pg\/mL; <i>p<\/i> = 0.019) compared to subjects without AKI. An optimal minimum collectrin cut-off value of 1606 [95% CI 1258 to 1954] pg\/mL was determined to detect AKI. In conclusion, urinary collectrin represents an indicator of AKI that, unlike all other established AKI biomarkers, decreases with stage of AKI and thus may be associated with a novel pathogenic pathway.","authors":"Pajenda, S., Wagner, L., Gerges, D., Herkner, H., Tevdoradze, T., Mechtler, K., Schmidt, A., Winnicki, W.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Life (Basel)","volume":"12","issue":"9","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35173350","title":"Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery.","abstract":"Nuclear Argonaute proteins, guided by small RNAs, mediate sequence-specific heterochromatin formation. The molecular principles that link Argonaute-small RNA complexes to cellular heterochromatin effectors on binding to nascent target RNAs are poorly understood. Here, we explain the mechanism by which the PIWI-interacting RNA (piRNA) pathway connects to the heterochromatin machinery in Drosophila. We find that Panoramix, a corepressor required for piRNA-guided heterochromatin formation, is SUMOylated on chromatin in a Piwi-dependent manner. SUMOylation, together with an amphipathic LxxLL motif in Panoramix's intrinsically disordered repressor domain, are necessary and sufficient to recruit Small ovary (Sov), a multi-zinc-finger protein essential for general heterochromatin formation and viability. Structure-guided mutations that eliminate the Panoramix-Sov interaction or that prevent SUMOylation of Panoramix uncouple Sov from the piRNA pathway, resulting in viable but sterile flies in which Piwi-targeted transposons are derepressed. Thus, Piwi engages the heterochromatin machinery specifically at transposon loci by coupling recruitment of a corepressor to nascent transcripts with its SUMOylation.","authors":"Andreev, VI., Yu, C., Wang, J., Schnabl, J., Tirian, L., Gehre, M., Handler, D., Duchek, P., Novatchkova, M., Baumgartner, L., Meixner, K., Sienski, G., Patel, DJ., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Struct Mol Biol","volume":"29","issue":"2","page":"130-142","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36195094","title":"A molecularly engineered, broad-spectrum anti-coronavirus lectin inhibits SARS-CoV-2 and MERS-CoV infection in\u00a0vivo.","abstract":"\"Pan-coronavirus\" antivirals targeting conserved viral components can be designed. Here, we show that the rationally engineered H84T-banana lectin (H84T-BanLec), which specifically recognizes high mannose found on viral proteins but seldom on healthy human cells, potently inhibits Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (including Omicron), and other human-pathogenic coronaviruses at nanomolar concentrations. H84T-BanLec protects against MERS-CoV and SARS-CoV-2 infection in\u00a0vivo. Importantly, intranasally and intraperitoneally administered H84T-BanLec are comparably effective. Mechanistic assays show that H84T-BanLec targets virus entry. High-speed atomic force microscopy depicts real-time multimolecular associations of H84T-BanLec dimers with the SARS-CoV-2 spike trimer. Single-molecule force spectroscopy demonstrates binding of H84T-BanLec to multiple SARS-CoV-2 spike mannose sites with high affinity and that H84T-BanLec competes with SARS-CoV-2 spike for binding to cellular ACE2. Modeling experiments identify distinct high-mannose glycans in spike recognized by H84T-BanLec. The multiple H84T-BanLec binding sites on spike likely account for the drug compound's broad-spectrum antiviral activity and the lack of resistant mutants.","authors":"Chan, JF., Oh, YJ., Yuan, S., Chu, H., Yeung, ML., Canena, D., Chan, CC., Poon, VK., Chan, CC., Zhang, AJ., Cai, JP., Ye, ZW., Wen, L., Yuen, TT., Chik, KK., Shuai, H., Wang, Y., Hou, Y., Luo, C., Chan, WM., Qin, Z., Sit, KY., Au, WK., Legendre, M., Zhu, R., Hain, L., Seferovic, H., Tamp\u00e9, R., To, KK., Chan, KH., Thomas, DG., Klausberger, M., Xu, C., Moon, JJ., Stadlmann, J., Penninger, JM., Oostenbrink, C., Hinterdorfer, P., Yuen, KY., Markovitz, DM.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Cell Rep Med","volume":null,"issue":null,"page":"100774","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36193674","title":"The <i>Drosophila<\/i> ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters.","abstract":"RNA interference systems depend on the synthesis of small RNA precursors whose sequences define the target spectrum of these silencing pathways. The <i>Drosophila<\/i> Heterochromatin Protein 1 (HP1) variant Rhino permits transcription of PIWI-interacting RNA (piRNA) precursors within transposon-rich heterochromatic loci in germline cells. Current models propose that Rhino's specific chromatin occupancy at piRNA source loci is determined by histone marks and maternally inherited piRNAs, but also imply the existence of other, undiscovered specificity cues. Here, we identify a member of the diverse family of zinc finger associated domain (ZAD)-C<sub>2<\/sub>H<sub>2<\/sub> zinc finger proteins, Kipferl, as critical Rhino cofactor in ovaries. By binding to guanosine-rich DNA motifs and interacting with the Rhino chromodomain, Kipferl recruits Rhino to specific loci and stabilizes it on chromatin. In <i>kipferl<\/i> mutant flies, Rhino is lost from most of its target chromatin loci and instead accumulates on pericentromeric Satellite arrays, resulting in decreased levels of transposon targeting piRNAs and impaired fertility. Our findings reveal that DNA sequence, in addition to the H3K9me3 mark, determines the identity of piRNA source loci and provide insight into how Rhino might be caught in the crossfire of genetic conflicts.","authors":"Baumgartner, L., Handler, D., Platzer, SW., Yu, C., Duchek, P., Brennecke, J.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Elife","volume":"11","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36187350","title":"The impact of heme biosynthesis regulation on glioma aggressiveness: Correlations with diagnostic molecular markers.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">36187350<\/PMID><DateRevised><Year>2022<\/Year><Month>10<\/Month><Day>04<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Print\">1662-5099<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>15<\/Volume><PubDate><Year>2022<\/Year><\/PubDate><\/JournalIssue><Title>Frontiers in molecular neuroscience<\/Title><ISOAbbreviation>Front Mol Neurosci<\/ISOAbbreviation><\/Journal><ArticleTitle>The impact of heme biosynthesis regulation on glioma aggressiveness: Correlations with diagnostic molecular markers.<\/ArticleTitle><Pagination><MedlinePgn>928355<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.3389\/fnmol.2022.928355<\/ELocationID><Abstract><AbstractText Label=\"Background\" NlmCategory=\"UNASSIGNED\">The prognosis of diffusely infiltrating glioma patients is dismal but varies greatly between individuals. While characterization of gliomas primarily relied on histopathological features, molecular markers increasingly gained importance and play a key role in the recently published 5 <i><sup>th<\/sup><\/i> edition of the World Health Organization (WHO) classification. Heme biosynthesis represents a crucial pathway due to its paramount importance in oxygen transport, energy production and drug metabolism. Recently, we described a \"heme biosynthesis mRNA expression signature\" that correlates with histopathological glioma grade and survival. The aim of the current study was to correlate this heme biosynthesis mRNA expression signature with diagnostic molecular markers and investigate its continued prognostic relevance.","authors":"Mischkulnig, M., Kiesel, B., R\u00f6tzer-Pejrimovsky, T., Borkovec, M., Lang, A., Millesi, M., Wadiura, LI., Hervey-Jumper, S., Penninger, JM., Berger, MS., Widhalm, G., Erhart, F.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Front Mol Neurosci","volume":"15","issue":null,"page":"928355","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36183858","title":"Carbon ion irradiation plus CTLA4 blockade elicits therapeutic immune responses in a murine tumor model.","abstract":"Radiotherapy can act as an in situ vaccine, activating preventive tumor-specific immune responses in patients. Although carbon ion radiotherapy has superior biophysical properties over conventional photon irradiation, the immunological effects induced by this radiation type are poorly understood. Multiple strategies combining radiotherapy with immune checkpoint inhibition (radioimmunotherapy) to enhance antitumor immunity have been described; however, immune cell composition in tumors following radioimmunotherapy with carbon ions remains poorly explored. We developed a bilateral tumor model based on time-shifted subcutaneous injection of murine Her2+ EO771 tumor cells into immune-competent mice followed by selective irradiation of the primary tumor. \u03b1CTLA4-, but not \u03b1PD-L1-based radioimmunotherapy, induced complete tumor rejection and mediated the eradication of even non-irradiated, distant tumors. Cured mice were protected against the EO771 rechallenge, indicating long-lasting, tumor-specific immunological memory. Single-cell RNA sequencing and flow cytometric analyses of irradiated tumors revealed activation of NK cells and distinct tumor-associated macrophage clusters with upregulated expression of TNF and IL1 responsive genes. Distant tumors in the irradiated mice showed higher frequencies of na\u00efve T cells activated upon the combination with CTLA4 blockade. Thus, radioimmunotherapy with carbon ions plus CTLA4 inhibition reshapes the tumor-infiltrating immune cell composition and can induce complete rejection even of non-irradiated tumors. Our data suggest combining radiotherapy approaches with CTLA4 blockade to achieve durable antitumor immunity. Evaluation of future radioimmunotherapy approaches should not be restricted to immunological impact at the irradiation site but should also consider systemic immunological effects on non-irradiated tumors.","authors":"Hartmann, L., Osen, W., Eichm\u00fcller, OL., Korda\u00df, T., Furkel, J., Dickes, E., Reid, C., Debus, J., Brons, S., Abdollahi, A., Moustafa, M., Rieken, S., Eichm\u00fcller, SB.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cancer Lett","volume":"550","issue":null,"page":"215928","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36213965","title":"Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell-like Program Conserved in HPV-Positive Cancers.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">36213965<\/PMID><DateCompleted><Year>2023<\/Year><Month>01<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2023<\/Year><Month>01<\/Month><Day>12<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">2159-8290<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>13<\/Volume><Issue>1<\/Issue><PubDate><Year>2023<\/Year><Month>Jan<\/Month><Day>09<\/Day><\/PubDate><\/JournalIssue><Title>Cancer discovery<\/Title><ISOAbbreviation>Cancer Discov<\/ISOAbbreviation><\/Journal><ArticleTitle>Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell-like Program Conserved in HPV-Positive Cancers.<\/ArticleTitle><Pagination><StartPage>70<\/StartPage><EndPage>84<\/EndPage><MedlinePgn>70-84<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1158\/2159-8290.CD-22-0489<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">The skin is exposed to viral pathogens, but whether they contribute to the oncogenesis of skin cancers has not been systematically explored. Here we investigated 19 skin tumor types by analyzing off-target reads from commonly available next-generation sequencing data for viral pathogens. We identified human papillomavirus 42 (HPV42) in 96% (n = 45\/47) of digital papillary adenocarcinoma (DPA), an aggressive cancer occurring on the fingers and toes. We show that HPV42, so far considered a nononcogenic, \"low-risk\" HPV, recapitulates the molecular hallmarks of oncogenic, \"high-risk\" HPVs. Using machine learning, we find that HPV-driven transformation elicits a germ cell-like transcriptional program conserved throughout all HPV-driven cancers (DPA, cervical carcinoma, and head and neck cancer). We further show that this germ cell-like transcriptional program, even when reduced to the top two genes (CDKN2A and SYCP2), serves as a fingerprint of oncogenic HPVs with implications for early detection, diagnosis, and therapy of all HPV-driven cancers.","authors":"Leiendecker, L., Neumann, T., Jung, PS., Cronin, SM., Steinacker, TL., Schleiffer, A., Schutzbier, M., Mechtler, K., Kervarrec, T., Laurent, E., Bachiri, K., Coyaud, E., Murali, R., Busam, KJ., Itzinger-Monshi, B., Kirnbauer, R., Cerroni, L., Calonje, E., R\u00fctten, A., Stubenrauch, F., Griewank, KG., Wiesner, T., Obenauf, AC.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Cancer Discov","volume":"13","issue":"1","page":"70-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36103529","title":"A self-generated Toddler gradient guides mesodermal cell migration.","abstract":"The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler\/ELABELA\/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor-based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo.","authors":"Stock, J., Kazmar, T., Schlumm, F., Hannezo, E., Pauli, A.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Sci Adv","volume":"8","issue":"37","page":"eadd2488","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.12.16.472981v1","articledate":"2022-09-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36189249","title":"Comprehensive CRISPR-Cas9 screen identifies factors which are important for plasmablast development.","abstract":"Plasma cells (PCs) and their progenitors plasmablasts (PBs) are essential for the acute and long-term protection of the host against infections by providing vast levels of highly specific antibodies. Several transcription factors, like Blimp1 and Irf4, are already known to be essential for PC and PB differentiation and survival. We set out to identify additional genes, that are essential for PB development by CRISPR-Cas9 screening of 3,000 genes for the loss of PBs by employing the <i>in vitro<\/i>-inducible germinal center B cell (iGB) culture system and Rosa26<sup>Cas9\/+<\/sup> mice. Identified hits in the screen were <i>Mau2<\/i> and <i>Nipbl<\/i>, which are known to contribute to the loop extrusion function of the cohesin complex. Other examples of promising hits were <i>Taf6<\/i>, <i>Stat3<\/i>, <i>Ppp6c<\/i> and <i>Pgs1<\/i>. We thus provide a new set of genes, which are important for PB development.","authors":"Pinter, T., Fischer, M., Sch\u00e4fer, M., Fellner, M., Jude, J., Zuber, J., Busslinger, M., W\u00f6hner, M.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Front Immunol","volume":"13","issue":null,"page":"979606","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36097293","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1.","abstract":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.","authors":"Prattes, M., Grishkovskaya, I., Hodirnau, VV., Hetzmannseder, C., Zisser, G., Sailer, C., Kargas, V., Loibl, M., Gerhalter, M., Kofler, L., Warren, AJ., Stengel, F., Haselbach, D., Bergler, H.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Struct Mol Biol","volume":"29","issue":"9","page":"942-953","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36074822","title":"Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins.","abstract":"Mammalian cells can generate amino acids through macropinocytosis and lysosomal breakdown of extracellular proteins, which is exploited by cancer cells to grow in nutrient-poor tumors. Through genetic screens in defined nutrient conditions, we characterized LYSET, a transmembrane protein (TMEM251) selectively required when cells consume extracellular proteins. LYSET was found to associate in the Golgi with GlcNAc-1-phosphotransferase, which targets catabolic enzymes to lysosomes through mannose-6-phosphate modification. Without LYSET, GlcNAc-1-phosphotransferase was unstable because of a hydrophilic transmembrane domain. Consequently, LYSET-deficient cells were depleted of lysosomal enzymes and impaired in turnover of macropinocytic and autophagic cargoes. Thus, LYSET represents a core component of the lysosomal enzyme trafficking pathway, underlies the pathomechanism for hereditary lysosomal storage disorders, and may represent a target to suppress metabolic adaptations in cancer.","authors":"Pechincha, C., Groessl, S., Kalis, R., de Almeida, M., Zanotti, A., Wittmann, M., Schneider, M., de Campos, RP., Rieser, S., Brandstetter, M., Schleiffer, A., M\u00fcller-Decker, K., Helm, D., Jabs, S., Haselbach, D., Lemberg, MK., Zuber, J., Palm, W.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Science","volume":"378","issue":"6615","page":"eabn5637","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35930970","title":"Structural basis of mRNA maturation: Time to put it together.","abstract":"In eukaryotes, the expression of genetic information begins in the cell nucleus with precursor messenger RNA (pre-mRNA) transcription and processing into mature mRNA. The mRNA is subsequently recognized and packaged by proteins into an mRNA ribonucleoprotein complex (mRNP) and exported to the cytoplasm for translation. Each of the nuclear mRNA maturation steps is carried out by a dedicated molecular machine. Here, we highlight recent structural and mechanistic insights into how these machines function, including the capping enzyme, the spliceosome, the 3'-end processing machinery, and the transcription-export complex. While we increasingly understand individual steps of nuclear gene expression, many questions remain. For example, we are only beginning to reveal how mature mRNAs are recognized and packaged for nuclear export and how mRNA maturation events are coupled to transcription and to each other. Advances in the preparation of recombinant and endogenous protein-nucleic acid complexes, cryo-electron microscopy, and machine learning promise exciting insights into the mechanisms of nuclear gene expression and its spatial organization.","authors":"Vorl\u00e4nder, MK., Pacheco-Fiallos, B., Plaschka, C.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Curr Opin Struct Biol","volume":"75","issue":null,"page":"102431","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36113480","title":"Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers.","abstract":"Gene transcription is a highly regulated process in all animals. In Drosophila, two major transcriptional programs, housekeeping and developmental, have promoters with distinct regulatory compatibilities and nucleosome organization. However, it remains unclear how the differences in chromatin structure relate to the distinct regulatory properties and which chromatin remodelers are required for these programs. Using rapid degradation of core remodeler subunits in Drosophila melanogaster S2 cells, we demonstrate that developmental gene transcription requires SWI\/SNF-type complexes, primarily to maintain distal enhancer accessibility. In contrast, wild-type-level housekeeping gene transcription requires the Iswi and Ino80 remodelers to maintain nucleosome positioning and phasing at promoters. These differential remodeler dependencies relate to different DNA-sequence-intrinsic nucleosome affinities, which favor a default ON state for housekeeping but a default OFF state for developmental gene transcription. Overall, our results demonstrate how different transcription-regulatory strategies are implemented by DNA sequence, chromatin structure, and remodeler activity.","authors":"Hendy, O., Serebreni, L., Bergauer, K., Muerdter, F., Huber, L., Nem\u010dko, F., Stark, A.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Mol Cell","volume":"82","issue":"19","page":"3598-3612.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36048956","title":"Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration.","abstract":"Salamanders are tetrapod models to study brain organization and regeneration; however, the identity and evolutionary conservation of brain cell types are largely unknown. We delineated the cell populations in the axolotl telencephalon during homeostasis and regeneration using single-cell genomic profiling. We identified glutamatergic neurons with similarities to amniote neurons of hippocampus, dorsal and lateral cortex, and conserved \u03b3-aminobutyric acid-releasing (GABAergic) neuron classes. We inferred transcriptional dynamics and gene regulatory relationships of postembryonic, region-specific neurogenesis and unraveled conserved differentiation signatures. After brain injury, ependymoglia activate an injury-specific state before reestablishing lost neuron populations and axonal connections. Together, our analyses yield insights into the organization, evolution, and regeneration of a tetrapod nervous system.","authors":"Lust, K., Maynard, A., Gomes, T., Fleck, JS., Camp, JG., Tanaka, EM., Treutlein, B.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Science","volume":"377","issue":"6610","page":"eabp9262","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35773262","title":"The specialist in regeneration-the Axolotl-a suitable model to study bone healing?","abstract":"While the axolotl's ability to completely regenerate amputated limbs is well known and studied, the mechanism of axolotl bone fracture healing remains poorly understood. One reason might be the lack of a standardized fracture fixation in axolotl. We present a surgical technique to stabilize the osteotomized axolotl femur with a fixator plate and compare it to a non-stabilized osteotomy and to limb amputation. The healing outcome was evaluated 3 weeks, 3, 6 and 9 months post-surgery by microcomputer tomography, histology and immunohistochemistry. Plate-fixated femurs regained bone integrity more efficiently in comparison to the non-fixated osteotomized bone, where larger callus formed, possibly to compensate for the bone fragment misalignment. The healing of a non-critical osteotomy in axolotl was incomplete after 9 months, while amputated limbs efficiently restored bone length and structure. In axolotl amputated limbs, plate-fixated and non-fixated fractures, we observed accumulation of PCNA<sup>+<\/sup> proliferating cells at 3 weeks post-injury similar to mouse. Additionally, as in mouse, SOX9-expressing cells appeared in the early phase of fracture healing and amputated limb regeneration in axolotl, preceding cartilage formation. This implicates endochondral ossification to be the probable mechanism of bone healing in axolotls. Altogether, the surgery with a standardized fixation technique demonstrated here allows for controlled axolotl bone healing experiments, facilitating their comparison to mammals (mice).","authors":"Polikarpova, A., Ellinghaus, A., Schmidt-Bleek, O., Grosser, L., Bucher, CH., Duda, GN., Tanaka, EM., Schmidt-Bleek, K.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"NPJ Regen Med","volume":"7","issue":"1","page":"35","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35587651","title":"Canonical Wnt signaling and the regulation of divergent mesenchymal Fgf8 expression in axolotl limb development and regeneration.","abstract":"The expression of fibroblast growth factors (Fgf) ligands in a specialized epithelial compartment, the Apical Ectodermal Ridge (AER), is a conserved feature of limb development across vertebrate species. In vertebrates, <i>Fgf 4<\/i>, <i>8<\/i>, <i>9<\/i>, and <i>17<\/i> are all expressed in the AER. An exception to this paradigm is the salamander (axolotl) developing and regenerating limb, where key Fgf ligands are expressed in the mesenchyme. The mesenchymal expression of Amex.<i>Fgf8<\/i> in axolotl has been suggested to be critical for regeneration. To date, there is little knowledge regarding what controls Amex.<i>Fgf8<\/i> expression in the axolotl limb mesenchyme. A large body of mouse and chick studies have defined a set of transcription factors and canonical Wnt signaling as the main regulators of epidermal <i>Fgf8<\/i> expression in these organisms. In this study, we address the hypothesis that alterations to one or more of these components during evolution has resulted in mesenchymal Amex.<i>Fgf8<\/i> expression in the axolotl. To sensitively quantify gene expression with spatial precision, we combined optical clearing of whole-mount axolotl limb tissue with single molecule fluorescent in situ hybridization and a semiautomated quantification pipeline. Several candidate upstream components were found expressed in the axolotl ectoderm, indicating that they are not direct regulators of Amex.<i>Fgf8<\/i> expression. We found that Amex.<i>Wnt3a<\/i> is expressed in axolotl limb epidermis, similar to chicken and mouse. However, unlike in amniotes, Wnt target genes are activated preferentially in limb mesenchyme rather than in epidermis. Inhibition and activation of Wnt signaling results in downregulation and upregulation of mesenchymal Amex.<i>Fgf8<\/i> expression, respectively. These results implicate a shift in tissue responsiveness to canonical Wnt signaling from epidermis to mesenchyme as one step contributing to the unique mesenchymal Amex.<i>Fgf8<\/i> expression seen in the axolotl.","authors":"Glotzer, GL., Tardivo, P., Tanaka, EM.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Elife","volume":"11","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35581155","title":"Inducible and tissue-specific cell labeling in Cre-ER<sup>T2<\/sup> transgenic Xenopus lines.","abstract":"Investigating cell lineage requires genetic tools that label cells in a temporal and tissue-specific manner. The bacteriophage-derived Cre-ER<sup>T2<\/sup> \/loxP system has been developed as a genetic tool for lineage tracing in many organisms. We recently reported a stable transgenic Xenopus line with a Cre-ER<sup>T2<\/sup> \/loxP system driven by the mouse Prrx1 (mPrrx1) enhancer to trace limb fibroblasts during the regeneration process (Prrx1:CreER line). Here we describe the detailed technological development and characterization of such line. Transgenic lines carrying a CAG promoter-driven Cre-ER<sup>T2<\/sup> \/loxP system showed conditional labeling of muscle, epidermal, and interstitial cells in both the tadpole tail and the froglet leg upon 4-hydroxytamoxifen (4OHT) treatment. We further improved the labeling efficiency in the Prrx1:CreER lines from 12.0% to 32.9% using the optimized 4OHT treatment regime. Careful histological examination showed that Prrx1:CreER lines also sparsely labeled cells in the brain, spinal cord, head dermis, and fibroblasts in the tail. This work provides the first demonstration of conditional, tissue-specific cell labeling with the Cre-ER<sup>T2<\/sup> \/loxP system in stable transgenic Xenopus lines.","authors":"Lin, TY., Taniguchi-Sugiura, Y., Murawala, P., Hermann, S., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Dev Growth Differ","volume":"64","issue":"5","page":"243-253","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35241664","title":"Tig1 regulates proximo-distal identity during salamander limb regeneration.","abstract":"Salamander limb regeneration is an accurate process which gives rise exclusively to the missing structures, irrespective of the amputation level. This suggests that cells in the stump have an awareness of their spatial location, a property termed positional identity. Little is known about how positional identity is encoded, in salamanders or other biological systems. Through single-cell RNAseq analysis, we identified Tig1\/Rarres1 as a potential determinant of proximal identity. Tig1 encodes a conserved cell surface molecule, is regulated by retinoic acid and exhibits a graded expression along the proximo-distal axis of the limb. Its overexpression leads to regeneration defects in the distal elements and elicits proximal displacement of blastema cells, while its neutralisation blocks proximo-distal cell surface interactions. Critically, Tig1 reprogrammes distal cells to a proximal identity, upregulating Prod1 and inhibiting Hoxa13 and distal transcriptional networks. Thus, Tig1 is a central cell surface determinant of proximal identity in the salamander limb.","authors":"Oliveira, CR., Knapp, D., Elewa, A., Gerber, T., Gonzalez Malagon, SG., Gates, PB., Walters, HE., Petzold, A., Arce, H., Cordoba, RC., Subramanian, E., Chara, O., Tanaka, EM., Simon, A., Yun, MH.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Nat Commun","volume":"13","issue":"1","page":"1141","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34607829","title":"Positional Memory in Vertebrate Regeneration: A Century's Insights from the Salamander Limb.","abstract":"Salamanders, such as axolotls and newts, can regenerate complex tissues including entire limbs. But what mechanisms ensure that an amputated limb regenerates a limb, and not a tail or unpatterned tissue? An important concept in regeneration is positional memory-the notion that adult cells \"remember\" spatial identities assigned to them during embryogenesis (e.g., \"head\" or \"hand\") and use this information to restore the correct body parts after injury. Although positional memory is well documented at a phenomenological level, the underlying cellular and molecular bases are just beginning to be decoded. Herein, we review how major principles in positional memory were established in the salamander limb model, enabling the discovery of positional memory-encoding molecules, and advancing insights into their pattern-forming logic during regeneration. We explore findings in other amphibians, fish, reptiles, and mammals and speculate on conserved aspects of positional memory. We consider the possibility that manipulating positional memory in human cells could represent one route toward improved tissue repair or engineering of patterned tissues for therapeutic purposes.","authors":"Otsuki, L., Tanaka, EM.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Cold Spring Harb Perspect Biol","volume":"14","issue":"6","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35926508","title":"The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T\u00a0cell function and immune homeostasis.","abstract":"FoxP3 is an essential transcription factor (TF) for immunologic homeostasis, but how it utilizes the common forkhead DNA-binding domain (DBD) to perform its unique function remains poorly understood. We here demonstrated that unlike other known forkhead TFs, FoxP3 formed a head-to-head dimer using a unique linker (Runx1-binding region [RBR]) preceding the forkhead domain. Head-to-head dimerization conferred distinct DNA-binding specificity and created a docking site for the cofactor Runx1. RBR was also important for proper folding of the forkhead domain, as truncation of RBR induced domain-swap dimerization of forkhead, which was previously considered the physiological form of FoxP3. Rather, swap-dimerization impaired FoxP3 function, as demonstrated with the disease-causing mutation R337Q, whereas a swap-suppressive mutation largely rescued R337Q-mediated functional impairment. Altogether, our findings suggest that FoxP3 can fold into two distinct dimerization states: head-to-head dimerization representing functional specialization of an ancient DBD and swap dimerization associated with impaired functions.","authors":"Leng, F., Zhang, W., Ramirez, RN., Leon, J., Zhong, Y., Hou, L., Yuki, K., van der Veeken, J., Rudensky, AY., Benoist, C., Hur, S.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Immunity","volume":"55","issue":"8","page":"1354-1369.e8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35700740","title":"Genetic tracing reveals transcription factor Foxp3-dependent and Foxp3-independent functionality of peripherally induced Treg cells.","abstract":"Regulatory T (Treg) cells expressing the transcription factor Foxp3 are an essential suppressive T\u00a0cell lineage of dual origin: Foxp3 induction in thymocytes and mature CD4<sup>+<\/sup> T\u00a0cells gives rise to thymic (tTreg) and peripheral (pTreg) Treg cells, respectively. While tTreg cells suppress autoimmunity, pTreg cells enforce tolerance to food and commensal microbiota. However, the role of Foxp3 in pTreg cells and the mechanisms supporting their differentiation remain poorly understood. Here, we used genetic tracing to identify microbiota-induced pTreg cells and found that many of their distinguishing features were Foxp3 independent. Lineage-committed, microbiota-dependent pTreg-like cells persisted in the colon in the absence of Foxp3. While Foxp3 was critical for the suppression of a Th17 cell program, colitis, and mastocytosis, pTreg cells suppressed colonic effector T\u00a0cell expansion in a Foxp3-independent manner. Thus, Foxp3 and the tolerogenic signals that precede and promote its expression independently confer distinct facets of pTreg functionality.","authors":"van der Veeken, J., Campbell, C., Pritykin, Y., Schizas, M., Verter, J., Hu, W., Wang, ZM., Matheis, F., Mucida, D., Charbonnier, LM., Chatila, TA., Rudensky, AY.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Immunity","volume":"55","issue":"7","page":"1173-1184.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34937932","title":"Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families.","abstract":"T cell activation, a key early event in the adaptive immune response, is subject to elaborate transcriptional control. In the present study, we examined how the activities of eight major transcription factor (TF) families are integrated to shape the epigenome of naive and activated CD4 and CD8 T cells. By leveraging extensive polymorphisms in evolutionarily divergent mice, we identified the 'heavy lifters' positively influencing chromatin accessibility. Members of Ets, Runx and TCF\/Lef TF families occupied the vast majority of accessible chromatin regions, acting as 'housekeepers', 'universal amplifiers' and 'placeholders', respectively, at sites that maintained or gained accessibility upon T cell activation. In addition, a small subset of strongly induced immune response genes displayed a noncanonical TF recruitment pattern. Our study provides a key resource and foundation for the understanding of transcriptional and epigenetic regulation in T cells and offers a new perspective on the hierarchical interactions between critical TFs.","authors":"Zhong, Y., Walker, SK., Pritykin, Y., Leslie, CS., Rudensky, AY., van der Veeken, J.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Immunol","volume":"23","issue":"1","page":"122-134","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-02-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36253568","title":"Human cerebral organoids - a new tool for clinical neurology research.","abstract":"The current understanding of neurological diseases is derived mostly from direct analysis of patients and from animal models of disease. However, most patient studies do not capture the earliest stages of disease development and offer limited opportunities for experimental intervention, so rarely yield complete mechanistic insights. The use of animal models relies on evolutionary conservation of pathways involved in disease and is limited by an inability to recreate human-specific processes. In vitro models that are derived from human pluripotent stem cells cultured in 3D have emerged as a new model system that could bridge the gap between patient studies and animal models. In this Review, we summarize how such organoid models can complement classical approaches to accelerate neurological research. We describe our current understanding of neurodevelopment and how this process differs between humans and other animals, making human-derived models of disease essential. We discuss different methodologies for producing organoids and how organoids can be and have been used to model neurological disorders, including microcephaly, Zika virus infection, Alzheimer disease and other neurodegenerative disorders, and neurodevelopmental diseases, such as Timothy syndrome, Angelman syndrome and tuberous sclerosis. We also discuss the current limitations of organoid models and outline how organoids can be used to revolutionize research into the human brain and neurological diseases.","authors":"Eichm\u00fcller, OL., Knoblich, JA.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Nat Rev Neurol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36068014","title":"Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS.","abstract":"This study demonstrates how the latest ultrahigh-performance liquid chromatography (UHPLC) technology can be combined with high-resolution accurate-mass (HRAM) mass spectrometry (MS) and long columns packed with fully porous particles to improve bottom-up proteomics analysis with nanoflow liquid chromatography-mass spectrometry (nanoLC-MS) methods. The increased back pressures from the UHPLC system enabled the use of 75 \u03bcm I.D. \u00d7 75 cm columns packed with 2 \u03bcm particles at a typical 300 nL\/min flow rate as well as elevated and reduced flow rates. The constant pressure pump operation at 1500 bar reduced sample loading and column washing\/equilibration stages and overall overhead time, which maximizes MS utilization time. The versatility of flow rate optimization to balance the sensitivity, throughput with sample loading amount, and capability of using longer gradients contributes to a greater number of peptide and protein identifications for single-shot bottom-up proteomics experiments. The routine proteome profiling and precise quantification of &gt;7000 proteins with single-shot nanoLC-MS analysis open possibilities for large-scale discovery studies with a deep dive into the protein level alterations. Data are available via ProteomeXchange with identifier PXD035665.","authors":"Zheng, R., Stejskal, K., Pynn, C., Mechtler, K., Boychenko, A.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"J Proteome Res","volume":"21","issue":"10","page":"2545-2551","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35576154","title":"Cryo-EM structure of the plant 26S proteasome.","abstract":"Targeted proteolysis is a hallmark of life. It is especially important in long-lived cells that can be found in higher eukaryotes, like plants. This task is mainly fulfilled by the ubiquitin-proteasome system. Thus, proteolysis by the 26S proteasome is vital to development, immunity, and cell division. Although the yeast and animal proteasomes are well characterized, there is only limited information on the plant proteasome. We determined the first plant 26S proteasome structure from Spinacia oleracea by single-particle electron cryogenic microscopy\u00a0at an overall resolution of 3.3\u00a0\u00c5. We found an almost identical overall architecture of the spinach proteasome compared with the known structures from mammals and yeast. Nevertheless, we noticed a structural difference in the proteolytic active \u03b21 subunit. Furthermore, we uncovered an unseen compression state by characterizing the proteasome's conformational landscape. We suspect that this new conformation of the 20S core protease, in correlation with a partial opening of the unoccupied gate, may contribute to peptide release after proteolysis. Our data provide a structural basis for the plant proteasome, which is crucial for further studies.","authors":"Kandolf, S., Grishkovskaya, I., Bela\u010di\u0107, K., Bolhuis, DL., Amann, S., Foster, B., Imre, R., Mechtler, K., Schleiffer, A., Tagare, HD., Zhong, ED., Meinhart, A., Brown, NG., Haselbach, D.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Plant Commun","volume":"3","issue":"3","page":"100310","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36261017","title":"SMC complexes can traverse physical roadblocks bigger than their ring size.","abstract":"Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in\u00a0vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to loop extrusion by yeast condensin. We find that even DNA-bound nanoparticles as large as 200\u00a0nm, much bigger than the SMC ring size, also translocate into DNA loops during extrusion by condensin and cohesin. This even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open to entrap DNA. The data show that SMC-driven loop extrusion has surprisingly little difficulty in accommodating large roadblocks into the loop. The findings also show that the extruded DNA does not pass through the SMC ring (pseudo)topologically, hence pointing to a nontopological mechanism for DNA loop extrusion.","authors":"Pradhan, B., Barth, R., Kim, E., Davidson, IF., Bauer, B., van Laar, T., Yang, W., Ryu, JK., van der Torre, J., Peters, JM., Dekker, C.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cell Rep","volume":"41","issue":"3","page":"111491","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.08.02.502451v1","articledate":"2022-10-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36333500","title":"DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions.","abstract":"Genomic imprinting is regulated by parental-specific DNA methylation of imprinting control regions (ICRs). Despite an identical DNA sequence, ICRs can exist in two distinct epigenetic states that are memorized throughout unlimited cell divisions and reset during germline formation. Here, we systematically study the genetic and epigenetic determinants of this epigenetic bistability. By iterative integration of ICRs and related DNA sequences to an ectopic location in the mouse genome, we first identify the DNA sequence features required for maintenance of epigenetic states in embryonic stem cells. The autonomous regulatory properties of ICRs further enabled us to create DNA-methylation-sensitive reporters and to screen for key components involved in regulating their epigenetic memory. Besides DNMT1, UHRF1 and ZFP57, we identify factors that prevent switching from methylated to unmethylated states and show that two of these candidates, ATF7IP and ZMYM2, are important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.","authors":"Butz, S., Schmolka, N., Karemaker, ID., Villase\u00f1or, R., Schwarz, I., Domcke, S., Uijttewaal, ECH., Jude, J., Lienert, F., Krebs, AR., de Wagenaar, NP., Bao, X., Zuber, J., Elling, U., Sch\u00fcbeler, D., Baubec, T.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Nat Genet","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-11-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36332029","title":"The HUSH complex controls brain architecture and protocadherin fidelity.","abstract":"The HUSH (human silencing hub) complex contains the H3K9me3 binding protein M-phase phosphoprotein 8 (MPP8) and recruits the histone methyltransferase SETDB1 as well as Microrchidia CW-type zinc finger protein 2 (MORC2). Functional and mechanistic studies of the HUSH complex have hitherto been centered around SETDB1 while the in vivo functions of MPP8 and MORC2 remain elusive. Here, we show that genetic inactivation of <i>Mphosph8<\/i> or <i>Morc2a<\/i> in the nervous system of mice leads to increased brain size, altered brain architecture, and behavioral changes. Mechanistically, in both mouse brains and human cerebral organoids, MPP8 and MORC2 suppress the repetitive-like protocadherin gene cluster in an H3K9me3-dependent manner. Our data identify MPP8 and MORC2, previously linked to silencing of repetitive elements via the HUSH complex, as key epigenetic regulators of protocadherin expression in the nervous system and thereby brain development and neuronal individuality in mice and humans.","authors":"Hagelkruys, A., Horrer, M., Taubenschmid-Stowers, J., Kavirayani, A., Novatchkova, M., Orthofer, M., Pai, TP., Cikes, D., Zhuk, S., Balma\u00f1a, M., Esk, C., Koglgruber, R., Moeseneder, P., Lazovic, J., Zopf, LM., Cronin, SJF., Elling, U., Knoblich, JA., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Sci Adv","volume":"8","issue":"44","page":"eabo7247","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-11-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36323866","title":"StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement.","abstract":"Cryogenic electron microscopy (cryo-EM) data represent density maps of macromolecular systems at atomic or near-atomic resolution. However, building and refining 3D atomic models by using data from cryo-EM maps is not straightforward and requires significant hands-on experience and manual intervention. We recently developed StarMap, an easy-to-use interface between the popular structural display program ChimeraX and Rosetta, a powerful molecular modeling engine. StarMap offers a general approach for refining structural models of biological macromolecules into cryo-EM density maps by combining Monte Carlo sampling with local density-guided optimization, Rosetta-based all-atom refinement and real-space B-factor calculations in a straightforward workflow. StarMap includes options for structural symmetry, local refinements and independent model validation. The overall quality of the refinement and the structure resolution is then assessed via analytical outputs, such as magnification calibration (pixel size calibration) and Fourier shell correlations. Z-scores reported by StarMap provide an easily interpretable indicator of the goodness of fit for each residue and can be plotted to evaluate structural models and improve local residue refinements, as well as to identify flexible regions and potentially functional sites in large macromolecular complexes. The protocol requires general computer skills, without the need for coding expertise, because most parts of the workflow can be operated by clicking tabs within the ChimeraX graphical user interface. Time requirements for the model refinement depend on the size and quality of the input data; however, this step can typically be completed within 1 d. The analytical parts of the workflow are completed within minutes.","authors":"Lugmayr, W., Kotov, V., Goessweiner-Mohr, N., Wald, J., DiMaio, F., Marlovits, TC.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Protoc","volume":"18","issue":"1","page":"239-264","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36356180","title":"Deep Proteome Profiling with Reduced Carryover Using Superficially Porous Microfabricated nanoLC Columns.","abstract":"In the field of liquid chromatography-mass spectrometry (LC-MS)-based proteomics, increases in the sampling depth and proteome coverage have mainly been accomplished by rapid advances in mass spectrometer technology. The comprehensiveness and quality of the data that can be generated do, however, also depend on the performance provided by nano-liquid chromatography (nanoLC) separations. Proper selection of reversed-phase separation columns can be important to provide the MS instrument with peptides at the highest possible concentration and separated at the highest possible resolution. In the current contribution, we evaluate the use of the prototype generation 2 \u03bcPAC nanoLC columns, which use C18-functionalized superficially porous micropillars as a stationary phase. When compared to traditionally used fully porous silica stationary phases, more precursors could be characterized when performing single shot data-dependent LC-MS\/MS analyses of a human cell line tryptic digest. Up to 30% more protein groups and 60% more unique peptides were identified for short gradients (10 min) and limited sample amounts (10-100 ng of cell lysate digest). With LC-MS gradient times of 10, 60, 120, and 180 min, respectively, we identified 2252, 6513, 7382, and 8174 protein groups with 25, 500, 1000, and 2000 ng of the sample loaded on the column. Reduction of sample carryover to the next run (up to 2 to 3%) and decreased levels of methionine oxidation (up to 3-fold) were identified as additional figures of merit. When analyzing a disuccinimidyl dibutyric urea-crosslinked synthetic library, 29 to 59 more unique crosslinked peptides could be identified at an experimentally validated false discovery rate of 1-2%.","authors":"Stejskal, K., Jeff, OB., Matzinger, M., D\u00fcrnberger, G., Boychenko, A., Jacobs, P., Mechtler, K.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Anal Chem","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-11-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36368996","title":"Clinical parameters obtained during tear film examination in domestic rabbits.","abstract":"on Status=\"MEDLINE\" IndexingMethod=\"Automated\" Owner=\"NLM\"><PMID Version=\"1\">36368996<\/PMID><DateCompleted><Year>2022<\/Year><Month>11<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2022<\/Year><Month>11<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1746-6148<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>18<\/Volume><Issue>1<\/Issue><PubDate><Year>2022<\/Year><Month>Nov<\/Month><Day>12<\/Day><\/PubDate><\/JournalIssue><Title>BMC veterinary research<\/Title><ISOAbbreviation>BMC Vet Res<\/ISOAbbreviation><\/Journal><ArticleTitle>Clinical parameters obtained during tear film examination in domestic rabbits.<\/ArticleTitle><Pagination><MedlinePgn>398<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12917-022-03492-1<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">One of the contributing factors to ocular surface health is a stable precorneal tear film. Considering the increasing interest in rabbits as pets and the limited literature available on domestic rabbit tearing, the aim of this study was to establish normative data for examination of the tear film in domestic rabbits.","authors":"Corsi, F., Arteaga, K., Corsi, F., Masi, M., Cattaneo, A., Selleri, P., Crasta, M., Peruccio, C., Guandalini, A.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"BMC Vet Res","volume":"18","issue":"1","page":"398","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-11-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36443325","title":"Targeting APLN\/APJ restores blood-testis barrier and improves spermatogenesis in murine and human diabetic models.","abstract":"Type 2 diabetes mellitus is one of the most prevalent metabolic diseases presenting with systemic pathologies, including reproductive disorders in male diabetic patients. However, the molecular mechanisms that contributing to spermatogenesis dysfunction in diabetic patients have not yet been fully elucidated. Here, we perform STRT-seq to examine the transcriptome of diabetic patients' testes at single-cell resolution including all major cell types of the testis. Intriguingly, whereas spermatogenesis appears largely preserved, the gene expression profiles of Sertoli cells and the blood-testis barrier (BTB) structure are dramatically impaired. Among these deregulate pathways, the Apelin (APLN) peptide\/Apelin-receptor (APJ) axis is hyper-activated in diabetic patients' testes. Mechanistically, APLN is produced locally by Sertoli cells upon high glucose treatment, which subsequently suppress the production of carnitine and repress the expression of cell adhesion genes in Sertoli cells. Together, these effects culminate in BTB structural dysfunction. Finally, using the small molecule APLN receptor antagonist, ML221, we show that blocking APLN\/APJ significantly ameliorate the BTB damage and, importantly, improve functional spermatogenesis in diabetic db\/db mice. We also translate and validate these findings in cultured human testes. Our findings identify the APLN\/APJ axis as a promising therapeutic target to improve reproduction capacity in male diabetic patients.","authors":"Song, K., Yang, X., An, G., Xia, X., Zhao, J., Xu, X., Wan, C., Liu, T., Zheng, Y., Ren, S., Wang, M., Chang, G., Cronin, SJF., Penninger, JM., Jing, T., Ou, X., Rao, S., Liu, Z., Zhao, XY.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Nat Commun","volume":"13","issue":"1","page":"7335","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-12-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36423263","title":"Zygotic genome activation by the totipotency pioneer factor Nr5a2.","abstract":"Life begins with a switch in genetic control from the maternal to the embryonic genome during zygotic genome activation (ZGA). Despite its importance, the essential regulators of ZGA remain largely unknown in mammals. Based on de novo motif searches, we identified the orphan nuclear receptor Nr5a2 as a key activator of major ZGA in mouse 2-cell embryos. Nr5a2 is required for progression beyond the 2-cell stage. It binds to its motif within <i>SINE B1\/Alu<\/i> retrotransposable elements found in <i>cis<\/i>-regulatory regions of ZGA genes. Chemical inhibition suggests that 72% of ZGA genes are regulated by Nr5a2 and potentially other orphan nuclear receptors. Nr5a2 promotes chromatin accessibility during ZGA and binds nucleosomal DNA in vitro. We conclude that Nr5a2 is an essential pioneer factor that regulates ZGA.","authors":"Gassler, J., Kobayashi, W., G\u00e1sp\u00e1r, I., Ruangroengkulrith, S., Mohanan, A., G\u00f3mez Hern\u00e1ndez, L., Kravchenko, P., K\u00fcmmecke, M., Lalic, A., Rifel, N., Ashburn, RJ., Zaczek, M., Vallot, A., Cuenca Rico, L., Ladst\u00e4tter, S., Tachibana, K.","publication_status":"aheadofprint","journalpubyear":"2022","journaltitle":"Science","volume":null,"issue":null,"page":"eabn7478","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-11-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36566234","title":"Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level.","abstract":"Recent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. We report that the Spike trimer acts as a highly dynamic molecular caliper, thereby forming up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) Variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, as opposed to the early Wuhan-1 isolate. Delta Spike shows rapid binding of all three Spike RBDs to three different ACE2 molecules with considerably increased bond lifetime when compared to the reference strain, thereby significantly amplifying avidity. Intriguingly, Omicron (B.1.1.529) Spike displays less multivalent bindings to ACE2 molecules, yet with a ten time longer bond lifetime than Delta. Delta and Omicron (B.1.1.529) Spike variants enhance and prolong viral attachment to the host, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncover distinct binding mechanisms and strategies at single-molecule resolution, employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.","authors":"Zhu, R., Canena, D., Sikora, M., Klausberger, M., Seferovic, H., Mehdipour, AR., Hain, L., Laurent, E., Monteil, V., Wirnsberger, G., Wieneke, R., Tamp\u00e9, R., Kienzl, NF., Mach, L., Mirazimi, A., Oh, YJ., Penninger, JM., Hummer, G., Hinterdorfer, P.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Nat Commun","volume":"13","issue":"1","page":"7926","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36545802","title":"Systematic identification and characterization of repressive domains in Drosophila transcription factors.","abstract":"All multicellular life relies on differential gene expression, determined by regulatory DNA elements and DNA-binding transcription factors that mediate activation and repression via cofactor recruitment. While activators have been extensively characterized, repressors are less well studied: the identities and properties of their repressive domains (RDs) are typically unknown and the specific co-repressors (CoRs) they recruit have not been determined. Here, we develop a high-throughput, next-generation sequencing-based screening method, repressive-domain (RD)-seq, to systematically identify RDs in complex DNA-fragment libraries. Screening more than 200,000 fragments covering the coding sequences of all transcription-related proteins in Drosophila melanogaster, we identify 195 RDs in known repressors and in proteins not previously associated with repression. Many RDs contain recurrent short peptide motifs, which are conserved between fly and human and are required for RD function, as demonstrated by motif mutagenesis. Moreover, we show that RDs that contain one of five distinct repressive motifs interact with and depend on different CoRs, such as Groucho, CtBP, Sin3A, or Smrter. These findings advance our understanding of repressors, their sequences, and the functional impact of sequence-altering mutations and should provide a valuable resource for further studies.","authors":"Klaus, L., de Almeida, BP., Vlasova, A., Nem\u010dko, F., Schleiffer, A., Bergauer, K., Hofbauer, L., Rath, M., Stark, A.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"EMBO J","volume":"42","issue":"3","page":"e112100","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36624495","title":"Electric field stimulation boosts neuronal differentiation of neural stem cells for spinal cord injury treatment via PI3K\/Akt\/GSK-3&#x3b2;\/&#x3b2;-catenin activation.","abstract":"on Status=\"PubMed-not-MEDLINE\" Owner=\"NLM\"><PMID Version=\"1\">36624495<\/PMID><DateRevised><Year>2023<\/Year><Month>01<\/Month><Day>12<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Print\">2045-3701<\/ISSN><JournalIssue CitedMedium=\"Print\"><Volume>13<\/Volume><Issue>1<\/Issue><PubDate><Year>2023<\/Year><Month>Jan<\/Month><Day>09<\/Day><\/PubDate><\/JournalIssue><Title>Cell &amp; bioscience<\/Title><ISOAbbreviation>Cell Biosci<\/ISOAbbreviation><\/Journal><ArticleTitle>Electric field stimulation boosts neuronal differentiation of neural stem cells for spinal cord injury treatment via PI3K\/Akt\/GSK-3&#x3b2;\/&#x3b2;-catenin activation.<\/ArticleTitle><Pagination><StartPage>4<\/StartPage><MedlinePgn>4<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">4<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13578-023-00954-3<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Neural stem cells (NSCs) are considered as candidates for cell replacement therapy in many neurological disorders. However, the propensity for their differentiation to proceed more glial rather than neuronal phenotypes in pathological conditions limits positive outcomes of reparative transplantation. Exogenous physical stimulation to favor the neuronal differentiation of NSCs without extra chemical side effect could alleviate the problem, providing a safe and highly efficient cell therapy to accelerate neurological recovery following neuronal injuries.","authors":"Liu, Q., Telezhkin, V., Jiang, W., Gu, Y., Wang, Y., Hong, W., Tian, W., Yarova, P., Zhang, G., Lee, SM., Zhang, P., Zhao, M., Allen, ND., Hirsch, E., Penninger, J., Song, B.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Cell Biosci","volume":"13","issue":"1","page":"4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36618345","title":"The Xbp1-regulated transcription factor Mist1 restricts antibody secretion by restraining Blimp1 expression in plasma cells.","abstract":"Antibody secretion by plasma cells provides acute and long-term protection against pathogens. The high secretion potential of plasma cells depends on the unfolded protein response, which is controlled by the transcription factor Xbp1. Here, we analyzed the Xbp1-dependent gene expression program of plasma cells and identified <i>Bhlha15<\/i> (Mist1) as the most strongly activated Xbp1 target gene. As Mist1 plays an important role in other secretory cell types, we analyzed in detail the phenotype of Mist1-deficient plasma cells in <i>Cd23<\/i>-Cre <i>Bhlha15<\/i> <sup>fl\/fl<\/sup> mice under steady-state condition or upon NP-KLH immunization. Under both conditions, Mist1-deficient plasma cells were 1.4-fold reduced in number and exhibited increased IgM production and antibody secretion compared to control plasma cells. At the molecular level, Mist1 regulated a largely different set of target genes compared with Xbp1. Notably, expression of the Blimp1 protein, which is known to activate immunoglobulin gene expression and to contribute to antibody secretion, was 1.3-fold upregulated in Mist1-deficient plasma cells, which led to a moderate downregulation of most Blimp1-repressed target genes in the absence of Mist1. Importantly, a 2-fold reduction of Blimp1 (<i>Prdm1<\/i>) expression was sufficient to restore the cell number and antibody expression of plasma cells in <i>Prdm1<\/i> <sup>Gfp\/+<\/sup> <i>Cd23<\/i>-Cre <i>Bhlha15<\/i> <sup>fl\/fl<\/sup> mice to the same level seen in control mice. Together, these data indicate that Mist1 restricts antibody secretion by restraining Blimp1 expression, which likely contributes to the viability of plasma cells.","authors":"W\u00f6hner, M., Pinter, T., B\u00f6nelt, P., Hagelkruys, A., Kostanova-Poliakova, D., Stadlmann, J., Konieczny, SF., Fischer, M., Jaritz, M., Busslinger, M.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Front Immunol","volume":"13","issue":null,"page":"859598","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36604593","title":"ZFP462 safeguards neural lineage specification by targeting G9A\/GLP-mediated heterochromatin to silence enhancers.","abstract":"ZNF462 haploinsufficiency is linked to Weiss-Kruszka syndrome, a genetic disorder characterized by neurodevelopmental defects, including autism. Though conserved in vertebrates and essential for embryonic development, the molecular functions of ZNF462 remain unclear. We identified its murine homologue ZFP462 in a screen for mediators of epigenetic gene silencing. Here we show that ZFP462 safeguards neural lineage specification of mouse embryonic stem cells (ESCs) by targeting the H3K9-specific histone methyltransferase complex G9A\/GLP to silence meso-endodermal genes. ZFP462 binds to transposable elements that are potential enhancers harbouring pluripotency and meso-endoderm transcription factor binding sites. Recruiting G9A\/GLP, ZFP462 seeds heterochromatin, restricting transcription factor binding. Loss of ZFP462 in ESCs results in increased chromatin accessibility at target sites and ectopic expression of meso-endodermal genes. Taken together, ZFP462 confers lineage and locus specificity to the broadly expressed epigenetic regulator G9A\/GLP. Our results suggest that aberrant activation of lineage non-specific genes in the neuronal lineage underlies ZNF462-associated neurodevelopmental pathology.","authors":"Yelagandula, R., Stecher, K., Novatchkova, M., Michetti, L., Michlits, G., Wang, J., Hofbauer, P., Vainorius, G., Pribitzer, C., Isbel, L., Mendjan, S., Sch\u00fcbeler, D., Elling, U., Brennecke, J., Bell, O.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Nat Cell Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36653451","title":"A molecular network of conserved factors keeps ribosomes dormant in the egg.","abstract":"Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed<sup>1-4<\/sup>. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4-eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1&#xa0;in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.","authors":"Leesch, F., Lorenzo-Orts, L., Pribitzer, C., Grishkovskaya, I., Roehsner, J., Chugunova, A., Matzinger, M., Roitinger, E., Bela\u010di\u0107, K., Kandolf, S., Lin, TY., Mechtler, K., Meinhart, A., Haselbach, D., Pauli, A.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.11.03.467131v1.article-metrics","articledate":"2023-01-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36688604","title":"MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search.","abstract":"Spectral library search can enable more sensitive peptide identification in tandem mass spectrometry experiments. However, its drawbacks are the limited availability of high-quality libraries and the added difficulty of creating decoy spectra for result validation. We describe MS Ana, a new spectral library search engine that enables high sensitivity peptide identification using either curated or predicted spectral libraries as well as robust false discovery control through its own decoy library generation algorithm. MS Ana identifies on average 36% more spectrum matches and 4% more proteins than database search in a benchmark test on single-shot human cell-line data. Further, we demonstrate the quality of the result validation with tests on synthetic peptide pools and show the importance of library selection through a comparison of library search performance with different configurations of publicly available human spectral libraries.","authors":"Dorl, S., Winkler, S., Mechtler, K., Dorfer, V.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"J Proteome Res","volume":"22","issue":"2","page":"462-470","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36669817","title":"Genotoxic effects of occupational exposure to glass fibres&#xa0;-&#xa0;A human biomonitoring study.","abstract":"As part of a large human biomonitoring study, we conducted occupational monitoring in a glass fibre factory in Slovakia. Shopfloor workers (n&#xa0;=&#xa0;80), with a matched group of administrators in the same factory (n&#xa0;=&#xa0;36), were monitored for exposure to glass fibres and to polycyclic aromatic hydrocarbons (PAHs). The impact of occupational exposure on chromosomal aberrations, DNA damage and DNA repair, immunomodulatory markers, and the role of nutritional and lifestyle factors, as well as the effect of polymorphisms in metabolic and DNA repair genes on genetic stability, were investigated. The (enzyme-modified) comet assay was employed to measure DNA strand breaks (SBs) and apurinic sites, oxidised and alkylated bases. Antioxidant status was estimated by resistance to H<sub>2<\/sub>O<sub>2<\/sub>-induced DNA damage. Base excision repair capacity was measured with an in vitro assay (based on the comet assay). Exposure of workers to fibres was low, but still was associated with higher levels of SBs, and SBs plus oxidised bases, and higher sensitivity to H<sub>2<\/sub>O<sub>2<\/sub>. Multivariate analysis showed that exposure increased the risk of high levels of SBs by 20%. DNA damage was influenced by antioxidant enzymes catalase and glutathione S-transferase (measured in blood). DNA repair capacity was inversely correlated with DNA damage and positively with antioxidant status. An inverse correlation was found between DNA base oxidation and the percentage of eosinophils (involved in the inflammatory response) in peripheral blood of both exposed and reference groups. Genotypes of XRCC1 variants rs3213245 and rs25487 significantly decreased the risk of high levels of base oxidation, to 0.50 (p&#xa0;=&#xa0;0.001) and 0.59 (p&#xa0;=&#xa0;0.001), respectively. Increases in DNA damage owing to glass fibre exposure were significant but modest, and no increases were seen in chromosome aberrations or micronuclei. However, it is of concern that even low levels of exposure to these fibres can cause significant genetic damage.","authors":"Ceppi, M., Smolkova, B., Staruchova, M., Kazimirova, A., Barancokova, M., Volkovova, K., Collins, A., Kocan, A., Dzupinkova, Z., Horska, A., Buocikova, V., Tulinska, J., Liskova, A., Mikusova, ML., Krivosikova, Z., Wsolova, L., Kuba, D., Rund\u00e9n-Pran, E., El Yamani, N., Longhin, EM., Hala\u0161ov\u00e1, E., Kyrtopoulos, S., Bonassi, S., Dusinska, M.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Mutat Res Genet Toxicol Environ Mutagen","volume":"885","issue":null,"page":"503572","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"30910006","title":"Werner syndrome helicase is a selective vulnerability of microsatellite instability-high tumor cells.","abstract":"Targeted cancer therapy is based on exploiting selective dependencies of tumor cells. By leveraging recent functional screening data of cancer cell lines we identify Werner syndrome helicase (WRN) as a novel specific vulnerability of microsatellite instability-high (MSI-H) cancer cells. MSI, caused by defective mismatch repair (MMR), occurs frequently in colorectal, endometrial and gastric cancers. We demonstrate that WRN inactivation selectively impairs the viability of MSI-H but not microsatellite stable (MSS) colorectal and endometrial cancer cell lines. In MSI-H cells, WRN loss results in severe genome integrity defects. ATP-binding deficient variants of WRN fail to rescue the viability phenotype of WRN-depleted MSI-H cancer cells. Reconstitution and depletion studies indicate that WRN dependence is not attributable to acute loss of MMR gene function but might arise during sustained MMR-deficiency. Our study suggests that pharmacological inhibition of WRN helicase function represents an opportunity to develop a novel targeted therapy for MSI-H cancers.","authors":"Lieb, S., Blaha-Ostermann, S., Kamper, E., Rippka, J., Schwarz, C., Ehrenh\u00f6fer-W\u00f6lfer, K., Schlattl, A., Wernitznig, A., Lipp, JJ., Nagasaka, K., van der Lelij, P., Bader, G., Koi, M., Goel, A., Neum\u00fcller, RA., Peters, JM., Kraut, N., Pearson, MA., Petronczki, M., W\u00f6hrle, S.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Elife","volume":"8","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-03-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"28943088","title":"BubR1 Promotes Bub3-Dependent APC\/C Inhibition during Spindle Assembly Checkpoint Signaling.","abstract":"The spindle assembly checkpoint (SAC) prevents premature sister chromatid separation during mitosis. Phosphorylation of unattached kinetochores by the Mps1 kinase promotes recruitment of SAC machinery that catalyzes assembly of the SAC effector mitotic checkpoint complex (MCC). The SAC protein Bub3 is a phospho-amino acid adaptor that forms structurally related stable complexes with functionally distinct paralogs named Bub1 and BubR1. A short motif (\"loop\") of Bub1, but not the equivalent loop of BubR1, enhances binding of Bub3 to kinetochore phospho-targets. Here, we asked whether the BubR1 loop directs Bub3 to different phospho-targets. The BubR1 loop is essential for SAC function and cannot be removed or replaced with the Bub1 loop. BubR1 loop mutants bind Bub3 and are normally incorporated in MCC in&#xa0;vitro but have reduced ability to inhibit the MCC target anaphase-promoting complex (APC\/C), suggesting that BubR1:Bub3 recognition and inhibition of APC\/C requires phosphorylation. Thus, small sequence differences in Bub1 and BubR1 direct Bub3 to different phosphorylated targets in the SAC signaling cascade.","authors":"Overlack, K., Bange, T., Weissmann, F., Faesen, AC., Maffini, S., Primorac, I., M\u00fcller, F., Peters, JM., Musacchio, A.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Curr Biol","volume":"27","issue":"19","page":"2915-2927.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-08-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36757845","title":"SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis.","abstract":"The maternal-to-zygotic transition (MZT) is a key developmental process in metazoan embryos that involves the activation of zygotic transcription (ZGA) and degradation of maternal transcripts. We employed metabolic mRNA sequencing (SLAMseq) to deconvolute the compound embryonic transcriptome in zebrafish. While mitochondrial zygotic transcripts prevail prior to MZT, we uncover the spurious transcription of hundreds of short and intron-poor genes as early as the 2-cell stage. Upon ZGA, most zygotic transcripts originate from thousands of maternal-zygotic (MZ) genes that are transcribed at rates comparable to those of hundreds of purely zygotic genes and replenish maternal mRNAs at distinct timescales. Rapid replacement of MZ transcripts involves transcript decay features unrelated to major maternal degradation pathways and promotes de novo synthesis of the core gene expression machinery by increasing poly(A)-tail length and translation efficiency. SLAMseq hence provides insights into the timescales, molecular features, and regulation of MZT during zebrafish embryogenesis.","authors":"Bhat, P., Cabrera-Quio, LE., Herzog, VA., Fasching, N., Pauli, A., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Cell Rep","volume":"42","issue":"2","page":"112070","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.06.01.494399v1.full","articledate":"2023-10-04","doi":"10.1016\/j.celrep.2023.112070","first_author":null,"corresponding_authors":null},{"pmid":"36736317","title":"A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination.","abstract":"Interactions between transcription and cohesin-mediated loop extrusion can influence 3D chromatin architecture. However, their relevance in biology is unclear. Here, we report a direct role for such interactions in the mechanism of antibody class switch recombination (CSR) at the murine immunoglobulin heavy chain locus (Igh). Using Tri-C to measure higher-order multiway interactions on single alleles, we find that the juxtaposition (synapsis) of transcriptionally active donor and acceptor Igh switch (S)&#xa0;sequences, an essential step in CSR, occurs via the interaction of loop extrusion complexes with a de novo topologically associating domain (TAD) boundary formed via transcriptional activity across S regions. Surprisingly, synapsis occurs predominantly in proximity to the 3' CTCF-binding element (3'CBE) rather than the Igh super-enhancer, suggesting a two-step mechanism whereby transcription of S regions is not topologically coupled to synapsis, as has been previously proposed. Altogether, these insights advance our understanding of how 3D chromatin architecture regulates CSR.","authors":"Costea, J., Schoeberl, UE., Malzl, D., von der Linde, M., Fitz, J., Gupta, A., Makharova, M., Goloborodko, A., Pavri, R.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Mol Cell","volume":"83","issue":"5","page":"681-697.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.04.26.489407v1","articledate":"2023-03-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36795852","title":"Blood Vessel Organoids for Development and Disease.","abstract":"Despite enormous advances, cardiovascular disorders are still a major threat to global health and are responsible for one-third of deaths worldwide. Research for new therapeutics and the investigation of their effects on vascular parameters is often limited by species-specific pathways and a lack of high-throughput methods. The complex 3-dimensional environment of blood vessels, intricate cellular crosstalks, and organ-specific architectures further complicate the quest for a faithful human in vitro model. The development of novel organoid models of various tissues such as brain, gut, and kidney signified a leap for the field of personalized medicine and disease research. By utilizing either embryonic- or patient-derived stem cells, different developmental and pathological mechanisms can be modeled and investigated in a controlled in vitro environment. We have recently developed self-organizing human capillary blood vessel organoids that recapitulate key processes of vasculogenesis, angiogenesis, and diabetic vasculopathy. Since then, this organoid system has been utilized as a model for other disease processes, refined, and adapted for organ specificity. In this review, we will discuss novel and alternative approaches to blood vessel engineering and explore the cellular identity of engineered blood vessels in comparison to in vivo vasculature. Future perspectives and the therapeutic potential of blood vessel organoids will be discussed.","authors":"Salewskij, K., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Circ Res","volume":"132","issue":"4","page":"498-510","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36758105","title":"Structural basis for regulation of apoptosis and autophagy by the BIRC6\/SMAC complex.","abstract":"Inhibitor of apoptosis proteins (IAPs) bind to pro-apoptotic proteases, keeping them inactive and preventing cell death. The atypical ubiquitin ligase BIRC6 is the only essential IAP, additionally functioning as a suppressor of autophagy. We performed a structure-function analysis of BIRC6 in complex with caspase-9, HTRA2, SMAC, and LC3B, which are critical apoptosis and autophagy proteins. Cryo-electron microscopy structures showed that BIRC6 forms a megadalton crescent shape that arcs around a spacious cavity containing receptor sites for client proteins. Multivalent binding of SMAC obstructs client binding, impeding ubiquitination of both autophagy and apoptotic substrates. On the basis of these data, we discuss how the BIRC6\/SMAC complex can act as a stress-induced hub to regulate apoptosis and autophagy drivers.","authors":"Ehrmann, JF., Grabarczyk, DB., Heinke, M., Deszcz, L., Kurzbauer, R., Hudecz, O., Shulkina, A., Gogova, R., Meinhart, A., Versteeg, GA., Clausen, T.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Science","volume":"379","issue":"6637","page":"1117-1123","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36762703","title":"Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy.","abstract":"UFMylation involves the covalent modification of substrate proteins with UFM1 (Ubiquitin-fold modifier 1) and is important for maintaining ER homeostasis. Stalled translation triggers the UFMylation of ER-bound ribosomes and activates C53-mediated autophagy to clear toxic polypeptides. C53 contains noncanonical shuffled ATG8-interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. However, the mechanistic basis of sAIM-mediated ATG8 interaction remains unknown. Here, we show that C53 and sAIMs are conserved across eukaryotes but secondarily lost in fungi and various algal lineages. Biochemical assays showed that the unicellular alga Chlamydomonas reinhardtii has a functional UFMylation pathway, refuting the assumption that UFMylation is linked to multicellularity. Comparative structural analyses revealed that both UFM1 and ATG8 bind sAIMs in C53, but in a distinct way. Conversion of sAIMs into canonical AIMs impaired binding of C53 to UFM1, while strengthening ATG8 binding. Increased ATG8 binding led to the autoactivation of the C53 pathway and sensitization of Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral role of sAIMs in UFMylation-dependent fine-tuning of C53-mediated autophagy activation.","authors":"Picchianti, L., S\u00e1nchez de Medina Hern\u00e1ndez, V., Zhan, N., Irwin, NA., Groh, R., Stephani, M., Hornegger, H., Beveridge, R., Sawa-Makarska, J., Lendl, T., Grujic, N., Naumann, C., Martens, S., Richards, TA., Clausen, T., Ramundo, S., Karag\u00f6z, GE., Dagdas, Y.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"EMBO J","volume":null,"issue":null,"page":"e112053","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35916241","title":"FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder.","abstract":"Whole-exome sequencing of two patients with idiopathic complex neurodevelopmental disorder (NDD) identified biallelic variants of unknown significance within FIBCD1, encoding an endocytic acetyl group-binding transmembrane receptor with no known function in the central nervous system. We found that FIBCD1 preferentially binds and endocytoses glycosaminoglycan (GAG) chondroitin sulphate-4S (CS-4S) and regulates GAG content of the brain extracellular matrix (ECM). In silico molecular simulation studies and GAG binding analyses of patient variants determined that such variants are loss-of-function by disrupting FIBCD1-CS-4S association. Gene knockdown in flies resulted in morphological disruption of the neuromuscular junction and motor-related behavioural deficits. In humans and mice, FIBCD1 is expressed in discrete brain regions, including the hippocampus. Fibcd1 KO mice exhibited normal hippocampal neuronal morphology but impaired hippocampal-dependent learning. Further, hippocampal synaptic remodelling in acute slices from Fibcd1 KO mice was deficient but restored upon enzymatically modulating the ECM. Together, we identified FIBCD1 as an endocytic receptor for GAGs in the brain ECM and a novel gene associated with an NDD, revealing a critical role in nervous system structure, function and plasticity.","authors":"Fell, CW., Hagelkruys, A., Cicvaric, A., Horrer, M., Liu, L., Li, JSS., Stadlmann, J., Polyansky, AA., Mereiter, S., Tejada, MA., Kokotovi\u0107, T., Achuta, VS., Scaramuzza, A., Twyman, KA., Morrow, MM., Juusola, J., Yan, H., Wang, J., Burmeister, M., Choudhury, B., Andersen, TL., Wirnsberger, G., Holmskov, U., Perrimon, N., \u017dagrovi\u0107, B., Monje, FJ., Moeller, JB., Penninger, JM., Nagy, V.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"EMBO Mol Med","volume":"14","issue":"9","page":"e15829","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-09-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36740985","title":"A whole-genome scan for Artemisinin cytotoxicity reveals a novel therapy for human brain tumors.","abstract":"The natural compound Artemisinin is the most widely used antimalarial drug worldwide. Based on its cytotoxicity, it is also used for anticancer therapy. Artemisinin and its derivates are endoperoxides that damage proteins in eukaryotic cells; their definite mechanism of action and host cell targets, however, have remained largely elusive. Using yeast and haploid stem cell screening, we demonstrate that a single cellular pathway, namely porphyrin (heme) biosynthesis, is required for the cytotoxicity of Artemisinins. Genetic or pharmacological modulation of porphyrin production is sufficient to alter its cytotoxicity in eukaryotic cells. Using multiple model systems of human brain tumor development, such as cerebral glioblastoma organoids, and patient-derived tumor spheroids, we sensitize cancer cells to dihydroartemisinin using the clinically approved porphyrin enhancer and surgical fluorescence marker 5-aminolevulinic acid, 5-ALA. A combination treatment of Artemisinins and 5-ALA markedly and specifically killed brain tumor cells in all model systems tested, including orthotopic patient-derived xenografts in&#xa0;vivo. These data uncover the critical molecular pathway for Artemisinin cytotoxicity and a sensitization strategy to treat different brain tumors, including drug-resistant human glioblastomas.","authors":"Taubenschmid-Stowers, J., Orthofer, M., Laemmerer, A., Krauditsch, C., R\u00f3zsov\u00e1, M., Studer, C., L\u00f6tsch, D., Gojo, J., Gabler, L., Dyczynski, M., Efferth, T., Hagelkruys, A., Widhalm, G., Peyrl, A., Spiegl-Kreinecker, S., Hoepfner, D., Bian, S., Berger, W., Knoblich, JA., Elling, U., Horn, M., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"EMBO Mol Med","volume":"15","issue":"3","page":"e16959","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36712238","title":"Cardiac regeneration: Options for repairing the injured heart.","abstract":"Cardiac regeneration is one of the grand challenges in repairing injured human hearts. Numerous studies of signaling pathways and metabolism on cardiac development and disease pave the way for endogenous cardiomyocyte regeneration. New drug delivery approaches, high-throughput screening, as well as novel therapeutic compounds combined with gene editing will facilitate the development of potential cell-free therapeutics. In parallel, progress has been made in the field of cell-based therapies. Transplantation of human pluripotent stem cell (hPSC)-derived cardiomyocytes (hPSC-CMs) can partially rescue the myocardial defects caused by cardiomyocyte loss in large animals. In this review, we summarize current cell-based and cell-free regenerative therapies, discuss the importance of cardiomyocyte maturation in cardiac regenerative medicine, and envision new ways of regeneration for the injured heart.","authors":"Wang, J., An, M., Haubner, BJ., Penninger, JM.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Front Cardiovasc Med","volume":"9","issue":null,"page":"981982","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36693323","title":"A cellular hierarchy of Notch and Kras signaling controls cell fate specification in the developing mouse salivary gland.","abstract":"The development of the mouse salivary gland involves a tip-driven process of branching morphogenesis that takes place in concert with differentiation into acinar, myoepithelial, and ductal (basal and luminal) sub-lineages. By combining clonal lineage tracing with a three-dimensional (3D) reconstruction of the branched epithelial network and single-cell RNA-seq analysis, we show that in tips, a heterogeneous population of renewing progenitors transition from a Krt14+ multipotent state to unipotent states via two transcriptionally distinct bipotent states, one restricted to the Krt14+ basal and myoepithelial lineage and the other to the Krt8+ acinar and luminal lineage. Using genetic perturbations, we show how the differential expression of Notch signaling correlates with spatial segregation, exits from multipotency, and promotes the Krt8+ lineage, whereas Kras activation promotes proacinar fate. These findings provide a mechanistic basis for how positional cues within growing tips regulate the process of lineage segregation and ductal patterning.","authors":"Chatzeli, L., Bordeu, I., Han, S., Bisetto, S., Waheed, Z., Koo, BK., Alcolea, MP., Simons, BD.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Dev Cell","volume":"58","issue":"2","page":"94-109.e6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36744771","title":"Generation of Human Blood Vessel Organoids from Pluripotent Stem Cells.","abstract":"An organoid is defined as an engineered multicellular in vitro tissue that mimics its corresponding in vivo organ such that it can be used to study defined aspects of that organ in a tissue culture dish. The breadth and application of human pluripotent stem cell (hPSC)-derived organoid research have advanced significantly to include the brain, retina, tear duct, heart, lung, intestine, pancreas, kidney, and blood vessels, among several other tissues. The development of methods for the generation of human microvessels, specifically, has opened the way for modeling human blood vessel development and disease in vitro and for the testing and analysis of new drugs or tissue tropism in virus infections, including SARS-CoV-2. Complex and lengthy protocols lacking visual guidance hamper the reproducibility of many stem cell-derived organoids. Additionally, the inherent stochasticity of organoid formation processes and self-organization necessitates the generation of optical protocols to advance the understanding of cell fate acquisition and programming. Here, a visually guided protocol is presented for the generation of 3D human blood vessel organoids (BVOs) engineered from hPSCs. Presenting a continuous basement membrane, vascular endothelial cells, and organized articulation with mural cells, BVOs exhibit the functional, morphological, and molecular features of human microvasculature. BVO formation is initiated through aggregate formation, followed by mesoderm and vascular induction. Vascular maturation and network formation are initiated and supported by embedding aggregates in a 3D collagen and solubilized basement membrane matrix. Human vessel networks form within 2-3 weeks and can be further grown in scalable culture systems. Importantly, BVOs transplanted into immunocompromised mice anastomose with the endogenous mouse circulation and specify into functional arteries, veins, and arterioles. The present visually guided protocol will advance human organoid research, particularly in relation to blood vessels in normal development, tissue vascularization, and disease.","authors":"Werschler, N., Penninger, J.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"J Vis Exp","volume":null,"issue":"191","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36731336","title":"Apelin expression is downregulated in T cells in a murine model of chronic colitis.","abstract":"Apelin (APL), an endogenous ligand for APJ, has been reported to be upregulated in a murine model of acute colitis induced by sodium dextran sulfate, as well as inflammatory bowel diseases (IBD) in humans. However, the mechanisms and functions of APL\/APJ axis in the pathogenesis of IBD are unclear. We herein analyzed CD4<sup>+<\/sup> T cells to determine the functions of APL in a murine model of chronic colitis induced in Rag deficient mice (Rag<sup>-\/-<\/sup>). In colonic tissues of wild-type mice (WT), we found that APL was expressed especially in the lamina propria lymphocytes, where CD4<sup>+<\/sup> T cells are dominant, rather than the epithelial cells. Unexpectedly, the APL expression was rather downregulated in the colonic tissue of the chronic colitis group compared to the control groups (Rag<sup>-\/-<\/sup> before colitis induction and WT). The APL expression was downregulated when na&#xef;ve T cells were differentiated into effecter T cells. A lack of APL resulted in decreased na&#xef;ve T cells and increased effecter T cells in secondary lymphoid organs. A synthetic APL peptide, [Pyr<sup>1<\/sup>]-APL-13, increased IL-10 and decreased IFN-&#x3b3; productions by effecter T cells. Administration of [Pyr<sup>1<\/sup>]-APL-13 improved survival rate in association with lessened colitis severity and decreased pro-inflammatory cytokine production. This is the first report showing immunological function of APL specifically on T cells, and these results indicate that APL\/APJ axis may be a novel therapeutic target for IBD.","authors":"Yamada, D., Kojima, Y., Hosoya, A., Suzuki, M., Watabe, T., Inoue, T., Tsugawa, N., Asakawa, T., Yonemoto, Y., Onizawa, M., Nemoto, Y., Oshima, S., Shimonaka, M., Kuba, K., Ishida, J., Fukamizu, A., Penninger, JM., Watanabe, M., Okamoto, R., Nagaishi, T.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Biochem Biophys Res Commun","volume":"647","issue":null,"page":"72-79","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36792779","title":"Generating human blastoids modeling blastocyst-stage embryos and implantation.","abstract":"Human early development sets the stage for embryonic and adult life but remains difficult to investigate. A solution came from the ability of stem cells to organize into structures resembling preimplantation embryos-blastocysts-that we termed blastoids. This embryo model is available in unlimited numbers and could thus support scientific and medical advances. However, its predictive power depends on how faithfully it recapitulates the blastocyst. Here, we describe how we formed human blastoids that (1) efficiently achieve the morphology of the blastocyst and (2) form lineages according to the pace and sequence of blastocyst development, (3) ultimately forming cells that transcriptionally reflect the blastocyst (preimplantation stage). We employ three different commercially available 96- and 24-well microwell plates with results similar to our custom-made ones, and show that blastoids form in clinical in vitro fertilization medium and can be cryopreserved for shipping. Finally, we explain how blastoids replicate the directional process of implantation into endometrial organoids, specifically when these are hormonally stimulated. It takes 4 d for human blastoids to form and 10 d to prepare the endometrial implantation assay, and we have cultured blastoids up to 6 d (time-equivalent of day 13). On the basis of our experience, we anticipate that a person with ~1 year of human pluripotent stem cell culture experience and of organoid culture should be able to perform the protocol. Altogether, blastoids offer an opportunity to establish scientific and biomedical discovery programs for early pregnancy, and an ethical alternative to the use of embryos.","authors":"Heidari Khoei, H., Javali, A., Kagawa, H., Sommer, TM., Sestini, G., David, L., Slovakova, J., Novatchkova, M., Scholte Op Reimer, Y., Rivron, N.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Nat Protoc","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36806919","title":"Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing.","abstract":"The ability to map a proteomic fingerprint to transcriptomic data would master the understanding of how gene expression translates into actual phenotype. In contrast to nucleic acid sequencing, in vitro protein amplification is impossible and no single cell proteomic workflow has been established as gold standard yet. Advances in microfluidic sample preparation, multi-dimensional sample separation, sophisticated data acquisition strategies, and intelligent data analysis algorithms have resulted in major improvements to successfully analyze such tiny sample amounts with steadily boosted performance. However, among the broad variation of published approaches, it is commonly accepted that highest possible sensitivity, robustness, and throughput are still the most urgent needs for the field. While many labs have focused on multiplexing to achieve these goals, label-free SCP is a highly promising strategy as well whenever high dynamic range and unbiased accurate quantification are needed. We here focus on recent advances in label-free single-cell mass spectrometry workflows and try to guide our readers to choose the best method or combinations of methods for their specific applications. We further highlight which techniques are most propitious in the future and which applications but also limitations we foresee for the field.","authors":"Matzinger, M., Mayer, RL., Mechtler, K.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Proteomics","volume":null,"issue":null,"page":"e2200162","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-01","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36802514","title":"Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics.","abstract":"The analysis of ultralow input samples or even individual cells is essential to answering a multitude of biomedical questions, but current proteomic workflows are limited in their sensitivity and reproducibility. Here, we report a comprehensive workflow that includes improved strategies for all steps, from cell lysis to data analysis. Thanks to convenient-to-handle 1 &#x3bc;L sample volume and standardized 384-well plates, the workflow is easy for even novice users to implement. At the same time, it can be performed semi-automatized using CellenONE, which allows for the highest reproducibility. To achieve high throughput, ultrashort gradient lengths down to 5 min were tested using advanced &#x3bc;-pillar columns. Data-dependent acquisition (DDA), wide-window acquisition (WWA), data-independent acquisition (DIA), and commonly used advanced data analysis algorithms were benchmarked. Using DDA, 1790 proteins covering a dynamic range of four orders of magnitude were identified in a single cell. Using DIA, proteome coverage increased to more than 2200 proteins identified from single-cell level input in a 20 min active gradient. The workflow enabled differentiation of two cell lines, demonstrating its suitability to cellular heterogeneity determination.","authors":"Matzinger, M., M\u00fcller, E., D\u00fcrnberger, G., Pichler, P., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Anal Chem","volume":"95","issue":"9","page":"4435-4445","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-07","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36815964","title":"Topological morphogenesis of neuroepithelial organoids.","abstract":"Animal organs exhibit complex topologies involving cavities and tubular networks, which underlie their form and function<sup>1-3<\/sup>. However, how topology emerges during the development of organ shape, or morphogenesis, remains elusive. Here we combine tissue reconstitution and quantitative microscopy to show that tissue topology and shape is governed by two distinct modes of topological transitions<sup>4,5<\/sup>. One mode involves the fusion of two separate epithelia and the other involves the fusion of two ends of the same epithelium. The morphological space is captured by a single control parameter that can be traced back to the relative rates of the two epithelial fusion modes. Finally, we identify a pharmacologically accessible pathway that regulates the frequency of two modes of epithelial fusion, and demonstrate the control of organoid topology and shape. The physical principles uncovered here provide fundamental insights into the self-organization of complex tissues<sup>6<\/sup>.","authors":"Ishihara, K., Mukherjee, A., Gromberg, E., Brugu\u00e9s, J., Tanaka, EM., J\u00fclicher, F.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Phys","volume":"19","issue":"2","page":"177-183","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36516856","title":"Developmental cell fate choice in neural tube progenitors employs two distinct cis-regulatory strategies.","abstract":"In many developing tissues, the patterns of gene expression that assign cell fate are organized by graded secreted signals. Cis-regulatory elements (CREs) interpret these signals to control gene expression, but how this is accomplished remains poorly understood. In the neural tube, a gradient of the morphogen sonic hedgehog (Shh) patterns neural progenitors. We identify two distinct ways in which CREs translate graded Shh into differential gene expression in mouse neural progenitors. In most progenitors, a common set of CREs control gene activity by integrating cell-type-specific inputs. By contrast, the most ventral progenitors use a unique set of CREs, established by the pioneer factor FOXA2. This parallels the role of FOXA2 in endoderm, where FOXA2 binds some of the same sites. Together, the data identify distinct cis-regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for FOXA2 across tissues.","authors":"Del\u00e1s, MJ., Kalaitzis, CM., Fawzi, T., Demuth, M., Zhang, I., Stuart, HT., Costantini, E., Ivanovitch, K., Tanaka, EM., Briscoe, J.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Dev Cell","volume":"58","issue":"1","page":"3-17.e8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36376278","title":"Altered developmental programs and oriented cell divisions lead to bulky bones during salamander limb regeneration.","abstract":"There are major differences in duration and scale at which limb development and regeneration proceed, raising the question to what extent regeneration is a recapitulation of development. We address this by analyzing skeletal elements using a combination of micro-CT imaging, molecular profiling and clonal cell tracing. We find that, in contrast to development, regenerative skeletal growth is accomplished based entirely on cartilage expansion prior to ossification, not limiting the transversal cartilage expansion&#xa0;and&#xa0;resulting in bulkier skeletal parts. The oriented extension of salamander cartilage and bone appear similar to the development of basicranial synchondroses in mammals, as we found no evidence for cartilage stem cell niches or growth plate-like structures during neither development nor regeneration. Both regenerative and developmental ossification in salamanders start from the cortical bone and proceeds inwards, showing the diversity of schemes for the synchrony of cortical and endochondral ossification among vertebrates.","authors":"Kaucka, M., Joven Araus, A., Tesarova, M., Currie, JD., Bostr\u00f6m, J., Kavkova, M., Petersen, J., Yao, Z., Bouchnita, A., Hellander, A., Zikmund, T., Elewa, A., Newton, PT., Fei, JF., Chagin, AS., Fried, K., Tanaka, EM., Kaiser, J., Simon, A., Adameyko, I.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Nat Commun","volume":"13","issue":"1","page":"6949","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-11-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36299593","title":"Muscles are barely required for the patterning and cell dynamics in axolotl limb regeneration.","abstract":"Regeneration of a complex appendage structure such as limb requires upstream and downstream coordination of multiple types of cells. Given type of cell may sit at higher upstream position to control the activities of other cells. Muscles are one of the major cell masses in limbs. However, the subtle functional relationship between muscle and other cells in vertebrate complex tissue regeneration are still not well established. Here, we use <i>Pax7<\/i> mutant axolotls, in which the limb muscle is developmentally lost, to investigate limb regeneration in the absence of skeletal muscle. We find that the pattern of regenerated limbs is relative normal in <i>Pax7<\/i> mutants compared to the controls, but the joint is malformed in the <i>Pax7<\/i> mutants. Lack of muscles do not affect the early regeneration responses, specifically the recruitment of macrophages to the wound, as well as the proliferation of fibroblasts, another major population in limbs. Furthermore, using single cell RNA-sequencing, we show that, other than muscle lineage that is mostly missing in <i>Pax7<\/i> mutants, the composition and the status of other cell types in completely regenerated limbs of <i>Pax7<\/i> mutants are similar to that in the controls. Our study reveals skeletal muscle is barely required for the guidance of other cells, as well the patterning in complex tissue regeneration in axolotls, and provides refined views of the roles of muscle cell in vertebrate appendage regeneration.","authors":"Hu, Y., Pan, X., Shi, Y., Qiu, Y., Wang, L., Murawala, P., Liu, Y., Xing, W., Tanaka, EM., Fei, JF.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Front Genet","volume":"13","issue":null,"page":"1036641","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36272091","title":"Artificial Insemination in Axolotl.","abstract":"In axolotls (Ambystoma mexicanum), fertilization takes place internally. After courtship, the male axolotl deposits spermatophores, which the female takes up into her cloaca in order to fertilize eggs internally. The success of axolotl breedings is subject to several poorly understood factors including age, pairing, and genotype. In some cases, individuals are unable to breed naturally despite having significant scientific value. Assisted reproductive technologies represent one approach to maintaining stocks of such individuals, as well as supplementing natural breedings of laboratory stocks.Here, we describe a protocol for artificial insemination--an assisted reproductive technology in which sperm is extracted from a male and transferred into the female cloaca, thus mimicking natural fertilization in axolotls. We believe that this simple method can be applied to other salamander species that have internal fertilization and also help restore endangered wild populations.","authors":"Taniguchi-Sugiura, Y., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Methods Mol Biol","volume":"2562","issue":null,"page":"417-423","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36272084","title":"Chromosome Conformation Capture for Large Genomes.","abstract":"The gigantic 32Gb Axolotl genome inspires fascinating questions such as: how such a big genome is organized and packed in nuclei and how regulation of gene transcription can happen over such large genomic distances. Currently, there are many technical challenges when we investigate chromatin architecture in axolotl. For example, probing promoter-enhancer interactions in such a large genome. Chromatin capture methods (e.g., Chromatin Conformation Capture) have been used in a variety of species. The large size of the axolotl nuclei and its genome requires the adaptation of such methods. Here, we describe a detailed protocol for high-throughput genome-wide conformation capture (Hi-C) using axolotl limb cells. This Hi-C library preparation protocol can also be used to prepare libraries from other nonmodel organisms such as Lungfish and Cephalopods. We believe that our protocol could be useful for a variety of animal systems including other salamanders.","authors":"Kawaguchi, A., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Methods Mol Biol","volume":"2562","issue":null,"page":"291-318","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-25","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36750319","title":"Effector-Triggered Immunity.","abstract":"The innate immune system detects pathogens via germline-encoded receptors that bind to conserved pathogen ligands called pathogen-associated molecular patterns (PAMPs). Here we consider an additional strategy of pathogen sensing called effector-triggered immunity (ETI). ETI involves detection of pathogen-encoded virulence factors, also called effectors. Pathogens produce effectors to manipulate hosts to create a replicative niche and\/or block host immunity. Unlike PAMPs, effectors are often diverse and rapidly evolving and can thus be unsuitable targets for direct detection by germline-encoded receptors. Effectors are instead often sensed indirectly via detection of their virulence activities. ETI is a viable strategy for pathogen sensing and is used across diverse phyla, including plants, but the molecular mechanisms of ETI are complex compared to simple receptor\/ligand-based PAMP detection. Here we survey the mechanisms and functions of ETI, with a particular focus on emerging insights from animal studies. We suggest that many examples of ETI may remain to be discovered, hiding in plain sight throughout immunology. Expected final online publication date for the <i>Annual Review of Immunology<\/i>, Volume 41 is April 2023. Please see http:\/\/www.annualreviews.org\/page\/journal\/pubdates for revised estimates.","authors":"Remick, BC., Gaidt, MM., Vance, RE.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Annu Rev Immunol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36578489","title":"Tumor necrosis factor is a necroptosis-associated alarmin.","abstract":"Necroptosis is a form of regulated cell death that can occur downstream of several immune pathways. While previous studies have shown that dysregulated necroptosis can lead to strong inflammatory responses, little is known about the identity of the endogenous molecules that trigger these responses. Using a reductionist <i>in vitro<\/i> model, we found that soluble TNF is strongly released in the context of necroptosis. On the one hand, necroptosis promotes TNF translation by inhibiting negative regulatory mechanisms acting at the post-transcriptional level. On the other hand, necroptosis markedly enhances TNF release by activating ADAM proteases. In studying TNF release at single-cell resolution, we found that TNF release triggered by necroptosis is activated in a switch-like manner that exceeds steady-state TNF processing in magnitude and speed. Although this shedding response precedes massive membrane damage, it is closely associated with lytic cell death. Further, we found that lytic cell death induction using a pore-forming toxin also triggers TNF shedding, indicating that the activation of ADAM proteases is not strictly related to the necroptotic pathway but likely associated with biophysical changes of the cell membrane upon lytic cell death. These results demonstrate that lytic cell death, particularly necroptosis, is a critical trigger for TNF release and thus qualify TNF as a necroptosis-associated alarmin.","authors":"Pinci, F., Gaidt, MM., Jung, C., Nagl, D., Kuut, G., Hornung, V.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Front Immunol","volume":"13","issue":null,"page":"1074440","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-12-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36384135","title":"IKK&#x3b2; primes inflammasome formation by recruiting NLRP3 to the trans-Golgi network.","abstract":"The NLRP3 inflammasome plays a central role in antimicrobial defense as well as in the context of sterile inflammatory conditions. NLRP3 activity is governed by two independent signals: the first signal primes NLRP3, rendering it responsive to the second signal, which then triggers inflammasome formation. Our understanding of how NLRP3 priming contributes to inflammasome activation remains limited. Here, we show that IKK&#x3b2;, a kinase activated during priming, induces recruitment of NLRP3 to phosphatidylinositol-4-phosphate (PI4P), a phospholipid enriched on the trans-Golgi network. NEK7, a mitotic spindle kinase that had previously been thought to be indispensable for NLRP3 activation, was redundant for inflammasome formation when IKK&#x3b2; recruited NLRP3 to PI4P. Studying iPSC-derived human macrophages revealed that the IKK&#x3b2;-mediated NEK7-independent pathway constitutes the predominant NLRP3 priming mechanism in human myeloid cells. Our results suggest that PI4P binding represents a primed state into which NLRP3 is brought by IKK&#x3b2; activity.","authors":"Schmacke, NA., O'Duill, F., Gaidt, MM., Szymanska, I., Kamper, JM., Schmid-Burgk, JL., M\u00e4dler, SC., Mackens-Kiani, T., Kozaki, T., Chauhan, D., Nagl, D., Stafford, CA., Harz, H., Fr\u00f6hlich, AL., Pinci, F., Ginhoux, F., Beckmann, R., Mann, M., Leonhardt, H., Hornung, V.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Immunity","volume":"55","issue":"12","page":"2271-2284.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36584678","title":"Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM.","abstract":"Molecular machines, such as polymerases, ribosomes, or proteasomes, fulfill complex tasks requiring the thermal energy of their environment. They achieve this by restricting random motion along a path of possible conformational changes. These changes are often directed through engagement with different cofactors, which can best be compared to a Brownian ratchet. Many molecular machines undergo three major steps throughout their functional cycles, including initialization, repetitive processing, and termination. Several of these major states have been elucidated by cryogenic electron microscopy (cryo-EM). However, the individual steps for these machines are unique and multistep processes themselves, and their coordination in time is still elusive. To measure these short-lived intermediate events by cryo-EM, the total reaction time needs to be shortened to enrich for the respective pre-equilibrium states. This approach is termed time-resolved cryo-EM (trEM). In this review, we sum up the methodological development of trEM and its application to a range of biological questions.","authors":"Amann, SJ., Keihsler, D., Bodrug, T., Brown, NG., Haselbach, D.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Structure","volume":"31","issue":"1","page":"4-19","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36931269","title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish.","abstract":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.","authors":"Huljev, K., Shamipour, S., Pinheiro, D., Preusser, F., Steccari, I., Sommer, CM., Naik, S., Heisenberg, CP.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Dev Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36897969","title":"Transcription shapes 3D chromatin organization by interacting with loop extrusion.","abstract":"Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. \"Loop extrusion\" can be impeded by chromatin-bound factors, such as CTCF, which generates characteristic and functional chromatin organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin and that active promoters are cohesin loading sites. However, the effects of transcription on cohesin have not been reconciled with observations of active extrusion by cohesin. To determine how transcription modulates extrusion, we studied mouse cells in which we could alter cohesin abundance, dynamics, and localization by genetic \"knockouts\" of the cohesin regulators CTCF and Wapl. Through Hi-C experiments, we discovered intricate, cohesin-dependent contact patterns near active genes. Chromatin organization around active genes exhibited hallmarks of interactions between transcribing RNA polymerases (RNAPs) and extruding cohesins. These observations could be reproduced by polymer simulations in which RNAPs were moving barriers to extrusion that obstructed, slowed, and pushed cohesins. The simulations predicted that preferential loading of cohesin at promoters is inconsistent with our experimental data. Additional ChIP-seq experiments showed that the putative cohesin loader Nipbl is not predominantly enriched at promoters. Therefore, we propose that cohesin is not preferentially loaded at promoters and that the barrier function of RNAP accounts for cohesin accumulation at active promoters. Altogether, we find that RNAP is an extrusion barrier that is not stationary, but rather, translocates and relocalizes cohesin. Loop extrusion and transcription might interact to dynamically generate and maintain gene interactions with regulatory elements and shape functional genomic organization.","authors":"Banigan, EJ., Tang, W., van den Berg, AA., Stocsits, RR., Wutz, G., Brand\u00e3o, HB., Busslinger, GA., Peters, JM., Mirny, LA.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Proc Natl Acad Sci U S A","volume":"120","issue":"11","page":"e2210480120","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.01.07.475367v2","articledate":"2023-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36941077","title":"Enhancers display constrained sequence flexibility and context-specific modulation of motif function.","abstract":"The information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers, sequence elements that comprise binding sites (motifs) for different transcription factors (TFs). Most of the research on enhancer sequences has been focused on TF motif presence, whereas the enhancer syntax, that is, the flexibility of important motif positions and how the sequence context modulates the activity of TF motifs, remains poorly understood. Here, we explore the rules of enhancer syntax by a two-pronged approach in <i>Drosophila melanogaster<\/i> S2 cells: we (1) replace important TF motifs by all possible 65,536 eight-nucleotide-long sequences and (2) paste eight important TF motif types into 763 positions within 496 enhancers. These complementary strategies reveal that enhancers display constrained sequence flexibility and the context-specific modulation of motif function. Important motifs can be functionally replaced by hundreds of sequences constituting several distinct motif types, but these are only a fraction of all possible sequences and motif types. Moreover, TF motifs contribute with different intrinsic strengths that are strongly modulated by the enhancer sequence context (the flanking sequence, the presence and diversity of other motif types, and the distance between motifs), such that not all motif types can work in all positions. The context-specific modulation of motif function is also a hallmark of human enhancers, as we demonstrate experimentally. Overall, these two general principles of enhancer sequences are important to understand and predict enhancer function during development, evolution, and in disease.","authors":"Reiter, F., de Almeida, BP., Stark, A.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Genome Res","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36906109","title":"MYC determines lineage commitment in kras driven primary liver cancer development.","abstract":"on Status=\"Publisher\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">36906109<\/PMID><DateRevised><Year>2023<\/Year><Month>03<\/Month><Day>11<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1600-0641<\/ISSN><JournalIssue CitedMedium=\"Internet\"><PubDate><Year>2023<\/Year><Month>Mar<\/Month><Day>09<\/Day><\/PubDate><\/JournalIssue><Title>Journal of hepatology<\/Title><ISOAbbreviation>J Hepatol<\/ISOAbbreviation><\/Journal><ArticleTitle>MYC determines lineage commitment in kras driven primary liver cancer development.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0168-8278(23)00175-7<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.jhep.2023.02.039<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\" NlmCategory=\"OBJECTIVE\">Primary liver cancer (PLC) comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), two frequent and lethal tumor types that differ regarding their tumor biology and responses to cancer therapies. Liver cells harbor a high degree of cellular plasticity and can give rise to either HCC or iCCA, however, little is known about the cell intrinsic mechanisms directing an oncogenically transformed liver cell either to HCC or iCCA. The scope of this study was to identify cell intrinsic factors determining lineage commitment in PLC.","authors":"D'Artista, L., Moschopoulou, AA., Barozzi, I., Craig, AJ., Seehawer, M., Herrmann, L., Minnich, M., Kang, TW., Rist, E., Henning, M., Klotz, S., Heinzmann, F., Harbig, J., Sipos, B., Longerich, T., Eilers, M., Dauch, D., Zuber, J., Wang, XW., Zender, L.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"J Hepatol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36416169","title":"X-linked inhibitor of apoptosis protein represents a promising therapeutic target for relapsed\/refractory ALL.","abstract":"Acute lymphoblastic leukemia (ALL) represents the most frequent malignancy in children, and relapse\/refractory (r\/r) disease is difficult to treat, both in children and adults. In search for novel treatment options against r\/r ALL, we studied inhibitor of apoptosis proteins (IAP) and Smac mimetics (SM). SM-sensitized r\/r ALL cells towards conventional chemotherapy, even upon resistance against SM alone. The combination of SM and chemotherapy-induced cell death via caspases and PARP, but independent from cIAP-1\/2, RIPK1, TNF&#x3b1; or NF-&#x3ba;B. Instead, XIAP was identified to mediate SM effects. Molecular manipulation of XIAP in&#xa0;vivo using microRNA-30 flanked shRNA expression in cell lines and patient-derived xenograft (PDX) models of r\/r ALL mimicked SM effects and intermediate XIAP knockdown-sensitized r\/r ALL cells towards chemotherapy-induced apoptosis. Interestingly, upon strong XIAP knockdown, PDX r\/r ALL cells were outcompeted in&#xa0;vivo, even in the absence of chemotherapy. Our results indicate a yet unknown essential function of XIAP in r\/r ALL and reveal XIAP as a promising therapeutic target for r\/r ALL.","authors":"Carlet, M., Schmelz, K., Vergalli, J., Herold, T., Senft, D., Jurinovic, V., Hoffmann, T., Proba, J., Weichert, N., Junghan\u00df, C., Roth, M., Eschenburg, G., Barz, M., Henze, G., Eckert, C., Eggert, A., Zuber, J., Hundsdoerfer, P., Jeremias, I.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"EMBO Mol Med","volume":"15","issue":"1","page":"e14557","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-19","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36630607","title":"SBNO2 is a critical mediator of STAT3-driven hematological malignancies.","abstract":"Gain-of-function mutations in the STAT3 gene are recurrently identified in patients suffering from large granular lymphocytic leukemia (LGLL) and some cases of T\/NK and adult T-cell leukemia\/lymphoma. To understand the consequences and molecular mechanisms contributing to disease development and oncogenic transformation we developed murine hematopoietic stem and progenitor cell models expressing mutated STAT3Y640F. The cells show accelerated proliferation and enhanced self-renewal potential. We integrated gene expression analyses and chromatin occupancy profiling of STAT3Y640F-transformed cells with T-LGLL patient data. This approach uncovered a conserved set of direct transcriptional targets of STAT3Y640F. Among those, the strawberry notch homolog 2 (SBNO2) represents an essential transcriptional target which was identified by a comparative genome-wide CRISPR\/Cas9-based loss-of-function (LOF) screen. The STAT3-SBNO2 axis is also present in NK-cell leukemia, T-cell non Hodgkin-lymphoma (T-NHL) and NPM-ALK-rearranged T-anaplastic large cell lymphoma (T-ALCL), which are driven by STAT3-hyperactivation\/mutation. In NPM-ALK T-ALCL patients, high SBNO2 expression correlates with shorter relapse-free- and overall survival. Our findings identify SBNO2 as potential therapeutic intervention site for STAT3-driven hematopoietic malignancies.","authors":"Brandstoetter, T., Schmoellerl, J., Grausenburger, R., Kollmann, S., Doma, E., Huuhtanen, J., Klampfl, T., Eder, T., Grebien, F., Hoermann, G., Zuber, J., Mustjoki, S., Maurer, B., Sexl, V.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Blood","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36310757","title":"Different Gene Sets Are Associated With Azacitidine Response In Vitro Versus in Myelodysplastic Syndrome Patients.","abstract":"Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic disorders characterized by dysplasia, ineffective hematopoiesis, and predisposition to secondary acute myeloid leukemias (sAML). Azacitidine (AZA) is the standard care for high-risk MDS patients not eligible for allogenic bone marrow transplantation. However, only half of the patients respond to AZA and eventually all patients relapse. Response-predicting biomarkers and combinatorial drugs targets enhancing therapy response and its duration are needed. Here, we have taken a dual approach. First, we have evaluated genes encoding chromatin regulators for their capacity to modulate AZA response. We were able to validate several genes, whose genetic inhibition affected the cellular AZA response, including 4 genes encoding components of Imitation SWItch chromatin remodeling complex pointing toward a specific function and co-vulnerability. Second, we have used a classical cohort analysis approach measuring the expression of a gene panel in bone marrow samples from 36 MDS patients subsequently receiving AZA. The gene panel included the identified AZA modulators, genes known to be involved in AZA metabolism and previously identified candidate modulators. In addition to confirming a number of previously made observations, we were able to identify several new associations, such as <i>NSUN3<\/i> that correlated with increased overall survival. Taken together, we have identified a number of genes associated with AZA response in vitro and in patients. These groups of genes are largely nonoverlapping suggesting that different gene sets need to be exploited for the development of combinatorial drug targets and response-predicting biomarkers.","authors":"Le Pann\u00e9rer, MM., Diesch, J., Casquero, R., Maher, M., Garcia, O., Haferlach, T., Zuber, J., K\u00fcndgen, A., G\u00f6tze, KS., Buschbeck, M.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Hemasphere","volume":"6","issue":"11","page":"e792","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-11-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36095844","title":"EVI1 drives leukemogenesis through aberrant ERG activation.","abstract":"Chromosomal rearrangements involving the MDS1 and EVI1 complex locus (MECOM) on chromosome 3q26 define an aggressive subtype of acute myeloid leukemia (AML) that is associated with chemotherapy resistance and dismal prognosis. Established treatment regimens commonly fail in these patients, therefore, there is an urgent need for new therapeutic concepts that will require a better understanding of the molecular and cellular functions of the ecotropic viral integration site 1 (EVI1) oncogene. To characterize gene regulatory functions of EVI1 and associated dependencies in AML, we developed experimentally tractable human and murine disease models, investigated the transcriptional consequences of EVI1 withdrawal in&#xa0;vitro and in&#xa0;vivo, and performed the first genome-wide CRISPR screens in EVI1-dependent AML. By integrating conserved transcriptional targets with genetic dependency data, we identified and characterized the ETS transcription factor ERG as a direct transcriptional target of EVI1 that is aberrantly expressed and selectively required in both human and murine EVI1-driven AML. EVI1 controls the expression of ERG and occupies a conserved intragenic enhancer region in AML cell lines and samples from&#xa0;patients with primary AML. Suppression of ERG induces terminal differentiation of EVI1-driven AML cells, whereas ectopic expression of ERG abrogates their dependence on EVI1, indicating that the major oncogenic functions of EVI1 are mediated through aberrant transcriptional activation of ERG. Interfering with this regulatory axis may provide entry points for the development of rational targeted therapies.","authors":"Schmoellerl, J., Barbosa, IAM., Minnich, M., Andersch, F., Smeenk, L., Havermans, M., Eder, T., Neumann, T., Jude, J., Fellner, M., Ebert, A., Steininger, M., Delwel, R., Grebien, F., Zuber, J.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Blood","volume":"141","issue":"5","page":"453-466","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35883003","title":"Discovery of potent and selective HER2 inhibitors with efficacy against HER2 exon 20 insertion-driven tumors, which preserve wild-type EGFR signaling.","abstract":"Oncogenic alterations in human epidermal growth factor receptor 2 (HER2) occur in approximately 2% of patients with non-small cell lung cancer and predominantly affect the tyrosine kinase domain and cluster in exon 20 of the ERBB2 gene. Most clinical-grade tyrosine kinase inhibitors are limited by either insufficient selectivity against wild-type (WT) epidermal growth factor receptor (EGFR), which is a major cause of dose-limiting toxicity or by potency against HER2 exon 20 mutant variants. Here we report the discovery of covalent tyrosine kinase inhibitors that potently inhibit HER2 exon 20 mutants while sparing WT EGFR, which reduce tumor cell survival and proliferation in vitro and result in regressions in preclinical xenograft models of HER2 exon 20 mutant non-small cell lung cancer, concomitant with inhibition of downstream HER2 signaling. Our results suggest that HER2 exon 20 insertion-driven tumors can be effectively treated by a potent and highly selective HER2 inhibitor while sparing WT EGFR, paving the way for clinical translation.","authors":"Wilding, B., Scharn, D., B\u00f6se, D., Baum, A., Santoro, V., Chetta, P., Schnitzer, R., Botesteanu, DA., Reiser, C., Kornigg, S., Knesl, P., H\u00f6rmann, A., K\u00f6ferle, A., Corcokovic, M., Lieb, S., Scholz, G., Bruchhaus, J., Spina, M., Balla, J., Peric-Simov, B., Zimmer, J., Mitzner, S., Fett, TN., Beran, A., Lamarre, L., Gerstberger, T., Gerlach, D., Bauer, M., Bergner, A., Schlattl, A., Bader, G., Treu, M., Engelhardt, H., Zahn, S., Fuchs, JE., Zuber, J., Ettmayer, P., Pearson, M., Petronczki, M., Kraut, N., McConnell, DB., Solca, F., Neum\u00fcller, RA.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Cancer","volume":"3","issue":"7","page":"821-836","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35794848","title":"BRD4 degradation blocks expression of MYC and multiple forms of stem cell resistance in Ph<sup>+<\/sup> chronic myeloid leukemia.","abstract":"In most patients with chronic myeloid leukemia (CML) clonal cells can be kept under control by BCR::ABL1 tyrosine kinase inhibitors (TKI). However, overt resistance or intolerance against these TKI may occur. We identified the epigenetic reader BRD4 and its downstream-effector MYC as growth regulators and therapeutic targets in CML cells. BRD4 and MYC were found to be expressed in primary CML cells, CD34<sup>+<\/sup> \/CD38<sup>-<\/sup> leukemic stem cells (LSC), and in the CML cell lines KU812, K562, KCL22, and KCL22<sup>T315I<\/sup> . The BRD4-targeting drug JQ1 was found to suppress proliferation in KU812 cells and primary leukemic cells in the majority of patients with chronic phase CML. In the blast phase of CML, JQ1 was less effective. However, the BRD4 degrader dBET6 was found to block proliferation and\/or survival of primary CML cells in all patients tested, including blast phase CML and CML cells exhibiting the T315I variant of BCR::ABL1. Moreover, dBET6 was found to block MYC expression and to synergize with BCR::ABL1 TKI in inhibiting the proliferation in the JQ1-resistant cell line K562. Furthermore, BRD4 degradation was found to overcome osteoblast-induced TKI resistance of CML LSC in a co-culture system and to block interferon-gamma-induced upregulation of the checkpoint antigen PD-L1 in LSC. Finally, dBET6 was found to suppress the in vitro survival of CML LSC and their engraftment in NSG mice. Together, targeting of BRD4 and MYC through BET degradation sensitizes CML cells against BCR::ABL1 TKI and is a potent approach to overcome multiple forms of drug resistance in CML LSC.","authors":"Peter, B., Eisenwort, G., Sadovnik, I., Bauer, K., Willmann, M., R\u00fclicke, T., Berger, D., Stefanzl, G., Greiner, G., Hoermann, G., Keller, A., Wolf, D., \u010culen, M., Winter, GE., Hoffmann, T., Schiefer, AI., Sperr, WR., Zuber, J., Mayer, J., Valent, P.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Am J Hematol","volume":"97","issue":"9","page":"1215-1225","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"35293570","title":"Dysregulated RNA polyadenylation contributes to metabolic impairment in non-alcoholic fatty liver disease.","abstract":"Pre-mRNA processing is an essential mechanism for the generation of mature mRNA and the regulation of gene expression in eukaryotic cells. While defects in pre-mRNA processing have been implicated in a number of diseases their involvement in metabolic pathologies is still unclear. Here, we show that both alternative splicing and alternative polyadenylation, two major steps in pre-mRNA processing, are significantly altered in non-alcoholic fatty liver disease (NAFLD). Moreover, we find that Serine and Arginine Rich Splicing Factor 10 (SRSF10) binding is enriched adjacent to consensus polyadenylation motifs and its expression is significantly decreased in NAFLD, suggesting a role mediating pre-mRNA dysregulation in this condition. Consistently, inactivation of SRSF10 in mouse and human hepatocytes in vitro, and in mouse liver in vivo, was found to dysregulate polyadenylation of key metabolic genes such as peroxisome proliferator-activated receptor alpha (PPARA) and exacerbate diet-induced metabolic dysfunction. Collectively our work implicates dysregulated pre-mRNA polyadenylation in obesity-induced liver disease and uncovers a novel role for SRSF10 in this process.","authors":"Jobbins, AM., Haberman, N., Artigas, N., Amourda, C., Paterson, HAB., Yu, S., Blackford, SJI., Montoya, A., Dore, M., Wang, YF., Sardini, A., Cebola, I., Zuber, J., Rashid, ST., Lenhard, B., Vernia, S.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nucleic Acids Res","volume":"50","issue":"6","page":"3379-3393","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36961408","title":"HUWE1 controls tristetraprolin proteasomal degradation by regulating its phosphorylation.","abstract":"Tristetraprolin (TTP) is a critical negative immune regulator. It binds AU-rich elements in the untranslated-regions of many mRNAs encoding pro-inflammatory mediators, thereby accelerating their decay. A key but poorly understood mechanism of TTP regulation is its timely proteolytic removal: TTP is degraded by the proteasome through yet unidentified phosphorylation-controlled drivers. In this study, we set out to identify factors controlling TTP stability. Cellular assays showed that TTP is strongly lysine-ubiquitinated, which is required for its turnover. A genetic screen identified the ubiquitin E3 ligase HUWE1 as a strong regulator of TTP proteasomal degradation, which we found to control TTP stability indirectly by regulating its phosphorylation. Pharmacological assessment of multiple kinases revealed that HUWE1-regulated TTP phosphorylation and stability was independent of the previously characterized effects of MAPK-mediated S52\/S178 phosphorylation. HUWE1 function was dependent on phosphatase and E3 ligase binding sites identified in the TTP C-terminus. Our findings indicate that while phosphorylation of S52\/S178 is critical for TTP stabilization at earlier times after pro-inflammatory stimulation, phosphorylation of the TTP C-terminus controls its stability at later stages.","authors":"Scinicariello, S., Soderholm, A., Sch\u00e4fer, M., Shulkina, A., Schwartz, I., Hacker, K., Gogova, R., Kalis, R., Froussios, K., Budroni, V., Bestehorn, A., Clausen, T., Kovarik, P., Zuber, J., Versteeg, GA.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Elife","volume":"12","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.08.29.505645v1","articledate":"2023-03-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37020021","title":"mRNA recognition and packaging by the human transcription-export complex.","abstract":"Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export<sup>1,2<\/sup>. However, the mechanisms of mRNP recognition and three-dimensional mRNP&#xa0;organization are poorly understood<sup>3<\/sup>. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export.","authors":"Pacheco-Fiallos, B., Vorl\u00e4nder, MK., Riabov-Bassat, D., Fin, L., O'Reilly, FJ., Ayala, FI., Schellhaas, U., Rappsilber, J., Plaschka, C.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-04-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36914898","title":"TurboID-based proteomic profiling of meiotic chromosome axes in Arabidopsis thaliana.","abstract":"During meiotic prophase I, sister chromatids are arranged in a loop-base array along a proteinaceous structure, called the meiotic chromosome axis. This structure is essential for synapsis and meiotic recombination progression and hence formation of genetically diverse gametes. Proteomic studies in plants aiming to unravel the composition and regulation of meiotic axes are constrained by limited meiotic cells embedded in floral organs. Here we report TurboID (TbID)-based proximity labelling (PL) in meiotic cells of Arabidopsis thaliana. TbID fusion to the two meiotic chromosome axis proteins ASY1 and ASY3 enabled the identification of their proximate 'interactomes' based on affinity purification coupled with mass spectrometry. We identified 39 ASY1 and\/or ASY3 proximate candidates covering most known chromosome axis-related proteins. Functional studies of selected candidates demonstrate that not only known meiotic candidates but also new meiotic proteins were uncovered. Hence, TbID-based PL in meiotic cells enables the identification of chromosome axis proximate proteins in A. thaliana.","authors":"Feng, C., Roitinger, E., Hudecz, O., Cuacos, M., Lorenz, J., Schubert, V., Wang, B., Wang, R., Mechtler, K., Heckmann, S.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Nat Plants","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36927757","title":"SPOC domain proteins in health and disease.","abstract":"Since it was first described &gt;20 yr ago, the SPOC domain (Spen paralog and ortholog C-terminal domain) has been identified in many proteins all across eukaryotic species. SPOC-containing proteins regulate gene expression on various levels ranging from transcription to RNA processing, modification, export, and stability, as well as X-chromosome inactivation. Their manifold roles in controlling transcriptional output implicate them in a plethora of developmental processes, and their misregulation is often associated with cancer. Here, we provide an overview of the biophysical properties of the SPOC domain and its interaction with phosphorylated binding partners, the phylogenetic origin of SPOC domain proteins, the diverse functions of mammalian SPOC proteins and their homologs, the mechanisms by which they regulate differentiation and development, and their roles in cancer.","authors":"Appel, LM., Benedum, J., Engl, M., Platzer, S., Schleiffer, A., Strobl, X., Slade, D.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Genes Dev","volume":"37","issue":"5-6","page":"140-170","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36941451","title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing.","abstract":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2\/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.","authors":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Torma, F., Orthofer, M., Yarwood, R., Heinz, LX., Sedlyarov, V., Miranda, ND., Taylor, A., Grapentine, S., Al-Murshedi, F., Abot, A., Weidinger, A., Kutchukian, C., Sanchez, C., Cronin, SJF., Novatchkova, M., Kavirayani, A., Schuetz, T., Haubner, B., Haas, L., Hagelkruys, A., Jackowski, S., Kozlov, AV., Jacquemond, V., Knauf, C., Superti-Furga, G., Rullman, E., Gustafsson, T., McDermot, J., Lowe, M., Radak, Z., Chamberlain, JS., Bakovic, M., Banka, S., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Metab","volume":"5","issue":"3","page":"495-515","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-30","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36990990","title":"Muscle cell-type diversification is driven by bHLH transcription factor expansion and extensive effector gene duplications.","abstract":"Animals are typically composed of hundreds of different cell types, yet mechanisms underlying the emergence of new cell types remain unclear. Here we address the origin and diversification of muscle cells in the non-bilaterian, diploblastic sea anemone Nematostella vectensis. We discern two fast and two slow-contracting muscle cell populations, which differ by extensive sets of paralogous structural protein genes. We find that the regulatory gene set of the slow cnidarian muscles is remarkably similar to the bilaterian cardiac muscle, while the two fast muscles differ substantially from each other in terms of transcription factor profiles, though driving the same set of structural protein genes and having similar physiological characteristics. We show that anthozoan-specific paralogs of Paraxis\/Twist\/Hand-related bHLH transcription factors are involved in the formation of fast and slow muscles. Our data suggest that the subsequent recruitment of an entire effector gene set from the inner cell layer into the neural ectoderm contributes to the evolution of a novel muscle cell type. Thus, we conclude that extensive transcription factor gene duplications and co-option of effector modules act as an evolutionary mechanism underlying cell type diversification during metazoan evolution.","authors":"Cole, AG., Jahnel, SM., Kaul, S., Steger, J., Hagauer, J., Denner, A., Murguia, PF., Taudes, E., Zimmermann, B., Reischl, R., Steinmetz, PRH., Technau, U.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"1747","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36989351","title":"mRNA translational specialization by RBPMS presets the competence for cardiac commitment in hESCs.","abstract":"The blueprints of developing organs are preset at the early stages of embryogenesis. Transcriptional and epigenetic mechanisms are proposed to preset developmental trajectories. However, we reveal that the competence for the future cardiac fate of human embryonic stem cells (hESCs) is preset in pluripotency by a specialized mRNA translation circuit controlled by RBPMS. RBPMS is recruited to active ribosomes in hESCs to control the translation of essential factors needed for cardiac commitment program, including Wingless\/Integrated (WNT) signaling. Consequently, RBPMS loss specifically and severely impedes cardiac mesoderm specification, leading to patterning and morphogenetic defects in human cardiac organoids. Mechanistically, RBPMS specializes mRNA translation, selectively via 3'UTR binding and globally by promoting translation initiation. Accordingly, RBPMS loss causes translation initiation defects highlighted by aberrant retention of the EIF3 complex and depletion of EIF5A from mRNAs, thereby abrogating ribosome recruitment. We demonstrate how future fate trajectories are programmed during embryogenesis by specialized mRNA translation.","authors":"Bartsch, D., Kalamkar, K., Ahuja, G., Lackmann, JW., Hescheler, J., Weber, T., Bazzi, H., Clamer, M., Mendjan, S., Papantonis, A., Kurian, L.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Sci Adv","volume":"9","issue":"13","page":"eade1792","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"36989136","title":"Integrated transcriptome and proteome analysis reveals posttranscriptional regulation of ribosomal genes in human brain organoids.","abstract":"During development of the human cerebral cortex, multipotent neural progenitors generate excitatory neurons and glial cells. Investigations of the transcriptome and epigenome have revealed important gene regulatory networks underlying this crucial developmental event. However, the posttranscriptional control of gene expression and protein abundance during human corticogenesis remains poorly understood. We addressed this issue by using human telencephalic brain organoids grown using a dual reporter cell line to isolate neural progenitors and neurons and performed cell class and developmental stage-specific transcriptome and proteome analysis. Integrating the two datasets revealed modules of gene expression during human corticogenesis. Investigation of one such module uncovered mTOR-mediated regulation of translation of the 5'TOP element-enriched translation machinery in early progenitor cells. We show that in early progenitors partial inhibition of the translation of ribosomal genes prevents precocious translation of differentiation markers. Overall, our multiomics approach proposes novel posttranscriptional regulatory mechanisms crucial for the fidelity of cortical development.","authors":"Sidhaye, J., Trepte, P., Sepke, N., Novatchkova, M., Schutzbier, M., D\u00fcrnberger, G., Mechtler, K., Knoblich, JA.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Elife","volume":"12","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37013908","title":"Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns.","abstract":"Recruitment of RNA polymerase II (Pol II) to promoters is essential for transcription. Despite conflicting evidence, the Pol II preinitiation complex (PIC) is often thought to have a uniform composition and to assemble at all promoters via an identical mechanism. Here, using Drosophila melanogaster S2 cells as a model, we demonstrate that different promoter classes function via distinct PICs. Promoter DNA of developmentally regulated genes readily associates with the canonical Pol II PIC, whereas housekeeping promoters do not, and instead recruit other factors such as DREF. Consistently, TBP and DREF are differentially required by distinct promoter types. TBP and its paralog TRF2 also function at different promoter types in a partially redundant manner. In contrast, TFIIA is required at all promoters, and we identify factors that can recruit and\/or stabilize TFIIA at housekeeping promoters and activate transcription. Promoter activation by tethering these factors is sufficient to induce the dispersed transcription initiation patterns characteristic of housekeeping promoters. Thus, different promoter classes utilize distinct mechanisms of transcription initiation, which translate into different focused versus dispersed initiation patterns.","authors":"Serebreni, L., Pleyer, LM., Haberle, V., Hendy, O., Vlasova, A., Loubiere, V., Nem\u010dko, F., Bergauer, K., Roitinger, E., Mechtler, K., Stark, A.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"EMBO J","volume":null,"issue":null,"page":"e113519","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-04-04","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37072184","title":"Low-density lipoprotein receptor-related protein 1 (LRP1) as an auxiliary host factor for RNA viruses.","abstract":"Viruses with an RNA genome are often the cause of zoonotic infections. In order to identify novel pro-viral host cell factors, we screened a haploid insertion-mutagenized mouse embryonic cell library for clones that are resistant to Rift Valley fever virus (RVFV). This screen returned the low-density lipoprotein receptor-related protein 1 (LRP1) as a top hit, a plasma membrane protein involved in a wide variety of cell activities. Inactivation of <i>LRP1<\/i> in human cells reduced RVFV RNA levels already at the attachment and entry stages of infection. Moreover, the role of LRP1 in promoting RVFV infection was dependent on physiological levels of cholesterol and on endocytosis. In the human cell line HuH-7, LRP1 also promoted early infection stages of sandfly fever Sicilian virus and La Crosse virus, but had a minor effect on late infection by vesicular stomatitis virus, whereas encephalomyocarditis virus was entirely LRP1-independent. Moreover, siRNA experiments in human Calu-3 cells demonstrated that also SARS-CoV-2 infection benefitted from LRP1. Thus, we identified LRP1 as a host factor that supports infection by a spectrum of RNA viruses.","authors":"Devignot, S., Sha, TW., Burkard, TR., Schmerer, P., Hagelkruys, A., Mirazimi, A., Elling, U., Penninger, JM., Weber, F.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Life Sci Alliance","volume":"6","issue":"7","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-04-20","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37094140","title":"In diverse conditions, intrinsic chromatin condensates have liquid-like material properties.","abstract":"Nuclear DNA in eukaryotes is wrapped around histone proteins to form nucleosomes on a chromatin fiber. Dynamic folding of the chromatin fiber into loops and variations in the degree of chromatin compaction regulate essential processes such as transcription, recombination, and mitotic chromosome segregation. Our understanding of the physical properties that allow chromatin to be dynamically remodeled even in highly compacted states is limited. Previously, we reported that chromatin has an intrinsic capacity to phase separate and form dynamic liquid-like condensates, which can be regulated by cellular factors [B. A. Gibson <i>et al.<\/i>, <i>Cell<\/i> <b>179<\/b>, 470-484.e421 (2019)]. Recent contradictory reports claim that a specific set of solution conditions is required for fluidity in condensates that would otherwise be solid [J. C. Hansen, K. Maeshima, M. J. Hendzel, <i>Epigenetics Chromatin<\/i> <b>14<\/b>, 50 (2021); H. Strickfaden <i>et al.<\/i>, <i>Cell<\/i> <b>183<\/b>, 1772-1784.e1713 (2020)]. We sought to resolve these discrepancies, as our ability to translate with confidence these biophysical observations to cells requires their precise characterization. Moreover, whether chromatin assemblies are dynamic or static affects how processes such as transcription, loop extrusion, and remodeling will engage them inside cells. Here, we show in diverse conditions and without specific buffering components that chromatin fragments form phase separated fluids in&#xa0;vitro. We also explore how sample preparation and imaging affect the experimental observation of chromatin condensate dynamics. Last, we describe how liquid-like in&#xa0;vitro behaviors can translate to the locally dynamic but globally constrained chromatin movement observed in cells.","authors":"Gibson, BA., Blaukopf, C., Lou, T., Chen, L., Doolittle, LK., Finkelstein, I., Narlikar, GJ., Gerlich, DW., Rosen, MK.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Proc Natl Acad Sci U S A","volume":"120","issue":"18","page":"e2218085120","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37085514","title":"Igh and Igk loci use different folding principles for V gene recombination due to distinct chromosomal architectures of pro-B and pre-B cells.","abstract":"Extended loop extrusion across the immunoglobulin heavy-chain (Igh) locus facilitates V<sub>H<\/sub>-DJ<sub>H<\/sub> recombination following downregulation of the cohesin-release factor Wapl by Pax5, resulting in global changes in the chromosomal architecture of pro-B cells. Here, we demonstrate that chromatin looping and V<sub>K<\/sub>-J<sub>K<\/sub> recombination at the Igk locus were insensitive to Wapl upregulation in pre-B cells. Notably, the Wapl protein was expressed at a 2.2-fold higher level in pre-B cells compared with pro-B cells, which resulted in a distinct chromosomal architecture with normal loop sizes in pre-B cells. High-resolution chromosomal contact analysis of the Igk locus identified multiple internal loops, which likely juxtapose V<sub>K<\/sub> and J<sub>K<\/sub> elements to facilitate V<sub>K<\/sub>-J<sub>K<\/sub> recombination. The higher Wapl expression in Ig&#x3bc;-transgenic pre-B cells prevented extended loop extrusion at the Igh locus, leading to recombination of only the 6 most 3' proximal V<sub>H<\/sub> genes and likely to allelic exclusion of all other V<sub>H<\/sub> genes in pre-B cells. These results suggest that pro-B and pre-B cells with their distinct chromosomal architectures use different chromatin folding principles for V gene recombination, thereby enabling allelic exclusion at the Igh locus, when the Igk locus is recombined.","authors":"Hill, L., Wutz, G., Jaritz, M., Tagoh, H., Calder\u00f3n, L., Peters, JM., Goloborodko, A., Busslinger, M.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"2316","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-04-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37100955","title":"Apoptotic cell death in disease-Current understanding of the NCCD 2023.","abstract":"Apoptosis is a form of regulated cell death (RCD) that involves proteases of the caspase family. Pharmacological and genetic strategies that experimentally inhibit or delay apoptosis in mammalian systems have elucidated the key contribution of this process not only to (post-)embryonic development and adult tissue homeostasis, but also to the etiology of multiple human disorders. Consistent with this notion, while defects in the molecular machinery for apoptotic cell death impair organismal development and promote oncogenesis, the unwarranted activation of apoptosis promotes cell loss and tissue damage in the context of various neurological, cardiovascular, renal, hepatic, infectious, neoplastic and inflammatory conditions. Here, the Nomenclature Committee on Cell Death (NCCD) gathered to critically summarize an&#xa0;abundant pre-clinical literature mechanistically linking the core apoptotic apparatus to organismal homeostasis in the context of disease.","authors":"Vitale, I., Pietrocola, F., Guilbaud, E., Aaronson, SA., Abrams, JM., Adam, D., Agostini, M., Agostinis, P., Alnemri, ES., Altucci, L., Amelio, I., Andrews, DW., Aqeilan, RI., Arama, E., Baehrecke, EH., Balachandran, S., Bano, D., Barlev, NA., Bartek, J., Bazan, NG., Becker, C., Bernassola, F., Bertrand, MJM., Bianchi, ME., Blagosklonny, MV., Blander, JM., Blandino, G., Blomgren, K., Borner, C., Bortner, CD., Bove, P., Boya, P., Brenner, C., Broz, P., Brunner, T., Damgaard, RB., Calin, GA., Campanella, M., Candi, E., Carbone, M., Carmona-Gutierrez, D., Cecconi, F., Chan, FK., Chen, GQ., Chen, Q., Chen, YH., Cheng, EH., Chipuk, JE., Cidlowski, JA., Ciechanover, A., Ciliberto, G., Conrad, M., Cubillos-Ruiz, JR., Czabotar, PE., D'Angiolella, V., Daugaard, M., Dawson, TM., Dawson, VL., De Maria, R., De Strooper, B., Debatin, KM., Deberardinis, RJ., Degterev, A., Del Sal, G., Deshmukh, M., Di Virgilio, F., Diederich, M., Dixon, SJ., Dynlacht, BD., El-Deiry, WS., Elrod, JW., Engeland, K., Fimia, GM., Galassi, C., Ganini, C., Garcia-Saez, AJ., Garg, AD., Garrido, C., Gavathiotis, E., Gerlic, M., Ghosh, S., Green, DR., Greene, LA., Gronemeyer, H., H\u00e4cker, G., Hajn\u00f3czky, G., Hardwick, JM., Haupt, Y., He, S., Heery, DM., Hengartner, MO., Hetz, C., Hildeman, DA., Ichijo, H., Inoue, S., J\u00e4\u00e4ttel\u00e4, M., Janic, A., Joseph, B., Jost, PJ., Kanneganti, TD., Karin, M., Kashkar, H., Kaufmann, T., Kelly, GL., Kepp, O., Kimchi, A., Kitsis, RN., Klionsky, DJ., Kluck, R., Krysko, DV., Kulms, D., Kumar, S., Lavandero, S., Lavrik, IN., Lemasters, JJ., Liccardi, G., Linkermann, A., Lipton, SA., Lockshin, RA., L\u00f3pez-Ot\u00edn, C., Luedde, T., MacFarlane, M., Madeo, F., Malorni, W., Manic, G., Mantovani, R., Marchi, S., Marine, JC., Martin, SJ., Martinou, JC., Mastroberardino, PG., Medema, JP., Mehlen, P., Meier, P., Melino, G., Melino, S., Miao, EA., Moll, UM., Mu\u00f1oz-Pinedo, C., Murphy, DJ., Niklison-Chirou, MV., Novelli, F., N\u00fa\u00f1ez, G., Oberst, A., Ofengeim, D., Opferman, JT., Oren, M., Pagano, M., Panaretakis, T., Pasparakis, M., Penninger, JM., Pentimalli, F., Pereira, DM., Pervaiz, S., Peter, ME., Pinton, P., Porta, G., Prehn, JHM., Puthalakath, H., Rabinovich, GA., Rajalingam, K., Ravichandran, KS., Rehm, M., Ricci, JE., Rizzuto, R., Robinson, N., Rodrigues, CMP., Rotblat, B., Rothlin, CV., Rubinsztein, DC., Rudel, T., Rufini, A., Ryan, KM., Sarosiek, KA., Sawa, A., Sayan, E., Schroder, K., Scorrano, L., Sesti, F., Shao, F., Shi, Y., Sica, GS., Silke, J., Simon, HU., Sistigu, A., Stephanou, A., Stockwell, BR., Strapazzon, F., Strasser, A., Sun, L., Sun, E., Sun, Q., Szabadkai, G., Tait, SWG., Tang, D., Tavernarakis, N., Troy, CM., Turk, B., Urbano, N., Vandenabeele, P., Vanden Berghe, T., Vander Heiden, MG., Vanderluit, JL., Verkhratsky, A., Villunger, A., von Karstedt, S., Voss, AK., Vousden, KH., Vucic, D., Vuri, D., Wagner, EF., Walczak, H., Wallach, D., Wang, R., Wang, Y., Weber, A., Wood, W., Yamazaki, T., Yang, HT., Zakeri, Z., Zawacka-Pankau, JE., Zhang, L., Zhang, H., Zhivotovsky, B., Zhou, W., Piacentini, M., Kroemer, G., Galluzzi, L.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Cell Death Differ","volume":null,"issue":null,"page":"1-58","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37076620","title":"CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion.","abstract":"In eukaryotes, genomic DNA is extruded into loops by cohesin<sup>1<\/sup>. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)<sup>2,3<\/sup> that have important roles in gene regulation and recombination during development and disease<sup>1,4-7<\/sup>. How CTCF establishes TAD boundaries and to what extent these are permeable to cohesin is unclear<sup>8<\/sup>. Here, to address these questions, we visualize interactions of single CTCF and cohesin molecules on DNA in vitro. We show that CTCF is sufficient to block diffusing cohesin, possibly reflecting how cohesive cohesin accumulates at TAD boundaries, and is also sufficient to block loop-extruding cohesin, reflecting how CTCF establishes TAD boundaries. CTCF functions asymmetrically, as predicted; however, CTCF is dependent on DNA tension. Moreover, CTCF regulates cohesin's loop-extrusion activity by changing its direction and by inducing loop shrinkage. Our data indicate that CTCF is not, as previously assumed, simply a barrier to cohesin-mediated loop extrusion but is an active regulator of this process, whereby the permeability of TAD boundaries can be modulated by DNA tension. These results reveal mechanistic principles of how CTCF controls loop extrusion and genome architecture.","authors":"Davidson, IF., Barth, R., Zaczek, M., van der Torre, J., Tang, W., Nagasaka, K., Janissen, R., Kerssemakers, J., Wutz, G., Dekker, C., Peters, JM.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nature","volume":"616","issue":"7958","page":"822-827","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.09.08.507093v2","articledate":"2023-04-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37188109","title":"Implementation of a Drug Screening Platform to Target<i>Gch1<\/i> Expression in Injured Mouse Dorsal Root Ganglion Neurons.","abstract":"Management of neuropathic pain is notoriously difficult; current analgesics, including anti-inflammatory- and opioid-based medications, are generally ineffective and can pose serious side effects. There is a need to uncover non-addictive and safe analgesics to combat neuropathic pain. Here, we describe the setup of a phenotypic screen whereby the expression of an algesic gene,<i>Gch1<\/i>, is targeted. GCH1 is the rate-limiting enzyme in the de novo synthesis of tetrahydrobiopterin (BH4), a metabolite linked to neuropathic pain in both animal models and in human chronic pain sufferers.<i>Gch1<\/i>is induced in sensory neurons after nerve injury and its upregulation is responsible for increased BH4 levels. GCH1 protein has proven to be a difficult enzyme to pharmacologically target with small molecule inhibition. Thus, by establishing a platform to monitor and target induced<i>Gch1<\/i> expression in individual injured dorsal root ganglion (DRG) neurons in vitro, we can screen for compounds that regulate its expression levels. This approach also allows us to gain valuable biological insights into the pathways and signals regulating GCH1 and BH4 levels upon nerve injury. This protocol is compatible with any transgenic reporter system in which the expression of an algesic gene (or multiple genes) can be monitored fluorescently. Such an approach can be scaled up for high-throughput compound screening and is amenable to transgenic mice as well as human stem cell-derived sensory neurons. Graphical overview.","authors":"Cronin, SJF., Davidow, LS., Arvanites, AC., Rubin, LL., Penninger, JM., Woolf, CJ.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Bio Protoc","volume":"13","issue":"9","page":"e4666","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37214906","title":"Pseudorabies virus hijacks DDX3X, initiating an addictive \"mad itch\" and immune suppression, to facilitate viral spread.","abstract":"Infections with defined Herpesviruses, such as Pseudorabies virus (PRV) and Varicella zoster virus (VZV) can cause neuropathic itch, referred to as \"mad itch\" in multiple species. The underlying mechanisms involved in neuropathic \"mad itch\" are poorly understood. Here, we show that PRV infections hijack the RNA helicase DDX3X in sensory neurons to facilitate anterograde transport of the virus along axons. PRV induces re-localization of DDX3X from the cell body to the axons which ultimately leads to death of the infected sensory neurons. Inducible genetic ablation of <i>Ddx3x<\/i> in sensory neurons results in neuronal death and \"mad itch\" in mice. This neuropathic \"mad itch\" is propagated through activation of the opioid system making the animals \"addicted to itch\". Moreover, we show that PRV co-opts and diverts T cell development in the thymus via a sensory neuron-IL-6-hypothalamus-corticosterone stress pathway. Our data reveal how PRV, through regulation of DDX3X in sensory neurons, travels along axons and triggers neuropathic itch and immune deviations to initiate pathophysiological programs which facilitate its spread to enhance infectivity.","authors":"Cronin, SJF., Tejada, MA., Song, R., Laval, K., Cikes, D., Ji, M., Brai, A., Stadlmann, J., Novatchikova, M., Perlot, T., Ali, OH., Botta, L., Decker, T., Lazovic, J., Hagelkruys, A., Enquist, L., Rao, S., Koyuncu, OO., Penninger, JM.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-05-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37226685","title":"FAM3C\/ILEI protein is elevated in psoriatic lesions and triggers psoriasiform hyperproliferation in mice.","abstract":"FAM3C\/ILEI is an important cytokine for tumor progression and metastasis. However, its involvement in inflammation remains elusive. Here, we show that ILEI protein is highly expressed in psoriatic lesions. Inducible keratinocyte-specific ILEI overexpression in mice (K5-ILEI<sup>ind<\/sup> ) recapitulates many aspects of psoriasis following TPA challenge, primarily manifested by impaired epidermal differentiation and increased neutrophil recruitment. Mechanistically, ILEI triggers Erk and Akt signaling, which then activates STAT3 via Ser727 phosphorylation. Keratinocyte-specific ILEI deletion ameliorates TPA-induced skin inflammation. A transcriptomic ILEI signature obtained from the K5-ILEI<sup>ind<\/sup> model shows enrichment in several signaling pathways also found in psoriasis and identifies urokinase as a targetable enzyme to counteract ILEI activity. Pharmacological inhibition of urokinase in TPA-induced K5-ILEI<sup>ind<\/sup> mice results in significant improvement of psoriasiform symptoms by reducing ILEI secretion. The ILEI signature distinguishes psoriasis from healthy skin with uPA ranking among the top \"separator\" genes. Our study identifies ILEI as a key driver in psoriasis, indicates the relevance of ILEI-regulated genes for disease manifestation, and shows the clinical impact of ILEI and urokinase as novel potential therapeutic targets in psoriasis.","authors":"Malik, B., Vokic, I., Mohr, T., Poppelaars, M., Holcmann, M., Novoszel, P., Timelthaler, G., Lendl, T., Krauss, D., Elling, U., Mildner, M., Penninger, JM., Petzelbauer, P., Sibilia, M., Csiszar, A.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"EMBO Mol Med","volume":"15","issue":"7","page":"e16758","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-07-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37251335","title":"Peripheralized sepiapterin reductase inhibition as a safe analgesic therapy.","abstract":"The development of novel analgesics for chronic pain in the last 2&#xa0;decades has proven virtually intractable, typically failing due to lack of efficacy and dose-limiting side effects. Identified through unbiased gene expression profiling experiments in rats and confirmed by human genome-wide association studies, the role of excessive tetrahydrobiopterin (BH4) in chronic pain has been validated by numerous clinical and preclinical studies. BH4 is an essential cofactor for aromatic amino acid hydroxylases, nitric oxide synthases, and alkylglycerol monooxygenase so a lack of BH4 leads to a range of symptoms in the periphery and central nervous system (CNS). An ideal therapeutic goal therefore would be to block excessive BH4 production, while preventing potential BH4 rundown. In this review, we make the case that sepiapterin reductase (SPR) inhibition restricted to the periphery (i.e., excluded from the spinal cord and brain), is an efficacious and safe target to alleviate chronic pain. First, we describe how different cell types that engage in BH4 overproduction and contribute to pain hypersensitivity, are themselves restricted to peripheral tissues and show their blockade is sufficient to alleviate pain. We discuss the likely safety profile of peripherally restricted SPR inhibition based on human genetic data, the biochemical alternate routes of BH4 production in various tissues and species, and the potential pitfalls to predictive translation when using rodents. Finally, we propose and discuss possible formulation and molecular strategies to achieve peripherally restricted, potent SPR inhibition to treat not only chronic pain but other conditions where excessive BH4 has been demonstrated to be pathological.","authors":"Cronin, SJF., Andrews, NA., Latremoliere, A.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Front Pharmacol","volume":"14","issue":null,"page":"1173599","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-05-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37137307","title":"Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival.","abstract":"The ClpC1:ClpP1P2 protease is a core component of the proteostasis system in mycobacteria. To improve the efficacy of antitubercular agents targeting the Clp protease, we characterized the mechanism of the antibiotics cyclomarin A and ecumicin. Quantitative proteomics revealed that the antibiotics cause massive proteome imbalances, including upregulation of two unannotated yet conserved stress response factors, ClpC2 and ClpC3. These proteins likely protect the Clp protease from excessive amounts of misfolded proteins or from cyclomarin A, which we show to mimic damaged proteins. To overcome the Clp security system, we developed a BacPROTAC that induces degradation of ClpC1 together with its ClpC2 caretaker. The dual Clp degrader, built from linked cyclomarin A heads, was highly efficient in killing pathogenic Mycobacterium tuberculosis, with&#xa0;&gt;100-fold increased potency over the parent antibiotic. Together, our data reveal Clp scavenger proteins as important proteostasis safeguards and highlight the potential of BacPROTACs as future antibiotics.","authors":"Hoi, DM., Junker, S., Junk, L., Schwechel, K., Fischel, K., Podlesainski, D., Hawkins, PME., van Geelen, L., Kaschani, F., Leodolter, J., Morreale, FE., Kleine, S., Guha, S., Rumpel, K., Schmiedel, VM., Weinstabl, H., Meinhart, A., Payne, RJ., Kaiser, M., Hartl, M., Boehmelt, G., Kazmaier, U., Kalscheuer, R., Clausen, T.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Cell","volume":"186","issue":"10","page":"2176-2192.e22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-05-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37208374","title":"Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments.","abstract":"DNA loop extrusion by structural-maintenance-of-chromosome (SMC) complexes has emerged as a primary organizing principle for chromosomes. The mechanism by which SMC motor proteins extrude DNA loops is still unresolved and much debated. The ring-like structure of SMC complexes prompted multiple models where the extruded DNA is topologically or pseudotopologically entrapped within the ring during loop extrusion. However, recent experiments showed the passage of roadblocks much bigger than the SMC ring size, suggesting a nontopological mechanism. Recently, attempts were made to reconcile the observed passage of large roadblocks with a pseudotopological mechanism. Here we examine the predictions of these pseudotopological models and find that they are not consistent with new experimental data on SMC roadblock encounters. Particularly, these models predict the formation of two loops and that roadblocks will reside near the stem of the loop upon encounter-both in contrast to experimental observations. Overall, the experimental data reinforce the notion of a nontopological mechanism for extrusion of DNA.","authors":"Barth, R., Pradhan, B., Kim, E., Davidson, IF., van der Torre, J., Peters, JM., Dekker, C.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Sci Rep","volume":"13","issue":"1","page":"8100","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-05-22","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37279615","title":"The material properties of mitotic chromosomes.","abstract":"Chromosomes transform during the cell cycle, allowing transcription and replication during interphase and chromosome segregation during mitosis. Morphological changes are thought to be driven by the combined effects of DNA loop extrusion and a chromatin solubility phase transition. By extruding the chromatin fibre into loops, condensins enrich at an axial core and provide resistance to spindle pulling forces. Mitotic chromosomes are further compacted by deacetylation of histone tails, rendering chromatin insoluble and resistant to penetration by microtubules. Regulation of surface properties by Ki-67 allows independent chromosome movement in early mitosis and clustering during mitotic exit. Recent progress has provided insight into how the extraordinary material properties of chromatin emerge from these activities, and how these properties facilitate faithful chromosome segregation.","authors":"Spicer, MFD., Gerlich, DW.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Curr Opin Struct Biol","volume":"81","issue":null,"page":"102617","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-06-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37293068","title":"Mast cell-derived BH4 is a critical mediator of postoperative pain.","abstract":"Postoperative pain affects most patients after major surgery and can transition to chronic pain. Here, we discovered that postoperative pain hypersensitivity correlated with markedly increased local levels of the metabolite BH4. Gene transcription and reporter mouse analyses after skin injury identified neutrophils, macrophages and mast cells as primary postoperative sources of GTP cyclohydrolase-1 ( <i>Gch1<\/i> ) expression, the rate-limiting enzyme in BH4 production. While specific <i>Gch1<\/i> deficiency in neutrophils or macrophages had no effect, mice deficient in mast cells or mast cell-specific <i>Gch1<\/i> showed drastically decreased postoperative pain after surgery. Skin injury induced the nociceptive neuropeptide substance P, which directly triggers the release of BH4-dependent serotonin in mouse and human mast cells. Substance P receptor blockade substantially ameliorated postoperative pain. Our findings underline the unique position of mast cells at the neuro-immune interface and highlight substance P-driven mast cell BH4 production as promising therapeutic targets for the treatment of postoperative pain.","authors":"Starkl, P., Jonsson, G., Artner, T., Turnes, BL., Serhan, N., Oliveira, T., Gail, LM., Stejskal, K., Channon, KM., K\u00f6cher, T., Stary, G., Klang, V., Gaudenzio, N., Knapp, S., Woolf, CJ., Penninger, JM., Cronin, SJF.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-06-13","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37316475","title":"Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries.","abstract":"Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer's evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization.","authors":"Gert, KRB., Panser, K., Surm, J., Steinmetz, BS., Schleiffer, A., Jovine, L., Moran, Y., Kondrashov, F., Pauli, A.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"3506","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.09.01.506233v1.abstract","articledate":"2023-06-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37357575","title":"Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase.","abstract":"Genetic information is stored in linear DNA molecules, which are highly folded inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in an intertwined arrangement. Dividing cells must disentangle and condense the sister chromatids into separate bodies such that a microtubule-based spindle can move them to opposite poles. While the spindle-mediated transport of sister chromatids has been studied in detail, the chromosome-intrinsic mechanics presegregating sister chromatids have remained elusive. Here, we show that human sister chromatids resolve extensively already during interphase, in a process dependent on the loop-extruding activity of cohesin, but not that of condensins. Increasing cohesin's looping capability increases sister DNA resolution in interphase nuclei to an extent normally seen only during mitosis, despite the presence of abundant arm cohesion. That cohesin can resolve sister chromatids so extensively in the absence of mitosis-specific activities indicates that DNA loop extrusion is a generic mechanism for segregating replicated genomes, shared across different Structural Maintenance of Chromosomes (SMC) protein complexes in all kingdoms of life.","authors":"Batty, P., Langer, CC., Tak\u00e1cs, Z., Tang, W., Blaukopf, C., Peters, JM., Gerlich, DW.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"EMBO J","volume":null,"issue":null,"page":"e113475","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-06-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37354885","title":"Loop extrusion rules: the next generation.","abstract":"The interphase genome of vertebrates contains roughly 100 000 dynamic loops&#xa0;formed by cohesins. These loops are thought to play important roles in many functions, but their exact contribution in each case remains hotly disputed. The key challenge in studying these loops is the lack of a single experimental technique that could reliably and comprehensively visualize their locations and dynamics. Yet, we can infer them using theoretical models that integrate complementary experimental observations. Modeling proved instrumental in showing that cohesins form loops via extrusion. The loop extrusion model made numerous successful qualitative and quantitative predictions and inspired many experiments. However, it also demonstrated limited accuracy in predicting contact maps. Recent research suggests that the original model did not fully account for the intricate details of the mechanism of loop extrusion and its complex regulation. Here, we review the progress in visualizing extrusion and characterizing the cohesin cofactors. These discoveries can be summarized as 'rules'&#xa0;of cohesin movement along chromosomes and incorporated into the next generation of models. Such improved models will enable more accurate inferences of positions and dynamics of cohesin loops and generate&#xa0;better predictions for designing experiments.","authors":"Corsi, F., Rusch, E., Goloborodko, A.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Curr Opin Genet Dev","volume":"81","issue":null,"page":"102061","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-06-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37317646","title":"A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans.","abstract":"Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. A defining feature of cilia is that they are evolutionarily ancient, yet not universally conserved. In this study, we have used the resulting presence and absence pattern in the genomes of diverse eukaryotes to identify a set of 386 human genes associated with cilium assembly or motility. Comprehensive tissue-specific RNAi in Drosophila and mutant analysis in C. elegans revealed signature ciliary defects for 70-80% of novel genes, a percentage similar to that for known genes within the cluster. Further characterization identified different phenotypic classes, including a set of genes related to the cartwheel component Bld10\/CEP135 and two highly conserved regulators of cilium biogenesis. We propose this dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and presents a valuable resource for future studies of cilium biology and associated disorders.","authors":"Dobbelaere, J., Su, TY., Erdi, B., Schleiffer, A., Dammermann, A.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"EMBO J","volume":null,"issue":null,"page":"e113616","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-06-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37384706","title":"Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities.","abstract":"Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode <i>Caenorhabditis briggsae<\/i>, we discovered that <i>Mavericks<\/i>, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that <i>Mavericks<\/i> gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.","authors":"Widen, SA., Bes, IC., Koreshova, A., Pliota, P., Krogull, D., Burga, A.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Science","volume":"380","issue":"6652","page":"eade0705","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-07-03","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37467143","title":"Histone variants shape chromatin states in Arabidopsis.","abstract":"How different intrinsic sequence variations and regulatory modifications of histones combine in nucleosomes remain unclear. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the <i>Arabidopsis thaliana<\/i> genome. We showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of constitutive heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.","authors":"Jamge, B., Lorkovi\u0107, ZJ., Axelsson, E., Osakabe, A., Shukla, V., Yelagandula, R., Akimcheva, S., Kuehn, AL., Berger, F.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Elife","volume":"12","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-07-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37572376","title":"Microfibrous Scaffolds Guide Stem Cell Lumenogenesis and Brain Organoid Engineering.","abstract":"3D organoids have been widely used as tractable in vitro models capable of elucidating aspects of human development and disease. However, the manual and low throughput culture methods coupled with a low reproducibility and geometric heterogeneity restricts the scope and application of organoid research. Combining expertise from stem cell biology and bioengineering offers a promising approach to address some of these limitations. Here, we use melt electrospinning writing to generate tuneable grid scaffolds that can guide the self-organization of pluripotent stem cells into patterned arrays of embryoid bodies. We show that grid geometry is a key determinant of stem cell self-organization, guiding the position and size of emerging lumens via curvature-controlled tissue growth. We report two distinct methods for culturing scaffold-grown embryoid bodies into either interconnected or spatially discrete cerebral organoids. These scaffolds provide a high-throughput method to generate, culture and analyse large numbers of organoids, substantially reducing the time investment and manual labour involved in conventional methods of organoid culture. We anticipate that this methodological development will open up new opportunities for guiding pluripotent stem cell culture, studying lumenogenesis, and generating large numbers of uniform organoids for high throughput screening. This article is protected by copyright. All rights reserved.","authors":"Ritzau-Reid, KI., Callens, SJP., Xie, R., Cihova, M., Reumann, D., Grigsby, CL., Prados-Martin, L., Wang, R., Moore, AC., Armstrong, JPK., Knoblich, JA., Stevens, MM.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Adv Mater","volume":null,"issue":null,"page":"e2300305","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37566781","title":"MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity.","abstract":"Cross-linking mass spectrometry has become a powerful tool for the identification of protein-protein interactions and for gaining insight into the structures of proteins. We previously published MS Annika, a cross-linking search engine which can accurately identify cross-linked peptides in MS2 spectra from a variety of different MS-cleavable cross-linkers. In this publication, we present MS Annika 2.0, an updated version implementing a new search algorithm that, in addition to MS2 level, only supports the processing of data from MS2-MS3-based approaches for the identification of peptides from MS3 spectra, and introduces a novel scoring function for peptides identified across multiple MS stages. Detected cross-links are validated by estimating the false discovery rate (FDR) using a target-decoy approach. We evaluated the MS3-search-capabilities of MS Annika 2.0 on five different datasets covering a variety of experimental approaches and compared it to XlinkX and MaXLinker, two other cross-linking search engines. We show that MS Annika detects up to 4 times more true unique cross-links while simultaneously yielding less false positive hits and therefore a more accurate FDR estimation than the other two search engines. All mass spectrometry proteomics data along with result files have been deposited to the ProteomeXchange consortium via the PRIDE partner repository with the dataset identifier PXD041955.","authors":"Birklbauer, MJ., Matzinger, M., M\u00fcller, F., Mechtler, K., Dorfer, V.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"J Proteome Res","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37609639","title":"Inhalation of ACE2 as a therapeutic target on sex-bias differences in SARS-CoV-2 infection and variant of concern.","abstract":"Despite similar infection rates, COVID-19 has resulted in more deaths in men than women. To understand the underlying mechanisms behind this sex-biased difference in disease severity, we infected K18-human angiotensin converting enzyme 2 (ACE2) mice of both sexes with SARS-CoV-2. Our study revealed a unique protein expression profile in the lung microenvironment of female mice. As a result, they were less vulnerable to severe infection, with higher ACE2 expression and a higher estrogen receptor &#x3b1; (ER&#x3b1;)\/androgen receptor (AR) ratio that led to increased antiviral factor levels. In male mice, inhaling recombinant ACE2 neutralized the virus and maintained the ER&#x3b1;\/AR ratio, thereby protecting the lungs. Our findings suggest that inhaling recombinant ACE2 could serve as a decoy receptor against SARS-CoV-2 and protect male mice by offsetting ER&#x3b1;-associated protective mechanisms. Additionally, our study supports the potential effectiveness of recombinant ACE2 therapy in human lung organoids infected with the Delta variant.","authors":"Onodera, Y., Liang, J., Li, Y., Griffin, B., Thanabalasingam, T., Lu, C., Zhu, J., Liu, M., Moraes, T., Zheng, W., Khateeb, J., Khang, J., Huang, Y., Jerkic, M., Nakane, M., Baker, A., Orser, B., Chen, YW., Wirnsberger, G., Penninger, JM., Rotstein, OD., Slutsky, AS., Li, Y., Mubareka, S., Zhang, H.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"iScience","volume":"26","issue":"8","page":"107470","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37591243","title":"Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms.","abstract":"Cohesin connects CTCF-binding sites and other genomic loci in cis to form chromatin loops and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here, we describe a cohesin hinge mutant that can extrude DNA into loops but is unable to mediate cohesion in human cells. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin's cohesion and loop extrusion activities can be partially separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wild-type cohesin. This suggests that cohesion establishment and cohesin's interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring.","authors":"Nagasaka, K., Davidson, IF., Stocsits, RR., Tang, W., Wutz, G., Batty, P., Panarotto, M., Litos, G., Schleiffer, A., Gerlich, DW., Peters, JM.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Mol Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37615576","title":"Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species.","abstract":"Methylation of cytosines in the CG context (mCG) is the most abundant DNA modification in vertebrates that plays crucial roles in cellular differentiation and identity. After fertilization, DNA methylation patterns inherited from parental gametes are remodelled into a state compatible with embryogenesis. In mammals, this is achieved through the global erasure and re-establishment of DNA methylation patterns. However, in non-mammalian vertebrates like zebrafish, no global erasure has been observed. To investigate the evolutionary conservation and divergence of DNA methylation remodelling in teleosts, we generated base resolution DNA methylome datasets of developing medaka and medaka-zebrafish hybrid embryos. In contrast to previous reports, we show that medaka display comparable DNA methylome dynamics to zebrafish with high gametic mCG levels (sperm: &#x223c;90%; egg: &#x223c;75%), and adoption of a paternal-like methylome during early embryogenesis, with no signs of prior DNA methylation erasure. We also demonstrate that non-canonical DNA methylation (mCH) reprogramming at TGCT tandem repeats is a conserved feature of teleost embryogenesis. Lastly, we find remarkable evolutionary conservation of DNA methylation remodelling patterns in medaka-zebrafish hybrids, indicative of compatible DNA methylation maintenance machinery in far-related teleost species. Overall, these results suggest strong evolutionary conservation of DNA methylation remodelling pathways in teleosts, which is distinct from the global DNA methylome erasure and reestablishment observed in mammals.","authors":"Ross, SE., V\u00e1zquez-Mar\u00edn, J., Gert, KRB., Gonz\u00e1lez-Rajal, \u00c1., Dinger, ME., Pauli, A., Mart\u00ednez-Morales, JR., Bogdanovic, O.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Nucleic Acids Res","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2023.05.24.542066v1","articledate":"2023-08-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37633982","title":"Mutational landscape of intestinal crypt cells after long-term in vivo exposure to high fat diet.","abstract":"Obesity is a modifiable risk factor in cancer development, especially for gastrointestinal cancer. While the etiology of colorectal cancer is well characterized by the adenoma-carcinoma sequence, it remains unclear how obesity influences colorectal cancer development. Dietary components of a high fat diet along with obesity have been shown to modulate the cancer risk by perturbing the homeostasis of intestinal stem cells, yet how adiposity impacts the development of genomic instability has not been studied. Mutational signatures are a powerful way to understand how a complex biological response impacts genomic stability. We utilized a mouse model of diet-induced obesity to study the mutational landscape of intestinal crypt cells after a 48-week exposure to an experimental high fat diet in vivo. By clonally enriching single crypt derived cells in organoid culture and obtaining whole genome sequences, we analyzed and compared the mutational landscape of intestinal epithelial cells from normal diet and high fat diet mice. Single nucleotide substitution signatures and indel signatures present in our cohort are found equally active in both diet groups and reflect biological processes of normal aging, cellular replication, and oxidative stress induced during organoid culturing. Thus, we demonstrate that in the absence of activating mutations or chemical exposure, high fat diet alone is not sufficient to increase genomic instability.","authors":"Meyenberg, M., Hakobyan, A., Papac-Milicevic, N., G\u00f6derle, L., Langner, FL., Markovic, M., Lee, JH., Koo, BK., Busslinger, GA., da Silva, IT., Binder, CJ., Menche, J., Loizou, JI.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Sci Rep","volume":"13","issue":"1","page":"13964","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37620393","title":"The ABL-MYC axis controls WIPI1-enhanced autophagy in lifespan extension.","abstract":"Human WIPI &#x3b2;-propellers function as PI3P effectors in autophagy, with WIPI4 and WIPI3 being able to link autophagy control by AMPK and TORC1 to the formation of autophagosomes. WIPI1, instead, assists WIPI2 in efficiently recruiting the ATG16L1 complex at the nascent autophagosome, which in turn promotes lipidation of LC3\/GABARAP and autophagosome maturation. However, the specific role of WIPI1 and its regulation are unknown. Here, we discovered the ABL-ERK-MYC signalling axis controlling WIPI1. As a result of this signalling, MYC binds to the WIPI1 promoter and represses WIPI1 gene expression. When ABL-ERK-MYC signalling is counteracted, increased WIPI1 gene expression enhances the formation of autophagic membranes capable of migrating through tunnelling nanotubes to neighbouring cells with low autophagic activity. ABL-regulated WIPI1 function is relevant to lifespan control, as ABL deficiency in C. elegans increased gene expression of the WIPI1 orthologue ATG-18 and prolonged lifespan in a manner dependent on ATG-18. We propose that WIPI1 acts as an enhancer of autophagy that is physiologically relevant for regulating the level of autophagic activity over the lifespan.","authors":"Sporbeck, K., Haas, ML., Pastor-Maldonado, CJ., Sch\u00fcssele, DS., Hunter, C., Takacs, Z., Diogo de Oliveira, AL., Franz-Wachtel, M., Charsou, C., Pfisterer, SG., Gubas, A., Haller, PK., Knorr, RL., Kaulich, M., Macek, B., Eskelinen, EL., Simonsen, A., Proikas-Cezanne, T.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Commun Biol","volume":"6","issue":"1","page":"872","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-28","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37440660","title":"Widespread regulatory specificities between transcriptional co-repressors and enhancers in <i>Drosophila<\/i>.","abstract":"Gene expression is controlled by the precise activation and repression of transcription. Repression is mediated by specialized transcription factors (TFs) that recruit co-repressors (CoRs) to silence transcription, even in the presence of activating cues. However, whether CoRs can dominantly silence all enhancers or display distinct specificities is unclear. In this work, we report that most enhancers in <i>Drosophila<\/i> can be repressed by only a subset of CoRs, and enhancers classified by CoR sensitivity show distinct chromatin features, function, TF motifs, and binding. Distinct TF motifs render enhancers more resistant or sensitive to specific CoRs, as we demonstrate by motif mutagenesis and addition. These CoR-enhancer compatibilities constitute an additional layer of regulatory specificity that allows differential regulation at close genomic distances and is indicative of distinct mechanisms of transcriptional repression.","authors":"Jacobs, J., Pagani, M., Wenzl, C., Stark, A.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Science","volume":"381","issue":"6654","page":"198-204","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-07-18","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37660160","title":"Ascl1 and Ngn2 convert mouse embryonic stem cells to neurons via functionally distinct paths.","abstract":"Ascl1 and Ngn2, closely related proneural transcription factors, are able to convert mouse embryonic stem cells into induced neurons. Despite their similarities, these factors elicit only partially overlapping transcriptional programs, and it remains unknown whether cells are converted via distinct mechanisms. Here we show that Ascl1 and Ngn2 induce mutually exclusive side populations by binding and activating distinct lineage drivers. Furthermore, Ascl1 rapidly dismantles the pluripotency network and installs neuronal and trophoblast cell fates, while Ngn2 generates a neural stem cell-like intermediate supported by incomplete shutdown of the pluripotency network. Using CRISPR-Cas9 knockout screening, we find that Ascl1 relies more on factors regulating pluripotency and the cell cycle, such as Tcf7l1. In the absence of Tcf7l1, Ascl1 still represses core pluripotency genes but fails to exit the cell cycle. However, overexpression of Cdkn1c induces cell cycle exit and restores the generation of neurons. These findings highlight that cell type conversion can occur through two distinct mechanistic paths, even when induced by closely related transcription factors.","authors":"Vainorius, G., Novatchkova, M., Michlits, G., Baar, JC., Raupach, C., Lee, J., Yelagandula, R., Wernig, M., Elling, U.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"5341","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-09-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37643759","title":"RNF43 and ZNRF3 in Wnt Signaling - A Master Regulator at the Membrane.","abstract":"The Wnt &#x3b2;-catenin signaling pathway is a highly conserved mechanism that plays a critical role from embryonic development and adult stem cell homeostasis. However, dysregulation of the Wnt pathway has been implicated in various diseases, including cancer. Therefore, multiple layers of regulatory mechanisms tightly control the activation and suppression of the Wnt signal. The E3 ubiquitin ligases RNF43 and ZNRF3, which are known negative regulators of the Wnt pathway, are critical component of Wnt signaling regulation. These E3 ubiquitin ligases control Wnt signaling by targeting the Wnt receptor Frizzled to induce ubiquitination-mediated endo-lysosomal degradation, thus controlling the activation of the Wnt signaling pathway. We also discuss the regulatory mechanisms, interactors, and evolution of RNF43 and ZNRF3. This review article summarizes recent findings on RNF43 and ZNRF3 and their potential implications for the development of therapeutic strategies to target the Wnt signaling pathway in various diseases, including cancer.","authors":"Farnhammer, F., Colozza, G., Kim, J.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Int J Stem Cells","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-29","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37603466","title":"The negative adipogenesis regulator <i>Dlk1<\/i> is transcriptionally regulated by <i>Ifrd1<\/i> (TIS7) and translationally by its orthologue <i>Ifrd2<\/i> (SKMc15).","abstract":"Delta-like homolog 1 (<i>Dlk1<\/i>), an inhibitor of adipogenesis, controls the cell fate of adipocyte progenitors. Experimental data presented here identify two independent regulatory mechanisms, transcriptional and translational, by which <i>Ifrd1<\/i> (TIS7) and its orthologue <i>Ifrd2<\/i> (SKMc15) regulate <i>Dlk1<\/i> levels. Mice deficient in both <i>Ifrd1<\/i> and <i>Ifrd2<\/i> (dKO) had severely reduced adipose tissue and were resistant to high-fat diet-induced obesity. Wnt signaling, a negative regulator of adipocyte differentiation, was significantly upregulated in dKO mice. Elevated levels of the Wnt\/&#x3b2;-catenin target protein Dlk1 inhibited the expression of adipogenesis regulators <i>Pparg<\/i> and <i>Cebpa<\/i>, and fatty acid transporter <i>Cd36<\/i>. Although both <i>Ifrd1<\/i> and <i>Ifrd2<\/i> contributed to this phenotype, they utilized two different mechanisms. <i>Ifrd1<\/i> acted by controlling Wnt signaling and thereby transcriptional regulation of <i>Dlk1<\/i>. On the other hand, distinctive experimental evidence showed that Ifrd2 acts as a general translational inhibitor significantly affecting Dlk1 protein levels. Novel mechanisms of <i>Dlk1<\/i> regulation in adipocyte differentiation involving <i>Ifrd1<\/i> and <i>Ifrd2<\/i> are based on experimental data presented here.","authors":"Vietor, I., Cikes, D., Piironen, K., Vasakou, T., Heimd\u00f6rfer, D., Gstir, R., Erlacher, MD., Tancevski, I., Eller, P., Demetz, E., Hess, MW., Kuhn, V., Degenhart, G., Rozman, J., Klingenspor, M., Hrabe de Angelis, M., Valovka, T., Huber, LA.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Elife","volume":"12","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-31","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37697643","title":"The promise of genetic screens in human <i>in&#xa0;vitro<\/i> brain models.","abstract":"Advances of <i>in&#xa0;vitro<\/i> culture models have allowed unprecedented insights into human neurobiology. At the same time genetic screening has matured into a robust and accessible experimental strategy allowing for the simultaneous study of many genes in parallel. The combination of both technologies is a newly emerging tool for neuroscientists, opening the door to identifying causal cell- and tissue-specific developmental and disease mechanisms. However, with complex experimental genetic screening set-ups new challenges in data interpretation and experimental scope arise that require a deep understanding of the benefits and challenges of individual approaches. In this review, we summarize the literature that applies genetic screening to <i>in&#xa0;vitro<\/i> brain models, compare experimental strengths and weaknesses and point towards future directions of these promising approaches.","authors":"Beirute-Herrera, J., L\u00f3pez-Amo Calvo, B., Edenhofer, F., Esk, C.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Biol Chem","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-09-12","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37706489","title":"Scavenger receptor endocytosis controls apical membrane morphogenesis in the <i>Drosophila<\/i> airways.","abstract":"The acquisition of distinct branch sizes and shapes is a central aspect in tubular organ morphogenesis and function. In the <i>Drosophila<\/i> airway tree, the interplay of apical ECM components with the underlying membrane and cytoskeleton controls tube elongation, but the link between ECM composition with apical membrane morphogenesis and tube size regulation is elusive. Here, we characterized Emp (epithelial membrane protein), a <i>Drosophila<\/i> CD36-homologue belonging to the scavenger receptor class B protein-family. <i>emp<\/i> mutant embryos fail to internalize the luminal chitin deacetylases Serp and Verm at the final stages of airway maturation and die at hatching with liquid filled airways. Emp localizes in apical epithelial membranes and shows cargo selectivity for LDLr-domain containing proteins. <i>emp<\/i> mutants also display over elongated tracheal tubes with increased levels of the apical proteins Crb, DE-cad and phosphorylated Src (p-Src). We show that Emp associates with and organizes the &#x3b2;H-Spectrin cytoskeleton and is itself confined by apical F-actin bundles. Overexpression or loss of its cargo protein Serp lead to abnormal apical accumulations of Emp and perturbations in p-Src levels. We propose that during morphogenesis, Emp senses and responds to luminal cargo levels by initiating apical membrane endocytosis along the longitudinal tube axis and thereby restricts airway elongation.","authors":"Pinheiro, AS., Tsarouhas, V., Senti, KA., Arefin, B., Samakovlis, C.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Elife","volume":"12","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-09-14","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37704762","title":"Single-cell brain organoid screening identifies developmental defects in autism.","abstract":"The development of the human brain involves unique processes (not observed in many other species) that can contribute to neurodevelopmental disorders<sup>1-4<\/sup>. Cerebral organoids enable the study of neurodevelopmental disorders in a human context. We have developed the CRISPR-human organoids-single-cell RNA sequencing&#xa0;(CHOOSE) system, which uses verified pairs of guide RNAs, inducible CRISPR-Cas9-based genetic disruption and single-cell transcriptomics for pooled loss-of-function screening in mosaic organoids. Here we show that&#xa0;perturbation of 36 high-risk autism spectrum disorder genes related to transcriptional regulation uncovers their effects on cell fate determination. We find that dorsal intermediate progenitors, ventral progenitors and upper-layer excitatory neurons are among the most vulnerable cell types. We construct a developmental gene regulatory network of cerebral organoids from single-cell transcriptomes and chromatin modalities and identify autism spectrum disorder-associated and perturbation-enriched regulatory modules. Perturbing members of the BRG1\/BRM-associated factor (BAF) chromatin remodelling complex leads to enrichment of ventral telencephalon progenitors. Specifically, mutating the BAF subunit ARID1B affects the fate transition of progenitors to oligodendrocyte and interneuron precursor cells, a phenotype that we confirmed in patient-specific induced pluripotent stem cell-derived organoids. Our study paves the way for high-throughput phenotypic characterization of disease susceptibility genes in organoid models with cell state, molecular pathway and gene regulatory network readouts.","authors":"Li, C., Fleck, JS., Martins-Costa, C., Burkard, TR., Themann, J., Stuempflen, M., Peer, AM., Vertesy, \u00c1., Littleboy, JB., Esk, C., Elling, U., Kasprian, G., Corsini, NS., Treutlein, B., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nature","volume":"621","issue":"7978","page":"373-380","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-09-15","doi":"10.1038\/s41586-023-06473-y","first_author":"Li, C.","corresponding_authors":"Knoblich, JA."},{"pmid":"37801801","title":"An update on human pre- and peri-implantation development: a blueprint for blastoids.","abstract":"Despite over 40 years following the first birth from medically assisted reproduction (MAR) technologies, mechanisms underlying the key developmental events during the first 7 days of human development, such as signaling pathway&#xa0;contribution, are remaining a mystery. An in-depth mechanistic understanding of how the human preimplantation embryo develops would support the optimization of embryo quality assessment methods and culturing conditions, thereby increasing the success rate of MAR. However, the limited availability of human embryos, legitimate ethical concerns, and regulations still present an obstacle toward our advancement of knowledge. Stem cell-based embryonic models, including blastoids than model blastocysts, offer unprecedented opportunities to fill knowledge gaps and complement animal models. Blastoids' predictive power depends on how faithfully they recapitulate the blastocyst. Here, we review the state of the art of human pre- and peri-implantation development and outline the specificities of human embryo research to clarify the framework for blastoid research.","authors":"David, L., Bruneau, A., Fr\u00e9our, T., Rivron, N., Van de Velde, H.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Curr Opin Genet Dev","volume":"83","issue":null,"page":"102125","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-10-06","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37486674","title":"Identification of potential classes of glycoligands mediating dynamic endothelial adhesion of human tumor cells.","abstract":"One critical step of metastasis formation is the extravasation of circulating tumor cells from the bloodstream. This process requires the dynamic interaction of cell adhesion molecules like E-selectin on endothelial cells with carbohydrate ligands on tumor cells. To characterize these glycans in a comprehensible approach, the rolling, tethering, and firm adhesion of nine human tumor cell lines on human umbilical vein endothelial cells was analyzed using laminar flow adhesion assays. The tumor cell lines were grouped into three subsets by their canonical E-selectin ligand status (sialyl-Lewis A and X +\/+, -\/+, -\/-) and their adhesiveness was compared after enzymatic, pharmacologic, chemical treatment or antibody blockade of the tumor cells or endothelial cells, respectively. Tumor cells were also screened regarding their glycosyltransferase expression profile. We found that although E-selectin and terminal &#x3b1;2,3-sialic acid largely determined firm adhesion, adhesive events did not exclusively depend on the presence of sialyl-Lewis A and\/or sialyl-Lewis X. Nevertheless, two of the three sialyl-Lewis A\/X-\/- tumor cells additionally or fully depended on vascular cell adhesion molecule-1 for firm adhesion. The significance of O-GalNAc- and N-glycans for adhesion varied remarkably among the tumor cells. The sialyl-Lewis A\/X+\/+ subset showed glycoprotein-independent adhesion, suggesting a role of glycolipids as well. All sialyl-Lewis A\/X-\/- tumor cells lacked FUT3 and FUT7 expression as opposed to sialyl-Lewis A\/X+\/+ or -\/+ cell lines. In summary, the glycans on tumor cells mediating endothelial adhesion are not as much restricted to sialyl-Lewis A \/X as previously assumed. The present study specifically suggests &#x3b1;2,3-linked sialic acid, O-GalNAc glycans, glycosphingolipids, and FUT3\/FUT7 products as promising targets for future studies.","authors":"Starzonek, S., Maar, H., Mereiter, S., Freytag, V., Haider, MT., Riecken, K., Huang, YL., Jacob, F., Wicklein, D., Schumacher, U., Lange, T.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Glycobiology","volume":"33","issue":"8","page":"637-650","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-10-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37846480","title":"The HACE1 E3 ligase mediates RAC1-dependent control of mTOR signaling complexes.","abstract":"HACE1 is a HECT family E3 ubiquitin-protein ligase with broad but incompletely understood tumor suppressor activity. Here, we report a previously unrecognized link between HACE1 and signaling complexes containing mammalian target of rapamycin (mTOR). HACE1 blocks mTORC1 and mTORC2 activities by reducing mTOR stability in an E3 ligase-dependent manner. Mechanistically, HACE1 binds to and ubiquitylates Ras-related C3 botulinum toxin substrate 1 (RAC1) when RAC1 is associated with mTOR complexes, including at focal adhesions, leading to proteasomal degradation of RAC1. This in turn decreases the stability of mTOR to reduce mTORC1 and mTORC2 activity. HACE1 deficient cells show enhanced mTORC1\/2 activity, which is reversed by chemical or genetic RAC1 inactivation but not in cells expressing the HACE1-insensitive mutant, RAC1<sup>K147R<\/sup> . In vivo, Rac1 deletion reverses enhanced mTOR expression in KRas<sup>G12D<\/sup> -driven lung tumors of Hace1<sup>-\/-<\/sup> mice. HACE1 co-localizes with mTOR and RAC1, resulting in RAC1-dependent loss of mTOR protein stability. Together, our data demonstrate that HACE1 destabilizes mTOR by targeting RAC1 within mTOR-associated complexes, revealing a unique ubiquitin-dependent process to control the activity of mTOR signaling complexes.","authors":"Turgu, B., El-Naggar, A., Kogler, M., Tortola, L., Zhang, HF., Hassan, M., Lizardo, MM., Kung, SH., Lam, W., Penninger, JM., Sorensen, PH.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"EMBO Rep","volume":null,"issue":null,"page":"e56815","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-10-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37842725","title":"Morphogenesis and development of human telencephalic organoids in the absence and presence of exogenous extracellular matrix.","abstract":"The establishment and maintenance of apical-basal polarity is a fundamental step in brain development, instructing the organization of neural progenitor cells (NPCs) and the developing cerebral cortex. Particularly, basally located extracellular matrix (ECM) is crucial for this process. In vitro, epithelial polarization can be achieved via endogenous ECM production, or exogenous ECM supplementation. While neuroepithelial development is recapitulated in neural organoids, the effects of different ECM sources in tissue morphogenesis remain underexplored. Here, we show that exposure to a solubilized basement membrane matrix substrate, Matrigel, at early neuroepithelial stages causes rapid tissue polarization and rearrangement of neuroepithelial architecture. In cultures exposed to pure ECM components or unexposed to any exogenous ECM, polarity acquisition is slower and driven by endogenous ECM production. After the onset of neurogenesis, tissue architecture and neuronal differentiation are largely independent of the initial ECM source, but Matrigel exposure has long-lasting effects on tissue patterning. These results advance the knowledge on mechanisms of exogenously and endogenously guided morphogenesis, demonstrating the self-sustainability of neuroepithelial cultures by endogenous processes.","authors":"Martins-Costa, C., Pham, VA., Sidhaye, J., Novatchkova, M., Wiegers, A., Peer, A., M\u00f6seneder, P., Corsini, NS., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"EMBO J","volume":"42","issue":"22","page":"e113213","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-14","doi":"10.15252\/embj.2022113213","first_author":null,"corresponding_authors":null},{"pmid":"37839701","title":"An automated nanowell-array workflow for quantitative multiplexed single-cell proteomics sample preparation at high sensitivity.","abstract":"Multiplexed and label-free mass spectrometry-based approaches with single-cell resolution have attributed surprising heterogeneity to presumed homogenous cell populations. Even though specialized experimental designs and instrumentation have demonstrated remarkable advances, the efficient sample preparation of single cells still lags. Here, we introduce the proteoCHIP, a universal option for single-cell proteomics sample preparation including multiplexed labeling up to 16-plex with high sensitivity and throughput. The automated processing using a commercial system combining single-cell isolation and picoliter dispensing, the cellenONE&#xae;, reduces final sample volumes to low nanoliters submerged in a hexadecane layer simultaneously eliminating error-prone manual sample handling and overcoming evaporation. The specialized proteoCHIP design allows direct injection of single cells via a standard autosampler resulting in around 1,500 protein groups per TMT10-plex with reduced or eliminated need for a carrier proteome. We evaluated the effect of wider precursor isolation windows at single-cell input levels and found that using 2 Da isolation windows increased overall sensitivity without significantly impacting interference. Using the dedicated MS acquisition strategies detailed here, we identified on average close to 2,000 proteins per TMT10-plex across 170 multiplexed single cells that readily distinguished human cell types. Overall, our workflow combines highly efficient sample preparation, chromatographic and ion mobility-based filtering, rapid wide-window DDA analysis and intelligent data analysis for optimal multiplexed single-cell proteomics. This versatile and automated proteoCHIP-based sample preparation approach is sufficiently sensitive to drive biological applications of single-cell proteomics and can be readily adopted by proteomics laboratories.","authors":"Ctortecka, C., Hartlmayr, D., Seth, A., Mendjan, S., Tourniaire, G., Udeshi, ND., Carr, SA., Mechtler, K.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Mol Cell Proteomics","volume":null,"issue":null,"page":"100665","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-10-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37848409","title":"Neural deficits in a mouse model of PACS1 syndrome are corrected with PACS1- or HDAC6-targeting therapy.","abstract":"PACS1 syndrome is a neurodevelopmental disorder (NDD) caused by a recurrent de novo missense mutation in PACS1 (p.Arg203Trp (PACS1<sup>R203W<\/sup>)). The mechanism by which PACS1<sup>R203W<\/sup> causes PACS1 syndrome is unknown, and no curative treatment is available. Here, we use patient cells and PACS1 syndrome mice to show that PACS1 (or PACS-1) is an HDAC6 effector and that the R203W substitution increases the PACS1\/HDAC6 interaction, aberrantly potentiating deacetylase activity. Consequently, PACS1<sup>R203W<\/sup> reduces acetylation of &#x3b1;-tubulin and cortactin, causing the Golgi ribbon in hippocampal neurons and patient-derived neural&#xa0;progenitor cells (NPCs) to fragment and overpopulate dendrites, increasing their arborization. The dendrites, however, are beset with varicosities, diminished spine density, and fewer functional synapses, characteristic of NDDs. Treatment of PACS1 syndrome mice or patient NPCs with PACS1- or HDAC6-targeting antisense oligonucleotides, or HDAC6 inhibitors, restores neuronal structure and synaptic transmission in prefrontal cortex, suggesting that targeting PACS1<sup>R203W<\/sup>\/HDAC6 may be an effective therapy for PACS1 syndrome.","authors":"Villar-Pazos, S., Thomas, L., Yang, Y., Chen, K., Lyles, JB., Deitch, BJ., Ochaba, J., Ling, K., Powers, B., Gingras, S., Kordasiewicz, HB., Grubisha, MJ., Huang, YH., Thomas, G.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"6547","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-10-23","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37890487","title":"Sequential multi-omics analysis identifies clinical phenotypes and predictive biomarkers for long COVID.","abstract":"The post-acute sequelae of COVID-19 (PASC), also known as long COVID, is often associated with debilitating symptoms and adverse multisystem consequences. We obtain plasma samples from 117 individuals during and 6&#xa0;months following their acute phase of infection to comprehensively profile and assess changes in cytokines, proteome, and metabolome. Network analysis reveals sustained inflammatory response, platelet degranulation, and cellular activation during convalescence accompanied by dysregulation in arginine biosynthesis, methionine metabolism, taurine metabolism, and tricarboxylic acid (TCA) cycle processes. Furthermore, we develop a prognostic model composed of 20 molecules involved in regulating T&#xa0;cell exhaustion and energy metabolism that can reliably predict adverse clinical outcomes following discharge from acute infection with 83% accuracy and an area under the curve (AUC) of 0.96. Our study reveals pertinent biological processes during convalescence that differ from acute infection, and it supports the development of specific therapies and biomarkers for patients suffering from long COVID.","authors":"Wang, K., Khoramjoo, M., Srinivasan, K., Gordon, PMK., Mandal, R., Jackson, D., Sligl, W., Grant, MB., Penninger, JM., Borchers, CH., Wishart, DS., Prasad, V., Oudit, GY.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Cell Rep Med","volume":null,"issue":null,"page":"101254","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37880247","title":"Identification of CCZ1 as an essential lysosomal trafficking regulator in Marburg and Ebola virus infections.","abstract":"Marburg and Ebola filoviruses are two of the deadliest infectious agents and several outbreaks have occurred in the last decades. Although several receptors and co-receptors have been reported for Ebola virus, key host factors remain to be elucidated. In this study, using a haploid cell screening platform, we identify the guanine nucleotide exchange factor CCZ1 as a key host factor in the early stage of filovirus replication. The critical role of CCZ1 for filovirus infections is validated in 3D primary human hepatocyte cultures and human blood-vessel organoids, both critical target sites for Ebola and Marburg virus tropism. Mechanistically, CCZ1 controls early to late endosomal trafficking of these viruses. In addition, we report that CCZ1 has a role in the endosomal trafficking of endocytosis-dependent SARS-CoV-2 infections, but not in infections by Lassa virus, which enters endo-lysosomal trafficking at the late endosome stage. Thus, we have identified an essential host pathway for filovirus infections in cell lines and engineered human target tissues. Inhibition of CCZ1 nearly completely abolishes Marburg and Ebola infections. Thus, targeting CCZ1 could potentially serve as a promising drug target for controlling infections caused by various viruses, such as SARS-CoV-2, Marburg, and Ebola.","authors":"Monteil, V., Kwon, H., John, L., Salata, C., Jonsson, G., Vorrink, SU., Appelberg, S., Youhanna, S., Dyczynski, M., Leopoldi, A., Leeb, N., Volz, J., Hagelkruys, A., Kellner, MJ., Devignot, S., Michlits, G., Foong-Sobis, M., Weber, F., Lauschke, VM., Horn, M., Feldmann, H., Elling, U., Penninger, JM., Mirazimi, A.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"6785","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-10-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37910614","title":"RANKL\/RANK is required for cytokine-induced beta cell death; osteoprotegerin, a RANKL inhibitor, reverses rodent type 1 diabetes.","abstract":"Treatment for type 1 diabetes (T1D) requires stimulation of functional &#x3b2; cell regeneration and survival under stress. Previously, we showed that inhibition of the RANKL\/RANK [receptor activator of nuclear factor kappa &#x392; (NF-&#x3ba;B) ligand] pathway, by osteoprotegerin and the anti-osteoporotic drug denosumab, induces rodent and human &#x3b2; cell proliferation. We demonstrate that the RANK pathway mediates cytokine-induced rodent and human &#x3b2; cell death through RANK-TRAF6 interaction and induction of NF-&#x3ba;B activation. Osteoprotegerin and denosumab protected &#x3b2; cells against this cytotoxicity. In human immune cells, osteoprotegerin and denosumab reduce proinflammatory cytokines in activated T-cells by inhibiting RANKL-induced activation of monocytes. In vivo, osteoprotegerin reversed recent-onset T1D in nonobese diabetic\/Ltj mice, reduced insulitis, improved glucose homeostasis, and increased plasma insulin, &#x3b2; cell proliferation, and mass in these mice. Serum from T1D subjects induced human &#x3b2; cell death and dysfunction, but not &#x3b1; cell death. Osteoprotegerin and denosumab reduced T1D serum-induced &#x3b2; cell cytotoxicity and dysfunction. Inhibiting RANKL\/RANK could have therapeutic potential.","authors":"Kondegowda, NG., Filipowska, J., Do, JS., Leon-Rivera, N., Li, R., Hampton, R., Ogyaadu, S., Levister, C., Penninger, JM., Reijonen, H., Levy, CJ., Vasavada, RC.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Sci Adv","volume":"9","issue":"44","page":"eadf5238","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-03","doi":"10.1126\/sciadv.adf5238","first_author":null,"corresponding_authors":null},{"pmid":"37725138","title":"Essential role of the Pax5 C-terminal domain in controlling B cell commitment and development.","abstract":"The B cell regulator Pax5 consists of multiple domains whose function we analyzed in vivo by deletion in Pax5. While B lymphopoiesis was minimally affected in mice with homozygous deletion of the octapeptide or partial homeodomain, both sequences were required for optimal B cell development. Deletion of the C-terminal regulatory domain 1 (CRD1) interfered with B cell development, while elimination of CRD2 modestly affected B-lymphopoiesis. Deletion of CRD1 and CRD2 arrested B cell development at an uncommitted pro-B cell stage. Most Pax5-regulated genes required CRD1 or both CRD1 and CRD2 for their activation or repression as these domains induced or eliminated open chromatin at Pax5-activated or Pax5-repressed genes, respectively. Co-immunoprecipitation experiments demonstrated that the activating function of CRD1 is mediated through interaction with the chromatin-remodeling BAF, H3K4-methylating Set1A-COMPASS, and H4K16-acetylating NSL complexes, while its repressing function depends on recruitment of the Sin3-HDAC and MiDAC complexes. These data provide novel molecular insight into how different Pax5 domains regulate gene expression to promote B cell commitment and development.","authors":"Gruenbacher, S., Jaritz, M., Hill, L., Sch\u00e4fer, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"J Exp Med","volume":"220","issue":"12","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-09-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37337907","title":"Enhancers of the PAIR4 regulatory module promote distal V<sub>H<\/sub> gene recombination at the Igh locus.","abstract":"While extended loop extrusion across the entire Igh locus controls V<sub>H<\/sub> -DJ<sub>H<\/sub> recombination, local regulatory sequences, such as the PAIR elements, may also activate V<sub>H<\/sub> gene recombination in pro-B-cells. Here, we show that PAIR-associated V<sub>H<\/sub> 8 genes contain a conserved putative regulatory element (V8E) in their downstream sequences. To investigate the function of PAIR4 and its V8.7E, we deleted 890&#x2009;kb containing all 14 PAIRs in the Igh 5' region, which reduced distal V<sub>H<\/sub> gene recombination over a 100-kb distance on either side of the deletion. Reconstitution by insertion of PAIR4-V8.7E strongly activated distal V<sub>H<\/sub> gene recombination. PAIR4 alone resulted in lower induction of recombination, indicating that PAIR4 and V8.7E function as one regulatory unit. The pro-B-cell-specific activity of PAIR4 depends on CTCF, as mutation of its CTCF-binding site led to sustained PAIR4 activity in pre-B and immature B-cells and to PAIR4 activation in T-cells. Notably, insertion of V8.8E was sufficient to activate V<sub>H<\/sub> gene recombination. Hence, enhancers of the PAIR4-V8.7E module and V8.8E element activate distal V<sub>H<\/sub> gene recombination and thus contribute to the diversification of the BCR repertoire in the context of loop extrusion.","authors":"Hill, L., Jaritz, M., Tagoh, H., Schindler, K., Kostanova-Poliakova, D., Sun, Q., Schwickert, TA., Leeb, M., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"EMBO J","volume":"42","issue":"15","page":"e112741","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37735619","title":"Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex\/cyclosome (APC\/C).","abstract":"Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight has thus far required artificially trapped structures to stabilize specific steps along the enzymatic process. So far, how any ubiquitin ligase builds a proteasomal degradation signal, which is canonically regarded as four or more ubiquitins, remains unclear. Here we present time-resolved cryogenic electron microscopy studies of the 1.2&#x2009;MDa E3 ubiquitin ligase, known as the anaphase-promoting complex\/cyclosome (APC\/C), and its E2 co-enzymes (UBE2C\/UBCH10 and UBE2S) during substrate polyubiquitination. Using cryoDRGN (Deep Reconstructing Generative Networks), a neural network-based approach, we reconstruct the conformational changes undergone by the human APC\/C during polyubiquitination, directly visualize an active E3-E2 pair modifying its substrate, and identify unexpected interactions between multiple ubiquitins with parts of the APC\/C machinery, including its coactivator CDH1. Together, we demonstrate how modification of substrates with nascent ubiquitin chains helps to potentiate processive substrate polyubiquitination, allowing us to model how a ubiquitin ligase builds a proteasomal degradation signal.","authors":"Bodrug, T., Welsh, KA., Bolhuis, DL., Paul\u0430konis, E., Martinez-Chacin, RC., Liu, B., Pinkin, N., Bonacci, T., Cui, L., Xu, P., Roscow, O., Amann, SJ., Grishkovskaya, I., Emanuele, MJ., Harrison, JS., Steimel, JP., Hahn, KM., Zhang, W., Zhong, ED., Haselbach, D., Brown, NG.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Struct Mol Biol","volume":"30","issue":"11","page":"1663-1674","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-15","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37409633","title":"Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5.","abstract":"UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an &#x3b1;-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.","authors":"Hod\u00e1kov\u00e1, Z., Grishkovskaya, I., Brunner, HL., Bolhuis, DL., Bela\u010di\u0107, K., Schleiffer, A., Kotisch, H., Brown, NG., Haselbach, D.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"EMBO J","volume":"42","issue":"16","page":"e113348","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37315536","title":"Tumor-derived prostaglandin E2 programs cDC1 dysfunction to impair intratumoral orchestration of anti-cancer T&#xa0;cell responses.","abstract":"Type 1 conventional dendritic cells (cDC1s) are critical for anti-cancer immunity. Protective anti-cancer immunity is thought to require cDC1s to sustain T&#xa0;cell responses within tumors, but it is poorly understood how this function is regulated and whether its subversion contributes to immune evasion. Here, we show that tumor-derived prostaglandin E2 (PGE<sub>2<\/sub>) programmed a dysfunctional state in intratumoral cDC1s, disabling their ability to locally orchestrate anti-cancer CD8<sup>+<\/sup> T&#xa0;cell responses. Mechanistically, cAMP signaling downstream of the PGE<sub>2<\/sub>-receptors EP2 and EP4 was responsible for the programming of cDC1 dysfunction, which depended on the loss of the transcription factor IRF8. Blockade of the PGE<sub>2<\/sub>-EP2\/EP4-cDC1 axis prevented cDC1 dysfunction in tumors, locally reinvigorated anti-cancer CD8<sup>+<\/sup> T&#xa0;cell responses, and achieved cancer immune control. In human cDC1s, PGE<sub>2<\/sub>-induced dysfunction is conserved and associated with poor cancer patient prognosis. Our findings reveal a cDC1-dependent intratumoral checkpoint for anti-cancer immunity that is targeted by PGE<sub>2<\/sub> for immune evasion.","authors":"Bayerl, F., Meiser, P., Donakonda, S., Hirschberger, A., Lacher, SB., Pedde, AM., Hermann, CD., Elewaut, A., Knolle, M., Ramsauer, L., Rudolph, TJ., Grassmann, S., \u00d6llinger, R., Kirchhammer, N., Trefny, M., Anton, M., Wohlleber, D., H\u00f6chst, B., Zaremba, A., Kr\u00fcger, A., Rad, R., Obenauf, AC., Schadendorf, D., Zippelius, A., Buchholz, VR., Schraml, BU., B\u00f6ttcher, JP.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Immunity","volume":"56","issue":"6","page":"1341-1358.e11","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-06-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37185990","title":"An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo.","abstract":"Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations of enhancers and minimal promoters are utilized to construct small, artificial promoters for gene delivery vectors. Large-scale functional screening methodology to construct genomic maps of enhancer activities has been successfully established in cultured cell lines, however, not yet applied to terminally differentiated cells and tissues in a living animal. Here, we transposed the Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) technique to the mouse brain using adeno-associated-viruses (AAV) for the delivery of a highly complex screening library tiling entire genomic regions and covering in total 3&#xa0;Mb of the mouse genome. We identified 483 sequences with enhancer activity, including sequences that were not predicted by DNA accessibility or histone marks. Characterizing the expression patterns of fluorescent reporters controlled by nine candidate sequences, we observed differential expression patterns also in sparse cell types. Together, our study provides an entry point for the unbiased study of enhancer activities in organisms during health and disease.","authors":"Chan, YC., Kienle, E., Oti, M., Di Liddo, A., Mendez-Lago, M., Aschauer, DF., Peter, M., Pagani, M., Arnold, C., Vonderheit, A., Sch\u00f6n, C., Kreuz, S., Stark, A., Rumpel, S.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Sci Rep","volume":"13","issue":"1","page":"6745","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-05-17","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37343338","title":"Transposon waves at the water-to-land transition.","abstract":"The major transitions in vertebrate evolution are associated with significant genomic reorganizations. In contrast to the evolutionary processes that occurred at the origin of vertebrates or prior to the radiation of teleost fishes, no whole-genome duplication events occurred during the water-to-land transition, and it remains an open question how did genome dynamics contribute to this prominent evolutionary event. Indeed, the recent sequencing of sarcopterygian and amphibian genomes has revealed that the extant lineages immediately preceding and succeeding this transition harbor an exceptional number of transposable elements and it is tempting to speculate that these sequences might have catalyzed the adaptations that enabled vertebrates to venture into land. Here, we review the genome dynamics associated with the major transitions in vertebrate evolution and discuss how the highly repetitive genomic landscapes revealed by recent efforts to characterize the genomes of amphibians and sarcopterygians argue for turbulent genome dynamics occurring before the water-to-land transition and possibly enabling it.","authors":"Falcon, F., Tanaka, EM., Rodriguez-Terrones, D.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Curr Opin Genet Dev","volume":"81","issue":null,"page":"102059","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-16","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37735473","title":"The NCOR-HDAC3 co-repressive complex modulates the leukemogenic potential of the transcription factor ERG.","abstract":"The ERG (ETS-related gene) transcription factor is linked to various types of cancer, including leukemia. However, the specific ERG domains and co-factors contributing to leukemogenesis are poorly understood. Drug targeting a transcription factor such as ERG is challenging. Our study reveals the critical role of a conserved amino acid, proline, at position 199, located at the 3' end of the PNT (pointed) domain, in ERG's ability to induce leukemia. P199 is necessary for ERG to promote self-renewal, prevent myeloid differentiation in hematopoietic progenitor cells, and initiate leukemia in mouse models. Here we show that P199 facilitates ERG's interaction with the NCoR-HDAC3 co-repressor complex. Inhibiting HDAC3 reduces the growth of ERG-dependent leukemic and prostate cancer cells, indicating that the interaction between ERG and the NCoR-HDAC3 co-repressor complex is crucial for its oncogenic activity. Thus, targeting this interaction may offer a potential therapeutic intervention.","authors":"Kugler, E., Madiwale, S., Yong, D., Thoms, JAI., Birger, Y., Sykes, DB., Schmoellerl, J., Drakul, A., Priebe, V., Yassin, M., Aqaqe, N., Rein, A., Fishman, H., Geron, I., Chen, CW., Raught, B., Liu, Q., Ogana, H., Liedke, E., Bourquin, JP., Zuber, J., Milyavsky, M., Pimanda, J., Priv\u00e9, GG., Izraeli, S.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"5871","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-09-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37726279","title":"ABCC1 and glutathione metabolism limit the efficacy of BCL-2 inhibitors in acute myeloid leukemia.","abstract":"The BCL-2 inhibitor Venetoclax is a promising agent for the treatment of acute myeloid leukemia (AML). However, many patients are refractory to Venetoclax, and resistance develops quickly. ATP-binding cassette (ABC) transporters mediate chemotherapy resistance but their role in modulating the activity of targeted small-molecule inhibitors is unclear. Using CRISPR\/Cas9 screening, we find that loss of ABCC1 strongly increases the sensitivity of AML cells to Venetoclax. Genetic and pharmacologic ABCC1 inactivation potentiates the anti-leukemic effects of BCL-2 inhibitors and efficiently re-sensitizes Venetoclax-resistant leukemia cells. Conversely, ABCC1 overexpression induces resistance to BCL-2 inhibitors by reducing intracellular drug levels, and high ABCC1 levels predicts poor response to Venetoclax therapy in patients. Consistent with ABCC1-specific export of glutathionylated substrates, inhibition of glutathione metabolism increases the potency of BCL-2 inhibitors. These results identify ABCC1 and glutathione metabolism as mechanisms limiting efficacy of BCL-2 inhibitors, which may pave the way to development of more effective therapies.","authors":"Ebner, J., Schmoellerl, J., Piontek, M., Manhart, G., Troester, S., Carter, BZ., Neubauer, H., Moriggl, R., Szak\u00e1cs, G., Zuber, J., K\u00f6cher, T., Andreeff, M., Sperr, WR., Valent, P., Grebien, F.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"5709","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-09-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37716355","title":"CBFA2T3-GLIS2-dependent pediatric acute megakaryoblastic leukemia is driven by GLIS2 and sensitive to navitoclax.","abstract":"Pediatric acute megakaryoblastic leukemia (AMKL) is an aggressive blood cancer associated with poor therapeutic response and high mortality. Here we describe the development of CBFA2T3-GLIS2-driven mouse models of AMKL that recapitulate the phenotypic and transcriptional signatures of the human disease. We show that an activating Ras mutation that occurs in human AMKL increases the penetrance and decreases the latency of CBF2AT3-GLIS2-driven AMKL. CBFA2T3-GLIS2 and GLIS2 modulate similar transcriptional networks. We identify the dominant oncogenic properties of GLIS2 that trigger AMKL in cooperation with oncogenic Ras. We find that both CBFA2T3-GLIS2 and GLIS2 alter the expression of a number of BH3-only proteins, causing AMKL cell sensitivity to the BCL2 inhibitor navitoclax both in&#xa0;vitro and in&#xa0;vivo, suggesting a potential therapeutic option for pediatric patients suffering from CBFA2T3-GLIS2-driven AMKL.","authors":"Neault, M., Lebert-Ghali, C\u00c9., Fournier, M., Capdevielle, C., Garfinkle, EAR., Obermayer, A., Cotton, A., Boulay, K., Sawchyn, C., St-Amand, S., Nguyen, KH., Assaf, B., Mercier, FE., Delisle, JS., Drobetsky, EA., Hulea, L., Shaw, TI., Zuber, J., Gruber, TA., Melichar, HJ., Mallette, FA.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Cell Rep","volume":"42","issue":"9","page":"113084","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-10-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37622993","title":"SPOP targets the immune transcription factor IRF1 for proteasomal degradation.","abstract":"Adaptation of the functional proteome is essential to counter pathogens during infection, yet precisely timed degradation of these response proteins after pathogen clearance is likewise key to preventing autoimmunity. Interferon regulatory factor 1 (IRF1) plays an essential role as a transcription factor in driving the expression of immune response genes during infection. The striking difference in functional output with other IRFs is that IRF1 also drives the expression of various cell cycle inhibiting factors, making it an important tumor suppressor. Thus, it is critical to regulate the abundance of IRF1 to achieve a 'Goldilocks' zone in which there is sufficient IRF1 to prevent tumorigenesis, yet not too much which could drive excessive immune activation. Using genetic screening, we identified the E3 ligase receptor speckle type BTB\/POZ protein (SPOP) to mediate IRF1 proteasomal turnover in human and mouse cells. We identified S\/T-rich degrons in IRF1 required for its SPOP MATH domain-dependent turnover. In the absence of SPOP, elevated IRF1 protein levels functionally increased IRF1-dependent cellular responses, underpinning the biological significance of SPOP in curtailing IRF1 protein abundance.","authors":"Schwartz, I., Vunjak, M., Budroni, V., Cantoran Garc\u00eda, A., Mastrovito, M., Soderholm, A., Hinterndorfer, M., de Almeida, M., Hacker, K., Wang, J., Froussios, K., Jude, J., Decker, T., Zuber, J., Versteeg, GA.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Elife","volume":"12","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-09-11","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37407816","title":"Cooperation between bHLH transcription factors and histones for DNA access.","abstract":"The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members<sup>1<\/sup>. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. <sup>2,3<\/sup>). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch<sup>4<\/sup>, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes<sup>5-7<\/sup> at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.","authors":"Michael, AK., Stoos, L., Crosby, P., Eggers, N., Nie, XY., Makasheva, K., Minnich, M., Healy, KL., Weiss, J., Kempf, G., Cavadini, S., Kater, L., Seebacher, J., Vecchia, L., Chakraborty, D., Isbel, L., Grand, RS., Andersch, F., Fribourgh, JL., Sch\u00fcbeler, D., Zuber, J., Liu, AC., Becker, PB., Fierz, B., Partch, CL., Menet, JS., Thom\u00e4, NH.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nature","volume":"619","issue":"7969","page":"385-393","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-07-26","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"37987220","title":"Adult neural stem cells and neurogenesis are resilient to intermittent fasting.","abstract":"Intermittent fasting (IF) is a promising strategy to counteract ageing shown to increase the number of adult-born neurons in the dentate gyrus of mice. However, it is unclear which steps of the adult neurogenesis process are regulated by IF. The number of adult neural stem cells (NSCs) decreases with age in an activation-dependent manner and, to counteract this loss, adult NSCs are found in a quiescent state which ensures their long-term maintenance. We aimed to determine if and how IF affects adult NSCs in the hippocampus. To identify the effects of every-other-day IF on NSCs and all following steps in the neurogenic lineage, we combined fasting with lineage tracing and label retention assays. We show here that IF does not affect NSC activation or maintenance and, that contrary to previous reports, IF does not increase neurogenesis. The same results are obtained regardless of strain, sex, diet length, tamoxifen administration or new-born neuron identification method. Our data suggest that NSCs maintain homeostasis upon IF and that this intervention is not a reliable strategy to increase adult neurogenesis.","authors":"Gabarr\u00f3-Solanas, R., Davaatseren, A., Kleifeld, J., Kep\u010dija, T., K\u00f6cher, T., Giralt, A., Crespo-Enr\u00edquez, I., Urb\u00e1n, N.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"EMBO Rep","volume":null,"issue":null,"page":"e57268","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-21","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38071364","title":"Loss of cohesin regulator PDS5A reveals repressive role of Polycomb loops.","abstract":"Polycomb Repressive Complexes 1 and 2 (PRC1, PRC2) are conserved epigenetic regulators that promote transcriptional gene silencing. PRC1 and PRC2 converge on shared targets, catalyzing repressive histone modifications. Additionally, a subset of PRC1\/PRC2 targets engage in long-range interactions whose functions in gene silencing are poorly understood. Using a CRISPR screen in mouse embryonic stem cells, we found that the cohesin regulator PDS5A links transcriptional silencing by Polycomb and 3D genome organization. PDS5A deletion impairs cohesin unloading and results in derepression of a subset of endogenous PRC1\/PRC2 target genes. Importantly, derepression is not linked to loss of Polycomb chromatin domains. Instead, PDS5A removal causes aberrant cohesin activity leading to ectopic insulation sites, which disrupt the formation of ultra-long Polycomb loops. We show that these loops are important for robust silencing at a subset of PRC1\/PRC2 target genes and that maintenance of cohesin-dependent genome architecture is critical for Polycomb regulation.","authors":"Bsteh, D., Moussa, HF., Michlits, G., Yelagandula, R., Wang, J., Elling, U., Bell, O.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"8160","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-12-09","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38052989","title":"In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain-striatum-cortex assembloids.","abstract":"Ventral midbrain dopaminergic neurons project to the striatum as well as the cortex and are involved in movement control and reward-related cognition. In Parkinson's disease, nigrostriatal midbrain dopaminergic neurons degenerate and cause typical Parkinson's disease motor-related impairments, while the dysfunction of mesocorticolimbic midbrain dopaminergic neurons is implicated in addiction and neuropsychiatric disorders. Study of the development and selective neurodegeneration of the human dopaminergic system, however, has been limited due to the lack of an appropriate model and access to human material. Here, we have developed a human in vitro model that recapitulates key aspects of dopaminergic innervation of the striatum and cortex. These spatially arranged ventral midbrain-striatum-cortical organoids (MISCOs) can be used to study dopaminergic neuron maturation, innervation and function with implications for cell therapy and addiction research. We detail protocols for growing ventral midbrain, striatal and cortical organoids and describe how they fuse in a linear manner when placed in custom embedding molds. We report the formation of functional long-range dopaminergic connections to striatal and cortical tissues in MISCOs, and show that injected, ventral midbrain-patterned progenitors can mature and innervate the tissue. Using these assembloids, we examine dopaminergic circuit perturbations and show that chronic cocaine treatment causes long-lasting morphological, functional and transcriptional changes that persist upon drug withdrawal. Thus, our method opens new avenues to investigate human dopaminergic cell transplantation and circuitry reconstruction as well as the effect of drugs on the human dopaminergic system.","authors":"Reumann, D., Krauditsch, C., Novatchkova, M., Sozzi, E., Wong, SN., Zabolocki, M., Priouret, M., Doleschall, B., Ritzau-Reid, KI., Piber, M., Morassut, I., Fieseler, C., Fiorenzano, A., Stevens, MM., Zimmer, M., Bardy, C., Parmar, M., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Methods","volume":"20","issue":"12","page":"2034-2047","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-12-10","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38052228","title":"Hypoblast from human pluripotent stem cells regulates epiblast development.","abstract":"Recently, several studies using cultures of human embryos together with single-cell RNA-seq analyses have revealed differences between humans and mice, necessitating the study of human embryos<sup>1-8<\/sup>. Despite the importance of human embryology, ethical and legal restrictions have limited post-implantation-stage studies. Thus, recent efforts have focused on developing in vitro self-organizing models using human stem cells<sup>9-17<\/sup>. Here, we report genetic and non-genetic approaches to generate authentic hypoblast cells (naive hPSC-derived hypoblast-like cells (nHyCs))-known to give rise to one of the two extraembryonic tissues essential for embryonic development-from naive human pluripotent stem cells (hPSCs). Our nHyCs spontaneously assemble with naive hPSCs to form a three-dimensional bilaminar structure (bilaminoids) with a pro-amniotic-like cavity. In the presence of additional naive hPSC-derived analogues of the second extraembryonic tissue, the trophectoderm, the efficiency of bilaminoid formation increases from 20% to 40%, and the epiblast within the bilaminoids continues to develop in response to trophectoderm-secreted IL-6. Furthermore, we show that bilaminoids robustly recapitulate the patterning of the anterior-posterior axis and the formation of cells reflecting the pregastrula stage, the emergence of which can be shaped by genetically manipulating the DKK1\/OTX2 hypoblast-like domain. We have therefore successfully modelled and identified the mechanisms by which the two extraembryonic tissues efficiently guide the stage-specific growth and progression of the epiblast as it establishes the post-implantation landmarks of human embryogenesis.","authors":"Okubo, T., Rivron, N., Kabata, M., Masaki, H., Kishimoto, K., Semi, K., Nakajima-Koyama, M., Kunitomi, H., Kaswandy, B., Sato, H., Nakauchi, H., Woltjen, K., Saitou, M., Sasaki, E., Yamamoto, T., Takashima, Y.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nature","volume":"626","issue":"7998","page":"357-366","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-13","doi":"10.1038\/s41586-023-06871-2","first_author":null,"corresponding_authors":null},{"pmid":"38042149","title":"u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions.","abstract":"We describe u-track3D, a software package that extends the versatile u-track framework established in 2D to address the specific challenges of 3D particle tracking. First, we present the performance of the new package in quantifying a variety of intracellular dynamics imaged by multiple 3D microcopy platforms and on the standard 3D test dataset of the particle tracking challenge. These analyses indicate that u-track3D presents a tracking solution that is competitive to both conventional and deep-learning-based approaches. We then present the concept of dynamic region of interest (dynROI), which allows an experimenter to interact with dynamic 3D processes in 2D views amenable to visual inspection. Third, we present an estimator of trackability that automatically defines a score for every trajectory, thereby overcoming the challenges of trajectory validation by visual inspection. With these combined strategies, u-track3D provides a complete framework for unbiased studies of molecular processes in complex volumetric sequences.","authors":"Roudot, P., Legant, WR., Zou, Q., Dean, KM., Isogai, T., Welf, ES., David, AF., Gerlich, DW., Fiolka, R., Betzig, E., Danuser, G.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Cell Rep Methods","volume":null,"issue":null,"page":"100655","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-12-02","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38029745","title":"Multi-chamber cardioids unravel human heart development and cardiac defects.","abstract":"The number one cause of human fetal death are defects in heart development. Because the human embryonic heart is inaccessible and the impacts of mutations, drugs, and environmental factors on the specialized functions of different heart compartments are not captured by in&#xa0;vitro models, determining the underlying causes is difficult. Here, we established a human cardioid platform that recapitulates the development of all major embryonic heart compartments, including right and left ventricles, atria, outflow tract, and atrioventricular canal. By leveraging 2D and 3D differentiation, we efficiently generated progenitor subsets with distinct first, anterior, and posterior second heart field identities. This advance enabled the reproducible generation of cardioids with compartment-specific in&#xa0;vivo-like gene expression profiles, morphologies, and functions. We used this platform to unravel the ontogeny of signal and contraction propagation between interacting heart chambers and dissect how mutations, teratogens, and drugs cause compartment-specific defects in the developing human heart.","authors":"Schmidt, C., Deyett, A., Ilmer, T., Haendeler, S., Torres Caballero, A., Novatchkova, M., Netzer, MA., Ceci Ginistrelli, L., Mancheno Juncosa, E., Bhattacharya, T., Mujadzic, A., Pimpale, L., Jahnel, SM., Cirigliano, M., Reumann, D., Tavernini, K., Papai, N., Hering, S., Hofbauer, P., Mendjan, S.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Cell","volume":"186","issue":"25","page":"5587-5605.e27","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-12-08","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38000028","title":"Intestinal Paneth cell differentiation relies on asymmetric regulation of Wnt signaling by Daam1\/2.","abstract":"The mammalian intestine is one of the most rapidly self-renewing tissues, driven by stem cells residing at the crypt bottom. Paneth cells form a major element of the niche microenvironment providing various growth factors to orchestrate intestinal stem cell homeostasis, such as Wnt3. Different Wnt ligands can selectively activate &#x3b2;-catenin-dependent (canonical) or -independent (noncanonical) signaling. Here, we report that the Dishevelled-associated activator of morphogenesis 1 (Daam1) and its paralogue Daam2 asymmetrically regulate canonical and noncanonical Wnt (Wnt\/PCP) signaling. Daam1\/2 interacts with the Wnt inhibitor RNF43, and Daam1\/2 double knockout stimulates canonical Wnt signaling by preventing RNF43-dependent degradation of the Wnt receptor, Frizzled (Fzd). Single-cell RNA sequencing analysis revealed that Paneth cell differentiation is impaired by Daam1\/2 depletion because of defective Wnt\/PCP signaling. Together, we identified Daam1\/2 as an unexpected hub molecule coordinating both canonical and noncanonical Wnt, which is fundamental for specifying an adequate number of Paneth cells.","authors":"Colozza, G., Lee, H., Merenda, A., Wu, SS., Catal\u00e0-Bordes, A., Radaszkiewicz, TW., Jordens, I., Lee, JH., Bamford, AD., Farnhammer, F., Low, TY., Maurice, MM., Bryja, V., Kim, J., Koo, BK.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Sci Adv","volume":"9","issue":"47","page":"eadh9673","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38086418","title":"Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.","abstract":"Enhancers control gene expression and have crucial roles in development and homeostasis<sup>1-3<\/sup>. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning to design tissue-specific enhancers for five tissues in the Drosophila melanogaster embryo:&#xa0;the central nervous system, epidermis, gut, muscle and brain. We first train convolutional neural networks using genome-wide single-cell assay for transposase-accessible chromatin with sequencing (ATAC-seq)&#xa0;datasets and then fine-tune the convolutional neural networks with smaller-scale data from in vivo enhancer activity assays, yielding models with 13% to 76% positive predictive value according to cross-validation. We designed and experimentally assessed 40 synthetic enhancers (8 per tissue) in vivo, of which 31 (78%) were active and 27 (68%) functioned in the target tissue (100% for central nervous system and muscle). The strategy of combining genome-wide and small-scale functional datasets by transfer learning is generally applicable and should enable the design of tissue-, cell type- and cell state-specific enhancers in any system.","authors":"de Almeida, BP., Schaub, C., Pagani, M., Secchia, S., Furlong, EEM., Stark, A.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nature","volume":"626","issue":"7997","page":"207-211","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-07","doi":"10.1038\/s41586-023-06905-9","first_author":null,"corresponding_authors":null},{"pmid":"38088903","title":"A High-Sensitivity Low-Nanoflow LC-MS Configuration for High-Throughput Sample-Limited Proteomics.","abstract":"This work demonstrates the utility of high-throughput nanoLC-MS and label-free quantification (LFQ) for sample-limited bottom-up proteomics analysis, including single-cell proteomics (SCP). Conditions were optimized on a 50 &#x3bc;m internal diameter (I.D.) column operated at 100 nL\/min in the direct injection workflow to balance method sensitivity and sample throughput from 24 to 72 samples\/day. Multiple data acquisition strategies were also evaluated for proteome coverage, including data-dependent acquisition (DDA), wide-window acquisition (WWA), and wide-window data-independent acquisition (WW-DIA). Analyzing 250 pg HeLa digest with a 10-min LC gradient (72 samples\/day) provided &gt;900, &gt;1,800, and &gt;3,000 protein group identifications for DDA, WWA, and WW-DIA, respectively. Total method cycle time was further reduced from 20 to 14.4 min (100 samples\/day) by employing a trap-and-elute workflow, enabling 70% mass spectrometer utilization. The method was applied to library-free DIA analysis of single-cell samples, yielding &gt;1,700 protein groups identified. In conclusion, this study provides a high-sensitivity, high-throughput nanoLC-MS configuration for sample-limited proteomics.","authors":"Zheng, R., Matzinger, M., Mayer, RL., Valenta, A., Sun, X., Mechtler, K.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Anal Chem","volume":"95","issue":"51","page":"18673-18678","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-12-27","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38132340","title":"Immunopeptidomics in the Era of Single-Cell Proteomics.","abstract":"Immunopeptidomics, as the analysis of antigen peptides being presented to the immune system via major histocompatibility complexes (MHC), is being seen as an imperative tool for identifying epitopes for vaccine development to treat cancer and viral and bacterial infections as well as parasites. The field has made tremendous strides over the last 25 years but currently still faces challenges in sensitivity and throughput for widespread applications in personalized medicine and large vaccine development studies. Cutting-edge technological advancements in sample preparation, liquid chromatography as well as mass spectrometry, and data analysis, however, are currently transforming the field. This perspective showcases how the advent of single-cell proteomics has accelerated this transformation of immunopeptidomics in recent years and will pave the way for even more sensitive and higher-throughput immunopeptidomics analyses.","authors":"Mayer, RL., Mechtler, K.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Biology (Basel)","volume":"12","issue":"12","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-12-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38238601","title":"Gpcpd1-GPC metabolic pathway is dysfunctional in aging and its deficiency severely perturbs glucose metabolism.","abstract":"Skeletal muscle plays a central role in the regulation of systemic metabolism during lifespan. With aging, this function is perturbed, initiating multiple chronic diseases. Our knowledge of mechanisms responsible for this decline is limited. Glycerophosphocholine phosphodiesterase 1 (Gpcpd1) is a highly abundant muscle enzyme that hydrolyzes glycerophosphocholine (GPC). The physiological functions of Gpcpd1 remain largely unknown. Here we show, in mice, that the Gpcpd1-GPC metabolic pathway is perturbed in aged muscles. Further, muscle-specific, but not liver- or fat-specific, inactivation of Gpcpd1 resulted in severely impaired glucose metabolism. Western-type diets markedly worsened this condition. Mechanistically, Gpcpd1 muscle deficiency resulted in accumulation of GPC, causing an 'aged-like' transcriptomic signature and impaired insulin signaling in young Gpcpd1-deficient muscles. Finally, we report that the muscle GPC levels are markedly altered in both aged humans and patients with type 2 diabetes, displaying a high positive correlation between GPC levels and chronological age. Our findings reveal that the muscle GPCPD1-GPC metabolic pathway has an important role in the regulation of glucose homeostasis and that it is impaired during aging, which may contribute to glucose intolerance in aging.","authors":"Cikes, D., Leutner, M., Cronin, SJF., Novatchkova, M., Pfleger, L., Klepochov\u00e1, R., Lair, B., Lac, M., Bergoglio, C., Viguerie, N., D\u00fcrnberger, G., Roitinger, E., Grivej, M., Rullman, E., Gustafsson, T., Hagelkruys, A., Tavernier, G., Bourlier, V., Knauf, C., Krebs, M., Kautzky-Willer, A., Moro, C., Krssak, M., Orthofer, M., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nat Aging","volume":"4","issue":"1","page":"80-94","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-08","doi":"10.1038\/s43587-023-00551-6","first_author":null,"corresponding_authors":null},{"pmid":"38177902","title":"eIF4E1b is a non-canonical eIF4E protecting maternal dormant mRNAs.","abstract":"Maternal mRNAs are essential for protein synthesis during oogenesis and early embryogenesis. To adapt translation to specific needs during development, maternal mRNAs are translationally repressed by shortening the polyA tails. While mRNA deadenylation is associated with decapping and degradation in somatic cells, maternal mRNAs with short polyA tails are stable. Here we report that the germline-specific eIF4E paralog, eIF4E1b, is essential for zebrafish oogenesis. eIF4E1b localizes to P-bodies in zebrafish embryos and binds to mRNAs with reported short or no polyA tails, including histone mRNAs. Loss of eIF4E1b results in reduced histone mRNA levels in early gonads, consistent with a role in mRNA storage. Using mouse and human eIF4E1Bs (in vitro) and zebrafish eIF4E1b (in vivo), we show that unlike canonical eIF4Es, eIF4E1b does not interact with eIF4G to initiate translation. Instead, eIF4E1b interacts with the translational repressor eIF4ENIF1, which is required for eIF4E1b localization to P-bodies. Our study is consistent with an important role of eIF4E1b in regulating mRNA dormancy and provides new insights into fundamental post-transcriptional regulatory principles governing early vertebrate development.","authors":"Lorenzo-Orts, L., Strobl, M., Steinmetz, B., Leesch, F., Pribitzer, C., Roehsner, J., Schutzbier, M., D\u00fcrnberger, G., Pauli, A.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"EMBO Rep","volume":"25","issue":"1","page":"404-427","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2023.06.10.544440v1","articledate":"2024-01-24","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"34812990","title":"The microbial metabolic activity on carbohydrates and polymers impact the biodegradability of landfilled solid waste.","abstract":"Biological waste degradation is the main driving factor for landfill emissions. In a 2-year laboratory experiment simulating different landfill in-situ aeration scenarios, the microbial degradation of solid waste under different oxygen conditions (treatments) was investigated. Nine landfill simulation reactors were operated in triplicates under three distinct treatments. Three were kept anaerobic, three were aerated for 706 days after an initial anaerobic phase and three were aerated for 244 days in between two anaerobic phases. In total, 36 solid and 36 leachate samples were taken. Biolog&#xae; EcoPlates&#x2122;&#xa0;were used to assess the functional diversity of the microbial community. It was possible to directly relate the functional diversity to the biodegradability of MSW (municipal solid waste), measured as RI<sub>4<\/sub> (respiration index after 4 days). The differences between the treatments in RI<sub>4<\/sub> as well as in carbon and polymer degradation potential were small. Initially, a RI<sub>4<\/sub> of about 6.5 to 8 mg O<sub>2<\/sub> kg<sup>-1<\/sup> DW was reduced to less than 1 mg O<sub>2<\/sub> kg<sup>-1<\/sup> DW within 114 days of treatment. After the termination of aeration, an increase 3 mg O<sub>2<\/sub> kg<sup>-1<\/sup> DW was observed. By calculating the integral of the Gompertz equation based on spline interpolation of the Biolog&#xae; EcoPlates&#x2122;&#xa0;results after 96 h two substrate groups mainly contributing to the biodegradability were identified: carbohydrates and polymers. The microbial activity of the respective microbial consortium could thus be related to the biodegradability with a multilinear regression model.","authors":"Brandstaetter, C., Fricko, N., Rahimi, MJ., Fellner, J., Ecker-Lala, W., Druzhinina, IS.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Biodegradation","volume":"33","issue":"1","page":"71-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-05-05","doi":null,"first_author":null,"corresponding_authors":null},{"pmid":"38477334","title":"The molecular mechanisms underpinning maternal mRNA dormancy.","abstract":"A large number of mRNAs of maternal origin are produced during oogenesis and deposited in the oocyte. Since transcription stops at the onset of meiosis during oogenesis and does not resume until later in embryogenesis, maternal mRNAs are the only templates for protein synthesis during this period. To ensure that a protein is made in the right place at the right time, the translation of maternal mRNAs must be activated at a specific stage of development. Here we summarize our current understanding of the sophisticated mechanisms that contribute to the temporal repression of maternal mRNAs, termed maternal mRNA dormancy. We discuss mechanisms at the level of the RNA itself, such as the regulation of polyadenine tail length and RNA modifications, as well as at the level of RNA-binding proteins, which often block the assembly of translation initiation complexes at the 5' end of an mRNA or recruit mRNAs to specific subcellular compartments. We also review microRNAs and other mechanisms that contribute to repressing translation, such as ribosome dormancy. Importantly, the mechanisms responsible for mRNA dormancy during the oocyte-to-embryo transition are also relevant to cellular quiescence in other biological contexts.","authors":"Lorenzo-Orts, L., Pauli, A.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Biochem Soc Trans","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-13","doi":"10.1042\/BST20231122","first_author":null,"corresponding_authors":null},{"pmid":"34694617","title":"Transcriptome-Wide Profiling of RNA Stability.","abstract":"Gene expression is controlled at multiple levels, including RNA transcription and turnover. But determining the relative contributions of RNA biogenesis and decay to the steady-state abundance of cellular transcripts remains challenging because conventional transcriptomics approaches do not provide the temporal resolution to derive the kinetic parameters underlying steady-state gene expression.Here, we describe a protocol that combines metabolic RNA labeling by 4-thiouridine with chemical nucleoside conversion and whole-transcriptome sequencing followed by bioinformatics analysis to determine RNA stability in cultured cells at a genomic scale. Time-resolved transcriptomics by thiol (SH)-linked alkylation for the metabolic sequencing of RNA (SLAMseq) provides accurate information on transcript half-lives across annotated features in the genome, including by-products of transcription, such as introns. We provide a step-by-step instruction for time-resolved transcriptomics, which enhances traditional RNA sequencing protocols to acquire the temporal resolution required to directly measure the cellular kinetics of RNA turnover under physiological conditions.","authors":"Fasching, N., Petr\u017e\u00edlek, J., Popitsch, N., Herzog, VA., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Methods Mol Biol","volume":"2404","issue":null,"page":"311-330","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-12-03","doi":"10.1007\/978-1-0716-1851-6_17","first_author":null,"corresponding_authors":null},{"pmid":"38310095","title":"Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications.","abstract":"Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (&#xb5;PACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data show that &#xb5;PACs identify &#x2264;50% more peptides and &#x2264;24% more proteins, while offering improved throughput, which is critical for large (clinical) proteomics studies. Combining wide precursor isolation widths of m\/z 4-12 with the CHIMERYS search engine identified +51-74% and +59-150% more proteins and peptides, respectively, for single cell, co-immunoprecipitation, and multi-species samples over a conventional workflow at well-controlled false discovery rates. The workflow further offers excellent precision, with CVs &lt;7% for low input bulk samples, and accuracy, with deviations &lt;10% from expected fold changes for regular abundance two-proteome mixes. Compared to a conventional workflow, our entire optimized platform discovered 92% more potential interactors in a protein-protein interaction study on the chromatin remodeler Smarca5\/Snf2h. These include previously described Smarca5 binding partners and undescribed ones including Arid1a, another chromatin remodeler with key roles in neurodevelopmental and malignant disorders.","authors":"Matzinger, M., Schm\u00fccker, A., Yelagandula, R., Stejskal, K., Kr\u0161\u0161\u00e1kov\u00e1, G., Berger, F., Mechtler, K., Mayer, RL.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"1019","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-05","doi":"10.1038\/s41467-024-45391-z","first_author":null,"corresponding_authors":null},{"pmid":"38365780","title":"A microfluidic platform integrating functional vascularized organoids-on-chip.","abstract":"The development of vascular networks in microfluidic chips is crucial for the long-term culture of three-dimensional cell aggregates such as spheroids, organoids, tumoroids, or tissue explants. Despite rapid advancement in microvascular network systems and organoid technologies, vascularizing organoids-on-chips remains a challenge in tissue engineering. Most existing microfluidic devices poorly reflect the complexity of in vivo flows and require complex technical set-ups. Considering these constraints, we develop a platform to establish and monitor the formation of endothelial networks around mesenchymal and pancreatic islet spheroids, as well as blood vessel organoids generated from pluripotent stem cells, cultured for up to 30 days on-chip. We show that these networks establish functional connections with the endothelium-rich spheroids and vascular organoids, as they successfully provide intravascular perfusion to these structures. We find that organoid growth, maturation, and function are enhanced when cultured on-chip using our vascularization method. This microphysiological system represents a viable organ-on-chip model to vascularize diverse biological 3D tissues and sets the stage to establish organoid perfusions using advanced microfluidics.","authors":"Quintard, C., Tubbs, E., Jonsson, G., Jiao, J., Wang, J., Werschler, N., Laporte, C., Pitaval, A., Bah, TS., Pomeranz, G., Bissardon, C., Kaal, J., Leopoldi, A., Long, DA., Blandin, P., Achard, JL., Battail, C., Hagelkruys, A., Navarro, F., Fouillet, Y., Penninger, JM., Gidrol, X.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"1452","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-19","doi":"10.1038\/s41467-024-45710-4","first_author":null,"corresponding_authors":null},{"pmid":"38374263","title":"Generation of complex bone marrow organoids from human induced pluripotent stem cells.","abstract":"The human bone marrow (BM) niche sustains hematopoiesis throughout life. We present a method for generating complex BM-like organoids (BMOs) from human induced pluripotent stem cells (iPSCs). BMOs consist of key cell types that self-organize into spatially defined three-dimensional structures mimicking cellular, structural and molecular characteristics of the hematopoietic microenvironment. Functional properties of BMOs include the presence of an in vivo-like vascular network, the presence of multipotent mesenchymal stem\/progenitor cells, the support of neutrophil differentiation and responsiveness to inflammatory stimuli. Single-cell RNA sequencing revealed a heterocellular composition including the presence of a hematopoietic stem\/progenitor (HSPC) cluster expressing genes of fetal HSCs. BMO-derived HSPCs also exhibited lymphoid potential and a subset demonstrated transient engraftment potential upon xenotransplantation in mice. We show that the BMOs could enable the modeling of hematopoietic developmental aspects and inborn errors of hematopoiesis, as shown for human VPS45 deficiency. Thus, iPSC-derived BMOs serve as a physiologically relevant in vitro model of the human BM microenvironment to study hematopoietic development and BM diseases.","authors":"Frenz-Wiessner, S., Fairley, SD., Buser, M., Goek, I., Salewskij, K., Jonsson, G., Illig, D., Zu Putlitz, B., Petersheim, D., Li, Y., Chen, PH., Kalauz, M., Conca, R., Sterr, M., Geuder, J., Mizoguchi, Y., Megens, RTA., Linder, MI., Kotlarz, D., Rudelius, M., Penninger, JM., Marr, C., Klein, C.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Nat Methods","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-19","doi":"10.1038\/s41592-024-02172-2","first_author":null,"corresponding_authors":null},{"pmid":"38402507","title":"Bioframe: operations on genomic intervals in Pandas dataframes.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">38402507<\/PMID><DateCompleted><Year>2024<\/Year><Month>03<\/Month><Day>04<\/Day><\/DateCompleted><DateRevised><Year>2024<\/Year><Month>03<\/Month><Day>04<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1367-4811<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>40<\/Volume><Issue>2<\/Issue><PubDate><Year>2024<\/Year><Month>Feb<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Bioframe: operations on genomic intervals in Pandas dataframes.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">btae088<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/bioinformatics\/btae088<\/ELocationID><Abstract><AbstractText Label=\"MOTIVATION\" NlmCategory=\"BACKGROUND\">Genomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from genes, to DNA binding sites, to disease variants. Operations on genomic intervals provide a language for asking questions about relationships between features. While there are excellent interval arithmetic tools for the command line, they are not smoothly integrated into Python, one of the most popular general-purpose computational and visualization environments.","authors":"Abdennur, N., Fudenberg, G., Flyamer, IM., Galitsyna, AA., Goloborodko, A., Imakaev, M., Venev, S.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Bioinformatics","volume":"40","issue":"2","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-04","doi":"10.1093\/bioinformatics\/btae088","first_author":null,"corresponding_authors":null},{"pmid":"38467836","title":"AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor.","abstract":"Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.","authors":"Trepte, P., Secker, C., Olivet, J., Blavier, J., Kostova, S., Maseko, SB., Minia, I., Silva Ramos, E., Cassonnet, P., Golusik, S., Zenkner, M., Beetz, S., Liebich, MJ., Scharek, N., Sch\u00fctz, A., Sperling, M., Lisurek, M., Wang, Y., Spirohn, K., Hao, T., Calderwood, MA., Hill, DE., Landthaler, M., Choi, SG., Twizere, JC., Vidal, M., Wanker, EE.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Mol Syst Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-25","doi":"10.1038\/s44320-024-00019-8","first_author":null,"corresponding_authors":null},{"pmid":"38452070","title":"Sister chromatid cohesion is mediated by individual cohesin complexes.","abstract":"Eukaryotic genomes are organized by loop extrusion and sister chromatid cohesion, both mediated by the multimeric cohesin protein complex. Understanding how cohesin holds sister DNAs together, and how loss of cohesion causes age-related infertility in females, requires knowledge as to cohesin's stoichiometry in vivo. Using quantitative super-resolution imaging, we identified two discrete populations of chromatin-bound cohesin in postreplicative human cells. Whereas most complexes appear dimeric, cohesin that localized to sites of sister chromatid cohesion and associated with sororin was exclusively monomeric. The monomeric stoichiometry of sororin:cohesin complexes demonstrates that sister chromatid cohesion is conferred by individual cohesin rings, a key prediction of the proposal that cohesion arises from the co-entrapment of sister DNAs.","authors":"Ochs, F., Green, C., Szczurek, AT., Pytowski, L., Kolesnikova, S., Brown, J., Gerlich, DW., Buckle, V., Schermelleh, L., Nasmyth, KA.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Science","volume":"383","issue":"6687","page":"1122-1130","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-11","doi":"10.1126\/science.adl4606","first_author":null,"corresponding_authors":null},{"pmid":"38448590","title":"Selfish conflict underlies RNA-mediated parent-of-origin effects.","abstract":"Genomic imprinting-the non-equivalence of maternal and paternal genomes-is a critical process that has evolved independently in many plant and mammalian species<sup>1,2<\/sup>. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles<sup>3,4<\/sup>. Yet, how these epigenetic differences evolve in the first place is poorly understood<sup>3,5,6<\/sup>. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals<sup>7-9<\/sup>. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1\/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1\/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs-but not SLOW-1 protein-are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.","authors":"Pliota, P., Marvanova, H., Koreshova, A., Kaufman, Y., Tikanova, P., Krogull, D., Hagm\u00fcller, A., Widen, SA., Handler, D., Gokcezade, J., Duchek, P., Brennecke, J., Ben-David, E., Burga, A.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-11","doi":"10.1038\/s41586-024-07155-z","first_author":null,"corresponding_authors":null},{"pmid":"38518768","title":"Spatially resolved proteomics of the Arabidopsis stomatal lineage identifies polarity complexes for cell divisions and stomatal pores.","abstract":"Cell polarity is used to guide asymmetric divisions and create morphologically diverse cells. We find that two oppositely oriented cortical polarity domains present during the asymmetric divisions in the Arabidopsis stomatal lineage are reconfigured into polar domains marking ventral (pore-forming) and outward-facing domains of maturing stomatal guard cells. Proteins that define these opposing polarity domains were used as baits in miniTurboID-based proximity labeling. Among differentially enriched proteins, we find kinases, putative microtubule-interacting proteins, and polar SOSEKIs with their effector ANGUSTIFOLIA. Using AI-facilitated protein structure prediction models, we identify potential protein-protein interaction interfaces among them. Functional and localization analyses of the polarity protein OPL2 and its putative interaction partners suggest a positive interaction with mitotic microtubules and a role in cytokinesis. This combination of proteomics and structural modeling with live-cell imaging provides insights into how polarity is rewired in different cell types and cell-cycle stages.","authors":"Wallner, ES., Mair, A., Handler, D., McWhite, C., Xu, SL., Dolan, L., Bergmann, DC.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Dev Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-22","doi":"10.1016\/j.devcel.2024.03.001","first_author":null,"corresponding_authors":null},{"pmid":"38548922","title":"Crimean-Congo haemorrhagic fever virus uses LDLR to bind and enter host cells.","abstract":"Climate change and population densities accelerated transmission of highly pathogenic viruses to humans, including the Crimean-Congo haemorrhagic fever virus (CCHFV). Here we report that the Low Density Lipoprotein Receptor (LDLR) is a critical receptor for CCHFV cell entry, playing a vital role in CCHFV infection in cell culture and blood vessel organoids. The interaction between CCHFV and LDLR is highly specific, with other members of the LDLR protein family failing to bind to or neutralize the virus. Biosensor experiments demonstrate that LDLR specifically binds the surface glycoproteins of CCHFV. Importantly, mice lacking LDLR exhibit a delay in CCHFV-induced disease. Furthermore, we identified the presence of Apolipoprotein E (ApoE) on CCHFV particles. Our findings highlight the essential role of LDLR in CCHFV infection, irrespective of ApoE presence, when the virus is produced in tick cells. This discovery holds profound implications for the development of future therapies against CCHFV.","authors":"Monteil, VM., Wright, SC., Dyczynski, M., Kellner, MJ., Appelberg, S., Platzer, SW., Ibrahim, A., Kwon, H., Pittarokoilis, I., Mirandola, M., Michlits, G., Devignot, S., Elder, E., Abdurahman, S., Bereczky, S., Bagci, B., Youhanna, S., Aastrup, T., Lauschke, VM., Salata, C., Elaldi, N., Weber, F., Monserrat, N., Hawman, DW., Feldmann, H., Horn, M., Penninger, JM., Mirazimi, A.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Nat Microbiol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-29","doi":"10.1038\/s41564-024-01672-3","first_author":null,"corresponding_authors":null},{"pmid":"38443338","title":"Homo-BacPROTAC-induced degradation of ClpC1 as a strategy against drug-resistant mycobacteria.","abstract":"Antimicrobial resistance is a global health threat that requires the development of new treatment concepts. These should not only overcome existing resistance but be designed to slow down the emergence of new resistance mechanisms. Targeted protein degradation, whereby a drug redirects cellular proteolytic machinery towards degrading a specific target, is an emerging concept in drug discovery. We are extending this concept by developing proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery. The anti-Mycobacterium tuberculosis (Mtb) BacPROTACs are derived from cyclomarins which, when dimerized, generate compounds that recruit and degrade ClpC1. The resulting Homo-BacPROTACs reduce levels of endogenous ClpC1 in Mycobacterium smegmatis and display minimum inhibitory concentrations in the low micro- to nanomolar range in mycobacterial strains, including multiple drug-resistant Mtb isolates. The compounds also kill Mtb residing in macrophages. Thus, Homo-BacPROTACs that degrade ClpC1 represent a different strategy for targeting Mtb and overcoming drug resistance.","authors":"Junk, L., Schmiedel, VM., Guha, S., Fischel, K., Greb, P., Vill, K., Krisilia, V., van Geelen, L., Rumpel, K., Kaur, P., Krishnamurthy, RV., Narayanan, S., Shandil, RK., Singh, M., Kofink, C., Mantoulidis, A., Biber, P., Gmaschitz, G., Kazmaier, U., Meinhart, A., Leodolter, J., Hoi, D., Junker, S., Morreale, FE., Clausen, T., Kalscheuer, R., Weinstabl, H., Boehmelt, G.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"2005","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-07","doi":"10.1038\/s41467-024-46218-7","first_author":null,"corresponding_authors":null},{"pmid":"38047596","title":"Cancer Evolution: A Multifaceted Affair.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">38047596<\/PMID><DateCompleted><Year>2024<\/Year><Month>01<\/Month><Day>15<\/Day><\/DateCompleted><DateRevised><Year>2024<\/Year><Month>01<\/Month><Day>23<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">2159-8290<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>14<\/Volume><Issue>1<\/Issue><PubDate><Year>2024<\/Year><Month>Jan<\/Month><Day>12<\/Day><\/PubDate><\/JournalIssue><Title>Cancer discovery<\/Title><ISOAbbreviation>Cancer Discov<\/ISOAbbreviation><\/Journal><ArticleTitle>Cancer Evolution: A Multifaceted Affair.<\/ArticleTitle><Pagination><StartPage>36<\/StartPage><EndPage>48<\/EndPage><MedlinePgn>36-48<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1158\/2159-8290.CD-23-0530<\/ELocationID><Abstract><AbstractText Label=\"UNLABELLED\">Cancer cells adapt and survive through the acquisition and selection of molecular modifications. This process defines cancer evolution. Building on a theoretical framework based on heritable genetic changes has provided insights into the mechanisms supporting cancer evolution. However, cancer hallmarks also emerge via heritable nongenetic mechanisms, including epigenetic and chromatin topological changes, and interactions between tumor cells and the tumor microenvironment. Recent findings on tumor evolutionary mechanisms draw a multifaceted picture where heterogeneous forces interact and influence each other while shaping tumor progression. A comprehensive characterization of the cancer evolutionary toolkit is required to improve personalized medicine and biomarker discovery.","authors":"Ciriello, G., Magnani, L., Aitken, SJ., Akkari, L., Behjati, S., Hanahan, D., Landau, DA., Lopez-Bigas, N., Lupi\u00e1\u00f1ez, DG., Marine, JC., Martin-Villalba, A., Natoli, G., Obenauf, AC., Oricchio, E., Scaffidi, P., Sottoriva, A., Swarbrick, A., Tonon, G., Vanharanta, S., Zuber, J.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Cancer Discov","volume":"14","issue":"1","page":"36-48","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-01-15","doi":"10.1158\/2159-8290.CD-23-0530","first_author":null,"corresponding_authors":null},{"pmid":"38129077","title":"Cohesin and CTCF do not assemble TADs in <i>Xenopus<\/i> sperm and male pronuclei.","abstract":"Paternal genomes are compacted during spermiogenesis and decompacted following fertilization. These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog <i>Xenopus laevis<\/i>, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically associating domains (TADs) at the mid-blastula transition (MBT). Why cohesin assembles TADs only at this stage is unknown. We first analyzed genome architecture in frog sperm and compared it to human and mouse. Our results indicate that sperm genome organization is conserved between frogs and humans and occurs without formation of TADs. TADs can be detected in mouse sperm samples, as reported, but these structures might originate from somatic chromatin contaminations. We therefore discuss the possibility that the absence of TADs might be a general feature of vertebrate sperm. To analyze sperm genome remodeling upon fertilization, we reconstituted male pronuclei in <i>Xenopus<\/i> egg extracts. In pronuclei, chromatin compartmentalization increases, but cohesin does not accumulate at CTCF sites and assemble TADs. However, if pronuclei are formed in the presence of exogenous CTCF, CTCF binds to its consensus sites, and cohesin accumulates at these and forms short-range chromatin loops, which are preferentially anchored at CTCF's N terminus. These results indicate that TADs are only assembled at MBT because before this stage CTCF sites are not occupied and cohesin only forms short-range chromatin loops.","authors":"Jessberger, G., V\u00e1rnai, C., Stocsits, RR., Tang, W., Stary, G., Peters, JM.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Genome Res","volume":"33","issue":"12","page":"2094-107","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-01-04","doi":"10.1101\/gr.277865.123","first_author":null,"corresponding_authors":null},{"pmid":"38176350","title":"Pulling the strings on solid-to-liquid phase transitions in cell collectives.","abstract":"Cell collectives must dynamically adapt to different biological contexts. For instance, in homeostatic conditions, epithelia must establish a barrier between body compartments and resist external stresses, while during development, wound healing or cancer invasion, these tissues undergo extensive remodeling. Using analogies from inert, passive materials, changes in cellular density, shape, rearrangements and\/or migration were shown to result in collective transitions between solid and fluid states. However, what biological mechanisms govern these transitions remains an open question. In particular, the upstream signaling pathways and molecular effectors controlling the key physical axes determining tissue rheology and dynamics remain poorly understood. In this perspective, we focus on emerging evidence identifying the first biological signals determining the collective state of living tissues, with an emphasis on how these mechanisms are exploited for functionality across biological contexts.","authors":"Pinheiro, D., Mitchel, J.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Curr Opin Cell Biol","volume":"86","issue":null,"page":"102310","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-14","doi":"10.1016\/j.ceb.2023.102310","first_author":null,"corresponding_authors":null},{"pmid":"38142424","title":"Tumor necrosis factor &#x3b1; promotes clonal dominance of KIT D816V+ cells in mastocytosis: role of survivin and impact on prognosis.","abstract":"Systemic mastocytosis (SM) is defined by the expansion and accumulation of neoplastic mast cells (MCs) in the bone marrow (BM) and extracutaneous organs. Most patients harbor a somatic KIT D816V mutation, which leads to growth factor-independent KIT activation and accumulation of MC. Tumor necrosis factor &#x3b1; (TNF) is a proapoptotic and inflammatory cytokine that has been implicated in the clonal selection of neoplastic cells. We found that KIT D816V increases the expression and secretion of TNF. TNF expression in neoplastic MCs is reduced by KIT-targeting drugs. Similarly, knockdown of KIT or targeting the downstream signaling cascade of MAPK and NF-&#x3ba;B signaling reduced TNF expression levels. TNF reduces colony formation in human BM cells, whereas KIT D816V+ cells are less susceptible to the cytokine, potentially contributing to clonal selection. In line, knockout of TNF in neoplastic MC prolonged survival and reduced myelosuppression in a murine xenotransplantation model. Mechanistic studies revealed that the relative resistance of KIT D816V+ cells to TNF is mediated by the apoptosis-regulator BIRC5 (survivin). Expression of BIRC5 in neoplastic MC was confirmed by immunohistochemistry of samples from patients with SM. TNF serum levels are significantly elevated in patients with SM and high TNF levels were identified as a biomarker associated with inferior survival. We here characterized TNF as a KIT D816V-dependent cytokine that promotes clonal dominance. We propose TNF and apoptosis-associated proteins as potential therapeutic targets in SM.","authors":"Greiner, G., Witzeneder, N., Klein, K., Tangermann, S., Kodajova, P., Jaeger, E., Ratzinger, F., Gerner, MC., Jawhar, M., Baumgartner, S., Fruehwirth, K., Schmetterer, KG., Zuber, J., Gleixner, KV., Mayerhofer, M., Schwarzinger, I., Simonitsch-Klupp, I., Esterbauer, H., Baer, C., Walter, W., Meggendorfer, M., Strassl, R., Haferlach, T., Hartmann, K., Kenner, L., Sperr, WR., Reiter, A., Sexl, V., Arock, M., Valent, P., Hoermann, G.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Blood","volume":"143","issue":"11","page":"1006-1017","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-15","doi":"10.1182\/blood.2023020515","first_author":null,"corresponding_authors":null},{"pmid":"38709825","title":"Cooltools: Enabling high-resolution Hi-C analysis in Python.","abstract":"Chromosome conformation capture (3C) technologies reveal the incredible complexity of genome organization. Maps of increasing size, depth, and resolution are now used to probe genome architecture across cell states, types, and organisms. Larger datasets add challenges at each step of computational analysis, from storage and memory constraints to researchers' time; however, analysis tools that meet these increased resource demands have not kept pace. Furthermore, existing tools offer limited support for customizing analysis for specific use cases or new biology. Here we introduce cooltools (https:\/\/github.com\/open2c\/cooltools), a suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Cooltools leverages the widely-adopted cooler format which handles storage and access for high-resolution datasets. Cooltools provides a paired command line interface (CLI) and Python application programming interface (API), which respectively facilitate workflows on high-performance computing clusters and in interactive analysis environments. In short, cooltools enables the effective use of the latest and largest genome folding datasets.","authors":"Abdennur, N., Abraham, S., Fudenberg, G., Flyamer, IM., Galitsyna, AA., Goloborodko, A., Imakaev, M., Oksuz, BA., Venev, SV., Xiao, Y.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"PLoS Comput Biol","volume":"20","issue":"5","page":"e1012067","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-05-06","doi":"10.1371\/journal.pcbi.1012067","first_author":null,"corresponding_authors":null},{"pmid":"38698465","title":"Neuropathological assessment of the olfactory bulb and tract in individuals with COVID-19.","abstract":"The majority of patients with Parkinson disease (PD) experience a loss in their sense of smell and accumulate insoluble &#x3b1;-synuclein aggregates in their olfactory bulbs (OB). Subjects affected by a SARS-CoV-2-linked illness (COVID-19) also frequently experience hyposmia. We previously postulated that microglial activation as well as &#x3b1;-synuclein and tau misprocessing can occur during host responses following microbial encounters. Using semiquantitative measurements of immunohistochemical signals, we examined OB and olfactory tract specimens collected serially at autopsies between 2020 and 2023. Deceased subjects comprised 50 adults, which included COVID19&#x2009;+&#x2009;patients (n&#x2009;=&#x2009;22), individuals with Lewy body disease (e.g., PD; dementia with Lewy bodies (n&#x2009;=&#x2009;6)), Alzheimer disease (AD; n&#x2009;=&#x2009;3), and other neurodegenerative disorders (e.g., progressive supranuclear palsy (n&#x2009;=&#x2009;2); multisystem atrophy (n&#x2009;=&#x2009;1)). Further, we included neurologically healthy controls (n&#x2009;=&#x2009;9), and added subjects with an inflammation-rich brain disorder as neurological controls (NCO; n&#x2009;=&#x2009;7). When probing for microglial and histiocytic reactivity in the anterior olfactory nuclei (AON) by anti-CD68 immunostaining, scores were consistently elevated in NCO and AD cases. In contrast, microglial signals on average were not significantly altered in COVID19&#x2009;+&#x2009;patients relative to healthy controls, although anti-CD68 reactivity in their OB and tracts declined with progression in age. Mild-to-moderate increases in phospho-&#x3b1;-synuclein and phospho-tau signals were detected in the AON of tauopathy- and synucleinopathy-afflicted brains, respectively, consistent with mixed pathology, as described by others. Lastly, when both sides were available for comparison in our case series, we saw no asymmetry in the degree of pathology of the left versus right OB and tracts. We concluded from our autopsy series that after a fatal course of COVID-19, microscopic changes in the rostral, intracranial portion of the olfactory circuitry -when present- reflected neurodegenerative processes seen elsewhere in the brain. In general, microglial reactivity correlated best with the degree of Alzheimer's-linked tauopathy and declined with progression of age in COVID19&#x2009;+&#x2009;patients.","authors":"Lengacher, NA., Tomlinson, JJ., Jochum, AK., Franz, J., Hasan Ali, O., Flatz, L., Jochum, W., Penninger, J., Stadelmann, C., Woulfe, JM., Schlossmacher, MG.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Acta Neuropathol Commun","volume":"12","issue":"1","page":"70","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-05-03","doi":"10.1186\/s40478-024-01761-8","first_author":null,"corresponding_authors":null},{"pmid":"38659940","title":"Rules of engagement for condensins and cohesins guide mitotic chromosome formation.","abstract":"During mitosis, interphase chromatin is rapidly converted into rod-shaped mitotic chromosomes. Using Hi-C, imaging, proteomics and polymer modeling, we determine how the activity and interplay between loop-extruding SMC motors accomplishes this dramatic transition. Our work reveals rules of engagement for SMC complexes that are critical for allowing cells to refold interphase chromatin into mitotic chromosomes. We find that condensin disassembles interphase chromatin loop organization by evicting or displacing extrusive cohesin. In contrast, condensin bypasses cohesive cohesins, thereby maintaining sister chromatid cohesion while separating the sisters. Studies of mitotic chromosomes formed by cohesin, condensin II and condensin I alone or in combination allow us to develop new models of mitotic chromosome conformation. In these models, loops are consecutive and not overlapping, implying that condensins do not freely pass one another but stall upon encountering each other. The dynamics of Hi-C interactions and chromosome morphology reveal that during prophase loops are extruded in vivo at ~1-3 kb\/sec by condensins as they form a disordered discontinuous helical scaffold within individual chromatids.","authors":"Samejima, K., Gibcus, JH., Abraham, S., Cisneros-Soberanis, F., Samejima, I., Beckett, AJ., Pu\u010dekov\u00e1, N., Abad, MA., Medina-Pritchard, B., Paulson, JR., Xie, L., Jeyaprakash, AA., Prior, IA., Mirny, LA., Dekker, J., Goloborodko, A., Earnshaw, WC.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-05-13","doi":"10.1101\/2024.04.18.590027","first_author":null,"corresponding_authors":null},{"pmid":"38659835","title":"Non-targeted isomer-sensitive N-glycome analysis reveals new layers of organ-specific diversity in mice.","abstract":"N-glycosylation is one of the most common protein modifications in eukaryotes, with immense importance at the molecular, cellular, and organismal level. Accurate and reliable N-glycan analysis is essential to obtain a systems-wide understanding of fundamental biological processes. Due to the structural complexity of glycans, their analysis is still highly challenging. Here we make publicly available a consistent N-glycome dataset of 20 different mouse tissues and demonstrate a multimodal data analysis workflow that allows for unprecedented depth and coverage of N-glycome features. This highly scalable, LC-MS\/MS data-driven method integrates the automated identification of N-glycan spectra, the application of non-targeted N-glycome profiling strategies and the isomer-sensitive analysis of glycan structures. Our delineation of critical sub-structural determinants and glycan isomers across the mouse N-glycome uncovered tissue-specific glycosylation patterns, the expression of non-canonical N-glycan structures and highlights multiple layers of N-glycome complexity that derive from organ-specific regulations of glycobiological pathways.","authors":"Stadlmann, J., Helm, J., Mereiter, S., Oliveira, T., Gattinger, A., Markovitz, D., Penninger, J., Altmann, F.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Res Sq","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-14","doi":"10.21203\/rs.3.rs-4130712\/v1","first_author":null,"corresponding_authors":null},{"pmid":"38656474","title":"Staying on track - Keeping things running in a high-end scientific imaging core facility.","abstract":"Modern life science research is a collaborative effort. Few research groups can single-handedly support the necessary equipment, expertise and personnel needed for the ever-expanding portfolio of technologies that are required across multiple disciplines in today's life science endeavours. Thus, research institutes are increasingly setting up scientific core facilities to provide access and specialised support for cutting-edge technologies. Maintaining the momentum needed to carry out leading research while ensuring high-quality daily operations is an ongoing challenge, regardless of the resources allocated to establish such facilities. Here, we outline and discuss the range of activities required to keep things running once a scientific imaging core facility has been established. These include managing a wide range of equipment and users, handling repairs and service contracts, planning for equipment upgrades, renewals, or decommissioning, and continuously upskilling while balancing innovation and consolidation.","authors":"Renaud, O., Aulner, N., Salles, A., Halidi, N., Brunstein, M., Mallet, A., Aumayr, K., Terjung, S., Levy, D., Lippens, S., Verbavatz, JM., Heuser, T., Santarella-Mellwig, R., Tinevez, JY., Woller, T., Botzki, A., Cawthorne, C., Munck, S.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"J Microsc","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-04-24","doi":"10.1111\/jmi.13304","first_author":null,"corresponding_authors":null},{"pmid":"38525542","title":"Apelin regulates skeletal muscle adaptation to exercise in a high-intensity interval training model.","abstract":"Plasma apelin levels are reduced in aging and muscle wasting conditions. We aimed to investigate the significance of apelin signaling in cardiac and skeletal muscle responses to physiological stress. Apelin knockout (KO) and wild-type (WT) mice were subjected to high-intensity interval training (HIIT) by treadmill running. The effects of apelin on energy metabolism were studied in primary mouse skeletal muscle myotubes and cardiomyocytes. Apelin increased mitochondrial ATP production and mitochondrial coupling efficiency in myotubes and promoted the expression of mitochondrial genes both in primary myotubes and cardiomyocytes. HIIT induced mild concentric cardiac hypertrophy in WT mice, whereas eccentric growth was observed in the left ventricles of apelin KO mice. HIIT did not affect myofiber size in skeletal muscles of WT mice but decreased the myofiber size in apelin KO mice. The decrease in myofiber size resulted from a fiber type switch toward smaller slow-twitch type I fibers. The increased proportion of slow-twitch type I fibers in apelin KO mice was associated with upregulation of myosin heavy chain slow isoform expression, accompanied with upregulated expression of genes related to fatty acid transport and downregulated expression of genes related to glucose metabolism. Mechanistically, skeletal muscles of apelin KO mice showed defective induction of insulin-like growth factor-1 signaling in response to HIIT. In conclusion, apelin is required for proper skeletal and cardiac muscle adaptation to high-intensity exercise. Promoting apelinergic signaling may have benefits in aging- or disease-related muscle wasting conditions.<b>NEW &amp; NOTEWORTHY<\/b> Apelin levels decline with age. This study demonstrates that in trained mice, apelin deficiency results in a switch from fast type II myofibers to slow oxidative type I myofibers. This is associated with a concomitant change in gene expression profile toward fatty acid utilization, indicating an aged-muscle phenotype in exercised apelin-deficient mice. These data are of importance in the design of exercise programs for aging individuals and could offer therapeutic target to maintain muscle mass.","authors":"Kilpi\u00f6, T., Skarp, S., Perj\u00e9s, \u00c1., Swan, J., Kaikkonen, L., Saarim\u00e4ki, S., Szokodi, I., Penninger, JM., Szab\u00f3, Z., Magga, J., Kerkel\u00e4, R.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Am J Physiol Cell Physiol","volume":"326","issue":"5","page":"C1437-C1450","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-04-30","doi":"10.1152\/ajpcell.00427.2023","first_author":null,"corresponding_authors":null},{"pmid":"38595939","title":"PRDM16 co-operates with LHX2 to shape the human brain.","abstract":"PRDM16 is a dynamic transcriptional regulator of various stem cell niches, including adipocytic, hematopoietic, cardiac progenitors, and neural stem cells. PRDM16 has been suggested to contribute to 1p36 deletion syndrome, one of the most prevalent subtelomeric microdeletion syndromes. We report a patient with a <i>de novo<\/i> nonsense mutation in the PRDM16 coding sequence, accompanied by lissencephaly and microcephaly features. Human stem cells were genetically modified to mimic this mutation, generating cortical organoids that exhibited altered cell cycle dynamics. RNA sequencing of cortical organoids at day 32 unveiled changes in cell adhesion and WNT-signaling pathways. ChIP-seq of PRDM16 identified binding sites in postmortem human fetal cortex, indicating the conservation of PRDM16 binding to developmental genes in mice and humans, potentially at enhancer sites. A shared motif between PRDM16 and LHX2 was identified and further examined through comparison with LHX2 ChIP-seq data from mice. These results suggested a collaborative partnership between PRDM16 and LHX2 in regulating a common set of genes and pathways in cortical radial glia cells, possibly via their synergistic involvement in cortical development.","authors":"Suresh, V., Bhattacharya, B., Tshuva, RY., Danan Gotthold, M., Olender, T., Bose, M., Pradhan, SJ., Zeev, BB., Smith, RS., Tole, S., Galande, S., Harwell, CC., Baizabal, JM., Reiner, O.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Oxf Open Neurosci","volume":"3","issue":null,"page":"kvae001","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-04-17","doi":"10.1093\/oons\/kvae001","first_author":null,"corresponding_authors":null},{"pmid":"38729677","title":"Neuromesodermal specification during head-to-tail body axis formation.","abstract":"The anterior-to-posterior (head-to-tail) body axis is extraordinarily diverse among vertebrates but conserved within species. Body axis development requires a population of axial progenitors that resides at the posterior of the embryo to sustain elongation and is then eliminated once axis extension is complete. These progenitors occupy distinct domains in the posterior (tail-end) of the embryo and contribute to various lineages along the body axis. The subset of axial progenitors with neuromesodermal competency will generate both the neural tube (the precursor of the spinal cord), and the trunk and tail somites (producing the musculoskeleton) during embryo development. These axial progenitors are called Neuromesodermal Competent cells (NMCs) and Neuromesodermal Progenitors (NMPs). NMCs\/NMPs have recently attracted interest beyond the field of developmental biology due to their clinical potential. In the mouse, the maintenance of neuromesodermal competency relies on a fine balance between a trio of known signals: Wnt\/&#x3b2;-catenin, FGF signalling activity and suppression of retinoic acid signalling. These signals regulate the relative expression levels of the mesodermal transcription factor Brachyury and the neural transcription factor Sox2, permitting the maintenance of progenitor identity when co-expressed, and either mesoderm or neural lineage commitment when the balance is tilted towards either Brachyury or Sox2, respectively. Despite important advances in understanding key genes and cellular behaviours involved in these fate decisions, how the balance between mesodermal and neural fates is achieved remains largely unknown. In this chapter, we provide an overview of signalling and gene regulatory networks&#xa0;in NMCs\/NMPs. We discuss mutant phenotypes associated with axial defects, hinting at the potential significant role of lesser studied proteins in the maintenance and differentiation of the progenitors that fuel axial elongation.","authors":"Martins-Costa, C., Wilson, V., Binagui-Casas, A.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Curr Top Dev Biol","volume":"159","issue":null,"page":"232-271","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-05-10","doi":"10.1016\/bs.ctdb.2024.02.012","first_author":null,"corresponding_authors":null},{"pmid":"38718796","title":"ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum.","abstract":"Mutations in ARID1B, a member of the mSWI\/SNF complex, cause severe neurodevelopmental phenotypes with elusive mechanisms in humans. The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions. Here, we find that neurons expressing SATB2, a determinant of callosal projection neuron (CPN) identity, show impaired maturation in ARID1B<sup>+\/-<\/sup> neural organoids. Molecularly, a reduction in chromatin accessibility of genomic regions targeted by TCF-like, NFI-like, and ARID-like transcription factors drives the differential expression of genes required for corpus callosum (CC) development. Through an in&#xa0;vitro model of the CC tract, we demonstrate that this transcriptional dysregulation impairs the formation of long-range axonal projections, causing structural underconnectivity. Our study uncovers new functions of the mSWI\/SNF during human corticogenesis, identifying cell-autonomous axonogenesis defects in SATB2<sup>+<\/sup> neurons as a cause of ACC in ARID1B patients.","authors":"Martins-Costa, C., Wiegers, A., Pham, VA., Sidhaye, J., Doleschall, B., Novatchkova, M., Lendl, T., Piber, M., Peer, A., M\u00f6seneder, P., Stuempflen, M., Chow, SYA., Seidl, R., Prayer, D., H\u00f6ftberger, R., Kasprian, G., Ikeuchi, Y., Corsini, NS., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Cell Stem Cell","volume":"31","issue":"6","page":"866-885.e14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-07","doi":"10.1016\/j.stem.2024.04.014","first_author":null,"corresponding_authors":null},{"pmid":"38714853","title":"Cerebral organoids display dynamic clonal growth and tunable tissue replenishment.","abstract":"During brain development, neural progenitors expand through symmetric divisions before giving rise to differentiating cell types via asymmetric divisions. Transition between those modes varies among individual neural stem cells, resulting in clones of different sizes. Imaging-based lineage tracing allows for lineage analysis at high cellular resolution but systematic approaches to analyse clonal behaviour of entire tissues are currently lacking. Here we implement whole-tissue lineage tracing by genomic DNA barcoding in 3D human cerebral organoids, to show that individual stem cell clones produce progeny on a vastly variable scale. By using stochastic modelling we find that variable lineage sizes arise because a subpopulation of lineages retains symmetrically dividing cells. We show that lineage sizes can adjust to tissue demands after growth perturbation via chemical ablation or genetic restriction of a subset of cells in chimeric organoids. Our data suggest that adaptive plasticity of stem cell populations ensures robustness of development in human brain organoids.","authors":"Lindenhofer, D., Haendeler, S., Esk, C., Littleboy, JB., Brunet Avalos, C., Naas, J., Pflug, FG., van de Ven, EGP., Reumann, D., Baffet, AD., von Haeseler, A., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nat Cell Biol","volume":"26","issue":"5","page":"710-718","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-05-16","doi":"10.1038\/s41556-024-01412-z","first_author":null,"corresponding_authors":null},{"pmid":"38000027","title":"Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous <i>Ptgs1<\/i> induction.","abstract":"Tissue regeneration after injury involves the dedifferentiation of somatic cells, a natural adaptive reprogramming that leads to the emergence of injury-responsive cells with fetal-like characteristics. However, there is no direct evidence that adaptive reprogramming involves a shared molecular mechanism with direct cellular reprogramming. Here, we induced dedifferentiation of intestinal epithelial cells using OSKM (Oct4, Sox2, Klf4, and c-Myc) in vivo. The OSKM-induced forced dedifferentiation showed similar molecular features of intestinal regeneration, including a transition from homeostatic cell types to injury-responsive-like cell types. These injury-responsive-like cells, sharing gene signatures of revival stem cells and atrophy-induced villus epithelial cells, actively assisted tissue regeneration following damage. In contrast to normal intestinal regeneration involving <i>Ptgs2<\/i> induction, the OSKM promotes autonomous production of prostaglandin E2 via epithelial <i>Ptgs1<\/i> expression. These results indicate prostaglandin synthesis is a common mechanism for intestinal regeneration but involves a different enzyme when partial reprogramming is applied to the intestinal epithelium.","authors":"Kim, J., Kim, S., Lee, SY., Jo, BK., Oh, JY., Kwon, EJ., Kim, KT., Adpaikar, AA., Kim, EJ., Jung, HS., Kim, HR., Roe, JS., Hong, CP., Kim, JK., Koo, BK., Cha, HJ.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Sci Adv","volume":"9","issue":"47","page":"eadi8454","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-27","doi":"10.1126\/sciadv.adi8454","first_author":null,"corresponding_authors":null},{"pmid":"38536720","title":"Exploration of drug resistance mechanisms in triple negative breast cancer cells using a microfluidic device and patient tissues.","abstract":"Chemoresistance is a major cause of treatment failure in many cancers. However, the life cycle of cancer cells as they respond to and survive environmental and therapeutic stress is understudied. In this study, we utilized a microfluidic device to induce the development of doxorubicin-resistant (DOXR) cells from triple negative breast cancer (TNBC) cells within 11 days by generating gradients of DOX and medium. In vivo chemoresistant xenograft models, an unbiased genome-wide transcriptome analysis, and a patient data\/tissue analysis all showed that chemoresistance arose from failed epigenetic control of the nuclear protein-1 (NUPR1)\/histone deacetylase 11 (HDAC11) axis, and high <i>NUPR1<\/i> expression correlated with poor clinical outcomes. These results suggest that the chip can rapidly induce resistant cells that increase tumor heterogeneity and chemoresistance, highlighting the need for further studies on the epigenetic control of the NUPR1\/HDAC11 axis in TNBC.","authors":"Lim, W., Hwang, I., Zhang, J., Chen, Z., Han, J., Jeon, J., Koo, BK., Kim, S., Lee, JE., Kim, Y., Pienta, KJ., Amend, SR., Austin, RH., Ahn, JY., Park, S.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Elife","volume":"12","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-29","doi":"10.7554\/eLife.88830","first_author":null,"corresponding_authors":null},{"pmid":"38359788","title":"Quantitative and qualitative mutational impact of ionizing radiation on normal cells.","abstract":"The comprehensive genomic impact of ionizing radiation (IR), a carcinogen, on healthy somatic cells remains unclear. Using large-scale whole-genome sequencing (WGS) of clones expanded from irradiated murine and&#xa0;human single cells, we revealed that IR induces a characteristic spectrum of short insertions or deletions (indels) and structural variations (SVs), including balanced inversions, translocations, composite SVs (deletion-insertion, deletion-inversion, and deletion-translocation composites), and complex genomic rearrangements (CGRs), including chromoplexy, chromothripsis, and SV by breakage-fusion-bridge cycles. Our findings suggest that 1&#xa0;Gy IR exposure causes an average of 2.33 mutational events per Gb genome, comprising 2.15 indels, 0.17 SVs, and 0.01 CGRs, despite a high level of inter-cellular stochasticity. The mutational burden was dependent on total irradiation dose, regardless of dose rate or cell type. The findings were further validated in IR-induced secondary cancers and single cells without clonalization. Overall, our study highlights a comprehensive and clear picture of IR effects on normal mammalian genomes.","authors":"Youk, J., Kwon, HW., Lim, J., Kim, E., Kim, T., Kim, R., Park, S., Yi, K., Nam, CH., Jeon, S., An, Y., Choi, J., Na, H., Lee, ES., Cho, Y., Min, DW., Kim, H., Kang, YR., Choi, SH., Bae, MJ., Lee, CG., Kim, JG., Kim, YS., Yu, T., Lee, WC., Shin, JY., Lee, DS., Kim, TY., Ku, T., Kim, SY., Lee, JH., Koo, BK., Lee, H., Yi, OV., Han, EC., Chang, JH., Kim, KS., Son, TG., Ju, YS.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Cell Genom","volume":"4","issue":"2","page":"100499","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-19","doi":"10.1016\/j.xgen.2024.100499","first_author":null,"corresponding_authors":null},{"pmid":"38862535","title":"Red2Flpe-SCON: a versatile, multicolor strategy for generating mosaic conditional knockout mice.","abstract":"Image-based lineage tracing enables tissue turnover kinetics and lineage potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco, which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion kinetics and neighboring effects of oncogenic clones to be dissected. We now report Red2Flpe-SCON: a mosaic knockout system that uses multicolor reporters to label both mutant and wild-type cells. We develop the Red2Flpe mouse line for red clone-specific Flpe expression, as well as the FRT-based SCON (Short Conditional IntrON) method to facilitate tunable conditional mosaic knockouts in mice. We use the Red2Flpe-SCON method to study Sox2 mutant clonal analysis in the esophageal epithelium of adult mice which reveal that the stem cell gene, Sox2, is less essential for adult stem cell maintenance itself, but rather for stem cell proliferation and differentiation.","authors":"Wu, SS., Kim, S., Lee, H., Lee, JH., Park, SY., Bakonyi, R., Teriyapirom, I., Hallay, N., Pilat-Carotta, S., Theussl, HC., Kim, J., Lee, JH., Simons, BD., Kim, JK., Colozza, G., Koo, BK.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"4963","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-11","doi":"10.1038\/s41467-024-49382-y","first_author":null,"corresponding_authors":null},{"pmid":"38809952","title":"Pairtools: From sequencing data to chromosome contacts.","abstract":"The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require high-performance and flexible processing of sequenced reads into contact pairs. To meet these challenges, we present pairtools-a flexible suite of tools for contact extraction from sequencing data. Pairtools provides modular command-line interface (CLI) tools that can be flexibly chained into data processing pipelines. The core operations provided by pairtools are parsing of.sam alignments into Hi-C pairs, sorting and removal of PCR duplicates. In addition, pairtools provides auxiliary tools for building feature-rich 3C+ pipelines, including contact pair manipulation, filtration, and quality control. Benchmarking pairtools against popular 3C+ data pipelines shows advantages of pairtools for high-performance and flexible 3C+ analysis. Finally, pairtools provides protocol-specific tools for restriction-based protocols, haplotype-resolved contacts, and single-cell Hi-C. The combination of CLI tools and tight integration with Python data analysis libraries makes pairtools a versatile foundation for a broad range of 3C+ pipelines.","authors":"Abdennur, N., Fudenberg, G., Flyamer, IM., Galitsyna, AA., Goloborodko, A., Imakaev, M., Venev, SV.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"PLoS Comput Biol","volume":"20","issue":"5","page":"e1012164","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-10","doi":"10.1371\/journal.pcbi.1012164","first_author":null,"corresponding_authors":null},{"pmid":"38788714","title":"A chromatin code for limb segment identity in axolotl limb regeneration.","abstract":"The salamander limb correctly regenerates missing limb segments because connective tissue cells have segment-specific identities, termed \"positional information\". How positional information is molecularly encoded at the chromatin level has been unknown. Here, we performed genome-wide chromatin profiling in mature and regenerating axolotl limb connective tissue cells. We find segment-specific levels of histone H3K27me3 as the major positional mark, especially at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. In the hand, the permissive chromatin state of the homeoprotein gene HoxA13 engages with the regeneration program bypassing the upper limb program. Comparison of regeneration regulatory elements with those found in other regenerative animals identified a core shared set of transcription factors, supporting an ancient, conserved regeneration program.","authors":"Kawaguchi, A., Wang, J., Knapp, D., Murawala, P., Nowoshilow, S., Masselink, W., Taniguchi-Sugiura, Y., Fei, JF., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Dev Cell","volume":"59","issue":"16","page":"2239-2253.e9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-20","doi":"10.1016\/j.devcel.2024.05.002","first_author":null,"corresponding_authors":null},{"pmid":"38783418","title":"Mechanistic insights into the function of 14-3-3 proteins as negative regulators of brassinosteroid signaling in Arabidopsis.","abstract":"Brassinosteroids (BRs) are vital plant steroid hormones sensed at the cell surface by a membrane signaling complex comprising the receptor kinase BRI1 and a SERK-family co-receptor kinase. Activation of this complex lead to dissociation of the inhibitor protein BKI1 from the receptor and to differential phosphorylation of BZR1\/BES1 transcription factors by the glycogen synthase kinase 3 protein BIN2. Many phosphoproteins of the BR signaling pathway, including BRI1, SERKs, BKI1 and BZR1\/BES1 can associate with 14-3-3 proteins. In this study, we use quantitative ligand binding assays to define the minimal 14-3-3 binding sites in the N-terminal lobe of the BRI1 kinase domain, in BKI1, and in BZR1 from Arabidopsis thaliana. All three motifs require to be phosphorylated to specifically bind 14-3-3s with mid- to low micromolar affinity. BR signaling components display minimal isoform preference within the 14-3-3 non-&#x3b5; subgroup. 14-3-3&#x3bb; and 14-3-3&#x3c9; isoform complex crystal structures reveal that BKI1 and BZR1 bind as canonical type II 14-3-3 linear motifs. Disruption of key amino acids in the phosphopeptide binding site through mutation impairs the interaction of 14-3-3&#x3bb; with all three linear motifs. Notably, quadruple loss-of-function mutants from the non-&#x3b5; group exhibit gain-of-function brassinosteroid signaling phenotypes, suggesting a role for 14-3-3 proteins as overall negative regulators of the BR pathway. Collectively, our work provides further mechanistic and genetic evidence for the regulatory role of 14-3-3 proteins at various stages of the brassinosteroid signaling cascade.","authors":"Obergfell, E., Hohmann, U., Moretti, A., Chen, H., Hothorn, M.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Plant Cell Physiol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-05-24","doi":"10.1093\/pcp\/pcae056","first_author":null,"corresponding_authors":null},{"pmid":"38776925","title":"Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition.","abstract":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable \"winning\" floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2<sup>+<\/sup> clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in&#xa0;vivo at mid\/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.","authors":"Krammer, T., Stuart, HT., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., Becerril Perez, F., Wang, J., Costantini, E., Lehr, S., Arbanas, L., H\u00f6rmann, A., Neum\u00fcller, RA., Elvassore, N., Siggia, E., Briscoe, J., Kicheva, A., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Dev Cell","volume":"59","issue":"15","page":"1940-1953.e10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-06","doi":"10.1016\/j.devcel.2024.04.021","first_author":null,"corresponding_authors":null},{"pmid":"38747650","title":"Striatin knock out induces a gain of function of I<sub>Na<\/sub> and impaired Ca<sup>2+<\/sup> handling in mESC-derived cardiomyocytes.","abstract":"on Status=\"Publisher\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">38747650<\/PMID><DateRevised><Year>2024<\/Year><Month>05<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1748-1716<\/ISSN><JournalIssue CitedMedium=\"Internet\"><PubDate><Year>2024<\/Year><Month>May<\/Month><Day>15<\/Day><\/PubDate><\/JournalIssue><Title>Acta physiologica (Oxford, England)<\/Title><ISOAbbreviation>Acta Physiol (Oxf)<\/ISOAbbreviation><\/Journal><ArticleTitle>Striatin knock out induces a gain of function of I<sub>Na<\/sub> and impaired Ca<sup>2+<\/sup> handling in mESC-derived cardiomyocytes.<\/ArticleTitle><Pagination><StartPage>e14160<\/StartPage><MedlinePgn>e14160<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1111\/apha.14160<\/ELocationID><Abstract><AbstractText Label=\"AIM\" NlmCategory=\"OBJECTIVE\">Striatin (Strn) is a scaffold protein expressed in cardiomyocytes (CMs) and alteration of its expression are described in various cardiac diseases. However, the alteration underlying its pathogenicity have been poorly investigated.","authors":"Benzoni, P., Arici, M., Giannetti, F., Cospito, A., Prevostini, R., Volani, C., Fassina, L., Rosato-Siri, MD., Metallo, A., Gennaccaro, L., Suffredini, S., Foco, L., Mazzetti, S., Calogero, A., Cappelletti, G., Leibbrandt, A., Elling, U., Broso, F., Penninger, JM., Pramstaller, PP., Piubelli, C., Bucchi, A., Baruscotti, M., Rossini, A., Rocchetti, M., Barbuti, A.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Acta Physiol (Oxf)","volume":null,"issue":null,"page":"e14160","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-05-15","doi":"10.1111\/apha.14160","first_author":null,"corresponding_authors":null},{"pmid":"38907142","title":"Label-Free Sample Preparation for Single-Cell Proteomics.","abstract":"In recent years, single-cell proteomics (SCP) has become a valuable addition to other single-cell omics technologies for studying cellular heterogeneity. The amount of protein in a single cell is very limited, and in contrast to sequencing techniques, there are currently no means for protein amplification. Therefore, most single-cell proteomics approaches aim to maximize sample preparation efficiency while minimizing peptide loss. By reducing processing volumes to sub-microliters and avoiding manual transfer steps that could lead to peptide loss, peptide recovery, and the robustness of SCP workflows have been significantly improved. In this chapter, we describe a protocol for label-free SCP sample preparation using the cellenONE<sup>&#xae;<\/sup> platform and the proteoCHIP LF 48 substrate prior to analysis with high-performance liquid chromatography-mass spectrometry.","authors":"Hartlmayr, D., Ctortecka, C., Mayer, R., Mechtler, K., Seth, A.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Methods Mol Biol","volume":"2817","issue":null,"page":"1-7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-21","doi":"10.1007\/978-1-0716-3934-4_1","first_author":null,"corresponding_authors":null},{"pmid":"38902237","title":"In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer.","abstract":"Functionally characterizing the genetic alterations that drive pancreatic cancer is a prerequisite for precision medicine. Here, we perform somatic CRISPR\/Cas9 mutagenesis screens to assess the transforming potential of 125 recurrently mutated pancreatic cancer genes, which revealed USP15 and SCAF1 as pancreatic tumor suppressors. Mechanistically, we find that USP15 functions in a haploinsufficient manner and that loss of USP15 or SCAF1 leads to reduced inflammatory TNF&#x3b1;, TGF-&#x3b2; and IL6 responses and increased sensitivity to PARP inhibition and Gemcitabine. Furthermore, we find that loss of SCAF1 leads to the formation of a truncated, inactive USP15 isoform at the expense of full-length USP15, functionally coupling SCAF1 and USP15. Notably, USP15 and SCAF1 alterations are observed in 31% of pancreatic cancer patients. Our results highlight the utility of in vivo CRISPR screens to integrate human cancer genomics and mouse modeling for the discovery of cancer driver genes with potential prognostic and therapeutic implications.","authors":"Martinez, S., Wu, S., Geuenich, M., Malik, A., Weber, R., Woo, T., Zhang, A., Jang, GH., Dervovic, D., Al-Zahrani, KN., Tsai, R., Fodil, N., Gros, P., Gallinger, S., Neely, GG., Notta, F., Sendoel, A., Campbell, K., Elling, U., Schramek, D.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"5266","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-20","doi":"10.1038\/s41467-024-49450-3","first_author":null,"corresponding_authors":null},{"pmid":"38918865","title":"Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework.","abstract":"Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing reads. Biases in mapping the resulting reads to reference genomes remain poorly understood. We present splice_sim, a splice-aware RNA-seq simulation and evaluation pipeline that introduces user-defined nucleotide conversions at set frequencies, creates mixture models of converted and unconverted reads, and calculates mapping accuracies per genomic annotation. By simulating nucleotide conversion RNA-seq datasets under realistic experimental conditions, including metabolic RNA labeling and RNA bisulfite sequencing, we measure mapping accuracies of state-of-the-art spliced-read mappers for mouse and human transcripts and derive strategies to prevent biases in the data interpretation.","authors":"Popitsch, N., Neumann, T., von Haeseler, A., Ameres, SL.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Genome Biol","volume":"25","issue":"1","page":"166","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-26","doi":"10.1186\/s13059-024-03313-8","first_author":null,"corresponding_authors":null},{"pmid":"38916145","title":"Synchronized development of thymic eosinophils and thymocytes.","abstract":"The thymus is an organ required for T cell development and is also an eosinophil-rich organ; however, the nature and function of thymic eosinophils remain unclear. Here, we characterized the gene expression and differentiation mechanism of thymic eosinophils in mice. Thymic eosinophils showed a distinct gene expression profile compared with other organ-resident eosinophils. The number of thymic eosinophils was controlled by medullary thymic epithelial cells. In Rag-deficient mice, the unique gene expression signature of thymic eosinophils was lost but restored by pre-T cell receptor signaling, which induces CD4+ CD8+ thymocyte differentiation, indicating that T cell differentiation beyond the CD4- CD8- stage is necessary and sufficient for the induction of thymic eosinophils. These results demonstrate that thymic eosinophils are quantitatively and qualitatively regulated by medullary thymic epithelial cells and developing thymocytes, respectively, suggesting that thymic eosinophils are a distinct, thymus-specific cell subset, induced by interactions with thymic cells.","authors":"Ota, A., Iguchi, T., Nitta, S., Muro, R., Mino, N., Tsukasaki, M., Penninger, JM., Nitta, T., Takayanagi, H.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Int Immunol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-25","doi":"10.1093\/intimm\/dxae037","first_author":null,"corresponding_authors":null},{"pmid":"38969721","title":"Proteome-scale tagging and functional screening in mammalian cells by ORFtag.","abstract":"The systematic determination of protein function is a key goal of modern biology, but remains challenging with current approaches. Here we present ORFtag, a versatile, cost-effective and highly efficient method for the massively parallel tagging and functional interrogation of proteins at the proteome scale. ORFtag uses retroviral vectors bearing a promoter, peptide tag and splice donor to generate fusions between the tag and endogenous open reading frames (ORFs). We demonstrate the utility of ORFtag through functional screens for transcriptional activators, repressors and posttranscriptional regulators in mouse embryonic stem cells. Each screen recovers known and identifies new regulators, including long ORFs inaccessible by other methods. Among other hits, we find that Zfp574 is a highly selective transcriptional activator and that oncogenic fusions often function as transactivators.","authors":"Nem\u010dko, F., Himmelsbach, M., Loubiere, V., Yelagandula, R., Pagani, M., Fasching, N., Brennecke, J., Elling, U., Stark, A., Ameres, SL.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Nat Methods","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-07-05","doi":"10.1038\/s41592-024-02339-x","first_author":null,"corresponding_authors":null},{"pmid":"39003739","title":"PP2A-B55 phosphatase counteracts Ki-67-dependent chromosome individualization during mitosis.","abstract":"Cell cycle progression is regulated by the orderly balance between kinase and phosphatase activities. PP2A phosphatase holoenzymes containing the B55 family of regulatory B subunits function as major CDK1-counteracting phosphatases during mitotic exit in mammals. However, the identification of the specific mitotic roles of these PP2A-B55 complexes has been hindered by the existence of multiple B55 isoforms. Here, through the generation of loss-of-function genetic mouse models for the two ubiquitous B55 isoforms (B55&#x3b1; and B55&#x3b4;), we report that PP2A-B55&#x3b1; and PP2A-B55&#x3b4; complexes display overlapping roles in controlling the dynamics of proper chromosome individualization and clustering during mitosis. In the absence of PP2A-B55 activity, mitotic cells display increased chromosome individualization in the presence of enhanced phosphorylation and perichromosomal loading of Ki-67. These data provide experimental evidence for a regulatory mechanism by which the balance between kinase and PP2A-B55 phosphatase activity controls the Ki-67-mediated spatial organization of the mass of chromosomes during mitosis.","authors":"Sanz-Flores, M., Ruiz-Torres, M., Aguirre-Portol\u00e9s, C., El Bakkali, A., Salvador-Barber\u00f3, B., Villarroya-Beltri, C., Ortega, S., Meg\u00edas, D., Gerlich, DW., \u00c1lvarez-Fern\u00e1ndez, M., Malumbres, M.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Cell Rep","volume":"43","issue":"7","page":"114494","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-07-14","doi":"10.1016\/j.celrep.2024.114494","first_author":null,"corresponding_authors":null},{"pmid":"38995818","title":"Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals.","abstract":"Members of the diverse heterochromatin protein 1 (HP1) family play crucial roles in heterochromatin formation and maintenance. Despite the similar affinities of their chromodomains for di- and tri-methylated histone H3 lysine 9 (H3K9me2\/3), different HP1 proteins exhibit distinct chromatin-binding patterns, likely due to interactions with various specificity factors. Previously, we showed that the chromatin-binding pattern of the HP1 protein Rhino, a crucial factor of the <i>Drosophila<\/i> PIWI-interacting RNA (piRNA) pathway, is largely defined by a DNA sequence-specific C<sub>2<\/sub>H<sub>2<\/sub> zinc finger protein named Kipferl (Baumgartner et al., 2022). Here, we elucidate the molecular basis of the interaction between Rhino and its guidance factor Kipferl. Through phylogenetic analyses, structure prediction, and in vivo genetics, we identify a single amino acid change within Rhino's chromodomain, G31D, that does not affect H3K9me2\/3 binding but disrupts the interaction between Rhino and Kipferl. Flies carrying the <i>rhino<sup>G31D<\/sup><\/i> mutation phenocopy <i>kipferl<\/i> mutant flies, with Rhino redistributing from piRNA clusters to satellite repeats, causing pronounced changes in the ovarian piRNA profile of <i>rhino<sup>G31D<\/sup><\/i> flies. Thus, Rhino's chromodomain functions as a dual-specificity module, facilitating interactions with both a histone mark and a DNA-binding protein.","authors":"Baumgartner, L., Ipsaro, JJ., Hohmann, U., Handler, D., Schleiffer, A., Duchek, P., Brennecke, J.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Elife","volume":"13","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-07-12","doi":"10.7554\/eLife.93194","first_author":null,"corresponding_authors":null},{"pmid":"38689024","title":"Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types.","abstract":"Many microRNAs (miRNAs) are expressed with high spatiotemporal specificity during organismal development, with some being limited to rare cell types, often embedded in complex tissues. Yet, most miRNA profiling efforts remain at the tissue and organ levels. To overcome challenges in accessing the microRNomes from tissue-embedded cells, we had previously developed mime-seq (miRNome by methylation-dependent sequencing), a technique in which cell-specific miRNA methylation in C. elegans and Drosophila enabled chemo-selective sequencing without the need for cell sorting or biochemical purification. Here, we present mime-seq 2.0 for profiling miRNAs from specific mouse cell types. We engineered a chimeric RNA methyltransferase that is tethered to Argonaute protein and efficiently methylates miRNAs at their 3'-terminal 2'-OH in mouse and human cell lines. We also generated a transgenic mouse for conditional expression of this methyltransferase, which can be used to direct methylation of miRNAs in a cell type of choice. We validated the use of this mouse model by profiling miRNAs from B cells and bone marrow plasma cells.","authors":"Mandlbauer, A., Sun, Q., Popitsch, N., Schwickert, T., Spanova, M., Wang, J., Ameres, SL., Busslinger, M., Cochella, L.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"EMBO J","volume":"43","issue":"12","page":"2506-2525","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-18","doi":"10.1038\/s44318-024-00102-8","first_author":null,"corresponding_authors":null},{"pmid":"39054317","title":"UNC-45 assisted myosin folding depends on a conserved FX<sub>3<\/sub>HY motif implicated in Freeman Sheldon Syndrome.","abstract":"Myosin motors are critical for diverse motility functions, ranging from cytokinesis and endocytosis to muscle contraction. The UNC-45 chaperone controls myosin function mediating the folding, assembly, and degradation of the muscle protein. Here, we analyze the molecular mechanism of UNC-45 as a hub in myosin quality control. We show that UNC-45 forms discrete complexes with folded and unfolded myosin, forwarding them to downstream chaperones and E3 ligases. Structural analysis of a minimal chaperone:substrate complex reveals that UNC-45 binds to a conserved FX<sub>3<\/sub>HY motif in the myosin motor domain. Disrupting the observed interface by mutagenesis prevents myosin maturation leading to protein aggregation in vivo. We also show that a mutation in the FX<sub>3<\/sub>HY motif linked to the Freeman Sheldon Syndrome impairs UNC-45 assisted folding, reducing the level of functional myosin. These findings demonstrate that a faulty myosin quality control is a critical yet unexplored cause of human myopathies.","authors":"Vogel, A., Arnese, R., Gudino Carrillo, RM., Sehr, D., Deszcz, L., Bylicki, A., Meinhart, A., Clausen, T.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"6272","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-07-25","doi":"10.1038\/s41467-024-50442-6","first_author":null,"corresponding_authors":null},{"pmid":"39013852","title":"Rational correction of pathogenic conformational defects in HTRA1.","abstract":"Loss-of-function mutations in the homotrimeric serine protease HTRA1 cause cerebral vasculopathy. Here, we establish independent approaches to achieve the functional correction of trimer assembly defects. Focusing on the prototypical R274Q mutation, we identify an HTRA1 variant that promotes trimer formation thus restoring enzymatic activity in vitro. Genetic experiments in Htra1<sup>R274Q<\/sup> mice further demonstrate that expression of this protein-based corrector in trans is sufficient to stabilize HtrA1-R274Q and restore the proteomic signature of the brain vasculature. An alternative approach employs supramolecular chemical ligands that shift the monomer-trimer equilibrium towards proteolytically active trimers. Moreover, we identify a peptidic ligand that activates HTRA1 monomers. Our findings open perspectives for tailored protein repair strategies.","authors":"Beaufort, N., Ingendahl, L., Merdanovic, M., Schmidt, A., Podlesainski, D., Richter, T., Neumann, T., Kuszner, M., Vetter, IR., Stege, P., Burston, SG., Filipovic, A., Ruiz-Blanco, YB., Bravo-Rodriguez, K., Mieres-Perez, J., Beuck, C., Uebel, S., Zobawa, M., Schillinger, J., Malik, R., Todorov-V\u00f6lgyi, K., Rey, J., Roberti, A., Hagemeier, B., Wefers, B., M\u00fcller, SA., Wurst, W., Sanchez-Garcia, E., Zimmermann, A., Hu, XY., Clausen, T., Huber, R., Lichtenthaler, SF., Schmuck, C., Giese, M., Kaiser, M., Ehrmann, M., Dichgans, M.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"5944","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-07-16","doi":"10.1038\/s41467-024-49982-8","first_author":null,"corresponding_authors":null},{"pmid":"38830897","title":"Sororin is an evolutionary conserved antagonist of WAPL.","abstract":"Cohesin mediates sister chromatid cohesion to enable chromosome segregation and DNA damage repair. To perform these functions, cohesin needs to be protected from WAPL, which otherwise releases cohesin from DNA. It has been proposed that cohesin is protected from WAPL by SORORIN. However, in vivo evidence for this antagonism is missing and SORORIN is only known to exist in vertebrates and insects. It is therefore unknown how important and widespread SORORIN's functions are. Here we report the identification of SORORIN orthologs in Schizosaccharomyces pombe (Sor1) and Arabidopsis thaliana (AtSORORIN). sor1&#x394; mutants display cohesion defects, which are partially alleviated by wpl1&#x394;. Atsororin mutant plants display dwarfism, tissue specific cohesion defects and chromosome mis-segregation. Furthermore, Atsororin mutant plants are sterile and separate sister chromatids prematurely at anaphase I. The somatic, but not the meiotic deficiencies can be alleviated by loss of WAPL. These results provide in vivo evidence for SORORIN antagonizing WAPL, reveal that SORORIN is present in organisms beyond the animal kingdom and indicate that it has acquired tissue specific functions in plants.","authors":"Prus\u00e9n Mota, I., Galova, M., Schleiffer, A., Nguyen, TT., Kovacikova, I., Farias Saad, C., Litos, G., Nishiyama, T., Gregan, J., Peters, JM., Schl\u00f6gelhofer, P.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"4729","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-03","doi":"10.1038\/s41467-024-49178-0","first_author":null,"corresponding_authors":null},{"pmid":"38925148","title":"Mechanism for the initiation of spliceosome disassembly.","abstract":"Precursor-mRNA&#xa0;(pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome<sup>1<\/sup>. Recent studies have shed light on spliceosome assembly and remodelling for catalysis<sup>2-6<\/sup>, but the mechanism of disassembly remains unclear. Here we report cryo-electron microscopy structures of nematode and human terminal intron lariat spliceosomes along with biochemical and genetic data. Our results uncover how four disassembly factors and the conserved RNA helicase DHX15 initiate spliceosome disassembly. The disassembly factors probe large inner and outer spliceosome surfaces to detect the release of ligated mRNA. Two of these factors, TFIP11 and C19L1, and three general spliceosome subunits, SYF1, SYF2 and SDE2, then dock and activate DHX15 on the catalytic U6 snRNA to initiate disassembly. U6 therefore controls both the start<sup>5<\/sup> and end of pre-mRNA&#xa0;splicing. Taken together, our results explain the molecular basis of&#xa0;the initiation of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes.","authors":"Vorl\u00e4nder, MK., Rothe, P., Kleifeld, J., Cormack, ED., Veleti, L., Riabov-Bassat, D., Fin, L., Phillips, AW., Cochella, L., Plaschka, C.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nature","volume":"632","issue":"8024","page":"443-450","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-07","doi":"10.1038\/s41586-024-07741-1","first_author":null,"corresponding_authors":null},{"pmid":"39015407","title":"Suppression of toxic transgene expression by optimized artificial miRNAs increases AAV vector yields in HEK-293 cells.","abstract":"Adeno-associated virus (AAV) vectors have become the leading platform for gene delivery in both preclinical research and therapeutic applications, making the production of high-titer AAV preparations essential. To date, most AAV-based studies use constitutive promoters (e.g., CMV, CAG), which are also active in human embryonic kidney (HEK)-293 producer cells, thus leading to the expression of the transgene already during production. Depending on the transgene's function, this might negatively impact producer cell performance and result in decreased AAV vector yields. Here, we evaluated a panel of diverse microRNA (miRNA)-based shRNA designs to identify a highly potent artificial miRNA for the transient suppression of transgenes during AAV production. Our results demonstrate that insertion of miRNA target sites into the 3' UTR of the transgene and simultaneous expression of the corresponding miRNA from the 3' UTR of conventional AAV production plasmids (rep\/cap, pHelper) enabled efficient silencing of toxic transgene expression, thereby increasing AAV vector yields up to 240-fold. This strategy not only allows to maintain the traditional triple-transfection protocol, but also represents a universally applicable approach to suppress toxic transgenes, thereby boosting vector yields with so far unprecedented efficiency.","authors":"Blahetek, G., Mayer, C., Zuber, J., Lenter, M., Strobel, B.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Mol Ther Methods Clin Dev","volume":"32","issue":"3","page":"101280","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-07-18","doi":"10.1016\/j.omtm.2024.101280","first_author":null,"corresponding_authors":null},{"pmid":"38926334","title":"Alkylamine-tethered molecules recruit FBXO22 for targeted protein degradation.","abstract":"Targeted protein degradation (TPD) relies on small molecules to recruit proteins to E3 ligases to induce their ubiquitylation and degradation by the proteasome. Only a few of the approximately 600 human E3 ligases are currently amenable to this strategy. This limits the actionable target space and clinical opportunities and thus establishes the necessity to expand to additional ligases. Here we identify and characterize SP3N, a specific degrader of the prolyl isomerase FKBP12. SP3N features a minimal design, where a known FKBP12 ligand is appended with a flexible alkylamine tail that conveys degradation properties. We found that SP3N is a precursor and that the alkylamine is metabolized to an active aldehyde species that recruits the SCF<sup>FBXO22<\/sup> ligase for FKBP12 degradation. Target engagement occurs via covalent adduction of Cys326 in the FBXO22 C-terminal domain, which is critical for ternary complex formation, ubiquitylation and degradation. This mechanism is conserved for two recently reported alkylamine-based degraders of NSD2 and XIAP, thus establishing alkylamine tethering and covalent hijacking of FBXO22 as a generalizable TPD strategy.","authors":"Kagiou, C., Cisneros, JA., Farnung, J., Liwocha, J., Offensperger, F., Dong, K., Yang, K., Tin, G., Horstmann, CS., Hinterndorfer, M., Paulo, JA., Scholes, NS., Sanchez Avila, J., Fellner, M., Andersch, F., Hannich, JT., Zuber, J., Kubicek, S., Gygi, SP., Schulman, BA., Winter, GE.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"5409","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-06-26","doi":"10.1038\/s41467-024-49739-3","first_author":null,"corresponding_authors":null},{"pmid":"38989621","title":"tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.","abstract":"tRNA genes exist in multiple copies in the genome of all organisms across the three domains of life. Besides the sequence differences across tRNA copies, extensive post-transcriptional modification adds a further layer to tRNA diversification. Whilst the crucial role of tRNAs as adapter molecules in protein translation is well established, whether all tRNAs are actually expressed, and whether the differences across isodecoders play any regulatory role is only recently being uncovered. Here we built upon recent developments in the use of NGS-based methods for RNA modification detection and developed tRAM-seq, an experimental protocol and in silico analysis pipeline to investigate tRNA expression and modification. Using tRAM-seq, we analysed the full ensemble of nucleo-cytoplasmic and mitochondrial tRNAs during embryonic development of the model vertebrate zebrafish. We show that the repertoire of tRNAs changes during development, with an apparent major switch in tRNA isodecoder expression and modification profile taking place around the start of gastrulation. Taken together, our findings suggest the existence of a general reprogramming of the expressed tRNA pool, possibly gearing the translational machinery for distinct stages of the delicate and crucial process of embryo development.","authors":"Rappol, T., Waldl, M., Chugunova, A., Hofacker, IL., Pauli, A., Vilardo, E.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Nucleic Acids Res","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.01.30.575011v1","articledate":"2024-07-11","doi":"10.1093\/nar\/gkae595","first_author":null,"corresponding_authors":null},{"pmid":"39251582","title":"FoxO transcription factors actuate the formative pluripotency specific gene expression programme.","abstract":"Na&#xef;ve pluripotency is sustained by a self-reinforcing gene regulatory network (GRN) comprising core and na&#xef;ve pluripotency-specific transcription factors (TFs). Upon exiting na&#xef;ve pluripotency, embryonic stem cells (ESCs) transition through a formative post-implantation-like pluripotent state, where they acquire competence for lineage&#xa0;choice. However, the mechanisms underlying disengagement from the na&#xef;ve GRN and initiation of the formative GRN are unclear. Here, we demonstrate that phosphorylated AKT acts as a gatekeeper that prevents nuclear localisation of FoxO TFs in na&#xef;ve ESCs. PTEN-mediated reduction of AKT activity upon exit from na&#xef;ve pluripotency allows nuclear entry of FoxO TFs, enforcing a cell fate transition by binding and activating formative pluripotency-specific enhancers. Indeed, FoxO TFs are necessary and sufficient for the activation of the formative pluripotency-specific GRN. Our work uncovers a pivotal role for FoxO TFs in establishing formative post-implantation pluripotency, a critical early embryonic cell fate transition.","authors":"Santini, L., Kowald, S., Cerron-Alvan, LM., Huth, M., Fabing, AP., Sestini, G., Rivron, N., Leeb, M.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"7879","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-09-09","doi":"10.1038\/s41467-024-51794-9","first_author":null,"corresponding_authors":null},{"pmid":"39178277","title":"Mast cell-derived BH4 and serotonin are critical mediators of postoperative pain.","abstract":"Postoperative pain affects most patients after major surgery and can transition to chronic pain. The considerable side effects and limited efficacy of current treatments underline the need for new therapeutic options. We observed increased amounts of the metabolites BH4 and serotonin after skin injury. Mast cells were primary postoperative sources of <i>Gch1<\/i>, the rate-limiting enzyme in BH4 synthesis, itself an obligate cofactor in serotonin production by tryptophan hydroxylase (Tph1). Mice deficient in mast cells or in mast cell-specific <i>Gch1<\/i> or <i>Tph1<\/i> showed drastically decreased postoperative pain. We found that injury induced the nociceptive neuropeptide substance P, mast cell degranulation, and granule nerve colocalization. Substance P triggered serotonin release in mouse and human mast cells, and substance P receptor blockade substantially ameliorated pain hypersensitivity. Our findings highlight the importance of mast cells at the neuroimmune interface and substance P-driven mast cell BH4 and serotonin production as a therapeutic target for postoperative pain treatment.","authors":"Starkl, P., Jonsson, G., Artner, T., Turnes, BL., Gail, LM., Oliveira, T., Jain, A., Serhan, N., Stejskal, K., Lakovits, K., Hladik, A., An, M., Channon, KM., Kim, H., K\u00f6cher, T., Weninger, W., Stary, G., Knapp, S., Klang, V., Gaudenzio, N., Woolf, CJ., Tikoo, S., Jain, R., Penninger, JM., Cronin, SJF.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Sci Immunol","volume":"9","issue":"98","page":"eadh0545","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-23","doi":"10.1126\/sciimmunol.adh0545","first_author":null,"corresponding_authors":null},{"pmid":"39119041","title":"Three-dimensional structural and metric characterisation of cardioids.","abstract":"Exact three-dimensional (3D) structural information of developing organoids is key for optimising organoid generation and for studying experimental outcomes in organoid models. We set up a 3D imaging technique and studied complexly arranged native and experimentally challenged cardioids of two stages of remodelling. The imaging technique we employed is S-HREM (Scanning High Resolution Episcopic Microscopy), a variant of HREM, which captures multiple images of subsequently exposed surfaces of resin blocks and automatically combines them to large sized digital volume data of voxels sizes below 1&#xa0;&#x3bc;m<sup>3<\/sup>. We provide precise volumetric information of the examined specimens and their single components and comparisons between stages in terms of volume and micro- and macroanatomic structure. We describe the 3D arrangement and lining of different types of cavities and their changes between day 10 and day 14 and map the various cell types to their precise spatial and structural environment. Exemplarily, we conducted semiautomatic counts of nuclei. In cryo-injured cardioids, we examined the extension and composition of the injured areas. Our results demonstrate the high quality and the great potential of digital volume data produced with S-HREM. It also provides sound metric and structural information, which assists production of native and experimentally challenged left ventricle cardioids and interpretation of their structural remodelling.","authors":"Geyer, SH., Ceci Ginistrelli, L., Ilmer, T., Schwendt, KM., Mendjan, S., Weninger, WJ.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Front Cell Dev Biol","volume":"12","issue":null,"page":"1426043","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-10","doi":"10.3389\/fcell.2024.1426043","first_author":null,"corresponding_authors":null},{"pmid":"39125467","title":"Identification of Pathogenic Pathways for Recurrence of Focal Segmental Glomerulosclerosis after Kidney Transplantation.","abstract":"Primary focal segmental glomerulosclerosis (FSGS) is a disease of the podocytes and glomerulus, leading to nephrotic syndrome and progressive loss of renal function. One of the most serious aspects is its recurrence of disease in over 30% of patients following allogeneic kidney transplantation, leading to early graft loss. This research investigates the individual genetic predispositions and differences in the immune responses leading to recurrence of FSGS after transplantation. We performed exome sequencing on six patients with recurrent FSGS to identify variants in fifty-one genes and found significant variations in the alpha-2-macroglobulin (A2M). Immunoblotting was used to investigate effects of specific gene variants at the protein level. Further expression analysis identified A2M, exophilin 5 (EXPH5) and plectin (PLEC) as specific proteins linked to podocytes, endothelial cells, and the glomerulus. Subsequent protein array screening revealed the presence of non-HLA-specific antibodies, including TRIM21, after transplantation. Using Metascape for pathway and process enrichment analysis, we focused on the IL-17 signaling and chemotaxis pathways. ELISA measurements showed significantly elevated IL-17 levels in patients with recurrent FSGS (32.30 &#xb1; 9.12 pg\/mL) compared to individuals with other glomerular diseases (23.16 &#xb1; 2.49 pg\/mL; <i>p<\/i> &lt; 0.01) and healthy subjects (22.28 &#xb1; 0.94 pg\/mL; <i>p<\/i> &lt; 0.01), with no significant difference in plasma CCL2\/MCP-1 levels between groups. This study explores the molecular dynamics underlying recurrence of FSGS after transplantation, offering insights into potential biomarkers and therapeutic targets for the future development of individualized treatments for transplant patients.","authors":"Pajenda, S., Gerges, D., Wagner, L., O'Connell, D., Aiad, M., Imre, R., Mechtler, K., Zimprich, A., Schmidt, A., Sengoelge, G., Winnicki, W.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Diagnostics (Basel)","volume":"14","issue":"15","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-12","doi":"10.3390\/diagnostics14151591","first_author":null,"corresponding_authors":null},{"pmid":"39332412","title":"mTOR activity paces human blastocyst stage developmental progression.","abstract":"Many mammals can temporally uncouple conception from parturition by pacing down their development around the blastocyst stage. In mice, this dormant state is achieved by decreasing the activity of the growth-regulating mTOR signaling pathway. It is unknown whether this ability is conserved in mammals in general and in humans in particular. Here, we show that decreasing the activity of the mTOR signaling pathway induces human pluripotent stem cells (hPSCs) and blastoids to enter a dormant state with limited proliferation, developmental progression, and capacity to attach to endometrial cells. These in&#xa0;vitro assays show that, similar to other species, the ability to enter dormancy is active in human cells around the blastocyst stage and is reversible at both functional and molecular levels. The pacing of human blastocyst development has potential implications for reproductive therapies.","authors":"Iyer, DP., Khoei, HH., van der Weijden, VA., Kagawa, H., Pradhan, SJ., Novatchkova, M., McCarthy, A., Rayon, T., Simon, CS., Dunkel, I., Wamaitha, SE., Elder, K., Snell, P., Christie, L., Schulz, EG., Niakan, KK., Rivron, N., Bulut-Karslio\u011flu, A.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-09-27","doi":"10.1016\/j.cell.2024.08.048","first_author":null,"corresponding_authors":null},{"pmid":"39349545","title":"Murine neonatal cardiac regeneration depends on Insulin-like growth factor 1 receptor signaling.","abstract":"Unlike adult mammals, the hearts of neonatal mice possess the ability to completely regenerate from myocardial infarction (MI). This observation has sparked vast interest in deciphering the potentially lifesaving and morbidity-reducing mechanisms involved in neonatal cardiac regeneration. In mice, the regenerative potential is lost within the first week of life and coincides with a reduction of Insulin-like growth factor 1 receptor (Igf1r) expression in the heart. Igf1r is a well-known regulator of cardiomyocyte maturation and proliferation in neonatal mice. To test the role of Igf1r as a pivotal factor in cardiac regeneration, we knocked down (KD) Igf1r specifically in cardiomyocytes using recombinant adeno-associated virus (rAAV) delivery and troponin T promotor driven shRNAmirs. Cardiomyocyte specific Igf1r KD versus control mice were subjected to experimental MI by permanent ligation of the left anterior descending artery (LAD). Cardiac functional and morphological data were analyzed over a 21-day period. Neonatal Igf1r KD mice showed reduced systolic cardiac function and increased fibrotic cardiac remodeling 21&#xa0;days post injury. This cardiac phenotype was associated with reduced cardiomyocyte nuclei mitosis and decreased AKT and ERK phosphorylation in Igf1r KD, compared to control neonatal mouse hearts. Our in vivo murine data show that Igf1r KD shifts neonatal cardiac regeneration to a more adult-like scarring phenotype, identifying cardiomyocyte-specific Igf1r signaling as a crucial component of neonatal cardiac regeneration.","authors":"Schuetz, T., Dolejsi, T., Beck, E., Fugger, F., Bild, A., Duin, MT., Gavranovic-Novakovic, J., Hilbold, E., Hoffmann, T., Zuber, J., Bauer, A., Ruschitzka, F., B\u00e4r, C., Penninger, JM., Haubner, BJ.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Sci Rep","volume":"14","issue":"1","page":"22661","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-09-30","doi":"10.1038\/s41598-024-72783-4","first_author":null,"corresponding_authors":null},{"pmid":"39304390","title":"Engineering next generation vascularized organoids.","abstract":"Organoids are self-organizing 3D cell culture models that are valuable for studying the mechanisms underlying both development and disease in multiple species, particularly, in humans. These 3D engineered tissues can mimic the structure and function of human organs in vitro. Methods to generate organoids have substantially improved to better resemble, in various ways, their in vivo counterpart. One of the major limitations in current organoid models is the lack of a functional vascular compartment. Here we discuss methodological approaches to generating perfusable blood vessel networks in organoid systems. Inclusion of perfused vascular compartments markedly enhances the physiological relevance of organoid systems and is a critical step in the establishment of next generation, higher-complexity in vitro systems for use in developmental, clinical, and drug-development settings.","authors":"Werschler, N., Quintard, C., Nguyen, S., Penninger, J.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Atherosclerosis","volume":null,"issue":null,"page":"118529","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-09-20","doi":"10.1016\/j.atherosclerosis.2024.118529","first_author":null,"corresponding_authors":null},{"pmid":"39294368","title":"A polarized FGF8 source specifies frontotemporal signatures in spatially oriented cell populations of cortical assembloids.","abstract":"Organoids generating major cortical cell types in distinct compartments are used to study cortical development, evolution and disorders. However, the lack of morphogen gradients imparting cortical positional information and topography in current systems hinders the investigation of complex phenotypes. Here, we engineer human cortical assembloids by fusing an organizer-like structure expressing fibroblast growth factor 8 (FGF8) with an elongated organoid to enable the controlled modulation of FGF8 signaling along the longitudinal organoid axis. These polarized cortical assembloids mount a position-dependent transcriptional program that in part matches the in vivo rostrocaudal gene expression patterns and that is lost upon mutation in the FGFR3 gene associated with temporal lobe malformations and intellectual disability. By producing spatially oriented cell populations with signatures related to frontal and temporal area identity within individual assembloids, this model recapitulates in part the early transcriptional divergence embedded in the protomap and enables the study of cortical area-relevant alterations underlying human disorders.","authors":"Bosone, C., Castaldi, D., Burkard, TR., Guzman, SJ., Wyatt, T., Cheroni, C., Caporale, N., Bajaj, S., Bagley, JA., Li, C., Sorre, B., Villa, CE., Testa, G., Krenn, V., Knoblich, JA.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Nat Methods","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-09-18","doi":"10.1038\/s41592-024-02412-5","first_author":null,"corresponding_authors":null},{"pmid":"39179932","title":"Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development.","abstract":"Early B cell lymphopoiesis depends on E2A, Ebf1, Pax5 and Ikaros family members. In the present study, we used acute protein degradation in mice to identify direct target genes of these transcription factors in pro-B, small pre-B and immature B cells. E2A, Ebf1 and Pax5 predominantly function as transcriptional activators by inducing open chromatin at their target genes, have largely unique functions and are essential for early B cell maintenance. Ikaros and Aiolos act as dedicated repressors to cooperatively control early B cell development. The surrogate light-chain genes Igll1 and Vpreb1 are directly activated by Ebf1 and Pax5 in pro-B cells and directly repressed by Ikaros and Aiolos in small pre-B cells. Pax5 and E2A contribute to V(D)J recombination by activating Rag1, Rag2, Dntt, Irf4 and Irf8. Similar to Pax5, Ebf1 also represses the cohesin-release factor gene Wapl to mediate prolonged loop extrusion across the Igh locus. In summary, in vivo protein degradation has provided unprecedented insight into the control of early B cell lymphopoiesis by five transcription factors.","authors":"Fedl, AS., Tagoh, H., Gruenbacher, S., Sun, Q., Schenk, RL., Froussios, K., Jaritz, M., Busslinger, M., Schwickert, TA.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nat Immunol","volume":"25","issue":"9","page":"1663-1677","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-29","doi":"10.1038\/s41590-024-01933-7","first_author":null,"corresponding_authors":null},{"pmid":"39402138","title":"Epigenetic regulation by polycomb repressive complex 1 promotes cerebral cavernous malformations.","abstract":"Cerebral cavernous malformations (CCMs) are anomalies of the cerebral vasculature. Loss of the CCM proteins CCM1\/KRIT1, CCM2, or CCM3\/PDCD10 trigger a MAPK-Kr&#xfc;ppel-like factor 2 (KLF2) signaling cascade, which induces a pathophysiological pattern of gene expression. The downstream target genes that are activated by KLF2 are mostly unknown. Here we show that Chromobox Protein Homolog 7 (CBX7), component of the Polycomb Repressive Complex 1, contributes to pathophysiological KLF2 signaling during zebrafish cardiovascular development. CBX7\/cbx7a mRNA is strongly upregulated in lesions of CCM patients, and in human, mouse, and zebrafish CCM-deficient endothelial cells. The silencing or pharmacological inhibition of CBX7\/Cbx7a suppresses pathological CCM phenotypes in ccm2 zebrafish, CCM2-deficient HUVECs, and in a pre-clinical murine CCM3 disease model. Whole-transcriptome datasets from zebrafish cardiovascular tissues and human endothelial cells reveal a role of CBX7\/Cbx7a in the activation of KLF2 target genes including TEK, ANGPT1, WNT9, and endoMT-associated genes. Our findings uncover an intricate interplay in the regulation of Klf2-dependent biomechanical signaling by CBX7 in CCM. This work also provides insights for therapeutic strategies in the pathogenesis of CCM.","authors":"Pham, VC., R\u00f6del, CJ., Valentino, M., Malinverno, M., Paolini, A., M\u00fcnch, J., Pasquier, C., Onyeogaziri, FC., Lazovic, B., Girard, R., Koskim\u00e4ki, J., Hu\u00dfmann, M., Keith, B., Jachimowicz, D., Kohl, F., Hagelkruys, A., Penninger, JM., Schulte-Merker, S., Awad, IA., Hicks, R., Magnusson, PU., Faurobert, E., Pagani, M., Abdelilah-Seyfried, S.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"EMBO Mol Med","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-10-14","doi":"10.1038\/s44321-024-00152-9","first_author":null,"corresponding_authors":null},{"pmid":"39397771","title":"Schizophrenia-associated changes in neuronal subpopulations in the human midbrain.","abstract":"Dysfunctional GABAergic and dopaminergic neurons are thought to exist in the ventral midbrain of patients with schizophrenia, yet transcriptional changes underpinning these abnormalities have not yet been localized to specific neuronal subsets. In the ventral midbrain, control over dopaminergic activity is maintained by both excitatory (glutamate) and inhibitory (GABA) input neurons. To elucidate neuron pathology at the single-cell level, we characterized the transcriptional diversity of distinct NEUN+ populations in the human ventral midbrain and then tested for schizophrenia-associated changes in neuronal subset proportions and gene activity changes within neuronal subsets. Combining single nucleus RNA-sequencing with fluorescence-activated sorting of NEUN+ nuclei, we analysed 31 669 nuclei. Initially, we detected 18 transcriptionally distinct neuronal populations in the human ventral midbrain, including two 'mixed' populations. The presence of neuronal populations in the midbrain was orthogonally validated with immunohistochemical stainings. 'Mixed' populations contained nuclei expressing transcripts for vesicular glutamate transporter 2 (SLC17A6) and glutamate decarboxylase 2 (GAD2), but these transcripts were not typically co-expressed by the same nucleus. Upon more fine-grained subclustering of the two 'mixed' populations, 16 additional subpopulations were identified that were transcriptionally classified as excitatory or inhibitory. In the midbrains of individuals with schizophrenia, we observed potential differences in the proportions of two (sub)populations of excitatory neurons, two subpopulations of inhibitory neurons, one 'mixed' subpopulation, and one subpopulation of TH-expressing neurons. This may suggest that transcriptional changes associated with schizophrenia broadly affect excitatory, inhibitory, and dopamine neurons. We detected 99 genes differentially expressed in schizophrenia compared to controls within neuronal subpopulations identified from the two 'mixed' populations, with most (67) changes within small GABAergic neuronal subpopulations. Overall, single-nucleus transcriptomic analyses profiled a high diversity of GABAergic neurons in the human ventral midbrain, identified putative shifts in the proportion of neuronal subpopulations, and suggested dysfunction of specific GABAergic subpopulations in schizophrenia, providing directions for future research.","authors":"Alsema, AM., Puvogel, S., Kracht, L., Webster, MJ., Shannon Weickert, C., Eggen, BJL., Sommer, IEC.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Brain","volume":"148","issue":"4","page":"1374-1388","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-24","doi":"10.1093\/brain\/awae321","first_author":null,"corresponding_authors":null},{"pmid":"39387203","title":"Lineage tracing of Shh+ floor plate cells and dynamics of dorsal-ventral gene expression in the regenerating axolotl spinal cord.","abstract":"Both development and regeneration depend on signaling centers, which are sources of locally secreted tissue-patterning molecules. As many signaling centers are decommissioned before the end of embryogenesis, a fundamental question is how signaling centers can be re-induced later in life to promote regeneration after injury. Here, we use the axolotl salamander model (Ambystoma mexicanum) to address how the floor plate is assembled for spinal cord regeneration. The floor plate is an archetypal vertebrate signaling center that secretes Shh ligand and patterns neural progenitor cells during embryogenesis. Unlike mammals, axolotls continue to express floor plate genes (including Shh) and downstream dorsal-ventral patterning genes in their spinal cord throughout life, including at steady state. The parsimonious hypothesis that Shh+ cells give rise to functional floor plate cells for regeneration had not been tested. Using HCR in situ hybridization and mathematical modeling, we first quantified the behaviors of dorsal-ventral spinal cord domains, identifying significant increases in gene expression level and floor plate size during regeneration. Next, we established a transgenic axolotl to specifically label and fate map Shh+ cells in vivo. We found that labeled Shh+ cells gave rise to regeneration floor plate, and not to other neural progenitor domains, after tail amputation. Thus, despite changes in domain size and downstream patterning gene expression, Shh+ cells retain their floor plate identity during regeneration, acting as a stable cellular source for this regeneration signaling center in the axolotl spinal cord.","authors":"Arbanas, LI., Cura Costa, E., Chara, O., Otsuki, L., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Dev Growth Differ","volume":"66","issue":"8","page":"414-425","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-10-25","doi":"10.1111\/dgd.12945","first_author":null,"corresponding_authors":null},{"pmid":"39423812","title":"A conserved fertilization complex bridges sperm and egg in vertebrates.","abstract":"Fertilization, the basis for sexual reproduction, culminates in the binding and fusion of sperm and egg. Although several proteins are known to be crucial for this process in vertebrates, the molecular mechanisms remain poorly understood. Using an AlphaFold-Multimer screen, we identified the protein Tmem81 as part of a conserved trimeric sperm complex with the essential fertilization factors Izumo1 and Spaca6. We demonstrate that Tmem81 is essential for male fertility in zebrafish and mice. In line with trimer formation, we show that Izumo1, Spaca6, and Tmem81 interact in zebrafish sperm and that the human orthologs interact in&#xa0;vitro. Notably, complex formation creates the binding site for the egg fertilization factor Bouncer in zebrafish. Together, our work presents a comprehensive model for fertilization across vertebrates, where a conserved sperm complex binds to divergent egg proteins-Bouncer in fish and JUNO in mammals-to mediate sperm-egg interaction.","authors":"Deneke, VE., Blaha, A., Lu, Y., Suwita, JP., Draper, JM., Phan, CS., Panser, K., Schleiffer, A., Jacob, L., Humer, T., Stejskal, K., Krssakova, G., Roitinger, E., Handler, D., Kamoshita, M., Vance, TDR., Wang, X., Surm, JM., Moran, Y., Lee, JE., Ikawa, M., Pauli, A.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Cell","volume":"187","issue":"25","page":"7066-7078.e22","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2023.07.27.550750v1","articledate":"2024-12-13","doi":"10.1016\/j.cell.2024.09.035","first_author":null,"corresponding_authors":null},{"pmid":"39090757","title":"Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">39090757<\/PMID><DateCompleted><Year>2024<\/Year><Month>08<\/Month><Day>02<\/Day><\/DateCompleted><DateRevised><Year>2024<\/Year><Month>08<\/Month><Day>04<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>25<\/Volume><Issue>1<\/Issue><PubDate><Year>2024<\/Year><Month>Aug<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria.<\/ArticleTitle><Pagination><StartPage>204<\/StartPage><MedlinePgn>204<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">204<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13059-024-03346-z<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">DNA methylation in the form of 5-methylcytosine (5mC) is the most abundant base modification in animals. However, 5mC levels vary widely across taxa. While vertebrate genomes are hypermethylated, in most invertebrates, 5mC concentrates on constantly and highly transcribed genes (gene body methylation; GbM) and, in some species, on transposable elements (TEs), a pattern known as \"mosaic\". Yet, the role and developmental dynamics of 5mC and how these explain interspecies differences in DNA methylation patterns remain poorly understood, especially in Spiralia, a large clade of invertebrates comprising nearly half of the animal phyla.","authors":"Guynes, K., Sarre, LA., Carrillo-Baltodano, AM., Davies, BE., Xu, L., Liang, Y., Mart\u00edn-Zamora, FM., Hurd, PJ., de Mendoza, A., Mart\u00edn-Dur\u00e1n, JM.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Genome Biol","volume":"25","issue":"1","page":"204","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-02","doi":"10.1186\/s13059-024-03346-z","first_author":null,"corresponding_authors":null},{"pmid":"39196027","title":"Egr1 regulates regenerative senescence and cardiac repair.","abstract":"Senescence plays a key role in various physiological and pathological processes. We reported that injury-induced transient senescence correlates with heart regeneration, yet the multi-omics profile and molecular underpinnings of regenerative senescence remain obscure. Using proteomics and single-cell RNA sequencing, here we report the regenerative senescence multi-omic signature in the adult mouse heart and establish its role in neonatal heart regeneration and agrin-mediated cardiac repair in adult mice. We identified early growth response protein 1 (Egr1) as a regulator of regenerative senescence in both models. In the neonatal heart, Egr1 facilitates angiogenesis and cardiomyocyte proliferation. In adult hearts, agrin-induced senescence and repair require Egr1, activated by the integrin-FAK-ERK-Akt1 axis in cardiac fibroblasts. We also identified cathepsins as injury-induced senescence-associated secretory phenotype components that promote extracellular matrix degradation and potentially assist in reducing fibrosis. Altogether, we uncovered the molecular signature and functional benefits of regenerative senescence during heart regeneration, with Egr1 orchestrating the process.","authors":"Zhang, L., Elkahal, J., Wang, T., Rimmer, R., Genzelinakh, A., Bassat, E., Wang, J., Perez, D., Kain, D., Lendengolts, D., Winkler, R., Bueno-Levy, H., Umansky, KB., Mishaly, D., Shakked, A., Miyara, S., Sarusi-Portuguez, A., Goldfinger, N., Prior, A., Morgenstern, D., Levin, Y., Addadi, Y., Li, B., Rotter, V., Katz, U., Tanaka, EM., Krizhanovsky, V., Sarig, R., Tzahor, E.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nat Cardiovasc Res","volume":"3","issue":"8","page":"915-932","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-28","doi":"10.1038\/s44161-024-00493-1","first_author":null,"corresponding_authors":null},{"pmid":"39521793","title":"Non-targeted N-glycome profiling reveals multiple layers of organ-specific diversity in mice.","abstract":"N-glycosylation is one of the most common protein modifications in eukaryotes, with immense importance at the molecular, cellular, and organismal level. Accurate and reliable N-glycan analysis is essential to obtain a systems-wide understanding of fundamental biological processes. Due to the structural complexity of glycans, their analysis is still highly challenging. Here we make publicly available a consistent N-glycome dataset of 20 different mouse tissues and demonstrate a multimodal data analysis workflow that allows for unprecedented depth and coverage of N-glycome features. This highly scalable, LC-MS\/MS data-driven method integrates the automated identification of N-glycan spectra, the application of non-targeted N-glycome profiling strategies and the isomer-sensitive analysis of glycan structures. Our delineation of critical sub-structural determinants and glycan isomers across the mouse N-glycome uncovered tissue-specific glycosylation patterns, the expression of non-canonical N-glycan structures and highlights multiple layers of N-glycome complexity that derive from organ-specific regulations of glycobiological pathways.","authors":"Helm, J., Mereiter, S., Oliveira, T., Gattinger, A., Markovitz, DM., Penninger, JM., Altmann, F., Stadlmann, J.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"9725","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-11-09","doi":"10.1038\/s41467-024-54134-z","first_author":null,"corresponding_authors":null},{"pmid":"39596877","title":"The Role of Epigenetic Switches in Polyphenism Control: Implications from a Nematode Model for the Developmental Regulation of Alternative Phenotypes.","abstract":"Polyphenisms, the capability of organisms to form two or more alternative phenotypes in response to environmental variation, are prevalent in nature. However, associated molecular mechanisms and potential general principles of polyphenisms among major organismal groups remain currently unknown. This review focuses on an emerging model system for developmental plasticity and polyphenism research, the nematode <i>Pristionchus pacificus<\/i> and explores mechanistic insight obtained through unbiased genetic, experimental and natural variation studies. Resulting findings identify a central role for epigenetic switches in the environmental control of alternative phenotypes and their micro-and macroevolution. Several features observed in <i>P. pacificus<\/i> are shared with insects and plants and might become general principles for the control of polyphenisms during development.","authors":"Wighard, S., Sommer, RJ.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Biology (Basel)","volume":"13","issue":"11","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-11-27","doi":"10.3390\/biology13110922","first_author":null,"corresponding_authors":null},{"pmid":"39572529","title":"Genome-wide profiling of DNA repair proteins in single cells.","abstract":"Accurate repair of DNA damage is critical for maintenance of genomic integrity and cellular viability. Because damage occurs non-uniformly across the genome, single-cell resolution is required for proper interrogation, but sensitive detection has remained challenging. Here, we present a comprehensive analysis of repair protein localization in single human cells using DamID and ChIC sequencing techniques. This study reports genome-wide binding profiles in response to DNA double-strand breaks induced by AsiSI, and explores variability in genomic damage locations and associated repair features in the context of spatial genome organization. By unbiasedly detecting repair factor localization, we find that repair proteins often occupy entire topologically associating domains, mimicking variability in chromatin loop anchoring. Moreover, we demonstrate the formation of multi-way chromatin hubs in response to DNA damage. Notably, larger hubs show increased coordination of repair protein binding, suggesting a preference for cooperative repair mechanisms. Together, our work offers insights into the heterogeneous processes underlying genome stability in single cells.","authors":"de Luca, KL., Rullens, PMJ., Karpinska, MA., de Vries, SS., Gacek-Matthews, A., Pongor, LS., Legube, G., Jachowicz, JW., Oudelaar, AM., Kind, J.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"9918","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-11-21","doi":"10.1038\/s41467-024-54159-4","first_author":null,"corresponding_authors":null},{"pmid":"39248702","title":"Zongertinib (BI 1810631), an Irreversible HER2 TKI, Spares EGFR Signaling and Improves Therapeutic Response in Preclinical Models and Patients with HER2-Driven Cancers.","abstract":"Mutations in ERBB2 (encoding HER2) occur in 2% to 4% of non-small cell lung cancer (NSCLC) and confer poor prognosis. ERBB-targeting tyrosine kinase inhibitors, approved for treating other HER2-dependent cancers, are ineffective in HER2-mutant NSCLC due to dose-limiting toxicities or suboptimal potency. We report the discovery of zongertinib (BI 1810631), a covalent HER2 inhibitor. Zongertinib potently and selectively blocks HER2, while sparing EGFR, and inhibits the growth of cells dependent on HER2 oncogenic driver events, including HER2-dependent human cancer cells resistant to trastuzumab deruxtecan. Zongertinib displays potent antitumor activity in HER2-dependent human NSCLC xenograft models and enhances the activities of antibody-drug conjugates and KRASG12C inhibitors without causing obvious toxicities. The preclinical efficacy of zongertinib translates in objective responses in patients with HER2-dependent tumors, including cholangiocarcinoma (SDC4-NRG1 fusion) and breast cancer (V777L HER2 mutation), thus supporting the ongoing clinical development of zongertinib. Significance: HER2-mutant NSCLC poses a challenge in the clinic due to limited options for targeted therapies. Pan-ERBB blockers are limited by wild-type EGFR-mediated toxicity. Zongertinib is a highly potent and wild-type EGFR-sparing HER2 inhibitor that is active in HER2-driven tumors in the preclinical and clinical settings.","authors":"Wilding, B., Woelflingseder, L., Baum, A., Chylinski, K., Vainorius, G., Gibson, N., Waizenegger, IC., Gerlach, D., Augsten, M., Spreitzer, F., Shirai, Y., Ikegami, M., Tilandyov\u00e1, S., Scharn, D., Pearson, MA., Popow, J., Obenauf, AC., Yamamoto, N., Kondo, S., Opdam, FL., Bruining, A., Kohsaka, S., Kraut, N., Heymach, JV., Solca, F., Neum\u00fcller, RA.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Cancer Discov","volume":"15","issue":"1","page":"119-138","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-01-13","doi":"10.1158\/2159-8290.CD-24-0306","first_author":null,"corresponding_authors":null},{"pmid":"39604727","title":"Cancer cells impair monocyte-mediated T cell stimulation to evade immunity.","abstract":"The tumour microenvironment is programmed by cancer cells and substantially influences anti-tumour immune responses<sup>1,2<\/sup>. Within the tumour microenvironment, CD8<sup>+<\/sup> T&#x2009;cells undergo full effector differentiation and acquire cytotoxic anti-tumour functions in specialized niches<sup>3-7<\/sup>. Although interactions with type&#x2009;1 conventional dendritic cells have been implicated in this process<sup>3-5,8-10<\/sup>, the underlying cellular players and molecular mechanisms remain incompletely understood. Here we show that inflammatory monocytes can adopt a pivotal role in intratumoral T&#x2009;cell stimulation. These cells express Cxcl9, Cxcl10 and Il15, but in contrast to type&#x2009;1 conventional dendritic cells, which cross-present antigens, inflammatory monocytes obtain and present peptide-major histocompatibility complex class&#x2009;I complexes from tumour cells through 'cross-dressing'. Hyperactivation of MAPK signalling in cancer cells hampers this process by coordinately blunting the production of type&#x2009;I interferon (IFN-I) cytokines and inducing the secretion of prostaglandin&#x2009;E<sub>2<\/sub> (PGE<sub>2<\/sub>), which impairs the inflammatory monocyte state and intratumoral T&#x2009;cell stimulation. Enhancing IFN-I cytokine production and blocking PGE<sub>2<\/sub> secretion restores this process and re-sensitizes tumours to T&#x2009;cell-mediated immunity. Together, our work uncovers a central role of inflammatory monocytes in intratumoral T&#x2009;cell stimulation, elucidates how oncogenic signalling disrupts T&#x2009;cell responses through counter-regulation of PGE<sub>2<\/sub> and IFN-I, and proposes rational combination therapies to enhance immunotherapies.","authors":"Elewaut, A., Estivill, G., Bayerl, F., Castillon, L., Novatchkova, M., Pottendorfer, E., Hoffmann-Haas, L., Sch\u00f6nlein, M., Nguyen, TV., Lauss, M., Andreatta, F., Vulin, M., Krecioch, I., Bayerl, J., Pedde, AM., Fabre, N., Holstein, F., Cronin, SM., Rieser, S., Laniti, DD., Barras, D., Coukos, G., Quek, C., Bai, X., Mu\u00f1oz I Ordo\u00f1o, M., Wiesner, T., Zuber, J., J\u00f6nsson, G., B\u00f6ttcher, JP., Vanharanta, S., Obenauf, AC.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nature","volume":"637","issue":"8046","page":"716-725","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-26","doi":"10.1038\/s41586-024-08257-4","first_author":null,"corresponding_authors":null},{"pmid":"39653126","title":"A framework for neural organoids, assembloids and transplantation studies.","abstract":"As the field of neural organoids and assembloids rapidly expands, there is an emergent need for guidance and advice on designing, conducting and reporting experiments to increase the reproducibility and utility of these models. Here, our consortium- representing specialized laboratories from around the world- presents a framework for the experimental process that ranges from ensuring the quality and integrity of human pluripotent stem cells to characterizing and manipulating neural cells in vitro, and from transplantation techniques to considerations for modeling human development, evolution, and disease. As with all scientific endeavors, we advocate for rigorous experimental designs tailored to explicit scientific questions, and transparent methodologies and data sharing, to provide useful knowledge for both current research practices and for developing regulatory standards.","authors":"Pa\u0219ca, SP., Arlotta, P., Bateup, HS., Camp, JG., Cappello, S., Gage, FH., Knoblich, JA., Kriegstein, AR., Lancaster, MA., Ming, GL., Novarino, G., Okano, H., Parmar, M., Park, IH., Reiner, O., Song, H., Studer, L., Takahashi, J., Temple, S., Testa, G., Treutlein, B., Vaccarino, FM., Vanderhaeghen, P., Young-Pearse, T.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-12-09","doi":"10.1038\/s41586-024-08487-6","first_author":null,"corresponding_authors":null},{"pmid":"39681701","title":"CRISPR-StAR enables high-resolution genetic screening in complex in vivo models.","abstract":"Pooled genetic screening with CRISPR-Cas9 has enabled genome-wide, high-resolution mapping of genes to phenotypes, but assessing the effect of a given genetic perturbation requires evaluation of each single guide RNA (sgRNA) in hundreds of cells to counter stochastic genetic drift and obtain robust results. However, resolution is limited in complex, heterogeneous models, such as organoids or tumors transplanted into mice, because achieving sufficient representation requires impractical scaling. This is due to bottleneck effects and biological heterogeneity of cell populations. Here we introduce CRISPR-StAR, a screening method that uses internal controls generated by activating sgRNAs in only half the progeny of each cell subsequent to re-expansion of the cell clone. Our method overcomes both intrinsic and extrinsic heterogeneity as well as genetic drift in bottlenecks by generating clonal, single-cell-derived intrinsic controls. We use CRISPR-StAR to identify in-vivo-specific genetic dependencies in a genome-wide screen in mouse melanoma. Benchmarking against conventional screening demonstrates the improved data quality provided by this technology.","authors":"Uijttewaal, ECH., Lee, J., Sell, AC., Botay, N., Vainorius, G., Novatchkova, M., Baar, J., Yang, J., Potzler, T., van der Leij, S., Lowden, C., Sinner, J., Elewaut, A., Gavrilovic, M., Obenauf, A., Schramek, D., Elling, U.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Nat Biotechnol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-12-16","doi":"10.1038\/s41587-024-02512-9","first_author":null,"corresponding_authors":null},{"pmid":"39755121","title":"The efflux pump ABCC1\/MRP1 constitutively restricts PROTAC sensitivity in cancer cells.","abstract":"Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that induce selective protein degradation by linking an E3 ubiquitin ligase enzyme to a target protein. This approach allows scope for targeting \"undruggable\" proteins, and several PROTACs have reached the stage of clinical candidates. However, the roles of cellular transmembrane transporters in PROTAC uptake and efflux remain underexplored. Here, we utilized transporter-focused genetic screens to identify the ATP-binding cassette transporter ABCC1\/MRP1 as a key PROTAC resistance factor. Unlike the previously identified inducible PROTAC exporter ABCB1\/MDR1, ABCC1 is highly expressed among cancers of various origins and constitutively restricts PROTAC bioavailability. Moreover, in a genome-wide PROTAC resistance screen, we identified candidates involved in processes such as ubiquitination, mTOR signaling, and apoptosis as genetic factors involved in PROTAC resistance. In summary, our findings reveal ABCC1 as a crucial constitutively active efflux pump limiting PROTAC efficacy in various cancer cells, offering insights for overcoming drug resistance.","authors":"Wolf, G., Craigon, C., Teoh, ST., Essletzbichler, P., Onstein, S., Cassidy, D., Uijttewaal, ECH., Dvorak, V., Cao, Y., Bensimon, A., Elling, U., Ciulli, A., Superti-Furga, G.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Cell Chem Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-01-04","doi":"10.1016\/j.chembiol.2024.11.009","first_author":null,"corresponding_authors":null},{"pmid":"39743223","title":"A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities.","abstract":"Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated in mass spectrometry-based proteomics laboratories. However, the lack of standardized quality control practices across laboratories poses challenges for data comparability and reproducibility. In response, we conducted a harmonization study within proteomics laboratories of the Core for Life alliance with the aim of establishing a common quality control framework, which facilitates comprehensive quality assessment and identification of potential sources of performance drift. Through collaborative efforts, we developed a consensus quality control standard for longitudinal assessment and adopted common processing software. We generated a 4-year longitudinal data set from multiple instruments and laboratories, which enabled us to assess intra- and interlaboratory variability, to identify causes of performance drift, and to establish community reference values for several quality control parameters. Our study enhances data comparability and reliability and fosters a culture of collaboration and continuous improvement within the proteomics community to ensure the integrity of proteomics data.","authors":"Chiva, C., Olivella, R., Staes, A., Mendes Maia, T., Panse, C., Stejskal, K., Douch\u00e9, T., Lombard, B., Schuhmann, A., Loew, D., Mechtler, K., Matondo, M., Rettel, M., Helm, D., Impens, F., Devos, S., Shevchenko, A., Nanni, P., Sabid\u00f3, E.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"J Proteome Res","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-01-01","doi":"10.1021\/acs.jproteome.4c00359","first_author":null,"corresponding_authors":null},{"pmid":"39718766","title":"Rnalib: a Python library for custom transcriptomics analyses.","abstract":"on Status=\"Publisher\" Owner=\"NLM\"><PMID Version=\"1\">39718766<\/PMID><DateRevised><Year>2024<\/Year><Month>12<\/Month><Day>24<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1367-4811<\/ISSN><JournalIssue CitedMedium=\"Internet\"><PubDate><Year>2024<\/Year><Month>Dec<\/Month><Day>24<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Rnalib: a Python library for custom transcriptomics analyses.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">btae751<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/bioinformatics\/btae751<\/ELocationID><Abstract><AbstractText Label=\"MOTIVATION\" NlmCategory=\"BACKGROUND\">The efficient and reproducible analysis of high-throughput sequencing datasets necessitates the development of methodical and robust computational pipelines that integrate established and bespoke bioinformatics analysis tools, often written in high-level programming languages such as Python. Despite the increasing availability of programming libraries for genomics, there is a noticeable lack of tools specifically focused on transcriptomics. Key tasks in this area include the association of gene features (e.g., transcript isoforms, introns or untranslated regions) with relevant subsections of (large) genomics datasets across diverse data formats, as well as efficient querying of these data based on genomic locations and annotation attributes.","authors":"Popitsch, N., Ameres, SL.","publication_status":"aheadofprint","journalpubyear":"2024","journaltitle":"Bioinformatics","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-12-24","doi":"10.1093\/bioinformatics\/btae751","first_author":null,"corresponding_authors":null},{"pmid":"39702463","title":"Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C\/D complex.","abstract":"The field of crosslinking mass spectrometry has seen substantial advancements over the past decades, enabling the structural analysis of proteins and protein complexes and serving as a powerful tool in protein-protein interaction studies. However, data analysis of large non-cleavable crosslink studies is still a mostly unsolved problem due to its n-squared complexity. We here introduce an algorithm for the identification of non-cleavable crosslinks implemented in our crosslinking search engine MS Annika that is based on sparse matrix multiplication and allows for proteome-wide searches on commodity hardware. We compare our algorithm to other state-of-the-art crosslinking search engines commonly used in the field and conclude that MS Annika unifies high sensitivity, accurate FDR estimation and computational performance, outperforming competing tools. Application of this algorithm enabled us to employ a proteome-wide search of C. elegans nuclei samples, where we were able to uncover previously unknown protein interactions and conclude a comprehensive structural analysis that provides a detailed view of the Box C\/D complex. Moreover, our algorithm will enable researchers to conduct similar studies that were previously unfeasible.","authors":"Birklbauer, MJ., M\u00fcller, F., Geetha, SS., Matzinger, M., Mechtler, K., Dorfer, V.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Commun Chem","volume":"7","issue":"1","page":"300","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-01-04","doi":"10.1038\/s42004-024-01386-x","first_author":null,"corresponding_authors":null},{"pmid":"39633049","title":"RANK drives structured intestinal epithelial expansion during pregnancy.","abstract":"During reproduction, multiple species such as insects and all mammals undergo extensive physiological and morphological adaptions to ensure health and survival of the mother and optimal development of the offspring. Here we report that the intestinal epithelium undergoes expansion during pregnancy and lactation in mammals. This enlargement of the intestinal surface area results in a novel geometry of expanded villi. Receptor activator of nuclear factor-&#x3ba;&#x392; (RANK, encoded by TNFRSF11A) and its ligand RANKL were identified as a molecular pathway involved in this villous expansion of the small intestine in vivo in mice and in intestinal mouse and human organoids. Mechanistically, RANK-RANKL protects gut epithelial cells from cell death and controls the intestinal stem cell niche through BMP receptor signalling, resulting in the elongation of villi and a prominent increase in the intestinal surface. As a transgenerational consequence, babies born to female mice that lack Rank in the intestinal epithelium show reduced weight and develop glucose intolerance after metabolic stress. Whereas gut epithelial remodelling in pregnancy\/lactation is reversible, constitutive expression of an active form of RANK is sufficient to drive intestinal expansion followed by loss of villi and stem cells, and prevents the formation of Apc<sup>min<\/sup>-driven small intestinal stem cell tumours. These data identify RANK-RANKL as a pathway that drives intestinal epithelial expansion in pregnancy\/lactation, one of the most elusive and fundamental tissue remodelling events in mammalian life history and evolution.","authors":"Onji, M., Sigl, V., Lendl, T., Novatchkova, M., Ullate-Agote, A., Andersson-Rolf, A., Kozieradzki, I., Koglgruber, R., Pai, TP., Lichtscheidl, D., Nayak, K., Zilbauer, M., Carranza Garc\u00eda, NA., Sievers, LK., Falk-Paulsen, M., Cronin, SJF., Hagelkruys, A., Sawa, S., Osborne, LC., Rosenstiel, P., Pasparakis, M., Ruland, J., Takayanagi, H., Clevers, H., Koo, BK., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nature","volume":"637","issue":"8044","page":"156-166","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-12-23","doi":"10.1038\/s41586-024-08284-1","first_author":null,"corresponding_authors":null},{"pmid":"39820751","title":"Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity.","abstract":"Despite significant advancements in sample preparation, instrumentation and data analysis, single-cell proteomics is currently limited by proteomic depth and quantitative performance. Here we demonstrate highly improved depth of proteome coverage as well as accuracy and precision for quantification of ultra-low input amounts. Using a tailored library, we identify up to 7,400 protein groups from as little as 250&#x2009;pg of HeLa cell peptides at a throughput of 50 samples per day. Using a two-proteome mix, we check for optimal parameters of quantification and show that fold change differences of 2 can still be successfully determined at single-cell-level inputs. Eventually, we apply our workflow to A549 cells, yielding a proteome coverage ranging from 1,801 to a maximum of &gt;5,300 protein groups from a single cell depending on cell size and search strategy used, which allows for the study of dependencies between cell size and cell cycle phase. Additionally, our workflow enables us to distinguish between in vitro analogs of two human blastocyst lineages: naive human pluripotent stem cells (epiblast) and trophectoderm-like cells. Our data harmoniously align with transcriptomic data, indicating that single-cell proteomics possesses the capability to identify biologically relevant differences within the blastocyst.","authors":"Bubis, JA., Arrey, TN., Damoc, E., Delanghe, B., Slovakova, J., Sommer, TM., Kagawa, H., Pichler, P., Rivron, N., Mechtler, K., Matzinger, M.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nat Methods","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-01-17","doi":"10.1038\/s41592-024-02559-1","first_author":null,"corresponding_authors":null},{"pmid":"39813297","title":"Multi-tissue characterization of the constitutive heterochromatin proteome in Drosophila identifies a link between satellite DNA organization and transposon repression.","abstract":"Noncoding satellite DNA repeats are abundant at the pericentromeric heterochromatin of eukaryotic chromosomes. During interphase, sequence-specific DNA-binding proteins cluster these repeats from multiple chromosomes into nuclear foci known as chromocenters. Despite the pivotal role of chromocenters in cellular processes like genome encapsulation and gene repression, the associated proteins remain incompletely characterized. Here, we use 2 satellite DNA-binding proteins, D1 and Prod, as baits to characterize the chromocenter-associated proteome in Drosophila embryos, ovaries, and testes through quantitative mass spectrometry. We identify D1- and Prod-associated proteins, including known heterochromatin proteins as well as proteins previously unlinked to satellite DNA or chromocenters, thereby laying the foundation for a comprehensive understanding of cellular functions enabled by satellite DNA repeats and their associated proteins. Interestingly, we find that multiple components of the transposon-silencing piRNA pathway are associated with D1 and Prod in embryos. Using genetics, transcriptomics, and small RNA profiling, we show that flies lacking D1 during embryogenesis exhibit transposon expression and gonadal atrophy as adults. We further demonstrate that this gonadal atrophy can be rescued by mutating the checkpoint kinase, Chk2, which mediates germ cell arrest in response to transposon mobilization. Thus, we reveal that a satellite DNA-binding protein functions during embryogenesis to silence transposons, in a manner that is heritable across later stages of development.","authors":"Chavan, A., Skrutl, L., Uliana, F., Pfister, M., Br\u00e4ndle, F., Tirian, L., Baptista, D., Handler, D., Burke, D., Sintsova, A., Beltrao, P., Brennecke, J., Jagannathan, M.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"PLoS Biol","volume":"23","issue":"1","page":"e3002984","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-01-15","doi":"10.1371\/journal.pbio.3002984","first_author":null,"corresponding_authors":null},{"pmid":"39946532","title":"Identification of a protective antigen reveals the trade-off between iron acquisition and antigen exposure in a global fungal pathogen.","abstract":"Systemic infections caused by <i>Cryptococcus<\/i> claim over 161,000 lives annually, with global mortality rate close to 70% despite antifungal therapies. Currently, no vaccine is available. To develop an effective multivalent vaccine against this free-living opportunistic eukaryotic pathogen, it is critical to identify protective antigens. We previously discovered <i>ZNF2<\/i><sup>oe<\/sup> strains elicit protective host immune responses and increase the abundance of antigens present in the capsule, which is required for its immunoprotection. Capsule is a defining feature of <i>Cryptococcus<\/i> species and composed of polysaccharides and mannoproteins. Here, we found increased levels of exposed mannoproteins in <i>ZNF2<\/i><sup>oe<\/sup> cells. As mannoproteins are the primary components recognized by anticryptococcal cell-mediated immune responses and few have been characterized, we systemically screened all 49 predicted GPI-mannoproteins in <i>Cryptococcus neoformans<\/i> for enhanced host recognition. We identified those highly present in <i>ZNF2<\/i><sup>oe<\/sup> cells and found Cig1 to be a protective antigen against cryptococcosis either as a recombinant protein vaccine or an mRNA vaccine. Cig1 is induced by iron limitation and is highly expressed by this fungus in infected mice and in patients with cryptococcal meningitis. Remarkably, iron restriction by the host induces cryptococcal cells to express iron-uptake proteins including Cig1, which act as cryptococcal antigens and in turn enhance host detection. Our results highlight an arms race between the pathogen and the host centered on iron competition, and the trade-off between cryptococcal iron acquisition and antigen exposure. These findings demonstrate the potential of leveraging this host-pathogen interaction for vaccine development.","authors":"Li, Y., Pham, T., Hipsher, K., Lee, CWJ., Jiao, J., Penninger, JM., Kronstad, JW., Fan, Y., Zhao, Y., Ambati, S., Meagher, RB., Xie, X., Lin, X.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Proc Natl Acad Sci U S A","volume":"122","issue":"7","page":"e2420898122","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-02-13","doi":"10.1073\/pnas.2420898122","first_author":null,"corresponding_authors":null},{"pmid":"36423299","title":"Scaling up complexity in synthetic developmental biology.","abstract":"The application of synthetic biology approaches to study development opens the possibility to build and manipulate developmental processes to understand them better. Researchers have reconstituted fundamental developmental processes, such as cell patterning and sorting, by engineering gene circuits in vitro. Moreover, new tools have been created that allow for the control of developmental processes in more complex organoids and embryos. Synthetic approaches allow testing of which components are sufficient to reproduce a developmental process and under which conditions as well as what effect perturbations have on other processes. We envision that the future of synthetic developmental biology requires an increase in the diversity of available tools and further efforts to combine multiple developmental processes into one system.","authors":"Mart\u00ednez-Ara, G., Stapornwongkul, KS., Ebisuya, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Science","volume":"378","issue":"6622","page":"864-868","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-11-30","doi":"10.1126\/science.add9666","first_author":null,"corresponding_authors":null},{"pmid":"33767424","title":"Generation of extracellular morphogen gradients: the case for diffusion.","abstract":"Cells within developing tissues rely on morphogens to assess positional information. Passive diffusion is the most parsimonious transport model for long-range morphogen gradient formation but does not, on its own, readily explain scaling, robustness and planar transport. Here, we argue that diffusion is sufficient to ensure robust morphogen gradient formation in a variety of tissues if the interactions between morphogens and their extracellular binders are considered. A current challenge is to assess how the affinity for extracellular binders, as well as other biophysical and cell biological parameters, determines gradient dynamics and shape in a diffusion-based transport system. Technological advances in genome editing, tissue engineering, live imaging and in vivo biophysics are now facilitating measurement of these parameters, paving the way for mathematical modelling and a quantitative understanding of morphogen gradient formation and modulation.","authors":"Stapornwongkul, KS., Vincent, JP.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Rev Genet","volume":"22","issue":"6","page":"393-411","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-27","doi":"10.1038\/s41576-021-00342-y","first_author":null,"corresponding_authors":null},{"pmid":"33060356","title":"Patterning and growth control in vivo by an engineered GFP gradient.","abstract":"Morphogen gradients provide positional information during development. To uncover the minimal requirements for morphogen gradient formation, we have engineered a synthetic morphogen in <i>Drosophila<\/i> wing primordia. We show that an inert protein, green fluorescent protein (GFP), can form a detectable diffusion-based gradient in the presence of surface-associated anti-GFP nanobodies, which modulate the gradient by trapping the ligand and limiting leakage from the tissue. We next fused anti-GFP nanobodies to the receptors of Dpp, a natural morphogen, to render them responsive to extracellular GFP. In the presence of these engineered receptors, GFP could replace Dpp to organize patterning and growth in vivo. Concomitant expression of glycosylphosphatidylinositol (GPI)-anchored nonsignaling receptors further improved patterning, to near-wild-type quality. Theoretical arguments suggest that GPI anchorage could be important for these receptors to expand the gradient length scale while at the same time reducing leakage.","authors":"Stapornwongkul, KS., de Gennes, M., Cocconi, L., Salbreux, G., Vincent, JP.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Science","volume":"370","issue":"6514","page":"321-327","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-27","doi":"10.1126\/science.abb8205","first_author":null,"corresponding_authors":null},{"pmid":"39491308","title":"Local cellular interactions during the self-organization of stem cells.","abstract":"Stem cell models for early mammalian development offer new experimental opportunities to access spatio-temporal details of the cell-cell interactions that govern cell differentiation and tissue patterning. This review summarizes recent studies that have used stem cell models to investigate the spatial range of developmental cell-cell communication systems. A key message from these works is that important biochemical signals for cell differentiation in these systems, such as Nodal and fibroblast growth factors (FGFs), often act over short distances of only a few cell diameters. The formation of long-range patterns at the tissue scale associated with these signals then results from signal relays and cell rearrangements. The modular view of differentiation and patterning emerging from research on stem cell models can offer a fresh perspective on the corresponding processes in the embryo.","authors":"Schr\u00f6ter, C., Stapornwongkul, KS., Trivedi, V.","publication_status":"aheadofprint","journalpubyear":"2023","journaltitle":"Curr Opin Cell Biol","volume":"85","issue":null,"page":"102261","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-11-04","doi":"10.1016\/j.ceb.2023.102261","first_author":null,"corresponding_authors":null},{"pmid":"27752079","title":"DIXDC1 contributes to psychiatric susceptibility by regulating dendritic spine and glutamatergic synapse density via GSK3 and Wnt\/&#x3b2;-catenin signaling.","abstract":"Mice lacking DIX domain containing-1 (DIXDC1), an intracellular Wnt\/&#x3b2;-catenin signal pathway protein, have abnormal measures of anxiety, depression and social behavior. Pyramidal neurons in these animals' brains have reduced dendritic spines and glutamatergic synapses. Treatment with lithium or a glycogen synthase kinase-3 (GSK3) inhibitor corrects behavioral and neurodevelopmental phenotypes in these animals. Analysis of DIXDC1 in over 9000 cases of autism, bipolar disorder and schizophrenia reveals higher rates of rare inherited sequence-disrupting single-nucleotide variants (SNVs) in these individuals compared with psychiatrically unaffected controls. Many of these SNVs alter Wnt\/&#x3b2;-catenin signaling activity of the neurally predominant DIXDC1 isoform; a subset that hyperactivate this pathway cause dominant neurodevelopmental effects. We propose that rare missense SNVs in DIXDC1 contribute to psychiatric pathogenesis by reducing spine and glutamatergic synapse density downstream of GSK3 in the Wnt\/&#x3b2;-catenin pathway.","authors":"Martin, PM., Stanley, RE., Ross, AP., Freitas, AE., Moyer, CE., Brumback, AC., Iafrati, J., Stapornwongkul, KS., Dominguez, S., Kivim\u00e4e, S., Mulligan, KA., Pirooznia, M., McCombie, WR., Potash, JB., Zandi, PP., Purcell, SM., Sanders, SJ., Zuo, Y., Sohal, VS., Cheyette, BNR.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Mol Psychiatry","volume":"23","issue":"2","page":"467-475","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-15","doi":"10.1038\/mp.2016.184","first_author":null,"corresponding_authors":null},{"pmid":"39947174","title":"FakET: Simulating cryo-electron tomograms with neural style transfer.","abstract":"In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750&#xd7;, uses 33&#xd7; less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https:\/\/github.com\/paloha\/faket\/.","authors":"Harar, P., Herrmann, L., Grohs, P., Haselbach, D.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Structure","volume":"33","issue":"4","page":"820-827.e4","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-07","doi":"10.1016\/j.str.2025.01.020","first_author":null,"corresponding_authors":null},{"pmid":"39799992","title":"The UBR Domain of Plant Ubr1 Homolog PRT6 Accommodates Basic and Hydrophobic Amino Termini for Substrate Recognition.","abstract":"N-degrons are amino-terminal degradation signals. Non-acetylated first residues with bulky side chains were the first discovered N-degrons. In yeast, their ability to destabilize a protein depends on ubiquitin ligase Ubr1, which has a binding site for basic first residues, the UBR box, and one for hydrophobic first residues, the N domain. We investigated PRT6, the Arabidopsis homolog of Ubr1, by expression in a yeast strain devoid of Ubr1. Phylogenetic analysis and structure prediction indicate that PRT6 lacks the N domain and thus should not accept hydrophobic N-degrons. However, we show that PRT6 mediates the turnover of proteins with Leu, Phe, Tyr and Trp as the first residue. By functional analysis in the heterologous host, we show that the PRT6 UBR box can accommodate these N-degrons. The data indicate a surprising evolutionary flexibility of the UBR box that may also be found in UBR box proteins of other organisms.","authors":"Rudi, O., Hodakova, Z., Farias Saad, C., Winter, N., Grishkovskaya, I., B\u00f6hm, J., Jarck, G., Schleiffer, A., Haselbach, D., Bachmair, A.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"J Mol Biol","volume":"437","issue":"4","page":"168939","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-02-07","doi":"10.1016\/j.jmb.2025.168939","first_author":null,"corresponding_authors":null},{"pmid":"39209816","title":"The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.","abstract":"The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities.","authors":"Kofler, L., Grundmann, L., Gerhalter, M., Prattes, M., Merl-Pham, J., Zisser, G., Grishkovskaya, I., Hodirnau, VV., Vareka, M., Breinbauer, R., Hauck, SM., Haselbach, D., Bergler, H.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"7511","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-08-29","doi":"10.1038\/s41467-024-51754-3","first_author":null,"corresponding_authors":null},{"pmid":"39641594","title":"Cryo-electron tomography: en route to the molecular anatomy of organisms and tissues.","abstract":"Cryo-electron tomography (cryo-ET) has become a key technique for obtaining structures of macromolecular complexes in their native environment, assessing their local organization and describing the molecular sociology of the cell. While microorganisms and adherent mammalian cells are common targets for tomography studies, appropriate sample preparation and data acquisition strategies for larger cellular assemblies such as tissues, organoids or small model organisms have only recently become sufficiently practical to allow for in-depth structural characterization of such samples in situ. These advances include tailored lift-out approaches using focused ion beam (FIB) milling, and improved data acquisition schemes. Consequently, cryo-ET of FIB lamellae from large volume samples can complement ultrastructural analysis with another level of information: molecular anatomy. This review highlights the recent developments towards molecular anatomy studies using cryo-ET, and briefly outlines what can be expected in the near future.","authors":"Schi\u00f8tz, OH., Klumpe, S., Plitzko, JM., Kaiser, CJO.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Biochem Soc Trans","volume":"52","issue":"6","page":"2415-2425","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-12-19","doi":"10.1042\/BST20240173","first_author":null,"corresponding_authors":null},{"pmid":"36258699","title":"Recovery of Conformational Continuum From Single-Particle Cryo-EM Images: Optimization of ManifoldEM Informed by Ground Truth.","abstract":"This work is based on the manifold-embedding approach to study biological molecules exhibiting continuous conformational changes. Previous work established a method-now termed ManifoldEM-capable of reconstructing 3D movies and accompanying free-energy landscapes from single-particle cryo-EM images of macromolecules exercising multiple conformational degrees of freedom. While ManifoldEM has proven its viability in several experimental studies, critical limitations and uncertainties have been found throughout its extended development and use. Guided by insights from studies with cryo-EM ground-truth data, simulated from atomic structures undergoing conformational changes, we have built a novel framework, ESPER, able to retrieve the free-energy landscape and respective 3D Coulomb potential maps for all states simulated. As shown by a direct comparison of ground truth vs. recovered maps, and analysis of experimental data from the 80S ribosome and ryanodine receptor, ESPER offers substantial improvements relative to the previous work.","authors":"Seitz, E., Acosta-Reyes, F., Maji, S., Schwander, P., Frank, J.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"IEEE Trans Comput Imaging","volume":"8","issue":"","page":"462-478","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-20","doi":"10.1109\/tci.2022.3174801","first_author":null,"corresponding_authors":null},{"pmid":"38306982","title":"Integrating cellular electron microscopy with multimodal data to explore biology across space and time.","abstract":"Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.","authors":"McCafferty, CL., Klumpe, S., Amaro, RE., Kukulski, W., Collinson, L., Engel, BD.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Cell","volume":"187","issue":"3","page":"563-584","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-02-06","doi":"10.1016\/j.cell.2024.01.005","first_author":null,"corresponding_authors":null},{"pmid":"35149681","title":"Allosteric control of Ubp6 and the proteasome via a bidirectional switch.","abstract":"The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by deubiquitinating enzyme Ubp6. The proteasome activates Ubp6, whereas Ubp6 inhibits the proteasome through deubiquitination and a noncatalytic effect. Here, we report cryo-EM structures of the proteasome bound to Ubp6, based on which we identify mutants in Ubp6 and proteasome subunit Rpt1 that abrogate Ubp6 activation. The Ubp6 mutations define a conserved region that we term the ILR element. The ILR is found within the BL1 loop, which obstructs the catalytic groove in free Ubp6. Rpt1-ILR interaction opens the groove by rearranging not only BL1 but also a previously undescribed&#xa0;network of three interconnected active-site-blocking loops. Ubp6 activation and noncatalytic proteasome inhibition are linked in that they are eliminated by the same mutations. Ubp6 and ubiquitin together drive proteasomes into a unique conformation associated with proteasome inhibition. Thus, a multicomponent allosteric switch exerts simultaneous control over both Ubp6 and the proteasome.","authors":"Hung, KYS., Klumpe, S., Eisele, MR., Elsasser, S., Tian, G., Sun, S., Moroco, JA., Cheng, TC., Joshi, T., Seibel, T., Van Dalen, D., Feng, XH., Lu, Y., Ovaa, H., Engen, JR., Lee, BH., Rudack, T., Sakata, E., Finley, D.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Nat Commun","volume":"13","issue":"1","page":"838","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-03-04","doi":"10.1038\/s41467-022-28186-y","first_author":null,"corresponding_authors":null},{"pmid":"36805107","title":"Cryo-plasma FIB\/SEM volume imaging of biological specimens.","abstract":"Serial focussed ion beam scanning electron microscopy (FIB\/SEM) enables imaging and assessment of subcellular structures on the mesoscale (10 nm to 10 &#xb5;m). When applied to vitrified samples, serial FIB\/SEM is also a means to target specific structures in cells and tissues while maintaining constituents' hydration shells for in situ structural biology downstream. However, the application of serial FIB\/SEM imaging of non-stained cryogenic biological samples is limited due to low contrast, curtaining, and charging artefacts. We address these challenges using a cryogenic plasma FIB\/SEM. We evaluated the choice of plasma ion source and imaging regimes to produce high-quality SEM images of a range of different biological samples. Using an automated workflow we produced three-dimensional volumes of bacteria, human cells, and tissue, and calculated estimates for their resolution, typically achieving 20-50 nm. Additionally, a tag-free localisation tool for regions of interest is needed to drive the application of in situ structural biology towards tissue. The combination of serial FIB\/SEM with plasma-based ion sources promises a framework for targeting specific features in bulk-frozen samples (&gt;100 &#xb5;m) to produce lamellae for cryogenic electron tomography.","authors":"Dumoux, M., Glen, T., Smith, JLR., Ho, EML., Perdig\u00e3o, LMA., Pennington, A., Klumpe, S., Yee, NBY., Farmer, DA., Lai, PYA., Bowles, W., Kelley, R., Plitzko, JM., Wu, L., Basham, M., Clare, DK., Siebert, CA., Darrow, MC., Naismith, JH., Grange, M.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Elife","volume":"12","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-10","doi":"10.7554\/eLife.83623","first_author":null,"corresponding_authors":null},{"pmid":"34166613","title":"Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity.","abstract":"Vesicle-inducing protein in plastids 1 (VIPP1) is essential for the biogenesis and maintenance of thylakoid membranes, which transform light into life. However, it is unknown how VIPP1 performs its vital membrane-remodeling functions. Here, we use cryo-electron microscopy to determine structures of cyanobacterial VIPP1 rings, revealing how VIPP1 monomers flex and interweave to form basket-like assemblies of different symmetries. Three VIPP1 monomers together coordinate a non-canonical nucleotide binding pocket on one end of the ring. Inside the ring's lumen, amphipathic helices from each monomer align to form large hydrophobic columns, enabling VIPP1 to bind and curve membranes. In&#xa0;vivo mutations in these hydrophobic surfaces cause extreme thylakoid swelling under high light, indicating an essential role of VIPP1 lipid binding in resisting stress-induced damage. Using cryo-correlative light and electron microscopy (cryo-CLEM), we observe oligomeric VIPP1 coats encapsulating membrane tubules within the Chlamydomonas chloroplast. Our work provides a structural foundation for understanding how VIPP1 directs thylakoid biogenesis and maintenance.","authors":"Gupta, TK., Klumpe, S., Gries, K., Heinz, S., Wietrzynski, W., Ohnishi, N., Niemeyer, J., Spaniol, B., Schaffer, M., Rast, A., Ostermeier, M., Strauss, M., Plitzko, JM., Baumeister, W., Rudack, T., Sakamoto, W., Nickelsen, J., Schuller, JM., Schroda, M., Engel, BD.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cell","volume":"184","issue":"14","page":"3643-3659.e23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-03","doi":"10.1016\/j.cell.2021.05.011","first_author":null,"corresponding_authors":null},{"pmid":"34951584","title":"A modular platform for automated cryo-FIB workflows.","abstract":"Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ablation rates of low Ga<sup>+<\/sup> ion beam currents required to maintain the structural integrity of vitreous specimens, common preparation protocols are time-consuming and labor intensive. The improved stability of new-generation cryo-FIB instruments now enables automated operations. Here, we present an open-source software tool, SerialFIB, for creating automated and customizable cryo-FIB preparation protocols. The software encompasses a graphical user interface for easy execution of routine lamellae preparations, a scripting module compatible with available Python packages, and interfaces with three-dimensional correlative light and electron microscopy (CLEM) tools. SerialFIB enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM-guided lamella preparation and in situ lamella lift-out procedures. Our software therefore provides a foundation for further development of advanced cryogenic imaging and sample preparation protocols.","authors":"Klumpe, S., Fung, HK., Goetz, SK., Zagoriy, I., Hampoelz, B., Zhang, X., Erdmann, PS., Baumbach, J., M\u00fcller, CW., Beck, M., Plitzko, JM., Mahamid, J.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Elife","volume":"10","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-20","doi":"10.7554\/eLife.70506","first_author":null,"corresponding_authors":null},{"pmid":"38110637","title":"Serial Lift-Out: sampling the molecular anatomy of whole organisms.","abstract":"Cryo-focused ion beam milling of frozen-hydrated cells and subsequent cryo-electron tomography (cryo-ET) has enabled the structural elucidation of macromolecular complexes directly inside cells. Application of the technique to multicellular organisms and tissues, however, is still limited by sample preparation. While high-pressure freezing enables the vitrification of thicker samples, it prolongs subsequent preparation due to increased thinning times and the need for extraction procedures. Additionally, thinning removes large portions of the specimen, restricting the imageable volume to the thickness of the final lamella, typically &lt;300&#x2009;nm. Here we introduce Serial Lift-Out, an enhanced lift-out technique that increases throughput and obtainable contextual information by preparing multiple sections from single transfers. We apply Serial Lift-Out to Caenorhabditis elegans L1 larvae, yielding a cryo-ET dataset sampling the worm's anterior-posterior axis, and resolve its ribosome structure to 7&#x2009;&#xc5; and a subregion of the 11-protofilament microtubule to 13&#x2009;&#xc5;, illustrating how Serial Lift-Out enables the study of multicellular molecular anatomy.","authors":"Schi\u00f8tz, OH., Kaiser, CJO., Klumpe, S., Morado, DR., Poege, M., Schneider, J., Beck, F., Klebl, DP., Thompson, C., Plitzko, JM.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Nat Methods","volume":"21","issue":"9","page":"1684-1692","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-09-13","doi":"10.1038\/s41592-023-02113-5","first_author":null,"corresponding_authors":null},{"pmid":"40049165","title":"In-cell structure and snapshots of copia retrotransposons in intact tissue by cryo-ET.","abstract":"Long terminal repeat (LTR) retrotransposons belong to the transposable elements (TEs), autonomously replicating genetic elements that integrate into the host's genome. Among animals, Drosophila melanogaster serves as an important model organism for TE research and contains several LTR retrotransposons, including the Ty1-copia family, which is evolutionarily related to retroviruses and forms virus-like particles (VLPs). In this study, we use cryo-focused ion beam (FIB) milling and lift-out approaches to visualize copia VLPs in ovarian cells and intact egg chambers, resolving the in situ copia capsid structure to 7.7&#xa0;&#xc5; resolution by cryoelectron tomography (cryo-ET). Although cytoplasmic copia VLPs vary in size, nuclear VLPs are homogeneous and form densely packed clusters, supporting a model in which nuclear import acts as a size selector. Analyzing flies deficient in the TE-suppressing PIWI-interacting RNA (piRNA) pathway, we observe copia's translocation into the nucleus during spermatogenesis. Our findings provide insights into the replication cycle and cellular structural biology of an active LTR retrotransposon.","authors":"Klumpe, S., Senti, KA., Beck, F., Sachweh, J., Hampoelz, B., Ronchi, P., Oorschot, V., Brandstetter, M., Yeroslaviz, A., Briggs, JAG., Brennecke, J., Beck, M., Plitzko, JM.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-03-14","doi":"10.1016\/j.cell.2025.02.003","first_author":null,"corresponding_authors":null},{"pmid":"33971286","title":"A streamlined workflow for automated cryo focused ion beam milling.","abstract":"Cryo-electron tomography (cryo-ET) is an emerging technique to study the cellular architecture and the structure of proteins at high resolution in situ. Most biological specimens are too thick to be directly investigated and are therefore thinned by milling with a focused ion beam under cryogenic conditions (cryo-FIB). This procedure is prone to contaminations, which makes it a tedious process, often leading to suboptimal results. Here, we present new hardware that overcomes the current limitations. We developed a new glove box and a high vacuum cryo transfer system and installed a stage heater, a cryo-shield and a cryo-shutter in the FIB milling microscope. This reduces the ice contamination during the transfer and milling process and simplifies the handling of the sample. In addition, we tested a new software application that automates the key milling steps. Together, these improvements allow for high-quality, high-throughput cryo-FIB milling. This paves the way for new types of experiments, which have been previously considered infeasible.","authors":"Tacke, S., Erdmann, P., Wang, Z., Klumpe, S., Grange, M., Plitzko, J., Raunser, S.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"J Struct Biol","volume":"213","issue":"3","page":"107743","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-04","doi":"10.1016\/j.jsb.2021.107743","first_author":null,"corresponding_authors":null},{"pmid":"34508074","title":"In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli.","abstract":"Ribosomes comprise a large (LSU) and a small subunit (SSU) which are synthesized independently in the nucleolus before being exported into the cytoplasm, where they assemble into functional ribosomes. Individual maturation steps have been analyzed in detail using biochemical methods, light microscopy and conventional electron microscopy (EM). In recent years, single particle analysis (SPA) has yielded molecular resolution structures of several pre-ribosomal intermediates. It falls short, however, of revealing the spatiotemporal sequence of ribosome biogenesis in the cellular context. Here, we present our study on native nucleoli in Chlamydomonas reinhardtii, in which we follow the formation of LSU and SSU precursors by in situ cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). By combining both positional and molecular data, we reveal gradients of ribosome maturation within the granular component (GC), offering a new perspective on how the liquid-liquid-phase separation of the nucleolus supports ribosome biogenesis.","authors":"Erdmann, PS., Hou, Z., Klumpe, S., Khavnekar, S., Beck, F., Wilfling, F., Plitzko, JM., Baumeister, W.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"5364","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-14","doi":"10.1038\/s41467-021-25413-w","first_author":null,"corresponding_authors":null},{"pmid":"32695274","title":"Exploring the catalytic cascade of cembranoid biosynthesis by combination of genetic engineering and molecular simulations.","abstract":"While chemical steps involved in bioactive cembranoid biosynthesis have been examined, the corresponding enzymatic mechanisms leading to their formation remain elusive. In the tobacco plant, <i>Nicotiana tabacum,<\/i> a putative cembratriene-ol synthase (CBTS) initiates the catalytic cascade that lead to the biosynthesis of cembratriene-4,6-diols, which displays antibacterial- and anti-proliferative activities. We report here on structural homology models, functional studies, and mechanistic explorations of this enzyme using a combination of biosynthetic and computational methods. This approach guided us to develop an efficient <i>de novo<\/i> production of five bioactive non- and monohydroxylated cembranoids. Our homology models in combination with quantum and classical simulations suggested putative principles of the CBTS catalytic cycle, and provided a possible rationale for the formation of premature olefinic side products. Moreover, the functional reconstruction of a <i>N. tabacum<\/i>-derived class II P450 with a cognate CPR, obtained by transcriptome mining provided for production of bioactive cembratriene-4,6-diols. Our combined findings provide mechanistic insights into cembranoid biosynthesis, and a basis for the sustainable industrial production of highly valuable bioactive cembranoids.","authors":"Schrepfer, P., Ugur, I., Klumpe, S., Loll, B., Kaila, VRI., Br\u00fcck, T.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Comput Struct Biotechnol J","volume":"18","issue":null,"page":"1819-1829","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-28","doi":"10.1016\/j.csbj.2020.06.030","first_author":null,"corresponding_authors":null},{"pmid":"39718850","title":"Point-spread-function engineering in MINFLUX: optimality of donut and half-moon excitation patterns.","abstract":"Localization microscopy enables imaging with resolutions that surpass the conventional optical diffraction limit. Notably, the Maximally INFormative LUminescence eXcitation (MINFLUX) method achieves super-resolution by shaping the excitation point spread function (PSF) to minimize the required photon flux for a given precision. Various beam shapes have recently been proposed to improve localization efficiency, yet their optimality remains an open question. In this work, we deploy a numerical and theoretical framework to determine optimal excitation patterns for MINFLUX. Such a computational approach allows us to search for new beam patterns in a fast and low-cost fashion and to avoid time-consuming and expensive experimental explorations. We show that the conventional donut beam is a robust optimum when the excitation beams are all constrained to the same shape. Further, our PSF engineering framework yields two pairs of half-moon beams (orthogonal to each other), which can improve the theoretical localization precision by a factor of about two.","authors":"Liu, Y., Dong, J., Augusto Maya, J., Balzarotti, F., Unser, M.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Opt Lett","volume":"50","issue":"1","page":"37-40","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-00-01","doi":"10.1364\/OL.543882","first_author":null,"corresponding_authors":null},{"pmid":"39879985","title":"Convergence of orphan quality control pathways at a ubiquitin chain-elongating ligase.","abstract":"Unassembled and partially assembled subunits of multi-protein complexes have emerged as major quality control clients, particularly under conditions of imbalanced gene expression such as stress, aging, and aneuploidy. The factors and mechanisms that eliminate such orphan subunits to maintain protein homeostasis are incompletely defined. Here, we show that the UBR4-KCMF1 ubiquitin ligase complex is required for the efficient degradation of multiple unrelated orphan subunits from the chaperonin, proteasome cap, proteasome core, and a protein targeting complex. Epistasis analysis in cells and reconstitution studies in&#xa0;vitro show that the UBR4-KCMF1 complex acts downstream of a priming ubiquitin ligase that first mono-ubiquitinates orphans. UBR4 recognizes both the orphan and its mono-ubiquitin and builds a K48-linked poly-ubiquitin degradation signal. The discovery of a convergence point for multiple quality control pathways may explain why aneuploid cells are especially sensitive to loss of UBR4 or KCMF1 and identifies a potential vulnerability across many cancers.","authors":"Carrillo Roas, S., Yagita, Y., Murphy, P., Kurzbauer, R., Clausen, T., Zavodszky, E., Hegde, RS.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Mol Cell","volume":"85","issue":"4","page":"815-828.e10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.08.07.607117v1.full","articledate":"2025-02-21","doi":"10.1016\/j.molcel.2025.01.002","first_author":null,"corresponding_authors":null},{"pmid":"39232338","title":"Friendly fire: recognition of self by the innate immune system.","abstract":"The innate immune system employs two different strategies to detect pathogens: first, it recognizes microbial components as ligands of pattern recognition receptors (pattern-triggered immunity [PTI]), and second, it detects the activities of pathogen-encoded effectors (effector-triggered immunity [ETI]). Recently, these pathogen-centric concepts were expanded to include sensing of self-derived signals during cellular distress or damage (damage-triggered immunity [DTI]). This extension relied on broadening the PTI model to include damage-associated molecular patterns (DAMPs). However, applying the pattern recognition framework of PTI to DTI overlooks the critical role of sterile activation of ETI pathways. We argue that both PTI and ETI pathways are prone to erroneous detection of self, which is largely attributable to 'friendly fire' rather than protective immune activation. This erroneous activation is inherent to the trade-off between sensitivity and specificity of immune sensing and might be tolerated because its detrimental effects emerge late in life, a phenomenon known as antagonistic pleiotropy.","authors":"Hornung, V., Gaidt, MM.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Curr Opin Immunol","volume":"90","issue":null,"page":"102457","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-09-11","doi":"10.1016\/j.coi.2024.102457","first_author":null,"corresponding_authors":null},{"pmid":"39824185","title":"SMC motor proteins extrude DNA asymmetrically and can switch directions.","abstract":"Structural maintenance of chromosomes (SMC) complexes organize the genome via DNA loop extrusion. Although some SMCs were reported to do so symmetrically, reeling DNA from both sides into the extruded DNA loop simultaneously, others perform loop extrusion asymmetrically toward one direction only. The mechanism underlying this variability remains unclear. Here, we examine the directionality of DNA loop extrusion by SMCs using in&#xa0;vitro single-molecule experiments. We find that cohesin and SMC5\/6 do not reel in DNA from both sides, as reported before, but instead extrude DNA asymmetrically, although the direction can switch over time. Asymmetric DNA loop extrusion thus is the shared mechanism across all eukaryotic SMC complexes. For cohesin, direction switches strongly correlate with the turnover of the subunit NIPBL, during which DNA strand switching may occur. Apart from expanding by extrusion, loops frequently diffuse and shrink. The findings reveal that SMCs, surprisingly, can switch directions.","authors":"Barth, R., Davidson, IF., van der Torre, J., Taschner, M., Gruber, S., Peters, JM., Dekker, C.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Cell","volume":"188","issue":"3","page":"749-763.e21","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-02-07","doi":"10.1016\/j.cell.2024.12.020","first_author":null,"corresponding_authors":null},{"pmid":"39786339","title":"Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis.","abstract":"How cells establish the interphase genome organization after mitosis is incompletely understood. Using quantitative and super-resolution microscopy, we show that the transition from a Condensin to a Cohesin-based genome organization occurs dynamically over 2 h. While a significant fraction of Condensins remains chromatin-bound until early G1, Cohesin-STAG1 and its boundary factor CTCF are rapidly imported into daughter nuclei in telophase, immediately bind chromosomes as individual complexes, and are sufficient to build the first interphase TAD structures. By contrast, the more abundant Cohesin-STAG2 accumulates on chromosomes only gradually later in G1, is responsible for compaction inside TAD structures, and forms paired complexes upon completed nuclear import. Our quantitative time-resolved mapping of mitotic and interphase loop extruders in single cells reveals that the nested loop architecture formed by the sequential action of two Condensins in mitosis is seamlessly replaced by a less compact but conceptually similar hierarchically nested loop architecture driven by the sequential action of two Cohesins.","authors":"Brunner, A., Morero, NR., Zhang, W., Hossain, MJ., Lampe, M., Pflaumer, H., Halavatyi, A., Peters, JM., Beckwith, KS., Ellenberg, J.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"J Cell Biol","volume":"224","issue":"3","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/pubmed.ncbi.nlm.nih.gov\/38854067\/","articledate":"2025-02-07","doi":"10.1083\/jcb.202405169","first_author":null,"corresponding_authors":null},{"pmid":"39748119","title":"Cohesin positions the epigenetic reader Phf2 within the genome.","abstract":"Genomic DNA is assembled into chromatin by histones, and extruded into loops by cohesin. These mechanisms control important genomic functions, but whether histones and cohesin cooperate in genome regulation is poorly understood. Here we identify Phf2, a member of the Jumonji-C family of histone demethylases, as a cohesin-interacting protein. Phf2 binds to H3K4me3 nucleosomes at active transcription start sites (TSSs), but also co-localizes with cohesin. Cohesin depletion reduces Phf2 binding at sites lacking H3K4me3, and depletion of Wapl and CTCF re-positions Phf2 together with cohesin in the genome, resulting in the accumulation of both proteins in chromosomal regions called vermicelli and cohesin islands. Conversely, Phf2 depletion reduces cohesin binding at TSSs lacking CTCF and decreases the number of short cohesin loops, while increasing the length of heterochromatic B compartments. These results suggest that Phf2 is an 'epigenetic reader', which is translocated through the genome by cohesin-mediated DNA loop extrusion, and which recruits cohesin to active TSSs and limits the size of B compartments. These findings reveal an unexpected degree of cooperativity between epigenetic and architectural mechanisms of eukaryotic genome regulation.","authors":"Tang, W., Costantino, L., Stocsits, R., Wutz, G., Ladurner, R., Hudecz, O., Mechtler, K., Peters, JM.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"EMBO J","volume":"44","issue":"3","page":"736-766","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-02-03","doi":"10.1038\/s44318-024-00348-2","first_author":null,"corresponding_authors":null},{"pmid":"39671477","title":"All eukaryotic SMC proteins induce a twist of -0.6 at each DNA loop extrusion step.","abstract":"Eukaryotes carry three types of structural maintenance of chromosome (SMC) protein complexes, condensin, cohesin, and SMC5\/6, which are ATP-dependent motor proteins that remodel the genome via DNA loop extrusion (LE). SMCs modulate DNA supercoiling but remains incompletely understood how this is achieved. Using a single-molecule magnetic tweezers assay that directly measures how much twist is induced by individual SMCs in each LE step, we demonstrate that all three SMC complexes induce the same large negative twist (i.e., linking number change [Formula: see text] of ~-0.6 at each LE step) into the extruded loop, independent of step size and DNA tension. Using ATP hydrolysis mutants and nonhydrolyzable ATP analogs, we find that ATP binding is the twist-inducing event during the ATPase cycle, coinciding with the force-generating LE step. The fact that all three eukaryotic SMC proteins induce the same amount of twist indicates a common DNA-LE mechanism among these SMC complexes.","authors":"Janissen, R., Barth, R., Davidson, IF., Peters, JM., Dekker, C.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Sci Adv","volume":"10","issue":"50","page":"eadt1832","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-12-13","doi":"10.1126\/sciadv.adt1832","first_author":null,"corresponding_authors":null},{"pmid":"39626663","title":"Enhancer cooperativity can compensate for loss of activity over large genomic distances.","abstract":"Enhancers are short DNA sequences that activate their target promoter from a distance; however, increasing the genomic distance between the enhancer and the promoter decreases expression levels. Many genes are controlled by combinations of multiple enhancers, yet the interaction and cooperation of individual enhancer elements are not well understood. Here, we developed a synthetic platform in mouse embryonic stem cells that allows building complex regulatory landscapes from the bottom up. We tested the system by integrating individual enhancers at different distances and confirmed that the strength of an enhancer contributes to how strongly it is affected by increased genomic distance. Furthermore, synergy between two enhancer elements depends on the distance at which the two elements are integrated: introducing a weak enhancer between a strong enhancer and the promoter strongly increases reporter gene expression, allowing enhancers to activate from increased genomic distances.","authors":"Thomas, HF., Feng, S., Haslhofer, F., Huber, M., Garc\u00eda Gallardo, M., Loubiere, V., Vanina, D., Pitasi, M., Stark, A., Buecker, C.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Mol Cell","volume":"85","issue":"2","page":"362-375.e9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-01-17","doi":"10.1016\/j.molcel.2024.11.008","first_author":null,"corresponding_authors":null},{"pmid":"39571581","title":"A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression.","abstract":"Differential gene transcription enables development and homeostasis in all animals and is regulated by two major classes of distal cis-regulatory DNA elements (CREs): enhancers and silencers. Although enhancers have been thoroughly characterized, the properties and mechanisms of silencers remain largely unknown. By an unbiased genome-wide functional screen in Drosophila melanogaster S2 cells, we discover a class of silencers that bind one of three transcription factors (TFs) and are generally not included in chromatin-defined CRE catalogs as they mostly lack detectable DNA accessibility. The silencer-binding TF CG11247, which we term Saft, safeguards cell fate decisions in&#xa0;vivo and functions via a highly conserved domain we term zinc-finger-associated C-terminal (ZAC) and the corepressor G9a, independently of G9a's H3K9-methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanisms has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes.","authors":"Hofbauer, L., Pleyer, LM., Reiter, F., Schleiffer, A., Vlasova, A., Serebreni, L., Huang, A., Stark, A.","publication_status":"ppublish","journalpubyear":"2024","journaltitle":"Mol Cell","volume":"84","issue":"23","page":"4503-4521.e14","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-12-06","doi":"10.1016\/j.molcel.2024.10.041","first_author":null,"corresponding_authors":null},{"pmid":"39362902","title":"Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila.","abstract":"Genomic enhancers are key transcriptional regulators which, upon the binding of sequence-specific transcription factors, activate their cognate target promoters. Although enhancers have been extensively studied in isolation, a substantial number of genes have more than one simultaneously active enhancer, and it remains unclear how these cooperate to regulate transcription. Using Drosophila melanogaster S2 cells as a model, we assay the activities of more than a thousand individual enhancers and about a million enhancer pairs toward housekeeping and developmental core promoters with STARR-seq. We report that housekeeping and developmental enhancers show distinct modes of enhancer-enhancer cooperativity: while housekeeping enhancers are additive such that their combined activity mirrors the sum of their individual activities, developmental enhancers are super-additive and combine multiplicatively. Super-additivity between developmental enhancers is promiscuous and neither depends on the enhancers' endogenous genomic contexts nor on specific transcription factor motif signatures. However, it can be further boosted by Twist and Trl motifs and saturates for the highest levels of enhancer activity. These results have important implications for our understanding of gene regulation in complex multi-enhancer developmental loci and genomically clustered housekeeping genes, providing a rationale to interpret the transcriptional impact of non-coding mutations at different loci.","authors":"Loubiere, V., de Almeida, BP., Pagani, M., Stark, A.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"8584","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-10-03","doi":"10.1038\/s41467-024-52921-2","first_author":null,"corresponding_authors":null},{"pmid":"40161635","title":"Direct cell-to-cell transmission of retrotransposons.","abstract":"Transposable elements are abundant in host genomes but are generally considered to be confined to the cell in which they are expressed, with the notable exception of endogenous retroviruses. Here, we identify a group of LTR retrotransposons that infect the germline from somatic cells within the <i>Drosophila<\/i> ovary, despite lacking the fusogenic Envelope protein typically required for retroviral entry. Instead, these elements encode a short transmembrane protein, sORF2, with structural features reminiscent of viral cell-cell fusogens. Through genetics, imaging, and electron microscopy, we show that sORF2 localizes to invasive somatic protrusions, enabling the direct transfer of retrotransposon capsids into the oocyte. Remarkably, sORF2-like proteins are widespread among insect retrotransposons and also occur in piscine nackednaviruses and avian picornaviruses. These findings reveal a noncanonical, Envelope-independent transmission mechanism shared by retrotransposons and non-enveloped viruses, offering important insights into host-pathogen evolution and soma-germline interactions.","authors":"Voichek, M., Bernhard, A., Novatchkova, M., Handler, D., M\u00f6seneder, P., Rafanel, B., Duchek, P., Senti, KA., Brennecke, J.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"bioRxiv","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-03-31","doi":"10.1101\/2025.03.14.642691","first_author":null,"corresponding_authors":null},{"pmid":"39970910","title":"Cold and hot fibrosis define clinically distinct cardiac pathologies.","abstract":"Fibrosis remains a major unmet medical need. Simplifying principles are needed to better understand fibrosis and to yield new therapeutic approaches. Fibrosis is driven by myofibroblasts that interact with macrophages. A mathematical cell-circuit model predicts two types of fibrosis: hot fibrosis driven by macrophages and myofibroblasts and cold fibrosis driven by myofibroblasts alone. Testing these concepts in cardiac fibrosis resulting from myocardial infarction (MI) and heart failure (HF), we revealed that acute MI leads to cold fibrosis whereas chronic injury (HF) leads to hot fibrosis. MI-driven cold fibrosis is conserved in pigs and humans. We computationally identified a vulnerability of cold fibrosis: the myofibroblast autocrine growth factor loop. Inhibiting this loop by targeting TIMP1 with neutralizing antibodies reduced myofibroblast proliferation and fibrosis post-MI in mice. Our study demonstrates the utility of the concepts of hot and cold fibrosis and the feasibility of a circuit-to-target approach to pinpoint a treatment strategy that reduces fibrosis. A record of this paper's transparent peer review process is included in the supplemental information.","authors":"Miyara, S., Adler, M., Umansky, KB., H\u00e4u\u00dfler, D., Bassat, E., Divinsky, Y., Elkahal, J., Kain, D., Lendengolts, D., Ramirez Flores, RO., Bueno-Levy, H., Golani, O., Shalit, T., Gershovits, M., Weizman, E., Genzelinakh, A., Kimchi, DM., Shakked, A., Zhang, L., Wang, J., Baehr, A., Petrover, Z., Sarig, R., Dorn, T., Moretti, A., Saez-Rodriguez, J., Kupatt, C., Tanaka, EM., Medzhitov, R., Kr\u00fcger, A., Mayo, A., Alon, U., Tzahor, E.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Cell Syst","volume":"16","issue":"3","page":"101198","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-03-20","doi":"10.1016\/j.cels.2025.101198","first_author":null,"corresponding_authors":null},{"pmid":"40042904","title":"Adeno-associated viruses for efficient gene expression in the axolotl nervous system.","abstract":"Axolotls are amphibian models for studying nervous system evolution, development, and regeneration. Tools to visualize and manipulate cells of the axolotl nervous system with high-efficiency, spatial and temporal precision are therefore greatly required. Recombinant adeno-associated viruses (AAVs) are frequently used for in vivo gene transfer of the nervous system but virus-mediated gene delivery to the axolotl nervous system has not yet been described. Here, we demonstrate the use of AAVs for efficient gene transfer within the axolotl brain, the spinal cord, and the retina. We show that serotypes AAV8, AAV9, and AAVPHP.eB are suitable viral vectors to infect both excitatory and inhibitory neuronal populations of the axolotl brain. We further use AAV9 to trace retrograde and anterograde projections between the retina and the brain and identify a cell population projecting from the brain to the retina. Together, our work establishes AAVs as a powerful tool to interrogate neuronal organization in the axolotl.","authors":"Lust, K., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Proc Natl Acad Sci U S A","volume":"122","issue":"10","page":"e2421373122","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-03-05","doi":"10.1073\/pnas.2421373122","first_author":null,"corresponding_authors":null},{"pmid":"40187387","title":"Optimized toolkit for the manipulation of immortalized axolotl fibroblasts.","abstract":"The axolotl salamander model has broad utility for regeneration studies, but this model is limited by a lack of efficient cell-culture-based tools. The Axolotl Limb-1 (AL-1) fibroblast line, the only available immortalized axolotl cell line, was first published over 20&#xa0;years ago, but many established molecular biology techniques, such as lipofectamine transfection, CRISPR-Cas9 mutagenesis, and antibiotic selection, work poorly or remain untested in AL-1 cells. Innovating technologies to manipulate AL-1 cells in culture and study their behavior following transplantation into the axolotl will complement in-vivo studies, decrease the number of animals used, and enable the faster, more streamlined investigation of regenerative biology questions. Here, we establish transfection, mutagenesis, antibiotic selection, and in-vivo transplantation techniques in axolotl AL-1 cells. These techniques will enable efficient culture with AL-1 cells and guide future tool development for the culture and manipulation of other salamander cell lines.","authors":"Tajer, BJ., Kalu, G., Jay, S., Wynn, E., Decaux, A., Gilbert, P., Singer, HD., Kidd, MD., Nelson, JA., Harake, N., Lopez, NJ., Souchet, NR., Luong, AG., Savage, AM., Min, S., Karabacak, A., B\u00f6hm, S., Kim, RT., Froitzheim, T., Sousounis, K., Courtemanche, K., Han, J., Payzin-Dogru, D., Blair, SJ., Roy, S., Fei, JF., Tanaka, EM., Whited, JL.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Methods","volume":"240","issue":null,"page":"21-34","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-05","doi":"10.1016\/j.ymeth.2025.03.019","first_author":null,"corresponding_authors":null},{"pmid":"40250419","title":"Fate and state transitions during human blood vessel organoid development.","abstract":"Human blood vessel organoids (hBVOs) have emerged as a system to model human vascular development and disease. Here, we use single-cell multi-omics together with genetic and signaling pathway perturbations to reconstruct hBVO development. Mesodermal progenitors bifurcate into endothelial and mural fates in&#xa0;vitro, and xenografted BVOs acquire definitive arteriovenous endothelial cell specification. We infer a gene regulatory network and use single-cell genetic perturbations to identify transcription factors (TFs) and receptors involved in cell fate specification, including a role for MECOM in endothelial and mural specification. We assess the potential of BVOs to generate organotypic states, identify TFs lacking expression in hBVOs, and find that induced LEF1 overexpression increases brain vasculature specificity. Finally, we map vascular disease-associated genes to hBVO cell states and analyze an hBVO model of diabetes. Altogether, we provide a comprehensive cell state atlas of hBVO development and illuminate the power and limitation of hBVOs for translational research.","authors":"Nikolova, MT., He, Z., Seimiya, M., Jonsson, G., Cao, W., Okuda, R., Wimmer, RA., Okamoto, R., Penninger, JM., Camp, JG., Treutlein, B.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-18","doi":"10.1016\/j.cell.2025.03.037","first_author":null,"corresponding_authors":null},{"pmid":"40279814","title":"Advancing autism research: Insights from brain organoid modeling.","abstract":"Autism Spectrum Disorders (ASD) are characterized by a variety of behavioral symptoms and a complex genetic architecture, posing significant challenges in understanding the mechanistic processes underlying their pathology. Despite extensive research, the mechanisms linking genetic variations to the phenotypic outcomes associated with ASD remain elusive. Consistent evidence indicates disruptions in early brain development among individuals with ASD. The advent of brain organoids offers a unique opportunity for uncovering, how brain development changes in ASD patients. Brain organoids are three-dimensional in&#xa0;vitro model systems derived from pluripotent stem cells that recapitulate early human brain development across multiple biological levels. They have become an invaluable tool for studying human-specific brain development processes and neurodevelopmental disorders. In this review, we discuss recent findings using brain organoid technologies to model ASD and discuss, how these new technologies can enhance our understanding of ASD genetics and pathology at the molecular, cellular, and tissue levels.","authors":"Li, CV., Knoblich, JA.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Curr Opin Neurobiol","volume":"92","issue":null,"page":"103030","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-25","doi":"10.1016\/j.conb.2025.103030","first_author":null,"corresponding_authors":null},{"pmid":"40262526","title":"A cost- and time-efficient method for high-throughput cryoprocessing and tissue analysis using multiplexed tissue molds.","abstract":"Cryosectioning remains the gold standard for antibody and transcriptomic\/in situ hybridization tissue analysis. However, tissue processing is time-consuming and costly, limiting routine and diagnostic use. Currently, no commercially available protocols or products exist for multiplexing this process. Here, we introduce multiplexed tissue molds (MTMs) that enable high-throughput cryoprocessing-cutting costs and workload by up to 96% while permitting the processing of tissues of various sizes and origins. We demonstrate compatibility with heterogeneous tissues by processing 19 different adult mouse tissues in parallel. Furthermore, we process up to &#x223c;110 neural organoids of different ages and sizes simultaneously and assess their neural differentiation marker expression. MTMs allow sectioning-based tissue analysis when labor, time, and cost are limiting factors. MTMs could be used to compare high specimen numbers in histopathological settings, organism-wide antigen and antibody targeting studies, high-throughput tissue screens, and defined tissue section positioning for, e.g., spatial transcriptomics experiments.","authors":"Reumann, D., Colombini, M., M\u00f6seneder, P., Piszczek, A., Knoblich, JA.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Cell Rep Methods","volume":"5","issue":"4","page":"101023","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-23","doi":"10.1016\/j.crmeth.2025.101023","first_author":null,"corresponding_authors":null},{"pmid":"40245870","title":"Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling.","abstract":"Metabolic pathways can influence cell fate decisions, yet their regulative role during embryonic development remains poorly understood. Here, we demonstrate an instructive role of glycolytic activity in regulating signaling pathways involved in mesoderm and endoderm specification. Using a mouse embryonic stem cell (mESC)-based in&#xa0;vitro model for gastrulation, we found that glycolysis inhibition increases ectodermal cell fates at the expense of mesodermal and endodermal lineages. We demonstrate that this relationship is dose dependent, enabling metabolic control of germ layer proportions through exogenous glucose levels. We further show that glycolysis acts as an upstream regulator of Nodal and Wnt signaling and that its influence on cell fate specification can be decoupled from its effects on growth. Finally, we confirm the generality of our findings using a human gastrulation model. Our work underscores the dependence of signaling pathways on metabolic conditions and provides mechanistic insight into the nutritional regulation of cell fate decision-making.","authors":"Stapornwongkul, KS., Hahn, E., Poli\u0144ski, P., Salam\u00f3 Palau, L., Arat\u00f3, K., Yao, L., Williamson, K., Gritti, N., Anlas, K., Osuna Lopez, M., Patil, KR., Heemskerk, I., Ebisuya, M., Trivedi, V.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Cell Stem Cell","volume":"32","issue":"5","page":"744-758.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-03","doi":"10.1016\/j.stem.2025.03.011","first_author":null,"corresponding_authors":null},{"pmid":"40355744","title":"Nicotinamide modulates gut microbial metabolic potential and accelerates recovery in mild-to-moderate COVID-19.","abstract":"Cellular NAD<sup>+<\/sup> depletion, altered tryptophan metabolism and gut microbiome dysbiosis are associated with disease progression and unfavourable clinical outcomes in COVID-19. Here, we show that supplementing tryptophan metabolism with nicotinamide alleviates COVID-19 symptoms. We evaluate a 4-week intervention with a novel nicotinamide formulation (1,000&#x2009;mg) in a prospective, double-blind, randomized, placebo-controlled trial in 900 symptomatic outpatients with PCR-proven COVID-19. In the primary analysis population of participants at risk for severe COVID-19, 57.6% of those receiving nicotinamide and 42.6% receiving placebo recover from their performance drop at week 2 (P&#x2009;=&#x2009;0.004). Nicotinamide is also beneficial for returning to normal activities (P&#x2009;=&#x2009;0.009). Effects on gut metagenomic signatures parallel clinical efficacy, suggesting that nicotinamide influences COVID-19-associated faecal microbiome changes. After 6 months, responders to nicotinamide in acute COVID-19 show fewer post-COVID symptoms than placebo responders (P&#x2009;=&#x2009;0.010). No relevant safety signals are observed. Overall, our results show that nicotinamide leads to faster recovery of physical performance and modulates COVID-19-associated faecal microbiome changes.","authors":"Schreiber, S., Waetzig, GH., L\u00f3pez-Agudelo, VA., Geisler, C., Schlicht, K., Franzenburg, S., di Giuseppe, R., Pape, D., Bahmer, T., Krawczak, M., Kokott, E., Penninger, JM., Harzer, O., Kramer, J., von Schrenck, T., Sommer, F., Zacharias, HU., Millet Pascual-Leone, B., Forslund, SK., Heyckendorf, J., Aden, K., Hollweck, R., Laudes, M., Rosenstiel, P.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nat Metab","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-12","doi":"10.1038\/s42255-025-01290-1","first_author":null,"corresponding_authors":null},{"pmid":"40339255","title":"Conservation and divergence of the molecular regulators of the vertebrate fertilization synapse.","abstract":"Fertilization - the process during which sperm and egg find each other, bind and eventually fuse - marks the beginning of a new individual. Research over the past years in vertebrates has shed new light on conserved and divergent molecular regulators that mediate the formation of the fertilization synapse, the close apposition of the two plasma membranes before fusion. Here, we review the known proteins that are required for sperm-egg interaction in mammals and fish from a phylogenetic perspective. While some sperm factors are only conserved in vertebrates and share phylogenetic and structural features, others have a longer evolutionary history. In contrast, the egg factors have changed even within vertebrates despite recognizing the preserved sperm machinery. Future functional work on these factors will be essential to understand the fusion mechanism of vertebrate sperm and egg.","authors":"Blaha, A., Schleiffer, A., Pauli, A.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Curr Opin Genet Dev","volume":"93","issue":null,"page":"102352","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-08","doi":"10.1016\/j.gde.2025.102352","first_author":null,"corresponding_authors":null},{"pmid":"40360510","title":"ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213.","abstract":"The giant E3 ubiquitin ligase RNF213 is a conserved component of mammalian cell-autonomous immunity, limiting the replication of bacteria, viruses and parasites. To understand how RNF213 reacts to these unrelated pathogens, we employ chemical and structural biology to find that ATP binding to its ATPases Associated with diverse cellular Activities (AAA) core activates its E3 function. We develop methodology for proteome-wide E3 activity profiling inside living cells, revealing that RNF213 undergoes a reversible switch in E3 activity in response to cellular ATP abundance. Interferon stimulation of macrophages raises intracellular ATP levels and primes RNF213 E3 activity, while glycolysis inhibition depletes ATP and downregulates E3 activity. These data imply that ATP bears hallmarks of a danger\/pathogen associated molecular pattern, coordinating cell-autonomous defence. Furthermore, quantitative labelling of RNF213 with E3-activity probes enabled us to identify the catalytic cysteine required for substrate ubiquitination and obtain a cryo-EM structure of the RNF213-E2-ubiquitin conjugation enzyme transfer intermediate, illuminating an unannotated E2 docking site. Together, our data demonstrate that RNF213 represents a new class of ATP-dependent E3 enzyme, employing distinct catalytic and regulatory mechanisms adapted to its specialised role in the broad defence against intracellular pathogens.","authors":"Ahel, J., Balci, A., Faas, V., Grabarczyk, DB., Harmo, R., Squair, DR., Zhang, J., Roitinger, E., Lamoliatte, F., Mathur, S., Deszcz, L., Bell, LE., Lehner, A., Williams, TL., Sowar, H., Meinhart, A., Wood, NT., Clausen, T., Virdee, S., Fletcher, AJ.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Nat Commun","volume":"16","issue":"1","page":"4414","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-14","doi":"10.1038\/s41467-025-59444-4","first_author":null,"corresponding_authors":null},{"pmid":"40399677","title":"Molecular basis of positional memory in limb regeneration.","abstract":"The amputation of a salamander limb triggers anterior and posterior connective&#xa0;tissue cells to form distinct signalling centres that together fuel regeneration<sup>1<\/sup>. Anterior and posterior identities are established during development and are thought to persist for the whole life in the form of positional memory<sup>2<\/sup>. However, the molecular basis of positional memory and whether positional memory can be altered remain unknown. Here, we identify a positive-feedback loop that is responsible for posterior identity in the limb of an axolotl (Ambystoma mexicanum). Posterior cells express residual Hand2 transcription factor from development, and this primes them to form a Shh signalling centre after limb amputation. During regeneration, Shh signalling is also upstream of Hand2 expression. After regeneration, Shh is shut down but Hand2 is sustained, safeguarding posterior memory. We used this regeneration circuitry to convert anterior cells to a posterior-cell memory state. Transient exposure of anterior&#xa0;cells to Shh during regeneration kick-started an ectopic Hand2-Shh loop, leading to stable Hand2 expression and lasting competence to express Shh. Our results implicate positive-feedback in the stability of positional memory and reveal that positional memory is reprogrammed more easily in one direction (anterior to posterior) than in the other. Modifying positional memory in regenerative cells changes their signalling outputs, which has implications for tissue engineering.","authors":"Otsuki, L., Plattner, SA., Taniguchi-Sugiura, Y., Falcon, F., Tanaka, EM.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nature","volume":"642","issue":"8068","page":"730-738","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-18","doi":"10.1038\/s41586-025-09036-5","first_author":"Otsuki, L.","corresponding_authors":"Tanaka, EM."},{"pmid":"40399606","title":"Bat organoids reveal antiviral responses at epithelial surfaces.","abstract":"Bats can host viruses of pandemic concern without developing disease. The mechanisms underlying their exceptional resilience to viral infections are largely unresolved, necessitating the development of physiologically relevant and genetically tractable research models. Here, we developed respiratory and intestinal organoids that recapitulated the cellular diversity of the in vivo epithelium present in Rousettus aegyptiacus, the natural reservoir for the highly pathogenic Marburg virus (MARV). In contrast to human counterparts, bat organoids and mucosal tissue exhibited elevated constitutive expression of innate immune effectors, including type I interferon-&#x3b5; (IFN&#x3b5;) and IFN-stimulated genes (ISGs). Upon infection with diverse zoonotic viruses, including MARV, bat organoids strongly induced type I and III IFN responses, which conferred robust antiviral protection. Type III IFN&#x3bb;3 additionally displayed virus-independent self-amplification, acting as an ISG to enhance antiviral immunity. Our organoid platform reveals key features of bat epithelial antiviral immunity that may inform therapeutic strategies for viral disease resilience.","authors":"Kellner, MJ., Monteil, VM., Zelger, P., Pei, G., Jiao, J., Onji, M., Nayak, K., Zilbauer, M., Balkema-Buschmann, A., Dorhoi, A., Mirazimi, A., Penninger, JM.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nat Immunol","volume":"26","issue":"6","page":"934-946","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-03","doi":"10.1038\/s41590-025-02155-1","first_author":null,"corresponding_authors":null},{"pmid":"40474005","title":"Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses.","abstract":"Transposable elements are major contributors to the evolution of their hosts, but the mechanisms driving their own diversification remain poorly understood. Here, we reveal key principles governing the evolution of insect endogenous retroviruses (ERVs), a class of infectious LTR-retrotransposons that encode an Envelope protein. Through comparative analyses and experimental studies of transposon replication cycles in Drosophila, we demonstrate how two crucial ERV traits-infectivity and spatiotemporal expression-co-evolve. We find that ERVs have adapted their cis-regulatory sequences to function across all ovarian cell types. Strikingly, infectious ERV lineages display distinct expression patterns in somatic cells, from where they infect the germline, whereas derived retroelement lineages that have lost infectivity are expressed exclusively in the germline. Co-evolutionary changes in the piRNA pathway, which integrates transposon promoter and sequence information into differentially expressed piRNA clusters, highlight the functional significance of the diverse ERV expression niches. By investigating a unique ERV lineage, rover, we reconstruct the molecular events that transformed an infectious ERV into a retroelement. Overall, our study uncovers fundamental mechanisms that drive the co-evolution of ERVs and their hosts, with important implications for understanding the functional diversification of LTR sequences.","authors":"Senti, KA., Rafanel, B., Handler, D., Kosiol, C., Schl\u00f6tterer, C., Brennecke, J.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"EMBO J","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-05","doi":"10.1038\/s44318-025-00471-8","first_author":null,"corresponding_authors":null},{"pmid":"40550823","title":"Developing a new cleavable crosslinker reagent for in-cell crosslinking.","abstract":"Crosslinking mass spectrometry (XL-MS) is a powerful technology that recently emerged as an essential complementary tool for elucidating protein structures and mapping interactions within a protein network. Crosslinkers which are amenable to post-linking backbone cleavage simplify peptide identification, aid in 3D structure determination and enable system-wide studies of protein-protein interactions (PPIs) in cellular environments. However, state-of-the-art cleavable linkers are fraught with practical limitations, including extensive evaluation of fragmentation energies and fragmentation behavior of the crosslinker backbone. We herein introduce DiSPASO (bis(2,5-dioxopyrrolidin-1-yl) 3,3'-((5-ethynyl-1,3-phenylene)bis(methylenesulfinyl))dipropanoate) as a lysine-selective, MS-cleavable crosslinker with an alkyne handle for affinity enrichment. DiSPASO was designed and developed for efficient cell membrane permeability and crosslinking while securing low cellular perturbation. We tested DiSPASO employing three different copper-based enrichment strategies using model systems with increasing complexity (Cas9-Halo, purified ribosomes, live cells). Fluorescence microscopy in-cell crosslinking experiments revealed a rapid uptake of DiSPASO into HEK 293 cells within 5 minutes. While DiSPASO represents progress in cellular PPI analysis, its limitations and low crosslinking yield in cellular environments require careful optimisation of the crosslinker design, highlighting the complexity of developing effective XL-MS tools and the importance of continuous innovation in accurately mapping PPI networks within dynamic cellular environments.","authors":"M\u00fcller, F., Brutiu, BR., Saridakis, I., Leischner, T., Birklbauer, MJ., Matzinger, M., Madalinski, M., Lendl, T., Shaaban, S., Dorfer, V., Maulide, N., Mechtler, K.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Commun Chem","volume":"8","issue":"1","page":"191","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-23","doi":"10.1038\/s42004-025-01568-1","first_author":null,"corresponding_authors":null},{"pmid":"40581115","title":"A Roadmap for Improving Reliability and Data Sharing in Crosslinking Mass Spectrometry.","abstract":"Crosslinking Mass Spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats, variable approaches to error control, and insufficient interoperability with global data repositories. Recent advances, especially in false discovery rate (FDR) models and pipeline benchmarking, show that Crosslinking MS data can reach a reliability that matches the demand of integrative structural biology. To drive meaningful progress, however, the community must agree on error estimation, open data formats, and streamlined repository submissions. This perspective highlights these challenges, clarifies remaining barriers, and frames practical next steps. Successful field harmonisation will enhance the acceptance of Crosslinking MS in the broader biological community and is critical for the dependability of the data, no matter where it is produced.","authors":"Rappsilber, J., Bruce, J., Combe, C., Fried, S., Graziadei, A., Heck, AJR., Iacobucci, C., Leitner, A., Mechtler, K., Novak, P., O'Reilly, F., Schriemer, DC., Sinz, A., Stengel, F., Thalassinos, K.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Mol Cell Proteomics","volume":null,"issue":null,"page":"101024","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-28","doi":"10.1016\/j.mcpro.2025.101024","first_author":null,"corresponding_authors":null},{"pmid":"40580953","title":"Regulation of somatic hypermutation by higher-order chromatin structure.","abstract":"The generation of protective antibodies by somatic hypermutation (SHM) is essential for antibody maturation and adaptive immunity. SHM involves co-transcriptional mutagenesis of immunoglobulin variable (V) regions regulated by enhancers located hundreds of kilobases away. How 3D chromatin topology affects SHM is poorly understood. Here, we measure higher-order interactions on single alleles of the human immunoglobulin heavy-chain locus (IGH) using Tri-C. We find that SHM is underpinned by a multiway hub wherein the V region is proximal to all enhancers. Cohesin-mediated loop extrusion is dispensable for IGH transcription and hub architecture. Transcription and mutagenesis of IGH switch regions, which are necessary for antibody class-switch recombination, create new chromatin loops that can form without cohesin. However, these additional loops do not compromise hub integrity, V region transcription, or SHM. Thus, antibody maturation occurs within a multiway hub accommodating several gene-enhancer loops in which transcription and mutagenesis of different segments occur non-competitively.","authors":"Schoeberl, UE., Fitz, J., von der Linde, M., Valieris, R., Bauer, B., Malzl, D., Froussios, K., Costea, J., Schmidt, F., Pflaum, J., Bartl, B., Albrecht, J., Wiedemann, EM., Garcia, AC., Peycheva, M., Rizzi, M., Goloborodko, A., Tojal da Silva, I., Pavri, R.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Mol Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-28","doi":"10.1016\/j.molcel.2025.06.003","first_author":null,"corresponding_authors":null},{"pmid":"40597406","title":"The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">40597406<\/PMID><DateCompleted><Year>2025<\/Year><Month>07<\/Month><Day>02<\/Day><\/DateCompleted><DateRevised><Year>2025<\/Year><Month>07<\/Month><Day>02<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>26<\/Volume><Issue>1<\/Issue><PubDate><Year>2025<\/Year><Month>Jul<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes.<\/ArticleTitle><Pagination><StartPage>186<\/StartPage><MedlinePgn>186<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13059-025-03653-z<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Many metazoan genomes are characterized by highly conserved chromosomal homologies that predate the ancient origin of this clade. This conservation has been tested by expansions of selfish DNA elements, in particular transposable elements (TEs). While comparative genomics studies have highlighted their diversity across animal genomes, common principles underlying their evolution along deeply conserved chromosomes have been elusive. A detailed mechanistic understanding from phylogenetically key and early branching animal species has been lacking.","authors":"Kon-Nanjo, K., Kon, T., Yu, TCK., Rodriguez-Terrones, D., Falcon, F., Mart\u00ednez, DE., Steele, RE., Tanaka, EM., Holstein, TW., Simakov, O.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Genome Biol","volume":"26","issue":"1","page":"186","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-07-02","doi":"10.1186\/s13059-025-03653-z","first_author":null,"corresponding_authors":null},{"pmid":"36450242","title":"Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription.","abstract":"Mammalian genomes are organized into three-dimensional DNA structures called A\/B compartments that are associated with transcriptional activity\/inactivity. However, whether these structures are simply correlated with gene expression or are permissive\/impermissible to transcription has remained largely unknown because we lack methods to measure DNA organization and transcription simultaneously. Recently, we developed RNA &amp; DNA (RD)-SPRITE, which enables genome-wide measurements of the spatial organization of RNA and DNA. Here we show that RD-SPRITE measures genomic structure surrounding nascent pre-mRNAs and maps their spatial contacts. We find that transcription occurs within B compartments-with multiple active genes simultaneously colocalizing within the same B compartment-and at genes proximal to nucleoli. These results suggest that localization near or within nuclear structures thought to be inactive does not preclude transcription and that active transcription can occur throughout the nucleus. In general, we anticipate RD-SPRITE will be a powerful tool for exploring relationships between genome structure and transcription.","authors":"Goronzy, IN., Quinodoz, SA., Jachowicz, JW., Ollikainen, N., Bhat, P., Guttman, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cell Rep","volume":"41","issue":"9","page":"111730","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-12-02","doi":"10.1016\/j.celrep.2022.111730","first_author":null,"corresponding_authors":null},{"pmid":"40659489","title":"A lyophilized open-source RT-LAMP assay for molecular diagnostics in resource-limited settings.","abstract":"A critical bottleneck for equitable access to population-scale molecular diagnostics is the limited availability of rapid, inexpensive point-of-care tests, especially in low- and middle-income countries. Here, we developed an open-source reverse transcription loop-mediated isothermal amplification (RT-LAMP) molecular assay for pathogen detection. It is based on nonproprietary enzymes, namely, HIV-1 reverse transcriptase, <i>Bst<\/i> LF DNA polymerase, and UDG BMTU thermolabile uracil-DNA glycosylase. Formulated as liquid or lyophilized reaction mixtures, these reagents enable sensitive colorimetric detection of respiratory samples without the need for prior nucleic acid isolation. We evaluated our lyophilized RT-LAMP assay on clinical samples with suspected COVID-19 infection, demonstrating high sensitivity and 100% specificity compared with the gold-standard RT-qPCR. Reaction performance was unaffected by prolonged storage of lyophilized reagents at ambient or elevated temperatures. As a proof of concept, we evaluated the robustness and ease of use of lyophilized RT-LAMP reaction mixes through independent laboratory testing of COVID-19 samples in Ghana. Overall, our open-source RT-LAMP assay provides a flexible and scalable point-of-care test that can be adapted for rapid detection of various pathogens in resource-limited settings.","authors":"Matl, M., Kellner, MJ., Ansah, F., Grishkovskaya, I., Handler, D., Heinen, R., Bauer, B., Men\u00e9ndez-Arias, L., Auer, TO., Prieto-Godino, LL., Penninger, JM., Awandare, GA., Brennecke, J., Pauli, A.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Life Sci Alliance","volume":"8","issue":"10","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-07-14","doi":"10.26508\/lsa.202403167","first_author":null,"corresponding_authors":null},{"pmid":"40702182","title":"Structural variation in 1,019 diverse humans based on long-read sequencing.","abstract":"Genomic structural variants (SVs) contribute substantially to genetic diversity and human diseases<sup>1-4<\/sup>, yet remain under-characterized in population-scale cohorts<sup>5<\/sup>. Here we conducted long-read sequencing<sup>6<\/sup> in 1,019 humans to construct an intermediate-coverage resource covering 26 populations from the 1000 Genomes Project. Integrating linear and graph genome-based analyses, we uncover over 100,000 sequence-resolved biallelic SVs and we genotype 300,000 multiallelic variable number of tandem repeats<sup>7<\/sup>, advancing SV characterization over short-read-based population-scale surveys<sup>3,4<\/sup>. We characterize deletions, duplications, insertions and inversions in distinct populations. Long interspersed nuclear element-1 (L1) and SINE-VNTR-Alu (SVA) retrotransposition activities mediate the transduction<sup>8,9<\/sup> of unique sequence stretches in 5' or 3', depending on source mobile element class and locus. SV breakpoint analyses point to a spectrum of homology-mediated processes contributing to SV formation and recurrent deletion events. Our open-access resource underscores the value of long-read sequencing in advancing SV characterization and enables guiding variant prioritization in patient genomes.","authors":"Schloissnig, S., Pani, S., Ebler, J., Hain, C., Tsapalou, V., S\u00f6ylev, A., H\u00fcther, P., Ashraf, H., Prodanov, T., Asparuhova, M., Magalh\u00e3es, H., H\u00f6ps, W., Sotelo-Fonseca, JE., Fitzgerald, T., Santana-Garcia, W., Moreira-Pinhal, R., Hunt, S., P\u00e9rez-Llanos, FJ., Wollenweber, TE., Sivalingam, S., Wieczorek, D., C\u00e1ceres, M., Gilissen, C., Birney, E., Ding, Z., Jensen, JN., Podduturi, N., Stutzki, J., Rodriguez-Martin, B., Rausch, T., Marschall, T., Korbel, JO.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-07-23","doi":"10.1038\/s41586-025-09290-7","first_author":null,"corresponding_authors":null},{"pmid":"40764806","title":"Functional divergence of conserved developmental plasticity genes between two distantly related nematodes.","abstract":"Genes diverge in form and function in multiple ways over time; they can be conserved, acquire new roles, or eventually be lost. However, the way genes diverge at the functional level is little understood, particularly in plastic systems. We investigated this process using two distantly related nematode species, Allodiplogaster sudhausi and Pristionchus pacificus. Both these nematodes display environmentally-influenced developmental plasticity of mouth-form feeding structures. This phenotype can be manipulated by growth on particular diets, making them ideal traits to investigate functional divergence of developmental plasticity genes between organisms. Using CRISPR-engineered mutations in A. sudhausi mouth-form genes, we demonstrate examples of the various ways ancestral genes regulate developmental plasticity and how these roles can progressively diverge. We examined four ancestral genes, revealing distinct differences in their conservation and divergence in regulating mouth phenotype in both species. Loss of certain genes results in similar developmental disruptions in both species, while for others they are distinct. Additionally, two ancestral genes retain their functions as switch genes, which completely prevent a phenotype, and the other two display quantitative effects, with knock-outs in these genes displaying intermediate phenotypes. Remarkably, despite the evolutionary distance, all genes examined were involved in mouth-form regulation. Finally, key sulfatase-encoding genes act downstream of the other genes, suggesting they play a major role in mouth-form plasticity. Together, this study represents the first mutant-based functional analysis of the evolution of developmental plasticity between two highly diverged species, offering new insights into the genetic mechanisms underlying phenotypic evolution.","authors":"Wighard, S., Witte, H., Sommer, RJ.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Sci Rep","volume":"15","issue":"1","page":"28518","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-06","doi":"10.1038\/s41598-025-14207-5","first_author":null,"corresponding_authors":null},{"pmid":"40804100","title":"In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies.","abstract":"Cross-linking mass spectrometry has evolved as a powerful technique to study protein-protein interactions and to provide structural information. Low reaction efficiencies, and complex matrices lead to challenging system wide crosslink analysis. We improved and streamlined an Azide-A-DSBSO based in vivo crosslinking workflow employing two orthogonal effective enrichment steps: Affinity enrichment and size exclusion chromatography (SEC). Combined, they allow an effective enrichment of DSBSO containing peptides and remove the background of linear as well as mono-linked peptides. We found that the analysis of a single SEC fraction is effective to yield ~90% of all crosslinks, which is important whenever measurement time is limited, and sample throughput is crucial. Our workflow resulted in more than 5000 crosslinks from K562 cells and generated a comprehensive PPI network. From 393 PPI found within the nucleus, 56 are novel. We further show, that by applying DSBSO to nuclear extracts we yield more crosslinks on lower abundant proteins and showcase this on the DEAD-box RNA helicase DDX39B which is predominantly expressed in the nucleus. Our data indicates that DDX39B might be present in monomeric and dimeric forms together with DDX39A within the nuclear extracts analyzed.","authors":"Br\u00e4uer, P., Tirian, L., M\u00fcller, F., Mechtler, K., Matzinger, M.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Commun Chem","volume":"8","issue":"1","page":"245","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-16","doi":"10.1038\/s42004-025-01644-6","first_author":null,"corresponding_authors":null},{"pmid":"40478934","title":"Inducible protein degradation reveals inflammation-dependent function of the T<sub>reg<\/sub> cell lineage-defining transcription factor Foxp3.","abstract":"Regulatory T cells (T<sub>reg<\/sub> cells) are immunosuppressive CD4 T cells defined by expression of the transcription factor Foxp3. Genetic loss-of-function mutations in <i>Foxp3<\/i> cause lethal multiorgan autoimmune inflammation resulting from defects in T<sub>reg<\/sub> cell development and suppressive activity. Whether T<sub>reg<\/sub> cells are continuously dependent on Foxp3 is still unclear. Here, we leveraged chemically induced protein degradation to show that functionally suppressive T<sub>reg<\/sub> cells in healthy organs can persist in the near-complete absence of Foxp3 protein for at least 10 days. Conversely, T<sub>reg<\/sub> cells responding to type 1 inflammation in settings of autoimmunity, viral infection, or cancer were selectively lost upon Foxp3 protein depletion. Acute degradation experiments revealed that Foxp3 acts mostly as a direct transcriptional repressor and modulates responsiveness to cytokine stimulation. This inflammation-dependent requirement for continuous Foxp3 activity enabled induction of a selective antitumor immune response upon systemic Foxp3 depletion, without causing deleterious T cell expansion in healthy organs.","authors":"J\u00e4ger, C., Dimitrova, P., Sun, Q., Tennebroek, J., Marchiori, E., Jaritz, M., Rauschmeier, R., Estivill, G., Obenauf, A., Busslinger, M., van der Veeken, J.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Sci Immunol","volume":"10","issue":"108","page":"eadr7057","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-06","doi":"10.1126\/sciimmunol.adr7057","first_author":null,"corresponding_authors":null},{"pmid":"40847602","title":"CLEC18A interacts with sulfated glycosaminoglycans and controls clear cell renal cell carcinoma progression.","abstract":"C-type lectins are a large protein family with essential functions in both health and disease. In cancer, some C-type lectins have been found to both promote and inhibit tumor growth, but many of the C-type lectins still remain uncharacterized. Here, we report a key role of the C-type lectin domain family 18 members (CLEC18 family) in the progression of clear cell renal cell carcinoma (ccRCC). The CLEC18 family is conserved across the entire Chordata phylum, with a high frequency of duplication events in humans compared to other species. We found that CLEC18A is exclusively expressed in the proximal tubule of the kidney and the medial habenula of the brain. We further identified sulfated glycosaminoglycans as the main CLEC18A ligand, making them unique among C-type lectins. In ccRCC patients, high expression of genes in the CLEC18 family in the tumor is associated with improved survival. In mouse models of ccRCC, deletion of the mouse ortholog, Clec18a, resulted in enhanced tumor growth. Our results establish CLEC18A as a newly identified and critical regulator of ccRCC tumor growth and highlight the potential benefit of modulating expression of CLEC18 family genes in the renal tumor microenvironment.","authors":"Jonsson, G., Hofmann, M., Mereiter, S., Hartley-Tassell, L., Onji, M., Sakic, I., Oliveira, T., Hoffmann, D., Novatchkova, M., Schleiffer, A., Penninger, JM.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"FEBS J","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-23","doi":"10.1111\/febs.70236","first_author":null,"corresponding_authors":null},{"pmid":"40840617","title":"Heart saver: Comprehensive investigation of (redox-) proteomic and thiol metabolite changes induced by Cana-, Dapa-, Empagliflozin treatment in 2D and 3D heart cell models reveals increased mitochondrial activity and glutathione redox defense and involvement of redox signaling.","abstract":"on Status=\"Publisher\" Owner=\"NLM\"><PMID Version=\"1\">40840617<\/PMID><DateRevised><Year>2025<\/Year><Month>08<\/Month><Day>21<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1879-0631<\/ISSN><JournalIssue CitedMedium=\"Internet\"><PubDate><Year>2025<\/Year><Month>Aug<\/Month><Day>19<\/Day><\/PubDate><\/JournalIssue><Title>Life sciences<\/Title><ISOAbbreviation>Life Sci<\/ISOAbbreviation><\/Journal><ArticleTitle>Heart saver: Comprehensive investigation of (redox-) proteomic and thiol metabolite changes induced by Cana-, Dapa-, Empagliflozin treatment in 2D and 3D heart cell models reveals increased mitochondrial activity and glutathione redox defense and involvement of redox signaling.<\/ArticleTitle><Pagination><StartPage>123923<\/StartPage><MedlinePgn>123923<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.lfs.2025.123923<\/ELocationID><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0024-3205(25)00558-2<\/ELocationID><Abstract><AbstractText Label=\"AIMS\" NlmCategory=\"OBJECTIVE\">Antidiabetic drugs, sodium-glucose co-transporter-2 inhibitors (SGLT-2i), have demonstrated heart-saving properties independently of the diabetes status of a patient. We aimed to discover SGLT-2i-specific cardiac targets.","authors":"Hoehlschen, J., Gosset, \u00c9., Hofreither, D., Jahnel, S., Mendjan, S., Schittmayer, M., Tomin, T., Birner-Gruenberger, R.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Life Sci","volume":null,"issue":null,"page":"123923","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-21","doi":"10.1016\/j.lfs.2025.123923","first_author":null,"corresponding_authors":null},{"pmid":"40950056","title":"An electrostatic repulsion model of centromere organisation.","abstract":"During cell division, chromosomes reorganise into compact bodies in which centromeres localise precisely at the chromatin surface to enable kinetochore-microtubule interactions essential for genome segregation. The physical principles guiding this centromere positioning remain unknown. Here, we reveal that human core centromeres are directed to the chromatin surface by repulsion of centromere-associated proteins - independent of condensin-mediated loop extrusion and microtubule engagement. Using cellular perturbations, biochemical reconstitution, and multiscale molecular dynamics simulations, we show that chromatin surface localisation emerges from repulsion between condensed chromatin and both the kinetochore and the highly negatively charged centromere protein, CENP-B. Together, these elements form a centromeric region composed of two domains with opposing affinities, one favouring integration within the mitotic chromosome and the other favouring exposure to the surrounding cytoplasm, thereby driving surface positioning. Tethering synthetic negatively charged proteins to chromatin was sufficient to recapitulate this surface localisation in cells and in vitro, indicating that electrostatic repulsion is a key determinant of surface localisation. These findings demonstrate that centromere layering is not hardwired by chromatin folding patterns but instead emerges from phase separation in chromatin. Our work uncovers electrostatic polarity as a general and programmable mechanism to spatially organise chromatin.","authors":"Bell, C., Chen, L., Maristany, MJ., Blaukopf, C., Zhou, H., Huertas, J., Perez Lopez, JI., Langer, CCH., Steinacker, TL., Schuette, N., Doolittle, L., Espinosa, JR., Redding, S., Collepardo-Guevara, R., Rosen, MK., Gerlich, DW.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-09-15","doi":"10.1101\/2025.09.01.673455","first_author":null,"corresponding_authors":null},{"pmid":"40876457","title":"A split-site E3 ligase mechanism enables ZNFX1 to ubiquitinate and cluster single-stranded RNA into ubiquitin-coated nucleoprotein particles.","abstract":"Eukaryotic cells use a multi-layered immune response to combat intracellular pathogens. The ubiquitin ligase ZNFX1 has emerged as a crucial yet little understood player that regulates the immune response while protecting against RNA viruses. Our study unveils the molecular mechanism of ZNFX1, mediated by the joint activity of a helicase serving as a nucleic acid sensor and a non-conventional E3 module featuring a split active site. We demonstrate that single-stranded RNA stimulates E3 activity by fostering dimerization of ZNFX1 subunits that translocate along nucleic acid tracks. Juxtaposed E3 domains complement each other, leading to the ubiquitination of ZNFX1 itself and engaged RNA molecules, while clustering nucleic acids into dense nucleoprotein particles. We show that the E3 ligase activity of ZNFX1 protects cells during an immune response and propose that ubiquitin-coated particles formed by ZNFX1 represent part of an ancient mechanism to regulate both foreign and host RNA in the cell.","authors":"Grabarczyk, DB., Aird, EJ., Reznikow, V., Kirchgatterer, PC., Ehrmann, JF., Kurzbauer, R., Bell, LE., Kellner, MJ., Aggarwal, R., Schleiffer, A., Faas, V., Deszcz, L., Meinhart, A., Versteeg, GA., Penninger, JM., Stelzl, LS., Gaidt, MM., Tessmer, I., Corn, JE., Clausen, T.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-28","doi":"10.1016\/j.cell.2025.08.006","first_author":null,"corresponding_authors":null},{"pmid":"40864552","title":"Quantitative profiling of human brain organoid cell diversity across four protocols and multiple cell lines.","abstract":"Human brain organoids are powerful in vitro models for brain development and disease. However, protocol and pluripotent cell line choices influence organoid variability and cell-type representation, complicating their use in biomedical research. Here, we systematically analyze the cellular and transcriptional landscape of brain organoids across multiple cell lines using four protocols aimed at recapitulating dorsal and ventral forebrain, midbrain, and striatum. We introduce the NEST-Score to evaluate cell-line- and protocol-driven differentiation propensities and comparisons to in vivo references. Thereby, we establish a set of protocols that together recreate the majority of cell types in the developing brain and provide a reference of cell-type recapitulation across cell lines and protocols. Additionally, we identify early gene expression signatures predicting protocol-driven organoid generation. We provide easy access to our data through a web explorer, creating a reference for brain organoid research and allowing straightforward protocol and cell-line performance validation.","authors":"Naas, J., Balma\u00f1a, M., Holcik, L., Novatchkova, M., Dobnikar, L., Krausgruber, T., Ladst\u00e4tter, S., Bock, C., von Haeseler, A., Esk, C., Knoblich, JA.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Cell Rep","volume":"44","issue":"9","page":"116168","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-27","doi":"10.1016\/j.celrep.2025.116168","first_author":null,"corresponding_authors":null},{"pmid":"40885716","title":"Targeting DDX3X suppresses progression of KRAS-driven lung cancer by disrupting antioxidative homeostasis and inducing ferroptosis.","abstract":"Approximately 30% of human cancers carry various RAS mutations, including KRAS, NRAS, and HRAS. Among these mutations, KRAS is the most prevalent isoform detected in lung cancer. While several small molecular inhibitors targeting specifically KRAS<sup>G12C<\/sup> have been developed and tested clinically, alternative approaches are still necessary due to expected drug resistance. In this study, we present evidence that the loss of DDX3X significantly delays tumor progression in various KRAS-driven lung cancer models. Inhibition of DDX3X disrupts cysteine and glutathione metabolism, thereby inducing ferroptosis in lung cancer cells. This effect is primarily mediated by the downregulation of Cystathionine-&#x3b2;-synthase (CBS), the rate-limiting enzyme in cysteine generation. Mechanistically, DDX3X directly binds to the transcription factor JUND, which mediates the transcriptional regulation of METTL16, a key N<sup>6<\/sup>-methyladenosine methyltransferase, and subsequently regulates m<sup>6<\/sup>A modification and translation of CBS transcripts. This cascade induces hypermethylation and high expression of CBS, consequently triggering cysteine production and maintaining antioxidative homeostasis, which is essential for the survival of KRAS-driven lung cancer cells. Finally, we demonstrate that a newly developed DDX3X PROTAC degrader J10 efficiently delays lung cancer progression with multiple advantages compared to DDX3X small molecular inhibitor RK-33 and limited side effects. These findings unveil the potential of DDX3X as a valuable target for adjuvant therapies in managing KRAS-driven lung cancer.","authors":"Dian, M., Yun, L., Meng, Q., Lin, S., Ji, M., Zhou, Y., Liu, W., Yang, Z., Zhao, Y., Li, G., Jiang, J., Hao, W., Chen, Z., Zhou, Z., Zhang, R., Liu, T., He, Y., Yan, T., Wang, H., Cronin, SJF., Penninger, JM., Cai, K., Rao, S.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Cell Death Dis","volume":"16","issue":"1","page":"660","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-30","doi":"10.1038\/s41419-025-07980-8","first_author":null,"corresponding_authors":null},{"pmid":"40993223","title":"Coordination of cardiogenesis in vivo and in vitro.","abstract":"Heart development has been extensively explored on the anatomical, cellular and molecular levels. Yet, the intricate interplay of tissue organization, cellular lineages and molecular factors that orchestrate heart development, culminating in forming a seamlessly synchronized functional heart, remains challenging to investigate. Mechanistic&#xa0;studies conducted both in vivo using animal models and in vitro stem-cell-derived systems aim to unravel this complexity. In this Review, we discuss how the recent surge in technological advancements in imaging and genomics, coupled with the evolution of next-generation cardiac organoid models, has provided profound insights into these processes, holding significant implications for the development of novel therapies for congenital or acquired heart diseases. We discuss the development of the heart as the first functional organ - from the morphogenesis of the mesoderm, heart tube and cardiac chambers to the establishment of the initial heartbeat and pacemaker and further how morphogenesis and function collaboratively drive heart maturation.","authors":"Mendjan, S., Deyett, A., Yelon, D.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nat Rev Mol Cell Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-09-24","doi":"10.1038\/s41580-025-00878-5","first_author":null,"corresponding_authors":null},{"pmid":"40855131","title":"The mitotic STAG3-cohesin complex shapes male germline nucleome.","abstract":"Germ cells are unique in that they tailor chromatin toward generating totipotency. Accordingly, mammalian spermatogonia, including spermatogonial stem cells that constitute the source for male gametes, acquire distinctive chromatin organization with weak insulation, but the underlying mechanism remains unknown. Here we show that STAG3, so far known to exclusively form meiotic cohesins, generates a mitotic cohesin for male germline nucleome programming in mice. Owing to its shorter chromatin residence, STAG3-cohesin attenuates topologically associating domains, rewires enhancer-promoter and Polycomb-mediated repressive interactions, and facilitates finer and more strengthened compartments, establishing a distinctive spermatogonial nucleome. Moreover, in the absence of STAG3-cohesin, spermatogonial stem cells show an impaired differentiation priming for spermatogenesis. Mitotic STAG3-cohesin is also expressed in human B cells and their malignant variations, promoting their propagation. Our findings on mitotic STAG3-cohesin elucidate a principle of male germline nucleome programming, demonstrate an unexpected mitotic role for STAG3 and might potentially improve understanding of human malignancies.","authors":"Nagano, M., Hu, B., Ogata, K., Umemura, F., Ishikura, Y., Suzuki, S., Katsifis, CC., Yoshinaga, M., Litos, G., Nagasaka, K., Tang, W., Nosaka, Y., Sasada, H., Wang, H., Kondo, D., Katou, Y., Mizuta, K., Yabuta, Y., Ohta, H., de Luna Vitorino, FN., Arima, H., Ichikawa, T., Gabriele, M., Majewski, J., Garcia, BA., Takeuchi, O., Yoshida, S., Hansen, AS., Peters, JM., Ishihama, Y., Saitou, M.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nat Struct Mol Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-25","doi":"10.1038\/s41594-025-01647-w","first_author":null,"corresponding_authors":null},{"pmid":"40763028","title":"NIPBL and STAG1 enable loop extrusion by providing differential DNA-cohesin affinity.","abstract":"DNA loop extrusion by cohesin has emerged as a critical pathway for chromosome organization. In vitro single-molecule experiments indicate that loop extrusion requires the assembly of a heteropentameric complex consisting of the SMC1\/SMC3 heterodimer, STAG1, NIPBL, and the kleisin SCC1. The complexity of the complete extrusion machinery, consisting of multiple subunits, DNA binding sites, and ATPases poses substantial challenges for revealing the underlying biomolecular mechanism. As a result, a number of different models have been proposed, many of which do not agree on key mechanistic aspects, such as the details of DNA loading, holoenzyme assembly, or the consequences of ATP binding and hydrolysis. Here, we use mass photometry to comprehensively quantify all the key biomolecular interactions required for DNA loop extrusion. We find that STAG1 binds tightly to the trimeric complex formed by the SMC1\/SMC3 heterodimer and SCC1, and together they weakly, but cooperatively, bind the DNA. Full-length NIPBL tightly binds DNA, acting as a DNA anchor during the mechanochemical loop extrusion cycle. Cohesin mutants incapable of head engagement, and those lacking DNA-binding domains in the ATPase heads show negligible differences in overall DNA-affinity, suggesting a minor role of these features for DNA binding. Instead, we find an ATP-modulated DNA binding site created by the interaction of STAG1 with SMC1\/SMC3\/SCC1, important for repeated grabbing and release of DNA critical to extrusion. Our results call for a careful reexamination of the proposed mechanisms and set energetic boundaries for future proposals.","authors":"van Wee, R., Asor, R., Li, Y., Drechsel, D., Popova, M., Litos, G., Davidson, IF., Peters, JM., Kukura, P.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Proc Natl Acad Sci U S A","volume":"122","issue":"32","page":"e2514190122","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-05","doi":"10.1073\/pnas.2514190122","first_author":null,"corresponding_authors":null},{"pmid":"40683887","title":"Nanoscale 3D DNA tracing in non-denatured cells&#xa0;resolves the Cohesin-dependent loop architecture of the genome in situ.","abstract":"The spatial organization of the genome is essential for its functions, including gene expression and chromosome segregation. Phase separation and loop extrusion have been proposed to underlie compartments and topologically associating domains, however, whether the fold of genomic DNA inside the nucleus is consistent with such mechanisms has been difficult to establish in situ. Here, we present a 3D DNA-tracing workflow that resolves genome architecture in single structurally well-preserved cells with nanometre resolution. Our findings reveal that genomic DNA generally behaves as a flexible random coil at the 100-kb scale. At CTCF sites however, we find Cohesin-dependent loops in a subset of cells, in variable conformations from the kilobase to megabase scale. The 3D-folds we measured in hundreds of single cells allowed us to formulate a computational model that explains how sparse and dynamic loops in single cells underlie the appearance of compact topological domains measured in cell populations.","authors":"Beckwith, KS., \u00d8deg\u00e5rd-Fougner, \u00d8., Morero, NR., Barton, C., Schueder, F., Tang, W., Alexander, S., Peters, JM., Jungmann, R., Birney, E., Ellenberg, J.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Nat Commun","volume":"16","issue":"1","page":"6673","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-07-19","doi":"10.1038\/s41467-025-61689-y","first_author":null,"corresponding_authors":null},{"pmid":"40516048","title":"Cohesin supercoils DNA during loop extrusion.","abstract":"Cohesin extrudes genomic DNA into loops that promote chromatin assembly, gene regulation, and gene recombination. Loop extrusion depends on large-scale conformational changes in cohesin, but how these translocate DNA is poorly understood. Here, we provide evidence that cohesin negatively supercoils DNA during loop extrusion. Supercoiling requires the engagement of cohesin's ATPase heads, DNA clamping by these heads, and a DNA-binding site on cohesin's hinge, indicating that cohesin twists DNA when constraining it between the hinge and the clamp. A cohesin mutant defective in negative supercoiling forms shorter loops in cells, and a similar, although weaker, phenotype is observed after the depletion of topoisomerase I. These results suggest that supercoiling is an integral part of the loop-extrusion mechanism and that relaxation of supercoiled DNA is required for cohesin-mediated loop extrusion and genome architecture.","authors":"Davidson, IF., Barth, R., Nagasaka, K., Tang, W., Wutz, G., Horn, S., Janissen, R., Stocsits, RR., Chlosta, E., Bauer, BW., Dekker, C., Peters, JM.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Cell Rep","volume":"44","issue":"6","page":"115856","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-27","doi":"10.1016\/j.celrep.2025.115856","first_author":null,"corresponding_authors":null},{"pmid":"41025451","title":"A fluorescence lifetime separation approach for FLIM live-cell imaging.","abstract":"Fluorescence lifetime imaging microscopy (FLIM) translates the duration of excited states of fluorophores into lifetime information as an additional source of contrast in images of biological samples. This offers the possibility to separate fluorophores particularly beneficial in case of similar excitation spectra. Here, we demonstrate the distinction of fluorescent molecules based on FLIM phasor analysis, called lifetime separation, in live-cell imaging using open-source software for analysis. We showcase two applications using Caenorhabditis elegans as a model system. First, we separated the highly spectrally overlapping fluorophores mCherry and mKate2 to distinctively track tagged proteins in six-dimensional datasets to investigate cell division in the developing early embryo. Second, we separated fluorescence of tagged proteins of interest from masking natural autofluorescence in adult hermaphrodites. For FLIM data handling and workflow implementation, we developed the open-source plugin napari-flim-phasor-plotter to implement conversion, visualisation, analysis and reuse of FLIM data of different formats. Our work thus advances technical applications and bioimage data management and analysis in FLIM microscopy for life science research.","authors":"Wetzker, C., Zoccoler, ML., Iarovenko, S., Okafornta, CW., Nobst, A., Hartmann, H., M\u00fcller-Reichert, T., Haase, R., Fabig, G.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"J Microsc","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-09-30","doi":"10.1111\/jmi.70036","first_author":null,"corresponding_authors":null},{"pmid":"40875847","title":"Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control.","abstract":"Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome system, where UBR4 acts as an essential E4 ubiquitin ligase, amplifying degradation marks on defective proteins. Cryo-electron microscopy analysis of UBR4 in complex with its cofactors KCMF1 and CALM1 reveals a massive 1.3-megadalton ring structure, featuring a central substrate-binding arena and flexibly attached catalytic units. Our structure shows how UBR4 binds substrate and extends lysine-48-specific ubiquitin chains. Efficient substrate targeting depends on both preubiquitination and specific N-degrons, with KCMF1 acting as a key substrate filter. The architecture of the E4 megacomplex is conserved across eukaryotes, but species-specific adaptations allow UBR4 to perform its precisely tuned quality control function in diverse cellular environments.","authors":"Grabarczyk, DB., Ehrmann, JF., Murphy, P., Yang, WS., Kurzbauer, R., Bell, LE., Deszcz, L., Neuhold, J., Schleiffer, A., Shulkina, A., Lee, J., Shin, JS., Meinhart, A., Versteeg, GA., Zavodszky, E., Song, HK., Hegde, RS., Clausen, T.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Science","volume":"389","issue":"6763","page":"909-914","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-28","doi":"10.1126\/science.adv9309","first_author":null,"corresponding_authors":null},{"pmid":"40274822","title":"TRIM52 maintains cellular fitness and is under tight proteolytic control by multiple giant E3 ligases.","abstract":"Tripartite motif 52 (TRIM52) exhibits strong positive selection in humans, yet is lost in many other mammals. In contrast to what one would expect for such a non-conserved factor, TRIM52 loss compromises cell fitness. We set out to determine the cellular function of TRIM52. Genetic and proteomic analyses revealed TRIM52 physically and functionally interacts with the DNA repair machinery. Our data suggest that TRIM52 limits topoisomerase 2 adducts, thereby preventing cell-cycle arrest. Consistent with a fitness-promoting function, TRIM52 is upregulated in various cancers, prompting us to investigate its regulatory pathways. We found TRIM52 to be targeted for ultra-rapid proteasomal degradation by the giant E3 ubiquitin ligases BIRC6, HUWE1, and UBR4\/KCMF1. BIRC6 mono-ubiquitinates TRIM52, with subsequent extension by UBR4\/KCMF1. These findings suggest a role for TRIM52 in maintaining genome integrity, and regulation of its own abundance through multi-ligase degradation.","authors":"Shulkina, A., Hacker, K., Ehrmann, JF., Budroni, V., Mandlbauer, A., Bock, J., Grabarczyk, DB., Edobor, G., Cochella, L., Clausen, T., Versteeg, GA.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Nat Commun","volume":"16","issue":"1","page":"3894","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-25","doi":"10.1038\/s41467-025-59129-y","first_author":null,"corresponding_authors":null},{"pmid":"40500448","title":"SP140-RESIST pathway regulates interferon mRNA stability and antiviral immunity.","abstract":"Type I interferons are essential for antiviral immunity<sup>1<\/sup> but must be tightly regulated<sup>2<\/sup>. The conserved transcriptional repressor SP140 inhibits interferon-&#x3b2; (Ifnb1) expression through an unknown mechanism<sup>3,4<\/sup>. Here we report that SP140 does not directly repress Ifnb1 transcription. Instead, SP140 negatively regulates Ifnb1 mRNA stability by directly repressing the expression of a previously uncharacterized regulator that we call RESIST (regulated stimulator of interferon via stabilization of transcript; previously annotated as annexin 2 receptor). RESIST promotes Ifnb1 mRNA stability by counteracting Ifnb1 mRNA destabilization mediated by the tristetraprolin (TTP) family of RNA-binding proteins and the CCR4-NOT deadenylase complex. SP140 localizes within punctate structures called nuclear bodies that have important roles in silencing DNA-virus gene expression in the nucleus<sup>3<\/sup>. Consistent with this observation, we find that SP140 inhibits replication of the gammaherpesvirus MHV68. The antiviral activity of SP140 is independent of its ability to regulate Ifnb1. Our results establish dual antiviral and interferon regulatory functions for SP140. We propose that SP140 and RESIST participate in antiviral effector-triggered immunity<sup>5,6<\/sup>.","authors":"Witt, KC., Dziulko, A., An, J., Pekovic, F., Cheng, AX., Liu, GY., Lee, OV., Turner, DJ., Lari, A., Gaidt, MM., Chavez, R., Fattinger, SA., Abraham, P., Dhaliwal, H., Lee, AY., Kotov, DI., Coscoy, L., Glaunsinger, BA., Valkov, E., Chuong, EB., Vance, RE.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nature","volume":"643","issue":"8074","page":"1372-1380","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/pubmed.ncbi.nlm.nih.gov\/39974928\/","articledate":"2025-07-30","doi":"10.1038\/s41586-025-09152-2","first_author":null,"corresponding_authors":null},{"pmid":"40909644","title":"Structural basis of NSD2 degradation via targeted recruitment of SCF-FBXO22.","abstract":"Targeted protein degradation (TPD) through the ubiquitin-proteasome system is driven by compound-mediated polyubiquitination of a protein-of-interest by an E3 ubiquitin (Ub) ligase. To date, relatively few E3s have been successfully utilized for TPD and the governing principles of functional ternary complex formation between the E3, degrader, and protein target remain elusive. FBXO22 has recently been harnessed by several groups to target different proteins for degradation. FBXO22 recruitment has been enabled through degraders that covalently modify its cysteine residues. Here, we reveal that the aldehyde derivative of UNC10088 promotes cooperative binding of FBXO22 to NSD2, a histone methyltransferase and oncogenic protein, leading to a cryo-EM structure of the full SKP1-CUL1-F-box (SCF)-FBXO22 complex with NSD2. This structure revealed a conformational change in the FBXO22 loop surrounding C326, further exposing the cysteine for covalent recruitment. Additional medicinal chemistry efforts led to the discovery of benzaldehyde-based non-prodrug degraders that similarly engage C326 of FBXO22 and potently degrade NSD2. Furthermore, unlike many degraders, our molecules recruit NSD2 to a different surface of FBXO22 than the known FBXO22 substrate BACH1, allowing for concurrent complex formation and degradation of both the neosubstrate and endogenous substrates. Overall, we demonstrate the biochemical and structural basis for NSD2 degradation, revealing key principles for efficient and selective TPD by SCF<sup>FBXO22<\/sup>.","authors":"Robertson, KC., Amann, SJ., Liu, T., Funk, AV., Wang, X., Grishkovskaya, I., Tabor, JR., Norris-Drouin, JL., Arrowsmith, CH., Collins, JL., Emanuele, MJ., Haselbach, D., James, LI., Brown, NG.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-09-15","doi":"10.1101\/2025.08.29.673087","first_author":null,"corresponding_authors":null},{"pmid":"40848707","title":"Cryo-focused ion beam milling for cryo-electron tomography: Shaping the future of in situ structural biology.","abstract":"Cryo-focused ion beam instruments to produce cellular thin sections for subsequent imaging by cryo-electron tomography have become an integral part of the methodologies for in situ structural biology, enabling high-resolution imaging of biological structures in their native environment. The application of these instruments has opened windows into cells that allowed unprecedented insights into the ultrastructure of cells and more recently, small multicellular organisms and tissues. While great strides have been made in the characterization of cryo-FIB milling and the streamlining of workflows with these tools, many limitations and technical challenges remain to be resolved. Here, we discuss the technical and technological challenges ahead to continue the steep rise of biological discoveries by in-cell cryo-electron tomography to enable cellular structural biology in the multicellular context.","authors":"Klumpe, S., Plitzko, JM.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Curr Opin Struct Biol","volume":"94","issue":null,"page":"103138","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-10-12","doi":"10.1016\/j.sbi.2025.103138","first_author":null,"corresponding_authors":null},{"pmid":"40829587","title":"The small GTPase Ran defines nuclear pore complex asymmetry.","abstract":"Nuclear pore complexes (NPCs) bridge across the nuclear envelope and mediate nucleocytoplasmic exchange. They consist of hundreds of nucleoporin building blocks and exemplify the structural complexity of macromolecular assemblies. To ensure transport directionality, different nucleoporin complexes are attached to the cytoplasmic and nuclear face of the NPC. How those asymmetric structures are faithfully assembled onto the symmetric scaffold architecture that exposes the same interaction surfaces to either side remained enigmatic. Here, we combine cryo-electron tomography, subtomogram averaging, and template matching with live imaging to address this question in budding yeast and Drosophila. We genetically induce ectopic nuclear pores and show that pores outside the nuclear envelope are symmetric. We furthermore demonstrate that the peripheral NPC configuration is affected by the nucleotide state of the small GTPase Ran. Our findings indicate that the nuclear transport system is self-regulatory, namely that the same molecular mechanism controls both transport and transport channel composition.","authors":"Sachweh, J., B\u00f6rmel, M., Klumpe, S., Becker, A., Taniguchi, R., Kuba\u0144ska, MA., Pintschovius, V., Kaindl, E., Plitzko, JM., Wilfling, F., Beck, M., Hampoelz, B.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-19","doi":"10.1016\/j.cell.2025.07.025","first_author":null,"corresponding_authors":null},{"pmid":"40467589","title":"Reduction of SEM charging artefacts in native cryogenic biological samples.","abstract":"Scanning electron microscopy (SEM) of frozen-hydrated biological samples allows imaging of subcellular structures at the mesoscale in a representation of their native state. Combined with focused ion beam milling (FIB), serial FIB\/SEM can be used to build a 3-dimensional model of cells and tissues. The correlation of specific regions of interest with cryo-electron microscopy (cryoEM) can additionally enable subsequent high-resolution analysis. However, the use of serial FIB\/SEM imaging-based methods is often limited due to charging artefacts arising from insulating areas of cryogenically preserved samples. Here, we demonstrate the use of interleaved scanning to attenuate these artefacts, allowing the observation of biological features that otherwise would be masked or distorted. We apply our method to samples where inherent features were not visible using conventional scanning. These examples include membrane contact sites within mammalian cells, visualisation of the degradation compartment in the algae E. gracilis and observation of a network of membranes within different types of axons in an adult mouse cortex. The proposed alternative scanning method could also be applied to imaging other non-conductive specimens in SEM.","authors":"Velazco, A., Glen, T., Klumpe, S., Pennington, A., Zhang, J., Smith, JLR., Glynn, C., Bowles, W., Kobylynska, M., Fleck, RA., Naismith, JH., Kim, JS., Darrow, MC., Grange, M., Kirkland, AI., Dumoux, M.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Nat Commun","volume":"16","issue":"1","page":"5204","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-13","doi":"10.1038\/s41467-025-60545-3","first_author":null,"corresponding_authors":null},{"pmid":"40633503","title":"Coping with uncertainty: Challenges for robust pattern formation in dynamical tissues.","abstract":"An outstanding question in biology is how tissue patterning emerges during development. The concept of positional information, which posits that gradients of morphogens instruct cell fate in a concentration-dependent manner, has been an influential framework to understand pattern formation. Recent studies, however, highlight that developing tissues are highly dynamic, with cellular movements, arising from local mechanical fluctuations or global morphogenetic forces, that often coincide with morphogen signaling and cell fate specification. This calls for a more dynamic understanding of pattern formation by explicitly investigating the interplay between signaling, cell fate and morphogenesis. In this review, we first discuss emerging evidence on the role of cellular movements in modulating signaling dosage and cell fate acquisition. We then examine the biophysical strategies employed by developing tissues to achieve robust patterning despite ongoing cellular dynamics and large-scale morphogenesis. While cellular movements may intuitively be viewed as disruptive to patterning programs, recent evidence suggests that when coupled with cell fate, they can act as a critical mechanism for generating and stabilizing precise tissue patterns during development.","authors":"Tsai, TY., Pinheiro, D.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Semin Cell Dev Biol","volume":"173","issue":null,"page":"103629","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-08-20","doi":"10.1016\/j.semcdb.2025.103629","first_author":null,"corresponding_authors":null},{"pmid":"41034156","title":"Mechanisms of Messenger RNA Packaging and Export.","abstract":"The packaging and export of messenger RNA (mRNA) are essential cellular pathways that bridge the nuclear and cytoplasmic phases of eukaryotic gene expression. During their nuclear maturation, mRNAs are packaged by proteins into mRNA ribonucleoproteins (mRNPs). Other proteins then assist in the export of mRNPs into the cytoplasm for translation. Together, these proteins play critical roles in compacting the mRNA, defining mRNA identity, preventing unwanted interactions, and orchestrating mRNA transport through the nuclear pore complex (NPC). Here, we review decades of genetics and biochemistry alongside recent structural and functional insights and outline a general framework for the late stages of nuclear mRNA biogenesis and export. We also highlight open questions, including the mechanisms of mRNP packaging, mRNP export through the NPC, and the regulation, quality control, and exploitation of the pathway.","authors":"Faraway, R., Zenklusen, D., Plaschka, C.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Annu Rev Cell Dev Biol","volume":"41","issue":"1","page":"479-504","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-10-01","doi":"10.1146\/annurev-cellbio-101123-045256","first_author":null,"corresponding_authors":null},{"pmid":"40993389","title":"Collective homeostasis of condensation-prone proteins via their mRNAs.","abstract":"The concentration of proteins containing intrinsically disordered regions must be tightly controlled to maintain cellular homeostasis<sup>1,2<\/sup>. However, mechanisms for collective control of these proteins, which tend to localize to membraneless condensates, are less understood than pathways mediated by membrane-bound organelles<sup>3,4<\/sup>. Here we report 'interstasis', a homeostatic mechanism in which increased concentration of proteins within RNA-protein condensates induces the sequestration of their own mRNAs. The selectivity of interstatic mRNA capture relies on the structure of the genetic code and conserved codon biases, which ensure that similar multivalent RNA regions encode similar low-complexity domains. For example, arginine-enriched mixed charge domains (R-MCDs) tend to be encoded by repetitive purine-rich sequences in mRNAs. Accumulation of proteins containing R-MCDs increases the cohesion of nuclear speckles, which induces selective capture of purine-rich multivalent mRNAs. The multivalent regions are bound by specific RNA-binding proteins, including TRA2 proteins, which relocalize to speckles upon interstasis to promote selective mRNA capture. CLK-mediated phosphorylation of TRA2 proteins counters their localization to speckles, thereby modulating interstasis. Thus, the condensation properties of nuclear speckles act as a sensor for interstasis, a collective negative-feedback loop that co-regulates mRNAs of highly dosage-sensitive genes, which primarily encode nuclear condensation-prone proteins.","authors":"Faraway, R., Costello Heaven, N., Digby, H., Kuret Hodnik, K., Rebselj, J., Wilkins, OG., Chakrabarti, AM., Iosub, IA., Vadnjal, N., Dore, R., Knez, L., Ameres, SL., Plaschka, C., Ule, J.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-10-01","doi":"10.1038\/s41586-025-09568-w","first_author":null,"corresponding_authors":null},{"pmid":"40912245","title":"Target RNA recognition drives PIWI<sup>&#x2217;<\/sup> complex assembly for transposon silencing.","abstract":"PIWI-clade Argonaute proteins and their associated PIWI-interacting RNAs (piRNAs) are essential guardians of genome integrity, silencing transposable elements through distinct nuclear and cytoplasmic pathways. Nuclear PIWI proteins direct heterochromatin formation at transposon loci, while cytoplasmic PIWIs cleave transposon transcripts to initiate piRNA amplification. Both processes rely on target RNA recognition by PIWI-piRNA complexes, yet how this leads to effector recruitment is unclear. Here, we show that target engagement triggers formation of complexes, termed PIWI<sup>&#x2217;<\/sup>-comprising a PIWI protein, a piRNA-target duplex, a GTSF family protein, and Maelstrom-that serve as molecular platforms recruiting downstream effectors. In Drosophila, nuclear Piwi<sup>&#x2217;<\/sup> engages the SFiNX complex to establish heterochromatin, while cytoplasmic Aubergine<sup>&#x2217;<\/sup> complexes recruit the helicase Spindle-E to promote piRNA biogenesis. Evolutionary analysis reveals that PIWI<sup>&#x2217;<\/sup> formation is conserved across metazoans, uncovering an ancient mechanism coupling piRNA-guided target recognition to effector function. These findings define a unifying molecular principle for PIWI-mediated silencing across cellular compartments.","authors":"Portell-Montserrat, J., Tirian, L., Yu, C., Silvestri, G., Hohmann, U., Handler, D., Duchek, P., Fin, L., Plaschka, C., Brennecke, J.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Mol Cell","volume":"85","issue":"17","page":"3288-3305.e6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-09-05","doi":"10.1016\/j.molcel.2025.08.007","first_author":"Portell-Montserrat, J.","corresponding_authors":"Plaschka, C., Brennecke, J."},{"pmid":"41000980","title":"ArchVelo: Archetypal Velocity Modeling for Single-cell Multi-omic Trajectories.","abstract":"Inferring dynamic cellular processes from static single-cell measurements remains a central challenge in genomics. Here we introduce ArchVelo, a new method for modeling gene regulation and inferring cell trajectories using single-cell simultaneous chromatin accessibility (scATAC-seq) and transcriptomic (scRNA-seq) profiling. ArchVelo represents chromatin accessibility as a set of archetypes-shared regulatory programs-and models their dynamic influence on transcription. Compared to previous methods, ArchVelo improves inference accuracy and gene-level latent time alignment, and enables identification of the underlying transcription factor activity. We benchmark ArchVelo on developing mouse brain and human hematopoiesis datasets and apply it to CD8 T cells responding to viral infection, revealing distinct trajectories of differentiation and proliferation. Focusing on the progenitor CD8 T cell population with key roles in sustaining immune responses and translationally linked to immunotherapy outcomes, we identify a previously uncharacterized differentiation trajectory from Ccr6 <sup>-<\/sup> to Ccr6 <sup>+<\/sup> progenitors, shared between acute and chronic infection. In sum, ArchVelo provides a principled framework for modeling dynamic gene regulation in multi-omic single-cell data across biological systems.","authors":"Avdeeva, M., Walker, S., van der Veeken, J., Rudensky, A., Pritykin, Y.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-09-26","doi":"10.1101\/2025.09.14.676182","first_author":null,"corresponding_authors":null},{"pmid":"40153488","title":"An aging bone marrow exacerbates lung fibrosis by fueling profibrotic macrophage persistence.","abstract":"Pulmonary fibrosis is an incurable disease that manifests with advanced age. Yet, how hematopoietic aging influences immune responses and fibrosis progression remains unclear. Using heterochronic bone marrow transplant mouse models, we found that an aged bone marrow exacerbates lung fibrosis irrespective of lung tissue age. Upon lung injury, there was an increased accumulation of monocyte-derived alveolar macrophages (Mo-AMs) driven by cell-intrinsic hematopoietic aging. These Mo-AMs exhibited an enhanced profibrotic profile and stalled maturation into a homeostatic, tissue-resident phenotype. This delay was shaped by cell-extrinsic environmental signals such as reduced pulmonary interleukin-10 (IL-10), perpetuating a profibrotic macrophage state. We identified regulatory T cells (T<sub>regs<\/sub>) as critical providers of IL-10 upon lung injury that promote Mo-AM maturation and attenuate fibrosis progression. Our study highlights the impact of an aging bone marrow on lung immune regulation and identifies T<sub>reg<\/sub>-mediated IL-10 signaling as a promising target to mitigate fibrosis and promote tissue repair.","authors":"Farhat, A., Radhouani, M., Deckert, F., Zahalka, S., Pimenov, L., Fokina, A., Hakobyan, A., Oberndorfer, F., Br\u00f6samlen, J., Hladik, A., Lakovits, K., Meng, F., Quattrone, F., Boon, L., Vesely, C., Starkl, P., Boucheron, N., Menche, J., van der Veeken, J., Ellmeier, W., Gorki, AD., Campbell, C., Gawish, R., Knapp, S.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Sci Immunol","volume":"10","issue":"105","page":"eadk5041","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-15","doi":"10.1126\/sciimmunol.adk5041","first_author":null,"corresponding_authors":null},{"pmid":"40596504","title":"Engineered microRNA scaffolds for potent gene silencing in vivo.","abstract":"RNA interference (RNAi) is emerging as a powerful strategy for therapeutic targeting of \"undruggable\" targets. However, efficacy of currently used siRNA-based therapies is often hindered by transient effects and limited modeling possibilities. Artificial microRNAs (amiRNAs or miRNA scaffolds) present a durable and precise approach to gene silencing, opening new avenues for developing long lasting targeted therapies. In this study, we engineered highly expressed primary miRNAs (pri-miRNAs) with sequence determinants known to enhance processing efficacy and precision. The resulting amiRNAs were extensively tested both in vitro and in vivo and proved to efficiently silence a target gene when virally delivered via adeno-associated virus (AAV) into mice brains. This study provides a set of novel amiRNAs with potential therapeutic application as well as a pipeline to generate and validate novel amiRNAs from endogenous pri-miRNAs.","authors":"Militello, G., Greig, A., Bi, C., Vasileva, A., Zavodszky, MI., Lo, SC., Guilmette, E., Clarner, P., Liu, B., Bhat, G., Suh, J., Dow, L., Zuber, J., Fellmann, C., Premsrirut, PK.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Sci Rep","volume":"15","issue":"1","page":"21419","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-07-02","doi":"10.1038\/s41598-025-07061-y","first_author":"Militello, G.","corresponding_authors":null},{"pmid":"40586312","title":"ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA.","abstract":"Type II interferon (IFN&#x3b3;) signaling is essential for innate immunity and critical for effective immunological checkpoint blockade in cancer immunotherapy. Genetic screen identification of post-transcriptional regulators of this pathway has been challenging since such factors are often essential for cell viability. Here, we utilize our inducible CRISPR\/Cas9 approach to screen for key post-transcriptional regulators of IFN&#x3b3; signaling, and in this way, we&#xa0;identify ERH and the ERH-associated splicing and RNA export factors MAGOH, SRSF1, and ALYREF. Loss of these factors impairs post-transcriptional mRNA maturation of JAK2, a crucial kinase for IFN&#x3b3; signaling, resulting in abrogated JAK2 protein levels and diminished IFN&#x3b3; signaling. Further analysis highlights a critical role for ERH in preventing intron retention in AU-rich regions in specific transcripts, such as JAK2. This regulation is markedly different from previously described retention of GC-rich introns. Overall, these findings reveal that post-transcriptional JAK2 processing is a critical rate-limiting step for the IFN&#x3b3;-driven innate immune response.","authors":"Soderholm, A., Vunjak, M., de Almeida, M., Popitsch, N., Podvalnaya, N., Araguas-Rodriguez, P., Scinicariello, S., Nischwitz, E., Butter, F., Ketting, RF., Ameres, SL., M\u00fcller-McNicoll, M., Zuber, J., Versteeg, GA.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nucleic Acids Res","volume":"53","issue":"12","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-30","doi":"10.1093\/nar\/gkaf545","first_author":null,"corresponding_authors":null},{"pmid":"40389480","title":"Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12.","abstract":"Nucleoporin 98 (NUP98) fusion oncoproteins are strong drivers of pediatric acute myeloid leukemia (AML) with poor prognosis. Here we show that NUP98 fusion-expressing AML harbors an epigenetic signature that is characterized by increased accessibility of hematopoietic stem cell genes and enrichment of activating histone marks. We employ an AML model for ligand-induced degradation of the NUP98::KDM5A fusion oncoprotein to identify epigenetic programs and transcriptional targets that are directly regulated by NUP98::KDM5A through CUT&amp;Tag and nascent RNA-seq. Orthogonal genome-wide CRISPR\/Cas9 screening identifies 12 direct NUP98::KDM5A target genes, which are essential for AML cell growth. Among these, we validate cyclin-dependent kinase 12 (CDK12) as a druggable vulnerability in NUP98::KDM5A-expressing AML. In line with its role in the transcription of DNA damage repair genes, small-molecule-mediated CDK12 inactivation causes increased DNA damage, leading to AML cell death. Altogether, we show that NUP98::KDM5A directly regulates a core set of essential target genes and reveal CDK12 as an actionable vulnerability in AML with oncogenic NUP98 fusions.","authors":"Troester, S., Eder, T., Wukowits, N., Piontek, M., Fern\u00e1ndez-Pernas, P., Schmoellerl, J., Haladik, B., Manhart, G., Allram, M., Maurer-Granofszky, M., Scheidegger, N., Nebral, K., Superti-Furga, G., Meisel, R., Bornhauser, B., Valent, P., Dworzak, MN., Zuber, J., Boztug, K., Grebien, F.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Nat Commun","volume":"16","issue":"1","page":"4656","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-19","doi":"10.1038\/s41467-025-59930-9","first_author":null,"corresponding_authors":null},{"pmid":"40328729","title":"mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery.","abstract":"Synthesizing the cellular proteome is a demanding process that is regulated by numerous signaling pathways and RNA modifications. How precisely these mechanisms control the protein synthesis machinery to generate specific proteome subsets remains unclear. Here, through genome-wide CRISPR screens we identify genes that enable mammalian cells to adapt to inactivation of the kinase mechanistic target of rapamycin complex 1 (mTORC1), the central driver of protein synthesis. When mTORC1 is inactive, enzymes that modify tRNAs at wobble uridines (U<sub>34<\/sub>-enzymes), Elongator and Ctu1\/2, become critically essential for cell growth in vitro and in tumors. By integrating quantitative nascent proteomics, steady-state proteomics and ribosome profiling, we demonstrate that the loss of U<sub>34<\/sub>-enzymes particularly impairs the synthesis of ribosomal proteins. However, when mTORC1 is active, this biosynthetic defect only mildly affects steady-state protein abundance. By contrast, simultaneous suppression of mTORC1 and U<sub>34<\/sub>-enzymes depletes cells of ribosomal proteins, globally inhibiting translation. Thus, mTORC1 cooperates with tRNA U<sub>34<\/sub>-enzymes to sustain the protein synthesis machinery and support the high translational requirements of cell growth.","authors":"Hermann, J., Borte\u00e7en, T., Kalis, R., Kowar, A., Pechincha, C., Vogt, V., Schneider, M., Helm, D., Krijgsveld, J., Loayza-Puch, F., Zuber, J., Palm, W.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Nat Commun","volume":"16","issue":"1","page":"4201","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-05-08","doi":"10.1038\/s41467-025-59185-4","first_author":null,"corresponding_authors":null},{"pmid":"41045457","title":"Human assembloid of human blood vessel organoids with pancreatic islets improves insulin secretion over time ex vivo.","abstract":"Pancreatic islet transplantation is a promising treatment strategy for type 1 diabetes patients; however, there are still major challenges to overcome, including vascularization. Despite a substantial need to understand the islet graft decline observed in patients 5-10 years post transplantation, clinical translation remains challenging, probably because of species-specific features and the lack of in vitro vascularized models. Here, we report results of a human assembloid composed of self-organizing 3D blood vessel organoids (BVOs) with human pancreatic islets. We demonstrate that co-culture of islets and BVOs ex vivo leads to an auto-organized assembloid (by light-sheet fluorescence microscopy) and improves insulin secretion over time (functionality assays) on 5 independent human islet donors (from 3 different hospital facilities). Taken together, this study could accelerate our understanding of type 1 diabetes and facilitate therapeutic development for type 1 diabetes patients.","authors":"Tubbs, E., Mehanovi\u0107, M., Lopes, M., Quintard, C., Combe, S., Pirlian, C., Armanet, M., Domet, T., Sabatier, J., Granziera, S., Bouzakri, K., Bietiger, W., Freida, D., Penninger, JM., Gidrol, X.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Cell Rep","volume":"44","issue":"10","page":"116378","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-10-04","doi":"10.1016\/j.celrep.2025.116378","first_author":null,"corresponding_authors":null},{"pmid":"41066575","title":"Acidosis orchestrates adaptations of energy metabolism in tumors.","abstract":"Malignant tumors are characterized by diverse metabolic stresses, including nutrient shortages, hypoxia, and buildup of metabolic by-products. To understand how cancer cells adapt to such challenges, we conducted sequential CRISPR screens to identify genes that affect cellular fitness under specific metabolic stress conditions in cell culture and to then probe their relevance in pancreatic tumors. Comparative analyses of hundreds of fitness genes revealed that cancer metabolism in vivo was shaped by bioenergetic adaptations to tumor acidosis. Mechanistically, acidosis suppressed cytoplasmic activity of extracellular signal-regulated kinase (ERK), thereby preventing oncogene-induced mitochondrial fragmentation and promoting fused mitochondria. The resulting boost in mitochondrial respiration supported cancer cell adaptations to various metabolic stresses. Thus, acidosis is an environmental factor that alters energy metabolism to promote stress resilience in cancer.","authors":"Groessl, S., Kalis, R., Snaebjornsson, MT., Wambach, L., Haider, J., Andersch, F., Schulze, A., Palm, W., Zuber, J.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Science","volume":"390","issue":"6769","page":"eadp7603","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-10-09","doi":"10.1126\/science.adp7603","first_author":"Groessl, S.","corresponding_authors":null},{"pmid":"41125852","title":"Germ granule localization of nematode Argonaute WAGO-4 ensures fidelity in small RNA loading.","abstract":"Germ granules are liquid-like condensates that regulate small RNA pathways and gene expression, ensuring genome stability and fertility in animals. In C. elegans, several Argonaute proteins, central players of small RNA pathways, localize to germ granules, yet the functional significance of this spatial enrichment remains unclear. Here, we disrupted the localization of the Argonaute WAGO-4 to germ granules by introducing targeted mutations in the FG repeats of Vasa-like GLH proteins. These mutations did not disrupt overall germ granule architecture but significantly reduced WAGO-4 partitioning, leading to its predominant localization in the cytoplasm. Functional analyses revealed that this mislocalization partially compromised WAGO-4 activity, resulting in reduced WAGO-4 binding of small RNAs targeting specific genes, particularly those not co-regulated by the Argonaute CSR-1. This selective effect highlights the importance of WAGO-4's spatial localization for efficient small RNA loading and gene regulation. Our findings demonstrate that germ granules serve as specialized compartments that fine-tune Argonaute function, emphasizing the role of phase-separated condensates in modulating RNA pathways and gene regulatory networks.","authors":"Jelenic, S., Renaud, MS., Del Borrello, S., Gokcezade, J., Bindics, J., Frasz, L., Czermak, P., Duchek, P., Claycomb, JM.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"EMBO J","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-10-22","doi":"10.1038\/s44318-025-00606-x","first_author":null,"corresponding_authors":null},{"pmid":"9141630","title":"Glycerol and polylysine synergize in their ability to rupture vesicular membranes: a mechanism for increased transferrin-polylysine-mediated gene transfer.","abstract":"The presence of about 1.2 M glycerol during transfection with DNA\/transferrin-polylysine and DNA\/polylysine complexes dramatically increases transgene expression in a variety of cell types, provided that the complexes have an excess of polylysine. We have characterized this phenomenon using a human melanoma cell line (H225). The addition of 1.2 M glycerol to the transfection medium has no influence on the internalization of DNA complexes or on the promoter activity used to direct reporter gene expression. Neither prenor postincubation of the cells with glycerol results in a notable increase in transgene expression. Bafilomycin A1 and chloroquine, two drugs affecting the endosomal pathway, both influenced transgene expression, indicating that glycerol acts on internal vesicles. Glycerol and polylysine synergized in their ability to lyse erythrocytes as well as internal vesicles (microsomes) isolated from H225 cells, indicating that the glycerol effect is due to a labilization of vesicular membranes, which facilitates membrane disruption by polylysine. Our current model suggests that the excess of polylysine in the DNA complexes disrupts vesicular membranes in the presence of glycerol, thus allowing the release of DNA complexes into the cytoplasm.","authors":"Zauner, W., Kichler, A., Schmidt, W., Mechtler, K., Wagner, E.","publication_status":"ppublish","journalpubyear":"1997","journaltitle":"Exp Cell Res","volume":"232","issue":"1","page":"137-45","pdf":null,"JrId":"3643","fulltextlink":null,"preprintlink":null,"articledate":"1997-06-11","doi":null,"first_author":"Zauner, W.","corresponding_authors":null},{"pmid":"41183210","title":"The RANK\/RANKL axis controls vascular dynamics in the bone marrow.","abstract":"Receptor activator of nuclear factor kappa B ligand (RANKL) is an essential cytokine that induces osteoclastic differentiation by monocyte-macrophage lineage precursors. Here, we showed that in addition to its conventional action, RANKL controls vascular permeability in the bone marrow, where it facilitates the mobilization of hematopoietic monocytic cells, including osteoclast precursors, and resultantly regulates bone metabolism. RANK, a cognate receptor for RANKL, is abundantly expressed in sinusoidal endothelial cells and controls vascular permeability by regulating the expression patterns of intercellular adhesion molecule 1 and vascular cell adhesion molecule 1. High RANKL expression was detected in perivascular C-X-C motif chemokine ligand 12-abundant reticular (CAR) stromal cells. Specific deletion of RANKL expression in CAR cells abrogated the vascular leakage, suggesting that perivascular RANKL is responsible for controlling permeability. In summary, our study revealed a role for RANK\/RANKL signaling as a gatekeeper of bone marrow sinusoids in vivo.","authors":"Kaneko, T., Yari, S., Kikuta, J., Omatsu, Y., Seno, S., Kikuchi, S., Sato, K., Fujii, K., Sudo, T., Hasegawa, T., Furuta, K., Guo, Q., Ibrahim, SH., Muraoka, K., Okada, Y., Kubota, Y., Okuzaki, D., Kobayashi, Y., Kumanogoh, A., Udagawa, N., Nagasawa, T., Penninger, JM., Ishii, M.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Proc Natl Acad Sci U S A","volume":"122","issue":"45","page":"e2425366122","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-11-03","doi":"10.1073\/pnas.2425366122","first_author":"Kaneko, T.","corresponding_authors":null},{"pmid":"41159548","title":"GTestimate: improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">41159548<\/PMID><DateCompleted><Year>2025<\/Year><Month>10<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2025<\/Year><Month>11<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">2047-217X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>14<\/Volume><PubDate><Year>2025<\/Year><Month>Jan<\/Month><Day>06<\/Day><\/PubDate><\/JournalIssue><Title>GigaScience<\/Title><ISOAbbreviation>Gigascience<\/ISOAbbreviation><\/Journal><ArticleTitle>GTestimate: improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">giaf084<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/gigascience\/giaf084<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Single-cell RNA-seq suffers from unwanted technical variation between cells, caused by its complex experiments and shallow sequencing depths. Many conventional normalization methods try to remove this variation by calculating the relative gene expression per cell. However, their choice of the maximum likelihood estimator is not ideal for this application.","authors":"Fahrenberger, M., Esk, C., Knoblich, JA., von Haeseler, A.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Gigascience","volume":"14","issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-10-29","doi":"10.1093\/gigascience\/giaf084","first_author":"Fahrenberger, M.","corresponding_authors":null},{"pmid":"41213913","title":"Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral.","abstract":"Crosslinking mass spectrometry is an essential tool for probing protein-protein interactions and structural organization. We here compare Orbitrap Astral and Orbitrap Eclipse instruments using Cas9 crosslinked with PhoX and DSSO under standardized chromatographic and acquisition conditions. The Astral identifies over 40% more unique residue pairs, largely due to increased MS1 sensitivity and efficient detection of low-abundance precursors. Implementation of high-field asymmetric ion mobility spectrometry further increases identifications by 30% through improved precursor filtering. On the Astral, single higher-energy collisional dissociation consistently outperforms stepped fragmentation, particularly at low sample amounts, whereas the Eclipse shows minimal dependence on fragmentation strategy. Gradient optimization experiments demonstrate that longer separations enhance identifications in purified crosslinked samples, while gains plateau in complex backgrounds, indicating the need for enrichment or isolation strategies. Column comparisons show that pore size and particle diameter affect separation efficiency, with the Aurora Ultimate column yielding sharper peaks and more crosslink identifications than PepMap. Together, these findings emphasize that instrument choice, fragmentation mode, and chromatographic design directly influence crosslinking performance. The Astral's combination of sensitivity and scan speed supports comprehensive detection of low-abundance crosslinks, providing deeper structural coverage of protein interaction networks.","authors":"M\u00fcller, F., Birklbauer, MJ., Bubis, J., Stejskal, K., Dorfer, V., Mechtler, K.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Nat Commun","volume":"16","issue":"1","page":"9877","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-11-10","doi":"10.1038\/s41467-025-64844-7","first_author":"M&#xfc;ller, F.","corresponding_authors":null},{"pmid":"41193641","title":"Notch signaling is a driver of glandular stem cell activity and regenerative migration after damage.","abstract":"Organoid models have significantly enhanced our understanding of adult stem cell function, however, uncovering regulatory mechanisms governing rare and often quiescent stem cells in glandular organs remains challenging. Here, we employ an integrative multi-omics approach, combining single-cell RNA sequencing, bulk ATAC and RNA sequencing, to profile the cellular populations and signaling pathways characterizing a mouse salivary gland organoid model across different temporal stages and after radiation-induced damage. Our findings identify Sox9- and Itgb1\/Cd44-expressing cells as primitive adult stem\/progenitor populations with a critical migratory role in tissue repair. Notch signaling is a key driver of self-renewal and migration in response to irradiation. Additionally, scRNA-seq analysis of irradiated salivary gland tissue confirms these findings in an in vivo setting. Extending these findings to murine and patient-derived salivary, mammary and thyroid gland organoids, we reveal the conserved role of Notch signaling in coordinating stem\/progenitor cell-mediated regeneration across glandular tissues. These insights position Notch signaling as a central regulator of glandular stem cell-like populations and as a promising therapeutic target for enhancing glandular tissue regeneration following cancer therapies.","authors":"Cinat, D., Maturi, R., Gunawan, JP., Jellema-de Bruin, AL., Kracht, L., Serrano Martinez, P., Wu, Y., Soto-Gamez, A., van Goethem, MJ., Holtman, IR., Pringle, S., Barazzuol, L., Coppes, RP.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"EMBO J","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-11-05","doi":"10.1038\/s44318-025-00607-w","first_author":"Cinat, D.","corresponding_authors":null},{"pmid":"41249498","title":"Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis.","abstract":"No genome on Earth is free of selfish genes. This reflects both their ability to subvert the laws of inheritance and their de novo emergence from host genes. Yet, despite their ubiquity and key role in driving innovation, the mechanisms responsible for their genesis remain largely unexplored. Here we report the discovery of three toxin-antidote elements in the nematode Caenorhabditis tropicalis. Toxin-antidote elements are selfish genes that increase their frequency in populations by poisoning non-carrier individuals. We find that all three novel toxins-klmt-1, pzl-1 and hyde-1-arose via gene duplication from fars-3, an essential subunit of the phenylalanyl tRNA synthetase. Their antidotes-KSS proteins-are rapidly evolving F-box proteins that degrade toxins via the SCF ubiquitin-ligase complex. Our phylogenetic and genomic analyses strongly suggest that the ancestor of all extant KSS antidotes fortuitously acquired affinity for FARS-3, much like 'self' proteins are targeted in autoimmune disease. This interaction neutralized the toxicity of future paralogues before it arose (presuppression), allowing otherwise deleterious mutant alleles to persist and ultimately evolve into selfish genes-consistent with the theory of constructive neutral evolution.","authors":"Tikanova, P., Ross, JJ., Hagm\u00fcller, A., P\u00fchringer, F., Pliota, P., Krogull, D., Stefania, V., Hunold, M., Koreshova, A., Koller, A., Ostapchuk, I., Okweri, J., Gokcezade, J., Duchek, P., Dong, G., Ben-David, E., Burga, A.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nat Ecol Evol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-11-17","doi":"10.1038\/s41559-025-02894-2","first_author":"Tikanova, P.","corresponding_authors":null},{"pmid":"41233617","title":"A mammalian-like piRNA pathway in Axolotl reveals the origins of piRNA-directed DNA methylation.","abstract":"The piRNA pathway protects animal germlines from active transposons. Mammals employ a cytoplasmic pathway to destroy transposon transcripts during germline reprogramming. This post-transcriptional mechanism is ancient and found throughout the animal kingdom. A nuclear piRNA pathway mediates transposon DNA re-methylation, which is believed to be bespoke to mammals. However, when exactly piRNA-directed DNA methylation evolved remains unknown. We found that a mammalian-like piRNA pathway evolved early in tetrapod evolution and is found and expressed in its current configuration in the axolotl salamander. Analysis of axolotl testes and oocytes revealed diverse repertoires of piRNAs and pervasive post-transcriptional targeting of young transposons. We identified high levels of genome methylation in axolotl spermatozoa, with full-length transposons being heavily methylated. Our findings reveal that the mammalian nuclear piRNA pathway has ancient vertebrate origins, and it has likely been safeguarding the germline throughout most of tetrapod evolution. Thus, the emergence of piRNA-directed DNA methylation is a pivotal epigenetic evolutionary event that may have laid the foundation for germline reprogramming and genomic imprinting.","authors":"Xiang, X., Gao, A., Handler, D., Falcon, F., Rodriguez-Terrones, D., Nowoshilow, S., Liu, W., Tanaka, EM., O'Carroll, D.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"EMBO J","volume":"45","issue":"6","page":"1933-1956","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-03-17","doi":"10.1038\/s44318-025-00631-w","first_author":"Xiang, X.","corresponding_authors":"O'Carroll, D."},{"pmid":"41279358","title":"WNK kinase regulates plasma membrane levels of the WNT inhibitor RNF43.","abstract":"The E3 ubiquitin ligases RNF43 and ZNRF3 are key negative regulators of canonical WNT signaling, promoting turnover of the WNT receptors FRIZZLED and LRP5\/6 at the plasma membrane. While their mechanism of action is well established, how RNF43\/ZNRF3 themselves are regulated remains unclear. Here, we identify WNK kinases as novel upstream regulators of RNF43 through proximity labeling proteomics. Using gain- and loss-of-function approaches, we show that WNKs control RNF43 surface localization and thereby its ability to ubiquitinate and downregulate WNT receptors. Pharmacological inhibition of WNKs increases RNF43 membrane abundance and enhances WNT suppression, an effect abolished in RNF43\/ZNRF3 double knockout cells and organoids. Mechanistically, WNK inhibition alters RNF43 trafficking and ubiquitination, revealing a role for WNKs in regulating its plasma membrane distribution. These findings define a new regulatory axis linking the pro-WNT activity of WNKs to RNF43\/ZNRF3-mediated feedback inhibition. Targeting WNK now offers a novel therapeutic strategy to restore WNT pathway control in cancers with RSPO fusions or RNF43 mutations.","authors":"Colozza, G., Jordens, I., Sosa, EA., Ha, J., Wu, S., Tavernini, K., Catala, A., Farnhammer, F., Urban Avellaneda, N., Maurice, M., Koo, BK.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-11-24","doi":"10.1101\/2025.10.08.681128","first_author":"Colozza, G.","corresponding_authors":null},{"pmid":"41264240","title":"Static morphogen scaling enables proportional growth in a tissue growth model inspired by axolotl limb regeneration.","abstract":"Axolotls can regenerate lost limbs throughout life, while they continue to grow. This poses the question of how the size and pattern of a regenerating limb is matched to a widely varying animal size. Two interacting signaling molecules, Sonic Hedgehog (SHH) and Fibroblast Growth Factor (FGF8), are produced at opposite sides of the regenerating limb and sustain tissue growth through a pair of oppositely oriented signaling gradients. As the size of the regrowing tissue can vary more than three-fold depending on the size of the animal, it is unclear how the activities of these mutually dependent morphogens are maintained and subsequently terminated to determine appropriate growth. Scaling of limb regeneration suggests a size-dependent adaptation of morphogen gradient parameters. Inspired by this biological example, we theoretically investigate general mechanisms of morphogen-controlled growth arrest and proportional growth. In the proposed mechanism, tissue growth increases the spatial distance between the two morphogen gradients, which eventually arrests morphogen activity and growth. We put forward two distinct scaling scenarios of morphogen gradients: either dynamic scaling with blastema size, where morphogen gradient parameters change dynamically with the growing tissue, or static scaling with animal size, where morphogen gradient parameters stay constant during blastema growth and only depend on animal size. We show that static scaling ensures proportional growth, but dynamic scaling does not. We compare theory predictions to experimental quantification of SHH and FGF8 morphogen gradient parameters at different time-points of regeneration in different-sized animals, indicating static scaling for some morphogen parameters, which is sufficient to ensure proportional growth in our model.","authors":"Lyubaykina, N., Knapp, D., Tardivo, P., Kotz, M., Sandoval-Guzm\u00e1n, T., Friedrich, BM.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Proc Natl Acad Sci U S A","volume":"122","issue":"47","page":"e2503086122","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-11-20","doi":"10.1073\/pnas.2503086122","first_author":"Lyubaykina, N.","corresponding_authors":null},{"pmid":"41326338","title":"Light-modulated stem cells in the camera-type eye of an annelid model for adult brain plasticity.","abstract":"Camera-type eyes in vertebrates and cephalopods are striking examples of parallel evolution of a complex structure. While comparisons have focused on these two groups, camera-type eyes with likely high functionality are also found in other invertebrate phyla with simpler brains. Employing single-cell RNA sequencing, we identify neurogenic cells in the adult eyes and brain of the marine annelid worm Platynereis dumerilii. Distinct neural stem cells in the camera-type adult eyes, located at the edge of the cup-shaped retina, and adjacent to the glass body\/lens, produce radial lines of cells, reminiscent of stem cells in ciliary marginal zones of vertebrate eyes exhibiting life-long growth. Normal proliferation in the eye depends on ambient light, a phenomenon that depends on the integrity of the photoreceptor gene c-opsin1, which is present in emerging rhabdomeric photoreceptors, and impacts on their differentiation. During reproductive maturation, proliferation in the eye as well as the entire brain sharply declines, while cells upregulate molecular characteristics of mammalian adult neural stem cell quiescence. Our data provide insights into the development and modulation of annelid head and brain cells, revealing similarities and differences to vertebrate eye development, neurogenesis and brain plasticity.","authors":"Milivojev, N., Scaramuzza, F., Brum, PO., Velastegui Gamboa, CL., Andreatta, G., Raible, F., Tessmar-Raible, K.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Nat Commun","volume":"16","issue":"1","page":"9861","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-01","doi":"10.1038\/s41467-025-65631-0","first_author":"Milivojev, N.","corresponding_authors":null},{"pmid":"41343653","title":"Cohesin guides homology search during DNA repair using loops and sister chromatid linkages.","abstract":"Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequence to faithfully restore damaged DNA, yet how broken DNA ends find homologous sites in a genome containing billions of bases remains unclear. Here, we introduce sister-pore-C, a high-resolution method to map intra- and intermolecular interactions in replicated chromosomes. We show how DSBs remodel chromosome architecture using two functionally distinct pools of cohesin. Loop-extruding cohesin accumulates across megabase-scale domains surrounding DSBs to control local homology sampling, whereas cohesive cohesin concentrates at break sites to tether DNA ends to the sister chromatid. This mechanism restricts the homology-sampling space, highlighting how chromosome conformation helps to preserve genomic integrity.","authors":"Teloni, F., Takacs, Z., Mitter, M., Langer, CCH., Prlesi, I., Steinacker, TL., Reuter, VP., Mylarshchikov, D., Gerlich, DW.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Science","volume":"390","issue":"6777","page":"eadw0566","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-04","doi":"10.1126\/science.adw0566","first_author":"Teloni, F.","corresponding_authors":null},{"pmid":"36780518","title":"Effective bet-hedging through growth rate dependent stability.","abstract":"Microbes in the wild face highly variable and unpredictable environments and are naturally selected for their average growth rate across environments. Apart from using sensory regulatory systems to adapt in a targeted manner to changing environments, microbes employ bet-hedging strategies where cells in an isogenic population switch stochastically between alternative phenotypes. Yet, bet-hedging suffers from a fundamental trade-off: Increasing the phenotype-switching rate increases the rate at which maladapted cells explore alternative phenotypes but also increases the rate at which cells switch out of a well-adapted state. Consequently, it is currently believed that bet-hedging strategies are effective only when the number of possible phenotypes is limited and when environments last for sufficiently many generations. However, recent experimental results show that gene expression noise generally decreases with growth rate, suggesting that phenotype-switching rates may systematically decrease with growth rate. Such growth rate dependent stability (GRDS) causes cells to be more explorative when maladapted and more phenotypically stable when well-adapted, and we show that GRDS can almost completely overcome the trade-off that limits bet-hedging, allowing for effective adaptation even when environments are diverse and change rapidly. We further show that even a small decrease in switching rates of faster-growing phenotypes can substantially increase long-term fitness of bet-hedging strategies. Together, our results suggest that stochastic strategies may play an even bigger role for microbial adaptation than hitherto appreciated.","authors":"de Groot, DH., Tjalma, AJ., Bruggeman, FJ., van Nimwegen, E.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Proc Natl Acad Sci U S A","volume":"120","issue":"8","page":"e2211091120","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-15","doi":"10.1073\/pnas.2211091120","first_author":"de Groot, DH.","corresponding_authors":null},{"pmid":"33511367","title":"Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks.","abstract":"The metabolic capabilities of cells determine their biotechnological potential, fitness in ecosystems, pathogenic threat levels, and function in multicellular organisms. Their comprehensive experimental characterization is generally not feasible, particularly for unculturable organisms. In principle, the full range of metabolic capabilities can be computed from an organism's annotated genome using metabolic network reconstruction. However, current computational methods cannot deal with genome-scale metabolic networks. Part of the problem is that these methods aim to enumerate all metabolic pathways, while computation of all (elementally balanced) conversions between nutrients and products would suffice. Indeed, the elementary conversion modes (ECMs, defined by Urbanczik and Wagner) capture the full metabolic capabilities of a network, but the use of ECMs has not been accessible until now. We explain and extend the theory of ECMs, implement their enumeration in ecmtool, and illustrate their applicability. This work contributes to the elucidation of the full metabolic footprint of any cell.","authors":"Clement, TJ., Baalhuis, EB., Teusink, B., Bruggeman, FJ., Planqu\u00e9, R., de Groot, DH.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Patterns (N Y)","volume":"2","issue":"1","page":"100177","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-01-30","doi":"10.1016\/j.patter.2020.100177","first_author":"Clement, TJ.","corresponding_authors":null},{"pmid":"31758233","title":"The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints.","abstract":"Living cells can express different metabolic pathways that support growth. The criteria that determine which pathways are selected in which environment remain unclear. One recurrent selection is overflow metabolism: the simultaneous usage of an ATP-efficient and -inefficient pathway, shown for example in Escherichia coli, Saccharomyces cerevisiae and cancer cells. Many models, based on different assumptions, can reproduce this observation. Therefore, they provide no conclusive evidence which mechanism is causing overflow metabolism. We compare the mathematical structure of these models. Although ranging from flux balance analyses to self-fabricating metabolism and expression models, we can rewrite all models into one standard form. We conclude that all models predict overflow metabolism when two, model-specific, growth-limiting constraints are hit. This is consistent with recent theory. Thus, identifying these two constraints is essential for understanding overflow metabolism. We list all imposed constraints by these models, so that they can hopefully be tested in future experiments.","authors":"de Groot, DH., Lischke, J., Muolo, R., Planqu\u00e9, R., Bruggeman, FJ., Teusink, B.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Cell Mol Life Sci","volume":"77","issue":"3","page":"441-453","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-02-14","doi":"10.1007\/s00018-019-03380-2","first_author":"de Groot, DH.","corresponding_authors":null},{"pmid":"40279435","title":"Growth rate controls the sensitivity of gene regulatory circuits.","abstract":"Microbes adapt to their environments using gene regulatory switches that sense environmental signals and induce target genes in response. Mathematical modeling predicts that, because growth rate sets the intracellular dilution rate, the sensitivity of regulatory switches to chemical cues systematically decreases with growth rate. We experimentally validate that the concentration of inducer required to activate <i>E. coli<\/i>'s <i>lac<\/i> operon increases quadratically with growth rate when varying nutrients but is invariant when varying growth rate through translation inhibition. We further establish that this growth-coupled sensitivity (GCS) allows bacteria to implement concentration-dependent sugar preferences, in which a new carbon source is used only if its concentration is sufficient to improve upon the current growth rate. Using microfluidics in combination with time-lapse microscopy, we validate this prediction at the single-cell level using mixtures of glucose and lactose. Overall, GCS causes cells to automatically become more sensitive to environmental signals when their growth rate decreases.","authors":"Julou, T., Gervais, T., de Groot, D., van Nimwegen, E.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Sci Adv","volume":"11","issue":"17","page":"eadu9279","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-26","doi":"10.1126\/sciadv.adu9279","first_author":"Julou, T.","corresponding_authors":null},{"pmid":"34330708","title":"Metabolic control of nitrogen fixation in rhizobium-legume symbioses.","abstract":"Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarboxylates to reduce atmospheric N<sub>2<\/sub> into ammonia. Despite the agricultural importance of this symbiosis, the mechanisms that govern carbon and nitrogen allocation in bacteroids and promote ammonia secretion to the plant are largely unknown. Using a metabolic model derived from genome-scale datasets, we show that carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules. Catabolism of dicarboxylates induces not only a higher oxygen demand but also a higher NADH\/NAD<sup>+<\/sup> ratio than sugars. Modeling and <sup>13<\/sup>C metabolic flux analysis indicate that oxygen limitation restricts the decarboxylating arm of the tricarboxylic acid cycle, which limits ammonia assimilation into glutamate. By tightly controlling oxygen supply and providing dicarboxylates as the energy and electron source donors for N<sub>2<\/sub> fixation, legumes promote ammonia secretion by bacteroids. This is a defining feature of rhizobium-legume symbioses.","authors":"Schulte, CCM., Borah, K., Wheatley, RM., Terpolilli, JJ., Saalbach, G., Crang, N., de Groot, DH., Ratcliffe, RG., Kruger, NJ., Papachristodoulou, A., Poole, PS.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Sci Adv","volume":"7","issue":"31","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-08-11","doi":"10.1126\/sciadv.abh2433","first_author":"Schulte, CCM.","corresponding_authors":null},{"pmid":"30783202","title":"In vivo characterisation of fluorescent proteins in budding yeast.","abstract":"Fluorescent proteins (FPs) are widely used in many organisms, but are commonly characterised in vitro. However, the in vitro properties may poorly reflect in vivo performance. Therefore, we characterised 27 FPs in vivo using Saccharomyces cerevisiae as model organism. We linked the FPs via a T2A peptide to a control FP, producing equimolar expression of the 2 FPs from 1 plasmid. Using this strategy, we characterised the FPs for brightness, photostability, photochromicity and pH-sensitivity, achieving a comprehensive in vivo characterisation. Many FPs showed different in vivo properties compared to existing in vitro data. Additionally, various FPs were photochromic, which affects readouts due to complex bleaching kinetics. Finally, we codon optimized the best performing FPs for optimal expression in yeast, and found that codon-optimization alters FP characteristics. These FPs improve experimental signal readout, opening new experimental possibilities. Our results may guide future studies in yeast that employ fluorescent proteins.","authors":"Botman, D., de Groot, DH., Schmidt, P., Goedhart, J., Teusink, B.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"Sci Rep","volume":"9","issue":"1","page":"2234","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-09-03","doi":"10.1038\/s41598-019-38913-z","first_author":"Botman, D.","corresponding_authors":null},{"pmid":"36808187","title":"ecmtool: fast and memory-efficient enumeration of elementary conversion modes.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">36808187<\/PMID><DateCompleted><Year>2023<\/Year><Month>03<\/Month><Day>06<\/Day><\/DateCompleted><DateRevised><Year>2023<\/Year><Month>03<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1367-4811<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>39<\/Volume><Issue>3<\/Issue><PubDate><Year>2023<\/Year><Month>Mar<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>ecmtool: fast and memory-efficient enumeration of elementary conversion modes.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">btad095<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/bioinformatics\/btad095<\/ELocationID><Abstract><AbstractText Label=\"MOTIVATION\">Characterizing all steady-state flux distributions in metabolic models remains limited to small models due to the explosion of possibilities. Often it is sufficient to look only at all possible overall conversions a cell can catalyze ignoring the details of intracellular metabolism. Such a characterization is achieved by elementary conversion modes (ECMs), which can be conveniently computed with ecmtool. However, currently, ecmtool is memory intensive, and it cannot be aided appreciably by parallelization.","authors":"Buchner, B., Clement, TJ., de Groot, DH., Zanghellini, J.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Bioinformatics","volume":"39","issue":"3","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-06","doi":"10.1093\/bioinformatics\/btad095","first_author":"Buchner, B.","corresponding_authors":null},{"pmid":"33919383","title":"Understanding FBA Solutions under Multiple Nutrient Limitations.","abstract":"Genome-scale stoichiometric modeling methods, in particular Flux Balance Analysis (FBA) and variations thereof, are widely used to investigate cell metabolism and to optimize biotechnological processes. Given (1) a metabolic network, which can be reconstructed from an organism's genome sequence, and (2) constraints on reaction rates, which may be based on measured nutrient uptake rates, FBA predicts which reactions maximize an objective flux, usually the production of cell components. Although FBA solutions may accurately predict the metabolic behavior of a cell, the actual flux predictions are often hard to interpret. This is especially the case for conditions with many constraints, such as for organisms growing in rich nutrient environments: it remains unclear why a certain solution was optimal. Here, we rationalize FBA solutions by explaining for which properties the optimal combination of metabolic strategies is selected. We provide a graphical formalism in which the selection of solutions can be visualized; we illustrate how this perspective provides a glimpse of the logic that underlies genome-scale modeling by applying our formalism to models of various sizes.","authors":"van Pelt-KleinJan, E., de Groot, DH., Teusink, B.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Metabolites","volume":"11","issue":"5","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-12","doi":"10.3390\/metabo11050257","first_author":"van Pelt-KleinJan, E.","corresponding_authors":null},{"pmid":"33953364","title":"Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth.","abstract":"As natural selection acts on individual organisms the evolution of costly cooperation between microorganisms is an intriguing phenomenon. Introduction of spatial structure to privatize exchanged molecules can explain the evolution of cooperation. However, in many natural systems cells can also grow to low cell concentrations in the absence of these exchanged molecules, thus showing \"cooperation-independent background growth\". We here serially propagated a synthetic cross-feeding consortium of lactococci in the droplets of a water-in-oil emulsion, essentially mimicking group selection with varying founder population sizes. The results show that when the growth of cheaters completely depends on cooperators, cooperators outcompete cheaters. However, cheaters outcompete cooperators when they can independently grow to only ten percent of the consortium carrying capacity. This result is the consequence of a probabilistic effect, as low founder population sizes in droplets decrease the frequency of cooperator co-localization. Cooperator-enrichment can be recovered by increasing the founder population size in droplets to intermediate values. Together with mathematical modelling our results suggest that co-localization probabilities in a spatially structured environment leave a small window of opportunity for the evolution of cooperation between organisms that do not benefit from their cooperative trait when in isolation or form multispecies aggregates.","authors":"van Tatenhove-Pel, RJ., de Groot, DH., Bisseswar, AS., Teusink, B., Bachmann, H.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"ISME J","volume":"15","issue":"10","page":"3050-3061","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-22","doi":"10.1038\/s41396-021-00986-y","first_author":"van Tatenhove-Pel, RJ.","corresponding_authors":null},{"pmid":"31986156","title":"Elementary Growth Modes provide a molecular description of cellular self-fabrication.","abstract":"In this paper we try to describe all possible molecular states (phenotypes) for a cell that fabricates itself at a constant rate, given its enzyme kinetics and the stoichiometry of all reactions. For this, we must understand the process of cellular growth: steady-state self-fabrication requires a cell to synthesize all of its components, including metabolites, enzymes and ribosomes, in proportions that match its own composition. Simultaneously, the concentrations of these components affect the rates of metabolism and biosynthesis, and hence the growth rate. We here derive a theory that describes all phenotypes that solve this circular problem. All phenotypes can be described as a combination of minimal building blocks, which we call Elementary Growth Modes (EGMs). EGMs can be used as the theoretical basis for all models that explicitly model self-fabrication, such as the currently popular Metabolism and Expression models. We then use our theory to make concrete biological predictions. We find that natural selection for maximal growth rate drives microorganisms to states of minimal phenotypic complexity: only one EGM will be active when growth rate is maximised. The phenotype of a cell is only extended with one more EGM whenever growth becomes limited by an additional biophysical constraint, such as a limited solvent capacity of a cellular compartment. The theory presented here extends recent results on Elementary Flux Modes: the minimal building blocks of cellular growth models that lack the self-fabrication aspect. Our theory starts from basic biochemical and evolutionary considerations, and describes unicellular life, both in growth-promoting and in stress-inducing environments, in terms of EGMs.","authors":"de Groot, DH., Hulshof, J., Teusink, B., Bruggeman, FJ., Planqu\u00e9, R.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"PLoS Comput Biol","volume":"16","issue":"1","page":"e1007559","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-04-06","doi":"10.1371\/journal.pcbi.1007559","first_author":"de Groot, DH.","corresponding_authors":null},{"pmid":"30856167","title":"The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates.","abstract":"Growth rate is a near-universal selective pressure across microbial species. High growth rates require hundreds of metabolic enzymes, each with different nonlinear kinetics, to be precisely tuned within the bounds set by physicochemical constraints. Yet, the metabolic behaviour of many species is characterized by simple relations between growth rate, enzyme expression levels and metabolic rates. We asked if this simplicity could be the outcome of optimisation by evolution. Indeed, when the growth rate is maximized-in a static environment under mass-conservation and enzyme expression constraints-we prove mathematically that the resulting optimal metabolic flux distribution is described by a limited number of subnetworks, known as Elementary Flux Modes (EFMs). We show that, because EFMs are the minimal subnetworks leading to growth, a small active number automatically leads to the simple relations that are measured. We find that the maximal number of flux-carrying EFMs is determined only by the number of imposed constraints on enzyme expression, not by the size, kinetics or topology of the network. This minimal-EFM extremum principle is illustrated in a graphical framework, which explains qualitative changes in microbial behaviours, such as overflow metabolism and co-consumption, and provides a method for identification of the enzyme expression constraints that limit growth under the prevalent conditions. The extremum principle applies to all microorganisms that are selected for maximal growth rates under protein concentration constraints, for example the solvent capacities of cytosol, membrane or periplasmic space.","authors":"de Groot, DH., van Boxtel, C., Planqu\u00e9, R., Bruggeman, FJ., Teusink, B.","publication_status":"epublish","journalpubyear":"2019","journaltitle":"PLoS Comput Biol","volume":"15","issue":"3","page":"e1006858","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-04-29","doi":"10.1371\/journal.pcbi.1006858","first_author":"de Groot, DH.","corresponding_authors":null},{"pmid":"41398956","title":"Epithelial WNT secretion drives niche escape of developing gastric cancer.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">41398956<\/PMID><DateCompleted><Year>2026<\/Year><Month>01<\/Month><Day>04<\/Day><\/DateCompleted><DateRevised><Year>2026<\/Year><Month>01<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1476-4598<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>25<\/Volume><Issue>1<\/Issue><PubDate><Year>2025<\/Year><Month>Dec<\/Month><Day>16<\/Day><\/PubDate><\/JournalIssue><Title>Molecular cancer<\/Title><ISOAbbreviation>Mol Cancer<\/ISOAbbreviation><\/Journal><ArticleTitle>Epithelial WNT secretion drives niche escape of developing gastric cancer.<\/ArticleTitle><Pagination><StartPage>1<\/StartPage><MedlinePgn>1<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">1<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12943-025-02543-z<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">WNT signaling plays a key role in maintaining the gastric epithelium and promoting tumorigenesis. However, how gastric tumors achieve WNT niche independence remains unclear, as mutations on APC or CTNNB1-common mechanisms of ligand-independent WNT activation in colorectal cancer-are infrequent in gastric cancer. Understanding how WNT self-sufficiency is acquired in the stomach is therefore critical.","authors":"Lee, J., Kim, S., Oh, Y., Jahn, SR., Kim, J., Kim, Y., Schm\u00e4che, T., Kim, SM., Teriyapirom, I., Gro\u00df, T., Kwon, O., Kim, J., Kim, S., Ada, AM., Catal\u00e0-Bordes, A., Cho, Y., Kim, J., Andersson-Rolf, A., Merker, SR., Lim, JY., Park, JY., Klompstra, TM., Yoon, KJ., Lim, DS., Lee, HS., Kim, JK., Choi, E., Goldenring, JR., Cheong, JH., Kim, H., Stange, DE., Lee, H., Koo, BK., Lee, JH.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Mol Cancer","volume":"25","issue":"1","page":"1","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-04","doi":"10.1186\/s12943-025-02543-z","first_author":"Lee, J.","corresponding_authors":null},{"pmid":"41397978","title":"Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma.","abstract":"Neutrophils are vital innate immune cells shown to infiltrate glioblastomas, however we currently lack the molecular understanding of their functional states within the tumour niche. Given that neutrophils are known to display a prominent discordance between mRNA and protein abundance, we developed ultra-sensitive mini-bulk and single cell proteomic (SCP) workflows to study the heterogeneity of peripheral blood and tumour associated neutrophils (TAN) from patients with glioblastoma. Mini-bulk analysis enabled a deeper protein coverage of circulating immature, mature and TAN populations, defining signatures of maturity and demonstrating that TANs resemble mature circulating neutrophils. Analysis of the SCP data results in the detection of &gt;1100 proteins from a single TAN providing a detailed characterization of neutrophil subsets in glioblastoma. Our approach shows evidence of pathogenic and anti-tumorigenic clusters and discovers cell states invisible to scRNAseq, opening new opportunities to selectively target pro-tumoural neutrophil states.","authors":"Sadiku, P., Brenes, AJ., Mayer, RL., Reyes, L., Coelho, P., van Stralen, G., Zhang, A., Sanchez-Garcia, MA., Watts, ER., Liaquat, I., Howden, AJM., Adekoya, I., Boldbaatar, A., MacRaild, A., Risbridger, S., Morrison, GM., MacPherson, H., Bruce, CM., Johnston, S., Grecian, R., Murphy, FA., Pollard, SM., Brennan, PM., Mechtler, K., Walmsley, SR.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nat Commun","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-15","doi":"10.1038\/s41467-025-67367-3","first_author":"Sadiku, P.","corresponding_authors":null},{"pmid":"41390669","title":"Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitment.","abstract":"During development, blood generation begins in the yolk sac with the differentiation of haemato-endothelial mesoderm forming haematopoietic progenitors. This study aims to identify the crucial molecular regulators of haemato-endothelial mesoderm formation and to extend our knowledge of the process in an unbiased way. We employ a murine embryonic stem cell model that recapitulates embryonic blood development, and perform targeted CRISPR-Cas9 knock out screens focusing on transcription factors and chromatin regulators. We identify the transcription factors ETV2, LDB1, SMAD1, SIX4 and ZBTB7b as regulators of haemato-endothelial mesoderm commitment. Embryonic stem cells lacking these regulators give rise to mesodermal subsets with a defined lineage differentiation bias, while transcriptome analysis of these cells uncovers the precise impact of each factor on gene expression in the developing mesoderm. Our study reveals molecular pathways governing mesodermal development crucial to allow endothelial and haematopoietic lineage specification and paves the way for future advances in haematopoietic stem cell applications.","authors":"Teske, M., Wertheimer, T., Butz, S., Zwicky, P., Mallona, I., Nopper, SL., M\u00fcnz, C., Elling, U., Lancrin, C., Becher, B., Grosso, AR., Baubec, T., Schmolka, N.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nat Commun","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-13","doi":"10.1038\/s41467-025-66230-9","first_author":"Teske, M.","corresponding_authors":null},{"pmid":"41372705","title":"Single cell transcriptional perturbome in pluripotent stem cell models.","abstract":"Functional genomics screens in human induced pluripotent stem cells (hiPSCs) remain challenging despite their transformative potential. We developed iPS2-seq: an inducible, clone-aware screening platform that enables phenotype-agnostic, single-cell resolved dissection of loss-of-function effects in hiPSC derivatives, including complex multicellular models such as organoids. iPS2-seq distinguishes true perturbation effects from genetic and epigenetic variability. It supports pooled and arrayed formats, integrates with microfluidic or split-pool single-cell RNA sequencing, and extends to multi-omic profiling of chromatin and proteins. A dedicated pipeline, catcheR, streamlines design and analysis. The platform enables stage-specific follow-up dissection of screen hits. We demonstrate this by targeting congenital heart disease-associated genes in monolayer cardiomyocytes and organoids. This reveals that epigenetic neuroectodermal priming interferes with germ layer differentiation in specific clones. Accounting for this bias, we show that SMAD2 controls cardiac progenitor specification, with knockdown redirecting cells toward fibroblast and epicardial fates. iPS2-seq unlocks rigorous functional genomics in hiPSC-based models.","authors":"Balmas, E., Ratto, ML., Snijders, KE., Becca, S., Liaci, C., Ricca, I., Merlo, GR., Calogero, RA., Alessandr\u00ec, L., Mendjan, S., Bertero, A.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Mol Syst Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-10","doi":"10.1038\/s44320-025-00172-8","first_author":"Balmas, E.","corresponding_authors":null},{"pmid":"41398412","title":"Mechanism of alternative splicing of yeast HEH1 through competing 5' splice sites.","abstract":"Alternative splicing of precursor-messenger RNAs (pre-mRNA) bearing introns with competing 5' splice sites (5'SS) produces two mRNAs. We investigated the mechanism of alternative splicing of the yeast HEH1\/SRC1 gene, which contains four nucleotide-apart competing 5'SS, by monitoring its RNA and protein products. HEH1 alternative splicing requires a sixteen-nucleotide pre-mRNA segment spanning its two 5'SS. The nucleotides are decoded by U5 and U6 small nuclear RNAs (snRNAs), supported by specific proteins of the spliceosomal B and Bact complexes, including Prp8. HEH1 alternative splicing became independent of the supporting proteins following recalibration of the pre-mRNA-snRNA base pairings through changes in the 5'SS or U5 and U6 snRNAs. Assisted by proteins that stabilize low-fidelity, high-efficiency spliceosome conformations, the competing HEH1 5'SS are marked for alternative splicing by U5 and U6 snRNAs during the B to Bact transition of the spliceosome.","authors":"Banyal, AK., Choudhuri, P., Pillai, BR., Varikkapulakkal, A., Mishra, SK.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nat Commun","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-15","doi":"10.1038\/s41467-025-67659-8","first_author":"Banyal, AK.","corresponding_authors":null},{"pmid":"41478878","title":"Organization of replicated chromosomes by DNA loops and sister chromatid cohesion.","abstract":"Cohesin is a key regulator of three-dimensional genome organization, contributing to gene regulation, recombination, DNA repair and chromosome segregation. Like other members of the evolutionary conserved structural maintenance of chromosomes (SMC) protein-complex family, cohesin folds DNA through motor-driven loop extrusion. Cohesin has a unique, second activity of genome organization: it physically links sister chromatids together in replicated chromosomes, a process termed sister chromatid cohesion. Sister chromatid cohesion and loop extrusion are mediated by two distinct pools of cohesin, which share common core subunits, but associate with distinct regulatory subunits to interact with chromosomes in fundamentally different ways. In this Review, we discuss how sister chromatid cohesion is established and regulated, and how an interplay between cohesion and chromatin loops organizes replicated chromosomes. We also discuss how cohesion supports chromosome segregation in mitosis and meiosis, and how it contributes to DNA double-strand break repair and age-related oocyte aneuploidy. We outline recent technological advances that provide new opportunities to study cohesion and the conformation of replicated chromosomes, and we provide a perspective on how these tools might be applied to answer fundamental questions in cohesin biology.","authors":"Ochs, F., Gerlich, DW.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Rev Mol Cell Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-01","doi":"10.1038\/s41580-025-00933-1","first_author":"Ochs, F.","corresponding_authors":null},{"pmid":"40495227","title":"A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">40495227<\/PMID><DateCompleted><Year>2025<\/Year><Month>06<\/Month><Day>10<\/Day><\/DateCompleted><DateRevised><Year>2025<\/Year><Month>06<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>26<\/Volume><Issue>1<\/Issue><PubDate><Year>2025<\/Year><Month>Jun<\/Month><Day>10<\/Day><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade.<\/ArticleTitle><Pagination><StartPage>160<\/StartPage><MedlinePgn>160<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">160<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13059-025-03626-2<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">The dynamic addition and removal of posttranslational modifications on eukaryotic histones define regulatory regions that play a central role in genome and chromatin biology. However, our understanding of these regulatory mechanisms in animals is primarily based on a few model systems, preventing a general understanding of how histone-based regulation directs and promotes phenotypic variation during animal embryogenesis.","authors":"Mart\u00edn-Zamora, FM., Cole, J., Donnellan, RD., Guynes, K., Carrillo-Baltodano, AM., Dickman, MJ., Hurd, PJ., Mart\u00edn-Dur\u00e1n, JM.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Genome Biol","volume":"26","issue":"1","page":"160","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-06-10","doi":"10.1186\/s13059-025-03626-2","first_author":"Mart&#xed;n-Zamora, FM.","corresponding_authors":null},{"pmid":"40220853","title":"Multi-omics driven genome-scale metabolic modeling improves viral vector yield in HEK293.","abstract":"HEK293 cells are a versatile cell line extensively used in the production of recombinant proteins and viral vectors, notably Adeno-associated virus (AAV) (Bulcha et al., 2021). Despite their high transfection efficiency and adaptability to various culture conditions, challenges remain in achieving sufficient yields of active viral particles. This study presents a comprehensive multi-omics analysis of two HEK293 strains under good manufacturing practice conditions, focusing on the metabolic and cellular responses during AAV production. The investigation included lipidomic, exometabolomic, and transcriptomic profiling across different conditions and time points. Genome-scale metabolic models (GSMMs) were reconstructed for these strains to elucidate metabolic shifts and identify potential bottlenecks in AAV production. Notably, the study revealed significant differences between a High-producing (HP) and a Low-producing (LP) HEK293 strains, highlighting pseudohypoxia in the LP strain. Key findings include the identification of hypoxia-inducible factor 1-alpha (HIF-1&#x3b1;) as a critical regulator in the LP strain, linking pseudohypoxia to poor AAV productivity. Inhibition of HIF-1&#x3b1; resulted in immediate cessation of cell growth and a 2.5-fold increase in viral capsid production, albeit with a decreased number of viral genomes, impacting the full-to-empty particle ratio. This trade-off is significant because it highlights a key challenge in AAV production: achieving a balance between capsid assembly and genome packaging to optimize the yield of functional viral vectors. Overall this suggests that while HIF-1&#x3b1; inhibition enhances capsid assembly, it simultaneously hampers nucleotide synthesis via the pentose phosphate pathway (PPP), necessary for nucleotide synthesis, and therefore for AAV genome replication.","authors":"Zehetner, L., Sz\u00e9liov\u00e1, D., Kraus, B., Hernandez Bort, JA., Zanghellini, J.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Metab Eng","volume":"91","issue":null,"page":"103-118","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-07-16","doi":"10.1016\/j.ymben.2025.03.011","first_author":"Zehetner, L.","corresponding_authors":"Zehetner, L., Sz&#xe9;liov&#xe1;, D., Hernandez Bort, JA., Zanghellini, J."},{"pmid":"41529658","title":"Exploring shaped focused ion beams for lamella preparation.","abstract":"Focused ion beams (FIB) are widely used instruments in transmission electron microscopy (TEM) sample preparation across scientific disciplines. Generally, site-specific ablation of material is achieved by scanning a highly focused probe across a selected area, leading to the removal of material. However, the geometries of TEM lamellae milled with the FIB are usually highly non-isometric, with their thickness generally being orders of magnitude smaller than their width and length. Here, we explore a changed probe shape for milling. Instead of using an ion beam with the standard, Gaussian-like probe, we characterize the use of the stigmator as quasi-cylindrical lens to create a highly astigmatic probe that we term 'ion knife'. Using the ion knife allows for material removal by spreading the current over a larger area and changes the dimension of the probe as observed in spot burn cross-sections. To allow for rapid alignment of parameters in beam shaping, we demonstrate a method to approximate the shapes of our probes by imaging. Finally, exploring shaped probes in cryogenic lamella preparation, we demonstrate the feasibility of cellular lamella milling and sectioning of cryo-lift-out volumes with the ion knife.","authors":"Brenner, J., Plitzko, JM., Klumpe, S.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Ultramicroscopy","volume":"282","issue":null,"page":"114302","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-13","doi":"10.1016\/j.ultramic.2025.114302","first_author":"Brenner, J.","corresponding_authors":"Plitzko, JM., Klumpe, S."},{"pmid":"41588252","title":"Putting mammalian early embryonic cells into dormancy.","abstract":"Mammalian development starts at fertilization and continually progresses until birth, except in cases in which an interruption is favorable to the embryo and the mother. Many mammals have the ability to pause development in case of suboptimal resources or routinely as part of their reproductive cycle-a phenomenon called 'embryonic diapause'. Diapause can be mimicked in vivo in mice via surgical removal of the ovaries or hormone injections. This procedure is laborious and invasive, ruling out its use across species. We have developed in vitro protocols through which mouse blastocysts, human blastoids and pluripotent stem cells from both species can be induced to enter a diapause-like dormant state via pharmacological inhibition of mTOR. Here, we describe in detail how embryos, blastoids and stem cells can be transitioned into and out of dormancy under different culture conditions. We further explain critical parameters to ensure success and propose experimental readouts. These in vitro embryonic dormancy setups can be used to uncover molecular mechanisms of dormancy, to test environmental or pharmacological effectors and to further innovate culture systems for species in which in vitro reproductive technologies are limited. We anticipate that researchers with ~1 year of embryo- and stem cell-handling experience should be able to achieve consistent results and evaluate outcomes. Altogether, inducing dormancy in vitro offers the possibility to slow down embryonic development for exploratory investigations of molecular mechanisms and eventually to expand the time window before implantation for clinical assays.","authors":"Iyer, DP., Heidari Khoei, H., Rivron, N., Bulut-Karslioglu, A.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Protoc","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-26","doi":"10.1038\/s41596-025-01303-z","first_author":"Iyer, DP.","corresponding_authors":null},{"pmid":"41571464","title":"Separable roles for Microprocessor and its cofactors, ERH and SAFB1\/2, during microRNA cluster assistance.","abstract":"While most conserved microRNA (miRNA) transcripts harbor a suite of features that mediate their efficient biogenesis into small RNAs, some loci bear suboptimal attributes that enable additional layers of processing regulation. A notable example is cluster assistance, whereby a miRNA hairpin with suboptimal nuclear biogenesis can be enhanced by an optimal neighbor. This process involves local transfer of the Microprocessor complex, composed of the RNase III enzyme Drosha and its partner, DGCR8, in concert with cofactors such as ERH and SAFB1\/2. However, the mechanisms that underlie miRNA cluster assistance remain largely unclear. Here, we gained insights into this process by integrating mutant cells of Microprocessor and its cofactors with analysis of miRNA structure-function variants, biochemical tests, and genome-wide profiling. We defined features of suboptimal miRNAs that render them dependent on cluster assistance and distinguished among a network of proposed interactions among Microprocessor and its cofactors to reveal a subset that is critical for cluster assistance. Most importantly, we used epistatic tests to separate and order the functional requirements for ERH and SAFB1\/2 into a pathway. Our data indicate that ERH may engage in the process of Microprocessor transfer between hairpins, while SAFB factors (especially SAFB2) mediate recognition and stable binding of a suboptimal miRNA hairpin after Microprocessor transfer. Finally, we show how cluster assistance integrates into a feedback regulatory loop on Microprocessor via Drosha-mediated cleavage of a suboptimal miRNA hairpin in the DGCR8 transcript. Altogether, our findings reveal complex regulatory transactions during biogenesis of clustered miRNAs.","authors":"Shang, R., Popitsch, N., Lee, S., Ameres, SL., Lai, EC.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Genes Dev","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-27","doi":"10.1101\/gad.353316.125","first_author":"Shang, R.","corresponding_authors":null},{"pmid":"41589062","title":"The Evolutionary Genomics of Meiotic Drive.","abstract":"Meiotic drivers are selfish genetic elements that gain transmission advantages by distorting equal, Mendelian segregation. For decades, biologists have considered meiotic drivers as interesting, albeit esoteric, case studies. It is now clear, however, that meiotic drive is more common and phylogenetically widespread than previously supposed. Indeed, intensive study of a few well-known cases has begun to reveal the evolutionary genomic consequences of meiotic drive. We argue here that many features of genome evolution, content, and organization that are seemingly inexplicable by organismal adaptation or nearly neutral processes are instead best accounted for by recurrent histories of meiotic drive. We review how meiotic drive can affect the evolution of sequences, gene copy numbers, genes with functions in meiosis and gametogenesis, signatures of \"selection\", chromosome rearrangements, and karyotype evolution. We also explore the interactions of meiotic drive elements with other classes of selfish genetic elements, including satellite DNAs, transposable elements, and with the endogenous host genes involved in drive suppression. Finally, we argue that some aspects of drive-mediated genome evolution are now sufficiently well established that we might reverse the direction of discovery- rather than ask how drive affects genome evolution, we can use genome data to discover new putative drive elements.","authors":"Presgraves, DC., Dawe, RK., Dyer, KA., Fishman, L., Bhide, SA., Bradshaw, SL., Brady, MJ., Burga, A., Courret, C., Fagen, BL., Ferretti, ABSM., Kelemen, RK., Kitano, J., Liu, Y., Mart\u00ed, E., Erlenbach, T., Reinhardt, JA., Ross, L., Runge, JN., Swanepoel, CM., Vicoso, B., Vogan, AA., Lindholm, AK., Larracuente, AM., Unckless, RL.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Mol Biol Evol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-27","doi":"10.1093\/molbev\/msag020","first_author":"Presgraves, DC.","corresponding_authors":null},{"pmid":"41616822","title":"The Stathmin 1-lineage Contributes to Acinar Regeneration but Not to Neoplasia Upon Oncogenic Kras Expression.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">41616822<\/PMID><DateCompleted><Year>2026<\/Year><Month>04<\/Month><Day>17<\/Day><\/DateCompleted><DateRevised><Year>2026<\/Year><Month>04<\/Month><Day>17<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">2352-345X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>20<\/Volume><Issue>5<\/Issue><PubDate><Year>2026<\/Year><\/PubDate><\/JournalIssue><Title>Cellular and molecular gastroenterology and hepatology<\/Title><ISOAbbreviation>Cell Mol Gastroenterol Hepatol<\/ISOAbbreviation><\/Journal><ArticleTitle>The Stathmin 1-lineage Contributes to Acinar Regeneration but Not to Neoplasia Upon Oncogenic Kras Expression.<\/ArticleTitle><Pagination><StartPage>101743<\/StartPage><MedlinePgn>101743<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">101743<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.jcmgh.2026.101743<\/ELocationID><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S2352-345X(26)00021-4<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\" NlmCategory=\"OBJECTIVE\">The exocrine pancreas has a limited regenerative capacity, but to what extent all acinar cells are involved in this process is unclear. Nevertheless, the heterogenous nature of acinar cells suggests that cells exhibiting higher plasticity might play a more prominent role in acinar regeneration. In that regard, stathmin 1 (Stmn1)-expressing acinar cells have been identified as potential facultative progenitor-like cells in the adult pancreas. Here, we studied Stmn1-progeny under physiological conditions, during regeneration, and in the context of Kras<sup>G12D<\/sup> expression.","authors":"Dahiya, S., Arbujas, JR., Hajihassani, A., Amini, S., Wageley, M., Gurbuz, K., Ma, Z., Copeland, C., Saleh, M., Gittes, GK., Koo, BK., DelGiorno, KE., Esni, F.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Cell Mol Gastroenterol Hepatol","volume":"20","issue":"5","page":"101743","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-04-17","doi":"10.1016\/j.jcmgh.2026.101743","first_author":"Dahiya, S.","corresponding_authors":"Esni, F."},{"pmid":"41613110","title":"Endocytosis and non-canonical autophagy mediate extracellular histones cytotoxicity in vascular models of sepsis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">41613110<\/PMID><DateCompleted><Year>2026<\/Year><Month>01<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2026<\/Year><Month>02<\/Month><Day>01<\/Day><\/DateRevised><Article PubModel=\"Electronic-eCollection\"><Journal><ISSN IssnType=\"Electronic\">1664-3224<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>16<\/Volume><PubDate><Year>2025<\/Year><\/PubDate><\/JournalIssue><Title>Frontiers in immunology<\/Title><ISOAbbreviation>Front Immunol<\/ISOAbbreviation><\/Journal><ArticleTitle>Endocytosis and non-canonical autophagy mediate extracellular histones cytotoxicity in vascular models of sepsis.<\/ArticleTitle><Pagination><StartPage>1650789<\/StartPage><MedlinePgn>1650789<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">1650789<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.3389\/fimmu.2025.1650789<\/ELocationID><Abstract><AbstractText Label=\"INTRODUCTION\" NlmCategory=\"UNASSIGNED\">Sepsis, a widespread global ailment, involves an exaggerated immune response, leading to hyperinflammation and immunosuppression. Extracellular histones, released during hyperinflammation as part of the defensive response against pathogens, significantly contribute to sepsis pathogenesis, compromising viability of the host's endothelial cells and contributing to organ failure.","authors":"Garc\u00e9s, C., Tasc\u00f3n, P., Diago-Domingo, L., Ib\u00e1\u00f1ez, AJ., Herrera, G., Rodr\u00edguez, LR., Salewskij, K., Jonsson, G., Penninger, JM., Rom\u00e1-Mateo, C., Pallard\u00f3, FV.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"Front Immunol","volume":"16","issue":null,"page":"1650789","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-30","doi":"10.3389\/fimmu.2025.1650789","first_author":"Garc&#xe9;s, C.","corresponding_authors":null},{"pmid":"41650255","title":"Divergent stem cell mechanisms govern the primary body axis and appendage regeneration in the axolotl.","abstract":"Exploring the fundamental mechanisms of organ regeneration is crucial for advancing regenerative medicine. The axolotl tail represents an opportunity to study regeneration of the primary axis including segmented muscle, vertebrae, and skin. During tail development, muscle stem cells (MuSCs) displayed expected specificity to the muscle lineage. Tail amputation, however, induced expansion of MuSC potential yielding clonal contribution to muscle, connective tissue including cartilage, pericytes, and fibroblasts. This expanded potential was not observed during limb regeneration, and cross-transplantation showed that these differences in potential are likely intrinsically determined. Single-cell RNA sequencing profiling revealed that tail MuSCs revert to an embryonic mesoderm-like state. Through genetic manipulation involving the overexpression of constitutively active transforming growth factor-&#x3b2; (TGF-&#x3b2;) receptors or <i>Smad7<\/i> (antagonist of TGF-&#x3b2; signaling) in MuSCs, we demonstrated that the levels of TGF-&#x3b2; signal determine the fate outcome of MuSCs to connective tissue lineage or muscle, respectively. Our findings illustrate that variation in MuSCs may represent a fundamental difference between regeneration of primary axis versus appendage.","authors":"Wang, L., Song, L., Yi, C., Zhou, J., Yong, Z., Hu, Y., Pan, X., Qiao, N., Cai, H., Zhao, W., Zhang, R., Yang, L., Liu, L., Peng, G., Tanaka, EM., Li, H., Liu, Y., Fei, JF.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Sci Adv","volume":"12","issue":"6","page":"eadx5697","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-02-06","doi":"10.1126\/sciadv.adx5697","first_author":"Wang, L.","corresponding_authors":null},{"pmid":"41644694","title":"Feeding-regulated glycogen metabolism drives rhythmic liver protein secretion.","abstract":"The liver has a key role in inter-organ communication by secreting most circulating plasma proteins. However, the mechanisms governing hepatic protein secretion remain unclear. Here we show that hepatic protein secretion follows a diurnal rhythm regulated by food intake in humans and mice. Using liver microsomal proteomics, we find that proteins implicated in the early secretory pathway, such as protein glycosylation and folding in the endoplasmic reticulum (ER) and Golgi apparatus, exhibit a rhythmic expression profile, which is abolished in Bmal1-knockout mice. Mechanistically, we show that hepatic glycogenolysis provides substrates for protein N-glycosylation. In mice, perturbing hepatic glycogenolysis with pharmacological or nutritional interventions leads to ER stress and attenuates diurnal protein secretion. We confirm these results in humans, as genetic variants associated with glycogen storage disease and congenital disorders of glycosylation also alter hepatic protein secretion. Overall, our work uncovers hepatic glycogen metabolism as a circadian regulator of protein secretion.","authors":"Weger, M., Mauvoisin, D., Hoyle, D., Wang, J., Martin, E., Rae, J., Ferguson, C., Klinke, G., Cielesh, M., Macauslane, KL., Larance, M., Quadroni, M., Templeman, I., Walhin, JP., Karagounis, LG., Betts, JA., Johnston, JD., Durussel, F., Firsov, D., Fournier, S., M\u00fcller, O., Schulz, BL., Parton, RG., Weger, BD., Gachon, F.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Metab","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-02-05","doi":"10.1038\/s42255-026-01453-8","first_author":"Weger, M.","corresponding_authors":null},{"pmid":"35687689","title":"Excessive local host-graft connectivity in aging and amyloid-loaded brain.","abstract":"Transplantation is a clinically relevant approach for brain repair, but much remains to be understood about influences of the disease environment on transplant connectivity. To explore the effect of amyloid pathology in Alzheimer's disease (AD) and aging, we examined graft connectivity using monosynaptic rabies virus tracing in APP\/PS1 mice and in 16- to 18-month-old wild-type (WT) mice. Transplanted neurons differentiated within 4 weeks and integrated well into the host visual cortex, receiving input from the appropriate brain regions for this area. Unexpectedly, we found a prominent several-fold increase in local inputs, in both amyloid-loaded and aged environments. State-of-the-art deep proteome analysis using mass spectrometry highlights complement system activation as a common denominator of environments promoting excessive local input connectivity. These data therefore reveal the key role of the host pathology in shaping the input connectome, calling for caution in extrapolating results from one pathological condition to another.","authors":"Thomas, J., Martinez-Reza, MF., Thorwirth, M., Zarb, Y., Conzelmann, KK., Hauck, SM., Grade, S., G\u00f6tz, M.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Sci Adv","volume":"8","issue":"23","page":"eabg9287","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-07-16","doi":"10.1126\/sciadv.abg9287","first_author":"Thomas, J.","corresponding_authors":null},{"pmid":"28018177","title":"Heterocellular Contacts with Mouse Brain Endothelial Cells <i>Via<\/i> Laminin and &#x3b1;6&#x3b2;1 Integrin Sustain Subventricular Zone (SVZ) Stem\/Progenitor Cells Properties.","abstract":"Neurogenesis in the subventricular zone (SVZ) is regulated by diffusible factors and cell-cell contacts. <i>In vivo<\/i>, SVZ stem cells are associated with the abluminal surface of blood vessels and such interactions are thought to regulate their neurogenic capacity. SVZ neural stem cells (NSCs) have been described to contact endothelial-derived laminin <i>via<\/i> &#x3b1;6&#x3b2;1 integrin. To elucidate whether heterocellular contacts with brain endothelial cells (BEC) regulate SVZ cells neurogenic capacities, cocultures of SVZ neurospheres and primary BEC, both obtained from C57BL\/6 mice, were performed. The involvement of laminin-integrin interactions in SVZ homeostasis was tested in three ways. Firstly, SVZ cells were analyzed following incubation of BEC with the protein synthesis inhibitor cycloheximide (CHX) prior to coculture, a treatment expected to decrease membrane proteins. Secondly, SVZ cells were cocultured with BEC in the presence of an anti-&#x3b1;6 integrin neutralizing antibody. Thirdly, BEC were cultured with &#x3b2;1<sup>-\/-<\/sup> SVZ cells. We showed that contact with BEC supports, at least in part, proliferation and stemness of SVZ cells, as evaluated by the number of BrdU positive (+) and Sox2+ cells in contact with BEC. These effects are dependent on BEC-derived laminin binding to &#x3b1;6&#x3b2;1 integrin and are decreased in cocultures incubated with anti-&#x3b1;6 integrin neutralizing antibody and in cocultures with SVZ &#x3b2;1<sup>-\/-<\/sup> cells. Moreover, BEC-derived laminin sustains stemness in SVZ cell cultures <i>via<\/i> activation of the Notch and mTOR signaling pathways. Our results show that BEC\/SVZ interactions involving &#x3b1;6&#x3b2;1 integrin binding to laminin, contribute to SVZ cell proliferation and stemness.","authors":"Rosa, AI., Grade, S., Santos, SD., Bernardino, L., Chen, TC., Relvas, J., Hofman, FM., Agasse, F.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Front Cell Neurosci","volume":"10","issue":null,"page":"284","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-01","doi":"10.3389\/fncel.2016.00284","first_author":"Rosa, AI.","corresponding_authors":null},{"pmid":"24578683","title":"Modulation of subventricular zone oligodendrogenesis: a role for hemopressin?","abstract":"Neural stem cells (NSCs) from the subventricular zone (SVZ) have been indicated as a source of new oligodendrocytes to use in regenerative medicine for myelin pathologies. Indeed, NSCs are multipotent cells that can self-renew and differentiate into all neural cell types of the central nervous system. In normal conditions, SVZ cells are poorly oligodendrogenic, nevertheless their oligodendrogenic potential is boosted following demyelination. Importantly, progressive restriction into the oligodendrocyte fate is specified by extrinsic and intrinsic factors, endocannabinoids being one of these factors. Although a role for endocannabinoids in oligodendrogenesis has already been foreseen, selective agonists and antagonists of cannabinoids receptors produce severe adverse side effects. Herein, we show that hemopressin (Hp), a modulator of CB1 receptors, increased oligodendroglial differentiation in SVZ neural stem\/progenitor cell cultures derived from neonatal mice. The original results presented in this work suggest that Hp and derivates may be of potential interest for the development of future strategies to treat demyelinating diseases.","authors":"Xapelli, S., Agasse, F., Grade, S., Bernardino, L., Ribeiro, FF., Schitine, CS., Heimann, AS., Ferro, ES., Sebasti\u00e3o, AM., De Melo Reis, RA., Malva, JO.","publication_status":"epublish","journalpubyear":"2014","journaltitle":"Front Cell Neurosci","volume":"8","issue":null,"page":"59","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-02-28","doi":"10.3389\/fncel.2014.00059","first_author":"Xapelli, S.","corresponding_authors":null},{"pmid":"17981398","title":"Methamphetamine induces alterations on hippocampal NMDA and AMPA receptor subunit levels and impairs spatial working memory.","abstract":"Methamphetamine (METH) is a powerful psychostimulant that increases glutamate (Glu) levels in the mammalian brain and it is currently known that hippocampi are particularly susceptible to METH. Moreover, it is well established that the overactivation of N-methyl-d-aspartate (NMDA) and AMPA ionotropic Glu receptors causes excitotoxicity. In the present study, we investigated the effect of acute (30 mg\/kg) versus escalating dose (ED) administration of METH on NMDA receptor 1, NMDA receptor 2 and glutamate receptor 2 (GluR2) subunit expression in the hippocampus and on memory. Adult Sprague-Dawley rats were injected s.c. during six consecutive days with saline (control and acute groups) or with a growing dose of METH (10, 15, 15, 20, 20, 25 mg\/kg\/day; ED group). On the 7th day, both METH groups were injected with a 'bolus' of 30 mg\/kg METH whereas controls received saline. Western blot analysis showed an increase of GluR2 and NR2A expression levels and no alterations on NR1 subunit in the acute group. On the other hand, in the ED group, GluR2 and NR2A expression levels were unaltered and there was a decrease on NR1 levels. Moreover, we did not observe neurodegeneration with both administration paradigms, as assessed by Fluoro-Jade C staining, but we did observe a strong astrogliosis in the acute administration group by using both immunohistochemistry and Western blot analysis. The impact of METH on working memory was evaluated using the Y maze test and revealed significant mnemonic deficit in the rats acutely treated with the drug. Overall, our results suggest a protection mechanism under conditions of METH administration by decreasing permeability and\/or functionality of NMDA and AMPA receptors, which has implications on memory. So, the participation of the glutamatergic system should be considered as an important pharmacological target to design new strategies to prevent or diminish the harmful effect of drug consumption.","authors":"Sim\u00f5es, PF., Silva, AP., Pereira, FC., Marques, E., Grade, S., Milhazes, N., Borges, F., Ribeiro, CF., Macedo, TR.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Neuroscience","volume":"150","issue":"2","page":"433-41","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-04-03","doi":null,"first_author":"Sim&#xf5;es, PF.","corresponding_authors":null},{"pmid":"18412629","title":"Interaction between neuropeptide Y (NPY) and brain-derived neurotrophic factor in NPY-mediated neuroprotection against excitotoxicity: a role for microglia.","abstract":"The neuroprotective effect of neuropeptide Y (NPY) receptor activation was investigated in organotypic mouse hippocampal slice cultures exposed to the glutamate receptor agonist alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA). Exposure of 2-week-old slice cultures, derived from 7-day-old C57BL\/6 mice, to 8 microm AMPA, for 24 h, induced degeneration of CA1 and CA3 pyramidal cells, as measured by cellular uptake of propidium iodide (PI). A significant neuroprotection, with a reduction of PI uptake in CA1 and CA3 pyramidal cell layers, was observed after incubation with a Y(2) receptor agonist [NPY(13-36), 300 nm]. This effect was sensitive to the presence of the selective Y(2) receptor antagonist (BIIE0246, 1 microm), but was not affected by addition of TrkB-Fc or by a neutralizing antibody against brain-derived neurotrophic factor (BDNF). Moreover, addition of a Y(1) receptor antagonist (BIBP3226, 1 microm) or a NPY-neutralizing antibody helped to disclose a neuroprotective role of endogenous NPY in CA1 region. Cultures exposed to 8 microm AMPA for 24 h, displayed, as measured by an enzyme-linked immunosorbent assay, a significant increase in BDNF. In such cultures there was an up-regulation of neuronal TrkB immunoreactivity, as well as the presence of BDNF-immunoreactive microglial cells at sites of injury. Thus, an increase of AMPA-receptor mediated neurodegeneration, in the mouse hippocampus, was prevented by neuroprotective pathways activated by NPY receptors (Y(1) and Y(2)), which can be affected by BDNF released by microglia and neurons.","authors":"Xapelli, S., Bernardino, L., Ferreira, R., Grade, S., Silva, AP., Salgado, JR., Cavadas, C., Grouzmann, E., Poulsen, FR., Jakobsen, B., Oliveira, CR., Zimmer, J., Malva, JO.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Eur J Neurosci","volume":"27","issue":"8","page":"2089-102","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-07-01","doi":"10.1111\/j.1460-9568.2008.06172.x","first_author":"Xapelli, S.","corresponding_authors":null},{"pmid":"18279032","title":"Response to histamine allows the functional identification of neuronal progenitors, neurons, astrocytes, and immature cells in subventricular zone cell cultures.","abstract":"Subventricular zone (SVZ) cell cultures contain mixed populations of immature cells, neurons, astrocytes, and progenitors in different stages of development. In the present work, we examined whether cell types of the SVZ could be functionally discriminated on the basis of intracellular free calcium level ([Ca(2+)](i)) variations following KCl and histamine stimulation. For this purpose, [Ca(2+)](i) were measured in SVZ cell cultures from neonatal P1-3 C57Bl\/6 donor mice, in single cells, after stimulation with 100 microM histamine or 50 mM KCl. MAP-2-positive neurons and doublecortin-positive neuroblasts were distinguished on the basis of their selective ratio of response to KCl and\/or histamine stimulation. Moreover, we could distinguish immature cells on the basis of the selective response to histamine via the histamine 1 receptor activation. Exposure of SVZ cultures to the pro-neurogenic stem cell factor (SCF) induced an increase in the number of cells responding to KCl and a decrease in the number of cells responding to histamine, consistent with neuronal differentiation. The selective response to KCl\/histamine in single cell calcium imaging analysis offers a rapid and efficient way for the functional discrimination of neuronal differentiation in SVZ cell cultures, opening new perspectives for the search of potential pro-neurogenic factors.","authors":"Agasse, F., Bernardino, L., Silva, B., Ferreira, R., Grade, S., Malva, JO.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Rejuvenation Res","volume":"11","issue":"1","page":"187-200","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-06-16","doi":"10.1089\/rej.2007.0600","first_author":"Agasse, F.","corresponding_authors":null},{"pmid":"18388302","title":"Neuropeptide Y promotes neurogenesis in murine subventricular zone.","abstract":"Stem cells of the subventricular zone (SVZ) represent a reliable source of neurons for cell replacement. Neuropeptide Y (NPY) promotes neurogenesis in the hippocampal subgranular layer and the olfactory epithelium and may be useful for the stimulation of SVZ dynamic in brain repair purposes. We describe that NPY promotes SVZ neurogenesis. NPY (1 microM) treatments increased proliferation at 48 hours and neuronal differentiation at 7 days in SVZ cell cultures. NPY proneurogenic properties are mediated via the Y1 receptor. Accordingly, Y1 receptor is a major active NPY receptor in the mouse SVZ, as shown by functional autoradiography. Moreover, short exposure to NPY increased immunoreactivity for the phosphorylated form of extracellular signal-regulated kinase 1\/2 in the nucleus, compatible with a trigger for proliferation, whereas 6 hours of treatment amplified the phosphorylated form of c-Jun-NH(2)-terminal kinase signal in growing axons, consistent with axonogenesis. NPY, as a promoter of SVZ neurogenesis, is a crucial factor for future development of cell-based brain therapy. Disclosure of potential conflicts of interest is found at the end of this article.","authors":"Agasse, F., Bernardino, L., Kristiansen, H., Christiansen, SH., Ferreira, R., Silva, B., Grade, S., Woldbye, DP., Malva, JO.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Stem Cells","volume":"26","issue":"6","page":"1636-45","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-08-06","doi":"10.1634\/stemcells.2008-0056","first_author":"Agasse, F.","corresponding_authors":null},{"pmid":"18583543","title":"Tumor necrosis factor-alpha modulates survival, proliferation, and neuronal differentiation in neonatal subventricular zone cell cultures.","abstract":"Tumor necrosis factor (TNF)-alpha has been reported to modulate brain injury, but remarkably, little is known about its effects on neurogenesis. We report that TNF-alpha strongly influences survival, proliferation, and neuronal differentiation in cultured subventricular zone (SVZ) neural stem\/progenitor cells derived from the neonatal P1-3 C57BL\/6 mice. By using single-cell calcium imaging, we developed a method, based on cellular response to KCl and\/or histamine, that allows the functional evaluation of neuronal differentiation. Exposure of SVZ cultures to 1 and 10 ng\/ml mouse or 1 ng\/ml human recombinant TNF-alpha resulted in increased differentiation of cells displaying a neuronal-like profile of [Ca2+](i) responses, compared with the predominant profile of immature cells observed in control, nontreated cultures. Moreover, by using neutralizing antibodies for each TNF-alpha receptor, we found that the proneurogenic effect of 1 ng\/ml TNF-alpha is mediated via tumor necrosis factor receptor 1 activation. Accordingly, the percentage of neuronal nuclear protein-positive neurons was increased following exposure to mouse TNF-alpha. Interestingly, exposure of SVZ cultures to 1 ng\/ml TNF-alpha induced cell proliferation, whereas 10 and 100 ng\/ml TNF-alpha induced apoptotic cell death. Moreover, we found that exposure of SVZ cells to TNF-alpha for 15 minutes or 6 hours caused an increase in the phospho-stress-activated protein kinase\/c-Jun N-terminal kinase immunoreactivity initially in the nucleus and then in growing axons, colocalizing with tau, consistent with axonogenesis. Taken together, these results show that TNF-alpha induces neurogenesis in neonatal SVZ cell cultures of mice. TNF-alpha, a proinflammatory cytokine and a proneurogenic factor, may play a central role in promoting neurogenesis and brain repair in response to brain injury and infection.","authors":"Bernardino, L., Agasse, F., Silva, B., Ferreira, R., Grade, S., Malva, JO.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Stem Cells","volume":"26","issue":"9","page":"2361-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-02-11","doi":"10.1634\/stemcells.2007-0914","first_author":"Bernardino, L.","corresponding_authors":null},{"pmid":"20230276","title":"Functional identification of neural stem cell-derived oligodendrocytes by means of calcium transients elicited by thrombin.","abstract":"Current immunosuppressive treatments for central nervous system demyelinating diseases fail to prevent long-term motor and cognitive decline in patients. Excitingly, glial cell transplantation arises as a promising complementary strategy to challenge oligodendrocytes loss occurring in myelination disorders. A potential source of new oligodendrocytes is the subventricular zone (SVZ) pool of multipotent neural stem cells. However, this approach has been handicapped by the lack of functional methods for identification and pharmacological analysis of differentiating oligodendrocytes, prior to transplantation. In this study, we questioned whether SVZ-derived oligodendrocytes could be functionally discriminated due to intracellular calcium level ([Ca(2+)](i)) variations following KCl, histamine, and thrombin stimulations. Previously, we have shown that SVZ-derived neurons and immature cells can be discriminated on the basis of their selective [Ca(2+)](i) rise upon KCl and histamine stimulation, respectively. Herein, we demonstrate that O4+ and proteolipid protein-positive (PLP+) oligodendrocytes do not respond to these stimuli, but display a robust [Ca(2+)](i) rise following thrombin stimulation, whereas other cell types are thrombin-insensitive. Thrombin-induced Ca(2+) increase in oligodendrocytes is mediated by protease-activated receptor-1 (PAR-1) activation and downstream signaling through G(q\/11) and phospholipase C (PLC), resulting in Ca(2+) recruitment from intracellular compartments. This method allows the analysis of functional properties of oligodendrocytes in living SVZ cultures, which is of major interest for the development of effective grafting strategies in the demyelinated brain. Additionally, it opens new perspectives for the search of new pro-oligodendrogenic factors to be used prior grafting.","authors":"Grade, S., Agasse, F., Bernardino, L., Silva, CG., Cortes, L., Malva, JO.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Rejuvenation Res","volume":"13","issue":"1","page":"27-37","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-06-02","doi":"10.1089\/rej.2009.0889","first_author":"Grade, S.","corresponding_authors":null},{"pmid":"21476976","title":"Functional evaluation of neural stem cell differentiation by single cell calcium imaging.","abstract":"Neurogenesis in the adult mammalian brain occurs in two specific brain areas, the subventricular zone (SVZ) bordering the lateral ventricles and the subgranular zone (SGZ) of the hippocampus. Although these regions are prone to produce new neurons, cultured cells from these neurogenic niches tend to be mixed cultures, containing both neurons and glial cells. Several reports highlight the potential of the self-healing capacity of the brain following injury. Even though much knowledge has been produced on the neurogenesis itself, brain repairing strategies are still far away from patients cure. Here we review general concepts in the neurogenesis field, also addressing the methods available to study neural stem cell differentiation. A major problem faced by research groups and companies dedicated to brain regenerative medicine resides on the lack of good methods to functionally identify neural stem cell differentiation and novel drug targets. To address this issue, we developed a unique single cell calcium imaging-based method to functionally discriminate different cell types derived from SVZ neural stem cell cultures. The unique functional profile of each SVZ cell type was correlated at the single cell level with the immunodetection of specific phenotypic markers. This platform was raised on the basis of the functional response of neurons, oligodendrocytes and immature cells to depolarising agents, to thrombin and to histamine, respectively. We also outline key studies in which our new platform was extremely relevant in the context of drug discovery and development in the area of brain regenerative medicine.","authors":"Eiriz, MF., Grade, S., Rosa, A., Xapelli, S., Bernardino, L., Agasse, F., Malva, JO.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Curr Stem Cell Res Ther","volume":"6","issue":"3","page":"288-96","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-01-09","doi":null,"first_author":"Eiriz, MF.","corresponding_authors":null},{"pmid":"21409522","title":"Functional identification of cell phenotypes differentiating from mice retinal neurospheres using single cell calcium imaging.","abstract":"Degeneration of neural retina causes vision impairment and can lead to blindness. Neural stem and progenitor cells might be used as a tool directed to regenerative medicine of the retina. Here, we describe a novel platform for cell phenotype-specific drug discovery and screening of proneurogenic factors, able to boost differentiation of neural retinal progenitor cells. By using single cell calcium imaging (SCCI) and a rational-based stimulation protocol, a diversity of cells emerging from differentiated retinal neurosphere cultures were identified. Exposure of retinal progenitor cultures to KCl or to &#x3b1;-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) stimulated Ca(2+) transients in microtubule-associated protein 2 (MAP-2) positive neurons. Doublecortin (DCX) and polysialated neural cell adhesion molecule (PSA-NCAM) positive neuroblasts were distinguished from differentiated neurons on the basis of their response to muscimol. Ca(2+) fluxes in glial fibrillary acidic protein (GFAP) or glutamine synthetase (GS) positive cells were induced by ATP. To validate the platform, neurospheres were treated with brain-derived neurotrophic factor (BDNF) (proneurogenic) or ciliary neurotrophic factor (CNTF) (gliogenic factor). BDNF increased the percentage of differentiated cells expressing Tuj-1 sensitive to KCl or AMPA and reduced the population of cells responding to muscimol. CNTF exposure resulted in a higher number of cells expressing GFAP responding to ATP. All together, our data may open new perspectives for cell type-specific discovery of drug targets and screening of novel proneurogenic factors to boost differentiation of neural retina cells to treat degenerative retinal diseases.","authors":"De Melo Reis, RA., Schitine, CS., K\u00f6falvi, A., Grade, S., Cortes, L., Gardino, PF., Malva, JO., de Mello, FG.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Cell Mol Neurobiol","volume":"31","issue":"6","page":"835-46","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-11-30","doi":"10.1007\/s10571-011-9673-6","first_author":"De Melo Reis, RA.","corresponding_authors":null},{"pmid":"22893458","title":"Histamine stimulates neurogenesis in the rodent subventricular zone.","abstract":"Neural stem\/progenitor cells present in the subventricular zone (SVZ) are a potential source of repairing cells after injury. Therefore, the identification of novel players that modulate neural stem cells differentiation can have a huge impact in stem cell-based therapies. Herein, we describe a unique role of histamine in inducing functional neuronal differentiation from cultured mouse SVZ stem\/progenitor cells. This proneurogenic effect depends on histamine 1 receptor activation and involves epigenetic modifications and increased expression of Mash1, Dlx2, and Ngn1 genes. Biocompatible poly (lactic-co-glycolic acid) microparticles, engineered to release histamine in a controlled and prolonged manner, also triggered robust neuronal differentiation in vitro. Preconditioning with histamine-loaded microparticles facilitated neuronal differentiation of SVZ-GFP cells grafted in hippocampal slices and in in vivo rodent brain. We propose that neuronal commitment triggered by histamine per se or released from biomaterial-derived vehicles may represent a new tool for brain repair strategies.","authors":"Bernardino, L., Eiriz, MF., Santos, T., Xapelli, S., Grade, S., Rosa, AI., Cortes, L., Ferreira, R., Bragan\u00e7a, J., Agasse, F., Ferreira, L., Malva, JO.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Stem Cells","volume":"30","issue":"4","page":"773-84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-12-20","doi":"10.1002\/stem.1042","first_author":"Bernardino, L.","corresponding_authors":null},{"pmid":"41603863","title":"In vivo CRISPR\/Cas9 screens identify new regulators of B cell activation and plasma cell differentiation.","abstract":"Immune responses to pathogens lead to the generation of plasma cells through a complex interplay of B cells with their microenvironment in lymphoid organs. To identify new regulators of B cell activation and plasmablast differentiation in the context of the splenic microenvironment, we established an in vivo system for pooled sgRNA CRISPR\/Cas9 screens in immunized mice. To improve the infection efficiency of na&#xef;ve B cells, we generated Cd23-Cre Rosa26LSL-EcoR\/+ mice exhibiting increased expression of the ecotropic lentivirus receptor EcoR on na&#xef;ve B cells. Upon adoptive B cell transfer and immunization of recipient mice, 379 sgRNAs, targeting genes with high expression in plasma cells, were analyzed for their effects on plasmablast generation. Gene hits, encoding 23 positive and 18 negative regulators of B cell activation, plasmablast differentiation, or homeostasis, were uniquely identified in these in vivo screens. Validated genes encoded proteins involved in cell adhesion, signal transduction, protein folding, iron transport, and enzymatic processes. Hence, our in vivo screening system identified novel regulators controlling B cell-mediated immune responses.","authors":"Calder\u00f3n, L., Sch\u00e4fer, M., Ron\u010devi\u0107, M., Rauschmeier, R., Jaritz, M., Schwickert, TA., Sun, Q., Pauli, A., Zuber, J., Busslinger, M.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"J Exp Med","volume":"223","issue":"3","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-28","doi":"10.1084\/jem.20250594","first_author":"Calder&#xf3;n, L.","corresponding_authors":null},{"pmid":"41557793","title":"BORC assemblies integrate BLOC-1 subunits to diversify endosomal trafficking functions.","abstract":"BORC and BLOC-1 are multisubunit complexes that regulate endolysosomal trafficking. Although they are presumed to be distinct, their paralogous origins and shared subunits suggest the potential for higher-order assembly. Here, we reveal the conserved octameric architecture of BORC formed by two intertwined tetramers and present the structure of C. elegans BORC. Through cross-linking mass spectrometry of endogenous complexes, we validate this model for human BORC and demonstrate that the integrity of the complex, which is essential for lysosomal transport, relies on specific interfacial residues. We also clarify the disruptive nature of disease-causing mutations and propose that the formation and function of BORC are likely regulated by specific cues. These cues might include the phosphorylation of Snapin and a pH-sensitive histidine residue in BORCS5. Additionally, we present direct biochemical and structural evidence of BORC-BLOC-1 hybrid complexes. Finally, we link a specific hybrid complex to the regulation of transferrin receptor recycling via interaction with the EARP complex. Our work challenges the paradigm of BORC and BLOC-1 as separate entities, establishing a model of dynamic complex formation wherein modular assembly creates functional specialization to meet diverse cellular demands.","authors":"de Araujo, MEG., J Amann, S., Stasyk, T., Schleiffer, A., Rauch, E., Fl\u00fcmann, P., Singer, II., Kremser, L., Dostal, V., Laopanupong, T., Obojes, N., Walln\u00f6fer, MH., Gradl, FS., Kurzbauer, R., Krebiehl, C., Kofler, S., Grishkovskaya, I., Vogel, GF., Hess, MW., Sarg, B., Clausen, T., Haselbach, D., Huber, LA.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Proc Natl Acad Sci U S A","volume":"123","issue":"4","page":"e2515691123","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-20","doi":"10.1073\/pnas.2515691123","first_author":"de Araujo, MEG.","corresponding_authors":null},{"pmid":"41554709","title":"Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity.","abstract":"APOBEC family members play crucial roles in antiviral restriction. However, certain APOBEC3 (A3) proteins drive harmful hypermutation in humans, contributing to cancer. The cancer-associated A3 proteins are capable of transiting from the cytosol to the nucleus, where they can cause genome mutations. Here, we uncover a specific set of cellular pathways that protect genomic DNA from the major cancer-associated A3 proteins. Through genetic and proteomic screening, we identify UBR4, UBR5, and HUWE1 as key ubiquitin E3 ligases marking cancer-associated A3B and A3H-I for degradation, thereby limiting A3-driven hypermutation. Mechanistically, UBR5 and HUWE1 recognize A3s in the absence of their RNA binding partner, thus promoting proteasomal degradation of APOBEC3 protein that is not engaged in its antiviral cellular function. Depletion or mutation of the E3 ligases in cells and human cancer samples increases A3-driven genome mutagenesis. Our findings reveal that UBR4, UBR5, and HUWE1 are crucial factors in a ubiquitination cascade that maintains human genome stability.","authors":"Schwartz, I., Budroni, V., Meyenberg, M., Hodakova, Z., Hornegger, H., Hacker, K., Schwartz, S., Grabarczyk, DB., Ehrmann, JF., Scinicariello, S., Haselbach, D., Menche, J., Clausen, T., Karag\u00f6z, GE., Versteeg, GA.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Commun","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-19","doi":"10.1038\/s41467-026-68420-5","first_author":"Schwartz, I.","corresponding_authors":null},{"pmid":"41499238","title":"PARG regulates the proteasomal degradation of TARG1.","abstract":"ADP-ribosylation (ADPr) is a reversible modification of macromolecules critical for the regulation of genome stability, stress responses, and proteostasis. While the roles of ADPr transferases such as PARP1\/2 and TNKS1\/2 are well established, the functions and regulatory mechanisms of ADPr hydrolases are still poorly understood. Here, we identify a function of the poly(ADP-ribose) glycohydrolase PARG in regulating protein degradation. Using quantitative proteomics, we show that PARG inhibition depletes protein levels of the mono-ADPr hydrolase TARG1. We demonstrate that this TARG1 depletion is both PAR and proteasome dependent and identify the E3 ubiquitin ligases HUWE1 and TRIP12 as mediators of this process. Our findings establish TARG1 as a substrate of PAR-dependent protein degradation and uncover a PARG-dependent mechanism controlling its stability. This work highlights an interplay between the two ADP-ribosyl hydrolases, with implications for the refinement of PARG-targeted therapeutic strategies.","authors":"Groslambert, J., Buch-Larsen, SC., Hendriks, IA., Kurzbauer, R., Elsborg, JD., Chatrin, C., Agnew, T., Henfrey, C., Tellier, M., Prokhorova, E., Hoang, SM., Barosso-Gonzalez, J., O'Sullivan, RJ., Clausen, T., Nielsen, ML., Ahel, I.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Cell Rep","volume":"45","issue":"1","page":"116789","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-30","doi":"10.1016\/j.celrep.2025.116789","first_author":"Groslambert, J.","corresponding_authors":"Ahel, I."},{"pmid":"41419192","title":"Structural basis for substrate recruitment and catalytic ubiquitin transfer by the E2\/E3 hybrid enzyme UBE2O.","abstract":"UBE2O is a promiscuous ubiquitin ligase involved in cellular quality control pathways. Along with BIRC6, UBE2O is one of only two E2 enzymes that can ubiquitinate substrates in an E3-independent manner. The E2\/E3 hybrid targets and multi-monoubiquitinates a multitude of orphan proteins; however, the mechanisms underlying substrate specificity and ubiquitin transfer remain poorly understood. By combining structural and biochemical approaches, we show that substrate binding by UBE2O occurs through a conserved acidic pocket formed by the N-terminal SH3-like domains and that this platform allows the recruitment of a broad range of proteins. Furthermore, we identified specific residues in the catalytic UBC domain that position ubiquitin in a closed state, confirming its confirmation, and priming it for nucleophilic attack by the incoming substrate. Importantly, the activated E2&#x223c;Ub conjugate is protected by a tryptophan residue, avoiding premature hydrolysis. By incorporating these findings into the UBC domain of BIRC6 our data provide the molecular basis of how specialized E2\/E3 hybrid proteins function as potent ubiquitination enzymes reminiscent of the catalytic principle of RING E3 ligases.","authors":"Kordic, D., Williams, TL., Deszcz, L., Ehrmann, JF., Arnese, R., Schleiffer, A., Clausen, T., Meinhart, A.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"J Biol Chem","volume":"302","issue":"2","page":"111073","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-23","doi":"10.1016\/j.jbc.2025.111073","first_author":"Kordic, D.","corresponding_authors":"Kordic, D., Meinhart, A."},{"pmid":"41678605","title":"Poxvirus attack of antiviral defense pathways unleashes an effector-triggered NF-&#x3ba;B response.","abstract":"Effector-triggered immunity (ETI) is a form of pathogen sensing that involves detection of pathogen-encoded virulence factors or \"effectors.\" To discover ETI pathways in mammals, we developed a screening approach in which we expressed individual virulence factors in a human monocyte cell line and assessed transcriptional responses by RNA sequencing. We identified a poxvirus effector, myxoma virus M3.1, which elicited an antiviral nuclear factor &#x3ba;B (NF-&#x3ba;B) response. NF-&#x3ba;B was unleashed by an ETI pathway that sensed M3.1 attack of two antiviral complexes: zinc finger antiviral protein and TBK1. NF-&#x3ba;&#x392; activation occurred because the proteins inhibited by M3.1-N4BP1, ZC3H12A, and TBK1-are negative regulators of NF-&#x3ba;B. Our study established a systematic approach for the discovery of ETI pathways, and the results illustrated how negative regulators of immune responses may function in pathogen sensing.","authors":"Remick, BC., Mao, JQ., Manford, AG., Gutierrez-Jensen, AD., Wagner, A., Rape, M., McFadden, G., Rahman, MM., Gaidt, MM., Vance, RE.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Science","volume":"391","issue":"6786","page":"eadw4937","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-02-12","doi":"10.1126\/science.adw4937","first_author":"Remick, BC.","corresponding_authors":null},{"pmid":"41639071","title":"A multivalent adaptor mechanism drives the nuclear import of proteasomes.","abstract":"Nuclear protein homeostasis, including transcription factor turnover, critically depends on the nuclear proteasomes that must be imported after cell division. This dynamic process requires AKIRIN2, a small unstructured protein whose mechanistic role has remained elusive despite its essential function. Using an integrated approach combining protein-wide saturation mutagenesis screens, cryo-EM, and biochemical reconstitution, we characterize AKIRIN2 as a scaffold protein that coordinates the assembly of an importin cluster around the proteasome. AKIRIN2 binds in multiple copies to the 20S proteasome and simultaneously interacts with importin IPO9 and the KPNA2\/KPNB1 heterodimer. In the nucleus, RanGTP triggers importin dissociation, releasing the proteasome, while AKIRIN2 undergoes ubiquitin-independent degradation. Our findings reveal how AKIRIN2's multivalency facilitates the recruitment of multiple importins to the proteasome, a critical adaptation for transporting this large macromolecular complex into the nucleus and maintaining the nuclear proteome.","authors":"Brunner, HL., Kalis, RW., Grundmann, L., Hod\u00e1kov\u00e1, Z., Koskova, Z., Grishkovskaya, I., de Almeida, M., Hinterndorfer, M., Knaudt, H., H\u00f6fflin, S., Andersch, F., Kotisch, H., Dickmanns, A., Cuylen-Haering, S., Zuber, J., Haselbach, D.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Commun","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.09.22.753668v1","articledate":"2026-02-04","doi":"10.1038\/s41467-026-69162-0","first_author":"Brunner, HL.","corresponding_authors":null},{"pmid":"41569156","title":"A comprehensive view on r-protein binding and rRNA domain structuring during early eukaryotic ribosome formation.","abstract":"Formation of the eukaryotic ribosomal subunits follows a strict regime to assemble ribosomal proteins (r-protein) with ribosomal RNAs (rRNA) while removing internal (ITS) and external (ETS) transcribed rRNA spacers. During the early stages of large subunit (LSU) formation, ITS2, together with six assembly factors, forms the characteristic foot structure of early nuclear pre-LSU particles. Here, we address the function of this foot structure during the early stages of ribosome assembly. We present cryo-EM structures from wild-type cells and cells depleted for the foot structure factor Rlp7. We show that compaction of domain I of the 25S rRNA is strictly dependent on the presence of foot factors, while domain II folds independently. Furthermore, Rlp7-depletion accumulated small subunit (SSU) processome intermediates prior to A1 cleavage and compaction of the individual domains of the 18S rRNA, providing also novel insights into the SSU-assembly process. SILAC labeling and affinity purification of co-transcriptionally assembled pre-ribosomes enabled us to resolve the assembly line of most early binding r-proteins step by step. This showed that incorporation of r-proteins in eukaryotes neither follows the bacterial regime nor a strict linear co-transcriptional mode. Instead, seed r-proteins might structurally define the individual rRNA domains before their compaction and fixation in the context of early pre-ribosomes.","authors":"Gerhalter, M., Prattes, M., Grundmann, LE., Grishkovskaya, I., Semeraro, EF., Zisser, G., Kotisch, H., Merl-Pham, J., Hauck, SM., Haselbach, D., Bergler, H.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Nucleic Acids Res","volume":"54","issue":"3","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-22","doi":"10.1093\/nar\/gkag036","first_author":"Gerhalter, M.","corresponding_authors":null},{"pmid":"41545346","title":"The cotranslational cycle of the ribosome-bound Hsp70 homolog Ssb.","abstract":"Coupling of ribosomal translation with cotranslational protein folding is essential for cellular homeostasis. In eukaryotes, Hsp70 and its J-domain cochaperone, the heterodimeric ribosome-associated complex (RAC), are central to this process; however, mechanistic insights into the coordination of Hsp70 function with translation remain limited. Here, we present two cryo-EM structures of the ribosome-bound yeast Hsp70 Ssb, identifying Rpl25\/uL23 as the ribosomal binding site and revealing its interaction with a model nascent chain. Together with detailed biochemical and mutational analyses, these structures enable us to delineate the intricate RAC-dependent cycle, which positions the substrate binding domain of Ssb-ATP close to the tunnel exit to receive nascent chains. This arrangement allows Ssb to undergo substantial conformational changes upon ATP hydrolysis without steric clashes with the ribosome, while the substrate binding domain of Ssb, now anchored by the tightly bound nascent chain, remains close to the tunnel exit.","authors":"Zhang, Y., Grundmann, L., Vollmar, L., Schimpf, J., H\u00fcbscher, V., Areeb, M., Grishkovskaya, I., Moddemann, A., Werner, K., Hugel, T., Haselbach, D., Rospert, S.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":"961","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-27","doi":"10.1038\/s41467-025-67685-6","first_author":"Zhang, Y.","corresponding_authors":null},{"pmid":"41174228","title":"Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape.","abstract":"Protein neofunctionalization is a key driver of cellular complexity. However, subunits of multimeric protein complexes are often thought to be evolutionarily constrained, limiting their capacity for functional divergence. This presents a paradox in plants, where the Exo70 subunit of the exocyst-an octameric complex essential for exocytosis-has undergone striking expansion and diversification. Here we show that electrostatic changes in the N-terminal helix of Exo70 facilitated its physical and functional dissociation from the exocyst, relieving constraints imposed by complex integration. Using Marchantia polymorpha and Arabidopsis thaliana, we demonstrate that this 'complex escape' enables Exo70 paralogues to acquire distinct localizations, interactomes and functions independent of canonical exocytosis. Ancestral reconstructions across land plants reveal that this electrostatic shift predates the extensive radiation of the plant Exo70 protein family, with some lineages later reassociating with the complex. Our findings reveal a reversible mechanism that enabled Exo70 to circumvent the evolutionary and biophysical constraints imposed by complex integration and diversify-a mechanism that could represent a generalizable route to protein neofunctionalization and cellular innovation.","authors":"De la Concepcion, JC., Duverge, H., Kim, Y., Julian, J., Xu, HD., Watt, MN., Ikene, SA., Bianchi, A., Grujic, N., Papareddy, RK., Grishkovskaya, I., Haselbach, D., Murray, DH., Clavel, M., Irwin, NAT., Dagdas, Y.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nat Plants","volume":"11","issue":"11","page":"2350-2367","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-11-19","doi":"10.1038\/s41477-025-02135-1","first_author":"De la Concepcion, JC.","corresponding_authors":null},{"pmid":"41420106","title":"Mechanisms of resistance to VHL loss-induced genetic and pharmacological vulnerabilities.","abstract":"The von Hippel-Lindau tumor suppressor (VHL) is a component of a ubiquitin ligase complex that controls cellular responses to hypoxia. Endogenous VHL is also utilized by proteolysis-targeting chimera (PROTAC) protein degraders, a promising class of anti-cancer agents. VHL is broadly essential for cell proliferation, yet it is a key tumor suppressor in renal cell carcinoma. To understand the functional consequences of VHL loss, and to identify targeted approaches for the elimination of VHL null cells, we have used genome-wide CRISPR-Cas9 screening in human renal epithelial cells. We find that, upon VHL loss, the HIF1A\/ARNT complex is the central inhibitor of cellular fitness, suppressing mitochondrial respiration, and that VHL null cells show HIF1A-dependent molecular vulnerabilities that can be targeted pharmacologically. Combined VHL\/HIF1A inactivation in breast and esophageal cancer cells can also provide resistance to ARV-771, a VHL-based bromodomain degrader that has anti-cancer activity. HIF1A stabilization can thus provide opportunities for early intervention in neoplastic VHL clones, and the VHL-HIF1A axis may be relevant for the development of resistance to the emerging class of PROTAC-based cancer therapies.","authors":"Ge, J., Hirosue, S., Castillon, L., Patel, SA., Wesolowski, L., Dyas, A., Yong, C., de Haan, S., Drost, J., Stewart, GD., Obenauf, AC., Mu\u00f1oz-Esp\u00edn, D., Vanharanta, S.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"EMBO Mol Med","volume":"18","issue":"2","page":"599-619","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-02-13","doi":"10.1038\/s44321-025-00361-w","first_author":"Ge, J.","corresponding_authors":null},{"pmid":"41497587","title":"Predictive design of tissue-specific mammalian enhancers that function <i>in vivo<\/i> in the mouse embryo.","abstract":"Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains unclear whether such approaches can operate within the regulatory complexity of mammalian tissues in vivo. Here, we present a general strategy for designing tissue-specific enhancers that function reliably in mice. We use deep learning to train compact convolutional neural networks (CNNs) on genome-wide chromatin accessibility and fine-tune them via transfer learning on validated human and mouse enhancers. Guided by these models, we design fifteen synthetic enhancers for the heart, limb, and central nervous system (CNS) in mouse embryos, all of which are active in their intended target tissue. Our work establishes a generalizable framework for programmable control of mammalian gene expression <i>in vivo<\/i>, opening new avenues in functional genomics, synthetic biology, and gene therapy.","authors":"Chen, S., Loubiere, V., Hollingsworth, EW., Jacinto, SH., Dizehchi, A., Schreiber, J., Kvon, EZ., Stark, A.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-12","doi":"10.64898\/2025.12.22.695948","first_author":"Chen, S.","corresponding_authors":null},{"pmid":"41332698","title":"Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways.","abstract":"Pathogens deploy effector proteins to exploit host cell biology, and most pathogen open reading frames (ORFs) are rapidly evolving and lack functional annotation. We developed the eORFeome, a scalable functional genomics platform encompassing 3,835 effector ORFs from diverse viruses, bacteria, and parasites. High-throughput barcoded screens across NF&#x3ba;B, apoptosis, p53, cGAS-STING and MHC-I pathways revealed functions for hundreds of uncharacterized eORFs, unexpected new activities for known effectors, and distinct pathway-specific functions encoded by single ORFs. Illustrating the power of the approach, we identify HHV6A U14 as a p53 antagonist, HHV7 U21 as a dual-function STING antagonist and MHC-I antigen display inhibitor, and adenoviral 13.6K\/i-leader protein as a <i>de novo<\/i> evolved TAP inhibitor that suppresses MHC-I display. These results establish a general framework for systematic effector annotation, uncover new mechanisms of host-pathogen interaction across kingdoms, and highlight pathogen effectors as a versatile toolkit for rewiring and probing human cellular pathways.","authors":"Pachano, T., Leng, H., Dugied, G., Tribble, T., Loubiere, V., Rauh, F., Lee, Y., Schleiffer, A., Young, V., Weller, B., Lyons, EA., Hass, MR., Kottayan, LC., Weirauch, MT., Fuxman Bass, JI., Newton, HJ., Ensminger, AW., Braun, PF., Schramek, D., Stark, A., Taipale, M.","publication_status":"epublish","journalpubyear":"2025","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-22","doi":"10.1101\/2025.11.17.687821","first_author":"Pachano, T.","corresponding_authors":null},{"pmid":"41451844","title":"Loss-of-function genetic screen unveils synergistic efficacy of PARG inhibition with combined 5-fluorouracil and irinotecan treatment in colorectal cancer.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">41451844<\/PMID><DateCompleted><Year>2025<\/Year><Month>12<\/Month><Day>26<\/Day><\/DateCompleted><DateRevised><Year>2026<\/Year><Month>01<\/Month><Day>02<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">2001-1326<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>15<\/Volume><Issue>12<\/Issue><PubDate><Year>2025<\/Year><Month>Dec<\/Month><\/PubDate><\/JournalIssue><Title>Clinical and translational medicine<\/Title><ISOAbbreviation>Clin Transl Med<\/ISOAbbreviation><\/Journal><ArticleTitle>Loss-of-function genetic screen unveils synergistic efficacy of PARG inhibition with combined 5-fluorouracil and irinotecan treatment in colorectal cancer.<\/ArticleTitle><Pagination><StartPage>e70543<\/StartPage><MedlinePgn>e70543<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">e70543<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1002\/ctm2.70543<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Colorectal cancer (CRC) remains a major global health concern, partly due to resistance to therapy and the lack of new effective treatments for advanced disease. The combination of 5-Fluorouracil (5FU, a thymidylate synthase inhibitor) and irinotecan (a topoisomerase 1 inhibitor) is widely used in first-line and subsequent treatments. This study aimed to identify novel therapeutic targets to enhance combinatorial therapy, improving treatment efficacy and durability of response.","authors":"Queralt, C., Moreta-Moraleda, C., Costa, M., Grau-Leal, F., Diesch, J., Vendrell-Ayats, C., Musul\u00e9n, E., Wright, RHG., Bug\u00e9s, C., Manzano, JL., Cabrero-de Las Heras, S., Zuber, J., Buschbeck, M., Forcales, SV., Mart\u00ednez-Balibrea, E.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Clin Transl Med","volume":"15","issue":"12","page":"e70543","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-26","doi":"10.1002\/ctm2.70543","first_author":"Queralt, C.","corresponding_authors":"Mart&#xed;nez-Balibrea, E."},{"pmid":"41296826","title":"Lymphotoxin alpha eradicates acute myeloid leukemia and simultaneously promotes healthy hematopoiesis in mice.","abstract":"Acute myeloid leukemia (AML) is characterized by frequent relapse, which is driven by resistant leukemic stem or progenitor cells (LSCs). Here, we reported on a tumor-suppressive mechanism that can be harnessed to simultaneously clear LSCs and promote healthy hematopoiesis. Genetic deletion of the tumor necrosis factor (TNF) superfamily member <i>lymphotoxin alpha<\/i> (<i>Lta<\/i>) blocked cell death and accelerated leukemogenesis in murine AML models. Accordingly, exposure of leukemic cells to exogenous recombinant lymphotoxin alpha (LT&#x3b1;<sub>3<\/sub>) induced myeloid differentiation and, in part, cell death in AML progenitors. In syngeneic and patient-derived xenograft mouse models, exposure to recombinant LT&#x3b1;<sub>3<\/sub> resulted in deep and durable remissions. LT&#x3b1;<sub>3<\/sub> repressed leukemia by depleting tumor necrosis factor receptor (TNFR)-associated factor 2 (TRAF2) through activation of TNF receptors TNFR1 and TNFR2. In contrast with conventional therapies, LT&#x3b1;<sub>3<\/sub> exerted only minimal toxicity on the healthy hematopoiesis but instead promoted hematopoietic progenitors. Leveraging this endogenous tumor-suppressive mechanism may decouple treatment efficacy on malignant cells from undesired bone marrow suppression.","authors":"H\u00f6ckendorf, U., Dutta, S., Kloos, A., Runtsch, M., Z\u00f6tsch, C., Vosberg, S., Wang, Y., Kienreich, S., Flasch, B., Malovan, G., J\u00e4ger, V., Stanzer, S., Prein, S., Odinius, TO., Wagner, CV., Buschhorn, L., Dill, V., Perfler, B., Haferlach, T., D\u00f6hner, K., G\u00f6tze, KS., Ruland, J., Bassermann, F., Wahida, A., Heikenw\u00e4lder, M., Branca, C., Schm\u00f6llerl, J., Zuber, J., Burk, AC., Zeiser, R., Sill, H., Jayavelu, AK., Zebisch, A., Heuser, M., Dengler, MA., Jost, PJ.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Sci Transl Med","volume":"17","issue":"826","page":"eadu3313","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-11-26","doi":"10.1126\/scitranslmed.adu3313","first_author":"H&#xf6;ckendorf, U.","corresponding_authors":null},{"pmid":"41060369","title":"MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia.","abstract":"The transcription factor MECOM, located at 3q26, is essential for hematopoietic stem cells in healthy individuals. Enhancer translocations, due to 3q26 rearrangements, drive out-of-context MECOM expression in one of the most aggressive subtypes of acute myeloid leukemia (AML). Aberrantly expressed MECOM is essential for the survival and immature phenotype of these leukemia cells. Direct depletion of MECOM using an endogenous auxin-inducible degron immediately upregulates expression of CEBPA, which encodes a transcription factor required for neutrophil development and is frequently mutated in other AML subtypes. MECOM depletion is accompanied by a severe loss of CD34 and gain of mature myeloid cell surface marker CD15. MECOM exerts its inhibitory effect on differentiation by binding to the +42-kilobase CEBPA enhancer. This is partially dependent on the interaction between MECOM and its corepressor CTBP2. We demonstrate that CEBPA overexpression can bypass the MECOM-mediated block of differentiation. In addition, patients with AML with MECOM overexpression through enhancer hijacking show significantly reduced CEBPA levels. Our study directly connects 2 major players in normal and malignant hematopoiesis, MECOM and CEBPA, and unveils how MECOM maintains self-renewal by repressing CEBPA-induced differentiation.","authors":"Pastoors, D., Havermans, M., Mulet-Lazaro, R., Smeenk, L., Ottema, S., Erpelinck-Verschueren, C., van Herk, S., Anthonissen, M., Grob, T., Subramanian, S., Thoms, JAI., Pimanda, JE., Wouters, BJ., Beverloo, B., Haferlach, T., Haferlach, C., Zuber, J., Bindels, E., Delwel, R.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Blood","volume":"146","issue":"25","page":"3098-3105","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-18","doi":"10.1182\/blood.2025028914","first_author":"Pastoors, D.","corresponding_authors":null},{"pmid":"41689039","title":"Axolotls retain fertility throughout lifespan.","abstract":"on Status=\"Publisher\" Owner=\"NLM\"><PMID Version=\"1\">41689039<\/PMID><DateRevised><Year>2026<\/Year><Month>02<\/Month><Day>14<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1741-7007<\/ISSN><JournalIssue CitedMedium=\"Internet\"><PubDate><Year>2026<\/Year><Month>Feb<\/Month><Day>14<\/Day><\/PubDate><\/JournalIssue><Title>BMC biology<\/Title><ISOAbbreviation>BMC Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Axolotls retain fertility throughout lifespan.<\/ArticleTitle><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s12915-026-02545-3<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Salamanders such as axolotls exhibit exceptional regenerative abilities and longevity. While many ectothermic species reproduce into old age, axolotls have been proposed to experience post-maturation fertility decline.","authors":"Haluza, Y., Gruhl, B., Wagner, A., Kurth, T., Tanaka, EM., Yun, MH.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"BMC Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-02-14","doi":"10.1186\/s12915-026-02545-3","first_author":"Haluza, Y.","corresponding_authors":"Yun, MH."},{"pmid":"41826699","title":"Riboflavin metabolism shapes FSP1-driven ferroptosis resistance.","abstract":"Membrane protection against oxidative insults is achieved by the concerted action of glutathione peroxidase 4 (GPX4) and endogenous lipophilic antioxidants such as ubiquinone and vitamin E. More recently, ferroptosis suppressor protein 1 (FSP1) was identified as a critical ferroptosis inhibitor, acting via the regeneration of membrane-embedded antioxidants. Yet, regulators of FSP1 are largely uncharacterized, and their identification is essential for understanding the mechanisms buffering phospholipid peroxidation and ferroptosis. Here we report a focused CRISPR-Cas9 screen to uncover factors influencing FSP1 function, identifying riboflavin (vitamin B<sub>2<\/sub>) as a modulator of ferroptosis sensitivity. We demonstrate that riboflavin supports FSP1 stability and the recycling of lipid-soluble antioxidants, thereby mitigating phospholipid peroxidation. Furthermore, we show that the riboflavin antimetabolite roseoflavin markedly impairs FSP1 function and sensitizes cancer cells to ferroptosis. Our findings provide a rational strategy to modulate the FSP1-antioxidant recycling pathway and underscore the therapeutic potential of targeting riboflavin metabolism, with implications for understanding the interaction of nutrients, as well as their contributions to a cell's antioxidant capacity.","authors":"Skafar, V., de Souza, I., Ghosh, B., Ferreira Dos Santos, A., Porto Freitas, F., Chen, Z., Sun, S., Donate Castillo, M., Nepachalovich, P., Seufert, L., Bothe, S., Tschuck, J., Mathur, A., Nunes-Alves, A., Buhr, J., Aponte-Santamar\u00eda, C., Schmitz, W., Mack, M., Eilers, M., Bargou, R., Chaufan, M., Kaur, M., Palma, M., Ubellacker, JM., Elling, U., Augustin, HG., Hadian, K., Meierjohann, S., Proneth, B., Conrad, M., Fedorova, M., Alborzinia, H., Friedmann Angeli, JP.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Cell Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-03-14","doi":"10.1038\/s41556-025-01856-x","first_author":"Skafar, V.","corresponding_authors":"Friedmann Angeli, JP."},{"pmid":"41888583","title":"PACS1 syndrome mutation disrupts dynein-mediated cargo transport via HDAC6 and BICD2.","abstract":"PACS1 syndrome is a neurodevelopmental disorder caused by a recurrent heterozygous missense mutation in PACS1 (p.R203W). We previously showed that PACS1<sup>R203W<\/sup> aberrantly potentiates HDAC6 activity, leading to Golgi fragmentation and neuronal deficits through an unresolved mechanism (Villar-Pazos and Thomas et al., Nature Commun. 14:6547-6564 (2023)). Here, we identify cytoplasmic dynein-1 heavy chain (DHC1) as a PACS1 interactor essential for maintaining furin localization at the trans-Golgi network. PACS1<sup>R203W<\/sup> induces a dynein loss-of-function phenotype that disrupts furin trafficking and Golgi organization. We demonstrate that PACS1<sup>R203W<\/sup>-HDAC6 recruits the adaptor BICD2, forming a complex that disperses the Golgi and impairs dynein function. Cargo motility assays revealed that PACS1<sup>R203W<\/sup> reduces dynein initiation frequency and velocity, defects rescued by HDAC6 inhibition or by expressing the dynein regulator Lis1. These findings uncover a pathogenic mechanism in which PACS1<sup>R203W<\/sup>-HDAC6-BICD2 disrupts dynein-driven transport, placing PACS1 syndrome within the broad spectrum of microtubule trafficking disorders.","authors":"Yang, Y., Thomas, L., Chen, K., Villar-Pazos, S., Haffey, WD., D'Agostino, A., Fanelli, K., Choi, YJ., Rathi, V., Matlapudi, MS., Greis, KD., Thomas, G.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Commun Biol","volume":"9","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-03-27","doi":"10.1038\/s42003-026-09924-0","first_author":"Yang, Y.","corresponding_authors":"Thomas, G."},{"pmid":"41951755","title":"A guide to using embedded ethics in human stem-cell-based embryo model research.","abstract":"Human stem-cell-based embryo models (hSCBEMs) offer unprecedented opportunities for basic and translational research. However, the rapid pace of scientific developments in the field challenges the slower, traditional modes of ethics evaluation. To facilitate responsible research and governance, and ensure public trust, we propose using 'embedded ethics' as a purpose-anchored, dynamic, iterative and integrative approach where ethicists and scientists engage in continuous dialogue to ethically assess ongoing research. We outline a nested benchmarking strategy to periodically evaluate the scientific and ethical status of hSCBEMs within a project, using the human embryo as a reference and weighting criteria along a hierarchy of features that chart embryo-likeness, completeness and the developmental stage modelled. Embedded ethics guides the definition of decision points and ethical boundaries through an iterative assessment of project purpose and ethical and regulatory frameworks, and enables early identification of emerging issues and the co-construction of responsible paths forward.","authors":"Bentzen, HB., Gaillard, M., Nachman, I., Reumann, D., Gadegaard, N., David, L., Lanner, F., Moris, N., Pasque, V., Rivron, N., Sozen, B., Isasi, R., Krauss, S., Veenvliet, JV.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Cell Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-04-08","doi":"10.1038\/s41556-026-01909-9","first_author":"Bentzen, HB.","corresponding_authors":"Veenvliet, JV."},{"pmid":"41951754","title":"Morally relevant features warranting ethical oversight in human stem cell-based embryo models.","abstract":"Stem cell-based embryo models provide innovative ways to explore the principles of human development but also pose new challenges for regulation. Recent guidelines have argued for case-by-case evaluation of stem cell-based embryo model research but it is still unclear what exactly such oversight should consider. Here we argue that effective review requires the identification of a set of attributes by which to evaluate research proposals. To define these, the underlying ethical values and morally relevant biological features present in embryo models must be identified to enable the practical implementation of oversight. We propose that developmental stage, tissue\/organ integrity, fetal potential and the capacity to form neural circuits should be used together for evaluation purposes. We also highlight the importance of the wider context, including the proposed uses of embryo models, public perception and individual researcher responsibilities, and thus provide a general framework for regulatory consideration of human embryo model research.","authors":"Moris, N., Martinez Arias, A., Pera, M., Rivron, N., Sermon, K., de Graeff, N.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Cell Biol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-04-08","doi":"10.1038\/s41556-026-01881-4","first_author":"Moris, N.","corresponding_authors":"de Graeff, N."},{"pmid":"41708383","title":"BacPROTAC-induced protein degradation as a new antibiotic concept.","abstract":"Antibiotic resistance is spreading worldwide, associated with more than 5 million deaths annually, yet few new antibiotics have emerged in recent years. This gap highlights the need for alternative strategies that enable the rational design of antibacterial agents. One promising approach is the development of proteolysis-targeting chimeras in bacteria (BacPROTACs), which can hijack endogenous degradation pathways. BacPROTACs tether selected proteins to caseinolytic proteases (Clp) to promote their degradation. Thus, unlike conventional inhibitors, they eliminate their targets, act in a catalytic manner, and can exploit weak binders. Furthermore, BacPROTACs have been shown to reach pathogens in infected cells, exhibiting potent activity against multidrug-resistant Mycobacterium tuberculosis. While challenges remain in cell entry, substrate selectivity, and pharmacokinetic optimization, BacPROTACs offer a promising route to develop next-generation antibiotics.","authors":"Junker, S., Clausen, T.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Trends Biochem Sci","volume":"51","issue":"3","page":"249-260","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-03-08","doi":"10.1016\/j.tibs.2025.12.012","first_author":"Junker, S.","corresponding_authors":"Junker, S., Clausen, T."},{"pmid":"42026065","title":"Structural basis of NSD2 degradation via targeted recruitment of SCF-FBXO22.","abstract":"Targeted protein degradation (TPD) through the ubiquitin-proteasome system is driven by compound-mediated polyubiquitination of a protein-of-interest by an E3 ubiquitin (Ub) ligase. Relatively few E3s have been successfully utilized for TPD and the governing principles of functional ternary complex formation between the E3, degrader, and protein target remain elusive. FBXO22 has recently been harnessed for TPD applications by degraders that covalently modify its cysteine residues. Here, we reveal that the aldehyde derivative of UNC10088 promotes cooperative binding of FBXO22 to NSD2, a histone methyltransferase and oncogenic protein, leading to a cryo-EM structure of the SKP1-CUL1-F-box (SCF)-FBXO22 complex with NSD2. This structure revealed a conformational change in the FBXO22 loop surrounding C326, further exposing the cysteine for covalent recruitment. Additional medicinal chemistry efforts led to the discovery of benzaldehyde-based non-prodrug degraders that similarly engage C326 of FBXO22 and potently degrade NSD2. Unlike many degraders, our molecules recruit NSD2 to a different surface of FBXO22 than the known FBXO22 substrate BACH1, allowing for concurrent complex formation and structural determination of SCF<sup>FBXO22<\/sup> bound to both the neosubstrate NSD2 and native substrate BACH1. Overall, we demonstrate the biochemical and structural basis for NSD2 degradation, revealing key principles for efficient and selective TPD by SCF<sup>FBXO22<\/sup>.","authors":"Robertson, KC., Amann, SJ., Liu, T., Funk, AV., Wang, X., Grishkovskaya, I., Mehmood, A., Tabor, JR., Norris-Drouin, JL., Arrowsmith, CH., Collins, JL., Miao, Y., Emanuele, MJ., Haselbach, D., James, LI., Brown, NG.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Commun","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-04-25","doi":"10.1038\/s41467-026-72235-9","first_author":"Robertson, KC.","corresponding_authors":"James, LI."},{"pmid":"41991342","title":"The microprotein SMIM26 connects metabolite transporters of the outer and inner mitochondrial membranes and is essential for respiratory chain function.","abstract":"Microproteins represent a class of short polypeptides with very diverse cellular functions. Microproteins frequently escape proteomics-based identification, making the extent and potential functions of small proteins largely elusive. Some microproteins originate from transcripts that are annotated as long noncoding RNAs (lncRNAs). Here, we functionally characterize SMIM26, a microprotein localized to mitochondria. In biochemical and single-molecule tracking studies, we found that SMIM26 interacts with VDAC1\/2 in the outer mitochondrial membrane and with SLC25A6 in the inner mitochondrial membrane. It spans the intermembrane space and is phosphorylated at distinct residues. Knockout cells are viable, but respiratory chain activity is strongly reduced. Interestingly, knockout mice are not viable and die at early developmental stages. Zebrafish homozygous <i>smim26<\/i> mutants are viable but show reduced fitness and survival compared with their wild-type or heterozygous siblings. Consistent with the mitochondrial phenotype in cell lines, respiration is also reduced in homozygous zebrafish embryos. Our work suggests that SMIM26 coordinates metabolite transport through the inner and outer mitochondrial membranes and is essential for respiratory chain function in vivo.","authors":"Heizler, K., Chugunova, A., Hofmann, M., Prochazkova, M., Proch\u00e1zka, J., Ho-Xuan, H., Fallmann, J., Stejskal, K., Krssakova, G., Bader, S., Kocak, E., Yasar, D., Luckner, P., Lehmann, G., K\u00f6ngeter, J., Riester, M., Roitinger, E., Wetzel, C., Diederichs, S., Sedlacek, R., Bruckmann, A., Gebhardt, JCM., Pauli, A., Meister, G.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Genes Dev","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-04-16","doi":"10.1101\/gad.353272.125","first_author":"Heizler, K.","corresponding_authors":"Meister, G."},{"pmid":"42030945","title":"PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes.","abstract":"Cohesin-NIPBL complexes extrude genomic DNA into loops that are constrained by CTCF boundaries. This process has important regulatory functions and weakens the separation between euchromatic and heterochromatic compartments. Cohesin can also bind PDS5 proteins, which do not support loop extrusion but are required for the formation of CTCF boundaries. How PDS5 proteins perform this function is unknown. Here we show, by in vitro single-molecule imaging, that human PDS5 proteins stop loop extrusion by facilitating the dissociation of NIPBL from cohesin. Hi-C experiments suggest that this function is required for the establishment of CTCF boundaries in cells. In silico modeling indicates that PDS5 proteins enable the separation between compartments by limiting cohesin's velocity and chromatin residence time. The degree of this compartmentalization depends on the frequency with which chromatin is extruded relative to the time it takes for compartments to form. These results identify PDS5 proteins as key regulators of genome organization.","authors":"Wutz, G., Davidson, IF., Banigan, EJ., Stocsits, RR., Kawasumi, R., Tang, W., Nagasaka, K., Costantino, L., Jansen, R., Hirota, K., Branzei, D., Mirny, LA., Peters, JM.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Mol Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-04-24","doi":"10.1016\/j.molcel.2026.03.025","first_author":"Wutz, G.","corresponding_authors":"Peters, JM."},{"pmid":"41349519","title":"Two CTCF motifs impede cohesin-mediated DNA loop extrusion.","abstract":"Human cohesin extrudes DNA into loops and is positioned along the genome by stalling at the human CCCTC-binding factor (CTCF) upon encountering its N-terminal region (NTR). The mechanism underlying this stalling, however, is unresolved. Using single-molecule assays that monitor DNA loop extrusion (LE) in the presence of NTR fragments, we identify two amino acid motifs, YDF and KTYQR, which hinder LE. KTYQR is found to completely block LE activity, while YDF hinders cohesin from completing LE step cycles and converts cohesin into a unidirectional extruder by strengthening the affinity of STAG1 to DNA. We thus identify two distinct NTR motifs that stall LE via different yet synergistic mechanisms, highlighting the multifaceted ways employed by CTCF to modulate LE to shape and regulate genomes.","authors":"Barth, R., Janissen, R., Muras, L., van der Torre, J., Litos, G., van der Sluis, E., van den Berg, A., Davidson, IF., Peters, JM., Dekker, C.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Mol Cell","volume":"85","issue":"23","page":"4304-4317.e9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-12-05","doi":"10.1016\/j.molcel.2025.11.001","first_author":"Barth, R.","corresponding_authors":"Dekker, C."},{"pmid":"41792242","title":"Functional genomic screens uncover FERMT2 as a critical regulator of YAP\/TAZ-driven tumorigenicity.","abstract":"YAP and TAZ are transcriptional regulators essential for mechanotransduction, development, and tissue homeostasis, whose dysregulation is implicated in multiple diseases, including cancer. To identify key regulators of YAP\/TAZ signaling required for breast cancer cell fitness, we performed CRISPR\/Cas9-based loss-of-function genetic screens both in vitro and in vivo. A custom sgRNA library targeting 216 candidate YAP\/TAZ modulators was screened across three breast cancer cell lines. Among these, FERMT2, a component of the integrin signaling pathway, consistently emerged as a strong drop-out hit, highlighting its essential role in sustaining YAP\/TAZ-dependent fitness. Bioinformatic analysis of large-scale cancer datasets further revealed genetic co-dependency between FERMT2, YAP, and TAZ, particularly in tumors with high YAP\/TAZ expression. Functional validation through FERMT2 knockout and silencing demonstrated its requirement for proliferation, anchorage-independent growth, and tumorigenicity in triple-negative breast cancer cells. FERMT2 loss impaired YAP\/TAZ nuclear accumulation, reduced the expression of YAP\/TAZ target genes, and decreased phosphorylation at key tyrosine residues. Mechanistically, FERMT2 regulates YAP\/TAZ independently of the canonical Hippo pathway through integrin-mediated activation of FAK. Consistent with this, glucocorticoid-driven FAK activation restored YAP\/TAZ signaling in FERMT2-depleted cells. Partial epistasis analyses also indicate that FERMT2 modulates actin-dependent regulation of YAP\/TAZ. Together, these findings identify FERMT2 as a pivotal upstream regulator of YAP\/TAZ via FAK signaling, demonstrate that YAP\/TAZ are principal effectors of integrin activity, and suggest that FERMT2 may represent a selective vulnerability in cancers with elevated YAP\/TAZ signaling.","authors":"Chiesa, A., Poli, V., Croci, O., Biagioni, F., Fuentes, P., Marenda, M., Dondi, A., Rodighiero, S., Filipuzzi, M., Sberna, S., Marzi, M., Nicassio, F., Zuber, J., Campaner, S.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Cell Death Differ","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-03-06","doi":"10.1038\/s41418-026-01694-w","first_author":"Chiesa, A.","corresponding_authors":"Campaner, S."},{"pmid":"42310446","title":"Molecular basis of polyadenylated RNA fate determination in the nucleus.","abstract":"Eukaryotic genomes generate a plethora of polyadenylated (pA<sup>+<\/sup>) RNAs<sup>1,2<\/sup>, which are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA<sup>+<\/sup> RNPs, including protein-coding RNPs, are exported to the cytoplasm, whereas transcripts within non-functional pA<sup>+<\/sup> RNPs are degraded in the nucleus<sup>1-4<\/sup>. How cells distinguish these opposing fates remains unknown. The DExD-box ATPase UAP56 (also known as DDX39B) is a central component of functional pA<sup>+<\/sup> RNPs, and promotes their docking to the nuclear pore complex-anchored TREX-2<sup>5,6<\/sup>, which triggers transcript release from UAP56 to facilitate export<sup>7<\/sup>. Here we reveal that the poly(A) tail exosome targeting (PAXT) connection<sup>8<\/sup> binds a TREX-2-like module, which releases pA<sup>+<\/sup> RNAs from UAP56 for decay by the nuclear exosome. The core of this module consists of a LENG8-PCID2-SEM1 trimer, which we show is structurally and biochemically equivalent to the central GANP-PCID2-SEM1 trimer of TREX-2. Mutagenesis and transcriptomic data demonstrate that the nuclear fate of pA<sup>+<\/sup> RNPs is governed by the contending actions of nucleoplasmic PAXT and nuclear pore complex-associated TREX-2, which interpret RNA-bound UAP56 as a signal for RNA decay or export, respectively. As RNA targets of PAXT are generally short and intron-poor, we propose an overall model for pA<sup>+<\/sup> RNP fate determination whereby the distinct sub-nuclear localizations of PAXT and TREX-2 govern the degradation of short non-functional pA<sup>+<\/sup> RNAs while allowing export of their longer and functional counterparts.","authors":"Bugai, A., Hohmann, U., Lorenzo, A., Graf, M., Fin, L., Rouvi\u00e8re, JO., Tirian, L., Dou, Y., Le Rest, M., Pol\u00e1k, P., Johnsen, D., Jakobsen, L., Andersen, JS., Brennecke, J., Plaschka, C., Jensen, TH.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Nature","volume":"655","issue":"8124","page":"1070-1078","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-22","doi":"10.1038\/s41586-026-10650-0","first_author":"Bugai, A.","corresponding_authors":"Jensen, TH."},{"pmid":"42059677","title":"Stress and conflict management in core facilities-News from an imaging survey.","abstract":"While conflict management is a well-known challenge for people working in the service sector, this topic remains largely unexplored in scientific imaging core facilities, despite frequent interactions with diverse users in environments with complex service demands. To address this gap, we conducted a survey to assess staff experiences, challenges, and the availability of institutional support. The 38-question survey, completed anonymously, covered three areas: (1) respondent background; (2) assessment of stress in core facilities and coping mechanisms and stress management resources; and (3) work environment challenges such as user interactions and overall work atmosphere. The results highlight the need for more awareness, targeted training, and organisational strategies to improve staff well-being and foster a collaborative work culture. By raising awareness and providing actionable insights, we aim to inform best practices for conflict de-escalation and, when necessary, conflict management in research infrastructure settings. While exemplified with scientific imaging facilities, we believe our survey results are easily transferable to other scientific cores and infrastructures with similar service and user interactions. In addition, the dataset is available to other researchers on figshare. Information concerning the data records, usage notes, code availability, and technical validation is presented.","authors":"Peychl, J., Rossi, C., Aulner, N., Salles, A., Halidi, N., Brunstein, M., Mallet, A., Aumayr, K., Verbavatz, JM., Heuser, T., Santarella-Mellwig, R., Dauphin, A., Parthoens, E., Gunkel, M., Fritsch, M., Bundschuh, ST., Chaabouni, R., Uhereczky, A., Tranfield, EM., Varas, PH., Munck, S.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"J Microsc","volume":"302","issue":"3","page":"370-381","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-15","doi":"10.1111\/jmi.70102","first_author":"Peychl, J.","corresponding_authors":"Munck, S."},{"pmid":"42069864","title":"Retrovirus insertions in host transcripts trigger de novo piRNA immunity.","abstract":"How host organisms adapt their defense systems to newly invading transposable elements remains poorly understood. Here, we show how Drosophila melanogaster acquired PIWI-interacting RNA (piRNA)-mediated immunity against the endogenous retrovirus Tirant. We uncover two distinct modes of de novo piRNA biogenesis by combining genetics, small RNA profiling, and population genomics. The primary route involves antisense insertions into the flamenco cluster, a master locus for transposon control. Unexpectedly, a second, equally potent mechanism arises from antisense Tirant insertions within host gene 3' UTRs. This process requires host gene transcription but is independent of host gene identity. Our findings challenge prevailing models that tie piRNA precursor specification to genomic origin or nuclear RNA processing context. Instead, they reveal a flexible mechanism that turns a critical vulnerability of transposons into an advantage for the host. When transposition occurs into host gene exons, chimeric antisense transcripts are exported to the cytoplasm, inadvertently initiating piRNA production and enabling rapid, adaptive genome defense against new invaders.","authors":"Rafanel, B., Protsenko, L., Handler, D., Brennecke, J., Senti, KA.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"EMBO J","volume":"45","issue":"11","page":"3833-3858","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-06-04","doi":"10.1038\/s44318-026-00777-1","first_author":"Rafanel, B.","corresponding_authors":"Senti, KA."},{"pmid":"42443208","title":"Structure of cytoplasmic RNA polymerase II.","abstract":"RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how this central multi-subunit enzyme is made and the role of dedicated assembly factors remains unclear. Here, we report the integrative structural analysis of a native human Pol II from the cytoplasm captured near the end of biogenesis. The complex contains Gdown1 and three biogenesis factors - RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the complex reveals how Gdown1 and RPAP2 associate with Pol II and prevent the premature association of transcription factors. Further biochemical and cryo-EM analysis reveals how RPAP2 tethers GPN1-GPN3 to the complex and how the assembly of the RPAP2-GPN1-GPN3 complex is controlled by GTP hydrolysis. The combined results uncover a network of interactions that chaperone cytoplasmic Pol II to prevent aberrant interactions, reveal a molecular switch regulating biogenesis factor association, and suggest a general mechanism for the action of GPN-loop GTPase family of enzymes.","authors":"Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., Bernecky, C.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Commun","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-13","doi":"10.1038\/s41467-026-75416-8","first_author":"Hlavata, A.","corresponding_authors":"Bernecky, C."},{"pmid":"42420286","title":"Molecular profiling of the single-cell proteome via gel electrophoresis and 3D single-molecule imaging.","abstract":"Recent advances in shotgun proteomics and immunoassays have yielded powerful single-cell proteomics technologies. However, current methods lack the sensitivity required to comprehensively quantify protein abundances in individual cells. Here, we present single-cell PAGE-PISA, an ultra-sensitive proteome profiling strategy that combines gel electrophoresis with 3D single-molecule fluorescence imaging. Our approach labels all proteins in single cells with fluorescent dyes, separates them by electrophoresis, and counts with single-molecule resolution. This technique quantified over 10<sup>7<\/sup> protein copies from a single mammalian cell with the sensitivity to detect low-abundance proteins down to 10<sup>5<\/sup> copies per species. Single-cell PAGE-PISA successfully classified cells into distinct cell types based on their proteomic profiles. Furthermore, our single-cell proteome data strongly correlated with predicted developmental states during cardiomyocyte differentiation, providing complementary information to single-cell transcriptome data. Together, single-cell PAGE-PISA enables highly sensitive and quantitative proteome profiling at the single-cell level, capturing subtle proteomic differences that distinguish diverse cellular states.","authors":"Kamarulzaman, L., Kim, S., Hidaka, T., Tsuchida, M., Taniguchi, Y.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-08","doi":"10.1038\/s41467-026-74840-0","first_author":"Kamarulzaman, L.","corresponding_authors":"Taniguchi, Y."},{"pmid":"42350674","title":"Cellular assembly and functional resilience of the mammalian RNA exosome.","abstract":"Most eukaryotic proteins assemble into multisubunit complexes that coordinate essential cellular functions, yet the principles governing their assembly and proteostatic control remain largely undefined. Here, we systematically dissect the cellular assembly and functional organization of the RNA exosome, an essential ribonucleolytic complex, using an inducible dual-guide CRISPR\/Cas9 system in mouse embryonic stem cells. We reveal a sequential assembly pathway where Exosc2, Exosc4, and Exosc7 initiate complex formation, facilitating the incorporation of barrel and cap subunits in a defined hierarchy. Unlike other structural subunits, the terminally incorporated cap subunit Exosc1 is dispensable for cell viability, revealing a modular, functionally resilient architecture. We demonstrate that orphan subunits are selectively degraded via the ubiquitin-proteasome system, enforcing stringent quality control over RNA exosome biogenesis. These findings define an assembly logic of of the mammalian exosome and uncover previously unrecognized plasticity in the composition and function of this essential ribonucleolytic complex.","authors":"Navalayeu, T., Beer, N., Bebjakov\u00e1, M., Kalis, RW., Hohmann, U., Stejskal, K., Kr\u0161\u0161\u00e1kov\u00e1, G., Fasching, N., Herzog, VA., Popitsch, N., Roitinger, E., Plaschka, C., Zuber, J., Ameres, SL.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"EMBO J","volume":"45","issue":"15","page":"5423-5456","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-08-04","doi":"10.1038\/s44318-026-00824-x","first_author":"Navalayeu, T.","corresponding_authors":"Ameres, SL."},{"pmid":"42321198","title":"Notch coordinates self-organization of germ layers and axial polarity in sea anemone gastruloids.","abstract":"Reaggregated early gastrula cells (\"gastruloids\") of the sea anemone Nematostella vectensis are able to regenerate into whole polyps within a few days. However, the cellular and molecular mechanisms underlying restoration of body axis and germ layers remains largely unknown. Here, we show that mesodermal cells sort to the periphery of the gastruloid, where they form cell clusters with hitchhiking endodermal cells. One of these clusters immigrates at one pole, forming the future pharynx and inner layer. This morphogenetic behavior that enables the symmetry break of the organizer tissue, requires a Wnt-Notch signaling feedback loop. This highlights a hitherto unknown role of Notch signaling in self-organizing gastruloids. Conservation of Notch-mediated boundary formation between germ layers mirrors similar mechanisms in bilaterians. This demonstrates how adoption of ancestral regulatory networks enables a morphospace converging to similar body plans, thus contributing to evolutionary robustness.","authors":"Narayanaswamy, S., Haas, F., Haillot, E., Cole, AG., Tanaka, EM., Technau, U.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-15","doi":"10.1038\/s41467-026-74441-x","first_author":"Narayanaswamy, S.","corresponding_authors":"Technau, U."},{"pmid":"42257675","title":"Mitochondria limit coenzyme Q export under cholesterol biosynthetic stress.","abstract":"Coenzyme Q (CoQ) is a hydrophobic lipid primarily synthesized in the mitochondria, though it is also present in non-mitochondrial membranes. However, the metabolic pathways that regulate intracellular CoQ distribution are unknown. This study identifies a key role for the mevalonate pathway in regulating CoQ distribution. The mevalonate pathway synthesizes isopentenyl pyrophosphate (IPP) as the precursor metabolite for both CoQ and cholesterol. We show that CoQ synthesis remains stable regardless of whether the mevalonate pathway is upregulated or downregulated. Upregulation of HMG-CoA reductase (HMGCR), indicative of increased mevalonate flux, enhances cholesterol ester synthesis without altering CoQ levels. When the pathway is downregulated, cholesterol synthesis declines, yet mitochondrial CoQ levels are preserved. Under these limiting conditions, mitochondria reduce CoQ export to maintain their internal CoQ pool. While this adaptation sustains mitochondrial respiration, it diminishes extramitochondrial CoQ availability and sensitizes cells to ferroptosis. These findings uncover a mitochondria-driven mechanism that preserves respiratory function by prioritizing CoQ retention during metabolic stress.","authors":"Ndoci, M., Bhattacharya, S., Agrawal, I., Hinze, Y., Lemke, K., Schumacher, AL., Uijttewaal, E., Elling, U., Lawo, S., Giavalisco, P., Langer, T., Deshwal, S.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"J Cell Biol","volume":"225","issue":"8","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-06-13","doi":"10.1083\/jcb.202507174","first_author":"Ndoci, M.","corresponding_authors":"Deshwal, S."},{"pmid":"42239165","title":"Hyaluronan Underlies the Emergence of Form, Fate, and Function in Human Cardioids.","abstract":"The extracellular matrix (ECM) is crucial for organ development and disease. Yet, the interplay among cells, function, and the ECM during human cardiogenesis remains obscure. Using human cardioids, we discovered that cardiac mesoderm-synthesized hyaluronan (HA) underlies early cardiac functional development. HA drives cardioid cavity formation through hydrogel swelling and bioscaffolding, critical functions of the cardiac jelly in the early vertebrate heart. During an early developmental window, HA is essential for establishing cardiac cell identity, while at later stages, HA-generated forces promote beating function through mechanosensitive channels. Chamber-specific differences in mechanical sensitivity ensure robust contractions in multi-chambered tissues. Our findings reveal how a single endogenous ECM component orchestrates the co-emergence of form, fate, and function during human organogenesis, opening new avenues for bioengineering physiologically relevant organ models.","authors":"Jahnel, SM., Dimitriadi, A., Kodnar, J., Gerakopoulos, V., Khurana, Y., Mayrhauser, M., Ilmer, T., Aguech, MA., Hall, AR., Ishihara, K., Mendjan, S.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-06-18","doi":"10.64898\/2026.01.26.700345","first_author":"Jahnel, SM.","corresponding_authors":"Mendjan, S."},{"pmid":"42225068","title":"Temporal control of sgRNA library activation unlocks large-scale in vivo CRISPR screens.","abstract":"CRISPR-StAR (stochastic activation by recombination) is an inducible pooled screening system that activates gene knockout after tumor engraftment and provides matched internal controls for guide-level normalization. In this study, we explore the scalability and reproducibility of this approach for in vivo cancer screens. Through barcode-embedded sequencing and the development of a Bayesian analysis pipeline, we screened a 30,000-sgRNA library in A549 xenografts, achieving reproducible dropout and enrichment phenotypes using just &#x223c;30 tumors. Across additional xenograft models, single tumors yielded reliable functional annotation for &#x223c;1,000 genes. Comparing in vivo and in vitro screens uncovered tumor suppressor effects detectable only in vivo; for example, KMT2C and KMT2D knockouts produced contrasting growth and transcriptional programs. Together with our R analysis package, we show that CRISPR-StAR enables scalable in vivo dependency mapping that complements in vitro resources and reduces animal use by up to 7-fold versus conventional dropout screens, improving methodological rigor at genome-scale clonal resolution.","authors":"Fenoglio, S., Yu, Y., Tepper, J., Grove, L., Bejnood, A., Meier, SR., Choi, AH., Wu, HJ., Devault, A., Liu, S., Shen, B., Khendu, T., Stowe, H., Uijttewaal, ECH., Zhang, M., Haines, BB., Wilker, E., Huang, A., Schramek, D., Elling, U., Pan, X., Andersen, JN., Teng, T.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Cell Rep Methods","volume":"6","issue":"7","page":"101470","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-20","doi":"10.1016\/j.crmeth.2026.101470","first_author":"Fenoglio, S.","corresponding_authors":"Teng, T."},{"pmid":"42182275","title":"Evolution of an Aurora Kinase A Inhibitor from an Essential tRNA Synthetase.","abstract":"Gene duplication is a major driver of evolution, yet how it generates fundamentally new molecular functions remains poorly understood. Here, we show how such novelty arose in KLMT-1, a selfish toxin that causes genetic incompatibilities in <i>Caenorhabditis tropicalis<\/i> . KLMT-1 evolved via duplication of an essential tRNA synthetase but, strikingly, lost its ancestral role in tRNA biology and translation. Instead, KLMT-1 localizes to centrosomes, where it targets Aurora kinase A (AIR-1). This innovation is mediated by a three-amino acid insertion that extends a &#x3b2;-hairpin loop, enabling electrostatic interaction with a regulatory interface on the kinase. Our results demonstrate how changes in selective pressure, combined with minimal modifications in neutrally evolving regions, allow duplicated proteins to access new functional space and evolve entirely new molecular activities.","authors":"Ross, JJ., Tikanova, P., Hagm\u00fcller, A., Krogull, D., Xiao, K., van Bavel, C., Balla, T., Liao, T., Echano, KA., Gokcezade, J., Duchek, P., Nedialkova, D., Jelier, R., Dong, G., Burga, A.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"bioRxiv","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-06-24","doi":"10.64898\/2026.05.15.725417","first_author":"Ross, JJ.","corresponding_authors":"Burga, A."},{"pmid":"42174701","title":"A reference genome for cultured Drosophila ovarian somatic cells enables studies of transposon and piRNA biology.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">42174701<\/PMID><DateCompleted><Year>2026<\/Year><Month>07<\/Month><Day>16<\/Day><\/DateCompleted><DateRevised><Year>2026<\/Year><Month>07<\/Month><Day>26<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>27<\/Volume><Issue>1<\/Issue><PubDate><Year>2026<\/Year><Month>May<\/Month><Day>22<\/Day><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>A reference genome for cultured Drosophila ovarian somatic cells enables studies of transposon and piRNA biology.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">227<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13059-026-04113-y<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Accurate reconstruction of repetitive genomic regions is essential to understand small RNA-mediated transposon silencing. In Drosophila ovarian somatic cells (OSCs), a primary model for nuclear PIWI-piRNA biology, reliance on the D. melanogaster reference (dm6) obscures cell-line-specific transposon insertions and the architecture of piRNA source loci.","authors":"Handler, D., Brennecke, J.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Genome Biol","volume":"27","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-16","doi":"10.1186\/s13059-026-04113-y","first_author":"Handler, D.","corresponding_authors":"Brennecke, J."},{"pmid":"42173905","title":"Tumor sialylation regulates G-CSF stability and promotes neutrophil-mediated immunosuppression in breast cancer.","abstract":"Breast cancer is the most prevalent cancer among women, yet immune checkpoint inhibitors remain largely ineffective in the majority of patients. Here we show that tumor sialylation is negatively associated with T cell infiltration across molecular breast cancer subtypes. In preclinical models, both genetic and pharmacologic inhibition of tumor cell sialylation reshape the tumor microenvironment by reducing immunosuppressive neutrophil infiltration, while CD8&#x207a; effector and Tcf7&#x207a; memory T cells are increased within the mammary tumors. Mechanistically, sialylation enhances the serum half-life of granulocyte colony-stimulating factor (G-CSF), a key driver of neutrophilic immunosuppression, and dampens tumor cell immunogenicity by limiting MHC-I surface expression. Disruption of sialylation sensitizes resistant mammary tumors to CD8&#x207a; T cell-mediated killing and anti-PD-1 therapy in multiple breast cancer models. These findings establish tumor sialylation as a key mechanism of immune evasion and a potential therapeutic target in breast cancer.","authors":"Mereiter, S., Jonsson, G., Oliveira, T., Garberis, IJ., Helm, J., Abeln, M., Jochum, AK., Jochum, W., Kellner, MJ., Feith, M., Tkalec, V., Wasilewska, K., Jiao, J., Hoffmann, D., Emsenhuber, L., Holstein, F., Obenauf, AC., Kroemer, G., Lacroix-Triki, M., Ali, OH., Flatz, L., Gerardy-Schahn, R., M\u00fcnster-K\u00fchnel, A., Stadlmann, J., Zitvogel, L., Penninger, JM.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-21","doi":"10.1038\/s41467-026-73401-9","first_author":"Mereiter, S.","corresponding_authors":"Penninger, JM."},{"pmid":"42127116","title":"PAM1 regulates meiosis by coupling RNA processing to the chromosome axis.","abstract":"Meiosis is a fundamental process responsible for sexual reproduction and generating genetic diversity in the progeny. Its successful completion requires fine-tuning of expression programs of many genes: promoting expression of genes involved in meiotic processes and suppressing genes whose expression may interfere with meiosis. Molecular mechanisms involved in meiotic transcriptome regulation and controlling meiosis progression vary between plants, animals, and fungi and remain elusive. We found that the <i>Plural abnormalities of meiosis1<\/i> (<i>Pam1<\/i>) gene in maize controls meiosis progression by tethering transcriptome processing to the meiosis-specific chromosome axis. <i>Pam1<\/i> encodes an RNA binding protein that becomes associated with chromosomes during early meiotic prophase I, binds transcripts of a large number of meiosis-related genes, and affects their splicing by interacting with the CCR4-NOT RNA processing protein complex. Disrupting <i>Pam1<\/i> function results in a wide array of severe meiosis defects affecting chromosome condensation and dynamics, nuclear envelope and cytoskeleton organization, as well as the overall meiosis progression. <i>Pam1<\/i> controls only a subset of meiotic genes and processes, indicating that several programs directing transcriptome architecture collectively regulate meiosis. RNA-binding proteins have been found to control meiosis progression in fungi and animals, and it is now shown to be also the case in plants. Interestingly, these proteins all exhibit distinct modes of action and evolutionary origins, presenting a remarkable case of convergent evolution. Uncovering mechanisms controlling meiosis progression should enable engineering meiosis to benefit crop improvement efforts.","authors":"Du, Q., Wang, M., Tiang, CL., Sheehan, MJ., Altendorf, P., Yu, JK., Hudecz, O., Roitinger, E., Wang, CR., Bukowski, R., Meeley, RB., Ko, C., Golubovskaya, IN., Pawlowski, WP.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Proc Natl Acad Sci U S A","volume":"123","issue":"20","page":"e2535316123","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-16","doi":"10.1073\/pnas.2535316123","first_author":"Du, Q.","corresponding_authors":"Pawlowski, WP."},{"pmid":"42556308","title":"A metabolic view of gastrulation: Coordinating signalling, epigenetics and morphogenesis.","abstract":"Gastrulation is the morphogenetic process by which the single-layered pluripotent epiblast is reorganised into the three germ layers and the basic body plan is established. While the metabolic state of pluripotent stem cells is well characterised, the metabolic remodelling that coincides with germ layer specification is less well understood. Emerging evidence suggests that metabolism functions as more than a passive housekeeping process and instead acts as a dynamic regulator of cell state during these developmental transitions. Here, we review recent work that implicates a role for metabolic pathways in regulating cell fate and morphogenesis during gastrulation. In particular, glucose metabolism appears to serve as a critical regulatory layer, modulating morphogen signalling to promote the emergence and function of mesodermal and endodermal populations. We also discuss the role of the tricarboxylic acid cycle and one-carbon metabolism in epigenetic remodelling and highlight the role of lipid metabolism in coupling the biophysical properties of membranes to cellular identity and morphogenetic movements. A current challenge is to distinguish in which situations metabolic shifts act as instructive drivers or permissive gatekeepers of development. Technological advances in spatial metabolomics, biosensors, and optogenetics are now facilitating the visualisation and manipulation of metabolic activity, paving the way for a mechanistic understanding of how metabolism shapes cell fate and behaviour during gastrulation.","authors":"Firfa, T., Civetta, T., Chan, EH., Stapornwongkul, KS.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Semin Cell Dev Biol","volume":"184","issue":null,"page":"103688","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-08-05","doi":"10.1016\/j.semcdb.2026.103688","first_author":"Firfa, T.","corresponding_authors":"Stapornwongkul, KS."},{"pmid":"42608481","title":"Nested TAD hierarchy defines cohesion zones on replicated chromosomes.","abstract":"During each cell cycle, cells must not only duplicate the DNA sequence but also preserve the three-dimensional genome architecture required for gene regulation and DNA repair. After replication, this requires coordination between cohesin-mediated loop extrusion and sister-chromatid cohesion for homology-directed DNA repair. Because extrusion promotes sister resolution whereas cohesion can impede extrusion, how both activities coexist on replicated chromosomes is unclear. Here we show that cohesin function is partitioned within the nested hierarchy of topologically associating domains (TADs): cohesive cohesin accumulates at high-level boundaries to form \"cohesion zones,\" while loop-extruding cohesin occupies boundaries across all hierarchical levels. Our data support a model in which this segregation emerges from dynamic interplay between cohesin pools and semi-permeable CTCF barriers, which act in cis and in trans to constrain sister-sister misalignment. Thus, a CTCF-defined boundary framework enables sister tethering while preserving dynamic loop folding, allowing replicated genomes to simultaneously support gene regulation and faithful DNA repair.","authors":"Takacs, Z., Mylarshchikov, D., Kolesnikova, S., Langer, CCH., Goloborodko, A., Gerlich, DW.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"EMBO J","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-08-18","doi":"10.1038\/s44318-026-00902-0","first_author":"Takacs, Z.","corresponding_authors":"Gerlich, DW."},{"pmid":"42599956","title":"A single-cell transcriptomic atlas reveals the emergence of medusa-specific cell states in the Aurelia coerulea scyphozoan.","abstract":"The life cycle of most medusozoan cnidarians is marked by the metagenesis from the asexually reproducing sessile polyp and the sexually reproducing motile medusa. At present, it is unknown to what extent this drastic morphological transformation is accompanied by molecular changes in the cell type composition. Here, we provide a single-cell transcriptome atlas of the cosmopolitan scyphozoan Aurelia coerulea focusing on changes in individual cell states during the transition from polyp to medusa. Notably, this transition is marked by an increase in cell type diversity, including an expansion of neural subtypes and the appearance of striated muscles. We find that two families of neuronal lineages are specified by homologous transcription factors in the sea anemone Nematostella vectensis and A. coerulea, suggesting an origin in the common ancestor of medusozoans and anthozoans about 500 Myr ago. Our analysis suggests that gene duplications might be drivers for the increase of cellular complexity during the evolution of cnidarian neuroglandular lineages and highlights the close relationship of neurons and muscles. One key medusozoan-specific cell type is the striated muscle in the subumbrella. Evaluating muscle types by fiber anatomy and gene expression validation of their individual molecular profiles made it possible for the first time to investigate transcriptome differences between smooth and striated muscles. Although smooth and striated muscles are phenotypically different, both have a similar regulation of the contractile complex, reminiscent to the regulation of smooth muscles in bilaterians. This contrasts with bilaterian striated muscles, where the regulation of muscle contraction involves Ca2+ binding troponins and their interaction with Tropomyosin. These data suggest that smooth muscle contraction regulation is ancestral and the use of troponins in striated muscles only evolved in bilaterians.","authors":"Link, O., Jahnel, SM., Janicek, K., Guerguerian, D., Kraus, J., Montenegro, JD., Zimmermann, B., Wick, B., Khalturin, K., Cole, AG., Technau, U.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"PLoS Biol","volume":"24","issue":"8","page":"e3003931","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-08-14","doi":"10.1371\/journal.pbio.3003931","first_author":"Link, O.","corresponding_authors":"Technau, U."},{"pmid":"42581140","title":"Urinary multi-omics reveal non-invasive diagnostic biomarkers in clear cell renal cell carcinoma.","abstract":"Clear cell renal cell carcinoma (ccRCC) is the most common kidney malignancy. Yet, no rapid, non-invasive biomarkers are available for diagnosis or screening. Urine represents an ideal analyte matrix due to its accessibility, low invasiveness, longitudinal sampling, and the kidney's central role in filtration. Here, we integrated proteomic, lipidomic, and metabolomic analyses of urine from ccRCC patients and controls to identify diagnostic biomarkers. Multi-omics profiling revealed urogenital metabolic dysregulation in ccRCC, including increased lipid metabolism, altered mitochondrial respiration signatures, and elevated urinary lipid content. We identified three urinary protein biomarkers: serum amyloid A1 (SAA1), haptoglobin (HP), and lipocalin 15 (LCN15). Using a parallel reaction monitoring mass spectrometry workflow, we developed a rapid and sensitive assay and combined these markers into a diagnostic UrineScore. The UrineScore achieved 0.96 in an area under the receiver operating characteristic curve analysis in the discovery cohort, and 0.95 in an independent validation cohort. Together, these results support the feasibility of multi-omics-guided urinary biomarker discovery and represent a step toward accessible diagnostic platforms for ccRCC.","authors":"Jonsson, G., Oliveira, T., Hofmann, M., Lemberger, U., Stejskal, K., Kr\u0161\u0161\u00e1kov\u00e1, G., Sakic, I., Novatchkova, M., Mereiter, S., Grabmann, G., K\u00f6cher, T., Koglgruber, R., Kikic, Z., Camano P\u00e1ez, S., Luna Sanchez, B., D\u00edez Nicol\u00e1s, V., Rechberger, GN., Z\u00fcllig, T., Hagelkruys, A., Englinger, B., Schmidinger, M., Penninger, JM.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"EMBO Mol Med","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-08-11","doi":"10.1038\/s44321-026-00498-2","first_author":"Jonsson, G.","corresponding_authors":"Penninger, JM."},{"pmid":"42507903","title":"BRIDGE: an interactive application for multi-omics data analysis, visualization and integration.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">42507903<\/PMID><DateCompleted><Year>2026<\/Year><Month>07<\/Month><Day>31<\/Day><\/DateCompleted><DateRevised><Year>2026<\/Year><Month>08<\/Month><Day>13<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1367-4811<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>42<\/Volume><Issue>7<\/Issue><PubDate><Year>2026<\/Year><Month>Jul<\/Month><Day>02<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>BRIDGE: an interactive application for multi-omics data analysis, visualization and integration.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">btag558<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/bioinformatics\/btag558<\/ELocationID><Abstract><AbstractText Label=\"SUMMARY\" NlmCategory=\"CONCLUSIONS\">BRIDGE is a Shiny-based application that provides an accessible, modular platform for individual and integrative multi-omics analysis. Using an independent SQLite database backend, it offers a local, private, and user-friendly environment that requires no prior computational expertise. The application supports proteomics, phospho-proteomics, and RNA-seq analyses through a comprehensive suite of visualization and analytical modules, together with an integrated multi-omics analysis pipeline. Built-in caching and asynchronous processing improve responsiveness, enabling efficient exploration, analysis, and visualization of multi-omics datasets on moderate hardware.","authors":"M\u00e1rquez-Oller, D., Pauli, A., Fallmann, J.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Bioinformatics","volume":"42","issue":"7","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-31","doi":"10.1093\/bioinformatics\/btag558","first_author":"M&#xe1;rquez-Oller, D.","corresponding_authors":"Fallmann, J."},{"pmid":"42430237","title":"ER-mitochondria contacts and mitochondrial fusion correlate with increased mitochondrial activity during vertebrate embryogenesis.","abstract":"Increased mitochondrial activity is essential for embryo development. Although conserved across organisms, the molecular basis of this increase is unknown, as detailed biochemical analysis in vertebrates is hampered by the limited availability of material. Using zebrafish as a model for vertebrate development, we comprehensively profile mitochondrial activity, morphology, metabolome, proteome, and phospho-proteome, as well as respiratory chain activity. Our data show that the mitochondrial proteome undergoes major changes during embryogenesis. While respiratory chain complex levels remain largely constant, we identify a marked increase in mitochondrial-ER association during early embryogenesis. Moreover, time-lapse imaging of mitochondrial dynamics reveals a transition from fragmented to elongated mitochondria starting during somitogenesis. Overall, our systematic profiling of the molecular and morphological changes of mitochondria during embryogenesis provides a valuable resource for further investigation of mitochondrial function. Our study reveals that increased mitochondrial-ER interaction and changes in mitochondrial morphology may contribute to its regulation during vertebrate development.","authors":"Chugunova, A., Sch\u00fctz, I., Keresztes, H., Kobylinska, R., Novatchkova, M., Lendl, T., Strobl, M., Fallmann, J., Oller, DM., Schutzbier, M., D\u00fcrnberger, G., Imre, R., Roitinger, E., Kidd, P., Pasierbek, P., Cencerrado, AM., Brandstetter, M., K\u00f6cher, T., Agerer, B., Genger, JW., Bergthaler, A., Pauli, A.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Cell Rep","volume":"45","issue":"7","page":"117615","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.06.11.598492v1","articledate":"2026-07-30","doi":"10.1016\/j.celrep.2026.117615","first_author":"Chugunova, A.","corresponding_authors":"Chugunova, A., Pauli, A."},{"pmid":"42629500","title":"Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data.","abstract":"Single-cell omics methods provide sparse, noisy measurements of high-dimensional cell states, whose underlying distributions remain poorly understood, raising an urgent need for exploratory analysis and visualization methods. However, current methods are ad hoc and uninterpretable, and they distort the structure in the data. We overcome these challenges by representing data on trees and present Bonsai, a method that reconstructs the most likely tree relating any set of high-dimensional objects with arbitrary heterogeneous measurement noise. Bonsai automatically regularizes noise, accurately recovers differentiation trajectories, preserves high-dimensional distances and improves nearest-neighbor identification. When applied to blood cell data, Bonsai not only accurately recovers known lineage relationships but also discovers a subtype of natural killer (NK) cells deriving from the myeloid lineage, pinpointing genes distinguishing myeloid NK from lymphoid NK cells. Bonsai has no tunable parameters, integrates downstream exploratory analyses methods with Bonsai-scout and scales to large datasets, making it applicable to visualizing the structure in any set of high-dimensional objects.","authors":"de Groot, DH., Morillo Leonardo, SX., Pachkov, M., van Nimwegen, E.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nat Biotechnol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-08-21","doi":"10.1038\/s41587-026-03220-2","first_author":"de Groot, DH.","corresponding_authors":"van Nimwegen, E."},{"pmid":"42236905","title":"Deletion of neurosecretory proteins GL and GM drives dual anti-obesity effects via appetite suppression and enhanced energy expenditure.","abstract":"Obesity results from an imbalance between energy intake and expenditure and is regulated by hypothalamic neuropeptide systems. The neurosecretory proteins GL (NPGL) and GM (NPGM) are expressed in the hypothalamus and promote feeding in gain-of-function studies; however, their endogenous physiological roles remain unclear. Here, we show that mice lacking both NPGL and NPGM display a lean phenotype driven by reduced food intake and increased energy expenditure. This anti-obesity phenotype is associated with increased expression of anorexigenic pro-opiomelanocortin in the hypothalamus and enhanced thermogenic activity in brown adipose tissue, marked by elevated uncoupling protein 1. Consistent with these findings, suppression of NPGL\/NPGM signaling reduces feeding and alters sympathetic nerve activity. In addition, genome-wide association analysis identifies an obesity-associated variant near the human NPGM locus, suggesting relevance to human energy balance. Together, these findings identify NPGL and NPGM as endogenous regulators of energy homeostasis with potential relevance to obesity.","authors":"Shikano, K., Yoshimura, M., Yahiro, T., Kurakazu, T., Saito, S., Teranishi, H., Higa, R., Umeda, R., Apolinario, MEC., Maruyama, T., Sasaki, AT., Hanada, T., Hikida, T., Ukena, K., Penninger, JM., Ueta, Y., Terao, C., Nakamura, K., Hanada, R.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Commun Biol","volume":"9","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-09-03","doi":"10.1038\/s42003-026-10405-7","first_author":"Shikano, K.","corresponding_authors":"Hanada, R."},{"pmid":"42704962","title":"Generation of high-quality reference control panels of human induced pluripotent stem cell clones from fibroblasts.","abstract":"Well-characterized iPSC reference panels are critical for developmental and disease-modeling research. We generated eleven iPSC clones from fibroblasts collected from four healthy, unrelated donors (two female, two male) using non-integrating Sendai virus reprogramming. Each clone was extensively validated according to current best practices, demonstrating genetic stability, high expression of markers for the undifferentiated state and robust trilineage differentiation potential. This collection is distinguished not only by the depth of characterization and standardized workflows, but also by the deliberate inclusion of multiple clones per donor to capture and control for clone&#x2011;to&#x2011;clone variability. All clones are available to academic and commercial researchers.","authors":"Mosca, E., Stein, E., John, J., Kinzer, M., Novatchkova, M., Scheuch, H., Agu, C., Stary, G., Penninger, JM., Meixner, A., Volz-Glaser, J.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Stem Cell Res","volume":"96","issue":null,"page":"104096","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-09-07","doi":"10.1016\/j.scr.2026.104096","first_author":"Mosca, E.","corresponding_authors":"Volz-Glaser, J."},{"pmid":"42642514","title":"Predictive design of tissue-specific mammalian enhancers that function in the mouse embryo.","abstract":"Enhancers control tissue-specific gene expression across animals<sup>1<\/sup>. Although deep learning<sup>2,3<\/sup> has enabled enhancer prediction and design in mammalian cell lines and non-mammalian model organisms<sup>4-10<\/sup> (reviewed in a previous publication<sup>11<\/sup>), it remains unclear whether such approaches can operate within the regulatory complexity of mammalian genomes and tissues in vivo. Here we present a general strategy for designing tissue-specific enhancers that function reliably in mice. We use deep learning to train compact convolutional neural networks on curated chromatin accessibility data and fine-tune them by transfer learning on validated human and mouse enhancers. Guided by these models, we design 15 synthetic enhancers for the heart, limb and central nervous system in mouse embryos, all of which are active in their intended target tissue. These results demonstrate that mammalian enhancer function can be reliably inferred from DNA sequence alone, enabling the predictive de novo design of tissue-specific synthetic enhancers from modest training sets. This work establishes a generalizable framework for programmable control of mammalian gene expression in vivo, opening new avenues in functional genomics, synthetic biology and gene therapy.","authors":"Chen, S., Loubiere, V., Hollingsworth, EW., Murakami, K., Mandlburger, N., Jacinto, SH., Dizehchi, A., Schreiber, J., Kvon, EZ., Stark, A.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Nat Genet","volume":"58","issue":"9","page":"2129-2133","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-09-09","doi":"10.1038\/s41588-026-02729-1","first_author":"Chen, S.","corresponding_authors":"Stark, A."},{"pmid":"41198879","title":"An ATP-gated molecular switch orchestrates human mRNA export.","abstract":"The nuclear export of mRNA is an important step in eukaryotic gene expression<sup>1<\/sup>. Despite recent molecular insights into how newly transcribed mRNAs are packaged into ribonucleoprotein complexes (mRNPs)<sup>2,3<\/sup>, the subsequent events that govern mRNA export are poorly understood. Here we uncover the molecular basis underlying key events of human mRNA export, including the remodelling of mRNP-bound transcription-export complexes (TREX), the formation of export-competent mRNPs, the docking of mRNPs at the nuclear pore complex (NPC), and the release of mRNPs at the NPC to initiate their export. Our biochemical and structural data show that the ATPase UAP56 (also known as DDX39) acts as a central molecular switch that directs nucleoplasmic mRNPs from TREX to NPC-anchored TREX-2 complexes through its ATP-gated mRNA-binding cycle. Collectively, these findings establish a mechanistic framework for a general and evolutionarily conserved mRNA&#xa0;export pathway.","authors":"Hohmann, U., Graf, M., Tiri\u00e1n, L., Pacheco-Fiallos, B., Schellhaas, U., Fin, L., Handler, D., Phillips, AW., Riabov-Bassat, D., Faraway, R., P\u00fchringer, T., Szalay, MF., Roitinger, E., Brennecke, J., Plaschka, C.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Nature","volume":"649","issue":"8098","page":"1042-1050","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-01-21","doi":"10.1038\/s41586-025-09832-z","first_author":"Hohmann, U.","corresponding_authors":"Plaschka, C."},{"pmid":"42691163","title":"Conformational asymmetry of replicated human chromosomes.","abstract":"DNA replication generates sister chromatids with identical sequence, yet its mechanism is fundamentally asymmetric: Chromatids inherit strands of opposite orientation, whereas forks synthesize new strands by distinct leading- and lagging-strand mechanisms. How this replication asymmetry affects chromosome organization is unknown. Using sister chromatid-sensitive conformation analysis, we found that human sister chromatids are consistently misaligned in the 5'&#x2192;3' direction of inherited DNA strands. This shift persisted without cohesin-mediated loop extrusion but was lost upon disruption of cohesion. Polymer modeling showed that modest directional misalignment of cohesive cohesins can explain the observed shift, and we propose two models for how such misalignment could originate from replication fork asymmetry. This register shift between sister chromatids has implications for homology search during DNA repair.","authors":"Corsi, F., Steinacker, TL., Kolesnikova, S., Tak\u00e1cs, Z., Batty, P., Mitter, M., Gerlich, DW., Goloborodko, A.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Science","volume":"393","issue":"6815","page":"eaea4611","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-09-03","doi":"10.1126\/science.aea4611","first_author":"Corsi, F.","corresponding_authors":"Goloborodko, A."},{"pmid":"42710430","title":"Generation of a human induced pluripotent stem cell panel from a family with a heterozygous RPS19 mutation including healthy wild-type, silent carrier and Diamond-Blackfan anemia individuals.","abstract":"Diamond-Blackfan anemia (DBA) is a rare inherited bone marrow failure syndrome characterized by defective erythropoiesis and increased risk of congenital malformations and cancer. Progress in understanding DBA pathophysiology has been hindered by the lack of physiologically relevant disease models, limited public funding, and low commercial interest. Here, we generated four induced pluripotent stem cell (iPSC) lines from peripheral blood mononuclear cells (PBMCs) obtained from members of a family carrying a heterozygous c.184C&#xa0;&gt;&#xa0;T RPS19 mutation (p.Arg62Trp) exhibiting variable clinical manifestations of DBA. This well-characterized iPSC resource facilitates disease modelling and therapeutic development and is available to both academic and commercial researchers.","authors":"Hagelkruys, A., Stein, E., Mosca, E., Leeb, N., Kinzer, M., Foong-Sobis, M., Gapp, BV., Tenorio, E., Aligianni, S., Meixner, A., Karger, L., Agu, C., Volz-Glaser, J., Penninger, JM.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Stem Cell Res","volume":"96","issue":null,"page":"104098","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-09-08","doi":"10.1016\/j.scr.2026.104098","first_author":"Hagelkruys, A.","corresponding_authors":"Volz-Glaser, J., Penninger, JM."},{"pmid":"42182320","title":"The SPARK complex forms the molecular basis of vertebrate fertilization.","abstract":"Fertilization requires gamete recognition and membrane fusion, yet the molecular basis of this process in vertebrates remains unknown. Here we identify SPARK (sperm protein assembly and receptor-binding key), a conserved multi-protein complex that integrates all known sperm fertilization factors, including TMEM81-IZUMO1-SPACA6 and DCST1\/2, together with two newly identified components, TMDD1 and FAM187A. SPARK subunits are mutually dependent for stability in mature sperm, and disruption of any single component causes male sterility in zebrafish and mice. Incubating zebrafish sperm with soluble egg receptor Bouncer partially rescues fertilization of Bouncer-deficient eggs in a SPARK-dependent manner, consistent with egg receptor binding priming the complex for fusion. Thus, we propose SPARK as a conserved molecular machine that couples gamete recognition to membrane fusion.","authors":"Deneke, VE., Suwita, JP., Wang, H., Tonai, S., Lu, Y., Panser, K., Schleiffer, A., Hollis, JA., Novatchkova, M., D\u00fcrnberger, G., Stejskal, K., Krssakova, G., Blaha, A., Andresan, AAR., Mirus, M., Marvanova, H., Chang, HY., Noda, T., Burga, A., Roitinger, E., Ikawa, M., Pauli, A.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"bioRxiv","volume":"","issue":"","page":"","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-06-08","doi":"10.64898\/2026.05.13.724128","first_author":"Deneke, VE.","corresponding_authors":"Pauli, A."},{"pmid":"41559218","title":"Impact and correction of segmentation errors in spatial transcriptomics.","abstract":"Spatial transcriptomics aims to elucidate how cells coordinate within tissues by connecting cellular states to their native microenvironments. Imaging-based assays are especially promising, capturing molecular and cellular features at subcellular resolution in three dimensions. Interpretation of such data, however, hinges on accurate cell segmentation. Assigning individual molecules to the correct cells remains challenging. Here we re-analyze data from multiple tissues and platforms to find that segmentation errors currently confound most downstream analysis of cellular state, including differential expression, neighbor influence and ligand-receptor interactions. The extent to which misassigned molecules impact the results can be striking, frequently dominating the results. Thus, we show that matrix factorization of local molecular neighborhoods can effectively identify and isolate such molecular admixtures, thereby reducing their impact on downstream analyses, in a manner analogous to doublet filtering in single-cell RNA sequencing. As the applications of spatial transcriptomics assays become more widespread, accounting for segmentation errors will be important for resolving molecular mechanisms of tissue biology.","authors":"Mitchel, J., Gao, T., Petukhov, V., Cole, E., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Nat Genet","volume":"58","issue":"2","page":"434-444","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-06-30","doi":"10.1038\/s41588-025-02497-4","first_author":"Mitchel, J.","corresponding_authors":"Kharchenko, PV."},{"pmid":"39313646","title":"Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition.","abstract":"Tissue-level and organism-level biological processes often involve the coordinated action of multiple distinct cell types. The recent application of single-cell assays to many individuals should enable the study of how donor-level variation in one cell type is linked to that in other cell types. Here we introduce a computational approach called single-cell interpretable tensor decomposition (scITD) to identify common axes of interindividual variation by considering joint expression variation across multiple cell types. scITD combines expression matrices from each cell type into a higher-order matrix and factorizes the result using the Tucker tensor decomposition. Applying scITD to single-cell RNA-sequencing data on 115 persons with lupus and 83 persons with coronavirus disease 2019, we identify patterns of coordinated cellular activity linked to disease severity and specific phenotypes, such as lupus nephritis. scITD results also implicate specific signaling pathways likely mediating coordination between cell types. Overall, scITD offers a tool for understanding the covariation of cell states across individuals, which can yield insights into the complex processes that define and stratify disease.","authors":"Mitchel, J., Gordon, MG., Perez, RK., Biederstedt, E., Bueno, R., Ye, CJ., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nat Biotechnol","volume":"43","issue":"7","page":"1192-1201","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-07-15","doi":"10.1038\/s41587-024-02411-z","first_author":"Mitchel, J.","corresponding_authors":"Kharchenko, PV."},{"pmid":"36163550","title":"Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes.","abstract":"Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. Single-cell RNA sequencing (scRNA-seq) has the potential to investigate both genetic and nongenetic sources of tumor heterogeneity in a single assay. Here we present a computational method, Numbat, that integrates haplotype information obtained from population-based phasing with allele and expression signals to enhance detection of copy number variations from scRNA-seq. Numbat exploits the evolutionary relationships between subclones to iteratively infer single-cell copy number profiles and tumor clonal phylogeny. Analysis of 22&#x2009;tumor samples, including multiple myeloma, gastric, breast and thyroid cancers, shows that Numbat can reconstruct the tumor copy number profile and precisely identify malignant cells in the tumor microenvironment. We identify genetic subpopulations with transcriptional signatures relevant to tumor progression and therapy resistance. Numbat requires neither sample-matched DNA data nor a priori genotyping, and is applicable to a wide range of experimental settings and cancer types.","authors":"Gao, T., Soldatov, R., Sarkar, H., Kurkiewicz, A., Biederstedt, E., Loh, PR., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Biotechnol","volume":"41","issue":"3","page":"417-426","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-20","doi":"10.1038\/s41587-022-01468-y","first_author":"Gao, T.","corresponding_authors":"Kharchenko, PV."},{"pmid":"34650268","title":"Cell segmentation in imaging-based spatial transcriptomics.","abstract":"Single-molecule spatial transcriptomics protocols based on in situ sequencing or multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However, distinguishing the boundaries of individual cells in such data is challenging and can hamper downstream analysis. Current methods generally approximate cells positions using nuclei stains. We describe a segmentation method, Baysor, that optimizes two-dimensional (2D) or three-dimensional (3D) cell boundaries considering joint likelihood of transcriptional composition and cell morphology. While Baysor can take into account segmentation based on co-stains, it can also perform segmentation based on the detected transcripts alone. To evaluate performance, we extend multiplexed error-robust fluorescence in situ hybridization (MERFISH) to incorporate immunostaining of cell boundaries. Using this and other benchmarks, we show that Baysor segmentation can, in some cases, nearly double the number of cells compared to existing tools while reducing segmentation artifacts. We demonstrate that Baysor performs well on data acquired using five different protocols, making it a useful general tool for analysis of imaging-based spatial transcriptomics.","authors":"Petukhov, V., Xu, RJ., Soldatov, RA., Cadinu, P., Khodosevich, K., Moffitt, JR., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Biotechnol","volume":"40","issue":"3","page":"345-354","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-21","doi":"10.1038\/s41587-021-01044-w","first_author":"Petukhov, V.","corresponding_authors":"Kharchenko, PV."},{"pmid":"30089906","title":"RNA velocity of single cells.","abstract":"RNA abundance is a powerful indicator of the state of individual cells. Single-cell RNA sequencing can reveal RNA abundance with high quantitative accuracy, sensitivity and throughput<sup>1<\/sup>. However, this approach captures only a static snapshot at a point in time, posing a challenge for the analysis of time-resolved phenomena such as embryogenesis or tissue regeneration. Here we show that RNA velocity-the time derivative of the gene expression state-can be directly estimated by distinguishing between unspliced and spliced mRNAs in common single-cell RNA sequencing protocols. RNA velocity is a high-dimensional vector that predicts the future state of individual cells on a timescale of hours. We validate its accuracy in the neural crest lineage, demonstrate its use on multiple published datasets and technical platforms, reveal the branching lineage tree of the developing mouse hippocampus, and examine the kinetics of transcription in human embryonic brain. We expect RNA velocity to greatly aid the analysis of developmental lineages and cellular dynamics, particularly in humans.","authors":"La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, ME., L\u00f6nnerberg, P., Furlan, A., Fan, J., Borm, LE., Liu, Z., van Bruggen, D., Guo, J., He, X., Barker, R., Sundstr\u00f6m, E., Castelo-Branco, G., Cramer, P., Adameyko, I., Linnarsson, S., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nature","volume":"560","issue":"7719","page":"494-498","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-02-20","doi":"10.1038\/s41586-018-0414-6","first_author":"La Manno, G.","corresponding_authors":"Kharchenko, PV."},{"pmid":"42711427","title":"Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover.","abstract":"The adult adrenal cortex undergoes constant renewal, yet underlying human-specific mechanisms remain poorly understood. Here we generated single-cell and spatial transcriptomic atlases of adult human and mouse adrenal glands, leveraging single-cell-resolution spatial data and a rare clonal mosaic case for lineage inference. In humans, we identified age-associated zona glomerulosa (ZG) cell states with direct cortisol synthesis capacity and sex-specific differences in inferred cholesterol balance. Cross-species comparison revealed conserved aldosterone-producing ZG but notable divergence in zona fasciculata markers, absence of zona reticularis homologs in mice and differential SHH-WNT4 signaling in proliferating cells. We uncovered human WT1<sup>-<\/sup> capsule-to-ZG transition and vascular smooth muscle cell-to-steroidogenic transitions supported by mosaic lineage evidence. We revealed dispersed proliferating cortical SF1<sup>+<\/sup>EZH2<sup>+<\/sup> cells throughout the human cortex in contrast with ZG restriction in mice. Taken together, our data expand the centripetal renewal model and establish a comparative framework for human adrenocortical biology.","authors":"Kastriti, ME., Maksimov, D., Krupinova, J., Utkina, M., Beltsevich, D., Roslyakova, A., Glazova, O., Kaziakhmedova, S., Ryabova, A., Kuznetsova, A., Shcherbakova, A., Bondarenko, E., Antysheva, Z., Albert, E., Urusova, L., Lapshina, A., Chevais, A., Avsievich, E., Trofimov, V., Melnichenko, G., Mokrysheva, N., Dedov, I., Englmaier, L., Petersen, J., Gusev, O., Heinzel, A., Oberbauer, R., Volchkov, P., Kharchenko, PV., Adameyko, I.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Nat Genet","volume":"58","issue":"9","page":"2270-2283","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-09-09","doi":"10.1038\/s41588-026-02737-1","first_author":"Kastriti, ME.","corresponding_authors":"Adameyko, I."},{"pmid":"42469240","title":"Embryonic and postnatal macrophages are necessary for proper tooth development and homeostasis.","abstract":"The role of macrophages in teeth, beyond their function in innate immunity, remains unexplored. This study demonstrates that macrophages populate dental tissues during early development and increase in number during pre-eruptive stages postnatally. In continuously growing teeth, they are associated with epithelial and mesenchymal stem cell niches throughout lifetime. To investigate their role in development, we genetically disrupt macrophage migration using neural-crest specific Wnt1<sup>Cre<\/sup>\/Csf1<sup>fl\/fl<\/sup> and general Csf1R knockout mouse models. This results in abnormal dentin and enamel deposition, eruption defects, early tooth mispatterning, and impaired osteogenesis. Notably, the phenotype is partially rescued via bone marrow transplantation. In addition, the short-term pharmacological depletion of macrophages in wildtype adult mice causes striking disintegration of both dentin and enamel in the apical part of continuously-growing teeth, which is restored after withdrawal of clodronate. Following treatment, macrophages rapidly repopulate dental tissue and the presence of M2 reparative state phenotype is observed by single-cell RNA-seq analysis. Overall, our findings reveal essential role of macrophages in the dental development and patterning of both mesenchymal and epithelial tooth compartments. This previously unrecognized role of macrophages in teeth is reminiscent of their function in complex tissue regeneration and requires future studies to dissect precise cellular and molecular mechanisms.","authors":"Gonzalez Lopez, M., Katsura, KA., Neves, VCM., Soldatov, R., Lavicky, J., Azam, M., Kavkova, M., Cigosova, K., Temsamrit, B., Bonnardel, J., Gong, H., Nemec, KM., Bennett, FC., Tuaima, H., Yianni, V., Sharpe, PT., Bajenoff, M., Kharchenko, P., Bennett, ML., Adameyko, I., Krivanek, J.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-17","doi":"10.1038\/s41467-026-75576-7","first_author":"Gonzalez Lopez, M.","corresponding_authors":"Krivanek, J."},{"pmid":"42310454","title":"Cortical development dynamics across autism spectrum disorder mouse models.","abstract":"Despite the functional diversity of over 100 causal genes<sup>1-3<\/sup>, phenotypic convergence across models may reveal common neurobiological processes in autism spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse models of ASD using single-nucleus multi-omic sequencing across three developmental stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. These alterations reflect a transient developmental delay rather than lasting lineage misspecification and resolve by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis showed molecular convergence across models within each developmental stage, suggesting that diverse mutations linked to ASD impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with female mice often displaying larger effect sizes than male mice. Together, our findings provide a comprehensive view of developmental cellular and molecular dynamics across models of ASD.","authors":"Schwarz, LA., Dotter, CP., Isaev, S., Lisi, M., Malzl, D., B\u00fcschl, C., Ladst\u00e4tter, S., Oliveira, B., Barel, M., Basilico, B., Chintaluri, C., Gorkiewicz, S., Goudarzi, M., Belinova, T., Reichl, S., Send\u017eikait\u0117, G., Jayaram, SA., Koppensteiner, P., Sommer, C., Vogels, TP., Menche, J., Adameyko, I., Kharchenko, PV., Bock, C., Novarino, G.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Nature","volume":"656","issue":"8126","page":"159-172","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-08-06","doi":"10.1038\/s41586-026-10679-1","first_author":"Schwarz, LA.","corresponding_authors":"Novarino, G."},{"pmid":"41986335","title":"Single-nucleus brain transcriptomics reveals microglia dysfunction in multiple system atrophy.","abstract":"Multiple system atrophy (MSA) is a rare, age-related neurodegenerative disease that shares clinical and pathological features with Parkinson's disease (PD) but presents a more devastating disease course. To elucidate the distinct cellular pathophysiology, we performed single-nucleus RNA sequencing on postmortem striatal brain tissue from 7 MSA and 12 PD patients, and 10 non-neurological cases. Here, we show significant compositional differences in astroglia and microglia subtypes, while oligodendroglia and neurons are comparable. PD brains show abundant microglia expressing MHC class II HLA haplotypes, indicative of a proinflammatory state, alongside more homeostatic astrocytes. In contrast, MSA lack activated microglia but has more reactive astrocytes compared to PD. Transcriptomic analysis suggests compromised oligodendrocyte signaling in MSA, with microglia being in a state of immune tolerance or exhaustion. Microglia derived from iPSC exposed to patient cerebrospinal fluid exhibit reduced phagocytic activity, especially in MSA. These findings underscore a dysfunctional immune response in MSA as a potential contributor to the more severe pathophysiology of MSA.","authors":"Rydbirk, R., S\u00f8rensen, FNF., Folke, J., Haukedal, H., Martinez, AA., Vargas, IL., McGarry, S., Hollmann, OC., Gherardelli, C., Sepulveda, S., Szafran, AT., Mancini, MA., Kaalund, SS., Brudek, T., Salvesen, L., Bech, S., Okarmus, J., Kharchenko, P., Meyer, M., Soto, C., Freude, K., Mukherjee, A., Aznar, S., Khodosevich, K.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-06-12","doi":"10.1038\/s41467-026-71525-6","first_author":"Rydbirk, R.","corresponding_authors":"Khodosevich, K."},{"pmid":"41803115","title":"Ribosomal modifications are associated with mesenchymal fate selection in the neural crest lineage.","abstract":"Neural crest cells contribute to craniofacial formation by differentiating into skeletogenic mesenchyme and neuro-glial lineages. Using Smart-seq2 single-cell transcriptomics, we show that mesenchymal fate commitment correlates specifically with the expression of rRNA-modifying and ribosome assembly factors, rather than structural ribosomal proteins. Notably, EMG1 and NHP2 introduce key post-transcriptional modifications into 18S rRNA, including m&#xb9;acp&#xb3;&#x3c8; at U1248, which requires TSR3 for final maturation. Disrupting NHP2 or TSR3 in vitro and in vivo perturbs cranial neural crest differentiation; post-migratory temporal knockout of Polr1a or Polr1c also causes craniofacial malformations. These findings align with cell type-specific m&#xb9;acp&#xb3;&#x3c8; levels during neural crest differentiation. Given the neural crest contribution to neuroblastoma, we analyze patient data to find that elevated ribosomal control and rRNA-modifying proteins predict poorer outcomes. Complementary experiments in neuroblastoma cell lines reveal functional roles for TSR3 and WDR74 in mesenchymal-like tumor states. Together, our results link rRNA modifications and ribosome assembly to fate decisions, suggesting ribosomal heterogeneity shapes both normal development and tumor progression.","authors":"Poverennaya, I., Murtazina, A., Li, L., Maili, L., Sourada, L., Montano-Gutierrez, LF., Galimullina, R., Steinschaden, T., Kaiser, M., Zikmund, T., Goralija, A., Gao, T., Attina, A., Clara, O., Bartenhagen, C., Erickson, AG., Gershtein, Y., Chen, S., Polaskova, K., Sterba, J., Semsch, B., Andersson, ER., Prakash, V., Vincent, T., Arceo, M., Kogner, P., Schlisio, S., Kharchenko, PV., David, A., Kaiser, J., Fischer, M., Skoda, J., Trainor, PA., Chagin, AS., Adameyko, I.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-10","doi":"10.1038\/s41467-026-70375-6","first_author":"Poverennaya, I.","corresponding_authors":"Adameyko, I."},{"pmid":"41723114","title":"Single-cell multiomic human brain atlas reveals regulatory drivers of cortical regionality.","abstract":"Distinct regional functionality of the human cortex is orchestrated by diverse cellular and molecular processes, yet the underlying regulatory mechanisms remain poorly understood. We performed multiomic single-cell and spatial characterization of nine regions of the human cortex to define the gene regulatory networks and transcription factors that govern cell-type and region specificity. With the combined data of over three million cells, two striking patterns of cortical neuron specialization were uncovered: a rostral-caudal spatial pattern of calcium regulatory machinery, and subunit switching of multiple signaling receptor families across the transmodal-sensory axis. Gene regulatory network analysis revealed putative transcriptional regulators of cortical neuron specialization with cell-type- and region-specific gene regulation patterns. While regionalization was observed in gene expression, chromatin accessibility, and spatial distributions, these modalities exhibited distinct cortical patterns. Our findings illuminate critical neuronal pathways that vary throughout the cortex and the gene regulatory networks that establish cortical regionalization in the human brain.","authors":"Palmer, CR., Song, J., Yang, B., Chen, CJ., Diep, D., Conklin, K., Plongthongkum, N., Indralingam, HS., Liu, CS., Kurtz, J., Hu, Q., Ransom, L., Shahnaee, A., Hiniker, A., Hodge, RD., Dirk Keene, C., Lein, E., Kharchenko, P., Zemke, NR., Chun, J., Ren, B., Zhang, K.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-07-08","doi":"10.1038\/s41467-026-69368-2","first_author":"Palmer, CR.","corresponding_authors":"Zhang, K."},{"pmid":"41168496","title":"Mesenchymal thymic niche cells enable regeneration of the adult thymus and T cell immunity.","abstract":"Thymic atrophy and the progressive immune decline that accompanies it is a major health problem, chronically with age and acutely with immune injury. No definitive solution is available. Here we demonstrate that one of the three mesenchymal cell subsets identified by single-cell analysis of human and mouse thymic stroma is a critical niche component for T lymphopoiesis. The Postn<sup>+<\/sup> subset is perivascular, and its depletion abrogates T cell progenitor recruitment, likely through production of the chemokine Ccl19. It markedly declines with age and in the acute setting of hematopoietic stem cell transplant conditioning. When isolated and adoptively transferred, Postn<sup>+<\/sup> cells durably engraft the atrophic thymus, recruit early T progenitors, increase T cell neogenesis and enhance T cell response to vaccination. More readily available mesenchymal populations expressing Ccl19 provide similar effects. These data define a thymus lymphopoietic niche cell type that may be manipulated therapeutically to regenerate T lymphopoiesis.","authors":"Gustafsson, K., Isaev, S., Mirsanaye, K., Hofmann, J., Kooshesh, KA., Baryawno, N., Kiem, A., Severe, N., Zhao, T., Scadden, EW., Spencer, JA., Burns, C., Akilan, K., Barkas, N., Gessessew, H., Kokkaliaris, KD., Lin, CP., Kharchenko, PV., Scadden, DT.","publication_status":"aheadofprint","journalpubyear":"2025","journaltitle":"Nat Biotechnol","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-08-13","doi":"10.1038\/s41587-025-02864-w","first_author":"Gustafsson, K.","corresponding_authors":"Scadden, DT."},{"pmid":"39808065","title":"Comparative Single-Cell Transcriptomics of Human Neuroblastoma and Preclinical Models Reveals Conservation of an Adrenergic Cell State.","abstract":"Transgenic mice and organoid models, such as three-dimensional tumoroid cultures, have emerged as powerful tools for investigating cancer development and targeted therapies. Yet, the extent to which these preclinical models recapitulate the cellular identity of heterogeneous malignancies, like neuroblastoma, remains to be validated. In this study, we characterized the transcriptional landscape of TH-MYCN tumors by single-cell RNA sequencing and developed ex vivo tumoroids. Integrated analysis with murine fetal adrenal samples confirmed that both TH-MYCN tumors and tumoroids closely mirror the cellular profiles of normal embryonic sympathoblasts and chromaffin cells. Comprehensive comparison between tumors from patients with neuroblastoma and TH-MYCN mice demonstrated similarities in adrenergic tumor cell composition. Ex vivo tumoroid cultures displayed histologic resemblance and shared transcriptional profiles with the originating TH-MYCN tumors and human neuroblastoma tumors. Importantly, subpopulations within tumoroids exhibited gene expression associated with poor survival of patients with neuroblastoma. Notably, recurrent observations of a low-proliferative chromaffin phenotype connected to the highly proliferative sympathetic phenotype suggested that pushing sympathoblasts into a chromaffin-like state may offer an interesting therapeutic strategy for neuroblastoma. Together, this study not only deepens our understanding of a widely used transgenic mouse neuroblastoma model but also introduces an ex vivo model that maintains critical adrenergic cell state identity, thereby enhancing its translational potential for neuroblastoma research. Significance: Transgenic mouse models and ex vivo tumoroids, characterized through single-cell RNA sequencing, faithfully recapitulate neuroblastoma cellular identity, offering a useful platform for investigating potential therapeutic strategies.","authors":"Embaie, BT., Sarkar, H., Alchahin, AM., Otte, J., Olsen, TK., T\u00fcmmler, C., Kameneva, P., Artemov, AV., Akkuratova, N., Adameyko, I., Stukenborg, JB., Wickstr\u00f6m, M., Kogner, P., Johnsen, JI., Mei, S., Kharchenko, PV., Baryawno, N.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Cancer Res","volume":"85","issue":"6","page":"1015-1034","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-03-14","doi":"10.1158\/0008-5472.CAN-24-1507","first_author":"Embaie, BT.","corresponding_authors":"Baryawno, N."},{"pmid":"39881190","title":"Niche-derived Semaphorin 4A safeguards functional identity of myeloid-biased hematopoietic stem cells.","abstract":"Somatic stem cell pools comprise diverse, highly specialized subsets whose individual contribution is critical for the overall regenerative function. In the bone marrow, myeloid-biased hematopoietic stem cells (myHSCs) are indispensable for replenishment of myeloid cells and platelets during inflammatory response but, at the same time, become irreversibly damaged during inflammation and aging. Here we identify an extrinsic factor, Semaphorin 4A (Sema4A), which non-cell-autonomously confers myHSC resilience to inflammatory stress. We show that, in the absence of Sema4A, myHSC inflammatory hyper-responsiveness in young mice drives excessive myHSC expansion, myeloid bias and profound loss of regenerative function with age. Mechanistically, Sema4A is mainly produced by neutrophils, signals via a cell surface receptor, Plexin D1, and safeguards the myHSC epigenetic state. Our study shows that, by selectively protecting a distinct stem cell subset, an extrinsic factor preserves functional diversity of somatic stem cell pool throughout organismal lifespan.","authors":"Toghani, D., Gupte, S., Zeng, S., Mahammadov, E., Crosse, EI., Seyedhassantehrani, N., Burns, C., Gravano, D., Radtke, S., Kiem, HP., Rodriguez, S., Carlesso, N., Pradeep, A., Georgiades, A., Lucas, F., Wilson, NK., Kinston, SJ., G\u00f6ttgens, B., Zong, L., Beerman, I., Park, B., Janssens, DH., Jones, D., Toghani, A., Nerlov, C., Pietras, EM., Mesnieres, M., Maes, C., Kumanogoh, A., Worzfeld, T., Cheong, JG., Josefowicz, SZ., Kharchenko, P., Scadden, DT., Scialdone, A., Spencer, JA., Silberstein, L.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nat Aging","volume":"5","issue":"4","page":"558-575","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-16","doi":"10.1038\/s43587-024-00798-7","first_author":"Toghani, D.","corresponding_authors":"Silberstein, L."},{"pmid":"39333268","title":"Vitessce: integrative visualization of multimodal and spatially resolved single-cell data.","abstract":"Multiomics technologies with single-cell and spatial resolution make it possible to measure thousands of features across millions of cells. However, visual analysis of high-dimensional transcriptomic, proteomic, genome-mapped and imaging data types simultaneously remains a challenge. Here we describe Vitessce, an interactive web-based visualization framework for exploration of multimodal and spatially resolved single-cell data. We demonstrate integrative visualization of millions of data points, including cell-type annotations, gene expression quantities, spatially resolved transcripts and cell segmentations, across multiple coordinated views. The open-source software is available at http:\/\/vitessce.io .","authors":"Keller, MS., Gold, I., McCallum, C., Manz, T., Kharchenko, PV., Gehlenborg, N.","publication_status":"ppublish","journalpubyear":"2025","journaltitle":"Nat Methods","volume":"22","issue":"1","page":"63-67","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2025-04-24","doi":"10.1038\/s41592-024-02436-x","first_author":"Keller, MS.","corresponding_authors":"Gehlenborg, N."},{"pmid":"38509069","title":"Mapping human tissues with highly multiplexed RNA in situ hybridization.","abstract":"In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in &lt;10&#x2009;h. We successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled &gt;20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.","authors":"Kalhor, K., Chen, CJ., Lee, HS., Cai, M., Nafisi, M., Que, R., Palmer, CR., Yuan, Y., Zhang, Y., Li, X., Song, J., Knoten, A., Lake, BB., Gaut, JP., Keene, CD., Lein, E., Kharchenko, PV., Chun, J., Jain, S., Fan, JB., Zhang, K.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Nat Commun","volume":"15","issue":"1","page":"2511","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-22","doi":"10.1038\/s41467-024-46437-y","first_author":"Kalhor, K.","corresponding_authors":"Zhang, K."},{"pmid":"38358826","title":"Single-cell analyses of metastatic bone marrow in human neuroblastoma reveals microenvironmental remodeling and metastatic signature.","abstract":"Neuroblastoma is an aggressive pediatric cancer with a high rate of metastasis to the BM. Despite intensive treatments including high-dose chemotherapy, the overall survival rate for children with metastatic neuroblastoma remains dismal. Understanding the cellular and molecular mechanisms of the metastatic tumor microenvironment is crucial for developing new therapies and improving clinical outcomes. Here, we used single-cell RNA-Seq to characterize immune and tumor cell alterations in neuroblastoma BM metastases by comparative analysis with patients without metastases. Our results reveal remodeling of the immune cell populations and reprogramming of gene expression profiles in the metastatic niche. In particular, within the BM metastatic niche, we observed the enrichment of immune cells, including tumor-associated neutrophils, macrophages, and exhausted T cells, as well as an increased number of Tregs and a decreased number of B cells. Furthermore, we highlighted cell communication between tumor cells and immune cell populations, and we identified prognostic markers in malignant cells that are associated with worse clinical outcomes in 3 independent neuroblastoma cohorts. Our results provide insight into the cellular, compositional, and transcriptional shifts underlying neuroblastoma BM metastases that contribute to the development of new therapeutic strategies.","authors":"Mei, S., Alchahin, AM., Embaie, BT., Gavriliuc, IM., Verhoeven, BM., Zhao, T., Li, X., Jeffries, NE., Pepich, A., Sarkar, H., Olsen, TK., Wickstr\u00f6m, M., Stenman, J., Reina-Bedoya, O., Kharchenko, PV., Saylor, PJ., Johnsen, JI., Sykes, DB., Kogner, P., Baryawno, N.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"JCI Insight","volume":"9","issue":"6","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-03-25","doi":"10.1172\/jci.insight.173337","first_author":"Mei, S.","corresponding_authors":"Baryawno, N."},{"pmid":"38273415","title":"Gene panel selection for targeted spatial transcriptomics.","abstract":"Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is their reliance on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method performing gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.","authors":"Zhang, Y., Petukhov, V., Biederstedt, E., Que, R., Zhang, K., Kharchenko, PV.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Genome Biol","volume":"25","issue":"1","page":"35","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-01-29","doi":"10.1186\/s13059-024-03174-1","first_author":"Zhang, Y.","corresponding_authors":"Kharchenko, PV."},{"pmid":"38281962","title":"Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">38281962<\/PMID><DateCompleted><Year>2024<\/Year><Month>01<\/Month><Day>30<\/Day><\/DateCompleted><DateRevised><Year>2024<\/Year><Month>10<\/Month><Day>23<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1756-994X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>16<\/Volume><Issue>1<\/Issue><PubDate><Year>2024<\/Year><Month>Jan<\/Month><Day>29<\/Day><\/PubDate><\/JournalIssue><Title>Genome medicine<\/Title><ISOAbbreviation>Genome Med<\/ISOAbbreviation><\/Journal><ArticleTitle>Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions.<\/ArticleTitle><Pagination><StartPage>1<\/StartPage><MedlinePgn>1<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">1<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13073-023-01272-6<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Despite therapeutic advances, once a cancer has metastasized to the bone, it represents a highly morbid and lethal disease. One third of patients with advanced clear cell renal cell carcinoma (ccRCC) present with bone metastasis at the time of diagnosis. However, the bone metastatic niche in humans, including the immune and stromal microenvironments, has not been well-defined, hindering progress towards identification of therapeutic targets.","authors":"Mei, S., Alchahin, AM., Tsea, I., Kfoury, Y., Hirz, T., Jeffries, NE., Zhao, T., Xu, Y., Zhang, H., Sarkar, H., Wu, S., Subtelny, AO., Johnsen, JI., Zhang, Y., Salari, K., Wu, CL., Randolph, MA., Scadden, DT., Dahl, DM., Shin, J., Kharchenko, PV., Saylor, PJ., Sykes, DB., Baryawno, N.","publication_status":"epublish","journalpubyear":"2024","journaltitle":"Genome Med","volume":"16","issue":"1","page":"1","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2024-01-30","doi":"10.1186\/s13073-023-01272-6","first_author":"Mei, S.","corresponding_authors":"Baryawno, N."},{"pmid":"37738974","title":"ZNF683 marks a CD8<sup>+<\/sup> T&#xa0;cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome.","abstract":"Unlike many other hematologic malignancies, Richter syndrome (RS), an aggressive B cell lymphoma originating from indolent chronic lymphocytic leukemia, is responsive to PD-1 blockade. To discover the determinants of response, we analyze single-cell transcriptome data generated from 17 bone marrow samples longitudinally collected from 6 patients with RS. Response is associated with intermediate exhausted CD8 effector\/effector memory T&#xa0;cells marked by high expression of the transcription factor ZNF683, determined to be evolving from stem-like memory cells and divergent from terminally exhausted cells. This signature overlaps with that of tumor-infiltrating populations from anti-PD-1 responsive solid tumors. ZNF683 is found to directly target key T&#xa0;cell genes (TCF7, LMO2, CD69) and impact pathways of T&#xa0;cell cytotoxicity and activation. Analysis of pre-treatment peripheral blood from 10 independent patients with RS treated with anti-PD-1, as well as patients with solid tumors treated with anti-PD-1, supports an association of ZNF683<sup>high<\/sup> T&#xa0;cells with response.","authors":"Parry, EM., Lemvigh, CK., Deng, S., Dangle, N., Ruthen, N., Knisbacher, BA., Bros\u00e9us, J., Hergalant, S., Gui\u00e8ze, R., Li, S., Zhang, W., Johnson, C., Long, JM., Yin, S., Werner, L., Anandappa, A., Purroy, N., Gohil, S., Oliveira, G., Bachireddy, P., Shukla, SA., Huang, T., Khoury, JD., Thakral, B., Dickinson, M., Tam, C., Livak, KJ., Getz, G., Neuberg, D., Feugier, P., Kharchenko, P., Wierda, W., Olsen, LR., Jain, N., Wu, CJ.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Cancer Cell","volume":"41","issue":"10","page":"1803-1816.e8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-03","doi":"10.1016\/j.ccell.2023.08.013","first_author":"Parry, EM.","corresponding_authors":"Wu, CJ."},{"pmid":"37904053","title":"A pan-tissue survey of mosaic chromosomal alterations in 948 individuals.","abstract":"Genetic mutations accumulate in an organism's body throughout its lifetime. While somatic single-nucleotide variants have been well characterized in the human body, the patterns and consequences of large chromosomal alterations in normal tissues remain largely unknown. Here, we present a pan-tissue survey of mosaic chromosomal alterations (mCAs) in 948 healthy individuals from the Genotype-Tissue Expression project, augmenting RNA-based allelic imbalance estimation with haplotype phasing. We found that approximately a quarter of the individuals carry a clonally-expanded mCA in at least one tissue, with incidence strongly correlated with age. The prevalence and genome-wide patterns of mCAs vary considerably across tissue types, suggesting tissue-specific mutagenic exposure and selection pressures. The mCA landscapes in normal adrenal and pituitary glands resemble those in tumors arising from these tissues, whereas the same is not true for the esophagus and skin. Together, our findings show a widespread age-dependent emergence of mCAs across normal human tissues with intricate connections to tumorigenesis.","authors":"Gao, T., Kastriti, ME., Ljungstr\u00f6m, V., Heinzel, A., Tischler, AS., Oberbauer, R., Loh, PR., Adameyko, I., Park, PJ., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Genet","volume":"55","issue":"11","page":"1901-1911","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-11-10","doi":"10.1038\/s41588-023-01537-1","first_author":"Gao, T.","corresponding_authors":"Kharchenko, PV."},{"pmid":"37468756","title":"Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP).","abstract":"The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale spatial atlas of the healthy human body at single-cell resolution by applying advanced technologies and disseminating resources to the community. As the HuBMAP moves past its first phase, creating ontologies, protocols and pipelines, this Perspective introduces the production phase: the generation of reference spatial maps of functional tissue units across many organs from diverse populations and the creation of mapping tools and infrastructure to advance biomedical research.","authors":"Jain, S., Pei, L., Spraggins, JM., Angelo, M., Carson, JP., Gehlenborg, N., Ginty, F., Gon\u00e7alves, JP., Hagood, JS., Hickey, JW., Kelleher, NL., Laurent, LC., Lin, S., Lin, Y., Liu, H., Naba, A., Nakayasu, ES., Qian, WJ., Radtke, A., Robson, P., Stockwell, BR., Van de Plas, R., Vlachos, IS., Zhou, M., B\u00f6rner, K., Snyder, MP.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Cell Biol","volume":"25","issue":"8","page":"1089-1100","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-08-14","doi":"10.1038\/s41556-023-01194-w","first_author":"Jain, S.","corresponding_authors":"Snyder, MP."},{"pmid":"36750562","title":"Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses.","abstract":"The treatment of low-risk primary prostate cancer entails active surveillance only, while high-risk disease requires multimodal treatment including surgery, radiation therapy, and hormonal therapy. Recurrence and development of metastatic disease remains a clinical problem, without a clear understanding of what drives immune escape and tumor progression. Here, we comprehensively describe the tumor microenvironment of localized prostate cancer in comparison with adjacent normal samples and healthy controls. Single-cell RNA sequencing and high-resolution spatial transcriptomic analyses reveal tumor context dependent changes in gene expression. Our data indicate that an immune suppressive tumor microenvironment associates with suppressive myeloid populations and exhausted T-cells, in addition to high stromal angiogenic activity. We infer cell-to-cell relationships from high throughput ligand-receptor interaction measurements within undissociated tissue sections. Our work thus provides a highly detailed and comprehensive resource of the prostate tumor microenvironment as well as tumor-stromal cell interactions.","authors":"Hirz, T., Mei, S., Sarkar, H., Kfoury, Y., Wu, S., Verhoeven, BM., Subtelny, AO., Zlatev, DV., Wszolek, MW., Salari, K., Murray, E., Chen, F., Macosko, EZ., Wu, CL., Scadden, DT., Dahl, DM., Baryawno, N., Saylor, PJ., Kharchenko, PV., Sykes, DB.","publication_status":"epublish","journalpubyear":"2023","journaltitle":"Nat Commun","volume":"14","issue":"1","page":"663","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-02-09","doi":"10.1038\/s41467-023-36325-2","first_author":"Hirz, T.","corresponding_authors":"Sykes, DB."},{"pmid":"36717627","title":"Dissection of gastric homeostasis in vivo facilitates permanent capture of isthmus-like stem cells in vitro.","abstract":"The glandular stomach is composed of two regenerative compartments termed corpus and antrum, and our understanding of the transcriptional networks that maintain these tissues is incomplete. Here we show that cell types with equivalent functional roles in the corpus and antrum share similar transcriptional states including the poorly characterized stem cells of the isthmus region. To further study the isthmus, we developed a monolayer two-dimensional (2D) culture system that is continually maintained by Wnt-responsive isthmus-like cells capable of differentiating into several gastric cell types. Importantly, 2D cultures can be converted into conventional three-dimensional organoids, modelling the plasticity of gastric epithelial cells in vivo. Finally, we utilized the 2D culture system to show that Sox2 is both necessary and sufficient to generate enterochromaffin cells. Together, our data provide important insights into gastric homeostasis, establish a tractable culture system to capture isthmus cells and uncover a role for Sox2 in enterochromaffin cells.","authors":"Huebner, AJ., Gorelov, RA., Deviatiiarov, R., Demharter, S., Kull, T., Walsh, RM., Taylor, MS., Steiger, S., Mullen, JT., Kharchenko, PV., Hochedlinger, K.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Nat Cell Biol","volume":"25","issue":"3","page":"390-403","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-03-16","doi":"10.1038\/s41556-022-01079-4","first_author":"Huebner, AJ.","corresponding_authors":"Hochedlinger, K."},{"pmid":"36394263","title":"scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Automated\"><PMID Version=\"1\">36394263<\/PMID><DateCompleted><Year>2023<\/Year><Month>01<\/Month><Day>03<\/Day><\/DateCompleted><DateRevised><Year>2025<\/Year><Month>05<\/Month><Day>30<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1367-4811<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>39<\/Volume><Issue>1<\/Issue><PubDate><Year>2023<\/Year><Month>Jan<\/Month><Day>01<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data.<\/ArticleTitle><ELocationID EIdType=\"pii\" ValidYN=\"Y\">btac746<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1093\/bioinformatics\/btac746<\/ELocationID><Abstract><AbstractText Label=\"SUMMARY\">scFates provides an extensive toolset for the analysis of dynamic trajectories comprising tree learning, feature association testing, branch differential expression and with a focus on cell biasing and fate splits at the level of bifurcations. It is meant to be fully integrated into the scanpy ecosystem for seamless analysis of trajectories from single-cell data of various modalities (e.g. RNA and ATAC).","authors":"Faure, L., Soldatov, R., Kharchenko, PV., Adameyko, I.","publication_status":"ppublish","journalpubyear":"2023","journaltitle":"Bioinformatics","volume":"39","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2023-01-03","doi":"10.1093\/bioinformatics\/btac746","first_author":"Faure, L.","corresponding_authors":"Adameyko, I."},{"pmid":"36424441","title":"Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.","abstract":"Tissue function depends on cellular organization. While the properties of individual cells are increasingly being deciphered using powerful single-cell sequencing technologies, understanding their spatial organization and temporal evolution remains a major challenge. Here, we present Image-seq, a technology that provides single-cell transcriptional data on cells that are isolated from specific spatial locations under image guidance, thus preserving the spatial information of the target cells. It is compatible with in situ and in vivo imaging and can document the temporal and dynamic history of the cells being analyzed. Cell samples are isolated from intact tissue and processed with state-of-the-art library preparation protocols. The technique therefore combines spatial information with highly sensitive RNA sequencing readouts from individual, intact cells. We have used both high-throughput, droplet-based sequencing as well as SMARTseq-v4 library preparation to demonstrate its application to bone marrow and leukemia biology. We discovered that DPP4 is a highly upregulated gene during early progression of acute myeloid leukemia and that it marks a more proliferative subpopulation that is confined to specific bone marrow microenvironments. Furthermore, the ability of Image-seq to isolate viable, intact cells should make it compatible with a range of downstream single-cell analysis tools including multi-omics protocols.","authors":"Haase, C., Gustafsson, K., Mei, S., Yeh, SC., Richter, D., Milosevic, J., Turcotte, R., Kharchenko, PV., Sykes, DB., Scadden, DT., Lin, CP.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Nat Methods","volume":"19","issue":"12","page":"1622-1633","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-12-06","doi":"10.1038\/s41592-022-01673-2","first_author":"Haase, C.","corresponding_authors":"Lin, CP."},{"pmid":"36223459","title":"Upper cortical layer-driven network impairment in schizophrenia.","abstract":"Schizophrenia is one of the most widespread and complex mental disorders. To characterize the impact of schizophrenia, we performed single-nucleus RNA sequencing (snRNA-seq) of &gt;220,000 neurons from the dorsolateral prefrontal cortex of patients with schizophrenia and matched controls. In addition, &gt;115,000 neurons were analyzed topographically by immunohistochemistry. Compositional analysis of snRNA-seq data revealed a reduction in abundance of GABAergic neurons and a concomitant increase in principal neurons, most pronounced for upper cortical layer subtypes, which was substantiated by histological analysis. Many neuronal subtypes showed extensive transcriptomic changes, the most marked in upper-layer GABAergic neurons, including down-regulation in energy metabolism and up-regulation in neurotransmission. Transcription factor network analysis demonstrated a developmental origin of transcriptomic changes. Last, Visium spatial transcriptomics further corroborated upper-layer neuron vulnerability in schizophrenia. Overall, our results point toward general network impairment within upper cortical layers as a core substrate associated with schizophrenia symptomatology.","authors":"Batiuk, MY., Tyler, T., Dragicevic, K., Mei, S., Rydbirk, R., Petukhov, V., Deviatiiarov, R., Sedmak, D., Frank, E., Feher, V., Habek, N., Hu, Q., Igolkina, A., Roszik, L., Pfisterer, U., Garcia-Gonzalez, D., Petanjek, Z., Adorjan, I., Kharchenko, PV., Khodosevich, K.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Sci Adv","volume":"8","issue":"41","page":"eabn8367","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-14","doi":"10.1126\/sciadv.abn8367","first_author":"Batiuk, MY.","corresponding_authors":"Khodosevich, K."},{"pmid":"36180422","title":"A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma.","abstract":"Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer in adults. When ccRCC is localized to the kidney, surgical resection or ablation of the tumor is often curative. However, in the metastatic setting, ccRCC remains a highly lethal disease. Here we use fresh patient samples that include treatment-naive primary tumor tissue, matched adjacent normal kidney tissue, as well as tumor samples collected from patients with bone metastases. Single-cell transcriptomic analysis of tumor cells from the primary tumors reveals a distinct transcriptional signature that is predictive of metastatic potential and patient survival. Analysis of supporting stromal cells within the tumor environment demonstrates vascular remodeling within the endothelial cells. An in silico cell-to-cell interaction analysis highlights the CXCL9\/CXCL10-CXCR3 axis and the CD70-CD27 axis as potential therapeutic targets. Our findings provide biological insights into the interplay between tumor cells and the ccRCC microenvironment.","authors":"Alchahin, AM., Mei, S., Tsea, I., Hirz, T., Kfoury, Y., Dahl, D., Wu, CL., Subtelny, AO., Wu, S., Scadden, DT., Shin, JH., Saylor, PJ., Sykes, DB., Kharchenko, PV., Baryawno, N.","publication_status":"epublish","journalpubyear":"2022","journaltitle":"Nat Commun","volume":"13","issue":"1","page":"5747","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-10-04","doi":"10.1038\/s41467-022-33375-w","first_author":"Alchahin, AM.","corresponding_authors":"Baryawno, N."},{"pmid":"35688160","title":"The immune cell atlas of human neuroblastoma.","abstract":"Understanding the complete immune cell composition of human neuroblastoma (NB) is crucial for the development of immunotherapeutics. Here, we perform single-cell RNA sequencing (scRNA-seq) on 19 human NB samples coupled with multiplex immunohistochemistry, survival analysis, and comparison with normal fetal adrenal gland data. We provide a comprehensive immune cell landscape and characterize cell-state changes from normal tissue to NB. Our analysis reveals 27 immune cell subtypes, including distinct subpopulations of myeloid, NK, B, and T&#xa0;cells. Several different cell types demonstrate a survival benefit. In contrast to adult cancers and previous NB studies, we show an increase in inflammatory monocyte cell state when contrasting normal and tumor tissue, while no differences in cytotoxicity and exhaustion score for T&#xa0;cells, nor in Treg activity, are observed. Our receptor-ligand interaction analysis reveals a highly complex interactive network of the NB microenvironment from which we highlight several interactions that we suggest for future therapeutic studies.","authors":"Verhoeven, BM., Mei, S., Olsen, TK., Gustafsson, K., Valind, A., Lindstr\u00f6m, A., Gisselsson, D., Fard, SS., Hagerling, C., Kharchenko, PV., Kogner, P., Johnsen, JI., Baryawno, N.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"Cell Rep Med","volume":"3","issue":"6","page":"100657","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-06-24","doi":"10.1016\/j.xcrm.2022.100657","first_author":"Verhoeven, BM.","corresponding_authors":"Baryawno, N."},{"pmid":"35074474","title":"Liver stromal cells restrict macrophage maturation and stromal IL-6 limits the differentiation of cirrhosis-linked macrophages.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Curated\"><PMID Version=\"1\">35074474<\/PMID><DateCompleted><Year>2022<\/Year><Month>04<\/Month><Day>20<\/Day><\/DateCompleted><DateRevised><Year>2022<\/Year><Month>06<\/Month><Day>08<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1600-0641<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>76<\/Volume><Issue>5<\/Issue><PubDate><Year>2022<\/Year><Month>May<\/Month><\/PubDate><\/JournalIssue><Title>Journal of hepatology<\/Title><ISOAbbreviation>J Hepatol<\/ISOAbbreviation><\/Journal><ArticleTitle>Liver stromal cells restrict macrophage maturation and stromal IL-6 limits the differentiation of cirrhosis-linked macrophages.<\/ArticleTitle><Pagination><StartPage>1127<\/StartPage><EndPage>1137<\/EndPage><MedlinePgn>1127-1137<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1016\/j.jhep.2021.12.036<\/ELocationID><ELocationID EIdType=\"pii\" ValidYN=\"Y\">S0168-8278(22)00007-1<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND &amp; AIMS\">Myeloid cells are key regulators of cirrhosis, a major cause of mortality worldwide. Because stromal cells can modulate the functionality of myeloid cells in&#xa0;vitro, targeting stromal-myeloid interactions has become an attractive potential therapeutic strategy. We aimed to investigate how human liver stromal cells impact myeloid cell properties and to understand the utility of a stromal-myeloid coculture system to study these interactions in the context of cirrhosis.","authors":"Buonomo, EL., Mei, S., Guinn, SR., Leo, IR., Peluso, MJ., Nolan, MA., Schildberg, FA., Zhao, L., Lian, C., Xu, S., Misdraji, J., Kharchenko, PV., Sharpe, AH.","publication_status":"ppublish","journalpubyear":"2022","journaltitle":"J Hepatol","volume":"76","issue":"5","page":"1127-1137","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-04-20","doi":"10.1016\/j.jhep.2021.12.036","first_author":"Buonomo, EL.","corresponding_authors":"Sharpe, AH."},{"pmid":"34719426","title":"Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment.","abstract":"Bone metastases are devastating complications of cancer. They are particularly common in prostate cancer (PCa), represent incurable disease, and are refractory to immunotherapy. We seek to define distinct features of the bone marrow (BM) microenvironment by analyzing single cells from bone metastatic prostate tumors, involved BM, uninvolved BM, and BM from cancer-free, orthopedic patients, and healthy individuals. Metastatic PCa is associated with multifaceted immune distortion, specifically exhaustion of distinct T&#xa0;cell subsets, appearance of macrophages with states specific to PCa bone metastases. The chemokine CCL20 is notably overexpressed by myeloid cells, as is its cognate CCR6 receptor on T&#xa0;cells. Disruption of the CCL20-CCR6 axis in mice with syngeneic PCa bone metastases restores T&#xa0;cell reactivity and significantly prolongs animal survival. Comparative high-resolution analysis of PCa bone metastases shows a targeted approach for relieving local immunosuppression for therapeutic effect.","authors":"Kfoury, Y., Baryawno, N., Severe, N., Mei, S., Gustafsson, K., Hirz, T., Brouse, T., Scadden, EW., Igolkina, AA., Kokkaliaris, K., Choi, BD., Barkas, N., Randolph, MA., Shin, JH., Saylor, PJ., Scadden, DT., Sykes, DB., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Cancer Cell","volume":"39","issue":"11","page":"1464-1478.e8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2022-01-05","doi":"10.1016\/j.ccell.2021.09.005","first_author":"Kfoury, Y.","corresponding_authors":"Baryawno, N., Kharchenko, PV."},{"pmid":"34616075","title":"A multimodal cell census and atlas of the mammalian primary motor cortex.","abstract":"Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization<sup>1-5<\/sup>. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.","authors":"","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature","volume":"598","issue":"7879","page":"86-102","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-01","doi":"10.1038\/s41586-021-03950-0","first_author":null,"corresponding_authors":null},{"pmid":"34616066","title":"A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.","abstract":"Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain<sup>1-3<\/sup>. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions<sup>4<\/sup>. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.","authors":"Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, RS., Aldridge, AI., Ament, SA., Bartlett, A., Behrens, MM., Van den Berge, K., Bertagnolli, D., de B\u00e9zieux, HR., Biancalani, T., Booeshaghi, AS., Bravo, HC., Casper, T., Colantuoni, C., Crabtree, J., Creasy, H., Crichton, K., Crow, M., Dee, N., Dougherty, EL., Doyle, WI., Dudoit, S., Fang, R., Felix, V., Fong, O., Giglio, M., Goldy, J., Hawrylycz, M., Herb, BR., Hertzano, R., Hou, X., Hu, Q., Kancherla, J., Kroll, M., Lathia, K., Li, YE., Lucero, JD., Luo, C., Mahurkar, A., McMillen, D., Nadaf, NM., Nery, JR., Nguyen, TN., Niu, SY., Ntranos, V., Orvis, J., Osteen, JK., Pham, T., Pinto-Duarte, A., Poirion, O., Preissl, S., Purdom, E., Rimorin, C., Risso, D., Rivkin, AC., Smith, K., Street, K., Sulc, J., Svensson, V., Tieu, M., Torkelson, A., Tung, H., Vaishnav, ED., Vanderburg, CR., van Velthoven, C., Wang, X., White, OR., Huang, ZJ., Kharchenko, PV., Pachter, L., Ngai, J., Regev, A., Tasic, B., Welch, JD., Gillis, J., Macosko, EZ., Ren, B., Ecker, JR., Zeng, H., Mukamel, EA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature","volume":"598","issue":"7879","page":"103-110","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-01","doi":"10.1038\/s41586-021-03500-8","first_author":"Yao, Z.","corresponding_authors":"Mukamel, EA."},{"pmid":"34616062","title":"Comparative cellular analysis of motor cortex in human, marmoset and mouse.","abstract":"The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals<sup>1<\/sup>. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.","authors":"Bakken, TE., Jorstad, NL., Hu, Q., Lake, BB., Tian, W., Kalmbach, BE., Crow, M., Hodge, RD., Krienen, FM., Sorensen, SA., Eggermont, J., Yao, Z., Aevermann, BD., Aldridge, AI., Bartlett, A., Bertagnolli, D., Casper, T., Castanon, RG., Crichton, K., Daigle, TL., Dalley, R., Dee, N., Dembrow, N., Diep, D., Ding, SL., Dong, W., Fang, R., Fischer, S., Goldman, M., Goldy, J., Graybuck, LT., Herb, BR., Hou, X., Kancherla, J., Kroll, M., Lathia, K., van Lew, B., Li, YE., Liu, CS., Liu, H., Lucero, JD., Mahurkar, A., McMillen, D., Miller, JA., Moussa, M., Nery, JR., Nicovich, PR., Niu, SY., Orvis, J., Osteen, JK., Owen, S., Palmer, CR., Pham, T., Plongthongkum, N., Poirion, O., Reed, NM., Rimorin, C., Rivkin, A., Romanow, WJ., Sede\u00f1o-Cort\u00e9s, AE., Siletti, K., Somasundaram, S., Sulc, J., Tieu, M., Torkelson, A., Tung, H., Wang, X., Xie, F., Yanny, AM., Zhang, R., Ament, SA., Behrens, MM., Bravo, HC., Chun, J., Dobin, A., Gillis, J., Hertzano, R., Hof, PR., H\u00f6llt, T., Horwitz, GD., Keene, CD., Kharchenko, PV., Ko, AL., Lelieveldt, BP., Luo, C., Mukamel, EA., Pinto-Duarte, A., Preissl, S., Regev, A., Ren, B., Scheuermann, RH., Smith, K., Spain, WJ., White, OR., Koch, C., Hawrylycz, M., Tasic, B., Macosko, EZ., McCarroll, SA., Ting, JT., Zeng, H., Zhang, K., Feng, G., Ecker, JR., Linnarsson, S., Lein, ES.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nature","volume":"598","issue":"7879","page":"111-119","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-01","doi":"10.1038\/s41586-021-03465-8","first_author":"Bakken, TE.","corresponding_authors":"Lein, ES."},{"pmid":"34493726","title":"Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors.","abstract":"Childhood neuroblastoma has a remarkable variability in outcome. Age at diagnosis is one of the most important prognostic factors, with children less than 1 year old having favorable outcomes. Here we study single-cell and single-nuclei transcriptomes of neuroblastoma with different clinical risk groups and stages, including healthy adrenal gland. We compare tumor cell populations with embryonic mouse sympatho-adrenal derivatives, and post-natal human adrenal gland. We provide evidence that low and high-risk neuroblastoma have different cell identities, representing two disease entities. Low-risk neuroblastoma presents a transcriptome that resembles sympatho- and chromaffin cells, whereas malignant cells enriched in high-risk neuroblastoma resembles a subtype of TRKB+ cholinergic progenitor population identified in human post-natal gland. Analyses of these populations reveal different gene expression programs for worst and better survival in correlation with age at diagnosis. Our findings reveal two cellular identities and a composition of human neuroblastoma tumors reflecting clinical heterogeneity and outcome.","authors":"Bedoya-Reina, OC., Li, W., Arceo, M., Plescher, M., Bullova, P., Pui, H., Kaucka, M., Kharchenko, P., Martinsson, T., Holmberg, J., Adameyko, I., Deng, Q., Larsson, C., Juhlin, CC., Kogner, P., Schlisio, S.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"5309","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-10-06","doi":"10.1038\/s41467-021-24870-7","first_author":"Bedoya-Reina, OC.","corresponding_authors":"Schlisio, S."},{"pmid":"34478631","title":"Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions.","abstract":"Human accelerated regions (HARs) are the fastest-evolving regions of the human genome, and many are hypothesized to function as regulatory elements that drive human-specific gene regulatory programs. We interrogate the in&#xa0;vitro enhancer activity and in&#xa0;vivo epigenetic landscape of more than 3,100 HARs during human neurodevelopment, demonstrating that many HARs appear to act as neurodevelopmental enhancers and that sequence divergence at HARs has largely augmented their neuronal enhancer activity. Furthermore, we demonstrate PPP1R17 to be a putative HAR-regulated gene that has undergone remarkable rewiring of its cell type and developmental expression patterns between non-primates and primates and between non-human primates and humans. Finally, we show that PPP1R17 slows neural progenitor cell cycle progression, paralleling the cell cycle length increase seen predominantly in primate and especially human neurodevelopment. Our findings establish HARs as key components in rewiring human-specific neurodevelopmental gene regulatory programs and provide an integrated resource to study enhancer activity of specific HARs.","authors":"Girskis, KM., Stergachis, AB., DeGennaro, EM., Doan, RN., Qian, X., Johnson, MB., Wang, PP., Sejourne, GM., Nagy, MA., Pollina, EA., Sousa, AMM., Shin, T., Kenny, CJ., Scotellaro, JL., Debo, BM., Gonzalez, DM., Rento, LM., Yeh, RC., Song, JHT., Beaudin, M., Fan, J., Kharchenko, PV., Sestan, N., Greenberg, ME., Walsh, CA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Neuron","volume":"109","issue":"20","page":"3239-3251.e7","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-08","doi":"10.1016\/j.neuron.2021.08.005","first_author":"Girskis, KM.","corresponding_authors":"Walsh, CA."},{"pmid":"34469751","title":"Diversity of developing peripheral glia revealed by single-cell RNA sequencing.","abstract":"The peripheral nervous system responds to a wide variety of sensory stimuli, a process that requires great neuronal diversity. These diverse neurons are closely associated with glial cells originating from the neural crest. However, the molecular nature and diversity among peripheral glia are not understood. Here, we used single-cell RNA sequencing to profile developing and mature glia from somatosensory dorsal root ganglia and auditory spiral ganglia. We found that glial precursors (GPs) in these two systems differ in their transcriptional profiles. Despite their unique features, somatosensory and auditory GPs undergo convergent differentiation to generate molecularly uniform myelinating and non-myelinating Schwann cells. By contrast, somatosensory and auditory satellite glial cells retain system-specific features. Lastly, we identified a glial signature gene set, providing new insights into commonalities among glia across the nervous system. This survey of gene expression in peripheral glia constitutes a resource for understanding functions of glia across different sensory modalities.","authors":"Tasdemir-Yilmaz, OE., Druckenbrod, NR., Olukoya, OO., Dong, W., Yung, AR., Bastille, I., Pazyra-Murphy, MF., Sitko, AA., Hale, EB., Vigneau, S., Gimelbrant, AA., Kharchenko, PV., Goodrich, LV., Segal, RA.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Dev Cell","volume":"56","issue":"17","page":"2516-2535.e8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-11-26","doi":"10.1016\/j.devcel.2021.08.005","first_author":"Tasdemir-Yilmaz, OE.","corresponding_authors":"Goodrich, LV., Segal, RA."},{"pmid":"34385354","title":"Population sequencing data reveal a compendium of mutational processes in the human germ line.","abstract":"Biological mechanisms underlying human germline mutations remain largely unknown. We statistically decompose variation in the rate and spectra of mutations along the genome using volume-regularized nonnegative matrix factorization. The analysis of a sequencing dataset (TOPMed) reveals nine processes that explain the variation in mutation properties between loci. We provide a biological interpretation for seven of these processes. We associate one process with bulky DNA lesions that are resolved asymmetrically with respect to transcription and replication. Two processes track direction of replication fork and replication timing, respectively. We identify a mutagenic effect of active demethylation primarily acting in regulatory regions and a mutagenic effect of long interspersed nuclear elements. We localize a mutagenic process specific to oocytes from population sequencing data. This process appears transcriptionally asymmetric.","authors":"Seplyarskiy, VB., Soldatov, RA., Koch, E., McGinty, RJ., Goldmann, JM., Hernandez, RD., Barnes, K., Correa, A., Burchard, EG., Ellinor, PT., McGarvey, ST., Mitchell, BD., Vasan, RS., Redline, S., Silverman, E., Weiss, ST., Arnett, DK., Blangero, J., Boerwinkle, E., He, J., Montgomery, C., Rao, DC., Rotter, JI., Taylor, KD., Brody, JA., Chen, YI., de las Fuentes, L., Hwu, CM., Rich, SS., Manichaikul, AW., Mychaleckyj, JC., Palmer, ND., Smith, JA., Kardia, SLR., Peyser, PA., Bielak, LF., O'Connor, TD., Emery, LS., Gilissen, C., Wong, WSW., Kharchenko, PV., Sunyaev, S.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Science","volume":"373","issue":"6558","page":"1030-1035","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-17","doi":"10.1126\/science.aba7408","first_author":"Seplyarskiy, VB.","corresponding_authors":"Sunyaev, S."},{"pmid":"34155396","title":"The triumphs and limitations of computational methods for scRNA-seq.","abstract":"The rapid progress of protocols for sequencing single-cell transcriptomes over the past decade has been accompanied by equally impressive advances in the computational methods for analysis of such data. As capacity and accuracy of the experimental techniques grew, the emerging algorithm developments revealed increasingly complex facets of the underlying biology, from cell type composition to gene regulation to developmental dynamics. At the same time, rapid growth has forced continuous reevaluation of the underlying statistical models, experimental aims, and sheer volumes of data processing that are handled by these computational tools. Here, I review key computational steps of single-cell RNA sequencing (scRNA-seq) analysis, examine assumptions made by different approaches, and highlight successes, remaining ambiguities, and limitations that are important to keep in mind as scRNA-seq becomes a mainstream technique for studying biology.","authors":"Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Methods","volume":"18","issue":"7","page":"723-732","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-09-20","doi":"10.1038\/s41592-021-01171-x","first_author":"Kharchenko, PV.","corresponding_authors":"Kharchenko, PV."},{"pmid":"33833454","title":"Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin.","abstract":"Characterization of the progression of cellular states during human embryogenesis can provide insights into the origin of pediatric diseases. We examined the transcriptional states of neural crest- and mesoderm-derived lineages differentiating into adrenal glands, kidneys, endothelium and hematopoietic tissue between post-conception weeks 6 and 14 of human development. Our results reveal transitions connecting the intermediate mesoderm and progenitors of organ primordia, the hematopoietic system and endothelial subtypes. Unexpectedly, by using a combination of single-cell transcriptomics and lineage tracing, we found that intra-adrenal sympathoblasts at that stage are directly derived from nerve-associated Schwann cell precursors, similarly to local chromaffin cells, whereas the majority of extra-adrenal sympathoblasts arise from the migratory neural crest. In humans, this process persists during several weeks of development within the large intra-adrenal ganglia-like structures, which may also serve as reservoirs of originating cells in neuroblastoma.","authors":"Kameneva, P., Artemov, AV., Kastriti, ME., Faure, L., Olsen, TK., Otte, J., Erickson, A., Semsch, B., Andersson, ER., Ratz, M., Fris\u00e9n, J., Tischler, AS., de Krijger, RR., Bouderlique, T., Akkuratova, N., Vorontsova, M., Gusev, O., Fried, K., Sundstr\u00f6m, E., Mei, S., Kogner, P., Baryawno, N., Kharchenko, PV., Adameyko, I.","publication_status":"ppublish","journalpubyear":"2021","journaltitle":"Nat Genet","volume":"53","issue":"5","page":"694-706","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-15","doi":"10.1038\/s41588-021-00818-x","first_author":"Kameneva, P.","corresponding_authors":"Adameyko, I."},{"pmid":"33686078","title":"Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.","abstract":"Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.","authors":"Kupari, J., Usoskin, D., Parisien, M., Lou, D., Hu, Y., Fatt, M., L\u00f6nnerberg, P., Sp\u00e5ngberg, M., Eriksson, B., Barkas, N., Kharchenko, PV., Lor\u00e9, K., Khoury, S., Diatchenko, L., Ernfors, P.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Nat Commun","volume":"12","issue":"1","page":"1510","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-03-22","doi":"10.1038\/s41467-021-21725-z","first_author":"Kupari, J.","corresponding_authors":"Ernfors, P."},{"pmid":"33504367","title":"Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Manual\"><PMID Version=\"1\">33504367<\/PMID><DateCompleted><Year>2021<\/Year><Month>12<\/Month><Day>14<\/Day><\/DateCompleted><DateRevised><Year>2024<\/Year><Month>03<\/Month><Day>30<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>22<\/Volume><Issue>1<\/Issue><PubDate><Year>2021<\/Year><Month>Jan<\/Month><Day>27<\/Day><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2.<\/ArticleTitle><Pagination><StartPage>50<\/StartPage><MedlinePgn>50<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"pii\" ValidYN=\"Y\">50<\/ELocationID><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/s13059-021-02267-5<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\">Macrophages are innate immune cells with diverse functional and molecular phenotypes. This diversity is largely unexplored at the level of single-cell proteomes because of the limitations of quantitative single-cell protein analysis.","authors":"Specht, H., Emmott, E., Petelski, AA., Huffman, RG., Perlman, DH., Serra, M., Kharchenko, P., Koller, A., Slavov, N.","publication_status":"epublish","journalpubyear":"2021","journaltitle":"Genome Biol","volume":"22","issue":"1","page":"50","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-12-14","doi":"10.1186\/s13059-021-02267-5","first_author":"Specht, H.","corresponding_authors":"Slavov, N."},{"pmid":"33028830","title":"Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis.","abstract":"Epilepsy is one of the most common neurological disorders, yet its pathophysiology&#xa0;is poorly understood due to the high complexity of affected neuronal circuits. To identify dysfunctional neuronal subtypes underlying seizure activity in the human brain, we have performed single-nucleus transcriptomics analysis of &gt;110,000 neuronal transcriptomes derived from temporal cortex samples of multiple temporal lobe epilepsy and non-epileptic subjects. We found that the largest transcriptomic changes occur in distinct neuronal subtypes from several families of principal neurons (L5-6_Fezf2 and L2-3_Cux2) and GABAergic interneurons (Sst and Pvalb), whereas other subtypes in the same families were less affected. Furthermore, the subtypes with the largest epilepsy-related transcriptomic changes may belong to the same circuit, since we observed coordinated transcriptomic shifts across these subtypes. Glutamate signaling exhibited one of the strongest dysregulations in epilepsy, highlighted by layer-wise transcriptional changes in multiple glutamate receptor genes and strong upregulation of genes coding for AMPA receptor auxiliary subunits. Overall, our data reveal a neuronal subtype-specific molecular phenotype of epilepsy.","authors":"Pfisterer, U., Petukhov, V., Demharter, S., Meichsner, J., Thompson, JJ., Batiuk, MY., Asenjo-Martinez, A., Vasistha, NA., Thakur, A., Mikkelsen, J., Adorjan, I., Pinborg, LH., Pers, TH., von Engelhardt, J., Kharchenko, PV., Khodosevich, K.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"5038","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-27","doi":"10.1038\/s41467-020-18752-7","first_author":"Pfisterer, U.","corresponding_authors":"Khodosevich, K."},{"pmid":"32968047","title":"Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth.","abstract":"Understanding cell types and mechanisms of dental growth is essential for reconstruction and engineering of teeth. Therefore, we investigated cellular composition of growing and non-growing mouse and human teeth. As a result, we report an unappreciated cellular complexity of the continuously-growing mouse incisor, which suggests a coherent model of cell dynamics enabling unarrested growth. This model relies on spatially-restricted stem, progenitor and differentiated populations in the epithelial and mesenchymal compartments underlying the coordinated expansion of two major branches of pulpal cells and diverse epithelial subtypes. Further comparisons of human and mouse teeth yield both parallelisms and differences in tissue heterogeneity and highlight the specifics behind growing and non-growing modes. Despite being similar at a coarse level, mouse and human teeth reveal molecular differences and species-specific cell subtypes suggesting possible evolutionary divergence. Overall, here we provide an atlas of human and mouse teeth with a focus on growth and differentiation.","authors":"Krivanek, J., Soldatov, RA., Kastriti, ME., Chontorotzea, T., Herdina, AN., Petersen, J., Szarowska, B., Landova, M., Matejova, VK., Holla, LI., Kuchler, U., Zdrilic, IV., Vijaykumar, A., Balic, A., Marangoni, P., Klein, OD., Neves, VCM., Yianni, V., Sharpe, PT., Harkany, T., Metscher, BD., Baj\u00e9noff, M., Mina, M., Fried, K., Kharchenko, PV., Adameyko, I.","publication_status":"epublish","journalpubyear":"2020","journaltitle":"Nat Commun","volume":"11","issue":"1","page":"4816","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2020-10-13","doi":"10.1038\/s41467-020-18512-7","first_author":"Krivanek, J.","corresponding_authors":"Adameyko, I."},{"pmid":"32938797","title":"Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect.","abstract":"Leukemic relapse remains a major barrier to successful allogeneic hematopoietic stem cell transplantation (allo-HSCT) for aggressive hematologic malignancies. The basis for relapse of advanced lymphoid malignancies remains incompletely understood and may involve escape from the graft-versus-leukemia (GvL) effect. We hypothesized that for patients with chronic lymphocytic leukemia (CLL) treated with allo-HSCT, leukemic cell-intrinsic features influence transplant outcomes by directing the evolutionary trajectories of CLL cells. Integrated genetic, transcriptomic, and epigenetic analyses of CLL cells from 10 patients revealed that the clinical kinetics of post-HSCT relapse are shaped by distinct molecular dynamics. Early relapses after allo-HSCT exhibited notable genetic stability; single CLL cell transcriptional analysis demonstrated a cellular heterogeneity that was static over time. In contrast, CLL cells relapsing late after allo-HSCT displayed notable genetic evolution and evidence of neoantigen depletion, consistent with marked single-cell transcriptional shifts that were unique to each patient. We observed a greater rate of epigenetic change for late relapses not seen in early relapses or relapses after chemotherapy alone, suggesting that the selection pressures of the GvL bottleneck are unlike those imposed by chemotherapy. No selective advantage for human leukocyte antigen (HLA) loss was observed, even when present in pretransplant subpopulations. Gain of stem cell modules was a common signature associated with leukemia relapse regardless of posttransplant relapse kinetics. These data elucidate the biological pathways that underlie GvL resistance and posttransplant relapse.","authors":"Bachireddy, P., Ennis, C., Nguyen, VN., Gohil, SH., Clement, K., Shukla, SA., Forman, J., Barkas, N., Freeman, S., Bavli, N., Elagina, L., Leshchiner, I., Mohammad, AW., Mathewson, ND., Keskin, DB., Rassenti, LZ., Kipps, TJ., Brown, JR., Getz, G., Ho, VT., Gnirke, A., Neuberg, D., Soiffer, RJ., Ritz, J., Alyea, EP., Kharchenko, PV., Wu, CJ.","publication_status":"ppublish","journalpubyear":"2020","journaltitle":"Sci Transl Med","volume":"12","issue":"561","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2021-06-23","doi":"10.1126\/scitranslmed.abb7661","first_author":"Bachireddy, P.","corresponding_authors":"Wu, CJ."},{"pmid":"31171666","title":"Spatiotemporal structure of cell fate decisions in murine neural crest.","abstract":"Neural crest cells are embryonic progenitors that generate numerous cell types in vertebrates. With single-cell analysis, we show that mouse trunk neural crest cells become biased toward neuronal lineages when they delaminate from the neural tube, whereas cranial neural crest cells acquire ectomesenchyme potential dependent on activation of the transcription factor <i>Twist1.<\/i> The choices that neural crest cells make to become sensory, glial, autonomic, or mesenchymal cells can be formalized as a series of sequential binary decisions. Each branch of the decision tree involves initial coactivation of bipotential properties followed by gradual shifts toward commitment. Competing fate programs are coactivated before cells acquire fate-specific phenotypic traits. Determination of a specific fate is achieved by increased synchronization of relevant programs and concurrent repression of competing fate programs.","authors":"Soldatov, R., Kaucka, M., Kastriti, ME., Petersen, J., Chontorotzea, T., Englmaier, L., Akkuratova, N., Yang, Y., H\u00e4ring, M., Dyachuk, V., Bock, C., Farlik, M., Piacentino, ML., Boismoreau, F., Hilscher, MM., Yokota, C., Qian, X., Nilsson, M., Bronner, ME., Croci, L., Hsiao, WY., Guertin, DA., Brunet, JF., Consalez, GG., Ernfors, P., Fried, K., Kharchenko, PV., Adameyko, I.","publication_status":"ppublish","journalpubyear":"2019","journaltitle":"Science","volume":"364","issue":"6444","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-11-20","doi":"10.1126\/science.aas9536","first_author":"Soldatov, R.","corresponding_authors":"Adameyko, I."},{"pmid":"29921301","title":"dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments.","abstract":"Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing and troubleshooting of these experiments, with few software options currently available. Here, we describe a flexible pipeline for processing droplet-based transcriptome data that implements barcode corrections, classification of cell quality, and diagnostic information about the droplet libraries. We introduce advanced methods for correcting composition bias and sequencing errors affecting cellular and molecular barcodes to provide more accurate estimates of molecular counts in individual cells.","authors":"Petukhov, V., Guo, J., Baryawno, N., Severe, N., Scadden, DT., Samsonova, MG., Kharchenko, PV.","publication_status":"epublish","journalpubyear":"2018","journaltitle":"Genome Biol","volume":"19","issue":"1","page":"78","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-10-30","doi":"10.1186\/s13059-018-1449-6","first_author":"Petukhov, V.","corresponding_authors":"Kharchenko, PV."},{"pmid":"29898899","title":"Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.","abstract":"Characterization of intratumoral heterogeneity is critical to cancer therapy, as the presence of phenotypically diverse cell populations commonly fuels relapse and resistance to treatment. Although genetic variation is a well-studied source of intratumoral heterogeneity, the functional impact of most genetic alterations remains unclear. Even less understood is the relative importance of other factors influencing heterogeneity, such as epigenetic state or tumor microenvironment. To investigate the relationship between genetic and transcriptional heterogeneity in a context of cancer progression, we devised a computational approach called HoneyBADGER to identify copy number variation and loss of heterozygosity in individual cells from single-cell RNA-sequencing data. By integrating allele and normalized expression information, HoneyBADGER is able to identify and infer the presence of subclone-specific alterations in individual cells and reconstruct the underlying subclonal architecture. By examining several tumor types, we show that HoneyBADGER is effective at identifying deletions, amplifications, and copy-neutral loss-of-heterozygosity events and is capable of robustly identifying subclonal focal alterations as small as 10 megabases. We further apply HoneyBADGER to analyze single cells from a progressive multiple myeloma patient to identify major genetic subclones that exhibit distinct transcriptional signatures relevant to cancer progression. Other prominent transcriptional subpopulations within these tumors did not line up with the genetic subclonal structure and were likely driven by alternative, nonclonal mechanisms. These results highlight the need for integrative analysis to understand the molecular and phenotypic heterogeneity in cancer.","authors":"Fan, J., Lee, HO., Lee, S., Ryu, DE., Lee, S., Xue, C., Kim, SJ., Kim, K., Barkas, N., Park, PJ., Park, WY., Kharchenko, PV.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Genome Res","volume":"28","issue":"8","page":"1217-1227","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-11-08","doi":"10.1101\/gr.228080.117","first_author":"Fan, J.","corresponding_authors":"Kharchenko, PV."},{"pmid":"29227469","title":"Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain.","abstract":"Detailed characterization of the cell types in the human brain requires scalable experimental approaches to examine multiple aspects of the molecular state of individual cells, as well as computational integration of the data to produce unified cell-state annotations. Here we report improved high-throughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq). We used each method to acquire nuclear transcriptomic and DNA accessibility maps for &gt;60,000 single cells from human adult visual cortex, frontal cortex, and cerebellum. Integration of these data revealed regulatory elements and transcription factors that underlie cell-type distinctions, providing a basis for the study of complex processes in the brain, such as genetic programs that coordinate adult remyelination. We also mapped disease-associated risk variants to specific cellular populations, which provided insights into normal and pathogenic cellular processes in the human brain. This integrative multi-omics approach permits more detailed single-cell interrogation of complex organs and tissues.","authors":"Lake, BB., Chen, S., Sos, BC., Fan, J., Kaeser, GE., Yung, YC., Duong, TE., Gao, D., Chun, J., Kharchenko, PV., Zhang, K.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Nat Biotechnol","volume":"36","issue":"1","page":"70-80","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-19","doi":"10.1038\/nbt.4038","first_author":"Lake, BB.","corresponding_authors":"Zhang, K."},{"pmid":"29224778","title":"Rapid Mobilization Reveals a Highly Engraftable Hematopoietic Stem Cell.","abstract":"Hematopoietic stem cell transplantation is a potential curative therapy for malignant and nonmalignant diseases. Improving the efficiency of stem cell collection and the quality of the cells acquired can broaden the donor pool and improve patient outcomes. We developed a rapid stem cell mobilization regimen utilizing a unique CXCR2 agonist, GRO&#x3b2;, and the CXCR4 antagonist AMD3100. A single injection of both agents resulted in stem cell mobilization peaking within 15&#xa0;min that was equivalent in magnitude to a standard multi-day regimen of granulocyte colony-stimulating factor (G-CSF). Mechanistic studies determined that rapid mobilization results from synergistic signaling on neutrophils, resulting in enhanced MMP-9 release, and unexpectedly revealed genetic polymorphisms in MMP-9 that alter activity. This mobilization regimen results in preferential trafficking of stem cells that demonstrate a higher engraftment efficiency than those mobilized by G-CSF. Our studies suggest a potential new strategy for the rapid collection of an improved hematopoietic graft.","authors":"Hoggatt, J., Singh, P., Tate, TA., Chou, BK., Datari, SR., Fukuda, S., Liu, L., Kharchenko, PV., Schajnovitz, A., Baryawno, N., Mercier, FE., Boyer, J., Gardner, J., Morrow, DM., Scadden, DT., Pelus, LM.","publication_status":"ppublish","journalpubyear":"2018","journaltitle":"Cell","volume":"172","issue":"1-2","page":"191-204.e10","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-12-31","doi":"10.1016\/j.cell.2017.11.003","first_author":"Hoggatt, J.","corresponding_authors":"Hoggatt, J., Scadden, DT., Pelus, LM."},{"pmid":"28729663","title":"A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA.","abstract":"Significant heterogeneities in gene expression among individual cells are typically interrogated using single whole cell approaches. However, tissues that have highly interconnected processes, such as in the brain, present unique challenges. Single-nucleus RNA sequencing (SNS) has emerged as an alternative method of assessing a cell's transcriptome through the use of isolated nuclei. However, studies directly comparing expression data between nuclei and whole cells are lacking. Here, we have characterized nuclear and whole cell transcriptomes in mouse single neurons and provided a normalization strategy to reduce method-specific differences related to the length of genic regions. We confirmed a high concordance between nuclear and whole cell transcriptomes in the expression of cell type and metabolic modeling markers, but less so for a subset of genes associated with mitochondrial respiration. Therefore, our results indicate that single-nucleus transcriptome sequencing provides an effective means to profile cell type expression dynamics in previously inaccessible tissues.","authors":"Lake, BB., Codeluppi, S., Yung, YC., Gao, D., Chun, J., Kharchenko, PV., Linnarsson, S., Zhang, K.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Sci Rep","volume":"7","issue":"1","page":"6031","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2019-01-29","doi":"10.1038\/s41598-017-04426-w","first_author":"Lake, BB.","corresponding_authors":"Zhang, K."},{"pmid":"28684471","title":"Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla.","abstract":"Adrenaline is a fundamental circulating hormone for bodily responses to internal and external stressors. Chromaffin cells of the adrenal medulla (AM) represent the main neuroendocrine adrenergic component and are believed to differentiate from neural crest cells. We demonstrate that large numbers of chromaffin cells arise from peripheral glial stem cells, termed Schwann cell precursors (SCPs). SCPs migrate along the visceral motor nerve to the vicinity of the forming adrenal gland, where they detach from the nerve and form postsynaptic neuroendocrine chromaffin cells. An intricate molecular logic drives two sequential phases of gene expression, one unique for a distinct transient cellular state and another for cell type specification. Subsequently, these programs down-regulate SCP-gene and up-regulate chromaffin cell-gene networks. The AM forms through limited cell expansion and requires the recruitment of numerous SCPs. Thus, peripheral nerves serve as a stem cell niche for neuroendocrine system development.","authors":"Furlan, A., Dyachuk, V., Kastriti, ME., Calvo-Enrique, L., Abdo, H., Hadjab, S., Chontorotzea, T., Akkuratova, N., Usoskin, D., Kamenev, D., Petersen, J., Sunadome, K., Memic, F., Marklund, U., Fried, K., Topilko, P., Lallemend, F., Kharchenko, PV., Ernfors, P., Adameyko, I.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Science","volume":"357","issue":"6346","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-11","doi":"10.1126\/science.aal3753","first_author":"Furlan, A.","corresponding_authors":"Adameyko, I."},{"pmid":"28679620","title":"Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia.","abstract":"Intra-tumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships, and probe genotype-phenotype relationships, we developed methods for targeted mutation detection in DNA and RNA isolated from thousands of single cells from five CLL samples. By clearly resolving phylogenic relationships, we uncovered mutated <i>LCP1<\/i> and <i>WNK1<\/i> as novel CLL drivers, supported by functional evidence demonstrating their impact on CLL pathways. Integrative analysis of somatic mutations with transcriptional states prompts the idea that convergent evolution generates phenotypically similar cells in distinct genetic branches, thus creating a cohesive expression profile in each CLL sample despite the presence of genetic heterogeneity. Our study highlights the potential for single-cell RNA-based targeted analysis to sensitively determine transcriptional and mutational profiles of individual cancer cells, leading to increased understanding of driving events in malignancy.","authors":"Wang, L., Fan, J., Francis, JM., Georghiou, G., Hergert, S., Li, S., Gambe, R., Zhou, CW., Yang, C., Xiao, S., Cin, PD., Bowden, M., Kotliar, D., Shukla, SA., Brown, JR., Neuberg, D., Alessi, DR., Zhang, CZ., Kharchenko, PV., Livak, KJ., Wu, CJ.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Genome Res","volume":"27","issue":"8","page":"1300-1311","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-30","doi":"10.1101\/gr.217331.116","first_author":"Wang, L.","corresponding_authors":"Wu, CJ."},{"pmid":"28484033","title":"Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma.","abstract":"To investigate the mechanism that drives dramatic mistargeting of active chromatin in NUT midline carcinoma (NMC), we have identified protein interactions unique to the BRD4-NUT fusion oncoprotein compared with wild-type BRD4. Using cross-linking, affinity purification, and mass spectrometry, we identified the EP300 acetyltransferase as uniquely associated with BRD4 through the NUT fusion in both NMC and non-NMC cell types. We also discovered ZNF532 associated with BRD4-NUT in NMC patient cells but not detectable in 293T cells. EP300 and ZNF532 are both implicated in feed-forward regulatory loops leading to propagation of the oncogenic chromatin complex in BRD4-NUT patient cells. Adding key functional significance to our biochemical findings, we independently discovered a <i>ZNF532-NUT<\/i> translocation fusion in a newly diagnosed NMC patient. ChIP sequencing of the major players NUT, ZNF532, BRD4, EP300, and H3K27ac revealed the formation of ZNF532-NUT-associated hyperacetylated megadomains, distinctly localized but otherwise analogous to those found in BRD4-NUT patient cells. Our results support a model in which NMC is dependent on ectopic NUT-mediated interactions between EP300 and components of BRD4 regulatory complexes, leading to a cascade of misregulation.","authors":"Alekseyenko, AA., Walsh, EM., Zee, BM., Pakozdi, T., Hsi, P., Lemieux, ME., Dal Cin, P., Ince, TA., Kharchenko, PV., Kuroda, MI., French, CA.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"Proc Natl Acad Sci U S A","volume":"114","issue":"21","page":"E4184-E4192","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-05-03","doi":"10.1073\/pnas.1702086114","first_author":"Alekseyenko, AA.","corresponding_authors":"French, CA."},{"pmid":"28482897","title":"Challenges and emerging directions in single-cell analysis.","abstract":"Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enabled systematic investigation of cellular heterogeneity in a wide range of tissues and cell populations, yielding fresh insights into the composition, dynamics, and regulatory mechanisms of cell states in development and disease. Despite substantial advances, significant challenges remain in the analysis, integration, and interpretation of single-cell omics data. Here, we discuss the state of the field and recent advances and look to future opportunities.","authors":"Yuan, GC., Cai, L., Elowitz, M., Enver, T., Fan, G., Guo, G., Irizarry, R., Kharchenko, P., Kim, J., Orkin, S., Quackenbush, J., Saadatpour, A., Schroeder, T., Shivdasani, R., Tirosh, I.","publication_status":"epublish","journalpubyear":"2017","journaltitle":"Genome Biol","volume":"18","issue":"1","page":"84","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-01-12","doi":"10.1186\/s13059-017-1218-y","first_author":"Yuan, GC.","corresponding_authors":"Tirosh, I."},{"pmid":"28087763","title":"Circadian Kinetics of Cell Cycle Progression in Adult Neurogenic Niches of a Diurnal Vertebrate.","abstract":"The circadian system may regulate adult neurogenesis via intracellular molecular clock mechanisms or by modifying the environment of neurogenic niches, with daily variation in growth factors or nutrients depending on the animal's diurnal or nocturnal lifestyle. In a diurnal vertebrate, zebrafish, we studied circadian distribution of immunohistochemical markers of the cell division cycle (CDC) in 5 of the 16 neurogenic niches of adult brain, the dorsal telencephalon, habenula, preoptic area, hypothalamus, and cerebellum. We find that common to all niches is the morning initiation of G<sub>1<\/sub>\/S transition and daytime S-phase progression, overnight increase in G<sub>2<\/sub>\/M, and cycle completion by late night. This is supported by the timing of gene expression for critical cell cycle regulators cyclins D, A2, and B2 and cyclin-dependent kinase inhibitor p20 in brain tissue. The early-night peak in <i>p20<\/i>, limiting G<sub>1<\/sub>\/S transition, and its phase angle with the expression of core clock genes, <i>Clock1<\/i> and <i>Per1<\/i>, are preserved in constant darkness, suggesting intrinsic circadian patterns of cell cycle progression. The statistical modeling of CDC kinetics reveals the significant circadian variation in cell proliferation rates across all of the examined niches, but interniche differences in the magnitude of circadian variation in CDC, S-phase length, phase angle of entrainment to light or clock, and its dispersion. We conclude that, in neurogenic niches of an adult diurnal vertebrate, the circadian modulation of cell cycle progression involves both systemic and niche-specific factors.<b>SIGNIFICANCE STATEMENT<\/b> This study establishes that in neurogenic niches of an adult diurnal vertebrate, the cell cycle progression displays a robust circadian pattern. Common to neurogenic niches located in diverse brain regions is daytime progression of DNA replication and nighttime mitosis, suggesting systemic regulation. Differences between neurogenic niches in the phase and degree of S-phase entrainment to the clock suggest additional roles for niche-specific regulatory mechanisms. Understanding the circadian regulation of adult neurogenesis can help optimize the timing of therapeutic approaches in patients with brain traumas or neurodegenerative disorders and preserve neural stem cells during cytostatic cancer therapies.","authors":"Akle, V., Stankiewicz, AJ., Kharchenko, V., Yu, L., Kharchenko, PV., Zhdanova, IV.","publication_status":"ppublish","journalpubyear":"2017","journaltitle":"J Neurosci","volume":"37","issue":"7","page":"1900-1909","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-08-18","doi":"10.1523\/JNEUROSCI.3222-16.2017","first_author":"Akle, V.","corresponding_authors":"Zhdanova, IV."},{"pmid":"27863245","title":"Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells.","abstract":"Stem cells determine homeostasis and repair of many tissues and are increasingly recognized as functionally heterogeneous. To define the extent of-and molecular basis for-heterogeneity, we overlaid functional, transcriptional, and epigenetic attributes of hematopoietic stem cells (HSCs) at a clonal level using endogenous fluorescent tagging. Endogenous HSC had clone-specific functional attributes over time in&#xa0;vivo. The intra-clonal behaviors were highly stereotypic, conserved under the stress of transplantation, inflammation, and genotoxic injury, and associated with distinctive transcriptional, DNA methylation, and chromatin accessibility patterns. Further, HSC function corresponded to epigenetic configuration but not always to transcriptional state.&#xa0;Therefore, hematopoiesis under homeostatic and stress conditions represents the integrated action of highly heterogeneous clones of HSC with epigenetically scripted behaviors. This high degree of epigenetically driven cell autonomy among HSCs implies that refinement of the concepts of stem cell plasticity and of the stem cell niche is warranted.","authors":"Yu, VWC., Yusuf, RZ., Oki, T., Wu, J., Saez, B., Wang, X., Cook, C., Baryawno, N., Ziller, MJ., Lee, E., Gu, H., Meissner, A., Lin, CP., Kharchenko, PV., Scadden, DT.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"167","issue":"5","page":"1310-1322.e17","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-04-07","doi":"10.1016\/j.cell.2016.10.045","first_author":"Yu, VWC.","corresponding_authors":"Kharchenko, PV., Scadden, DT."},{"pmid":"27818134","title":"Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia.","abstract":"Mutations in SF3B1, which encodes a spliceosome component, are associated with poor outcome in chronic lymphocytic leukemia (CLL), but how these contribute to CLL progression remains poorly understood. We undertook a transcriptomic characterization of primary human CLL cells to identify transcripts and pathways affected by SF3B1 mutation. Splicing alterations, identified in the analysis of bulk cells, were confirmed in single SF3B1-mutated CLL cells and also found in cell lines ectopically expressing mutant SF3B1. SF3B1 mutation was found to dysregulate multiple cellular functions including DNA damage response, telomere maintenance, and Notch signaling (mediated through KLF8 upregulation, increased TERC and TERT expression, or altered splicing of DVL2 transcript, respectively). SF3B1 mutation leads to diverse changes in CLL-related pathways.","authors":"Wang, L., Brooks, AN., Fan, J., Wan, Y., Gambe, R., Li, S., Hergert, S., Yin, S., Freeman, SS., Levin, JZ., Fan, L., Seiler, M., Buonamici, S., Smith, PG., Chau, KF., Cibulskis, CL., Zhang, W., Rassenti, LZ., Ghia, EM., Kipps, TJ., Fernandes, S., Bloch, DB., Kotliar, D., Landau, DA., Shukla, SA., Aster, JC., Reed, R., DeLuca, DS., Brown, JR., Neuberg, D., Getz, G., Livak, KJ., Meyerson, MM., Kharchenko, PV., Wu, CJ.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cancer Cell","volume":"30","issue":"5","page":"750-763","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-06-01","doi":"10.1016\/j.ccell.2016.10.005","first_author":"Wang, L.","corresponding_authors":"Wu, CJ."},{"pmid":"27565344","title":"Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex.","abstract":"Alternative splicing is prevalent in the mammalian brain. To interrogate the functional role of alternative splicing in neural development, we analyzed purified neural progenitor cells (NPCs) and neurons from developing cerebral cortices, revealing hundreds of&#xa0;differentially spliced exons that preferentially alter key protein domains-especially in cytoskeletal proteins-and can harbor disease-causing mutations. We show that Ptbp1 and Rbfox proteins antagonistically govern the NPC-to-neuron transition by regulating neuron-specific exons. Whereas Ptbp1 maintains apical progenitors partly through suppressing a poison exon of Flna in NPCs, Rbfox proteins promote neuronal differentiation by switching Ninein from a centrosomal splice form in NPCs to a non-centrosomal isoform in neurons. We further uncover an intronic human mutation within a PTBP1-binding site that disrupts normal skipping of the FLNA poison exon in NPCs and causes a brain-specific malformation. Our study indicates that dynamic control of alternative splicing governs cell fate in cerebral cortical development.","authors":"Zhang, X., Chen, MH., Wu, X., Kodani, A., Fan, J., Doan, R., Ozawa, M., Ma, J., Yoshida, N., Reiter, JF., Black, DL., Kharchenko, PV., Sharp, PA., Walsh, CA.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell","volume":"166","issue":"5","page":"1147-1162.e15","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-12-29","doi":"10.1016\/j.cell.2016.07.025","first_author":"Zhang, X.","corresponding_authors":"Zhang, X., Walsh, CA."},{"pmid":"27524439","title":"Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem\/Progenitor Cell Regulators.","abstract":"Physiological stem cell function is regulated by secreted factors produced by niche cells. In this study, we describe an unbiased approach based on the differential single-cell gene expression analysis of mesenchymal osteolineage cells close to, and further removed from, hematopoietic stem\/progenitor cells (HSPCs) to identify candidate niche factors. Mesenchymal cells displayed distinct molecular profiles based on their relative location. We functionally examined, among the genes that were preferentially expressed in proximal cells, three secreted or cell-surface molecules not previously connected to HSPC biology-the secreted RNase angiogenin, the cytokine IL18, and the adhesion molecule Embigin-and discovered that all of these factors are HSPC quiescence regulators. Therefore, our proximity-based differential single-cell approach reveals molecular heterogeneity within niche cells and can be used to identify novel extrinsic stem\/progenitor cell regulators. Similar approaches could also be applied to other&#xa0;stem cell\/niche pairs to advance the understanding of microenvironmental regulation of stem cell function.","authors":"Silberstein, L., Goncalves, KA., Kharchenko, PV., Turcotte, R., Kfoury, Y., Mercier, F., Baryawno, N., Severe, N., Bachand, J., Spencer, JA., Papazian, A., Lee, D., Chitteti, BR., Srour, EF., Hoggatt, J., Tate, T., Lo Celso, C., Ono, N., Nutt, S., Heino, J., Sipil\u00e4, K., Shioda, T., Osawa, M., Lin, CP., Hu, GF., Scadden, DT.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Cell Stem Cell","volume":"19","issue":"4","page":"530-543","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2017-07-19","doi":"10.1016\/j.stem.2016.07.004","first_author":"Silberstein, L.","corresponding_authors":"Hu, GF., Scadden, DT."},{"pmid":"27199251","title":"Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition.","abstract":"Resistance to the Bruton's tyrosine kinase (BTK) inhibitor ibrutinib has been attributed solely to mutations in BTK and related pathway molecules. Using whole-exome and deep-targeted sequencing, we dissect evolution of ibrutinib resistance in serial samples from five chronic lymphocytic leukaemia patients. In two patients, we detect BTK-C481S mutation or multiple PLCG2 mutations. The other three patients exhibit an expansion of clones harbouring del(8p) with additional driver mutations (EP300, MLL2 and EIF2A), with one patient developing trans-differentiation into CD19-negative histiocytic sarcoma. Using droplet-microfluidic technology and growth kinetic analyses, we demonstrate the presence of ibrutinib-resistant subclones and estimate subclone size before treatment initiation. Haploinsufficiency of TRAIL-R, a consequence of del(8p), results in TRAIL insensitivity, which may contribute to ibrutinib resistance. These findings demonstrate that the ibrutinib therapy favours selection and expansion of rare subclones already present before ibrutinib treatment, and provide insight into the heterogeneity of genetic changes associated with ibrutinib resistance.","authors":"Burger, JA., Landau, DA., Taylor-Weiner, A., Bozic, I., Zhang, H., Sarosiek, K., Wang, L., Stewart, C., Fan, J., Hoellenriegel, J., Sivina, M., Dubuc, AM., Fraser, C., Han, Y., Li, S., Livak, KJ., Zou, L., Wan, Y., Konoplev, S., Sougnez, C., Brown, JR., Abruzzo, LV., Carter, SL., Keating, MJ., Davids, MS., Wierda, WG., Cibulskis, K., Zenz, T., Werner, L., Dal Cin, P., Kharchencko, P., Neuberg, D., Kantarjian, H., Lander, E., Gabriel, S., O'Brien, S., Letai, A., Weitz, DA., Nowak, MA., Getz, G., Wu, CJ.","publication_status":"epublish","journalpubyear":"2016","journaltitle":"Nat Commun","volume":"7","issue":null,"page":"11589","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2018-09-20","doi":"10.1038\/ncomms11589","first_author":"Burger, JA.","corresponding_authors":"Wu, CJ."},{"pmid":"26816381","title":"Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin.","abstract":"Genes encoding human &#x3b2;-type globin undergo a developmental switch from embryonic to fetal to adult-type expression. Mutations in the adult form cause inherited hemoglobinopathies or globin disorders, including sickle cell disease and thalassemia. Some experimental results have suggested that these diseases could be treated by induction of fetal-type hemoglobin (HbF). However, the mechanisms that repress HbF in adults remain unclear. We found that the LRF\/ZBTB7A transcription factor occupies fetal &#x3b3;-globin genes and maintains the nucleosome density necessary for &#x3b3;-globin gene silencing in adults, and that LRF confers its repressive activity through a NuRD repressor complex independent of the fetal globin repressor BCL11A. Our study may provide additional opportunities for therapeutic targeting in the treatment of hemoglobinopathies.","authors":"Masuda, T., Wang, X., Maeda, M., Canver, MC., Sher, F., Funnell, AP., Fisher, C., Suciu, M., Martyn, GE., Norton, LJ., Zhu, C., Kurita, R., Nakamura, Y., Xu, J., Higgs, DR., Crossley, M., Bauer, DE., Orkin, SH., Kharchenko, PV., Maeda, T.","publication_status":"ppublish","journalpubyear":"2016","journaltitle":"Science","volume":"351","issue":"6270","page":"285-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-02-16","doi":"10.1126\/science.aad3312","first_author":"Masuda, T.","corresponding_authors":"Maeda, T."},{"pmid":"26575630","title":"Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer.","abstract":"Aberrant transcription of the pericentromeric human satellite II (HSATII) repeat is present in a wide variety of epithelial cancers. In deriving experimental systems to study its deregulation, we observed that HSATII expression is induced in colon cancer cells cultured as xenografts or under nonadherent conditions in vitro, but it is rapidly lost in standard 2D cultures. Unexpectedly, physiological induction of endogenous HSATII RNA, as well as introduction of synthetic HSATII transcripts, generated cDNA intermediates in the form of DNA\/RNA hybrids. Single molecule sequencing of tumor xenografts showed that HSATII RNA-derived DNA (rdDNA) molecules are stably incorporated within pericentromeric loci. Suppression of RT activity using small molecule inhibitors reduced HSATII copy gain. Analysis of whole-genome sequencing data revealed that HSATII copy number gain is a common feature in primary human colon tumors and is associated with a lower overall survival. Together, our observations suggest that cancer-associated derepression of specific repetitive sequences can promote their RNA-driven genomic expansion, with potential implications on pericentromeric architecture.","authors":"Bersani, F., Lee, E., Kharchenko, PV., Xu, AW., Liu, M., Xega, K., MacKenzie, OC., Brannigan, BW., Wittner, BS., Jung, H., Ramaswamy, S., Park, PJ., Maheswaran, S., Ting, DT., Haber, DA.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Proc Natl Acad Sci U S A","volume":"112","issue":"49","page":"15148-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-05-03","doi":"10.1073\/pnas.1518008112","first_author":"Bersani, F.","corresponding_authors":"Haber, DA."},{"pmid":"26220994","title":"The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains.","abstract":"NUT midline carcinoma (NMC), a subtype of squamous cell cancer, is one of the most aggressive human solid malignancies known. NMC is driven by the creation of a translocation oncoprotein, BRD4-NUT, which blocks differentiation and drives growth of NMC cells. BRD4-NUT forms distinctive nuclear foci in patient tumors, which we found correlate with &#x223c;100 unprecedented, hyperacetylated expanses of chromatin that reach up to 2 Mb in size. These \"megadomains\" appear to be the result of aberrant, feed-forward loops of acetylation and binding of acetylated histones that drive transcription of underlying DNA in NMC patient cells and na&#xef;ve cells induced to express BRD4-NUT. Megadomain locations are typically cell lineage-specific; however, the cMYC and TP63 regions are targeted in all NMCs tested and play functional roles in tumor growth. Megadomains appear to originate from select pre-existing enhancers that progressively broaden but are ultimately delimited by topologically associating domain (TAD) boundaries. Therefore, our findings establish a basis for understanding the powerful role played by large-scale chromatin organization in normal and aberrant lineage-specific gene transcription.","authors":"Alekseyenko, AA., Walsh, EM., Wang, X., Grayson, AR., Hsi, PT., Kharchenko, PV., Kuroda, MI., French, CA.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Genes Dev","volume":"29","issue":"14","page":"1507-23","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-10-13","doi":"10.1101\/gad.267583.115","first_author":"Alekseyenko, AA.","corresponding_authors":"French, CA."},{"pmid":"26077710","title":"DAZL regulates Tet1 translation in murine embryonic stem cells.","abstract":"Embryonic stem cell (ESC) cultures display a heterogeneous gene expression profile, ranging from a pristine na&#xef;ve pluripotent state to a primed epiblast state. Addition of inhibitors of GSK3&#x3b2; and MEK (so-called 2i conditions) pushes ESC cultures toward a more homogeneous na&#xef;ve pluripotent state, but the molecular underpinnings of this na&#xef;ve transition are not completely understood. Here, we demonstrate that DAZL, an RNA-binding protein known to play a key role in germ-cell development, marks a subpopulation of ESCs that is actively transitioning toward na&#xef;ve pluripotency. Moreover, DAZL plays an essential role in the active reprogramming of cytosine methylation. We demonstrate that DAZL associates with mRNA of Tet1, a catalyst of 5-hydroxylation of methyl-cytosine, and enhances Tet1 mRNA translation. Overexpression of DAZL in heterogeneous ESC cultures results in elevated TET1 protein levels as well as increased global hydroxymethylation. Conversely, null mutation of Dazl severely stunts 2i-mediated TET1 induction and hydroxymethylation. Our results provide insight into the regulation of the acquisition of na&#xef;ve pluripotency and demonstrate that DAZL enhances TET1-mediated cytosine hydroxymethylation in ESCs that are actively reprogramming to a pluripotent ground state.","authors":"Welling, M., Chen, HH., Mu\u00f1oz, J., Musheev, MU., Kester, L., Junker, JP., Mischerikow, N., Arbab, M., Kuijk, E., Silberstein, L., Kharchenko, PV., Geens, M., Niehrs, C., van de Velde, H., van Oudenaarden, A., Heck, AJ., Geijsen, N.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"EMBO Rep","volume":"16","issue":"7","page":"791-802","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-04-20","doi":"10.15252\/embr.201540538","first_author":"Welling, M.","corresponding_authors":"Geijsen, N."},{"pmid":"25639793","title":"Epstein-Barr virus oncoprotein super-enhancers control B cell growth.","abstract":"Super-enhancers are clusters of gene-regulatory sites bound by multiple transcription factors that govern cell transcription, development, phenotype, and oncogenesis. By examining Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs), we identified four EBV oncoproteins and five EBV-activated NF-&#x3ba;B subunits co-occupying &#x223c;1,800 enhancer sites. Of these, 187 had markedly higher and broader histone H3K27ac signals, characteristic of super-enhancers, and were designated \"EBV super-enhancers.\" EBV super-enhancer-associated genes included the MYC and BCL2 oncogenes, which enable LCL proliferation and survival. EBV super-enhancers were enriched for B cell transcription factor motifs and had high co-occupancy of STAT5 and NFAT transcription factors (TFs). EBV super-enhancer-associated genes were more highly expressed than other LCL genes. Disrupting EBV super-enhancers by the bromodomain inhibitor JQ1 or conditionally inactivating an EBV oncoprotein or NF-&#x3ba;B decreased MYC or BCL2 expression and arrested LCL growth. These findings provide insight into mechanisms of EBV-induced lymphoproliferation and identify potential therapeutic interventions.","authors":"Zhou, H., Schmidt, SC., Jiang, S., Willox, B., Bernhardt, K., Liang, J., Johannsen, EC., Kharchenko, P., Gewurz, BE., Kieff, E., Zhao, B.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Cell Host Microbe","volume":"17","issue":"2","page":"205-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-11-25","doi":"10.1016\/j.chom.2014.12.013","first_author":"Zhou, H.","corresponding_authors":"Kieff, E., Zhao, B."},{"pmid":"25559106","title":"BioTAP-XL: Cross-linking\/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes.","abstract":"In order to understand how chromatin complexes function in the nucleus, it is important to obtain a comprehensive picture of their protein, DNA, and RNA components, as well as their mutual interactions. This unit presents a chromatin cross-linking approach (BioTAP-XL) that utilizes a special BioTAP-tagged transgenic protein bait along with mass spectrometry to identify protein complex components, and high-throughput sequencing to identify RNA components and DNA binding sites. Full protocols are provided for Drosophila cells and for human cells in culture, along with an additional protocol for Drosophila embryos as the source material. A key element of the approach in all cases is the generation of control data from input chromatin samples.","authors":"Alekseyenko, AA., McElroy, KA., Kang, H., Zee, BM., Kharchenko, PV., Kuroda, MI.","publication_status":"epublish","journalpubyear":"2015","journaltitle":"Curr Protoc Mol Biol","volume":"109","issue":null,"page":"21.30.1-21.30.32","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2016-09-07","doi":"10.1002\/0471142727.mb2130s109","first_author":"Alekseyenko, AA.","corresponding_authors":"Kuroda, MI."},{"pmid":"25540416","title":"Epstein-Barr virus nuclear antigen 3A partially coincides with EBNA3C genome-wide and is tethered to DNA through BATF complexes.","abstract":"Epstein-Barr Virus (EBV) conversion of B-lymphocytes to Lymphoblastoid Cell Lines (LCLs) requires four EBV nuclear antigen (EBNA) oncoproteins: EBNA2, EBNALP, EBNA3A, and EBNA3C. EBNA2 and EBNALP associate with EBV and cell enhancers, up-regulate the EBNA promoter, MYC, and EBV Latent infection Membrane Proteins (LMPs), which up-regulate BCL2 to protect EBV-infected B-cells from MYC proliferation-induced cell death. LCL proliferation induces p16(INK4A) and p14(ARF)-mediated cell senescence. EBNA3A and EBNA3C jointly suppress p16(INK4A) and p14(ARF), enabling continuous cell proliferation. Analyses of the EBNA3A human genome-wide ChIP-seq landscape revealed 37% of 10,000 EBNA3A sites to be at strong enhancers; 28% to be at weak enhancers; 4.4% to be at active promoters; and 6.9% to be at weak and poised promoters. EBNA3A colocalized with BATF-IRF4, ETS-IRF4, RUNX3, and other B-cell Transcription Factors (TFs). EBNA3A sites clustered into seven unique groups, with differing B-cell TFs and epigenetic marks. EBNA3A coincidence with BATF-IRF4 or RUNX3 was associated with stronger EBNA3A ChIP-Seq signals. EBNA3A was at MYC, CDKN2A\/B, CCND2, CXCL9\/10, and BCL2, together with RUNX3, BATF, IRF4, and SPI1. ChIP-re-ChIP revealed complexes of EBNA3A on DNA with BATF. These data strongly support a model in which EBNA3A is tethered to DNA through a BATF-containing protein complexes to enable continuous cell proliferation.","authors":"Schmidt, SC., Jiang, S., Zhou, H., Willox, B., Holthaus, AM., Kharchenko, PV., Johannsen, EC., Kieff, E., Zhao, B.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Proc Natl Acad Sci U S A","volume":"112","issue":"2","page":"554-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-04-30","doi":"10.1073\/pnas.1422580112","first_author":"Schmidt, SC.","corresponding_authors":"Zhao, B."},{"pmid":"25490447","title":"Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.","abstract":"Intratumoral heterogeneity plays a critical role in tumor evolution. To define the contribution of DNA methylation to heterogeneity within tumors, we performed genome-scale bisulfite sequencing of 104 primary chronic lymphocytic leukemias (CLLs). Compared with 26 normal B cell samples, CLLs consistently displayed higher intrasample variability of DNA methylation patterns across the genome, which appears to arise from stochastically disordered methylation in malignant cells. Transcriptome analysis of bulk and single CLL cells revealed that methylation disorder was linked to low-level expression. Disordered methylation was further associated with adverse clinical outcome. We therefore propose that disordered methylation plays a similar role to that of genetic instability, enhancing the ability of cancer cells to search for superior evolutionary trajectories.","authors":"Landau, DA., Clement, K., Ziller, MJ., Boyle, P., Fan, J., Gu, H., Stevenson, K., Sougnez, C., Wang, L., Li, S., Kotliar, D., Zhang, W., Ghandi, M., Garraway, L., Fernandes, SM., Livak, KJ., Gabriel, S., Gnirke, A., Lander, ES., Brown, JR., Neuberg, D., Kharchenko, PV., Hacohen, N., Getz, G., Meissner, A., Wu, CJ.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Cancer Cell","volume":"26","issue":"6","page":"813-825","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-02-13","doi":"10.1016\/j.ccell.2014.10.012","first_author":"Landau, DA.","corresponding_authors":"Meissner, A., Wu, CJ."},{"pmid":"25420068","title":"Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing.","abstract":"The primary sensory system requires the integrated function of multiple cell types, although its full complexity remains unclear. We used comprehensive transcriptome analysis of 622 single mouse neurons to classify them in an unbiased manner, independent of any a priori knowledge of sensory subtypes. Our results reveal eleven types: three distinct low-threshold mechanoreceptive neurons, two proprioceptive, and six principal types of thermosensitive, itch sensitive, type C low-threshold mechanosensitive and nociceptive neurons with markedly different molecular and operational properties. Confirming previously anticipated major neuronal types, our results also classify and provide markers for new, functionally distinct subtypes. For example, our results suggest that itching during inflammatory skin diseases such as atopic dermatitis is linked to a distinct itch-generating type. We demonstrate single-cell RNA-seq as an effective strategy for dissecting sensory responsive cells into distinct neuronal types. The resulting catalog illustrates the diversity of sensory types and the cellular complexity underlying somatic sensation.","authors":"Usoskin, D., Furlan, A., Islam, S., Abdo, H., L\u00f6nnerberg, P., Lou, D., Hjerling-Leffler, J., Haeggstr\u00f6m, J., Kharchenko, O., Kharchenko, PV., Linnarsson, S., Ernfors, P.","publication_status":"ppublish","journalpubyear":"2015","journaltitle":"Nat Neurosci","volume":"18","issue":"1","page":"145-53","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2015-03-06","doi":"10.1038\/nn.3881","first_author":"Usoskin, D.","corresponding_authors":"Ernfors, P."},{"pmid":"25164756","title":"Comparative analysis of metazoan chromatin organization.","abstract":"Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms. Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths. To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.","authors":"Ho, JW., Jung, YL., Liu, T., Alver, BH., Lee, S., Ikegami, K., Sohn, KA., Minoda, A., Tolstorukov, MY., Appert, A., Parker, SC., Gu, T., Kundaje, A., Riddle, NC., Bishop, E., Egelhofer, TA., Hu, SS., Alekseyenko, AA., Rechtsteiner, A., Asker, D., Belsky, JA., Bowman, SK., Chen, QB., Chen, RA., Day, DS., Dong, Y., Dose, AC., Duan, X., Epstein, CB., Ercan, S., Feingold, EA., Ferrari, F., Garrigues, JM., Gehlenborg, N., Good, PJ., Haseley, P., He, D., Herrmann, M., Hoffman, MM., Jeffers, TE., Kharchenko, PV., Kolasinska-Zwierz, P., Kotwaliwale, CV., Kumar, N., Langley, SA., Larschan, EN., Latorre, I., Libbrecht, MW., Lin, X., Park, R., Pazin, MJ., Pham, HN., Plachetka, A., Qin, B., Schwartz, YB., Shoresh, N., Stempor, P., Vielle, A., Wang, C., Whittle, CM., Xue, H., Kingston, RE., Kim, JH., Bernstein, BE., Dernburg, AF., Pirrotta, V., Kuroda, MI., Noble, WS., Tullius, TD., Kellis, M., MacAlpine, DM., Strome, S., Elgin, SC., Liu, XS., Lieb, JD., Ahringer, J., Karpen, GH., Park, PJ.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Nature","volume":"512","issue":"7515","page":"449-52","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-10-24","doi":"10.1038\/nature13415","first_author":"Ho, JW.","corresponding_authors":"Park, PJ."},{"pmid":"24990964","title":"Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs.","abstract":"Heterochromatin protein 1 (HP1a) has conserved roles in gene silencing and heterochromatin and is also implicated in transcription, DNA replication, and repair. Here we identify chromatin-associated protein and RNA interactions of HP1a by BioTAP-XL mass spectrometry and sequencing from Drosophila S2 cells, embryos, larvae, and adults. Our results reveal an extensive list of known and novel HP1a-interacting proteins, of which we selected three for validation. A strong novel interactor, dADD1 (Drosophila ADD1) (CG8290), is highly enriched in heterochromatin, harbors an ADD domain similar to human ATRX, displays selective binding to H3K9me2 and H3K9me3, and is a classic genetic suppressor of position-effect variegation. Unexpectedly, a second hit, HIPP1 (HP1 and insulator partner protein-1) (CG3680), is strongly connected to CP190-related complexes localized at putative insulator sequences throughout the genome in addition to its colocalization with HP1a in heterochromatin. A third interactor, the histone methyltransferase MES-4, is also enriched in heterochromatin. In addition to these protein-protein interactions, we found that HP1a selectively associated with a broad set of RNAs transcribed from repetitive regions. We propose that this rich network of previously undiscovered interactions will define how HP1a complexes perform their diverse functions in cells and developing organisms.","authors":"Alekseyenko, AA., Gorchakov, AA., Zee, BM., Fuchs, SM., Kharchenko, PV., Kuroda, MI.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Genes Dev","volume":"28","issue":"13","page":"1445-60","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-09-02","doi":"10.1101\/gad.241950.114","first_author":"Alekseyenko, AA.","corresponding_authors":"Kuroda, MI."},{"pmid":"24550272","title":"Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification.","abstract":"Understanding the composition of epigenetic regulators remains an important challenge in chromatin biology. Traditional biochemical analysis of chromatin-associated complexes requires their release from DNA under conditions that can also disrupt key interactions. Here we develop a complementary approach (BioTAP-XL), in which cross-linking (XL) enhances the preservation of protein interactions and also allows the analysis of DNA targets under the same tandem affinity purification (BioTAP) regimen. We demonstrate the power of BioTAP-XL through analysis of human EZH2, a core subunit of polycomb repressive complex 2 (PRC2). We identify and validate two strong interactors, C10orf12 and C17orf96, which display enrichment with EZH2-BioTAP at levels similar to canonical PRC2 components (SUZ12, EED, MTF2, JARID2, PHF1, and AEBP2). ChIP-seq analysis of BioTAP-tagged C10orf12 or C17orf96 revealed the similarity of each binding pattern with the location of EZH2 and the H3K27me3-silencing mark, validating their physical interaction with PRC2 components. Interestingly, analysis by mass spectrometry of C10orf12 and C17orf96 interactions revealed that these proteins may be mutually exclusive PRC2 subunits that fail to interact with each other or with JARID2 and AEBP2. C10orf12, in addition, shows a strong and unexpected association with components of the EHMT1\/2 complex, thus potentially connecting PRC2 to another histone methyltransferase. Similarly, results from CBX4-BioTAP protein pulldowns are consistent with reports of a diversity of PRC1 complexes. Our results highlight the importance of reciprocal analyses of multiple subunits and suggest that iterative use of BioTAP-XL has strong potential to reveal networks of chromatin-based interactions in higher organisms.","authors":"Alekseyenko, AA., Gorchakov, AA., Kharchenko, PV., Kuroda, MI.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Proc Natl Acad Sci U S A","volume":"111","issue":"7","page":"2488-93","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-04-15","doi":"10.1073\/pnas.1400648111","first_author":"Alekseyenko, AA.","corresponding_authors":"Kuroda, MI."},{"pmid":"24344258","title":"Epstein-Barr virus nuclear antigen 3C binds to BATF\/IRF4 or SPI1\/IRF4 composite sites and recruits Sin3A to repress CDKN2A.","abstract":"Epstein-Barr virus nuclear antigen 3C (EBNA3C) repression of CDKN2A p14(ARF) and p16(INK4A) is essential for immortal human B-lymphoblastoid cell line (LCL) growth. EBNA3C ChIP-sequencing identified &gt;13,000 EBNA3C sites in LCL DNA. Most EBNA3C sites were associated with active transcription; 64% were strong H3K4me1- and H3K27ac-marked enhancers and 16% were active promoters marked by H3K4me3 and H3K9ac. Using ENCODE LCL transcription factor ChIP-sequencing data, EBNA3C sites coincided (&#xb1;250 bp) with RUNX3 (64%), BATF (55%), ATF2 (51%), IRF4 (41%), MEF2A (35%), PAX5 (34%), SPI1 (29%), BCL11a (28%), SP1 (26%), TCF12 (23%), NF-&#x3ba;B (23%), POU2F2 (23%), and RBPJ (16%). EBNA3C sites separated into five distinct clusters: (i) Sin3A, (ii) EBNA2\/RBPJ, (iii) SPI1, and (iv) strong or (v) weak BATF\/IRF4. EBNA3C signals were positively affected by RUNX3, BATF\/IRF4 (AICE) and SPI1\/IRF4 (EICE) cooccupancy. Gene set enrichment analyses correlated EBNA3C\/Sin3A promoter sites with transcription down-regulation (P &lt; 1.6 &#xd7; 10(-4)). EBNA3C signals were strongest at BATF\/IRF4 and SPI1\/IRF4 composite sites. EBNA3C bound strongly to the p14(ARF) promoter through SPI1\/IRF4\/BATF\/RUNX3, establishing RBPJ-, Sin3A-, and REST-mediated repression. EBNA3C immune precipitated with Sin3A and conditional EBNA3C inactivation significantly decreased Sin3A binding at the p14(ARF) promoter (P &lt; 0.05). These data support a model in which EBNA3C binds strongly to BATF\/IRF4\/SPI1\/RUNX3 sites to enhance transcription and recruits RBPJ\/Sin3A- and REST\/NRSF-repressive complexes to repress p14(ARF) and p16(INK4A) expression.","authors":"Jiang, S., Willox, B., Zhou, H., Holthaus, AM., Wang, A., Shi, TT., Maruo, S., Kharchenko, PV., Johannsen, EC., Kieff, E., Zhao, B.","publication_status":"ppublish","journalpubyear":"2014","journaltitle":"Proc Natl Acad Sci U S A","volume":"111","issue":"1","page":"421-6","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-03-12","doi":"10.1073\/pnas.1321704111","first_author":"Jiang, S.","corresponding_authors":"Zhao, B."},{"pmid":"24183666","title":"\"Jump start and gain\" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts.","abstract":"Dosage compensation in Drosophila is mediated by the MSL complex, which increases male X-linked gene expression approximately 2-fold. The MSL complex preferentially binds the bodies of active genes on the male X, depositing H4K16ac with a 3' bias. Two models have been proposed for the influence of the MSL complex on transcription: one based on promoter recruitment of RNA polymerase II (Pol II), and a second featuring enhanced transcriptional elongation. Here, we utilize nascent RNA sequencing to document dosage compensation during transcriptional elongation. We also compare X and autosomes from published data on paused and elongating polymerase in order to assess the role of Pol II recruitment. Our results support a model for differentially regulated elongation, starting with release from 5' pausing and increasing through X-linked gene bodies. Our results highlight facilitated transcriptional elongation as a key mechanism for the coordinated regulation of a diverse set of genes.","authors":"Ferrari, F., Plachetka, A., Alekseyenko, AA., Jung, YL., Ozsolak, F., Kharchenko, PV., Park, PJ., Kuroda, MI.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Rep","volume":"5","issue":"3","page":"629-36","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-08-28","doi":"10.1016\/j.celrep.2013.09.037","first_author":"Ferrari, F.","corresponding_authors":"Kuroda, MI."},{"pmid":"24167291","title":"Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2.","abstract":"Epstein-Barr virus (EBV) nuclear antigens EBNALP (LP) and EBNA2 (E2) are coexpressed in EBV-infected B lymphocytes and are critical for lymphoblastoid cell line outgrowth. LP removes NCOR and RBPJ repressive complexes from promoters, enhancers, and matrix-associated deacetylase bodies, whereas E2 activates transcription from distal enhancers. LP ChIP-seq analyses identified 19,224 LP sites of which ~50% were &#xb1; 2 kb of a transcriptional start site. LP sites were enriched for B-cell transcription factors (TFs), YY1, SP1, PAX5, BATF, IRF4, ETS1, RAD21, PU.1, CTCF, RBPJ, ZNF143, SMC3, NF&#x3ba;B, TBLR, and EBF. E2 sites were also highly enriched for LP-associated cell TFs and were more highly occupied by RBPJ and EBF. LP sites were highly marked by H3K4me3, H3K27ac, H2Az, H3K9ac, RNAPII, and P300, indicative of activated transcription. LP sites were 29% colocalized with E2 (LP\/E2). LP\/E2 sites were more similar to LP than to E2 sites in associated cell TFs, RNAPII, P300, and histone H3K4me3, H3K9ac, H3K27ac, and H2Az occupancy, and were more highly transcribed than LP or E2 sites. Gene affected by CTCF and LP cooccupancy were more highly expressed than genes affected by CTCF alone. LP was at myc enhancers and promoters and of MYC regulated ccnd2, 23 med complex components, and MYC regulated cell survival genes, igf2r and bcl2. These data implicate LP and associated TFs and DNA looping factors CTCF, RAD21, SMC3, and YY1\/INO80 chromatin-remodeling complexes in repressor depletion and gene activation necessary for lymphoblastoid cell line growth and survival.","authors":"Portal, D., Zhou, H., Zhao, B., Kharchenko, PV., Lowry, E., Wong, L., Quackenbush, J., Holloway, D., Jiang, S., Lu, Y., Kieff, E.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Proc Natl Acad Sci U S A","volume":"110","issue":"46","page":"18537-42","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-01-08","doi":"10.1073\/pnas.1317608110","first_author":"Portal, D.","corresponding_authors":"Kieff, E."},{"pmid":"23775117","title":"Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters.","abstract":"Polycomb group (PcG)-mediated repression is an evolutionarily conserved process critical for cell fate determination and maintenance of gene expression during embryonic development. However, the mechanisms underlying PcG recruitment in mammals remain unclear since few regulatory sites have been identified. We report two novel prospective PcG-dependent regulatory elements within the human HOXB and HOXC clusters and compare their repressive activities to a previously identified element in the HOXD cluster. These regions recruited the PcG proteins BMI1 and SUZ12 to a reporter construct in mesenchymal stem cells and conferred repression that was dependent upon PcG expression. Furthermore, we examined the potential of two DNA-binding proteins, JARID2 and YY1, to regulate PcG activity at these three elements. JARID2 has differential requirements, whereas YY1 appears to be required for repressive activity at all 3 sites. We conclude that distinct elements of the mammalian HOX clusters can recruit components of the PcG complexes and confer repression, similar to what has been seen in Drosophila. These elements, however, have diverse requirements for binding factors, which, combined with previous data on other loci, speaks to the complexity of PcG targeting in mammals.","authors":"Woo, CJ., Kharchenko, PV., Daheron, L., Park, PJ., Kingston, RE.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Mol Cell Biol","volume":"33","issue":"16","page":"3274-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-10-23","doi":"10.1128\/MCB.00275-13","first_author":"Woo, CJ.","corresponding_authors":"Kingston, RE."},{"pmid":"23665121","title":"Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming.","abstract":"The chromatin state of pluripotency genes has been studied extensively in embryonic stem cells (ESCs) and differentiated cells, but their potential interactions with other parts of the genome remain largely unexplored. Here, we identified a genome-wide, pluripotency-specific interaction network around the Nanog promoter by adapting circular chromosome conformation capture sequencing. This network was rearranged during differentiation and restored in induced pluripotent stem cells. A large fraction of Nanog-interacting loci were bound by Mediator or cohesin in pluripotent cells. Depletion of these proteins from ESCs resulted in a disruption of contacts and the acquisition of a differentiation-specific interaction pattern prior to obvious transcriptional and phenotypic changes. Similarly, the establishment of Nanog interactions during reprogramming often preceded transcriptional upregulation of associated genes, suggesting a causative link. Our results document a complex, pluripotency-specific chromatin \"interactome\" for Nanog and suggest a functional role for long-range genomic interactions in the maintenance and induction of pluripotency.","authors":"Apostolou, E., Ferrari, F., Walsh, RM., Bar-Nur, O., Stadtfeld, M., Cheloufi, S., Stuart, HT., Polo, JM., Ohsumi, TK., Borowsky, ML., Kharchenko, PV., Park, PJ., Hochedlinger, K.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Cell Stem Cell","volume":"12","issue":"6","page":"699-712","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2014-12-19","doi":"10.1016\/j.stem.2013.04.013","first_author":"Apostolou, E.","corresponding_authors":"Hochedlinger, K."},{"pmid":"23295261","title":"Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila.","abstract":"X-chromosome dosage compensation by the MSL (male-specific lethal) complex is required in Drosophila melanogaster to increase gene expression from the single male X to equal that of both female X chromosomes. Instead of focusing solely on protein complexes released from DNA, here we used chromatin-interacting protein MS (ChIP-MS) to identify MSL interactions on cross-linked chromatin. We identified MSL-enriched histone modifications, including histone H4 Lys16 acetylation and histone H3 Lys36 methylation, and CG4747, a putative Lys36-trimethylated histone H3 (H3K36me3)-binding protein. CG4747 is associated with the bodies of active genes, coincident with H3K36me3, and is mislocalized in the Set2 mutant lacking H3K36me3. CG4747 loss of function in vivo results in partial mislocalization of the MSL complex to autosomes, and RNA interference experiments confirm that CG4747 and Set2 function together to facilitate targeting of the MSL complex to active genes, validating the ChIP-MS approach.","authors":"Wang, CI., Alekseyenko, AA., LeRoy, G., Elia, AE., Gorchakov, AA., Britton, LM., Elledge, SJ., Kharchenko, PV., Garcia, BA., Kuroda, MI.","publication_status":"ppublish","journalpubyear":"2013","journaltitle":"Nat Struct Mol Biol","volume":"20","issue":"2","page":"202-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-02","doi":"10.1038\/nsmb.2477","first_author":"Wang, CI.","corresponding_authors":"Kuroda, MI."},{"pmid":"22955616","title":"An integrated encyclopedia of DNA elements in the human genome.","abstract":"The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.","authors":"","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Nature","volume":"489","issue":"7414","page":"57-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-10-17","doi":"10.1038\/nature11247","first_author":null,"corresponding_authors":null},{"pmid":"23028361","title":"Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.","abstract":"Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP-chip) analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in euchromatin or pericentric heterochromatin: while there is a depletion of silencing marks at the transcription start sites (TSSs), HP1a and H3K9me3, but not H3K9me2, are enriched strongly over gene bodies. Intriguingly, genes on chromosome 4 are less frequently associated with paused polymerase. However, when the chromatin is altered by depleting HP1a or POF, the RNA pol II enrichment patterns of many chromosome 4 genes shift, showing a significant decrease over gene bodies but not at TSSs, accompanied by lower expression of those genes. Chromosome 4 genes have a low incidence of TRL\/GAGA factor binding sites and a low T(m) downstream of the TSS, characteristics that could contribute to a low incidence of RNA polymerase pausing. Our data also indicate that EGG and POF jointly regulate H3K9 methylation and promote HP1a binding over gene bodies, while HP1a targeting and H3K9 methylation are maintained at the repeats by an independent mechanism. The HP1a-enriched, POF-associated chromatin structure over the gene bodies may represent one type of adaptation for genes embedded in repetitive DNA.","authors":"Riddle, NC., Jung, YL., Gu, T., Alekseyenko, AA., Asker, D., Gui, H., Kharchenko, PV., Minoda, A., Plachetka, A., Schwartz, YB., Tolstorukov, MY., Kuroda, MI., Pirrotta, V., Karpen, GH., Park, PJ., Elgin, SC.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"9","page":"e1002954","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-04","doi":"10.1371\/journal.pgen.1002954","first_author":"Riddle, NC.","corresponding_authors":"Elgin, SC."},{"pmid":"22955991","title":"ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.","abstract":"Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http:\/\/encodeproject.org\/ENCODE\/) and modENCODE (http:\/\/www.modencode.org\/) portals.","authors":"Landt, SG., Marinov, GK., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, BE., Bickel, P., Brown, JB., Cayting, P., Chen, Y., DeSalvo, G., Epstein, C., Fisher-Aylor, KI., Euskirchen, G., Gerstein, M., Gertz, J., Hartemink, AJ., Hoffman, MM., Iyer, VR., Jung, YL., Karmakar, S., Kellis, M., Kharchenko, PV., Li, Q., Liu, T., Liu, XS., Ma, L., Milosavljevic, A., Myers, RM., Park, PJ., Pazin, MJ., Perry, MD., Raha, D., Reddy, TE., Rozowsky, J., Shoresh, N., Sidow, A., Slattery, M., Stamatoyannopoulos, JA., Tolstorukov, MY., White, KP., Xi, S., Farnham, PJ., Lieb, JD., Wold, BJ., Snyder, M.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genome Res","volume":"22","issue":"9","page":"1813-31","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-01-24","doi":"10.1101\/gr.136184.111","first_author":"Landt, SG.","corresponding_authors":"Snyder, M."},{"pmid":"22767387","title":"Nature and function of insulator protein binding sites in the Drosophila genome.","abstract":"Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but only at a small number of Polycomb target regions and only to prevent repressive histone methylation within adjacent genes that are already transcriptionally inactive. RNAi knockdown of insulator proteins in cultured cells does not lead to major alterations in genome expression. Taken together, these observations argue against the concept of a genome partitioned by specialized boundary elements and suggest that insulators are reserved for specific regulation of selected genes.","authors":"Schwartz, YB., Linder-Basso, D., Kharchenko, PV., Tolstorukov, MY., Kim, M., Li, HB., Gorchakov, AA., Minoda, A., Shanower, G., Alekseyenko, AA., Riddle, NC., Jung, YL., Gu, T., Plachetka, A., Elgin, SC., Kuroda, MI., Park, PJ., Savitsky, M., Karpen, GH., Pirrotta, V.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Genome Res","volume":"22","issue":"11","page":"2188-98","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2013-04-11","doi":"10.1101\/gr.138156.112","first_author":"Schwartz, YB.","corresponding_authors":"Pirrotta, V."},{"pmid":"22745252","title":"Landscape of somatic retrotransposition in human cancers.","abstract":"Transposable elements (TEs) are abundant in the human genome, and some are capable of generating new insertions through RNA intermediates. In cancer, the disruption of cellular mechanisms that normally suppress TE activity may facilitate mutagenic retrotranspositions. We performed single-nucleotide resolution analysis of TE insertions in 43 high-coverage whole-genome sequencing data sets from five cancer types. We identified 194 high-confidence somatic TE insertions, as well as thousands of polymorphic TE insertions in matched normal genomes. Somatic insertions were present in epithelial tumors but not in blood or brain cancers. Somatic L1 insertions tend to occur in genes that are commonly mutated in cancer, disrupt the expression of the target genes, and are biased toward regions of cancer-specific DNA hypomethylation, highlighting their potential impact in tumorigenesis.","authors":"Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, LJ., Lohr, JG., Harris, CC., Ding, L., Wilson, RK., Wheeler, DA., Gibbs, RA., Kucherlapati, R., Lee, C., Kharchenko, PV., Park, PJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Science","volume":"337","issue":"6097","page":"967-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-13","doi":"10.1126\/science.1222077","first_author":"Lee, E.","corresponding_authors":"Park, PJ."},{"pmid":"22570616","title":"Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.","abstract":"The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at \"entry sites\" that contain a consensus sequence motif (\"MSL recognition element\" or MRE). However, this motif is only &#x223c;2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells (which contain MSL complex) and female Kc cells (which lack the complex), we find that the presence of active chromatin modifications, together with an elevated local GC content in the surrounding sequences, has strong predictive value for functional MSL entry sites, independent of MSL binding. We tested these sites for function in Kc cells by RNAi knockdown of Sxl, resulting in induction of MSL complex. We show that ectopic MSL expression in Kc cells leads to H4K16 acetylation around these sites and a relative increase in X chromosome transcription. Collectively, our results support a model in which a pre-existing active chromatin environment, coincident with H3K36me3, contributes to MSL entry site selection. The consequences of MSL targeting of the male X chromosome include increase in nucleosome lability, enrichment for H4K16 acetylation and JIL-1 kinase, and depletion of linker histone H1 on active X-linked genes. Our analysis can serve as a model for identifying chromatin and local sequence features that may contribute to selection of functional protein binding sites in the genome.","authors":"Alekseyenko, AA., Ho, JW., Peng, S., Gelbart, M., Tolstorukov, MY., Plachetka, A., Kharchenko, PV., Jung, YL., Gorchakov, AA., Larschan, E., Gu, T., Minoda, A., Riddle, NC., Schwartz, YB., Elgin, SC., Karpen, GH., Pirrotta, V., Kuroda, MI., Park, PJ.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"PLoS Genet","volume":"8","issue":"4","page":"e1002646","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-09-26","doi":"10.1371\/journal.pgen.1002646","first_author":"Alekseyenko, AA.","corresponding_authors":"Park, PJ."},{"pmid":"22337862","title":"Heterogeneity of the transition\/transversion ratio in Drosophila and Hominidae genomes.","abstract":"Mutation rate varies between sites in the genome. Part of this variation can be explained by well-recognized short nucleotide contexts, but a large component of this variation remains cryptic. We used data on interspecies divergence and intraspecies polymorphism in Drosophila and Hominidae to analyze variation of the average rate of the 12 possible kinds of single-nucleotide mutations and in the transition\/transversion ratio &#x3ba; at single-nucleotide resolution. Both the average mutation rate and &#x3ba; vary by a factor of ~3 between nucleotide sites. The characteristic scale of variation in &#x3ba; is up to at least ~30 nucleotides in Drosophila and ~5 nucleotides in Hominidae. Genome segments with locally elevated mutation rates possess lower values of &#x3ba;; however, a substantial fraction of variation in &#x3ba; cannot be directly explained by the local mutation rates.","authors":"Seplyarskiy, VB., Kharchenko, P., Kondrashov, AS., Bazykin, GA.","publication_status":"ppublish","journalpubyear":"2012","journaltitle":"Mol Biol Evol","volume":"29","issue":"8","page":"1943-55","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-11-28","doi":"10.1093\/molbev\/mss071","first_author":"Seplyarskiy, VB.","corresponding_authors":"Bazykin, GA."},{"pmid":"22143764","title":"The genomic binding sites of a noncoding RNA.","abstract":"Long noncoding RNAs (lncRNAs) have important regulatory roles and can function at the level of chromatin. To determine where lncRNAs bind to chromatin, we developed capture hybridization analysis of RNA targets (CHART), a hybridization-based technique that specifically enriches endogenous RNAs along with their targets from reversibly cross-linked chromatin extracts. CHART was used to enrich the DNA and protein targets of endogenous lncRNAs from flies and humans. This analysis was extended to genome-wide mapping of roX2, a well-studied ncRNA involved in dosage compensation in Drosophila. CHART revealed that roX2 binds at specific genomic sites that coincide with the binding sites of proteins from the male-specific lethal complex that affects dosage compensation. These results reveal the genomic targets of roX2 and demonstrate how CHART can be used to study RNAs in a manner analogous to chromatin immunoprecipitation for proteins.","authors":"Simon, MD., Wang, CI., Kharchenko, PV., West, JA., Chapman, BA., Alekseyenko, AA., Borowsky, ML., Kuroda, MI., Kingston, RE.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Proc Natl Acad Sci U S A","volume":"108","issue":"51","page":"20497-502","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2012-03-09","doi":"10.1073\/pnas.1113536108","first_author":"Simon, MD.","corresponding_authors":"Kingston, RE."},{"pmid":"21179089","title":"Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.","abstract":"Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short\/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.","authors":"Kharchenko, PV., Alekseyenko, AA., Schwartz, YB., Minoda, A., Riddle, NC., Ernst, J., Sabo, PJ., Larschan, E., Gorchakov, AA., Gu, T., Linder-Basso, D., Plachetka, A., Shanower, G., Tolstorukov, MY., Luquette, LJ., Xi, R., Jung, YL., Park, RW., Bishop, EP., Canfield, TK., Sandstrom, R., Thurman, RE., MacAlpine, DM., Stamatoyannopoulos, JA., Kellis, M., Elgin, SC., Kuroda, MI., Pirrotta, V., Karpen, GH., Park, PJ.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nature","volume":"471","issue":"7339","page":"480-5","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-05-02","doi":"10.1038\/nature09725","first_author":"Kharchenko, PV.","corresponding_authors":"Park, PJ."},{"pmid":"21368835","title":"X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila.","abstract":"The evolution of sex chromosomes has resulted in numerous species in which females inherit two X chromosomes but males have a single X, thus requiring dosage compensation. MSL (Male-specific lethal) complex increases transcription on the single X chromosome of Drosophila males to equalize expression of X-linked genes between the sexes. The biochemical mechanisms used for dosage compensation must function over a wide dynamic range of transcription levels and differential expression patterns. It has been proposed that the MSL complex regulates transcriptional elongation to control dosage compensation, a model subsequently supported by mapping of the MSL complex and MSL-dependent histone 4 lysine 16 acetylation to the bodies of X-linked genes in males, with a bias towards 3' ends. However, experimental analysis of MSL function at the mechanistic level has been challenging owing to the small magnitude of the chromosome-wide effect and the lack of an in vitro system for biochemical analysis. Here we use global run-on sequencing (GRO-seq) to examine the specific effect of the MSL complex on RNA Polymerase II (RNAP II) on a genome-wide level. Results indicate that the MSL complex enhances transcription by facilitating the progression of RNAP II across the bodies of active X-linked genes. Improving transcriptional output downstream of typical gene-specific controls may explain how dosage compensation can be imposed on the diverse set of genes along an entire chromosome.","authors":"Larschan, E., Bishop, EP., Kharchenko, PV., Core, LJ., Lis, JT., Park, PJ., Kuroda, MI.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Nature","volume":"471","issue":"7336","page":"115-8","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-03-21","doi":"10.1038\/nature09757","first_author":"Larschan, E.","corresponding_authors":"Kuroda, MI."},{"pmid":"21356108","title":"ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Manual\"><PMID Version=\"1\">21356108<\/PMID><DateCompleted><Year>2011<\/Year><Month>06<\/Month><Day>27<\/Day><\/DateCompleted><DateRevised><Year>2021<\/Year><Month>10<\/Month><Day>20<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2164<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>12<\/Volume><PubDate><Year>2011<\/Year><Month>Feb<\/Month><Day>28<\/Day><\/PubDate><\/JournalIssue><Title>BMC genomics<\/Title><ISOAbbreviation>BMC Genomics<\/ISOAbbreviation><\/Journal><ArticleTitle>ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.<\/ArticleTitle><Pagination><StartPage>134<\/StartPage><MedlinePgn>134<\/MedlinePgn><\/Pagination><ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1186\/1471-2164-12-134<\/ELocationID><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip\/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster.","authors":"Ho, JW., Bishop, E., Karchenko, PV., N\u00e8gre, N., White, KP., Park, PJ.","publication_status":"epublish","journalpubyear":"2011","journaltitle":"BMC Genomics","volume":"12","issue":null,"page":"134","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-06-27","doi":"10.1186\/1471-2164-12-134","first_author":"Ho, JW.","corresponding_authors":"Park, PJ."},{"pmid":"21177973","title":"Chromatin signatures of the Drosophila replication program.","abstract":"DNA replication initiates from thousands of start sites throughout the Drosophila genome and must be coordinated with other ongoing nuclear processes such as transcription to ensure genetic and epigenetic inheritance. Considerable progress has been made toward understanding how chromatin modifications regulate the transcription program; in contrast, we know relatively little about the role of the chromatin landscape in defining how start sites of DNA replication are selected and regulated. Here, we describe the Drosophila replication program in the context of the chromatin and transcription landscape for multiple cell lines using data generated by the modENCODE consortium. We find that while the cell lines exhibit similar replication programs, there are numerous cell line-specific differences that correlate with changes in the chromatin architecture. We identify chromatin features that are associated with replication timing, early origin usage, and ORC binding. Primary sequence, activating chromatin marks, and DNA-binding proteins (including chromatin remodelers) contribute in an additive manner to specify ORC-binding sites. We also generate accurate and predictive models from the chromatin data to describe origin usage and strength between cell lines. Multiple activating chromatin modifications contribute to the function and relative strength of replication origins, suggesting that the chromatin environment does not regulate origins of replication as a simple binary switch, but rather acts as a tunable rheostat to regulate replication initiation events.","authors":"Eaton, ML., Prinz, JA., MacAlpine, HK., Tretyakov, G., Kharchenko, PV., MacAlpine, DM.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Genome Res","volume":"21","issue":"2","page":"164-74","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-04","doi":"10.1101\/gr.116038.110","first_author":"Eaton, ML.","corresponding_authors":"MacAlpine, DM."},{"pmid":"21177972","title":"Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin.","abstract":"Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis of histone modifications and chromosomal proteins. As anticipated, the pericentric heterochromatin and chromosome 4 are on average enriched for the \"silencing\" marks H3K9me2, H3K9me3, HP1a, and SU(VAR)3-9, and are generally depleted for marks associated with active transcription. The locations of the euchromatin-heterochromatin borders identified by these marks are similar in animal tissues and most cell lines, although the amount of heterochromatin is variable in some cell lines. Combinatorial analysis of chromatin patterns reveals distinct profiles for euchromatin, pericentric heterochromatin, and the 4th chromosome. Both silent and active protein-coding genes in heterochromatin display complex patterns of chromosomal proteins and histone modifications; a majority of the active genes exhibit both \"activation\" marks (e.g., H3K4me3 and H3K36me3) and \"silencing\" marks (e.g., H3K9me2 and HP1a). The hallmark of active genes in heterochromatic domains appears to be a loss of H3K9 methylation at the transcription start site. We also observe complex epigenomic profiles of intergenic regions, repeated transposable element (TE) sequences, and genes in the heterochromatic extensions. An unexpectedly large fraction of sequences in the euchromatic chromosome arms exhibits a heterochromatic chromatin signature, which differs in size, position, and impact on gene expression among cell types. We conclude that patterns of heterochromatin\/euchromatin packaging show greater complexity and plasticity than anticipated. This comprehensive analysis provides a foundation for future studies of gene activity and chromosomal functions that are influenced by or dependent upon heterochromatin.","authors":"Riddle, NC., Minoda, A., Kharchenko, PV., Alekseyenko, AA., Schwartz, YB., Tolstorukov, MY., Gorchakov, AA., Jaffe, JD., Kennedy, C., Linder-Basso, D., Peach, SE., Shanower, G., Zheng, H., Kuroda, MI., Pirrotta, V., Park, PJ., Elgin, SC., Karpen, GH.","publication_status":"ppublish","journalpubyear":"2011","journaltitle":"Genome Res","volume":"21","issue":"2","page":"147-63","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-10-04","doi":"10.1101\/gr.110098.110","first_author":"Riddle, NC.","corresponding_authors":"Karpen, GH."},{"pmid":"22022339","title":"Analysis of primary structure of chromatin with next-generation sequencing.","abstract":"The recent development of next-generation sequencing technology has enabled significant progress in chromatin structure analysis. Here, we review the experimental and bioinformatic approaches to studying nucleosome positioning and histone modification profiles on a genome scale using this technology. These studies advanced our knowledge of the nucleosome positioning patterns of both epigenetically modified and bulk nucleosomes and elucidated the role of such patterns in regulation of gene expression. The identification and analysis of large sets of nucleosome-bound DNA sequences allowed better understanding of the rules that govern nucleosome positioning in organisms of various complexity. We also discuss the existing challenges and prospects of using next-generation sequencing for nucleosome positioning analysis and outline the importance of such studies for the entire chromatin structure field.","authors":"Tolstorukov, MY., Kharchenko, PV., Park, PJ.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Epigenomics","volume":"2","issue":"2","page":"187-197","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-03-01","doi":null,"first_author":"Tolstorukov, MY.","corresponding_authors":"Park, PJ."},{"pmid":"21177974","title":"Identification of functional elements and regulatory circuits by Drosophila modENCODE.","abstract":"To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.","authors":"Roy, S., Ernst, J., Kharchenko, PV., Kheradpour, P., Negre, N., Eaton, ML., Landolin, JM., Bristow, CA., Ma, L., Lin, MF., Washietl, S., Arshinoff, BI., Ay, F., Meyer, PE., Robine, N., Washington, NL., Di Stefano, L., Berezikov, E., Brown, CD., Candeias, R., Carlson, JW., Carr, A., Jungreis, I., Marbach, D., Sealfon, R., Tolstorukov, MY., Will, S., Alekseyenko, AA., Artieri, C., Booth, BW., Brooks, AN., Dai, Q., Davis, CA., Duff, MO., Feng, X., Gorchakov, AA., Gu, T., Henikoff, JG., Kapranov, P., Li, R., MacAlpine, HK., Malone, J., Minoda, A., Nordman, J., Okamura, K., Perry, M., Powell, SK., Riddle, NC., Sakai, A., Samsonova, A., Sandler, JE., Schwartz, YB., Sher, N., Spokony, R., Sturgill, D., van Baren, M., Wan, KH., Yang, L., Yu, C., Feingold, E., Good, P., Guyer, M., Lowdon, R., Ahmad, K., Andrews, J., Berger, B., Brenner, SE., Brent, MR., Cherbas, L., Elgin, SC., Gingeras, TR., Grossman, R., Hoskins, RA., Kaufman, TC., Kent, W., Kuroda, MI., Orr-Weaver, T., Perrimon, N., Pirrotta, V., Posakony, JW., Ren, B., Russell, S., Cherbas, P., Graveley, BR., Lewis, S., Micklem, G., Oliver, B., Park, PJ., Celniker, SE., Henikoff, S., Karpen, GH., Lai, EC., MacAlpine, DM., Stein, LD., White, KP., Kellis, M.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Science","volume":"330","issue":"6012","page":"1787-97","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2011-01-20","doi":"10.1126\/science.1198374","first_author":"Roy, S.","corresponding_authors":"Kellis, M."},{"pmid":"20085705","title":"A region of the human HOXD cluster that confers polycomb-group responsiveness.","abstract":"Polycomb group (PcG) proteins are essential for accurate axial body patterning during embryonic development. PcG-mediated repression is conserved in metazoans and is targeted in Drosophila by Polycomb response elements (PREs). However, targeting sequences in humans have not been described. While analyzing chromatin architecture in the context of human embryonic stem cell (hESC) differentiation, we discovered a 1.8kb region between HOXD11 and HOXD12 (D11.12) that is associated with PcG proteins, becomes nuclease hypersensitive, and then shows alteration in nuclease sensitivity as hESCs differentiate. The D11.12 element repressed luciferase expression from a reporter construct and full repression required a highly conserved region and YY1 binding sites. Furthermore, repression was dependent on the PcG proteins BMI1 and EED and a YY1-interacting partner, RYBP. We conclude that D11.12 is a Polycomb-dependent regulatory region with similarities to Drosophila PREs, indicating conservation in the mechanisms that target PcG function in mammals and flies.","authors":"Woo, CJ., Kharchenko, PV., Daheron, L., Park, PJ., Kingston, RE.","publication_status":"ppublish","journalpubyear":"2010","journaltitle":"Cell","volume":"140","issue":"1","page":"99-110","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2010-02-04","doi":"10.1016\/j.cell.2009.12.022","first_author":"Woo, CJ.","corresponding_authors":"Kingston, RE."},{"pmid":"19797766","title":"Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X.","abstract":"Dosage compensation in Drosophila melanogaster males is achieved via targeting of male-specific lethal (MSL) complex to X-linked genes. This is proposed to involve sequence-specific recognition of the X at approximately 150-300 chromatin entry sites, and subsequent spreading to active genes. Here we ask whether the spreading step requires transcription and is sequence-independent. We find that MSL complex binds, acetylates, and up-regulates autosomal genes inserted on X, but only if transcriptionally active. We conclude that a long-sought specific DNA sequence within X-linked genes is not obligatory for MSL binding. Instead, linkage and transcription play the pivotal roles in MSL targeting irrespective of gene origin and DNA sequence.","authors":"Gorchakov, AA., Alekseyenko, AA., Kharchenko, P., Park, PJ., Kuroda, MI.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genes Dev","volume":"23","issue":"19","page":"2266-71","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-10-14","doi":"10.1101\/gad.1840409","first_author":"Gorchakov, AA.","corresponding_authors":"Kuroda, MI."},{"pmid":"19246569","title":"Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes.","abstract":"Eukaryotic DNA is wrapped around a histone protein core to constitute the fundamental repeating units of chromatin, the nucleosomes. The affinity of the histone core for DNA depends on the nucleotide sequence; however, it is unclear to what extent DNA sequence determines nucleosome positioning in vivo, and if the same rules of sequence-directed positioning apply to genomes of varying complexity. Using the data generated by high-throughput DNA sequencing combined with chromatin immunoprecipitation, we have identified positions of nucleosomes containing the H2A.Z histone variant and histone H3 trimethylated at lysine 4 in human CD4(+) T-cells. We find that the 10-bp periodicity observed in nucleosomal sequences in yeast and other organisms is not pronounced in human nucleosomal sequences. This result was confirmed for a broader set of mononucleosomal fragments that were not selected for any specific histone variant or modification. We also find that human H2A.Z nucleosomes protect only approximately 120 bp of DNA from MNase digestion and exhibit specific sequence preferences, suggesting a novel mechanism of nucleosome organization for the H2A.Z variant.","authors":"Tolstorukov, MY., Kharchenko, PV., Goldman, JA., Kingston, RE., Park, PJ.","publication_status":"ppublish","journalpubyear":"2009","journaltitle":"Genome Res","volume":"19","issue":"6","page":"967-77","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-08-03","doi":"10.1101\/gr.084830.108","first_author":"Tolstorukov, MY.","corresponding_authors":"Park, PJ."},{"pmid":"19029915","title":"Design and analysis of ChIP-seq experiments for DNA-binding proteins.","abstract":"Recent progress in massively parallel sequencing platforms has enabled genome-wide characterization of DNA-associated proteins using the combination of chromatin immunoprecipitation and sequencing (ChIP-seq). Although a variety of methods exist for analysis of the established alternative ChIP microarray (ChIP-chip), few approaches have been described for processing ChIP-seq data. To fill this gap, we propose an analysis pipeline specifically designed to detect protein-binding positions with high accuracy. Using previously reported data sets for three transcription factors, we illustrate methods for improving tag alignment and correcting for background signals. We compare the sensitivity and spatial precision of three peak detection algorithms with published methods, demonstrating gains in spatial precision when an asymmetric distribution of tags on positive and negative strands is considered. We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites.","authors":"Kharchenko, PV., Tolstorukov, MY., Park, PJ.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Nat Biotechnol","volume":"26","issue":"12","page":"1351-9","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2009-02-05","doi":"10.1038\/nbt.1508","first_author":"Kharchenko, PV.","corresponding_authors":"Park, PJ."},{"pmid":"18724933","title":"A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome.","abstract":"The Drosophila MSL complex associates with active genes specifically on the male X chromosome to acetylate histone H4 at lysine 16 and increase expression approximately 2-fold. To date, no DNA sequence has been discovered to explain the specificity of MSL binding. We hypothesized that sequence-specific targeting occurs at \"chromatin entry sites,\" but the majority of sites are sequence independent. Here we characterize 150 potential entry sites by ChIP-chip and ChIP-seq and discover a GA-rich MSL recognition element (MRE). The motif is only slightly enriched on the X chromosome ( approximately 2-fold), but this is doubled when considering its preferential location within or 3' to active genes (&gt;4-fold enrichment). When inserted on an autosome, a newly identified site can direct local MSL spreading to flanking active genes. These results provide strong evidence for both sequence-dependent and -independent steps in MSL targeting of dosage compensation to the male X chromosome.","authors":"Alekseyenko, AA., Peng, S., Larschan, E., Gorchakov, AA., Lee, OK., Kharchenko, P., McGrath, SD., Wang, CI., Mardis, ER., Park, PJ., Kuroda, MI.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Cell","volume":"134","issue":"4","page":"599-609","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-09-10","doi":"10.1016\/j.cell.2008.06.033","first_author":"Alekseyenko, AA.","corresponding_authors":"Kuroda, MI."},{"pmid":"18723689","title":"Nucleosome positioning in human HOX gene clusters.","abstract":"The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and is thought to influence gene regulation through modulation of DNA accessibility. However, properties of nucleosome organization remain poorly understood, particularly in mammalian genomes. Toward this goal we used tiled microarrays to identify stable nucleosome positions along the HOX gene clusters in human cell lines. We show that nucleosome positions exhibit sequence properties and long-range organization that are different from those characterized in other organisms. Despite overall variability of internucleosome distances, specific loci contain regular nucleosomal arrays with 195-bp periodicity. Moreover, such arrays tend to occur preferentially toward the 3' ends of genes. Through comparison of different cell lines, we find that active transcription is correlated with increased positioning of nucleosomes, suggesting an unexpected role for transcription in the establishment of well-positioned nucleosomes.","authors":"Kharchenko, PV., Woo, CJ., Tolstorukov, MY., Kingston, RE., Park, PJ.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Genome Res","volume":"18","issue":"10","page":"1554-61","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-12-10","doi":"10.1101\/gr.075952.107","first_author":"Kharchenko, PV.","corresponding_authors":"Park, PJ."},{"pmid":"18477461","title":"Differential H3K4 methylation identifies developmentally poised hematopoietic genes.","abstract":"Throughout development, cell fate decisions are converted into epigenetic information that determines cellular identity. Covalent histone modifications are heritable epigenetic marks and are hypothesized to play a central role in this process. In this report, we assess the concordance of histone H3 lysine 4 dimethylation (H3K4me2) and trimethylation (H3K4me3) on a genome-wide scale in erythroid development by analyzing pluripotent, multipotent, and unipotent cell types. Although H3K4me2 and H3K4me3 are concordant at most genes, multipotential hematopoietic cells have a subset of genes that are differentially methylated (H3K4me2+\/me3-). These genes are transcriptionally silent, highly enriched in lineage-specific hematopoietic genes, and uniquely susceptible to differentiation-induced H3K4 demethylation. Self-renewing embryonic stem cells, which restrict H3K4 methylation to genes that contain CpG islands (CGIs), lack H3K4me2+\/me3- genes. These data reveal distinct epigenetic regulation of CGI and non-CGI genes during development and indicate an interactive relationship between DNA sequence and differential H3K4 methylation in lineage-specific differentiation.","authors":"Orford, K., Kharchenko, P., Lai, W., Dao, MC., Worhunsky, DJ., Ferro, A., Janzen, V., Park, PJ., Scadden, DT.","publication_status":"ppublish","journalpubyear":"2008","journaltitle":"Dev Cell","volume":"14","issue":"5","page":"798-809","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2008-05-29","doi":"10.1016\/j.devcel.2008.04.002","first_author":"Orford, K.","corresponding_authors":"Scadden, DT."},{"pmid":"17563360","title":"Chromosomal periodicity of evolutionarily conserved gene pairs.","abstract":"Chromosomes are compacted hundreds of times to fit in the cell, packaged into dynamic folds whose structures are largely unknown. Here, we examine patterns in gene locations to infer large-scale features of bacterial chromosomes. Specifically, we analyzed &gt;100 genomes and identified thousands of gene pairs that display two types of evolutionary correlations: a tendency to co-occur and a tendency to be located close together in many genomes. We then analyzed the detailed distribution of these pairs in Escherichia coli and found that genes in a pair tend to be separated by integral multiples of 117 kb along the genome and to be positioned in a 117-kb grid of genomic locations. In addition, the most pair-dense locations coincide with regions of intense transcriptional activity and the positions of top transcribed and conserved genes. These patterns suggest that the E. coli chromosome may be organized into a 117-kb helix-like topology that localizes a subset of the most essential and highly transcribed genes along a specific face of this structure. Our approach indicates an evolutionarily maintained preference in the spacing of genes along the chromosome and offers a general comparative genomics framework for studying chromosome structure, broadly applicable to other organisms.","authors":"Wright, MA., Kharchenko, P., Church, GM., Segr\u00e8, D.","publication_status":"ppublish","journalpubyear":"2007","journaltitle":"Proc Natl Acad Sci U S A","volume":"104","issue":"25","page":"10559-64","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-08-15","doi":null,"first_author":"Wright, MA.","corresponding_authors":"Segr&#xe8;, D."},{"pmid":"16684370","title":"Influence of metabolic network structure and function on enzyme evolution.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Manual\"><PMID Version=\"1\">16684370<\/PMID><DateCompleted><Year>2006<\/Year><Month>08<\/Month><Day>29<\/Day><\/DateCompleted><DateRevised><Year>2022<\/Year><Month>03<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print-Electronic\"><Journal><ISSN IssnType=\"Electronic\">1474-760X<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><Issue>5<\/Issue><PubDate><Year>2006<\/Year><\/PubDate><\/JournalIssue><Title>Genome biology<\/Title><ISOAbbreviation>Genome Biol<\/ISOAbbreviation><\/Journal><ArticleTitle>Influence of metabolic network structure and function on enzyme evolution.<\/ArticleTitle><Pagination><StartPage>R39<\/StartPage><MedlinePgn>R39<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. In the present work we connect molecular evolution on the gene level with system properties of a cellular metabolic network. In contrast to protein interaction networks, where several previous studies investigated the molecular evolution of proteins, metabolic networks have a relatively well-defined global function. The ability to consider fluxes in a metabolic network allows us to relate the functional role of each enzyme in a network to its rate of evolution.","authors":"Vitkup, D., Kharchenko, P., Wagner, A.","publication_status":"ppublish","journalpubyear":"2006","journaltitle":"Genome Biol","volume":"7","issue":"5","page":"R39","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-08-29","doi":null,"first_author":"Vitkup, D.","corresponding_authors":"Wagner, A."},{"pmid":"16571130","title":"Identifying metabolic enzymes with multiple types of association evidence.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Manual\"><PMID Version=\"1\">16571130<\/PMID><DateCompleted><Year>2006<\/Year><Month>08<\/Month><Day>03<\/Day><\/DateCompleted><DateRevised><Year>2023<\/Year><Month>04<\/Month><Day>15<\/Day><\/DateRevised><Article PubModel=\"Electronic\"><Journal><ISSN IssnType=\"Electronic\">1471-2105<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>7<\/Volume><PubDate><Year>2006<\/Year><Month>Mar<\/Month><Day>29<\/Day><\/PubDate><\/JournalIssue><Title>BMC bioinformatics<\/Title><ISOAbbreviation>BMC Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Identifying metabolic enzymes with multiple types of association evidence.<\/ArticleTitle><Pagination><StartPage>177<\/StartPage><MedlinePgn>177<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"BACKGROUND\" NlmCategory=\"BACKGROUND\">Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes.","authors":"Kharchenko, P., Chen, L., Freund, Y., Vitkup, D., Church, GM.","publication_status":"epublish","journalpubyear":"2006","journaltitle":"BMC Bioinformatics","volume":"7","issue":null,"page":"177","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-08-03","doi":null,"first_author":"Kharchenko, P.","corresponding_authors":"Church, GM."},{"pmid":"16729051","title":"Expression dynamics of a cellular metabolic network.","abstract":"Toward the goal of understanding system properties of biological networks, we investigate the global and local regulation of gene expression in the Saccharomyces cerevisiae metabolic network. Our results demonstrate predominance of local gene regulation in metabolism. Metabolic genes display significant coexpression on distances smaller than the average network distance, a behavior supported by the distribution of transcription factor binding sites in the metabolic network and genome context associations. Positive gene coexpression decreases monotonically with distance in the network, while negative coexpression is strongest at intermediate network distances. We show that basic topological motifs of the metabolic network exhibit statistically significant differences in coexpression behavior.","authors":"Kharchenko, P., Church, GM., Vitkup, D.","publication_status":"ppublish","journalpubyear":"2005","journaltitle":"Mol Syst Biol","volume":"1","issue":null,"page":"2005.0016","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2006-08-11","doi":null,"first_author":"Kharchenko, P.","corresponding_authors":"Vitkup, D."},{"pmid":"15262797","title":"Filling gaps in a metabolic network using expression information.","abstract":"on Status=\"MEDLINE\" Owner=\"NLM\" IndexingMethod=\"Manual\"><PMID Version=\"1\">15262797<\/PMID><DateCompleted><Year>2007<\/Year><Month>08<\/Month><Day>27<\/Day><\/DateCompleted><DateRevised><Year>2019<\/Year><Month>12<\/Month><Day>10<\/Day><\/DateRevised><Article PubModel=\"Print\"><Journal><ISSN IssnType=\"Electronic\">1367-4811<\/ISSN><JournalIssue CitedMedium=\"Internet\"><Volume>20 Suppl 1<\/Volume><PubDate><Year>2004<\/Year><Month>Aug<\/Month><Day>04<\/Day><\/PubDate><\/JournalIssue><Title>Bioinformatics (Oxford, England)<\/Title><ISOAbbreviation>Bioinformatics<\/ISOAbbreviation><\/Journal><ArticleTitle>Filling gaps in a metabolic network using expression information.<\/ArticleTitle><Pagination><StartPage>i178<\/StartPage><EndPage>i185<\/EndPage><MedlinePgn>i178-85<\/MedlinePgn><\/Pagination><Abstract><AbstractText Label=\"MOTIVATION\" NlmCategory=\"BACKGROUND\">The metabolic models of both newly sequenced and well-studied organisms contain reactions for which the enzymes have not been identified yet. We present a computational approach for identifying genes encoding such missing metabolic enzymes in a partially reconstructed metabolic network.","authors":"Kharchenko, P., Vitkup, D., Church, GM.","publication_status":"ppublish","journalpubyear":"2004","journaltitle":"Bioinformatics","volume":"20 Suppl 1","issue":null,"page":"i178-85","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2007-08-27","doi":null,"first_author":"Kharchenko, P.","corresponding_authors":"Church, GM."},{"pmid":"14583118","title":"From annotated genomes to metabolic flux models and kinetic parameter fitting.","abstract":"Significant advances in system-level modeling of cellular behavior can be achieved based on constraints derived from genomic information and on optimality hypotheses. For steady-state models of metabolic networks, mass conservation and reaction stoichiometry impose linear constraints on metabolic fluxes. Different objectives, such as maximization of growth rate or minimization of flux distance from a reference state, can be tested in different organisms and conditions. In particular, we have suggested that the metabolic properties of mutant bacterial strains are best described by an algorithm that performs a minimization of metabolic adjustment (MOMA) upon gene deletion. The increasing availability of many annotated genomes paves the way for a systematic application of these flux balance methods to a large variety of organisms. However, such a high throughput goal crucially depends on our capacity to build metabolic flux models in a fully automated fashion. Here we describe a pipeline for generating models from annotated genomes and discuss the current obstacles to full automation. In addition, we propose a framework for the integration of flux modeling results and high throughput proteomic data, which can potentially help in the inference of whole-cell kinetic parameters.","authors":"Segr\u00e8, D., Zucker, J., Katz, J., Lin, X., D'haeseleer, P., Rindone, WP., Kharchenko, P., Nguyen, DH., Wright, MA., Church, GM.","publication_status":"ppublish","journalpubyear":"2003","journaltitle":"OMICS","volume":"7","issue":"3","page":"301-16","pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2004-05-27","doi":null,"first_author":"Segr&#xe8;, D.","corresponding_authors":"Church, GM."},{"pmid":"42777706","title":"Direct cell-to-cell transmission of retrotransposons.","abstract":"Transposable elements are abundant in host genomes but are generally considered to be confined to the cell in which they are expressed, with the notable exception of endogenous retroviruses. Here, we identify a group of long terminal repeat (LTR) retrotransposons that infect the germline from somatic cells within the Drosophila ovary, despite lacking the fusogenic Envelope protein typically required for retroviral entry. Instead, these elements encode a short transmembrane protein, sORF2, which bears structural features reminiscent of viral cell-cell fusogens. Through genetics, imaging, and electron microscopy, we show that sORF2 localizes to invasive somatic protrusions that contain retroviral capsids and establish physical contact with the oocyte membrane. In the absence of sORF2, protrusion formation and soma-to-germline transmission of capsids are abolished. Remarkably, sORF2-like proteins are widespread among insect retrotransposons and also occur in piscine nackednaviruses and avian picornaviruses. These findings reveal a noncanonical, Envelope-independent transmission mechanism shared by retrotransposons and non-enveloped viruses.","authors":"Voichek, M., Bernhard, A., Lauterjung, L., Novatchkova, M., Handler, D., M\u00f6seneder, P., Protsenko, L., Rafanel, B., Iarovenko, S., Duchek, P., Senti, KA., Brennecke, J.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Cell","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-09-29","doi":"10.1016\/j.cell.2026.08.047","first_author":"Voichek, M.","corresponding_authors":"Senti, KA., Brennecke, J."},{"pmid":"42720090","title":"Immune regulation of neuronal stem cells in the medaka retina.","abstract":"Stem cell populations in tissues require precise regulation of their number and quality to maintain proper organ growth. Among the various regulatory mechanisms, immune cells are emerging to directly regulate stem cell populations. The medaka retinal stem cell (RSC) niche, a model for lifelong neurogenic growth, provides a system for studying immune-stem cell interactions. We investigate how microglia, which are resident macrophages of the central nervous system, regulate the RSC niche. We identify that bona fide RSCs express the chemokine Ccl25b, while its cognate receptor, Ccr9a, is expressed in microglia. These microglia form a surveillance ring adjacent to the RSC niche and actively phagocytose RSCs. Interference with microglia by deletion of spi1b reveals that microglia absence leads to increased numbers of ccl25b-positive RSCs and results in morphological defects of the retina. Targeted mutation of ccl25b specifically affects microglia mobility under injury conditions; however, we did not observe any morphological defects, indicating that Ccl25b-Ccr9a signaling is not essential for stem cell maintenance. Overall, our data show that, under homeostatic conditions, the individual RSCs, which are essential for proper eye development, are actively phagocytosed by immune surveillance.","authors":"Agarwal, R., Benjaminsen, J., Lust, K., Julseth, C., Fuchs, N., Hasel de Carvalho, E., Eggeler, F., El Said Ibrahim, O., Aghaallaei, N., Bajoghli, B., Wittbrodt, J.","publication_status":"ppublish","journalpubyear":"2026","journaltitle":"Development","volume":"153","issue":"17","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-09-10","doi":"10.1242\/dev.205198","first_author":"Agarwal, R.","corresponding_authors":"Wittbrodt, J."},{"pmid":"42823412","title":"Pushing the limits of single-cell proteomics to investigate bacterial heterogeneity using bacSCP.","abstract":"Single-cell proteomics (SCP) has emerged as a powerful approach to quantify protein expression variability at cellular resolution, yet most state-of-the-art workflows are tailored to eukaryotic cells with only one study exploring how single bacteria can be analyzed by mass spectrometry. Here, we established bacSCP, a protocol extending SCP to bacterial cells, facing analytical challenges such as the thick bacterial cell wall hampering lysis, the extremely small cell size and resultant low protein content, and the comparatively high level of contaminating proteins from external sources. Using this bacSCP pipeline, we quantified more than 50 bacterial proteins from single Bacillus subtilis and Escherichia coli cells. Upon heat stress, we reproducibly observed up to 8-fold upregulation of chaperones including GroEL, GroES, and ClpC for a B. subtilis &#x394;mcsB strain. Importantly, single-cell measurements revealed potential heterogeneity within the heat-stressed subpopulation, enabling interrogation of stress-response variability at the proteome level. These results demonstrate the feasibility of bacSCP and provide a foundation for studying bacterial stress adaptation and phenotypic diversity with single-cell proteomic resolution.","authors":"Leodolter, J., Thierer, T., Mechtler, K., Matzinger, M.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-10-01","doi":"10.1038\/s41467-026-77426-y","first_author":"Leodolter, J.","corresponding_authors":"Matzinger, M."},{"pmid":"42818913","title":"Chromatin remodeling coordinates chromosome compaction, synaptonemal complex architecture and meiotic crossing-over.","abstract":"Crossing-over between maternal and paternal chromosomes during meiosis relies on the maturation of recombination intermediates within the synaptonemal complex (SC). These events unfold within a hierarchically organized environment, in which linear arrays of chromatin loops are anchored to the axes of meiotic chromosomes. Yet, how chromatin organization is integrated with crossover maturation remains poorly understood. Here, we identify the nucleosome remodeler CHD1 as a previously unrecognized component of the mammalian SC. CHD1 localizes at the interface of synapsed homologs through direct interaction with the SC central-element protein SYCE1 and regulates meiotic chromosome organization. Conditional depletion of CHD1 in meiocytes increases chromatin accessibility at recombination hotspots, disrupts chromosome compaction, and reduces the spatial separation between homolog axes. These meiosis-specific structural defects are accompanied by impaired stabilization of crossover-promoting factors at incipient crossover sites. Together, our findings demonstrate that CHD1-mediated nucleosome remodeling shapes meiotic chromosome organization across scales, creating a chromatin environment that supports crossover maturation and fertility.","authors":"Matos, J., Palmer, N., Khauratovich, U., Toe, LD., Hartmann, F., Pavlova, A., Khanal, S., Patel, R., Petroulaki, V., Bl\u00e1hov\u00e1, V., Hunter, N., Robert, T., Goloborodko, A.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Res Sq","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-10-01","doi":"10.21203\/rs.3.rs-10849354\/v1","first_author":"Matos, J.","corresponding_authors":"Goloborodko, A."},{"pmid":"42834077","title":"Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS.","abstract":"Crosslinking mass spectrometry has become the method of choice for the identification of protein-protein interactions and for gaining insight into the structures of proteins in vivo. However, connecting crosslink search engine results with down-stream analysis tools, and therefore gaining biological insight from crosslink identifications, has remained a manual and cumbersome step in the analysis that often requires expert bioinformatics knowledge. Here we introduce pyXLMS, a python package and public web application which aims to simplify and streamline this intermediate step, enabling researchers even without bioinformatics knowledge to conduct in-depth crosslink analyses. In its current state pyXLMS supports input from more than seven different crosslink search engines, as well as the mzIdentML format of the HUPO Proteomics Standards Initiative. Data processing and quality control is facilitated by functionality that is directly available within pyXLMS such as aggregation, validation, annotation, filtering, and visualization. In addition, the data can easily be exported to more than ten supported down-stream analysis tools and formats. We demonstrate the applicability and benefits of pyXLMS by re-analyzing a publicly available crosslink dataset with a variety of different search engines and show how the same data analysis workflow can be applied using pyXLMS.","authors":"Birklbauer, MJ., Buur, LM., Kaser, S., M\u00fcller, F., Matzinger, M., Mechtler, K., Winkler, S., Dorfer, V.","publication_status":"epublish","journalpubyear":"2026","journaltitle":"Nat Commun","volume":"17","issue":"1","page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-10-05","doi":"10.1038\/s41467-026-77407-1","first_author":"Birklbauer, MJ.","corresponding_authors":"Dorfer, V."},{"pmid":"42844479","title":"Mechanism of spliceosome termination.","abstract":"After excising an intron from pre-mRNA, the spliceosome remains trapped in a non-productive complex bound to the intron<sup>1-5<\/sup>. Termination of this complex is critical for spliceosome recycling and intron decay<sup>6<\/sup>, but the mechanism remains unknown. Here we present cryo-electron microscopy structures of human spliceosomes at two sequential stages of termination. First, the RNA helicases DHX15 and Aquarius unwind the RNA active site of the spliceosome, releasing bound components including U2 snRNA and extracting the buried intron-lariat branch point. The branch point is then debranched by the spliceosome-tethered enzyme DBR1, generating the previously unknown debranched intron spliceosome. This state recruits the RNA helicase DHX35 with its co-factors GPATCH1-WDR83, assisted by YJU2B. DHX35 ejects the debranched intron from the U6 snRNA-5' splice site duplex, driving spliceosome disassembly and intron turnover. In defective spliceosomes stalled on aberrant introns, YJU2B partners with LENG1 to guide DHX35-GPATCH1-WDR83 for termination through spliceosome quality control. Together, we reveal the mechanism of regular spliceosome termination and its parallels with spliceosome quality control, ensuring accurate and efficient pre-mRNA splicing.","authors":"Boreikaite, V., Faraway, R., Vorl\u00e4nder, MK., Phillips, AW., Opitz, L., Wanke, M., Yakoub, G., Raffl, G., Fin, L., Gonz\u00e1lez-Prieto, R., Luijsterburg, MS., Ameres, SL., Plaschka, C.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"Nature","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-10-07","doi":"10.1038\/s41586-026-11101-6","first_author":"Boreikaite, V.","corresponding_authors":"Plaschka, C."},{"pmid":"42888264","title":"Electrostatic control of chromatin compaction safeguards against apoptotic DNA release.","abstract":"Apoptosis involves extensive intracellular reorganisation to facilitate the clearance of dying cells. A key step in this process is the destruction of the genome through fragmentation by caspase-activated DNase (CAD). Rather than dispersing after CAD-mediated cleavage, DNA fragments are compacted into a dense chromatin compartment, but the underlying mechanism and biological relevance of this compaction remain unknown. Here we show that global deacetylation of histone tails promotes chromatin compaction during apoptosis, preventing DNA release into apoptotic extracellular vesicles. Using synthetic effectors that modulate nucleosome electrostatics independently of histone modifications, we demonstrate that electrostatic attraction alone is sufficient to compact and sequester fragmented chromatin. These findings reveal a mechanism by which global reprogramming of histone modifications coordinates genome fragmentation with its physical sequestration during apoptosis. Our synthetic approach further provides a tool to probe how physical forces contribute to genome organisation across diverse biological contexts.","authors":"Spicer, MFD., Wijma, S., Sch\u00fctte, N., Huertas, J., Maristany, MJ., P\u00e9rez L\u00f3pez, JI., Chen, L., Alaabo, M., Rosen, MK., Collepardo-Guevara, R., Gerlich, DW.","publication_status":"aheadofprint","journalpubyear":"2026","journaltitle":"EMBO J","volume":null,"issue":null,"page":null,"pdf":null,"JrId":null,"fulltextlink":null,"preprintlink":null,"articledate":"2026-10-16","doi":"10.1038\/s44318-026-00932-8","first_author":"Spicer, MFD.","corresponding_authors":"Gerlich, DW."}]